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Preface to the Second Edition | |
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Preface | |
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List of Symbols | |
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Introduction | |
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Basics | |
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Statistical Mechanics | |
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Entropy and Temperature | |
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Classical Statistical Mechanics | |
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Ergodicity | |
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Questions and Exercises | |
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Monte Carlo Simulations | |
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The Monte Carlo Method | |
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Importance Sampling | |
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The Metropolis Method | |
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A Basic Monte Carlo Algorithm | |
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The Algorithm | |
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Technical Details | |
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Detailed Balance versus Balance | |
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Trial Moves | |
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Translational Moves | |
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Orientational Moves | |
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Applications | |
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Questions and Exercises | |
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Molecular Dynamics Simulations | |
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Molecular Dynamics: The Idea | |
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Molecular Dynamics: A Program | |
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Initialization | |
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The Force Calculation | |
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Integrating the Equations of Motion | |
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Equations of Motion | |
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Other Algorithms | |
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Higher-Order Schemes | |
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Liouville Formulation of Time-Reversible Algorithms | |
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Lyapunov Instability | |
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One More Way to Look at the Verlet Algorithm | |
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Computer Experiments | |
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Diffusion | |
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Order-n Algorithm to Measure Correlations | |
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Some Applications | |
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Questions and Exercises | |
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Ensembles | |
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Monte Carlo Simulations in Various Ensembles | |
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General Approach | |
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Canonical Ensemble | |
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Monte Carlo Simulations | |
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Justification of the Algorithm | |
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Microcanonical Monte Carlo | |
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Isobaric-Isothermal Ensemble | |
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Statistical Mechanical Basis | |
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Monte Carlo Simulations | |
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Applications | |
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Isotension-Isothermal Ensemble | |
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Grand-Canonical Ensemble | |
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Statistical Mechanical Basis | |
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Monte Carlo Simulations | |
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Justification of the Algorithm | |
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Applications | |
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Questions and Exercises | |
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Molecular Dynamics in Various Ensembles | |
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Molecular Dynamics at Constant Temperature | |
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The Andersen Thermostat | |
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Nose-Hoover Thermostat | |
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Nose-Hoover Chains | |
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Molecular Dynamics at Constant Pressure | |
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Questions and Exercises | |
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Free Energies and Phase Equilibria | |
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Free Energy Calculations | |
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Thermodynamic Integration | |
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Chemical Potentials | |
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The Particle Insertion Method | |
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Other Ensembles | |
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Overlapping Distribution Method | |
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Other Free Energy Methods | |
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Multiple Histograms | |
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Acceptance Ratio Method | |
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Umbrella Sampling | |
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Nonequilibrium Free Energy Methods | |
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Questions and Exercises | |
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The Gibbs Ensemble | |
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The Gibbs Ensemble Technique | |
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The Partition Function | |
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Monte Carlo Simulations | |
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Particle Displacement | |
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Volume Change | |
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Particle Exchange | |
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Implementation | |
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Analyzing the Results | |
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Applications | |
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Questions and Exercises | |
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Other Methods to Study Coexistence | |
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Semigrand Ensemble | |
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Tracing Coexistence Curves | |
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Free Energies of Solids | |
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Thermodynamic Integration | |
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Free Energies of Solids | |
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Atomic Solids with Continuous Potentials | |
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Free Energies of Molecular Solids | |
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Atomic Solids with Discontinuous Potentials | |
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General Implementation Issues | |
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Vacancies and Interstitials | |
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Free Energies | |
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Numerical Calculations | |
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Free Energy of Chain Molecules | |
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Chemical Potential as Reversible Work | |
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Rosenbluth Sampling | |
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Macromolecules with Discrete Conformations | |
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Extension to Continuously Deformable Molecules | |
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Overlapping Distribution Rosenbluth Method | |
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Recursive Sampling | |
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Pruned-Enriched Rosenbluth Method | |
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Advanced Techniques | |
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Long-Range Interactions | |
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Ewald Sums | |
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Point Charges | |
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Dipolar Particles | |
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Dielectric Constant | |
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Boundary Conditions | |
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Accuracy and Computational Complexity | |
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Fast Multipole Method | |
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Particle Mesh Approaches | |
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Ewald Summation in a Slab Geometry | |
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Biased Monte Carlo Schemes | |
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Biased Sampling Techniques | |
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Beyond Metropolis | |
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Orientational Bias | |
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Chain Molecules | |
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Configurational-Bias Monte Carlo | |
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Lattice Models | |
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Off-lattice Case | |
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Generation of Trial Orientations | |
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Strong Intramolecular Interactions | |
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Generation of Branched Molecules | |
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Fixed Endpoints | |
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Lattice Models | |
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Fully Flexible Chain | |
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Strong Intramolecular Interactions | |
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Rebridging Monte Carlo | |
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Beyond Polymers | |
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Other Ensembles | |
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Grand-Canonical Ensemble | |
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Gibbs Ensemble Simulations | |
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Recoil Growth | |
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Algorithm | |
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Justification of the Method | |
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Questions and Exercises | |
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Accelerating Monte Carlo Sampling | |
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Parallel Tempering | |
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Hybrid Monte Carlo | |
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Cluster Moves | |
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Clusters | |
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Early Rejection Scheme | |
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Tackling Time-Scale Problems | |
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Constraints | |
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Constrained and Unconstrained Averages | |
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On-the-Fly Optimization: Car-Parrinello Approach | |
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Multiple Time Steps | |
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Rare Events | |
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Theoretical Background | |
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Bennett-Chandler Approach | |
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Computational Aspects | |
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Diffusive Barrier Crossing | |
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Transition Path Ensemble | |
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Path Ensemble | |
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Monte Carlo Simulations | |
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Searching for the Saddle Point | |
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Dissipative Particle Dynamics | |
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Description of the Technique | |
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Justification of the Method | |
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Implementation of the Method | |
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DPD and Energy Conservation | |
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Other Coarse-Grained Techniques | |
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Appendices | |
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Lagrangian and Hamiltonian | |
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Lagrangian | |
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Hamiltonian | |
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Hamilton Dynamics and Statistical Mechanics | |
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Canonical Transformation | |
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Symplectic Condition | |
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Statistical Mechanics | |
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Non-Hamiltonian Dynamics | |
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Theoretical Background | |
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Non-Hamiltonian Simulation of the N, V, T Ensemble | |
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The Nose-Hoover Algorithm | |
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Nose-Hoover Chains | |
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The N, P, T Ensemble | |
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Linear Response Theory | |
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Static Response | |
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Dynamic Response | |
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Dissipation | |
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Electrical Conductivity | |
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Viscosity | |
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Elastic Constants | |
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Statistical Errors | |
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Static Properties: System Size | |
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Correlation Functions | |
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Block Averages | |
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Integration Schemes | |
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Higher-Order Schemes | |
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Nose-Hoover Algorithms | |
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Canonical Ensemble | |
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The Isothermal-Isobaric Ensemble | |
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Saving CPU Time | |
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Verlet List | |
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Cell Lists | |
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Combining the Verlet and Cell Lists | |
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Efficiency | |
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Reference States | |
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Grand-Canonical Ensemble Simulation | |
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Statistical Mechanics of the Gibbs "Ensemble" | |
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Free Energy of the Gibbs Ensemble | |
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Basic Definitions | |
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Free Energy Density | |
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Chemical Potential in the Gibbs Ensemble | |
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Overlapping Distribution for Polymers | |
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Some General Purpose Algorithms | |
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Small Research Projects | |
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Adsorption in Porous Media | |
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Transport Properties in Liquids | |
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Diffusion in a Porous Media | |
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Multiple-Time-Step Integrators | |
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Thermodynamic Integration | |
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Hints for Programming | |
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Bibliography | |
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Author Index | |
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Index | |