Students

Graduate Students

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SADJAD ARZASH - Rice University
My overall research interests include understanding the mechanical and dynamic properties of soft and biological materials. Biopolymers, as well as carbon nanotubes can be characterized as semiflexible polymers, which have been shown to exhibit elastic and relaxational properties that differ strongly from flexible polymers. By simulating networks of semiflexible polymers, we can predict their mechanical response, as well as the dynamics of their stress relaxation.

Melia

MELIA BONOMO - Rice University
My research investigates modular structure and function in a variety of biological topics. In CRISPR-Cas, I model the kinetics of crRNA:Cas9 recognition of invading DNA to understand how modularity contributes to specificity and efficiency. In the human immune system, I model vaccine efficacy against influenza based on antibody recognition of modular sites on the virus's hemagglutinin protein. In the human brain, I analyze network modularity in fMRI data of people listening to music to work towards personalizing music therapy. I also model brain network changes that lead to cognitive impairment and analyze MEG data from patients with dementia.

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CARLOS BUENO - Rice University
The goal of my work is to improve the models used to predict the stability of proteins. I use several methods including direct coupling analysis, the AWSEM forcefield and normal mode analysis. The insights obtained by these analyses can also be used to analyze the movement of the protein during allosteric regulation.

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SANDRA BYJU - Northeastern University
My work focuses on molecular dynamics of large-scale biomolecular assemblies. I adopt the simplified structure-based models, for which the Whitford group is well known, to study the changes in the energy landscape of the ribosome, which is the sole producer of proteins in the cell. More specifically, I study the conformational rearrangements and dynamics during the early translocation stages of protein elongation using SBM and molecular dynamics simulations.

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SIHAN CHEN - Rice University
I’m interested in dynamic properties of soft materials such as semiflexible biopolymers. Currently, I’m working on non-equilibrium force generation in actin filaments..

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XUN CHEN - Rice University
My research mainly focuses on the dynamics of protein and DNA in vivo, included protein aggregation, protein-DNA interaction and membrane protein. The transition of molecular structure in vivo determine their function in human life. I want to use physical tools to understand these kind of action better. At the same time, I am also interested in develop the Hamiltonian of AWSEM model to describe the protein folding, which also can help us understand the protein function better.

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BEN CLAUSS - Northeastern University
I am interested in the regulatory interactions that govern early embryonic development. I am currently developing a method to identify key regulatory interactions for multi-state transitions through a combination of mathematical modeling and statistics. My future interests lie in incorporating chromatin landscape information into quantitative models and identifying specific perturbations that alter state distributions during development.

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SETH COLEMAN - Rice University
My work focuses on modeling the cell-fate decision in bacteriophage lambda. My goal is to quantitatively describe the gene expression kinetics of the lambda decision and to identify and characterize the main factors that drive it.

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LUCAS HILDEBRAND PIRES DA CUNHA - Rice University
My overall research interest is in the mechanical behaviour of complex fluids in the microscale. In the past years, I have worked with numerical simulations of droplets flowing through microchannels and magnetic droplets under the influence of external magnetic fields and imposed flows. Recently, I got interested in the use of chains of magnetic colloidal particles as tools to understand the rheological response of biological materials.

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YOUYUAN DENG - Rice University
My current research models patterns of cell motility, interactions between cells and ECM (extra-cellular matrices). In pursuit of science goals, I'm also interested in good, modern practices for scientific computing.

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ERDONG DING - Rice University
My research mainly focuses on computational methods and their application on biosystems. Currently, I am working on the behavior of a certain kind of RNA called riboswitch via SMOG forcefield and other methods developed by our group.

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ESTEBAN DODERO-ROJAS - Rice University
My research is focused on exploring the folding landscape of viral proteins, currently applied to the SARS-CoV-2 Spike protein. This project aims to expose important features of viral membrane fusion which can be later used to trigger, reduce efficiency, or deny such process. Moreover, my work covers epigenetics marks prediction, this is done from an information theory framework in which a great compilation of data allows us to extract correlation and anticorrelation between histone modifications and transcriptor factors.

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WINTER DOUGLASS - Northeastern University
My research focuses on using mathematical models and computer simulations to study biological tissues. I'm particularly interested in cell motility under conditions relevant to cancer metastasis and tumor invasion.

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YOSSI ELIAZ - University of Houston
We seek to understand the physics of living systems. Specifically, I study the theory of active matter inside a cell. I am highly interested how actomyosin networks evolve and store information as mechano-biological machines. By harnessing ideas from computer science and applied mathematics, we aim to explain the physical principles of self-assembly in biological matter. The end goal is to elucidate how long-term memory is formed and maintained.

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MADELINE GALBRAITH - Rice University
I'm interested in the mechanism of cancer metastases and pathways that can be targeted to slow/stop cancer growth. My research focuses on using mathematical models of the gene networks involved, such as the notch signaling pathway.

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ANDREI GASIC - University of Houston
Inside a living cell, there is an immensely complex and crowded environment—this is far from the ideal test-tube setting. Our under-standing of how proteins and other biomolecules function in this environment is largely unknown. Using both theory and computer simulations, my research aims to answer important questions at the interface of physics and biology, spanning from the single protein scale to cellular scales. The thrusts of my research consists of understanding the following: i.) the effects of the cellular environment on protein folding; ii.) criticality of proteins and the effects of macromolecular crowding; iii.) the physics of hierarchical protein-complex assemblies and the "structure" of the cytosol.

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DANIEL "DANYA" GORDON - Northeastern University
My research focuses on systems biology approaches to the study of gene regulatory dynamics. Specifically, I use mathematical modeling and bioinformatics tools to simulate, visualize and analyze the behavior of gene regulatory networks. My work explores a variety of topics including network inference, network refinement, model development, multi-omics data integration, and parameter optimization.

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XINYU GU - Rice University
I'm interested in computational and theoretical chemistry, especially in topics about biological systems, like proteins. My recent research direction aims at improving protein structure prediction, basing on AWSEM coarse grain model.

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ASEM HASSAN - Northeastern University
My research focuses on computational modeling and simulation of ribosomes. I use structure-based models and molecular dynamics simulation techniques to study dynamical processes in the ribosome. My current research emphasis is on the elongation cycle of translation, studying various dynamical events during elongation and characterizing their energetics. I am also working on improving descriptions of domain motions in the ribosome and developing guiding protocols to detect and differentiate between these motions experimentally.

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EUGEN HRUSKA - Rice University
My research focuses on the analysis of macromolecular dynamics and the development of new strategies for enhanced sampling. Current methods for adaptive sampling are mostly based on dimensionality reduction tools, but the speed-up achieved for complex systems is still limited. Analyzing the shortcomings of the current methods allows us to improve these methods and develop new approaches, in order to better simulate and characterize protein dynamics over long timescales.

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JUNXIANG HUANG - Northeastern University
My research involves modeling the rigidity transition and rheology of epithelial tissues using computational simulation and statistical physics analysis.

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HANA JAAFARI - Rice University
My research interests center on employing computational modeling and theoretical physics to explore the dynamics of biological systems. I currently study the role evolution plays on the energy landscapes of proteins by examining pseudogenes, using our AWSEM coarse grain model and DCA model.

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WEN JIA - Rice University / Northeastern University
My research mainly focuses on cancer system biology. Transitions between epithelial and mesenchymal phenotypes play important roles in both tissue repair and cancer metastasis. Currently, I’m investigating the influences of new feedback terms on EMT and MET. Some would have significant effects on the transitions and need to be further studied.

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SHIKAI JIN - Rice University
My research interests include protein structure prediction and application in solving crystallographic phasing problem. The phasing problem, which arises from the fact that X-ray diffraction experiments only record the intensities, but not the phases, of the diffracting electromagnetic waves. With de novo predicted structure, we can solve phasing problem by molecular replacement and get real structure from X-ray data. This method will greatly broadens the protein structure database.

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SAYANTANI "SAYAN" KAYAL - Northeastern University
I am interested in collective cell migrations and pattern formations in confluent tissues. Currently I am studying the influences of cell-level heterogeneities (mechanical heterogeneity, heterogeneity in the motility of cells etc.) in epithelial tissues to examine if these induce any emergent phenomena in the system.

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JULES NDE KENGNE - University of Houston
My research focuses on understanding the role of calcium-binding proteins in regulating actomyosin networks using coarse-grained models and physics-based approaches.

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KAITLIN KNAPP - Rice University
My research interests include computational modeling and analysis of biomolecular dynamics and applications of machine learning. I am particularly interested in coarse-grained network modeling and the interplay of flexibility and frustration in the large scale conformational changes that accompany biomolecular functions.

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PRATHAMESH KULKARNI - Rice University
I am interested in polymer behavior in biological systems using theory and simulation techniques. Theoretical understanding of semiflexible polymers can be used to predict and explain the behavior of actin filaments that constitute the cytoskeleton in cells. Currently, my research focuses on studying the stress relaxation in actin filament networks.

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CHENGXUAN LI - University of Houston
My research focuses on coarse-grained modelling of active networks in biological systems and investigating the impact of actin-binding proteins on actomyosin network dynamics.

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XINZHI LI - Northeastern University
I am interested in nonequilibrium systems and their collective behaviors. Both theoretical and numerical simulations are used in understanding various biological and non-biological systems. Focusing on the following areas: (1) amorphous materials with complete photonic band gap based on self-propelled Voronoi model; (2) how does variability of single cell affect the jamming behavior of the system; (3) Mechanical metamaterials with phonon band gaps inspired by biological tissues.

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JAMES LIMAN - Rice University
I am currently working on understanding long-term morphological plasticity of dendritic spines by computationally integrating known short-term biochemical signals and actin cytoskeleton reorganization. This study, when successful, will considerably advance our understanding of cellular mechanism of learning and memory.

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WEI LU - Rice University
Membrane proteins account for more than 20 percent of all human protein-coding genes and more than 50 percent of the drug targets using today. My current research focuses on the studying of force induced membrane protein unfolding dynamics using our coarse grain model (AWSEM).

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WEIQI LU - Rice University
My research interests include the modeling and computational simulation and analysis of biomolecular architecture. Currently, I am mainly focused on the chromosome conformation, to be more specific, how the Minimal Chromatin Model (MichroM) would work on higher-ordered contacts within a single chromosome.

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KAREEM MEHRABIANI - Rice University
My research involves the Prediction of Actin-Actin interactions via co-evolutionary sequence analysis and molecular dynamics simulation.

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ANANYA MONDAL - University of Houston
My research is focused on understanding how robust cellular mechanisms evolve at the mesoscale from noisy molecular level structure and dynamics of biopolymers. A major challenge in probing a living cell is its highly heterogeneous and crowded environment. To this end, a combination of bottom-up approaches such as coarse-grained theoretical modeling and single molecule force-extension experiments have helped capture the generic features of semiflexible biopolymers (for example DNA, actin bundles) and elucidate key biological questions. I apply mean-field theory together with computation to study the effects of variable tensile forces like electrophoretic stretching on the statistics and rheology of charged biopolymers (polyelectrolytes). The aim is to explain the eventual consequences of non-uniform tension on biologically relevant processes like DNA-histone packaging.

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KEVIN NG CHAU - Northeastern University
My main interest is the modelling of physical phenomena from the mathematical and computational standpoints. In particular, my current research centers on understanding how the adaptive immune system is able to discriminate self from foreign cells and healthy from cancer cells by formulating models describing the interaction of immune system's T cells with antigens at a molecular and at a repertoire level, in hope that such understanding can help in advancing immunotherapy as a successful treatment for cancer.

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THAO NGUYEN - Rice University
I am interested in studying biophysical systems by means of theoretical and computational methods. My current research topics include the development of a novel stochastic model that describes the mechanism of antimicrobial peptides on bacteria.

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ATRAYEE SARKAR - University of Houston
My objective is to develop a theoretical model to understand the principles of emerging protein-complex assemblies in signalling pathways using a statistical mechanical framework.

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JORDAN SHIVERS - Rice University
I am interested in the elastic properties of semi-flexible polymer networks. In living systems, such networks provide striking nonlinear mechanical behavior to cells and tissues, including strain stiffening and negative normal stresses. Currently, I am working to characterize the dependence of negative normal stress on network structure and applied strain.

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JACOB TINNIN - University of Houston
My research focuses on understanding the structure-function relationship of organic photovoltaic materials. Currently we are focusing on electron donor-acceptor heterojunctions such as C60-SubPC and C70-DBP. We model the interface using molecular dynamics and obtain significant structures using statistical mechanics and machine learning techniques. We then compute charge transfer statistics using quantum chemistry and link this to device performance using a kinetic Monte Carlo method. This link between interfacial geometry and device performance is up-to-now unknown and will allow for the creation of improved solar technology.

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SHUBHAM TRIPATHI - Rice University / Northeastern University
My research work focuses on the mechanisms underlying the phenotypic heterogeneity and plasticity exhibited by tumor cells, including functional, metabolic, and epigenetic heterogeneity. I use concepts from physics to understand how such behavior can arise and how it can contribute towards the emergence of drug resistance in tumor cells.

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TIANYOU YAO - Baylor College of Medicine / University of Illinois Urbana-Champaign
I am a graduate student in the department of Biochemistry and Molecular Biology at Baylor College of Medicine, working in the lab of Dr. Ido Golding. I am working on the system comprising the bacterium E. coli and phage lambda. My goal is to discover the undetected variables that contribute to the heterogeneity of lambda gene expression and the resulting decision between lysis and lysogeny.

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FENGDAN YE - Rice University
My research focuses on quantitative modeling of complex biological systems. Such systems include gene interaction networks in cancer cells, functional connectivity in human brain, genome-scale metabolic network of E.coli, and so on. I use methods such as network clustering, dimensionality reduction, neural networks, and flux balance analysis. The overall goal of my research is to understand the relation between the structure and function of biological networks.

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JIANGGUO ZHANG - Rice University
My primary research interest centers on applying multi-disciplinary models into biological research. I am taking advantage of deep learning to transfer phase-contrast images of Myxococcus xanthus into fluorescent images, which can be easily interpreted to cell density maps. I am also working on extracting Myxo cell aggregation features, which will be helpful to cluster mutant strains into different genetic pathways.


Undergraduate Students

William

WILLIAM CUTLER - Northeastern University
I am an undergraduate Computer Science and Physics combined major at Northeastern University (Class of 2023) who actively seeks to leverage knowledge from both fields to participate in novel research. I am specifically interested in applying machine learning techniques to solve problems in genomics. I am also an avid clarinetist, performing for NEU’s Wind Ensemble and Symphony Orchestra, and an Eagle Scout.

Daniel

DANIEL RAMIREZ - Northeastern University
My work focuses primarily on the behavior and properties of gene regulatory networks in simulated and experimental single-cell data. My current projects include investigating the role of epithelial-mesenchymal transition in cancer and mammalian development at the single-cell level. My overall interest is in developing computational methods for efficiently and robustly interpreting single-cell transcriptomics.