مدل شبیه سازی برای مولکول های آمفیفیلیک در حلال mesoscale
|کد مقاله||سال انتشار||تعداد صفحات مقاله انگلیسی||ترجمه فارسی|
|9344||2008||12 صفحه PDF||سفارش دهید|
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Publisher : Elsevier - Science Direct (الزویر - ساینس دایرکت)
Journal : Computers & Mathematics with Applications, Volume 55, Issue 7, April 2008, Pages 1469–1480
We present a stochastic rotation dynamics model of amphiphilic molecules. Vesicle formation of amphiphilic molecules in a thermal fluctuating fluid is demonstrated in this paper. In the model, the interaction of amphiphilic molecules is represented by Lennard–Jones potentials, and stochastic rotation dynamics [T. Ihle, D.M. Kroll, Stochastic rotation dynamics: A Galilean-invariant mesoscopic model for fluid flow, Phys. Rev. E 63 (2001) 020201(R)] of mesoscopic particles has been adopted to reproduce the correct hydrodynamics of solvent fluids at the macroscopic scale. The amphiphilic molecules and the solvent particles interact via Boltzmann sampling of a color potential as suggested in a previous paper [Y. Inoue, Y. Chen, H. Ohashi, A mesoscopic simulation model for immiscible multiphase fluids, J. Comput. Phys. 201 (2004) 191] to reproduce a phase separation between hydrophobic atoms and solvent fluids.
A vesicle is a spherical closed bilayer formed by amphiphilic molecules. Investigations of both vesicles and their dynamics are important for our understanding of biology because vesicles can be regarded as a simple cellular model in biological systems. A large variety of simulation models which reproduce the self-assembly of vesicles has been developed. Noguchi and Takasu  have shown Brownian dynamics (BD) simulations of amphiphilic particles self-assembling into a vesicle without solvent particles, where the amphiphilic particle consists of one hydrophilic particle and two hydrophobic particles. They defined a multi-body potential energy between hydrophobic parts to mimic the so-called hydrophobic effect. However, because of the lack of the explicit solvent, the BD model may not capture how hydrodynamics affects the macroscopic dynamics of amphiphilic molecules. Yamamoto et al.  have developed a dissipative particle dynamics (DPD) model of amphiphilic molecules, in which the DPD amphiphilic molecules can spontaneously assemble into a vesicle when suspended amongst explicit solvent particles. Since DPD features a soft repulsive force between particles, one can use a relatively large time step compared to that used in molecular dynamics simulations. Thus, DPD can access the hydrodynamic regime but is restricted to small simulation boxes due to the high computational cost. A more realistic molecular model, but still at the mesoscale, has been suggested by Marrink and Mark , in which DPPC lipids are represented by twelve coarse-grained atoms and the water molecules are represented by single coarse-grained atoms. Their result of the electron density distribution measured along the bilayer normal quantitatively agrees with those obtained by atomistic molecular dynamics simulations; coarse-grained DPPC showed spontaneous aggregation into vesicles. All the models mentioned above can reproduce spontaneous aggregation into a vesicle. However, simulations of dynamics of vesicles with hydrodynamics at the sub-micrometer scale are impossible for BD  due to the lack of hydrodynamics, and impracticable for DPD  and MD  due to the computational costs of the calculations of many solvent particles. Thus, a novel simulation model, which would be capable of simulations of vesicles on long time scales and over long distances, is required.
نتیجه گیری انگلیسی
We developed an stochastic rotation dynamics model of amphiphilic molecules to simulate the dynamics of vesicles in fluids. We constructed a 3D color method which bridges stochastic rotation dynamics and molecular dynamics. Our simulation results of both the probability distribution function for segments and the sealing process qualitatively agree with that obtained in previous studies involving molecular dynamics and dissipative particle dynamics simulations. However, our simulation done here is very limited to a few examples. We have not clarified how each approximation makes errors yet. We should achieve further simulations from the grand scope to test our model.