Related papers: Membrane simulation models from nm to $\mu$m scale
A good representation of mesoscopic fluids is required to combine with molecular simulations at larger length and time scales (De Fabritiis {\it et. al}, Phys. Rev. Lett. 97, 134501 (2006)). However, accurate computational models of the…
Biomembranes play a central role in various phenomena like locomotion of cells, cell-cell interactions, packaging of nutrients, and in maintaining organelle morphology and functionality. During these processes, the membranes undergo…
We review recent molecular dynamics simulations of thermally activated undulations and defects in the lamellar $L_\alpha$ phase of a binary amphiphile-solvent mixture, using an idealized molecular coarse-grained model: Solvent particles are…
The behavior of lipid bilayer is important to understand the functionality of cells like the trafficking of ions between cells. Standard procedures to explore the properties of lipid bilayer and hemifused states typically use either…
It is well known that the number of particles should be scaled up to enable industrial scale simulation. The calculations are more computationally intensive when the motion of the surrounding fluid is considered. Besides the advances in…
The aim of this paper is to propose a new numerical model to simulate 2D vesicles interacting with a newtonian fluid. The inextensible membrane is modeled by a chain of circular rigid particles which are maintained in cohesion by using two…
We study membrane-protein interactions and membrane-mediated protein-protein interactions by Monte Carlo simulations of a generic coarse-grained model for lipid bilayers with cylindrical hydrophobic inclusions. The strength of the…
This paper considers membranes of globular structure in the framework of the cell model technique. Coupled micropolar and Brinkman-type equations are used to model the flow of micropolar fluid through a spherical cell, consisting of solid…
first-principles numerical simulation model for crumpling of a stiff tethered membrane is introduced. In our model membranes, wrinkles, ridge formation, ridge collapse, as well as the initiation of stiffness divergence, are observed. The…
Membrane organization is essential for cellular functions such as signal transduction and membrane trafficking. A major challenge is to understand the lateral heterogeneous structures in membranes and membrane fluidity in the presence of…
This work aims to describe a mathematical model and a numerical method to simulate a thin anisotropic composite membrane moving and deforming in 3D space under a dynamic load of an arbitrary time and space profile. The model and the method…
This paper presents a numerical method for the simulation of multiscale materials composed of an elastic matrix and slender active inclusions. The setting is motivated by the modeling of vascularized tissues and by problems arising in the…
We study the indentation of a free-standing lipid membrane suspended over a nanopore on a hydrophobic substrate by means of molecular dynamics simulations. We find that in the course of indentation, the membrane bends at the point of…
For a wide range of applications, we need DEM simulations of granular matter in contact with flexible elastic boundaries. We present a novel method to describe the interaction between granular particles and a flexible elastic membrane.…
Dense suspensions of particles dispersed in liquids are central to industrial and geophysical processes and serve as model systems for out-of-equilibrium soft matter. At high particle concentrations, they exhibit stress-dependent rheology,…
In experiments on model membranes, a formation of large domains of different lipid composition is readily observed. However, no such phase separation is observed in the membranes of intact cells. Instead, a structure of small transient…
The diffusion coefficient of a circular shaped inclusion in a liquid membrane is investigated by taking into account the interaction between membranes and bulk solvents of arbitrary thickness. As illustrative examples, the diffusion…
Biomembranes, which are mainly composed of neutral and charged lipids, exhibit a large variety of functional structures and dynamics. Here, we report a coarse-grained molecular dynamics (MD) simulation of the phase separation and…
A variety of computational models have been developed to describe active matter at different length and time scales. The diversity of the methods and the challenges in modeling active matter---ranging from molecular motors and cytoskeletal…
A large number of powerful, high-quality, and open-source simulation packages exist to efficiently perform molecular dynamics simulations, and their prevalence has greatly accelerated discoveries across a wide range of scientific domains.…