Course name : Introduction to Computational Biophysics
Course Code : 04710262
Textbook :
Lecture notes, posted ahead of class (usually one day earlier)
Frenkel, and Smit, 《Understanding Molecular Simulations》 2nd edition，2002
Reference :
- Thomas Creighton 《Proteins: Structures and Molecular properties》
- D. C. Rapaport《The Art of Molecular Dynamics Simulation》 2nd Edition
- https://learnpythonthehardway.org/book/
Time : Thursday afternoon, Spring, 2023
Room : F201
Lecture 1. Statistical Thermodynamics: Basic Concepts and Hypothesis
Lecture 2. Statistical Thermodynamics: Ensemble
Lecture 3. Statistical Thermodynamics: Interacting and Noninteracting Systems
Lecture 4. Statistical Thermodynamics: Zimm-Bragg Theory and Helix-Coil Equilibrium
Lecture 5. Statistical Thermodynamics: Fluctuation and Ensemble Equivalence
Lecture 6. Monte Carlo Simulation: Basics
Lecture 7. Monte Carlo Simulation: Lennard-Jones Fluid and Temperature Control
Lecture 8. Monte Carlo Simulation: Pressure Calculation
Lecture 9. Monte Carlo Simulation: Pressure Control
Lecture 10. Monte Carlo Simulation: Chemical Potential and Open Systems
Lecture 11. Free Energy Calculation: Thermodynamic Integration and Widom Testing Particle Insertion
Lecture 12. Free Energy Calculation: Overlapping Method, Acceptance Ratio Method and Weighted Histogram Method