Comprehensive biophysics: biophysics techniques for structural characterization of macromolecules/ edited by Edward H. Egelma,

VOLUME 9 Simulation and Modeling
Volume Introduction
9.1 Theoretical Biophysics: Cornerstone of Understanding in Modem Biology and
Biomedicine H Weinstein I
In Silico Approaches to Structures and Function of Cell Components and Their Aggregates
9.2 Coarse-Grained Methods: Theory RElber and AE Cardenas 2
9.3 In Silico Coarse-Grained Approaches to Structural Dynamics and Function of Proteins and
their
Assemblies P Doruker, YLiu, Z Yang, and I Bahar 27
9.4 Coarse Grained Methods: Applications to Membranes D Harries and Khelashvili 53
9.5 Dynamics of Very Large Systems: The Ribosome KY Sanbonmatsu, SC Blanchard, and
PC Whitford
9.6 New Technologies for Molecular Dynamics Simulations EChow, JL Klepeis, CA Rendleman,
RO Dror, and DEShaw '
Simulations of Molecular Mechanisms
9.7 Molecular Modeling and Simulations of Transporter Proteins - The Transmembrane
Allosteric Machinery L Shi
9.8 Gene Protein Coupled Receptors DProvasi and M Filizola 123
9.9 Quantum Mechanical Methods for Enzyme Modeling: Accurate Computation of Kinetic
Isotope Effects / Gao 2^^
9.10 MNDO-PSDCI and the Analysis of the Photophysical Properties of Visual Chromophores and
Retinal Proteins DJ Sandberg, NL Wagner, MN Sandberg, JM Crowley, and RR Birge 162
In Silico Approaches to Structure and Function of Cell Components and Their Assemblies
9.11 Molecular Electrostatics and Solvent Effects SA Hassan and EL Mehler 190
9.12 Interactions of the Cell Membrane with Integral Proteins SMondal, H Weinstein, and
9.13 Theory and Mathematical Methods }Gunawardena 243
Mathematical Modeling of Complex Biological Systems
9.14 From Genes and Molecules to Organs and Organisms: Heart YRudy 268
9.15 Biophysical Representation of Kidney Function AM Weinstein 328
9.16 Systems Immunology: A Primer for Biophysicists GAltan-Bonnet and TEmonet 389
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