相关论文: Simulating the chromatin mediated phase separation…

Phase separation of two phase separating solutes in a common solvent can result in mesoscale (micron-sized) droplets with complex topologies of the domains of each solute within each droplet. Such topologies have been observed in-vitro in…

A coarse-grained model for solutions of polymers in supercritical fluids is introduced and applied to the system of hexadecane and carbon dioxide as a representative example. Fitting parameters of the model to the gas-liquid critical point…

Polariton condensates occur away from thermal equilibrium, in an open system where heat and particles are continually exchanged with reservoirs. These phenomena have been extensively analyzed in terms of kinetic equations. Based on the…

This study presents an enhanced method for analyzing cluster dynamics, with a particular focus on tracking clusters' continuity over time using time-series data from molecular dynamics (MD) simulation. The proposed method was applied to…

Given the wide range of length scales, the analysis of polymer systems often requires coarse-graining, for which various levels of description may be possible depending on the phenomenon under consideration. Here, we provide a super-coarse…

During the eukaryotic cell cycle, chromatin undergoes several conformational changes, which are believed to play key roles in gene expression regulation during interphase, and in genome replication and division during mitosis. In this…

Phase-separated biomolecular condensates containing proteins and RNAs can assemble into higher-order structures by forming thermodynamically stable interfaces between immiscible phases. Using a minimal model of a protein/RNA interaction…

The liquid-liquid phase separation of biomolecules is an important process for intracellular organization. Biomolecular sequence combinatorics leads to a large variety of proteins and nucleic acids which can interact to form a diversity of…

The spatio-temporal organization of proteins and the associated morphological changes in membranes are of importance in cell signaling. Several mechanisms that promote the aggregation of proteins at low cell surface concentrations have been…

This chapter reviews how molecular dynamics simulations, experimental data, and Markov state models can synergize to map-out the mechanism of protein-protein association and dissociation.

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…

Colloid-polymer mixtures may undergo either fluid-fluid phase separation or gelation. This depends on the depth of the quench (polymer concentration) and polymer-colloid size ratio. We present a real-space study of dynamics in phase…

One of the most important problems in development is how epigenetic domains can be first established, and then maintained, within cells. To address this question, we propose a framework which couples 3D chromatin folding dynamics, to a…

Depletion forces play a role in the compaction and de-compation of chromosomal material in simple cells but it remains debatable whether they are sufficient to account for chromosomal collapse. We present coarse-grained molecular dynamics…

We discover a new type of nonequilibrium phase transition in a model of chromatin dynamics, which accounts for the coherent motions that have been observed in experiment. The coherent motion is due to the long-range cooperation of molecular…

We report a numerical simulation for the phase diagram of a simple two dimensional model, similar to one proposed by Noro and Frenkel [J. Chem. Phys. \textbf{114}, 2477 (2001)] for membrane proteins, but one that includes the role of the…

Cells regulate gene expression in part by forming DNA-protein condensates in the nucleus. While existing theories describe the equilibrium size and stability of such condensates, their dynamics remain less understood. Here, we use…

Cells operate in part by compartmentalizing chemical reactions. For example, recent work has shown that chromatin, the material that contains the cell's genome, can auto-regulate its structure by utilizing reaction products (proteins, RNA)…

We solve a hydrodynamic model of active chromatin dynamics, within a confined geometry simulating the cell nucleus. Using both analytical and numerical methods, we describe the behavior of the chromatin polymer driven by the activity of…

A physical scenario accounting for the existence of size-limited submicrometric domains in cell membranes is proposed. It is based on the numerical investigation of the counterpart, in lipidic membranes where proteins are diffusing, of the…