The Resource Ab initio computational applications to complex biomolecular systems, Lei Liang, (electronic resource)

Ab initio computational applications to complex biomolecular systems, Lei Liang, (electronic resource)

Label
Ab initio computational applications to complex biomolecular systems
Title
Ab initio computational applications to complex biomolecular systems
Statement of responsibility
Lei Liang
Creator
Contributor
Thesis advisor
Subject
Genre
Language
eng
Summary
A series of biomaterial related systems - including water and DNA molecules - have been studied using ab initio (first-principles) methods. By investigating the properties of water as the preliminary step, the hydrogen bond (HB) interactions, which play important roles in biomolecules, were better understood from the quantum mechanical viewpoint. The calculated K-edge x-ray absorption near edge structure (XANES) spectra of all 340 oxygen atoms in the model have been accumulated to reproduce the experimental one. The spectra were shown to be very sensitive to the HB configurations of O atoms, which could be used to elucidate the subtle structural variations in complex biomolecules. The simulation of singlemolecule DNA overstretching experiments under torsionally constrained condition has been carried out afterwards. The initial DNA models were stretched stepwisely and eventually gained an extension of 1.5-fold (150% x the original length). The variation of total energy, atomic configuration, and the electronic structure during this process were analyzed in details. At the extension of 1̃.3-fold, the ring opening reactions occurred in the backbones. The backbone nicks appeared at elongations of 1̃.40-fold. The whole process was accompanied by HB breaking and charge transfers. We have proposed an overstretched structure named O-DNA (Opened-DNA) to clarify the confusion in understanding the behavior of DNA under high force load. With more experiences gained, a comprehensive methodology revealing the underlying principles of bioprocesses from the quantum mechanical viewpoint eventually come up. For the purpose of better computational accuracy, the scheme of implementing the generalized gradient approximation (GGA) exchangecorrelation functionals into the Orthogonalized Linear Combination of Atomic Orbitals (OLCAO) program suite has been discussed, and the computational efficiency has been analyzed correspondingly. Moreover, the parallel strategy for performing evaluation on a regular mesh and relevant updates to the file system were also presented. All the fundamental works above paved the way for more sophisticated study on wet DNA model and interfaces between biomolecules and bioceramic materials in the future
Cataloging source
UMK
http://library.link/vocab/creatorDate
1984-
http://library.link/vocab/creatorName
Liang, Lei
Degree
Ph.D.
Dissertation year
2011.
Granting institution
Dept. of Physics and Dept. of Mathematics and Statistics. University of Missouri-Kansas City
Illustrations
illustrations
Index
no index present
Literary form
non fiction
Nature of contents
  • dictionaries
  • bibliography
  • theses
http://library.link/vocab/relatedWorkOrContributorName
Ching, Wai-Yim
http://library.link/vocab/subjectName
  • Biomolecules
  • Electronic structure
  • Biomedical materials
Label
Ab initio computational applications to complex biomolecular systems, Lei Liang, (electronic resource)
Instantiates
Publication
Note
  • "A dissertation in Physics and Math & Statistics."
  • Advisor: Wai-Yim Ching
  • Vita
Antecedent source
not applicable
Bibliography note
Includes bibliographical references (pages 119-129)
Carrier category
online resource
Carrier category code
cr
Carrier MARC source
rdacarrier
Color
black and white
Content category
text
Content type code
txt
Content type MARC source
rdacontent
Contents
Introduction -- Theoretical methods -- Case studies -- Future work -- Appendix A. VASP relaxation running time comparison -- Appendix B. Typical initial datasets of oxygen atomic orbitals -- Appendix D. Abbreviaitons
Control code
801056752
Dimensions
unknown
Extent
1 online resource (147 pages)
File format
one file format
Form of item
online
Level of compression
mixed
Media category
computer
Media MARC source
rdamedia
Media type code
c
Other physical details
color illustrations
Quality assurance targets
not applicable
Specific material designation
remote
System control number
(OCoLC)801056752
System details
  • The full text of the dissertation is available as an Adobe Acrobat .pdf file; Adobe Acrobat Reader required to view the file
  • Mode of access: World Wide Web
Label
Ab initio computational applications to complex biomolecular systems, Lei Liang, (electronic resource)
Publication
Note
  • "A dissertation in Physics and Math & Statistics."
  • Advisor: Wai-Yim Ching
  • Vita
Antecedent source
not applicable
Bibliography note
Includes bibliographical references (pages 119-129)
Carrier category
online resource
Carrier category code
cr
Carrier MARC source
rdacarrier
Color
black and white
Content category
text
Content type code
txt
Content type MARC source
rdacontent
Contents
Introduction -- Theoretical methods -- Case studies -- Future work -- Appendix A. VASP relaxation running time comparison -- Appendix B. Typical initial datasets of oxygen atomic orbitals -- Appendix D. Abbreviaitons
Control code
801056752
Dimensions
unknown
Extent
1 online resource (147 pages)
File format
one file format
Form of item
online
Level of compression
mixed
Media category
computer
Media MARC source
rdamedia
Media type code
c
Other physical details
color illustrations
Quality assurance targets
not applicable
Specific material designation
remote
System control number
(OCoLC)801056752
System details
  • The full text of the dissertation is available as an Adobe Acrobat .pdf file; Adobe Acrobat Reader required to view the file
  • Mode of access: World Wide Web

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