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Modeling and Simulation of Cells
Linköping University, Department of Electrical Engineering, Information Coding. Linköping University, The Institute of Technology.
2011 (English)Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
Abstract [en]

The aim of this thesis is to create a computer program that simulates the motionof cells in a developing embryo. The resulting simulator is to be used by in the CellLineage project (Robert Forchheimer et al.) as an input to their genetic model, themeta-Boolean model [18]. This genetic model is not the focus of this work. Sincethe simulated system is highly complex, with fluids and deforming soft bodies, itis unfeasible to simulate the system in a physically realistic manner while keepingexecution time to reasonable values. Therefore some physical realism is sacrificedin favor of simulation stability and execution speed.The resulting simulator, Cell-Lab, uses Position Based Dynamics (PBD) [17] toimplement a number of different models for the cell’s mechanical properties. PBDis well suited for this purpose since it, while not taking excessively long time toexecute, guarantees an unconditionally stable simulation. The simulator includesa hard eggshell surrounding the cells. Cells can be split during the simulation,emulating mitosis. There is also the possibility to simulate cell adhesion usinga cadherin like mechanism. To control when and how cells are split and fetchinformation about the current state of the simulation there is an interface to beused by external applications. The meta-Boolean model can be implemented insuch an application

Place, publisher, year, edition, pages
2011. , 79 p.
Keyword [en]
Theoretical biology, C. Elegans, Meta-Boolean, Embryogenesis, Soft-body simula- tion, Position based dynamics
National Category
Engineering and Technology
URN: urn:nbn:se:liu:diva-110121ISRN: LiTH-ISY-EX--11/4365--SEOAI: diva2:743653
Subject / course
Information Coding
Available from: 2014-09-05 Created: 2014-09-02 Last updated: 2014-09-05Bibliographically approved

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