Related papers: Grand-canonical-like molecular-dynamics simulation…
The reaction-diffusion master equation (RDME) is commonly used to model processes where both the spatial and stochastic nature of chemical reactions need to be considered. We show that the RDME in many cases is inconsistent with a…
For a gas-solid interfacial system where chemical species undergo reversible adsorption, we develop a mesoscopic stochastic modeling method that simulates both gas-phase hydrodynamics and surface coverage dynamics by coupling the Langmuir…
Let $\mathcal{D}$ be the dictionary of Gaussian mixtures: the functions created by affine change of variables of a single Gaussian in $n$ dimensions. $\mathcal{D}$ is used pervasively in scientific applications to a degree that…
Molecular dynamics (MD) simulations are used in biochemistry, physics, and other fields to study the motions, thermodynamic properties, and the interactions between molecules. Computational limitations and the complexity of these problems,…
We present a coupled atomistic-continuum method for the modeling of defects and interface dynamics of crystalline materials. The method uses atomistic models such as molecular dynamics near defects and interfaces, and continuum models away…
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…
Searching for potential active compounds in large databases is a necessary step to reduce time and costs in modern drug discovery pipelines. Such virtual screening methods seek to provide predictions that allow the search space to be…
We present a novel multiscale numerical approach that combines parallel-in-time computation with hybrid domain adaptation for linear collisional kinetic equations in the diffusive regime. The method addresses the computational challenges of…
Mass-conserving reaction-diffusion (MCRD) systems are widely used to model phase separation and pattern formation in cell polarity, biomolecular condensates, and ecological systems. Numerical simulations and formal asymptotic analysis…
We propose a fourth-order cut-cell method for solving the two-dimensional advection-diffusion equation with moving boundaries on a Cartesian grid. We employ the ARMS technique to give an explicit and accurate representation of moving…
Diffusion models (DMs) have exhibited remarkable efficacy in various image restoration tasks. However, existing approaches typically operate within the high-dimensional pixel space, resulting in high computational overhead. While methods…
The model of transient enhanced diffusion of ion-implanted As is formulated and the finite-difference method for numerical solution of the system of equations obtained is developed. The nonuniform distribution of point defects near the…
The accurate determination of atom numbers is an ubiquitous problem in the field of ultracold atoms. For modest atom numbers, absolute calibration techniques are available, however, for large numbers and high densities, the available…
Gaussian process (GP) regression provides a strategy for accelerating saddle point searches on high-dimensional energy surfaces by reducing the number of times the energy and its derivatives with respect to atomic coordinates need to be…
Stochastic simulation methods can be applied successfully to model exact spatio-temporally resolved reaction-diffusion systems. However, in many cases, these methods can quickly become extremely computationally intensive with increasing…
Diffusion-based Generative Models (DGMs) have achieved unparalleled performance in synthesizing high-quality visual content, opening up the opportunity to improve image super-resolution (SR) tasks. Recent solutions for these tasks often…
We report adaptive resolution molecular dynamics simulations of a flexible linear polymer in solution. The solvent, i.e., a liquid of tetrahedral molecules, is represented within a certain radius from the polymer's center of mass with a…
Idealized and comprehensive ocean models at low resolutions cannot reproduce nominally-resolved flow structures similar to those presented in the high-resolution solution. Although there are various underlying physical reasons for this,…
We have developed a three-dimensional radiative transfer method designed specifically for use with parallel adaptive mesh refinement hydrodynamics codes. This new algorithm, which we call hybrid characteristics, introduces a novel form of…
Finite temperature calculations, based on ab initio molecular dynamics (AIMD) simulations, are a powerful tool able to predict material properties that cannot be deduced from ground state calculations. However, the high computational cost…