- APICe
- Publications
- Stochastic simulation of the spatio-temporal dynamics of reaction-diffusion systems: the case for the bicoid gradient
Stochastic simulation of the spatio-temporal dynamics of reaction-diffusion systems: the case for the bicoid gradient
- Manage
- Copy
- Actions
- Export
- Annotate
- Print Preview
Choose the export format from the list below:
- Office Formats (1)
-
Export as Portable Document Format (PDF) using the Web Browser
-
- Other Formats (2)
-
-
Export as HyperText Markup Language (HTML)
-
Paola Lecca, Adaoha E. C. Ihekwaba, Lorenzo Dematté, Corrado Priami
Journal of Integrative Bioinformatics 7(1)
2010
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 represen- tation 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 non- homogeneous and structured media the assumption of constant intracellular diffusion co- efficient 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 bicoid- enhanced green fluorescent protein. |
Publications / Personal
Publications / Views
Home
— clouds
tags | authors | editors | journals
— per year
2023 | 2022 | 2021 | 2020 | 2019 | 2018 | 2017 | 2016 | 2015 | 2014–1927
— per sort
in journal | in proc | chapters | books | edited | spec issues | editorials | tech reps | phd th | others
— per status
online | in press | proof | camera-ready | revised | accepted | revision | submitted | draft | note
— services
ACM Digital Library | DBLP | IEEE Xplore | IRIS | PubMed | Google Scholar | Scopus | Semantic Scholar | Web of Science | DOI
Publication
— authors
Paola Lecca, Adaoha E. C. Ihekwaba, Lorenzo Dematté, Corrado Priami
— status
published
— sort
article in journal
— publication date
2010
— journal
Journal of Integrative Bioinformatics
— volume
7
— issue
1
identifiers
— DOI