| On the Relevance of Diffusion-Controlled Reactions for Understanding Living Cell Biochemistry |
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| Zoran Konkoli. On the Relevance of Diffusion-Controlled Reactions for Understanding Living Cell Biochemistry. International Journal of Software and Informatics, 2013,7(4):675~694 |
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| Abstract:In recent years, a considerable portion of the computer science community has focused its attention on studying the living cell biochemistry. Efforts to understand such complicated reaction environments have stimulated a range of activities, from the ones focusing on the systems biology techniques, through network analysis (motif identification), towards developing languages and simulations for low-level biochemical processes. The approaches that do not use computer simulation techniques, frequently employ mean field equations or, equivalently, classical chemical kinetics. The central quantity of interest is the concentration of reactants, and (mean field) equations describe the time evolution of this quantity. Such equations are used to address various issues among which stability, robustness, or sensitivity analysis. Rarely is the validity of mean field equations questioned. This paper will discuss various situations when mean field equations fail and should not be used. These equations can be derived from the more general theory of diffusion-controlled reactions by assuming that reactants mix well. |
| keywords:diffusion-limited reactions fluctuation-dominated kinetics living cell biochemistry role of dimensionality |
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