CSE Annual Report 2013/2014 (PDF, 9.8 MB)

Computational Science and Engineering (CSE) Annual Report 2013/2014

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CSEComputational Science and Engineering

Annual Report2013 / 2014

July 2013 to July 2014

Impressum:

© 2014 ETH Zürich Editors: Vasile Gradinaru, Ralf Hiptmair, Markus Reiher ETH Zürich PDF files of this report are available from: Dr. Vasile Gradinaru Seminar for Applied Mathematics Tel.: +41 44 632 3448 E-mail: [email protected] or may be downloaded from: www.rw.ethz.ch/dokumente/cse_annual_report_1314.pdf CSE curricula at ETH Zürich on the internet: www.rw.ethz.ch or www.cse.ethz.ch Cover: Ensemble forecast with a horizontal resolution of 2.2 km of the probability to exceed a precipitation amount of 5mm/6h for four different 6h time intervals of Monday September 22, 2014.

Groups having contributed to this report

Research Group Institute Projects Publs.

P. Arbenz Computer Science 42 212

S. Bonhoeffer Experimental and Theoretical Biology 214

K. Boulouchos Engines and Combustion Laboratory 48 216

C. Coperet Anorganic Chemistry 61

V. Gradinaru Seminar for Applied Mathematics 63

C. Hafner Electromagnetic Fields 64

D. Helbing Sociology 66 217

H. Herrmann Building Materials 69

R. Hiptmair Seminar for Applied Mathematics 76

P. Hora Virtual Manufacturing 84

P. Hünenberger Physical Chemistry 89 219

A. Jackson Geophysics 95

P. Jenny Fluid Dynamics 99 221

L. Kleiser Fluid Dynamics 109 225

M. Kröger Polymer Physics 113 227

M. Luisier Integrated Systems Laboratory 114 229

S. Mishra Seminar for Applied Mathematics 116 231

M. Parrinello Computational Science & USI 119 233

R. Peikert Visual Computing 127

M. Quack Physical Chemistry 130 234

M. Reiher Physical Chemistry 141 236

C. Schär Atmospheric and Climate Science 167 239

C. Schwab Seminar for Applied Mathematics 168 242

P. Tackley Geophysics 174 245

M. Troyer Theoretical Physics 248

W. van Gunsteren Physical Chemistry 192 253

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Table of Contents

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1 Introduction

2 Education

3 CSE Case Studies Seminar

4 Computational Highlight

5 CSE Research Projects

6 High-performance Hardware

6.1 Competence Center for Computational Chemistry

6.2 Information Technology Services

7 Publications in 2013/2014 211

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1

Introduction

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The year 2014 may be remembered as an important year for Computational Scienceand Engineering at ETHZ, because it saw the founding of the

Zurich Graduate School in Computational Science1 (ZHCS).

The initiative was launched by Petros Koumoutsakos (ETHZ, D-MAVT) and RomainTeyssier (UZH), inspired by the successful graduate schools in mathematics2 and lifesciences3, both run jointly by ETH and the University of Zurich.

The main goals of this new graduate school are:

• to attract and facilitate the recruitment of talented PhD students in the field ofComputational Science,

• to strengthen existing activities and enhance the visibility of Computational Sciencein Zurich,

• to offer a platform for communication and interaction between researchers and PhDstudents from different fields interested in Computational Science.

Facilities and activities of the ZHCS include

• a web platform (expected launch, Spring 2015) to facilitate the application process,following the example of the Graduate School in Mathematics

• the advertising of the ZHCS to students from around the world,

• block courses in Computational Science taught by ZHCS faculty. PhD students ofZHCS can earn credits for their degree by attending theses block courses.

• an annual retreat with a scientific and social programme for ZHCS PhD students,faculty and staff.

• the Academia-Industry Modeling Weeks where groups of PhD students tackle aopen problems proposed by representatives from industry and try to find a feasiblesolution under their guidance. The first of these took place Oct 27-31, 2014, andwas a big success.

• the Distinguished Lecture Series in Computational Science, attracting to Zurichworld leaders in the field to present their work and to meet with ZHCS members.

ZHCS can be expected to be fully operational by mid 2015. More information can beobtained from its website, see Figure 1.

All faculty of ETH Zurich and the University of Zurich with activities andinterest in computer simulation in science are invited to join the new ZHCSgraduate school as members.

As December 2014, 48 researchers from both universities have already enrolled.

1I assume that computational engineering is covered, because all fields of engineering have a legitimateclaim to be included into the wider category of science.

2www.zgms.ch3www.lifescience-graduateschool.ch

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Figure 1: ZHCS home page, www.zhcs.ch

Zurich, November 16, 2011Ralf Hiptmair,

Director of Studies CSE, member of the CSE Committee

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Education

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In September 2013, 26 new students started their CSE Bachelor studies, 19 in the firstsemester and 7 in the third semester. From outside ETH 13 students entered the CSE Mastercurriculum.

The total number of CSE students enrolled at the end of the academic year 2012/2013 was98 (61 in the BSc program and 37 in the MSc program).

In the past academic year 24 students have successfully finished a CSE curriculum, 10Bachelor students and 14 Master students, and have received a CSE degree, some with verygood scores. In the following list we give the name of the student, the title of theBachelor/Master thesis and the name and the department of the advisor.

The Willi Studer Preis 2014 for the best CSE Master Diploma in the past academic year wasawarded to Ruben Michaël Dezeure.

Number of CSE students in the curriculum; dark = number of new students

Number of CSE graduates

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Bachelor Theses

Stephania Deflorin: Predicting webcam images using weather measurements(Luc Van Gool, D-ITET)

Matthias Frey: Parallelization of a Differential Algebra Framework(Andreas Adelmann, D-INFK, PSI and Ralf Hiptmair, D-MATH)

Kelly Steich: Simultaneous Segmentation and Annotation of Video Semantics via Implicit Crowdsourcing(Gerhard Tröster, D-ITET)

Tobias Rechtenbacher: A Literature Search for “Preindustrial” Aerosol(Ulrike Lohmann, D-USYS)

Master Theses

Nikhil Biyani: Improving biomolecular structure refinement using Hamiltonian replica exchange simulations.(Wilfried van Gunsteren, D-CHAB)

Stefan Bucher: Reproducing Network Dynamics of a Neocortical Microcircuit with Point-Neuron Models(Ruedi Stoop, ZNZ)

Stephania Deflorin: Image-based Analysis and Visualization of Blood Flow in Choroidal Vessels(Markus Gross, D-INFK)

Dominik Eugster: Semi-Automated 3D Object Recognition in Electron Microscopy Image Data(Gabor Szekely, D-ITET)

Alessandro Felder: Twiner: A Physics-Based Approach for Synthesizing Vine Overgrowth(Markus Gross, D-INFK)

Shubham Gupta: HLLC Solver for the Reduced Model of Multiphase Compressible Flows(Patrick Jenny, D-MAVT)

Nicolo Lardelli: Explicit Horizontal Diffusion in the COSMO CCLM meteorological model with a Domain-Specific Embedded Language based on C++(Christian Schär, D-USYS)

Jakob Progsch: BRDF Fitting using Nonlinear Optimization Methods(Markus Gross, D-INFK)

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Yann Poltera: Multilevel Monte Carlo - Finite Differences method for 2D statistical solutions of the Navier-Stokes equations (Christoph Schwab, D-MATH)

Term Papers

Kushagra Alankar: Implementation and performance study of an ARM-based Visible Light Communication system(Thomas Gross, D-INFK)

Stefano Battaglia: Implementation of the Relativistic (Four-Component) DMRG approach in Maquis(Markus Reiher, D-CHAB)

Daniele Casati: Analysis of 2009’s Complete Twitter Digraph(Frank Schweitzer, D-MTEC)

Arthur Schwaninger: A Comparison between Panel and Panel-Free Methods to enforce Boundary Conditions for Viscous Vortex Methods(Patrik Jenny, D-MAVT)

Each semester on Thursdays, 15 - 17 hours, the CSE Case Studies Seminar takes place.Speakers from ETH, from other universities as well as from industry are invited to give a2x45 minutes talk on an applied topic. The seminar talks of the past academic year are listedin Chapter 3 of the report. Beside the scientific talks the CSE students are asked to give shortpresentations (10 minutes) on their Bachelor theses or on published papers out of a list. Thesepresentations help the students to practise giving talks. Students are also asked to give talks ontheir term papers and voluntarily on their Master theses (if there are free time slots).

Zürich, November 24, 2014Vasile Gradinaru, Advisor of Student Studies CSE and member of the CSE Committee(Fachberater RW und Mitglied des Ausschusses Rechnergestützte Wissenschaften)

For detailed information on the RW/CSE curricula at ETH Zürich see: www.cse.ethz.ch

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http://www.cse.ethz.ch/

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CSE Case Studies Seminar

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The CSE Case Studies Seminar takes place each semester on Thursdays, 15 - 17 hours. Speakers from ETH, from other universities as well as from industry are invited to give a 2x45 minutes talk on an applied topic. The idea is to show the students a case study of an application problem containing the problem setting, the modelling, the mathematical approach and the simulation on a computer. In addition, such a case study should show what is going on in the field of CSE and what are the job perspectives for a CSE engineer. The seminars of the past academic year are given in the two following lists. Case Studies Seminar HS13 26.09.13 Matthias Troyer, Theoretical Physics

Annealing as an Optimization Method on Classical and Quantum Hardware

10.10.13 Torsten Hoefler, Computer Systems Modeling Communication in Cache-Coherent SMP Systems – A Case-Study with Xeon Phi 17.10.13 Stefan Bühler, Institute of Fluid Dynamics Numerical Simulation of Nozzle-Jet Flows and their Sound 31.10.13 Peter Bastian, Universität Heidelberg Numerical Simulation of Multiphase Flows in Porous Media 14.11.13 Christoph Winkelmann, Seminar for Applied Mathematics (SAM)

Efficient Algorithms for Disperse and Resolved Multiphase Flow Problems

05.12.13 Simon Stingelin, Endress+Hauser Flowtec AG, Reinach BL Numerical Simulation of Electromagnetic Flowmeter

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Case Studies Seminar FS14 27.02.14 Oliver Sander, RWTH Aachen The Distributed and Unified Numerics Environment (Dune) 06.03.14 Claudia Schillings, Seminar for Applied Mathematics (SAM)

Optimal Aerodynamic Design under Uncertainty - Identification, Quantification and Minimization of Uncertainties Arising in the Formulation of Aerodynamic Design Tasks

13.03.14 Florian Fruth, Formerly KTH Stockholm, Aeroelasticity Group Reduction of Aerodynamic Forcing in Transonic Turbomachinery 15.05.14 Jonas Buchli, Robotics Software for Modeling, Simulation and Real-Time Control of Legged Robots in Complex Environments

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Computational Highlight

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Towards weather and climate modeling on heterogeneous

high-performance computing architectures

O. Fuhrer1, C. Schär

2, A. Arteaga

3, N. Ban

2, M. Bianco

4, T. Gysi

5, X. Lapillonne

3,

D. Leutwyler2, C. Osuna

3, S. Rüdisühli

3, T. Schulthess

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1Federal Institute of Meteorology and Climatology MeteoSwiss

2Institute of Atmospheric and Climate Science, ETH Zurich 3Center of Climate Systems Modeling C2SM, ETH Zurich

4Swiss National Supercomputing Centre CSCS, ETH Zurich

5Department of Computer Science, ETH Zurich 6Institute of Theoretical Physics, ETH Zurich

Abstract

Accurate forecasts of the evolution of weather and climate are of high societal and

economic value. Over the last decades, numerical atmospheric models have

become the central methodological element for these forecasts. Ever increasing

high-performance computing resources have led to a continuous increase of the

computational resolution of these models. Higher resolution allows better

representing topography and key physical processes such as moist atmospheric

convection. But emerging high-performance computing architectures are

undergoing dramatic changes, typically employing heterogeneous node

architectures with mixtures of traditional CPUs and accelerators. Achieving a high

efficiency on such heterogeneous architectures requires significant refactoring of

atmospheric models. The COSMO model, an atmospheric model widely used for

numerical weather prediction and regional climate modeling, has recently been

ported to such an architecture. Here we briefly summarize the governing

equations, the main numerical algorithms, and the adaption to massively parallel,

heterogeneous architectures. Using four applications we illustrate its usefulness

and versatility for weather and climate applications.

1 Introduction

The development of weather and climate models has a long and fascinating history. For long,

weather prediction had been based on subjective and semi-empirical procedures. Two

scientific advances that paved the way towards today’s numerical models are worth

mentioning: The first is the early work of the Norwegian physicist and meteorologist Vilhelm

Bjerknes. In 1904, Bjerknes recognized that „weather forecasting should be considered as an

initial value problem of mathematical physics.“ He and his collaborators experimented for

several decades with graphical methods to integrate a simplified version of the governing

equations, but they ultimately failed.

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The first attempt to numerically integrate the governing equations were published in 1922 by

Lewis F. Richardson. He designed a finite-difference scheme on a three-dimensional grid.

Richardson is famous for the following quote: “If the coordinate chequer were 200 km square

in plan, [...] 64,000 computers would be needed to race the weather. In any case, the

organisation indicated is a central forecast-factory” (Lynch 2014). Note that the “computers”

in this quote relate to human computers – digital computers were still unheard of.

Richardson’s attempt to coordinate the work of a 64,000 staff can be considered as one of the

first thrusts to parallelize a large computational problem into a huge number of small parallel

tasks, a theme that is still common today in the realm of modern weather and climate models.

After Richardson, it took another three decades until the first research-style simulations were

published, and only in the 1970s numerical weather prediction (NWP) started to shape

operational weather forecasting.

The exponential increase of available computing power in conjunction with a multitude of

model improvements led to a rapid increase in model performance (Simmons and

Hollingsworth, 2002). For instance, today’s 5-day global weather forecasts of the European

Center for Medium Range Weather Forecasting (ECMWF) have the same quality1 as the 1-

day forecasts in 1982 (Richardson et al. 2013). While this improvement is also due to the

assimilation of additional measurement data such as satellite radiances, and the use of more

sophisticated numerical schemes, it has strongly relied on an increase of the available

computing power. When refining today’s models, in order to represent the atmosphere using

finer computational grids and more detailed descriptions of underlying physical processes, the

availability of high-performance computing systems still plays a central role.

One obvious motivation behind using high grid resolution is the important role of topography

on atmospheric flows, as well as weather and climate in general. Around 1980, the highest-

resolution global NWP models had a horizontal grid spacing of merely 100 km. As many grid

points are needed to represent a flow structure, even complex topographic barriers such as the

Alps were misrepresented as smooth gentle obstacles, and even prominent inner-Alpine

features such as the Rhine, Rhone or Inn valley were not present in the model topography.

Similarly, the topographic height and slope, and thus the blocking effect of the mountain

barrier were seriously underestimated. As a result, NWP provided merely a useful

continental-scale picture, but the weather forecast for specific locations had to be supplied

either by statistical methods or the know-how of experienced forecasters.

Atmospheric models are often community models where the development and maintenance

burden is shared among scientists from a consortium of institutions and countries. Currently,

the main workhorse for national weather prediction and regional climate simulation in

Switzerland is the model of the Consortium for Small-scale Modeling (COSMO). It is

developed and applied by over 7 national weather services and countless universities. The

COSMO model (Steppeler et al. 2003; Doms et al. 2011) can be applied with horizontal

resolutions ranging from 100 m to 100 km. Since its introduction into operational service at

MeteoSwiss in the year 2000, the horizontal resolution of this model has been continuously

refined.

One important motivation behind further refining atmospheric atmospheric models is moist

convection – the driving physical process behind thunderstorms and rain showers. Most of the

atmospheric flow normally takes place along quasi-horizontal surfaces with small vertical

1 Measured in terms of 500 hPa anomaly skill scores for the northern hemisphere extratropics.

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motions of typically less than 10 cm/s. This fundamental property of the atmosphere is due to

its density stratification, which acts to suppress vertical motions. However, diabatic heating

related to the condensation of water vapor may lead to a local destabilization that implies

large vertical motions, often exceeding 10 m/s. Over continental Europe, convective

precipitation is particularly common in the summer season and over topography. The

spectrum of atmospheric phenomena related to this process includes a wide range of features,

including cumulus clouds, rain showers, and thunderstorms (Houze 1994). The societal

importance of these events is of great significance, due to their role in heavy precipitation,

windstorm and flash flood events, and timely warnings against convective systems is thus a

key challenge to any weather service. MeteoSwiss has made major efforts in numerical

modeling to address this quest.

Representing convection explicitly rather than with parameterization schemes requires a

horizontal resolution of at least 2–4 km (Langhans et al. 2012), and thus represents a major

computational task. One of the first real-time applications of a convection-resolving model

took place during the field phase of the Mesoscale Alpine Programme (MAP) in the fall of

1999 (Benoit et al. 2002). This project was based on a collaborative effort between

MeteoSwiss, ETH, CSCS and Environment Canada. Due to computational constraints, the

simulations had to be restricted to a lead time of 27 hours, and the results became available

only 7–8 hours after the nominal model start.

Today, MeteoSwiss runs two operational models: COSMO-7 with a horizontal grid-spacing

of 6.6 km over a European domain and COSMO-2 with a horizontal grid-spacing of 2.2 km.

While COSMO-7 is run twice daily (00 UTC and 12 UTC) out to three days, COSMO-2 runs

in a so called rapid update cycle where a 33 hour forecast integrating the latest observations is

started every three hours. Both models have very strict time-to-solution requirements. In order

to be useful, a time-compression factor of at least 1:60 has to be achieved, meaning that a

one-day forecast has to complete in 24 minutes of wall-clock time. Together with the size of

the computational problem and the parallel performance of the atmospheric model, these

severe time-to-solution requirements determine the size of the required high-performance

computing system. The high-resolution of COSMO-2 allows resolving atmospheric

convection explicitly and is thus especially useful for providing advance guidance and

warnings for intense precipitation events.

In relation to climate and climate change, atmospheric convection is also of paramount

importance to the European water cycle. Normally the large-scale water cycle is characterized

by a net flux of water from ocean to land, but during the European summer season this cycle

is inverted (Hirschi et al. 2006), i.e. there is a net atmospheric water transport from land to

ocean. A key element of this inverted cycle is atmospheric convection, which moistens the

upper troposphere by extracting moisture from the boundary layer and the land surface.

Previous studies have shown that the underlying feedbacks include small-scale structures that

cannot adequately be represented in conventional models (Hohenegger et al. 2009;

Froideveaux et al. 2014).

2 Overview of the simulation approach

Weather and climate models include two categories of numerical procedures. The first

addresses the resolved fluid dynamical motions within the density-stratified atmosphere on a

rotating planet. The underlying equations are closely related to the Navier-Stokes equations,

although these equations are approximated in ways briefly discussed below.

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The second category of numerical procedures relates to a large number of physical processes

that operate at sub-grid scales, which cannot fully be resolved on the numerical mesh

considered. This includes the transfer of and interaction with electromagnetic radiation in a

broad spectral range, interactions with the water cycle (clouds, precipitation), turbulent

processes in the boundary layer and the free atmosphere, and others.

2.1 Dynamical Equations

The fluid dynamical problem has a complex character. Although sound waves do not affect

weather or climate, the respective wave propagation is an (unwanted) side effect of the

atmospheric compressibility, and thus part of the full problem. While an accurate integration

of sound modes is not needed, the fast speed of acoustic modes implies serious constraints for

the time stepping (see Section 2.3). Until about 10 years ago, most weather models were thus

using a simplified version of the governing equations, and most global climate models still do

so today. In particular, conventional weather prediction and climate models use the

hydrostatic approximation, which assumes a balance between the pressure gradient force and

the gravitational force in the vertical direction. This approximation suppresses vertical sound

propagation and the resulting simplifications have shaped the numerical schemes of most

current atmospheric models.

However, the hydrostatic approximation becomes invalid at horizontal scales below about

10 km. Overcoming this challenge, a number of filtered equations have been considered

(Durran 1989; Durran 2008; Smolarkiewicz et al. 2014), which may work well at high-

resolution in small computational domains, but have disadvantages at large scales

(>1000 km). The COSMO model thus employs the fully compressible equations (Doms et al.

2011). In a simplified form, they may be written as

dv

dt + 1

ρ∇p + gk + 2Ω× v = F (1)

∂ρ∂t

+ ∇⋅ ρv( ) = 0

(2)

dT

dt +

p

cvρ∇⋅v =

Q

cvρ

(3)

p = ρRd (1+α)T (4)

dqw

dt = ρSw (5)

This set of equations is referred to as the Euler equations. The first equation is the advective

form of the momentum equation, where v is the three-dimensional wind vector, and

is the total (Lagrangian) derivative following the motion of the flow. The

second term is the pressure gradient force, and the third term the Coriolis force with Ω

denoting the angular velocity of the rotating Earth. In comparison to the Navier-Stokes

equations, the viscous terms are omitted. This is due to the large Reynolds numbers of

atmospheric flows, which implies the use of a turbulence model represented by the force F.

d dt = ∂ ∂t + v ⋅∇

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Equations (2) and (3) relate to the mass continuity and the thermodynamic equations,

respectively, with pressure p, density ρ and absolute temperature T. These two equations are

complemented with the gas law for moist air (4), where Rd is the gas constant for dry air, and

α a factor to account for atmospheric moisture (water vapor).

The last equation (5) relates to the mass fractions of different water species. This includes

water vapor qv, cloud water qc, cloud ice qi, which are transported by the resolved wind

subject to sources and sinks Sw. In addition and depending on the model setup, precipitating

particles such as rain, snow, graupel and hail are also considered.

The terms on the right-hand side of (1-5) relate to a non-conservative force F, a diabatic

heating Q, and source terms Sw relating to the different water species. In general, these terms

also include sub-grid scale fluxes, and they are specified through the parameterization

packages.

2.2 Parameterizations

In essence, parameterizations are designed to provide an estimate of subgrid-scale fluxes and

sources/sinks as a function of the explicitly resolved variables. Typical parameterization

packages include a boundary-layer and turbulence scheme to account for the turbulent

transport of momentum, energy and moisture; a land-surface scheme to represent temperature

and soil moisture conditions in the uppermost meters of the soil, as needed for the

computation of evapotranspiration and surface heat fluxes; a radiation scheme that computes

the transfer of radiation in a broad spectral range (covering solar and terrestrial radiation from

the far infrared to ultraviolet) as well as the emission, absorption and scattering of radiation

by the underlying surface, atmospheric gases, as well as aerosol and cloud particles; a

microphysics scheme that provides the source and sink terms for the different water species,

which may result from condensation of water vapor and ensuing cloud microphysical

processes; and a parameterization of convective clouds which must represents the associated

vertical exchange of heat and moisture and the ensuing formation of clouds and precipitation.

Some aspects in these parameterizations can be formulated close to their underlying physical

principles, as for instance the radiative transfer in moist air. Other aspects rely on semi-

empirical approaches and may include tunable parameters, as for instance in the convection

and the land-surface schemes. It is thus evident that replacing a parameterization by an

explicit treatment is a promising strategy, as it will reduce uncertainties and render the model

closer to first principles.

2.3 Discretization

A complete description of the computational grid, horizontal and vertical coordinate

transformation, as well as the finite-difference methods employed to discretize the above

equations is given in Steppeler et al. (2003) and Doms et al. (2011). The following is a

summary of the main methods employed.

Before discretizing the governing equations (1)–(5), two coordinate transformations are

applied. The governing equations are formulated with respect to the rotating Earth and are

thus valid for any coordinate system rotating with the Earth. The most natural and convenient

way to take the spherical shape of the Earth into account is via a spherical coordinate system.

In order to avoid convergence of the meridians and pole singularities we use rotated spherical

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coordinates (λ, ϕ, z) in which λ is longitude, ϕ is latitude, and z = r – rearth is the geometrical

height above mean sea level. In a rotated spherical coordinate system the pole is tilted and can

be positioned such that the equator runs through the center of the model domain, such as to

ensure a fairly isotropic grid. For very small domains with negligible impact of the curvature

of the Earth’s surface, the transformed equations become identical to those for a tangential

Cartesian coordinate system.

Figure 1: Vertical cross-section illustrating the vertical distribution of model levels for a vertical coordinate

spacing of Dz = 1 km. The domain has a length of 150 km and shows the Alpine topography at 7.87°E

extending from the Po valley over the Monte Rosa massif and the Bernese Alps to the Rhine (from left to

right).

Furthermore, most atmospheric models employ a terrain-following vertical coordinate system

(e.g. Gal-Chen and Sommerville 1975; Schär et al. 2002). Terrain-following vertical

coordinate transformations map the atmospheric domain under consideration upon a

rectangular computational mesh and significantly simplify the formulation of the lower

boundary condition. Figure 1 shows the vertical coordinates for a vertical cross-section

through the Alps. The use of terrain-following coordinates implies truncation errors with the

same leading order as present in the underlying scheme. It is thus relevant to use a coordinate

transformation with smooth coordinate surfaces (Schär et al. 2002, Leuenberger et al. 2010).

This is illustrated in Figure 1, where the small-scale topographic features are no longer

present at upper levels.

The physical modes of meteorological importance (Rossby waves, baroclinic and buyancy

waves, advection) represented by equations (1)–(5) are typically of much lower frequency

than the highest-frequency modes permitted by the equations (acoustic modes, Lamb waves).

Similar to many other models, COSMO employs a time-splitting method (Marchuk 1974)

integrating the lower frequency modes with a larger timestep. To this end, the terms in the

prognostic equations (1)–(3) are split into fast and slow terms.

∂φ∂t

= Pf φ( )+Ps φ( ) , (6)

where φ stands for any of (v, p, T) and the two terms on the right-hand side correspond to the

fast and slow terms, respectively. For instance, in the thermodynamic equation (3) the second

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term is categorized as fast, and the term on the right-hand side as slow. The time-

discretization follows closely the splitting method proposed by Wicker and Skamarock

(2002), where a three-stage Runge-Kutta scheme (RK3WS) is employed for the large

timestep Δt, while sub-stepping is used with a small timestep Δτ for the fast processes. In

more detail this is:

1st RK-stage !φ* −φn

Δt / 3= P

s!φ*,φn( ) (7)

Sub-stepping φυ+1 = φυ +Δτ Pf φυ+1,φυ( )+ Ps !φ*,φn( )"#$

%&'

for φ n ⇒ φ* (8)

2nd RK-stage !φ** −φn

Δt / 2= P

s!φ**,φn( ) (9)

Sub-stepping φυ+1 = φυ +Δτ Pf φυ+1,φυ( )+ Ps !φ**,φn( )"#$

%&'

for φ n ⇒ φ** (10)

3rd RK-stage !φ*** −φ n

Δt= P

s

!φ***,φ n( ) (11)

Sub-stepping φυ+1 = φυ +Δτ Pf φυ+1,φυ( )+ Ps !φ***,φn( )"#$

%&'

for φ n ⇒ φ*** (12)

The slow tendencies are kept constant during the sub-stepping procedure in Equations (8),

(10), and (12). Due to implicit treatment of vertical terms both in the fast and slow modes, an

tridiagonal linear system has to solved for each Runge-Kutta stage and for each small

timestep Δτ. This is reflected in the fact that all Ps- and Pf-terms in (7-12) depend upon two

time levels. For the COSMO model with 2.2 km horizontal resolution, the large and small

timesteps typically are set to Δt = 20 s and Δτ = 3.33 s, respectively.

The RK3WS scheme is formally only 2nd

-order accurate in time (Baldauf 2008; Baldauf et al.

2011) but is mainly used for its efficiency and in order to stabilize the 5th

-order upwind

advection. As compared to Wicker and Skamarock (2002), the time-splitting scheme in

COSMO is extended by an implicit vertical advection calculation (contained in Ps) using a

Crank-Nicholson scheme, spatially discretized using 2nd

-order centered differences. The main

reasons for this choice are the much smaller grid spacing in the vertical direction as compared

to the horizontal directions and the occurrence of large vertical velocities due to explicitly

resolved atmospheric convection.

For the advection of scalar fields such as the water constituents of the atmosphere (LHS of

Equation (5)) the COSMO model has several options. The most frequently used scheme is a

three-dimensional extension of the Bott scheme (Bott 1989) in a mass-consistent manner

(Easter 1993) and usable for Courant numbers larger than unity (Skamarock 2006). While this

scheme excels with its mass conservation properties, its application in combination with a

terrain-following coordinate transformation over steep terrain can sometimes be problematic.

2.4 Implementation on hybrid architectures

Over the past four years, in a joint effort by MeteoSwiss, CSCS and ETH, a version of the

COSMO model capable of executing on hardware with graphics processing units (GPUs) has

Ps

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been developed. The current official release version of the COSMO model source code has

been written almost two decades ago and is implemented as a monolithic Fortran 90 code

comprised of approximately 300,000 lines of code. Here, the term “monolithic” refers to a

source code with almost no external dependencies, written entirely in a single programming

language, and which does not make extensive use of modern software engineering concepts

such as modular programming or encapsulation. While such a software architecture may also

have certain advantages, achieving performance portability across a wide range of emerging

high-performance computing architectures, while retaining a single maintainable source code

is a formidable challenge. Here we briefly outline the different porting strategies employed in

the different parts of the source code (see Fuhrer et al. 2014 for more details).

Figure 2: Software architecture of the COSMO version capable of running on hybrid architectures. Red

colors correspond to user code, purple colors are for re-usable middleware tools, blue is for I/O and system

libraries (from Fuhrer et al. 2014).

The part of the source code which solves the discretized Euler equations (cf. Sections 2.1 and

2.3) is referred to as the dynamical core. For typical weather and climate applications, the

dynamical core requires approximately 60% of the total runtime and is thus the most

performance critical part of the model. With a total of 60,000 lines of code, it has been

completely rewritten with a disruptive programming model using C++. The central emphasis

of the new implementation was to allow for a separation of concerns between the user-

specified parts (equations, discretization, algorithm) and the architecture-specific, optimized

implementation. Figure 2 illustrates the software architecture of the refactored dynamical core

(in red and purple). The implementation is heavily based on a domain-specific language

(DSL) named STELLA (Gysi et al., in preparation; Fuhrer et al. 2014) which allows for a

high-level specification of the required finite-difference operators. Similarly, the boundary

conditions and ghost-cell updates required as a consequence of the domain-decomposition

across compute nodes are built upon a re-usable software framework and a generic

communication library (GCL). All architectural details and optimizations are hidden from the

user-code, which allows retaining a single, performance portable source code.

For all remaining parts of the COSMO code (main, physical parametrizations, assimilation) a

less disruptive porting strategy based on compiler directives (OpenACC) has been employed

(Lapillonne and Fuhrer 2014). The choice to leave these parts of the code in their original

Fortran form was a pragmatic one due to limited resources for refactoring and to minimize the

impact of changes on the existing developer community.

29

3 Applications

3.1 Numerical weather prediction

Since almost a decade, high-resolution numerical weather prediction (NWP) models are

routinely run, resolving explicitly deep convection at a horizontal mesh size of a few

kilometers. This is a major step forward since the parameterization of deep convection is a

large source of uncertainty for lower-resolution models. Several studies have shown that

convection-resolving models provide significantly better quantitative precipitation forecasts

(Clark et al. 2007; Lean et al. 2008; Weusthoff et al. 2010). On the other hand, due to the high

spatial and temporal resolution, the convection-resolving models are more expensive in terms

of calculation capacity than their lower-resolution counterparts.

Numerical weather prediction is also a central element of weather forecasting at MeteoSwiss.

MeteoSwiss has access to several global models, most importantly IFS-HRES model from the

European Center for Medium Range Weather Forecasting (ECMWF). It uses forecasts of the

IFS-HRES model as lateral boundary conditions for running its own regional models using

COSMO, which are currently COSMO-7 and COSMO-2 (see Introduction). Figure 3 shows

the whole modeling “chain” used for operational weather forecasting at MeteoSwiss, where

the convection-permitting high-resolution model COSMO-2 comes at the very end of the

modeling chain. Forecasters use these models as the basis for issuing daily forecasts and

weather warnings to the general public as well as to key clients from the public, aviation,

agriculture, and industrial sectors. The simulations are executed on a dedicated high-

performance computing system at the Swiss National Supercomputing Centre (CSCS) in

Lugano and must satisfy very high requirements in terms of timeliness and reliability.

Figure 3: Modeling chain use for operational weather forecasting at MeteoSwiss. The global model IFS-

HRES from the European Center for Medium Range Weather Prediction (ECMWF) provides boundary

conditions for COSMO-7. COSMO-2 in turn is nested into the domain of COSMO-7 and receives its

boundary conditions from there.

Many important weather phenomena over the Alps such as diurnal convection, Foehn, and

fog are strongly influenced by the underlying complex topography. Even with a grid spacing

of 2.2 km only deep and organized convection can reasonably resolved and small and medium

sized Alpine valleys are still not well represented. In the framework of a development effort

since 2012, MeteoSwiss is developing the capability to run COSMO with a horizontal grid

30

spacing of 1.1 km (COSMO-1). COSMO-1 will have a total number of 1158x774x80

gridpoints, cover a domain slightly larger than COSMO-2 and run in a similar forecasting

cycle as COSMO-2 with 8 forecasts per day ranging to at least +24 hours. Figure 4 shows a

comparison of 10 m wind fields for COSMO-2 and COSMO-1 illustrating the more detailed

and realistic flow structures that can be achieved by increasing the horizontal resolution.

Figure 4: Wind forecast for COSMO-2 (left) and COSMO-1 (right) at 10 m above ground for an area in

southeastern Switzerland showing the finer details that are available in the COSMO-1 forecast. The upper

panels show the wind speed (contours) and the wind barbs at 10 m height. The bottom panels show the

topography (contours) overlaid with wind barbs.

Nevertheless, accurate prediction of convective-scale severe weather events continues to be a

major challenge. The inherent nonlinearity of the their dynamics and physics and the small

spatial and temporal scales render deterministic forecasts of a single model simulation highly

uncertain (Hohenegger and Schär 2007). A way to address the inherently limited

predictability of high-resolution forecasts is through the development of ensemble prediction

systems (EPS) (Schwartz et al. 2010). An EPS consists of multiple forecasts covering the

same time period (members) but with perturbed initial conditions, boundary conditions and

model physics in order to attempt the generation of a representative sample of possible future

states of the atmosphere. EPS allow to assess the uncertainty of a specific forecast and are

superior to deterministic forecasts at providing guidance for rare events, such as severe

thunderstorms or heavy precipitation (Murphy 1991).

Similar to many Monte Carlo approaches, ensembles are trivially parallel and do not pose a

challenge in terms of scalability of the atmospheric model. But in order to have a good sample

of the probability distribution function of possible atmospheric states, there is a strong

pressure to have ensembles with a large number of ensemble members (Richardson 2000).

MeteoSwiss is currently developing a convection-permitting ensemble system (COSMO-E)

with a total of 21 members and a horizontal resolution of 2.2 km. Figure 5 shows an ensemble

forecast from COSMO-E for the probability of exceeding a certain threshold of precipitation.

In general, ensemble forecast products provide uncertainty information since it is essential to

31

estimate the impact of uncertainties on forecast accuracy. No weather prediction can be

considered complete without a forecast of the associated flow-dependent predictability

(Palmer 2000).

As compared to COSMO-7 and COSMO-2, COSMO-1 and COSMO-E comprise an increase

of computational problem size of a factor of ~40. Mapping such a large computational

problem onto a high-performance computing system without a drastic increase in investment

and running costs is only possible with the use of the GPU-capable version of COSMO and

through a reduction of the floating point arithmetic precision from double (8 bytes per

floating point number) to single (4 bytes per floating point number).

Figure 5: Ensemble forecast with a horizontal resolution of 2.2 km of the probability to exceed a

precipitation amount of 5mm/6h for four different 6h time intervals of Monday September 22, 2014.

3.2 Regional climate simulations

The mean summer climate of Central and Southern European is projected to warm by about

3-7ºC by the end of the century, if anthropogenic greenhouse gas emissions should proceed

on a business-as-usual pathway (IPCC 2013). These projections represent a serious challenge

to climate science, as they exceed past historical variations (Luterbacher et al. 2004), and as

extreme summers are expected to warm even stronger (Schär et al. 2004; Fischer and Schär

2010). Besides the warming, simulations also suggest a pronounced reduction of summer

precipitation, in particular in the Mediterranean region, and the warming and drying are

intimately linked to each other (Seneviratne et al. 2006). This illustrates that the simulation of

the European climate must consider the whole water cycle, including the challenging

convective events that are characteristic for the summer season.

Representing moist convection in an explicit rather than parameterized fashion is thus an

attractive way to proceed. However, due to the high computational costs, the use of

convection-resolving models in climate studies is very limited, typically restricted to

relatively small domains and/or few seasons (Grell et al. 2000; Hohenegger et al. 2008; Knote

et al. 2010; Prein et al. 2013). Only a very limited number of studies have addressed sizable

32

domains exceeding scales of 500 km (Kendon et al. 2014; Ban et al. 2014, 2015), and these

have demonstrated a significant improvement in skill regarding short-term heavy precipitation

events.

For further illustration, Figure 6 shows a validation in an extended Alpine domain, using a

computational mesh of 500x500x60 gridpoints with a horizontal grid spacing of 2.2 km using

a version of the COSMO model (Ban et al. 2014). For validation purposes, the simulations are

driven at the lateral boundaries by reanalysis data (which represents the actual meteorological

conditions as closely as possible), and the simulated precipitation is compared against

observations from a set of 62 rain gauges (that provide hourly data throughout the period).

Figure 6 shows the mean diurnal cycle of precipitation amounts, heavy precipitation events

(based on the 99th

percentile of events), and the average diurnal cycle on heavy precipitation

days (with peak precipitation exceeding the 95th

percentile). Blue and red lines, respectively,

show the 12km-resolution simulation using parameterized convection, and the 2km

simulation using explicit convection. A dramatic improvement is evident with high resolution.

This demonstrates the promising potential of high-resolution climate simulations.

Figure 6: Validation of summer (June-July-August) precipitation against 62 Swiss rain gauge stations in the

period 1998–2007. Observations are shown in black, a simulations with 12 km resolution and parameterized

convection in blue, and the high-resolution simulation with 2 km resolution in red. The panels show the mean

diurnal cycles of (left) mean precipitation, (middle) heavy hourly precipitation defined by the 99th percentile,

and (right) precipitation on extreme precipitation days defined by the top 5% precipitation days. The

validation is performed using a reanalysis driven simulation (courtesy of Nikolina Ban, ETH Zürich, Ban et

al. 2015).

The set-up of the previous study has recently been used to conduct scenario simulations

covering decade-long time slices of current and future climate conditions under anthropogenic

greenhouse gas scenarios (Ban et al. 2015). For the summer season, results confirm a

pronounced reduction of mean precipitation (by more than 30%) that is familiar from

previous studies. However, despite this drying, the intensity of heavy hourly precipitation

events is projected to increase with the event size, by up to about 20%. This increase has been

shown to be consistent with the Clausius-Clapeyron relation and amounts to about 6-7% per

degree large-scale warming (Ban et al. 2015).

In an on-going project, the refactored GPU-enabled COSMO version is used to extend these

simulations to European scales, using a domain size of 1500x1500x60 gridpoints. This

domain requires about 10 times more computing resources than that of Ban et al. (2014,

2015). The simulations only become feasible when exploiting a GPU-based high-performance

computing system. The testing of the GPU-enabled version in its climate set-up is currently in

an advanced phase using seasonal and year-long integrations. Figure 7 shows a snapshot from

OBS

2 km

12 km

33

an extended simulation covering the winter storm Kyrill in January 2007. Comparison against

conventional-resolution climate simulation (left panel) reveals a more realistic cloud field, as

well as high-resolution details and an enhanced level of organization in the precipitation

distribution.

In summary, recent results demonstrate that high-resolution COSMO simulations using the

GPU-enabled version represent a highly promising avenue in continental scale climate

studies. High-resolution simulations enable addressing short-term heavy precipitation events

(which are not amenable in conventional models) and raise the credibility of the simulations

(as they are much closer to the underlying physical principles). There is also a thrust towards

the use of kilometer-scale global model simulations (Palmer 2014). The regional simulations

using the new COSMO version on heterogeneous architectures are an attractive tool to

approach this goal.

Figure 7: Visualization of cloud pattern (grey scale) and hourly precipitation rate (color scale, in mm/hour)

for a prototype convection-resolving simulation covering the European continent. Left and right-hand panels

relate to simulations with 50 and 2 km grid spacing, respectively. Differences to note include: the fine-scale

precipitation systems such as the cold frontal-rainbands or the prefrontal convective activity, the more

realistic organization of convective elements to the rear of the simulated storm, and the rich details evident in

the cloud pattern. The convection-resolving simulation has been run on a heterogeneous compute

architecture with GPUs, using a mesh of 1500x1500x60 grid points (courtesy of David Leutwyler, ETH

Zurich).

4 Parallel performance

The COSMO model employs a two-dimensional domain decomposition along the two

horizontal directions to distribute work across compute nodes (see Figure 8). The vertical

direction is not decomposed, due to the abundance of vertically implicit discretizations which

require the solution of banded small linear systems. Inter-node communication is dominated

by nearest neighbor communication between adjoining sub-domains. On the node, there are

two levels of parallelism. The sub-domain is further split into coarse-grained blocks which are

mapped onto OpenMP threads or CUDA blocks, which require only very little

synchronization. Within the blocks, horizontal grid-points are mapped onto SIMD vectors or

CUDA threads, which execute in lock-step. The three levels of parallelism allow for a flexible

mapping of the application to different hardware architectures. The number of horizontal

0.1 0.2 0.5 1 2 5

34

gridpoints per sub-domains Nsub and per block Nblock are tunable parameters for optimal

efficiency on different hardware architectures.

Figure 8: Two-dimensional domain decomposition onto compute nodes along the latitudinal and longitudinal

direction. Each sub-domain is mapped onto a compute-node. Shown is the topography (in meters) of the

operational 2 km model of MeteoSwiss (COSMO-2). Size of ghost-cell regions is exaggerated for illustration

purposes.

Figure 9: Scaling results on a hybrid Cray XC30 (Piz Daint). Left: Weak scaling for sub-domains with Nsub =

128 x 128 (solid lines) and Nsub = 64 x 64 (dashed lines) gridpoints per node. Right: Strong scaling for total

domain sizes Ntot = 512 x 512 (solid line) and Ntot = 256 x 256 (dashed line). Colors indicate results using

the original Fortran version on CPU (blue), the refactored version on CPU (red) and on GPU (orange).

Runtime is given in seconds and corresponds to a total of 100 timesteps (from Fuhrer et al. 2014).

In the following, we present performance results on a hybrid Cray XC30 (Piz Daint) at the

Swiss National Supercomputing Centre (CSCS) in Lugano. Piz Daint has a hybrid node

architecture with an Intel Xeon E5-2670 CPU with 32 GB of host memory, and a NVIDIA

Tesla K20X GPU with 6 GB of GDDR5 memory. The CPU and GPU are connected via the

PCIe bus and the compute nodes are interconnected with Cray’s proprietary Aries network

that has a three-level dragonfly topology. Performance results have been measured using the

original Fortran code (running on CPU) compared against the refactored code (running both

on CPU or GPU).

We first consider weak scalability: The left panel of Figure 9 shows near perfect weak

scalability of the code in all configurations up to 1000 nodes (i.e. 16,000 CPU cores or

35

2,688,000 GPU cores). Two configurations with Nsub = 128 x 128 and Nsub = 64 x 64

horizontal gridpoints per node with 60 vertical levels have been chosen for these experiments.

Comparing the CPU results from the current Fortran code (blue) and the refactored code (red)

one can observe that a speedup of approximately 1.5x has been achieved by the refactoring.

Moving the refactored code from the CPU (red) to the hybrid mode with GPUs (orange)

results in a further speedup of 3.0x.

Strong scalability is the more relevant test for weather and climate codes, since often a fixed

problem size has to be solved below a certain threshold in time-to-solution threshold, in order

to be useful (see Introduction). Typical problem sizes for the COSMO model range from 300

x 300 to 2000 x 2000 gridpoints. The right panel of Figure 9 shows results from two

configurations, on with a total domain size of Ntot = 256 x 256 and one with Ntot = 512 x 512

horizontal gridpoints. Each configuration has 60 vertical levels. While the CPU results show

good scalability up to high node counts – performance start leveling off at around 10

horizontal gridpoints per core – the GPU results saturate at much lower node counts. A

minimum number of horizontal gridpoints (i.e. CUDA threads) is required to efficiently use

the GPU. The horizontal black line in the right panel of Figure 9 delimits the typical time-to-

solution requirement for the Ntot = 512 x 512 problem size. Thus, while the refactored code

requires 48 CPU nodes (with one Intel Xeon E5-2670) to achieve the time-to-solution limit,

the same code requires only 14 hybrid nodes (each with one Intel Xeon E5-2670 and a K20X

GPU).

While the community is still mesmerized by the astronomical number of floating point

operations a supercomputer can execute per second (FLOP/s), the power consumption of the

fastest supercomputers has already exceeded a megawatt (MW) of electricity. As a

consequence, the cost of electricity to run these systems has become substantial and engineers

designing supercomputers as well a computer centers have begun to take interest in the energy

efficiency. A natural metric for measuring en energy efficiency of supercomputers is the

number of floating point operations per second per watt (FLOPS/s/W) and has become

widespread. For COSMO, energy-to-solution decreases even more (approximately by a factor

7x) than time-to-solution when moving from a pure CPU-based system to a system with a

hybrid node architecture with an accelerator. The main reason is that COSMO is a memory

bound application and that a GPU only uses less than ~60% of its total power envelope when

running COSMO. In contrast, CPUs in use today for high-performance computing systems

still use over ~80% of their power envelope, even when running idle.

5 Conclusions and Outlook

An atmospheric model (COSMO) and its underlying governing equations and numerical

algorithms have been presented. It is based on a dynamical core which integrates the Euler

equations, and a set of physical parametrizations which describe sub-grid scale processes and

source terms. COSMO is the first atmospheric model which has been fully ported to hybrid

high-performance computing architectures with GPUs that can be used productively for

numerical weather prediction and regional climate modeling. The refactoring for hybrid

architectures has been done using different porting approaches for different parts of the

model. The dynamical core has been rewritten in C++ and is based on a generic library that

provides a domain-specific language for stencil computations. The physical parameterizations

as well as the rest of the model code have been retained in Fortran and ported using compiler

directives. While to former allows to retain a single high-level source code that gives near

36

optimal performance for different hardware architectures, using compiler directives has

proven to give good performance but also increased the complexity of the code and led to

hardware specific code in performance critical sections. The adaption of the source code of

COSMO to hybrid architectures was a significant investment and required over 15 man-years.

In this process, the readiness to abandon the usual practices for new programming paradigms

and the intense collaboration of an interdisciplinary team ranging from atmospheric scientists

to computer scientist were key elements for success. Using different applications from

weather and climate research, we have demonstrated that the hybrid version of COSMO can

already be applied for a wide range of applications.

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.

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5

CSE Research Projects

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Title: Multi-level µ-FE analysis for human bone structures

Researchers: Peter Arbenz?

Cyril Flaig?

G. Harry van Lenthe†

Ralph Muller†

Erhan Turan?

Institute/ ?Computer Science Department, ETH ZurichGroup: †Institute for Biomechanics, ETH Zurich

Description:

Micro-structural finite element (µFE) analysis based on high-resolution computed tomog-raphy represents the current gold standard to predict bone stiffness and strength. Recentprogress in solver technology makes possible simulations on large supercomputers thatinvolve billions of degrees of freedom.In order to be effectively solved quickly and reliably on state-of-the-art parallel com-puters, the resulting µFE models require advanced solution techniques. We developedan improved solver that has a significantly smaller memory footprint compared to thecurrently used solvers. This new approach fully exploits the information that is con-tained in the underlying CT image itself. It admits to execute all steps in the underlyingmultigrid-preconditioned conjugate gradient algorithm in matrix-free form.The reduced memory footprint allows to solve bigger bone models on a given hardware.It is an important step forward to the clinical usage of µFE simulations.

References:

P. Arbenz, C. Flaig, D. Kellenberger: Bone structure analysis on multiple GPGPUs. J.Parallel Distrib. Comput. 74, 2941–2950 (2014),

E. Turan, P. Arbenz: Preconditioning aspects of large scale micro finite element analysisof 3D bone poroelasticity. Parallel Comput. 40, 239–250 (2014).

P. Arbenz, E. Turan: Preconditioning for large scale micro finite element analyses of 3Dporoelasticity. In: Applied Parallel and Scientific Computing (PARA 2012). P. Manninen,P. Oster (eds.). LNCS 7782, pp. 361–374. Springer, Heidelberg, 2013.

C. Flaig, P. Arbenz: A highly scalable matrix-free multigrid solver for µFE analysis basedon a pointer-less octree. In Large Scale Scientific Computing LSSC’11. I. Lirkov, S.Margenov, J. Wasniewski (eds.). LNCS 7116, pp. 498–506. Springer, Heidelberg, 2012.

C. Bekas, A. Curioni, P. Arbenz, C. Flaig, G.H. van Lenthe, R. Muller, A.J. Wirth:Massively parallel graph partitioning: A case in human bone simulations. In Combinato-rial Scientific Computing. Uwe Naumann, Olaf Schenk (eds.). Chapman and Hall/CRC,2012. pp. 407–425.

42

C. Flaig, P. Arbenz: A scalable memory efficient multigrid solver for micro-finite elementanalyses based on CT images. Parallel Comput. 37 (12): 846-854 (2011).

43

Title: A self-consistent particle-in-cell finite element timedomain solver for large accelerator structures


Andreas Adelmann†

Yves Ineichen?,†

Institute/ ?Computer Science Department, ETH ZurichGroup: †Paul Scherrer Institute, Villigen

Description:

This research project focuses on efficiently solving self-consistent Maxwell’s equationsin large and complex shaped accelerator structures primarily in the light of the firstpart of the PSI-FEL/LEG1 project. Our prime goal is a quantitative and self-consistentmodeling of the injector in the PSI-FEL/LEG project.A novel parallel multi-scale modeling code is developed, using knowledge on paralleliza-tion, numerical methods and accelerator modeling developed in recent projects. Particle-in-cell (PIC) methods combined with novel finite element discretization techniques andparallel implementation will enable us to build up the unique capabilities with respectto quantitative modeling, needed in order to predict with sufficient accuracy beam andfield properties in the detailed design and optimization of the PSI-FEL/LEG project.Benchmarking and code comparison will be done in collaboration with researchers fromLawrence Berkeley Laboratory (LBL) and CERN.

References:

Y. Ineichen: Toward massively parallel multi-objective optimization with application toparticle accelerators, PhD thesis, Computer Science Department, ETH Zurich, January2013. http://dx.doi.org/10.3929/ethz-a-009792359

Y. Ineichen, A. Adelmann, A. Kolano, C. Bekas, A. Curioni, P. Arbenz: A parallelgeneral purpose multi-objective optimization framework, with application to beam dynam-ics. Technical report arXiv:1302.2889v1 [physics.acc-ph], February 2013, http:

//arxiv.org/abs/1302.2889.

Y. Ineichen, A. Adelmann, C. Bekas, A. Curioni, P. Arbenz: A fast and scalable lowdimensional solver for charged particle dynamics in large particle accelerators. Comput.Sci. Res. Dev. 28 (2-3): 185–192 (2013).

Y. Ineichen, A. Adelmann, C. Bekas, A. Curioni, P. Arbenz: A massively parallel gen-eral purpose multi-objective optimization framework, applied to beam dynamic studies.Proceedings of ICAP2012, Rostock-Warnemunde, Germany, 2012, pp. 62–66.

44

Title: A self-consistent particle-in-cell time-domain solverincorporating radiative losses and interaction


Andreas Adelmann†

Christof Metzger-Kraus?


Description:

The simulation of radiative interactions in a particle accelerator is a challenging problem.Existing codes reduce the dimensionality of the problem, neglect transient effects or limitthe number of particles and the complexity of the geometry. Our plan is to computethe electromagnetic field of the particles in time domain on a hierarchy of meshes. Toreduce the memory consumption we plan to embed co-moving finer meshes in a coarsermesh. Even with this reduction the computation of the resulting problem will have to becarried out on thousands of compute nodes.The resulting tool will be seamlessly integrated into the particle tracker Object Ori-ented Parallel Accelerator Library (OPAL) that has been developed at PSI allowing forsimulations of particle accelerators from start to end (S2E) including magnetic chicanesconsisting of four deflecting dipoles.

References:

C. Kraus, A. Adelmann, P. Arbenz: Perfectly matched layers in a divergence preservingADI scheme for electromagnetics. J. Comput. Phys. 231 (1): 39-44 (2012).

C. Metzger-Kraus: A self-consistent particle-in-cell time-domain solver incorporating ra-diative interaction. ETH Zurich, PhD Thesis No. 22154, 2014. http://dx.doi.org/10.3929/ethz-a-010261293.

45

Title: Resonant lossy electromagnetic structures


Hua Guo?

Yoichi Matsuo?‡

Benedikt Oswald†


‡Department of Mathematics, Keio University, Japan

Description:Resonant electromagnetic cavity structures are used in virtually all types of particleaccelerators. The X-ray free electron laser currently under study at the Paul ScherrerInstitute, is no exception and will consist of a large variety of radio frequency (RF)structures for guiding and accelerating electrons from the photo-cathode through thelinear accelerator section.We introduce a 3-dimensional electromagnetic eigenmodal algorithm for the theoreticalanalysis of resonating nano-optical structures. The method, a variant of the Jacobi-Davidson algorithm, solves the electric field vector wave, or curl-curl, equation for theelectromagnetic eigenmodes of resonant optical structures with a finite element method.In particular, the method includes transparent boundary conditions that enable the anal-ysis of resonating structures in unbounded space.

References:

Y. Matsuo, H. Guo, P. Arbenz: Experiments on a Parallel Nonlinear Jacobi–DavidsonAlgorithm. Procedia Comput. Sci. 29, 565-575 (2014), Proceedings of the InternationalConference on Computational Science (ICCS) 2014.

H. Guo, P. Arbenz, B. Oswald: A large-scale nonlinear eigensolver for the analysis ofdispersive nanostructures. Computer Phys. Comm. 184 (8): 1898-1906 (2013).

H. Guo, B. Oswald, P. Arbenz: 3-dimensional eigenmodal analysis of plasmonic nanos-tructures. Optics Express. 20 (5): 5481-5500 (2012)

H. Guo: 3-dimensional eigenmodal analysis of electromagnetic structures. ETH Zurich,PhD Thesis No. 20947, 2012. doi:10.3929/ethz-a-007599690.

46

Title: Parallelization of the time integration for time-periodic flow problems


Daniel Hupp?

Dominik Obrist†

Institute/ ?Computer Science Department, ETH ZurichGroup: †Institute of Fluid Dynamics, ETH Zurich

Description:We investigate parallel algorithms for the solution of flow problems that are periodic intime. Finite difference approximations on a mesh in space-time are used. For periodicsolutions, the discretized problem can be written as a large non-linear system of equations.This system of equations is solved by a Newton-Krylov method, using a preconditionedGMRES solver. The parallel performance of this algorithm is illustrated by a number ofnumerical experiments in one and two space dimensions.

References:

P. Arbenz, D. Hupp, D. Obrist: A parallel solver for the time-periodic Navier–Stokesequations. In: Parallel Processing and Applied Mathematics (PPAM 13), Part II. R.Wyrzykowski, J. Dongarra, K. Karczewski, J. Wasniewski (eds.). Lecture Notes in Com-puter Science 8385, pp. 291–300. Springer, Berlin, 2014.

P. Arbenz, A. Hiltebrand, D. Obrist: A parallel space-time finite difference solver forperiodic solutions of the shallow-water equation. In Parallel Processing and AppliedMathematics (PPAM 11), Part II. R. Wyrzykowski, J. Dongarra, K. Karczewski, J.Wasniewski (eds.). Lecture Notes in Computer Science 7204, pp. 302–312. Springer,Berlin, 2012.

47

Title: Direct numerical simulation of multiple cycles in a valve/piston as-sembly and the effect of compression on the flow, temperature andcomposition under engine-like conditions

Institute/Group:

M. Schmitt1, C.E. Frouzakis1, A.G. Tomboulides2, Y.M. Wright1,K. Boulouchos11Aerothermochemistry and Combustion Systems Laboratory, ETHZ2Department of Mechanical Engineering, University of WesternMacedonia, 50100 Kozani, Greece

The dynamics and multiple-cycle evolution of the incompressible flow induced by a movingpiston through the open valve of a motored piston-cylinder assembly was investigated usingdirect numerical simulation (DNS). A spectral element solver, adapted for moving geometriesusing an Arbitrary Lagrange/Eulerian formulation, was employed. Eight cycles were simulatedand the ensemble- and azimuthally-averaged data were found to be in good agreement withexperimentally determined means and fluctuations at all measured points and times. Duringthe first half of the intake stroke the flow field is dominated by the dynamics of the incomingjet and the vortex rings it creates. With decreasing piston speed a large central ring becomesthe dominant flow feature until the top dead center. The flow field at the end of the previouscycle is found to have a dominant effect on the jet breakup and the vortex ring dynamics belowthe valve and on the observed significant cyclic variations. Based on statistical averaging, theevolution of the turbulent flow field during the first half of the intake stroke is dominated by thejet breakup process leading to a strongly anisotropic behavior. In the second part of the intakestroke, the decrease of the incoming jet velocity results in a more isotropic behavior.

The effect of compression on the flow, temperature and composition inside a cylinder wasalso investigated using DNS. The initial conditions were obtained from a separate DNS of theintake stroke in the open-valve setup and includes thermal and species mixing. The results showsignificant changes of the turbulence and temperature fields during compression: The decreaseof kinematic viscosity resulting from the increasing pressure results in smaller turbulent lengthscales and higher dissipation rates. Temperature fluctuations away from the walls decreaseslightly during the first half but increase strongly during the second half of the compressionstroke towards the Top Dead Center (TDC) due to heat transfer to and from the walls and turbu-lent transport. At TDC the turbulent flow field is anisotropic, and the axial fluctuation velocityis approximately 30% smaller than the fluctuation velocities in the radial and azimuthal direc-tions. The integral length scale of temperature is approximately 25% higher than the integrallength scale of turbulent kinetic energy. The stratification in the species concentration is foundto be practically negligible.

References:• M. Schmitt, C.E. Frouzakis, A. Tomboulides, Y.M. Wright, K. Boulouchos, Direct numericalsimulation of multiple cycles in a valve/piston assembly, Phys. Fluids, 26, 035105, (2014)• M. Schmitt, C.E. Frouzakis, A. Tomboulides, Y.M. Wright, K. Boulouchos, Direct numericalsimulation of the effect of compression on the flow, temperature and composition under engine-

48

A B

C

36°CA 90°CA72°CA51.5°CA

5000 0

Vorticity magnitude [m2/s3]

(a)

Figure 1: (a) volume renderings of the instantaneous vorticity magnitude at different times during theexpansion of the first cycle, Velocity magnitude, temperature and H2O mass fraction on a vertical sliceat (b) BDC and (c) on a horizontal slice 3.75 mm below the cylinder head at TDC.

like conditions, Proc. Combust. Inst., (in press)

49

Title: Entropy production analysis for mechanism reduction

Institute/Group:

M. Kooshkbaghi, C.E. Frouzakis, K. Boulouchos, I.V. KarlinAerothermochemistry and Combustion Systems Laboratory, ETHZ

A systematic approach based on the relative contribution of each elementary reaction to thetotal entropy production is developed for eliminating species from detailed reaction mechanismsin order to generate skeletal schemes. The approach is applied to a database of solutions forhomogeneous constant pressure auto-ignition of n-heptane to construct two skeletal schemesfor different threshold values defining the important reactions contributing to the total entropyproduction. The accuracy of the skeletal mechanisms is evaluated in spatially homogeneoussystems for ignition delay time, a single-zone engine model, and a perfectly stirred reactor ina wide range of thermodynamic conditions. High accuracy is also demonstrated for the speedand structure of spatially-varying premixed laminar flames.

References:• M. Kooshkbaghi, C.E. Frouzakis, K. Boulouchos, I.V. Karlin, Entropy production analysisfor mechanism reduction, Combust. Flame, 161(6), 1507–1515, (2014)

50

Title: The global relaxation redistribution method for reduction of com-bustion kinetics

Institute/Group:

M. Kooshkbaghi, C.E. Frouzakis, K. Boulouchos, I.V. KarlinAerothermochemistry and Combustion Systems Laboratory, ETHZ

An algorithm based on the Relaxation Redistribution Method (RRM) is proposed for con-structing the Slow Invariant Manifold (SIM) of a chosen dimension to cover a large fractionof the admissible composition space that includes the equilibrium and initial states. The man-ifold boundaries are determined with the help of the Rate Controlled Constrained Equilibriummethod, which also provides the initial guess for the SIM. The latter is iteratively refined untilconvergence and the converged manifold is tabulated. A criterion based on the departure frominvariance is proposed to find the region over which the reduced description is valid. The globalrealization of the RRM algorithm is applied to constant pressure auto-ignition and adiabaticpremixed laminar flames of hydrogen-air mixtures.

References:• M. Kooshkbaghi1, C.E. Frouzakis, E. Chiavazzo, K. Boulouchos, I.V. Karlin, The globalrelaxation redistribution method for reduction of combustion kinetics, J. Chem. Phys. 141,044102, (2014)

51

Title: Detailed transient numerical simulation of H2/air hetero-/homogeneous combustion in platinum-coated channels withconjugate heat transfer

Institute/Group:

A. Brambilla1,2, C.E. Frouzakis1,2, J. Mantzaras2, A. Tomboulides3,S. Kerkemeier1, K. Boulouchos11Aerothermochemistry and Combustion Systems Laboratory, ETHZ2Combustion Research, Paul Scherrer Institute, CH-5232 Villigen3Department of Mechanical Engineering, University of WesternMacedonia, 50100 Kozani, Greece

Transient 2-D simulations of fuel-lean H2/air combustion were performed in a 2-mm-heightplanar channel coated with platinum, using detailed hetero-/homogeneous chemistry and trans-port as well as heat conduction in the solid wall. The developed model resolved, for the firsttime, all relevant spatiotemporal scales in a practical channel-flow reactor configuration. Aparametric study was carried out to investigate the effects of wall material, inlet velocity, andinlet temperature on the fundamental catalytic and gas-phase combustion processes. Computa-tional singular perturbation (CSP) analysis identified the key catalytic reactions affecting light-off and homogeneous ignition. Homogeneous ignition crucially depended on the OH desorbingfluxes from the catalyst, while flame propagation and stabilization involved time scales of a fewmilliseconds. During the short duration of the light-off event, the ensuing Stefan velocity ap-preciably altered the flow field. Predictions of time accurate numerical simulations were furthercompared against those of a code relying on the quasisteady state assumption, and the specificconditions under which the latter was invalidated were identified.

012

(a)

0

1

2(b)

0

12

(c)

0 2 4 6 8 10x [mm]

0

1

2(d)

y [m

m]

0.00E+00

0.00E+00

0.00E+00

0.00E+00

2.38E-05

2.42E-03

1.67E-03

2.32E-04

Figure 2: 2-D maps of OH radical mass fraction during gas-phase ignition in a channel with FeCr-alloywall and inlet conditions TIN = 650 K, UIN = 10 m/s) at (a) t = 250 ms, (b) t = 258 ms, (c) t = 267.2ms and (d) t = 270 ms.

References:• A. Brambilla, C.E. Frouzakis, J. Mantzaras, A. Tomboulides, S. Kerkemeier, K. Boulou-chos, Detailed transient numerical simulation of H2/air hetero-/homogeneous combustion inplatinum-coated channels with conjugate heat transfer Combust. Flame, 161, 2692–2707,(2014)

52

Title: An experimental and numerical investigation of premixed syngascombustion dynamics in mesoscale channels with controlled walltemperature profiles

Institute/Group:

A. Brambilla1,2, M. Schultze2, C.E. Frouzakis1, J. Mantzaras2, RolfBombach2, Konstantinos Boulouchos11Aerothermochemistry and Combustion Systems Laboratory, ETHZ2Combustion Research, Paul Scherrer Institute, CH-5232 VilligenPSI

The dynamics in H2/CO/O2/N2 premixed combustion was investigated experimentally andnumerically in a 7-mm height mesoscale channel at atmospheric pressure, fuellean equivalenceratios 0.250.42, volumetric CO:H2 ratios 1:1 to 20:1, and wall temperatures 5501320 K. Exper-iments were performed in an optically-accessible channel-flow reactor and involved high-speed(up to 1 kHz) planar laser induced fluorescence (LIF) of the OH radical and thermocouple mea-surements of the upper and lower channel wall temperatures. Simulations were carried out witha transient 2-D code, which included an elementary syngas reaction mechanism and detailedspecies transport. Demarcation of the experimentally-observed parameter space separating sta-tionary and oscillatory combustion modes indicated that the former were favored at the higherwall temperatures and higher CO:H2 volumetric ratios, while the latter predominately appearedat the lower wall temperatures and lower CO:H2 ratios. The numerical model reproducedvery well all stationary combustion modes, which included V-shaped and asymmetric (upperor lower) modes, in terms of flame shapes and flame anchoring positions. Simulations of theoscillatory flames, which appeared in the form of ignition/extinction events of varying spatialextents, were very sensitive to the specific boundary conditions and reproduced qualitatively theflame topology, the ignition sequence (including the periodic reversion from upper-asymmetricto lower-asymmetric flame propagation), and the range of measured oscillation frequencies.Predicted emissions in the stationary modes ranged from 25 to 94 ppm-mass for CO and from0.1 to 0.3 ppm-mass for H2, while in the oscillatory modes incomplete combustion of both COand H2 was attested during their oscillation period.

References:• A. Brambilla, M. Schultze, C.E. Frouzakis, J. Mantzaras, R. Bombach, K. Boulouchos, An ex-perimental and numerical investigation of premixed syngas combustion dynamics in mesoscalechannels with controlled wall temperature profiles, Proc. Combust. Inst., (in press)

53

Title: Direct numerical simulation of circular expanding premixed flamesin a lean quiescent hydrogen-air mixture: Phenomenology and de-tailed flame front analysis

Institute/Group:

C. Altantzis1, C.E. Frouzakis1, A.G. Tomboulides2, K. Boulouchos11Aerothermochemistry and Combustion Systems Laboratory, ETHZ2Department of Mechanical Engineering, University of WesternMacedonia, 50100 Kozani, Greece

The transition to cellularity and the dynamics of lean premixed hydrogen/air flames prop-agating outwards in 2D circular domains under the combined influence of the hydrodynamicand thermodiffusive instabilities is investigated computationally using detailed chemistry andtransport. In response to monochromatic (single wavelength) and polychromatic perturbationsimposed initially on the flame, the non-monotonic rate of increase of the surface area reflects thetransitions of the perturbed front dynamics. The relation of the wavelength of the cellular struc-tures with the growth rate of their amplitude is investigated separately during the initial intervalof accelerated growth marking the onset of cellularity as well as during later times when thewrinkled front undergoes a continuous process of cell creation and annihilation. As the flameexpands, the local minima of the initial perturbation determine the primary troughs which havea dominant effect on the long term evolution since they constrain the waveangle over whichsecondary cells can form and interact and define the periodicity of the problem. During thetime interval of propagation considered in this study, it is found that the temporal evolution ofthe mean flame radius does not follow a power law, but varies almost linearly in time.

Figure 3: Contour plots of OH mass fractions at different times for a circular H2/air premixed flameinitially located at Rig = 10 and perturbed to R(θ) = Rig(1 + 0.001 cos(28θ)).

References:• C. Altantzis, C.E. Frouzakis, A.G. Tomboulides, K. Boulouchos, Direct numerical simulationof circular expanding premixed flames in a lean quiescent hydrogen-air mixture: Phenomenol-ogy and detailed flame front analysis, Combust. Flame, (in press)

54

Title: Consistent definitions of “Flame Displacement Speed” and “Mark-stein Length” for premixed flame propagation

Institute/Group:

G.K. Giannakopoulos1, A. Gatzoulis1, C.E. Frouzakis2, M.Matalon3, A.G. Tomboulides11Department of Mechanical Engineering, University of WesternMacedonia, 50100 Kozani, Greece2Aerothermochemistry and Combustion Systems Laboratory, ETHZ3Department of Mechanical Science and Engineering, University ofIllinois, Urbana-Champaign, USA

The definition of the flame displacement speed (FDS), often used to characterize the dy-namical properties of premixed flames, is generally ambiguous because, except for a steadilypropagating planar flame, the mass flow rate through the combustion region varies with distancethrough the flame and one is therefore faced with the difficulty of choosing a proper iso-surfaceto represent the flame surface. A directly related issue is the determination of the proportionalitycoefficient in the linear flame speed-flame stretch relation of weakly-stretched flames, knownas the Markstein length, which depends strongly on the location inside the flame zone where itis measured or calculated. The objective of the present study is to identify an iso-surface andthereby a definition of the FDS that is well conditioned and less prone to uncertainties, and aconsistent and unambiguous expression for the Markstein length. In this study we examine thespherical flame geometry, a setup that provides an independent determination of the FDS that isnot contingent upon an arbitrary selection of the flame surface and thus permits a proper eval-uation of the two FDS definitions. A number of simulations of premixed spherical propane/airflames with equivalence ratio ranging from 0.8 to 1.4 were carried out at various temperaturesand pressures using both global single-step and detailed reaction schemes. Outwardly propagat-ing spherical (or cylindrical) flames and inwardly propagating stationary spherical flames wereexamined. The dependence of the flame speed and flame temperature on stretch, and the corre-sponding Markstein length were identified for different isotherms selected to represent the flamesurface, and the results were carefully compared to the asymptotic theory of weakly-stretchedflames. The excellent agreement between theory and simulations provides a clear explanationand quantification of the differences found between the trends in the flame speed-flame stretchrelation and the corresponding Markstein lengths, exhibited when the FDS was calculated basedon an isotherm in the burned or unburned sides of the flame. We show that the proper isothermfor the evaluation of the FDS which is well-conditioned and properly accounts for the physicsmust be sufficiently close to the burned side of the flame.

References:• G.K. Giannakopoulos, A. Gatzoulis, C.E. Frouzakis, M. Matalon, A.G. Tomboulides, Con-sistent definitions of “Flame Displacement Speed” and “Markstein Length” for premixed flamepropagation, Combust. Flame, (in press)

55

Title: Numerical study of unstable hydrogen/air flames: Shape and propa-gation speed

Institute/Group:

C.E. Frouzakis1, N.Fogla2, A.G. Tomboulides3, C. Altantzis4, M.Matalon2,1Aerothermochemistry and Combustion Systems Laboratory, ETHZ2Department of Mechanical Science and Engineering, University ofIllinois, Urbana-Champaign, USA3Department of Mechanical Engineering, University of WesternMacedonia, 50100 Kozani, Greece4Department of Mechanical Engineering, Massachusetts Institute ofTechnology, USA

Extensive numerical simulations with detailed chemistry and transport are performed toidentify the range of dominance (in terms of equivalence ratio and domain size) of the hydro-dynamic instability, the shape of the structures that evolve at long times, and their propagationspeed. The calculations were performed in two-dimensional domains of lateral extent 3100flame thicknesses. Hydrogen/air mixtures ranging from rich (φ=2) to lean conditions (φ=0.5)were considered, expecting that thermo-diffusive effects will start becoming important only atthe lean end. The initial growth of a perturbed planar flame front is found to agree qualitatively,and to a large extent even quantitatively, with the asymptotic theoretical predictions. Beyondlinearity it is shown that the dynamics depend strongly on the equivalence ratio (or on the ef-fective Lewis number of the mixture) and the domain lateral size. For stoichiometric and richmixtures, the flame shape is generally characterized by a single-cusp structure that propagatesat a constant speed. The propagation speed increases with increasing lateral domain size andasymptotes to a value nearly 24% larger than the laminar flame speed. For the lean mixtures, theflame does not assume a well-defined structure even after a long time. It is regularly contam-inated by small cells that result from thermo-diffusive effects and cause a significant increasein the propagation speed (nearly 60% above the laminar flame speed) that varies continuouslyin time. Except for the lean cases, the simulation results compare well with the asymptotichydrodynamic theory both in the flame shape and propagation speed.

References:• C.E. Frouzakis, N.Fogla, A.G. Tomboulides, C. Altantzis, M. Matalon Numerical study ofunstable hydrogen/air flames: Shape and propagation speed, Proc. Combust. Inst., (in press)

56

Title: The curvature Markstein length and the definition of flame displace-ment speed for stationary spherical flames

Institute/Group:

G.K. Giannakopoulos, M. Matalon, C.E. Frouzakis, A.G.Tomboulides1Department of Mechanical Engineering, University of WesternMacedonia, 50100 Kozani, Greece2Department of Mechanical Science and Engineering, University ofIllinois, Urbana-Champaign, USA3Aerothermochemistry and Combustion Systems Laboratory, ETHZ

The separate effects of flame stretch and flame curvature are investigated in the presentstudy considering a stationary spherical flame configuration that experiences no stretch but hasa finite curvature. A theoretical expression for the flame displacement speed, derived fromasymptotic analysis, is compared with numerical simulations exhibiting very good agreementbetween the two. The notion of the curvature Markstein length is introduced, a coefficient whichis independent from diffusion and chemical reaction effects, in contrast to the Markstein lengthassociated with total flame stretch. It is shown that its value depends strongly on the iso-surfacechosen to define the flame, exhibiting large variations in the preheat zone and more insensitivebehavior close to the burned side.

References:• G.K. Giannakopoulos, M. Matalon, C.E. Frouzakis, A.G. Tomboulides, The curvature Mark-stein length and the definition of flame displacement speed for stationary spherical flames, Proc.Combust. Inst., (in press)

57

Title: Gibbs’ principle for the lattice-kinetic theory of fluid dynamicsI. V. Karlin1, F. Bosch1, S. S. Chikatamarla1

Institute/Group:

1Aerothermochemistry and Combustion Systems Laboratory,ETHZ

Gibbs’ seminal prescription for constructing optimal states by maximizing the entropy un-der pertinent constraints is used to derive a lattice kinetic theory for the computation of highReynolds number flows. The notion of modifying the viscosity to stabilize subgrid simulationsis challenged in this kinetic framework. A lattice Boltzmann model for direct simulation ofturbulent flows is presented without any need for tunable parameters and turbulent viscosity.Simulations at very high Reynolds numbers demonstrate a major extension of the operationrange for fluid dynamics.

Figure 1: Snapshot of a fully developed turbulent flow past a round cylinder at Re = 140000.Vorticity iso-surface is shown colored with the velocity magnitude.

References:• I. V. Karlin, F. Bosch, S. S. Chikatamarla, Gibbs’ principle for the lattice-kinetic theory offluid dynamics, Phys. Rev. E, 90, 031302(R), 2014.

58

Title: Multispeed entropic lattice Boltzmann model for thermal flowsN. Frapolli1, S. S. Chikatamarla1, I. V. Karlin1

Institute/Group:


An energy-conserving lattice Boltzmann (LB) model based on the entropic theory of admis-sible higher-order lattice is presented in detail. The entropy supporting zero-one-three latticeis used to construct a model capable of reproducing the full Fourier-Navier-Stokes equations atlow Mach numbers. The proposed direct approach of constructing thermal models overcomesthe shortcomings of existing models and retains one of the most important advantages of the LBmethods, the exact space discretization of the advection step, thus paving the way for direct nu-merical simulation of thermal flows. New thermal wall boundary condition capable of handlingcurved geometries immersed in a multispeed lattice is proposed by extending the Tamm-Mott-Smith boundary condition. Entropic realization of the current model ensures stability of themodel also for subgrid simulations. Numerical validation and thermodynamic consistency isdemonstrated with classical setups such as thermal Couette flow, Rayleigh-Benard natural con-vection, acoustic waves, speed of sound measurements, and shock tube simulations.

Figure 2: Forced (left) and natural (right) convection past a hot cylinder. Shown is the temper-ature profile.

References:• N. Frapolli, S. S. Chikatamarla, and I. V. Karlin, Multispeed entropic lattice Boltzmann modelfor thermal flows, Phys. Rev. E, 90, 043306, 2014

59

Title: Entropic lattice Boltzmann method for multiphase flowsA. Mazloomi1, S. S. Chikatamarla1, I. V. Karlin1

Institute/Group:


A novel lattice Boltzmann model which enables dynamical effects of two-phase fluids isdeveloped. The key innovation is the application of the entropic lattice Boltzmann stabilizationmechanism to control the dynamics at the liquid-vapor interface. This allows us to present anumber of simulations of colliding droplets, including complex phenomena such as the forma-tion of a stable lamella film. Excellent agreement of the simulation with recent experimentsdemonstrates viability of the present approach to simulation of complex dynamic phenomenaof multiphase fluids.

Figure 3: Dynamics of the droplets collision for different impact parameter.

References:• A. Mazloomi, S. S. Chikatamarla, and I. V. Karlin, Phys. Rev. Lett., (under review) 2014

60

Title: Understanting Surface Chemistry at the molecular level through computational chemistry

Researchers: Prof. C. CopéretDr. A. Comas-VivesDr. F. Nunez-Zazur

Institute: Department of Chemistry and Applied Biosciences Institute of Inorganic Chemistry

Group: C. Copéret

Description:

A major research effort in our group aims at understanding at the molecular level the active sites of supported catalysts by combining selective surface preparation methods, characterization through advanced spectroscopic techniques, in particular IR and NMR, and computational chemistry. This approach has allowed to reveal (i) detailed information about the structure of the active sites of the Ziegler-Natta pre-catalysts and the Philipps catalysts, two of the major polymerization industrial processes, (ii) the surface chemistry of surface defects in highly dehydroxylated silica, (iii) the origin of the selectivity of Ag nanoparticles in the semi-hydrogenation of alkynes, and (iv) the nature of the active sites in Sn-beta zeolites, Al-based co-catalysts and (v) the limitation of NMR spectroscopy in determining the structure of the surface sites in oxide surface.

References:

[1] Spectral Signatures of the Active Sites in Sn– Zeolite. Wolf, P. Valla, M. Rossini, A. J., Comas-Vives, A.; Núñez-Zarur, F.; Malaman, B.; Lesage, A.; Emsley, L.; Copéret, C.; Hermans, I. Angew. Chem. Int. Ed. 2014, DOI: 10.1002/anie.201403905.

[2] On the Visibility of Al Surface Sites of -Alumina: a Combined Computational and Experimental Point of View. Wischert, R.; Florian, P.; Copéret, C.; Massiot, D.; Sautet P. J. Phys. Chem. C. 2014, Article ASAP. DOI: 10.1021/jp503277m.

[3] Proton Transfers Are Key Elementary Steps in Ethylene Polymerization on Isolated Chromium(III) Silicates. Delley, M.F.; Núñez-Zarur, F.; Conley, M, P.;Comas-Vives, A.; Siddiqi, G.; Norsic, S.; Monteil, V.; Safonova, O. V.; Copéret, C. Proc. Nat. Acad. Sci. 2014, In press. DOI: 10.1073/pnas.1405314111.

[4] Silica–surface reorganization during organotin grafting evidenced by 119Sn DNP SENS: a tandem reaction of gem-silanols and strained siloxane bridges. Conley, M.P.; Rossini, A.J.; Comas Vives, A.; Valla, M.; Casano, G.; Ouari, O;

61

Tordo, P; Lesage,A.; Emsley, L.; Copéret, C. Phys. Chem. Chem. Phys. 2014, in press. DOI: 10.1039/C4CP01973C.

[5] Chlorodiethylaluminum supported on silica: a dinuclear aluminum surface species with bridging 2-Cl-ligand as a highly efficient co-catalyst for the Ni-catalyzed dimerization of ethene, A. Kermagoret, R. N. Kerber, M. P Conley, E. Callens, P. Florian, D. Massiot, F. Delbecq, X. Rozanska, P. Sautet, C. Copéret, J. Catal. 2014, 313, 46-54.

[6] Silver nanoparticles for olefin production: a paradigm shift in the mechanistic description of catalyzed hydrogenations. G. Vilé, D. Baudouin, C. Copéret, N. López, and J. Pérez-Ramírez, ChemCatChem 2013, 5 (12), 3750-3759.

[7] Triisobutylaluminum: bulkier and yet more reactive towards silica surfaces than triethyl or trimethylaluminum. A. Kermagoret, R. Nathaniel Kerber, M. P.Conley, E. Callens, P. Florian, D. Massiot, C. Copéret, F. Delbecq, X. Rozanska, P. Sautet Dalton Trans., 2013, 42, 12681-12687.

[8] Tetrahydrofuran in TiCl4/THF/MgCl2: a Non-Innocent Ligand for Supported Ziegler-Natta Polymerization Catalysts. E. Grau, A. Lesage, S. Norsic, C. Copéret, V. Monteil, P. Sautet, ACS Catalysis, 2013, 3, 52–56.

62

Title: Numerical Semiclassical Quantum Dynamics with Wavepackets

Researchers: Vasile Gradinaru (SAM), Raoul Bourquin (SAM)George Hagedorn (Virginia Tech)

Institute: Seminar for Applied Mathematics, ETH ZurichVirginia Polytechnic Institute and State University, USA

Funding: SNF Grant 200021 140688

Description:

The computer simulation of the solution of the time dependent Schrodinger equation (TDSE) playsa fundamental role in the modern quantum chemistry. This project considers the TDSE for nuclei inits semiclassical formulation which features the presence of several scales and many space dimensions.The project aims at a rigorous understanding and consistent assessment of the properties of the numer-ical methods based on semiclassical wavepackets for quantum dynamics. The project uses techniques,methods and knowledge from theoretical chemistry, mathematical physics and modelling, and numericalmathematics. New algorithms for the numerical integration of the semiclassical Schrodinger equationwere found.

References:

[1] V. Gradinaru and G. A. Hagedorn A timesplitting for the semiclassical Schrdinger equation,Numerische Mathematik (2013)

[2] R. Bourquin and V. Gradinaru and G. A. Hagedorn Non-adiabatic transitions near avoided cross-ings: theory and numerics, Journal of Math. Chemistry (2011), pp. 1-18

63

Title: Numerical methods for electromagnetics and optimization Researchers: Christian Hafner Jürg Fröhlich

Jens Niegemann Sascha Schnepp Mustafa Boyvat

Nikolay Komarvesky Aytac Alparslan Mengyu Wang

Christoph Böcklin Alexander Dorodnyy

Sahar Sargheini Pegah Souzanghar

Institute Institute of Electromagnetic Fields Description: We develop various numerical methods and software packages for computational electromagnetics and optimal design with applications ranging from very low up to optical frequencies. These codes, free software (freeFEM++, NGsolve, Concepts) and commercial packages (Comsol, CST, HFSS, etc.) are applied to 1) metamaterials for magnetic field shielding, radar absorption, thermal protection, and efficient solar cells; 2) photonic crystals and dielectric waveguide structures for optical frequencies and for fast interconnects in the mm wave range; 3) design of antenna structures ranging from radio frequencies up to optical frequencies, e.g., plasmonic nano antennas for bio sensing; 4) analysis and design of scanning probe tips for microwaves, optics, and electron emission; 5) devices for biology and medicine; etc. Currently we develop and combine various field solvers based on boundary discretization methods such as the Multiple Multipole Program (MMP) as well as domain discretization methods in frequency and time domain, namely Finite Elements Methods (FEM), Discontinuous Galerkin (DG), Fourier Modal Method (FMM), etc. The semi-analytic MMP method provides high accuracy, robustness, numerical efficiency for 2D applications, and exhibits no problems with material dispersion and loss. For 3D simulations, TD-FEM and DG-FEM are favorable for the analysis of geometrically complicated structures. Our MMP and FDTD codes are contained in the OpenMaXwell platform, which is an OpenSource project (see http://openmax.ethz.ch/). References: From fall 2013 till fall 2014, 11 papers on various topics of computational electromagnetics were published in reviewed journals.

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Group of Ch. Hafner Reviewed Journals

1. F. Kretzschmar, S. M. Schnepp, I. Tsukerman, T. Weiland, Discontinuous Galerkin Methods with Trefftz Approximation, Journal of Computational and Applied Mathematics (JCAM), Vol. 270, pp.211-222, November 2014.

2. S. M. Schnepp, Error-Driven Dynamical hp-Meshes for the Discontinuous Galerkin Method in Time-Domain, Journal of Computational and Applied Mathematics (JCAM), Vol. 270, pp.353-368, November 2014.

3. Ch. Hafner, N. Komarevsky, A. Dorodnyy, M. Boyvat, Electromagnetic Metamaterials-Promises, Design, and Applications, Quantum Matter, Vol. 3, Issue 4, pp.328-338, August 2014.

4. J. Mihaljevic, J. Niegemann, S. M. Schnepp, Ch. Hafner, On the Numerical Modeling of Sharp Metallic Tips, Quantum Matter, Vol. 3, Issue 4, pp.344-354, August 2014.

5. M. Boyvat, C. Hafner, J. Leuthold, Wireless control and selection of forces and torques - towards wireless engines, Scientific Reports, Vol. 4, July 2014.

6. C. Böcklin, D. Baumann, J. Fröhlich, New approach for absolute fluence distribution calculations in Monte Carlo simulations of light propagation in turbid media, Journal of Applied Physics, Vol. 115, Issue 6, pp.DOI: 10.1063/1.4865171, February 2014.

7. M. Wang, A. Alparslan, S. M. Schnepp, Ch. Hafner, Optimization of a Plasmon-Assisted Waveguide Coupler Using FEM and MMP, PIER B, Vol. 59, pp.219-229, 2014.

8. M. Husnik, J. Niegemann, K. Busch, M. Wegener, Quantitative spectroscopy on individual wire, slot, bow-tie, rectangular, and square-shaped optical antennas, Optics Letters, Vol. 38, Issue 22, pp.4597-4600, November 2013.

9. M. Husnik, F. von Cube, S. Irsen, S. Linden, J. Niegemann, K. Busch, M. Wegener, Comparison of electron energy-loss and quantitative optical spectroscopy on individual optical gold antennas, Nanophotonics, Vol. 2, Issue 4, pp.241-245, October 2013.

10. Dorodnyy, V. Shklover, Ch. Hafner, Hybrid FEM-FMM Approach For Efficient Calculations Of Periodic Photonic Structures, Progress In Electromagnetics Research, Vol. 33, pp.121-135, October 2013.

11. J. Mihaljevic, Ch. Hafner, A. J. Meixner, Simulation of a metallic SNOM tip illuminated by a parabolic mirror, Optics Express, Vol. 21, Issue 22, pp.25926-25943, October 2013.

65

Title: Planetary Nervous SystemResearchers: Dirk Helbing et al.Institute/Group: Chair of Sociology, in particular

of Modeling and Simulation

Description:

The Planetary Nervous System is a large-scaledistributed research platform that provides real-timesocial mining services as a public good. Existing BigData systems threaten social cohesion as they aredesigned to be closed, proprietary, privacy-intrusiveand discriminatory. In contrast, the PlanetaryNervous System is an open, privacy-preserving andparticipatory platform designed to be collectivelybuilt by citizens and for citizens.

The Planetary Nervous System is enabled by Internetof Things technologies and aims at seamlesslyinterconnecting a large number of different pervasivedevices, e.g. mobile phones, smart sensors, etc. Forthis purpose, several universal state-of-the-artprotocols and communication means are introduced.A novel social mining paradigm shift is engineered:Users are provided with freedom and incentives toshare, collect and, at the same time, protect data oftheir digital environment in real-time. In this way, social mining turns into a knowledgeextraction service of public good.

The social mining services of the Planetary Nervous System can be publicly used for buildingnovel innovative applications. Whether you would like to detect an earthquake, perform asecure evacuation or discover the hot spots of a visited city, the Planetary Nervous systemmakes this possible by collectively mining social activity of participatory citizens.

References:

• F. Giannotti, D. Pedreschi, P. Lukowicz, D. Kossmann, J. Crowley and D. Helbing (2013). A planetary nervous system for social mining and collective awareness. arXiv preprint arXiv:1304.3700.

• D. Helbing (2013). New Ways to Promote Sustainability and Social Well-Being in a Complex, Strongly Interdependent World: The FuturICT Approach. arXiv preprint arXiv:1310.3498.

• D. Helbing (2011). FuturICT-New science and technology to manage our complex, strongly connected world. arXiv preprint arXiv:1108.6131.

66

Title: MomentumResearchers: Dirk Helbing et al.Institute/Group: Chair of Sociology, in particular of

Modeling and Simulation

Description:

The Momentum project, funded by an ERC Advanced Investigator Grant with 2.5 millioneuros, is a five-year project of the SOMS group that has just started. Its central innovation isto explain the emergence of social behavior and institutions from very first principles, makinguse of large-scale agent-based simulations. These agents will be equipped with artificialbrains (neural networks), allowing them to develop and employ new behavioral rules to studyunder which conditions social institutions can emerge and become globally accepted norms.

Understanding social systems from fundamental principles is one of the most importantscientific challenges of the modern area. The main objective of the simulation of sophisticatedinteracting agents is to show how other-regarding human behavior (characterizing a “homosocialis”) can be the result of competition and the co-evolution of social mechanisms. Ourmodels will not assume that actors are equipped with certain social institutions already at theoutset of the evolutionary process. We want to demonstrate that, for example, socialcooperation and social norms are not static features of societies, but rather emergent outcomesof repeated and multifaceted interactions between many individuals. Rather thanimplementing “homophily”, cooperation, norms, inequality, conflict etc. as features of oursimulated model societies, we want to understand them as outcomes of a co-evolutionaryprocess in which individual behaviors, social interactions, learning processes and theirinterplay evolve over time. We seek to develop a model of human societies where eachmember can invent new behavioral rules, imitate successful behavior of others, and improveexisting rules. Thus, besides the complexity that results from the interaction between agents,our model adds a lot of complexity on the level of the individuals, as each individual needs tobe equipped with a “brain” that allows her to invent and improve behavioral rules. To simulatethese kinds of complex behaviors, our virtual agents will have a small virtual brain in the formof an artificial neural network. We plan to simulate 1,000 agents with 1,000 brains, eachrunning on a separate processor core in a computer cluster.

References:

• Helbing, D., Yu, W., and Rauhut, H. (2011) Self-organization and Emergence in SocialSystems: Modeling the Coevolution of Social Environments and Cooperative Behavior. Journal of Mathematical Sociology 35:177-208.

• Helbing, D. and W. Yu (2010) The future of social experimenting. Proceedings of the National Academy of Sciences USA (PNAS) 107(12): 5265-5266.

• Helbing, D. and Yu, W. (2009) The outbreak of cooperation among success-driven individuals under noisy conditions. PNAS 106(10)

• Helbing, D. and A. Johansson (2010) Cooperation, norms, and revolutions: A unified game-theoretical approach. PLoS ONE 5(10): e12530.

• Helbing, D., A. Szolnoki, M. Perc, and G. Szabó (2010) Evolutionary Establishment of Moral and Double Moral Standards through Spatial Interactions. PLoS Computational Biology 6(4): e1000758.

67

Title: Innovation AcceleratorResearchers: Dirk Helbing et al.Institute/Group: Chair of Sociology, in particular of

Modeling and Simulation

Description:

This project focusses on the long-term vision of creating an “Innovation Accelerator”: ageneral platform to monitor the latest developments in science, detect emerging trends andinnovations, find the best experts for projects, and support the distributed generation of newknowledge, thereby promoting innovation.

To that aim, an ecosystem of interconnected, open tools has been developed: Vijo (vijo.inn.ac)is an interface where users can create “virtual journals,” consisting of articles published inregular journals but dynamically compiled based on filters defined and shared by individualusers or communities. Living Science (livingscience.ethz.ch) is a platform to observe andanalyze scientific publications and activities. Living Archive (livingarchive.eu) is an onlinecatalog of open datasets. Nanobrowser (nanobrowser.inn.ac) is an interface for browsing andpublishing “nanopublications,” i.e. tiny pieces of scientific results represented together withtheir provenance and metadata in a formal Semantic Web language.

References:

• Helbing, D. and Balietti, S. (2011) How to create an innovation accelerator. EPJ ST 195(1)

• van Harmelen, F., Kampis, G., Börner, K., van den Besselaar, P., Schultes, E. and others. (2012) Theoretical and technological building blocks for an innovation accelerator. EPJ ST 214(1)

• Kuhn, T., Barbano, P.E., Nagy, M.L., and Krauthammer, M. (2013) Broadening the Scope of Nanopublications. Proc. of ESWC 2013

• Kuhn, T. and Krauthammer, M. (2012) Underspecified Scientific Claims in Nanopublications. Proc. of WoLE 2012

68

Title: Modelling the influence of photospheric turbulence on solarflare statistics

Researchers: Dr. M. MendozaMr. A. KaydulProf. Dr. L. de ArcangelisProf. Dr. J.S. Soares Jr.Prof. Dr. H. J. Herrmann

Institute: Institute for Building MaterialsETH Zurich

Description:

Solar flares stem from the reconnection of twisted magnetic field lines in the solar pho-tosphere. The energy and waiting time distributions of these events follow complexpatterns that have been carefully considered in the past and that bear some resemblancewith earthquakes and stockmarkets. Here we explore in detail the tangling motion of in-teracting flux tubes anchored in the plasma and the energy ejections resulting when theyrecombine. The mechanism for energy accumulation and release in the flow is reminiscentof self-organized criticality. From this model we suggest the origin for two important andwidely studied properties of solar flare statistics, including the time-energy correlations.We first propose that the scale-free energy distribution of solar flares is largely due tothe twist exerted by the vorticity of the turbulent photosphere. Second, the long-rangetemporal and time-energy correlations appear to arise from the tube-tube interactions.The agreement with satellite measurements is encouraging.

References:

[1] M. Mendoza, A. Kaydul, L. de Arcangelis, J. S. Andrade Jr, and H. J. Herrmann,Modelling the influence of photospheric turbulence on solar flare statistics, Nat.Commun. 5:5035 doi: 10.1038/ncomms6035 (2014).

69

Title: Kinetic Formulation of the Kohn-Sham Equations for abinitio Electronic Structure Calculations

Researchers: Dr. M. MendozaDr. S. SucciProf. Dr. H. J. Herrmann


Description:

We introduce a new connection between density functional theory and kinetic theory. Inparticular, we show that the Kohn-Sham (KS) equations can be reformulated as a macro-scopic limit of the steady-state solution of a suitable single-particle kinetic equation. Wederive a Boltzmann-like equation for a gas of quasi-particles, where the potential playsthe role of an external source that generates and destroys particles, so as to drive thesystem towards its ground state. The ions are treated as classical particles, by usingeither the Born-Oppenheimer (BO) dynamics or by imposing concurrent evolution withthe electronic orbitals. In order to provide quantitative support to our approach, weimplement a discrete (lattice) kinetic model and compute the exchange and correlationenergies of simple atoms and the geometrical configuration of the methane molecule.Moreover, we also compute the first vibrational mode of the hydrogen molecule, withboth BO and concurrent dynamics. Excellent agreement with values in the literature isfound in all cases.

References:

[1] M. Mendoza, S. Succi, and H. J. Herrmann, Kinetic Formulation of the Kohn-ShamEquations for ab initio Electronic Structure Calculations, Phys. Rev. Lett. 113,096402 (2014)

70

Title: Grain Scale Modelling of Triggering Mechanisms of RainfallInduced Slope Failures

Researchers: K. MelnikovDr. F. WittelProf. H. J. Herrmann


Description:

Rainfall induced slope failures are a common phenomenon in mountainous regions afterlong periods of rains. These failures sometimes lead to initiation of landslides which aretogether with debris flows highly dangerous for both people and infrastructure. The goalof our research project is to model triggering mechanisms of rainfall induced slope failuresat the grain scale. To reach this goal we developed a model of granular material withstationary particles that can account for arbitrary water saturation levels. A certainminimum water saturation level is required to cause the loss of cohesion in the soil.This saturation level lies beyond the well-studied capillary bridge regime and thus anew approach should be considered. We solve this problem by assuming that the water-air interface in the material has a locally spherical shape in form of menisci which arelocated between three grains. The propagation of the interface through the material istriggered by local instabilities which are described by a set of rules based on experimentalobservations (e.g. Haines jumps). With this approximation it is possible to account forincreasing water saturation level in an initially unsaturated granular material due towater infiltration and thus to model the loss of cohesion.

In the next step moving particles will be considered. We use the contact dynamicsapproach to model the particle interactions. The cohesion force at the surface of waterstructures will be approximated with the cohesion force of single liquid bridges. In orderto model the loss of cohesion the capillary force will be set to zero for fully immersedparticles. With this model it is possible to investigate the influence of the inhomogenityand structure of granular material as well as the influence of the initial water content onthe triggering process.

71

Title: Usage Leading to an Abrupt Collapse

Researchers: D. V. StagerDr. N. A. M. AraujoProf. H. J. Herrmann


Description:

Network infrastructures are essential for the distribution of resources such as electricityand water. Typical strategies to assess their resilience focus on the impact of a sequenceof random or targeted failures of network nodes or links. Here we consider a more real-istic scenario, where elements fail based on their usage. We propose a dynamic model oftransport based on the Bak-Tang-Wiesenfeld sandpile model where links fail after theyhave transported more than an amount µ (threshold) of the resource and we investi-gate it on the square lattice. As we deal with a new model, we provide insight on itsfundamental behavior and dependence on parameters. We observe that for low valuesof the threshold due to a positive feedback of link failure, an avalanche develops thatleads to an abrupt collapse of the lattice. By contrast, for high thresholds the latticebreaks down in an uncorrelated fashion. We determine the critical threshold µ∗ separat-ing these two regimes and show how it depends on the toppling threshold of the nodesand the mass increment added stepwise to the system. We find that the time of majordisconnection is well described with a linear dependence on µ. Furthermore, we propose alower bound for µ∗ by measuring the strength of the dynamics leading to abrupt collapses.

References:

[1] D. V. Stager, N. A. M. Araujo, and H. J. Herrmann, Usage Leading to an AbruptCollapse, Physical Review E (2014), submitted

72

Title: Scale and Conformal invariance in Graphene

Researchers: I. GiordanelliDr. M. MendozaProf. H. J. Herrmann


Description:

We present interesting statistical properties of suspended graphene sheets at finite tem-perature. Due to thermal fluctuations, suspended graphene possesses strong height fluc-tuations, where isolines of zero height can be well defined. We show that those isolines,and the area enclosed by them, are scale invariant. Furthermore, we provide numericalevidence that the isolines curves share the same statistical properties as Schramm-Lownerevolution (SLEκ) curves, implying that these curves are conformal invariant. From ourresults we conjecture that they belong to the same universality class as the Loop ErasedRandom Walk (LERW). Understanding the intrinsic symmetries of suspended graphenerepresents a key step in the unification of 2D physics within the framework of scale andconformal symmetries.

73

Title: Transport Properties of Campylotic Media

Researchers: J.-D. DebusDr. M. MendozaProf. S. SucciProf. H. J. Herrmann


Description:

We investigate the transport properties of intrinsically curved (campylotic) media, equippedwith localized metric perturbations (curvatons). To this end, we study the flux of a fluiddriven through the campylotic medium in dependence of the spatial deformation, charac-terized by the curvaton parameters (amplitude, range and density). We observe that theflux through a campylotic medium depends only on a specific combination of curvatonparameters which we identify as the average curvaton strength. We find an empiricalflux law which is universal in the sense that – within the parameter range considered – itdepends neither on the specific curvaton shape nor on the spatial order of the curvatonsand is valid both for two- and three-dimensional systems. We have also compared campy-lotic media with porous media, finding that the flux in a campylotic medium also satisfiesDarcy’s law, where the permeability is closely related to the flux law. For the purposeof this study, we have improved and validated our recently developed lattice Boltzmannmodel in curved space by canceling discrete lattice effects.

References:

[1] J.-D. Debus, M. Mendoza, S. Succi, and H. J. Herrmann, Transport Properties of

Campylotic Media, in preparation

74

Title: Packing of Slender Objects in Deformable Confinements

Researchers: R. VetterF. K. WittelH. J. Herrmann


Description:

Morphogenesis can be intriguingly complex in Nature, and the variety of morphologiesemerging from simple geometrical constraints is often compelling in self-organized sys-tems. We have carried out finite element simulations showing that the shape of fixedgeometrical confinement can have dramatic influence on the packing process of elasticfilaments that are fed in [1]. However, Nature’s tight spatial constraints are seldom rigid.Rather, cell walls, buds and giant vesicles are quite flexible and conforming when actingas containers for stiffer objects. How do thin bodies crumple, fold and pack in such de-formable confinements? How can the non-linear interplay between touching flexible thinstructures be characterized, and what morphologies emerge from such interactions? Weseek to answer these questions using numerical simulations of tightly packed, mutuallyinteracting slender objects, accompanied by table-top experiments conducted on off-the-shelf materials. Flexible confinement is modeled using a highly efficient thin shell finiteelement approach using Loop subdivision surfaces [2]. A large-scale parameter study [3]revealed that four morphologies develop when elastic ring-like filaments grow within asoft membrane, controlled by flexibility and size ratios, as well as friction. These fourdifferent configurations constitute morphological phases and the transition between themcan be characterized by symmetry-breaking phase transitions.

References:

[1] R. Vetter, F. K. Wittel, N. Stoop, H. J. Herrmann, Finite element simulation ofdense wire packings, Eur. J. Mech. A 37, 160–171 (2013)

[2] R. Vetter, N. Stoop, T. Jenni, F. K. Wittel, H. J. Herrmann, Subdivision shellelements with anisotropic growth, Int. J. Numer. Meth. Eng. 95, 791–810 (2013)

[3] R. Vetter, F. K. Wittel, H. J. Herrmann, Morphogenesis of filaments growing inflexible confinements, Nat. Commun. 5, 4437 (2014)

75

Title: Shape optimization by pursuing diffeomorphisms

Researchers: Alberto Paganini, Prof. Ralf HiptmairInstitute: Seminar for Applied Mathematics, ETH Zurich

Description: We consider PDE constrained shape optimization based on finite elementdiscretization of the underlying boundary value problem (the state problem). We de-velop an accurate and reliable optimization algorithm that preserves and exploits theapproximation properties offered by the finite element method.

The set of admissible shapes is constructed by letting diffeomorphisms act on an initialshape Ω0 (the initial guess). We employ transformation techniques to recast the shapeoptimization problem as an optimal control problem on the fixed shape Ω0: optimizationis then carried out by searching the optimal diffeomorphisms. We pursue a Ritz approachand state the optimal control problem on a conforming finite dimensional trial space ofdiffeomorphisms based on multivariate cubic B-splines.

Then, approximate optimal shapes can be retrieved with descent methods based on theFrechet derivative of the cost functional. Both functionals depend on the solution of thestate problem, and can be approximated by replacing it with a finite element solution.This introduces a perturbation error that, with our approach, can be guaranteed todecrease algebraically with a rate equal two, when the state is approximated with linearLagrangian finite elements (super-convergence). This rate is reflected in the quality ofthe retrieved optimal solution.

Figure 1: Numerical experiment. Left: B-splines are generated on a regular grid thatcovers the initial guess Ω0. The finite element grid is drawn in purple. Right: Aftertwelve iterations of a descent method, we recover a decent approximation (blue line) ofthe target boundary (cyan line). Red lines indicate the boundary of the initial guess Ω0.

Publications

[1] R. Hiptmair and A. Paganini, Approximate shape gradients for interface problems, SAM-Report 2014-12, Seminar for Applied Mathematics, ETH Zurich, 2014.

[2] , Shape optimization by pursuing diffeomorphisms, SAM-Report 2014-27, Seminar forApplied Mathematics, ETH Zurich, 2014.

[3] R. Hiptmair, A. Paganini, and S. Sargheini, Comparison of approximate shape gradi-

ents, BIT Numerical Mathematics, (2014), published online.

76

Title: Generalized Advection Problemwith Discrete Differential Forms

Researchers: Cecilia PagliantiniProf. Ralf HiptmairProf. Siddhartha Mishra

Institute: Seminar for Applied Mathematics, ETH Zurich

Funding: Swiss NSF Grant No. 146355.

Description: We formulate and implement an Eulerian stabilized Galerkin methodfor the generalized advection problem for a differential k-form based on structure pre-serving spatial discretizations relying on discrete differential forms. The method allowsthe use of both fully discontinuous (DG) and conforming finite elements in space andimplicit/explicit time-stepping. Moreover, it accommodates jump discontinuity in thevelocity field which are the natural outcome of hyperbolic problems such as the magne-tohydrodynamics (MHD) equations. In particular, the advection problem for 1-forms isnumerically tackled as a building block for the solution of the resistive MHD system.

−A2, time t = 1, edge elements

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A1, time t = 1, edge elements

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Figure 1: Vector components of the magnetic potential obtained as solution of the mag-netic advection problem for the 2D Orszag-Tang benchmark. The numerical discretiza-tion is based on the stabilized scheme with upwind fluxes, lowest order rotated Raviart-Thomas elements and implicit Euler time-stepping.

77

Title: Well-Conditioned Second Kind Single Trace BEM forAcoustic Scattering

Researchers: Elke Spindler (SAM),Prof. Ralf Hiptmair (SAM),Xavier Claeys (Paris UPMC)


Description:

Acoustic scattering at penetrable and impenetrable composite objects is considered.Classical first-kind approaches are ill-conditioned and there is no suitable preconditioneravailable. We establish a well-conditioned second-kind boundary element approach thatis formulated in L2 using discontinuous ansatz and test functions to approximate theunknown boundary data.

101

102

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1/h

L2−

err

or

Dirichlet first−kind lin

Dirichlet second−kind const

Dirichlet second−kind lin

Dirichlet first−kind quad

Dirichlet second−kind quad

Neumann first−kind const

Neumann second−kind const

Neumann second−kind lin

Neumann first−kind lin

Neumann second−kind quad

Dirichlet second−kind proj const

Dirichlet second−kind proj lin

Dirichlet second−kind proj quad

Figure 1: Studies of the 2-norm condition number of the Galerkin matrices. The given3D-model problem has the geometry of a ball with radius r = 0.5 divided into two halfballs with wave numbers κ1 = 2, κ2 = 3, respectively, and wave number κ0 = 1 in theexterior.

Implementations of both approaches have been done in 2D (in Matlab) as wellas in 3D based on the C++ Boundary Element Template Library (BETL2) by LarsKielhorn (SAM). So far experiments in 2D have been done using piecewise constantansatz functions for the traces. In 3D we did experiments with boundary elements upto third order. The results show competitive accuracy of the new approach (see Fig.1), bounded condition numbers of the Galerkin matrices (see Fig. 2(b)) and superiorconvergence of GMRES. Several tests indicate the absence of spurious modes in our newformulation.

Publications:

[1] X. Claeys, A single trace integral formulation of the second-kind for multiple sub-

domain scattering, Tech. Rep. 2011-14, Seminar for Applied Mathematics, ETHZurich, Zurich, Switzerland, 2011.

78

−2 −1 0 1 2

−2

−1

0

1

2

−2

−1.5

−1

−0.5

0

0.5

1

1.5

Ω3

Ω2

Ω1

Ω0

(a) Plot of the real part of the solution to acomplex scattering problem in 2D. The upperhalf disc Ω1 is impenetrable, the lower halfdisc is penetrable with wave number κ2 = 10.Ω3 is penetrable with wave number κ3 = 15and the exterior domain is also penetrablewith wave number κ0 = 5.

100

101

101

102

103

104

105

106

1/h

cond

2(G

)

p = 2.91

p = 0.26

second−kind, const

first−kind, const−linear

first−kind, linear−quadratic

second−kind, linear

(b) Convergence results of the error of theboundary data with respect to the highestresolution result in L2-norm. The given 3D-model problem is a ball with radius r = 0.5divided into two half balls with wave num-bers κ1 = 2, κ2 = 3, respectively, and wavenumber κ0 = 1 in the exterior.

Figure 2: some results of numerical experiments

[2] X. Claeys, and R. Hiptmair, and E. Spindler, A second-kind Galerkin bound-

ary element method for scattering at composite objects, BIT Numerical Mathematics,Springer Netherlands, 2014.

79

Title: BETL2 — A new Boundary Element Template Library

Researchers: Dr. Lars KielhornProf. Dr. Ralf Hiptmair

Institute: Seminar for Applied MathematicsETH Zurich

Description:

The Boundary Element Template Library (BETL2) is a successor of BETL (Hiptmairand Kielhorn, 2012). It provides building blocks for the Galerkin discretisation of bilinearforms as they occur in Finite and Boundary Element Methods—both 2d and 3d.

As of October 2014 the library supports hybrid grid structures up to degree two fordomain and boundary meshes in two- and three-dimensional space. Additionially, itprovides higher order approximations of the unknown quantities which may be definedeither by Lagrangian basis or by Nedelec-type basis functions.

BETL2 is developed in tight collaboration with an industry partner such that perfor-mance is a major design goal. Therefore, utmost emphasis is put on an efficient imple-mentation with little to no runtime overhead. For this reason BETL2 is entirely writtenin C++11 fully incorporating the language’s strong generic programming facilities.

(a) Eddy currents in a plate(Hiptmair, 2007) (b) Magnetic field

(c) Magnetic field (Hiptmair,2002)

Figure 1: Electromagnetic computations. left: pure BEM , center: pure FEM, right: coupled compu-tation FEM/BEM

References

R. Hiptmair. Symmetric Coupling for Eddy Current Problems. SIAM Journal on Nu-merical Analysis, 40(1):41–65, 2002. doi: 10.1137/S0036142900380467.

R. Hiptmair. Boundary element methods for eddy current computation. In M. Schanzand O. Steinbach, editors, Boundary Element Analysis, volume 29 of Lecture Notes inApplied and Computational Mechanics, pages 213–248. Springer Berlin / Heidelberg,2007. ISBN 978-3-540-47465-4.

R. Hiptmair and L. Kielhorn. BETL – A Boundary Element Template Library.Technical Report 2012-36, Seminar for Applied Mathematics, ETH Zurich, 2012.http://www.sam.math.ethz.ch/betl.

80

Title: High Resolution Simulation Tool for Power Devices

Researchers: Raffael CasagrandeDr. Christoph WinkelmannDr. Joerg OstrowskiProf. Ralf Hiptmair

Institute: Seminar for Applied Mathematics, ETH ZurichABB Corporate Reasearch, Baden-Dattwil

Description:The goal of the project is to enable arc-simulations of circuit breakers on hybrid,

moving meshes. For this purpose the electromagnetic field solver HyDi is weakly coupledto the commercial fluid solver ANSYS-FLUENT.

HyDi is an extensible, modern C++ FEM Solver that supports moving, hybrid sub-meshes as they appear in the simulation of circuit breakers. The non-conforming inter-faces between the different sub-meshes are treated with the Interior Penalty/Nitsche’sMethod. This allows us to use standard, H(curl) conforming FEM discretizations insidethe sub-meshes and couple them together by penalizing discontinuities.

Figure 1: Magnetic Field (right) for a configuration (left) with two copper electrodes anda plasma chamber in which the electric arc is burning.

References

[1] R. Casagrande and R. Hiptmair, An a priori error estimate for interior penaltydiscretizations of the curl-curl operator on non-conforming meshes, sam report, ETHZurich, 2014.

[2] R. Casagrande, C. Winkelmann, R. Hiptmair, and J. Ostrowski, Dg treat-ment of non-conforming interfaces in 3d curl-curl problems, in Mathematics in In-dustry, Springer, 2015.

81

Title: Far-field calculations in half space

Researchers: Sahar Sargheini (SAM & IFH) ,Prof. Ralf Hiptmair (SAM)


Funding: ETH CHIRP project CH1-01 11-1

Description: In many electromagnetic scattering problems, the key quantity of concernis the field value at far distances. Numerical methods like Finite Elements or FiniteDifference provide the solution to Maxwell’s equations within some finite region of space,i.e. the field inside the computational domain. It is very expensive to consider thesolution domain so big that the far-field data can be evaluated directly.Field values at far distances can be obtained using a post-processing procedure callednear-field to far-field mapping. The mapping is a linear functional of the near-fieldsolution. The procedure of far-field calculations for structures in free space is well known.However, for structures located above a substrate, the calculations are more challenging.we present an asymptotic analysis for outgoing electromagnetic waves and derive a closedform for the field of a dipole over a substrate at far distances. Far-field functionals arestated in terms of a boundary integral over a surface surrounding the scatterer. Sinceboundary integrals are not well-defined on the natural variational space, we reformulatethe far-field mapping in terms of a volume integral [1].In our implementations, we use 3rd order Nedelec finite elements on a quasi-uniformtetrahedral mesh to solve Maxwell’s equations in 3D structures The experiments arebased on a finite element library NGSolve developed by Joachim Schoeberl at Universityof Vienna.

Figure 1: The far-field patternof an electric dipole, calculatedusing volume based formulationand the method of multiple mul-tipoles (MMP) for φ = 0 and0 < θ < π

2. The dipole is located

at z′ = 0.5λ, perpendicular to thesubstrate. ε1

ε0= 1 and ε2

ε0= 2

are the relative permittivities forz > 0 and z < 0, respectively.

00

0.2

0.4

0.6

0.8

1

θ

|E∞

|2

MMP method

Volume based far−field integral method

π/3 π/2π/6

References

[1] R. Hiptmair and S. Sargheini, Far-field calculations in half space, SAM report,2014.

82

Title: Numerical simulation of the time-dependent and spatially-inhomogeneous Boltzmann equation

Researchers: Simon PintarelliProf. Philipp GrohsProf. Ralf Hiptmair

Institute: Seminar for Applied Mathematics, ETH ZurichFunding: SNF grant 200020 146356/1

Description: The time-dependent and spatially-inhomogeneous Boltzmann equation isconsidered. We use SUPG stabilized finite elements in space and a spectral discretizationin velocity without truncation. In our scheme, the 3-dimensional scattering tensor can beprecomputed, with the advantage that highly accurate quadrature is feasible. For this,previous work from [1] has been extended to obtain a conservative polar spectral dis-cretization with good approximation properties across varying temperatures. Boundaryconditions are enforced in a weak sense using a penalty term in the variational formula-tion. We have developped a parallel Code in C++, which is running on the Brutus clusterof ETH. Future work focuses on the extension to 3-dimensions and the exploration offurther possibilities to reduce the computational complexity.

(a) Time evolution of an inital distributionf(x,v) = F (x)||v||2e−||v||2/2. Periodic boundaryconditions in x. Total DoFs: 21.2 × 106, VelocityDoFs: 1275, z-axis: density, Coloring: tempera-ture.

0 5 10 15t

10-9

10-8

10-7

10-6

10-5

10-4

10-3

10-2

Abs.

Err

or

K=50, β=1.00

K=50, β=1.20

K=50, β=1.50

K=50, β=2.00

K=80, β=1.00

K=80, β=1.20

K=80, β=1.50

K=80, β=2.00

(b) L2-errors vs. time. Spatially homo-geneous case with analytically known so-lution. β-values correspond to conform-ing and non-conforming temperatures.K: max. polynomial degree in one di-rection.

Publications

[1] E. Fonn, P. Grohs, and R. Hiptmair, Polar spectral scheme for the spatiallyhomogeneous boltzmann equation, Tech. Rep. 2014-13, Seminar for Applied Mathe-matics, ETH Zurich, Switzerland, 2014.

83

Title: Innovative finite element method for extrusion processes Researchers: L. Tong C. Becker P. Hora Institute/ Institute of Virtual Manufacturing Group: Description: For design purposes of extrusion dies and to determine the material flow inside the toolings FE simulations are quite often used. The filling of the dies and the subsequent extrusion of the profile are in general simulated using two different numerical approaches. The filling process is commonly simulated using the Updated-Lagrange (UL) framework which generally suffers from mesh distortion and thus requires frequent and costly remeshing operations. Small time increments and high simulation time are the result. On the other hand the extrusion process is commonly simulated by the Arbitrary Lagrangian Eulerian method (ALE) which enables an efficient simulation of the extruded profile if a filled tool is provided. In the present work an advanced simulation technique for the virtual modelling of extrusion processes was developed. The new developed technique uses a predefined mesh for the filled tool, the elements of which are initially deactivated. The computed material flow thus leads to the progressive activation of the elements and the filling of the tools is achieved. The material free surface is furthermore tracked to obtain accurate results. This approach enables a very fast and accurate computation of the filling process, as the mesh quality is ensured in the beginning and no distortion occurs. Furthermore advanced friction modelling techniques enable the realistic simulation of the process [1].

Velocity distribution during the filling process of the extrusion die.

Velocity distribution during the extrusion process. References: [1] Hora P., Becker C., Tong L., Maier J., Müller S.: Advanced frictional models for extrusion application, Key Engineering Materials Vol. 585, pp. 41-48, 2014.

84

Title: Multiscale modeling of failure initiation in a ferritic-pearlitic steel Researchers: B. Berisha C. Raemy C. Becker P. Hora Institute/ Institute of Virtual Manufacturing Group: Description:

A RVE-based strategy for modeling the hardening and failure behavior of a ferritic-pearlitic steel at different length scales - mesoscale and microscale - is presented. Firstly, micrographs taken on the undeformed material were adapted to a FE-mesh by using the software OOF2. Boundary conditions of the RVE were defined based on the macroscopic deformation history of an interest region of an axisymmetric impact extrusion part. Crack initiation in pearlite is modeled within the XFEM framework as shown in Figure 1b), where the pearlite properties were considered as isotropic and homogeneous. Figure 1 a) shows the distribution of the cementite lamella (average distance of app. 300 nm) inside the pearlite region. Therefore, modeling of the inhomogeneous pearlite structure requires a high resolution of the mesh. For this purpose, in addition to RVEs based on finite element modeling (Figure 1b), a spectral solver of the code DAMASK was applied to model strain localizations at grain level, see Figure 1c) and d). X-ray measurements were carried out to determine orientation of ferrite grains and to fit parameters of the applied crystal plasticity material model. Figure 1d) shows strain localizations caused by the inhomogeneous structure of pearlite. These results corresponds to the observed failure phenomena presented in [1].

The concept of coupling the FE-Method and the spectral solver leads to a very efficient strategy, because of the high efficiency of the spectral solver for RVE computations for large problems.

a) b) c) d) Figure 1: a) Micrograph showing pearlite cracking, b) Failure modeling at mesoscale based on XFEM, c) Modeling of pearlite microstructure based on crystal plasticity, where the colors represent different grain orientation and the straight lines represent cementite lamellae, d) Simulation results of the spectral solver showing strain localization regions: orientation of the cementite lamella have a strong influence on the inhomogeneity of the strain distribution.

References: [1] Berisha B., Raemy C., Becker C., Hora P.: Modeling of microstructure evolution and failure

initiation during impact extrusion of a ferritic-perlitic steel. EMMC14 – Europian Mechanics of Materials Conference, Gothenburg, Sweden, 2014.

85

Title: Determination of macroscopic material properties by crystal plasticity simulations

Researchers: C. Raemy

B. Berisha P. Hora

Institute/ Institute of Virtual Manufacturing Group: Description: In order to increase the accuracy of metal forming simulations, more and more complex material models are developed. However, considerable experimental work is necessary to obtain the parameters for these models. This study aimed to substitute some of the laboratory experiments by multiscale simulations. Specifically, a yield locus of deep drawing steel in raw state and after prestraining was calculated. The measured microstructure of the investigated material was approximated by a few grains and a representative volume element (RVE) was built accordingly. The material properties needed for the crystal plasticity (CP) simulations were fitted with a simple tensile test. Several biaxial plane stress states were simulated to determine the onset yielding and thus to get the yield locus – a macroscopic description of the behavior of the material. A so called spectral solver was used, which is based on fast Fourier transform. Since this kind of solver inherently produces periodic solutions, it is especially suited for the investigation of RVEs. Compared to similar FE-simulations, where the constitutive laws are implemented via material user subroutines, a decrease of computational time of up to two orders of magnitude could be observed. The simulated yield loci were in good to very good agreement to laboratory experiments.

RVE Initial yield locus After prestraining

References: [1] Roters F. et al.: “ DAMASK: the Düsseldorf Advanced MAterial Simulation Kit for studying crystal plasticity using an FE based or a spectral numerical solver”. In: Procedia IUTAM 2 (2012), pp. 3-10 [2] Raemy C.: Master Thesis, ETHZ 2014

86

Title: Development of an intelligent planning- and an on-line process monitoring system for optimal design and monitoring of the metal spinning process

Researchers: B. Rentsch

P. Hora

Institute/ Institute of Virtual Manufacturing

Group:

Description:

A new class of forming processes known as Incremental sheet forming (ISF) has raised a lot of attention in the last two decades. These processes are characterized by the fact that at any time only a small part of the product is actually being formed and this area of local deformation is moving over the entire product. A particular incremental sheet metal forming process is metal spinning, used for the manufacturing of rotational parts in low to medium series [1]. Plenty of research has been done in this field, however the use of numerical simulation techniques in the design of the process remains very limited. The rapidly changing contact states complicate the application of implicit FEM solvers. For this reason, explicit solvers with very small time steps are applied [2]. This method is bound to enormous computing times. An optimization of the tool path, which perhaps may require the tracing of several hundred variants, is hardly feasible due to time constraints. In the scope of the project a semi-analytical model (spinPlan) of the metal spinning process is developed, aiming to map an optimized initial design of the intermediate stages with reduced requirements in computing time. Concurrently sophisticated material models and failure criteria, which properly reflect the material behaviour in incremental sheet forming are implemented in the commercial FE code LS-DYNA through user subroutines. In a later stage, experiments will be conducted on a CNC lathe and the resulting data compared to the output of LS-DYNA Explicit solver (Figure 1) and spinPlan (Figure 2).

Figure 1: Full-scale 3D-Model in LS-DYNA Figure 2: Semi-analytical model in spinPlan

References

[1] W. C. Emmens, G. Sebastiani und A. H. Van den Boogard, „The technology of Incremental Sheet Forming - A brief review of the history,“ Journal of Materials Processing Technology, Bd. 210, pp. 981-997, 2010.

[2] J. Li, P. Geng und J. Shen, „Numerical simulation and experimental investigation of multistage incremental sheet forming,“ International Journal of Advanced Manufacturing Technology, Nr. 68, pp. 2637-2644, 2013.

87

88

Title: Local elevation umbrella sampling applied to the calculation of al-chemical free-energy changes via λ-dynamics: The λ-LEUS scheme.

Researchers: N.S. Bieler∗

R. Hauselmann∗

P.H. Hunenberger∗

Institute/Group:

∗ Laboratory of Physical Chemistry

Description :

When using molecular dynamics (MD) simulations for the calculation of alchemi-cal free-energy changes, λ-dynamics (λD) in its currently available implementationsdoes not compare very favorably with thermodynamic integration (TI) in terms ofrobustness, efficiency and accuracy, although it is in principle easier to set up, post-process and automatize. In the present article, the main shortcomings of the λDapproach are carefully analyzed, and possible remedies are proposed. The resultingscheme, called λ-LEUS, involves: (i) the use of a simple non-invertible coordinatetransformation ensuring a finite sampling of the two physical end states; (ii) theapplication of the local elevation umbrella sampling (LEUS) memory-based biasingscheme to enforce homogeneous sampling and overcome barriers along the alchemi-cal coordinate; (iii) recommendations concerning the choice of the mass parameterand of the temperature-coupling scheme for this coordinate; (iv) the use of a second-order splines basis set for the memory-based biasing functions. The λ-LEUS schemeis described and tested considering the perturbation of hydroquinone to benzene inwater. The results are compared to those of TI calculations and exhibit a superioraccuracy-to-efficiency ratio. Therefore, λ-LEUS combines the practical advantagesof λD with the robustness of TI, simultaneously affording a slightly enhanced com-putational efficiency.

References: N.S. Bieler, R. Hauselmann, and P.H. HunenbergerJ. Chem. Theory. Comput. 10 (2014) 3006-3022.

89

Title: Effect of the cosolutes trehalose and methanol on the equilibriumand phase-transition properties of glycerol-monopalmitate lipidbilayers investigated using molecular dynamics simulations.

Researchers: M. Laner∗

B.A.C. Horta∗∗

P.H. Hunenberger∗

Institute/Group:

∗ Laboratory of Physical Chemistry∗∗ Dpto. de Ciencias Biologicas, UEZO, Rio de Janeiro, Brazil

Description :

The influence of the cosolutes trehalose and methanol on the structural, dynamic andthermodynamic properties of a glycerol-1-monopalmitate (GMP) bilayer and on itsmain transition temperature Tm is investigated using atomistic molecular dynamicssimulations (600 ns) of a GMP bilayer patch (2×8×8 lipids) at different temperaturesin the range 302 – 338 K and considering three different cosolute concentrations.Depending on the environment and temperature, these simulations present no or asingle GL→LC, LC→GL or LC→ID transition, where LC, GL and ID are the liquidcrystal, gel and interdigitated phases, respectively. The trehalose molecules form acoating layer at the bilayer surface, promote the hydrogen-bonded bridging of thelipid headgroups, preserve the interaction of the headgroups with trapped water andinduce a slight lateral expansion of the bilayer in the LC phase, observations thatmay have implications for the phenomenon of anhydrobiosis. However, this cosolutedoes not affect Tm and its dependence on hydration in the concentration rangeconsidered. On the other hand, methanol molecules intercalate between the lipidheadgroups, promote a lateral expansion of the bilayer in the LC phase and induce aconcentration dependent decrease of Tm, observations that may have implications forthe phenomenon of anesthesia. The occurrence of an ID phase in the presence of thiscosolute may be viewed as an extreme consequence of lateral expansion. The analysisof the simulations also suggests the existence of two basic conservation principles: (i)the hydrogen-bond saturation principle rests on the observation that for all speciespresent in the different systems, the total numbers of hydrogen-bonds per moleculeis essentially constant, the only factor of variability being their distribution amongdifferent partners; (ii) the densest packing principle rests on the observation that theeffective volume per methylene group in the bilayer interior is only weakly sensitiveto the environment, with values comparable to those for liquid (LC) and solid (ID)alkanes, or intermediate (GL).

References: Laner, M., Horta, B.A.C. Huenberger, P.H.Eur. Biophys. J. (2014) in press (available on-line).

90

Title: Long-timescale motions in glycerol-monopalmitate lipid bilayersinvestigated using molecular dynamics simulation.


B.A.C. Horta∗∗

P.H. Hunenberger∗

Institute/Group:

∗ Laboratory of Physical Chemistry∗∗ Dpto. de Ciencias Biologicas, UEZO, Rio de Janeiro, Brazil

Description :

The occurrence of long-timescale motions in glycerol-1-monopalmitate (GMP) lipidbilayers is investigated based on previously reported 600 ns molecular dynamicssimulations of a 2× 8× 8 GMP bilayer patch in the temperature range 302 to 338K, performed at three different hydration levels, or in the presence of the cosolutesmethanol or trehalose at three different concentrations. The types of long-timescalemotions considered are: (i) the possible phase transitions; (ii) the precession ofthe relative collective tilt-angle of the two leaflets in the gel phase; (iii) the trans-gauche isomerization of the dihedral angles within the lipid aliphatic tails; (iv) theflipping of single lipids across the two leaflets. The results provide a picture of GMPbilayers involving a rich spectrum of events occurring on a wide range of timescales,from the 100-ps range isomerization of single dihedral angles, via the 100-ns range oftilt precession motions, to the multi-µs range of phase transitions and lipid-flippingevents.

References: M. Laner, B.A.C. Horta and P.H. HunenbergerJ. Mol. Graph. Model (2014) submitted.

91

Title: Effect of methanol on the phase-transition properties of glycerol-monopalmitate lipid bilayers investigated using molecular dynamicssimulations: In quest of the biphasic effect.


P.H. Hunenberger∗

Institute/Group:


Description :

The effect of methanol on the phase and phase-transition properties of a 2×8×8glycerol-1-monopalmitate bilayer patch is investigated using a series of 239 moleculardynamics simulations on the 180 ns timescale, considering methanol concentrationscM and temperatures T in the ranges 0-12.3 M and 302-338 K, respectively. Theresults in the form of hysteresis-corrected transition temperatures Tm are compatiblewith the expected features of the biphasic effect, with a reversal concentration crevof about 5.2 M. Below this concentration, the main transition is between the liquidcrystal (LC) and gel (GL) phase, and Tm decreases upon increasing cM . Abovethis concentration, the interdigitated (ID) phase is the stable ordered phase instead,and Tm slightly increases upon interasing T up to about 10 M. The analysis ofthe structural and dynamical properties also reveals very different sensitivities andresponses of the three phases to changes in cM . In particular, the properties of theGL phase are insensitive to cM , whereas those of the LC and ID phases are alteredvia an increase of the area per lipid. For the LC phase, increasing cM promotesdisorder and fluidity. For the ID phase, in contrast, increasing cM up to about 10M slightly increases the ordering and rigidity. Two side issues are also addressed,concerning: (i) the occurrence tilt-precession motions in the GL and ID phases; (ii)the influence of the pressure coupling scheme employed in the simulations, semi- orfully-anisotropic, on the simulation results.

References: M. Laner, B.A.C. Horta and P.H. HunenbergerJ. Mol. Graph. Model (2014) submitted.

92

Title: Estimating the initial biasing potential for λ-local-elevationumbrella-sampling (λ-LEUS) simulations via slow growth.

Researchers: N.S. Bieler∗

P.H. Hunenberger∗

Institute/Group:


Description :

In a recent article [Bieler et al., JCTC, 10 (2014) pp 3006-3022], we introduced acombination of the λ-dynamics (lD) approach for calculating alchemical free-energydifferences and of the local-elevation umbrella-sampling (LEUS) memory-based bias-ing method to enhance the sampling along the alchemical coordinate. The combinedscheme, referred to as λ-LEUS, was applied to the perturbation of hydroquinone tobenzene in water as a test system, and found to represent an improvement overthermodynamic integration (TI) in terms of sampling efficiency at equivalent accu-racy. However, the preoptimization of the biasing potential required in the λ-LEUSmethod requires filling up all the basins in the potential of mean force. This intro-duces a non-productive pre-sampling time that is system-dependent, and generallyexceeds the corresponding equilibration time in a TI calculation. In this letter,a remedy is proposed to this problem, termed the slow growth memory guessing(SGMG) approach. Instead of initializing the biasing potential to zero at the startof the preoptimization, an approximate potential of mean force is estimated from ashort slow growth calculation, and its negative used to construct the initial memory.Considering the same test system as in the preceding article, it is shown that ofthe application of SGMG in λ-LEUS permits to reduce the preoptimization time byabout a factor four.

References: N.S. Bieler and P.H. HunenbergerJ. Chem. Theory. Comput. Lett. (2014) submitted.

93

Title: Phase-transition properties of glycerol-dipalmitate lipid bilayersinvestigated using molecular dynamics simulation.


P.H. Hunenberger∗

Institute/Group:


Description :

The phase- and phase-transition properties of glycerol-dipalmitate (GDP) bilayerpatches are investigated using molecular dynamics simulations. This permits tocharacterize the influence of introducing a second aliphatic lipid tail by comparisonto previously reported simulations of glycerol-1-monopalmitate (GMP). To this pur-pose, a set 67 simulations (up to 300 ns duration) of 2×8×8 GDP bilayer patchesare performed, considering the two isomers glycerol-1,3-dipalmitate (13GDP) andglycerol-1,2-dipalmitate (12GDP; racemic), two hydration levels (12GDP only), andtemperatures in the range 250-370 K. In agreement with experiment, the GDP simu-lations reveal an increase in the main transition temperature by about 30 K relativeto GMP, and the occurrence of non-bilayer phases at high temperatures (inverted-cylinder or stacked conformations). Structurally, the GDP system tends to evidencea tighter packing of the chains, a reduced extent of tilting, increased order param-eters and a reduced fluidity. These differences are easily interpreted in terms oftwo key changes in molecular properties when going from from GMP and GDP: (i)the reduction of the headgroup polarity and hydration (from two hydroxyl groupsto a single one); (ii) the increase in the effective tail cross-section relative to the(hydrated) headgroup cross-section, conferring to GDP a particuliar wedge shape.These two effects contribute to the relative instability of the liquid-crystalline phase,the stability being recovered in nature when the diglyceride headgroup is function-alized by a bulky or/and polar substituent.

References: M. Laner, B.A.C. Horta and P.H. HunenbergerMol. Simul. (2014) to be submitted.

94

Title: Precession driven dynamos in a full sphere

Researchers: Y. Lin (1)

P. Marti (1,2)

J. Noir (1)

A. Jackson (1)

Institute/ (1) EPM, Institut fur Geophysik, ETH Zurich, Switzerland

Group: (2) Department of Applied Mathematics, University of Colorado Boulder, USA.

Description:

Precession is a change in the orientation of the rotation axis of a rotating body. The earth

goes through one full precessional period over a duration of approximately 26000 years due to

the luni-solar tidal torque acting on the Earth’s equatorial bulge. From an energetic point of

view, precession is a possible driving mechanism for the generation of Earths magnetic field

through the so-called dynamo process (Bullard, 1949). Recent numerical simulations have

shown that precession driven flows can power dynamos in spherical and spheroidal containers

(Tilgner, 2005; Wu & Roberts, 2009). But it is still an open question whether precession is

responsible for the geodynamo because numerical models are far away from the Earth’s param-

eter regime. The present study aims at shedding further lights on the role of precession in the

geomagnetic field generation. The fully nonlinear Navier-Stokes equation and magnetic field

diffusion equation are solved using a highly parallelized spectral code (Marti, 2012). Firstly,

we investigate hydrodynamical instability of precession driven flow in a sphere in which only

the Navier-Stokes equations are considered . As the precession rate is above a threshold, the

flow becomes unstable through a parametric resonance of two inertial waves with the distortion

of streamlines. The dynamo simulations show that both hydrodynamical stable flow (laminar)

and unstable flow (disorganized) are capable to sustain dynamos. The laminar flow operates a

dynamo with equatorial dipolar magnetic field, whereas the disorganized flow generates a mag-

netic field dominated by small scale structures. The effect of a thin conducting outer layer is

also considered.

Reference:

Bullard, E. C. (1949). The Magnetic Field within the Earth. Proceedings of the Royal Society

A: Mathematical, Physical and Engineering Sciences, 197:433453.

Tilgner, A. (1949). Precession driven dynamos. Phys. Fluids , 17:034104.

Wu, C. C., & Roberts, P. H. (2009). On a dynamo driven by topographic precession. Geophys-

ical & Astrophysical Fluid Dynamics, 103(6), 467501.

Marti, P. (2012). Convection and boundary driven flows in a sphere. PhD thesis, ETH Zurich.

1

95

Title: Electrically-driven MHD flow in a modified cylindrical annulus

Researchers: Z. Stelzer (1)

D. Cebron (1,2)

S. Vantieghem (1)

A. Jackson (1)

Institute/ (1) EPM, Institute for Geophysics, ETH Zurich, Switzerland

Group: (2) Geodynamo, ISTerre, Universite Grenoble Alpes, CNRS, France

Description:

The dynamics of liquid metal flow under the influence of a magnetic field is relevant in the

geophysical context for the generation of planetary magnetic fields as well as in engineering

applications like liquid metal pumps and flow control. Systems of electrically conducting flu-

ids interacting with magnetic fields are governed by the equations of magnetohydrodynamics

(MHD). A special limit of MHD is the quasi-static approximation where induced magnetic

fields are negligible compared to the imposed one. This limit applies to most laboratory appli-

cations as well as the small-scale motions in the Earth’s core.

Our system under consideration is a cylindrical annulus. The flow is driven by the Lorentz

force resulting from an imposed radial current between the inner and outer ring electrodes in

an axial magnetic field. We are interested in the dynamics of the flow, especially in differ-

ent flow regimes and criteria for instability. In order to complement our laboratory experiment

ZUCCHINI (ZUrich Cylindrical CHannel INstability Investigation) which uses the liquid metal

alloy GaInSn, we perform finite-element (FE) simulations of this system. In this context, it is

crucial to resolve the thin Hartmann layers on walls perpendicular to the magnetic field which

scale inversely with the magnetic field strength.

We employ a 2D3C (2 dimensions, 3 components) FE model of the setup to study numerically

the base flow and the threshold of linear instability. The predominantly azimuthal base flow

is in good agreement with theory and experiments. The subsequent linear stability analysis

builds upon the base flow model. Separating the governing equations in modes with different

azimuthal wave numbers, we retrieve the most unstable modes and the onset of linear instability.

In agreement with the experiment, the first instability occurs in the Shercliff layer parallel to the

magnetic field. We also determine the scaling of this onset of instability in terms of dimensional

and nondimensional quantities.

Reference:

Experimental and numerical study of electrically-driven MHD flow in a modified cylindrical

annulus: (1) Base flow, in prep. for submission to Physics of Fluids.

Experimental and numerical study of electrically-driven MHD flow in a modified cylindrical

annulus: (2) Instabilities, in prep. for submission to Physics of Fluids.

2

96

Title: Latidunal libration driven flows in a triaxial ellipsoid

Researchers: S. Vantieghem (1)

D. Cebron (1,2)

J. Noir (1)


Group: (2) Geodynamo, ISTerre, Universite Grenoble Alpes, CNRS, France

Description:

The aim of our research is to understand planetary core flows and their ability to generate

and sustain magnetic fields. Conventional dynamo models assume that these flows are driven

by thermochemical convection. However, for some planets and satellites, such as the ancient

Moon, Mercury and Jupiter’s moon Ganymede, simple models of convectively driven core flows

are difficult to reconcile with observational constraints. Therefore, it has been proposed that

other mechanisms could give rise to vigorous core flows, and thus drive a dynamo. More

precisely, it has been proposed that a combination of tidal deformation and variations in the

rotation rate of a planet may be at the origin hydrodynamic instabilities.

In this context, we have studied flows driven by libration in latitude, i.e. a north-south-like

oscillation of the figure axes of a planet with respect to its spin axis. The planet itself is mod-

eled as a triaxial ellipsoid. This is a source of major computational challenge. Indeed, many

existing codes assume that a planet is spherically symmetric and exploit this symmetry by using

a decomposition of the relevant physical quantities in terms of spherical harmonics. Such an

approach is not possible in the presence of boundary deformation, and therefore, we have to

recur to local discretisation methods. In particular, we have taken advantage of the unstructured

finite- volume code that we have been developing over the past few years.

In our study, we have identified two mechanisms that allow libration in latitude to drive vigorous

flows. Both mechanisms are related to resonant drivings of inertial modes, i.e. eigenmodes of

the Coriolis operator. More specifically, the first mechanism is a direct forcing of the spin-over

inertial mode that can occur if the libration frequency matches its eigenfrequency. The second

mechanism is a so-called inertial instability, whereby the strain imposed by the triaxial geometry

can resonantly couple two inertial modes of the unforced system. Whether these mechanisms

are such that they can also drive a dynamo, is currently under investigation.

Reference:

Vantieghem S., Cebron D., Noir, J. Latitudinal libration driven flows in a triaxial ellipsoid. J.

Fluid Mech. In review.

3

97

Title: Variational data assimilation for a forced, inertia-free magnetohydrodynamic

dynamo model

Researchers: K. Li (1)

A. Jackson (1)

P. W. Livermore (2)


Group: (2) School of Earth and Environment, University of Leeds, UK

Description:

Earth’s magnetic field is generated by fluid motions in its electrically-conducting liquid outer

core, whereby convective motions are thought to be driven by cooling of the Earth and crys-

tallization of the solid inner core. This system is governed by a set of three coupled equations

that describe the conservation of momentum, energy and the evolution in time of the spatially-

varying magnetic field. The resulting magnetic field permeates the silicate mantle and is observ-

able at the Earth’s surface, thus providing a window into the dynamics of the core. The ultimate

goal of this study is to quantify the trajectory of these coupled fields in the core and to predict

the geomagnetic field evolution in the future. This year, we study the variational data assimila-

tion for a forced, inertia-free magnetohydrodynamic dynamo model with the control parameter

similar to Earth’s dynamo system and find varies strategist to retrieve the entire trajectory of

this system accurately. The results suggest the possibility of retrieving the entire trajectory of

the geodynamo system using the 400-year model of secular variation gufm1.

Reference:

Li, K., Livermore, P.W. and Jackson, A. (2011) Variational data assimilation for the initial value

dynamo problem, Phys. Rev. E , Vol. 84, 056321.

Li, K., Jackson, A. and Livermore, P.W. (2014) Variational data assimilation for a forced,

inertia-free magnetohydrodynamic dynamo model, GJI, accecpted.

4

98

Title: Turbulence modeling and turbulent reactive flow Researchers: Benedikt Dorschner

Valentin GiddeyDaniel MeyerHeng Xiao (now AP TT at Virginia Tech)Patrick Jenny

Institute/Group: Institute of Fluid Dynamics/Prof. Patrick Jenny

General description: Most flows involving human made devices or flows in the environment are turbulent and involve a large range of length and time scales. Consequently such flows are expensive to solve numerically. To reduce the computational burden, methods are applied that solve only for a fraction of these scales but require turbulence models to incorporate effects that result from neglected scales. Most important are Reynolds-averaged Navier-Stokes (RANS) models, large eddy simulation (LES) and probability density function (PDF) methods.

Worldwide, more than 80% of the consumed energy is converted by burning fossil fuels. Therefore, improving emission rates and efficiency of combustion devices automatically has a significant impact on our environment and is of crucial importance. To achieve such improvements, however, the capability of accurately predicting the governing physical processes (which involve turbulence-reaction interaction) is essential. A modeling approach, which proved to be very general and powerful, is based on solving a joint PDF transport equation. Opposed to other approaches, such PDF methods require no model for turbulent convection and there exist no closure issues with averaging the reaction source terms.

Development of PDF solution algorithms: Compared with RANS models, PDF methods are computationally more expensive and challenging. Due to its high dimensionality, the PDF transport equation is typically solved with a particle method.

Currently, with the objective to address more realistic reactive flow problems, an improved hybrid FV/MC solution algorithm is implemented. To this end, we plan to make use of new concepts stemming from the simulation of rarefied gas flows like statistical noise reduction techniques [1].

Modeling of group effect in turbulent spray combustion: The combustion of fuel sprays plays a role, for example, in aircraft turbines and Diesel combustion engines. Despite the importance of these devices, the formation and combustion of droplet groups is not yet well understood [2]. Our research in this area is focused on direct numerical simulation (DNS) of the underlying processes to gain a better understanding of the governing physiochemical effects. In a second step, we plan to formulate improved models to accurately account for group combustion effects in PDF method simulations.

Hybrid LES/RANS modeling framework: While LES is a very powerful approach to model turbulent flows, it is not yet widely used in industrial workflows. This is mainly due to the high computational cost, which is Reynolds

99

number dependent, if wall turbulence is involved. Another difficulty is the choice of an appropriate computational grid. Motivated by these shortcomings, various hybrid LES/RANS methods have been proposed. A major challenge thereby is to determine the RANS and LES regions and to provide valid boundary conditions between them. We follow a new approach which is based on simultaneous LES and RANS simulations, which are coupled via forcing terms to ensure internal consistency [3, 4]. This allows to overcome most of the problems at RANS/LES interfaces, which are intrinsic in other hybrid methods.

It has been demonstrated that robust and consistent coupling of an LES and a RANS simulation, which employ different grids, can be achieved. Recently, we have proposed and successfully tested an improved resolution evaluation criterion [5]. This criterion is applied in hybrid RANS/LES simulations to determine the RANS and LES regions in the computational domain.

!

100

Title: Flow and transport in porous and fractured media Researchers: Davide Cortinovis

Rajdeep DebKarim KhayratFlorian MüllerDaniel MeyerPatrick Jenny


General description: Flow and transport in porous media has many applications in earth science, energy science and many other areas. Examples in which we are interested are oil and gas recovery, CO2 storage in geological subsurface formations, geothermal power exploration and uncertainty assessment of flow and transport.

Multi-scale modeling: This is a collaboration with Dr. Seong Lee (Chevron). One of the major challenges in macroscopic simulations is the correct treatment of complex permeability distributions with strong variations and many length scales. To deal with this issue, various upscaling and multi-scale methods have been developed. In collaboration with the company Chevron we devised and developed a new multi-scale finite-volume (MSFV) algorithm, which has several advantageous properties compared with previous multi-scale methods. The MSFV method allows for very efficient studies of realistic multi-phase flow scenarios in heterogeneous porous media.

Recently, we investigated a more robust version of the MSFV method that performs better for high permeability contrast than earlier MSFV variants. The new iterative Galerkin-enriched MSFV method retains the capabilities of the existing MSFV method, but provides significantly higher convergence speeds [6].

!

! Figure: Nodal basis functions of the standard MSFV method (top figures). Nodal basis functions (4 center figures) after the insertion of two additional degrees of freedom. The corresponding enrichment functions are shown in the bottom figures.

Figure 4: Nodal basis functions of the standard MSFV method (top figures) associated to the dual cell containing the L-shaped shale layers shown in Fig. 3(a). Nodal basis functions (4 center figures) after the insertion of two additional DoF. Thecorresponding enrichment functions are shown in the bottom figures.

while the correction functions (including iterative improvements of the localization assumption) now satisfy233

r · ( ·re()h

) = r · h+ q in d

h

(31)

r? · ( ·r?e()h

) = r? · ( ·r?p()s

) on @d

h

(32)

e()h

(xc

l

) = 0 (33)

e()h

(xa

l

) = 0 (34)

e()h

(x) = 0 8x 2 \ d

h

. (35)

Finally, the enrichment functions associated with the additional DoF locations are numerical solutions of234

r · ( ·r e,h

) = 0 in d

h

(36)

r? · ( ·r? e,h

) = 0 on @d

h

(37)

e,h

(xc

l

) = 0 (38)

e,h

(xa

l

) = el

(39)

e,h

(x) = 0 8x 2 \ d

h

(40)

computed in each dual cell with at least one additional DoF located somewhere on its boundary.235

The correction term e() is assembled exactly as for the standard i-MSFV method (see Eq. (25)), while236

the N = Nc

+Na

interpolators in Eq. (2) are now given by237

k

=

8<

:

PNd

h=1 k,h if k Nc

PNd

h=1 e=kNc,h if k > Nc

. (41)

Note that Eqs. (28), (29), (38) and (39) ensure that k

Nk=1 forms a partition of unity in . The correction238

term is the same as in the standard i-MSFV method.239

8

101

!Hierarchical model of fractured reservoirs: This is an interdisciplinary collaboration with various earth scientists of ETH Zürich. In the context of geothermal power production, a modeling framework for flow and transport in fractured porous media has been created [7]. It has proper interfaces which allow to interfere with rock mechanics and rock chemistry models. Moreover, everything is coupled with heat conduction in the rock. Due to the very large number of fractures, only the large ones are resolved. The cloud of small fractures is treated by effective permeabilities.

Our recent research is focused on the seismicity and the feedback of rock mechanics on the flow or more precisely the porosity and permeability of the fractured reservoir [8]. To this end, we are developing computationally efficient methods to account for shear and tensile failures of fractures. These take place at time scales that are much shorter compared to the time scales relevant for the management of geothermal reservoirs leading to a stiff simulation problem.

Uncertainty assessment of flow and transport in porous media: This is a collaboration with Prof. Christoph Schwab, Prof. Siddhartha Mishra (both SAM, ETHZ), Prof. Peter Arbenz (D-INF, ETHZ) and Prof. Hamdi Tchelepi (Stanford University). The transport of chemical substances in the subsurface is relevant in many different applications. For example, for the assessment of nuclear waste deposition sites or for the coordination of remediation actions after a contamination hazard, predictive simulation tools are required. These tools have to account for the uncertainty in the soil parameters, since measurements of the subsurface structure are typically very scarcely available.

One of our goals is the development of a simulation framework for flow and transport that provides probabilistic information about local tracer concentrations or oil saturations. A probability density function (PDF) method was proposed that is applicable for highly heterogeneous porous media thanks to newly-developed Markovian velocity processes (MVPs). Currently, we are extending this method for two-phase flow applications.

In addition, a multi-level Monte Carlo (MLMC) method has been developed [9], which allows to combine expensive high fidelity methods with cheap approximate solvers to achieve output statistics more efficiently [10]. Recently, we have devised an MLMC method that balances sampling and discretization errors to achieve an optimal total work vs. total error convergence [11].

Prediction of non-equilibrium multi-phase flow: Currently, storing CO2 in geological subsurface formations seems to be one of the most promising feasible technologies to stabilize the CO2 concentration in the Earth’s atmosphere. The prime objective of our research is to improve our understanding of how the physics and dynamics at the pore scale is linked to the macro-scale description that is used for predictions at the formation scale.

To this end, we have devised new model equations for sub-phase saturations. The resulting equation set is able to model hysteric effects. It requires, however, empirical constitutive

102

relations that are calibrated by means of pore network simulations. Moreover, in connection with pore network simulation we are developing a multi-scale simulation approach that couples pore-scale subnetworks with a meso-scale description to simulate large pore networks at small computational cost. Meso-scale flow equations are solved with the flow properties derived from the subnetwork two-phase configuration. The subnetwork configurations are then evolved in time in a physically consistent manner. In addition, our meso-scale representation can account for non-equilibrium effects.

!

! Figure: Simulation of viscous fingering for viscosity ratio 10 using the multi-scale pore network model. Grid cells encapsulate different coupled subnetworks. Shown in white are subnetworks tubes that are filled with invading non-wetting fluid. The meso-scale saturation of non-wetting fluid is shown in color (red 0.93, blue 0).

!Non-equilibrium effects result as well from density differences between CO2-saturated brine and pure brine. With the non-wetting CO2 phase typically sitting on top of the wetting brine phase, so-called gravity fingers form at the phase interface with CO2 diffusing into the brine and increasing the brine density. The resulting finger-like structures are much smaller than the formation scale and therefore cannot be resolved numerically. In our recent research, we have developed a scale analysis that implies opportunities for different modeling approaches [12]. These approaches do not require the resolution of the underlying fine-scale structures.

!

103

Title: Fluid dynamics in biological systems and biomedical optics Researchers: Thomas Kummer

Adrien LückerFranca SchmidPatrick Jenny


General description: Fluid dynamics in biological systems is a research area, which is mainly driven by questions related to life sciences. In many cases, the background of biologists and medical doctors is not suited to investigate complex transport processes of various fluid compositions, which often are crucial for a deep understanding of the problems at hand. Therefore, bio-fluid dynamics is a very interdisciplinary field, which necessarily involves tight collaborations between life scientists, physicists and engineers.

Dynamics of flow with particles (erythrocytes) in capillary networks: This is a collaboration with Dr. Dominik Obrist (ARTORG Center, University of Bern), Prof. Bruno Weber (University of Zürich) and Prof. Alfred Buck (University Hospital Zürich). The rheological influence of red blood cells (RBCs) is an active field of research. While hematocrit dependent viscosity and other phenomena are well described in the literature, the dramatic impact of RBCs on blood flow in capillary networks has not been sufficiently appreciated. A discrete simulation framework was developed in which the erythrocytes are resolved. The number of RBCs in any given capillary relates linearly to the pressure drop along the vessel. At bifurcations, a simple but well confirmed rule is applied to determine the direction of RBC flow, namely that the red cells follow the path of the steepest (local) pressure gradient. The application of the bifurcation rule and RBC-dependent resistance has strong impact on the flow and transport processes within the capillary network. RBC seeded flow differs fundamentally from pure blood-plasma flow (i.e. different flow patterns rather than simple rescaling). A continuum model was devised in which the average number of red cells in a capillary segment is treated as a real number. It has the advantage of being applicable to large capillary networks, where a discrete treatment of RBCs would be computationally too expensive. The continuum model has been extended to work with vascular networks that contain both capillaries and non-capillaries. The goal was to perform blood flow simulations on large, physiological networks that explicitly take the rheological influence of red cells into account. This provides a unique opportunity to study the fascinating self-regulation of blood flow mediated by RBCs and will have enormous impact on our understanding of cerebral blood flow in general and Oxygen supply in particular.

Recently, we extended the discrete treatment of RBCs to enable the simulation of large and realistic microvascular networks. The current investigation focus on the neurovascular coupling or more precisely the up-regulation of the Oxygen supply at a local level.

Oxygen transport in the microcirculation: The most fundamental function of the blood circulation is Oxygen transport to the tissue. Gas and nutrient exchange mostly occurs at the capillary level due to their large total surface area. In organs such as the brain or in muscles, Oxygen supply is a dynamic process that is strongly

104

linked to the metabolism. The mechanisms involved in this coupling are only partly understood, especially at capillary level, but are of fundamental importance. A correct interpretation of functional magnetic resonance imaging requires a sound understanding of the link between neuronal activity and cerebral blood flow (known as neurovascular coupling). Besides, disorders such as Alzheimer’s disease are often related to abnormalities in the microcirculation. However, these phenomena are very difficult to observe experimentally due to the small size of capillaries and the challenges of in vivo experimentation.

In collaboration with Prof. Bruno Weber (University of Zürich), a new model for Oxygen transport from capillaries to the tissue has been developed. The presence of individual moving red blood cells in this model allows us to capture the spatial and temporal heterogeneity of blood flow and its influence on tissue Oxygenation. After a successful comparison with recent Oxygen measurements in the rodent brain [13], we are developing a multi-scale model that couples Oxygen transport with the discrete red blood cell transport model developed at the Institute of Fluid Dynamics. Next, we will focus on candidate mechanisms for neurovascular coupling and quantify their influence on tissue Oxygenation.

!

! Figure: a) Computational domain with a fixed tissue region and red blood cells moving in a capillary. b) Longitudinal partial oxygen pressure profiles at three radial positions. The thick lines indicate the red blood cell locations.

!

a) b)

105

Title: Rarefied gas kinetics Researchers: Nemanja Andric

Hossein GorjiStephan KüchlinPatrick Jenny


General description: It is well known that the Navier-Stokes equations become invalid for large Knudsen numbers, i.e. if the mean free path length is significant compared to the scale of observation. Such scenarios can occur e.g. in nano-scale devices, at re-entry of a space vehicle, in plasma flows and in the presence of very strong shocks.

Stochastic particle method based Fokker-Planck model: This project started as a collaboration with Prof. Manuel Torrilhon (ETH Zürich) and Prof. Stefan Heinz (University of Wyoming). A stochastic model and a solution algorithm to simulate the flow of gases, which are not in thermodynamic equilibrium was developed. For the interaction of a particle with others, statistical moments of the local ensemble have to be evaluated, but unlike in molecular dynamics simulations or DSMC, no collisions between computational particles are considered. In addition, a novel integration technique allows for time steps independent of the stochastic time scale. The stochastic model represents a Fokker-Planck (FP) equation in the kinetic description, which can be viewed as an approximation to the Boltzmann equation. This allows for a rigorous investigation of the relation between the new model and classical fluid and kinetic equations. The fluid dynamic equations of Navier-Stokes and Fourier are fully recovered for small relaxation times, while for larger values the new model extends into the kinetic regime. It could be demonstrated that the stochastic model is consistent with Navier-Stokes in that limit, but also that the results become significantly different, if the conditions for equilibrium are invalid. It could also be shown that the mass flow rate through a channel is correctly predicted as a function of the Knudsen number. By introducing a cubic non-linear drift term, the model leads to the correct Prandtl number of 2/3 for monatomic gas, which is crucial to study heat transport phenomena. Moreover, a highly accurate scheme to evolve the computational particles in velocity and physical space is constructed. An important property of this integration scheme is that it ensures energy conservation and honors the tortuosity of particle trajectories. Especially in situations with small to moderate Knudsen numbers this allows to proceed with much larger time steps than with direct simulation Monte Carlo (DSMC), i.e. the mean collision time not necessarily has to be resolved and thus leads to more efficient simulations.

Recently, besides algorithmic improvements [1, 14], the model was generalized for complex gas flows including mixtures and diatomic molecules [15]. Currently, a new separation device concept based on electromagnetic excitation of gas species is being developed [16]. Moreover, a hybrid DSMC/FP solution algorithm is devised, which is applicable for the whole range of Knudsen numbers. Finally, a novel variance reduction scheme was proposed for computationally efficient simulations of low Mach-number gas flows.

!

106

Title: Morphing wing aerodynamics Researchers: Vitaly Dmitriev

Patrick Jenny Institute/Group: Institute of Fluid Dynamics/Prof. Patrick Jenny

Description: The technology of morphing wings has a high potential, since many more degrees of freedom can be employed to adapt and control a wing for different purposes in different environments. This project is a collaboration with Profs. Paolo Ermanni, Eduardo Mazza and Manfred Morari (ETH Zürich). Our role is to build predictive virtual models, which allow to design the required structure and control algorithms.

It was demonstrated that it is possible to extract energy from shear flows. However, the amount is relatively small in realistic turbulent atmospheres [17]. As a next step, the aerodynamics of an oscillating ring wing and a diamond-shaped wing was simulated [18]. Moreover, optimization studies concerned with the flapping and morphing dynamics were conducted.

!

107

Title: Numerical schemes and solution algorithms Researchers: Halvor Lund

Florian MüllerPatrick Jenny


Description: The numerical integration of the Navier-Stokes equations for incompressible flows has always been a central topic of numerical fluid mechanics. One possible approach consists in computing the pressure and the velocity vector at discrete grid points by solving a system of algebraic equations obtained by discretization of the momentum and continuity equations. Easy analytical manipulations provide then an independent Poisson equation for the pressure. In terms of computational efficiency, the solution of the elliptic pressure equation is the bottle neck in most cases and much effort has been made to improve the computational efficiency for this step.

We focus on the development of an accurate Rankine-Hugoniot-Riemann (RHR) solver [19]. In this finite-volume approach, viscous terms, source terms and cross flux variations (in multi-dimensions) are consistently treated as singularities at the cell centers. In contrast to many other schemes treating multidimensionality and source terms, there is no need for special Riemann solvers. Moreover, it has been proven that this solver is second order accurate and studies reveal that the error is approximately one order of magnitude smaller than other established methods of the same spatial order.

!

! Figure: Advection of a scalar Gaussian profile with different numerical schemes including the newly developed RHR scheme.

!

the following we first show how the RHR relations are solved for theisothermal Euler equations, followed by a brief description of thecharacteristic solver used to solve the resulting Riemann problems.Finally, we present numerical results for a manufactured steadysolution demonstrating second order.

4.4.1. Solving the RHR relationsTo calculate the half-states ui;j;E, ui;j;W;ui;j;S and ui;j;N, we need to

solve the RHR relations given by Eqs. (10)–(13). This is a straight-forward process for the advection equation we have considered sofar, but slightly more complex for the isothermal Euler equations.

In the following, we only consider the solution procedure forui;j;E, as the procedure for ui;j;N is completely analogous. The statesui;j;W and ui;j;S are then given by Eqs. (10) and (11). Using Eq. (10),we replace ui;j;W in Eq. (12), which then reads

1Dxðf ðuEÞ # f ð2u# uEÞÞ ¼ qx; ð49Þ

where we have omitted the spatial indices i and j. The flux functionf is given by

f ðuÞ ¼qu

qðu2 þ c2Þquv

2

64

3

75 ¼u2

u22=u1 þ u1c2

u2u3=u1

2

64

3

75; ð50Þ

where u1 ¼ q;u2 ¼ qu and u3 ¼ qv . Substitution into Eq. (49) leadsto

u2;E

u22;E=u1;Eþu1;Ec2

u2;Eu3;E=u1;E

2

6664

3

7775#

2u2#u2;E

ð2u2#u2;EÞ2=ð2u1#u1;EÞþð2u1#u1;EÞc2

ð2u2#u2;EÞð2u3#u3;EÞ=ð2u1#u1;EÞ

2

6664

3

7775¼Dxqx:

ð51Þ

The first component of Eq. (51) is easily solved for u2;E, i.e.

u2;E ¼Dx2

qx;1 þ u2: ð52Þ

Next, we solve the second component of Eq. (51) for u1;E. Aftersubstituting n ¼ u1 # u1;E one obtains the cubic equation

n3 þDxqx;2

2c2 n2 þ2u2

2;E # 2u21c2 þ 4u2ðu2 # u2;EÞ

2c2 n

þ#4u2u1ðu2 # u2;EÞ # Dxqx;2u2

1

2c2 ¼ 0 ð53Þ

for n. This equation may be solved either numerically usingNewton’s method with good starting values, or analytically usingan exact solution formula, of which we have used the latter. Inour analytical solution of Eq. (53), we choose the root yielding apositive density u1;E and minimising the jump n between u1;E and u1.

Having found n and thus u1;E, one can calculate u3;E using thethird component of Eq. (51) and obtains

u3;E ¼ð2u2#u2;EÞ2u3

2u1#u1;Eþ Dxqx;3

u2;Eu1;Eþ ð2u2#u2;EÞ

2u1#u1;E

: ð54Þ

In summary, Eqs. (52)–(54) yield ui;j;E, and similarly ui;j;N can becalculated.

Fig. 10. Advection of a scalar Gaussian profile (16) with velocity ða; bÞ> ¼ ð1; 0:5Þ> , on a 20& 20 grid with Dx ¼ Dy ¼ 1:8.

Table 1Computational cost per time step for advection of a scalar on a80 & 80 grid.

Method Cost (ms)

RHR no lim. 8.8RHR lim. 8.8MUSCL minmod 8.6MUSCL van Albada 8.7

H. Lund et al. / Computers & Fluids 101 (2014) 1–14 9

108

Title: Fluid Mechanics of the Inner Ear

Researchers: Francesco Boselli, Elisabeth Edom, Bernhard Grieser, LeonhardKleiser and Dominik Obrist

Institute/ Institute of Fluid DynamicsGroup: Prof. L. Kleiser

Description:

The inner ear hosts the senses for balance (vestibular system) and hearing (cochlea). Westudy the (patho-)physiology of the inner ear by numerical simulations.Inside each semicircular canal (SCC) of the vestibular system an elastic membranouslabyrinth holds a lymphatic fluid (endolymph) which develops a quasi-steady Poiseuilleflow profile across the SCC lumen during head rotation. This flow leads to the perceptionof angular motion, and it results in eye motions that stabilize our vision.It has been observed that, without head motion, the rare presence of a dehiscence inthe bony roof of the canals can cause upward-torsional eye movements when exposed tosound of a certain amplitude (> 80dB SPL) and frequency (ca. 500 − 3000Hz), resultingin dizziness and vertigo (Tullio phenomenon) which may originate from an induced flow inthe respective SCC. Sound waves propagate from the stapes not only through the cochlea,but also towards the dehiscence which serves as a third window. In interaction with theflexible membranous labyrinth we observe nonlinear effects that lead to an energy trans-fer from the highly oscillating stapes into the low-frequency domain of the balance sense,causing a uni-directional second-order flow inside the SCC.In another project we compute a particle-laden endolymph flow by the Multilayer Methodof Fundamental Solutions (MFS) in combination with the Force Coupling Method (FCM)which was applied to a realistic three-dimensional SCC during head rotation. This setupenabled us to study a pathological condition where free-floating particles disturb the en-dolymph flow. Such a condition can cause benign paroxysmal positional vertigo (BPPV),which is arguably the most common form of vertigo in humans.The cochlea converts oscillations of the middle ear ossicles into traveling waves of theperilymphatic fluid and of its sensory structures. These movements lead to hearing. Westudy the cochlear mechanics with the massively-parallel Navier-Stokes solver IMPACTdeveloped in our group. The mechanical structures and their interaction with the fluidflow are integrated with an immersed boundary approach. We investigate a nonlineareffect of the fluid motion which is known as steady streaming. This flow might stimulatethe sensory cells in the cochlea and also help to transport ions in the cochlear fluid whichare crucial for the hearing. Further, we address the influence of different stimulationmodes on the hearing.

References: See separate list.

109

Title: Prediction of Jet Flows, Aeroacoustic Jet Noise and Sta-bility of Swirling Jets using Large-Eddy Simulation

Researchers: Stefan Buhler, Tobias Luginsland, Michael Gloor,Leonhard Kleiser


Description:

The reduction of aeroacoustic noise is an important goal in the design process of modernjet engines. Our research helps to improve the understanding of the relevant mechanismsthat are responsible for the noise production in turbulent flow fields in the exhaust ofsuch engines. In order to study jet noise phenomena, high-order numerical schemes weredeveloped for solving the compressible Navier-Stokes equations.The flow conditions at the jet nozzle exit have a significant impact on the radiated noise.However, little physical insight is currently available on how sound generation mechanismsare influenced by the character of the flow disturbances. We therefore study the flow de-velopment and sound emission from initially laminar, transitional and turbulent nozzleboundary layers for isothermal single jet flows. The findings confirm the sensitivity ofthe flow development and sound radiation on the details of the inflow conditions. Soundpressure spectra obtained in the acoustic near-field agree well with experimental data.In addition to the research on isothermal single jets, we study coaxial jet flows with aheated core stream to represent realistic flow conditions in the exhaust of modern bypassjet engines. By performing large-scale simulations we study the influence of the jet-to-ambient temperature ratio and the core-to-bypass velocity ratio. The results show thatan increase of sound pressure levels can be observed for strongly heated jets because ofincreased fluctuation levels in the flow region close to the end of the potential core. Ad-ditionally, the bypass velocity has a complex influence on the jet-flow development bymodifying the Kelvin-Helmholtz instabilities that lead to the transition of the initiallylaminar shear layers.Furthermore, we investigate the stability and transitional behavior of swirling jets atmedium to high swirl numbers. At sufficiently high azimuthal velocity the jets breakdown and a recirculation zone around the centerline develops. This flow state is governedby strong helical modes dominating the conical shear layers. We study the influence ofthe nozzle on the breakdown behavior of the swirling jet. The nozzle lip has an importantimpact on the mode selection in the flow region behind the nozzle together with the az-imuthal shear layers within and outside the nozzle. The influence of physical parameters(Re, Ma, swirl number S) on the breakdown behavior is additionally investigated.


110

Title: Instability and Transition Near the Leading Edge of Swept Wings

Researchers: Michael John, Dominik Obrist and Leonhard Kleiser


Description:

Flow instability, which makes laminar flow become turbulent, is one of the canonical prob-lems of fluid dynamics. Various techniques exist to investigate the different instabilities,such as linear primary, secondary or non-linear analyses. For the late stages of transitionto turbulence direct numerical simulations (DNS) of the flow field, which directly resolveall nonlinearities, are very important.

We investigate the instability of the swept Hiemenz boundary layer (SHBL), which is amodel for the flow along the leading edge of swept airplane wings. It is an inherentlythree-dimensional flow, and the instability is of the so-called “subcritical” type. Thismeans that instabilities arise which are due to nonlinear effects even when the flow isstable according to the simpler, linear theory. The project is structured in three parts.The fist part treats a new class of exact Navier-Stokes solutions which better describe thelaminar flow analytically. The second part investigates the linear primary and secondaryinstability of the boundary layer flow without and with a finite primary disturbance,respectively. The third part consist of an investigation of a nonlinear bypass transitionmechanism by means of very large DNS with our high-fidelity in-house simulation codeIMPACT.

The first part of this work contributes to the theoretical understanding of the instability ofthree-dimensional boundary layers. This mathematical investigation of subcritical, non-linear instability of differential equations is of high academic value. The second and thirdpart may contribute to the solution of the practical problem of transition prediction andlaminar-flow control on swept airplane wings. Ultimately, our simulations may contributeto a delay of turbulent flow near the leading edge of swept wings and hence to substantialdrag reduction and reduced fuel consumption of airplanes.


111

Title: Simulation of Particle-Laden Flows

Researchers: Yvonne Reinhardt, Tarun Chadha and Leonhard Kleiser


Description:

We study particle-laden flows with direct and large-eddy simulations. Such flows are par-tially governed by density differences, which are either due to different densities of theinvolved fluids or due to suspended particles. For the simulations we use a highly scalableand high order (up till 10th order) code for incompressible flows which has been devel-oped in-house. It employs compact finite differences on staggered grids in space and afully-explicit or semi-implicit time integration scheme. To increase the Reynolds numberrange, we use different sub-grid scale models to perform large-eddy simulations.To model density differences (e.g. due to salinity or suspended particles), additional trans-port equations are solved. In this regard the fluid phase is described in an Eulerianframework, with or without the Boussinesq assumption. The particle/dispersed phase isrepresented as an Eulerian concentration field or as discrete particles using a Lagrangianparticle approach, wherein transport equations are solved for each particle. The effectof transported concentrations and particles appears as an additional force term in theNavier-Stokes equations (two-way coupling). Currently, the flow solver is applied to dif-ferent multiphase flows such as turbidity currents. A model configuration known as thelock-exchange setup is used. This configuration is widely used in the study of gravity cur-rents produced by an instant release mechanism. In this configuration the spatial domainis a rectangular box in which an initially fixed volume of fluid suspended with particlesis separated from the clear fluid by a barrier. At the start of the simulation/experiment,the barrier is removed giving rise to a bottom-propagating turbidity current. The effectof various parameters on front propagation and spatially averaged quantities such as theenergy budget and suspended particle mass is studied. Furthermore, instantaneous fea-tures such as the Kelvin-Helmholtz and the lobe-and-cleft instabilities appearing in theseflows are studied in detail. The results from the simulations are compared with the ex-perimental observations and data.In a second project we focus on the development and validation of computational methodsthat can be employed for industrial applications of multiphase flows. Main interest is puton abrasive water jet cutting, which has become increasingly popular for material cuttingapplications. The aim of this project is to model the mixing process between particlesand the jet in the cutting head and the evolution of the flow in the focusing tube. Forthe computations, the open-source framework of OpenFOAM is used.


112

Title: Multiscale modeling of polymers, dendronized polymers, actinfilaments, primitive path statistics

Researchers: Prof. Martin Kroger 1

Prof. Avraham Halperin 2

Prof. Igal Szleifer & Ying Li 3

Prof. Andreas Bausch 4

Prof. Juan J. de Pablo 5

Institutes: 1 Computational Polymer Physics, D-MATL, ETH Zurich2 CEA Grenoble, France3 Northwestern University, Chicago, CA, USA4 TU Munich, Germany5 University of Wisconsin, Madison, WI, USA

Description:

We recently focused our attention on the dynamics of polymer chains in the vicinity of non-attractive nanoparticles [1], primitive-path statistics of entangled polymers and the mapping ofmulti-chain simulations onto single-chain mean-field models [2], interactions in dendronized poly-mers [3], the microscopic origin of the non-Newtonian viscosity of semiflexible polymer solutions[4], the effect of polymer solvent on the mechanical properties of entangled polymer gels [5],organization and characterization of dendronized polymers at the atomistic level [6,7], the effectof charge, hydrophobicity, and sequence of nucleoporins on the translocation of model particlesthrough the nuclear pore complex [7], branching defects in dendritic molecules [8], the directobservation of the dynamics of semiflexible polymers in shear flow [9], and reviewed challengesin multiscale modeling of polymer dynamics [10]. Details available at www.complexfluids.ethz.ch

[1] Y. Li, M. Kroger, W.K. Liu, Soft Matter 10 (2014) 1723.[2] R.J.A. Steenbakkers, C. Tzoumanekas, Y. Li, W.K. Liu, M. Kroger, J.D. Schieber, New J. Phys.

16 (2014) 015027.[3] E. Cordova-Mateo, O. Bertran, B. Zhang, D. Vlassopoulos, R. Pasquino, A.D. Schluter, M. Kroger,

C. Aleman, Soft Matter 10 (2014) 1032.[4] B. Huber, M. Harasim, B. Wunderlich, M. Kroger, A.R. Bausch, ACS Macro Lett. 3 (2014) 136.[5] Y.R. Sliozberg, R.A. Mrozek, J.D. Schieber, M. Kroger, J.L. Lenhart, J.W. Anzelm, Polymer 54

(2013) 2555.[6] O. Bertran, B. Zhang, A.D. Schluter, A. Halperin, M. Kroger, C. Aleman, RSC Adv. 3 (2013) 126.[7] O. Bertran, B. Zhang, A. D. Schluter, M. Kroger, C. Aleman, J. Phys. Chem. B 117 (2013) 6007.[8] M. Tagliazucchi, O. Peleg, M. Kroger, Y. Rabin, I. Szleifer, Proc. Natl. Acad. Sci. 110 (2013)

3363.[9] M. Kroger, A.D. Schluter, A. Halperin, Macromolecules 46 (2013) 7550.[10] M.B. Harasim, B. Wunderlich, O. Peleg, M. Kroger, A.R. Bausch, Phys. Rev. Lett. 110 (2013)

108302.[11] Y. Li, B.C. Abberton, M. Kroger, W.K. Liu, Polymers 5 (2013) 751.

113

Title: Accelerating Quantum Transport Calculations through the FEAST Algorithm

Researchers: Sascha Brück Mauro Calderara Mathieu Luisier Institute/ Integrated Systems Laboratory/ Group: Nano-TCAD Group Description: Quantum transport (QT) simulations of devices with realistic dimensions pose a serious com-putational challenge and demand therefore for a high level of parallelization. At each energy point required to evaluate the charge and current density of a given structure, a polynomial ei-genvalue problem must be solved to obtain the so-called open boundary conditions. This op-eration scales with the system size to the power of three. However, not all the eigenvalues are needed, but only those with an absolute value close to one. As a solution the FEAST algo-rithm is used because it allows for a reduction of the problem size down to the number of de-sired eigenvalues and for a drastic acceleration of the computation time. To determine the re-duced system, the integration of a matrix function along a complex contour enclosing the de-sired eigenvalues is necessary. This contour is chosen as two concentric circles around the unit circle, as depicted below. At each integration point, a linear system of equations must be solved. It is generally the most time consuming part of the algorithm, but it can be performed in parallel. This results in total speed-ups that exceed the number of available CPUs, when compared to standard methods. With FEAST ab-initio QT simulations with more than 10.000 atoms are now possible. A nanowire field-effect transistor is shown below as an example.

Top: Nanowire field-effect transistor Right: Concentric circles in the complex

plane with integration points. The desired eigenvalues are located in the light blue area.

Reference: S. Brück, M. Calderara, M. H. Bani-Hashemian, J. VandeVondele and M. Luisier, “Towards ab-initio simulations of nanowire field-effect transistors”, Proceedings of the IWCE 17, DOI: 10.1109/IWCE.2014.6865831, 2014, Paris, France, June 2014.

114

Title: SplitSolve: a GPU-Accelerated Sparse System Solver for Quantum Transport

Researchers: Mauro Calderara Sascha Brück Mathieu Luisier Institute/ Integrated Systems Laboratory/ Group: Nano-TCAD Group Description: SplitSolve in an algorithm for solving sparse linear systems as encountered in quantum transport (QT) simulations based on the Wave Function (WF) formalism. In QT the system to solve consists of an energy-dependent Hamiltonian matrix augmented with open boundary self-energies for the contacts (OBCs). The OBCs blocks have a much lower rank than the Hamiltonian itself. The right hand sides have non-zero entries only in the top and bottom rows, matching the rows containing the updates in the Hamiltonian. This structure can be leveraged to interleave the computation of the OBCs and the solution of the sparse linear systems, i.e. the Hamiltonian matrix can be preprocessed before knowing the exact form of the OBCs updates. After completing the interleaved tasks, the final solution to the system can be computed as a correction to the solution obtained during preprocessing. SplitSolve uses dense linear algebra for pre- and post-processing and is thus well suited to accelerators such as GPUs. Our benchmarks show that due to the prowess of accelerators at dense linear algebra the overall time to solve the WF equations with SplitSolve is considerably smaller than when using a generic sparse linear solver such as MUMPS. The speedup is further increased by the interleaving strategy that is not possible otherwise. Simulations on hybrid architectures featuring accelerators thus see an increased usage of the computational resources and shorter run times, as illustrated below.

References:

M.Calderara, S. Brück, P. Ferry, and M. Luisier, “Accelerating Quantum Transport Simulations on Massively Parallel Computing Architectures”, PASC Conference, ETH Zurich, June 2014. S. Brück, M. Calderara, M. H. Bani-Hashemian, J. VandeVondele and M. Luisier, “Towards ab-initio simulations of nanowire field-effect transistors”, Proceedings of the IWCE 17, DOI: 10.1109/IWCE.2014.6865831, 2014, Paris, France, June 2014.

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Title: Computation of measure valued solutions of the equations of fluiddynamics.

Insitute: SAM.Researchers: S. Mishra, R. Kappeli, S. Lanthaler, F. Leonardi, U. S.Fjordholm (NTNU, Trondheim, Norway).Description: Measure valued solutions are a new paradigm in CFD thatappear to be promising as the appropriate solution framework of both theincompressible as well as compressible Euler equations of fluid dynamics.These solutions are space-time parametrized probability measures that rep-resent (weak) limit of approximation schemes, such as numerical methods.A new ensemble based sampling algorithm is proposed to approximatemeasure valued solutions and is shown to converge as the mesh parameterstend to zero. Statistical quantities of interest, such as the mean, variance,pdfs and multi-point correlation functions can be computed in a conver-gent manner.Publications:

• U. S. Fjordholm, R. Kappeli, S. Mishra and E. Tadmor, Construc-tion of approximate entropy measure valued solutions for hyperbolicsystems of conservation laws. Preprint, available as arXiv:1402.0909[math.NA].

• S. Lanthaler and S. Mishra, Computation of measure valued solutionsof the incompressible Euler equations, preprint, 2014.

116

Title: High resolution entropy stable finite volume and space-time Dis-continuous Galerkin methods for approximating compressible Euler andNavier-Stokes equations on unstructured grids.

Insitute: SAM.Researchers: S. Mishra, A. Hiltebrand, S. May, D. Ray and P. Chan-drasekher (TIFR Bangalore, India), U. S. Fjordholm (NTNU, Norway).Description: We design entropy stable high-resolution finite volume schemesfor the Euler and Navier-Stokes equations, based on a judicious combina-tion of entropy conservative fluxes, numerical diffusion operators and signpreserving limiters. Similarly, space-time shock capturing DG methods arealso designed to be entropy stable. Both sets of methods are designed onunstructured grids to approximate realistic flows on domains with complexgeometry.Publications:

• P. Chandrasekhar, U. S. Fjordholm, S. Mishra and D. Ray, Entropystable schemes on two-dimensional unstructured grids, preprint 2014.

• A. Hiltebrand and S. Mishra, Efficient computation of all speed flowsusing an entropy stable shock-capturing space-time discontinuous Galerkinmethod, Research report 2014-17, SAM ETH Zurich.

• A. Hiltebrand and S. Mishra, Efficient pre conditioners for a shockcapturing space-time discontinuous Galerkin method for systems ofconservation laws, Research report 2014-04, SAM ETH Zurich.

117

Title: Multi-level Monte Carlo methods for UQ in CFD.

Insitute: SAM.Researchers: S. Mishra, C. Schwab, J. Sukys, K. Lye.Description: Multi-level Monte Carlo (MLMC) methods are developedand employed to efficiently compute uncertainty in nonlinear hyperbolicsystems of conservation laws. A massively parallel code is designed forthis purpose and is applied to a wide variety of problems such as Eulerand MHD equations with uncertain initial data, shallow water equationswith uncertain topography and material parameters, acoustic wave equa-tions with uncertain rock properties as well as the computation of measurevalued and statistical solutions of the fundamental equations of fluid dy-namics.Publications:

• S. Mishra, Ch. Schwab and J. Sukys, Multi-Level Monte Carlo Fi-nite Volume methods for uncertainty quantification of acoustic wavepropagation in random heterogeneous layered medium, Research report2014-22, SAM ETH Zurich.

• C. Sanchez-Linares, M. de la asuncion, M. Castro, S. Mishra and J.Sukys, Multi-level Monte Carlo finite volume method for shallow waterequations with uncertain parameters applied to landslides-generatedtsunamis, Research report 2014-24, SAM ETH Zurich.

118

Title: Free-energy landscape of protein oligomerization from atomistic simulations

Researchers: A. Barducci1

M. Bonomi3

M. K. Prakash2

Michele Parrinello2 Institute/Group: 1 Laboratoire de Biophysique Statistique, École Polytechnique Fédérale de

Lausanne, CH-1015 Lausanne, Switzerland; 2 Department of Chemistry and Applied Biosciences, Eidgenössische Technische Hochschule Zürich, CH-8006 Zurich, Switzerland and Facoltà di Informatica, Istituto di Scienze Computazionali, Università della Svizzera Italiana, CH-6900 Lugano, Switzerland 3 Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biosciences, University of California, San Francisco, CA 94158

Description: In the realm of protein–protein interactions, the assembly process of homooligomers plays a fundamental role because the majority of proteins fall into this category. A comprehensive understanding of this multistep process requires the characterization of the driving molecular interactions and the transient intermediate species. The latter are often short-lived and thus remain elusive to most experimental investigations. Molecular simulations provide a unique tool to shed light onto these complex processes complementing experimental data. Here we combine advanced sampling techniques, such as metadynamics and parallel tempering, to characterize the oligomerization landscape of fibritin foldon domain. This system is an evolutionarily optimized trimerization motif that represents an ideal model for experimental and computational mechanistic studies. Our results are fully consistent with previous experimental nuclear magnetic resonance and kinetic data, but they provide a unique insight into fibritin foldon assembly. In particular, our simulations unveil the role of nonspecific interactions and suggest that an interplay between thermodynamic bias toward native structure and residual conformational disorder may provide a kinetic advantage. References: PNAS, 2013, 110 (49) pp E4708-E4713 DOI: 10.1073/pnas.1320077110

119

Title: Evaluating functions of positive-definite matrices using colored-noise thermostats

Researchers: M. Nava1

M. Ceriotti2

C. Dryzun1

M. Parrinello1

Institute/Group: 1 Department of Chemistry and Applied Biosciences, Eidgenössische

Technische Hochschule Zürich, CH-8006 Zurich, Switzerland and Facoltà di Informatica, Istituto di Scienze Computazionali, Università della Svizzera Italiana, CH-6900 Lugano, Switzerland 2 Laboratory of Computational Science and Modeling, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland

Description:

Many applications in computational science require computing the elements of a function of a large matrix. A commonly used approach is based on the the evaluation of the eigenvalue decomposition, a task that, in general, involves a computing time that scales with the cube of the size of the matrix. We present here a method that can be used to evaluate the elements of a function of a positive-definite matrix with a scaling that is linear for sparse matrices and quadratic in the general case. This methodology is based on the properties of the dynamics of a multidimensional harmonic potential coupled with colored-noise, generalized Langevin equation thermostats. This “f-thermostat” approach allows us to calculate directly elements of functions of a positive-definite matrix by carefully tailoring the properties of the stochastic dynamics. We demonstrate the scaling and the accuracy of this approach for both dense and sparse problems and compare the results with other established methodologies.

References: Phys. Rev. E, 2014, 89, 023302 DOI: 10.1103/PhysRevE.89.023302

120

Title: Anomalous water diffusion in salt solutions

Researchers: Y. Ding1

A. A. Hassanali2

M. Parrinello1


Technische Hochschule Zurich and Facoltà di Informatica, Instituto di Scienze Computationali, Università della Svizzera Italiana, CH-6900 Lugano, Switzerland 2 The Abdus Salam International Centre for Theoretical Physics, I-34151 Trieste, Italy

Description:

Liquid water remains one of the most important environments in which physical, chemical, and biological processes occur. One such process involves the solvation of ions. Understanding the perturbation that ions make on the hydrogen bond network of water remains an open question. Here, using state-of-the-art simulation methods, we show that treating the electronic degrees of freedom explicitly is required to reproduce the experimentally observed water diffusion trends in CsI and NaCl solutions, where ab initio water is characterized by dynamic heterogeneity. We find that the ions do not disrupt the network in any significant manner and provide some nuances to classical ideas in physical chemistry regarding the “structure-making” and “structure-breaking” properties of ions. References: PNAS, 2014, 111 (9) pp 3310-3315

DOI: 10.1073/pnas.1400675111

121

Title: Aqueous solutions: state of the art in ab initio molecular dynamics Researchers: A. A. Hassanali1

J. Cuny2

V. Verdolino1

M. Parrinello1

Institute/Group: 1 Department of Chemistry and Applied Biosciences, ETH Zurich,

and Facoltà di Informatica, Istituto di Scienze Computazionali, Università della Svizzera Italiana, 6900 Lugano Switzerland 2 Laboratoire de Chimie et Physique Quantiques—UMR 5626, Toulouse, France

Description: The simulation of liquids by ab initio molecular dynamics (AIMD) has been a subject of intense activity over the last two decades. The significant increase in computational resources as well as the development of new and efficient algorithms has elevated this method to the status of a standard quantum mechanical tool that is used by both experimentalists and theoreticians. As AIMD computes the electronic structure from first principles, it is free of ad hoc parametrizations and has thus been applied to a large variety of physical and chemical problems. In particular, AIMD has provided microscopic insight into the structural and dynamical properties of aqueous solutions which are often challenging to probe experimentally. In this review, after a brief theoretical description of the Born–Oppenheimer and Car–Parrinello molecular dynamics formalisms, we show how AIMD has enhanced our understanding of the properties of liquid water and its constituent ions: the proton and the hydroxide ion. Thereafter, a broad overview of the application of AIMD to other aqueous systems, such as solvated organic molecules and inorganic ions, is presented. We also briefly describe the latest theoretical developments made in AIMD, such as methods for enhanced sampling and the inclusion of nuclear quantum effects. References: Phil. Trans. R. Soc. A, 2014, 372 (2011) 20120482

DOI: 10.1098/rsta.2012.0482

122

Title: Assessing the Reliability of the Dynamics Reconstructed from Metadynamics

Researchers: M. Salvalaglio1,2

P. Tiwary2

M. Parrinello2

Institute/Group: 1 Institute of Process Engineering, ETH Zurich, CH-8092 Zurich,

Switzerland 2 Department of Chemistry and Applied Biosciences, ETH Zurich, 8092 Zurich, Switzerland and Facoltà di Informatica, Istituto di Scienze Computazionali, Università della Svizzera Italiana, Via G. Buffi 13, 6900 Lugano, Switzerland

Description:

Sampling a molecular process characterized by an activation free energy significantly larger than kBT is a well-known challenge in molecular dynamics simulations. In a recent work [Tiwary and Parrinello, Phys. Rev. Lett. 2013, 111, 230602], we have demonstrated that the transition times of activated molecular transformations can be computed from well-tempered metadynamics provided that no bias is deposited in the transition state region and that the set of collective variables chosen to enhance sampling does not display hysteresis. Ensuring though that these two criteria are met may not always be simple. Here we build on the fact that the times of escape from a long-lived metastable state obey Poisson statistics. This allows us to identify quantitative measures of trustworthiness of our calculation. We test our method on a few paradigmatic examples. References: J. Chem. Theory Comput., 2014, 10 (4), pp 1420–1425

DOI: 10.1021/ct500040r

123

Title: The role of the umbrella inversion mode in proton diffusion

Researchers: A. A. Hassanali1

F. Giberti2

G. C. Sosso2

M. Parrinello2

Institute/Group: 1 The Abdus Salaam International Center for Theoretical Physics, Strada

Costiera, 11, I-34151 Trieste, Italy 2 Department of Chemistry and Applied Biosciences, Eidgenössische Technische Hochschule Zürich, CH-8093 Zurich, Switzerland and Facoltà di Informatica, Istituto di Scienze Computazionali, Università della Svizzera Italiana, 6900 Lugano, Switzerland

Description:

Here, using ab initio molecular dynamics (AIMD) simulations, we elucidate the role of the umbrella inversion mode of the hydronium in proton transfer (PT) in liquid water. The hydrophobic face of the hydronium oxygen experiences asymmetries in the solvent potential along the inversion coordinate and this has a rather drastic effect on the barrier for proton transfer. This behavior is coupled to the fluctuations of voids or cavities in the vicinity of the hydronium in the water network. The peculiar inversion mode can either trap or release the proton from different parts of the water network.

References: J. Chem. Phys. Lett., 2014, 599, pp 133-138

DOI: 10.1016/j.cplett.2014.03.034

124

Title: Well-Tempered Metadynamics Concerges Asymptotically

Researchers: J. F. Dama1

M. Parrinello2

G. A. Voth1

Institute/Group: 1 Department of Chemistry, James Franck Institute, Institute for

Biophysical Dynamics, and Computation Institute, University of Chicago, Chicago, Illinois 60637, USA 2 Department of Chemistry and Applied Biosciences, Eidgenössische Technische Hochschule Zürich, CH-8093 Zurich, Switzerland and Facoltà di Informatica, Istituto di Scienze Computazionali, Università della Svizzera Italiana, 6900 Lugano, Switzerland

Description:

Metadynamics is a versatile and capable enhanced sampling method for the computational study of soft matter materials and biomolecular systems. However, over a decade of application and several attempts to give this adaptive umbrella sampling method a firm theoretical grounding prove that a rigorous convergence analysis is elusive. This Letter describes such an analysis, demonstrating that well-tempered metadynamics converges to the final state it was designed to reach and, therefore, that the simple formulas currently used to interpret the final converged state of tempered metadynamics are correct and exact. The results do not rely on any assumption that the collective variable dynamics are effectively Brownian or any idealizations of the hill deposition function; instead, they suggest new, more permissive criteria for the method to be well behaved. The results apply to tempered metadynamics with or without adaptive Gaussians or boundary corrections and whether the bias is stored approximately on a grid or exactly.

References: Phys. Rev. Lett., 2014, 112, 240602 DOI: 10.1103/PhysRevLett.112.240602

125

Title: A Time-Independent Free Energy Estimator for Metadynamics Researchers: P. Tiwary1

M. Parrinello1


Technische Hochschule (ETH) Zürich, CH-8093 Zurich, Switzerland and Facoltà di Informatica, Istituto di Scienze Computazionali, Università della Svizzera Italiana, 6900 Lugano, Switzerland

Description:

Metadynamics is a powerful and well-established enhanced sampling method for exploring and quantifying free energy surfaces of complex systems as a function of appropriately chosen variables. In the limit of long simulation time, metadynamics converges to the exact free energy surface plus a time-dependent constant. In this article, we analyze in detail this time-dependent constant. We show an easy way to calculate it, and by explicitly calculating the time dependence of this constant, we are able to derive a time-independent and locally convergent free energy estimator for metadynamics. We also derive an alternate procedure for obtaining the full unbiased distributions of generic operators from biased metadynamics simulations and explicitly test its usefulness. References: J. Phys. Chem. B, 2014, accepted DOI: 10.1021/jp504920s

126

Title: A Comparison of Finite-Time and Finite-Size Lyapunov Exponents

Researchers: R. Peikert, A. Pobitzer, F. Sadlo and B. Schindler

Institute/ Department of Computer Science / Group: Scientific Visualization Group Description: Finite-time and finite-size Lyapunov exponents are related concepts that have been used for the purpose of identifying transport structures in time-dependent flow. The preference for one or the other concept seems to be based more on a tradition within a scientific community than on proven advantages. In this study, we demonstrate that with the two concepts highly similar visualizations can be produced, by maximizing a simple similarity measure. Furthermore, we show that results depend crucially on the numerical implementation of the two concepts. References: Topological Methods in Data Analysis and Visualization III, Springer, pp. 187-200, 2014. DOI: 10.1007/978-3-319-04099-8_12

127

Title: Smart transparency for illustrative visualization of complex flow surfaces

Researchers: R. Carnecky, R. Fuchs, Y. Jang and R. Peikert

Institute/ Information Technology and Education / Group: Scientific Visualization Group Description: The perception of transparency and the underlying neural mechanisms have been subject to extensive research in the cognitive sciences. However, we have yet to develop visualization techniques that optimally convey the inner structure of complex transparent shapes. In this paper, we apply the findings of perception research to develop a novel illustrative rendering method that enhances surface transparency non-locally. Rendering of transparent geometry is computationally expensive since many optimizations, such as visibility culling, are not applicable and fragments have to be sorted by depth for correct blending. In order to overcome these difficulties efficiently, we propose the illustration buffer. This novel data structure combines the ideas of the A and G-buffers to store a list of all surface layers for each pixel. A set of local and nonlocal operators is then used to process these depth lists to generate the final image. Our technique is interactive on current graphics hardware and is only limited by the available graphics memory. Based on this framework, we present an efficient algorithm for a nonlocal transparency enhancement that creates expressive renderings of transparent surfaces. A controlled quantitative double blind user study shows that the presented approach improves the understanding of complex transparent surfaces significantly. References: IEEE Transactions on Visualization and Computer Graphics, 19(5), pp. 838-851, 2013.

128

Title: Multiverse data-flow control

Researchers: B. Schindler, R. Fuchs, R. Peikert

Institute/ Information Technology and Education / Group: Scientific Visualization Group Description: In this paper, we present a data-flow system which supports comparative analysis of time-dependent data and interactive simulation steering. The system creates data on-the-fly to allow for the exploration of different parameters and the investigation of multiple scenarios. Existing data-flow architectures provide no generic approach to handle modules that perform complex temporal processing such as particle tracing or statistical analysis over time. Moreover, there is no solution to create and manage module data, which is associated with alternative scenarios. Our solution is based on generic data-flow algorithms to automate this process, enabling elaborate data-flow procedures, such as simulation, temporal integration or data aggregation over many time steps in many worlds. To hide the complexity from the user, we extend the World Lines interaction techniques to control the novel data-flow architecture. The concept of multiple, special-purpose cursors is introduced to let users intuitively navigate through time and alternative scenarios. Users specify only what they want to see, the decision which data are required is handled automatically. The concepts are explained by taking the example of the simulation and analysis of material transport in levee-breach scenarios. To strengthen the general applicability, we demonstrate the investigation of vortices in an offline-simulated dam-break data set. References: IEEE Transactions on Visualization and Computer Graphics, 19(6), pp. 1005-1019, 2013.

129

Title: Höchstauflösende FTIR-Spektroskopie. Trendbericht Physikalische Chemie 2013

Researchers: S. Albert*/** M. Quack* Institute/Group: * Group for Molecular Kinetics and Spectroscopy, Physical

Chemistry, ETH Zürich, CH-8093 Zurich, Switzerland ** Swiss Light Source, Paul Scherrer Institute, CH-5232 Villigen

PSI, Switzerland Description: Höchstauflösende Fourier-Transform-Infrarot-(FTIR)-Spektroskopie liefert Informationen über interstellare IR-Banden, Tunneldynamik, chirale Moleküle sowie Methan auf Planeten und Monden. Die Analyse der höchstaufgelösten Spektren erfordert umfangreiche numerische, rechnergestützte Auswertungen. References: S. Albert and M. Quack, Nachrichten aus der Chemie 62, 313 – 318 (2014), DOI. 10.1515/nachrchem.2014.62.3.313

130

Title: Synchrotron based FTIR spectroscopy of the chiral molecules CDBrClF and CHBrIF

Researchers: S. Albert*/** S. Bauerecker*/*** K. Keppler Ph. Lerch** M. Quack*

Institute/Group: * Group for Molecular Kinetics and Spectroscopy, Physical


PSI, Switzerland *** Institut für Physikalische und Theoretische Chemie, Technische

Universität Braunschweig, D-38106 Braunschweig, Germany Description: We report the analysis of the high resolution spectra of the title compounds, making use of extensive computational pattern recognition and simulation tools. References: S. Albert, S. Bauerecker, K. Keppler, Ph. Lerch and M. Quack, in “Proceedings of the 19th Symposium on Atomic, Cluster and Surface Physics 2014 (SASP 2014), Obergurgl, Austria, 8 to 14 February 2014”, pages 152 – 155, (D. Stock, R. Wester, P. Scheier eds., Innsbruck University Press (IUP), Innsbruck, 2014), ISBN 978-3-902936-26-4

131

Title: Two Photon IR-Laser Induced Population Transfer in NH3 – First Steps to Measure Parity Violation in Chiral Molecules

Researchers: P. Dietiker E. Milogyadov M. Quack A. Schneider G. Seyfang

Institute/Group: Group for Molecular Kinetics and Spectroscopy, Physical Chemistry,

ETH Zürich, CH-8093 Zurich, Switzerland Description: The title topic is described with the first proof of principle experiments so far on an achiral molecule. Computational simulations of the experiments provide a perfect match. References: P. Dietiker, E. Milogyadov, M. Quack, A. Schneider, G. Seyfang, in “Proceedings of the 19th Symposium on Atomic, Cluster and Surface Physics 2014 (SASP 2014), Obergurgl, Austria, 8 to 14 February 2014”, pages 226 – 229, (D. Stock, R. Wester, P. Scheier eds., Innsbruck University Press (IUP), Innsbruck, 2014), ISBN 978-3-902936-26-4.

132

Title: Highest resolution FTIR spectroscopy of indene (C9H8) with synchrotron radiation

Researchers: S. Albert*/** Ph. Lerch** M. Quack* A. Wokaun**



PSI, Switzerland Description: We report the analysis of the high resolution spectra of the title compound, making use of extensive computational pattern recognition and simulation tools. References: S. Albert, Ph. Lerch, M. Quack and A. Wokaun, in “Proceedings of the 19th Symposium on Atomic, Cluster and Surface Physics 2014 (SASP 2014), Obergurgl, Austria, 8 to 14 February 2014”, pages 240 – 243, (D. Stock, R. Wester, P. Scheier eds., Innsbruck University Press (IUP), Innsbruck, 2014), ISBN 978-3-902936-26-4 .

133

Title: The infrared spectrum of methane up to 12000 cm–1 Researchers: O. N. Ulenikov*/** E. S. Bekhtereva*/** S. Albert*/*** S. Bauerecker*/****

H.-M. Niederer*

M. Quack*


Chemistry, ETH Zürich, CH-8093 Zurich, Switzerland ** Laboratory of Molecular Spectroscopy, Physics Department,

Tomsk National Research University, RU-634055 Tomsk, Russia *** Swiss Light Source, Paul Scherrer Institute, CH-5232 Villigen

PSI, Switzerland **** Institut für Physikalische und Theoretische Chemie, Technische

Universität Braunschweig, DE-38106 Braunschweig, Germany Description: We report the analysis of the high resolution spectra of methane, making use of extensive computational pattern recognition and simulation tools. References: O. N. Ulenikov, E. S. Bekhtereva, S. Albert, S. Bauerecker, H.-M. Niederer, and M. Quack, in “Proceedings of the 19th Symposium on Atomic, Cluster and Surface Physics 2014 (SASP 2014), Obergurgl, Austria, 8 to 14 February 2014”, pages 244– 247, (D. Stock, R. Wester, P. Scheier eds., Innsbruck University Press (IUP), Innsbruck, 2014),, Innsbruck, 2014), ISBN 978-3-902936-26-4

134

Title: On the “Expanded Local Mode” Approach Applied to the Methane Molecule: Isotopic Substitution CH3D ← CH4 and CHD3 ← CH4

Researchers: O. N. Ulenikov** E. S. Bekhtereva**

A. L. Fomchenko**/***

A. G. Litvinovskaya**

C. Leroy*/***

M. Quack* Institute/Group: * Group for Molecular Kinetics and Spectroscopy, Physical

Chemistry, ETH Zürich, CH-8093 Zurich, Switzerland ** Institute of Physics and Technology, National Research Tomsk

Polytechnic University, RU-634050 Tomsk, Russia and

Physics Department, National Research Tomsk State University, RU-634050 Tomsk, Russia

*** Laboratoire Interdisciplinaire Carnot de Bourgogne, UMR CNRS 6303, Université de Bourgogne, F-21078 Dijon Cedex, France

Description: Operator perturbation theory and the symmetry properties of the axially symmetric XYZ3 (C3v) type molecules are used for the determination of the spectroscopic parameters in the form of functions of structural parameters and parameters of the intramolecular potential function. Several relations between sets of spectroscopic parameters of these molecules are obtained. The ‘expanded local mode’ model and the general isotopic substitution theory are used to estimate the relations between spectroscopic parameters of CH3D and CHD3, on the one hand, and with the Td symmetric isotopic species, CH4, on the other hand. Test calculations with the isotopic relations show that even without including prior information about the CH3D and CHD3 species, numerical results of calculations are in a good agreement both with experimental data and with results of ab initio calculations. References: O. N. Ulenikov, E. S. Bekhtereva, A. L. Fomchenko, A. G. Litvinovskaya, C. Leroy, and M. Quack, Mol. Phys, 112, 2529 – 2556 (2014)

135

Title: The Concept of Law and Models in Chemistry Researchers: M. Quack Institute/Group: Group for Molecular Kinetics and Spectroscopy, Physical Chemistry,

ETH Zürich, CH-8093 Zurich, Switzerland Description: After a brief introduction to the basic concepts including some questions of language, the first part of this paper provides a brief survey of the historical development of laws and models in Chemistry, in particular atomic and molecular models. In the second part this paper deals with the fundamental role of the observation of symmetry violations in physics and chemistry in understanding the most ‘fundamental laws’ and current efforts towards such studies by means of high resolution spectroscopy of molecules. We conclude with a brief discussion of the implications for current unsolved problems in astrophysics and biology. The role of computational models derived from theory is discussed as well. References: M. Quack, European Review, 22/Supplement S1, pp S50-S86, doi:10.1017/S106279871300077X

136

Title: On the Emergence of Simple Structures in Complex Phenomena: Concepts and Some Numerical Examples

Researchers: M. Quack


ETH Zürich, CH-8093 Zurich, Switzerland Description: We provide a conceptual review of the title subject, illustrated with numerical examples. References: M. Quack, Adv. Chem. Phys., 157, 97 – 116 (2014)

137

Title: On Biomolecular Homochirality as a Quasi-Fossil of the Evolution of Life Researchers: M. Quack


ETH Zürich, CH-8093 Zurich, Switzerland Description: We provide a review of the title subject including also theoretical and experimental aspects of molecular parity violation. References: M. Quack, Adv. Chem. Phys., 157, 249 – 290 (2014)

138

Title: Myths, Challenges, Risks and Opportunities in Evaluating and Supporting Scientific Research

Researchers: M. Quack


ETH Zürich, CH-8093 Zurich, Switzerland Description: The methods for evaluating and supporting scientific research are discussed pointing out, in particular, the fallacies of a purely statistical-numerical-approach by numerical bibliometry and the like. References: M. Quack, in “Incentives and performance: Governance of research organizations”, pages 000-000, I. M. Welpe, J. Wollersheim, S. Ringelhan, and M. Osterloh, M. (Eds.), Springer International Publishing, Cham (2014)

139

Title: Survey of the High Resolution Infrared Spectrum of Methane (12CH4 and 13CH4): Partial Vibrational Assignment Extended Towards 12000 cm−1

Researchers: O. N. Ulenikov*/** E. S. Bekhtereva*/** S. Albert*/*** S. Bauerecker*/****

H.-M. Niederer*

M. Quack*


Chemistry, ETH Zürich, CH-8093 Zurich, Switzerland ** Institute of Physics and Technology, National Research Tomsk

Polytechnic University, RU-634050 Tomsk, Russia *** Swiss Light Source, Paul Scherrer Institute, CH-5232 Villigen

PSI, Switzerland **** Institut für Physikalische und Theoretische Chemie, Technische

Universität Braunschweig, DE-38106 Braunschweig, Germany Description: We have recorded the complete infrared spectrum of methane 12CH4 and its second most abundant isotopomer 13CH4 extending from the fundamental range starting at 1000 cm−1 up to the overtone region near 12’000 cm−1 in the near infrared at the limit towards the visible range, at temperatures of about 80 K and also at 298 K with Doppler limited resolution in the gas phase by means of interferometric Fourier transform spectroscopy using the Bruker IFS 125 HR prototype (ZP 2001) of the ETH Zürich laboratory. This provides the so far most complete data set on methane spectra in this range at high resolution. In the present work we report in particular those results, where the partial rovibrational analysis allows for the direct assignment of pure (J = 0) vibrational levels including high excitation. These results substantially extend the accurate knowledge of vibrational band centers to higher energies and provide a benchmark for both the comparison with theoretical results on the one hand and atmospheric spectroscopy on the other hand. We also present a simple effective Hamiltonian analysis, which is discussed in terms of vibrational level assignments and 13C isotope effects. References: O. N. Ulenikov, E. S. Bekhtereva, S. Albert, S. Bauerecker, H. M. Niederer, and M. Quack J. Chem. Phys. (2014) in press

140

Title: Theoretical 57Fe Mossbauer Spectroscopy for Structure Elucida-tion of [Fe] Hydrogenase Active Site Intermediates

Researchers: Joel Gubler1

Arndt R. Finkelmann1

Markus Reiher1

Institute/Group: 1Laboratorium fur Physikalische Chemie, ETH Zurich, 8093Zurich

Description:

[Fe] hydrogenase is a hydrogen activating enzyme that features a mono-iron active sitewhich can be well characterized by Mossbauer spectroscopy. Mossbauer spectra havebeen measured of the CO and CN− inhibited species as well as under turnover con-ditions [S. Shima et al., J. Am. Chem. Soc., 2005, 127, 10430]. In this project wecalculated Mossbauer parameters for various active-site models of [Fe] hydrogenase toprovide structural information about the species observed in experiment. As theoreticalMossbauer spectroscopy requires the parametrization of observables from first-principlescalculations (i.e., electric-field gradients and contact densities) to the experimental ob-servables (i.e., quadrupole splittings and isomer shifts), non-relativistic and relativisticdensity functional theory methods were parametrized against a reference set of Fe com-plexes specifically selected for the application to the Fe center in [Fe] hydrogenase. Withthis methodology the measured parameters for the CO and CN− inhibited complexescould be reproduced. Evidence for the protonation states of the hydroxyl group in closeproximity to the active site and for the thiolate ligand, which could participate in protontransfer, was obtained. The unknown resting state measured in the presence of the sub-strate and under pure H2 atmosphere was identified to be a water-coordinated complex.Consistent with previous assignments based on infrared and X-ray absorption near-edgespectroscopy, all measured Mossbauer data could be reproduced with the active site’siron atom being in oxidation state +II.

References: J. Gubler, A. R. Finkelmann, M. Reiher, Inorg. Chem., 2013, 52,14205–14215.

141

Title: Assessment of Charge-Transfer Excitations with Time-Dependent,Range-Separated Density Functional Theory based on Long-Range MP2 and Multiconfigurational Self-Consistent Field WaveFunctions

Researchers: Erik Donovan Hedegard1

Frank Heiden1

Stefan Knecht1,2

Emmanuel Fromager3

Hans Jørgen Aagaard Jensen1

Institute/Group: 1Department of Physics, Chemistry and Pharmacy, University ofSouthern Denmark, 5230 Odense, Denmark2Laboratorium fur Physikalische Chemie, ETH Zurich, 8093Zurich3Laboratoire de Chimie Quantique, Institut de Chimie, CNRS etUniversite de Strasbourg, 67000 Strasbourg, France

Description:

Charge transfer excitations can be described within Time-Dependent Density FunctionalTheory (TD-DFT), not only by means of the Coulomb Attenuated Method (CAM) butalso with our recently developed combination of wave function theory and TD-DFTbased on range separation [J. Chem. Phys. 2013, 138, 084101]. The latter approach en-ables a rigorous formulation of multi-determinantal TD-DFT schemes where excitationclasses, which are absent in conventional TD-DFT spectra (like for example double exci-tations), can be addressed. We investigate the combination of both the long-range Multi-Configuration Self-Consistent Field (MCSCF) and Second Order Polarization Propaga-tor Approximation (SOPPA) ansatze with a short-range DFT (srDFT) description. Wefind that the combinations of SOPPA or MCSCF with TD-DFT yield better resultsthan could be expected from the pure wave function schemes. For the Time-DependentMCSCF short-range DFT ansatz (TD-MC-srDFT) excitation energies calculated over alarger benchmark set of molecules with predominantly single reference character yieldgood agreement with their reference values, and are in general comparable to the CAM-B3LYP functional. Beyond proof-of-principle calculations, we additionally study thelow-lying singlet excited states (S1 and S2) of the retinal chromophore. The chromophoredisplays multireference character in the ground state and both excited states exhibit con-siderable double excitation character, which in turn cannot be described within standardTD-DFT, due to the adiabatic approximation. However, a TD-MC-srDFT approach canaccount for the multireference character, and excitation energies are obtained with ac-curacy comparable to CASPT2, although using a much smaller active space.

References: E. D. Hedegaard, F. Heiden, S. Knecht, E. Fromager,H. J. Aa. Jensen, J. Chem. Phys., 2013, 139, 184308.

142

Title: Toward Reliable Prediction of the Energy Ladder in Multichro-mophoric Systems: A Benchmark Study on the FMO Light-Harvesting Complex

Researchers: Nanna Holmgaard List1

Carles Curutchet2

Stefan Knecht1,3

Benedetta Mennucci4

Jacob Kongsted1

Institute/Group: 1Department of Physics, Chemistry and Pharmacy, University ofSouthern Denmark, 5230 Odense, Denmark2Departament de Fisicoquımica, Facultat de Farmacia, Universitatde Barcelona, 08028 Barcelona, Spain3Laboratorium fur Physikalische Chemie, ETH Zurich, 8093Zurich4Dipartimento di Chimica e Chimica Industriale, Universita diPisa, 56126 Pisa, Italy

Description:

We present an evaluation of the performance of various single-reference QM methods forthe prediction of the relative site energies and transition moments of the Q bands in thebacteriochlorophyll a (BChl a) pigments of the FennaMatthewOlson (FMO) complex.We examine the relative merits of ZINDO, CIS, TD-DFT (with the functionals PBE,BLYP, PBE0, B3LYP, and CAM-B3LYP) and RI-CC2 in reproducing the variationsacross the pigments that occur as a consequence of geometrical and electrostatic effectsof the FMO complex by comparison to DFT-BHLYP/MRCI. We find that these pigmentsare near-multiconfigurational in nature and, thus, constitute critical cases for the RI-CC2method. The commonly used ZINDO method is fairly reliable for the site energies of theisolated pigments; however, it overestimates the coupling to the environment, therebyleading to variations across the embedded pigments that are too drastic. The overallbest performance in comparison to DFT/MRCI is provided by the TD-DFT methods,where the hybrid functional PBE0 is slightly superior to the other functionals comprisedin our test set.

References: N. H. List, C. Curutchet, S. Knecht, B. Mennucci, J. Kongsted,J. Chem. Theory Comput., 2013, 9, 4928.

143

Title: On the Photophysics of Carotenoids: A Multireference DFT Studyof Peridinin

Researchers: Stefan Knecht1,2

Christel M. Marian3

Jacob Kongsted2

Benedetta Mennucci4

Institute/Group: 1Laboratorium fur Physikalische Chemie, ETH Zurich, 8093Zurich2Department of Physics, Chemistry and Pharmacy, University ofSouthern Denmark, 5230 Odense, Denmark3Institute of Theoretical and Computational Chemistry, Univer-sity of Dusseldorf, 40225 Dusseldorf, Germany4Dipartimento di Chimica e Chimica Industriale, Universita diPisa, 56126 Pisa, Italy

Description:

We present a quantum-mechanical investigation of the photophysics of a specificcarotenoid, peridinin, which is present in light-harvesting complexes. The fundamentalrole played by the geometry in determining the position and character of its low-lyingsinglet electronic states is investigated using a multireference DFT approach in combina-tion with a continuum solvation model. The main photophysical properties of peridininappear to be governed by the lowest two singlet excited states, as no evidence pointsto an intermediate S∗ state and the energies of the upper excited states are too high toallow their population with excitation in the visible range. These two excited states (S1,21A−g and S2, 11B+

u ) are highly connected through the conjugation path here character-ized by the value of the bond length alternation (BLA). The S1 and S2 states presentdistinct natures for small BLA values, whereas for larger ones they become more similarin terms of both brightness and dipolar character and their energies become closer. Thegeometrical issue is thus of fundamental importance for a correct interpretation of thespectroscopic signatures of peridinin.

References: S. Knecht, C. M. Marian, J. Kongsted, B. Mennucci,J. Phys. Chem. B, 2013, 117, 13808.

144

Title: Unravelling the quantum-entanglement effect of noble gas coordi-nation on the spin ground state of CUO

Researchers: Pawel Tecmer1

Katharina Boguslawski1

O. Legeza2

Markus Reiher1

Institute/Group: 1Laboratorium fur Physikalische Chemie, ETH Zurich, 8093Zurich2Wigner Research Center for Physics, H-1525 Budapest

Description:

The accurate description of the complexation of the CUO molecule by Ne and Ar noblegas matrices represents a challenging task for present-day quantum chemistry. Especially,the accurate prediction of the spin ground state of different CUOnoble-gas complexesremains elusive. In this work, the interaction of the CUO unit with the surroundingnoble gas matrices is investigated in terms of complexation energies and dissected intoits molecular orbital quantum entanglement patterns. Our analysis elucidates the antic-ipated singlettriplet ground-state reversal of the CUO molecule diluted in different noblegas matrices and demonstrates that the strongest uraniumnoble gas interaction is foundfor CUOAr4 in its triplet configuration.

References: P. Tecmer, K Boguslawski, O. Legeza, M. Reiher, Phys. Chem.Chem. Phys., 2014, 16, 719–727.

145

Title: Significant Substituent Effect on the Anomerization ofPyranosides

Researchers: Shino Manab1

Hiroko Satoh2

Jurg Hutter3

Hans Peter Luthi4

Teodoro Laino5

Yukishige Ito1

Institute/Group: 1RIKEN, Synthetic Cellular Chemistry Laboratory, Hirosawa,Wako, Saitama 351-01982National Institute of Informatics (NII), Hitotsubashi, Chiyoda-ku, Tokyo 101-84303Institute of Physical Chemistry, University of Zurich, 8057 Zurich4Laboratorium fur Physikalische Chemie, ETH Zurich, 8093Zurich5IBM Research Zurich, 8803 Ruschlikon

Description:

Aminoglycosides containing a 2,3-trans carbamate group easily undergo anomerizationfrom the 1,2-trans glycoside to the 1,2-cis isomer under mild acidic conditions. TheN-substituent of the carbamate has a significant effect on the anomerization reaction;in particular, an N-acetyl group facilitated rapid and complete -anomerization. The dif-ferences in reactivity due to the various N-substituents were supported by the resultsof DFT calculations; the orientation of the acetyl carbonyl group close to the anomericposition was found to contribute significantly to the directing of the anomerization re-action. By exploiting this reaction, oligoaminoglycosides with multiple 1,2-cis glycosidicbonds were generated from 1,2-trans glycosides in a one-step process.

References: S. Manab, H. Satoh, J. Hutter, H.P. Luthi, T. Laino, Y. Ito, Chem.Eur. J., 2014, 20, 124–132.

146

Title: Theoretical 57Fe Mossbauer Spectroscopy: Isomer shifts of [Fe]-Hydrogenase Intermediates

Researchers: Erik Donovan Hedegard1

Stefan Knecht2

Ulf Ryde3

Jacob Kongsted1

Trond Saue4

Institute/Group: 1Laboratorium fur Physikalische Chemie, ETH Zurich, 8093Zurich2Department of Physics, Chemistry and Pharmacy, University ofSouthern Denmark3Department of Theoretical Chemistry, Lund University4Laboratoire de Chimie et Physique Quantiques, Universite PaulSabatier

Description:

Mossbauer spectroscopy is an indispensable spectroscopic technique and analytical toolin iron coordination chemistry. The linear correlation between the electron density atthe nucleus (“contact density”) and experimental isomer shifts has been used to linkcalculated contact densities to experimental isomer shifts. Here we have investigated forthe first time relativistic methods of systematically increasing sophistication, includingthe eXact 2-Component (X2C) Hamiltonian and a finite-nucleus model, for the calcu-lation of isomer shifts of iron compounds. While being of similar accuracy as the fullfour-component treatment, X2C calculations are far more efficient. We find that effectsof spin-orbit coupling can safely be neglected, leading to further speedup. Linear cor-relation plots using effective densities rather than contact densities versus experimentalisomer shift lead to a correlation constant which is close to an experimentally derivedvalue. Isomer shifts of similar quality can thus be obtained both with and without fitting,which is not the case if one pursues a priori a non-relativistic model approach. As anapplication for a biologically relevant system, we have studied three recently proposed[Fe]-hydrogenase intermediates. The structures for these intermediates were extractedfrom QM/MM calculations using large QM regions surrounded by the full enzyme anda solvation shell of water molecules. We show that a comparison between calculatedand experimentally observed isomer shifts can be used to discriminate between differ-ent intermediates, whereas calculated atomic charges do not necessarily correlate withMossbauer isomer shifts. Detailed analysis reveals that the difference in isomer shiftsbetween two intermediates is due to an overlap effect.

References: E. D. Hedegaard, S. Knecht, U. Ryde, J. Kongsted, T. Saue, Phys.Chem. Chem. Phys., 2014, 16, 4853.

147

Title: Four-Component Density Matrix Renormalization Group

Researchers: Stefan Knecht1

Ors Legeza2

Markus Reiher1

Institute/Group: 1Laboratorium fur Physikalische Chemie, ETH Zurich, 8093Zurich2Wigner Research Centre, H-1525 Budapest, Hungary

Description:

We present the first implementation of the relativistic quantum chemical two- and four-component density matrix renormalization group algorithm that includes a variationaldescription of scalar-relativistic effects and spin-orbit coupling. Numerical results basedon the four-component Dirac-Coulomb Hamiltonian are presented and compared to “tra-ditional” ab initio wave function configuration interaction and coupled cluster approachesfor the standard reference molecule for correlated relativistic benchmarks: thallium hy-dride.

References: S. Knecht, O. Legeza, M. Reiher, J. Chem. Phys., 2014, 140,041101.

148

Title: Quantum entanglement in carbon-carbon, carbon-phosphorus andsilicon-silicon bond

Researchers: Matthieu Mottet1

Pawel Tecmer1

Katharina Boguslawski1

Ors Legeza2

Markus Reiher1

Institute/Group: 1Laboratorium fur Physikalische Chemie, ETH Zurich, 8093Zurich2Wigner Research Centre, H-1525 Budapest, Hungary

Description:

The chemical bond is an important local concept to understand chemical compoundsand processes. Unfortunately, like most local concepts, the chemical bond and the bondorder do not correspond to any physical observable and thus cannot be determinedas an expectation value of a quantum chemical operator. We recently demonstrated[Boguslawski et al., J. Chem. Theory Comput., 2013, 9, 2959–2973] that one- andtwo-orbital-based entanglement measures can be applied to interpret electronic wavefunctions in terms of orbital correlation. Orbital entanglement emerged as a powerfultool to provide a qualitative understanding of bond-forming and bond-breaking processes,and allowed for an estimation of bond orders of simple diatomic molecules beyond theclassical bonding models. In this article we demonstrate that the orbital entanglementanalysis can be extended to polyatomic molecules to understand chemical bonding.

References: M. Mottet, P. Tecmer, K. Boguslawski, O. Legeza, M. Reiher,Phys. Chem. Chem. Phys, 2014, 16, 8872–8880

149

Title: A Role for [Fe4S4] Clusters in tRNA Recognition — A TheoreticalStudy

Researchers: Martin T. Stiebritz1


Description:

Over the past several years, structural studies have led to the unexpected discovery ofiron-sulfur clusters in enzymes that are involved in DNA replication/repair and pro-tein biosynthesis. Although these clusters are generally well studied cofactors, theirsignificance in the new contexts often remains elusive. One fascinating example is atryptophanyl-tRNA synthetase from the thermophilic bacterium Thermotoga maritima,TmTrpRS, that has recently been structurally characterized. It represents an unprece-dented connection among a primordial iron-sulfur cofactor, RNA, and protein biosyn-thesis. A possible role of the [Fe4S4] cluster in tRNA anticodon-loop recognition wasinvestigated by means of density functional theory and comparison with the structure ofa human tryptophanyl-tRNA synthetase/tRNA complex. It turned out that a cluster-coordinating cysteine residue, R224, and polar main chain atoms form a characteristicstructural motif for recognizing a putative 5′ cytosine or 5′ 2-thiocytosine moiety inthe anticodon loop of the tRNA molecule. This motif provides not only affinity but alsospecificity by creating a structural and energetical penalty for the binding of other bases,such as uracil.

References: M. T. Stiebritz, Nucl. Acids Res., 2014, 42, 5426.

150

Title: Code Interoperability and Standard Data Formats in QuantumChemistry and Quantum Dynamics

Researchers: Elda Ross1

Stefano Evangelisti2

Antonio Lagana3

Hans Peter Luthi4 et al.

Institute/Group: 1SuperComputing Applications and Innovation Department,CINECA, via Magnanelli, 6/3, Casalecchio di Reno/Bologna, I-400332Laboratoire de Physique Quantique, UMR 5626, Universite deToulouse et CNRS 118, Route de Narbonne, Toulouse Cedex, F-310623Department of Chemistry, University of Perugia, Via Elce disotto, 8, Perugia, I-061234Laboratorium fur Physikalische Chemie, ETH Zurich, 8093Zurich

Description:

Code interoperability and the search for domain-specific standard data formats representa critical issue in many areas of computational science. The advent of novel computinginfrastructures such as computational grids and clouds made these issues even moreurgent. The design and implementation of a common data format for quantum chemistryand quantum dynamics computer programs is discussed with reference to the researchperformed in the course of two COST Actions. The specific data models adopted, Q5costand D5cost, are shown to work for a number of interoperating codes, regardless of thetype and amount of information (small or large data sets) to be exchanged. The codesare either interfaced directly, or transfer data by means of wrappers; both types of dataexchange are supported by the Q5/D5cost library. Further, the exchange of data betweenquantum chemistry and quantum dynamics codes is addressed. As a proof of concept,the H + H2 reaction is discussed. The proposed scheme is shown to provide an excellentbasis for cooperative code development, even across domain boundaries. Moreover, thescheme presented is found to be useful also as a production tool in the Grid distributedcomputing environment.

References: E. Ross, S. Evangelisti, A. Lagana, H.P. Luthi et al, J. Comp.Chem., 2014, 35, 611–621.

151

Title: Gradient-driven molecule construction: An inverse approach ap-plied to the design of small-molecule fixating catalysts

Researchers: Thomas Weymuth1

Markus Reiher1


Description:

Rational design of molecules and materials usually requires extensive screening of molec-ular structures for the desired property. The inverse approach to deduce a structure fora predefined property would be highly desirable, but is, unfortunately, not well defined.However, feasible strategies for such an inverse design process may be successfully de-veloped for specific purposes. We discuss options for calculating jacket potentials thatfulfill a predefined target requirementa concept that we recently introduced (Weymuthand Reiher, MRS Proceedings 2013, 1524, DOI:10.1557/opl.2012.1764). We consider thecase of small-molecule activating transition metal catalysts. As a target requirementwe choose the vanishing geometry gradients on all atoms of a subsystem consisting ofa metal center binding the small molecule to be activated. The jacket potential can berepresented within a full quantum model or by a sequence of approximations of which afield of electrostatic point charges is the simplest. In a second step, the jacket potentialneeds to be replaced by a chemically viable chelate-ligand structure for which the geom-etry gradients on all of its atoms are also required to vanish. To analyze the feasibility ofthis approach, we dissect a known dinitrogen-fixating catalyst to study possible designstrategies that must eventually produce the known catalyst.

References: T. Weymuth, M. Reiher, Int. J. Quantum Chem., 2014, 114,838–850.

152

Title: Inaccessibility of the µ-hydride species in [FeFe] hydrogenases

Researchers: Arndt R. Finkelmann1

Martin T. Stiebritz1

Markus Reiher1


Description:

[FeFe] hydrogenases catalyse the reversible formation and oxidation of H2. They pre-sumably feature a hydride species as a key intermediate. The H− ligand can either bebound between the iron atoms of the [2Fe]H subsite (µ-H) or terminally to the distaliron atom of the active site (terminal-H). Although the µ-H species is thermodynami-cally most stable, experimental evidence points to the terminal-H species as the relevantintermediate. In order to understand these contradictory results, we investigated thecatalytic cycle of [FeFe] hydrogenases (including transition states) with a special focuson the role of the two possible hydride intermediates. For this, density functional theorycalculations were carried out for a large quantum mechanical active-site model. It wasshown that formation of the µ-H intermediate is prohibited by high activation barrierswhich are caused by interactions of the H cluster with surrounding amino acids. Weprovided direct evidence for the anchoring of the H cluster in the protein to be decisivefor the kinetic hinderance of µ-H formation.

References: A. R. Finkelmann, M. T. Stiebritz, M. Reiher, Chem. Sci., 2014,5, 215–221.

153

Title: Facile Synthesis and Theoretical Conformation Analysis of aTriazine-Based Double-Decker Rotor Molecule with Three An-thracene Blades

Researchers: Max Kory1

Maike Bergeler2

Markus Reiher2

A. Dieter Schluter1

Institute/Group: 1Laboratorium fur Polymer Chemie, ETH Zurich, 8093 Zurich2Laboratorium fur Physikalische Chemie, ETH Zurich, 8093Zurich

Description:

The facile synthesis of a rotor-shaped compound with two stacked triazine units, whichare symmetrically connected by three anthracene blades through oxygen linkers, is pre-sented. This new double-decker, which is a potential monomer for two-dimensionalpolymerization, was synthesized by using readily available, cheap building blocks, ex-ploiting the known selectivity difference for the nucleophilic substitution of cyanuricchloride. The crystal structure of a C3h symmetric rotor-shaped compound with 9,10-dihydroanthracene blades, which is a direct precursor to the targeted monomer, andthe crystal structure of the new double-decker with the desired C3h symmetry, are alsoreported. The synthetic efforts were preceded by a computational analysis, which wastriggered by the question of conformational stability of the potential monomer. Twostable conformers could be found, and the barrier for the transition path in the gasphase between these conformers was determined by quantum chemical calculations. Ex-ploratory BornOppenheimer molecular-dynamics simulations revealed a strong influenceof solventsolute interactions on the stability of the conformers, which resulted in anenergetic preference of the C3h symmetric conformation of the double-decker.

References: M. Kory, M. Bergeler, M. Reiher and A. D. Schluter, Chem. Eur.J., 2014, 20, 6934.

154

Title: Inaccessibility of the µ-hydride species in [FeFe] hydrogenases


Hans M. Senn2

Markus Reiher1

Institute/Group: 1Laboratorium fur Physikalische Chemie, ETH Zurich, 8093Zurich2WestCHEM and School of Chemistry, University of Glasgow,Glasgow G12 8QQ, UK

Description:

When investigating the mode of hydrogen activation by [Fe] hydrogenases, not only thechemical reactivity at the active site is of importance but also the large-scale confor-mational change between the so-called open and closed conformations, which leads to aspecial spatial arrangement of substrate and iron cofactor. To study H2 activation, acomplete model of the solvated and cofactor-bound enzyme in complex with the sub-strate methenyl-H4MPT+ was constructed. Both the closed and open conformationswere simulated with classical molecular dynamics on the 100 ns time scale. Quantum-mechanics/molecular-mechanics calculations on snapshots then revealed the features ofthe active site that enable the facile H2 cleavage. The hydroxyl group of the pyridinolligand can easily be deprotonated. With the deprotonated hydroxyl group and the struc-tural arrangement in the closed conformation, H2 coordinated to the Fe center is subjectto an ionic and orbital push–pull effect and can be rapidly cleaved with a concertedhydride transfer to methenyl-H4MPT+. An intermediary hydride species is not formed.

References: A. R. Finkelmann, H. M. Senn, M. Reiher, Chem. Sci., 2014, 5,4474–4482.

155

Title: Relativistic Fock-Space Coupled Cluster Study of Small BuildingBlocks of Larger Uranium Complexes

Researchers: Pawe l Tecmer1

Andre Severo Pereira Gomes2

Stefan Knecht3

Lucas Visscher1

Institute/Group: 1Amsterdam Center for Multiscale Modeling (ACMM), VU Uni-versity Amsterdam, 1081 HV Amsterdam, The Netherlands2Laboratoire PhLAM, CNRS, UMR 8523, Universite de Lille 1,59655 Villeneuve dAscq Cedex, France3Laboratorium fur Physikalische Chemie, ETH Zurich, 8093Zurich

Description:

We present a study of the electronic structure of the [UO2]+, [UO2]

2+, [UO2]3+, NUO,

[NUO]+, [NUO]2+, [NUN]−, NUN and [NUN]+ molecules with the intermediate Hamil-tonian Fock-space coupled cluster method. The accuracy of mean-field approaches basedon the eXact-2-Component Hamiltonian to incorporate spin–orbit coupling and Gauntinteractions are compared to results obtained with the Dirac–Coulomb Hamiltonian.Furthermore, we assess the reliability of calculations employing approximate densityfunctionals in describing electronic spectra and quantities useful in rationalizing Ura-nium(VI) species reactivity (hardness, electronegativity and electrophilicity).

References: P. Tecmer, A. S. P. Gomes, S. Knecht, L. Visscher, J. Chem. Phys.,2014, 141, 041107.

156

Title: New Benchmark Set of Transition-Metal Coordination Reactionsfor the Assessment of Density Functional


Erik P. A. Couzijn2

Peter Chen2

Markus Reiher1

Institute/Group: 1Laboratorium fur Physikalische Chemie, ETH Zurich, 8093Zurich2Laboratorium fur Organische Chemie, ETH Zurich, 8093 Zurich.

Description:

We present the WCCR10 data set of 10 ligand dissociation energies of large cationic tran-sition metal complexes for the assessment of approximate exchangecorrelation function-als. We analyze nine popular functionals, namely BP86, BP86-D3, B3LYP, B3LYP-D3,B97-D-D2, PBE, TPSS, PBE0, and TPSSh by mutual comparison and by comparison toexperimental gas-phase data measured with well-known precision. The comparison of allcalculated data reveals a large, system-dependent scattering of results with nonnegligibleconsequences for computational chemistry studies on transition metal compounds. Con-sidering further the comparison with experimental results, the nonempirical functionalsPBE and TPSS turn out to be among the best functionals for our reference data set.The deviation can be lowered further by including HartreeFock exchange. Accordingly,PBE0 and TPSSh are the two most accurate functionals for our test set, but also thesefunctionals exhibit deviations from experimental results by up to 50 kJ mol1 for indi-vidual reactions. As an important result, we found no functional to be reliable for allreactions. Furthermore, for some of the ligand dissociation energies studied in this work,invoking semiempirical dispersion corrections yields results which increase the deviationfrom experimental results. This deviation increases further if structure optimization in-cluding such dispersion corrections is performed, although the contrary should be thecase, pointing to the need to develop the currently available dispersion corrections fur-ther. Finally, we compare our results to other benchmark studies and highlight thatthe performance assessed for different density functionals depends significantly on thereference molecule set chosen.

References: T. Weymuth, E.P.A. Couzijn, P. Chen, M. Reiher, J. Chem. The-ory Comput., 2014, 10, 3092–3103

157

Title: The Impact of Structure and Bonding on the Reactivity of λ3-Iodanes

Researchers: Halua Pinto de Magalhaes1

Hans Peter Luthi1

Antonio Togni2

Institute/Group: 1Laboratorium fur Physikalische Chemie, ETH Zurich, 8093Zurich2Laboratorium fur Anorganische Chemie, ETH Zurich, 8093Zurich.

Description:

Diaryliodonium salts have gained considerable attention in synthesis as they performreductive elimination reactions leading to functionalization of arenes under mild condi-tions. Mechanistic studies have shown that the formation of corresponding λ3-iodaneintermediates takes a key role, as they determine course and selectivity of the reac-tion. Bridged diaryliodonium salts, featuring a heterocyclic moiety involving the iodineatom, were shown to exhibit a distinctly different reactivity leading to different prod-ucts. These products may also arise via radical mechanisms. Our investigations revealthat the λ3-iodane intermediate is the ”gateway” also for reactions that are only ob-served for strained bridged systems. At the same time we find a remarkable affinityof the hypervalent region to planarity for all reaction mechanisms. In addition, usingmodel compounds, some of the basic features governing the reactivity of λ3-iodanes areelucidated.

References: H. Pinto de Magalhaes, H.P. Luthi, A. Togni, J. Org. Chem.,2014, 79 (17), 8374–8382.

158

Title: Investigation of the Solvent Effect on Two Limiting ReactionMechanisms Involving Hypervalent Iodine Reagents (λ3-Iodanes)

Researchers: Oliver Sala1,2

Hans Peter Luthi1

Antonio Togni2

Institute/Group: 1Laboratorium fur Physikalische Chemie, ETH Zurich, 8093Zurich2Laboratorium fur Anorganische Chemie, ETH Zurich, 8093Zurich

Description:

Trifluoromethylation of acetonitrile with 3,3-dimethyl-1-(trifluoromethyl)-1λ3,2-benziodoxol is assumed to occur via reductive elimination (RE) of the electrophilic CF3-ligand and MeCN bound to the hypervalent iodine atom. Computations in gas phaseshowed that the reaction might also occur via an SN2. There is a substantial solventeffect present for both reaction mechanisms, and their energies of activation are verysensitive towards the solvent model used (implicit, microsolvation, cluster-continuum).With PCM-based methods, the SN2 mechanism becomes less favourable. Applying thecluster-continuum model, using a shell of solvent molecules derived from ab-initio-MD(AIMD) simulations, the gap between the two activation barriers (∆∆G‡) is lowered toa few kcal mol−1 and also shows that the activation entropies for the two mechanismsdiffer substantially.

References: O. Sala, H. P. Luthi, A. Togni, J. Comput. Chem., 2014, 35,2122–2131.

159

Title: Determining Factors for the Accuracy of DMRG

Researchers: Sebastian Keller1

Markus Reiher1


Description:

The Density Matrix Renormalization Group (DMRG) algorithm has been a rising starfor the accurate ab initio exploration of Born-Oppenheimer potential energy surfacesin theoretical chemistry. However, owing to its iterative numerical nature, pitfalls thatcan affect the accuracy of DMRG energies need to be circumvented. Here, after a briefintroduction into this quantum chemical method, we discuss criteria that determine theaccuracy of DMRG calculations.

References: S. Keller, M. Reiher, Chimia, 2014, 68.

160

Title: Development of Hypervalent Iodine Reagents: a Collaboration ofChemical Synthesis with Modeling and Simulation

Researchers: Hans Peter Luthi1

Antonio Togni2

Institute/Group: 1Laboratorium fur Physikalische Chemie, ETH Zurich, 8093Zurich2Laboratorium fur Anorganische Chemie, ETH Zurich, 8093Zurich

Description:

Much of the focus of quantum chemical modeling and simulation is on understandingchemical phenomena and in assisting experiment to further improve and develop the re-spective chemistry. Given the computational tools available today, rather than assistingthe development of new chemicals, modeling and simulation is in the process of makingthe step towards guiding experiment towards novel targets. In this article we show howan intense collaboration between chemical synthesis and computation lead to a betterunderstanding of hypervalent iodine reagents and how modeling and simulation maydirect the search of novel reagents.

References: H.P. Luthi, A. Togni, Chimia, 2014, 68, 624–628.

161

Title: Studying Chemical Reactivity in a Virtual Environment

Researchers: Moritz P. HaagMarkus Reiher

Institute/Group: Laboratorium fur Physikalische Chemie, ETH Zurich, 8093 ZurichReiher Research Group

Description:

Chemical reactivity of a set of reactants is determined by its potential (electronic) energy(hyper)surface. The high dimensionality of this surface renders it difficult to efficientlyexplore reactivity in a large reactive system. Exhaustive sampling techniques and searchalgorithms are not straightforward to employ as it is not clear which explored path willeventually produce the minimum energy path of a reaction passing through a transitionstructure. Here, the chemist’s intuition would be of invaluable help, but it cannot beeasily exploited because (1) no intuitive and direct tool for the scientist to manipulatemolecular structures is currently available and because (2) quantum chemical calculationsare inherently expensive in terms of computational effort. In this project, we elaboratedon how the chemist can be reintroduced into the exploratory process within a virtual en-vironment that provides immediate feedback and intuitive tools to manipulate a reactivesystem. We worked out in detail how this immersion should take place. We provided ananalysis of modern semi-empirical methods which already today are candidates for theinteractive study of chemical reactivity. Implications of manual structure manipulationsfor their physical meaning and chemical relevance were carefully analysed in order toprovide sound theoretical foundations for the interpretation of the interactive reactivityexploration.

References: M. P. Haag, M. Reiher, Faraday Discuss., 2014, 169,DOI: 10.1039/c4fd00021h.

162

Title: Interactive Chemical Reactivity Exploration

Researchers: Moritz P. Haag1

Alain C. Vaucher1

Mael Bosson2

Stephane Redon2

Markus Reiher1

Institute/Group: 1Laboratorium fur Physikalische Chemie, ETH Zurich, 8093Zurich / Reiher Research Group

2INRIA Grenoble–Rhone-Alpes and CNRS Laboratoire JeanKuntzmann, 655, avenue de l’Europe Montbonnot, 38334 SaintIsmier Cedex (France) / NANO-D Group

Description:

Elucidating chemical reactivity in complex molecular assemblies of a few hundred atomsis, despite the remarkable progress in quantum chemistry, still a major challenge. Black-box search methods to find intermediates and transition-state structures might fail insuch situations because of the high-dimensionality of the potential energy surface. Inthis project, we developed the concept of interactive chemical reactivity explorationto effectively introduce the chemists intuition into the search process. We employ ahaptic pointer device with force feedback to allow the operator the direct manipulationof structures in three dimensions along with simultaneous perception of the quantummechanical response upon structure modification as forces. We elaborated on the detailsof how such an interactive exploration should proceed and which technical difficultiesneed to be overcome. All reactivity-exploration concepts developed for this purpose havebeen implemented in the SAMSON programming environment.

References: M. P. Haag, A. C. Vaucher, M. Bosson, S. Redon, M. Reiher,ChemPhysChem, 2014, 15, 3301–3319.

163

Title: Systematic Dependence of Transition-Metal Coordination Ener-gies on Density-Functional Parametrizations


Markus Reiher1


Description:

In recent years, the calibration of parameters in approximate exchange-correlation den-sity functionals was intensified by the proposition of diverse and increasingly unbiasedreference datasets. It is, however, not obvious how sensitive the accuracy of a givenfunctional is with respect to a small change of its parameters. Knowledge about thissensitivity would be desirable for the assessment of the general accuracy that can be ex-pected for the calculation of a given observableespecially for notorious cases as found, forinstance, in coordination chemistry. At the example of the well-known BP86 exchange-correlation functional, we investigate the dependence of the coordination energies in theWCCR10 reference set [Weymuth et al., J. Chem. Theory Comput. 2014, 10, 3092]on the empirical parameters of this density functional. The WCCR10 reactions werefound to be a true challenge for contemporary density functionals. Here, we find thatthe parameter dependence is qualitatively the same for all reactions. This observation isimportant in view of the fact that the BP86 functional was never parametrized againsttransition-metal data. Still, within the parameter intervals investigated, the individualreaction energies vary significantly, which seems to suggest a reoptimization of the empir-ical parameters. However, it turns out that the overall description of all 10 reactions canbe improved by only 9.5 kJ/mol, and therefore, such a reoptimization is not advisable.

References: T. Weymuth, M. Reiher, Int. J. Quantum Chem., 2014,DOI: 10.1002/qua.24800.

164

Title: Activation barriers of oxygen transformation at the active site of[FeFe] hydrogenases


Martin T. Stiebritz1

Markus Reiher1


Description:

Oxygen activation at the active sites of [FeFe] hydrogenases has been proposed to bethe initial step of irreversible oxygen-induced inhibition of these enzymes. Based on afirst theoretical study into the thermodynamics of O2 activation [Inorg. Chem. 2009,48, 7127] we investigated the kinetics of possible reaction paths at the distal iron atomof the active site by means of density functional theory in this project. A sequence ofsteps was proposed to either form a reactive oxygen species (ROS) or fully reduce O2 towater. In this reaction cascade, two branching points were identified where water forma-tion directly competes with harmful oxygen activation reactions. The latter are waterformation by O–O bond cleavage of a hydrogen-peroxide-bound intermediate competingwith H2O2 dissociation and CO2 formation by a putative iron-oxo species competingwith protonation of the iron-oxo species to form a hydroxyo ligand. Furthermore, weshowed that proton transfer to activated oxygen is fast and that proton supply to theactive site is vital to prevent ROS dissociation. If sufficiently many reduction equivalentsare available, oxygen activation reactions are accelerated and oxygen reduction to waterbecomes possible.

References: A. R. Finkelmann, M. T. Stiebritz, M. Reiher, Inorg. Chem.,2014, in press.

165

Title: Electric Transition Dipole Moment in pre-Born–OppenheimerMolecular Structure Theory

Researchers: Benjamin Simmen1

Edit Matyus2

Markus Reiher1

Institute/Group: 1Laboratorium fur Physikalische Chemie, ETH Zurich, 8093Zurich2Institute of Chemistry, Eovtos University, H-1518 Budapest 112,Hungary

Description:

We focus on the calculation of the electric transition dipole moment in a pre-Born–Oppenheimer framework for transitions between two rovibronic levels of the H2 moleculeassignable to the lowest rovibrational states of the X 1Σ+

g and B 1Σ+u electronic states in

the clamped-nuclei framework. Electrons and nuclei are treated equally in terms of theparametrization of the non-relativistic total wave function, which is written as a linearcombination of basis functions constructed with explicitly correlated Gaussian functionsand the global vector representation. This is the first evaluation of this quantity in a fullquantum mechanical treatment without relying on the Born–Oppenheimer approxima-tion. The integrals of the electric transition dipole moment are derived corresponding tothese basis functions in both the length and the velocity representation. The completederivation and the calculations are performed in laboratory-fixed Cartesian coordinateswithout relying on coordinates which separate the center of mass from the translationallyinvariant degrees of freedom. The effect of the overall motion is eliminated via trans-lationally invariant integral expressions. As a numerical example the electric transitiondipole moment is calculated

References: B. Simmen, E. Matyus and M. Reiher, J. Chem. Phys., 2014,in press

166

Title: Climate change and the water cycle: processes and scenarios Researchers: Nikolina Ban, Omar Bellprat, Tanja Dallafior, Erich Fischer, Doris Folini,

Maria Hakuba, Hanieh Hassanzadeh, Michael Keller, Sven Kotlarski, Nico Kröner, Wolfgang Langhans, David Leutwyler, Daniel Lüthi, Anna Possner, Jan Rajczak, Christoph Schär, Linda Schlemmer, Jürg Schmidli, Ana Sesartic, Martin Wild.

Institute/Group: Institute for Atmospheric and Climate Science Group of Christoph Schär

Description: We are using global and regional atmospheric models on a wide range of temporal and spatial scales. The high-resolution regional modeling uses the COSMO-CLM limited-area atmospheric model. Comprehensive European-scale climate-change scenario simulations were conducted in the framework of the COordinated Regional climate Downscaling Experiment (Euro-CORDEX) at horizontal resolutions of 12 and 50 km covering the period 1950- 2100. Recent work in this context is addressing a standard validation of all models participating in Euro-CORDEX, the calibration of the COSMO-CLM, the analysis of changes in heat-wave, heavy precipitation events and snow cover, the height-dependence of the climate change signals, the representation of aerosol effects, and the quantification of different drivers behind the European summer climate. In parallel, we are further developing a high-resolution climate simulation capability with horizontal resolutions at the km-scale. Both idealized and real-case simulations are conducted. 10 year long simulations for present and future climate conditions for the whole Alpine area were performed at this resolution. They showed especially an improved representation of precipitation on the sub-daily time scale. The long simulations are complemented by detailed analyses of convective processes over mountainous terrain using a combination of satellite data and idealized large-eddy simulations. The main motivation behind this work is the desire to explicitly simulate convective clouds (as opposed to using convective cloud parameterization schemes in lower-resolution models). We have also started using a recent GPU version of the COSMO model (jointly developed in HP2C projects by MeteoSwiss, ETH/C2SM and CSCS). This allows to extend the simulation domain for convection-resolving simulations to the European continent. The use of the COSMO-CLM is coordinated by Drs. D. Lüthi, J. Schmidli and S. Kotlarski. The global scale simulations are carried out with the climate model ECHAM6-HAM, developed at the Max Planck Institute in Hamburg, Germany. This work is led by Prof. Martin Wild and Dr. Doris Folini, and it also exploits collaborations with the group of Prof. Ulrike Lohmann. The model contains sophisticated aerosol and cloud microphysics schemes. These are essential for realistic simulations of radiation and precipitation processes in the atmosphere. This model is used to study the link between anthropogenic and natural perturbations of the radiation balance and the intensity of the hydrological cycle. The time period under consideration covers 1870-2100. The global model simulations provide also boundary conditions to drive the regional model. Currently, ECHAM6-HAM is expanded into a coupled atmosphere-ocean climate modeling system, which allows to exploit the full response of the climate system in general and the water cycle in particular to the imposed radiative forcings in transient mode.

References: A series of papers has been published (see references for further details).

167

Title: Computational Reduction for Bayesian Inverse Problems.

Researchers: Dr. Peng ChenProf. Christoph Schwab


Description:

This project aims at development and analysis of efficient and accurate computationalreduction techniques to solve Bayesian inverse problems (BIP). BIP can be generallyformulated as given some prior information of the unknown system inputs, typicallydescribed by high or infinite dimensional random fields prescribed with certain probabilitydistribution, and given observational data of the system outputs, to evaluate the posteriordistribution of the unknown inputs as well as some related quantity of interests (QoIs).

Solution of BIP with the underlying system modelled by partial differential equations(PDEs) brings several computational challenges, among which one typically faces i) curseof dimensionality : in the case of high or infinite dimensional random inputs, one has tosolve the underlying PDEs for at an excessively large number of samples in order toachieve the required accuracy; ii) large-scale computation: solution of the PDEs at eachof the sample is very expensive, so that only a small number of solutions are affordable.

To tackle these great computational challenges, we exploit the sparsity and reducibilityof the solution and its related QoIs and develop an effective computational reductionframework based on sparse grid and reduced basis methods. Best approximation propertyof this framework will be shown for both linear and nonlinear problems. Through severalpractical BIP, we demonstrate that this framework can effectively break the curse ofdimensionality and considerably alleviate the large-scale computational burden.

100

101

102

10−9

10−8

10−7

10−6

10−5

10−4

10−3

10−2

# reduced bases

max

y |

Θh(y

) −

ΘN(y

)|/Θ

c N(y

)

LS fitted rate = −3.0021

Convergence of approximation error of QoI w.r.t. # reduced bases in 256 dimensions.

References:

[1] P. Chen and Ch. Schwab, Sparse grid, reduced basis approximation of Bayesianinverse problems, in preparation

168

Title: Numerical analysis of stochastic partial differentialequations

Researchers: Lukas HerrmannProf. Christoph Schwab


Description:

Random fields are used to model random quantities that arise in science and engineeringin a mathematical way. Isotropic covariance kernels of these fields result in variousproperties of the random fields.

Isotropic spherical random fields are defined and analyzed, especially isotropic Gaus-sian spherical random fields. The connection between the angular power spectrum, thepath regularity and the integrability of these fields is in particular investigated. Appli-cations of this are the discussion of the stochastic heat equation with additive isotropicQ-Wiener noise and unique solvability and Holder regularity of second order, ellipticpartial differential equations on the sphere with lognormal isotropic coefficients.

In this project we further focus on the numerical analysis of problems of this kind aswell as on numerical experiments to confirm theoretical results.

References:

[1] L. Herrmann, Isotropic random fields on the sphere – regularity of random ellipticPDEs, Master’s thesis, ETH Zurich, 2013

[2] A. Lang and Ch. Schwab, Isotropic Gaussian random fields on the sphere: regular-ity, fast simulation, and stochastic partial differential equations, Ann. Appl. Prob.,to appear, 2014

[3] L. Herrmann, A. Lang and Ch. Schwab, in preparation

169

Title: Low-rank tensor-structured solution of differentialequations

Researchers: Vladimir KazeevChristoph Schwab


Description:

The project focuses on the numerical solution of high-dimensional ODEs and PDEs inlow-parametric representations known as tensor decompositions. Naive FDM or FEMdiscretizations constructed on extremely fine uniform tensor-product meshes are usuallynot employed in advanced numerical algorithms due to an excessively large number ofdegrees of freedom. The key idea of the project is combining such discretizations withnon-linear approximations based on the separation of variables, so that the solution,operator and the intermediate data are represented efficiently. The full discretizationsare never supposed to be dealt with immediately; instead, adaptive algorithms of the low-rank tensor recompression, which have to underlie any tensor-structured computation,are exploited as the tool extracting the “effective” degrees of freedom.

The tensor format we employ is the newly introduced tensor train decomposition,which generalizes the SVD of matrices differently from the well-known canonical polyadicand Tucker representations. It enjoys the major advantages of the two. Namely, linear(with respect to the dimensionality) complexity and the availability of a stable arithmeticbased on standard matrix decompositions (SVD and QR, in particular). Being coupledwith quantization, which means splitting each “physical” dimension of a vector or matrixinto multiple “virtual” dimensions, it gives rise to the quantized tensor train decomposi-tion. The latter, in some cases, allows to achieve even logarithmic (with respect to thenumber of “uncompressed” degrees of freedom) complexity of representing the data andperforming the basic operations of linear algebra on it.

The major challenges within the project are: theoretical analysis of the TT and QTTstructure of the operators and solutions; investigation of appropriate discretizations inspace and time (for evolution problems); solution of linear systems in the TT format;high-performance implementation of the TT arithmetic.

References:

[1] V. Kazeev, M. Khammash, M. Nip, and C. Schwab, Direct solution of the ChemicalMaster Equation using Quantized Tensor Trains, Technical Report 3, March 2014.

[2] V. Kazeev and I. Oseledets, The tensor structure of a class of adaptive algebraicwavelet transforms, Research Report 28, Seminar for Applied Mathematics, ETH

170

Zurich, 2013

[3] V. Kazeev, O. Reichmann, and C. Schwab, hp-DG-QTT solution of high-dimensionaldegenerate diffusion equations, Report 11, Seminar for Applied Mathematics, ETHZurich, 2012

[4] V. Kazeev, O. Reichmann, and C. Schwab, Low-rank tensor structure of lineardiffusion operators in the TTand QTT formats, Linear Algebra and its Applications,438(11):4204–4221, 2013

[5] V. Kazeev and C. Schwab, Tensor approximation of stationary distributions ofchemical reaction networks, Research Report 18, Seminar for Applied Mathematics,ETH Zurich, 2013

171

Title: Finite Elements with mesh refinement for linear, second-order hyperbolic PDEs on polygons and polyhedra.

Researchers: Fabian L. MullerProf. Christoph Schwab


Description:

Linear, second-order hyperbolic PDEs play an important role in modeling various evo-lution phenomena in applications, such as acoustic, seismic and electromagnetic wavepropagation. Simulations are usually performed using a method of lines with semi-discretization in space done by Finite Elements, followed by a time-stepping scheme.

The convergence rates of this discretization strategy depend on the regularity of theexact solution. On polygonal domains, or in the presence of jumps in the materialcoefficients (“interface problem”), this is an issue yielding severly reduced convergencerates.

In this project, we investigate mesh refinement techniques to recover quasi-optimalconvergence rates for the h-version of Finite Elements. For the semi-discretization inspace, similar classes of locally refined meshes as known for stationary cases can be ap-plied. Moreover, we study the use of local space-time refinements in order to resolvesingularities in the time-variable and investigate the convergence of the resulting fullydiscretized method for the acoustic and the elastic wave equation with smooth coeffi-cients on polygonal domains and the acoustic interface problem.

References:

[1] F. Muller and Ch. Schwab, Finite Elements with mesh refinement for wave equationsin polygons, Seminar for applied Mathematics, ETH Zurich, 2013, Report 11.

[2] F. Muller and Ch. Schwab, Finite Elements with mesh refinement for elastic wavepropagation in polygons, under review.

172

Title: Sparse techniques for parametric differential equations

Researchers: Dr. Claudia Schillings,Robert N. Gantner,Prof. Christoph Schwab

Institute: Seminar for Applied Mathematics (SAM)

Description:

The focus of the project is on the efficient numerical approximation of parametric dif-ferential equations. In particular, we are interested in methods which are dimensionallyrobust, i.e. whose efficiency (meaning accuracy versus computational cost measured interms of the total number of floating point operations to achieve this accuracy) is provablyrobust with respect to the number of parameters.

In order to allow for efficient approximations of the parametric solutions on the entire,possibly infinite dimensional parameter space, some form of sparsity in the parametric de-pendence of the solution is necessary. Problem classes are identified, so that the solutionsof the parametric problems admit sparse expansions in terms of tensorized polynomialsystems in the infinite dimensional parameter space, under the provision of sparsity ofthe random input. We deduce rates of convergence of N -term truncated approximationsof expansions of the parametric solutions.

Based on the theoretical results, a major goal of the project is to develop numericalalgorithms which allow to exploit computationally the sparse parameter dependence ofthe solutions and, hence, to achieve the optimal complexity by the sparse approxima-tions. In the references below, we present an adaptive approach for computing sparse,approximate representations of the parametric solutions in large parameter dimensions.References:

[1] C. Schillings and Ch. Schwab, Sparsity in Bayesian inversion of parametric operatorequations, Inverse Problems, 30 (2014), p. 065007.

[2] R.N. Gantner, C. Schillings and Ch. Schwab, Binned Multilevel Monte Carlo forBayesian Inverse Problems with Large Data, Proc. Intl. Conf. Domain Decomposi-tion DD22, (2014) (to appear).

[3] C. Schillings and Ch. Schwab, Scaling Limits in Computational Bayesian Inversion,(in preparation).

[4] C. Schillings, Ch. Schwab, J. Stelling, M. Sunnaker, Efficient Characterization ofParametric Uncertainty of Complex (Bio)chemical Networks, (in preparation).

[5] R.N. Gantner, Ch. Schwab, Computational Higher Order Quasi-Monte Carlo Inte-gration, (submitted).

173

Title: Numerical modelling of continental collision zones Researchers: Taras Gerya, Thibault Duretz, Elena Sizova, Jonas Ruh, Ria Fisher, Chen Lin Institute: Institute of Geophysics, D-ERDW, ETH-Zurich Group: Geophysical Fluid Dynamics Description: Various aspects of continental collision zones and accretionary wedges dynamics are modelled in 2D and 3D with the use of the original codes I2ELVIS and I3ELVIS combining finite differences on a fully staggered rectangular Eulerian grid and Lagrangian marker-in-cell technique for solving momentum, continuity and temperature equations:

• Slab detachment during laterally variable continental collision (Duretz et al., 2014) • Intracratonic geodynamics (Gorczyk et al., 2013) • Dynamics of accretionary wedges (Fig.2) (Ruh et al., 2014) • Collision of continental corner (Fig. 2)(Li et al., 2013) • Slab rollback processes and surface deformation (Sternai et al., 2014) • Styles of Precambrian collision (Sizova et al., 2013)

Fig. 2. Internal structures and faulting patterns in accretionary wedges (Ruh et al., 2014).

References: Duretz, T., Gerya, T.V., Spakman, W. (2014) Slab detachment in laterally varying subduction

zones: 3-D numerical modeling. Geophysical Research Letters, 41, 1951-1956. Gorczyk, W., Hobbs, B., Gessner, K., Gerya, T. (2013) Intracratonic geodynamics.

Gondwana Research, 24, 838-848. Ruh, J.B., Gerya, T., Burg, J-P. (2014) 3D effects of strain vs. velocity weakening on

deformation patterns in accretionary wedges. Tectonophysics, 615, 122-141. Sternai, P., Jolivet, L., Menant, A., Gerya, T. (2014) Driving the upper plate surface

deformation by slab rollback and mantle flow. Earth and Planetary Science Letters, 405, 110-118.

174

Title: Numerical modelling of planetary processes and surface structures Researchers: Taras Gerya, Stefan Brändly, Paul Tackley, Cyrill Bösch Institute: Institute of Geophysics, D-ERDW, ETH-Zurich Group: Geophysical Fluid Dynamics Description: Coupled planetary surface and interior evolution processes are modeled in 3D with the use of the original code I3ELVIS combining finite differences on a fully staggered rectangular Eulerian grid and Lagrangian marker-in-cell technique for solving momentum, continuity and temperature equations:

• Plume-induced crustal convection on Venus (Fig. 3) (Gerya, 2014): https://www.ethz.ch/de/news-und-veranstaltungen/eth-news/news/2014/02/hotspot-venus.html

•

Fig. 3. Modeled (left) vs. observed (right) surface structures on Venus (Gerya, 2014). References: Gerya, T.V. (2014) Plume-induced crustal convection: 3D thermomechanical model and

implications for the origin of novae and coronae on Venus. EPSL, 391, 183-192.Liao, J.,

175

Title: Numerical modelling of lithospheric extension and faulting processes Researchers: Taras Gerya, Jie Liao, Noel Aman Institute: Institute of Geophysics, D-ERDW, ETH-Zurich Group: Geophysical Fluid Dynamics Description: Various aspects of lithospheric extension processes are modelled in 2D and 3D with the use of the original codes I2ELVIS and I3ELVIS combining finite differences on a fully staggered rectangular Eulerian grid and Lagrangian marker-in-cell technique for solving momentum, continuity and temperature equations:

• Plume-lithosphere interaction and continental breakup (Fig.4) (Burov and Gerya, 2014): https://www.ethz.ch/en/news-and-events/eth-news/news/2014/09/mantle-plumes-crack-continents.html

• Layered lithosphere extension (Liao et al., 2013; Liao and Gerya, 2014)

Fig. 4. Plume-induced continental breakup (Burov and Gerya, 2013) References: Burov, E., Gerya, T. (2014) Asymmetric three-dimensional topography over mantle plumes.

Nature, 513, 85–89. Liao, J., Gerya, T.V., Wang, Q. (2013) Layered structure of the lithospheric mantle changes

dynamics of craton extension. Geophys. Res. Lett., 40, 1-6. Liao, J., Gerya, T. (2014) Influence of lithospheric mantle stratification on craton extension:

Insight from two-dimensional thermo-mechanical modeling. Tectonophysics, 631, 50–64.

176

Title: Development of new numerical geodynamic modeling techniques Researchers: Taras Gerya, Dave May Institute: Institute of Geophysics, D-ERDW, ETH-Zurich Group: Geophysical Fluid Dynamics Description: Further development of numerical modeling approaches for geodynamic problems:

• New numerical approach to the Stokes problem with high contrasts in viscosity (Lobanov et al., 2014)

• New analytical solutions for benchmarking of 2-D and 3-D geodynamic Stokes problems with variable viscosity. (Popov et al., 2014)

• Development of new numerical modeling method for coupled visco-plastic rocks deformation and fluid percolation (Fig. 5) (Dymkova and Gerya, 2013)

Fig. 5. Coupled deformation and fluid flow during subduction (Dymkova and Gerya, 2013) References: Dymkova, D., Gerya, T. (2013) Porous fluid flow enables oceanic subduction initiation on

Earth. Geophysical Research Letters, 40, 5671–5676. Lobanov, I.S., Popov, I.Yu., Popov, A.I., Gerya, T.V. (2014) Numerical approach to the

Stokes problem with high contrasts in viscosity. Applied Mathematics and Computation, 235, 17-25.

Popov, I.Yu., Lobanov, I.S., Popov, S.I., Popov, A.I., Gerya, T.V. (2014) Practical analytical solutions for benchmarking of 2-D and 3-D geodynamic Stokes problems with variable viscosity. Solid Earth, 5, 461–476.

177

Title: Numerical modelling of subduction zones Researchers: Guizhi Zhu, Katharina Vogt, Taras Gerya, Diana Dymkova, Thibault Duretz, Bettina Baitsch-Ghirardello, Ria Fisher, Dave May Institute: Institute of Geophysics, D-ERDW, ETH-Zurich Group: Geophysical Fluid Dynamics Description: Various aspects of subduction zones dynamics, seismicity, magmatic activities, fluid regimes and geochemical transport are modelled in 2D and 3D with the use of the original codes I2ELVIS and I3ELVIS combining finite differences on a fully staggered rectangular Eulerian grid and Lagrangian marker-in-cell technique for solving momentum, continuity and temperature equations: • Geochemical processes and trace elements transport in subduction zones (Baitsch-

Ghirardello et al., 2014; Vogt et al., 2013) • Subduction triggering by porous fluid flow (Dymkova et al., 2013) • Subduction of oceanic fracture zones (Fig. 1) (Manea et al., 2014) • Subduction initiation at curved and straight continental margins (Marques et al., 2014) • Seismicity of subduction zones (Van Dinther et al., 2014a,b) • Plate serpentinization and skinning of subducting slabs (Vogt and Gerya, 2014)

Fig. 1. Ordinary subduction (a) vs. subduction of a fracture zone (b) (Manea et al., 2014).

References: Baitsch-Ghirardello, B., Stracke, A., Connolly, J.A.D., Nikolaeva, K.M., Gerya, T.V. (2014)

Lead transport in intra-oceanic subduction zones: 2D geochemical–thermo-mechanical modeling of isotopic signatures. Lithos, 208–209, 265-280.

Dymkova, D., Gerya, T. (2013) Porous fluid flow enables oceanic subduction initiation on Earth. Geophysical Research Letters, 40, 5671–5676.

Manea, V.C., Leeman,W.P., Gerya, T., Manea, M., Zhu, G. (2014) Subduction of fracture zones controls mantle melting and geochemical signature above slabs. Nature Communications, 5, Article number: 5095.

Marques, F.O., Cabral, F.R., Gerya, T.V., Zhu, G., May, D.A. (2014) Subduction initiates at straight passive margins. Geology, 42, 331-334.

178

van Dinther, Y., Gerya, T.V., Dalguer, L.A., Mai, P.M., Morra, G., Giardini, D. (2013) The seismic cycle at subduction thrusts: Insights from seismo-thermo-mechanical models. J. Geophys. Res., 118, 1502–1525.

van Dinther, Y., Gerya, T.V., Dalguer, L.A., Corbi, F., Funiciello, F., Mai, P.M. (2014) Modeling the seismic cycle in subduction zones: The role and spatiotemporal occurrence of off-megathrust earthquakes. Geophysical Research Letters, 41, 1194-1201.

Vogt, K., Castro, A., Gerya, T. (2013) Numerical modeling of geochemical variations cause by crustal relamination, G3, 14, 470–487). Geochem. Geophys. Geosys., 14, 1131–1155.

Vogt, K., Gerya, T. (2014) Deep plate serpentinization triggers skinning of subducting slabs. Geology, 42, 723-726.

179

Figure: Long-term evolution of mantle convection considering the influence of grain size evolution.

Title: Coupled modelling of atmosphere and mantle evolution Researchers: C. Gillmann, P. J. Tackley, G. J. Golabek Institute/Group: Institute of Geophysics/Geophysical Fluid Dynamics We use Venus as test bed for our numerical model of the evolution of the atmosphere of terrestrial planets, as an intermediary between life-sustaining Earth and yet to be discovered exoplanets. Here, we focus on mechanisms that deplete or replenish the atmosphere: volcanic degassing and atmospheric escape. These processes are linked together to obtain a coupled model, using retroaction of the atmosphere on the mantle. We study potential divergent evolutions this could cause. Two aspects of the atmospheric escape are taken into account. During early evolution, hydrodynamic escape is dominant. We use a model developed to take into account the linked escape of Hydrogen and Oxygen. A significant portion of the early atmosphere can be removed this way. For later evolution, we focus on non-thermal escape. Post 4 Ga escape is low. Water escapes moderately, while we are not able to detect the present-day escape of CO2. The atmosphere is replenished by volcanic degassing, bringing volatiles from the mantle to the surface. Volcanic activity is obtained by adapting the finite difference/finite volume code StagYY for Venus. Volatile fluxes are estimated for different mantle compositions and partitioning ratios.Surface conditions are estimated by tracking the amount of CO2 and water in the atmosphere and computing the surface temperature with a gray radiative-convective atmosphere model. These surface conditions in turn act as a boundary condition for the mantle dynamic model and have an influence on convection, volcanism and subsequent degassing. Our results show that we are able to obtain a Venus-like behavior for the solid planet, with resurfacing events which constitute an efficient way of losing Venus’ internal heat. We are able to create evolution leading to present conditions. CO2 pressure seems unlikely to vary much over the history of the planet, only slightly increasing due to degassing. A late build-up of the atmosphere with several resurfacing events seems unlikely. On the other hand, water pressure is strongly sensitive to volcanic activity and varies rapidly. This leads to variations in surface temperatures of up to 200 K, which have been identified to have an effect on volcanic activity. While a positive feedback (increasing atmosphere temperature leading to increasing mantle temperatures and melting) is not immediately apparent, we observe a clear link between temperature changes and volcanic spikes, in particular a strong correlation between large temperature drops and increased volcanism. Mobilization of the upper layers occurs, which imply that our coupling is not complete without taking into account rehydratation of the mantle. This depends on the surface alteration processes and could have important effects.

180

Title: Numerical models of the thermomechanical evolution of planetesimals: Application to the acapulcoite-lodranite parent body

Researchers: G. J. Golabek, B. Bourdon, T. V. Gerya Institute/Group: Institute of Geophysics/Geophysical Fluid Dynamics The acapulcoite-lodranite meteorites are members of the primitive achondrite class. The observation of partial melting and resulting partial removal of Fe-FeS indicates that this meteorite group could be an important link between achondrite and iron meteorites on the one hand and chondrite meteorites on the other. Thus a better understanding of the thermomechanical evolution of the parent body of this meteorite group can help to improve our understanding of the evolution of early planetesimals. Here we use 2D and 3D finite-difference numerical models to determine the formation time, initial radius of the parent body of the acapulcoite-lodranite meteorites and their formation depth inside the body by applying available geochronological, thermal and textural constraints to our numerical data. Our results indicate that the best fit to the data can be obtained for a parent body with 25-65 km radius, which formed around 1.3 Ma after CAI. The 2D and 3D results considering various initial temperatures and the effect of porosity indicate possible formation depths of the acapulcoite-lodranite meteorites of 9-19 and 14-25 km, respectively. Our data also suggest that other meteorite classes could form at different depths inside the same parent body, supporting recently proposed models.

Figure: 3D model of early thermomechanical evolution of an early-formed planetesimal.

References:

G. J. Golabek, B. Bourdon and T.V. Gerya, Numerical models of the thermomechanical evolution of planetesimals: Application to the acapulcoite-lodranite parent body. Meteorit. Planet. Sci., 49, 1083-1099 (2014).

181

Title: Combined modelling of planetary accretion and differentiation Researchers: G. J. Golabek, R. Morishima, T. V. Gerya, P. J. Tackley, S. Labrosse Institute/Group: Institute of Geophysics/Geophysical Fluid Dynamics Results of current 1D models on planetesimal accretion yield an onion-like thermal structure with very high internal temperatures due to powerful short-lived radiogenic heating in the planetesimals. These lead to extensive silicate melting in the parent bodies. Yet, magma ocean and impact processes are not considered in these models and core formation is, if taken into account, assumed to be instantaneous with no feedback on the mantle evolution. It was pointed out that impacts can not only deposit heat deep into the target body, which is later buried by ejecta of further impacts, but also that impacts expose in the crater region originally deep-seated layers, thus cooling the interior. This combination of impact effects becomes even more important when we consider that planetesimals of all masses contribute to planetary accretion. This leads occasionally to collisions between bodies with large ratios between impactor and target mass. Thus, all these processes can be expected to have a profound effect on the thermal evolution during the epoch of planetary accretion and may have implications for the onset of mantle convection and cannot be described properly in 1D geometry. Here we present a new methodology, which can be used to simulate the internal evolution of a planetary body during accretion and differentiation: Using the N-body code PKDGRAV we simulate the accretion of planetary embryos from an initial annulus of several thousand planetesimals. The growth history of the largest resulting planetary embryo is used as an input for the thermomechanical 2D code I2ELVIS. The thermomechanical model takes recent parametrizations of impact processes like impact heating and crater excavation into account. Results show that late-formed planetesimals do not experience silicate melting and avoid thermal alteration, whereas in early-formed bodies accretion and iron core growth occur almost simultaneously and magma oceans develop in the interior of these bodies. These tend to form first close to the core-mantle boundary and migrate upwards with growing internal pressure.

182

Figure: 2D model of thermochemical evolution of an accreting protoplanet.

Title: Towards coupled giant impact and long term interior evolution models

Researchers: G. J. Golabek, M. Jutzi, T. V. Gerya, E. I. Asphaug Institute/Group: Institute of Geophysics/Geophysical Fluid Dynamics The crustal dichotomy is the dominant geological feature on planet Mars. The exogenic approach to the origin of the crustal dichotomy (Wilhelms and Squyres, 1984; Frey and Schultz, 1988; Andrews-Hanna et al., 2008; Marinova et al., 2008; Nimmo et al., 2008) assumes that the northern lowlands correspond to a giant impact basin formed after primordial crust formation. However these simulations only consider the impact phase without studying the long-term repercussions of such a collision. The endogenic approach, suggesting a degree-1 mantle upwelling underneath the southern highlands, relies on a high Rayleigh number and a particular viscosity profile to form a low degree convective pattern within the geological constraints for the dichotomy formation. Such vigorous convection, however, results in continuous magmatic resurfacing, destroying the initially dichotomous crustal structure in the long-term. A further option is a hybrid exogenic–endogenic approach, which proposes an impact-induced magma ocean and subsequent superplume in the southern hemisphere. However these models rely on simple scaling laws to impose the thermal effects of the collision. Here we performed impact simulations with a SPH code and coupled it serially with geodynamical computations performed using the code I3VIS to improve the latter approach and test it against observations. We are exploring collisions varying the impactor velocities, impact angles and target body properties, and are gauging the sensitivity to the handoff from SPH to I3VIS. As expected, our first results indicate the formation of a transient hemispherical magma ocean in the impacted hemisphere, and the merging of the cores. We also find that impact angle and velocity have a strong effect on the post-impact temperature field and on the timescale and nature of core merger.

183

Title: The dynamics of primordial reservoirs in the Earth’s mantle Researchers: Y. Li, F. Deschamps, P.J. Tackley Institute/ Institute of Geophysics Group: Geophysical Fluid Dynamics, D-ERDW Description: Large-scale chemical lateral heterogeneities are inferred in the Earth’s lowermost mantle by seismological studies. We explore the model space of thermochemical convection that can maintain reservoirs of dense material for a long period of time, in 3-D spherical geometry. In this study, we focus on the parameters thought to be important in controlling the stability and structure of primordial dense reservoirs in the lower mantle. Varying buoyancy ratio leads to different flow patterns, from rapid upwelling to stable layering; and large thermal viscosity contrasts are required to generate long wavelength chemical structures in the lower mantle. Chemical viscosity contrasts in a reasonable range have a second-order role in modifying the stability of the dense anomalies. The volume fraction of the initial primordial dense material does not effect the results with large thermal viscosity contrasts, but has significant effects on calculations with intermediate and small thermal viscosity contrasts. The volume fraction of dense material at which the flow pattern changes from unstable to stable depends on buoyancy ratio and thermal viscosity contrast. An endothermic phase transition at 660 km depth acts as a ‘filter’ allowing cold slabs to penetrate while blocking most of the dense material from penetrating to the upper mantle.

Figure. Composition (left) and temperature (right) isosurfaces for numerical simulations of mantle convection with an initial dense layer. References: Li, Y., F. Deschamps and P.J. Tackley (2014) Effects of low-viscosity post-perovskite on the stability and structure of primordial reservoirs in the mantle, doi:10.1002/2014GL061362. Li, Y., F. Deschamps and P. J. Tackley (2014) The stability and structure of primordial reservoirs in the lower mantle: insight from models of thermo-chemical convection in spherical geometry, Geophys. J. Int., 199(2), 914-930, doi:10.1093/gji/ggu295.

184

Title: Robust non-linear methods for studying 3D shear bands

Researchers: Dave A. May

Institute/ Geophysical Fluid Dynamics Group: Department of Earth Sciences

Description:

Understanding the development and evolution of individual faults, and fault systems is a fundamental aspect of lithospheric deformation. Many studies treating the lithosphere as a visco-plastic (Mises or Drucker Prager) material have been conducted in 2D. However, natural systems are inherently three-dimensional, thus to study non-cylindrical structures requires 3D numerical simulations.

To date, little research has been conducted using numerical models which examine the behaviour of visco-plastic fault systems in 3D and development of efficient Newton based non-linear solver. We have developed our understanding of faults and how they develop in complex continental rifting scenarios using anew parallel finite element code pTatin3d.

Below we show the evolution of topography (H) and basin structures from a rifting experiment ~10 Myrs after breakup occurred. Passive margins (topographic lows), are accurately simulated via the free surface. The second invariant of the strain- rate tensor (eII) highlights the complex geometry of cross-cutting faults that intersect the isolated basin. We employed 2 mm/yr shortening which resulted in the development of oblique active structures (yellow iso-surfaces).

References:

D. A. May, J. Brown & L. Le Pourhiet, A scalable, matrix-free Stokes discretisation for geodynamic applications, Computer Methods in Applied Mechanics and Engineering (2014) [under review]

M. Spiegelman, D. A. May & C. R. Wilson. Lessons and insights into effective solvers for visco-plasticity in geodynamics, Geochemisty, Geophysics, Geosystems (2014) [in preparation]

185

Title: Influence of combined primordial layering and recycled MORB on the coupled thermal evolution of Earth’s mantle and core

Researchers: T. Nakagawa, P. J. Tackley Institute/Group: Institute of Geophysics/Geophysical Fluid Dynamics Description: A thermo-chemical mantle convection model with both primordial compositional layering and recycling of mid-ocean ridge basalt (MORB) coupled to a parameterized core heat balance model is used to investigate how the thermo-chemical evolution of the mantle affects the thermal history of the core including primordial material proposed by early Earth hypotheses. The amount of MORB that accumulates above the CMB is strongly dependent on effective Rayleigh number, such that more accumulates at higher Ra (lower viscosity), but a continuous layer of MORB is not obtained here. With initial primordial layering, large-scale thermo-chemical anomalies are found in the deep mantle, which are generated mainly by the primordial material with small amount of segregated basaltic material on top of it, localized in the hot upwelling region. A successful core evolution can only be obtained when initial primordial layering is present. In conclusion, primordial material above the CMB originated from early mantle differentiation might be needed to construct a realistic model of a coupled mantle and core evolution.

Figure. Infuence of buoyancy ratio of primordial material on the thermochemical structure after 4.5 billion years. References: Nakagawa, T. and P. J. Tackley (2014) Influence of combined primordial layering and recycled MORB on the coupled thermal evolution of Earth’s mantle and core, Geochem., Geophys. Geosys. 15, 69-633, doi:10.1002/2013GC005128.

186

Title: Non-Newtonian geodynamics of Enceladus

Researchers: A. Rozel, G. Golabek, J. Besserer, M. Kaplan, P. Tackley

Institute/Group: Institute of Geophysics/Geophysical Fluid Dynamics

The dynamics of Enceladus, an icy satellite of Saturn presenting an intense activity at its south pole, has been intensively investigated through several sets of numerical simulations during the year 2014. A publication in JGR Planets has been accepted (Self-consistent generation of single-plume state for Enceladus using non-Newtonian rheology, A. Rozel, J. Besserer, G. Golabek, M. Kaplan, P. Tackley, JGR Planets, 119, 3, p416-439) and a second one is in preparation.

In the published study, we have shown that the large heat flux detected at the south pole can be explained by a large convection pattern, only if the rheology of the ice is non-Newtonian. In this case only, a single plume can remain stable at the south pole without distabilizing the surrounding mantle.

This figure shows that several types of convection pattern can be reached considering the additional contribution of tidal heating in the ice shell. We provide a map of the single-plume state for several tidal heating power, according to the optimal viscosity and the Rayleigh number used. Several simulations of this study also reproduced the heat flux detected at the south pole.

187

Title: Generating the tiger stripes of Enceladus

Researchers: A. Rozel, G. Golabek, J. Besserer, P. Tackley


In this second study, we keep investigating the dynamics of Enceladus, an intriging icy satellite of Saturn, adding some complexity to the pre-existing study. The presence of a basal ocean has been shown to be of particular interest to describe the possible mechanical state of the convecting body. We have implemented an ice melting model in which hot ice crossing the solidus can generate the basal ocean (only if sufficient tidal heating is provided). A porosity field (stored and advected in a tracer field) is also generated to account for mass conservation. The porous ice being significantly lighter than the ambiant mantle, we find that melting may largely influence the ice's non-Newtonian viscosity, adding a non-negligible additional amount of stress.

The model also accounts for the freezing of the basal ocean, when the downwellings produce a large heat flux. The porosity becomes quite important in some long-term simulations, which requires the addition of a compaction model, still in development. In a scenario in which porosity becomes large enough (likely to happen regarding our tests), a compaction model would produce some subsidence of the south polar region, which would be in adequation with the observed depression of the polar terrains. To account for the localization of deformation, called “tiger-stripes” on Enceladus, we have also implemented a model in which the gaz, produced by melting, propagates upward through preferential paths. We are intensively working on a self-consistent model for this upward heat propagation, coupled with the porosity field.

The figure below shows a typical porosity field obtained in our simulations. Important porosity lateral anomalies can be seen at the bottom of the model.

188

Title: Scaling laws for the internal temperature and the heat flux in the stagnant lid regime for pressure-dependent fluids.

Researchers: A. Rozel


Scaling laws for the internal temperature reached in a convecting system with a non-Newtonian temperature-pressure-dependent rheology are derived analytically and confronted to a large set of numerical simulations. The study has been submitted to Journal of Fluid Mechanics.

In a convecting domain, when the viscosity strongly depends on temperature, a thick “stagnant lid” forms at the top. An internal temperature can be obtained using the temperature-dependence of the viscosity. In this paper, it is shown that usual model fail to predict this internal temperature when the viscosity also depends on pressure. Indeed, when pressure significantly increases the viscosity, the bottom boundary layer becomes also thick, which decreases the internal temperature obtained at steady state. Lateral and vertical viscosity contrasts are incorporated in a new upgraded version of the boundary layer theory. This new ambiant mantle temperature also strongly influences the heat flux reached at the equilibrium, which might be very important for the thermal evolution of convecting bodies of the solar system. This figure shows a comparison of the new model compared to the previous approach.

189

Title: Grain size evolution in the mantle of the Earth

Researchers: A. Rozel, G. Golabek, P. Tackley


A new model of grain size evolution in the mantle, accounting for phase transition and potential localization of deformation has been implemented in the convection code StagYY. Preliminary tests show that deformation is likely to localize below the lithosphere where large stress and strain rate can be reached.

In this model for grain size evolution, rock aggregates are represented by assemblages of two phases. Grains in each phase can independently grow until a large size is reached, where the two phases start to interact significantly. On top of this, deformation decreases the grain size, using a self-consistent thermodynamical approach previously published. The interface between the two phases is also explicitly treated by the formalism (following an expression similar to what is used for the average grain size evolution itself). Phase transitions are now carefully treated by the model, which considers the (olivine/ringwoodite)-(pyroxene/garnet) system in the upper mantle and the (Mg-perovskite)-(Ca-perovskite/Magnesowustite) system in the lower mantle.

The following figures shows that grain size evolution strongly influence the dynamics of the lithosphere, which can easily delaminate through a self-lubricating process. A parametric study is now required to provide scaling laws and convection maps for a satisfying understanding of the impact of grain size on the dynamics of the Earth.

190

Title: Stagnant lid convection in dwarf planets and icy moons Researchers: C. Yao, F. Deschamps, J.P. Lowman, C. Sanchez-Valle, P.J. Tackley Institute/ Institute of Geophysics Group: Geophysical Fluid Dynamics, D-ERDW Description: Because the viscosity of ice is strongly temperature dependent, convection in the ice layers of icy moons and dwarf planets likely operates in the stagnant lid regime, in which a rigid lid forms at the top of the fluid and reduces the heat transfer. A detailed modeling of the thermal history and radial structure of icy moons and dwarf planets thus requires an accurate description of stagnant lid convection. We performed numerical experiments of stagnant lid convection in 3-D spherical geometries for various ice shell curvatures f (measured as the ratio between the inner and outer radii), effective Rayleigh number Ram, and viscosity contrast Δη. From our results, we derived scaling laws for the average temperature of the well-mixed interior, θm, and the heat flux transported through the shell. Our models also show that the development of the stagnant lid regime depends on f. For given values of Ram and Δη, the stagnant lid is less developed as the shell's curvature increases (i.e., as f decreases), leading to improved heat transfer. Therefore, as the outer ice shells of icy moons and dwarf planets grow, the effects of a stagnant lid are less pronounced.

Figure. Influence of core radius on convection in an icy moon or dwarf planet. References: Yao, C., F. Deschamps, J.P. Lowman, C. Sanchez-Valle and P.J. Tackley (2014) Stagnant lid convection in bottom-heated thin 3D spherical shells: Infuence of curvature and implications for dwarf planets and icy moons, J. Geophys. Res., doi:10.1002/2014JE004653.

191

Group of W.F. van Gunsteren Title: On the use of one-step perturbation to investigate the dependence of NOE

derived atom-atom distance bound violations of peptides upon a variation of force-field parameters

Researchers: Z. Lin C. Oostenbrink* W.F. van Gunsteren

Institute/Group: Institute of Molecular Modeling and Simulation (MMS), University of Natural Resources and Life Sciences, Vienna, Austria* Laboratory of Physical Chemistry, ETH Zürich, Switzerland

Description:

The method of one-step perturbation can be used to predict from a single molecular dynamics simulation the values of observable quantities as functions of variations in the parameters of the Hamiltonian or biomolecular force field used in the simulation. The method is used to predict violations of nuclear Overhauser effect (NOE) distance bounds measured in nuclear magnetic resonance (NMR) experiments by atom - atom distances of the NOE atom pairs when varying force-field parameters. Predictions of NOE distance bound violations between different versions of the GROMOS force field for a hexa- β-peptide in solution show that the technique works for rather large force-field parameter changes as well as for very different NOE bound violation patterns. The effect of changing individual force-field parameters on the NOE distance bound violations of the β-peptide and an α-peptide was investigated too. One-step perturbation, which in this case is equivalent to reweighting configurations, constitutes an efficient technique to predict many values of different quantities from a single conformational ensemble for a particular system, which makes it a powerful force-field development technique that easily reduces the number of required separate simulations by an order of magnitude

References: Eur. Biophys. J. 43 (2014) 113-119 DOI 10.1007/s00249-014-0943-3

192

Title: A Polarizable Empirical Force Field for Molecular Dynamics Simulation of Liquid Hydrocarbons

Researchers: Oliwia M. Szklarczyk Stephan J. Bachmann Wilfred F. van Gunsteren

Institute/Group: Laboratory of Physical Chemistry, ETH Zürich, Switzerland

Description:

Electronic polarisability is usually treated implicitly in molecular simulations, which may lead to imprecise or even erroneous molecular behaviour in spatially electronically inhomogeneous regions of systems such as proteins, membranes, interfaces between compounds, or mixtures of solvents. The majority of available molecular force fields and molecular dynamics simulation software packages does not account explicitly for electronic polarization. Even the simplest charge-on-spring (COS) models have only been developed for few types of molecules. In this work, we report a polarizable COS model for cyclohexane, as this molecule is a widely used solvent, and for linear alkanes, which are also used as solvents, and are the precursors of lipids, amino acid side chains, carbohydrates, or nucleic acid backbones. The model is an extension of a non-polarisable united-atom model for alkanes that had been calibrated against experimental values of the density, the heat of vaporization and the Gibbs free energy of hydration for each alkane. The latter quantity was used to calibrate the parameters governing the interaction of the polarizable alkanes with water. Subsequently, the model was tested for other structural, thermodynamic, dielectric, and dynamic properties such as trans/gauche ratios, excess free energy, static dielectric permittivity, and self-diffusion. A good agreement with the experimental data for a large set of properties for each considered system was obtained, resulting in a transferable set of polarizable force-field parameters for CH2, CH3, and CH4 moieties.

References: Journal of Computational Chemistry, 35 (2014) 789–801 DOI: 10.1002/jcc.23551

193

Title: Rapid sampling of folding equilibria of β-peptides in methanol using a supra-molecular solvent model

Researchers: W. Huang S. Riniker W.F. van Gunsteren


Description:

Molecular dynamics simulation of biomolecules in solvent using an atomic model for both the biomolecules and the solvent molecules is still computationally rather demanding considering the time scale of the biomolecular motions. The use of a supra-molecular coarse-grained (CG) model can speed up the simulation considerably, but it also reduces the accuracy inevitably. Combining an atomic fine-grained (FG) level of modelling for the biomolecules and a supra-molecular CG level for the solvent into a hybrid system, the increased computational efficiency may outweigh the loss of accuracy with respect to the biomolecular properties in the hybrid FG/CG simulation. Here, a previously published CG methanol model is reparametrized, and then a 1:1 mixture of FG and CG methanol is used to calibrate the FG-CG interactions using thermodynamic and dielectric screening data for liquid methanol. The FG-CG interaction parameter set is applied in hybrid FG/CG solute/solvent simulations of the folding equilibria of three β-peptides that adopt different folds. The properties of the peptides are compared with those obtained in FG solvent simulations and with experimental NMR data. The comparison shows that the folding equilibria in the pure CG solvent simulations are different from those in the FG solvent simulations because of the lack of hydrogen-bonding partners in the supra-molecular CG solvent. Next, we introduced an FG methanol layer around the peptides in CG solvent to recover the hydrogen-bonding pattern of the FG solvent simulations. The result shows that with the FG methanol layer, the folding equilibria of the three β-peptides are very similar to those in the FG solvent simulations, while the computational efficiency is at least 3 times higher and the cutoff radius for nonbonded interactions could be increased from 1.4 to 2.0 nm.

References: J. Chem. Theory Comput. 10 (2014) 2213−2223 DOI 10.1021/ct500048c incl. supp. mat.

194

Title: The use of enveloping distribution sampling to evaluate important characteristics of biomolecular force fields

Researchers: W. Huang Z. Lin W.F. van Gunsteren


Description:

The predictive power of biomolecular simulation critically depends on the quality of the force field or molecular model used and on the extent of conformational sampling that can be achieved. Both issues are addressed. First, it is shown that widely used force fields for simulation of proteins in aqueous solution appear to have rather different propensities to stabilize or destabilize α-, π-, and 310-helical structures, which is an important feature of a biomolecular force field due to the omni-presence of such secondary structure in proteins. Second, the relative stability of secondary structure elements in proteins can only be computationally determined through so-called free-energy calculations, the accuracy of which critically depends on the extent of configurational sampling. It is shown that the method of enveloping distribution sampling is a very efficient method to extensively sample different parts of configurational space.

References: J. Phys. Chem. 118 (2014) 6424–6430 DOI: 10.1021/jp411005x, incl. supp. mat.

195

Title: Polarizable Model for DMSO and DMSO−Water Mixtures

Researchers: S.J. Bachmann W.F. van Gunsteren


Description:

Starting from a non-polarisable rigid molecular model for DMSO, a polarizable rigid model for DMSO in the liquid phase is proposed. The molecular polarisability is represented by a charge-on-spring (COS) inducible dipole at the sulfur atom and its polarization is damped for large values of the electric field strength. Some parameters of the model, the partial charge distribution, the polarisability, the value of the electric field at which damping sets in, were varied, and the overall depth and repulsion strength of the Lennard - Jones interactions were scaled with the aim of reproducing the experimental values for the molecular dipole moment, the density, heat of vaporization, and static dielectric constant of liquid DMSO at ambient temperature and pressure. The polarizable DMSO/D model well reproduces the experimental data, such as excess free energy, surface tension, translational, and rotational diffusion, for liquid DMSO. The model is further tested in mixtures with polarizable water models and in mixtures with non-polarisable DMSO. The latter results suggest that it could serve as model for polarizable co-solvent in aqueous solutions. References: J. Phys. Chem. B 118 (2014) 10175−10186

DOI: org/10.1021/jp5035695

196

Title: Practical aspects of free-energy calculations: A review

Researchers: N. Hansen* W.F. van Gunsteren

Institute/Group: Institute of Thermodynamics and Thermal Process Engineering, University of Stuttgart, Germany*

Laboratory of Physical Chemistry, ETH Zürich, Switzerland

Description:

Free-energy calculations in the framework of classical molecular dynamics simulations are nowadays used in a wide range of research areas including solvation thermodynamics, molecular recognition, and protein folding. The basic components of a free-energy calculation, that is, a suitable model Hamiltonian, a sampling protocol, and an estimator for the free energy, are independent of the specific application. However, the attention that one has to pay to these components depends considerably on the specific application. Here, we review six different areas of application and discuss the relative importance of the three main components to provide the reader with an organigram and to make non-experts aware of the many pitfalls present in free energy calculations.

References: J. Chem. Theory Comput. 10 (2014) 2632−2647 DOI: 10.1021/ct500161f

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Title: On the compatibility of polarisable and non-polarisable models for liquid water



Description:

The properties of water at physiological conditions can be modelled at different levels of resolution: (1) sub-atomic models that take into account electronic degrees of freedom, (2) atomic models that only account for atomic degrees of freedom and (3) supra-molecular models that only involve some supra-molecular degrees of freedom. To enhance the computational efficiency of molecular simulation, models at different levels of resolution should be simultaneously usable for different parts of a system for which the level of detail of interest is different. This requires these different types of models to be compatible with each other. In the present study, the compatibility of two polarisable models for liquid water, COS/G2 and COS/D, with a non-polarisable model for liquid water, SPC, is investigated. It is shown that these models are compatible. The polarisable models can thus be used to solvate biomolecules described by a biomolecular force field that is compatible with the SPC water model.

References: Mol. Phys. 112 (2014) 2761 - 2780 DOI: 10.1080/00268976.2014.910317

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Title: An improved polarisable water model for use in biomolecular simulation



Description:

The accuracy of biomolecular simulations depends to some degree on the accuracy of the water model used to solvate the biomolecules. Because many biomolecules such as proteins are electrostatically rather inhomogeneous, containing apolar, polar, and charged moieties or side chains, a water model should be able to represent the polarisation response to a local electrostatic field, while being compatible with the force field used to model the biomolecules or protein. The two polarisable water models, COS/G2 and COS/D, that are compatible with the GROMOS biomolecular force fields leave room for improvement. The COS/G2 model has a slightly too large dielectric permittivity and the COS/D model displays a much too slow dynamics. The proposed COS/D2 model has four interaction sites: only one Lennard-Jones interaction site, the oxygen atom, and three permanent charge sites, the two hydrogens, and one massless off-atom site that also serves as charge-on-spring (COS) polarisable site with a damped or sub-linear dependence of the induced dipole on the electric field strength for large values of the latter. These properties make it a cheap and yet realistic water model for biomolecular solvation.

References: J. Chem. Phys. 141 (2014) online DOI: 10.1063/1.4897976

199

Title: Time-averaged order parameter restraints in molecular dynamics simulations

Researchers: N. Hansen* F. Heller, N Schmid W.F. van Gunsteren

Institute/Group: Laboratory of Physical Chemistry, ETH Zürich, Switzerland Institute of Thermodynamics and Thermal Process Engineering, University of Stuttgart, Germany*

Description:

A method is described that allows experimental S2 order parameters to be enforced as a time-averaged quantity in molecular dynamics simulations. The two parameters that characterize time-averaged restraining, the memory relaxation time and the weight of the restraining potential energy term in the potential energy function used in the simulation, are systematically investigated based on two model systems, a vector with one end restrained in space and a pentapeptide. For the latter it is shown that the backbone N–H order parameter of individual residues can be enforced such that the spatial fluctuations of quantities depending on atomic coordinates are not significantly perturbed. The applicability to realistic systems is illustrated for the B3 domain of protein G in aqueous solution.

References: J. Biomol. NMR 60 (2014) 169–187 DOI: 10.1007/s10858-014-9866-7

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Title: Challenge of representing entropy at different levels of resolution in molecular Simulation

Researchers: W. Huang W.F. van Gunsteren


Description:

The role of entropic contributions in processes involving biomolecules is illustrated using the process of vaporization or condensation of the solvents water and methanol and the process of polypeptide folding in solution using molecular models at different levels of resolution: subatomic, atomic, supra-atomic, and supra-molecular. For the folding process, a β-hexapeptide that adopts, as inferred from NMR experiments, both a right-handed 2.710/12-helical fold and a left-handed 314-helical fold in methanol, is used to illustrate the challenge of modelling thermodynamically driven processes at different levels of resolution.

References: J. Phys. Chem. B (2014) online, incl. supp. mat. DOI: org/10.1021/jp505045m

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Title: On the use of a supra-molecular coarse-grained model for the solvent in simulations of the folding equilibrium of an octa-beta-peptide in methanol and water

Researchers: W. Huang N. Hansen* W.F. van Gunsteren

Institute/Group: Laboratory of Physical Chemistry, ETH Zürich, Switzerland Institute of Thermodynamics and Thermal Process Engineering, University of Stuttgart, Germany*

Description:

Molecular dynamics (MD) simulation can give a detailed picture of conformational equilibria of biomolecules, but it is only reliable if the force field used in the simulation is accurate, and the sampling of the conformational space accessible to the biomolecule shows many (un)folding transitions to allow for precise averages of observable quantities. Here, the use of coarse-grained (CG) solvent MeOH and H2O models to speed up the sampling of the conformational equilibria of an octa--peptide is investigated. This peptide is thought to predominantly adopt a 314-helical fold when solvated in MeOH, and a hairpin fold when solvated in H2O on the basis of the NMR data. Various factors such as the chirality of a residue, a force-field modification for the solute, coarse-graining of the solvent model, and an extension of the non-bonded interaction cut-off radius are shown to influence the simulated conformational equilibria and the agreement with the experimental NMR data for the octa--peptide.

References: Helv. Chem. Acta (2014) in press DOI: 10.1002/hlca.201400219

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Title: Pyranose Dehydrogenase Ligand Promiscuity: A Generalized Approach to Simulate Monosaccharide Solvation, Binding, and Product Formation

Researchers: M.H. Graf* Z. Lin U. Bren* D. Haltrich* W.F. van Gunsteren C. Oostenbrink*

Institute/Group: Institute of Molecular Modeling and Simulation (MMS), University of Natural Resources and Life Sciences, Vienna, Austria* Laboratory of Physical Chemistry, ETH Zürich, Switzerland

Description:

The flavoenzyme pyranose dehydrogenase (PDH) from the litter decomposing fungus Agaricus meleagris oxidizes many different carbohydrates occurring during lignin degradation. This promiscuous substrate specificity makes PDH a promising catalyst for bioelectrochemical applications. A generalized approach to simulate all 32 possible aldohexopyranoses in the course of one or a few molecular dynamics (MD) simulations is reported. Free energy calculations according to the one-step perturbation (OSP) method revealed the solvation free energies (ΔGsolv) of all 32 aldohexopyranoses in water, which have not yet been reported in the literature. The free energy difference between β- and α-anomers (ΔGβ-α) of all D-stereoisomers in water were compared to experimental values with a good agreement. Moreover, the free-energy differences (ΔG) of the 32 stereoisomers bound to PDH in two different poses were calculated from MD simulations. The relative binding free energies (ΔΔGbind) were calculated and, where available, compared to experimental values, approximated from Km values. The agreement was very good for one of the poses, in which the sugars are positioned in the active site for oxidation at C1 or C2. Distance analysis between hydrogens of the monosaccharide and the reactive N5-atom of the flavin adenine dinucleotide (FAD) revealed that oxidation is possible at HC1 or HC2 for pose A, and at HC3 or HC4 for pose B. Experimentally detected oxidation products could be rationalized for the majority of monosaccharides by combining ΔΔGbind and a reweighted distance analysis. Furthermore, several oxidation products were predicted for sugars that have not yet been tested experimentally, directing further analyses. This study rationalizes the relationship between binding free energies and substrate promiscuity in PDH, providing novel insights for its applicability in bioelectrochemistry. The results suggest that a similar approach could be applied to study promiscuity of other enzymes.

References: PLOS Computational Biology (2014) in press

203

Title: Characterisation of the flexible lip regions in bacteriophage lambda lysozyme using MD simulations

Researchers: L.J. Smith* W.F. van Gunsteren N. Hansen**

Institute/Group: Inorganic Chemistry Laboratory, University of Oxford, United Kingdom* Laboratory of Physical Chemistry, ETH Zürich, Switzerland Institute of Thermodynamics and Thermal Process Engineering, University of Stuttgart, Germany**

Description:

The upper and lower lip regions in lysozyme from bacteriophage lambda (-lysozyme) are flexible in solution and exhibit two different conformations in crystal structures of the protein. MD simulations have been used to characterise in detail the structure and dynamics of these lip regions, which surround the active site. By applying a limited number of conservative NOE distance and 1H-15N order parameter restraints, simulation trajectories have been calculated which reproduce the experimental data. These show that the lower lip region, although undergoing considerable backbone fluctuations, contains two persistent -strands. In the upper lip region a wide range of conformations are populated, although it is not clear from the available data whether some helical secondary structure is present. The work provides a clear example of the advantages of combining MD simulations with experimental data. In this case, time-averaged order parameter restraining has played an essential role in enabling convergence between two different starting structures and identifying the extent to which flexible regions in solution can contain persistent secondary structure.

References: FEBS J. (2014) submitted

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6

High-performance Hardware

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6.1 C4: The Year in Review

The Competence Center for Computational Chemistry (C4) is a network of researchersinterested in theory and computation of the IBM Zürich Research Laboratory, the Universityof Zürich, and the ETH Zürich. The goal of C4 is to move the frontiers in molecular modelingand simulation, to cater to the flow of know-how within this growing community, and to serveas a platform for the interaction with partners from other areas of science or from outsideacademia. Today, the C4 network covers a broad spectrum of research activities involvingabout fifteen research groups from ten different institutes (see also www.c4.ethz.ch).

The C4 Steering CommitteeThe Steering Committee consists of Prof. Alessandro Curioni, head of computational sciencesat IBM Zürich Research, Profs. Jürg Hutter (University of Zürich), and PD Dr. Hans P. Lüthi(chair; ETH Zürich).

C4 Seminar The actual “backbone” of C4 is its Seminar Program. During the 2013 Fall- and 2014 Spring-Term the C4 Seminar Program covered 10 lectures, again some of them presented by leadersin the field of computational chemistry. The seminar enjoys a remarkable popularity bringingtogether between forty and sixty students and researchers each time. One C4 seminar washosted by the IBM Research Laboratory, and another two seminars were hosted by theUniversity of Zürich. One of the seminars, presented by Prof. K. Morokuma (Kobe andEmory Universities), was part of a Swiss Chemical Society Lectureship.

Compute ResourceSince many of the members of the computational chemistry community have their owncomputing facilities, or were granted compute time by the Centro Svizzero die CalcoloScientifico (CSCS), the compute resource offered by C4 in recent years became less and less“mission critical”. C4 holds a number of nodes on the ETH Brutus cluster that are open to allETH computational chemists.

C4 TutorialsWith CECAM being established in Switzerland, the offering for tutorials and workshops hasincreased considerably, both, in number and in the spectrum of topics covered. The CECAMZurich node is lead by our colleague Prof. Matthias Troyer of the Institute of TheoreticalPhysics. C4 did not offer its own tutorials.

The IBM Research AwardIn 2007, the ETH Schulleitung approved the “IBM Research Forschungspreis”, an award foroutstanding MSc and PhD theses sponsored by the IBM Zürich Research Laboratory. Thisyear, the prize was awarded to Carlo Weingart of the group of Prof. Nicola Spaldin (ETH D-MATL) for his MSc thesis entitled “Origin of Spin Canting in Multiferroic Perovskites”. Theaward jury consisted of Professors U.W. Suter (chairperson; former VP Research ETHZürich), Hans P. Lüthi (ETH), Jürg Hutter (UZH) and Alessandro Curioni (IBM Research).

The 2013 Award Ceremony took place at the ETH Tag with the Rector, Prof. Lino Guzzella,handing out the award to the winner. The laureate, Carlo Weingart, now computationalscientist at Autoform Development GmbH in Zürich, also presented his research at theoccasion of a special C4 Seminar held at the IBM Research Laboratory in Rüschlikon onApril 10, 2014.

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OutlookA network such as C4 plays an important role when it comes to the exchange of informationwithin a relatively large and distributed community. Modeling and Simulation have becomeestablished tools also for researchers with an experimental background, and the C4 networkgives them access to the state-of-the-art methodologies and computational know-how. Also inthe next year we will make sure that C4 is a valuable platform for its stakeholders.

Hans P. Lüthi, Leiter C4November 17, 2014

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6.2 Information Technology Services

The IT Services of ETH are currently managing two large Linux clusters called BRUTUS (“Better Reliability and Usability Thanks to Unified System”) and EULER (Erweiterbarer, Umwelfreundlicher, Leistungfähiger ETH Rechner”).

Both clusters have been financed and are operated according to a “shareholder” model. Professors, institutes and even whole departments can become shareholders by financing a number of compute nodes in the cluster. In return, they are guaranteed a share of CPU time proportional to their investment. The share financed by the IT Services is made available to the whole scientific community of ETH at no cost.

To make it easier for users to switch back and forth between Brutus and Euler, both clusters use the same operating system (CentOS), batch system (Platform LSF), development tools (GNU, Intel and PGI compilers) and applications.

Brutus

The Brutus cluster has been in operation at ETH since 2008 and has been regularly upgraded and expanded over the years. As a result Brutus is very heterogeneous; there are 10 different types of compute nodes, containing from 4 to 48 cores and between 16 GB and 1024 GB of memory. The cluster’s software environment has been designed from the start to hide this complexity and to present Brutus as a monolithic system to its users.

Currently Brutus contains 1,004 compute nodes with a total of 19,824 processor cores and 50 GPUs, giving it a peak performance of 200 TF.

Two Lustre parallel file systems, with a capacity of 400 TB each, are configured respectively as permanent and non-permanent (scratch) storage for the most data-intensive applications. A Panasas parallel file system with a capacity of 75 TB is configured as medium-term storage for less demanding applications. Lastly, an NFS file system with a capacity of 50 TB, based on four redundant Solaris ZFS servers, is used for home directories and centrally installed applications. This NFS file system is backed up every night to the ETH’s central tape archive (TSM).

All compute nodes are connected to the cluster’s internal Ethernet network via 1 Gb/s links. The login nodes are connected to this network and to the ETH’s network via 10 Gb/s links. The vast majority of the compute nodes are connected to a low-latency 40 Gb/s InfiniBand QDR network.

The two Lustre file systems are attached directly to the cluster’s InfiniBand QDR network. The Panasas and NFS file systems, as well as the ETH’s central NAS, are connected to the cluster’s Ethernet network via 10 Gb/s links.

Euler

The new Euler cluster was commissioned at the end of 2013 and installed in the spring of 2014. Due to lack of space, power and cooling in the computer rooms at ETH in Zurich, this system is housed in CSCS’s new data center in Lugano and managed remotely from Zurich by the IT Services.

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Euler does not replace Brutus but complements it. Whereas Brutus was designed primarily for high-throughput computations, Euler is designed for high-performance. This goal has been achieved by combining the most powerful x86-64 processor on the market (Intel’s 12-core Xeon E5-2697v2) together with two high-speed networks (56 Gb/s InfiniBand FDR and 10 Gb/s Ethernet). Most of the compute nodes are equipped with 64 GB of memory; 32 nodes contain 128 GB and 64 nodes contain 256 GB.

Currently Euler contains 448 compute nodes with a total of 10,752 processor cores, giving it a peak performance of 260 TF. Another 320 compute nodes / 7680 cores are scheduled to be added at the beginning of 2015.

Due to the distance (latency) between Zurich and Lugano, it was decided early on that Euler would need its own local storage systems. A Panasas parallel file system with a capacity of 240 TB is configured as permanent and non-permanent (scratch) storage for data-intensive applications. An NFS file system with a capacity of 200 TB, based on two redundant NetApp servers, is used for home directories, centrally installed applications, as well as long-term storage for specific projects. Like Brutus, the NFS file system of Euler is backed up every night to the ETH’s central tape archive (TSM) in Zurich.

All compute nodes are connected to the 56 Gb/s InfiniBand FDR and 10 Gb/s Ethernet networks. The former is dedicated to inter-node communication (typically MPI); the latter is used for file access and for global communication (system management, monitoring, batch system, etc.)

A core feature of Euler is the extensive use of virtualization. As one can see in the picture below, the head nodes (login and management nodes) of Euler are not physical servers but virtual machines. The underlying virtualization layer, based on VMware, makes it possible to create virtual compute nodes or even offer complete clusters to customers who cannot or do not want to use the Euler cluster in a traditional manner.

Euler concept

This concept forms the basis of a new range of cloud services (IaaS, PaaS, SaaS) that will complement the traditional HPC offering of IT Services in the future.

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Publications*

*only CSE-related articlesin refereed journals

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Group of P. Arbenz

P. Arbenz, C. Flaig, D. Kellenberger: Bone structure analysis on multiple GPGPUs. J.Parallel Distrib. Comput. 74, 2941–2950 (2014),

E. Turan, P. Arbenz: Preconditioning aspects of large scale micro finite element analysisof 3D bone poroelasticity. Parallel Comput. 40, 239–250 (2014).

S. Pauli, M. Kohler, P. Arbenz: A fault tolerant implementation of multi-level MonteCarlo methods. Parallel Computing: Accelerating Computational Science and Engineer-ing (CSE). M. Bader et al. (eds.). Parallel Computing: Accelerating ComputationalScience and Engineering (CSE), Advances in Parallel Computing 25, IOS Press, 2014,pp. 471–480.

M. Toggweiler, A. Adelmann, P. Arbenz, J. J. Yang: A novel adaptive time steppingvariant of the Boris-Buneman integrator applied to particle accelerator simulation withspace charge. J. Comput. Phys. 273, 255–267 (2014).

Y. Matsuo, H. Guo, P. Arbenz: Experiments on a Parallel Nonlinear Jacobi–DavidsonAlgorithm. Procedia Comput. Sci. 29, 565-575 (2014), Proceedings of the InternationalConference on Computational Science (ICCS) 2014.

P. Arbenz, D. Hupp, D. Obrist: A parallel solver for the time-periodic Navier–Stokesequations. In: Parallel Processing and Applied Mathematics (PPAM 13), Part II. R.Wyrzykowski, J. Dongarra, K. Karczewski, J. Wasniewski (eds.). Lecture Notes in Com-puter Science 8385, pp. 291–300. Springer, Berlin, 2014.

C. Metzger-Kraus: A self-consistent particle-in-cell time-domain solver incorporating ra-diative interaction. ETH Zurich, PhD Thesis No. 22154, 2014. http://dx.doi.org/10.3929/ethz-a-010261293.

H. Guo, P. Arbenz, B. Oswald: A large-scale nonlinear eigensolver for the analysis ofdispersive nanostructures. Computer Phys. Comm. 184 (8): 1898–1906 (2013).

P. Arbenz, E. Turan: Preconditioning for large scale micro finite element analyses of 3Dporoelasticity. In: Applied Parallel and Scientific Computing (PARA 2012). P. Manni-nen, P. Oster (eds.). Lecture Notes in Computer Science 7782, pp. 361–374. Springer,Heidelberg, 2013.

Y. Ineichen: Toward massively parallel multi-objective optimization with application toparticle accelerators, PhD thesis, Computer Science Department, ETH Zurich, January2013. http://dx.doi.org/10.3929/ethz-a-009792359

C. Flaig, P. Arbenz: A highly scalable matrix-free multigrid solver for µFE analysis basedon a pointer-less octree. In Large Scale Scientific Computing LSSC’11. I. Lirkov, S.

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Margenov, J. Wasniewski (eds.). Lecture Notes in Computer Science 7116, pp. 498–506.Springer, Heidelberg, 2012.

C. Bekas, A. Curioni, P. Arbenz, C. Flaig, G.H. van Lenthe, R. Muller, A.J. Wirth:Massively parallel graph partitioning: A case in human bone simulations. In Combinato-rial Scientific Computing. Uwe Naumann, Olaf Schenk (eds.). Chapman and Hall/CRC,2012. pp. 407–425.

Y. Ineichen, A. Adelmann, C. Bekas, A. Curioni, P. Arbenz: A fast and scalable lowdimensional solver for charged particle dynamics in large particle accelerators. Comput.Sci. Res. Dev. 28 (2-3): 185–192 (2013).

A. Adelmann, P. Arbenz, Y. Ineichen: Improvements of a fast parallel Poisson solveron irregular domains. In Applied Parallel and Scientific Computing (PARA 2010). K.Jonasson (ed.). Part I, Lecture Notes in Computer Science 7133, pp. 65–74. Springer,Heidelberg, 2012.

P. Arbenz, A. Hiltebrand, D. Obrist: A parallel space-time finite difference solver for pe-riodic solutions of the shallow-water equation. In Parallel Processing and Applied Mathe-matics (PPAM 11) Part II. R. Wyrzykowski, J. Dongarra, K. Karczewski, J. Wasniewski(eds.). Lecture Notes in Computer Science 7204, pp. 302–312. Springer, Berlin, 2012.

C. Kraus, A. Adelmann, P. Arbenz: Perfectly matched layers in a divergence preservingADI scheme for electromagnetics. J. Comput. Phys. 231 (1): 39–44 (2012).

H. Guo, B. Oswald, P. Arbenz: 3-dimensional eigenmodal analysis of plasmonic nanos-tructures. Optics Express. 20 (5): 5481-5500 (2012)

Y. Ineichen, A. Adelmann, C. Bekas, A. Curioni, P. Arbenz: A massively parallel gen-eral purpose multi-objective optimization framework, applied to beam dynamic studies.Proceedings of ICAP2012, Rostock-Warnemunde, Germany, 2012, pp. 62–66.

H. Guo: 3-dimensional eigenmodal analysis of electromagnetic structures. ETH Zurich,PhD Thesis No. 20947, 2012. doi:10.3929/ethz-a-007599690.

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Publication List: Group of Sebastian Bonhoeffer

Hool A, Gabriel Leventhal, Sebastian Bonhoeffer Virus-induced target cell activation reconciles set-point viral load heritability and within-host evolution. 2013, Epidemics

Samuel Tazzyman, Sebastian Bonhoeffer Fixation probability of mobile genetic elements such as plasmids. 2013, Theoretical population biology

Magnus C, Brandenberg OF, Rusert P, Trkola A, Roland Regoes Mathematical models: a key to understanding HIV envelope interactions? 2013, Journal of immunological methods

Kaiser P, Slack E, Grant AJ, Hardt WD, Roland Regoes Lymph node colonization dynamics after oral salmonella typhimurium infection in mice. 2013, PLoS pathogens

Wu T, Feng Fu, Zhang Y, Wang L Adaptive tag switching reinforces the coevolution of contingent cooperation and tag diversity. 2013, J Theor Biol

Alex Hall Genotype-by-environment interactions due to antibiotic resistance and adaptation in Escherichia coli. 2013, J Evol Biol

Tanja Stadler, Sebastian Bonhoeffer Uncovering epidemiological dynamics in heterogeneous host populations using phylogenetic methods. 2013, Philosophical transactions of the Royal Society of London. Series B, Biological sciences

Saenz RA, Sebastian Bonhoeffer Nested model reveals potential amplification of an HIV epidemic due to drug resistance. 2013, Epidemics

Victor Garcia Palencia, Roland Regoes Stabilization of cooperative virulence by the expression of an avirulent phenotype 2013, nature

Diard M, Garcia V, Maier L, Remus-Emsermann MN, Roland Regoes, Ackermann M, Hardt WD Stabilization of cooperative virulence by the expression of an avirulent phenotype. 2013, Nature

Inglis RF, Alex Hall, Buckling A The role of 'soaking' in spiteful toxin production in Pseudomonas aeruginosa. 2013, Biology letters

214

Roland Regoes, Hamblin S, Tanaka MM Viral mutation rates: modelling the roles of within-host viral dynamics and the trade-off between replication fidelity and speed. 2013, Proceedings. Biological sciences / The Royal Society

Tanja Stadler, Denise Kühnert, Sebastian Bonhoeffer, Drummond AJ Birth-death skyline plot reveals temporal changes of epidemic spread in HIV and hepatitis C virus (HCV). 2013, Proceedings of the National Academy of Sciences of the United States of America

Oña L, Kouyos RD, Lachmann M, Sebastian Bonhoeffer On the role of resonance in drug failure under HIV treatment interruption. 2013, Theoretical biology & medical modelling

Zhang Y, Feng Fu, Wu T, Xie G, Wang L A tale of two contribution mechanisms for nonlinear public goods. 2013, Sci Rep

Seich Al Basatena NK, Chatzimichalis K, Graw F, Frost SD, Roland Regoes, Asquith B Can non-lytic CD8+ T cells drive HIV-1 escape? 2013, PLoS pathogens

Wu T, Feng Fu, Zhang Y, Wang L The increased risk of joint venture promotes social cooperation. 2013, PLoS One

Daniel Angst, Alex Hall The cost of antibiotic resistance depends on evolutionary history in Escherichia coli. 2013, BMC evolutionary biology

Shirado H, Feng Fu, Fowler JH, Christakis NA Quality versus quantity of social ties in experimental cooperative networks. 2013, Nat Commun

Wu T, Feng Fu, Zhang Y, Wang L Adaptive role switching promotes fairness in networked ultimatum game. 2013, Sci Rep

215

Group of K. Boulouchos publications

1. M. Schmitt, C.E. Frouzakis, A. Tomboulides, Y.M. Wright, K. Boulouchos, Direct numer-ical simulation of multiple cycles in a valve/piston assembly, Phys. Fluids, 26, 035105,(2014)

2. M. Schmitt, C.E. Frouzakis, A. Tomboulides, Y.M. Wright, K. Boulouchos, Direct nu-merical simulation of the effect of compression on the flow, temperature and compositionunder engine-like conditions, Proc. Combust. Inst., (in press)

3. M. Kooshkbaghi, C.E. Frouzakis, K. Boulouchos, I.V. Karlin, Entropy production analy-sis for mechanism reduction, Combust. Flame, 161(6), 1507–1515, (2014)

4. M. Kooshkbaghi1, C.E. Frouzakis, E. Chiavazzo, K. Boulouchos, I.V. Karlin, The globalrelaxation redistribution method for reduction of combustion kinetics, J. Chem. Phys.141, 044102, (2014)

5. A. Brambilla, C.E. Frouzakis, J. Mantzaras, R. Bombach, K. Boulouchos, Flame dynam-ics in lean premixed CO/H2/air combustion in a mesocale channel, Combust. Flame,161(5), 1268–1281, (2014)

6. A. Brambilla, M. Schultze, C.E. Frouzakis, J. Mantzaras, R. Bombach, K. Boulouchos,An experimental and numerical investigation of premixed syngas combustion dynamicsin mesoscale channels with controlled wall temperature profiles, Proc. Combust. Inst.,(in press)

7. A. Brambilla, C.E. Frouzakis, J. Mantzaras, A. Tomboulides, S. Kerkemeier, K. Boulou-chos, Detailed transient numerical simulation of H2/air hetero-/homogeneous combustionin platinum-coated channels with conjugate heat transfer Combust. Flame, 161(5), 2692–2707, (2014)

8. C. Altantzis, C.E. Frouzakis, A.G. Tomboulides, K. Boulouchos, Direct numerical sim-ulation of circular expanding premixed flames in a lean quiescent hydrogen-air mixture:Phenomenology and detailed flame front analysis, Combust. Flame, (in press)

9. G.K. Giannakopoulos, A. Gatzoulis, C.E. Frouzakis, M. Matalon, A.G. Tomboulides,Consistent definitions of “Flame Displacement Speed and “Markstein Length for pre-mixed flame propagation, Combust. Flame, (in press)

10. C.E. Frouzakis, N.Fogla, A.G. Tomboulides, C. Altantzis, M. Matalon Numerical studyof unstable hydrogen/air flames: Shape and propagation speed, Proc. Combust. Inst., (inpress)

11. G.K. Giannakopoulos, M. Matalon, C.E. Frouzakis, A.G. Tomboulides, The curvatureMarkstein length and the definition of flame displacement speed for stationary sphericalflames, Proc. Combust. Inst., (in press)

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Group name: Chair of Sociology, in particular of Modeling and Simulation

List of publications in 2013 and 2014:

• M. Schich, C. Song, Y. Y. Ahn, A. Mirsky, M. Martino, A. L. Barabási, and Helbing, D. (2014) “A network framework of cultural history.” Science 345(6196), 558-562.

• D. Helbing, W. Yu, K. D. Opp, and H. Rauhut (2014) “Conditions for the Emergence of Shared Norms in Populations with Incompatible Preferences.” PLOS one, 9(8), e104207.

• G. L. Ciampaglia, S. Lozano, and D. Helbing (2014) “Power and fairness in a generalized ultimatum game.” PLOS ONE, 9(6), e99039.

• D. Helbing, D. Brockmann, T. Chadefaux, K. Donnay, U. Blanke, O. Woolley-Meza,M. Moussaid, A. Johansson, J. Krause, S. Schutte, and M. Perc (2014) “Saving HumanLives: What Complexity Science and Information Systems can Contribute.” Journal ofStatistical Physics, 1-47.

• R. Carvalho, L. Buzna, F. Bono, M. Masera, D. K. Arrowsmith, and D. Helbing (2014)“Resilience of natural gas networks during conflicts, crises and disruptions.” PLOSONE, 9(3), e90265.

• Tobias Kuhn and Michel Dumontier. Trusty URIs: Verifiable, Immutable, andPermanent Digital Artifacts for Linked Data. In Proceedings of the 11th ExtendedSemantic Web Conference (ESWC). Springer, 2014.

• Tobias Kuhn. A Survey and Classification of Controlled Natural Languages.Computational Linguistics, 40(1), 2014.

• D. Brockmann and D. Helbing (2013) “The hidden geometry of complex, network-driven contagion phenomena”. Science 342(6164), 1337–1342.

• D. Helbing (2013). “Globally networked risks and how to respond.” Nature, 497, 51–59.

• Leduc, C., K. Padberg-Gehle, V. Varga, D.Helbing, S. Diez, and J. Howard (2012) “Molecular crowding creates traffic jams of kinesin motors on microtubules.” PNAS 16: 6100-6105.

• R. Bhavnani, K. Donnay, D. Miodownik, M. Mor, and D. Helbing (2013) Group segregation and urban violence. American Journal of Political Science, in print (DOI: 10.1111/ajps.12045).

• F. Winter, H. Rauhut and D. Helbing (2012) “How norms can generate confict: an experiment on the failure of cooperative micro-motives on the macro-level.” Social Forces 90(3): 919-946.

• T. Chadefaux, D. Helbing (2012) “The rationality of prejudices.” PLoS ONE 7(2): e30902.

• R. Berger, H. Rauhut, S. Prade, and D. Helbing (2012) “Bargaining over waiting time in ultimatum game experiments.” Social Science Research 41: 372-379.

• Heliövaara, S., H. Ehtamo, D. Helbing, T. Korhonen (2013) “Patient and impatient pedestrians in a spatial game for egress congestion.” Physical Review E 87: 012802.

• Helbing, D. and P. Mukerji (2012) “Crowd disasters as systemic failures: Analysis of the Love Parade disaster.” EPJ Data Science 1:7.

• Helbing, D. (2013) "Economics 2.0: The natural step towards a self-regulating, participatory market society", Evolutionary and Institutional Economics Review.

• Helbing, D. and A. Kirman (2013) "Rethinking economics using complexity theory",

217

Real-World Economics Review, in print. • Parisi, D.R., D. Sornette, and D. Helbing (2013) "Financial price dynamics and

pedestrian counterflows: A comparison of statistical stylized facts." Physical Review E87: 012804.

218

Group of P.H. Hunenberger

M. Laner, B.A.C. Horta and P.H. HunenbergerPhase-transition properties of glycerol-monopalmitate lipid bilayers investigated bymolecular dynamics simulation: Influence of the system size and force-field param-eters.Mol. Simul. 39 (2013) 563-583.

N. Hansen, P.H. Hunenberger and W.F. van Gunsteren.Efficient combination of environment change and alchemical perturbation within theenveloping distribution sampling (EDS) scheme: Twin-system EDS and applicationto the determination of octanol-water partition coefficients.J. Chem. Theory Comput. 9 (2013) 1334-1346.

D. Wang, M.L. Amundadotir, W.F. van Gunsteren and P.H. Hunenberger.Intramolecular hydrogen-bonding in aqueous carbohydrates as a cause or conse-quence of conformational preferences: A molecular dynamics study of cellobiosestereoisomers.Eur. Biophys. J. 42 (2013) 521-537.

G.J. Rocklin, D.L. Mobley, K.A. Dill and P.H. Hunenberger.Calculating the binding free energies of charged species based on explicit-solventsimulations employing lattice-sum methods: An accurate correction scheme for elec-trostatic finite-size effects.J. Chem. Phys. 139 (2013) 184103/1-184103/32.

N.S. Bieler, R. Hauselmann and P.H. Hunenberger.Local elevation umbrella sampling applied to the calculation of alchemical free-energy changes via λ-dynamics: The λ-LEUS scheme.J. Chem. Theory. Comput. 10 (2014) 3006-3022.

M. Laner, B.A.C. Horta and P.H. Hunenberger.Effect of the cosolutes trehalose and methanol on the equilibrium and phase-transitionproperties of glycerol-monopalmitate lipid bilayers investigated using molecular dy-namics simulations.Eur. Biophys. J. (2014) in press (available on-line).

M. Laner, B.A.C. Horta and P.H. Hunenberger.Long-timescale motions in glycerol-monopalmitate lipid bilayers investigated usingmolecular dynamics simulation.J. Mol. Graph. Model. (2014) submitted.

219

M. Laner and P.H. Hunenberger.Effect of methanol on the phase-transition properties of glycerol-monopalmitate lipidbilayers investigated using molecular dynamics simulations: In quest of the biphasiceffect.J. Mol. Graph. Model. (2014) submitted (2014).

N.S. Bieler and P.H. Hunenberger.Estimating the initial biasing potential for λ-local-elevation umbrella-sampling (λ-LEUS) simulations via slow growth.J. Chem. Theory. Comput. Lett. (2014) submitted.

220

Publications since 2012: 1. Gorji, M.H., Fokker-Planck Solution Algorithm for Rarefied Gas Flows and Applications

of Complex Gas-Surface Interactions. 2014, ETH-Zürich. 2. Jenny, P., D. Roekaerts, and N. Beishuizen, Modeling of turbulent dilute spray

combustion. Progress in Energy and Combustion Science, 2012. 38(6): p. 846-887.3. Xiao, H. and P. Jenny, A Consistent Dual-Mesh Framework for Hybrid LES/RANS

Modeling. Journal of Computational Physics, 2012. 231(4): p. 1848-1865.4. Xiao, H., et al., Coupling of solvers with non-conforming computational domains in a

dual-mesh hybrid LES/RANS framework. Computers & Fluids, 2013. 88: p. 653-662.5. Xiao, H., J.X. Wang, and P. Jenny, Dynamic Evaluation of Mesh Resolution and Its

Application in Hybrid LES/RANS Methods. Flow Turbulence and Combustion, 2014.93(1): p. 141-170.

6. Cortinovis, D. and P. Jenny, Iterative Galerkin-enriched multiscale finite-volume method.Journal of Computational Physics, 2014. 277: p. 248-267.

7. Karvounis, D.C., Simulations of Enhanced Geothermal Systems with an AdaptiveHierarchical Fracture Representation. 2013, ETH.

8. Deb, R. and P. Jenny. Modeling of Failure along Predefined Planes in FracturedReservoirs. in Thirty-Ninth Workshop on Geothermal Reservoir Engineering. 2014.Stanford University, Stanford, California.

9. Müller, F., P. Jenny, and D.W. Meyer, Multilevel Monte Carlo for two phase flow andBuckley–Leverett transport in random heterogeneous porous media. Journal ofComputational Physics, 2013. 250: p. 685-702.

10. Müller, F., D.W. Meyer, and P. Jenny, Solver-based vs. grid-based multilevel Monte Carlofor two phase flow and transport in random heterogeneous porous media. Journal ofComputational Physics, 2014. 268: p. 39-50.

11. Müller, F., Stochastic methods for uncertainty quantification in subsurface flow andtransport problems. 2014, ETH.

12. Jenny, P., J.S. Lee, D.W. Meyer, and H.A. Tchelepi, Scale analysis of miscible density-driven convection in porous media. Journal of Fluid Mechanics, 2014. 749: p. 519-541.

13. Lücker, A., B. Weber, and P. Jenny, A dynamic model of oxygen transport from capillariesto tissue with moving red blood cells. AJP-Heart and Circulatory Physiology, 2014.accepted.

14. Gorji, M.H. and P. Jenny, An efficient particle Fokker-Planck algorithm for rarefied gasflows. Journal of Computational Physics, 2014. 262: p. 325-343.

15. Gorji, H. and P. Jenny, A gas-surface interaction kernel for diatomic rarefied gas flowsbased on the Cercignani-Lampis-Lord model. Physics of Fluids, 2014. accepted.

16. Gorji, M.H. and P. Jenny, A Device Concept for Demixing of Gas Species based onExcitation of Internal Energy Modes, in ASME 2013 11th International Conference onNanochannels, Microchannels, and Minichannels. 2013, ASME: Sapporo, Japan.

Group of P. Jenny

221

17. Dmitriev, V. and P. Jenny, Energy Extraction from Onflow Inhomogeneity in the Spanwise Direction. A Theoretical Study. Journal of Intelligent & Robotic Systems, 2013. 69(1-4): p. 83-89.

18. Dmitriev, V. and P. Jenny, Concept for Flapping Annular Wing UAV, in 12th AIAA Aviation Technology, Integration, andOperations (ATIO) Conference and 14th AIAA/ISSMO MultidisciplinaryAnalysis and Optimization Conference. 2012, AIAA: Indianapolis, IN, USA.

19. Lund, H., F. Muller, B. Muller, and P. Jenny, Rankine-Hugoniot-Riemann solver for steady multidimensional conservation laws with source terms. Computers & Fluids, 2014. 101: p. 1-14.

20. Dmitriev, V. and P. Jenny, Energy Extraction from Wind Inhomogeneity by Means of Wing Morphing, in Proceedings of the 12th AIAA AviationTechnology, Integration, and Operations (ATIO) Conference and 14thAIAA/ISSMO Multidisciplinary Analysis and Optimization Conference. 2012, Kluwer: Indianapolis, IN, USA. p. 83-89.

21. Erbertseder, K.M., et al., A Coupled Discrete/Continuum Model for Describing Cancer- Therapeutic Transport in the Lung. PLoS one, 2012. 7(3): p. e31966-.

22. Gorji, H. and P. Jenny, A Kinetic Model for Gas Mixtures Based on a Fokker-Planck Equation. Journal of Physics: Conference Series, 2012. 362(1): p. 012042-.

23. Hajibeygi, H., S.H. Lee, and I. Lunati, Accurate and Efficient Simulation of Multiphase Flow in a Heterogeneous Reservoir With Error Estimate and Control in the Multiscale Finite-Volume Framework. SPE Journal, 2012. 17(4): p. 1071-1083.

24. Hegetschweiler, M., B. Zoller, and P. Jenny, Reactive Parametrized Scalar Profile (R- PSP) Mixing Model for Partially Premixed Combustion. Combustion and Flame, 2012. 159(2): p. 734-747.

25. Hirsch, S., et al., Topology and hemodynamics of the cortical cerebrovascular system. Journal of Cerebral Blood Flow & Metabolism, 2012. 32(6): p. 952-967.

26. Jenny, P. and D.W. Meyer, Transported Probability and Mass Density Function (PDF/ MDF) Methods for Uncertainty Assessment and Multi-Scale Problems. 2012, Springer. p. 35-65.

27. Kang, J., N.I. Prasianakis, and J. Mantzaras, Development of an LB Model for Non- Isothermal Mixture Flows, in 21st Conference on Discrete Simulation of Fluid Dynamics. 2012: Bangalore, India.

28. Karvounis, D. and P. Jenny, Modeling of Flow and Transport for EGS Cost Optimization Problems, in Thirty-Seventh Workshop on Geothermal Reservoir Engineering. 2012: Stanford, CA, USA.

29. Meyer, D.W., Modelling of turbulence modulation in particle- or droplet-laden flows. Journal of Fluid Mechanics, 2012. 706: p. 251-273.

30. Meyer, D.W. and R. Deb, Modeling molecular mixing in a spatially inhomogeneous turbulent flow. Physics of Fluids, 2012. 24(2): p. 025103-.

31. Misselwitz, B., et al., Near Surface Swimming of Salmonella Typhimurium Explains Target-Site Selection and Cooperative Invasion. PLoS pathogens, 2012. 8(7): p. e1002810-.

222

32. Rosén, T., et al., Saturation Dependent Effective Transport Properties of PEFC Gas Diffusion Layers. Journal of The Electrochemical Society, 2012. 159(9): p. F536-F544.

33. Schneider, M., et al., Tissue Metabolism Driven Arterial Tree Generation. Medical Image Analysis, 2012. 16(7): p. 1397-1414.

34. Sormaz, M. and P. Jenny, Empirical model for target depth estimation used in the time- domain subsurface imaging. Journal of the Optical Society of America A, 2012. 29(10).

35. Šormaz, M. and P. Jenny, Empirical model for target depth estimation used in the time- domain subsurface imaging. Journal of the Optical Society of America A, 2012. 29(10): p. 2174-2180.

36. Gorji, M.H. and P. Jenny, A Fokker-Planck based kinetic model for diatomic rarefied gas flows. Physics of Fluids, 2013. 25(6): p. 062002-.

37. Gorji, M.H., S. Küchlin, and P. Jenny, A Hybrid Fokker-Planck-DSMC Solution Algorithm for the Whole Range of Knudsen Numbers, in ASME 2013 11th International Conference on Nanochannels, Microchannels, and Minichannels. 2013, ASME 2013 11th International Conference on Nanochannels, Microchannels, and Minichannels: Sapporo, Japan.

38. Hack, M.L. and P. Jenny, Joint PDF Closure of Turbulent Premixed Flames. Flow, Turbulence and Combustion, 2013. 90(2): p. 373-386.

39. Kang, J., Lattice Boltzmann method for reactive thermal multicomponent flows. 2013, ETH-Zürich.

40. Kang, J., N.I. Prasianakis, and J. Mantzaras, Lattice Boltzmann model for thermal binary- mixture gas flows. Physical Review E, Statistical, nonlinear, and soft matter physics, 2013. 87(5): p. 053304-.

41. Küchlin, S., Multipurpose synthetic particle image velocimetry. 2013, ETH-Zürich. 42. Meyer, D.W., H.A. Tchelepi, and P. Jenny, A fast simulation method for uncertainty

quantification of subsurface flow and transport. Water Resources Research, 2013. 49(5): p. 2359-2379.

43. Meyer, D.W. and P. Jenny, Accurate and computationally efficient mixing models for the simulation of turbulent mixing with PDF methods. Journal of Computational Physics, 2013. 247: p. 192-207.

44. Tritarelli, R.C. and L. Kleiser. Heat release and high-temperature gas effects in shock/ shear-layer interaction. in Proceedings of the second TRR40 Summer Program 2013. 2013.

45. Wild, M.A., General purpose PDF solution algorithm for reactive flow simulations in OpenFOAM. 2013, ETH.

46. Zoller, B.T., M.L. Hack, and P. Jenny, A PDF combustion model for turbulent premixed flames. Proceedings of the Combustion Institute, 2013. 34: p. 1421-1428.

47. Zoller, B.T., Scale Separation Modeling of Turbulent Gas-Phase Combustion Using PDF Methods. 2013, ETH.

223

48. Deb, R. and P. Jenny, Modeling of Failure along Predefined Planes in Fractured Reservoirs, in Thirty-Ninth Workshop on Geothermal Reservoir Engineering. 2014, Curran: Stanford, California, USA.

49. Gloor, M. and P. Jenny, Efficient and Adaptive Algorithm for Aerodynamic Investigations of Micro Helicopters, in 32nd AIAA Applied Aerodynamics Conference. 2014, American Institute of Aeronautics and Astronautics: Atlanta, GA, USA.

50. Jenny, P., M. Sormaz, and S. Mourad, Computer Models for Digital Imaging, in Handbook of Digital Imaging, M.A. Kriss, Editor. 2014, John Wiley & Sons.

51. Meyer, D.W. and M.L. Eggersdorfer, Simulating particle collisions in homogeneous turbulence with kinematic simulation: A validation study. Colloids and surfaces A, Physicochemical and engineering aspects, 2014. 454: p. 57-64.

52. Meyer, D.W., Stochastic Models of Particle Dynamics in Turbulent and Subsurface Flows. 2014, ETH.

!!

224

Group of L. Kleiser

References

[1] John, Michael O., Obrist Dominik, and Kleiser, Leonhard A class of exact Navier-Stokes solutions for homogeneous flat-plate boundary layers and their linear stability.Journal of Fluid Mechanics, 752:462-484, 2014

[2] Edom, Elisabeth, Obrist Dominik, and Kleiser, Leonhard Steady streaming in atwo-dimensional box model of a passive cochlea. Journal of Fluid Mechanics, 753:254-278, 2014

[3] Pfenniger, Alois, Stahel, Andreas, Koch, Volker M., Obrist, Dominik, and Vogel, RolfEnergy harvesting through arterial wall deformation. Applied Mathematical Mod-elling, 38(13):3325-3338, 2014

[4] Luginsland, Tobias Numerical investigation of vortex breakdown in compressible,swirling nozzle-jet flows. Diss ETH no. 21616, 2014

[5] John, Michael O., Obrist Dominik, and Kleiser, Leonhard Stabilization of subcrit-ical bypass transition in the leading-edge boundary layer by suction. Journal ofTurbulence, 15(11):795-805, 2014

[6] Buhler, Stefan, Obrist, Dominik, and Kleiser, Leonhard Near-field and far-field acous-tics of laminar and turbulent nozzle-jet flows. 19th AIAA/CEAS Aeroacoustics Con-ference, p. 187, 2013

[7] Pfenniger, Alois, Obrist, Dominik, Stahel, Andreas, Koch, Volker M., and Vogel, RolfEnergy harvesting through arterial wall deformation. Medical & Biological Engineer-ing & Computing, 51(7):741-755, 2013

[8] Landolt, Andrin, Obrist, Dominik, Wyss, Matthias, Barrett, Matthew, Langer, Do-minik, Jolivet, Renaud, Soltisynki, Tomasz, Weber, Bruno, and Rosgen, ThomasTwo-photon microscopy with double-circle trajectories for in vivo cerebral bloodflow measurements. Experiments in Fluids, 54(5):1523-, 2013

[9] Boselli, Francesco, Obrist, Dominik, and Kleiser, Leonhard Vortical flow in the utricleand the ampulla. Biomechanics and Modeling in Mechanobiology, 12(2):335-348, 2013

[10] Buhler, Stefan Numerical Simulation of Laminar and Turbulent Nozzle-Jet Flowsand Their Sound. Diss ETH no. 21483, 2013

[11] Borer, D., Yammine, S., Singer, F., Rosgen, T,, Latzin, P,, and Obrist, D. A ComputerModel for Single-Breath Washout with Double-Tracer Gas to Help UnderstandingVentilation Inhomogeneity. Biomedizinische Technik - Biomedical engineering, 58(Supplement 1), 2013

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[12] Radu, M.D., Pfenniger, A., Raber, L., Marchi, S.F. de, Obrist, D., Kelbk, H., Windecker, S., Ser-ruys, P.W., and Vogel, R. Flow disturbances in stent-related coronary evaginations.EuroIntervention, 9(7), 2013

226

Martin Kroger www.complexfluids.ethz.ch

Y. Li, M. Kroger, W.K. Liu, Dynamic structure of unentangled polymer chains in the vicinityof non-attractive nanoparticles,Soft Matter 10 (2014) 1723-1737.

R.J.A. Steenbakkers, C. Tzoumanekas, Y. Li, W.K. Liu, M. Kroger, J.D. Schieber, Primitive-path statistics of entangled polymers: Mapping multi-chain simulations onto single-chainmean-field models,New J. Phys. 16 (2014) 015027.

E. Cordova-Mateo, O. Bertran, B. Zhang, D. Vlassopoulos, R. Pasquino, A.D. Schluter,M. Kroger, C. Aleman, Interactions in dendronized polymers: Intramolecular dominatesintermolecular,Soft Matter 10 (2014) 1032-1044.

B. Huber, M. Harasim, B. Wunderlich, M. Kroger, A.R. Bausch, Microscopic origin of thenon-Newtonian viscosity of semiflexible polymer solutions in the semidilute regime,ACS Macro Lett. 3 (2014) 136-140.

Y.R. Sliozberg, R.A. Mrozek, J.D. Schieber, M. Kroger, J.L. Lenhart, J.W. Anzelm, Effectof polymer solvent on the mechanical properties of entangled polymer gels: Coarse-grainedmolecular simulation,Polymer 54 (2013) 2555-2564.

Y. Li, B.C. Abberton, M. Kroger, W.K. Liu, Challenges in multiscale modeling of polymerdynamics,Polymers 5 (2013) 751-832.

O. Bertran, B. Zhang, A.D. Schluter, A. Halperin, M. Kroger, C. Aleman, Computer simu-lations of dendronized polymers: organization and characterization at the atomistic level,RSC Adv. 3 (2013) 126-140.

O. Bertran, B. Zhang, A. D. Schluter, M. Kroger, C. Aleman, Computer simulation of fifthgeneration dendronized polymers: Impact of charge on internal organization,J. Phys. Chem. B 117 (2013) 6007-6017.

M. Tagliazucchi, O. Peleg, M. Kroger, Y. Rabin, I. Szleifer, Effect of charge, hydrophobicity,and sequence of nucleoporins on the translocation of model particles through the nuclearpore complex (vol 110, pg 3363, 2013),Proc. Natl. Acad. Sci. 110 (2013) 10336-10337.

M. Tagliazucchi, O. Peleg, M. Kroger, Y. Rabin, I. Szleifer, Effect of charge, hydrophobicityand sequence of nucleoporins on the translocation of model particles through the nuclearpore complex,Proc. Natl. Acad. Sci. 110 (2013) 3363-3368.

227

M. Sadati, C. Luap, B. Luthi, M. Kroger, H.C. Ottinger, Application of full flow field recon-struction to a viscoelastic liquid in a 2D cross-slot channel,J. Non-Newtonian Fluid Mech. 192 (2013) 10-19.

M. Kroger, A.D. Schluter, A. Halperin, Branching defects in dendritic molecules: Couplingefficiency and congestion effects,Macromolecules 46 (2013) 7550-7564.

M.B. Harasim, B. Wunderlich, O. Peleg, M. Kroger, A.R. Bausch, Direct observation of thedynamics of semiflexible polymers in shear flow,Phys. Rev. Lett. 110 (2013) 108302.

E. Panagiotou, M. Kroger, K.C. Millet, Writhe and mutual entanglement combine to givethe entanglement length,Phys. Rev. E 88 (2013) 062604.

228

Group of M. Luisier 1. A. Szabo, S. J. Koester, and M. Luisier, “Metal-dichalcogenide hetero-TFETs: are they a

viable option for low power electronics?”, Proceedings of the 72 Device Research Con-ference (DRC), pp. 19-20, 2014, Santa Barbara, USA, June 2014.

2. R. Rhyner and M. Luisier, “Influence of anharmonic phonon decay on self-heating in Si

nanowire transistors”, Proceedings of the International Workshop on Computational Na-noelectronics (IWCE) 17, DOI: 10.1109/IWCE.2014.6865826, 2014, Paris, France, June 2014.

3. S. Brück, M. Calderara, M. H. Bani-Hashemian, J. VandeVondele, and M. Luisier, “To-wards ab-initio simulations of nanowire field-effect transistors”, Proceedings of the Inter-national Workshop on Computational Nanoelectronics (IWCE) 17, DOI: 10.1109/IWCE.2014.6865831, 2014, Paris, France, June 2014.

4. D. Areshkin and M. Luisier, “System-dependent modified Becke-Johnson exchange for

quantum transport simulations”, Proceedings of the International Workshop on Computa-tional Nanoelectronics (IWCE) 17, DOI: 10.1109/IWCE.2014.6865841, 2014, Paris, France, June 2014.

5. M. Calderara, S. Brück, P. Ferry, and M. Luisier, “Accelerating quantum transport simula-

tions on massively parallel computing architectures”, Platform for Advanced Scientific Computing (PASC) Conference, Zurich, Switzerland, June 2014.

6. R. Rhyner and M. Luisier, “Self-Heating Effects in Ultra-Scaled Si Nanowire Transis-tors”, IEDM 2013, Washington DC, USA, December 2013.

7. A. Szabo and M. Luisier, “Full-Band Simulation of p-Type Ultra-Scaled Silicon Nanowire Transistors”, 2013 Proceedings of the European Solid-State Device Research Conference (ESSDERC), 2013, pp. 77–80, Bucharest, Romania, September 2013.

8. M. Luisier, P. Ferry, A. Kuzmin, and O. Schenk, “Accelerating nanoelectronic device si-

mulation through massive parallelization”, Theory, Modelling and Computational Me-thods for Semiconductors Workshop (TMCS IV), Manchester, England, January 2014.

9. M. Luisier and R. Rhyner, “Atomistic Simulation of Electron and Phonon Transport in

Nano-Devices”, 2013 Proceedings of the European Solid-State Device Research Con-ference (ESSDERC), 2013, pp. 308-313, Bucharest, Romania, September 2013.

10. R. Rhyner and M. Luisier, “Influence of anharmonic phonon decay on self-heating in Si

nanowire transistors”, App. Phys. Lett. 105, 062113 (2014). 11. A. Pedersen and M. Luisier, “Bowl breakout: Escaping the positive region when searching

for saddle points”, J. Chem. Phys. 141, 024109 (2014). 12. S. G. Kim, M. Luisier, T. B. Boykin, and G. Klimeck, “Computational study of hete-

229

rojunction graphene nanoribbon tunneling transistors with p-d orbital tight-binding me-thod”, App. Phys. Lett. 104, 243113 (2014).

13. R. Rhyner and M. Luisier, “Atomistic modeling of coupled electron-phonon transport in

nanowire transistors”, Phys. Rev. B 89, 235311 (2014).

14. M. Luisier, “Atomistic simulation of transport phenomena in nanoelectronic devices”, Chemical Society Reviews 43, 4357 (2014).

15. R. Rhyner and M. Luisier, “Phonon-limited low-field mobility in silicon: Quantum trans-

port vs. linearized Boltzmann Transport Equation”, J. App. Phys. 114, 223708 (2013).

230

Group of S. Mishra

Published papers

1. U.S. Fjordholm, S. Mishra and E. Tadmor, ENO reconstruction and ENO interpo-lation are stable, Found. Comput. Math, 13 (2), 2013, 139-159.

2. A. Hiltebrand and S. Mishra, Entropy stable shock capturing streamline diffusionspace-time discontinuous Galerkin (DG) methods for systems of conservation laws,Numer. Math, 126 (1), 2014, 103-151.

3. G.M. Coclite, L. Di Ruvo, J. Ernest and S. Mishra, Convergence of vanishing capil-larity approximations for scalar conservation laws with discontinuous fluxes, Netw.Heterog. Media 8 (4), 2013, 969-984

4. R. Kappeli and S. Mishra, Well-balanced schemes for the Euler equations withgravitation, J. Comput. Phys., 259, 2014, 199-219.

5. P. LeFloch and S. Mishra, Numerical methods with controlled dissipation for small-scale dependent shocks Acta Numerica, 23, 2014, 743-816

6. I. Averbukh, D. Ben-Zvi, S. Mishra and N. Barkai, Scaling morphogen gradientsduring tissue growth by a cell division rule, Development, 141, 2014, 2150-2156.

In Press

7. G. M. Coclite, S. Mishra, N. H. Risebro and F. Weber, Analysis and Numericalapproximation of Brinkmann regularization of two phase flows in porous media,Comp. GeoSci., to appear, 2014.

8. S. Mishra and L.V. Spinolo Accurate numerical schemes for approximating intitial-boundary value problems for systems of conservation laws , Jl. Hyp. Diff. Eqns.,to appear, 2014.

Preprints

9. U. Koley, S. Mishra, N. H. Risebro and F. R. Weber, Robust finite difference schemesfor a nonlinear variational wave equation modeling liquid crystals, Research report2013-43, SAM ETH Zurich.

10. R. Kappeli and S. Mishra, Structure preserving schemes, Research report 2014-02,SAM ETH Zurich.

11. A. Hiltebrand and S. Mishra, Efficient pre conditioners for a shock capturing space-time discontinuous Galerkin method for systems of conservation laws, Research re-port 2014-04, SAM ETH Zurich.

12. U. S. Fjordholm, R. Kappeli, S. Mishra and E. Tadmor, Construction of approxi-mate entropy measure valued solutions for hyperbolic systems of conservation laws.Preprint, available as arXiv:1402.0909 [math.NA].

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13. A. Hiltebrand and S. Mishra, Efficient computation of all speed flows using anentropy stable shock-capturing space-time discontinuous Galerkin method, Researchreport 2014-17, SAM ETH Zurich

14. S. Mishra, Ch. Schwab and J. Sukys, Multi-Level Monte Carlo Finite Volumemethods for uncertainty quantification of acoustic wave propagation in random het-erogeneous layered medium, Research report 2014-22, SAM ETH Zurich.

15. C. Sanchez-Linares, M. de la asuncion, M. Castro, S. Mishra and J. Sukys, Multi-level Monte Carlo finite volume method for shallow water equations with uncertainparameters applied to landslides-generated tsunamis, Research report 2014-24, SAMETH Zurich

16. P. Chandrasekhar, U. S. Fjordholm, S. Mishra and D. Ray, Entropy stable schemeson two-dimensional unstructured grids, preprint 2014.

232

Group of M. Parrinello P. Tiwary and M. Parrinello

From Metadynamics to Dynamics Phys. Rev. Lett., 111 (23), 230602 (2013), DOI: 10.1103/PhysRevLett.111.230602 O. Valsson and M. Parrinello Thermodynamical Description of a Quasi-First-Order Phase Transition from the Well-

Tempered Ensemble J. Chem. Theory Comput., 9, 5267-5276 (2013), DOI: 10.1021/ct400589f A. Barducci, M. Bonomi, M. K. Prakash and M. Parrinello Free-energy landscape of protein oligomerization from atomistic simulations” PNAS, 110 (49), E4708-E4713 (2013), DOI: 10.1073/pnas.1320077110 M. Salvalaglio, T. Vetter, M. Mazzotti and M. Parrinello Controlling and Predicting Crystal Shapes: The Case of Urea Anges. Chem. Int. Ed., 52, 13369 – 13372 (2013), DOI: 10.1002/anie.201304562

M. Salvalaglio, F. Giberti and M. Parrinello 1,3,5-Tris(4-bromophenyl)benzeneprenucleation clusters from meta-dynamics” ActaCryst., C70, 132–136 (2014), DOI:10.1107/S2053229613026946 M. Nava, M. Ceriotti, C. Dryzun and M. Parrinello Evaluating functions of positive-definite matrices using colored-noise thermostats Phys. Rev. E, 89 (2), 023302 (2014), DOI: 10.1103/PhysRevE.89.023302 Y. Ding, A. A. Hassanali and M. Parrinello Anomalous water diffusion in salt solutions PNAS, 111 (9), 3310-3315 (2014), DOI: 10.1073/pnas.1400675111 A. A. Hassanali, J. Cuny, V. Verdolino and M. Parrinello Aqueous solutions: state of the art in ab initio molecular dynamics Phil. Trans. R. Soc. A, 372, 20120482 (2014), DOI: 10.1098/rsta.2012.0482 M. Salvalaglio, P. Tiwary and M. Parrinello Assessing the Reliability of the Dynamics Reconstructed from Metadynamics J. Chem. Theory Comput., 10, 1420-1425 (2014), DOI: 10.1021/ct500040r A. A. Hassanali, F. Giberti, G. C. Sosso and M. Parrinello The role of the umbrella inversion mode in proton diffusion Chem. Phys. Lett., 599, 133-138 (2014), DOI: 10.1016/j.cplett.2014.03.034 J. F. Dama, M. Parrinello and G. A. Voth Well-Tempered Metadynamics Converges Asymptotically Phys. Rev. Lett., 112, 240602 (2014), DOI: 10.1103/PhysRevLett.112.240602

233

Group of M. Quack

S. Albert and M. Quack Höchstauflösende FTIR-Spektroskopie. Trendbericht Physikalische Chemie 2013 Nachrichten aus der Chemie 62, 313 – 318 (2014), DOI. 10.1515/nachrchem.2014.62.3.313 S. Albert, S. Bauerecker, K. Keppler, Ph. Lerch and M. Quack Synchrotron based FTIR spectroscopy of the chiral molecules CDBrClF and CHBrIF in “Proceedings of the 19th Symposium on Atomic, Cluster and Surface Physics 2014 (SASP 2014), Obergurgl, Austria, 8 to 14 February 2014”, pages 152 – 155, (D. Stock, R. Wester, P. Scheier eds., Innsbruck University Press (IUP), Innsbruck, 2014), ISBN 978-3-902936-26-4. P. Dietiker, E. Milogyadov, M. Quack, A. Schneider, G. Seyfang Two Photon IR-Laser Induced Population Transfer in NH3 – First Steps to Measure Parity Violation in Chiral Molecules in “Proceedings of the 19th Symposium on Atomic, Cluster and Surface Physics 2014 (SASP 2014), Obergurgl, Austria, 8 to 14 February 2014”, pages 226 – 229, (D. Stock, R. Wester, P. Scheier eds., Innsbruck University Press (IUP), Innsbruck, 2014), ISBN 978-3-902936-26-4. S. Albert, Ph. Lerch, M. Quack and A. Wokaun Highest resolution FTIR spectroscopy of indene (C9H8) with synchrotron radiation in “Proceedings of the 19th Symposium on Atomic, Cluster and Surface Physics 2014 (SASP 2014), Obergurgl, Austria, 8 to 14 February 2014”, pages 240 – 243, (D. Stock, R. Wester, P. Scheier eds., Innsbruck University Press (IUP), Innsbruck, 2014), ISBN 978-3-902936-26-4 O. N. Ulenikov, E. S. Bekhtereva, S. Albert, S. Bauerecker, H.-M. Niederer, and M. Quack The infrared spectrum of methane up to 12000 cm–1 in “Proceedings of the 19th Symposium on Atomic, Cluster and Surface Physics 2014 (SASP 2014), Obergurgl, Austria, 8 to 14 February 2014”, pages 244– 247, (D. Stock, R. Wester, P. Scheier eds., Innsbruck University Press (IUP), Innsbruck, 2014),, Innsbruck, 2014), ISBN 978-3-902936-26-4 O. N. Ulenikov, E. S. Bekhtereva, A. L. Fomchenko, A. G. Litvinovskaya, C. Leroy, and M. Quack On the “Expanded Local Mode” Approach Applied to the Methane Molecule: Isotopic Substitution CH3D ← CH4 and CHD3 ← CH4 Mol. Phys, 112, 2529 – 2556 (2014) M. Quack The Concept of Law and Models in Chemistry European Review, 22/Supplement S1, pp S50-S86, doi:10.1017/S106279871300077X

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M. Quack On the Emergence of Simple Structures in Complex Phenomena: Concepts and Some Numerical Examples, Adv. Chem. Phys., 157, 97 – 116 (2014) M. Quack On Biomolecular Homochirality as a Quasi-Fossil of the Evolution of Life Adv. Chem. Phys., 157, 249 – 290 (2014) M. Quack Myths, Challenges, Risks and Opportunities in Evaluating and Supporting Scientific Research in “Incentives and performance: Governance of research organizations”, I. M. Welpe, J. Wollersheim, S. Ringelhan, and M. Osterloh, M. (Eds.), Springer International Publishing, Cham (2014) Survey of the High Resolution Infrared Spectrum of Methane (12CH4 and 13CH4): Partial Vibrational Assignment Extended Towards 12000 cm−1 O. N. Ulenikov, E. S. Bekhtereva, S. Albert, S. Bauerecker, H. M. Niederer, and M. Quack J. Chem. Phys. (2014) in press

235

Group of Prof. M. Reiher

J. Gubler, A. R. Finkelmann, M. Reiher,Theoretical 57Fe Mssbauer Spectroscopy for Structure Elucidation of [Fe] Hydrogenase Ac-tive Site IntermediatesInorg. Chem., 2013, 52, 14205–14215.

E. D. Hedegard, F. Heiden, S. Knecht, E. Fromager, H. J. Aa. Jensen,Assessment of charge-transfer excitations with time-dependent, range-separated densityfunctional theory based on long-range MP2 and multiconfigurational self-consistent fieldwave functionsJ. Chem. Phys., 2013, 139, 184308.

N. H. List, C. Curutchet, S. Knecht, B. Mennucci, J. Kongsted,Toward Reliable Prediction of the Energy Ladder in Multichromophoric Systems: A Bench-mark Study on the FMO Light-Harvesting ComplexJ. Chem. Theory Comput., 2013, 9, 4928.

S. Knecht, C. M. Marian, J. Kongsted, B. Mennucci,On the Photophysics of Carotenoids: A Multireference DFT Study of PeridininJ. Phys. Chem. B, 2013, 117, 13808.

P. Tecmer, K Boguslawski, O. Legeza, M. Reiher,Unravelling the quantum-entanglement effect of noble gas coordination on the spin groundstate of CUOPhys. Chem. Chem. Phys., 2014, 16, 719–727.

S. Manab, H. Satoh, J. Hutter, H.P. Luthi, T. Laino, Y. ItoSignificant Substituent Effect on the Anomerization of Pyranosides: Mechanism of Anomer-ization and Synthesis of a 1,2-cis Glucosamine Oligomer from the 1,2-trans AnomerChem. Eur. J., 2014, 20, 124–132.

E. D. Hedegaard, S. Knecht, U. Ryde, J. Kongsted, T. Saue,Theoretical 57Fe Mssbauer spectroscopy: isomer shifts of [Fe]-hydrogenase intermediatesPhys. Chem. Chem. Phys., 2014, 16, 4853.

S. Knecht, O. Legeza, M. Reiher,Communication: Four-component density matrix renormalization groupJ. Chem. Phys., 2014, 140, 041101.

M. Mottet, P. Tecmer, K. Boguslawski, O. Legeza, M. Reiher Quantum entanglement incarbon-carbon, carbon-phosphorus and silicon-silicon bondPhys. Chem. Chem. Phys, 2014, 16, 8872–8880.

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M. T. Stiebritz,A role for [Fe4S4] clusters in tRNA recognitiona theoretical studyNucl. Acids Res., 2014, 42, 5426.

E. Ross, S. Evangelisti, A. Lagana, H.P. Luthi et alCode Interoperability and Standard Data Formats in Quantum Chemistry and QuantumDynamics: The Q5/D5Cost Data ModelJ. Comp. Chem., 2014, 35, 611–621.

T. Weymuth, M. ReiherGradient-driven molecule construction: An inverse approach applied to the design of small-molecule fixating catalystsInt. J. Quantum Chem., 2014, 114, 838–850.

A. R. Finkelmann, M. T. Stiebritz, M. Reiher,Accesibility of µ-hydride species in [FeFe] hydrogenasesChem. Sci., 2014, 5, 215–221.

M. Kory, M. Bergeler, M. Reiher and A. D. Schluter,Facile Synthesis and Theoretical Conformation Analysis of a Triazine-Based Double-DeckerRotor Molecule with Three Anthracene BladesChem. Eur. J., 2014, 20, 6934.

A. R. Finkelmann, H. M. Senn, M. Reiher,Hydrogen-Activation Mechanism of [Fe] Hydrogenase Revealed by Multi-Scale ModelingChem. Sci., 2014, 5, 4474–4482.

P. Tecmer, A. S. P. Gomes, S. Knecht, L. Visscher,Communication: Relativistic Fock-space coupled cluster study of small building blocks oflarger uranium complexesJ. Chem. Phys., 2014, 141, 041107.

T. Weymuth, E.P.A. Couzijn, P. Chen, M. ReiherNew Benchmark Set of Transition-Metal Coordination Reactions for the Assessment ofDensity FunctionalsJ. Chem. Theory Comput., 2014, 10, 3092–3103.

H. Pinto de Magalhaes, H.P. Luthi, A. Togni,Breaking Down the Reactivity of λ3-Iodanes: The Impact of Structure and Bonding onCompeting Reaction MechanismsJ. Org. Chem., 2014, 79 (17), 8374–8382.

O. Sala, H. P. Luthi, A. Togni,The solvent effect on two competing reaction mechanisms involving hypervalent iodinereagents (λ3-iodanes): Facing the limit of the stationary quantum chemical approachJ. Comput. Chem., 2014, 35, 2122–2131.

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S. Keller, M. Reiher,Determining Factors for the Accuracy of DMRGChimia, 2014, 68.

H.P. Luthi, A. TogniWhy and How it Works: The Development of Hypervalent Iodine Reagents as an Illustra-tion for the Collaboration of Chemical Synthesis with Modeling and SimulationChimia, 2014, 68, 624–628.

M. P. Haag, M. Reiher,Studying chemical reactivity in a virtual environmentFaraday Discuss., 2014, 169, DOI: 10.1039/c4fd00021h.

M. P. Haag, A. C. Vaucher, M. Bosson, S. Redon, M. Reiher,Interactive Chemical Reactivity ExplorationChemPhysChem, 2014, 15, 3301–3319.

T. Weymuth, M. Reiher,Systematic Dependence of Transition-Metal Coordination Energies on Density-FunctionalParametrizationsInt. J. Quantum Chem., 2014, DOI: 10.1002/qua.24800

A. R. Finkelmann, M. T. Stiebritz, M. Reiher,Activation barriers of oxygen transformation at the active site of [FeFe] hydrogenasesInorg. Chem., 2014, in press.

B. Simmen, E. Matyus and M. Reiher,Electric Transition Dipole Moment in pre-Born–Oppenheimer Molecular Structure TheoryJ. Chem. Phys., 2014, in press.

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Published: Allen, R.J., Norris, J.R., and Wild, M. 2013: Evaluation of multidecadal variability in CMIP5 surface solar radiation and inferred underestimation of aerosol direct effects over Europe, China, Japan, and India, J. Geophys. Res. Atmos., 118, 6311–6336, doi:10.1002/jgrd.50426. Auchmann, R., Arfeuille, F., Wegmann, J., Franke, J., Barriendos, M., Prohom, M., Sanchez-Lorenzo, A., Bhend, J., Wild, M., Folini, D., Stepanek, P., and Brönnimann, S. 2013: Impact of volcanic stratospheric aerosols on diurnal temperature range (DTR) in Europeover the past 200 years:Observations versusmodel simulations, J. Geophys. Res. Atmos., 118, 9064–9077, doi:10.1002/jgrd.50759. Ban, N., J. Schmidli, and C. Schär (2014), Evaluation of the convection-resolving regional climate modeling approach in decade-long simulations, J. Geophys. Res. Atmos., 119, 7889–7907, doi:10.1002/2014JD021478 Bellprat, O., S. Kotlarski, D. Lüthi, and C. Schär, 2014: Physical constraints for temperature biases in climate models, Geophys. Res. Lett., 40, 4042–4047, doi:10.1002/grl.50737. Bichet, A., Folini, D., Wild, M., and Schär, C., 2014: Enhanced Central European summer precipitation in the late 19th century: A link to the Tropics. Quart. J. Roy. Met. Soc., 140, 111-123, DOI: 10.1002/qj.2111. Bosshard, T., Kotlarski, S., Zappa, M., and Schär, C., 2014: Hydrological Climate-Impact Projections for the Rhine River: GCM–RCM Uncertainty and Separate Temperature and Precipitation Effects. J. Hydrometeor, 15, 697–713. doi: 10.1175/JHM-D-12-098.1 Bosshard, T., Carambia, M., Görgen, K., Kotlarski, S., Krahe, P., Zappa, M., Schär, C., 2013: Quantifying uncertainty sources in an ensemble of hydrological climate-impact projections.Water Resour. Res. 49, 3: 1523-1536. doi:10.1029/2011WR011533 Calisto, M., Folini, D., Wild, M., and Bengtsson, L., 2014: Cloud radiative forcing intercomparison between fully coupled CMIP5 models and CERES satellite data, Ann. Geophys., 32, 793-807, doi:10.5194/angeo-32-793-2014, 2014. Cherian, R., Quaas, J., Salzmann, M., Wild, M., 2014: Pollution trends over Europe constrain global aerosol forcing as simulated by climate models, Geophys. Res. Lett., 41, 2176-2181 DOI: 10.1002/2013GL058715. Emanuel, K., Solomon, S., Folini, D., Davis, S., and Cagnazzo, C., 2013: Influence of Tropical Tropopause Layer Cooling on Atlantic Hurricane Activity, J. Clim., 26, 7, Doi:10.1175/JCLI-D-12-00242.1 Gobiet, A., S. Kotlarski, M. Beniston, G. Heinrich, J. Rajczak, M. Stoffel, 2014: 21st century climate change in the European Alps — a review, Sci Total Environ, 493, 1138–1151. DOI: 10.1016/j.scitotenv.2013.07.050 Jacob, D. and ... and Kotlarski, S. and ..., 2013: EURO-CORDEX: New high-resolution climate change projections for European impact research, Reg. Environ. Change, 14, 563-578. doi: 10.1007/s10113-013-0499-2 Kothe, S., Lüthi, D. and Ahrens, B., 2014: Analysis of the West African Monsoon system in the regional climate model COSMO-CLM. Int. J. Climatol., 34, 481–493. doi: 10.1002/joc.3702 Kotlarski, S., Keuler, K., Christensen, O. B., Colette, A., Déqué, M., Gobiet, A., Goergen, K., Jacob, D., Lüthi, D., van Meijgaard, E., Nikulin, G., Schär, C., Teichmann, C., Vautard, R., Warrach-Sagi, K., and Wulfmeyer, V., 2014: Regional climate modeling on European scales: a joint standard evaluation of the EURO-CORDEX RCM ensemble, Geosci. Model Dev., 7, 1297-1333, doi:10.5194/gmd-7-1297-2014, 2014

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Group of C. Schär

http://dx.doi.org/10.1175/JHM-D-12-098.1

Langhans, W., J. Schmidli, O. Fuhrer, S. Bieri and C. Schär, 2013: Long-Term Simulations of Thermally Driven Flows and Orographic Convection at Convection-Parameterizing and Cloud-Resolving Resolutions. J. Appl. Meteor. Climatol., 52, 1490–1510. doi: 10.1175/JAMC-D-12-0167.1 Ma, Q., Wang, K. C., and Wild, M., 2014: Evaluation of atmospheric downward longwave radiation from 44 coupled general circulation models of CMIP5, J. Geophys. Res. Atmos., 119, 4486–4497, doi:10.1002/2013JD021427. Panitz, H.-J., A. Dosio, M. Büchner, D. Lüthi, K. Keuler, 2013: COSMO-CLM (CCLM) climate simulations over CORDEX Africa domain: analysis of the ERA-Interim driven simulations at 0.44° and 0.22° resolution., Clim. Dyn., 42, 3015-3038. doi: 10.1007/s00382-013-1834-5 Possner, A., E. Zubler, O. Fuhrer, U. Lohmann and C. Schär, 2014: A Case Study in Modeling Low-Lying Inversions and Stratocumulus Cloud Cover in the Bay of Biscay. Wea. Forecasting, 29, 289–304. doi: 10.1175/WAF-D-13-00039.1 Schaller, N., Cermak, J., Wild, M., and Knutti, R. 2013: The sensitivity of the modeled energy budget and hydrological cycle to CO2 and solar forcing, Earth Syst. Dynam., 4, 253-266, doi:10.5194/esd-4-253-2013. Schmidli, J., 2013: Daytime Heat Transfer Processes over Mountainous Terrain. J. Atmos. Sci., 70, 4041–4066. doi: 10.1175/JAS-D-13-083.1 Steger, C., Kotlarski, S., Jonas, T. and Schär, C., 2013: Alpine snow cover in a changing climate: a regional climate model perspective. Clim. Dyn., 41, 735-754. doi: 10.1007/s00382-012-1545-3 Vautard, R. and ... Kotlarski, S. and ..., 2013: The simulation of European heat waves from an ensemble of regional climate models within the EURO-CORDEX project. Clim. Dyn., 41, 2555-2575. doi: 10.1007/s00382-013-1714-z Wegmann, M., Bronnimann, S., Bhend, J., Franke, J., Folini, D., Wild, M., and Luterbacher, J., 2014: Volcanic Influence on European Summer Precipitation through Monsoons: Possible Cause for "Years without Summer'', J. Climate, 27, 3683-3691, doi: 10.1175/JCLI-D-13-00524.1. Wild M., Folini D., Schär C., Loeb N., Dutton E.G., and König-Langlo G., 2013: The global energy balance from a surface perspective. Clim. Dyn., 40, 3107–3134, DOI 10.1007/s00382-012-1569-8 You, Q., Sanchez-Lorenzo, A., Wild, M., Folini, D., Fraedrich, K., Ren, G., and Kang, S., 2013: Decadal variation of surface solar radiation in the Tibetan Plateau from observations, reanalysis and model simulations, Clim. Dyn., 40, 2073-2086, DOI: 10.1007/s00382-012-1383-3. In press, accepted, submitted: Ban, N., J. Schmidli, and C. Schär, 2014: Heavy precipitation in a changing climate: Does short-term summer precipitation increase faster? (submitted) Chiacchio,, M., Solmon,, F., Giorgi,, F., Stackhouse, P., Wild, M., 2014: Evaluation of the radiation budget with a regional climate model over Europe and inspection of dimming and brightening (submitted). Dosio, A. and Panitz, H.-J. and Schubert-Frisius, M. and Lüthi, D., 2014: Dynamical downscaling of CMIP5 global circulation models over CORDEX-Africa with COSMO-CLM: evaluation over the present climate and analysis of the added value, Clim. Dyn., (in press). Hassanzadeh, H., J. Schmidli, W. Langhans, L. Schlemmer, C. Schär, 2014: Impact of topography on diurnal cycle of summertime moist convection in idealized simulations. (submitted)

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Nabat, P., Somot, S., Mallet, M., Sanchez-Lorenzo, A., and Wild, M., 2014: Contribution of anthropogenic sulfate aerosols to the changing Euro-Mediterranean climate since 1980, Geophys. Res. Lett., DOI: 10.1002/2014GL060798 (in press). Nabat, P., Somot, S., Mallet, M., Sevault, F., Chiacchio, M., and Wild, M., 2013: Direct and semi-direct aerosol radiative effect on the Mediterranean climate variability using a coupled Regional Climate System Model, Clim. Dyn., (in press). Possner, A., Zubler, E., Lohmann, U., and Schär, C., 2014: Real-case simulations of aerosol-cloud interactions in ship tracks over the Bay of Biscay, Atmos. Chem. Phys. Discuss., 14, 26721-26764, doi:10.5194/acpd-14-26721-2014. (submitted) Prein, A.F, W. Langhans, G. Fosser, A. Ferrone, N. Ban, K. Goergen, M. Keller, M. Tölle, O. Gutjahr, F. Feser, E. Brisson, S. Kollet, J. Schmidli, N.P.M. van Lipzig, R.L. Leung, 2014: A review of convection permitting climate modelling: Demonstrations, prospects, and challenges. (submitted) Wild, M. Folini, D., Hakuba, M., Schär, C., Seneviratne, S., Loeb, N.G., Rutan, D., Kato, S., and König-Langlo, G, 2014: The energy balance over land and sea: An assessment based on direct observations and CMIP5 models (submitted).

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Group of Prof. Dr. Christoph Schwab

A. Buffa and G. Sangalli and Ch. SchwabExponential convergence of the hp version of isogeometric analysis in 1D.Proc. ICOSAHOM2012, Carthage Tunisia, 95 (2014) , pp. 191-203, SAM Report 2012-39.

P. Chen and Ch. SchwabSparse grid, reduced basis approximation of Bayesian inverse problems.Seminar of Applied Mathematics, ETH Zurich, 2014, preprint.

A. Chkifa and A. Cohen and Ch. SchwabHigh-Dimensional Adaptive Sparse Polynomial Interpolation and Applications to Para-metric PDEs.Journ. Found. Comp. Math., 14/4 (2014) , pp. 601-633, SAM Report 2012-22

A. Cohen and A. Chkifa and Ch. SchwabBreaking the curse of dimensionality in sparse polynomial approximation of parametricPDEs.Journ. Math. Pures et Appliquees (2014), SAM Report 2013-25

J. Dick and Q.T. LeGia and Ch. SchwabHigher order Quasi Monte Carlo integration for holomorphic, parametric operator equa-tions.(in review)

J. Dick and F.Y. Kuo and Q.T. LeGia and Ch. SchwabMulti-level higher order QMC Galerkin discretization for affine parametric operator equa-tions.(submitted)

J. Dolz and H. Harbrecht and Ch. SchwabCovariance regularity and H-matrix approximation for rough random fields.(submitted)

M. Eigel and C. J. Gittelson and Ch. Schwab and E. ZanderA convergent adaptive stochastic Galerkin finite element method with quasi-optimal spa-tial meshes.(submitted)

M. Eigel and C.J. Gittelson and Ch. Schwab and E. ZanderAdaptive stochastic Galerkin FEM.Comp. Meth. Appl. Mech. Engg., 270 (2014) , pp. 247-269, SAM Report 2013-01.

R.N. Gantner, C. Schillings and Ch. Schwab.Binned Multilevel Monte Carlo for Bayesian Inverse Problems with Large Data.Proc. Intl. Conf. Domain Decomposition DD22, (2014) (submitted).

242

R.N. Gantner and Ch. Schwab.Computational Higher Order Quasi-Monte Carlo Integration.(in review)

C.J. Gittelson and R. Andreev and Ch. SchwabOptimality of Adaptive Galerkin methods for random parabolic partial differential equa-tions.Journal of Computational and Applied Mathematics, 263 (2014) , pp. 189-201, SAMReport 2013-09

R. Guberovic and Ch. Schwab and R. StevensonSpace-time variational saddle point formulations of Stokes and Navier-Stokes equations.ESAIM: Mathematical Modelling and Numerical Analysis, 48/3 (2014) , pp. 875-894,SAM Report 2011-66

L. HerrmannIsotropic random fields on the sphere – regularity of random elliptic PDEsMaster’s thesis, ETH Zurich, 2013

L. Herrmann, A. Lang and Ch. Schwabin preparation

V.H. Hoang and Ch. Schwab and A.M. StuartSparse MCMC gpc Finite Element Methods for Bayesian Inverse Problems.Inverse Problems (2014), SAM Report 2012-23

V.H. Hoang and Ch. SchwabN-term Wiener Chaos Approximation Rates for elliptic PDEs with lognormal Gaussianrandom inputs.Math. Mod. Meth. Appl. Sci. , 24/4 (2014) , pp. 797-826, SAM Report 2011-59

V. Kazeev, M. Khammash, M. Nip, and Ch. SchwabDirect solution of the Chemical Master Equation using Quantized Tensor TrainsTechnical Report 3, March 2014.

V. Kazeev and I. OseledetsThe tensor structure of a class of adaptive algebraic wavelet transformsResearch Report 28, Seminar for Applied Mathematics, ETH Zurich, 2013

V. Kazeev, O. Reichmann, and Ch. Schwabhp-DG-QTT solution of high-dimensional degenerate diffusion equationsReport 11, Seminar for Applied Mathematics, ETH Zurich, 2012

V. Kazeev, O. Reichmann, and Ch. SchwabLow-rank tensor structure of linear diffusion operators in the TTand QTT formatsLinear Algebra and its Applications, 438(11):4204–4221, 2013

V. Kazeev and Ch. SchwabTensor approximation of stationary distributions of chemical reaction networksResearch Report 18, Seminar for Applied Mathematics, ETH Zurich, 2013

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R. Kornhuber and Ch. Schwab and M. WolfMulti-Level Monte-Carlo Finite Element Methods for stochastic elliptic variational in-equalities.SIAM J. Numerical Analysis (2014) , SAM Report 2013-12

S. Mishra and Ch. Schwab and J. SukysMulti-Level Monte Carlo Finite Volume methods for uncertainty quantification of acousticwave propagation in random heterogeneous layered medium.(submitted)

F. Muller and Ch. SchwabFinite Elements with mesh refinement for elastic wave propagation in polygons.under review.

F. Muller and Ch. SchwabFinite Elements with mesh refinement for wave equations in polygonsSeminar for applied Mathematics, ETH Zurich, 2013, Report 11.

Ch. Schwab and C. SchillingsSparse Quadrature Approach to Bayesian Inverse Problems.Oberwolfach-Report 2014 (accepted)

C. Schillings and Ch. Schwab.Sparsity in Bayesian inversion of parametric operator equations.Inverse Problems, 30 (2014), p. 065007.

C. Schillings and Ch. Schwab.Scaling Limits in Computational Bayesian Inversion.(in preparation).

C. Schillings, Ch. Schwab, J. Stelling, M. Sunnaker.Efficient Characterization of Parametric Uncertainty of Complex (Bio)chemical Networks(in preparation).

D. Schotzau and Ch. Schwab and T. Wihler and M. WirzExponential convergence of hp-DGFEM for elliptic problems in polyhedral domains.Proc. ICOSAHOM2012, Carthage Tunisia, 95 (2014) , pp. 57-73, SAM Report 2012-40

Ch. SchwabExponential convergence of simplicial hp-FEM for H1-functions with isotropic singulari-ties.(in review)

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Publication list 2013-14

Group name: Geophysical Fluid Dynamics, D-ERDW (Prof. P. J. Tackley)

Baitsch-Ghirardello, B., Stracke, A., Connolly, J.A.D., Nikolaeva, K.M., Gerya, T.V. (2014)Lead transport in intra-oceanic subduction zones: 2D geochemical–thermo-mechanicalmodeling of isotopic signatures. Lithos, 208–209, 265-280.

Bello, L., N. Coltice, T. Rolf and P. J. Tackley, On the predictability limit of convection models of the Earth's mantle, Geochem. Geophys. Geosys., doi:10.1002/2014GC005254 (2014).

Burov, E., Gerya, T. (2014) Asymmetric three-dimensional topography over mantle plumes.Nature, 513, 85–89.

Collignon, M., B. J. P. Kaus, D. A. May & N. Fernandez, “Influences of surface processes onfold growth during 3-D detachment folding”, Geochemistry, Geophysics, Geosystems, 15 (18), 3281–3303, 2014, DOI: 10.1002/2014GC005450.

Coltice, N., T. Rolf and P. J. Tackley, Seafloor spreading evolution in response to continentalgrowth (2014), Geology, doi:10.1130/G35062.1.

Coltice, N., M. Seton, T. Rolf, R.D. Müller and P.J. Tackley (2013) Convergence of tectonic reconstructions and mantle convection models for significant fluctuations in seafloor spreading, Earth Planet. Sci. Lett. 383, 92-100, doi:10.1016/j.epsl.2013.09.032.

Crameri, F. and P. J. Tackley, Spontaneous development of arcuate single-sided subduction inglobal 3-D mantle convection models with a free surface, J. Geophys. Res., 119(7), 5921-5942, doi:10.1001/2014JB010939 (2014).

Dymkova, D., Gerya, T. (2013) Porous fluid flow enables oceanic subduction initiation onEarth. Geophysical Research Letters, 40, 5671–5676.

Duretz, T., Gerya, T.V., Spakman, W. (2014) Slab detachment in laterally varying subductionzones: 3-D numerical modeling. Geophysical Research Letters, 41, 1951-1956.

Fox, M., L. Goren, D. A. May and S. D. Willett, “Inversion of fluvial channels for paleo-rockuplift rates in Taiwan”, Journal of Geophysical Research: Earth Surface, 2014, DOI: 10.1002/2014JF003196.

Gerya, T.V. (2014) Plume-induced crustal convection: 3D thermomechanical model andimplications for the origin of novae and coronae on Venus. EPSL, 391, 183-192.

Gillmann, C. and P. J. Tackley, Atmosphere/mantle coupling and feedbacks on Venus, J. Geophys. Res., doi:10.1002/2013JE004505 (2014).

Golabek, G.J., Bourdon, B., Gerya, T.V. (2014) Numerical models of the thermomechanicalevolution of planetesimals: Application to the acapulcoite-lodranite parent body. Meteoritics& Planetary Science, 49, 1083-1099.

245

Gorczyk, W., Hobbs, B., Gessner, K., Gerya, T. (2013) Intracratonic geodynamics. Gondwana Research, 24, 838-848.

Lechmann, S. M. Schmalholz, G. Hetenyi, D. A. May & B. J. P. Kaus, “Quantifying the impact of mechanical layering and underthrusting on the dynamics of the modern India-Asia collisional system with 3-D numerical models”, Journal of Geophysical Research-Solid Earth, 119 (1), 616–644, 2014, DOI: 10.1002/2012JB009748.

Li, Y., F. Deschamps and P. J. Tackley (2014) Effects of low-viscosity post-perovskite on the stability and structure of primitive reservoirs in the lower mantle, Geophys. Res. Lett. 41, doi:10.1002/2014GL061362.

Li, Y., F. Deschamps and P. J. Tackley (2014) The stability and structure of primordial reservoirs in the lower mantle: insight from models of thermo-chemical convection in spherical geometry, Geophys. J. Int., 199(2), 914-930, doi:10.1093/gji/ggu295.

Liao, J., Gerya, T.V., Wang, Q. (2013) Layered structure of the lithospheric mantle changesdynamics of craton extension. Geophys. Res. Lett., 40, 1-6.

Liao, J., Gerya, T. (2014) Influence of lithospheric mantle stratification on craton extension:Insight from two-dimensional thermo-mechanical modeling. Tectonophysics, 631, 50–64.

Lobanov, I.S., Popov, I.Yu., Popov, A.I., Gerya, T.V. (2014) Numerical approach to the Stokesproblem with high contrasts in viscosity. Applied Mathematics and Computation, 235, 17-25.

May, D. A., J. Brown & L. Le Pourhiet, “pTatin3D: High-Performance Methods for Long-Term Lithospheric Dynamics”, Published in: SC ’14 Proceedings of the International Conference for High Performance Com- puting, Networking, Storage and Analysis , 274–284, 2014, DOI: 10.1109/SC.2014.28.

Manea,V.C., Leeman, W.P., Gerya, T., Manea, M., Zhu, G. (2014) Subduction of fracturezones controls mantle melting and geochemical signature above slabs. NatureCommunications, 5, Article number: 5095.

Marques, F.O., Cabral, F.R., Gerya, T.V., Zhu, G., May, D.A. (2014) Subduction initiates atstraight passive margins. Geology, 42, 331-334.

Nakagawa, T. and P. J. Tackley (2014), Influence of combined primordial layering and recycled MORB on the coupled thermal evolution of Earth's mantle and core, Geochem. Geophys. Geosyst. 15. 619-633, doi:10.1002/2013GC005128.

Popov, I.Yu., Lobanov, I.S., Popov, S.I., Popov, A.I., Gerya, T.V. (2014) Practical analyticalsolutions for benchmarking of 2-D and 3-D geodynamic Stokes problems with variableviscosity. Solid Earth, 5, 461–476.

Rolf, T., N. Coltice and P. J. Tackley (2014), Statistical cyclicity of the supercontinent cycle, Geophys. Res. Lett. 41, doi:10.1002/2014GL059595.

246

Rozel, A., J. Besserer, G. J. Golabek, M. Kaplan, T. W. Becker and P. J. Tackley (2014), Self-consistent generation of single plume state for Enceladus using non-Newtonian rheology, J. Geophys. Res. (2014)

Ruh, J.B., Gerya, T., Burg, J-P. (2014) 3D effects of strain vs. velocity weakening ondeformation patterns in accretionary wedges. Tectonophysics, 615, 122-141.

Sternai, P., Jolivet, L., Menant, A., Gerya, T. (2014) Driving the upper plate surfacedeformation by slab rollback and mantle flow. Earth and Planetary Science Letters, 405, 110-118.

Thielmann, M., D. A. May & B. J. P. Kaus, “Discretization errors in the hybrid finite elementparticle-in-cell method”, Pure and Applied Geophysics, 171, 2165–2184, 2014, DOI: 10.1007/s00024-014-0808-9.

van Dinther, Y., Gerya, T.V., Dalguer, L.A., Mai, P.M., Morra, G., Giardini, D. (2013) Theseismic cycle at subduction thrusts: Insights from seismo-thermo-mechanical models. J.Geophys. Res., 118, 1502–1525.

van Dinther, Y., Gerya, T.V., Dalguer, L.A., Corbi, F., Funiciello, F., Mai, P.M. (2014)Modeling the seismic cycle in subduction zones: The role and spatiotemporal occurrence ofoff-megathrust earthquakes. Geophysical Research Letters, 41, 1194-1201.

Vogt, K., Castro, A., Gerya, T. (2013) Numerical modeling of geochemical variations causeby crustal relamination, G3, 14, 470–487). Geochem. Geophys. Geosys., 14, 1131–1155.

Vogt, K., Gerya, T. (2014) Deep plate serpentinization triggers skinning of subducting slabs.Geology, 42, 723-726.

Yao, C., F. Deschamps, J. Lowman, C. Sanchez-Valle and P. J. Tackley (2014) Stagnant-lid convection in bottom-heated thin 3-D spherical shells: influence of curvature and implications for dwarf planets and icy moons, J. Geophys. Res. 119, 1895-1913, doi:10.1002/2014JE004653.

Submitted or in press

Crameri, F. and P. J. Tackley, Parameters controlling dynamically self-consistent plate tectonics and single-sided subduction in global models of mantle convection, J. Geophys. Res.

Petersen, R. I., D. Stegman and P.J. Tackley, A regime diagram of mobile lid convection with plate-like behavior, Phys. Earth Planet. Inter..

Leone, G., P. J. Tackley, T. V. Gerya, D. May and G. Zhu, 3-D simulations of the southernpolar giant impact hypothesis for the origin of the martian dichotomy, Geophys. Res. Lett.

247

Group of M. Troyer

Bela Bauer, Roman M. Lutchyn, Matthew B. Hastings, Matthias TroyerEffect of thermal fluctuations in topological p-wave superconductorsPhys. Rev. B 87, 014503 (2013)

Didier Poilblanc, Adrian Feiguin, Matthias Troyer, Eddy Ardonne, Parsa BondersonOne-dimensional itinerant interacting non-Abelian anyonsPhys. Rev. B 87, 085106 (2013)

T. Uehlinger, D. Greif, G. Jotzu, L. Tarruell, T. Esslinger, Lei Wang, M. TroyerDouble transfer through Dirac points in a tunable honeycomb optical latticeEur. Phys. J. Special Topics 217, 12 (2013)

Lei Wang, Alexey A. Soluyanov, Matthias TroyerDirect measurement of topological invariants in optical latticesPhys. Rev. Lett. 110, 166802 (2013)

Bela Bauer and Liza Huijse and Erez Berg and Matthias Troyer and Kareljan SchoutensStrong finite-size corrections for lattice fermions at a supersymmetric multicritical pointPreprint, Phys. Rev. B 87, 165145 (2013)

E. Kozik, E. Burovski, V.W. Scarola, M. TroyerNéel temperature and thermodynamics of the half-filled 3D Hubbard model by DiagrammaticDeterminant Monte CarloPhys. Rev. B 87, 205102 (2013)

C. Gils, E. Ardonne, S. Trebst, D.A. Huse, A.W.W. Ludwig, Matthias Troyer, Z. WangAnyonic quantum spin chains: Spin-1 generalizations and topological stabilityPhys. Rev. B. 87, 235120 (2013)

Paul Fendley, Sergei V. Isakov, Matthias TroyerFibonacci topological order from quantum netsPhys. Rev. Lett. 110, 260408 (2013)

Lei Wang, Matthias Troyer, Xi DaiTopological charge pumping in a one-dimensional optical latticePhys. Rev. Lett. 111, 026802 (2013)

Hsiang-Hsuan Hung, Lei Wang, Zheng-Cheng Gu, Gregory A. Fiete Topological phase transition in a generalized Kane-Mele-Hubbard model: A combined Quantum Monte Carlo and Green’s function study. Phys. Rev. B, 87, 121113, (2013).

248

http://arxiv.org/find/cond-mat/1/au:+Wang_Z/0/1/0/all/0/1

http://arxiv.org/find/cond-mat/1/au:+Troyer_M/0/1/0/all/0/1

http://arxiv.org/find/cond-mat/1/au:+Ludwig_A/0/1/0/all/0/1

http://arxiv.org/find/cond-mat/1/au:+Huse_D/0/1/0/all/0/1

http://arxiv.org/find/cond-mat/1/au:+Trebst_S/0/1/0/all/0/1

http://arxiv.org/find/cond-mat/1/au:+Ardonne_E/0/1/0/all/0/1

http://arxiv.org/find/cond-mat/1/au:+Gils_C/0/1/0/all/0/1


http://arxiv.org/find/cond-mat/1/au:+Soluyanov_A/0/1/0/all/0/1

http://arxiv.org/find/cond-mat/1/au:+Wang_L/0/1/0/all/0/1


http://arxiv.org/find/cond-mat/1/au:+Wang_L/0/1/0/all/0/1

http://arxiv.org/find/cond-mat/1/au:+Esslinger_T/0/1/0/all/0/1

http://arxiv.org/find/cond-mat/1/au:+Tarruell_L/0/1/0/all/0/1

http://arxiv.org/find/cond-mat/1/au:+Jotzu_G/0/1/0/all/0/1

http://arxiv.org/find/cond-mat/1/au:+Greif_D/0/1/0/all/0/1

http://arxiv.org/find/cond-mat/1/au:+Uehlinger_T/0/1/0/all/0/1


http://arxiv.org/find/cond-mat/1/au:+Hastings_M/0/1/0/all/0/1

http://arxiv.org/find/cond-mat/1/au:+Lutchyn_R/0/1/0/all/0/1

http://arxiv.org/find/cond-mat/1/au:+Bauer_B/0/1/0/all/0/1

Lei Wang, Alexey A. Soluyanov and Matthias Troyer, Proposal for direct measurement of topological invariants in optical lattices. Phys. Rev. Lett., 110, 166802, (2013).

Bela Bauer and Liza Huijse and Erez Berg and Matthias Troyer and Kareljan SchoutensStrong finite-size corrections for lattice fermions at a supersymmetric multicritical pointPreprint, Phys. Rev. B 87, 165145 (2013)

S. Boixo, T. Rønnow, S. Isakov, Z.H. Wang, D. Wecker, D. Lidar, J. Martinis, M. TroyerEvidence for Quantum annealing on more than a hundred qubitsNature Physics 10, 218 (2014)

Johannes Schachenmayer, Lode Pollet, Matthias Troyer, Andrew John DaleySpontaneous emissions and thermalization of cold bosons in optical latticesPhys. Rev. A 89, 011601 (2014)

S. Pilati, I. Zintchenko, M. TroyerFerromagnetism of a Repulsive Atomic Fermi gas in an Optical Lattice: a Quantum Monte Carlo study Phys. Rev. Lett. 112, 015301 (2014)

Lei Wang, Matthias TroyerSeeing Hofstadter's Butterfly in Atomic Fermi GasesPhys. Rev. A 89, 011603 (2014)

Jakub Imriška, Mauro Iazzi, Lei Wang, Emanuel Gull, Daniel Greif, Thomas Uehlinger, Gregor Jotzu, Leticia Tarruell, Tilman Esslinger, Matthias TroyerThermodynamics and magnetic properties of the anisotropic 3D Hubbard modelPhys. Rev. Lett. 112, 115301 (2014)

T. T. Nguyen, A. J. Herrmann, M. Troyer, S. PilatiCritical Temperature of Interacting Bose Gases in Periodic PotentialsPhys. Rev. Lett. 112, 170402 (2014)

Iztok Pizorn, Viktor Eisler, Sabine Andergassen, Matthias TroyerReal time evolution at finite temperatures with operator space matrix product statesNew J. Phys. 16, 073007 (2014)

Hiroshi Shinaoka, Michele Dolfi, Matthias Troyer, Philipp WernerHybridization expansion Monte Carlo simulation of multi-orbital quantum impurity problems: matrix product formalism and improved Monte Carlo samplingJ. Stat. Mech., P0601 (2014)

Philippe Corboz, T. M. Rice, Matthias TroyerCompeting states in the t-J model: uniform d-wave state versus stripe statePhys. Rev. Lett. 113, 046402 (2014)

249

http://arxiv.org/find/cond-mat/1/au:+Werner_P/0/1/0/all/0/1


http://arxiv.org/find/cond-mat/1/au:+Dolfi_M/0/1/0/all/0/1

http://arxiv.org/find/cond-mat/1/au:+Shinaoka_H/0/1/0/all/0/1

Troels F. Rønnow, Zhihui Wang, Joshua Job, Sergio Boixo, Sergei V. Isakov, David Wecker, John M. Martinis, Daniel A. Lidar, Matthias TroyerDefining and detecting quantum speedupScience 345, 420 (2014)

Dave Wecker, Bela Bauer, Bryan K. Clark, Matthew B. Hastings, Matthias TroyerCan quantum chemistry be performed on a small quantum computer?Phys. Rev. A 90, 022305 (2014)

M. Dolfi, B. Bauer, S. Keller, A. Kosenkov, T. Ewart, A. Kantian, T. Giamarchi, M. TroyerMatrix Product State applications for the ALPS projectComputer Physics Communications 185, 3430 (2014).

M. B. Hastings, D. Wecker, B. Bauer, M. TroyerImproving Quantum Algorithms for Quantum ChemistryQuantum Information and Communication (in press)

Lei Wang, Matthias TroyerRenyi Entanglement Entropy of Interacting Fermions Calculated Using Continuous-Time Quantum Monte Carlo MethodPhys. Rev. Lett. 113, 110401 (2014)

D. Poulin, M. B. Hastings, D. Wecker, N. Wiebe, A. C. Doherty, Matthias TroyerThe Trotter Step Size Required for Accurate Quantum Simulation of Quantum ChemistryQuantum Information and Communication (in press)

M. O. J. Heikkinen, D.-H. Kim, M. Troyer, P. TörmäNon-local quantum fluctuations and fermionic superfluidity in the attractive Hubbard modelPhys. Rev. Lett. 113, 185301 (2014)

Lei Wang, Philippe Corboz, Matthias TroyerFermionic Quantum Critical Point of Spinless Fermions on a Honeycomb LatticeNew J. Phys. 16, 103008 (2014)

J. Gukelberger, E. Kozik, L. Pollet, N.V. Prokof'ev, M. Sigrist, B.V. Svistunov, M. Troyerp-wave Superfluidity by Spin-Nematic Fermi Surface DeformationPhys. Rev. Lett. 113, 195301 (2014)

Lei Wang, Hsiang-Hsuan Hung, Matthias TroyerTopological Phase Transition in the Hofstadter-Hubbard ModelPhys. Rev. B 90, 205111 (2014)

Juan Osorio Iregui, Philippe Corboz, Matthias TroyerProbing the stability of the spin liquid phases in the Kitaev-Heisenberg model using tensor network algorithmsPhys. Rev. B (in press)

250


http://arxiv.org/find/cond-mat/1/au:+Svistunov_B/0/1/0/all/0/1

http://arxiv.org/find/cond-mat/1/au:+Sigrist_M/0/1/0/all/0/1

http://arxiv.org/find/cond-mat/1/au:+Prokofev_N/0/1/0/all/0/1

http://arxiv.org/find/cond-mat/1/au:+Pollet_L/0/1/0/all/0/1

http://arxiv.org/find/cond-mat/1/au:+Kozik_E/0/1/0/all/0/1

http://arxiv.org/find/cond-mat/1/au:+Gukelberger_J/0/1/0/all/0/1

S.V. Isakov, I.N. Zintchenko, T.F. Rønnow, M. TroyerOptimized simulated annealing for Ising spin glassesPreprint

M. Dolfi, J. Gukelberger, A. Hehn, J. Imriška, K. Pakrouski, T. F. Rønnow, M. Troyer, I. Zintchenko, F. Chirigati, J. Freire, D. ShashaA model project for reproducible papers: critical temperature for the Ising model on a squarelatticePreprint

Arash Bellafard, Sudip Chakravarty, Matthias Troyer, Helmut G. KatzgraberThe effect of quenched bond disorder on first-order phase transitionsPreprint

Mauro Iazzi, Alexey Soluyanov and Matthias TroyerTopological origin of the fermionic sign problemPreprint, submitted to Phys. Rev. Lett

Ilia Zintchenko, Matthew B. Hastings, Matthias TroyerFrom local to global ground states in Ising spin glassesPreprint, submitted to Phys. Rev. B

Johannes Schachenmayer, Lode Pollet, Matthias Troyer, Andrew J. DaleyThermalization of strongly interacting bosons after spontaneous emissions in optical latticesPreprint, submitted to EPJ-ST

Michele Dolfi, Adrian Kantian, Bela Bauer and Matthias TroyerMinimizing Non-Adiabadicities In Optical Lattice LoadingPreprint, submitted to Phys. Rev. Lett.

Mauro Iazzi and Matthias TroyerEfficient continuous-time quantum Monte Carlo algorithm for fermionic lattice modelsPreprint, submitted to Phys. Rev. Lett

Bettina Heim, Troels F. Rønnow, Sergei V. Isakov, and Matthias TroyerQuantum versus Classical Annealing of Ising Spin GlassesPreprint

Tameem Albash, Troels F. Rønnow, Matthias Troyer, Daniel A. LidarReexamining classical and quantum models for the D-Wave One processorPreprint, submitted to EJP

Hiroshi Shinaoka, Rei Sakuma, Philipp Werner, Matthias TroyerAccuracy of downfolding based on the constrained random phase approximationPreprint, submitted to Phys. Rev. B

251

http://arxiv.org/find/quant-ph/1/au:+Lidar_D/0/1/0/all/0/1

http://arxiv.org/find/quant-ph/1/au:+Troyer_M/0/1/0/all/0/1

http://arxiv.org/find/quant-ph/1/au:+Ronnow_T/0/1/0/all/0/1

http://arxiv.org/find/quant-ph/1/au:+Albash_T/0/1/0/all/0/1

http://arxiv.org/find/cond-mat/1/au:+Daley_A/0/1/0/all/0/1


http://arxiv.org/find/cond-mat/1/au:+Pollet_L/0/1/0/all/0/1

http://arxiv.org/find/cond-mat/1/au:+Schachenmayer_J/0/1/0/all/0/1


http://arxiv.org/find/cond-mat/1/au:+Hastings_M/0/1/0/all/0/1

http://arxiv.org/find/cond-mat/1/au:+Zintchenko_I/0/1/0/all/0/1

[222] K. Pakrouski, M.R. Peterson, T. Jolicoeur, V.W. Scarola, C. Nayak, Matthias TroyerThe Phase Diagram of the =5/2 Fractional Quantum Hall Effect: Effects of Landau Level νMixing and Non-Zero WidthPreprint, submitted to Phys. Rev. X

252

Group of W.F. van Gunsteren W.F. van Gunsteren The seven sins in academic behavior in the natural sciences Angew. Chem. Int. Ed. 52 (2013) 118-122, DOI: 10.1002/anie.201204076 Angew. Chem. 125 (2013) 128-132, DOI: 10.1002/ange.201204076

L.J. Smith, W.F. van Gunsteren, J.R. Allison Multiple binding modes for palmitate to barley lipid transfer protein facilitated by the presence of proline 12 Prot. Sci. 22 (2013) 56-64, DOI: 10.1002/pro.2184, incl. supp. mat M.M. Müller, J.R. Allison, N. Hongdilokkul, L. Gaillon, P. Kast, W.F. van Gunsteren, P. Marliére, D. Hilvert Directed evolution of a model primordial enzyme provides insights into the development of the genetic code PLoS Genet 9 (2013) e1003187, DOI:10.1371/journal.pgen.1003187, incl. supp. mat.

A. Choutko, W.F. van Gunsteren Conformational preferences of a β-octapeptide as function of solvent and force-field parameters Helv. Chim. Acta 96 (2013) 189-200, DOI: 10.1002/hlca.201200173, incl. supp. mat.

Z. Lin, W.F. van Gunsteren On the choice of a reference state for one-step perturbation calculations between polar and non-polar molecules in a polar environment J. Comput. Chem. 34 (2013) 387-393, DOI: 10.1002/jcc.23146, incl. supp. mat.

K. Meier, A. Choutko, J. Dolenc, A.P. Eichenberger, S. Riniker, W.F. van Gunsteren Multi-resolution simulation of biomolecular systems: a review of methodological issues Angew. Chem. Int. Ed. 52 (2013) 2820-2834, DOI: 10.1002/anie.201205408 Angew. Chem. 125 (2013) 2-19, DOI: 10.1002/ange.201205408

Z. Lin, S. Riniker, W.F. van Gunsteren Free enthalpy differences between -, π-, and 310-helices of an atomic level fine-grained alanine deca-peptide solvated in supra-molecular coarse-grained water J. Chem. Theory Comput. 9 (2013) 1328-1333, DOI: 10.1021/ct3010497

N. Hansen, P.H. Hünenberger, W.F. van Gunsteren Efficient combination of environment change and alchemical perturbation within the enveloping distribution sampling (EDS) scheme: twin system EDS and application to the determination of octanol-water partition coefficients J. Chem. Theory Comput. 9 (2013) 1334-1346, DOI: 10.1021/ct300933y, incl. supp. mat.

K. Meier, W.F. van Gunsteren On the use of advanced modelling techniques to investigate the conformational discrepancy between two X-ray structures of the AppA BLUF domain Mol. Sim. 39 (2013) 472-486, DOI: 10.1080/08927022.2012.743659

253

Z. Lin, W.F. van Gunsteren Combination of enveloping distribution sampling (EDS) of a soft-core reference-state Hamiltonian with one-step perturbation to predict the effect of side chain substitution on the relative stability of right- and left-helical folds of β-peptides J. Chem. Theory Comput. 9 (2013) 126-134, DOI: 10.1021/ct300929q A.P. Eichenberger, W.F. van Gunsteren, L.J. Smith Structure of hen egg-white lysozyme solvated in TFE/water: a molecular dynamics simulation study based on NMR data J. Biomol. NMR 55 (2013) 339-353, DOI: 10.1007/s10858-013-9717-y, incl. supp. mat.

A. Choutko, A.P. Eichenberger, W.F. van Gunsteren, J. Dolenc Exploration of swapping enzymatic function between two proteins: a simulation study of chorismate mutase and isochorismate pyruvate lyase Prot. Sci. 22 (2013) 809-822, DOI: 10.1002/pro.2264, incl. supp. mat.

D. Wang, M.L. Amundadottir, W.F. van Gunsteren, P.H. Hünenberger Intramolecular hydrogen-bonding in aqueous carbohydrates as a cause or consequence of conformational preferences: a molecular dynamics study of cellobiose stereoisomers Eur. Biophys. J. 42 (2013) 521-537, DOI: 10.1007/s00249-013-0901-5 Z. Lin, W.F. van Gunsteren Influence of variation of a side chain on the folding equilibrium of a β-peptide: limitations of one-step perturbation J. Comput. Chem. 34 (2013) 1899-1906, DOI: 10.1002/jcc.23331 N. Hansen, J.R. Allison, F. Hodel, W.F. van Gunsteren Relative free enthalpies for point mutations in two proteins with highly similar sequence but different folds Biochemistry 52 (2013) 4962–4970, DOI: 10.1021/bi400272q Z. Lin, W.F. van Gunsteren The effect of branched side chains on the relative stability of α- and π- helices: a combination of the enveloping distribution sampling and one-step perturbation methods Mol. Phys. 111 (2013) 2126-2130, DOI: 10.1080/00268976.2013.793828, incl. supp. mat. S.J. Bachmann, J. Dolenc, W.F. van Gunsteren On the use of one-step perturbation to investigate the dependence of different properties of liquid water upon a variation of model parameters from a single simulation Mol. Phys. 111 (2013) 2334-2344 L. Smith, Y. Roby, J.R. Allison, W.F. van Gunsteren MD simulations of barley and maize lipid transfer proteins show different ligand binding preferences in agreement with experimental data Biochemistry 52 (2013) 5029-5038, DOI: 10.1021/bi4006573

254

D. Wang, A. Böckmann, J. Dolenc, B. Meier, W.F. van Gunsteren On the behavior of water at subfreezing temperatures in a protein crystal: evidence of higher mobility than in bulk water J. Phys. Chem. B. 117 (2013) 11433–11447, DOI: 10.1021/jp400655v incl. supp. mat. M. Pechlaner, R.K.O. Sigel, W.F. van Gunsteren, J. Dolenc Structure and conformational dynamics of the domain 5 RNA hairpin of a bacterial group II intron revealed by solution NMR and molecular dynamics simulations Biochemistry 52 (2013) 7099–7113, DOI: 10.1021/bi400784r, incl. supp. mat.

Z. Lin, W.F. van Gunsteren Enhanced conformational sampling using enveloping distribution sampling J. Chem. Phys. 139 (2013) 144105, DOI: 10.1063/1.4824391 Z. Lin, W.F. van Gunsteren Refinement of the application of the GROMOS 54A7 force field to β-peptides J. Comput. Chem. 34 (2013) 2796-2805, DOI: 10.1002/jcc.23459, incl. supp. mat. Z. Lin, C. Necula, W.F. van Gunsteren

-peptide with a very unstable folded conformation in solution: The advantage of focused sampling using EDS Chem. Phys. 428 (2014) 156-163, DOI: 10.1016/j.chemphys.2013.11.016, incl. supp. mat. S.J. Bachmann, Z. Lin, T. Stafforst, W.F. van Gunsteren, J. Dolenc On the sensitivity of peptide nucleic acid duplex formation and crystal dissolution to a variation of force-field parameters J. Chem. Theory Comput. 10 (2013) 391-400, DOI: 10.1021/ct400652w Z. Lin, C. Oostenbrink, W.F. van Gunsteren On the use of one-step perturbation to investigate the dependence of NOE derived atom-atom distance bound violations of peptides upon a variation of force-field parameters Eur. Biophys. J. 43 (2014) 113-119, DOI 10.1007/s00249-014-0943-3 O.M. Szklarczyk, S.J. Bachmann, W.F. van Gunsteren A polarisable empirical force field for molecular dynamics simulation of liquid hydrocarbons J. Comput. Chem. 35 (2014) 789–801, DOI: 10.1002/jcc.23551 W. Huang, S. Riniker, W.F. van Gunsteren Rapid sampling of folding equilibria of β-peptides in methanol using a supramolecular solvent model J. Chem. Theory Comput. 10 (2014) 2213−2223, DOI 10.1021/ct500048c incl. supp. mat. W. Huang, Z. Lin, W.F. van Gunsteren The use of enveloping distribution sampling to evaluate important characteristics of biomolecular force fields J. Phys. Chem. 118 (2014) 6424–6430, DOI: 10.1021/jp411005x, incl. supp. mat.

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S.J. Bachmann, W.F. van Gunsteren Polarisable model for DMSO and DMSO-water mixtures J. Phys. Chem. B 118 (2014) 10175-10186, DOI: 10.1021/jp5035695 N. Hansen, W.F. van Gunsteren Practical aspects of free-energy calculations: A review J. Chem. Theory Comput. 10 (2014) 2632−2647, DOI: 10.1021/ct500161f S.J. Bachmann, W.F. van Gunsteren On the compatibility of polarisable and non-polarisable models for liquid water Mol. Phys. (2014) online, DOI: 10.1080/00268976.2014.910317 S.J. Bachmann, W.F. van Gunsteren An improved polarisable water model for use in biomolecular simulation J. Chem. Phys. 141 (2014) online, DOI: 10.1063/1.4897976 In press or submitted

N. Hansen, F. Heller, N Schmid, W.F. van Gunsteren Time-averaged order parameter restraints in molecular dynamics simulations J. Biomol. NMR (2014) in press W. Huang, W.F. van Gunsteren On the challenge of representing entropy at different levels of resolution in molecular simulation J. Phys. Chem. B (2014) in press, incl. supp. mat. W. Huang, N. Hansen, W.F. van Gunsteren On the use of a supra-molecular coarse-grained model for the solvent in simulations of the folding equilibrium of an octa-beta-peptide in methanol and water Helv. Chem. Acta (2014) in press M.H. Graf, Z. Lin, U. Bren, D. Haltrich, W.F. van Gunsteren, C. Oostenbrink Pyranose Dehydrogenase Ligand Promiscuity: A Generalized Approach to Simulate Monosaccharide Solvation, Binding, and Product Formation PLOS Computational Biology (2014) in press L.J. Smith, W.F. van Gunsteren. N. Hansen Characterisation of the flexible lip regions in bacteriophage lambda lysozyme using MD simulations FEBS J. (2014) submitted

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Computational Science

and Engineering (CSE)

Annual Report

2013/2014

ETH Zurich

Rämistrasse 101

8092 Zurich

www.rw.ethz.ch

Documents

CSE Annual Report 2013/2014 (PDF, 9.8 MB)