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Simulation of transport of lipophilic compounds in complex cell geometry
KTH, School of Computer Science and Communication (CSC), Numerical Analysis, NA. (Numerical Analysis)
KTH, School of Computer Science and Communication (CSC), Numerical Analysis, NA.ORCID iD: 0000-0003-4950-6646
Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden.
2009 (English)In: Proceedings of the COMSOL Conference, Milan, 2009, 2009Conference paper, Published paper (Refereed)
Place, publisher, year, edition, pages
2009.
Keyword [en]
complex cellular architecture, reaction and diffusion system, homogenization, metabolism in biological cells
National Category
Computational Mathematics
Identifiers
URN: urn:nbn:se:kth:diva-32381OAI: oai:DiVA.org:kth-32381DiVA: diva2:410355
Note
QC 20110413Available from: 2011-04-13 Created: 2011-04-13 Last updated: 2011-04-13Bibliographically approved
In thesis
1. Numerical Approximation of Reaction and Diffusion Systems in Complex Cell Geometry
Open this publication in new window or tab >>Numerical Approximation of Reaction and Diffusion Systems in Complex Cell Geometry
2010 (English)Licentiate thesis, comprehensive summary (Other academic)
Abstract [en]

The mathematical modelling of the reaction and diffusion mechanism of lipophilic toxic compounds in the mammalian cell is a challenging task because of its considerable complexity and variation in the architecture of the cell. The heterogeneity of the cell regarding the enzyme distribution participating in the bio-transformation, makes the modelling even more difficult. In order to reduce the complexity of the model, and to make it less computationally expensive and numerically treatable, Homogenization techniques have been used. The resulting complex system of Partial Differential Equations (PDEs), generated from the model in 2-dimensional axi-symmetric setting is implemented in Comsol Multiphysics. The numerical results obtained from the model show a nice agreement with the in vitro cell experimental results. The model can be extended to more complex reaction systems and also to 3-dimensional space. For the reduction of complexity and computational cost, we have implemented a model of mixed PDEs and Ordinary Differential Equations (ODEs). We call this model as Non-Standard Compartment Model. Then the model is further reduced to a system of ODEs only, which is a Standard Compartment Model. The numerical results of the PDE Model have been qualitatively verified by using the Compartment Modeling approach. The quantitative analysis of the results of the Compartment Model shows that it cannot fully capture the features of metabolic system considered in general. Hence we need a more sophisticated model using PDEs for our homogenized cell model.

Place, publisher, year, edition, pages
Stockholm: KTH, 2010. xi, 38 p.
Series
Trita-CSC-A, ISSN 1653-5723 ; 2010:04
Keyword
Complex Cell Geometry, Reaction and Diffusion System, Metabolism in Biological Cells, Homogenization, Compartment Modelling
National Category
Computational Mathematics
Identifiers
urn:nbn:se:kth:diva-12099 (URN)978-91-7415-586-0 (ISBN)
Presentation
2010-03-30, E2, KTH Main building, Lindstedtsv. 3, 100 44 Stockholm, 13:00 (English)
Opponent
Supervisors
Projects
Computational Modelling of the Mammalian Cell and Membrane Protein Enzymology
Available from: 2010-03-05 Created: 2010-03-03 Last updated: 2011-04-13

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Hanke, Michael

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Citation style
  • apa
  • harvard1
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