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The explicit polarization theory as ...

Mazack, Michael John Morgan.

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The explicit polarization theory as a quantum mechanical force field and the development of coarse-grained models for simulating crowded systems of many proteins.

Record Type:	Electronic resources : Monograph/item
Title/Author:	The explicit polarization theory as a quantum mechanical force field and the development of coarse-grained models for simulating crowded systems of many proteins./
Author:	Mazack, Michael John Morgan.
Description:	304 p.
Notes:	Source: Dissertation Abstracts International, Volume: 76-08(E), Section: B.
Contained By:	Dissertation Abstracts International76-08B(E).
Subject:	Physical chemistry. -
Online resource:	http://pqdd.sinica.edu.tw/twdaoapp/servlet/advanced?query=3686954
ISBN:	9781321639599

The explicit polarization theory as a quantum mechanical force field and the development of coarse-grained models for simulating crowded systems of many proteins.
Mazack, Michael John Morgan.

The explicit polarization theory as a quantum mechanical force field and the development of coarse-grained models for simulating crowded systems of many proteins. - 304 p.

Source: Dissertation Abstracts International, Volume: 76-08(E), Section: B.

Thesis (Ph.D.)--University of Minnesota, 2014.

This dissertation consists of two parts. The first part concerns the use of explicit polarization theory (X-Pol), the semiempirical polarized molecular orbital (PMO) method, and the dipole preserving, polarization consistent (DPPC) charge model as a quantum mechanical force field (QMFF). A detailed discussion of Hartree-Fock theory and X-Pol is provided, along with expressions for the energy and the analytical first derivative of this QMFF. Test cases for this QMFF with extensive comparisons to experimental data and other models are provided for water (XP3P) and hydrogen fluoride (XPHF), showing that the PMO/X-Pol/DPPC approach discussed in this dissertation is competitive with the most accurate models for those two chemical species over a wide range of chemical and physical properties.

ISBN: 9781321639599Subjects--Topical Terms:

1981412
Physical chemistry.

The explicit polarization theory as a quantum mechanical force field and the development of coarse-grained models for simulating crowded systems of many proteins.
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100 1 $a Mazack, Michael John Morgan. $3 3179540
245 1 4 $a The explicit polarization theory as a quantum mechanical force field and the development of coarse-grained models for simulating crowded systems of many proteins.
300 $a 304 p.
500 $a Source: Dissertation Abstracts International, Volume: 76-08(E), Section: B.
500 $a Adviser: Jiali Gao.
502 $a Thesis (Ph.D.)--University of Minnesota, 2014.
520 $a This dissertation consists of two parts. The first part concerns the use of explicit polarization theory (X-Pol), the semiempirical polarized molecular orbital (PMO) method, and the dipole preserving, polarization consistent (DPPC) charge model as a quantum mechanical force field (QMFF). A detailed discussion of Hartree-Fock theory and X-Pol is provided, along with expressions for the energy and the analytical first derivative of this QMFF. Test cases for this QMFF with extensive comparisons to experimental data and other models are provided for water (XP3P) and hydrogen fluoride (XPHF), showing that the PMO/X-Pol/DPPC approach discussed in this dissertation is competitive with the most accurate models for those two chemical species over a wide range of chemical and physical properties.
520 $a The second part of this dissertation concerns the development and application of coarse-grained models for protein dynamics. First, a coarse-grained force field (CGFF) for macromolecules in crowded environments is introduced and described along with a visualization environment for the cartoon-like rendering of biomolecules in vivo. This CGFF is tested against experimental diffusion coefficients for myoglobin (Mb) at a wide range of concentrations, including volume fractions as high as 40%, finding it to be surprisingly accurate for its simplicity and level of coarseness. Second, an analytical coarse-grained (ACG) model for mapping the internal dynamics of proteins into a spherical harmonic expansion is described.
590 $a School code: 0130.
650 4 $a Physical chemistry. $3 1981412
650 4 $a Biophysics. $3 518360
650 4 $a Applied mathematics. $3 2122814
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710 2 $a University of Minnesota. $b Scientific Computation. $3 3179541
773 0 $t Dissertation Abstracts International $g 76-08B(E).
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791 $a Ph.D.
792 $a 2014
793 $a English
856 4 0 $u http://pqdd.sinica.edu.tw/twdaoapp/servlet/advanced?query=3686954