title: Stochastic simulation of the spatio-temporal dynamics of reaction-diffusion systems: the case for the bicoid gradient.
abstract: 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.
authors.affiliation: The Microsoft Research - University of Trento, Centre for Computational and Systems Biology, Povo (Trento), Italy.
authors.forename: Paola
authors.initials: P
authors.lastname: Lecca
authors.forename: Adaoha E C
authors.initials: AE
authors.lastname: Ihekwaba
authors.forename: Lorenzo
authors.initials: L
authors.lastname: Dematté
authors.forename: Corrado
authors.initials: C
authors.lastname: Priami
mesh_terms: D000465:Algorithms; D000818:Animals; D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D004058:Diffusion; D029721:Drosophila Proteins; D004331:Drosophila melanogaster; D049452:Green Fluorescent Proteins / Q000378:metabolism; D018398:Homeodomain Proteins / Q000235:genetics* / Q000502:physiology*; D015233:Models, Statistical; D011381:Programming Languages; D012997:Solvents / Q000737:chemistry; D013269:Stochastic Processes; D015534:Trans-Activators / Q000235:genetics* / Q000502:physiology*; D019076:Transgenes; D014783:Viscosity
chemical_list: D029721:Drosophila Proteins; D018398:Homeodomain Proteins; D012997:Solvents; D015534:Trans-Activators; C056478:bcd protein, Drosophila; C485184:enhanced green fluorescent protein; D049452:Green Fluorescent Proteins