Analysis of Biochemical Mechanisms using Mathematica with Applications

Authors

  • Nikolay Kyurkchiev Institute of Mathematics and Informatics Bulgarian Academy of Sciences Acad. G. Bonchev Str., Bl. 8 1113 Sofia, Bulgaria
  • Svetoslav Markov Institute of Mathematics and Informatics Bulgarian Academy of Sciences Acad. G. Bonchev Str., Bl. 8 1113 Sofia, Bulgaria
  • Maya Mincheva Department of Math. Sciences Northern Illinois University DeKalb, IL 60115, USA

DOI:

https://doi.org/10.55630/sjc.2016.10.63-78

Keywords:

biochemical mechanism, mass–action kinetics, stoichiometric matrix, rate functions, conservation relations, bipartite graph, double phosphorylation

Abstract

Biochemical mechanisms with mass action kinetics are usually modeled as
systems of ordinary differential equations (ODE) or bipartite graphs.

We present a software module for the numerical analysis of ODE models of
biochemical mechanisms of chemical species and elementary reactions
(BMCSER) within the programming environment of CAS Mathematica.

The module BMCSER also visualizes the bipartite graph of biochemical
mechanisms. Numerical examples, including a double phosphorylation model,
are presented demonstrating the scientific applications and the visualization
properties of the module.

ACM Computing Classification System (1998): G.4.

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Published

2017-02-17

Issue

Vol. 10 No. 1 (2016)

Section

Articles