Related papers: A tutorial for mesoscale computer simulations of l…
Solvent-free coarse grained models represent one of the most promising approaches for molecular simulations of mesoscopically large membranes. In these models, the size of the simulated membrane is limited by the slow relaxation time of…
The biological membrane, which compartmentalizes the cell and its organelles, exhibit wide variety of macroscopic shapes of varying morphology and topology. A systematic understanding of the relation of membrane shapes to composition,…
Computational determination of the equilibrium state of heterogeneous phospholipid mem-branes is a significant challenge. We wish to explore the rich phase diagram of these multi-component systems. However, the diffusion and mixing times in…
Lipid bilayers often form high-curvature configurations due to self-assembly conditions or certain biological processes. However, particle-based simulations of lipid membranes are predominantly of flat lipid membranes because planar…
Filaments are ubiquitous within the microscopic world. They occur frequently in both biological and industrial environments and display varied and rich dynamics. Their wide range of applications has spurred the development of a special…
We review a scalable two- and three-dimensional computer code for low-temperature plasma simulations in multi-material complex geometries. Our approach is based on embedded boundary (EB) finite volume discretizations of the minimal…
We present a method for simulating fluid vesicles with in-plane orientational ordering. The method involves computation of local curvature tensor and parallel transport of the orientational field on a randomly triangulated surface. It is…
An overview of computer simulations of tribology is presented. The chapter begins with a brief overview of simulation techniques and the special requirements for simulations of tribological processes. Then simple one-dimensional models of…
Model biomembrane systems play a crucial role in advancing biomedical research by providing simplified yet effective platforms for exploring complex biological mechanisms. These systems span a wide range of scales, from…
Narrow membrane tubes are commonly pulled out from the surface of phospholipid vesicles using forces applied either through laser or magnetic tweezers or through the action of processive motor proteins. Recent examples have emerged where…
We describe a complete methodology to bridge the scales between nanoscale Molecular Dynamics and (micrometer) mesoscale Monte Carlo simulations in lipid membranes and vesicles undergoing phase separation, in which curving molecular species…
Many coarse-grained models have been developed for equilibrium studies of lipid bilayer membranes. To achieve in simulations access to length-scales and time-scales difficult to attain in fully atomistic molecular dynamics, these…
Biological membranes constitute boundaries of cells and cell organelles. Physico-chemical mechanisms at the atomic scale are dictated by protein-lipid interaction strength, lipid composition, lipid distribution in the vicinity of the…
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…
We present a simple coarse-grained bead-and-spring model for lipid bilayers. The system has been developed to reproduce the main (gel-liquid) transition of biological membranes on intermediate length scales of a couple of nanometres and is…
Background: Monte Carlo simulations of diffusion are commonly used as a model validation tool as they are especially suitable for generating the diffusion MRI signal in complicated tissue microgeometries. New method: Here we describe the…
We study the stress distribution profiles and the height and thickness fluctuations of lipid membranes in the tilted gel state by Monte Carlo simulations of a generic coarse-grained model for lipid membranes, which reproduces many known…
Generic coarse-grained models are designed such that they are (i) simple and (ii) computationally efficient. They do not aim at representing particular materials, but classes of materials, hence they can offer insight into universal…
Membrane phase-separation is a mechanism that biological membranes often use to locally concentrate specific lipid species in order to organize diverse membrane processes. Phase separation has also been explored as a tool for the design of…
Blebs are balloon-shaped membrane protrusions that form during many physiological processes. Using computer simulation of a particle-based model for self-assembled lipid bilayers coupled to an elastic meshwork, we investigated the phase…