A Simulation for Better Understanding of Integrin Clustering and Activation

Shams, Shahab | 2016

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  1. Type of Document: M.Sc. Thesis
  2. Language: Farsi
  3. Document No: 48541 (19)
  4. University: Sharif University of Technology
  5. Department: Computer Engineering
  6. Advisor(s): Motahhari, Abolfazl
  7. Abstract:
  8. Today, computer simulations are employed prevalently by researchers to understand biological processes. The tendency to use computational methods has been increased recently due to the high costs and errors of experimental methods. Integrins are membrane proteins that mechanically attach cells to the extra cellular matrix (ECM) and derive some behaviors such as cell migration. Moreover, integrins have biochemical functions. They transduce environment signals and trigger chemical pathways. As a result, integrins regulate cell shape, motility, etc. The investigation of integrin behavior in a real environment is very difficult due to the presence of many other proteins that interfere with the integrin activity process. The importance of integrine’s role and difficulties in experimental observations led the researchers to use computer simulations to understand the behavior of these important proteins. In this project, the behavior of integrins in the phenomenon of clustering and adhesion formation is surveyed by simulating the cell membrane. First, the effective factors are defined according to the current literature on the nature of the adhesion formation. Then, the environment of the membrane and affecting factors on integrin clustering are simulated by using agent-based models. The model presented here provides satisfactory results, comparing to the previous experimental studies that introduced the impacts of factors such as ECM ligands and the structure of the cytoskeleton on cell environment.

  9. Keywords:
  10. Focal Adhesion ; Computational Biology ; Agent Based Model ; Integrin Clustering ; Computatianal Physics

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