ChemCell : a particle-based model of protein chemistry and diffusion in microbial cells.

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Prokaryotic single-cell microbes are the simplest of all self-sufficient living organisms. Yet microbes create and use much of the molecular machinery present in more complex organisms, and the macro-molecules in microbial cells interact in regulatory, metabolic, and signaling pathways that are prototypical of the reaction networks present in all cells. We have developed a simple simulation model of a prokaryotic cell that treats proteins, protein complexes, and other organic molecules as particles which diffuse via Brownian motion and react with nearby particles in accord with chemical rate equations. The code models protein motion and chemistry within an idealized cellular geometry. ... continued below

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31 p.

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Plimpton, Steven James & Slepoy, Alexander December 1, 2003.

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Description

Prokaryotic single-cell microbes are the simplest of all self-sufficient living organisms. Yet microbes create and use much of the molecular machinery present in more complex organisms, and the macro-molecules in microbial cells interact in regulatory, metabolic, and signaling pathways that are prototypical of the reaction networks present in all cells. We have developed a simple simulation model of a prokaryotic cell that treats proteins, protein complexes, and other organic molecules as particles which diffuse via Brownian motion and react with nearby particles in accord with chemical rate equations. The code models protein motion and chemistry within an idealized cellular geometry. It has been used to simulate several simple reaction networks and compared to more idealized models which do not include spatial effects. In this report we describe an initial version of the simulation code that was developed with FY03 funding. We discuss the motivation for the model, highlight its underlying equations, and describe simulations of a 3-stage kinase cascade and a portion of the carbon fixation pathway in the Synechococcus microbe.

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31 p.

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  • Report No.: SAND2003-4509
  • Grant Number: AC04-94AL85000
  • DOI: 10.2172/918231 | External Link
  • Office of Scientific & Technical Information Report Number: 918231
  • Archival Resource Key: ark:/67531/metadc878810

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Office of Scientific & Technical Information Technical Reports

Reports, articles and other documents harvested from the Office of Scientific and Technical Information.

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  • December 1, 2003

Added to The UNT Digital Library

  • Sept. 22, 2016, 2:13 a.m.

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  • Nov. 22, 2016, 10:21 p.m.

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Plimpton, Steven James & Slepoy, Alexander. ChemCell : a particle-based model of protein chemistry and diffusion in microbial cells., report, December 1, 2003; United States. (digital.library.unt.edu/ark:/67531/metadc878810/: accessed April 20, 2018), University of North Texas Libraries, Digital Library, digital.library.unt.edu; crediting UNT Libraries Government Documents Department.