Molecular Simulations

1. INTRODUCTION Motivation: Relating Microscopic Molecular Properties to Macroscopic / Thermodynamic Behavior of Bulk Systems Molecular Dynamics and Monte Carlo Simulations for Modeling Macroscopic Scale Experiment Scope of the Book and Background Needed 2. CLASSICAL MECHANICS FOR MANY-MOLECULE SYSTEMS Newton's Equations of Motion for Many-Molecule Systems Analytical Solution of Newton's Equations for Simple Systems The Concept of Trajectory and Phase Space Numerical Solution of Newton's Equations, Finite-Difference Method The Verlet and Leapfrog Time Progression Algorithms The Trajectory for a Many-Particle System 3. FORCE FIELD MODELS IN CLASSICAL MOLECULAR SIMULATIONS Summary of the Quantum Mechanics of Molecular Force Fields Modeling the Potential Energy Surface of Non-Reactive Systems Inter- and Intra-Molecular Force Fields Design and Choice of Force Fields Calculation of the Force Field Parameters Using Quantum Chemistry, Spectroscopy, and Modeling 4. INTRODUCTION TO PROBABILITY CONCEPTS Basic Concepts of Probability Theory: Single and Multiple Variable Probabilities, Discrete and Continuous Probabilities, the Central Limit Theorem Maxwell-Boltzmann Probability Distribution for Molecular Velocity, Speed Maxwell-Boltzmann Energy Distribution for Single Molecules and Collections of Molecules Probability Distributions of Large Collections of Molecules Assigning Molecular Velocities in Molecular Simulations from the Maxwell-Boltzmann Probability Distribution 5. INTRODUCTION TO STATISTICAL MECHANICS Statistical Mechanics in Classical Mechanics Language The Concept of Partition Function and Ensembles in Statistical Mechanics: Canonical (Isothermal Isochoric), Isothermal Isobaric, Grand-Canonical and Other Ensembles Thermodynamic Properties: Energy, Temperature, Pressure, Entropy, Free Energy, Fluctuations in These Quantities in Microscopic Systems The Quantum Mechanical Approach to Statistical Mechanics 6. MOLECULAR DYNAMICS (MD) SIMULATIONS 1 Periodic Boundary

Saman Alavi is Adjunct Professor at the Department of Chemical and Biological Engineering at the University of British Columbia (Vancouver, Canada) and at the Department of Chemistry and Biomolecular Sciences at the University of Ottawa (Canada). After obtaining his PhD from the University of British Columbia, he spent research periods in the National Research Council of Canada, at Oklahoma State University (USA) and the University of Ottawa (Canada). Saman Alavi has authored over 120 scientific publications on molecular simulations of different classes of materials.