Abstract
Many students are familiar with the idea of modeling chemical reactions in terms of ordinary differential equations. However, these deterministic reaction rate equations are really a certain large-scale limit of a sequence of finer-scale probabilistic models. In studying this hierarchy of models, students can be exposed to a range of modern ideas in applied and computational mathematics. This article introduces some of the basic concepts in an accessible manner and points to some challenges that currently occupy researchers in this area. Short, downloadable MATLAB codes are listed and described.
| Original language | English |
|---|---|
| Pages (from-to) | 347-368 |
| Number of pages | 22 |
| Journal | Siam review |
| Volume | 50 |
| Issue number | 2 |
| DOIs | |
| Publication status | Published - 5 May 2008 |
Keywords / Materials (for Non-textual outputs)
- Euler-Maruyama
- Gillespie
- Michaelis-Menten
- birth-and-death process
- chemical Langevin
- chemical master equation
- kinetic Monte Carlo
- law of mass action
- reaction rate equation
- stochastic simulation algorithm
- stoichiometric vector
- tau-leaping