Lattice-Boltzmann Modeling of Multicomponent Systems: An Introduction
Modeling Mechanochemistry from First Principles
Mapping Energy Transport Networks in Proteins
The Role of Computations in Catalysis
The Construction of Ab Initio Based Potential Energy Surfaces
Uncertainty Quantification for Molecular Dynamics
Table of Contents
List of Contributors ix
Preface xi
Contributors to Previous Volumes xv
1 Lattice-Boltzmann Modeling of Multicomponent Systems: An Introduction 1
Ulf D. Schiller and Olga Kuksenok
Introduction 1
The Lattice Boltzmann Equation: A Modern Introduction 4
A Brief History of the LBM 5
The Lattice Boltzmann Equation 7
The Fluctuating Lattice Boltzmann Equation 23
Boundary Conditions 25
Fluid-Particle Coupling 30
LBM for Multiphase Fluids 37
Governing Continuum Equations 37
Lattice Boltzmann Algorithm for Binary Fluid: Free-Energy Approach 42
Minimizing Spurious Velocities 47
Conclusions 50
References 51
2 Mapping Energy Transport Networks in Proteins 63
David M. Leitner and Takahisa Yamato
Introduction 63
Thermal and Energy Flow in Macromolecules 65
Normal Modes of Proteins 65
Simulating Energy Transport in Terms of Normal Modes 69
Energy Diffusion in Terms of Normal Modes 70
Energy Transport from Time Correlation Functions 73
Energy Transport in Proteins is Inherently Anisotropic 75
Locating Energy Transport Networks 77
Communication Maps 77
CURrent calculations for Proteins (CURP) 80
Applications 83
Communication Maps: Illustrative Examples 83
CURP: Illustrative Examples 89
Future Directions 98
Summary 99
Acknowledgments 100
References 100
3 Uncertainty Quantification for Molecular Dynamics 115
Paul N. Patrone and Andrew Dienstfrey
Introduction 115
From Dynamical to Random: An Overview of MD 118
System Specification 119
Interatomic Potentials 121
Hamilton’s Equations 123
Thermodynamic Ensembles 128
Where Does This Leave Us? 131
Uncertainty Quantification 131
What is UQ? 132
Tools for UQ 136
UQ of MD 143
Tutorial: Trajectory Analysis 143
Tutorial: Ensemble Verification 148
Tutorial: UQ of Data Analysis for the Glass-Transition Temperature 151
Concluding Thoughts 161
References 162
4 The Role of Computations in Catalysis 171
Horia Metiu, Vishal Agarwal, and Henrik H. Kristoffersen
Introduction 171
Screening 172
Sabatier Principle 173
Scaling Relations 175
BEP Relationship 176
Volcano Plots 180
Some Rules for Oxide Catalysts 189
Let Us Examine Some Industrial Catalysts 191
Sometimes Selectivity is More Important than Rate 191
Sometimes We Want a Smaller Rate! 191
Sometimes Product Separation is More Important than the Reaction Rate 193
Some Reactions are Equilibrium-limited 193
The Cost of Making the Catalyst is Important 194
The Catalyst Should Contain Abundant Elements 194
A Good Catalyst Should not be Easily Poisoned 195
Summary 195
References 196
5 The Construction of Ab Initio-Based Potential Energy Surfaces 199
Richard Dawes and Ernesto Quintas-Sánchez
Introduction and Overview 199
What is a PES? 199
Significance and Range of Applications of PESs 204
Challenges for Theory 207
Terminology and Concepts 209
The Schrödinger Equation 209
The BO Approximation 210
Mathematical Foundations of (Linear) Fitting 215
Quantum Chemistry Methods 221
General Considerations 221
Single Reference Methods 223
Multireference Methods 225
Compound Methods or Protocols 227
Fitting Methods 229
General Considerations and Desirable Attributes of a PES 229
Non-Interpolative Fitting Methods 231
Interpolative Fitting Methods 239
Applications 242
The Automated Construction of PESs 242
Concluding Remarks 248
Acknowledgements 250
Acronyms/Abbreviations 250
References 251
6 Modeling Mechanochemistry from First Principles 265
Heather J. Kulik
Introduction and Scope 265
Potential Energy Surfaces and Reaction Coordinates 266
Theoretical Models of Mechanochemical Bond Cleavage 268
Linear Model (Kauzmann, Eyring, and Bell) 268
Tilted Potential Energy Profile Model 270
First-Principles Models for Mechanochemical Bond Cleavage 271
Constrained Geometries Simulate External Force (COGEF) 271
Force-Modified Potential Energy Surfaces 273
Covalent Mechanochemistry 278
Overview of Characterization Methods 278
Representative Mechanophores 280
Representative Mechanochemistry Case Studies 281
Benzocyclobutene 281
gem-Difluorocyclopropane 285
PPA: Heterolytic Bond Cleavage 288
Mechanical Force for Sampling: Application to Lignin 292
Best Practices for Mechanochemical Simulation 296
Conclusions 298
Acknowledgments 299
References 300
Index 313
