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Simulating Kinetic Processes in Time and Space on aLattice

Published online by Cambridge University Press:  05 October 2011

J. P. Gill ,
K. M. Shaw ,
B. L. Rountree ,
C. E. Kehl  and
H. J. Chiel
J. P. Gill*
Affiliation:
Department of Biology
K. M. Shaw
Affiliation:
Department of Biology
B. L. Rountree
Affiliation:
Center for Applied Scientific Computing, Lawrence Livermore National Laboratory, Livermore, CA 94550
C. E. Kehl
Affiliation:
Department of Biology
H. J. Chiel
Affiliation:
Department of Biology Department of Neurosciences Department of Biomedical Engineering, Case Western Reserve University, Cleveland, OH, 44106
*
⋆ Corresponding author. E-mail: [email protected]
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Abstract

We have developed a chemical kinetics simulation that can be used as both an educationaland research tool. The simulator is designed as an accessible, open-source project thatcan be run on a laptop with a student-friendly interface. The application can potentiallybe scaled to run in parallel for large simulations. The simulation has been successfullyused in a classroom setting for teaching basic electrochemical properties. We have shownthat this can be used for simulating fundamental molecular and chemical processes and evensimplified models of predator–prey interactions. By giving the simulated entities spatialextent in the lattice, the particles do not interpenetrate, and clusters of particles canspatially exclude one another. Our simulation demonstrates that spatial inhomogeneityleads to different results than those that are obtained by using standard ordinarydifferential equation models, as previously reported.

Keywords

education in biomathematicslattice modelsartificial chemistrysimulationopen-sourceautopoiesisorigin of lifediffusionNernst potentialresting potentialDonnan equilibriumchemical reactionskineticsMichaelis–Mentenenzyme kineticsLotka–Volterrapredator–prey model
Type
Research Article
Information
Mathematical Modelling of Natural Phenomena , Volume 6 , Issue 6: Biomathematics Education , 2011 , pp. 159 - 197
Copyright
© EDP Sciences, 2011

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