Moscow State University supercomputing applications

1

2

Contents

Regional atmospheric modeling 4

Supercomputer-aided drug design 5

Self-organization of amphiphilic macromolecules with helical secondary structure 6

SparseLinSol – library for solving large sparse systems of linear algebraic equations 7

Numerical simulations of acoustic liners 8

Numerical simulations of the airframe noise 9

Simulation of processors cooler system 10

Methods of the wave tomography in medicine, geophysics, industry 11

Microphase separation of random copolymers by DPD 12

New drag suppressive technique in turbulent flow 13

High-energy pulse compression through an off-axial beam dynamics in a laser-induced filament 14

Electro-catalysis for hydrogen-air fuel cells on the base of nano-sized platinum 15

Modelling of thermodynamics and mechanics of nanostructured systems in presence of polyelectrolytes 16

Atomic and molecular dynamics in strong laser fields 17

Molecular modeling of enzymatic reactions 18

Computer modeling of macromolecular systems, containing amphiphilic units 19

Molecular modeling of enzymatic activity 20

Computer modeling of bilayer with mobile grafting points 21

New properties and possible applications of ferroelectric superlattices: the results of first-principles studies 22

Extendable CFD computing platform FlowVision 23

Phase diagram of diblock copolymer melt obtained by dissipative particle dynamics simulation 24

Mesoscale simulation of organic-inorganic nanocomposite synthesis by anionic polymerization of silicon spiro compounds 25

3

Research of fundamental structural and conductive properties of linear-chain carbon 26

Molecular dynamics simulations of ion conduction through bacterial potassium channel 27

Numerical simulation of galactic and extragalactic objects: the dynamics of multicomponent sys-tems and the role of dark matter 28

Rational design of drugs on base of G-quadruplex containing apatamers 29

Identification of minimal Zn(2+) binding site of amyloid-β 30

Molecular mechanisms of chromosome movements during cell division 31

Search for new PGHS inhibitors as potential anti-inflammatory drugs 32

TIP4P water diffusion factor calculation 33

Simulation of oil deposit recovery by water flooding 34

Climate modeling (climate change prediction by using coupled atmospheric and oceanic general circulation model) 35

Large eddy simulation of geophysical turbulent flows 36

Surface-related multiple noise elimination for 3D seismic data 37

Electrochemical oxidation of cerium and other metal atoms inside the carbon cage as studied by density functional theory 38

Interpretation of the hyperfine structure in the electron paramagnetic resonance spectra of large fullerene-based perfluoroalkyl-radicals 39

4 R E G I O N A L A T M O S P H E R I C M O D E L I N G

Regional atmospheric modeling

The need for improvement of climate and weather prediction at a regional scaleSTRATEGY Regional non-hydrostatic atmospheric model with horizontal resolution 2-10 km is being developed by including sophisticated parameter-izations of physical and biogeochemical processes occurring in both the atmosphere and in the active layer of land surface. This enables to explicitly reproduce in the model many feedbacks between land and atmosphere that are relevant to climate change. The emphasis is made on simulating meso-scale atmospheric dynamics and greenhouse gases concentrations at high latitudes, namely, in Arctic region and permafrost area.

OBJECTIVE Development of parallel computa-tional technology capable of correctly reproducing regional weather and land surface dynamics in mid- and high latitudes for use in a wide range of environmental applications and climate studies.

IMPACT Improving the knowledge of key process-es in regional climate systems of high latitudes.

USAGE Climate and weather prediction.

AUTHOR Stepanenko V.M., Chechin D.G., Yurova A.Y., Lykosov V.N. (Research Computing Center, Moscow State University)

EMAIL [email protected], lykossov@ inm. ras. ru

5S T R U C T U R A L - B A S E D C O M P U T E R - A I D E D D R U G D E S I G N

Supercomputer-aided drug design

STRATEGY Virtual screening of databases of ligands by means of docking, quantum chemistry and molecular dynamics methods for estimation of protein-ligand binding energies.

OBJECTIVE Create original molecular modeling tools with high ability to predict efficient inhibitors for a given target-protein. Higher accuracy of the protein-ligand binding energy calculations leads to the better prediction of new inhibitors. Auto-matic preparation of hundreds of target-proteins and millions of small molecules for docking and calculations of protein-ligand binding energies. Ef-fective virtual screening of millions of molecules at supercomputers, effective parallel implementations of docking and quantum chemistry methods.

IMPACT Efficient, quick and cheap rational devel-opment of new drugs.

USAGE New inhibitors development for a given target-protein.

AUTHOR V.B.Sulimov, A.N.Romanov, O.A.Kondakova (RCC Lomonosov Moscow State University), A.V.Sulimov, I.V.Oferkin, E.V.Katkova, C.M.Fedulov (Dimonta, Ltd, Moscow).

EMAIL [email protected], sulimovv@ mail.ru

Design of new inhibitors for a given target-protein based on molecular modeling

Program SOL Docking: global energy minimum search. Space ≤ 21 dimensions. Internal torsions ≤ 15. Ligand interaction with all protein atoms is represented by a set of grids of potentials in the cube 22 x 22 x 22. 1 ligand 1 CPU: 1-3 hours.

6 P O L Y M E R S C I E N C E

Self-organization of amphiphilic macromolecules with helical secondary structure

DRIVER Interaction mechanisms in some biologi-cal and synthetic macromolecules are still unclear.

STRATEGY Study the structure formation in con-centrated solutions of macromolecules with local helicity.

OBJECTIVE Find chain length and concentration dependencies of the aggregation behavior.

IMPACT Explanation of viscosity phenomena in some polysaccharides, creation of advanced materials.

USAGE Better understanding of aggregation mechanisms in helical macromolecules.

AUTHOR M. K. Glagolev (Faculty of Physics, Mos-cow State University), V. V. Vasilevskaya (A. N. Nes-meyanov Institute of Organoelement Compounds RAS), A. R. Khokhlov (Faculty of Physics, Moscow State University; A. N. Nesmeyanov Institute of Organoelement Compounds RAS).

EMAIL [email protected], vvvas@ polly. phys.msu.ru, khokhlov@ polly. phys. msu.ru

7N U M E R I C A L M E T H O D S

SparseLinSol – library for solving large sparse systems of linear algebraic equations

DRIVER: Needs for effective scalable numerical methods and their implementations for solving large sparse systems of linear algebraic equations

STRATEGY: Development of a library of multigrid and Krylov subspace iterative methods.

OBJECTIVE: Analysis of different approaches and technologies for parallelization of numerical methods. Implementation of a library of numerical methods for solving large sparse systems of linear algebraic equations using the selected approach: hybrid model MPI+ShM.

IMPACT: Increasing the efficiency of usage the computing resources in applied calculations makes possible to increase the resolution of computational grids and results precision and to decrease the solu-tion time.

USAGE: Any application, that uses computational grids for solving partial differential equations, in particular — CFD-applications (computational fluid dynamics). For example, modeling of cooling systems for modern supercomputers.

AUTHOR B.I. Krasnopolsky (Institute of Mechan-ics, Lomonosov Moscow State University)

EMAIL [email protected]

8 A E R O A C O U S T I C S . A C O U S T I C L I N E R S

Numerical simulations of acoustic liners

DRIVER Need in predicting the sound-absorption properties of cells of acoustic liners and revealing possibilities for the optimization.

STRATEGY Large-scale predictions based on direct numerical simulation (DNS) approach implement-ed with the help of higher-accuracy finite-volume methods for unstructured grids.

OBJECTIVE To create virtual testing tool providing the valid computational experiments on systems of liner cells of different configurations.

IMPACT Reduction of fan noise towards quieter aircraft.

USAGE Aircraft design.

AUTHOR I. V. Abalakin, A. P. Duben, A. V. Goro-bets, T. K. Kozubskaya (Keldysh institute of applied mathematics RAS, Moscow, Russia)

EMAIL [email protected], [email protected]

9A E R O A C O U S T I C S . A I R F R A M E N O I S E

Numerical simulations of the airframe noise

DRIVER Need in deeper understanding of air-frame-noise generation mechanisms, and finding the ways of noise-source damping.

STRATEGY Large-scale turbulent-flow predic-tions based on (Delayed) Detached Eddy Simula-tion ((D)DES) approach implemented with the help of higher-accuracy finite-volume methods for unstructured grids.

OBJECTIVE To predict the localization of the airframe-noise sources and their spectral properties for generic cases representing the airframe noise.

IMPACT Reduction of airframe noise towards quieter aircraft.

USAGE Aircraft design.

AUTHOR I. V. Abalakin, A. P. Duben, A. V. Goro-bets, T. K. Kozubskaya (Keldysh institute of applied mathematics RAS, Moscow, Russia)


10 H E A T T R A N S F E R

DRIVER Accurate simulation of processor coolers.

STRATEGY Highly resolved simulation of heat flow using Direct Numerical Simulation.

OBJECTIVE Implement mathematically consistent algorithms for multiscale modeling of heat transfer in the processor cooler.

IMPACT Better, safer cooler design.

Simulation of processors cooler system

AUTHOR S.V.Polyakov, M.V. Iakobovski (Keldysh Institute of Applied Mathematics)


Accurate simulation of processor coolers

11W A V E T O M O G R A P H Y

Methods of the wave tomography in medicine, geophysics, industryNon-destructive investigation of the internal structure of the object DRIVER Non-destructive investigation of the internal structure of the object.

STRATEGY Solution of three-dimensional nonlin-ear coefficient inverse problems for wave equa-tions on supercomputers.

OBJECTIVE Study of the internal structure of the object by wave sounding with super resolution

IMPACT Break-throw technology of computer aid-ed non-destructive diagnostics with wave sounding.

USAGE Ultrasound tomography in medi-cine, wave sounding of the surface layers of the Earth, industrial tomography.

AUTHOR A.V. Goncharsky, S.Yu.Romanov (Scien-tific and Research Computer Center of MSU)


12

Microphase separation of random copolymers by DPD

STRATEGY Study microphase separation in dif-ferent types of random copolymers. Use polymer reactions for self-organization in polymer melt.

OBJECTIVE Use DPD (dissipative particle dy-namics) to investigate phase diagrams of random diblock and multiblock copolymers. Apply polymer reactions, taking place in random copolymers, to propose mechanism of polymer films self-organiza-tion near some template surface.

IMPACT Propose new polymer systems for nano-technology applications.

USAGE Modern nanocomposite materials, organic electronics, fotonic crystals, functional membranes.

Need for robust nanostructures via simple and cheap polymers

AUTHOR A.A. Gavrilov, P.G. Khalatur, A.V. Cher-tovich (Lomonosov Moscow State University, Phys-ics Department)


P O L Y M E R S C I E N C E

13T U R B U L E N C E M O D E L I N G

New drag suppressive technique in turbulent flowFind a new way to reduce turbulent friction drag in gas or liquid flows near solid surfaceSTRATEGY Use direct numerical simulation for fundamental studies of the microphysics of turbu-lent flows with different boundary conditions.

OBJECTIVE Make an assumption about mecha-nism of turbulent energy production in wall-bounded flows.

IMPACT Better and more clear understanding of mysterious phenomenon - turbulence.

USAGE Decreasing fuel transportation costs.

AUTHOR N.V. Nikitin, I.S. Vodopyanov (Lomono-sov Moscow State University, Institute of Mechanics)


14 N O N L I N E A R O P T I C S

High-energy pulse compression through an off-axial beam dynamics in a laser-induced filamentDRIVER Laser-induced filamentation is a promis-ing technique of infrared radiation energy transfer and a powerful method of ultrashort pulse com-pression.

STRATEGY As a physical phenomenon, filamenta-tion involves a complex, strongly coupled spatio-temporal dynamics of optical field waveforms in nonlinear, fast-ionizing media. 3+1-dimensional simulations on supercomputers allow us to predict the unique regimes of ultrafast electrodynamics.

OBJECTIVE Proper management of the spatial chirp of a laser beam in a filament can substantially improve the efficiency of pulse compression thus allowing generation of terawatt CEP-stable few- and single-cycle electromagnetic field waveforms. IMPACT In ultrafast optical science, laser filamen-tation finds growing applications as a powerful technique of pulse compression, enabling the gen-eration of high-peak-power carrier-envelope-phase stable few-cycle optical field waveforms within a broad frequency range from the deep ultraviolet to the near- and mid-infrared.

USAGE Remote sensing of the atmosphere, electro-magnetic radiation energy transfer.

AUTHOR A.A. Voronin (Lomonosov Moscow State University, Physics Department, International Laser Center), A.M. Zheltikov (Lomonosov Moscow State University, Physics Department, International Laser Center; Department of Physics and Astronomy, Texas A&M University, College Station TX)

EMAIL [email protected], zheltikov@ phys.msu.ru

15H Y D R O G E N E N E R G Y

Electro-catalysis for hydrogen-air fuel cells on the base of nano-sized platinum — semi-conducting oxides composites: size ef fects, inf luence of substrate, peculiarit ies of adsorption and electrochemical processes

DRIVER Improve electrochemical fuel cells ef-ficiency, stability and reduce costs.

STRATEGY Understanding of elementary steps of processes in electrochemical fuel cells. Elucidate factors determining efficiency and stability of com-posite catalysts based on nano-sized metal particles on proton-conducting oxide substrates.

OBJECTIVE Use ab initio DFT-based techniques to model interactions of oxygen and fuel molecules with metal surfaces up to dissociation, moving of atoms and functional groups from metal to sub-strate (spillover-effect), migration of atoms along catalyst and substrate surfaces, interaction between metal particles and substrate. Elucidate factors de-termining molecule activation on catalyst particles, proton conductivity trough the composite system and fastening of metal particles on substrate.

IMPACT Design of electrochemical fuel cells with high stability and low content of platinum metals. Electro-catalysis for hydrogen-air fuel cells on the base of nano-sized platinum – semi-conducting ox-ides composites: size effects, influence of substrate, peculiarities of adsorption and electrochemical processes.

USAGE Catalysis, fuel cells.

Moving of atom H from metal cluster Pt19 to substrate SnO2(001) (spillover-effect). Structures of isomers and corresponding potential curve (E, eV).

AUTHOR Yu.A. Dobrovolskii, A.S. Zyubin, T.S. Zyubina, V.M. Volochov (Institute of Problems of Chemical Physics, Russian Academy of Sciences, Chernogolovka)

EMAIL [email protected], [email protected], vvm@ icp.ac.ru

16 S O F T M A T T E R

Modelling of thermodynamics and mechanics of nanostructured systems in presence of polyelectrolytesDRIVER Development of novel micro- and na-noscale drug carriers in fluidic systems. Attempt to understand the role of polyions in their stability and transport, and thermodynamics of multicom-partment nanosystems.

STRATEGY We do Langevin dynamics simulation of fluidic systems with liquid-vapour interfaces and membranes in presence of asymmetric electrolytes.The model includes all small ions and polyions explicitly and employs the Ewald summation tech-nique for electrostatic interactions. The dependences of the osmotic pressure, disjoining pressure between the interfaces, and surface charging on the electro-lyte concentration and polyion structure are studied.

OBJECTIVE We aim to quantify the electrostatic contributions to thermodynamics and stability of heterogeneous nanostructured fluidic systems including semipermeable membranes and nano-bubbles. We develop and test the theories predict-ing the mechanical and electrokinetic properties of these structures.

IMPACT We hope to achieve control over mecha-nisms of stabilization and transport of micro- and nanocapsules, natural and synthetic cells used in chemical technology, biotechnology, and pharma-ceutics.

USAGE Microfluidic devices for biotechnology, pharmaceutics.

AUTHOR Bogdanov A.N. , Ivanov V.A. (Lomono-sov Moscow State University, Faculty of Physics), Lobaskin V.A. (University College Dublin), Vino-gradova O.I. (Lomonosov Moscow State University, Faculty of Chemistry)

EMAIL [email protected], [email protected], [email protected]

17A T O M I C A N D L A S E R P H Y S I C S

Atomic and molecular dynamics in strong laser fields

STRATEGY Development of new effective codes for numerical integration of stationary and nonsta-tionary Shroedinger equations on two- and three-dimensional spatial grids.

OBJECTIVE Direct solution of the nonstationary Schroednger equation for modeling of the quantum system behavior in external electromagnetic fields.

IMPACT Fundamental knowledge on quantum systems behavior under high intensity and ulrashort laser pulses action and possible applications for spectroscopy with subfemtosecond temporal and subangstrom spatial resolution.

USAGE Nonlinear optics, atomic spectroscopy.

AUTHOR E.A.Volkova, A.M.Popov, O.V.Tikhonova (Institute of Nuclear Physics, Moscow State Univer-sity, 119991, Moscow, Russia)

EMAIL [email protected], [email protected], ovtikhonova@ mail.ru

Need for simulation of strong laser fields interaction with atoms and molecules

18 E N Z Y M O L O G Y

Molecular modeling of enzymatic reactions

STRATEGY Use supercomputers to investigate catalytic mechanisms of native and modified enzymes through building of reactions elementary steps energy profiles using combined quantum and molecular mechanics method.

OBJECTIVE Mechanisms of enzyme catalytic ac-tions are to be understood at the level of elementary chemical events in order to design rationally new therapeutic agents. The main target groups under consideration are inhibitors of certain enzymes; physiologically-active supramolecular structures and modified enzymes with desired catalytic prop-erties.

IMPACT Better understanding of chemical basis of enzymes action and rational design of new thera-peutic agents.

USAGE New medical treatments and prophylaxis for humans.

AUTHOR S.V. Lushchekina, A.V. Nemukhin, S.D. Varfolomeev (Lomonosov Moscow State Uni-versity, Chemistry Department; Emanuel Institute of Biochemical Physics, RAS)


Need for new therapeutic agents with desired action mechanisms

19P O L Y M E R S C I E N C E

Computer modeling of macromolecular systems, containing amphiphilic unitsStudy of self-assembly in macromolecular systems, containing units with different affinity to a solventSTRATEGY Investigate behavior of systems with large number of particles by means of computer simulation.

OBJECTIVE (a) Simulation of microphase separa-tion in a melt of comb-coil diblock copolymers. (b) Simulation of adsorption of a comb-like macromol-ecule on patterned surface.

IMPACT Development of new materials from mac-romolecules with amphiphilic groups for techno-logical applications (membranes, nanoelectronics, etc).

USAGE (a) transport in membranes, new materials with controllable properties; (b) patterned surfaces, nanoelectronics.

AUTHOR A. A. Glagoleva (Faculty of Phys-ics, Moscow State University), V. V. Vasilevskaya (A.N. Nesmeyanov Institute of Organoelement Compounds RAS), A. R. Khokhlov (Faculty of Physics, Moscow State University; A. N. Nesmeya-nov Institute of Organoelement Compounds RAS)

EMAIL [email protected], vvvas@ polly. phys.msu.ru

20 M O L E C U L A R M O D E L I N G

Molecular modeling of enzymatic activityAccurately predict energy and geometric characteristics of enzyme-substrate complexes.STRATEGY Apply molecular docking and mo-lecular dynamics techniques to simulate substrate binding and substrate transformation by mutant forms of an enzyme.

OBJECTIVE Elaboration of methodology of free energy calculation considering the specifics of stud-ied enzyme. In silico screening for mutant forms of an enzyme with increased substrate affinity and catalytic activity.

IMPACT Development of improved biocatalysts on a basis of a native enzyme.

USAGE Pharmacology, biotechnology.

AUTHOR D.K. Nilov (Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University), V.K. Švedas (Belozersky Institute of Physicochemical Biology, Lomonosov Moscow State University)

EMAIL [email protected], vytas@ belozersky.msu.ru

21P O L Y M E R S C I E N C E

Computer modeling of bilayer with mobile grafting pointsNeed for patterned surfaces with specific propertiesSTRATEGY Introduce the new model of bilayer, corresponding to certain kinds of systems, and study it by means of computer simulation.

OBJECTIVE Study the distribution patterns of the upper layer in weak and strong segregation modes.

IMPACT Fabrication of nanodevices, biologically active surfaces, nanolitography.

USAGE Fabrication of patterned surfaces.

AUTHOR M. K. Glagolev (Faculty of Physics, Mos-cow State University), V. V. Vasilevskaya (A. N. Nes-meyanov Institute of Organoelement Compounds RAS), A. R. Khokhlov (Faculty of Physics, Moscow State University; A. N. Nesmeyanov Institute of Organoelement Compounds RAS).

EMAIL [email protected], vvvas@ polly. phys.msu.ru, khokhlov@ polly. phys. msu.ru

22 E L E C T R O N I C S

New properties and possible applications of ferroelectric superlattices: the results of first-principles studiesDRIVER Use of artificial ferroelectric nanostruc-tures— ferroelectric superlattices and wires—in electronics, in particular in nonvolatile memory devices (ferroelectric RAM); possible application of ferroelectric superlattices as a medium for 3D information recording.

STRATEGY Very thin domain walls and small critical size for appearance of ferroelectricity in ferroelectrics make them promising materials for next generation of electronic memory devices. First-principles calculations are capable to take into account all physical interactions in these complex materials and reliably predict their properties.

OBJECTIVE First-principles density-functional-theory calculations are used to predict properties of various nanostructures (superlattices, wires) and to find new artificial materials with advanced ferro-electric, dielectric, piezoelectric, nonlinear optical and electrical properties.

IMPACT New advanced materials for electronics.

USAGE New advanced materials for electronics, nonvolatile memory devices.

AUTHOR A.I. Lebedev (Physics Department, Mos-cow State University)


23I N D U S T R I A L H Y D R O D Y N A M I C S

Extendable CFD computing platform FlowVision

DRIVER Need for simulating large industrial problems with multiphase and multi-physics phe-nomena in computational domains with arbitrary complex shape and moving/deformable bodies.

STRATEGY Automatic mesh generation with dynamic local adaptation, high accuracy implicit numerical schemes. This requires powerful and scalable approaches for solving coupled non-linear equations of fluid motion on modern supercom-puter architecture.

OBJECTIVE Create powerful and extendable CFD computing platform for virtual fluid engineering of large and complex industrial design projects in areas of automotive, shipbuilding, atomic energy and aerospace.

IMPACT Reduced simulation time and increased accuracy result in reducing design time and in-creasing design reliability.

USAGE It is a base technology for design in in-dustries: automotive, shipbuilding, nuclear power, wind turbines, etc.

AUTHOR A.Aksenov, A.Dyadkin, V.Pokhilko, V.Kutin, S.Kharchenko, S.Zluktov (All - TESIS Ltd., Russia)


24 C H E M I S T R Y

Phase diagram of diblock copolymer melt obtained by dissipative particle dynamics simulationDRIVER Study behavior of diblock-copolymer melts.

STRATEGY Dissipative particle dynamics simula-tion of diblock copolymer melts in the wide range of characterizing system parameters with presence of fluctuations.

OBJECTIVE Obtain phase diagram of diblock copolymer melt, with focus on the studying of the region of stability of gyroid structure.

IMPACT Fundamental understanding of self-assembly in diblock copolymer melts.

USAGE Nanostructured materials, photonic crys-tals.

AUTHOR E.S. Patyukov, I.I. Potemkin (Physics Department, Moscow State University; Department of Polymer Science, University of Ulm, Germany); P.G. Khalatur (Department of Polymer Science, University of Ulm, Germany; Institute of Organo-element Compounds, Russian Academy of Science, Moscow, Russia)

EMAIL [email protected], igor@ polly. phys.msu.ru, khalatur@ polly. phys. msu. ru

25P H Y S I C A L C H E M I S T R Y O F P O L Y M E R S

Mesoscale simulation of organic-inorganic nanocomposite synthesis by anionic polymerization of silicon spiro compoundsDRIVER Need for one-stage synthesis of nano-structured polymeric/inorganic composites.

STRATEGY Understand mechanism of nanocom-posite formation by twin-polymerization.

OBJECTIVE Develop universal mesoscale molecu-lar simulation technique for multiple competing chemical reactions in polymer systems. Quanti-tative prediction of cationic ring-opening twin polymerization kinetics, and structure of resulting nanocomposite by complementary usage of quan-tum mechanics, classical molecular dynamics, and kinetic Monte Carlo approaches.

IMPACT Synthesis of polymeric/inorganic nano-composites of predefined structure and properties.

USAGE Computer-aided design of porous thermo/chemically stable adsorbents, membranes, catalytic substrates, electrodes.

AUTHOR Berezkin A.V., Auer A.A. (Max-Planck Institut für Eisenforschung GmbH, Max-Planck-Straße 1, 40237 Düsseldorf, Germany), Guseva D.V.: (Lomonosov Moscow State University, Physics Department, Leninskie gory, 1, build. 2., 119991 Moscow, Russian Federation)

EMAIL [email protected], guseva@ polly.phys.msu.ru

26 M A T E R I A L S S C I E N C E

Research of fundamental structural and conductive properties of linear-chain carbon

DRIVER Need for accurate calculations of struc-tural properties of polyatomic systems of linear carbon chains.

STRATEGY Resolving of Schrodinger equation for different forms of linear-chain carbon.

OBJECTIVE Explain stability of different forms of linear-chain carbon, their experimentally observed properties and create theory of atomic and electron structure of such materials.

IMPACT Create materials for nanoelectronic, such as quantum wires.

USAGE New materials for nanoelectronic and medicine.

AUTHOR Korobova J.G., Bazhanov D.I., Guseva M.B., Khvostov V.V. (MSU, physical department)


27B I O L O G Y

Molecular dynamics simulations of ion conduction through bacterial potassium channel

DRIVER Voltage-gated ion channels are respon-sible for production and propagation of nerve impulses along neuronal structures and across syn-apses. They present both fundamental and practical interest as potential drug targets.

STRATEGY Molecular dynamics simulations of ion transfer through bacterial potassium channel KcsA at atomic resolution. Calculation of Potential of Mean Force profile for potassium ions in the channel pore.

OBJECTIVE Study ion conduction mechanism from first principles. Understand the key interac-tions between potassium ion and protein’s elements which are responsible for fast gating transitions at the selectivity filter.

IMPACT Simulations of physical mechanisms underlying the conductivity of ion channels will contribute to our fundamental understanding of the cellular processes and will possible have biomedical applications. USAGE Fundamental sci-ence, medicine.

AUTHOR M.A. Kasimova, A.K. Shaytan, K.V. Shaytan (Biology Department, Moscow State University, 119991 Moscow, Russia)

EMAIL [email protected], alex@ molsim.org

28 A S T R O P H Y S I C S

Numerical simulation of galactic and extragalactic objects: the dynamics of multicomponent systems and the role of dark matterDRIVER Spiral structure in galaxies and influence of dark mass on structure and evolution of galaxies.

STRATEGY Estimation of dark matter mass and its spatial distribution.

OBJECTIVE The properties of visible baryon sub-stance depend on a dark massive halo: a kinemat-ics of stellar and gaseous components, central bar, spiral structure, polar rings IMPACT Predictive numerical simulations of galaxies dynamics will enable our fundamental understanding of the large-scale structure of our Universe

USAGE New models for understanding of nature and structure of the Universe.

AUTHOR A.V.Khoperskov, S.A.Khoperskov (Vol-gograd State University), A.V.Zasov, N.V.Tyurina (Moscow State University)


A S T R O P H Y S I C S

29B I O L O G Y

Rational design of drugs on base of G-quadruplex containing apatamers

DRIVER Rational design of small DNA molecules inhibiting thrombin to prevent clot formation with-out toxic effects.

STRATEGY Understand molecular dynamics and stability of G-quadruplex containing DNA.

OBJECTIVE Dynamical structure model and structure annotation of DNA aptamer inhibiting thrombin.

IMPACT Simulations and structure annotation will provide unique details to successful design drug against thrombosis and modern strategy to develop new generation drugs.

USAGE New medical treatments for humans.

AUTHOR Andrey V. Golovin, Roman V. Reshet-nikov (Lomonosov Moscow State University Bioen-gineering and Bioinformatics Department)


B I O L O G Y

30 B I O L O G Y

Identification of minimal Zn(2+) binding site of amyloid-βStudy of role of peptide ion interaction in amyloid agrgation to find drug target in Alzheimer disease therapy

STRATEGY Research of Zn+2 coordination in am-yloid beta peptides by hybrid QM/MM approach.

OBJECTIVE Three dimensional structure of Zn+2 binding site in amyloid peptides and ion binding mechanism, dynamical models and structural an-notation.

IMPACT Characterization of possible drug target site may lead to new drug creation in Alzheimer disease therapy.


AUTHOR Andrey V. Golovin (Lomonosov Moscow State University Bioengineering and Bioinformat-ics Department); Philipp O. Tsvetkov, Alexander A. Makarov (Engelhardt Institute of Molecular Biol-ogy, Russian Academy of Sciences, Moscow)

EMAIL [email protected], vizlipuzli@ gmail.com, [email protected]

31B I O L O G Y

Molecular mechanisms of chromosome movements during cell division

DRIVER Understand mechanisms that drive chro-mosome movements during cell division and create effective anti-cancer strategies.

STRATEGY Study molecular mechanism of action of key kinetochore proteins that drive chromosome motion during cell division.

OBJECTIVE Create new molecular-mechanical approach to model dynamics of complex protein polymers and assemblies and study their action on biological time scales (seconds to minutes).

IMPACT Develop strategy for new type of anti-cancer therapy less toxic that existing now.


AUTHOR Maxim I. Molodtsov, Pavel N. Zakharov (Center for theoretical problems of physicochemi-cal pharmacology RAS, Moscow, Russia), Andrey O. Zheleznyakov (Lomonosov Moscow State Uni-versity, Moscow, Russia), Ekaterina L. Grishchuk (Department of Physiology, University of Pennsyl-vania School of Medicine, Philadelphia, PA USA), Fazly I.Ataullakhanov (National Research Center for Hematology RAMS, Moscow, Russia)


32 B I O L O G Y

Search for new PGHS inhibitors as potential anti-inflammatory drugsStudy mechanisms of converting arachidonic acid to prostaglandin by Prostaglandin synthase-1 enzyme (PGHS-1)

STRATEGY Model reaction mechanism and its intermediates by quantum chemistry and molecular dynamics methods.

OBJECTIVE PGHS-1 is important pharmacologi-cally as it is a target of aspirin and other nonste-roidal anti-inflammatory drugs. Understanding of prostaglandin synthesis mechanism will help to develop new specific inhibitors for PGHS-1.

IMPACT Produce alternative anti-inflammatory drugs with significantly reduced side effects.


AUTHOR E.E. Khrameeva, I.S.Filimonov, P.V.Vrzhesch (Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow 119992, Russia), I.S.Filimonov, P.V.Vrzhesch (International Research Center for Biochemical Technology, Lomonosov Moscow State University, Moscow 119992, Rus-sia)


33D R U G D E S I G N

TIP4P water diffusion factor calculationNeed for accurate calculation of diffusion factors in a various biological macromolecular systemsSTRATEGY Detailed comparison of different ap-proaches to diffusion factor calculation in water reveals advantages and faults of them and allows in future make a reliable estimations of this factor in a complex molecular models.

OBJECTIVE Making a molecular simulations of liquid water under different pressures and tem-peratures and calculation of water diffusion factors in this models. Comparison values calculated in a different manner with experimental ones and deter-mination in a such way restrictions and accuracy of different methods.

IMPACT Our results allow to make a reliable esti-mations of diffusion factors in a different molecular models.

USAGE Drug design.

AUTHOR Dmitry V. Zlenko (MSU, Biological Fac-ulty, Biophysical Chair, ERG Research Group)


34 O I L R E C O V E R Y

Simulation of oil deposit recovery by water floodingDynamic percolation model for optimization of oil recoverySTRATEGY Simulation of oil and water flows in the fractal structure of the oil layer.

OBJECTIVE Implement dynamic percolation approach for accurate modeling of some special features of oil reservoir.

IMPACT Optimization of oil recovery.

USAGE Spread of contaminants in soil.

AUTHOR M.N. Voronyuk (MSTU “Stankin”), M.V. Iakobovski (Keldysh Institute of Applied Mathematics)


35C L I M A T E M O D E L I N G

Climate modeling (climate change prediction by using coupled atmospheric and oceanic general circulation model)DRIVER Adequate representation of current climate using global climate models and forecast its short-and long-term variations.

STRATEGY Develop more accurate global climate models by representing key physical processes responsible for the formation of atmospheric and oceanic circulation.

OBJECTIVE Improve the accuracy of climate change predictions. Configure atmospheric, ocean, terrestrial, and cryospheric component models to answer policy and planning relevant questions about specific climate change adaptation and miti-gation scenarios.

IMPACT Mitigate deleterious effects of global climate change using modern global climate models as a tool for simulation and prediction.

USAGE Global climate models, climate change prediction, global warming.

AUTHOR E.M. Volodin (Institute of Numerical Mathematics of the Russian Academy of Sciences), D.V. Kulyamin (Research Computer Center of Lomonosov Moscow State University)


36 L O C A L - S C A L E A T M O S P H E R I C M O D E L I N G

Large eddy simulation of geophysical turbulent flowsFine modeling of turbulent processes in atmospheric flowsSTRATEGY Development of high-resolution numerical models of turbulent flows. Large Eddy Simulation of the turbulence in atmospheric boundary layer above heterogeneous surfaces under different meteorological conditions. Statistical analysis of the results. Investigation and param-eterization of the turbulent momentum, heat and moisture exchange.

OBJECTIVE Evaluation of local risks due to climate change and human activity. Improvement of param-eterizations of turbulent process in atmospheric boundary layer for advance in climate modeling and weather prediction.

IMPACT Improved technologies for numerical modeling of the atmospheric circulation on differ-ent scales.

USAGE Weather and climate prediction.

AUTHOR Glazunov A.V., Lykosov V.N. (Institute of Numerical Mathematics RAS, Research Com-puting Center Moscow State University), Mor-tikov E.V. (Research Computing Center Moscow State University)


37E N E R G Y

Surface-related multiple noise elimination for 3D seismic dataNeed for highly reliable and noise-free images of the Earth subsurface in seismic exploration for oil and gasSTRATEGY Studying possibilities of regular noise attenuation, in particular eliminating surface-re-lated multiple reflections from seismic records, for arbitrary 2D and 3D seismic acquisition patterns.

OBJECTIVE Developing a robust data-driven (model-free) algorithm for prediction and subse-quent adaptive subtraction of surface-related mul-tiple reflections. Implementing the algorithm as a software package for scalable seismic data process-ing on petascale compute clusters.

IMPACT The application of the software developed will enable to extract previously masked-by-noise information about oil and gas reservoirs in complex geological settings.

USAGE Exploration for oil and gas.

AUTHOR Evgeny Kurin, Mikhail Denisov (GEO-LAB Ltd.)


38 C H E M I S T R Y

Electrochemical oxidation of cerium and other metal atoms inside the carbon cage as studied by density functional theory

DRIVER Develop efficient electron acceptors with long charge-separation time.

STRATEGY Study isomeric forms of endohedral metallofullerenes in different charge states.

OBJECTIVE Apply density functional theory to study the electron transfer in endohedral metallofullerenes – hollow carbon clusters with en-capsulations of metallic atoms in their inner space – and determine energetic characteristics and mecha-nism of the electron transfer, especially focusing on the molecules with the endohedral redox activity (i.e., when the electron transfer to the molecule changes the charge state on the endohedral metal atoms while the carbon cage remains intact).

IMPACT Improve photovoltaic characteristic of the fullerene-based donor-acceptor dyads.

USAGE Photovoltaics, spintronics.

AUTHOR A.A. Popov (Chemistry Department, Moscow State Univeristy), L. Dunsch (Leibniz-Institute for Solid State and Materials Research, Dresden, Germany)


39C H E M I S T R Y

Interpretation of the hyperfine structure in the electron paramagnetic resonance spectra of large fullerene-based perfluoroalkyl-radicals

DRIVER Develop the scheme of the interpreta-tion of the hyperfine structure of anion-radicals of perfluoroalkylated fullerenes.

STRATEGY Study spin-density distribution in anion-radicals with different addition patterns.

OBJECTIVE Apply density functional theory to study spin-density distribution and hyperfine struc-ture in anion-radicals of perfluoroalkylated fuller-enes – study basis-set dependence of the predicted coupling constants – apply DFT-computed cou-pling constants in simulation of ESR spectra with subsequent inverse-problem solution – determine spatial localization of spin density and frontier orbitals to predict electron-accepting properties.

IMPACT Improve approach for interpretation of hyperfine structure in the spectra of electron paramagnetic resonance USAGE Photovoltaics, interpretation of ESR spectra of radicals, electro-chemistry.

AUTHOR A.A. Popov (Chemistry Department, Moscow State Univeristy), L. Dunsch (Leibniz-Institute for Solid State and Materials Research, Dresden, Germany)


40

Documents

Moscow State University supercomputing applications