Related papers: Membrane simulation models from nm to $\mu$m scale
Relatively short peptides, such as toxins and antimicrobial-peptides, are known to insert themselves into cell membranes. On the basis of simple bead-spring models for the membrane lipids, the peptide, and water, detailed processes of the…
We propose a robust simulation method for phospholipid membranes. It is based on a mixed three-field formulation that accounts for tangential fluidity (Boussinesq-Scriven law), bending elasticity (Canham-Helfrich model) and inextensibility.…
Over times shorter than that required for relaxation of enthalpy, a liquid can exhibit striking heterogeneities. The picture of these heterogeneities is complex with transient patches of rigidity, irregular yet persistent, intersected by…
Particle simulations confined by sharp walls usually develop an oscillatory density profile. For some applications, most notably soft matter liquids, this behavior is often unrealistic and one expects a monotonic density climb instead. To…
Massively-parallel molecular dynamics simulation is applied to systems containing electrolytes, vapour-liquid interfaces, and biomolecules in contact with water-oil interfaces. Novel molecular models of alkali halide salts are presented and…
A theoretical model of a two-component fluid membrane containing lipids and two-state active inclusions is presented. Under strong inclusion activities the membrane can be unstable due to pump-driven undulation or aggregation of high…
As a complementary tool to laboratory experiments, discrete numerical simulation, applied to granular materials, provides valuable information on the grain and contact scale microstructure, thereby enabling one to better understand the…
We consider the hydrodynamics of lipid bilayers containing transmembrane proteins of arbitrary shape. This biologically-motivated problem is relevant to the cell membrane, whose fluctuating dynamics play a key role in phenomena ranging from…
This paper presents a phase-field model for simulating the three-dimensional deformation of vesicle membranes, incorporating area-difference elasticity, with constraints on bulk volume and surface area. We develop efficient numerical…
Quantum chemical calculations on quantum computers have been focused mostly on simulating molecules in gas-phase. Molecules in liquid solution are however most relevant for Chemistry. Continuum solvation models represent a good compromise…
A new method is presented for mesoscopic simulations of particle dispersions in liquid crystal solvents. It allows efficient first-principle simulations of the dispersions involving many particles with many-body interactions mediated by the…
We consider a discrete-continuum model of a biomembrane with embedded particles. While the membrane is represented by a continuous surface, embedded particles are described by rigid discrete objects which are free to move and rotate in…
Accurate modeling of the solvent environment for biological molecules is crucial for computational biology and drug design. A popular approach to achieve long simulation time scales for large system sizes is to incorporate the effect of the…
Machine learning (ML) is transforming all areas of science. The complex and time-consuming calculations in molecular simulations are particularly suitable for a machine learning revolution and have already been profoundly impacted by the…
In this paper we study newly developed methods for linear elasticity on polyhedral meshes. Our emphasis is on applications of the methods to geological models. Models of subsurface, and in particular sedimentary rocks, naturally lead to…
We describe a numerical method to simulate an elastic shell immersed in a viscous incompressible fluid. The method is developed as an extension of the immersed boundary method using shell equations based on the Kirchhoff-Love and the planar…
The distances over which biological molecules and their complexes can function range from a few nanometres, in the case of folded structures, to millimetres, for example during chromosome organization. Describing phenomena that cover such…
Molecular dynamics simulation has been used to model pattern formation in three-dimensional Rayleigh--Benard convection at the discrete-particle level. Two examples are considered, one in which an almost perfect array of hexagonally-shaped…
The Cellular Potts Model (CPM) succesfully simulates drainage and shear in foams. Here we use the CPM to investigate instabilities due to the flow of a single large bubble in a dry, monodisperse two-dimensional flowing foam. As in…
The great challenge with biological membrane systems is the wide range of scales involved, from nanometers and picoseconds for individual lipids, to the micrometers and beyond millisecond for cellular signalling processes. While…