相关论文: Simulating the chromatin mediated phase separation…
The point-curvature model for membrane protein inclusions is shown to capture multibody interactions very well. Using this model, we find that the interplay between membrane tension and multibody interactions results in a collective…
Native extracellular matrices (ECMs), such as those of the human brain and other neural tissues, exhibit networks of molecular interactions between specific matrix proteins and other tissue components. Guided by these naturally…
We use computer simulations to study the dynamics of a physical gel at high densities where gelation and the glass transition interfere. We report and provide detailed physical understanding of complex relaxation patterns for time…
Polymer blends offer an exciting material for various potential applications due to their tunable properties by varying constituting components and their relative composition. Our simulation results unravel an intrinsic relationship between…
Liquid mixtures of many interacting components often exhibit numerous coexisting types of droplets. An exciting example is the cytosol of biological cells, where diverse droplets, called condensates, are essential for cellular function.…
We study interacting bosons in optical lattices in the weak-tunneling regime in systems that exhibit the coexistence of Mott-insulating and condensed phases. We discuss the nature of the condensed ground state in this regime and the…
Scaffold proteins organize cellular processes by bringing signaling molecules into interaction, sometimes by forming large signalosomes. Several of these scaffolds are known to polymerize. Their assemblies should therefore not be understood…
We present molecular dynamics simulations on the structural relaxation of a simple bead-spring model for polymer blends. The introduction of a different monomer size induces a large time scale separation for the dynamics of the two…
The purpose of this work is to use active particles to study the effect of facilitation on supercooled liquids. To this end we investigate the behavior of a model supercooled liquid doped with intermittently active and intermittently slowed…
Hybrid molecular dynamics/Monte Carlo simulations used to study melts of unentangled, thermoreversibly associating supramolecular polymers. In this first of a series of papers, we describe and validate a model that is effective in…
Despite more than 100 years of study, it is unclear if the movement of proteins inside the cell is best described as a mosh pit or an exquisitely choreographed dance. Recent studies suggest the latter. Local interactions induce molecular…
Recent work has highlighted roles for thermodynamic phase behavior in diverse cellular processes. Proteins and nucleic acids can phase separate into three-dimensional liquid droplets in the cytoplasm and nucleus and the plasma membrane of…
Using dissipative particle dynamics (DPD) simulation method, we study the phase separation dynamics in block copolymer (BCP) melt in $d=3$, subjected to external stimuli such as light. An initial homogeneous BCP melt is rapidly quenched to…
The interplay between phase separation and wetting of multicomponent mixtures is ubiquitous in nature and technology and recently gained significant attention across scientific disciplines, due to the discovery of biomolecular condensates.…
We study the aggregation of peptides using the discrete molecular dynamics simulations. At temperatures above the alpha-helix melting temperature of a single peptide, the model peptides aggregate into a multi-layer parallel beta-sheet…
The eukaryotic cell nucleus harbors the DNA genome that is organized in a dynamic chromatin network and embedded in a viscous crowded fluid. This environment directly affects enzymatic reactions and target search processes that access the…
The extent of coupling between the folding of a protein and its binding to a substrate varies from protein to protein. Some proteins have highly structured native states in solution, while others are natively disordered and only fold fully…
We propose a microscopic simulation for quark many-body system based on molecular dynamics. Using color confinement and one-gluon exchange potentials together with the meson exchange potentials between quarks, we construct nucleons and…
This paper reviews recent Monte Carlo simulation studies of the glassy behavior in thin polymer films. The simulations employ a version of the bond-fluctuation lattice model, in which the glass transition is driven by the competition…
Two ring polymers close to each other in space may be either in a segregated phase if there is a strong repulsion between monomers in the polymers, or intermingle in a mixed phase if there is a strong attractive force between the monomers.…