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1. Lattice–Boltzmann Modeling of Multicomponent Systems: An IntroductionUlf D. Schiller and Olga Kuksenok Introduction The Lattice Boltzmann Equation: A Modern Introduction A Brief History of the Lattice Boltzmann Method The Lattice Boltzmann Equation Continuum Kinetic Theory Discrete Velocity Models Space–Time Discretization Common Lattice Boltzman Models Parameter Choice in Lattice Boltzmann Simulations The Fluctuating Lattice Boltzmann Equation Boundary Conditions Fluid–Particle Coupling LBM for Multiphase Fluids Governing Continuum Equations Lattice Boltzmann Algorithm for Binary Fluid: A Free Energy Approach Minimizing Spurious Velocities Conclusions References 2. Mapping Energy Transport Networks in ProteinsDavid M. Leitner and Takahisa Yamato Introduction Thermal and Energy Flow in Macromolecules Normal Modes of Proteins Simulating Energy Transport in Terms of Normal Modes Energy Diffusion in Terms of Normal Modes Energy Transport from Time Correlation Functions Energy Transport in Proteins is Inherently Anisotropic Locating Energy Transport Networks Communication Maps Current calculations for Proteins (CURP) Applications Communication Maps: Illustrative Examples CURP: Illustrative Examples Future Directions Summary Acknowledgements References 3. Uncertainty Quantification for Molecular DynamicsPaul N. Patrone and Andrew Dienstfrey Introduction From Dynamical to Random: Overview of MD System Specification Inter–atomic Potentials Hamilton’s Equations Thermodynamic Ensembles Uncertainty Quantification What is UQ? Tools for Uncertainty Quantification Maximum Likelihood Estimation Spectral Approach to Non–Parametric Inference Uncertainty Propagation UQ of MD Tutorial: Trajectory Analysis Background Tutorial: Ensemble Verification Background and Main Ideas Example: Application to Water Simulations Tutorial: UQ of Data Analysis for the Glass–Transition Temperature Background and Underlying Ideas Simulations and Tg Estimates Within–uncertainty Estimate for Tg Between Uncertainty and Weighted–Mean Averages Concluding Thoughts References 4. The Role of Computations in CatalysisHoria Metiu, Vishal Agarwal, and Henrik H. Kristoffersen Introduction Screening Sabatier Principle Scaling Relations Brønstead–Evans–Polanyi Relationship Volcano Plots Some Rules for Oxide Catalysts Let us Examine Some Industrial Catalysts Sometimes Selectivity is More Important than Rate Sometimes We Want a Smaller Rate! Sometimes Product Separation is More Important than Reaction Rate Some Reactions are Equilibrium–Limited The Cost of Making the Catalyst is Important The Catalyst Should Contain Abundant Elements A Good Catalyst Should Not be Easily Poisoned Summary References 5. The Construction of Ab Initio Based Potential Energy SurfacesRichard Dawes and Ernesto Quintas Sánchez Introduction and Overview What is a PES? Scope of This Review Significance and Range of Applications of PESs Challenges for Theory Terminology and Fundamental Concepts The Schrödinger Equation The Born–Oppenheimer Approximation Mathematical Foundations of (Linear) Fitting Moving Least Squares Fitting IMLS Method L–IMLS Method Quantum Chemistry Methods General Considerations Single Reference Methods Multireference Methods Compound Methods or Protocols Fitting Methods General Considerations and Desirable Attributes of a PES Non–Interpolative Fitting Methods Interpolative Fitting Methods Applications The Automated Construction of PESs Concluding Remarks Acknowledgements List of References 6. Modeling Mechanochemistry from First PrinciplesHeather J. Kulik Introduction and Scope Potential Energy Surfaces and Reaction Coordinates Theoretical Models of Mechanochemical Bond Cleavage Linear Model (Kauzmann, Eyring, and Bell) Tilted Energy Profile Model First–Principles Models for Mechanochemical Bond Cleavage Constrained Geometries Simulate External Force (COGEF) Force–Modified Potential Energy Surfaces Covalent Mechanochemistry Overview of Characterization Methods Representative Mechanophores Representative Mechanochemistry Case Studies Benzylcyclobutene gem–Difluorocyclopropane PPA: Heterolytic Bond Cleavage Mechanical Force for Sampling: Application to Lignin Best Practices for Mechanochemical Simulation Conclusions Acknowledgments References Bibliography Subject Index