An overview of spatial microscopic and accelerated kinetic Monte Carlo methods
A Chatterjee, DG Vlachos - Journal of computer-aided materials design, 2007 - Springer
The microscopic spatial kinetic Monte Carlo (KMC) method has been employed extensively
in materials modeling. In this review paper, we focus on different traditional and multiscale …
in materials modeling. In this review paper, we focus on different traditional and multiscale …
When polymer reaction engineers play dice: applications of Monte Carlo models in PRE
ALT Brandao, JBP Soares, JC Pinto… - Macromolecular …, 2015 - Wiley Online Library
Monte Carlo methods are heuristic algorithms that use probabilities to select an outcome
among several possible events in a given process. Monte Carlo methods are useful in …
among several possible events in a given process. Monte Carlo methods are useful in …
BioNetGen 2.2: advances in rule-based modeling
BioNetGen is an open-source software package for rule-based modeling of complex
biochemical systems. Version 2.2 of the software introduces numerous new features for both …
biochemical systems. Version 2.2 of the software introduces numerous new features for both …
Perspective: Stochastic algorithms for chemical kinetics
We outline our perspective on stochastic chemical kinetics, paying particular attention to
numerical simulation algorithms. We first focus on dilute, well-mixed systems, whose …
numerical simulation algorithms. We first focus on dilute, well-mixed systems, whose …
Master equations and the theory of stochastic path integrals
This review provides a pedagogic and self-contained introduction to master equations and
to their representation by path integrals. Since the 1930s, master equations have served as …
to their representation by path integrals. Since the 1930s, master equations have served as …
Biochemical simulations: stochastic, approximate stochastic and hybrid approaches
J Pahle - Briefings in bioinformatics, 2009 - academic.oup.com
Computer simulations have become an invaluable tool to study the sometimes
counterintuitive temporal dynamics of (bio-) chemical systems. In particular, stochastic …
counterintuitive temporal dynamics of (bio-) chemical systems. In particular, stochastic …
Lattice microbes: High‐performance stochastic simulation method for the reaction‐diffusion master equation
Spatial stochastic simulation is a valuable technique for studying reactions in biological
systems. With the availability of high‐performance computing (HPC), the method is poised to …
systems. With the availability of high‐performance computing (HPC), the method is poised to …
Spatial stochastic intracellular kinetics: A review of modelling approaches
Abstract Models of chemical kinetics that incorporate both stochasticity and diffusion are an
increasingly common tool for studying biology. The variety of competing models is vast, but …
increasingly common tool for studying biology. The variety of competing models is vast, but …
Simulation of biochemical reactions with time-dependent rates by the rejection-based algorithm
We address the problem of simulating biochemical reaction networks with time-dependent
rates and propose a new algorithm based on our rejection-based stochastic simulation …
rates and propose a new algorithm based on our rejection-based stochastic simulation …
Spatially extended hybrid methods: a review
Many biological and physical systems exhibit behaviour at multiple spatial, temporal or
population scales. Multiscale processes provide challenges when they are to be simulated …
population scales. Multiscale processes provide challenges when they are to be simulated …