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We develop a novel method of replica-exchange molecular dynamics (REMD) simulation, mass-scaling REMD (MSREMD) method, which improves trajectory accuracy at high temperatures, and thereby contributes to numerical stability. In addition, the…

Statistical Mechanics · Physics 2015-06-19 Tetsuro Nagai , Takuya Takahashi

This paper proposes a novel reaction-diffusion system approximation tailored for singular diffusion problems, typified by the fast diffusion equation. While such approximation methods have been successfully applied to degenerate parabolic…

Analysis of PDEs · Mathematics 2026-04-01 Hideki Murakawa , Florian Salin

Pore-scale simulations accurately describe transport properties of fluids in the subsurface. These simulations enhance our understanding of applications such as assessing hydrogen storage efficiency and forecasting CO$_2$ sequestration…

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

The reaction-diffusion master equation (RDME) is a model that allows for efficient on-lattice simulation of spatially resolved stochastic chemical kinetics. Compared to off-lattice hard-sphere simulations with Brownian Dynamics (BD) or…

Numerical Analysis · Mathematics 2017-09-06 Stefan Hellander , Andreas Hellander , Linda Petzold

Understanding grain-surface processes is crucial to interpreting the chemistry of the ISM. However, accurate surface chemistry models are computationally expensive and are difficult to integrate with gas-phase simulations. A new…

Astrophysics · Physics 2009-11-13 R. T. Garrod

The development of computational models for the numerical simulation of chemically reacting flows operating in the turbulent regime requires the solution of partial differential equations that represent the balance of mass, linear momentum,…

Fluid Dynamics · Physics 2021-06-03 Americo Cunha , Luis Fernando Figueira da Silva

A combination of reaction-diffusion models with moving-boundary problems yields a system in which the diffusion (spreading and penetration) and reaction (transformation) evolve the system's state and geometry over time. These systems can be…

Computational Engineering, Finance, and Science · Computer Science 2020-08-26 Mojtaba Barzegari , Liesbet Geris

In recent years, reduced basis methods (RBMs) have been adapted to the many-body eigenvalue problem and they have been used, largely in nuclear physics, as fast emulators able to bypass expensive direct computations while still providing…

Superconductivity · Physics 2023-04-19 Virgil V. Baran , Denis R. Nichita

We present a simple finite element formulation of mass-consistent approximation, and a fast multigrid iterative method with adaptive semicoarsening, which maintains the convergence of the iterations over a range of grids and penalty…

Numerical Analysis · Mathematics 2022-01-19 J. Mandel , A. Farguell , A. K. Kochanski , D. V. Mallia , K. Hilburn

Reaction networks in the bulk and on surfaces are widespread in physical, chemical and biological systems. In macroscopic systems, which include large populations of reactive species, stochastic fluctuations are negligible and the reaction…

Statistical Mechanics · Physics 2007-10-12 Baruch Barzel , Ofer Biham , Raz Kupferman

Diffusion behaviors of heterogeneous materials are of paramount importance in many engineering problems. Numerical models that take into account the internal structure of such materials are robust but computationally very expensive. This…

Numerical Analysis · Mathematics 2023-12-18 Jan Eliáš , Hao Yin , Gianluca Cusatis

39 detailed mechanisms for combustion of hydrogen, carbon monoxide and methanol are investigated using ReactionKinetics, a Mathematica based package. The obtained results in most cases do not depend on the choice of reaction rate…

Chemical Physics · Physics 2013-08-06 J. Tóth , A. L. Nagy , I. Zsély

This is the first part of a series of two articles describing the ARP-GEM global atmosphere model version 1 and its evaluation in simulations from 55 km to 6 km resolutions. This article provides a complete description of ARP-GEM1, focusing…

Atmospheric and Oceanic Physics · Physics 2024-10-01 David Saint-Martin , Olivier Geoffroy

We present an acceleration method for sequences of large-scale linear systems, such as the ones arising from the numerical solution of time-dependent partial differential equations coupled with algebraic constraints. We discuss different…

Numerical Analysis · Mathematics 2024-03-29 Margherita Guido , Daniel Kressner , Paolo Ricci

As inverter-based resources (IBRs) penetrate power systems, the dynamics become more complex, exhibiting multiple timescales, including electromagnetic transient (EMT) dynamics of power electronic controllers and electromechanical dynamics…

Systems and Control · Electrical Eng. & Systems 2025-03-17 Kaiyang Huang , Min Xiong , Yang Liu , Kai Sun

In this paper, we present a study on how to develop an efficient multiscale simulation strategy for the dynamics of chemically active systems on low-dimensional supports. Such reactions are encountered in a wide variety of situations,…

Computational Physics · Physics 2015-06-04 Giacomo Mazzi , Yannick De Decker , Giovanni Samaey

This paper presents a heterogeneous adaptive mesh refinement (AMR) framework for efficient simulation of moderately stiff reactive problems. This framework features an elaborate subcycling-in-time algorithm along with a specialized…

Computational Physics · Physics 2025-06-04 Yuqi Wang , Yadong Zeng , Ralf Deiterding , Jianhan Liang

The multi-grid reaction-diffusion master equation (mgRDME) provides a generalization of stochastic compartment-based reaction-diffusion modelling described by the standard reaction-diffusion master equation (RDME). By enabling different…

Quantitative Methods · Quantitative Biology 2024-05-06 Radek Erban , Stefanie Winkelmann

In atomistic simulations, pseudo-dynamics relaxation schemes often exhibit better performance and accuracy in finding local minima than line-search-based descent algorithms like steepest descent or conjugate gradient. Here, an improved…