I am interested in single-cell responses to internal and external signals and in emerging mechanisms governing collective cell behavior. In my endeavors, I use methods of synthetic and quantitative biology (i.e. controlled microenvironments, synthetic gene networks, microfluidics, nanomaterials and quantitative microscopy), complementing standard biological assays. Together with Prof. Dr. Balázsi, we develop gene regulation systems allowing to explore and control cancer metastasis and to counteract viral infection. By monitoring the single-cell expression of disease-related genes and correlating it with phenotype profiles (e.g. cell motility) we aim to gain quantitative insights into emergence and dynamics of those complex pathologies.

Balázsi Lab

Rafal.Krzyszton@stonybrook.edu

I work on the integration of Elastic Network Models (ENMs) into various biological systems, aiming to provide a more comprehensive understanding of the intricate relationship between the structural characteristics and functional properties of biomolecules. My research interests primarily revolve around the advancement of protein engineering frameworks, designed to measure and assess the consequences of diverse modifications on a protein's structural dynamics and functional attributes. Through an interdisciplinary approach, I contribute to shedding light on critical biological mechanisms, aiding in the development of novel therapeutic strategies and a deeper understanding of complex disease processes.

Bahar Lab

Anupam.Banerjee@stonybrook.edu

I am interested in developing methods for more efficient molecular dynamics simulations that enable more ambitious applications. During my PhD at the University of Pittsburgh in the lab of Lillian Chong, I worked on the weighted ensemble method, which uses splitting and merging to achieve more efficient sampling. I was a core developer of the WESTPA software package for weighted ensemble simulations. As a postdoc, I am now interested in how the MELD sampling strategy, possibly combined with ENM methods, can further enhance molecular dynamics simulations and enable even more ambitious applications.

Bahar Lab | Dill Lab

anthony.bogetti@stonybrook.edu

I attained my PhD in the lab of Sunil Saxena at the University of Pittsburgh, where I worked on electron paramagnetic resonance spectroscopy and molecular dynamics simulations. As a postdoctoral researcher in the lab of Ivet Bahar, I am interested in integrating experimental data into computational modeling to achieve a more complete understanding of protein dynamics and interactions.

Bahar Lab

xiaowei.bogetti@stonybrook.edu

I am interested in the development of geometric methods to study the structure-function relationship of molecules. By using geometry methods, we have developed a robust numerical algorithm for the solutions of inverse kinematics problems arising in molecular structure studies, and a numerical method to compute the molecular surface areas and volumes which are playing significant roles in the solvation of molecules. My current work focuses on the applications of the methods to the quantitative evaluation of molecular interactions and to the efficient exploration of molecular shape spaces, such as macrocycles, loop regions in proteins, and RNAs.

Coutsias Lab

xin.cao@stonybrook.edu

I research the biophysics of adaptivity. Living organisms are unique among physical systems in that they are self-sustaining entities that are able to sense their environments and respond in self-serving ways. This adaptive behavior happens at all scales, from the individual level where single cells maintain homeostasis by regulating their protein expression in response to environmental stimuli, to the population level where Darwinian evolution selects winners of resource competitions in its hallmark fitness ratcheting process. I want to bridge the scales of adaptivity and develop new mathematical tools to understand it.

Dill Lab

charles.kocher@stonybrook.edu

Rostam applies tools from statistical mechanics to elucidate underlying forces in biological phenomena, such as “Why do proteins evolve differently?”, “What causes cells to age?” and “How do brain networks transition?” Emphasis is placed on developing biophysical models for which mathematical equations with experimentally measured parameters can be derived.

Bahar Lab | Dill Lab

rostam.razban@stonybrook.edu

I completed my Ph.D. in Chemistry from IISER Pune in 2024. My research focuses on the aggregation mechanisms of proteins like alpha-synuclein, Aβ42, and gamma-crystallin, which are implicated in Parkinson’s, Alzheimer’s, and cataracts. I am also interested in biomolecular condensates and liquid-liquid phase separation. Characterizing protein condensates and understanding how their conformations and biophysical properties vary between the bulk and condensed phases remain challenging. My research employs high-throughput disulfide scanning to map distinct conformations within biomolecular aggregates and condensates.

Serebryany Lab

aslam.uddin@stonybook.edu

I am interested in molecular-level motions of chemical, physical, and biophysical systems in solvents which manifest interesting microscopic phenomena such as phase separation, aggregation, and nucleation that eventually dictate macroscopic behaviors. My current work focuses on the development of a statistical mechanical water model which will significantly reduce the time and computational cost required to simulate complex phenomena (e.g. protein-ligand complexation dynamics).

Dill Lab

lakshmanji.verma@stonybrook.edu

I have a deep-seated interest in the confluence of synthetic biology and cancer biology. My ambition is to seamlessly intertwine these two domains, aiming to produce groundbreaking, quantitative insights into phenotypic landscapes in cancer models. While pursuing my PhD at Stony Brook University under the expert guidance of Dr. Gabor Balázsi, our team harnessed these synthetic biological tools to forge a novel quantitative understanding of a pivotal cancer metastasis regulator, BACH1. Our discoveries revealed that BACH1 regulates cancer invasion in a non-monotonic fashion while consistently inhibiting cell proliferation. As I transition into my postdoctoral role in the Balázsi lab, my vision is to craft cutting-edge, multi-functional cellular platforms. These platforms, boasting expanded dimensions and capabilities, will be instrumental in delving deeper into the quantitative nuances of cancer models and serve as the foundation for safe and efficacious therapeutic interventions.

Balázsi Lab

yiming.wan@stonybrook.edu

Yiming’s website

Thermodynamic/energetic principles can be formulated for stochastic dynamical models of complex systems. These principles include fluctuation-dissipation relations, the landscape theory in stochastic thermodynamics, and the statistical thermodynamics of entropic forces. They are formulated purely from time symmetries and the limit theorems of stochastic models in the ideal data infinitus limit and are thus universal. I am generally interested in developing these theories and applying them to solve problems in cellular biology, neuroscience, and evolution biology.

Dill Lab

ying-jen.yang@stonybrook.edu