Simulating active machines in a lipid bilayer
| Autor: | Mu-Jie Huang, 黃慕傑 |
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| Rok vydání: | 2012 |
| Druh dokumentu: | 學位論文 ; thesis |
| Popis: | 101 This thesis discusses an efficient method to simulate the dynamics of active molecular machines in a lipid bilayer embedded in a solvent. A molecular machine is modeled as an elastic network (EN) that can change its conformations, a lipid chain is modeled by a single bead-spring chain, and the dynamics of the solvent is carried out using multiparticle collision dynamics. This simulation method reproduces liquid and gel phases of a lipid membrane. In the liquid phase, the bending and stretching moduli are found to be comparable to the experimental measurements. Analyzing velocity correlation between two lipid domains at different separations, lipid bilayers are found to indeed behave as two-dimensional (2D) fluids. Simulations of a toy machine representing nano swimmer in such 2D fluid have been performed. We find that this swimmer propels itself over long distances against thermal nosies. Using EN model, the effects of both passive and active molecular machines on the membrane are investigated. For passive machine, the membranes are found to be strongly deformed when the machine is in its ligand-free conformation state. When the active machine is considered, we find that the membrane shape fluctuations modified by machine activities. Moreover, the cyclic conformation transitions of the machine induces a long-ranged lipid flow field. |
| Databáze: | Networked Digital Library of Theses & Dissertations |
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