Modern Methods for Theoretical Physical Chemistry of Biopolymers book cover

Modern Methods for Theoretical Physical Chemistry of Biopolymers

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.

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

Hardbound, 604 Pages

Published: July 2006

Imprint: Elsevier

ISBN: 978-0-444-52220-7

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

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