How is stochastic simulation useful for describing biological systems?
Biological systems can be described as a system of biochemical reactions, including processes such as metabolism, signal transduction, and gene expression. The reactions may involve bond-breaking (as in the classic definition of a chemical reaction) or may only involve strong non-covalent interactions between molecules, such as hydrogen bonding, salt bridges, or hydrophobic ‘forces’. Either way, one may measure the thermodynamics and kinetics of these reactions and quantitatively describe their rates. Traditionally, the dynamics of a system of reactions is described using ordinary differential equations (ODEs). With ODEs, the trajectory of the state moves deterministically through time to some attractor (ie. starting from the same initial condition, the trajectory will always be the same and no two trajectories may ever cross). However, through both analysis of theory and experimental observation, it has been noted that ODEs do not adequately describe the dynamics of biological systems
