A Multi-Scale Approach to Modeling E. coli Chemotaxis
| Autor: | Ryan K. Spangler, Eran Agmon |
|---|---|
| Jazyk: | angličtina |
| Rok vydání: | 2020 |
| Předmět: |
multi-scale simulation
Computer science General Physics and Astronomy lcsh:Astrophysics Flagellum medicine.disease_cause Article Cellular life 03 medical and health sciences 0302 clinical medicine computational systems biology lcsh:QB460-466 medicine Escherichia coli chemotaxis lcsh:Science 030304 developmental biology 0303 health sciences Modelling biological systems Chemotaxis model integration lcsh:QC1-999 Model integration Biophysical Process lcsh:Q Gene sequence Biological system 030217 neurology & neurosurgery lcsh:Physics |
| Zdroj: | Entropy, Vol 22, Iss 1101, p 1101 (2020) Entropy Volume 22 Issue 10 |
| ISSN: | 1099-4300 |
| Popis: | The degree to which we can understand the multi-scale organization of cellular life is tiedto how well our models can represent this organization and the processes that drive its evolution.This paper uses Vivarium&mdash an engine for composing heterogeneous computational biology modelsinto integrated, multi-scale simulations. Vivarium&rsquo s approach is demonstrated by combining severalsub-models of biophysical processes into a model of chemotactic E. coli that exchange molecules withtheir environment, express the genes required for chemotaxis, swim, grow, and divide. This modelis developed incrementally, highlighting cross-compartment mechanisms that link E. coli to itsenvironment, with models for: (1) metabolism and transport, with transport moving nutrients acrossthe membrane boundary and metabolism converting them to useful metabolites, (2) transcription,translation, complexation, and degradation, with stochastic mechanisms that read real gene sequencedata and consume base pairs and ATP to make proteins and complexes, and (3) the activity of flagellaand chemoreceptors, which together support navigation in the environment. |
| Databáze: | OpenAIRE |
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