Modern Methods for Theoretical Physical Chemistry of Biopolymers

Modern Methods for Theoretical Physical Chemistry of Biopolymers

1st Edition - July 4, 2006

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  • Editors: Evgeni Starikov, James Lewis, Shigenori Tanaka
  • eBook ISBN: 9780080461014
  • Hardcover ISBN: 9780444522207

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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.

Key Features

· 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


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

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 Hamiltonians
    Chapter 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 Properties
    Chapter 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

Product details

  • No. of pages: 604
  • Language: English
  • Copyright: © Elsevier Science 2006
  • Published: July 4, 2006
  • Imprint: Elsevier Science
  • eBook ISBN: 9780080461014
  • Hardcover ISBN: 9780444522207

About the Editors

Evgeni Starikov

Affiliations and Expertise

Institute für Theoretische Festkorperphysik, Universitat Karlsruhe, Karlsruhe Germany

James Lewis

Affiliations and Expertise

Department of Physics and Astronomy, Brigham Young University, Provo, Utah, USA

Shigenori Tanaka

Affiliations and Expertise

Graduate School of Science and Technology, Kobe University, Kobe, Japan

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