Exact Stochastic Simulation of Coupled Chemical Reactions
- Manage
- Copy
- Actions
- Export
- Annotate
- Print Preview
Choose the export format from the list below:
- Office Formats (1)
-
Export as Portable Document Format (PDF) using Apache Formatting Objects Processor (FOP)
-
- Other Formats (1)
-
Export as HyperText Markup Language (HTML)
-
Daniel T. Gillespie
The Journal of Physical Chemistry 81(25), pages 2340-2361
December 1977
There are two formalisms for mathematically describing the time behavior of a spatially homogeneous chemical system: The ~deterministic approach~ regards the time evolution as a continuous, wholly predictable process which is governed by a set of coupled, ordinary differential equations (the "reaction-rate equations"); the ~stochastic approach~ regards the time evolution as a kind of random-walk process which is governed by a single differential-difference equation (the "master equation"). Fairly simple kinetic theory arguments show that the stochastic formulation of chemical kinetics has a firmer physical basis than the deterministic formulation, but unfortunately the stochastic master equation is often mathematically intractable. There is, however, a way to make exact numerical calculations within the framework of the stochastic formulation without having to deal with the master equation directly. It is a relatively simple digital computer algorithm which uses a rigorously derived Monte Carlo procedure to ~numerically simulate~ the time evolution of the given chemical system. Like the master equation, this "stochastic simulation algorithm" correctly accounts for the inherent fluctuations and correlations that are necessarily ignored in the deterministic formulation. In addition, unlike most procedures for numerically solving the deterministic reaction-rate equations, this algorithm never approximates infinitesimal time increments d~t~ by finite time steps Δ~t~. The feasibility and utility of the simulation algorithm are demonstrated by applying it to several well-known model chemical systems, including the Lotka model, the Brusselator, and the Oregonator. |
Publications / Personal
Publications / Views
Home
— clouds
tags | authors | editors | journals
— per year
2023 | 2022 | 2021 | 2020 | 2019 | 2018 | 2017 | 2016 | 2015 | 2014–1927
— per sort
in journal | in proc | chapters | books | edited | spec issues | editorials | entries | manuals | tech reps | phd th | others
— per status
online | in press | proof | camera-ready | revised | accepted | revision | submitted | draft | note
— services
ACM Digital Library | DBLP | IEEE Xplore | IRIS | PubMed | Google Scholar | Scopus | Semantic Scholar | Web of Science | DOI
Publication
— authors
Daniel T. Gillespie
— status
published
— sort
article in journal
— publication date
December 1977
— journal
The Journal of Physical Chemistry
— volume
81
— issue
25
— pages
2340-2361
URLs
identifiers
— DOI