Related papers: Coarse-grained molecular dynamics simulation of bi…
A question of considerable interest to cell membrane biology is whether phase segregated domains across an asymmetric bilayer are strongly correlated with each other and whether phase segregation in one leaflet can induce segregation in the…
We report on the results of a molecular dynamics simulation study of binodal glassy systems, formed in the process of isochoric rapid quenching from a high-temperature fluid phase. The transition to vitreous state occurs due to concurrent…
In this paper we present the results of a large-scale numerical investigation of structural properties of a model of cell membrane, simulated as a bilayer of flexible molecules in vacuum. The study was performed by carrying out extensive…
We perform extensive numerical simulations of a paradigmatic model glass former, the hard-sphere fluid with 10% polydispersity. We sample from the ensemble of trajectories with fixed observation time, whereby single trajectories are…
The filtration of fluid in 2D porous medium is simulated by the molecular dynamics technique. The high concentration of fluid is created at the initial point in time and the number of fluid particles is investigated in all porous. The…
We review a few representative examples of granular experiments or models where phase separation, accompanied by domain coarsening, is a relevant phenomenon. We first elucidate the intrinsic non-equilibrium, or athermal, nature of granular…
This paper presents a model and numerical analysis (simulations) of transmembrane potential induced in biological cell membrane under the influence of externally applied electric field (i.e., electroporation). This model differs from the…
We computationally studied the phase behavior and dynamics of binary mixtures of active particles, where each 'species' had distinct activities leading to distinct velocities, fast and slow. We obtained phase diagrams demonstrating…
We propose a simple microscopic model of molecular dynamics simulation to study orientational glass in three dimensions. We present simulation results for mixtures of mildly anisotropic particles and spherical impurities. We realize fcc…
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…
We numerically investigate the hydrodynamics and membrane dynamics of multicomponent vesicles in two strongly confined geometries. This serves as a simplified model for red blood cells undergoing large deformations while traversing narrow…
Probably the most fundamental processes for biological systems is their ability to create themselves through the use of cell division and cell differentiation. In this work a simple physical model is proposed for biological cell division.…
We show here a general model of phase separation in isotropic condensed matter, namely, a viscoelastic model. We propose that the bulk mechanical relaxation modulus that has so far been ignored in previous theories plays an important role…
Complex fluids exhibit structure on a wide range of length and time scales, and hierarchical approaches are necessary to investigate all facets of their often unusual properties. The study of idealized coarse-grained models at different…
Accurate modelling of electrostatic interactions and charge transfer is fundamental to computational chemistry, yet most machine learning interatomic potentials (MLIPs) rely on local atomic descriptors that cannot capture long-range…
The kinetics of dislocations is studied with computer simulation at loadings of different intensity. It is established that the dislocations have a few different structural states. The dislocations "with the micropore" play important role…
Using a multi-phase field model, we examine how particle deformability, which is a proxy for cell stiffness, affects motility induced phase separation (MIPS). We show that purely repulsive deformable, i.e., squishy, cells phase separate…
Lipid membranes are abundant in living organisms, where they constitute a surrounding shell for cells and their organelles. There are many circumstances in which the deformations of lipid membranes are involved in living cells: fusion and…
Many biological processes are supported by special molecules, called motor proteins or molecular motors, that transport cellular cargoes along linear protein filaments and can reversibly associate to their tracks. Stimulated by these…
A binary mixture of particles interacting with spherically-symmetric potentials leading to microsegregation is studied by theory and molecular dynamics (MD) simulations. We consider spherical particles with equal diameters and volume…