Related papers: Surface reaction-diffusion kinetics on lattice at …
Boiling is a complex phenomenon where different non-linear physical interactions take place and for which the quantitative modeling of the mechanism involved is not fully developed yet. In the last years, many works have been published…
Many complex multiphysics systems in fluid dynamics involve using solvers with varied levels of approximations in different regions of the computational domain to resolve multiple spatiotemporal scales present in the flow. The accuracy of…
We report developments of the kinetic Monte Carlo (KMC) method with improved accuracy and increased versatility for the description of atomic diffusivity on metal surfaces. The on-lattice constraint built into our recently proposed…
Random lateral translocation of lipids and proteins is a universal process on membrane surfaces. Local aggregation or organization of lipids and proteins can be induced when this lateral random diffusion is mediated by the electrostatic…
Background: Monte Carlo simulations of diffusion are commonly used as a model validation tool as they are especially suitable for generating the diffusion MRI signal in complicated tissue microgeometries. New method: Here we describe the…
We discuss the Lattice Boltzmann-Particle Dynamics (LBPD) multiscale paradigm for the simulation of complex states of flowing matter at the interface between Physics, Chemistry and Biology. In particular, we describe current large-scale…
We employ a multiscale approach to model the translocation of biopolymers through nanometer size pores. Our computational scheme combines microscopic Langevin molecular dynamics (MD) with a mesoscopic lattice Boltzmann (LB) method for the…
Particle-based stochastic reaction-diffusion (PBSRD) models are a popular approach for capturing stochasticity in reaction and transport processes across biological systems. In some contexts, the overdamped approximation inherent in such…
The Lattice Boltzmann Method (LBM) is a computational technique of Computational Fluid Dynamics (CFD) that has gained popularity due to its high parallelism and ability to handle complex geometries with minimal effort. Although LBM…
Exploring the hydrodynamic boundary of a surface by approaching a colloidal sphere and measuring the occurring drag force is a common experimental technique. However, numerous parameters like the wettability and surface roughness influence…
Stochastic lattice models (sLMs) are computational tools for simulating spatiotemporal dynamics in physics, computational biology, chemistry, ecology, and other fields. Despite their widespread use, it is challenging to fit sLMs to data, as…
A new upscaling procedure that provides 1D representations of 2D mixing-limited reactive transport systems is developed and applied. A key complication with upscaled models in this setting is that the procedure must differentiate between…
In this paper, a new progressive mesh algorithm is introduced in order to perform fast physical simulations by the use of a lattice Boltzmann method (LBM) on a single-node multi-GPU architecture. This algorithm is able to mesh automatically…
The immersed boundary lattice Boltzmann method (IB-LBM) has been widely used in the simulation of fluid-solid interaction and particulate flow problems, since proposed in 2004. However, it is usually a non-trivial task to retain the…
We propose a multiscale computational method for thin-layer flows of complex fluids, termed the synchronized molecular dynamics (SMD) method, which directly couples local molecular dynamics (MD) simulations with a macroscopic lubrication…
In this paper, an algorithm is presented to calculate the transition rates between adjacent mesoscopic subvolumes in the presence of flow and diffusion. These rates can be integrated in stochastic simulations of reaction-diffusion systems…
Protein aggregation on the plasma membrane (PM) is of critical importance to many cellular processes such as cell adhesion, endocytosis, fibrillar conformation, and vesicle transport. Lateral diffusion of protein aggregates or clusters on…
We study numerically the nature of the diffusion process on a honeycomb and a quasi-lattice, where a point particle, moving along the bonds of the lattice, scatters from randomly placed scatterers on the lattice sites according to strictly…
Diffusion mediated reaction models are particularly ubiquitous in the description of physical, chemical or biological processes. The random walk schema is a useful tool for formulating these models. Recently, evanescent random walk models…
In this paper, a diffuse-interface lattice Boltzmann method (DI-LBM) is developed for fluid-particle interaction problems. In this method, the sharp interface between the fluid and solid is replaced by a thin but nonzero thickness…