相关论文: Active Hydrodynamic Theory of Euchromatin and Hete…
We investigate the hydrodynamic stability and the formation of patterns in a continuum model of epithelial layers, able to account for the interplay between mechanical activity, lateral adhesion and the $6-$fold orientational order…
The baseline level of transcription, which is variable and difficult to quantify, seriously complicates the normalization of comparative transcriptomic data, but its biological importance remains unappreciated. We show that this currently…
Systemic properties of living cells are the result of molecular dynamics governed by so-called genetic regulatory networks (GRN). These networks capture all possible features of cells and are responsible for the immense levels of adaptation…
Living cells provide a fluctuating, out-of-equilibrium environment in which genes must coordinate cellular function. DNA looping, which is a common means of regulating transcription, is very much a stochastic process; the loops arise from…
Nucleosome organization in eukaryotic genomes has a deep impact on gene function. Although progress has been recently made in the identification of various concurring factors influencing nucleosome positioning, it is still unclear whether…
The hydrodynamic theory of active nematics has been often used to describe the spatio-temporal dynamics of cell flows and motile topological defects within soft confluent tissues. Those theories, however, often rely on the assumption that…
The structure and dynamics of important biological quasi-two-dimensional systems, ranging from cytoskeletal gels to tissues, are controlled by nematic order, flow, defects and activity. Continuum hydrodynamic descriptions combined with…
Water and water-mediated interactions determine thermodynamic and kinetics of protein folding, protein aggregation and self-assembly in confined spaces. To obtain insights into the role of water in the context of folding problems, we…
Hydrodynamic theories effectively describe many-body systems out of equilibrium in terms of a few macroscopic parameters. However, such hydrodynamic parameters are difficult to derive from microscopics. Seldom is this challenge more…
We derive hydrodynamics of a prototypical one dimensional model, having variable-range hopping, which mimics passive diffusion and ballistic motion of active, or self-propelled, particles. The model has two main ingredients - the hardcore…
DNA methylation is a primary layer of epigenetic modification that plays a pivotal role in the regulation of development, aging, and cancer. The concurrent activity of opposing enzymes that mediate DNA methylation and demethylation gives…
Water plays a major role in bio-systems, greatly contributing to determine their structure, stability and even function. It is well know, for instance, that proteins require a minimum amount of water to be functionally active. Since the…
Inspired by dense contractile tissues, where cells are subject to periodic deformation, we formulate and study a generic hydrodynamic theory of pulsating active liquids. Combining mechanical and phenomenological arguments, we postulate that…
Biomolecular condensates are essential for cellular organization and result from phase separation in systems far from thermodynamic equilibrium. Among various models, chemically active droplets play a significant role, consisting of…
We incorporate hydrodynamic interactions in a structure-based model of ubiquitin and demonstrate that the hydrodynamic coupling may reduce the peak force when stretching the protein at constant speed, especially at larger speeds.…
A general theoretical framework is put forth to organize and understand various observed phenomena and mathematical relationships in the field of molecular biology. By modeling each cell in eukaryotic organisms as a processor having a…
Lamina-associated domains (LADs) cover a large part of the human genome and are thought to play a major role in shaping the nuclear architectural landscape. Here, we perform polymer simulations, microscopy and mass spectrometry to dissect…
Biological membranes and vesicles play a central role in living systems, forming dynamic interfaces that regulate cellular organization and function. Classical descriptions of membrane mechanics that are rooted in equilibrium statistical…
Communities of swimming microorganisms often thrive near liquid-air interfaces. We study how such `active carpets' shape their aquatic environment by driving biogenic transport in the water column beneath them. The hydrodynamic stirring…
We investigate proteins within heterogeneous cell membranes where non-equilibrium phenomena arises from spatial variations in concentration and temperature. We develop simulation methods building on non-equilibrium statistical mechanics to…