| Summary: | The degree to which we can understand the multi-scale organization of cellular life is tied<br />to how well our models can represent this organization and the processes that drive its evolution.<br />This paper uses Vivarium—an engine for composing heterogeneous computational biology models<br />into integrated, multi-scale simulations. Vivarium’s approach is demonstrated by combining several<br />sub-models of biophysical processes into a model of chemotactic E. coli that exchange molecules with<br />their environment, express the genes required for chemotaxis, swim, grow, and divide. This model<br />is developed incrementally, highlighting cross-compartment mechanisms that link E. coli to its<br />environment, with models for: (1) metabolism and transport, with transport moving nutrients across<br />the membrane boundary and metabolism converting them to useful metabolites, (2) transcription,<br />translation, complexation, and degradation, with stochastic mechanisms that read real gene sequence<br />data and consume base pairs and ATP to make proteins and complexes, and (3) the activity of flagella<br />and chemoreceptors, which together support navigation in the environment.
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