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Molecular dynamics simulations of gr...

Atherton, Stephanie Jane.

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Molecular dynamics simulations of gramicidin A: Dynamics of permeation.

Record Type:	Electronic resources : Monograph/item
Title/Author:	Molecular dynamics simulations of gramicidin A: Dynamics of permeation./
Author:	Atherton, Stephanie Jane.
Description:	94 p.
Notes:	Source: Dissertation Abstracts International, Volume: 66-07, Section: B, page: 3725.
Contained By:	Dissertation Abstracts International66-07B.
Subject:	Chemistry, Physical. -
Online resource:	http://pqdd.sinica.edu.tw/twdaoapp/servlet/advanced?query=3180844
ISBN:	9780542216978

Molecular dynamics simulations of gramicidin A: Dynamics of permeation.
Atherton, Stephanie Jane.

Molecular dynamics simulations of gramicidin A: Dynamics of permeation. - 94 p.

Source: Dissertation Abstracts International, Volume: 66-07, Section: B, page: 3725.

Thesis (Ph.D.)--The University of Utah, 2005.

The permeation of the model ion channel gramicidin A (gA) is investigated using molecular dynamics simulation. Using the Multi-State Empirical Valence Bond (MS-EVBII) water model, the dynamics and potential of mean force of proton permeation through the unrestrained channel in fully-hydrated lipid bilayer is calculated. The permeation pathway is compared to that of sodium in the same system. Due to the unrestrained nature of the system, an internal reaction coordinate with which these studies are conducted is developed and compared to previously-published molecular dynamics results. The sampling undertaken is much greater than previous studies and illustrates the glassy nature of the protein motions. Aspects of the proton profile in particular are discussed, including consideration of the thermostat used and the effect of restraints on the umbrella sampling.

ISBN: 9780542216978Subjects--Topical Terms:

560527
Chemistry, Physical.

Molecular dynamics simulations of gramicidin A: Dynamics of permeation.
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020 $a 9780542216978
035 $a (UnM)AAI3180844
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100 1 $a Atherton, Stephanie Jane. $3 1914215
245 1 0 $a Molecular dynamics simulations of gramicidin A: Dynamics of permeation.
300 $a 94 p.
500 $a Source: Dissertation Abstracts International, Volume: 66-07, Section: B, page: 3725.
500 $a Adviser: Gregory A. Voth.
502 $a Thesis (Ph.D.)--The University of Utah, 2005.
520 $a The permeation of the model ion channel gramicidin A (gA) is investigated using molecular dynamics simulation. Using the Multi-State Empirical Valence Bond (MS-EVBII) water model, the dynamics and potential of mean force of proton permeation through the unrestrained channel in fully-hydrated lipid bilayer is calculated. The permeation pathway is compared to that of sodium in the same system. Due to the unrestrained nature of the system, an internal reaction coordinate with which these studies are conducted is developed and compared to previously-published molecular dynamics results. The sampling undertaken is much greater than previous studies and illustrates the glassy nature of the protein motions. Aspects of the proton profile in particular are discussed, including consideration of the thermostat used and the effect of restraints on the umbrella sampling.
590 $a School code: 0240.
650 4 $a Chemistry, Physical. $3 560527
650 4 $a Biophysics, General. $3 1019105
690 $a 0494
690 $a 0786
710 2 0 $a The University of Utah. $3 1017410
773 0 $t Dissertation Abstracts International $g 66-07B.
790 1 0 $a Voth, Gregory A., $e advisor
790 $a 0240
791 $a Ph.D.
792 $a 2005
856 4 0 $u http://pqdd.sinica.edu.tw/twdaoapp/servlet/advanced?query=3180844