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Simulation of stochastic reaction-diffusion processes on lower dimensional manifolds with application in molecular biology
Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology.
2012 (English)Independent thesis Advanced level (degree of Master (Two Years)), 30 credits / 45 HE creditsStudent thesis
Abstract [la]

In this thesis, we simulate stochastically the reaction-diffusion processes in a living cell. The simulation is done in three dimension (3D) by MATLAB. The one dimensional (1D) polymers are embedded in the 3D space. The reaction and diffusion events occur both in the space and on the polymers. There is also a possibility for the molecule to jump between the 3D space and 1D polymers. Two simulation levels are used: mesoscopic and microscopic. An accurate and efficient algorithm is developed for the mesoscopic simulation. The corresponding microscopic Smoluchowski equation is solved numerically by a finite difference method in a specific coordinate system adapted to its boundary conditions. The comparison between the result of the mesoscopic simulation and the solution of the microscopic Smoluchowski equation is provided. Good agreement is observed in the experiments.

Place, publisher, year, edition, pages
IT, 12 045
National Category
Engineering and Technology
URN: urn:nbn:se:uu:diva-181613OAI: diva2:557115
Educational program
Master Programme in Computational Science
Available from: 2012-09-27 Created: 2012-09-27 Last updated: 2012-09-27Bibliographically approved

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