A Multi-Scale Approach to Modeling E. coli Chemotaxis

Entropy

RyanK. Spangler¹  Eran Agmon¹ 

[1] Department of Bioengineering, Stanford University, Stanford, CA 94305, USA;

关键词: Escherichia coli;    chemotaxis;    computational systems biology;    multi-scale simulation;    model integration;   

DOI  :  10.3390/e22101101

来源: DOAJ

【 摘 要 】

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 metabolism converting them to useful metabolites, (2) transcription,
translation, complexation, and degradation, with stochastic mechanisms that read real gene sequence
data and consume base pairs and ATP to make proteins and complexes, and (3) the activity of flagella
and chemoreceptors, which together support navigation in the environment.

【 授权许可】

Unknown