Simulation studies in biochemical signaling and enzyme reactions

Sudarshan R. Nelatury, Mary C. Vagula

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

Biochemical pathways characterize various biochemical reaction schemes that involve a set of species and the manner in which they are connected. Determination of schematics that represent these pathways is an important task in understanding metabolism and signal transduction. Examples of these Pathways are: DNA and protein synthesis, and production of several macro-molecules essential for cell survival. A sustained feedback mechanism arises in gene expression and production of mRNA that lead to protein synthesis if the protein so synthesized serves as a transcription factor and becomes a repressor of the gene expression. The cellular regulations are carried out through biochemical networks consisting of reactions and regulatory proteins. Systems biology is a relatively new area that attempts to describe the biochemical pathways analytically and develop reliable mathematical models for the pathways. A complete understanding of chemical reaction kinetics is prohibitively hard thanks to the nonlinear and highly complex mechanisms that regulate protein formation, but attempting to numerically solve some of the governing differential equations seems to offer significant insight about their biochemical picture. To validate these models, one can perform simple experiments in the lab. This paper introduces fundamental ideas in biochemical signaling and attempts to take first steps into the understanding of biochemical oscillations. Initially, the two-pool model of calcium is used to describe the dynamics behind the oscillations. Later we present some elementary results showing biochemical oscillations arising from solving differential equations of Elowitz and Leibler using MATLAB software.

Original languageEnglish (US)
Title of host publicationSensing Technologies for Global Health, Military Medicine, and Environmental Monitoring IV
PublisherSPIE
ISBN (Print)9781628410495
DOIs
StatePublished - Jan 1 2014
EventSensing Technologies for Global Health, Military Medicine, and Environmental Monitoring IV - Baltimore, MD, United States
Duration: May 5 2014May 7 2014

Publication series

NameProceedings of SPIE - The International Society for Optical Engineering
Volume9112
ISSN (Print)0277-786X
ISSN (Electronic)1996-756X

Other

OtherSensing Technologies for Global Health, Military Medicine, and Environmental Monitoring IV
CountryUnited States
CityBaltimore, MD
Period5/5/145/7/14

Fingerprint

protein synthesis
enzymes
Pathway
Enzymes
gene expression
Simulation Study
proteins
Proteins
oscillations
reaction kinetics
differential equations
Protein Synthesis
Oscillation
Protein
Gene expression
simulation
circuit diagrams
Gene Expression
metabolism
biology

All Science Journal Classification (ASJC) codes

  • Electronic, Optical and Magnetic Materials
  • Condensed Matter Physics
  • Computer Science Applications
  • Applied Mathematics
  • Electrical and Electronic Engineering

Cite this

Nelatury, S. R., & Vagula, M. C. (2014). Simulation studies in biochemical signaling and enzyme reactions. In Sensing Technologies for Global Health, Military Medicine, and Environmental Monitoring IV [91121D] (Proceedings of SPIE - The International Society for Optical Engineering; Vol. 9112). SPIE. https://doi.org/10.1117/12.2053197
Nelatury, Sudarshan R. ; Vagula, Mary C. / Simulation studies in biochemical signaling and enzyme reactions. Sensing Technologies for Global Health, Military Medicine, and Environmental Monitoring IV. SPIE, 2014. (Proceedings of SPIE - The International Society for Optical Engineering).
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Nelatury, SR & Vagula, MC 2014, Simulation studies in biochemical signaling and enzyme reactions. in Sensing Technologies for Global Health, Military Medicine, and Environmental Monitoring IV., 91121D, Proceedings of SPIE - The International Society for Optical Engineering, vol. 9112, SPIE, Sensing Technologies for Global Health, Military Medicine, and Environmental Monitoring IV, Baltimore, MD, United States, 5/5/14. https://doi.org/10.1117/12.2053197

Simulation studies in biochemical signaling and enzyme reactions. / Nelatury, Sudarshan R.; Vagula, Mary C.

Sensing Technologies for Global Health, Military Medicine, and Environmental Monitoring IV. SPIE, 2014. 91121D (Proceedings of SPIE - The International Society for Optical Engineering; Vol. 9112).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

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Nelatury SR, Vagula MC. Simulation studies in biochemical signaling and enzyme reactions. In Sensing Technologies for Global Health, Military Medicine, and Environmental Monitoring IV. SPIE. 2014. 91121D. (Proceedings of SPIE - The International Society for Optical Engineering). https://doi.org/10.1117/12.2053197