Modern Methods for Theoretical Physical Chemistry of Biopolymers

Edited by

  • Evgeni Starikov, Institute für Theoretische Festkorperphysik, Universitat Karlsruhe, Karlsruhe Germany
  • James Lewis, Department of Physics and Astronomy, Brigham Young University, Provo, Utah, USA
  • Shigenori Tanaka, Graduate School of Science and Technology, Kobe University, Kobe, Japan

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.
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Senior pre-graduates, doctoral students, and younger postdocs in the field of theoretical physical chemistry/chemical physics of biopolymers


Book information

  • Published: July 2006
  • Imprint: ELSEVIER
  • ISBN: 978-0-444-52220-7

Table of Contents

SECTION 1. Quantum Chemistry Chapter 1. Theoretical development of the fragment molecular orbital (FMO) method
Chapter 2. Developments and applications of ABINIT-MP software based on the Fragment Molecular Orbital
Chapter 3. Combined DFT and electrostatic calculations of pKa's in proteins: Study of cytochrome c oxidase
Chapter 4. Watson-Crick hydrogen bonds: Nature and role in DNA replication
Chapter 5. Quantum chemical modeling of charge transfer in DNA

SECTION 2. Molecular Mechanics Chapter 6. Solvent effects on biomolecular dynamics simulations: A comparison between TIP3P, SPC and SPC/E water models acting on the glucocorticoid receptor DNA-binding domain
Chapter 7. Computer simulations of DNA stretching
Chapter 8. On the art of computing the IR spectra of molecules in condensed phase
Chapter 9. High Throughput in-silico screening of large ligand databases for rational drug design
Chapter 10. Enzymatic recognition of radiation produced oxidative DNA lesion.Molecular dynamics approach
Chapter 11. Nucleation of polyglutamine amyloid fibres modelling using molecular dynamics
Chapter 12. Drug discovery using grid technology
Chapter 13. Simple models for nonlinear states of double stranded DNA
Chapter 14. Thermodynamics and kinetic analysis of FoF1-ATPase

SECTION 3. Statistical Methods Chapter 15. Monte Carlo method: Some applications to problems in protein science
Chapter 16. Protein structure generation and elucidation: Applications of automated histogram filtering cluster analysis
Chapter 17. All atom protein folding with stochastic optimization methods

SECTION 4. Model HamiltoniansChapter 18. The effects of bridge motion on electron transfer reactions mediated by tunneling
Chapter 19. Modeling molecular conduction in DNA wires: Charge transfer theories and dissipative quantum transport
Chapter 20. Electronic structure of DNA derivatives and mimics by Density Functional Theory
Chapter 21. Electronic structure theory of DNA: from semi-empirical theory
Chapter 22. Electronic transport and localization in short and long DNA
Chapter 23. Polaronic charge transport mechanism in DNA
Chapter 24. Atomistic models of biological charge transfer
Chapter 25. Nonlinear Models in DNA conductivity

SECTION 5. Electric PropertiesChapter 26. Embedding method for conductance studies of large molecules
Chapter 27. Ballistic conductance for all-atom models of native and chemically modified DNA: a review of Kubo-formula-based approach