Simulating the Interactions of Genes, Proteins, and Metabolities in Cell-Like Entities

Abstract

The goal of this project was to create software to model Cell-Like Entities, and to perform initial simulations. A software package was written in Matlab that performs stochastic simulations using a Gillespie-based algorithm of biomolecular networks. Biochemical processes that can be modeled include binding, unbinding, transcription, translation, Michaelis-Menten, and n-th order processes. Models and parameters are defined using several text files. The software package was designed to enable simple porting to high-performance computing platforms. A model to simulate a prototype CLE that responds to an external chemical with production of a particular protein was developed. This detection CLE was further analyzed to quantify the level of stochastic fluctuations over multiple runs, and to determine a combination of input parameters that optimized the detection task.

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Document Details

Document Type
Technical Report
Publication Date
Sep 01, 2005
Accession Number
ADA438522

Entities

People

  • Brent D. Foy

Organizations

  • Wright State University

Tags

Communities of Interest

  • Biomedical

DTIC Thesaurus Topics

  • Air Force
  • Algorithms
  • Chemical Kinetics
  • Chemistry
  • Complex Systems
  • Computational Biology
  • Detection
  • Equations
  • High Performance Computing
  • Metabolites
  • Models
  • Molecular Dynamics
  • Molecules
  • Mrna
  • Simulations
  • Systems Biology
  • Transcription Factors

Readers

  • Computational Fluid Dynamics (CFD)
  • Nanoscale Plasmonic Nanotechnology
  • Software Engineering.