Graduate Students

Daniel Ajuzie

DANIEL AJUZIE - Rice University
My work in the May-MIDAS lab focuses on developing in-silico models of bacterial stress response. More specifically, I combine mathematical differential equation-based models and statistical gene models to study bacterial response to environmental or host-induced iron and hydrogen peroxide stress. Along this line, I am also developing models for multi-phenotype parametrization and optimization of dynamical system models.

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NATE AVISH - Northeastern University
I use computational tools and structure-based models to study the conformational dynamics of biomolecular systems. My current research focus looks at the regulatory effects of diffuse ions on the stability and dynamics of RNA assemblies.


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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BEN CLAUSS - Tufts 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.

Joel Gard

JOEL GARD - Rice University
I am interested in computational and coarse-grained modeling as a means to better understand the behavior of semi-flexible biopolymers. Currently, my research is focused on the behavior of biopolymers within various geometries with the purpose of understanding how conformational properties of biopolymers, such as DNA and actin, are effected by confinement.

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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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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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My research is focused on unraveling how different DNA spatial configurations affect the search target process for different proteins. By developing and solving discrete state stochastic analytic models and using different simulation methods we are able to explain how different proteins are able to find genes or form loops, for example.

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YASMENE WANG ELHADY - University of Washington
I am interested in understanding the structure-function relationship of organic photovoltaic materials. I model the interface using molecular dynamics and obtain significant structures using statistical mechanics and machine learning techniques. This connection 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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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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My research involves studying the mechanics and dynamic properties of soft polymer networks. I'm using polypeptoids to mimic these soft biological networks and study the influence of valence and physical associations.

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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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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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LIJIA HUANG - Rice University / Northeastern University
My research interest is to understand how complex circuits of interacting genes and proteins enable cells to sense and respond to signals, communicate, remember information, and develop into multicellular organisms. These circuits use non-intuitive designs. Making sense of those designs is essential for understanding, predicting, and controlling natural cellular behaviors.

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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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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 Washington
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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CHRIS KIRKUP - Northeastern University
Information forthcoming.

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ALENA KLINDZIUK - Rice University
My research goal is to uncover the molecular mechanisms that govern DNA transcription dynamics and generate gene expression noise. To this end, I develop, solve and simulate stochastic models of the complex physical and chemical processes that are implicated in the copying and replication of DNA such as the cooperation of RNA Polymerases, supercoiling of DNA, the enzymatic activity of Topoisomerases, and much more.

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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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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 Washington
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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MATHEUS MELLO - Rice University
My work focuses on the investigation of chromosome behavior and structure and their influence on gene activity. By using coarse-grained models, we study chromatin phase separation and inter-chromosome interactions in systems with multiple chromosomes, seeking to have a deeper understanding of how they affect each other and how the nucleus behaves as a whole during interphase.

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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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ANH NGUYEN - Rice University / Northeastern University
I am interested in collective cells migration. My current research involves modeling the epithelial-mesenchymal transition (EMT) using the SPV model. I want to study how cell-cell viscous adhesion affects the collective motion of the system and the EMT.

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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.


UMA SAXENA - Northeastern University
Research statement coming.

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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.


AMOOLYA SRINIVAS - Northeastern University
Research statement coming.

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YIWEN TANG - Northeastern University
I am interested in the emergent collective behavior of cells in dense biological tissues, which is relevant in a broad range of biological processes, including cancer invasion and embryonic development. Currently I am trying to understand how topological defects are generated by the active forces of cell division and apoptosis in homeostatic tissues. I am also working to understand the organization and dynamics of topological charges in a cell layer confined to a spherical surface.

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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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GEORGE WANES - Northeastern University
My research focuses on using molecular dynamics in studying the energy landscape of biomolecules based on structure-based models. Currently, I am working on developing a force field that can capture the effect of the chelated ions on the energetics of biomolecular assemblies.

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DOUGLAS WHITE - Northeastern University
I use statistical physics and machine learning to look at how a genome's 3-D structure affects protein production. The 1-D structure can be related with the 3-D structure using Hi-C experiments. Dr. Di Pierro and I seek to find a better way to study the 3-D structure.

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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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YUKAI YOU - Northeastern University
I am interested in using mathematical and computational methods to reveal the nature and inner links of genes and gene networks. At present, I am working on building core gene networks based on the Single-cell RNA-seq data with different methods.

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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.

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CHONGBIN ZHENG - Rice University
My research interest is in using ideas from physics, such as non-equilibrium statistical mechanics and topology in condensed matter theory, to understand the behavior and robust functions that arise from stochastic biological systems. Currently I am working on a model that attempts to explain the dynamic instability of microtubules and the consequences of topology in such systems.

Undergraduate Students


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.

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KAITLYN RAMESH - Rice University / Northeastern University
Provided soon ...


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.