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Participating Groups

The following faculty currently own shares in Proteus:

Garritt Tucker (Materials Science and Engineering, College of Engineering)
The Materials Modeling for Extreme Environments (MMEE) research group in the MSE department at Drexel University pursues fundamental research in nanostructured materials for enhanced mechanical and radiation tolerance in extreme environments using ab initio, atomistic, mesoscale, and multiscale modeling techniques. Our specific aim is to elucidate structural/compositional effects that drive enhanced functionality in novel materials by employing a variety of computational methods and forming synergistic efforts with experiments.

Gail Rosen (Electrical and Computer Engineering, College of Engineering)
The EESI Lab makes computational methods to study ecology and evolution, especially studies of microbial communities.  Such environmental and health studies can comprise terabytes of data and require sophisticated machine learning and signal processing algorithms.

Kurt Sjoblom (Civil, Architectural, and Environmental Engineering, College of Engineering)
Looking at how the microfabric of clay soils evolve during shear using molecular dynamic simulations. This work will lead to better predictions of macro material responses due to loading events, e.g., reactivation of a landslide induced by heavy rainfall.

Yared Shifferaw Bayleyegn (Civil, Architectural, and Environmental Engineering, College of Engineering)
Computational and experimental mechanics, structural stability, optimization, health monitoring and hazard mitigation, sustainable structures, emerging materials, thin-walled structures and metallic structures.

 

The following faculty currently have user access to Proteus' University Block:

Cameron Abrams (Chemical and Biological Engineering, College of Engineering)
Molecular simulations in biology and materials; enhanced sampling for structure prediction and transport property estimation.

Hasan Ayaz (Biomedical Engineering, School of Biomedical Engineering, Science and Health Systems)
We are investigating the potential of brain computer interface development using optical brain imaging sensors.

Marcello Balduccini (College of Computing and Informatics)
Knowledge representation and reasoning, including ontologies, agent architectures, commonsense, natural language understanding, and constraint satisfaction.

Sebastien Bradley (Economics, LeBow College of Business)
This project examines the impact of preferential tax regimes for patent and IP income on innovation, income reallocation, and cross-border mergers and acquisitions activity.

Shannon Capps (Civil, Architectural, and Environmental Engineering, College of Engineering)
Air quality modeling: estimating influences of emissions sources; evaluating health, ecosystem and climate impacts of pollutants;
assimilating observations to improve models.

Oben Ceryan (Decision Sciences and MIS, LeBow College of Business)
Computing optimal policies and evaluating heuristics for dynamic pricing and replenishment decisions for multiple substitutable products.

Luis Cruz Cruz (Physics, College of Arts & Sciences)
Our group studies properties and firing dynamics of neural microcolumns, specifically focusing on abnormalities found in aging and autistic tissue.

Mian Dai (Economics, LeBow College of Business)
We estimate models of competition under various contexts such as airline, venture capital, and health care providers etc. Our approach helps predict counterfactual market outcomes under alternative policy interventions. 

Casey Dougal (Finance, LeBow College of Business)
This research investigates the role of firm- and manager-specific heterogeneity in firm outcomes.

Evan Forman (Psychology, College of Arts & Sciences)
Permutation test will be conducted in order to examine the ability of our machine learning algorithm to predict dietary lapses at a level that is better than chance.

Matthew Freedman (Economics, LeBow College of Business)
I am leveraging administrative and survey data to examine how federal, state, and local housing and economic development programs affect neighborhoods and shape broader patterns of economic activity within regions.

Gary Friedman (Electrical and Computer Engineering, College of Engineering)
Modeling of dynamic properties of magnetic nanoparticles for applications in medical imaging and detection of biomarkers.

Neal D. Goldstein (Epidemiology & Biostatistics, Dornsife School of Public Health)
This work simulates a hospital’s intensive care unit for neonates, and informs infection prevention efforts on how factors such as hand hygiene and patient contact correlate to risk for communicable disease.

Mary Katherine Gonder (Biology, College of Arts and Sciences)
We will be using whole genome sequences of chimpanzee subspecies to develop a high-resolution single nucleotide polymorphism (SNP) typing scheme. This will help to quickly type and analyze newly collected samples for use in population genomic analyses. 

Allon Guez (Electrical and Computer Engineering, College of Engineering)
Classification of simulated cardiac tissue dynamics based on spiral wave behaviors.

Frank Ji (Chemistry, College of Arts and Sciences)
The RelA/SpoT homologue is an understudied drug target for mediating bacteria biofilm synthesis. Some antibiotic resistances, for example, have been partially attributed to bacteria’s ability to produce biofilm, which shields them from hostile environments. Utilizing computational molecular dynamics, diverse ligand sets can be screened to yield structural and chemical data pertinent to designing inhibitors and potential drug candidates for the RelA/SpoT complex.

Marilyn Jorns (Biochemistry and Molecular Biology, College of Medicine)
Use computational molecular replacement approaches to solve the phase problem and generate high resolution protein crystal structures.

Vibha Kalra (Chemical & Biological Engineering, College of Engineering)
Molecular Dynamics Study on Self Assembly of Conjugated Polymers under Shear Flow.

Antonios Kontsos (Mechanical Engineering & Mechanics, College of Engineering)
A systematic effort to introduce physics-based damage laws in computational studies of deformation and damage of advanced composites is performed in an Integrated Computational Materials Engineering (ICME) framework.

Sandhya Kortagere (Microbiology and Immunology, College of Medicine)
Design and development of small molecule modulators of protein-protein interactions and other proteins of therapeutic relevance using Structure Based Drug Design techniques.

J. Yasha Kresh (Cardiothoracic Surgery, College of Medicine)
We aim to develop of a computational fluid-dynamic (CFD) model of the circulation that will allow comparisons of complex flow dynamics and parameters (i.e. velocity, pressure, wall-shear stress) between helical and non-helical flow measured in benchtop experimental morphologically realistic models of human regional arterial circulation.

André Kurmann (School of Economics, LeBow College of Business)
We estimate a New Keynesian Dynamic General Equilibrium model to evaluate its ability to match impulse responses to a productivity news shock observed in U.S. data. 

Christopher Laincz (School of Economics, LeBow College of Business)
The research agenda examines the optimal R&D subsidy policy when the government conditions its subsidy on observable firm characteristics such as size, e.g. policy of the Small Business Administration.  The research also investigates the impact of R&D knowledge spillovers between firms on welfare and competition levels.

Leslie Lamberson (Mechanical Engineering & Mechanics, College of Engineering)
This work is conducting finite element simulations to virtually explore the use of an energy balance method to determining dynamic fracture properties of brittle solids. 

Hualou Liang (School of Biomedical Engineering, Science and Health Systems)
Computational analysis of large-scale brain networks, and biomedical signal processing.

Chuanren Liu (Decision Sciences, LeBow College of Business)
Temporal correlation in sequential pattern analysis: buying path/stage of business customers, predictive modelling with electronic health records.

Tatyana Livshultz (Biodiversity, Earth & Environmental Sciences, College of Arts & Sciences)
The phylogeny of the genus Hoya (Apocynaceae, Asclepiadoideae), a group of ca. 200 Southeast Asian epiphytes, has remained unresolved in previous analyses using small amounts of sequence data. In this study, we are assembling whole chloroplast genomes to resolve the relationships among the species of Hoya and between Hoya and closely related genera, Dischidia and Oreosparte

Geoffrey Mainland (Computer Science, College of Computing and Informatics)
We are developing language and compiler technology to compile high-level languages to efficient, low-level code.

Richard McCourt (Biodiversity, Earth & Environmental Science/Acad. of Natural Sciences, College of Arts and Sciences)
Next generation sequencing of algae in culture often reveal the presence of bacteria that grow in the cultures.  We will survey the diversity of bacteria associated with several green algae in culture to see if the bacteria present are common contaminants or possibly mutualistic partners that help the algae to grow.

Steve McMillan (Physics, College of Arts and Sciences)
Radiation magnetohydrodynamic simulations of star-forming regions.

Joshua Chang Mell (Microbiology and Immunology, College of Medicine)
The Mell Group uses genomics to investigate the mechanism, consequences and evolution of genetic recombination, especially in pathogenic bacteria.

Daniel Mirman (Psychology, College of Arts and Sciences)
An evaluation of methods for multiple comparison correction in voxel-based lesion-symptom mapping. The overall goal is to identify methods that optimize the trade-off between statistical power (detecting true effects) and avoiding false positives

Andréia C. K. Mortensen (Pharmacology & Physiology, College of Medicine)
This work is focused on understanding mechanisms of regulation of the human glutamate transporter EAAT2, using molecular modeling of the homologous bacterial transporter GltPh.

Shae Padrick (Biochemistry & Molecular Biology, College of Medicine)
The Padrick lab uses Proteus for experiment driven numerical modeling of regulated actin dynamics.

Genevieve Pham-Kanter (Health Management & Policy, Dornsife School of Public Health)
This research examines financial conflicts of interest in medicine and their effects on policy-making and on population health.

Tristan Potter (School of Economics, LeBow College of Business)
I use high-frequency longitudinal data to study the determinants of individuals’ job search decisions during unemployment.

Jacob Russell (Biology, College of Arts and Sciences)
We perform metagenomic analyses to elucidate the functions of symbiotic gut bacteria from ants.

Christopher Sales (Civil, Architectural, and Environmental Engineering, College of Engineering)
Our group analyzes chemical data and molecular biology sequences collected from natural and engineered environmental systems. Advances in analytical chemistry and molecular biology techniques have enabled high-throupghput production of large amounts of data that requires significant computing power to analyze.

Ioannis Savidis (Electrical and Computer Engineering, College of Engineering)
Ioannis's research focus is on the improvement of high performance integrated circuits through accurate and efficient analysis and design. Although simulation on an entire integrated circuit containing over one billion transistors is prohibitively expensive, computing clusters are exploited to model and analyze larger circuit sub-blocks for functionality and timing. Through proper analysis, improvements in circuit performance are achieved while meeting the noise constraints and power requirements ofan integrated circuit.

Ali Shokoufandeh (Computer Science, College of Computing and Informatics)
This project focuses on graph matching problem and its applications on several real life problems in the field of pattern recognition and user association.

Gideon Simpson (Mathematics, College of Arts and Sciences)
My active areas of research include partial differential equations, molecular dynamics and statistical inverse problems.  This includes solving time dependent nonlinear wave equations using finite differences, finite elements, and spectral methods.

Srinivas Somarowthu (Biochemistry and Molecular Biology, College of Medicine)
Phylogenetic analysis of long non-coding RNAs.RNA-Seq data analysis

Masoud Soroush (Chemical and Biological Engineering, College of Engineering)
Molecular dynamics simulations will be conducted to predict material properties of nanostructures, and kinetics of polymerization reactions will be studied using quantum chemical calculations.

Jonathan Spanier (Materials Science and Engineering, College of Engineering)
We seek to carry out finite-difference Poisson-Schrodinger calculations of electrostatic potential and charge density in complete oxide heterostructures. Simulation code has been developed within the Spanier group.

Kara Spiller (School of Biomedical Engineering, Science and Health Systems)
The goal of the Biomaterials and Regenerative Medicine Laboratory at Drexel University is to understand the mechanisms by which the inflammatory response orchestrates successful tissue regeneration and to develop novel biomaterial strategies that apply these principles to situations in which tissue regeneration is impaired.

Loni Philip Tabb (Epidemiology and Biostatistics, Dornsife School of Public Health)
Research carried out involves building Markov chain Monte Carlo algorithms for Bayesian multilevel models, as well as analyses of zero-inflated (longitudinal) count data in application areas ranging from environmental to health disparities.

Baris Taskin (Electrical and Computer Engineering, College of Engineering)
Design space exploration of a hardware-software design platform for chip multiprocessors and network-on-chips.

Amy Throckmorton (School of Biomedical Engineering, Science and Health Systems)
As a new innovative treatment strategy for patients with congestive heart failure, we are developing a unique a unique hybrid-design, continuous flow, implantable, magnetically levitated, TAH (Dragon Heart), and we employ the URCF resources to perform computational  studies of design optimization.

Catherine von Reyn (School of Biomedical Engineering, Science and Health Systems)
Cell type-specific genetic engineering, whole-cell patch clamp in behaving animals, modeling, and detailed behavioral analysis to identify and characterize sensorimotor circuits.

Steven Weber (Electrical and Computer Engineering, College of Engineering)
Large graph search algorithm performance analysis, optimization, and design.

Jason D. Weckstein (Biodiversity, Earth and Environmental Sciences, College of Arts and Sciences)
My laboratories work uses DNA sequence data to reconstuct the evolutionary history of birds and their parasites. We will use Proteus to analyze various next generation DNA sequencing libraries for our research.

Matthew Weinberg (Economics, LeBow College of Business)
A project that tests how the merger of Miller and Coors beer companies changed the market for beer.

Christopher Weinberger (Mechanical Engineering and Mechanics, College of Engineering)
Dr. Weinberger's research focuses on the development of analytical and computer models to describe the mechanical and structural properties of ceramics, metals and their alloys at the nano- micro- and macro-scales. The goal of this work is to link atomic bonding, defects and microstructure to material performance at the macroscale.

Ming Xiao (Biomedical Engineering, School of Biomedical Engineering, Science and Health Systems)
Whole genome mapping and sequencing for human genomic structural variation analysis.

Mark Zarella (Department of Pathology & Laboratory Medicine, College of Medicine)
Dr. Zarella incorporates concepts in digital imaging, signal processing, and bioinformatics toward the goal of understanding biological systems.

Fengqing Zoe Zhang (Psychology, College of Arts and Sciences)
The massive neuroimaging data present opportunities for new discoveries as well as unique computational and statistical challenges. My research focuses on statistical modeling for high dimensional structured data with application to neuroimaging.

 

The following faculty currently have hardware hosted in the URCF: