Rulong Ma, Postdoctoral Fellow, University of Houston
My research focuses on the computational biophysical investigation of protein structure and function. I have strong expertise in all-atom molecular dynamics simulations using NAMD and VMD. My work has elucidated the transport mechanism of the sarco/endoplasmic reticulum Ca²⁺-ATPase (SERCA) and revealed the inhibitory mechanism of the human SERCA2b C-terminal extension. More recently, I have been investigating the mechanisms of photodamage resistance in photosystem II (PSII) complex by combining bioinformatics analysis with molecular dynamics simulations.

Matheus Mello, Graduate Student, Rice University
My work focuses on genome organization and chromosome structure and dynamics. Using coarse-grained theoretical models, I study the organization of the chromosomes in the nucleus, how chromosomes interact, and how active and inactive chromatin phase-separates in the nuclear environment. I am also interested in the interaction of chromatin with other nuclear bodies and in the chromosome structural changes over the cell cycle.

My research interests lie in approaching cancer systems from a theoretical and mathematical perspective. I am currently developing a framework to better understand how tumor cells adapt to stressful conditions and prolong their survival through various interrelated mechanisms. For example, many tumor cells exhibit drug-tolerant persistence and/or dormancy when exposed to cytotoxic agents. I aim to continue investigating diverse dynamical phenomena within the tumor microenvironment with the goal of contributing to the development and optimization of therapeutic interventions in oncology.

Aviva Presser Aiden, Assistant Professor, Baylor College of Medicine
I am working on multiple aspects of 3D-genomics. I am using these tools to explore how structural factors affect different organs’ development. I am also using these tools to explore mosquito and blood meal genomics, and metagenomics/diagnostics applications.

Mehmet Velat Inci, Graduate Student, Northeastern University
I’m interested in the coevolutionary dynamics between adaptive immune systems and evolving viruses—specifically the CRISPR-Cas bacterial immune system and its interactions with bacteriophages. I use stochastic algorithms to simulate host-pathogen interactions and to analyze population dynamics, immune functionality, and viral evolution.

Carlos Bueno, Postdoctoral Scholar, Rice University
My research focuses on actin networks, a gel-like substance that regulates the plasticity and motility of most cells, and plays a crucial role in processes such as memory formation. I’m fascinated by the complexity that originates from simple interaction rules and how complex structures arise by influencing parameters such as crosslinker length, shape, and concentration. I use a variety of models at different scales, from molecular mechanics simulations to mathematical models, to understand how the interactions between proteins generate diverse structures and to predict how changes in protein interactions can alter cellular processes.

Marina Slawinski, Graduate Student, University of Wisconsin – Madison
Immune response to tuberculosis (TB) infection generates granulomas, which are organized clusters of immune cells that surround bacteria in an attempt to physically contain and clear infection. The granulomas can either successfully eliminate infection or contain the bacteria with ~10% risk of dissemination depending on various risk factors, including comorbidities. Given that about one quarter of the world’s population is currently infected with TB, it is of great importance to understand and model how various risk factors impact granuloma formation and disease outcome to predict which demographics are most at risk of developing active infection and target therapies accordingly. To this end, we infect fluorescently labeled macrophages with mycobacteria as an in vitro model of TB, and will analyze confocal microscopy data to characterize differences in macrophage spatiotemporal dynamics and phenotypic changes with the goal of informing a computational model of granuloma formation.

Akza Ahmed, Graduate Student, University of Wisconsin, Madison
My work in May-MIDAS lab focuses on developing in silico models to study the combined effect of vitamin D3 and alcohol metabolism on modulation of key inflammatory cytokines and effector molecules produced by macrophages during Mycobacterium tuberculosis (Mtb) infection. More specifically, the mathematical model is formulated in MATLAB using a system of ordinary differential equations (ODEs) to depict signal transduction pathways that arise from Mtb lipoarabinomannan (LAM) activation of pro and anti-inflammatory cytokines such as IL-12, IFN-y, IL-10, and effector molecules including H2O2 and NO. A current project in our lab involves developing regression-based models for existing experimental data and determining cell death pathways in murine macrophages.

Aviva Presser Aiden, Assistant Professor, Baylor College of Medicine
I am working on multiple aspects of 3D-genomics. I am using these tools to explore how structural factors affect different organs’ development. I am also using these tools to explore mosquito and blood meal genomics, and metagenomics/diagnostics applications.

Vinicius Contessoto, Postdoctoral Scholar, Rice University
My research centers on the development and application of theoretical biophysics models combined with computational simulations to investigate the dynamics and function of chromosomes and proteins. I’m particularly interested in understanding structural changes in chromosomes throughout the cell cycle and the interplay between chromatin organization and gene expression. Additionally, I explore protein folding and engineering, with a focus on computational methods for predicting epitopes in immunization strategies and identifying mutations that enhance enzyme thermostability.

Max Hall-Brown, Graduate Student, Rice University
My work centers generally on the cytoskeleton, and more specifically on how material and structural properties can emerge in biological context. Central to this problem are ideas borrowed from the physics of amorphous glassy materials, which have a complicated and intricate set of behaviors in their own right. These ideas are useful for understanding systems such as biomolecular condensates, actin-myosin networks, the dendritic spine, protein folding, and many others. I’ll mostly work on biomolecular condensates and actin-myosin networks in the near future, as well as more fundamental physics work in the field of glasses.

Praveen Kumar, Postdoctoral Scholar, Northeastern University
I am interested in a wide range of soft matter physics problems, spanning both biological and non-biological systems. My current research interests are focused on comprehending the mechanics and collective behaviors in biological tissue systems through the use of theoretical modeling and computer simulations. I apply tools from statistical and soft matter physics to understand and predict emergent phenomena in these dynamic systems.

Matheus Mello, Graduate Student, Rice University
My work focuses on genome organization and chromosome structure and dynamics. Using coarse-grained theoretical models, I study the organization of the chromosomes in the nucleus, how chromosomes interact, and how active and inactive chromatin phase-separates in the nuclear environment. I am also interested in the interaction of chromatin with other nuclear bodies and in the chromosome structural changes over the cell cycle.

Ronaldo Oliveira, Postdoctoral Scholar, Rice University
We’ve been working on problems related to protein folding dynamics and chromatin organization. These studies primarily involve molecular dynamics simulations of coarse-grained models, through which we characterize the kinetics and thermodynamics of the biomolecules under investigation. Recently, our focus has shifted to studying the association mechanism between two intrinsically flexible proteins and exploring the minimal chromatin model.

Christina Palma, Postdoctoral Scholar, Rice University
My work focuses on gene regulatory mechanisms that allow bacteria to adapt and survive to stress conditions. For this, I combine computational methodologies, including stochastic and deterministic models, statistics, and signal processing techniques, with experimental data obtained from a spectrum of techniques such as microscopy, flow-cytometry, and RNA-seq. Specifically, I study the cellular adaptation mechanisms, on a systems level, by focusing on different regulatory factors such as transcription factors, DNA supercoiling and post-translational interactions.

Daniel Ramirez, Graduate Student, Northeastern University
My research focuses on combining mathematical modeling and bioinformatics to construct, refine, and simulate gene regulatory networks, in particular concerning cellular state transitions. Among other tools, we use stochastic differential equations, single-cell transcriptomics, and machine learning approaches to study processes including the cell cycle and epithelial-mesenchymal transition. Eventually, our aim is to create data-driven dynamical models to understand the fundamentals of cellular information processing.

George Wanes, Graduate Student, 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 model that can capture the effects of the ions on the dynamics of large-scale assemblies, including the ribosome.

Douglas White, Graduate Student, Northeastern University
Chromatin is an amalgam of DNA and proteins within a cell’s nucleus. I model chromatin with course-grained polymers, each bead of which represents a segment of DNA. To do this, I use molecular dynamics to sample a free energy landscape of 3D structures. I would also be interested in applying statistical mechanical methods and abstract math to the nucleus and beyond. Wild ideas beyond the scope described above are welcome as well; the wilder the better.

Yukai You, Graduate Student, Northeastern University
My research seeks to unravel the complexities of cellular state transitions, such as differentiation and immune activation, by constructing precise gene regulatory networks through nonlinear ordinary differential equations, leveraging single-cell genomics data. My approach aims to enhance our comprehension of cellular behaviors and their continuous dynamics, offer deeper insights for potential therapeutic developments, and provide a robust understanding of life’s fundamental biological processes.

Nate Avish, Graduate Student, Northeastern University
I am interested in understanding how to predict the dynamics of individual biomolecules, such as RNA and proteins. My current projects include the development of new theoretical models for ions, as well as calculating how molecular flexibility can enable chemical reactions in enzymes.

Carlos Bueno, Postdoctoral Scholar, Rice University
My research focuses on actin networks, a gel-like substance that regulates the plasticity and motility of most cells, and plays a crucial role in processes such as memory formation. I’m fascinated by the complexity that originates from simple interaction rules and how complex structures arise by influencing parameters such as crosslinker length, shape, and concentration. I use a variety of models at different scales, from molecular mechanics simulations to mathematical models, to understand how the interactions between proteins generate diverse structures and to predict how changes in protein interactions can alter cellular processes.

Esteban Dodero-Rojas, Graduate Student, Rice University
My research has three main focuses: molecular mechanisms related to the SARS-CoV-2 virus infection and recognition; analysis of DNA behavior under interaction with nuclear bodies; and DNA loop formation through molecular motors such as condensin. We use molecular dynamics simulations and machine learning algorithms to investigate properties and mechanisms that drive these biological systems to perform their role.

Joel Gard, Graduate Student, University of Houston
My current research is focused on understanding the role confinement plays in the active and passive processes of biopolymers such as DNA and actin. Confinement induces large scale configurational changes in an ensemble by constraining its entropy, yet differing geometries can produce markedly different effects. I utilize coarse grained modeling and both molecular dynamics and Monte Carlo simulations to analyze these effects and gain a deeper understanding of their influence on biopolymers in vivo and in vitro.

Max Hall-Brown, Graduate Student, Rice University

Andrei Gasic, Postdoctoral Scholar, Rice University
My main research interest lies at the interaction of two areas of condensed matter physics: active matter and glasses. Using ideas from these two subfields, my goal is to develop theories and mathematical models for understanding the behavior of actomyosin networks. I also have various interests spanning from the single protein scale to cellular scales, such as the physics of protein-complex assemblies and biocondensates.

I study drug development for cancer and bacteria infection with theoretical models and computer algorithms for making predictions about potential drug efficacy. This work focuses on antimicrobial peptides, short proteins in the innate immune system of many different organisms including humans, that can be used as treatments for multiple diseases.

Matheus Mello, Graduate Student, Rice University
My work focuses on the investigation of chromosome behavior and structure. 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.

Tripti Midha, Postdoctoral Scholar, Rice University
My present research focuses on analyzing the interplay of speed and accuracy of fundamental biological processes such as DNA replication, RNAP transcription elongation, and protein synthesis translation. I aim to develop stochastic models to investigate the various mechanisms of proofreading using theoretical and computational methods.

Alex Moffett, Postdoctoral Scholar, Northeastern University
I am interested in a broad range of problems in evolutionary biology and ecology. My current projects include applying methods from theoretical ecology to model cancer-immune interactions and examining the evolution of mammalian genomes.

Alex Raterink, Graduate Student, Rice University
I am interested in studying the biophysics of gene regulation at the single-cell level. To do this, I use microscopy techniques, particularly 3D single-particle tracking, with novel live-cell fluorescent labeling methods. My goal is to measure the spatiotemporal dynamics of specific sites in the human genome in live cells, and to quantify the effect of these dynamics on gene expression.