Lattice-based simulations of microscopic reaction-diffusion models in a crowded environment

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 eva...

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Main Author: Eriksson, Markus
Format: Others
Language:English
Published: Uppsala universitet, Avdelningen för beräkningsvetenskap 2016
Online Access:http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-297856
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spelling ndltd-UPSALLA1-oai-DiVA.org-uu-2978562016-07-01T05:32:30ZLattice-based simulations of microscopic reaction-diffusion models in a crowded environmentengEriksson, MarkusUppsala universitet, Avdelningen för beräkningsvetenskap2016Molecules 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. Student thesisinfo:eu-repo/semantics/bachelorThesistexthttp://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-297856UPTEC F, 1401-5757 ; 16033application/pdfinfo:eu-repo/semantics/openAccess
collection NDLTD
language English
format Others
sources NDLTD
description 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.
author Eriksson, Markus
spellingShingle Eriksson, Markus
Lattice-based simulations of microscopic reaction-diffusion models in a crowded environment
author_facet Eriksson, Markus
author_sort Eriksson, Markus
title Lattice-based simulations of microscopic reaction-diffusion models in a crowded environment
title_short Lattice-based simulations of microscopic reaction-diffusion models in a crowded environment
title_full Lattice-based simulations of microscopic reaction-diffusion models in a crowded environment
title_fullStr Lattice-based simulations of microscopic reaction-diffusion models in a crowded environment
title_full_unstemmed Lattice-based simulations of microscopic reaction-diffusion models in a crowded environment
title_sort lattice-based simulations of microscopic reaction-diffusion models in a crowded environment
publisher Uppsala universitet, Avdelningen för beräkningsvetenskap
publishDate 2016
url http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-297856
work_keys_str_mv AT erikssonmarkus latticebasedsimulationsofmicroscopicreactiondiffusionmodelsinacrowdedenvironment
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