ArticleThe Journal of chemical physics2013
Perspective: Stochastic algorithms for chemical kinetics.
Article in The Journal of chemical physics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 76 papers.
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Who cites it
76 citing papers in PubMed.
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- Assessment of simulation-based inference methods for stochastic compartmental models in epidemiological research.PloS one · 2026Article
- Nuclear deformation by microtubule molecular motors.PLoS computational biology · 2025Article
- Investigation of hydrogen peroxide yields and oxygen consumption in high dose rate irradiation: a TOPAS-nBio Monte Carlo study.Physics in medicine and biology · 2024Article
- AI-powered simulation-based inference of a genuinely spatial-stochastic gene regulation model of early mouse embryogenesis.PLoS computational biology · 2024Article
- Review of chemical models and applications in Geant4-DNA: Report from the ESA BioRad III Project.Medical physics · 2024Review
- Approximate Bayesian computation for inferring Waddington landscapes from single-cell data.Royal Society open science · 2024Article
- Maboss for HPC environments: implementations of the continuous time Boolean model simulator for large CPU clusters and GPU accelerators.BMC bioinformatics · 2024Article
- Fostering discoveries in the era of exascale computing: How the next generation of supercomputers empowers computational and experimental biophysics alike.Biophysical journal · 2023Review
- Analysing ill-conditioned Markov chains.Philosophical transactions. Series A, Mathematical, physical, and engineering sciences · 2023Article
- An integrated Monte Carlo track-structure simulation framework for modeling inter and intra-track effects on homogenous chemistry.Physics in medicine and biology · 2023Article
- Epigenetics as a mediator of plasticity in cancer.Science (New York, N.Y.) · 2023Review
- GillesPy2: A Biochemical Modeling Framework for Simulation Driven Biological Discovery.Letters in biomathematics · 2023Article
- Multi-scale models of whole cells: progress and challenges.Frontiers in cell and developmental biology · 2023Review
- Interpretable and tractable models of transcriptional noise for the rational design of single-molecule quantification experiments.Nature communications · 2022Article
- Close agreement between deterministic versus stochastic modeling of first-passage time to vesicle fusion.Biophysical journal · 2022Article
- Systematic comparison of modeling fidelity levels and parameter inference settings applied to negative feedback gene regulation.PLoS computational biology · 2022Article
- Scalable and flexible inference framework for stochastic dynamic single-cell models.PLoS computational biology · 2022Article
16 more citing papers are in PubMed but not listed here.
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3 authors.
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Abstract
We outline our perspective on stochastic chemical kinetics, paying particular attention to numerical simulation algorithms. We first focus on dilute, well-mixed systems, whose description using ordinary differential equations has served as the basis for traditional chemical kinetics for the past 150 years. For such systems, we review the physical and mathematical rationale for a discrete-stochastic approach, and for the approximations that need to be made in order to regain the traditional continuous-deterministic description. We next take note of some of the more promising strategies for dealing stochastically with stiff systems, rare events, and sensitivity analysis. Finally, we review some recent efforts to adapt and extend the discrete-stochastic approach to systems that are not well-mixed. In that currently developing area, we focus mainly on the strategy of subdividing the system into well-mixed subvolumes, and then simulating diffusional transfers of reactant molecules between adjacent subvolumes together with chemical reactions inside the subvolumes.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.