Diffusion Controlled Reactions, Fluctuation Dominated Kinetics, and Living Cell Biochemistry

Zoran Konkoli

In recent years considerable portion of the computer science community has focused its attention on understanding living cell biochemistry and efforts to understand such complication reaction environment have spread over wide front, ranging from systems biology approaches, through network analysis (motif identification) towards developing language and simulators for low level biochemical processes. Apart from simulation work, much of the efforts are directed to using mean field equations (equivalent to the equations of classical chemical kinetics) to address various problems (stability, robustness, sensitivity analysis, etc.). Rarely is the use of mean field equations questioned. This review will provide a brief overview of the situations when mean field equations fail and should not be used. These equations can be derived from the theory of diffusion controlled reactions, and emerge when assumption of perfect mixing is used.

In S. Barry Cooper and Vincent Danos: Proceedings Fifth Workshop on Developments in Computational Models — Computational Models From Nature (DCM 2009), Rhodes, Greece, 11th July 2009, Electronic Proceedings in Theoretical Computer Science 9, pp. 98–107.
Published: 15th November 2009.

ArXived at: http://dx.doi.org/10.4204/EPTCS.9.11 bibtex PDF

Comments and questions to: eptcs@eptcs.org
For website issues: webmaster@eptcs.org