Multiscale simulation of microbe structure and dynamics

Harshad Joshi, Abhishek Singharoy, Yuriy V. Sereda, Srinath C. Cheluvaraja, Peter J. Ortoleva

Research output: Contribution to journalArticle

25 Citations (Scopus)

Abstract

A multiscale mathematical and computational approach is developed that captures the hierarchical organization of a microbe. It is found that a natural perspective for understanding a microbe is in terms of a hierarchy of variables at various levels of resolution. This hierarchy starts with the N -atom description and terminates with order parameters characterizing a whole microbe. This conceptual framework is used to guide the analysis of the Liouville equation for the probability density of the positions and momenta of the N atoms constituting the microbe and its environment. Using multiscale mathematical techniques, we derive equations for the co-evolution of the order parameters and the probability density of the N-atom state. This approach yields a rigorous way to transfer information between variables on different space-time scales. It elucidates the interplay between equilibrium and far-from-equilibrium processes underlying microbial behavior. It also provides framework for using coarse-grained nanocharacterization data to guide microbial simulation. It enables a methodical search for free-energy minimizing structures, many of which are typically supported by the set of macromolecules and membranes constituting a given microbe. This suite of capabilities provides a natural framework for arriving at a fundamental understanding of microbial behavior, the analysis of nanocharacterization data, and the computer-aided design of nanostructures for biotechnical and medical purposes. Selected features of the methodology are demonstrated using our multiscale bionanosystem simulator DeductiveMultiscaleSimulator. Systems used to demonstrate the approach are structural transitions in the cowpea chlorotic mosaic virus, RNA of satellite tobacco mosaic virus, virus-like particles related to human papillomavirus, and iron-binding protein lactoferrin.

Original languageEnglish (US)
Pages (from-to)200-217
Number of pages18
JournalProgress in Biophysics and Molecular Biology
Volume107
Issue number1
DOIs
StatePublished - Oct 1 2011
Externally publishedYes

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Tobacco mosaic satellite virus
Comovirus
Iron-Binding Proteins
Computer-Aided Design
Lactoferrin
Nanostructures
Virion
RNA
Membranes

Keywords

  • Deductive multiscale analysis
  • Langevin dynamics
  • Microbial systems
  • Multiscale modeling
  • Order parameters

ASJC Scopus subject areas

  • Biophysics
  • Molecular Biology

Cite this

Multiscale simulation of microbe structure and dynamics. / Joshi, Harshad; Singharoy, Abhishek; Sereda, Yuriy V.; Cheluvaraja, Srinath C.; Ortoleva, Peter J.

In: Progress in Biophysics and Molecular Biology, Vol. 107, No. 1, 01.10.2011, p. 200-217.

Research output: Contribution to journalArticle

Joshi, Harshad ; Singharoy, Abhishek ; Sereda, Yuriy V. ; Cheluvaraja, Srinath C. ; Ortoleva, Peter J. / Multiscale simulation of microbe structure and dynamics. In: Progress in Biophysics and Molecular Biology. 2011 ; Vol. 107, No. 1. pp. 200-217.
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