Related papers: Hydrodynamics of Diffusion in Lipid Membrane Simul…
Hydrodynamic theories effectively describe many-body systems out of equilibrium in terms of a few macroscopic parameters. However, such hydrodynamic parameters are difficult to derive from microscopics. Seldom is this challenge more…
In hydrodynamic descriptions of lipid bilayers, the membrane is often approximated as being impermeable to the surrounding, solute-containing fluid. However, biological and in vitro lipid membranes are influenced by their permeability and…
We investigate the process of biopolymer translocation through a narrow pore using a multiscale approach which explicitly accounts for the hydrodynamic interactions of the molecule with the surrounding solvent. The simulations confirm that…
We present Monte Carlo simulations of an ultra coarse-grained lipid bilayer with different number of lipids on both leaflets. In the simulations, we employ a new method for measuring the elastic parameters of the membrane, including the…
In this review we discuss the recent progress in the simulation of soft active matter systems and in particular the hydrodynamics of microswimmers using the method of multiparticle collision dynamics, which solves the hydrodynamic flows…
The partitioning of small molecules in cell membranes---a key parameter for pharmaceutical applications---typically relies on experimentally-available bulk partitioning coefficients. Computer simulations provide a structural resolution of…
We study compressible fluid flow in narrow two-dimensional channels using a novel molecular dynamics simulation method. In the simulation area, an upstream source is maintained at constant density and temperature while a downstream…
In living cells, protein-rich condensates can wet the cell membrane and surfaces of membrane-bound organelles. Interestingly, many phase-separating proteins also bind to membranes leading to a molecular layer of bound molecules. Here we…
One of the principal mechanisms by which surfaces and interfaces affect microbial life is by perturbing the hydrodynamic flows generated by swimming. By summing a recursive series of image systems we derive a numerically tractable…
Explicit simulations of fluid mixtures of highly size-dispersed particles are constrained by numerical challenges associated with identifying pair-interaction neighbors. Recent algorithmic developments have ameliorated these difficulties to…
Membrane bending is an extensively studied problem from both modeling and experimental perspectives because of the wide implications of curvature generation in cell biology. Many of the curvature generating aspects in membranes can be…
A theory of a lateral stress relaxation in a fluid bilayer membrane under a step-like pressure pulse is proposed. It is shown theoretically that transfer of lipid molecules into a strained region may lead to a substantial decrease of the…
We present predictions for the statistical error due to finite sampling in the presence of thermal fluctuations in molecular simulation algorithms. Specifically, we establish how these errors depend on Mach number, Knudsen number, number of…
Cell membranes phase separate into ordered ${\rm L_o}$ and disordered ${\rm L_d}$ domains depending on their compositions. This membrane compartmentalization is heterogeneous and regulates the localization of specific proteins related to…
The influence of periodic and random surface textures on the flow structure and effective slip length in Newtonian fluids is investigated by molecular dynamics (MD) simulations. We consider a situation where the typical pattern size is…
Molecular dynamics simulations are a powerful tool to study diffusion processes in battery electrolyte and electrode materials. From a single molecular dynamics simulation many properties relevant to diffusion can be obtained, including the…
By adopting the approximations suggested in the theory of thin shells, the hydrodynamic theory of liquid crystals established by Eriksen [Arch. Rational Mech. Anal. 4 (1960) 231; Trans. Soc. Rheol. 4 (1960) 29] and Leslie [Adv. Liq. Cryst.…
In this paper, we explore osmotic transport by means of molecular dynamics (MD) simulations. We first consider osmosis through a membrane, and investigate the reflection coefficient of an imperfectly semi-permeable membrane, in the dilute…
We derive the Hydrodynamics for a system of N active, spherical, underdamped particles, interacting through conservative forces. At the microscopic level, we represent the evolution of the particles in terms of the Kramers equation for the…
We show that long-time, long-distance fluctuations of plane-symmetric horizons exhibit universal hydrodynamic behavior. By considering classical fluctuations around black-brane backgrounds, we find both diffusive and shear modes. The…