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Dynamic Modeling and Simulation of Biological Membranes

Bahrami, Amir Houashang | 2011

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  1. Type of Document: Ph.D. Dissertation
  2. Language: Farsi
  3. Document No: 41328 (08)
  4. University: Sharif University of Technology
  5. Department: Mechanical Engineering
  6. Advisor(s): Jalali, Mir Abbas
  7. Abstract:
  8. Phospholipid membranes and vesicles play important roles in the cellular functioning, otein signaling and material transport inside cells. Protein-embedded vesiclesare also used for targeted drug delivery. In this thesis, we use molecular dynamicsmethods and study (i) the formation of vesicles from flat lipid bilayers (ii) the mechanicalproperties of vesicles under compressive forces (iii) the shape variations ofvesicles with and without transmembrane proteins (iv) protein clustering.We grow our vesicles from lipid bilayers, which may contain proteins with differentconcentrations. We start with a random initial distribution of proteins that allowsus to monitor the clustering and fragmentation of proteins. As clusters are formed,they locally flatten their host vesicles and increase the bending energy of the system.We measure such deformations by modeling the outer surface of vesicles and computethe local (and averaged) mean and Gaussian curvatures. This helps us understandthe evolution of clusters and the maximum bending energy that a protein-embeddedvesicle can tolerate. We also introduce an indicator for the population of proteins inclusters and use it to distinguish the roles of depletion force and curvature-mediatedinteractions in the formation of clusters. Our results confirm previous predictionsthat vesicles can host bigger clusters than flat bilayers, but we show that there is anupper bound on the size of clusters in vesicles.The mechanical properties of vesicles, like the density and pressure distributionin the water and lipid components, are also investigated. By applying a compressiveforce on our vesicles, we obtain the force-displacement relation, which showsa nonlinear stiffening with apparently piecewise linear segments. A major part ofmaterial is transported from/into cells through nanoscale transmembrane pores. Weshow that spontaneous liquid flow in nanotubes follows macroscale rules and differencesbetween the wetting properties of liquids can lead to efficient material transportthrough transmembrane pores
  9. Keywords:
  10. Molecular Dynamics ; Proteins ; Capillary Tube ; Biological Membrane ; Vesicle Shape Transformation ; Vesicle Curvature

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