Han Group
Computational Biology and Biophysics Group

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 :

  1. Thomas Creighton 《Proteins: Structures and Molecular properties》
  2. D. C. Rapaport《The Art of Molecular Dynamics Simulation》 2nd Edition
  3. 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


Lecture 13. Free Energy Calculation: Implementation of  WHAM 

Lecture 14. Free Energy Calculation: Umbrella Sampling

Lecture 15. Molecular Dynamics Simulation: Basics, Integrators and Thermostats

Lecture 16. Summary