Anisimov / Stewart Introduction to Quantum Biology

Topics in Computational Biophysics, Theory, and Implementation
1. Auflage 2012
ISBN: 978-1-4398-3906-5
Verlag: Taylor & Francis
Format: PDF
Kopierschutz: Adobe DRM (»Systemvoraussetzungen)

E-Book, Englisch, 460 Seiten

This book introduces the reader to the theory and methodology of quantum-mechanical modeling of chemical and biological systems. Given the immense complexity of such systems, there is a constant search for new methods. The goal of this text is to derive approximate (semi-empirical) methods to address this class of problems and to provide insight for their continued development. The authors cover such important topics as molecular dynamics, high performance computing, free energy calculations, statistical mechanics, long-range electrostatics, and many-electron systems. They also discuss applications for water salvation, chemical reactions, conformational sampling, and structure relaxation.

Zielgruppe

Anyone interested in molecular modeling of biological systems or method development. This includes students (undergraduate and graduate), academics, and researchers in industry in chemistry, chemical physics, biophysics, structure based drug design, and other related areas of molecular modeling.

Autoren/Hrsg.

Anisimov, Victor

Stewart, James J.P.

Fachgebiete

• Mathematik | Informatik EDV | Informatik Angewandte Informatik Bioinformatik
• Naturwissenschaften Biowissenschaften Angewandte Biologie Bioinformatik
• Naturwissenschaften Chemie Physikalische Chemie Quantenchemie, Theoretische Chemie

Inhaltsverzeichnis

Introduction to Biomolecular Simulations
Dawn of Quantum Biology
What Makes Biomolecules Special
Matching Computational and Experimental Conditions
Mathematical Preliminaries
Linear Algebra
Spherical Coordinates
Internal Coordinates
Coordinate Transformation
Differential and Integral Calculus
Dirac Delta Function
Linear Operators
Function Minimization
Mathematical Statistics
Classical Mechanics
The Newton Laws
The Lagrange Equation
Classical Electrostatics
Electrostatic Potential
Electric Field
Curl and Divergence
Gauss' Law
Poisson and Laplace Equations
The Legendre Polinomials
Spherical Harmonics
Multipole Expansion
Fourier Series
Many-Electron Systems
The Schrodinger Equation
The Born-Oppenheimer Approximation
Variation Principle
Perturbation Theory
The Hartree-Fock Approximation
Geometry Optimization
Constrained Optimization using Lagrange Multipliers
Coupled Perturbed Hartree-Fock Theory
Vibrational Analysis
The Semiempirical Theory
The NDDO Approximation
Energy Derivatives
Linear Scaling Methods
Initial Guess
VFL Approximation and LocalSCF Method
Multiple-Layer QM Models
Implicit Solvent Model COSMO
Classical Biomolecular Force Fields
Mean Field Approximation
Simulation of Bulk Liquids
Determination of Electrostatic and Lennard-Jones Parameters
Biomolecular Force Fields and Programs
Long-Range Electrostatics
Fast Multipole Method
Ewald Sums Method
Condensed Phase
Translational Symmetry
Periodic Structures
Hartree-Fock Method for Periodic Systems
Statistical Mechanics
Statistical Ensembles
Configuration Space
Entropy
Time-Correlation Function
Radial Distribution Function
Molecular Dynamics
Hamiltonian Dynamics
Langevin Dynamics
Non-Hamiltonian Dynamics
Constrained Dynamics
Free Energy Calculations
Free Energy Problem
Potential of Mean Force
Free Energy Pe11urbation
Thermodynamic Integration
The Weighted Histogram Analysis Method
Sample Applications
Structure Preconditioning
Water Solvation
Adding Ions
Structure Relaxation by Using Force Fields
Quantum Mechanical Molecular Dynamics
Chemical Reactions
Conformational Sampling
Protein-Ligand Binding Free Energy
High Performance Computing
MPI Basics
Submitting Multiple Jobs on Multiple Processors

Über Autor(innen)

Victor M. Anisimov is a Postdoctoral Fellow at the School of Health Information Science at the University of Texas, Houston. James J. P. Stewart is the Owner of Stewart Computational Chemistry, Colorado Springs.