SubjectsSubjects(version: 949)
Course, academic year 2019/2020
Advanced methods of molecular dynamics - AP403005
Title: Advanced methods of molecular dynamics
Guaranteed by: Department of Physical Chemistry (403)
Faculty: Faculty of Chemical Engineering
Actual: from 2019
Semester: summer
Points: summer s.:0
E-Credits: summer s.:0
Examination process: summer s.:
Hours per week, examination: summer s.:2/1, other [HT]
Capacity: unlimited / unlimited (unknown)
Min. number of students: unlimited
Language: English
Teaching methods: full-time
Teaching methods: full-time
For type: doctoral
Note: course is intended for doctoral students only
can be fulfilled in the future
Guarantor: Heyda Jan doc. RNDr. Mgr. Ph.D.
Kolafa Jiří prof. RNDr. CSc.
Malijevský Alexandr prof. Mgr. Ph.D., DSc.
Interchangeability : P403005
Examination dates   Schedule   
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: Pátková Vlasta (08.06.2018)

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

Literature -
Last update: Heyda Jan doc. 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: Pátková Vlasta (08.06.2018)

Teaching methods -
Last update: Pátková Vlasta (08.06.2018)

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

Syllabus -
Last update: Pátková Vlasta (08.06.2018)

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: Pátková Vlasta (08.06.2018)

Good knowledge of thermodynamics and statistical thermodynamics.

Basic knowledge of simulation methods MC, MD.

Registration requirements -
Last update: Řehák Karel doc. Ing. CSc. (10.10.2018)

M403002 Statistická termodynamika, molekulové modelování a simulace (Statistical thermodynamics, molecular modeling and simulation)

Course completion requirements -
Last update: Pátková Vlasta (08.06.2018)

active participation in seminars (50 %)

oral exam (50 %)