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Tools and Methodology for the Adapti...

Duster, Adam William.

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Tools and Methodology for the Adaptive Multiscale Simulation of Proton Transport in Complex Environments.

Record Type:	Electronic resources : Monograph/item
Title/Author:	Tools and Methodology for the Adaptive Multiscale Simulation of Proton Transport in Complex Environments./
Author:	Duster, Adam William.
Published:	Ann Arbor : ProQuest Dissertations & Theses, : 2017,
Description:	104 p.
Notes:	Source: Masters Abstracts International, Volume: 56-04.
Contained By:	Masters Abstracts International56-04(E).
Subject:	Biophysics. -
Online resource:	http://pqdd.sinica.edu.tw/twdaoapp/servlet/advanced?query=10272892
ISBN:	9781369774146

Tools and Methodology for the Adaptive Multiscale Simulation of Proton Transport in Complex Environments.
Duster, Adam William.

Tools and Methodology for the Adaptive Multiscale Simulation of Proton Transport in Complex Environments. - Ann Arbor : ProQuest Dissertations & Theses, 2017 - 104 p.

Source: Masters Abstracts International, Volume: 56-04.

Thesis (M.S.)--University of Colorado at Denver, 2017.

This thesis reports three developments in the combined quantum-mechanics/molecular-mechanics (QM/MM) methodology and software. First, an interface between the program QMMM and the MM package NAMD was implemented, substantially increasing the computational efficiency of MM calculations. Second, the permuted adaptive partitioning QM/MM algorithm implemented in the QMMM software package was parallelized using the OpenMP protocol. The algorithm can scale approximately linearly when the number of buffer groups vastly exceeds the number of threads requested. These two improvements will increase the scope and scale of future calculations conducted with QMMM. Finally, the feasibility of using a restrained proton indicator in biased (MD) simulations was investigated. A harmonic restraint potential was imposed on an existing proton indicator, the position of which approximates the location of an excess proton in water. When applied to a carbon nanotube model system, the restrained proton accelerated water recruitment into the nanotube when it was restrained above the nanotube opening, in agreement with previous simulations in the literature, where a different algorithm for proton representation was used.

ISBN: 9781369774146Subjects--Topical Terms:

518360
Biophysics.

Tools and Methodology for the Adaptive Multiscale Simulation of Proton Transport in Complex Environments.
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300 $a 104 p.
500 $a Source: Masters Abstracts International, Volume: 56-04.
500 $a Adviser: Hai Lin.
502 $a Thesis (M.S.)--University of Colorado at Denver, 2017.
520 $a This thesis reports three developments in the combined quantum-mechanics/molecular-mechanics (QM/MM) methodology and software. First, an interface between the program QMMM and the MM package NAMD was implemented, substantially increasing the computational efficiency of MM calculations. Second, the permuted adaptive partitioning QM/MM algorithm implemented in the QMMM software package was parallelized using the OpenMP protocol. The algorithm can scale approximately linearly when the number of buffer groups vastly exceeds the number of threads requested. These two improvements will increase the scope and scale of future calculations conducted with QMMM. Finally, the feasibility of using a restrained proton indicator in biased (MD) simulations was investigated. A harmonic restraint potential was imposed on an existing proton indicator, the position of which approximates the location of an excess proton in water. When applied to a carbon nanotube model system, the restrained proton accelerated water recruitment into the nanotube when it was restrained above the nanotube opening, in agreement with previous simulations in the literature, where a different algorithm for proton representation was used.
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