相关论文: Parametrization of coarse grained force fields for…
We construct a coarse-grained (CG) model for dipalmitoylphosphatidylcholine (DPPC)/cholesterol bilayers and apply it to large-scale simulation studies of lipid membranes. Our CG model is a two-dimensional representation of the membrane,…
Separation of salt ions from seawater using graphene oxide (GO) membrane is an emerging desalination method. Here, we investigate the dynamic behavior of water, sodium, and chloride ions inside GO membrane using a computational approach.…
In unresolved flow CFD-DEM simulations, the porosity values for each CFD cell are determined using a coarse-graining algorithm. While this approach enables coupled simulations of representative numbers of particles, the influence of the…
The Eulerian-Lagrangian approach based on Large-Eddy Simulation (LES) is one of the most promising and viable numerical tools to study turbulent dispersed flows when the computational cost of Direct Numerical Simulation (DNS) becomes too…
Shear transformations (i.e., localised rearrangements of particles resulting in the shear deformation of a small region of the sample) are the building blocks of mesoscale models for the flow of disordered solids. In order to compute the…
Diffusion of particles in complex fluids and gels is difficult to describe and often lies beyond the scope of the classical Stokes-Einstein relation. One of the main lines of research over the past few decades has sought to relate…
Ionic Liquids feature thermophysical properties that are of interest in solvents, energy storage materials and tenable lubrication applications. Recently, a series of coarse grained (CG) models was developed to investigate…
We use a coarse-grained molecular dynamics simulation to investigate the interaction between neutral or charged nanoparticles (NPs) and a vesicle consisting of neutral and negatively charged lipids. We focus on the interaction strengths of…
In this work, we review previously developed coarse-grained (CG) particle models for biological membrane and red blood cells (RBCs) and discuss the advantages of the CG particle method over the continuum and atomic simulations on modeling…
We review some recent coarse-graining and multi-scale methods, but also put forward some new ideas for addressing such issues. We find that, if one is guided by nonequilibrium statistical mechanics and thermodynamics, it is possible to…
Molecular dynamics (MD) simulation is essential for various scientific domains but computationally expensive. Learning-based force fields have made significant progress in accelerating ab-initio MD simulation but are not fast enough for…
Composite of two kinds of grains is modeled in two-dimension and the elasticity is calculated using molecular dynamics method implementing Gear predictor-corrector of fifth order. It has been observed that same composite concentration can…
Coarse-grained (CG) molecular dynamics enables simulations of atomic systems such as biomolecules at timescales inaccessible to all-atom (AA) methods, but existing CG neural potentials trained via force matching capture only the gradient of…
In this work, we address the systematic biases and random errors stemming from finite step sizes encountered in diffusion simulations. We introduce the Effective Geometry Monte Carlo (EG-MC) simulation algorithm which modifies the geometry…
A brief review of modeling and simulation methods for a study of polymers at interfaces is provided. When studying truly multiscale problems as provided by realistic polymer systems, coarse graining is practically unavoidable. In this…
Recent developments in vortex particle methods for simulating three-dimensional incompressible flows are presented. A lightweight, dynamic Large-Eddy Simulation model is tested, featuring a dynamic procedure that relies solely on Lagrangian…
We present a systematic study of the self-diffusion coefficient for a fluid of particles interacting via the square-well pair potential by means of molecular dynamics simulations in the canonical (N,V,T) ensemble. The discrete nature of the…
We present a general approach to isolate chemical reaction mechanism as an independently controllable variable across chemically distinct systems. Modern approaches to reduce the computational expense of molecular dynamics simulations often…
A parameterization strategy for molecular models on the basis of force fields is proposed, which allows a rapid development of models for small molecules by using results from quantum mechanical (QM) ab initio calculations and thermodynamic…
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…