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In recent years, the modeling interest has increased significantly from the molecular level to the atomic and quantum scale. The field of computational chemistry plays a significant role in designing computational models for the operation…

Formal Languages and Automata Theory · Computer Science 2020-07-09 Amandeep Singh Bhatia , Shenggen Zheng

We treat the accurate simulation of the calcination reaction in particles, where the particles are large and, thus, the inner-particle processes must be resolved. Because these processes need to be described with coupled partial…

Fluid Dynamics · Physics 2023-11-28 Lucas Reineking , Torben Bergold , Enric Illana , Viktor Scherer , Martin Mönnigmann

We describe a new computational method for the numerically stable particle-based simulation of open-boundary flows, including volume conserving chemical reactions. The novel method is validated for the case of heterogeneous catalysis…

Adaptation and Self-Organizing Systems · Physics 2020-10-09 Sebastian Mühlbauer , Severin Strobl , Thorsten Pöschel

We present a computational study of static and dynamic linear polarizabilities in solution. We use different theoretical approaches to describe solvent effects, ranging from quantum mechanics/molecular mechanics (QM/MM) to quantum embedding…

Chemical Physics · Physics 2022-12-07 Linda Goletto , Sara Gómez , Josefine H. Andersen , Henrik Koch , Tommaso Giovannini

Despite its numerical challenges, finite element method is used to compute viscous fluid flow. A consensus on the cause of numerical problems has been reached; however, general algorithms---allowing a robust and accurate simulation for any…

Computational Engineering, Finance, and Science · Computer Science 2019-02-05 Bilen Emek Abali

Reaction diffusion systems describe the behaviour of dynamic, interacting, particulate systems. Quantum stochastic processes generalise Brownian motion and Poisson processes, having operator valued It\^{o} calculus machinery. Here it is…

Mathematical Physics · Physics 2023-05-31 Chris D Greenman

A hydrogeological model for the spread of pollution in an aquifer is considered. The model consists in a convection-diffusion-reaction equation involving the dispersion tensor which depends nonlinearly of the fluid velocity. We introduce an…

Numerical Analysis · Mathematics 2020-06-05 Éloïse Comte

Spatial reaction-diffusion models have been employed to describe many emergent phenomena in biological systems. The modelling technique most commonly adopted in the literature implements systems of partial differential equations (PDEs),…

Quantitative Methods · Quantitative Biology 2015-10-05 Christian A. Yates , Mark B. Flegg

An understanding of the hydrodynamics of multiphase processes is essential for their design and operation. Multiphase computational fluid dynamics (CFD) simulations enable researchers to gain insight which is inaccessible experimentally.…

Numerical Analysis · Mathematics 2021-01-18 Tanyakarn Treeratanaphitak , Nasser Mohieddin Abukhdeir

We discuss algorithms applicable to the numerical solution of second-order ordinary differential equations by finite-differences. We make particular reference to the solution of the dissipative particle dynamics fluid model, and present…

Soft Condensed Matter · Physics 2016-08-31 Keir E. Novik , Peter V. Coveney

We consider adaptive finite element methods for solving a multiscale system consisting of a macroscale model comprising a system of reaction-diffusion partial differential equations coupled to a microscale model comprising a system of…

Numerical Analysis · Mathematics 2015-06-22 A. Johansson , J. H. Chaudry , V. Carey , D. Estep , V. Ginting , M. Larson , S. Tavener

The primary goal of this paper is to characterize solutions to coupled reaction-diffusion systems. Indeed, we use operators theory to show that under suitable assumptions, then the solutions to the reaction-diffusion equations exist. As…

Analysis of PDEs · Mathematics 2007-05-23 Toka Diagana

Various biological system models have been proposed in systems biology, which are based on the complex biological reactions kinetic of various components. These models are not practical because we lack of kinetic information. In this paper,…

Quantitative Methods · Quantitative Biology 2011-02-19 Weidong Huang , Chundu Wu , Bingjia Xiao , Weidong Xia

We develop numerical methods for reaction-diffusion systems based on the equations of fluctuating hydrodynamics (FHD). While the FHD formulation is formally described by stochastic partial differential equations (SPDEs), it becomes similar…

Fluid Dynamics · Physics 2018-01-17 Changho Kim , Andy Nonaka , John B. Bell , Alejandro L. Garcia , Aleksandar Donev

Partial differential equation (PDE) models with multiple temporal/spatial scales are prevalent in several disciplines such as physics, engineering, and many others. These models are of great practical importance but notoriously difficult to…

Numerical Analysis · Mathematics 2023-04-17 Junpeng Hu , Shi Jin , Lei Zhang

Physics-guided sampling with diffusion model priors has shown promise for solving partial differential equation (PDE) governed problems, but applications to chemically meaningful reaction-transport systems remain limited. We apply…

Chemical Physics · Physics 2026-03-06 Andrew Millard , Henrik Pedersen

A numerical method is presented to obtain approximate solutions to problems arising from sedimentation models. These processes are widely utilized in minery for recovering water from suspensions coming out of flotation processes. The main…

Numerical Analysis · Mathematics 2008-06-23 Ricardo Ruiz Baier

The modelling of electrokinetic flows is a critical aspect spanning many industrial applications and research fields. This has introduced great demand in flexible numerical solvers to describe these flows. The underlying phenomena are…

Numerical Analysis · Mathematics 2023-11-08 Robert Barnett , Federico Municchi , John King , Matteo Icardi

We discuss a method to describe the qualitative dynamics of chemical reaction networks in terms of symbolic dynamics. The method, that can be applied to mass-action reaction networks with separated timescales, uses solutions of the partial…

Molecular Networks · Quantitative Biology 2022-05-17 Aurélien Desoeuvres , Peter Szmolyan , Ovidiu Radulescu

This review describes the theory and implementation of implicit solvation models based on continuum electrostatics. Within quantum chemistry this formalism is sometimes synonymous with the polarizable continuum model, a particular…

Chemical Physics · Physics 2022-03-15 John M. Herbert