相关论文: Simulating the chromatin mediated phase separation…

We present molecular dynamics simulations of a simple model for polymer melts with intramolecular barriers. We investigate structural relaxation as a function of the barrier strength. Dynamic correlators can be consistently analyzed within…

The fractal globule state is a popular model for describing chromatin packing in eukaryotic nuclei. Here we provide a scaling theory and dissipative particle dynamics (DPD) computer simulation for the thermal motion of monomers in the…

The aim of this paper is to develop suitable models for the phenomenon of cell blebbing, which allow for computational predictions of mechanical effects including the crucial interaction of the cell membrane and the actin cortex. For this…

We study the formation of protein-protein encounter complexes with a Langevin equation approach that considers direct, steric and thermal forces. As three model systems with distinctly different properties we consider the pairs…

We investigate the phase transition properties of the polymer-Potts model, a chain composed of monomers with magnetic degrees of freedom, with the motivation to study the conformation and mark switching dynamics of chromatin. By the…

Suspensions of swimming particles exhibit complex collective behaviors driven by hydrodynamic interactions, showing persistent large-scale flows and long-range correlations. While heavily studied, it remains unclear how such structures…

In view of the notorious complexity of protein--protein interactions, simplified models of proteins treated as patchy particles offer a promising strategy to obtain insight into the mechanism of crystallization. Here we report…

Phase separation, crucial for spatially segregating biomolecules in cells, is well-understood in the simple case of a few components with pairwise interactions. Yet, biological cells challenge the simple picture in at least two ways: First,…

Fluid-structure interactions between active and passive components are important for many biological systems to function. A particular example is chromatin in the cell nucleus, where ATP-powered processes drive coherent motions of the…

We report theoretical and simulation studies of phase coexistence in model globular protein solutions, based on short-range, central, pair potential representations of the interaction among macro-particles. After reviewing our previous…

We study equilibrium properties of polymer films and droplets on a solid substrate employing particle-based simulation techniques (Molecular Dynamics) and a continuum description. Parameter-passing techniques are explored that facilitate a…

Cells contain multiple condensates which spontaneously form due to the heterotypic interactions between their components. Although the proteins and disordered region sequences that are responsible for condensate formation have been…

Experimental approaches have been applied to address questions in understanding three-dimensional chromatin organisation and function. As datasets increase in size and complexity, it becomes a challenge to reach a mechanistic interpretation…

Motivated by the biologically important and complex phenomena of A\beta\ peptide aggregation in Alzheimer's disease, we introduce a model and simulation methodology for studying protein aggregation that includes extra-cellular aggregation,…

Liquid-liquid phase separation plays a major role in the formation and maintenance of various membrane-less subcellular structures in the cytoplasm and nucleus of cells. Biological condensates contain enhanced concentrations of proteins and…

In a companion paper, we put forth a thermodynamic model for complex formation via a chemical reaction involving multiple macromolecular species, which may subsequently undergo liquid-liquid phase separation and a further transition into a…

Phase separation is as familiar as watching vinegar separating from oil in vinegrette. The observation that phase separation of proteins and nucleic acids is widespread in living cells has opened an entire field of research into the…

Chromatin is known to be organized into multiple domains of varying sizes and compaction. While these domains are often imagined as static structures, they are highly dynamic and show cell-to-cell variability. Since processes such as gene…

DNA is now firmly established as a versatile and robust platform for achieving synthetic nanostructures. While the folding of single molecules into complex structures is routinely achieved through engineering basepair sequences, much less…

The diffusion of small molecular penetrants through polymeric materials represents an important fundamental problem, relevant to the design of materials for applications such as coatings and membranes. Polymer networks hold promise in these…