Postdoctoral Fellows

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I am interested in building mathematical models aimed at understanding how protein-mediated physical manipulation of the chromosomal polymer at hundreds-of-nanometers length scale may lead to large scale structural reorganization and topological disentanglement, also interesting are the associated time scales. Such models not only have the potential to make our notion of the inner workings of the cellular machinery more nuanced via interpreting existing observations, but can also predict new experiments.

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CONSTANTIN "CRISTIAN" CARANICA - Northeastern University
My research is focused on integrating ensemble methods from statistical physics and data-driven analysis to simulate biological processes at the cell level. I used such methods to unravel stochastic clock networks in Neurosporra crassa driven by a stochastic resonance phenomenon. I am also using optimization methods to integrate mathematical modeling and bioinformatics to model gene regulatory networks driving cellular state transitions.

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RYAN CHENG - Rice University
My research at the CTBP involves quantifying the essential features of large biological datasets. I have primarily worked on inferring fitness landscapes for bacterial signaling proteins to better understand the origin of interaction specificity, “cross-talk,” and mutational phenotypes. Recently, I am also working in a collaborative effort to elucidate the biochemical origins of the 3D spatial organization of human chromosomes.

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AMIT DAS - Northeastern University
I am interested in active biological matter and multiscale modeling. I use various computational tools of soft condensed matter to understand the mechanics and dynamical behaviors of subcellular to tissue-level active processes.

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OLGA DUDCHENKO - Baylor College of Medicine
I am currently working towards understanding how genomes fold in three dimensions. We probe the 3D architecture of whole genomes by coupling proximity-based ligation with massively parallel sequencing – the Hi-C method. I am particularly interested in large-scale genome remodeling events associated with the process known as X chromosome inactivation: a mechanism that ensures that males who possess one X chromosome and females with two X chromosomes exhibit similar gene expression levels.

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DONGYA JIA - Rice University
I use systems biology approaches to uncover the principles underlying the phenotypic plasticity and cell-fate decision making in cancer. Specifically, I integrate mathematical modeling and data analysis to elucidate the emergent dynamics of cellular networks governing metastasis and cancer metabolism. My work contributes to a systems-level understanding of tumorigenesis and metastasis and eventually facilitates the personalized therapeutic strategies for patients.

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DANA KREPEL - Rice University
The aim of my current research is to shed light on the enigma of three-dimensional chromatin structure, a complex of DNA and proteins. As a first step, I am working on better understanding of the cohesion complex, which is considered as the motor, translocating segments of chromatin to form structural loops.

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JOEL D. MALLORY - Rice University
My research centers on exploring the thermodynamic efficiency of driven, nonequilibrium cycles that are fundamentally important for cellular information processing, namely those of DNA replication by the T7DNA polymerase enzyme and protein translation by the E. Coli ribosome. The thermodynamic efficiency of these molecular machines is assessed by their ability to keep unnecessary stochastic fluctuations and errors under control while at the same time to minimize the rate of heat dissipated to the environment. The trade-off between these two competing objectives is captured by a quantity called the uncertainty measure, which should be small and suppressed for an efficient molecular machine operating in a nonequilibrium steady state.

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TOMER MARKOVICH - Rice University
I am interested in the nonequilibrium statistical mechanics of active matter systems, including self-propelled particles and living cells. My main focus is active gels, and specifically understanding their departure from equilibrium and the breakage of time-reversal-symmetry. I further study the consequences of this breakage of time-reversal-symmetry on biological systems and in the formulation of general continuum theories.

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MIKITA MISIURA - Rice University
My current research includes studies of ERK and kinesin motor proteins. I use both theoretical methods and computational tools (such as molecular dynamics, docking, etc.) to understand their properties and their role in the living cells.

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MRINMOY MUKHERJEE - Northeastern University
My current research includes understanding of epithelial-mesenchymal transition using mathematical modeling. I use both coarse-grained and agent-based modeling approach to understand the physical phenomena in biological pattern formation in the context of developmental and cancer biology.

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PATRICK MURPHY - Rice University
My research focuses on emergent behavior in bacteria such as Myxococcus xanthus, which are known for a diverse set of communal behaviors under various conditions. I focus on quantifying changes in collective cellular behavior under starvation conditions that lead to the formation of fruiting bodies, particularly during later stages of aggregation, using data-driven modeling. My research also focuses on analyzing mathematical models of neumatic alignment, where crowded cellular environments and subsequent cell-to-cell collisions aid in aligning neighboring cells.

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My research at the CTBP involves the investigation of chromatin dynamics, studying the 3D spatial organization of chromosomes by using High-Performance Computer (HPC). I am also interested in exploring models to visualize energy landscapes via multidimensional reduction methods.

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OLGA SAMOYLOVA - Rice University
My project is the study of dynamics and aggregation of tumor suppressor protein p53 (wild type and mutants) using molecular modeling, investigation of mechanisms of dense liquid condensates formations and its role in the nucleation and growth of amyloid fibrils.

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JAEOH SHIN - Rice University
My research aims to unravel the fundamental physics principles behind complex biological processes. I am working on the process of protein reaching a specific target sequence on a DNA by using the theory of stochastic processes and numerical simulations. More recently, I am also working on how the fundamental property of transition time symmetry can be broken in non-equilibrium biological processes.

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HAMID TEIMOURI - Rice University
My current research focuses on developing quantitative models for understanding the role of stochasticity in biological processes. In particular, I am interested in investigating the role of stochasticity in dynamics of cancer initiation, antibiotic-induced bacterial clearance, T cell activation, and cell-size control in bacteria. I perform my research projects by combining analytical solutions, computer simulations, machine learning methods and statistical hypothesis testing. An indispensable part of my work is to test my theoretical predictions with the available experimental data.