| Computations in Treating Fullerenes and Carbon Aggregates / Christian Ochsenfeld ; Patrice Koehl1： |
| Peptide Mimetic Design with the Aid of Computational Chemistry |
| Pseudopotential Calculations of Transitions Metals Compounds-Scope and Limitation / R. Judson ; M. Murcko ; M. Francl ; Geoff M. Downs |
| Free Energy by Molecular Simulation |
| Effective Core Potential Approaches to the Chemistry of the Heavier Elements / Sason Shaik ; Roberto Dovesi ; Jorg Kussmann |
| The Application of Molecular Modeling Techniques to the Determination of Oligosaccaride Solution Conformations |
| Genetic Algorithms and Their Use in Chemistry |
| Recent Advances in Ligand Design Methods |
| Protein Structure Classification / L. Chirlian ; John M. Barnard |
| Relativistic Effects in Chemistry |
| Molecular Mechanics Calculated Conformational Energies of Organic Molecules |
| The Ab Initio Computation of Nuclear Magnetic Resonance Chemical Shielding / E. Martin, et al. ; D. Clark, et al. ; Philippe C. Hiberty ; Bartolomeo Civalleri ; Daniel S. Lambrecht |
| A Comparison of Force Fields |
| The Pluses and Minuses of Mapping Atomic Charges to Electrostatic Potentials |
| Clustering Methods and Their Uses in Computational Chemistry |
| Introduction |
| Indexes |
| Molecular Shape Descriptors |
| Does Combinatorial Chemistry Obviate Computer-Aided Drug Design? |
| Current Issues in De Novo Molecular Design |
| Valence Bond Theory, Its History, Fundamentals, and Applications: A Primer / T. Crawford ; Hans-Joachim Bouml;hm |
| Classification and Biology / Roberto Orlando |
| The Biomolecular Revolution / R. Topper ; T. Oprea |
| Linear-Scaling Methods in Quantum Chemistry |
| A Story of Valence Bond Theory, Its Rivalry with Molecular Orbital Theory, Its Demise, and Eventual Resurgence / H. Schaefer ; Martin Stahl |
| Basic Principles of Protein Structure / Carla Roetti |
| Visualizing Molecular Phase Space: Nonstatistical Effects in Reaction Dynamics |
| Roots of VB Theory / C. Waller |
| Visualization |
| An Introduction to Coupled Cluster Theory for Computational Chemists / R. Larter |
| The Use of Scoring Functions in Drug Discovery Applications |
| Origins of MO Theory and the Roots of VB-MO Rivalry |
| Protein Building Blocks / Victor R. Saunders |
| Theoretical and Practical Aspects of Three-Dimensional Quantitative Structure-Activity Relationships |
| The ''Dance'' of Two Theories: One Is Up, the Other Is Down / B. van de Graaf, et al. ; Steven W. Rick |
| Protein Structure Hierarchy |
| Some Basics of SCF Theory |
| Are the Failures of VB Theory Real Ones? / K. Showalter ; G. Greco, et al. |
| Ab Initio Quantum Simulation in Solid State Chemistry 1 |
| Three Types of Proteins |
| Introduction to Zeolite Modeling |
| Modern VB Theory: VB Theory Is Coming of Age / Steven J. Stuart |
| Geometry of Globular Proteins / 2： |
| Direct SCF Methods and Two-Electron Integral Screening |
| Computational Studies in Nonlinear Dynamics |
| Approaches to Three-Dimensional Quantitative Structure-Activity Relationships |
| Basic VB Theory / S. Price |
| Protein Domains / Patrick Bultinck |
| Potentials and Algorithms for Incorporating Polarizability in Computer Simulations / S. Smith ; P. Carrupt, et al. |
| Writing and Representing VB Wave Functions |
| Resources on Protein Structures |
| Schwarz Integral Estimates |
| Towards More Accurate Model Intermolecular Potentials for Organic Molecules |
| The Relationship between MO and VB Wave Functions / Dmitry V. Matyushov |
| Protein Structure Comparison / Xavier Girones |
| Computational Approaches to Lipophilicity: Methods and Applications / B. Sutcliffe |
| Formalism Using the Exact Hamiltonian / C. Mundy, et al. |
| Automatic Identification of Protein Structural Domains |
| Multipole-Based Integral Estimates (MBIE) |
| Qualitative VB Theory / G. Ravishanker, et al. ; Gregory A. Voth |
| The Rigid-Body Transformation Problem / Ramon Carbo-Dorca |
| The Development of Computational Chemistry in the United Kingdom |
| Nonequilibrium Molecular Dynamics |
| Some Simple Formulas for Elementary Interactions |
| Protein Structure Superposition |
| Calculation of Integrals via Multipole Expansion |
| Treatment of Counterions in Computer Simulations of DNA |
| New Developments in the Theoretical Description of Charge-Transfer Reactions in Condensed Phases / D. Boyd |
| Insights of Qualitative VB Theory |
| Molecular Quantum Similarity: Theory and Applications |
| cRMS: An Ambiguous Measure of Similarity |
| Appendix |
| Are the ''Failures'' of VB Theory Real? / George R. Famini |
| Differential Geometry and Protein Structure Comparison / 3： |
| A First Example |
| Can VB Theory Bring New Insight into Chemical Bonding? / K. Lipkowitz |
| Upcoming Challenges for Protein Structure Comparison / Jean-Loup Faulon |
| VB Diagrams for Chemical Reactivity / Leland Y. Wilson |
| Derivation of the Multipole Expansion |
| History of the Gordon Research Conferences on Computational Chemistry |
| VBSCD: A General Model for Electronic Delocalization and Its Comparison with the Pseudo-Jahn-Teller Model |
| The Structure Classification of Proteins (SCOP) / Donald P. Visco, Jr. |
| Linear Free Energy Relationships Using Quantum Mechanical Descriptors |
| What Is the Driving Force, s or p, Responsible for the D6h Geometry of Benzene? |
| The CATH Classification |
| The Fast Multipole Method: Breaking the Quadratic Wall |
| VBSCD: The Twin-State Concept and Its Link to Photochemical Reactivity / Sigrid D. Peyerimhoff |
| The DALI Domain Dictionary (DDD) / Diana Roe |
| The Spin Hamiltonian VB Theory |
| Comparing SCOP, CATH, and DDD |
| Fast Multipole Methods for Continuous Charge Distributions |
| The Development of Computational Chemistry in Germany |
| Theory |
| Enumerating Molecules |
| Conclusions |
| Applications |
| Acknowledgments / 4： |
| Other Approaches |
| Ab Initio VB Methods / Donald B. Boyd |
| Orbital-Optimized Single-Configuration Methods / David J. Livingstone |
| References |
| Exchange-Type Contractions |
| Orbital-Optimized Multiconfiguration VB Methods / Kenny B. Lipkowitz |
| Prospective / David W. Salt |
| The Exchange-Correlation Matrix of KS-DFT / Emilio Xavier Esposito |
| Examination of the Employment Environment for Computational Chemistry |
| Variable Selection-Spoilt for Choice? |
| Author Index |
| Avoiding the Diagonalization Step-Density Matrix-Based SCF / Dror TobiA.1： |
| Subject Index |
| Expansion of MO Determinants in Terms of AO Determinants |
| General Remarks / Nathan A. Baker ; Jeffry D. MaduraA.2： |
| Guidelines for VB Mixing |
| Biomolecular Applications of Poisson-Boltzmann Methods |
| Comparative Protein Modeling / A.3： |
| Tensor Formalism |
| Computing Mono-Determinantal VB Wave Functions with Standard Ab Initio Programs |
| Anatomy of a Comparative Model / Baltazar D. Aguda |
| Properties of the One-Particle Density Matrix |
| Searching for Related Sequences and Structures / Georghe CraciunStep 1： |
| Density Matrix-Based Energy Functional |
| Expert Protein Analysis System (ExPASy) / Nikita Matsunaga ; Rengul Cetin-Atalay |
| BLAST and PSI-BLAST |
| "Curvy Steps" in Energy Minimization |
| Data Sources and Computational Approaches for Generating Models of Gene Regulatory Networks / Shiro Koseki |
| Protein Data Bank (PDB) |
| Sequence Alignment and Modeling System with Hidden Markov Models |
| Density Matrix-Based Quadratically Convergent SCF (D-QCSCF) |
| Modeling of Spin-Forbidden Reactions |
| Index Subject |
| Threading |
| Overview of Reactions Requiring Two States |
| Threader |
| Implications for Linear-Scaling Calculation of SCF Energies |
| Spin-Forbidden Reaction, Intersystem Crossing |
| Example: Finding Related Sequences and 3-D Structures |
| Spin-Orbit Coupling as a Mechanism for Spin-Forbidden Reaction |
| SCF Energy Gradients / Step 2： |
| General Considerations |
| Sequence Alignment |
| Atomic Spin-Orbit Coupling |
| Preparing the Sequences |
| Molecular Response Properties at the SCF Level |
| Molecular Spin-Orbit Coupling |
| Alignment Basics |
| Crossing Probability |
| Similarity Matrices |
| Vibrational Frequencies |
| Fermi Golden Rule |
| Clustal |
| Landau-Zener Semiclassical Approximation |
| Tree-Based Consistency Objective Function for Alignment Evaluation (T-Coffee) |
| NMR Chemical Shieldings |
| Methodologies for Obtaining Spin-Orbit Matrix Elements |
| Divide-and-Conquer Alignment (DCA) |
| Electron Spin in Nonrelativistic Quantum Mechanics |
| Example: Aligning Sequences |
| Density Matrix-Based Coupled Perturbed SCF (D-CPSCF) |
| Klein-Gordon Equation |
| Dirac Equation / Step 3： |
| Selecting Templates and Improving Alignments |
| Outlook on Electron Correlation Methods for Large Systems |
| Foldy-Wouthuysen Transformation |
| Selecting Templates |
| Breit-Pauli Hamiltonian |
| Improving Sequence Alignments With Primary and Secondary Structure Analysis |
| Long-Range Behavior of Correlation Effects |
| Z eff Method |
| Example: Aligning the Target to the Selected Template |
| Effective Core Potential-Based Method |
| Rigorous Selection of Transformed Products via Multipole-Based Integral Estimates (MBIE) / Step 4： |
| Model Core Potential-Based Method |
| Constructing Protein Models |
| Douglas-Kroll Transformation |
| Satisfaction of Spatial Restraints |
| Implications |
| Potential Energy Surfaces |
| Segment Match Modeling |
| Minimum Energy Crossing-Point Location |
| Multiple Template Method |
| Available Programs for Modeling Spin-Forbidden Reactions |
| 3D-Jigsaw |
| Applications to Spin-Forbidden Reactions |
| Overall Protein Model Construction Methods |
| Diatomic Molecules |
| Example: Constructing a Protein Model |
| Polyatomic Molecules |
| Phenyl Cation / Spiridoula MatsikaStep 5： |
| Refinement of Protein Models |
| Norborene |
| Side-Chains with Rotamer Library (SCWRL) |
| Conjugated Polymers |
| Energy Minimization |
| Conical Intersections in Molecular Systems |
| CH( 2 II) + N2 -- HCN + N( 4 S) |
| Molecular Dynamics |
| Blast and PSI-Blast |
| Molecular Properties |
| Molecular Dynamics with Simulated Annealing |
| Dynamical Aspects |
| Other Reactions / Step 6： |
| Evaluating Protein Models |
| General Theory |
| Biological Chemistry |
| Procheck |
| Concluding Remarks |
| Verify3D |
| The Born-Oppenhemier Approximation and its Breakdown: Nonadiabatic Processes |
| Errat |
| Protein Structure Analysis (ProSa) |
| Adiabatic-Diabatic Representation |
| Protein Volume Evaluation (PROVE) |
| Model Clustering Analysis / Stefan Grimme |
| The Noncrossing Rule |
| Example: Evaluation of Protein Models |
| Calculation of the Electronic Spectra of Large Molecules |
| The Geometric Phase Effect |
| Types of Electronic Spectra |
| Conical Intersections and Symmetry |
| Types of Excited States |
| The Branching Plane / Joan-Emma Shea |
| Excitation Energies |
| Transition Moments / Miriam R. Friedel |
| Characterizing Conical Intersections: Topography |
| Vibrational Structure |
| Quantum Chemical Methods / Andrij Baumketner |
| Derivative Coupling |
| Case Studies |
| Simulations of Protein Folding |
| Vertical Absorption Spectra |
| Electronic Structure Methods for Excited States |
| Circular Dichroism |
| Theoretical Framework |
| Energy Landscape Theory |
| Multiconfiguration Self-Consistent Field (MCSCF) |
| Summary and Outlook |
| Thermodynamics and Kinetics of Folding: Two-State and Multistate Folders |
| Protein Models |
| Multireference Configuration Interaction (MRCI) |
| Introduction and General Simulation Techniques |
| Coarse-Grained Protein Models |
| Complete Active Space Second-Order Perturbation Theory (CASPT2) |
| Fully Atomic Simulations / Raymond Kapral |
| Advanced Topics: The Transition State Ensemble for Folding |
| Single Reference Methods |
| Simulating Chemical Waves and Patterns |
| Transition State and Two-State Kinetics |
| Methods for Identifying the TSE |
| Choosing Electronic Structure Methods for Conical Intersections |
| Reaction-Diffusion Systems |
| Conclusions and Future Directions |
| Cellular Automata |
| Locating Conical Intersections |
| Coupled Map Lattices |
| Mesoscopic Models |
| Dynamics |
| Summary |
| Conical Intersections in Biologically Relevant Systems / Marco Saraniti ; Shela Aboud ; Costel Sa?rbu |
| Beyond the Double Cone / Robert Eisenberg ; Horia F. Pop |
| The Simulation of Ionic Charge Transport in Biological Ion Channels: An Introduction to Numerical Methods |
| Fuzzy Soft-Computing Methods and Their Applicationsin Chemistry |
| Three-State Conical Intersections |
| System Components |
| Methods for Exploratory Data Analysis |
| Time and Space Scale |
| Spin-Orbit Coupling and Conical Intersections |
| Visualization of High-Dimensional Data |
| Experiments |
| Clustering Methods |
| Electrostatics |
| Projection |
| Long-Range Interaction |
| Short-Range Interaction |
| Boundary Conditions |
| Particle-Based Simulation |
| Implicit Solvent: Brownian Dynamics |
| Explicit Solvent: Molecular Dynamics |
| Flux-Based Simulation / Antonio Fernandez-Ramos |
| Nernst-Planck Eq" |
| Variational Transition State Theory with Multidimensional Tunneling / Benjamin A. Ellingson ; Bruce C. Garrett ; Donald G. Truhlar |
| Variational Transition State Theory for Gas-Phase Reactions |
| Conventional Transition State Theory |
| Canonical Variational Transition State Theory |
| Other Variational Transition State Theories |
| Quantum Effects on the Reaction Coordinate |
| Practical Methods for Quantized VTST Calculations |
| The Reaction Path |
| Evaluation of Partition Functions |
| Harmonic and Anharmonic Vibrational Energy Levels |
| Calculations of Generalized Transition State Number of States |
| Quantum Effects on Reaction Coordinate Motion |
| Multidimensional Tunneling Corrections Based on the Adiabatic Approximation |
| Large Curvature Transmission Coefficient |
| The Microcanonically Optimized Transmission Coefficient |
| Building the PES from Electronic Structure Calculation |
| Direct Dynamics with Specific Reaction Parameters |
| Interpolated VTST |
| Dual-Level Dynamics |
| Reactions in Liquids |
| Ensemble-Averaged Variational Transition State Theory |
| Gas-Phase Example: H + CH[subscript 4] |
| Liquid-Phase Example: Menshutkin Reaction |
| Coarse-Grain Modeling of Polymers / Roland Faller |
| Defining the System |
| Choice of Model |
| Interaction Sites on the Coarse-Grained Scale |
| Static Mapping |
| Single-Chain Distribution Potentials |
| Simplex |
| Iterative Structural Coarse-Graining |
| Mapping Onto Simple Models |
| Dynamic Mapping |
| Mapping by Chain Diffusion |
| Mapping through Local Correlation Times |
| Direct Mapping of the Lennard-Jones Time |
| Coarse-Grained Monte Carlo Simulations |
| Reverse Mapping |
| A Look Beyond Polymers |
| Nernst-Planck Equation |
| The Poisson-Nernst-Planck (NP) Method |
| Hierarchical Simulation Schemes / Jeffrey W. Godden |
| Future Directions and Concluding Remarks / Jurgen Bajorath |
| Analysis of Chemical Information Content Using Shannon Entropy |
| Shannon Entropy Concept / C. Matthew Sundling ; Nagamani Sukumar |
| Descriptor Comparison / Hongmei Zhang |
| Influence of Boundary Effects / Mark J. Embrechts |
| Extension or SE Analysis for Profiling of Chemical Libraries / Curt M. Breneman |
| Information Content of Organic Molecules |
| Wavelets in Chemistry and Chemoinformatics |
| Shannon Entropy in Quantum Mechanics, Molecular Dynamics, and Modeling |
| Preface |
| Examples of SE and DSE Analysis |
| Introduction to Wavelets |
| Fourier Transform |
| Continuous Fourier Transform |
| Short-Time Fourier Transformation / Ovidiu Ivanciuc |
| Wavelet Transform |
| Applications of Support Vector Machines in Chemistry |
| Continuous Wavelet Transform |
| Discrete Wavelet Transform |
| A Nonmathematical Introduction to SVM |
| Wavelet Packet Transform |
| Pattern Classification |
| Wavelets vs. Fourier Transforms: A Summary |
| The Vapnik-Chervonenkis Dimension |
| Application of Wavelets in Chemistry |
| Pattern Classification with Linear Support Vector Machines |
| Smoothing and Denoising |
| SVM Classification for Linearly Separable Data |
| Signal Feature Isolation |
| Linear SVM for the Classification of Linearly Non-Separable Data |
| Signal Compression |
| Nonlinear Support Vector Machines |
| Quantum Chemistry |
| Mapping Patterns to a Feature Space |
| Classification, Regression, and QSAR/QSPR |
| Feature Functions and Kernels |
| Kernel Functions for SVM |
| Hard Margin Nonlinear SVM Classification |
| Soft Margin Nonlinear SVM Classification |
| v-SVM Classification |
| Weighted SVM for Imbalanced Classification |
| Multi-class SVM Classification |
| SVM Regression |
| Optimizing the SVM Model |
| Descriptor Selection |
| Support Vectors Selection |
| Jury SVM |
| Kernels for Biosequences |
| Kernels for Molecular Structures |
| Practical Aspects of SVM Classification |
| Predicting the Mechanism of Action for Polar and Nonpolar Narcotic Compounds |
| Predicting the Mechanism of Action for Narcotic and Reactive Compounds |
| Predicting the Mechanism of Action from Hydrophobicity and Experimental Toxicity |
| Classifying the Carcinogenic Activity of Polycyclic Aromatic Hydrocarbons |
| Structure-Odor Relationships for Pyrazines |
| Practical Aspects of SVM Regression |
| SVM Regression QSAR for the Phenol Toxicity to Tetrahymena pyriformis |
| SVM Regression QSAR for Benzodiazepine Receptor Ligands |
| SVM Regression QSAR for the Toxicity of Aromatic Compounds to Chlorella vulgaris |
| SVM Regression QSAR for Bioconcentration Factors |
| Review of SVM Applications in Chemistry |
| Recognition of Chemical Classes and Drug Design |
| QSAR |
| Genotoxicity of Chemical Compounds |
| Chemometrics |
| Sensors |
| Chemical Engineering |
| Text Mining for Scientific Information |
| SVM Resources on the Web |
| SVM Software |
| How Computational Chemistry Became Important in the Pharmaceutical Industry / 7： |
| Germination: The 1960s |
| Gaining a Foothold: The 1970s |
| Growth: The 1980s |
| Gems Discovered: The 1990s |
| Final Observations |
| Determining the Glass Transition in Polymer Melts / Wolfgang Paul |
| Phenomenology of the Glass Transition |
| Model Building |
| Chemically Realistic Modeling |
| Coarse-Grained Models |
| Coarse-Grained Models of the Bead-Spring Type |
| The Bond-Fluctuation Lattice Model |
| Simulation Methods |
| Monte Carlo Methods |
| Molecular Dynamics Method |
| Thermodynamic Properties |
| Dynamics in Super-Cooled Polymer Melts |
| Dynamics in the Bead-Spring Model |
| Dynamics in 1,4-Polybutadiene |
| Dynamic Heterogeneity |
| Atomistic Modeling of Friction / Nicholas J. Mosey ; Martin H. Muser |
| Theoretical Background |
| Friction Mechanisms |
| Load-Dependence of Friction |
| Velocity-Dependence of Friction |
| Role of Interfacial Symmetry |
| Computational Aspects |
| Surface Roughness |
| Imposing Load and Shear |
| Imposing Constant Temperature |
| Bulk Systems |
| Computational Models |
| Selected Case Studies |
| Instabilities, Hysteresis, and Energy Dissipation |
| The Role of Atomic-Scale Roughness |
| Superlubricity |
| Self-Assembled Monolayers |
| Tribochemistry |
| Computing Free Volume, Structural Order, and Entropy of Liquids and Glasses / Jeetain Mittal ; William P. Krekelberg ; Jeffrey R. Errington ; Thomas M. Truskett |
| Metrics for Structural Order |
| Crystal-Independent Structural Order Metrics |
| Structural Ordering Maps |
| Free Volume |
| Identifying Cavities and Computing Their Volumes |
| Computing Free Volumes |
| Computing Thermodynamics from Free Volumes |
| Relating Dynamics to Free Volumes |
| Entropy |
| Testing the Adam-Gibbs Relationship |
| An Alternative to Adam-Gibbs? |
| The Reactivity of Energetic Materials at Extreme Conditions / Laurence E. Fried |
| Chemical Equilibrium |
| Atomistic Modeling of Condensed-Phase Reactions |
| First Principles Simulations of High Explosives |
| Magnetic Properties of Atomic Clusters of the Transition Elements / Julio A. Alonso |
| Basic Concepts |
| Experimental Studies of the Dependence of the Magnetic Moments with Cluster Size |
| Simple Explanation of the Decay of the Magnetic Moments with Cluster Size |
| Tight Binding Method |
| Tight Binding Approximation for the d Electrons |
| Introduction of s and p Electrons |
| Formulation of the Tight Binding Method in the Notation of Second Quantization |
| Spin-Density Functional Theory |
| General Density Functional Theory |
| Spin Polarization in Density Functional Theory |
| Local Spin-Density Approximation (LSDA) |
| Noncollinear Spin Density Functional Theory |
| Measurement and Interpretation of the Magnetic Moments of Nickel Clusters |
| Interpretation Using Tight Binding Calculations |
| Influence of the s Electrons |
| Density Functional Calculations for Small Nickel Clusters |
| Orbital Polarization |
| Clusters of Other 3d Elements |
| Chromium and Iron Clusters |
| Manganese Clusters |
| Clusters of the 4d Elements |
| Rhodium Clusters |
| Ruthenium and Palladium Clusters |
| Effect of Adsorbed Molecules |
| Determination of Magnetic Moments by Combining Theory and Photodetachment Spectroscopy |
| Summary and Prospects |
| Calculation of the Density of Electronic States within the Tight Binding Theory by the Method of Moments / Appendix： |
| Transition Metal- and Actinide-Containing Systems Studied with Multiconfigurational Quantum Chemical Methods / Laura Gagliardi |
| The Multiconfigurational Approach |
| The Complete Active Space SCF Method |
| Multiconfigurational Second-Order Perturbation Theory, CASPT2 |
| Treatment of Relativity |
| Relativistic AO Basis Sets |
| The Multiple Metal-Metal Bond in [Characters not reproducible] and Related Systems |
| The Cr-Cr Multiple Bond |
| Cu[subscript 2]O[subscript 2] Theoretical Models |
| Spectroscopy of Triatomic Molecules Containing One Uranium Atom |
| Actinide Chemistry in Solution |
| The Actinide-Actinide Chemical Bond |
| Inorganic Chemistry of Diuranium |
| Recursive Solutions to Large Eigenproblems in Molecular Spectroscopy and Reaction Dynamics / Hua Guo |
| Quantum Mechanics and Eigenproblems |
| Discretization |
| Direct Diagonalization |
| Scaling Laws and Motivation for Recursive Diagonalization |
| Recursion and the Krylov Subspace |
| Lanczos Recursion |
| Exact Arithmetic |
| Finite-Precision Arithmetic |
| Extensions of the Original Lanczos Algorithm |
| Transition Amplitudes |
| Expectation Values |
| Chebyshev Recursion |
| Chebyshev Operator and Cosine Propagator |
| Spectral Method |
| Filter-Diagonalization |
| Filter-Diagonalization Based on Chebyshev Recursion |
| Low-Storage Filter-Diagonalization |
| Filter-Diagonalization Based on Lanczos Recursion |
| Bound States and Spectroscopy |
| Reaction Dynamics |
| Lanczos vs. Chebyshev |
| Development and Uses of Artificial Intelligence in Chemistry / Hugh Cartwright8： |
| Evolutionary Algorithms |
| Principles of Genetic Algorithms |
| Genetic Algorithm Implementation |
| Why Does the Genetic Algorithm Work? |
| Where Is the Learning in the Genetic Algorithm? |
| What Can the Genetic Algorithm Do? |
| What Can Go Wrong with the Genetic Algorithm? |
| Neural Networks |
| Neural Network Principles |
| Neural Network Implementation |
| Why Does the Neural Network Work? |
| What Can We Do with Neural Networks? |
| What Can Go Wrong? |
| Self-Organizing Maps |
| Where Is The Learning? |
| Some Applications of SOMs |
| Expert Systems |
| Conclusion |
| Computer-Aided Molecular Diversity Analysis and Combinatorial Library Design / Richard A. Lewis ; Stephen D. Pickett ; David E. Clark1.： |
| Molecular Recognition: Similarity and Diversity |
| Describing Diversity Space |
| Types of Descriptor |
| Choosing Appropriate Descriptors |
| Validation of Descriptors |
| Diversity Analysis |
| Combinatorial Library Design |
| Diversity Is Not the Be-All and End-All! |
| Current Issues and Future Directions |
| Diversity Descriptors |
| Library Design |
| Speed Requirement |
| "Quick and Dirty" QSAR |
| Integration with Other Modeling Tools |
| Persuading the Customers |
| Artificial Neural Networks and Their Use in Chemistry / Keith L. Peterson2.： |
| Overview and Goals |
| What Are Artificial Neural Networks? |
| Analogy with the Brain |
| Artificial Neural Networks |
| Summary of Neural Network Operation |
| Brief History of Neural Networks |
| What Can Neural Networks Be Used for and When Should You Use Them? |
| Classification |
| Modeling |
| Mapping and Associations |
| General Comments on ANNs, Statistics, and Artificial Intelligence |
| Processing Elements |
| Summation Functions |
| Transfer Functions |
| Output Functions |
| Error Functions |
| Learning Rules |
| Collections of Processing Elements |
| Different Types of Artificial Neural Network |
| Adaptive Resonance Theory (ART) Networks |
| Backpropagation (BP) and Related Networks |
| Biassociative Memory (BAM) Networks |
| Counterpropagation Networks |
| Generalized Regression Networks (GRN) |
| Hopfield Networks |
| Kohonen Self-Organizing Map (SOM) Networks |
| Perceptron Networks |
| Radial Basis Function (RBF) Networks |
| Recirculation Networks |
| Miscellaneous Networks |
| Practical Considerations in Solving Problems with Neural Networks |
| What Type of Network? |
| Data Preprocessing |
| Variable Selection, Reduction, and Orthogonalization |
| Training and Testing Sets |
| Training the Network |
| Learning Versus Generalization |
| Performance Metrics |
| Classification Problems |
| Nonclassification, Supervised Learning Problems |
| Miscellaneous Remarks |
| Analysis of Neural Networks |
| Neural Network Software |
| Use of Force Fields in Materials Modeling / Jorg-Rudiger Hill ; Clive M. Freeman ; Lalitha Subramanian3.： |
| The Force Field Approach to Describing Structures of Materials |
| What Are Force Fields? |
| Ion Pair and Shell Model Potentials |
| Molecular Mechanics Force Fields |
| Comparison of Ion Pair and Molecular Mechanics Force Fields |
| Force Field Parameterization |
| Ab Initio Based Force Fields |
| Empirical Force Fields |
| Transferability |
| Rule-Based Force Fields |
| Application of Force Fields in Materials Science |
| Metal Oxides and Ceramics |
| Superconductors |
| Zeolites and Related Microporous Materials |
| Glasses |
| Polymers |
| Free Energy Calculations: Use and Limitations in Predicting Ligand Binding Affinities / M. Rami Reddy ; Mark D. Erion ; Atul Agarwal4.： |
| Methodology Overvie |
| Computational Details |
| Treatment of Long-Range Forces |
| Polarization |
| Bond Length Constraints |
| Treatment of Boundaries |
| Solvent Models |
| Convergence of Free Energy Results |
| Free Energy Perturbation Calculations for Small Molecules |
| Tautomerization |
| Ionization |
| Log P |
| Covalent Hydration |
| Solvation |
| Free Energy Perturbation Calculations for Macromolecules |
| Nonprotein-Ligand Complexes |
| Protease Inhibitors |
| Lyases |
| Oxidases and Reductases |
| Allosteric Binding Site Ligands |
| DNA Binding Proteins |
| Miscellaneous Studies |
| Guide to Structure-Based Ligand Optimization |
| Computer Model |
| Characterization of the Binding Site |
| Lead Generation |
| Optimization of Lead Compounds |
| Optimization of Ligands to HIV-1 Protease: Using the FEP Method |
| Design Considerations |
| X-Ray Structures of HIV-1 Protease Complexes |
| Force Field Parameters |
| Computational Details for Solvent |
| Computational Details for Complex |
| Computer Model Validation |
| Validation of FEP Methodology |
| Convergence and Error Analysis |
| Binding Affinity Predictions |
| Advantages of Free Energy Calculations |
| Limitations of Free Energy Calculations |
| Brief Guide for Free Energy Calculations and Their Use in Ligand Optimization |
| Small Molecule Docking and Scoring / Ingo Muegge ; Matthias Rarey |
| Algorithms for Molecular Docking |
| The Docking Problem |
| Placing Fragments and Rigid Molecules |
| Flexible Ligand Docking |
| Handling Protein Flexibility |
| Docking of Combinatorial Libraries |
| Scoring |
| Shape and Chemical Complementary Scores |
| Force Field Scoring |
| Empirical Scoring Functions |
| Knowledge-Based Scoring Functions |
| Comparing Scoring Functions in Docking Experiments: Consensus Scoring |
| From Molecular Docking to Virtual Screening |
| Protein Data Preparation |
| Ligand Database Preparation |
| Docking Calculation |
| Postprocessing |
| Docking as a Virtual Screening Tool |
| Docking as a Ligand Design Tool |
| Protein-Protein Docking / Lutz P. Ehrlich ; Rebecca C. Wade |
| Why This Topic? |
| Protein-Protein Binding Data |
| Challenges for Computational Docking Studies |
| Computational Approaches to the Docking Problem |
| Docking = Sampling + Scoring |
| Rigid-Body Docking |
| Flexible Docking |
| Example |
| Estimating the Extent of Conformational Change upon Binding |
| Flexible Docking with Side-Chain Flexibility |
| Flexible Docking with Full Flexibility |
| Future Directions |
| Spin-Orbit Coupling in Molecules / Christel M. Marian |
| What It Is All About |
| The Fourth Electronic Degree of Freedom |
| The Stern-Gerlach Experiment |
| Zeeman Spectroscopy |
| Spin Is a Quantum Effect |
| Angular Momenta |
| Orbital Angular Momentum |
| General Angular Momenta |
| Spin Angular Momentum |
| Spin-Orbit Hamiltonians |
| Full One- and Two-Electron Spin-Orbit Operators |
| Valence-Only Spin-Orbit Hamiltonians |
| Effective One-Electron Spin-Orbit Hamiltonians |
| Symmetry |
| Transformation Properties of the Wave Function |
| Transformation Properties of the Hamiltonian |
| Matrix Elements |
| Examples |
| Evaluation of Spin-Orbit Integrals |
| Perturbational Approaches to Spin-Orbit Coupling |
| Variational Procedures |
| Comparison of Fine-Structure Splittings with Experiment |
| First-Order Spin--Orbit Splitting |
| Second-Order Spin--Orbit Splitting |
| Spin-Forbidden Transitions |
| Radiative Transitions |
| Nonradiative Transitions |
| Cellular Automata Models of Aqueous Solution Systems / Lemont B. Kier ; Chao-Kun Cheng ; Paul G. Seybold |
| Historical Background |
| The General Structure |
| Cell Movement |
| Movement (Transition) Rules |
| Collection of Data |
| Aqueous Solution Systems |
| Water as a System |
| The Molecular Model |
| Significance of the Rules |
| Studies of Water and Solution Phenomena |
| A Cellular Automata Model of Water |
| The Hydrophobic Effect |
| Solute Dissolution |
| Aqueous Diffusion |
| Immiscible Liquids and Partitioning |
| Micelle Formation |
| Membrane Permeability |
| Acid Dissociation |
| Percolation |
| Solution Kinetic Models |
| First-Order Kinetics |
| Kinetic and Thermodynamic Reaction Control |
| Excited-State Kinetics |
| Second-Order Kinetics |
| Enzyme Reactions |
| An Anticipatory Model |
| Chromatographic Separation |
| Books Published on the Topics of Computational Chemistry |
| Computers in Chemistry |
| Chemical Information |
| Computational Chemistry |
| Artificial Intelligence and Chemometrics |
| Crystallography, Spectroscopy, and Thermochemistry |
| Fundamentals of Quantum Theory |
| Applied Quantum Chemistry |
| Crystals, Polymers, and Materials |
| Selected Series and Proceedings from Long-Running Conferences |
| Molecular Modeling |
| Molecular Simulation |
| Molecular Design and Quantitative Structure-Activity Relationships |
| Graph Theory in Chemistry |
| Trends |
| Clustering Algorithms |
| Hierarchical Methods |
| Nonhierarchical Methods |
| Progress in Clustering Methodology |
| Algorithm Developments |
| Comparative Studies on Chemical Data Sets |
| How Many Clusters? |
| Chemical Applications |
| The use of Scoring Functions in Drug Discovery Applications / Hans-Joachim Bohm |
| The Process of Virtual Screening |
| Major Contributions to Protein--Ligand Interactions |
| Description of Scoring Functions for Receptor--Ligand Interactions |
| Force Field-Based Methods |
| Knowledge-Based Methods |
| Critical Assessment of Current Scoring Functions |
| Influence of the Training Data |
| Molecular Size |
| Other Penalty Terms |
| Specific Attractive Interactions |
| Water Structure and Protonation State |
| Performance in Structure Prediction |
| Rank Ordering Sets of Related Ligands |
| Application of Scoring Functions in Virtual Screening |
| Seeding Experiments |
| Hydrogen Bonding versus Hydrophobic Interactions |
| Finding Weak Inhibitors |
| Consensus Scoring |
| Successful Identification of Novel Leads through Virtual Screening |
| Outlook |
| Nonpolarizable Models |
| Polarizable Point Dipoles |
| Shell Models |
| Electronegativity Equalization Models |
| Semiempirical Models |
| Water |
| Proteins and Nucleic Acids |
| Comparison of the Polarization Models |
| Mechanical Polarization |
| Computational Efficiency |
| Hyperpolarizability |
| Charge-Transfer Effects |
| The Electrostatic Potential |
| Summary and Conclusions |
| Paradigm of Free Energy Surfaces |
| Formulation |
| Two-State Model |
| Heterogeneous Discharge |
| Beyond the Parabolas |
| Bilinear Coupling Model |
| Electron Transfer in Polarizable Donor--Acceptor Complexes |
| Nonlinear Solvation Effects |
| Electron-Delocalization Effects |
| Nonlinear Solvation versus Intramolecular Effects |
| Optical Band Shape |
| Optical Franck--Condon Factors |
| Absorption Intensity and Radiative Rates |
| Electron-Transfer Matrix Element |
| Electronically Delocalized Chromophores |
| Polarizable Chromophores |
| Hybrid Model |
| LFER Methodology / 5.： |
| Background |
| Computational Methods |
| Linear Free Energy Relationships |
| Descriptors |
| Classifications |
| Quantum Mechanical Descriptors |
| Quantum Mechanical Calculations |
| Statistical Procedures |
| Multiple Regression Analysis |
| Examples of LFER Equations |
| Model-Based Methods |
| Nonmodel-Based Methods |
| Computer Development / 6.： |
| The ZUSE Computers |
| The G1, G2, and G3 of Billing in Gottingen |
| Computer Development at Universities |
| The Analog Computer in Chemistry |
| Quantum Chemistry, A New Start |
| Theoretical Chemistry 1960-1970 |
| The Deutsche Rechenzentrum at Darmstadt |
| Formation of Theoretical Chemistry Groups |
| Deutsche Forschungsgemeinschaft--Schwerpunktprogramm Theoretische Chemie |
| Theoretical Chemistry Symposia |
| Scientific Developments |
| Computational Chemistry 1970-1980 |
| European Efforts |
| Computer-Aided Synthesis |
| Progress in Quantum Chemical Methods |
| Beyond 1980 |
| Hiring Trends / Appendix.： |
| Skills in Demand |
| The Broader Context |
| Salaries |
| Computations of Noncovalent ? Interactions / C. David Sherrill |
| Challenges for Computing ? Interactions |
| Electron Correlation Problem |
| Basis Set Problem |
| Basis Set Superposition Errors and the Counterpoise Correction |
| Additive Basis/Correlation Approximations |
| Reducing Computational Cost |
| Truncated Basis Sets |
| Pauling Points |
| Resolution of the Identity and Local Correlation Approximations |
| Spin-Component-Scaled MP2 |
| Explicitly Correlated R12 and F12 Methods |
| Density Functional Approaches |
| Semiempirical Methods and Molecular Mechanics |
| Analysis Using Symmetry-Adapted Perturbation Theory |
| Appendix: Extracting Energy Components from the SAPT2006 Program |
| Reliable Electronic Structure Computations for Weak Noncovalent Interactions in Clusters / Gregory S. Tschumper |
| Introduction and Scope |
| Clusters and Weak Noncovalent Interactions |
| Weak Noncovalent Interactions |
| Historical Perspective |
| Some Notes about Terminology |
| Fundamental Concepts: A Tutorial |
| Model Systems and Theoretical Methods |
| Rigid Monomer Approximation |
| Supermolecular Dissociation and Interaction Energies |
| Counterpoise Corrections for Basis Set Superposition Error |
| Two-Body Approximation and Cooperative/Nonadditive Effects |
| Size Consistency and Extensivity of the Energy |
| Summary of Steps in Tutorial |
| High-Accuracy Computational Strategies |
| Primer on Electron Correlation |
| Primer on Atomic Orbital Basis Sets |
| Scaling Problem |
| Estimating Eint at the CCSD(T) CBS Limit: Another Tutorial |
| Accurate Potential Energy Surfaces |
| Less Demanding Computational Strategies |
| Second-Order Møller-Plesset Perturbation Theory |
| Density Functional Theory |
| Guidelines |
| Other Computational Issues |
| Basis Set Superposition Error and Counterpoise Corrections |
| Beyond Interaction Energies: Geometries and Vibrational Frequencies |
| Excited States from Time-Dependent Density Functional Theory / Peter Elliott ; Filipp Furche ; Kieron Burke |
| Overview |
| Ground-State Review |
| Formalism |
| Approximate Functionals |
| Basis Sets |
| Time-Dependent Theory |
| Runge-Gross Theorem |
| Kohn-Sham Equations |
| Linear Response |
| Approximations |
| Implementation and Basis Sets |
| Density Matrix Approach |
| Convergence for Naphthalene |
| Double-Zeta Basis Sets |
| Polarization Functions |
| Triple-Zeta Basis Sets |
| Diffuse Functions |
| Resolution of the Identity |
| Performance |
| Example: Naphthalene Results |
| Influence of the Ground-State Potential |
| Analyzing the Influence of the XC Kernel |
| Errors in Potential vs. Kernel |
| Understanding Linear Response TDDFT |
| Atoms as a Test Case |
| Quantum Defect |
| Testing TDDFT |
| Saving Standard Functionals |
| Electron Scattering |
| Beyond Standard Functionals |
| Double Excitations |
| Solids |
| Charge Transfer |
| Other Topics |
| Ground-State XC Energy |
| Strong Fields |
| Electron Transport |
| Computing Quantum Phase Transitions / Thomas Vojta |
| Preamble: Motivation and History |
| Phase Transitions and Critical Behavior |
| Landau Theory |
| Scaling and the Renormalization Group |
| Finite-Size Scaling |
| Quenched Disorder |
| Quantum vs. Classical Phase Transitions |
| How Important Is Quantum Mechanics? |
| Quantum Scaling and Quantum-to-Classical Mapping |
| Beyond the Landau-Ginzburg-Wilson Paradigm |
| Impurity Quantum Phase Transitions |
| Quantum Phase Transitions: Computational Challenges |
| Classical Monte Carlo Approaches |
| Method: Quantum-to-Classical Mapping and Classical Monte Carlo Methods |
| Transverse-Field Ising Model |
| Bilayer Heisenberg Quantum Antiferromagnet |
| Dissipative Transverse-Field Ising Chain |
| Diluted Bilayer Quantum Antiferromagnet |
| Random Transverse-Field Ising Model |
| Dirty Bosons in Two Dimensions |
| Quantum Monte Carlo Approaches |
| World-Line Monte Carlo |
| Stochastic Series Expansion |
| Spin1/2 Quantum Heisenberg Magnet |
| Diluted Heisenberg Magnets |
| Superfluid-Insulator Transition in an Optical Lattice |
| Fermions |
| Other Methods and Techniques |
| Real-Space and Multigrid Methods in Computational Chemistry / Thomas L. Beck |
| Physical Systems: Why Do We Need Multiscale Methods? |
| Why Real Space? |
| Real-Space Basics |
| Equations to Be Solved |
| Finite-Difference Representations |
| Finite-Element Representations |
| Iterative Updates of the Functions, or Relaxation |
| What Are the Limitations of Real-Space Methods on a Single Fine Grid? |
| Multigrid Methods |
| How Does Multigrid Overcome Critical Slowing Down? |
| Full Approximations Scheme (FAS) Multigrid, and Full Multigrid (FMG) |
| Eigenvalue Problems |
| Multigrid for the Eigenvalue Problem |
| Self-Consistency |
| Linear Scaling for Electronic Structure? |
| Other Nonlinear Problems: The Poisson-Boltzmann and Poisson-Nernst-Planck Equations |
| Poisson-Boltzmann Equation |
| Poisson-Nernst-Planck (PNP) Equations for Ion Transport |
| Some Advice on Writing Multigrid Solvers |
| Applications of Multigrid Methods in Chemistry, Biophysics, and Materials Nanoscience |
| Electronic Structure |
| Transport Problems |
| Existing Real-Space and Multigrid Codes |
| Transport |
| Some Speculations on the Future |
| Chemistry and Physics: When Shall the Twain Meet? |
| Elimination of Molecular Orbitals? |
| Larger Scale DFT, Electrostatics, and Transport |
| Reiteration of "Why Real Space?" |
| Hybrid Methods for Atomic-Level Simulations Spanning Multiple-Length Scales in the Solid State / Francesca Tavazza ; Lyle E. Levine ; Anne M. Chaka |
| General Remarks about Hybrid Methods |
| Complete-Spectrum Hybrid Methods |
| About this Review |
| Atomistic/Continuum Coupling |
| Zero-Temperature Equilibrium Methods |
| Finite-Temperature Equilibrium Methods |
| Dynamical Methods |
| Classical/Quantum Coupling |
| Static and Semistatic Methods |
| Dynamics Methodologies |
| Conclusions: The Outlook |
| Appendix: A List of Acronyms |
| Extending the Time Scale in Atomically Detailed Simulations / Alfredo E. Cárdenas ; Eric Barth |
| The Verlet Method |
| Molecular Dynamics Potential |
| Multiple Time Steps |
| Reaction Paths |
| Multiple Time-Step Methods |
| Splitting the Force |
| Numerical Integration with Force Splitting: Extrapolation vs. Impulse |
| Fundamental Limitation on Size of MTS Methods |
| Langevin Stabilization |
| Further Challenges and Recent Advances |
| An MTS Tutorial |
| Extending the Time Scale: Path Methodologies |
| Transition Path Sampling |
| Maximization of the Diffusive Flux (MaxFlux) |
| Discrete Path Sampling and String Method |
| Optimization of Action |
| Boundary Value Formulation in Length |
| Use of SDEL to Compute Reactive Trajectories: Input Parameters, Initial Guess, and Parallelization Protocol |
| Applications of the Stochastic Difference Equation in Length |
| Recent Advances and Challenges |
| Appendix: MATLAB Scripts for the MTS Tutorial |
| Acknowledgment |
| Atomistic Simulation of Ionic Liquids / Edward J. Maginn |
| Short (Pre)History of Ionic Liquid Simulations |
| Earliest Ionic Liquid Simulations |
| More Systems and Refined Models |
| Force Fields and Properties of Ionic Liquids Having Dialkylimidazolium Cations |
| Force Fields and Properties of Other Ionic Liquids |
| Solutes in Ionic Liquids |
| Implications of Slow Dynamics when Computing Transport Properties |
| Computing Self-Diffusivities, Viscosities, Electrical Conductivities, and Thermal Conductivities for Ionic Liquids |
| Nonequilibrium Methods for Computing Transport Properties |
| Ab Initio Molecular Dynamics |
| How to Carry Out Your Own Ionic Liquid Simulations |
| What Code? |
| Force Fields |
| Data Analysis |
| Operating Systems and Parallel Computing |
| Brittle Fracture: From Elasticity Theory to Atomistic Simulations / Stefano Giordano ; Alessandro Mattoni ; Luciano Colombo |
| 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 |
| 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 |
| 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 |
| Griffith Criterion for Failure |
| Failure in Complex Systems |
| Stress Shielding at Crack-Tip |
| Appendix: Notation |
| Dissipative Particle Dynamics / Igor V. Pivkin ; Bruce Caswell ; George Em Kamiadakis |
| Fundamentals of DPD |
| Mathematical Formulation |
| Units in DPD |
| Thermostat and Schmidt Number |
| Integration Algorithms |
| Extensions of DPD |
| DPD with Energy Conservation |
| Fluid Particle Model |
| DPD for Two-Phase Flows |
| Other Extensions |
| Polymer Solutions and Melts |
| Binary Mixtures |
| Amphiphilic Systems |
| Red Cells in Microcirculation |
| Trajectory-Based Rare Event Simulations / Peter G. Bolhuis ; Christoph Dellago |
| 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 |
| 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 |
| Understanding Metal/Metal Electrical Contact Conductance from the Atomic to Continuum Scales / Douglas L. Irving |
| Factors That Influence Contact Resistance |
| 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 |
| Conduction Through Metallic Nanowires |
| Multiscale Methods Applied to Metal/Metal Contacts |
| Molecular Detailed Simulations of Lipid Bilayers / Max L. Berkowitz ; James T. Kindt |
| Membrane Simulation Methodology |
| Choice of the Ensemble |
| Verification of the Force Field |
| Monte Carlo Simulation of Lipid Bilayers |
| Detailed Simulations of Bilayers Containing Lipid Mixtures |
| Semiclassical Bohmian Dynamics / Sophya Garashchuk ; Vitaly Rassolov ; Oleg Prezhdo |
| The Formalism and Its Features |
| The Trajectory Formulation |
| Features of the Bohmian Formulation |
| The Classical Limit of the Schrödinger 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 |
| Conservation of Density within a Volume Element / Appendix A： |
| Quantum Trajectories in Arbitrary Coordinates / Appendix B： |
| Optimal Parameters of the Linearized Momentum on Spatial Domains in Many Dimensions / Appendix C： |
| Prospects for Career Opportunities in Computational Chemistry |
| Introduction and Overview |
| Methodology and Results |
| Proficiencies in Demand |
| Analysis |
| An Aside: Economics 101 |
| Prognosis |
| Appendix: List of Computational Molecular Scientists |
