A hierarchical approach to model decision making: a study in chemotactic behavior of Escherichia coli

Reducing the complex behavior of living entities to its underlying physical and chemical processes is a formidable task in biology. Complex behaviors can be characterized as decision making: the ability to process the incoming information via an intracellular network and act upon this information to...

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Bibliographic Details
Published inbioRxiv
Main Authors Safar Vafadar, Kavousi, Kaveh, Safdari, Hadiseh, Kalirad, Ata, Sadeghi, Mehdi
Format Paper
LanguageEnglish
Published Cold Spring Harbor Cold Spring Harbor Laboratory Press 07.03.2019
Subjects
Chemical reactions
Chemotaxis
Decision making
E coli
Flagella
Information processing
Motility
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Summary:Reducing the complex behavior of living entities to its underlying physical and chemical processes is a formidable task in biology. Complex behaviors can be characterized as decision making: the ability to process the incoming information via an intracellular network and act upon this information to choose appropriate strategies. Motility is one such behavior that has been the focus many modeling efforts in the past. Our aim is to reduce the chemotactic behavior in E. coli to its molecular constituents in order to paint a comprehensive and end-to-end picture of this intricate behavior. We utilize a hierarchical approach, consisting of three layers, to achieve this goal: at the first level, chemical reactions involved in chemotaxis are simulated. In the second level, the chemical reactions give rise to the mechanical movement of six independent flagella. At the last layer, the two lower layers are combined to allow a digital bacterium to receive information from its environment and swim through it with verve. Our results are in concert with the experimental studies concerning the motility of E. coli cells. In addition, we show that our detailed model of chemotaxis is reducible to a non-homogeneous Markov process. Footnotes * https://github.com/safarvafadar/chemotaxis
DOI:10.1101/569277