Related papers: Multiscale modeling of solute diffusion in tribloc…
In this paper we introduce a novel method to simulate lateral diffusion of inclusions in a fluctuating membrane. The regarded systems are governed by two dynamic processes: the height fluctuations of the membrane and the diffusion of the…
We expand on a recent study of a lattice model of interacting particles [Phys. Rev. Lett. 111, 110601 (2013)]. The adsorption isotherm and equilibrium fluctuations in particle number are discussed as a function of the interaction. Their…
A multi-scale framework was recently proposed for more realistic molecular dynamics simulations in continuum solvent models by coupling a molecular mechanics treatment of solute with a fluid mechanics treatment of solvent, where we…
In this work we study the diffusion mechanisms in lithium disilicate melt using molecular dynamics simulation, which has an edge over other simulation methods because it can track down actual atomic rearrangements in materials once a…
KMCLib is a general framework for lattice kinetic Monte Carlo (KMC) simulations. The program can handle simulations of the diffusion and reaction of millions of particles in one, two, or three dimensions, and is designed to be easily…
Recently, hybrid models have emerged that combine microscopic and mesoscopic regimes in a single stochastic reaction-diffusion simulation. Microscopic simulations track every individual molecule and are generally more accurate. Mesoscopic…
The simulation of fluid flow in real, multiscale porous media remains challenging due to the complexity of nanoscale phenomena and the difficulty of developing upscaling methodologies. In this study, we introduce a multiscale filtration…
Multi-layered materials are everywhere, from fiber-reinforced polymer composites (FRPCs) to plywood sheets to layered rocks. When in service, these materials are often exposed to long-term environmental factors, like moisture, temperature,…
Despite the wide existence of vesicles in living cells as well as their important applications like drug-delivery, the underlying mechanism of vesicle fusion/fission remains under debate. Here, we develop a constrained self-consistent field…
We generalize to three dimensions (3D) a recently developed improved multi-component pseudopotential lattice Boltzmann method and analyze its applicability to simulate flows through realistic porous media. The model is validated and…
Three dimensional implementations of liquid state theories offer an efficient alternative to computer simulations for the atomic-level description of aqueous solutions in complex environments. In this context, we present a (classical)…
Kinetic Monte-Carlo (KMC) simulations are a well-established numerical tool to investigate the time-dependent surface morphology in molecular beam epitaxy (MBE) experiments. In parallel, simplified approaches such as limited mobility (LM)…
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…
A hybrid numerical model previously developed for combustion simulations is extended in this article to describe flame propagation and stabilization in porous media. The model, with a special focus on flame/wall interaction processes, is…
We have conducted a triple-scale simulation of liquid water by concurrently coupling atomistic, mesoscopic, and continuum models of the liquid. The presented triple-scale hydrodynamic solver for molecular liquids enables the insertion of…
Detailed understanding of the coupling between fluid flow and solid deformation in porous media is crucial for the development biomedical devices and novel energy technologies relating to a wide range of geological and biological processes.…
We use Langevin dynamics (LD) simulations to investigate single-file diffusion (SFD) in a dilute solution of flexible linear polymers inside a narrow tube with periodic boundary conditions (a torus). The transition from SFD, where the time…
This paper presents an algorithm for Monte Carlo fixed-lag smoothing in state-space models defined by a diffusion process observed through noisy discrete-time measurements. Based on a particles approximation of the filtering and smoothing…
We have used the Scheutjens-Fleer self-consistent field (SF-SCF) method to predict the self-assembly of triblock copolymers with a solvophilic middle block and sufficiently long solvophobic outer blocks. We model copolymers consisting of…
Stochastic models of reaction-diffusion systems are important for the study of biochemical reaction networks where species are present in low copy numbers or if reactions are highly diffusion limited. In living cells many such systems…