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Lattice-based simulations of microscopic reaction-diffusion models in a crowded environment
Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing.
2016 (English)Independent thesis Advanced level (professional degree), 20 credits / 30 HE creditsStudent thesis
Abstract [en]

Molecules inside living cells move by diffusion and can react with each other upon

collision. Living cells are occupied by macromolecules which limits the available space

for the particles to diffuse in. The effect caused by these crowders has been modeled

and the accuracy of the models has been evaluated. We investigate two models that

follows individual particle trajectories. The more accurate model samples Brownian

Dynamics in a continuous space. The second computationally more efficient model,

uses discrete space were the particles move on a lattice. The result shows that the

lattice model under-estimates the crowding effect on the diffusive behavior. The

reaction rates were both increased and decreased depending on the time and amount

of crowders when comparing the lattice model to the model using Brownian

Dynamics. This also prove the importance to model the particles with realistic sizes

when simulating reaction-diffusion in a crowded environment.

Place, publisher, year, edition, pages
2016. , 34 p.
UPTEC F, ISSN 1401-5757 ; 16033
National Category
Bioinformatics and Systems Biology
URN: urn:nbn:se:uu:diva-297856OAI: oai:DiVA.org:uu-297856DiVA: diva2:943858
Educational program
Master Programme in Engineering Physics
Available from: 2016-06-30 Created: 2016-06-28 Last updated: 2016-06-30Bibliographically approved

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