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Simulation of transport of lipophilic compounds in complex cell geometry
KTH, Skolan för datavetenskap och kommunikation (CSC), Numerisk analys, NA. (Numerical Analysis)
KTH, Skolan för datavetenskap och kommunikation (CSC), Numerisk analys, NA.ORCID-id: 0000-0003-4950-6646
Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden.
2009 (Engelska)Ingår i: Proceedings of the COMSOL Conference, Milan, 2009, 2009Konferensbidrag, Publicerat paper (Refereegranskat)
Ort, förlag, år, upplaga, sidor
2009.
Nyckelord [en]
complex cellular architecture, reaction and diffusion system, homogenization, metabolism in biological cells
Nationell ämneskategori
Beräkningsmatematik
Identifikatorer
URN: urn:nbn:se:kth:diva-32381OAI: oai:DiVA.org:kth-32381DiVA, id: diva2:410355
Anmärkning
QC 20110413Tillgänglig från: 2011-04-13 Skapad: 2011-04-13 Senast uppdaterad: 2011-04-13Bibliografiskt granskad
Ingår i avhandling
1. Numerical Approximation of Reaction and Diffusion Systems in Complex Cell Geometry
Öppna denna publikation i ny flik eller fönster >>Numerical Approximation of Reaction and Diffusion Systems in Complex Cell Geometry
2010 (Engelska)Licentiatavhandling, sammanläggning (Övrigt vetenskapligt)
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.

Ort, förlag, år, upplaga, sidor
Stockholm: KTH, 2010. s. xi, 38
Serie
Trita-CSC-A, ISSN 1653-5723 ; 2010:04
Nyckelord
Complex Cell Geometry, Reaction and Diffusion System, Metabolism in Biological Cells, Homogenization, Compartment Modelling
Nationell ämneskategori
Beräkningsmatematik
Identifikatorer
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 (Engelska)
Opponent
Handledare
Projekt
Computational Modelling of the Mammalian Cell and Membrane Protein Enzymology
Tillgänglig från: 2010-03-05 Skapad: 2010-03-03 Senast uppdaterad: 2011-04-13

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