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 :  Monday afternoon, Spring, 2018

Room : E104

Lecture 1. Introduction to Molecular Simulations

Lecture 2. Statistical Thermodynamics Basics: Fluctuations

Lecture 3.intro-computer-Biophys-is

Lecture 4.intro-computer-Biophys-ii

Lecture 5.intro-computer-Biophys-iii

Lecture 6. Monte Carlo Simulations: Overview

Lecture 7. Monte Carlo Basics and Technical Details

Lecture 8. Monte Carlo Simulations in Various Ensembles

Lecture 9. Biased Monte Carlo Schemes

Lecture 10. Monte Carlo Sampling for Chain Molecules: Simple Sampling and Rosenbluth Sampling

Lecture 11. Monte Carlo Sampling for Chain Molecules: Dynamic Methods

Lecture 12. Free Energy Calculations: Thermodynamic Integration and Partical Insertion

Lecture 13. Chemical Potentials of Chain Molecules

Lecture 14. Multiple Histogram Method and Acceptance Ratio Method

Lecture 15.  Statistical Mechanics of Binding Affinity Calculation: Basics

Lecture 16.  Statistical Mechanics of Binding Affinity Calculation: Advanced Topics

2019 Lecture Note 1

2019 Lecture Note 2

2019 Lecture Note 3-MC

2019 Lecture Note 4-freeEnergy

Homework 1.