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Reflected diffusions in polyhedral domains are commonly used as approximate models for stochastic processing networks in heavy traffic. Stationary distributions of such models give useful information on the steady state performance of the…
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…
Mathematically modeling complex transport phenomena at the molecular level can be a powerful tool for identifying transport mechanisms and predicting macroscopic properties. We use two different stochastic time series models, parameterized…
In this work we propose a novel space-dependent multiscale model for the spread of infectious diseases in a two-dimensional spatial context on realistic geographical scenarios. The model couples a system of kinetic transport equations…
The dynamics of the discrete Gaussian model for the surface of a crystal deposited on a disordered substrate is investigated by Monte Carlo simulations. The mobility of the growing surface was studied as a function of a small driving force…
We demonstrate that a simple model based on reaction-diffusion-advection (RDA) equation forced by realistic surface velocities and nutrients is skilled in reproducing the distributions of the surface phytoplankton chlorophyll in the…
Achieving dynamic manipulation and control of single molecules at high spatio-temporal resolution is pivotal for advancing atomic-scale computing and nanorobotics. However, this endeavour is critically challenged by complex nature of atomic…
Monolayer cluster growth in far-from-equilibrium systems is investigated by applying simulation and analytic techniques to minimal hard core particle (exclusion) models. The first model (I), for post-deposition coarsening dynamics, contains…
Using kinetic Monte-Carlo simulations of a Solid-on-Solid model we investigate the influence of step edge diffusion (SED) and evaporation on Molecular Beam Epitaxy (MBE). Based on these investigations we propose two strategies to optimize…
This Letter introduces an approach for precisely designing surface friction properties using a conditional generative machine learning model, specifically a diffusion denoising probabilistic model (DDPM). We created a dataset of synthetic…
We present a comprehensive theoretical and computational model that explores the behavior of a thin hydrated film bonded to a non-hydrated / impermeable soft substrate in the context of surface and bulk elasticity coupled with surface…
We have combined the original diffusion-limited aggregation model introduced by Witten and Sander with the surface thermodynamics of the growing solid aggregate. The theory is based on the consideration of the surface chemical potential as…
We consider a generalization of the classical logistic growth model introducing more than one inflection point. The growth, called multi-sigmoidal, is firstly analyzed from a deterministic point of view in order to obtain the main…
Reaction-diffusion equations describe various spatially extended processes that unfold as traveling fronts moving at constant velocity. We introduce and solve analytically a model that, besides such fronts, supports solutions advancing as…
We propose improved versions of the standard diffusion Monte Carlo (DMC) and the lattice regularized diffusion Monte Carlo (LRDMC) algorithms. For the DMC method, we refine a scheme recently devised to treat non-local pseudopotential in a…
We investigate by Montecarlo simulation the linear response function of three dimensional structural glass models defined by short-range kinetic constraints and a trivial equilibrium Boltzmann-Gibbs measure. The breakdown of the…
Models with mixed origins of anomalous subdiffusion have been considered important for understanding transport in biological systems. Here, one such mixed model, the quenched trap model (QTM) on fractal lattices, is investigated. It is…
We present an investigation into diffusion models for molecular generation, with the aim of better understanding how their predictions compare to the results of physics-based calculations. The investigation into these models is driven by…
The Diffusion Monte Carlo method is devoted to the computation of electronic ground-state energies of molecules. In this paper, we focus on implementations of this method which consist in exploring the configuration space with a {\bf fixed}…
We study diffusive dynamics of phase separation in a binary mixture, following critical quench, both in spatial dimensions $d=2$ and $d=3$. Particular focus in this work is to obtain information about effects of system size and correction…