Diffusion Controlled Reactions and Living Cell Biochemistry

Mar 18, 2010, 11:45 AM
Nordita Seminar Room 132:028 (Nordita)

Nordita Seminar Room 132:028



Zoran Konkoli


The talk will discuss how Statistical Physics tools can be used to understand biochemistry of the living cell. Structures found in the living cell are rather special and to achieve such task techniques used in the field of Statistical Physics need to be slightly modified. A critical reflection is needed on which techniques to use and for what purpose. As an example the theory of diffusion controlled reactions will be reviewed with a purpose of using it for understanding spatio-temporal organization of the living cell. It will be argued that formalism of diffusion controlled reactions is a suitable framework for describing living cell and the scope and the limitations of such approach will be discussed. Informal discussion will be given around problems (and possible traps) one meets when trying to compute properties of biochemical reactions in the cell interior. For example, mean field calculations are routinely used to model cell biochemistry and there usage is rarely questioned. The validity of mean field equations will be critically reviewed. Some situations when these equations do not work will be mentioned (low dimension, fluctuation dominated kinetics). The generic features of spatio temporal organization of the living cell biochemistry will be discussed with particular emphasis on geometrical (spatial) features, ranging from shape of reactants towards spatial organization of intracellular reaction volumes. There is a great need for developing analysis tools that could help us understand intracellular organization and geometry and it will be argued that the theory of diffusion controlled reactions can be useful in the context. As an example, the brief overview of Geometry-Reaction InterPlay framework (GRIP) will be given. KEYWORDS: fluctuation dominated kinetics, diffusion controlled reactions, reaction-geometry interplay, reactions in restricted geometries, shape of reactants, shape of reaction volume, topology of pathway graph

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