SubjectsSubjects(version: 890)
Course, academic year 2020/2021
Advanced methods of molecular dynamics - P403005
Title: Pokročilé metody molekulové dynamiky
Guaranteed by: Department of Physical Chemistry (403)
Actual: from 2020
Semester: summer
Points: summer s.:0
E-Credits: summer s.:0
Examination process: summer s.:
Hours per week, examination: summer s.:2/1 other [hours/week]
Capacity: unlimited / unlimited (unknown)
Min. number of students: unlimited
Language: Czech
Teaching methods: full-time
For type: doctoral
Note: can be fulfilled in the future
Guarantor: Heyda Jan RNDr. Mgr. Ph.D.
Kolafa Jiří prof. RNDr. CSc.
Malijevský Alexandr doc. Mgr. Ph.D., DSc.
Is interchangeable with: AP403005
Annotation -
Last update: Matějka Pavel prof. Dr. RNDr. (16.06.2019)
The course covers advanced methods of molecular and coarse-grained computer simulations with applications in biology, thermodynamics of solutions, and theory of phase transitions. The selection of applications will be tailored to the group of Ph.D. students.
Aim of the course -
Last update: Kolafa Jiří prof. RNDr. CSc. (28.05.2018)

Student will receive an overview of modern MC and MD simulation methods of molecular systems.

Literature -
Last update: Heyda Jan RNDr. Mgr. Ph.D. (06.09.2019)

K. Binder and D. Heermann: Monte Carlo Simulation in Statistical Physics: An Introduction (Springer International, 6th Edition, 2019);

Ch. Chipot and A. Pohorille: Free Energy Calculations Theory and Applications in Chemistry and Biology (Springer-Verlag 2007);

D. Frenkel and B. Smit: Understanding Molecular Simulation (Academic Press, 1996, 2002);

M.P. Allen and D.J. Tildesley: Computer Simulation of Liquids (Clarendon Press, Oxford 1986, 2002);

U.R. Pedersen: Direct calculation of the solid-liquid Gibbs free energy difference in a single equilibrium simulation, J. Chem. Phys. 139, 104102 (2013);

J.R. Espinosa, C. Vega, E. Sanz: The mold integration method for the calculation of the crystal-fluid interfacial free energy from simulations, J. Chem. Phys. 141, 134709 (2014);

M. Dinpajooh, P. Bai, D.A. Allan, and J.I. Siepmann: Accurate and precise determination of critical properties from Gibbs ensemble Monte Carlo simulations, J. Chem. Phys. 143, 114113 (2015);

and selected articles

Learning resources -
Last update: Heyda Jan RNDr. Mgr. Ph.D. (29.05.2018)

Teaching methods -
Last update: Kolafa Jiří prof. RNDr. CSc. (28.05.2018)

Lectures (50 %) and seminars (50 %) from hot topics.

Syllabus -
Last update: Kolafa Jiří prof. RNDr. CSc. (28.05.2018)

1. Parallel tempering – Replica Exchange Molecular Dynamics.

2. Metadynamics – application of adjustable external potential.

3. Kinetics of rare events techniques – transition path sampling.

4. Generalized Monte Carlo methods – Wang-Landa algorithm.

5. Statistical thermodynamics of solutions – Kirkwood-Buff theory.

6. Free energy functional theory – mean-field theories, Flory-de-Gennes theory.

7. Langevin equation, fluctuation-dissipation theorem. Stochastic thermostats.

8. Brownian dynamics, dissipative particle dynamics.

9. Special ensembles in MC: from the grand canonical ensemble to Gibbs ensemble to reaction ensemble. Osmotic ensemble in MC and MD.

10. Phase equilibria. Slab geometry, chemical potential of liquids and crystals.

11. Surface tension and interfacial energy of crystals.

12. Critical point: how to beat critical slowing-down, finite-size scaling, renormalization group.

13. MD and MC simulations of polarizable molecules.

14. Kinetic quantities (viscosity, el. conductivity, diffusivity). EMD: Linear Response Theory, Green-Kubo formulas, Einstein relations. NEMD, SLODD.

Entry requirements -
Last update: Kolafa Jiří prof. RNDr. CSc. (28.05.2018)

Good knowledge of thermodynamics and statistical thermodynamics.

Basic knowledge of simulation methods MC, MD.

Course completion requirements -
Last update: Kolafa Jiří prof. RNDr. CSc. (28.05.2018)

active participation in seminars (50 %)

oral exam (50 %)