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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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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ANDREA FALCON - Northeastern University
Info forthcoming.

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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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ANDREI GASIC - 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.

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DIMOS GKOUNTAROULIS - Baylor College of Medicine
My research focuses on quantifying the topology of biopolymers using computational pipelines based on formal low-dimensional topology and knot theory. I am particularly interested in the interaction between mathematical topology and chromatin tracing: image-based methods that determine the actual spatial coordinates of consecutive genomic loci of single cells.

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TOMAR 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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My research involves the Prediction of Actin-Actin interactions via co-evolutionary sequence analysis and molecular dynamics simulation.

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TRIPTI MIDHA - Rice University
My research focuses on analyzing the interplay of speed and accuracy of fundamental biological processes such as DNA replication and protein synthesis translation. I aim at developing the stochastic models to investigate the various mechanisms of proof-reading using the theoretical and computational methods.

Alex Moffett

ALEX MOFFETT - Northeastern UniversityI’m interested in ecology and evolution. Currently, I am working on problems related to the population dynamics of cancer and microbial infection. I’m also generally interested in developing mathematical/computational tools for biological problems, including methods for comparing biomolecular structures and for modeling biochemical signaling pathways.

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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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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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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.

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AILUN WANG - Northeastern University
I am interested in investigating the dynamical behaviors of biological systems in a wide range. I use molecular dynamics simulations with various computational tools and analysis methods to understand the dynamics properties in biological processes, such as the protein-peptide interaction, nucleosome and chromatin dynamics and the conformational dynamics of ribosomes.

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BERNARD ZUBILLAGA HERRERA - Northeastern University
I am interested in using computational tools such as molecular dynamics and Monte Carlo simulations in order to probe the statistical mechanics behind Hi-C methods. Theoretical modeling of virtual Hi-C experiments may provide insights into the limitations of real Hi-C experiments, shedding light on current issues and unanswered questions concerning the experimental Hi-C methodology.