Molecular Dynamics and Simulations
( 25 Modules )

Module #1
Introduction to Molecular Dynamics
Overview of molecular dynamics, its importance, and applications in various fields

Module #2
Classical Mechanics and Statistical Mechanics
Review of classical mechanics and statistical mechanics principles, including equations of motion and thermodynamic ensembles

Module #3
Molecular Dynamics Simulation Methods
Introduction to molecular dynamics simulation methods, including Cartesian and Lagrangian coordinates

Module #4
Force Fields and Potential Energy Surfaces
Introduction to force fields and potential energy surfaces, including functional forms and parameterization

Module #5
Simulation Algorithms
Overview of simulation algorithms, including Verlet, Velocity Verlet, and leap-frog methods

Module #6
Boundary Conditions and Periodic Systems
Discussion of boundary conditions and periodic systems in molecular dynamics simulations

Module #7
Thermostats and Barostats
Introduction to thermostats and barostats, including Nose-Hoover and Berendsen methods

Module #8
Equilibration and Production Runs
Discussion of equilibration and production runs in molecular dynamics simulations

Module #9
Analysis of Simulation Data
Introduction to analysis of simulation data, including structural, thermodynamic, and dynamic properties

Module #10
Visualization of Simulation Data
Introduction to visualization of simulation data using visualization tools and programming languages

Module #11
Basics of Quantum Mechanics and Electronic Structure
Review of quantum mechanics and electronic structure principles, including Schrödinger equation and Hartree-Fock method

Module #12
Density Functional Theory (DFT)
Introduction to density functional theory (DFT), including functional forms and approximations

Module #13
Hybrid Quantum-Classical Methods
Discussion of hybrid quantum-classical methods, including QM/MM and FEP methods

Module #14
Molecular Dynamics in Materials Science
Applications of molecular dynamics in materials science, including metals, semiconductors, and polymers

Module #15
Molecular Dynamics in Biophysics and Biochemistry
Applications of molecular dynamics in biophysics and biochemistry, including protein-ligand interactions and enzymatic reactions

Module #16
Molecular Dynamics in Chemical Engineering
Applications of molecular dynamics in chemical engineering, including catalysis and separations

Module #17
Advanced Topics in Molecular Dynamics
Discussion of advanced topics in molecular dynamics, including enhanced sampling methods and machine learning applications

Module #18
High-Performance Computing in Molecular Dynamics
Introduction to high-performance computing in molecular dynamics, including parallelization and GPU acceleration

Module #19
Molecular Dynamics Software Packages
Overview of popular molecular dynamics software packages, including GROMACS, AMBER, and LAMMPS

Module #20
Case Studies in Molecular Dynamics
Case studies of molecular dynamics simulations in various fields, including materials science, biophysics, and chemical engineering

Module #21
Error Analysis and Validation
Discussion of error analysis and validation methods in molecular dynamics simulations

Module #22
Advanced Simulation Techniques
Discussion of advanced simulation techniques, including umbrella sampling, free energy perturbation, and metadynamics

Module #23
Coarse-Graining and Multiscale Modeling
Introduction to coarse-graining and multiscale modeling techniques in molecular dynamics

Module #24
Machine Learning in Molecular Dynamics
Introduction to machine learning applications in molecular dynamics, including force field development and property prediction

Module #25
Course Wrap-Up & Conclusion
Planning next steps in Molecular Dynamics and Simulations career

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Molecular Dynamics and Simulations ( 25 Modules )

Molecular Dynamics and Simulations
( 25 Modules )