A Multi-Scale Approach to Modeling E. coli Chemotaxis.

ABSTRACT: The degree to which we can understand the multi-scale organization of cellular life is tied to how well our models can represent this organization and the processes that drive its evolution. This paper uses Vivarium-an engine for composing heterogeneous computational biology models into integrated, multi-scale simulations. Vivarium's approach is demonstrated by combining several sub-models of biophysical processes into a model of chemotactic E. coli that exchange molecules with their environment, express the genes required for chemotaxis, swim, grow, and divide. This model is developed incrementally, highlighting cross-compartment mechanisms that link E. coli to its environment, with models for: (1) metabolism and transport, with transport moving nutrients across the membrane boundary and

SUBMITTER: Agmon E 

PROVIDER: S-EPMC7597207 | biostudies-literature | 2020 Sep

REPOSITORIES: biostudies-literature