Related papers: Scalable and fast heterogeneous molecular simulati…

We present and compare distributed parallelization strategies for the particle-in-Fourier (PIF) schemes used in kinetic plasma simulations. The different strategies are i) domain decomposition, where both the particles and Fourier modes are…

In spatial regression models, spatial heterogeneity may be considered with either continuous or discrete specifications. The latter is related to delineation of spatially connected regions with homogeneous relationships between variables…

The multi-level hp-refinement scheme is a powerful extension of the finite element method that allows local mesh adaptation without the trouble of constraining hanging nodes. This is achieved through hierarchical high-order overlay meshes,…

To facilitate rational molecular and materials design, this research proposes an integrated computational framework that combines stochastic simulation, ab initio quantum chemistry, and molecular docking. The suggested workflow allows…

This paper presents a neural network--enhanced surrogate modeling approach for diffusion problems with spatially varying random field coefficients. The method builds on numerical homogenization, which compresses fine-scale coefficients into…

Comprehensive simulations of the entire biochemistry of cells have great potential to help physicians treat disease and help engineers design biological machines. But such simulations must model networks of millions of molecular species and…

This paper presents our work on developing parallel computational methods for two-phase flow on modern parallel computers, where techniques for linear solvers and nonlinear methods are studied and the standard and inexact Newton methods are…

We present a domain decomposition approach for the simulation of charge transport in heterojunction semiconductors. The problem is characterized by a large variation of primary variables across an interface region of a size much smaller…

We present a new adaptive resolution technique for efficient particle-based multiscale molecular dynamics (MD) simulations. The presented approach is tailor-made for molecular systems where atomistic resolution is required only in spatially…

Numerical algorithms for solving problems of mathematical physics on modern parallel computers employ various domain decomposition techniques. Domain decomposition schemes are developed here to solve numerically initial/boundary value…

Motivated by the idea of imposing paralleling computing on solving stochastic differential equations (SDEs), we introduce a new Domain Decomposition Scheme to solve forward-backward stochastic differential equations (FBSDEs) parallely. We…

Molecular dynamics (MD) simulations are powerful tools for elucidating the macroscopic physical properties of materials from microscopic atomic behaviors. However, the massive, high-dimensional datasets generated by MD simulations pose a…

We consider a variational method to solve the optical flow problem with varying illumination. We apply an adaptive control of the regularization parameter which allows us to preserve the edges and fine features of the computed flow. To…

Sampling the phase space of molecular systems -- and, more generally, of complex systems effectively modeled by stochastic differential equations -- is a crucial modeling step in many fields, from protein folding to materials discovery.…

This paper investigates a computational strategy for studying the interactions between multiple through-the-width delaminations and global or local buckling in composite laminates taking into account possible contact between the delaminated…

In this paper we develop and analyse domain decomposition methods for linear systems of equations arising from conforming finite element discretisations of positive Maxwell-type equations. Convergence of domain decomposition methods rely…

Solving multiscale diffusion problems is often computationally expensive due to the spatial and temporal discretization challenges arising from high-contrast coefficients. To address this issue, a partially explicit temporal splitting…

Multiple Sequences Alignment (MSA) of biological sequences is a fundamental problem in computational biology due to its critical significance in wide ranging applications including haplotype reconstruction, sequence homology, phylogenetic…

Hydrogen is vital for sectors like chemicals and others, driven by the need to reduce carbon emissions. Proton Electrolyte Membrane Water Electrolysis (PEMWE) is a key technology for the production of green hydrogen under fluctuating…

In this paper, we develop a general framework for multicontinuum homogenization in perforated domains. The simulations of problems in perforated domains are expensive and, in many applications, coarse-grid macroscopic models are developed.…