From CA to gene expression: Machines and mechanisms

Chowdhury, Debashish, Garai, Ashok, Greulich, Philip, Nishinari, Katsuhiro, Schadschneider, Andreas, Tripathy, T. and Wang, J.-S. (2008) From CA to gene expression: Machines and mechanisms. Umeo, H., Morishita, S., Nishinari, K., Komatsuzaki, T. and Bandini, S. (eds.) In Cellular Automata. ACRI 2008. vol. 5191, Springer.. (doi:10.1007/978-3-540-79992-4_1).

Abstract

Molecular motors are proteins or macromolecular complexes which use input energy to perform mechanical work. Some of these motors move on filamentous proteins whereas other move on DNA or RNA strands. Often, many such motors move simultaneously on the same track and their collective movement is similar to vehicular traffic on highways. We have developed theoretical models of different types of molecular motor traffic by appropriately extending the totally asymmetric simple exclusion process (TASEP). Thus, our models of molecular motor traffic belong to the broad class of driven-diffusive lattice gas models which have close relations with cellular automata. By drawing analogy with vehicular traffic, we have introduced novel quantities for characterizing the nature of the spatio-temporal organization of molecular motors on their tracks. We show how the mechano-chemistry of the individual motors influence the traffic-like intracellular collective phenomena.

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Contributors

Author: Philip Greulich

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