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Modern methods for theoretical physical chemistry of biopolymers
1 online resource (604 pages, 21 unnumbered pages of plates) : illustrations (some color)
Modern Methods for Theoretical Physical Chemistry of Biopolymers provides an interesting selection of contributions from an international team of researchers in theoretical chemistry. This book is extremely useful for tackling the complicated scientific problems connected with biopolymers' physics and chemistry. The applications of both the classical molecular-mechanical and molecular-dynamical methods and the quantum chemical methods needed for bridging the gap to structural and dynamical properties dependent on electron dynamics are explained. Also included are ways to deal with complex problems when all three approaches need to be considered at the same time. The book gives a rich spectrum of applications: from theoretical considerations of how ATP is produced and used as energy currency in the living cell, to the effects of subtle solvent influence on properties of biopolymers and how structural changes in DNA during single-molecule manipulation may be interpreted. Presents modern successes and trends in theoretical physical chemistry/chemical physics of biopolymers Topics covered are of relevant importance to rapidly developing areas in science such as nanotechnology and molecular medicine Quality selection of contributions from renowned scientists in the field.
Theoretical development of the fragment molecular orbital (FMO) method / Dmitri G. Fedorov and Kazuo Kitaura -- Developments and applications of ABINIT-MP software based on the fragment molecular orbital method / Tatsuya Nakano, Yuji Mochizuki, Kaori Fukuzawa, Shinji Amari and Shigenori Tanaka -- Combined DFT and electrostatic calculations of pKas in proteins : study of cytochrome c oxidase / Dragan M. Popovic, Jason Quenneville and Alexei A. Stuchebrukhov -- Watson-Crick hydrogen bonds : nature and role in DNA replication / Célia Fonseca Guerra and F. Matthias Bickelhaupt -- Quantum chemical modeling of charge transfer in DNA / Alexander A. Voityuk -- Solvent effects on biomolecular dynamics simulations : a comparison between TIP3P, SPC and SPC/E water models acting on the Glucocorticoid receptor DNA-binding domain / Johan Bredenberg, Pekka Mark and Lennart Nilsson -- Computer simulations of DNA stretching / Raimo A. Lohikoski, Martin Dahlberg and Aatto Laaksonen -- On the art of computing the IR spectra of molecules in the condensed phase / Matthias Schmitz and Paul Tavan -- High throughput in-silico screening of large ligand databases for rational drug design / H. Merlitz, B. Fischer and W. Wenzel -- Enzymatic recognition of radiation-produced oxidative DNA lesion : molecular dynamics approach / Miroslav Pinak -- Nucleation of polyglutamine amyloid fibres modelling using molecular dynamics / James Elliott, Evgeni B. Starikov, Jane Crawshaw, Peter Claiden, Lennart Nilsson and Alan Windle -- Drug discovery using grid technology / Hitoshi Goto, Sigeaki Obata, Toshiyuki Kamakura, Naofumi Nakayama, Mitsuhisa Sato, Yoshihiro Nakajima, Umpei Nagashima, Toshio Watanabe, Yuichi Inadomi, Masakatsu Ito, Takeshi Nishikawa, Tatsuya Nakano, Lennart Nilsson, Shigenori Tanaka, Kaori Fukuzawa, Yuichiro Inagaki, Michiaki Hamada and Hiroshi Chuman -- Thermodynamics and kinetic analysis of F₀F₁-ATPase / Yi Qin Gao, Wei Yang and Martin Karplus -- Monte Carlo method : Some applications to problems in protein science / Petras J. Kundrotas -- Protein structure generation and elucidation : applications of automated histogram filtering cluster analysis -- Heather L. Gordon and Stuart M. Rothstein -- All-atom protein folding with stochastic optimization methods / A. Schug, A. Verma, K.H. Lee and W. Wenzel -- Simple models for nonlinear states of double-helix DNA / Raimo A. Lohikoski and Aatto Laaksonen -- The effects of bridge motion on electron transfer reactions mediated by tunneling / Spiros S. Skourtis, Jianping Lin and David N. Beratan -- Modelling molecular conduction in DNA wires : charge transfer theories and dissipative quantum transport / Ralf Bulla, Rafael Gutierrez and Gianaurelio Cuniberti -- Electronic structure theory of DNA : from semi-empirical theory of the [pi]-stack to ab initio calculations of the optical conductivity / Robert G. Endres, Arnd Hübsch, Daniel L. Cox and Rajiv R.P. Singh -- Electronic transport and localization in short and long DNA / H. Wang, R. Marsh, J.P. Lewis and R.A. Römer -- Polaronic charge transport mechanism in DNA / D. Hennig and J.F.R. Archilla -- Atomistic models of biological charge transfer / Thorsten Koslowski, Tobias Cramer and Nadine Utz -- Nonlinear models in DNA conductivity / Victor D. Lakhno -- Electronic structure of DNA derivatives and mimics by density functional theory / Rosa Di Felice and Arrigo Calzolari -- Embedding method for conductance studies of large molecules / Owen R. Davies and John E. Inglesfield -- Ballistic conductance for all-atom models of native and chemically modified DNA : a review of a Kubo-formula-based approach / Ewgeni B. Starikov, Shigenori Tanaka, Noriyuki Kurita, Yasuo Sengoku, Takayuki Natsume, Aina Quintilla and Wolfgang Wenzel.
editors, Evgeni B. Starikov, James P. Lewis, Shigenori Tanaka.
Includes bibliographical references and index.
114705:114799 Elsevier Science & Technology