Prof. Alfonso Gautieri, Politecnico di Milano, Italy
Сourse Objective: ....
The objective is to introduce atomistic modeling techniques and motivate its potential for solving problems in molecular biology and biomolecular engineering, with a particular emphasis on protein investigation. We demonstrate how atomistic modeling can be used to evaluate thermodynamic averages by molecular dynamics, including accelerated sampling for the study of rare events. Students will learn the basics of atomistic modeling, including choosing interatomic potentials, visualization and analysis of data. We will discuss limitations and potentials of atomistic modeling of biological molecules. In the second part of the class, students will work on hands-on projects in computational lab. All simulation codes and numerical tools will be explained in detail, and will be provided to participants.
Course Main Topics:
1. Introduction to Molecular Modelling
2. Force fields for biomolecular modelling
3. Energy minimization algorithms
4. Molecular dynamics principles
5. Advanced modelling (Replica Exchange Molecular Dynamics, Metadynamics, …)
6. Coarse-Grained Modelling
7. Example and applications
Auxilary References:
1. Leach, A. R. (2001) Molecular Modelling: Principles and Applications, 2nd Edn. Pearson Prentice Hall.
2. Kukol A. (2008) Molecular Modeling of Proteins, Springer.
Prerequirements of the Course: ....
Linear algebra, statistics and probability theory, Basic experience with Linux environment.