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- Type of Document: M.Sc. Thesis
- Language: Farsi
- Document No: 43915 (08)
- University: Sharif University of Tecnology
- Department: Mechanical Engineering
- Advisor(s): Saeedi, Mohammad Saeed; Firoozabadi, Bahar
- Abstract:
- By studying change of ion concentrations in animal cells, researchers have reach to important information about cell cycles such as cell growth, muscle cell contraction and cell migration. Manner and amount of passage of ions through cell membrane are basic information that for studying the cell cycle is required. In this thesis, by using two methods, Forward-Reverse constant velocity Steered Molecular Dynamics (FR-cv-SMD) and classical Equilibrium Molecular Dynamics (EMD), diffusion coefficient and Potential of Mean Force (PMF) of sodium and potassium permeation through their protein channels are obtained. For verification the molecular dynamics (MD) methods, diffusion coefficient of K+ through water box is obtained that was compatible with pervious experimental results. The all atom MD simulations are executed on GPU and CPU together. Results show that by using Device and increasing the nodes number, CPU time decreasing exponentially. The classical mathematical model for predicting the mass transport phenomena in continuum region is the Fick's Law. In this thesis a lagged model for predicting this phenomena is presented. Using Laplace Transform and Inversion Theorem in complex plain, the lagged and Fick's models in a case study mass transport phenomena are solved analytically. By applying MD simulation of argon, the results are compared with Fick's and the lagged models. The results show that the relaxation time has a great influence on the concentration distribution of atoms in the box. Furthermore, the shock expected in the lagged model mass transfer is close to the results obtained from MD simulation. According to MD simulation results, as the lagged model shows, there is a mass shock moving to the end of the box with constant velocity. Velocity of information transfer is obtained analytically. Using diffusion coefficient and PMF of Na channel obtained from FR-cv-SMD Simulation and Langevin equation of motion, permeation of Na+ through Na channel is studying. From the simulation speed of computation increased extraordinary. Results shown that ion concentration distribution in membrane protein channel is closed to that the lagged model predict. Velocity of information transfer in Na channel is obtained 1.2 [m/s] that indicates inherent delay in biological systems
- Keywords:
- Molecular Dynamics ; Mass Transfer ; Nano Channel ; Parallel Processing ; Drug Delivery ; Information Transfer in Nano Scale Velocity ; Bionanomembrane
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