Related papers: Surface reaction-diffusion kinetics on lattice at …
In limited mobility (LM) models of thin film deposition, the final position of each atom or molecule is chosen according to a set of stochastic rules before the incidence of another atom or molecule. Here we investigate the possibility of a…
Immersed boundary-lattice Boltzmann method (IB-LBM) has been widely used for simulation of particle-laden flows recently. However, it was limited to small-scale simulations with no more than O(103) particles. Here, we expand IB-LBM for…
Kinetic Monte Carlo (kMC) simulations have emerged as a key tool for microkinetic modeling in heterogeneous catalysis and other materials applications. Systems, where site-specificity of all elementary reactions allows a mapping onto a…
The mesoscopic reaction-diffusion master equation (RDME) is a popular modeling framework, frequently applied to stochastic reaction-diffusion kinetics in systems biology. The RDME is derived from assumptions about the underlying physical…
A novel approach to simulate simple protein-ligand systems at large time- and length-scales is to couple Markov state models (MSMs) of molecular kinetics with particle-based reaction-diffusion (RD) simulations, MSM/RD. Currently, MSM/RD…
In this work, we investigate the interaction of free and porous media flow by large scale lattice Boltzmann simulations. We study the transport phenomena at the porous interface on multiple scales, i.e., we consider both, computationally…
This paper presents a generic framework for the numerical simulation of transformation-diffusion processes in complex volume geometric shapes. This work follows a previous one devoted to the simulation of microbial degradation of organic…
Complex biological and physical transport processes are often described through systems of interacting particles. Excluded-volume effects on these transport processes are well studied, however the interplay between volume exclusion and…
The lattice Boltzmann model is a simplified kinetic method based on the particle distribution function. We use this method to simulate problems in MEMS, in which the velocity slip near the wall plays an important role. It is demonstrated…
We study a lattice model for the spreading of fluid films, which are a few molecular layers thick, in narrow channels with inert lateral walls. We focus on systems connected to two particle reservoirs at different chemical potentials,…
Reaction networks in the bulk and on surfaces are widespread in physical, chemical and biological systems. In macroscopic systems, which include large populations of reactive species, stochastic fluctuations are negligible and the reaction…
Chemical reactions inside cells are generally considered to happen within fixed-size compartments. Needless to say, cells and their compartments are highly dynamic. Thus, such stringent assumptions may not reflect biochemical reality, and…
We have extended the multilevel summation (MLS) method, originally developed to evaluate long-range Coulombic interactions in molecular dynamics (MD) simulations [Skeel et al., J. Comput. Chem., 23, 673 (2002)], to handle dispersion…
Nanoscopic diffusion at surfaces normally takes place when an adsorbate jumps from one adsorption site to the other. Jump diffusion can be measured via quasi-elastic scattering experiments, and the results can often be interpreted in terms…
Double-diffusive convection in porous media is a common phenomenon in nature, and has received considerable attention in a wide variety of engineering applications. In this paper, a multiple-relaxation-time (MRT) lattice Boltzmann (LB)…
Diffusion-limited association reactions are ubiquitous in nature. They are particularly important for biological reactions, where the reaction rates are often determined by the diffusive transport of the molecules on two-dimensional…
This paper presents an enhancement to the free surface lattice Boltzmann method (FSLBM) for the simulation of bubbly flows including rupture and breakup of bubbles. The FSLBM uses a volume of fluid approach to reduce the problem of a…
It is well known that there are two integral steps of streaming and collision in the lattice Boltzmann method (LBM). This concept has been changed by the author's recently proposed macroscopic lattice Boltzmann method (MacLAB) to solve the…
Lattice Boltzmann method (LBM) simulations of incompressible flows are nowadays common and well-established. However, for compressible turbulent flows with strong variable density and intrinsic compressibility effects, results are…
Four different kinds of laminar flows between two parallel plates are investigated using the Lattice Boltzmann Method (LBM). The LBM accuracy is estimated in two cases using numerical fits of the parabolic velocity profiles and the kinetic…