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Studies on ion and nucleotide force ...

The University of Utah.

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Studies on ion and nucleotide force fields used in biomolecular simulations.

Record Type:	Electronic resources : Monograph/item
Title/Author:	Studies on ion and nucleotide force fields used in biomolecular simulations./
Author:	Joung, In Suk.
Description:	263 p.
Notes:	Source: Dissertation Abstracts International, Volume: 70-04, Section: B, page: 2322.
Contained By:	Dissertation Abstracts International70-04B.
Subject:	Biophysics, General. -
Online resource:	http://pqdd.sinica.edu.tw/twdaoapp/servlet/advanced?query=3353977
ISBN:	9781109111309

Studies on ion and nucleotide force fields used in biomolecular simulations.
Joung, In Suk.

Studies on ion and nucleotide force fields used in biomolecular simulations. - 263 p.

Source: Dissertation Abstracts International, Volume: 70-04, Section: B, page: 2322.

Thesis (Ph.D.)--The University of Utah, 2009.

Pair-potential models in molecular dynamics simulations are actively utilized in various fields and have been shown to accurately model and reveal a variety of phenomena occurring at the atomistic level. However, the models still have room for improvement. Changing parameters involved in the pair-potential can completely change the potential energy map of systems. Since there are too many degrees of freedom in the determination of the parameters, obtaining the most optimized parameters is almost impossible. For this reason, any pre-existing parameters can be challenged whenever new methods of optimization are discovered. In particular, the parameters for alkali and halide ions had an urgent need for revision due to serious artifacts, such as early precipitation below saturation concentration. We presumed that the problems were mainly caused by not considering ion-ion interactions in the parameterization. Lattice constants and lattice energy of alkali-halide salts were used to reparametrize in addition to hydration free energies. The revised ion parameters were tested and they were good at reproducing the new target properties as well as hydration free energies, which were traditionally regarded as important properties for the ions. Other various properties of the ions related to ion dynamics and energetics in aqueous solutions were measured and compared with those from old parameters and experimental results. Some properties showed qualitative agreements with experimental results but some did not. In parallel with the investigation on ion parameters, AMBER nucleotide force fields were tested. Recently, the AMBER nucleotide force field was revised because alpha/gamma dihedral angles of the backbone of polynucleotides were wrongly populated. To test the new force field called parmbsc0, we attempted to reveal coralyne-poly(dA) duplex structures utilizing both old and new force fields. We detected slight difference between them but overall, two force fields gave similar prediction. However, the readjustment of the new force field showed clear improvement in the population of the backbone torsions.

ISBN: 9781109111309Subjects--Topical Terms:

1019105
Biophysics, General.

Studies on ion and nucleotide force fields used in biomolecular simulations.
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245 1 0 $a Studies on ion and nucleotide force fields used in biomolecular simulations.
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500 $a Source: Dissertation Abstracts International, Volume: 70-04, Section: B, page: 2322.
502 $a Thesis (Ph.D.)--The University of Utah, 2009.
520 $a Pair-potential models in molecular dynamics simulations are actively utilized in various fields and have been shown to accurately model and reveal a variety of phenomena occurring at the atomistic level. However, the models still have room for improvement. Changing parameters involved in the pair-potential can completely change the potential energy map of systems. Since there are too many degrees of freedom in the determination of the parameters, obtaining the most optimized parameters is almost impossible. For this reason, any pre-existing parameters can be challenged whenever new methods of optimization are discovered. In particular, the parameters for alkali and halide ions had an urgent need for revision due to serious artifacts, such as early precipitation below saturation concentration. We presumed that the problems were mainly caused by not considering ion-ion interactions in the parameterization. Lattice constants and lattice energy of alkali-halide salts were used to reparametrize in addition to hydration free energies. The revised ion parameters were tested and they were good at reproducing the new target properties as well as hydration free energies, which were traditionally regarded as important properties for the ions. Other various properties of the ions related to ion dynamics and energetics in aqueous solutions were measured and compared with those from old parameters and experimental results. Some properties showed qualitative agreements with experimental results but some did not. In parallel with the investigation on ion parameters, AMBER nucleotide force fields were tested. Recently, the AMBER nucleotide force field was revised because alpha/gamma dihedral angles of the backbone of polynucleotides were wrongly populated. To test the new force field called parmbsc0, we attempted to reveal coralyne-poly(dA) duplex structures utilizing both old and new force fields. We detected slight difference between them but overall, two force fields gave similar prediction. However, the readjustment of the new force field showed clear improvement in the population of the backbone torsions.
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650 4 $a Chemistry, Biochemistry. $3 1017722
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