Rensselaer Polytechnic Institute Graduate Research ... · The nuclear extracts are incubated with streptavidin magnetic beads coated with biotin-modified G4 oligonucleotides or control

Rensselaer Polytechnic Institute

Graduate Research Symposium

March 23th-24th 2018

ABSTRACTS

2

Contents Garo Agopian ................................................................................................................................................ 4

Anna Thonis .................................................................................................................................................. 5

Hayley McCullough ...................................................................................................................................... 6

Kathleen Morrissey ....................................................................................................................................... 7

Clifford Morrison .......................................................................................................................................... 8

Nathaniel Anderson ...................................................................................................................................... 9

Colin Garvey ............................................................................................................................................... 10

Indrani Bhattacharya ................................................................................................................................... 11

Abhishek Choudhary .................................................................................................................................. 12

Courtney Walton ......................................................................................................................................... 13

Ellie Irons .................................................................................................................................................... 14

Jennifer Howell-Clark ................................................................................................................................. 15

Tyree Ratcliff .............................................................................................................................................. 16

Montwaun Young ....................................................................................................................................... 17

Akashdeep Singh Virk ................................................................................................................................ 18

Mohammad Islam ....................................................................................................................................... 19

Siddharth Sundararaman ............................................................................................................................. 20

Majeed Simaan............................................................................................................................................ 21

Rufeng Ma .................................................................................................................................................. 22

Fangheng Sun.............................................................................................................................................. 23

Charles Hathaway ....................................................................................................................................... 24

Alagu Chidambaram ................................................................................................................................... 25

Brian Molnar ............................................................................................................................................... 26

Garett MacLean .......................................................................................................................................... 27

Matthew Dellehunt ...................................................................................................................................... 28

Jonathan Kulwatno ...................................................................................................................................... 29

Stephanie Jennings ...................................................................................................................................... 30

Xiangyu Gong ............................................................................................................................................. 31

Ashok Williams .......................................................................................................................................... 32

Jane Thibeault ............................................................................................................................................. 33

Amelia Peterson .......................................................................................................................................... 34

Robert Altman ............................................................................................................................................. 35

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James Hu ..................................................................................................................................................... 36

Carlos Ivan Rivera-Gonzalez ...................................................................................................................... 37

Diana Ramirez-Rios .................................................................................................................................... 38

Jennifer Rico-Varela ................................................................................................................................... 39

Rachel Dass ................................................................................................................................................. 40

Dhruv Patel ................................................................................................................................................. 41

Manish Bhat ................................................................................................................................................ 42

Anirban Chandra ......................................................................................................................................... 43

Zhongqian Lin ............................................................................................................................................. 44

Syed Islam ................................................................................................................................................... 45

Michael Jenkinson ...................................................................................................................................... 46

Antwane Mason .......................................................................................................................................... 47

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Garo Agopian1, Gina O'Connor1

1Rensselaer Polytechnic Institute

Establishing a Breakthrough Innovation Capability: The Case of SE Denmark

This case study explores a complex social phenomenon: establishing a breakthrough innovation

(BI) capability in a large, mature company under threat. The initiation and emergence of the capability are

the focus of the study. SE Denmark, a Danish energy and utilities company, is the subject case. Data

include depth interviews with company executives. Process mapping was used to analyze the data. The

research questions are based on Van de Ven and Huber’s (1990) framework for organizational change.

The analysis suggest that a newly established BI capability cannot start out working in a vacuum,

especially when the company has not had innovation as part of its ongoing business environment; it must

partner with existing business units and start out with aligned opportunities. While BI is the objective,

sometimes companies are so atrophied in their ability to innovate that this function starts with incremental

ideas; with time, the innovation group learns and becomes more trusted throughout the organization, and

the degree of innovativeness increases. The external threat creates enough urgency for company

executives to continue to improve this capability rather than backing away, as many companies do.

5

Anna Thonis1, Bradford Lister1


Predicting Climate-Induced Distributional Shifts for Puerto Rican Anoles

With some 400 known species, the lizard genus Anolis is the most speciose group of terrestrial

vertebrates in the world. Widely distributed, they occur throughout Central and South America, the West

Indies, and the southeastern United States. Although anoles have emerged as paradigmatic species in

ecology and evolution, relatively little research has addressed the effects of climate change on their

distributions. Over the past 40 years, Puerto Rico has experienced steady increases in ambient

temperature with mean maximum temperatures rising by as much as 2°C. Using distribution data from the

Puerto Rico Gap Analysis, WorldClim bioclimatic variables, and MaxEnt niche modeling software, we

projected potential changes in the distribution of ten species of Puerto Rican anoles for 2050 and 2070.

Our models used the HadGEM2-AO Global Climate Model paired with the IPCC’s Representative

Concentration Pathways (RCPs). RCP8.5 was chosen as it represents a likely scenario of continued high

greenhouse gas emissions through 2100. Under HadGEM2-AO RCP8.5 for 2050, Anolis krugi, A.

evermanni, and A. gundlachi are the most negatively impacted species, while for 2070 the most

negatively impacted species are A. gundlachi, A. evermanni, and A. cristatellus. The model also predicts

reductions in most suitable habitat across all ten Anolis species, ranging from -29.4% by 2050 to -39.6%

by 2070. Our study provides insights into the potential impact of continued climate change on Puerto

Rican anoles, and most likely other West Indian Anolis species, and has important implications for future

conservation efforts.

6

Hayley McCullough1


A Linguistic Analysis of the Rhetoric of Academic Articles in Psychology

The present study explores rhetoric in a quantitative manner by using integrative complexity and

its subtypes – linguistic variables that measure differentiation and integration – as dependent variables to

test possible correlations between the complexity of a published, peer-reviewed psychology article and

the number of times it is subsequently cited after publication. Eighty articles were randomly selected and

scored for complexity using the Automated Integrative Complexity (Conway et al., 2014; Houck et al.,

2014). Individual one-way ANOVAs revealed statistically significant main effects for all three types of

complexity, revealing predominantly curvilinear mean patterns: the lowest complexity scores appearing at

the two extreme of the spectrum and the highest complexity scores appearing in the middle. These

findings provide unique insight into the underlining psychology of the academic publication process and

into how rhetoric manifests across the quality spectrum, suggesting a general preference towards

simplicity in writing amongst academics; however, these findings also show that factors beyond

integrative complexity also influence an article’s subsequent citation count. Overall, the consistency and

overall strength of the present study’s results, despite the novelty and exploratory nature, provide a solid

foundation and justification for future quantitative rhetoric explorations in this research vein.

7

Kathleen Morrissey1


Potential G-quadruplex Forming Aptamers using a Genome-Inspired Reverse Selection Approach

Aptamers have become one of the leading alternatives to antibodies as affinity reagents to a wide

variety of targets including proteins. They were first discovered in 1990 using the process known as

Systematic Evolution of Ligands by Exponential Enrichment (SELEX). In this process, oligonucleotides

are selected from a combinatorial library for high affinity, highly selective binding to a specific target.

SELEX has discovered many aptamers but it does come with limitations that can hinder the process of

aptamer discovery, particularly in the case of potential aptamers that form multi-tier G-quadruplexes

(G4). G-quadruplex-forming sequences are found throughout the human genome and merit investigation

as potential aptamers. In our lab, we have developed a new genome-inspired, reverse selection approach

that allows us to explore these and other challenging secondary structures. In the reverse selection

approach, a specific DNA sequence from the human genome is used for affinity capture of proteins from

natural pools such as nuclear extracts. The nuclear extracts are incubated with streptavidin magnetic

beads coated with biotin-modified G4 oligonucleotides or control oligonucleotides. A rapid screening for

captured proteins is performed using MALDI-TOF MS to determine if there is any affinity capture of

proteins specific for the G4 DNA. If affinity capture is established, the capture experiments are repeated

on a larger scale and captured proteins are separated by gel electrophoresis. Bands specific for G4 DNA

are analyzed by LC-MS/MS to produce a list of possible protein matches. This list is used to guide our

selection of proteins for further interrogation using Western blots. Here we will present our results for

genomic-G4 forming sequences from the promoter regions of the human oncogenes c-myc, Rb, and

VEGF as potential aptamers toward proteins in nuclear extracts from the basal breast cancer cell line

MDA-MB-468.

8

Clifford Morrison1


Electrochemical Bioreactor Technology for Chemical and Biological Applications

Two seemingly distinct fields, industrial biocatalysis and microbial electrosynthesis, will be

viewed together through the lens of electrochemical bioreactor technology in order to highlight the

challenges that exist in creating a versatile platform technology for use in chemical and biological

applications. Industrial biocatalysis applications requiring NAD(P)H to perform redox transformations

often necessitates convoluted coupled-enzyme regeneration systems to regenerate reduced cofactor,

NAD(P)H from oxidized cofactor, NAD(P). Renewed interest in continuously recycling the cofactor via

electrochemical reduction is motivated by the low cost of performing electrochemical reactions, easy

monitoring of the reaction progress, and straightforward product recovery. However, electrochemical

cofactor regeneration methods invariably produce adventitious reduced cofactor side products which

result in unproductive loss of input NAD(P). Strategies for mitigating the loss of cofactor material in

industrially-scalable systems will be discussed. Microbial electrosynthesis is a form of microbially-driven

catalysis in which electricity is supplied to living microorganisms for the production of industrially-

relevant chemical products at higher carbon efficiencies and yields as compared to traditional, non-

electrically driven, fermentations. The biological engineering challenges involved in this task, and the

ways in which these challenges inform better electrochemical bioreactor design, will be discussed.

9

Nathaniel Anderson1, Peter Dinolfo2, Xing Wang2


2Center for Biotechnology and Interdisciplinary Studies

Center for Biotechnology and Interdisciplinary Studies

The ability to position light absorbing molecules with precision in the nanoscale has a large effect

on the efficiency of the transfer of energy between chromophores. Solar energy producing technologies

rely heavily on this performance and how well that energy can be passed into the system. Utilizing the

self-assembly of DNA nanostructures gives the ability to position and orient such chromophores with

nanometer resolution. In this work, DNA nanostructures combined with the versatile CuAAC click

chemistry reactivity is used to form a new scaffold onto which energy donor molecules can be positioned

around a central attachment point. The scaffold is built using a porphyrin molecule as the attachment

point allowing for convenient morphology for multiple single-stranded oligonucleotides to be covalently

bound. The porphyrin also acts as an energy transfer acceptor through Förster Resonance Energy

Transfer. This new scaffold has been purified, characterized, and used as an energy transfer system with

transfer efficiency nearing 90%. It provides a model system to identify parameters important to designing

robust energy transfer systems without the need for more complicated and potentially low yielding

chemistry necessary for nanoscale positioning.

10

Colin Garvey1

1 Rensselaer Polytechnic Institute

On the Democratization of Artificial Intelligence

Recently the "democratization" of artificial intelligence (AI) has been taken by several major tech

companies. What does this explicitly political claim mean? Some companies are offering APIs, libraries,

and developer tools online for free. There are two problems with calling this "democracy." First, how

does it differ from earlier "open source" efforts? Even where resources are made available, scarcities in

access make widespread participation practically unrealizable; a "digital divide" separates haves from

have-nots. Second, it is unclear that open access to datasets and AI tools online will contribute in any

meaningful way to improved democratic governance of society, or AI R&D itself. A stronger sense of

political democracy is needed. What would it mean to take seriously the political dimensions of the

"democratization" of AI? Applying Woodhouse's 20-point framework for demo-cratic decision making

through intelligent trial and error (ITE), our evaluation of AI R&D found considerable barriers to

democratization. 1) public deliberation is impaired by deterministic framings of AI's developmental

trajectory, prohibiting partisan disagreement and restricting discussion to a narrow set of concerns; (2)

most decision making processes are opaque, exclude most stakeholders, and allocate authority to

technical experts and business executives; (3) the rapid pace of AI R&D mitigates against stringent initial

precautions and disallows time for social organizations to learn and respond. Because addressing these

issues requires changes to the AI R&D process, the democratization of AI therefore requires social

innovations.

11

Indrani Bhattacharya1, Richard Radke1


Cognitive Environments that Facilitate Group Decision Making

Humans invest substantial time, energy, and money in group meetings in professional

environments every day. However, meetings are often inefficient, unfocused, and poorly documented.

Our vision is to create a multi-modal sensor-enabled room with advanced cognitive computing

capabilities. These include actively tracking the location, pose, and visual focus of attention of the

participants; distinguishing and clearly isolating the speech of several people talking at the same time;

learning and remembering the context of previous meetings; generating automated summaries; analyzing

participation shifts and meeting productivity; and ultimately contributing in real time to facilitate group

decision making. In addition to its potential economic impact, research in this domain will also assist

social psychologists interested in studying human interaction patterns in group meetings. Since meeting

participants could feel uncomfortable, self-conscious, or inhibited in the presence of active video cameras,

we instead propose privacy-preserving methods for human tracking using a sparse array of ceiling

mounted time-of-flight sensors. By integrating these with non-verbal audio information (speaker

segmentation, interruptions, tone of voice, prosody), we can study participation shifts, interaction links

between participants, and emergent leadership in groups. We evaluate our system on a lunar survival task

dataset collected in the Smart Conference Room at RPI.

12

Abhishek Choudhary1

Peter Kramer1


Mathematical Modeling of Intracellular Transport

We present a mathematical framework to analyze the intracellular transport inside an axon. Our

model captures the spatial dynamics and interactions of motor and cargo through a system of coupled

stochastic differential equations. Using the techniques of asymptotic analysis, the first passage time for

the reattachment of a tethered motor is computed. Through the application of renewal-reward theory we

are able to derive the key quantities of interest for the transport processes spanning over multiple attached

and detached phases of a single molecular motor and cargo complex.

13

Courtney Walton1, Judy Wu1, Jacob Shelley1


Detection and Sequencing of Biomolecules using Solution-Cathode Glow Discharge Mass Spectrometry

Many fields, especially those considered –omics, i.e. metabolomics, proteomics are in need of

fast, sensitive methods that can provide molecular information. Mass spectrometry is an analytical

technique that provides such information for biomolecules, but continues to rely on complex and costly

instruments capable of controllably fragmenting biopolymers for structural elucidation. Therefore, it

would be advantageous to develop an ionization source that, when paired with any mass spectrometer,

could tunably produce intact molecular ions and information-rich fragments.

We have recently found an ionization source capable of this feat: the solution-cathode glow

discharge (SCGD), which is an atmospheric-pressure glow discharge. The plasma of the SCGD is

sustained between a metal anode and a flowing, conductive solution, which serves as the cathode.

Analytes within the liquid stream are sputtered from solution and ionized by the glow discharge. The

SCGD is unique in that it produces both intact, gas-phase ions from labile biomolecules and with

parameter changes yields fragmentation of the species within the source. This presentation will focus on

the SCGD as an ionization source for biomolecule mass spectrometry. Recent progress in the detection

and tunable fragmentation of biomolecules including the ability to couple this source with high-

performance liquid chromatography (HPLC) will be demonstrated.

14

Ellie Irons1


Social-Ecological Art and Public Fieldwork in the (so-called) Anthropocene

This talk explores socially-engaged, environmentally oriented art in the context of the

Anthropocene debate, through the lens of my engagement with weedy plants and urban ecology. Focusing

on my collaborative project the Environmental Performance Agency (EPA*), I trace an interdisciplinary

path from feminist land art of the 1960s through social practice art and tactical biopolitics in the 2000s,

setting the stage for my current commitment to an artistic methodology I call “public fieldwork”. Drawing

on EPA* activities, I investigate the benefits of open, publicly accessible exchange between art and

ecology, and between humans and other life forms. Responding to Born and Berry’s concept of the

“public experiment” I explore tactics for resisting damaging dualisms arising from the simplification of

fields like Invasion Biology and Restoration Ecology. The artist/fieldworker becomes an intermediary to

dispel plant blindness and encourage place-based awareness of the more-than-human habitats we create in

constructing our cities.

*Named in response to the proposed defunding of the US Environmental Protection Agency, the

Environmental Performance Agency has no affiliation with the US EPA, but has consciously chosen to

appropriate its acronym."

15

Jennifer Howell-Clark1, Christian Wetzel1, T. Paul Chow1, Zhibo Guo1


Impurity Control for High Performance Gallium Nitride Devices

Gallium Nitride (GaN) is an attractive choice for high-voltage power devices due to its high

breakdown field (> 3 MV/cm). This property, stemming from its wide band gap of 3.4 eV, allows for

large voltages to be supported on thinner, more heavily doped layers than would be possible for

conventional materials like silicon, which have smaller critical fields. Consequently, the on-resistance of

high voltage power devices can be reduced, improving the design tradeoffs of semiconductor power

devices by an order of magnitude or more; these improvements allow for more efficient power electronic

systems.

However, the material properties of GaN present several practical challenges which are not

encountered in silicon. Many of these challenges center on doping and impurities. Magnesium is the only

impurity that has been shown to reliably result in p-type conductivity in GaN, but Mg performs poorly in

comparison to p-type doping in silicon. We seek to both improve upon existing Mg doping techniques,

and to explore alternate impurities and methods for use in high-voltage power devices. In device

structures where Mg is not necessary, we are investigating the feasibility of using carbon as an acceptor

impurity, enabling device structures and designs that would otherwise not be possible.

16

Tyree Ratcliff1


Development of a Transferable Atom Equivalent method for Materials QSPR (Quantitive Structure

Property Relationship) modeling of metal containing systems.

The Quantum Theory of Atoms in Molecules is used to build a library of Transferable Atom

Equivalent (TAE) descriptors capable of adequately describing the quantum-chemical properties of metal-

containing organometallic materials. The development of metal-based TAE descriptors allows for more

precise description of the chemical space with greatly diminished calculation time, providing better

modeling potential. The goal of this project is to facilitate the advancement and development of novel

materials that are capable of meeting the demands of a growing technological age. With the development

of TAE techniques for coordination environments, metal TAE descriptors can be developed and applied

to a range of molecular environments. Once developed, these descriptors will be capable of capturing the

electronic properties of metal systems without a large computational overhead.

17

Montwaun Young1, Sunil Badal1, Jessica Hellinger1, Jacob Shelley1

Rensselaer Polytechnic Institute

Development of a Simultaneous Multimodal Chemical Imaging Platform Based on Optical and Mass

Spectrometries

Recent advances in mass-spectrometry instrumentation have led to several new capabilities,

including the ability to generate chemical images from solid samples. However, unequivocal analyte

identification in these imaging experiments requires multiple analytical approaches performed on the

same sample, termed 'multimodal chemical imaging'. Success in generating high-resolution chemical

images has been achieved with instruments based around mass spectrometry due its high selectivity and

specificity. Several mass-spectral imaging (MSI) techniques have been developed which provide either

molecular or elemental maps as is dictated by the ionization source used. However, mass spectrometry is

inherently a destructive technique (i.e. the analyzed sample is consumed during the analysis). Therefore,

combining MSI with approaches that simultaneously provide orthogonal analytical information would be

most advantageous.

Here, we describe a new multimodal chemical imaging approach to simultaneously provide

molecular and elemental chemical information of solid samples with little to no sample preparation. The

dual imaging approach is achieved through laser sampling followed by simultaneous mass-spectrometric

and optical-emission measurements. Molecular chemical images are obtained by laser ablation followed

by flowing atmospheric-pressure afterglow (FAPA) mass spectrometry. At the same time, optical

emission from a laser-induced plasma is used to provide elemental information. Instrument design and

preliminary figures-of-merit will be presented.

18

Akashdeep Singh Virk1, Zvi Rusak1


Transonic flow of steam with non-equilibrium and homogeneous condensation

A small-disturbance model for studying the physical behavior of a steady transonic flow of steam

with non-equilibrium and homogeneous condensation around a thin airfoil is derived. The steam

thermodynamic behavior is described by van der Waals equation of state. The water condensation rate is

calculated according to classical nucleation and droplet growth models. The current study is based on an

asymptotic analysis of the fluid flow and condensation equations and boundary conditions in terms of the

small thickness of the airfoil, small angle of attack, closeness of upstream flow Mach number to unity and

small amount of condensate. The asymptotic analysis gives the similarity parameters that govern the

problem. The flow field may be described by a non-homogeneous transonic small-disturbance equation

coupled with a set of four ordinary differential equations for the calculation of the condensate mass

fraction. An iterative numerical scheme which combines Murman & Cole's (1971) method with

Simpson's integration rule is applied to solve the coupled system of equations. The model is used to study

the effects of energy release from condensation on the aerodynamic performance of airfoils/blades

operating in steam at high pressures and temperatures and near the vapor-liquid saturation conditions.

19

Mohammad Islam1


Morphology and mechanics of fungal mycelium

We study here a unique biomaterial developed from fungal mycelium, the vegetative part and the

root structure of fungi. Mycelium has a porous and filamentous network like structure, in which the

mechanics is predominantly determined by individual filament properties and network architecture. We

aim to identify the system parameters that control the mechanical behavior of mycelium based materials

and to develop relevant material design rules. To this end, we report the morphological and mechanical

characterization of mycelium through a synergetic combination of microscopic imaging, mechanical

testing and computational modeling. Our experimental results reveal that mycelium exhibits significant

non-linear stress-strain behavior both under tension and compression. Significantly, we observe that

mycelium exhibits considerable strain hardening before rupture under tension and it mimics open cell

foam behavior under compression with strain dependent hysteresis and stress softening behavior under

cyclic loading condition. Based on our morphological characterization and experimental observations, we

have developed a topologically equivalent random fiber network model which provides further insight

into the microstructural origin of mycelium’s mechanical response.

20

Siddharth Sundararaman1, Liping Huang1, Walter Kob2, Simona Ispas2

1 Rensselaer Polytechnic Institute

2University of Montpellier, Montpellier, France

New Optimization Scheme for Potential Development for Multi-component Oxide Glasses

A dearth of satisfactory interaction potentials for multi-component oxide glasses that can

reasonably describe a variety of properties is a major stumbling block facing the glass community. In this

work, a new optimization scheme was developed to parameterize effective pairwise potentials for

molecular dynamic (MD) simulations of multi-component oxide glasses. Our approach was to fit to

results from accurate first principles calculations and explicitly incorporate the radial distribution function

(RDF) of the equilibrium liquid at multiple temperatures, the vibration density of states (VDOS) and the

density of glass at different pressures into the cost function of the fitting scheme. This new optimization

scheme has successfully improved potentials for silica glass and alkali silicate glasses, which can not only

predict the elastic moduli at ambient conditions, but also their response to external stimuli like high

pressure and temperature. This new optimization schedule is being extended to multi-component oxide

glasses.

21

Majeed Simaan1


Estimation Risk and Implicit Value of Index-Tracking

I study Roll’s (1992) conjecture that there may exist an implicit value in index-tracking relative to

forming MV-optimal portfolios. I show, analytically, that the conjectured implicit value is evident in

terms of lower estimation error and higher out-of-sample utility. The implicit value improves with risk

tolerance, asset betas, and the number of assets, however, diminishes with market volatility and sample

size. A battery of empirical tests supports my analytical conclusions and indicate that the implicit value is

most evident in cases associated with high estimation error. The improvement implies higher risk-

adjusted returns, lower volatility, higher Sharpe-ratio, lower turnover, and larger opportunity cost.

22

Rufeng Ma1, Kristen Mills1


Mechanosensitivity and motility of NF1+/-, NF2+/- and healthy dermal fibroblasts

Cells sense the physical properties of their extracellular environment and translate them into

biochemical signals. Neurofibromatosis type 1 (NF1) and Neurofibromatosis type 2 (NF2) are two tumor-

associated genetic disorders in which the proteins encoded are involved in the cell mechanosensing or

motility pathways. The neoplastic origin of neurofibromas, benign tumors associated with the disease, are

believed to be NF1-deficient (NF1-/-) Schwann cells, but haploinsufficient (NF1+/-) stromal cells, such as

fibroblasts, are suspected to play a role in the development of tumors associated with the disease. Little

work has been invested to study the mechanobiology of these cells. Here, we present a detailed study of

the influence of local variations in substrate geometry on the spreading, orientation, and stress fiber

expression of dermal fibroblasts (DFs).

23

Fangheng Sun1, Sunil Badal1, Jessica Hellinger1, Jacob Shelley1


Mixed-gas Flowing Atmospheric-Pressure Afterglow as an Atmospheric Pressure Chemical- and Photo-

ionization Source for Mass Spectrometry

Plasma-based ambient desorption/ionization (ADI) techniques, which rely on low power

electrical discharges to desorb/ionize analytes from their native environment, have received considerable

attention due to their simple construction and operation, rapid sample analysis times, and high sensitivity.

Most plasma-based ADI sources generally use helium as the discharge gas due to the large reaction cross

section of excited helium species with atmospheric gases, such as N2 and H2O, which leads to substantial

reagent-ion densities and, ultimately, better sensitivity. Despite the extensive use of helium, some mixed-

gas systems have been shown to improve the analytical performance. In the present study, we explore

changes in discharge processes and ionization chemistry, through optical and mass spectrometries, with

the addition of molecular gases to the helium discharge gas of a flowing atmospheric pressure afterglow

(FAPA) ADI source. Furthermore, the role of photons emitted by FAPA glow discharge in analyte

ionization was also studied. The chemical reagent ions and photons were separated by MgF2 window and

only photons were used for analyte ionization. Mass spectra for a range of analytes were collected with

FAPA glow discharge as a photoionization source. Effects of discharge current, discharge gas

composition, and dopants on photoionization characteristics will also be discussed in this presentation.

24

Charles Hathaway1


Broadening the Applicability of Software Metrics with Biological BROADENING THE

APPLICABILITY OF SOFTWARE COMPLEXITY METRICS WITH BIOLOGICAL Analogues

Software metrics represent an application of conventional computer science to itself in an attempt

to quantify the complexity of software systems. Many of the conventional metrics proposed in academia

and industry find their roots in a top-down composition that is so similar to the way conventional AI has

been done prior to the surge in machine learning techniques. As software becomes increasingly

networked together, the opportunity for bottom-up approaches to software complexity becomes more

apparent. The complexity concepts created for biological systems, such as ecological biodiversity, neural

pattern recognition, and genetic mutation rate, offer "proof of concept" illustrations that useful global

measures can offer insights into the behavior of complex systems. Thus computational analogs to these

biological complexity metrics may offer deeper understanding of how complexity occurs in contemporary

networked computing systems. We compare traditional software metrics to these bio-inspired measures in

many contexts, such as bug-finding, measuring student comprehension, and using metrics as a way of

quantifying generative justice.

25

Alagu Chidambaram1


Electrical Stimulation increases primary human Schwann cell number and supports angiogenesis.

Neurofibromatosis Type 2 (NF2) is an autosomal dominant genetic disorder characterized by

multiple tumors to the nervous system, with the most common being vestibular Schwannoma or acoustic

neuroma. To date, changes to NF-2 Schwannoma cells caused by electrical stimulation have not been

examined. Furthermore, a composite model of the local tumor environment, including vasculature has not

been developed. Human Schwann cells are seeded onto a coverslip and exposed to an electric field. HSC

proliferation was estimated by counting nuclei and comparing to unstimulated control. Early

reorganization of HUVECs was characterized using a 2D angiogenesis kit. Electrical stimulation

increases the growth rate of wild type human Schwann cells and supports angiogenesis. Schwann cell

conditioned medium also supported 2D angiogenesis.

26

Brian Molnar1, Sunil Badal1, Jacob Shelley1


Rapid, Plasma-Assisted Synthesis of Unsaturated Carbonyls from n-Alkanes

Unsaturated carbonyl compounds are used extensively as starting materials in industrial and

pharmaceutical syntheses. Well-established synthetic methods such as the aldol condensation offer yields

between 60-80%. However, the requirement for two starting materials and heat can increase production

costs. Furthermore, to improve the reaction yield further requires reaction times in excess of 12 hours and

sometimes additional materials, such as catalysts. Gas-phase synthesis could be an attractive alternative

because it allows for much faster reaction rates by increasing the rate of diffusion and lowering the energy

barrier of the reaction. However, traditional gas-phase synthesis can still proceed slowly. Reaction rates

could be much improved by using gas-phase ion-molecule chemistry. In this work, the afterglow of a

helium atmospheric pressure glow discharge is used to produce gaseous reactant ions, which react rapidly

with neutral aliphatic compounds to yield unique products. Specifically, a method for regioselectively

synthesizing unsaturated carbonyls from n-alkanes was observed. Reaction products were characterized

online during the reaction with high resolution mass spectrometry, which revealed that these reactions

occur on a sub-millisecond timescale. Efforts to scale up these reactions as well as characterization of

these reaction mixtures with other analytical methods will also be described.

27

Garett MacLean1, Jacob Shelley1


Uranium Isotope Ratio Analysis with Solution-Cathode Glow Discharge Mass Spectrometry

The International Atomic Energy Agency (IAEA) monitors the enrichment of uranium at

production facilities by collecting and shipping samples to designated laboratories for analysis and sets

International Target Values (ITVs) for uncertainty goals to ensure the reliability of an analytical technique

for isotope-ratio measurements. Increasing restrictions on the transport of enriched uranium samples has

created a demand for rapid, on-site methods of uranium-enrichment assay. Here, a new ionization source

for mass spectrometry (MS), the solution cathode glow discharge (SCGD), is evaluated as a potential

ionization source for U-isotope ratio measurements when coupled with an Exactive Plus Orbitrap mass

spectrometer. The SCGD consists of a low-power (70 W) direct current plasma between an anode and the

surface of a flowing, conductive sample solution with ambient air serving as the discharge gas.

Preliminary optimizations have resulted in 235U/238U precisions as low as 0.09% relative standard

deviation (RSD) for a 500 part-per-billion U-solution of 0.37% 235U abundance. The precisions attained

demonstrate that SCGD-MS is capable of exceeding the IAEA’s ITVs for established techniques, and

shows great promise as a transportable ionization source for on-site isotope-ratio measurements.

28

Matthew Dellehunt1


Mc Br Es -- Micro-climate Bio-remediation Ecological System

This project aims to remediate the Heat Island effect in New York City by deploying an Oyster

and micro-Algae Ecological System into the environment, providing cleaner air, through a CO2

absorption and bio-remediation process of the Algae. Through lower CO2 levels and evaporative cooling,

Micro-climate will be formed around each food cart and around the commissary.

This project also aims to clean and utilize the Hudson river shed to grow and produce oysters and

algae for human consumption. To do this, water bio-remediation treatment occurs to remove PCBs

through algae consumption, then is passed through pressurized barriers to the oyster habitats where

sediment and further organic material is remove, finally passing back out into the Hudson water shed as

fully cleaned water

29

Jonathan Kulwatno1, Kristen Mills1, Mihaela Skobe2, Matthew Getzin1 Ruth Griswold2

1Rensselaer Polytechnic Institute, 2Ichan School of Medicine, Mount Sinai

Tumor Growth in Vessel-Like Microchannels

Metastases account for approximately 90% of deaths associated with cancer. They are secondary

tumors that develop from the metastatic cells of a primary tumor, where the lymphatic system has shown

to be a major contributor. Here, the lymphatic vasculature can act as a conduit for the dissemination of

tumor cells, but also a niche for which tumor cells can develop within the vessel and form so called

intralymphatic tumors. In this project, we explore how the geometry and mechanical constraint as by a

lymphatic vessel contributes to the growth and morphology of such intralymphatic tumors. HCT116

human colon cancer cells were introduced and allowed to growth within a hollow microchannel made in

bioinert agarose. The concentration of agarose was adjusted to provide different mechanical stiffness that

mimicked the stiffness of healthy and diseased tissues. As a result, the stiffness of the geometric

constraint influenced the overall shape of the tumors, but did not affect the volumetric growth rate.

30

Stephanie Jennings1


The Horrors of Transcendent Knowledge: A Feminist-Epistemological Approach to Video Games

The purpose of this presentation is to advance strategies for understanding video games from

situated perspectives. I outline a subjective, intersectional framework that draws upon feminist-

epistemological theories to call attention to ways that players may generate feminist ways of knowing

through their own playful experiences of video games.

To demonstrate this framework in action, I explicate sections of my own playthrough of From

Software’s (2015) Bloodborne. While the Dark Souls franchise—of which Bloodborne is a part—could

be critiqued as a violent masculine power fantasy, I suggest that women may find enjoyment in

Bloodborne’s violence and difficulty. I understand Bloodborne as dealing expressly with epistemological

concerns, functioning largely as a critique of traditional Western knowledge production. As such, I

suggest that women may experience the game’s violence as a symbolic language of liberatory power

against oppressive patriarchal structures.

My account of Bloodborne is just one example of how to broaden understandings of play-styles,

demonstrating a resistant channel for situated knowledge and experience. By offering insight into the

possible pleasures, desires, and experiences of playing video games as a woman, I argue that Bloodborne

reveals the horrifying consequences of the pursuit for transcendent, rational, objective—yet

hegemonically male-centered—knowledge.

31

Xiangyu Gong1, Kristen Mills1


Cell division in multicellular tumor ellipsoids in a non-adhesive 3D environment

Mechanical stress, a key factor in the tumor microenvironment, is known to play a role in cell

division and tumor growth. Our current research aims to reveal the links between the biomechanical

environment, the force generating capability of cells, and tumor shape. Our in vitro 3D tumor models

have shown that tumor shape is a function of the stiffness of the mechanical environment. Tumors adopt

ellipsoidal shape in stiffer, non-adhesive, inert hydrogels. Similar shapes have also been observed by in

vivo studies. However, the perturbation of the tumor shape and the interplay between this shape and cell

divisions in a tumor still remain elusive. Here, our tumor growth monitoring from the single-cell level

over a week via brightfield time-lapse imaging captured the symmetry breaking moment of tumor

ellipsoid development. Furthermore, 3D time-lapse confocal imaging on a fluorescence-labeled tumor

ellipsoid embedded in agarose hydrogel over a 24-hour period allowed us to visualize and map all cell

divisions in this complex 3D shape. The preliminary results suggest a unique distribution of cell division

events in a 3D ellipsoidal tumor.

32

Ashok Williams1, Kristen Mills1, Rachel Dass1, Elizabeth Pontius1, James Nowak1, Johnson Samuel1


Electrospinning of Hybrid Scaffolds to Mimic the Tumor Microenvironment

The extracellular matrix (ECM) provides structural, biophysical, and biologically active support

to the cells within the microenvironment. During the progression of solid tumors, the ECM is altered

through deregulated fiber growth, and increased fiber reorganization. The biomechanical interactions of

cancer cells with the extracellular matrix are of key interest when developing in vitro cancer models

because tumor behaviors are highly influenced by their microenvironments. Specific biophysical variables

are necessary to recapitulate the in vivo environment. Previous research has focused on 2D structures to

monitor cell growth, or simple hydrogel models to produce a 3D environment. We aim to produce a

fibrous hydrogel to recapitulate native ECM that physiologically and mechanically mimic the tumor

microenvironment. Tunable electrospun fibrous mats composed of polycaprolactone (PCL) were

manufactured to assess cell interactions as a preliminary step to developing 3D in vitro models. This

process of electrospinning was then used in conjunction with agarose formation to produce a uniformly

mixed fibrous hydrogel to encapsulate cells.

33

Jane Thibeault1


Expression of Kinetically Stable Proteins in Pseudomonas aeruginosa and Staphylococcus aureus

While most proteins are susceptible to denaturants, detergents, and proteases, hyperstable or

kinetically stable proteins (KSPs) are highly resistant to such degradation and unfolding. Of particular

interest, KSPs are resistant to denaturation induced by the detergent sodium dodecyl sulfide (SDS). The

gel electrophoresis method diagonal two-dimensional (D2D) SDS-PAGE exploits this SDS-resistance and

is coupled with MALDI-TOF MS in order to explore the presence and roles of KSPs in complex

biological lysates. This study will apply the D2D SDS PAGE method to the pathogenic model systems

Pseudomonas aeruginosa and Staphylococcus aureus to further elucidate structural and functional trends

common to hyperstable proteins. Further experimentation with modified environmental conditions,

including changing growth phase, co-culturing the two systems, and altering the active respiration

pathways, will modulate transcription and ultimately the protein and KSP expression in the systems.

These modifications mimic naturally occurring growth environments for P aeruginosa and S. aureus

which may allow for additional KSP identifications not seen under the standard laboratory growth

conditions. Analysis of all the KSPs identified will advance the understanding of protein kinetic stability

and may provide information applicable to science and engineering endeavors with medical and

biotechnological relevance.

34

Amelia Peterson1, Shayla Sawyer1


An ultrasensitive ultraviolet (UV) photodetector is created through the integration of a UV-

sensitive ZnO quantum dot (QD) layer, a highly conductive graphene channel, and a 10-

decyltrichlorosilane SAM spacer for mitigation of mobility deterioration in the graphene. The synergistic

combination of these nanocomposite materials yields excellent device performance relative to commercial

UV photodetectors, and its applications include space-to-space communications, environment monitoring,

and missile plume detection. Experimental results from our fabricated device show a high

photoresponsivity of 108 A/W, a photodetectivity of 5.1x1013 Jones at 368nm and room temperature, a

high phototransistor gain of 3x109 and a UV to visible light rejection ratio of 103. To improve upon the

overall performance of this UV photodetector, potential device and nanostructure geometries are explored

through simulation in NEMO5 and Sentaurus. The simulation setup is confirmed by comparison to

measurements of the fabricated device from published results. Generated plots include photocurrent as a

function of drain-source voltage, photoresponsivity, gain, and transient response. The effect of graphene

defects on dark current is investigated, and the relationship between graphene layer geometry and overall

device performance is explored. The results found in this work will guide the development of future

device designs and fabrication methodology for this UV sensor.

35

Robert Altman1, Xiangyu Gong1, Kristen Mills1


Microfluidic Drop Patterning Chip

Cancer treatment relies heavily on selecting the proper cocktail of drugs specific to a patient’s

individual cancer cells. Selection of this cocktail is done by growing the cancer cells in vitro (outside of

living body) in the 2d environment of a petri dish. A 3d encapsulation of the cells would provide a more

accurate representation of the in vivo (within living body) environment. Cells grow differently in a 3d

environment than in 2d, and this difference could change how the cancer cells react to the cancer

treatment drugs. The goal of my research is to develop a method of depositing cells well aligned to a grid

and a single layer within the 3d agarose substrate to allow for automated imaging. First, to accomplish

this, a microfluidic device is used to capture the cells in the desired pattern, then the cells space above the

cells is flooded with agarose. Once covered in agarose the device is inverted allowing for the cells to

drop. By varying the curing time in relation to the mass of the captured cells, the cells can be embedded

on the same plane as well as in the array of the microfluidic device.

36

James Hu1


Engineering Microbial Electrosynthesis in Escherichia coli for Enhanced Carbon Efficiency

Microbial electrosynthesis, a process by which electrons are supplied to microorganisms through

an electric current, allows for enhanced carbon efficiency in industrially-relevant bioprocesses.

Artificially providing reducing equivalents by supplying an electron mediator allows cells to shuttle

electrons in, increasing the carbon efficiencies and theoretical yields of chemical reactions for high value

products. This changes the stoichiometry of industrially-relevant bioprocesses that rely on redox

reactions, resulting in more efficient utilization of carbonaceous reactants.

Several organisms have been identified as being able to naturally conduct electricity; in anoxic

environments Shewanella oneidensis produces electrically-conductive nanowires to reduce metals while

organisms such as Gallionella capsiferriformans and Sideroxydans lithotrophicus have naturally occurring

metal-oxidizing pathways. Replicating these pathways in Escherichia coli would allow for the wide-

spread use of microbial electrosynthesis for enhanced industrial bioprocesses.

Creating a genetic platform for inserting the various combinations of electrosynthetic pathway

components into the microorganism is crucial for the development of a relatively straightforward

approach for optimizing electron uptake in E. coli. Novel analytical techniques will be developed to

determine the engineered organism’s electrosynthetic capabilities. The techniques, challenges, and future

work will be discussed.

37

Carlos Ivan Rivera-Gonzalez1, Diana Ramirez-Rios1,

Cara Wang1, Jose Holguin-Veras1, Joshua Schmid1


Public Opinion Towards Crowd Deliveries in New York State

Crowd deliveries is a business model in freight deliveries that is part of the new trend of shared

economies. It matches excess vehicle capacity from the common person or crowd (who act as the courier)

with the demand of others geographically dispersed individuals who require their merchandize to be

delivered. In the last few years, there are more than 40 start-up companies in the U.S and more than 50

worldwide that use this new concept. This innovative model has shown to make urban freight more

efficient particularly in the last-mile delivery, showing potential reductions for both transportation costs

and environmental impacts. This study is intended to understand the shopping behaviors of individuals

and their acceptance, or not, of these alternate delivery services, such as crowd deliveries, and their

feasibility in accordance to today’s market conditions. Initial empirical findings in New York State

suggest that there is still some resistance in accepting Crowd Deliveries but some segments of the

population are more inclined to accept this new trend of deliveries.

38

Diana Ramirez-Rios1, Jose Holguin-Veras1, Shama Campbell1,

Lokesh Kalahasthi1, Carlos Gonzalez-Calderon1, Jeffrey Wojtowicz1


Quantification of Freight and Service Activity Trends in Cities

The purpose of this presentation is to demonstrate the potential of freight trip generation and

service trip attraction models in studying freight and service activity (FSA) patterns for cities of various

sizes. Models that estimate freight and service vehicle trips were incorporated in a software that uses as

inputs the publically available ZIP code business patterns data for various industry sectors at ZIP code

level. Three city sizes were considered: Small, Intermediate and Large and the North American Industry

Classification System (NAICS) at 2-digit level was considered for industry type. The results shown

correspond to eight cities (two small, three intermediate, and three large) that correspond to different

ranking percentiles of population density. The cities were compared with respect to various metrics of

FSA estimates. These ZIP code level estimates are very helpful in identifying zones with high freight or

service activity. The results show that the distribution of NAICS and the size of the firms play a

significant role in the generation FSA.

39

Jennifer Rico-Varela1, Leo Q. Wan1, Kathryn Worley1


Cellular Chirality as a New Screening Platform for Human Laterality Disorders

During early stages of pregnancy, exposure to certain pharmaceutical drugs can lead to human

laterality disorders, resulting in improper positioning and shaping of visceral organs within the body.

Heterotaxy and isomerism are the most common types of laterality disorders, and related to the

disturbance in the establishment of left-right (LR) asymmetry. The LR symmetry, also known as chirality,

is a conserved property of organisms. The LR axis is developed from the pre-establishment of the

anterior-posterior (AP) and dorsal-ventral (DV). Due to the lack of in vitro high-throughput platforms for

testing the effects of drugs during pregnancy, the underlying mechanisms of disorders are understudied.

Recently increasing evidences suggest that embryonic LR asymmetry may arise from cellular LR

asymmetry or cell chirality. Our objective is to mimic LR symmetry breaking during embryogenesis by

combining microtechnologies with the culture of human embryonic stem cells (hESCs). Herein, we

screened dozens of stem cell signaling small-molecule drugs using an in vitro platform, which

recapitulates the complexity of in vivo chiral morphogenesis in 3D at the cellular level. For this purpose,

we embedded single hESCs within a Matrigel bilayer of different concentrations (100% bottom and 2%

top layers), and exposed them to different chemicals such as regulators of JAK/STAT, GSK3, Wnt, and

TGF-beta. From our preliminary results, we observed significant changes in rotation directionality

compared to the control groups. Interestingly, these respective signaling pathways play an important role

in the establishment of embryonic LR asymmetry, demonstrating the value of in vitro screening. In

ongoing studies, we are exploring a new microfluidic approach to better recapitulate the cellular

microenvironment at which the aforementioned axes are established via morphogen gradients utilized in

embryogenesis. Such platforms can become powerful tools to not only study embryogenesis, but also to

identify teratogens for birth defects prevention.

40

Rachel Dass1, Ashok Williams1, Kristen Mills1, James Nowak1, Johnson Samuel1


Manufacturing of 3D Fiber-Reinforced Hydrogels for Tumor Growth Studies

It is well established that tumor growth and tumor cell behaviors are significantly affected by

increased stiffness that takes place, in part due to increased fiber density. The full extent to which

microenvironmental mechanics plays a role in tumor growth and progression is still unknown. Current

models to study these behaviors are limited to 2D or include only the fiber or gel portion of the ECM. In

order to isolate the effects of the fiber-gel composite ECM morphology and mechanics, we have

developed a 3D fiber-reinforced hydrogel consisting of biocompatible polymer fibers to study the growth

of cancerous tumors. By varying process parameters, we can create 3D fiber-reinforced hydrogels that

mimic the morphology and mechanics of healthy and diseased tissue.

41

Dhruv Patel1

1 Rensselaer Polytechnic Institute, Scientific Computation Research Center

It is a well known fact that benign tumors tend to be mechanically homogeneous, while malignant

tumors are more heterogeneous. Likewise, benign tumors are elastically linear, whereas malignant tumors

are non-linear. Traditional elastography techniques use these differences to diagnose disease and/or

classify tumors. However, these techniques require the solution of an inverse elasticity problem, which is

quite expensive, and often difficult to solve. Inspired by the recent developments in computer vision and

deep learning, we propose a different strategy and use deep neural networks to classify the tumor based

on its mechanical properties without solving an inverse problem. We train a Convolution Neural Network

(CNN) on in-silico displacement data for this classification task. We also investigate the effectiveness of

transfer learning in this context to mitigate the problem of non-availability of sufficient labeled data in

medical imaging domain.

42

Manish Bhat1, Steven Cramer1, Akshat Mullerpatan1, Anurag Rathore2

1Rensselaer Polytechnic Institute, 2Indian Institute of Technology, Delhi

Continuous Precipitation of Antibodies

Since starting out as an undergrad, I have worked on making drugs that can cure cancer cheaper.

The drug, I am working on is mAb( monoclonal antibody). 70% of the cost is due to purifying it. I am

trying to replace a standard method used currently called Protein-A chromatography with continuous

precipitation. It is cheaper but, can also achieve the same level of purity. This sounds awesome, what is

the catch? Protein-A chromatography has been done for almost 4 decades. It is a very reliable method to

purify drugs. I need more data to fully confirm the high level of purity of continuous precipitation.

Ultimately, the safety of the patient matters the most, and thus reliability is key. This is why, I have come

to RPI to continue my research into continuous precipitation under Professor Cramer who has done some

really fascinating research in the field of drug purification.

43

Anirban Chandra1, Fan Yang1, Yu Zhang1, Onkar Sahni1, Assad Oberai1, Mark Shephard1


Solving Phase change problems using Unstructured Finite Elements

Interfacial phase-change processes such as evaporation/condensation of a liquid (or combustion

of a solid) are commonplace in several engineering applications. Numerical modeling of such physical

phenomenon necessitates some special attention because of large density ratio over phases, discontinuous

fields at the interface and rapidly evolving geometries. Here we present a mathematically consistent and

robust computational approach to address these issues. Stabilized finite element methods on mixed

topology unstructured grids is utilized for solving the compressible Navier-Stokes equations. Flux jump

conditions derived from conservation laws at the interface are handled by using discontinuous

interpolations, while the continuity of temperature and tangential velocity is ensured using a penalty

parameter. The Arbitrary Lagrangian-Eulerian (ALE) technique is utilized to explicitly track the interface

motion - the mesh at the interface is constrained to move with the interface while elsewhere in the

domain it is moved using the linear elasticity analogy. In addition, mesh modification is done when the

mesh becomes too distorted.

44

Zhongqian Lin1


The Structural Study of the HINT Domain of the Hedgehog Protein

Hedgehog signaling pathway is a developmental pathway that is essential for adult stem cell

maintenance. The malfunction of this pathway is associated with a variety of cancer such as prostate

cancer and basal cell. In this study, we purified a mutant segment of the Hedgehog ligand precursor and

study its structure using Nuclear Magnetic Resonance. Studying the structure of the protein's potential

active site would allow us to learn about the detailed mechanism of the pathway activation and provide a

new approach to understand cancer development.

45

Syed Islam1, Ji Jiang1, Qiaobei Dong1, Huazheng Li1, Miao Yu1


High Temperature Separation of H2/N2 using SAPO-34 Membranes

Synthesized on Ceramic Hollow Fibers

Zeolite membrane has drawn tremendous interest in gas and liquid separations due to its well-

defined pores and channel structure. With the advantages of high chemical, thermal and mechanical

stability, zeolite membranes could be used in harsh environment such as high temperature and pressure.

In this study, SAPO-34 membranes were successfully synthesized on the outside of ceramic hollow fibers

by secondary growth method. The influence of synthesis parameters, such as precursor composition, seed

particle size, morphology, concentration and stabilizer concentration in the seed suspension, and seeding

conditions, and of pore size of support, on the separation performance of SAPO-34 membranes was

studied in detail. The results indicated that high quality SAPO-34 membranes with thickness of < 5 µm

could be achieved by using high aspect ratio zeolites as seeds. The as-synthesized membranes exhibited a

high H2 permeance of 2.9×10-7 mol/(m2·s·Pa) and H2/N2 separation selectivity of 19 at 400 oC and

pressure drop of 100 psig. Further, the membranes were stable at temperature up to 400 oC and pressure

drop up to 100 psig for > 2.5 h, which make it very suitable for industrial applications such as the

decomposition of NH3 for the production of high purity H2.

46

Michael Jenkinson1, Jeffrey Banks1, William Henshaw1, Jordan Angel1, Donald Schwendeman 1


A High-order Accurate Scheme for Maxwell's Equations with a Generalized Dispersion Model

A high-order accurate scheme for solving the time-domain Maxwell's equations with a

generalized dispersion model is described. Maxwell's equations are solved in second-order form for the

electric field. General dispersion models are treated with the addition of one or more polarization vectors

which are coupled to the electric field and its time-derivative through a set of second-order ordinary

differential equations (the so-called auxiliary differential equation (ADE) approach). Single-stage three-

level space-time schemes are developed for both second-order and fourth-order accuracy in space and

time which lead to very efficient schemes with a large CFL "one'' time-step. The equations are discretized

in space using finite-difference and conservative finite-difference approximations. Since the equations are

in second-order form it is straight-forward to discretize the equations in a compact manner on collocated

grids without the need for staggering. Composite overlapping grids are used to treat complex geometry

with boundary conforming grids. A high-order upwind dissipation is added to the scheme to ensure a

robust and stable approximation on overlapping grids. Numerical results in two and three space

dimensions confirm the accuracy and stability of the new schemes.

47

Antwane Mason1


Reuse Opportunities in Software Quality Assurance

Our research goal is to lower time and effort required to perform both testing and formal

verification, two important quality assurance (QA) activities. We wish to achieve this goal by developing

theory, tools, and automation for reuse of software artifacts and processes between both QA activities. To

this end, we explore existing software artifacts and processes that can be reused between the two

activities. We also explore a branch of mathematics called category theory to serve as a tool for theory

development.

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Rensselaer Polytechnic Institute Graduate Research ... · The nuclear extracts are incubated with streptavidin magnetic beads coated with biotin-modified G4 oligonucleotides or control