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Computational studies of the amphiph...

He, Xibing.

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Computational studies of the amphiphilic molecules with all-atom and coarse-grained molecular dynamics simulations.

Record Type:	Language materials, printed : Monograph/item
Title/Author:	Computational studies of the amphiphilic molecules with all-atom and coarse-grained molecular dynamics simulations./
Author:	He, Xibing.
Description:	140 p.
Notes:	Source: Dissertation Abstracts International, Volume: 71-07, Section: B, page: 4269.
Contained By:	Dissertation Abstracts International71-07B.
Subject:	Chemistry, Physical. -
Online resource:	http://pqdd.sinica.edu.tw/twdaoapp/servlet/advanced?query=3414216
ISBN:	9781124064208

Computational studies of the amphiphilic molecules with all-atom and coarse-grained molecular dynamics simulations.
He, Xibing.

Computational studies of the amphiphilic molecules with all-atom and coarse-grained molecular dynamics simulations. - 140 p.

Source: Dissertation Abstracts International, Volume: 71-07, Section: B, page: 4269.

Thesis (Ph.D.)--University of Pennsylvania, 2010.

This thesis deals with two types of systems -- surfactants and phospholipids, which are amphiphilic molecules composed of hydrophilic head-groups and hydrophobic tail-groups. Molecular dynamics (MD) simulations with atomistic forcefield were carried out on monolayers of a series of linear alkylbenzene sulfonates (LAS), which are the most popular synthetic surfactant family, at the water/air interface. The structures and properties, such as surface tension, tilt angles, solubility, mobility, are investigated and compared for different LAS homologs and isomers. A set of coarse-grained (CG) model was developed for studying the phase behaviors of LAS surfactant molecules. First of all, a variety of simple CG models of water, with different resolutions, interaction potentials (Lennard-Jones, Morse), and cut-off distances, were systematically examined. The relationships between the parameters and the thermodynamic properties, such as density, surface tension, and compressibility, were found to fit simple mathematical equations. The limits of applicability of these CG water models were explored by checking the melting temperature. One specific CG water model, W3-LJ124-rc15, was chosen based on the balance between efficiency and accuracy. The LAS CG model was systematically developed by fitting the thermodynamic data from experiments and structural data obtained from all-atom MD for the NaCl solutions, aliphatic and aromatic alkanes, alkyl sulfonates and LAS solutions. An extensive evaluation of the parameters provides a reliable, transferable and computationally efficient CG model, which can be easily employed to simulate the self-assembly of LAS aqueous solutions into different morphologies starting from random configurations. The CG model was shown to accurately reproduce the phase behavior of solutions of pure isomers of sodium dodecylbenzene sulfonate, despite the fact that phase behavior was not directly taken into account in the forcefield parameterization. CG MD simulations were also performed to calculate the free energy profiles of the aggregation of two trans-membrane inclusions in the phospholipid dimyristoylphosphatidylcholine (DMPC) bilayer, and the free energy profile of the membrane meniscus caused by the hydrophobic mismatch between the hydrophobic length of the trans-membrane inclusions and the hydrophobic thickness of the DMPC bilayer.

ISBN: 9781124064208Subjects--Topical Terms:

560527
Chemistry, Physical.

Computational studies of the amphiphilic molecules with all-atom and coarse-grained molecular dynamics simulations.
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245 1 0 $a Computational studies of the amphiphilic molecules with all-atom and coarse-grained molecular dynamics simulations.
300 $a 140 p.
500 $a Source: Dissertation Abstracts International, Volume: 71-07, Section: B, page: 4269.
500 $a Adviser: Michael L. Klein.
502 $a Thesis (Ph.D.)--University of Pennsylvania, 2010.
520 $a This thesis deals with two types of systems -- surfactants and phospholipids, which are amphiphilic molecules composed of hydrophilic head-groups and hydrophobic tail-groups. Molecular dynamics (MD) simulations with atomistic forcefield were carried out on monolayers of a series of linear alkylbenzene sulfonates (LAS), which are the most popular synthetic surfactant family, at the water/air interface. The structures and properties, such as surface tension, tilt angles, solubility, mobility, are investigated and compared for different LAS homologs and isomers. A set of coarse-grained (CG) model was developed for studying the phase behaviors of LAS surfactant molecules. First of all, a variety of simple CG models of water, with different resolutions, interaction potentials (Lennard-Jones, Morse), and cut-off distances, were systematically examined. The relationships between the parameters and the thermodynamic properties, such as density, surface tension, and compressibility, were found to fit simple mathematical equations. The limits of applicability of these CG water models were explored by checking the melting temperature. One specific CG water model, W3-LJ124-rc15, was chosen based on the balance between efficiency and accuracy. The LAS CG model was systematically developed by fitting the thermodynamic data from experiments and structural data obtained from all-atom MD for the NaCl solutions, aliphatic and aromatic alkanes, alkyl sulfonates and LAS solutions. An extensive evaluation of the parameters provides a reliable, transferable and computationally efficient CG model, which can be easily employed to simulate the self-assembly of LAS aqueous solutions into different morphologies starting from random configurations. The CG model was shown to accurately reproduce the phase behavior of solutions of pure isomers of sodium dodecylbenzene sulfonate, despite the fact that phase behavior was not directly taken into account in the forcefield parameterization. CG MD simulations were also performed to calculate the free energy profiles of the aggregation of two trans-membrane inclusions in the phospholipid dimyristoylphosphatidylcholine (DMPC) bilayer, and the free energy profile of the membrane meniscus caused by the hydrophobic mismatch between the hydrophobic length of the trans-membrane inclusions and the hydrophobic thickness of the DMPC bilayer.
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773 0 $t Dissertation Abstracts International $g 71-07B.
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791 $a Ph.D.
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