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Journal of Integrative Bioinformatics

Editor-in-Chief: Schreiber, Falk / Hofestädt, Ralf

Managing Editor: Sommer, Björn

Ed. by Baumbach, Jan / Chen, Ming / Orlov, Yuriy / Allmer, Jens

Editorial Board: Giorgetti, Alejandro / Harrison, Andrew / Kochetov, Aleksey / Krüger, Jens / Ma, Qi / Matsuno, Hiroshi / Mitra, Chanchal K. / Pauling, Josch K. / Rawlings, Chris / Fdez-Riverola, Florentino / Romano, Paolo / Röttger, Richard / Shoshi, Alban / Soares, Siomar de Castro / Taubert, Jan / Tauch, Andreas / Yousef, Malik / Weise, Stephan / Hassani-Pak, Keywan


CiteScore 2018: 0.90

SCImago Journal Rank (SJR) 2018: 0.315

Open Access
Online
ISSN
1613-4516
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Volume 7, Issue 1

Issues

Stochastic simulation of the spatio-temporal dynamics of reaction-diffusion systems: the case for the bicoid gradient

Paola Lecca
  • Corresponding author
  • The Microsoft Research - University of Trento, Centre for Computational and Systems Biology, Povo (Trento), http://www.cosbi.eu, Italy
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ Adaoha E. C. Ihekwaba
  • The Microsoft Research - University of Trento, Centre for Computational and Systems Biology, Povo (Trento), http://www.cosbi.eu, Italy
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ Lorenzo Dematté
  • The Microsoft Research - University of Trento, Centre for Computational and Systems Biology, Povo (Trento), http://www.cosbi.eu, Italy
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ Corrado Priami
  • The Microsoft Research - University of Trento, Centre for Computational and Systems Biology, Povo (Trento), http://www.cosbi.eu Italy
  • DISI, University of Trento,http://www.disi.unitn.it, Italy
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
Published Online: 2016-10-18 | DOI: https://doi.org/10.1515/jib-2010-150

Summary

Reaction-diffusion systems are mathematical models that describe how the concentrations of substances distributed in space change under the influence of local chemical reactions, and diffusion which causes the substances to spread out in space. The classical representation of a reaction-diffusion system is given by semi-linear parabolic partial differential equations, whose solution predicts how diffusion causes the concentration field to change with time. This change is proportional to the diffusion coefficient. If the solute moves in a homogeneous system in thermal equilibrium, the diffusion coefficients are constants that do not depend on the local concentration of solvent and solute. However, in nonhomogeneous and structured media the assumption of constant intracellular diffusion coefficient is not necessarily valid, and, consequently, the diffusion coefficient is a function of the local concentration of solvent and solutes. In this paper we propose a stochastic model of reaction-diffusion systems, in which the diffusion coefficients are function of the local concentration, viscosity and frictional forces. We then describe the software tool Redi (REaction-DIffusion simulator) which we have developed in order to implement this model into a Gillespie-like stochastic simulation algorithm. Finally, we show the ability of our model implemented in the Redi tool to reproduce the observed gradient of the bicoid protein in the Drosophila Melanogaster embryo. With Redi, we were able to simulate with an accuracy of 1% the experimental spatio-temporal dynamics of the bicoid protein, as recorded in time-lapse experiments obtained by direct measurements of transgenic bicoidenhanced green fluorescent protein.

About the article

Published Online: 2016-10-18

Published in Print: 2010-03-01


Citation Information: Journal of Integrative Bioinformatics, Volume 7, Issue 1, Pages 140–171, ISSN (Online) 1613-4516, DOI: https://doi.org/10.1515/jib-2010-150.

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© 2010 The Author(s). Published by Journal of Integrative Bioinformatics.. This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 License. BY-NC-ND 4.0

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