Reviews in Computational Chemistry / Reviews in Computational Chemistry, Volume 27

Name: Reviews in Computational Chemistry / Reviews in Computational Chemistry, Volume 27
Brand: Wiley
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Kenny B. Lipkowitz(Herausgeber*in)

Wiley (Verlag)

2. Auflage

Erschienen am 29. September 2010

400 Seiten

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Reviews in Computational Chemistry 27
Preface
Contents
Contributors
Contributors to Previous Volumes
CHAPTER 1 Brittle Fracture: From Elasticity Theory to Atomistic Simulations
INTRODUCTION
ESSENTIAL CONTINUUM ELASTICITY THEORY
Conceptual Layout
The Concept of Strain
The Concept of Stress
The Formal Structure of Elasticity Theory
Constitutive Equations
The Isotropic and Homogeneous Elastic Body
Governing Equations of Elasticity and Border Conditions
Elastic Energy
MICROSCOPIC THEORY OF ELASTICITY
Conceptual Layout
Triangular Lattice with Central Forces Only
Triangular Lattice with Two-Body and Three-Body Interactions
Interatomic Potentials for Solid Mechanics
Atomic-Scale Stress
LINEAR ELASTIC FRACTURE MECHANICS
Conceptual Layout
Stress Concentration
The Griffith Energy Criterion
Opening Modes and Stress Intensity Factors
Some Three-Dimensional Configurations
Elastic Behavior of Multi Fractured Solids
Atomistic View of Fracture
ATOMISTIC INVESTIGATIONS ON BRITTLE FRACTURE
Conceptual Layout
Griffith Criterion for Failure
Failure in Complex Systems
Stress Shielding at Crack-Tip
ACKNOWLEDGMENTS
APPENDIX: NOTATION
REFERENCES
CHAPTER 2 Dissipative Particle Dynamics
INTRODUCTION
FUNDAMENTALS OF DPD
Mathematical Formulation
Units in DPD
Thermostat and Schmidt Number
Integration Algorithms
Boundary Conditions
EXTENSIONS OF DPD
DPD with Energy Conservation
Fluid Particle Model
DPD for Two-Phase Flows
Other Extensions
APPLICATIONS
Polymer Solutions and Melts
Binary Mixtures
Amphiphilic Systems
Red Cells in Microcirculation
SUMMARY
REFERENCES
CHAPTER 3 Trajectory-Based Rare Event Simulations
INTRODUCTION
Simulation of Rare Events
Rare Event Kinetics from Transition State Theory
The Reaction Coordinate Problem
Accelerating Dynamics
Trajectory-Based Methods
Outline of the Chapter
TRANSITION STATE THEORY
Statistical Mechanical Definitions
Rate Constants
Rate Constants from Transition State Theory
Variational TST
The Harmonic Approximation
REACTIVE FLUX METHODS
The Bennett-Chandler Procedure
The Effective Positive Flux
The Ruiz-Montero-Frenkel-Brey Method
TRANSITION PATH SAMPLING
Path Probability
Order Parameters
Sampling the Path Ensemble
Shooting Move
Sampling Efficiency
Biasing the Shooting Point
Aimless Shooting
Stochastic Dynamics Shooting Move
Shifting Move
Flexible Time Shooting
Which Shooting Algorithm to Choose?
The Initial Pathway
The Complete Path Sampling Algorithm
Enhancement of Sampling by Parallel Tempering
Multiple-State TPS
Transition Path Sampling Applications
COMPUTING RATES WITH PATH SAMPLING
The Correlation Function Approach
Transition Interface Sampling
Partial Path Sampling
Replica Exchange TIS or Path Swapping
Forward Flux Sampling
Milestoning
Discrete Path Sampling
MINIMIZING THE ACTION
Nudged Elastic Band
Action-Based Sampling
Transition Path Theory and the String Method
IDENTIFYING THE MECHANISM FROM THE PATH ENSEMBLE
Reaction Coordinate and Committor
Transition State Ensemble and Committor Distributions
Genetic Neural Networks
Maximum Likelihood Estimation
CONCLUSIONS AND OUTLOOK
ACKNOWLEDGMENTS
REFERENCES
CHAPTER 4 Understanding Metal/Metal Electrical Contact Conductance from the Atomic to Continuum Scales
INTRODUCTION
FACTORS THAT INFLUENCE CONTACT RESISTANCE
Surface Roughness
Local Heating
Intermixing and Interfacial Contamination
Dimensions of Contacting Asperities
COMPUTATIONAL CONSIDERATIONS
Atomistic Methods
Calculating Conductance of Nanoscale Asperities
Hybrid Multiscale Methods
Characterization of Defected Atoms
SELECTED CASE STUDIES
Conduction Through Metallic Nanowires
Multiscale Methods Applied to Metal/Metal Contacts
CONCLUDING REMARKS
ACKNOWLEDGMENTS
REFERENCES
CHAPTER 5 Molecular Detailed Simulations of Lipid Bilayers
INTRODUCTION
MEMBRANE SIMULATION METHODOLOGY
Force Fields
Choice of the Ensemble
Verification of the Force Field
Monte Carlo Simulation of Lipid Bilayers
DETAILED SIMULATIONS OF BILAYERS CONTAINING LIPID MIXTURES
CONCLUSIONS
REFERENCES
CHAPTER 6 Semiclassical Bohmian Dynamics
INTRODUCTION
THE FORMALISM AND ITS FEATURES
The Trajectory Formulation
Features of the Bohmian Formulation
The Classical Limit of the Schr ¨ odinger Equation and the Semiclassical Regime of Bohmian Trajectories
Using Quantum Trajectories in Dynamics of Chemical Systems
BOHMIAN QUANTUM-CLASSICAL DYNAMICS
Mean-Field Ehrenfest Quantum-Classical Dynamics
Quantum-Classical Coupling via Bohmian Particles
Numerical Illustration of the Bohmian Quantum-Classical Dynamics
Properties of the Bohmian Quantum-Classical Dynamics
HYBRID BOHMIAN QUANTUM-CLASSICAL PHASE-SPACE DYNAMICS
THE INDEPENDENT TRAJECTORY METHODS
The Derivative Propagation Method
The Bohmian Trajectory Stability Approach. Calculation of Energy Eigenvalues by Imaginary Time Propagation
Bohmian Mechanics with Complex Action
DYNAMICS WITH THE GLOBALLY APPROXIMATED QUANTUM POTENTIAL (AQP)
Global Energy-Conserving Approximation of the Nonclassical Momentum
Approximation on Subspaces or Spatial Domains
Nonadiabatic Dynamics
TOWARD REACTIVE DYNAMICS IN CONDENSED PHASE
Stabilization of Dynamics by Balancing Approximation Errors
Bound Dynamics with Tunneling
CONCLUSIONS
ACKNOWLEDGMENTS
APPENDIX A: CONSERVATION OF DENSITY WITHIN A VOLUME ELEMENT
APPENDIX B: QUANTUM TRAJECTORIES IN ARBITRARY COORDINATES
APPENDIX C: OPTIMAL PARAMETERS OF THE LINEARIZED MOMENTUM ON SPATIAL DOMAINS IN MANY DIMENSIONS
REFERENCES
CHAPTER 7 Prospects for Career Opportunities in Computational Chemistry
INTRODUCTION AND OVERVIEW
METHODOLOGY AND RESULTS
PROFICIENCIES IN DEMAND
ANALYSIS
AN ASIDE: ECONOMICS 101
PROGNOSIS
ACKNOWLEDGMENTS
REFERENCES
Appendix: List of Computational Molecular Scientists
Subject Index

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