- Inter-faculty Studies in Bioinformatics and Systems Biology
- Bachelor's degree, first cycle programme, Computer Science
- Bachelor's degree, first cycle programme, Mathematics
- Master's degree, second cycle programme, Bioinformatics and Systems Biology
- Master's degree, second cycle programme, Computer Science
- Master's degree, second cycle programme, Mathematics
Molecular modeling 1200-MMOL-OG
The role of molecular modeling in science. Basic techniques of molecular mechanics and their relations with physical experiments. Selected software packages and databases. Molecular dynamics - algorithms and stability of MD. Brownian dynamics. The problem of the finite size of model systems. Force fields in MD. Monte Carlo methods. Various statistical ensembles in MC. Generalized ensemble MC. Replica Exchange MC. Applications of various techniques of molecular modeling to the global energy minimum problem. Studying phase transitions and diffusion - selection of methods and boundary conditions -critical slow down. Mesoscopic and reduced models. Modeling of macromolecules and large biomolecular systems. Ligand docking. Membranes. Reduction of conformational space. Potentials of mean force and statistical potentials. Multiscale modeling. Realtions between Monte Carlo dynamics and classical molecular dynamics
Type of course
Prerequisites (description)
Course coordinators
Learning outcomes
Basic knowledge of molecular modeling methods, including energy minimization, Molecular Dynamics, molecular Monte Carlo. Practical skils in applications of molecular modeling in physical chemistry and in organic chemistry.
Assessment criteria
Written test, containing 15 closed questions and 5 open questions, conducted off-line (in a class room) or an oral exam - possibly online
Practical placement
does not concern
Bibliography
1. P. von Rague Schleyer, Encyclopedia of Compuational Chemistry, Wiley 1998
2. K. Binder, D. W. Heermann, Monte Carlo Simulations in Statistical Physics, Springer 2002
3. D. Frenkel, B. Smit, Understanding Molecular Simulation, Academic Press, 2001
Additional information
Information on level of this course, year of study and semester when the course unit is delivered, types and amount of class hours - can be found in course structure diagrams of apropriate study programmes. This course is related to the following study programmes:
- Inter-faculty Studies in Bioinformatics and Systems Biology
- Bachelor's degree, first cycle programme, Computer Science
- Bachelor's degree, first cycle programme, Mathematics
- Master's degree, second cycle programme, Bioinformatics and Systems Biology
- Master's degree, second cycle programme, Computer Science
- Master's degree, second cycle programme, Mathematics
Additional information (registration calendar, class conductors, localization and schedules of classes), might be available in the USOSweb system: