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.
Last update: Matějka Pavel prof. Dr. RNDr. (16.06.2019)
Předmět pokrývá pokročilé metody molekulových i hrubozrnných počítačových simulací s aplikacemi v biologii, termodynamice roztoků i v teorii fázových přechodů. Výběr aplikací bude uzpůsoben aktuální skupině doktorandů.
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.
Last update: Kolafa Jiří prof. RNDr. CSc. (28.05.2018)
Posluchači se budou orientovat v moderních MC a MD simulačních metodách molekulových systémů.
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
Last update: Heyda Jan RNDr. Mgr. Ph.D. (06.09.2019)
K. Binder a D. Heermann: Monte Carlo Simulation in Statistical Physics: An Introduction (Springer International, 6th Edition, 2019);
Ch. Chipot a A. Pohorille: Free Energy Calculations Theory and Applications in Chemistry and Biology (Springer-Verlag 2007);
D. Frenkel a B. Smit: Understanding Molecular Simulation (Academic Press, 1996, 2002);
M.P. Allen a 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, J.I. Siepmann: Accurate and precise determination of critical properties from Gibbs ensemble Monte Carlo simulations, J. Chem. Phys. 143, 114113 (2015);
vybrané články
Learning resources -
Last update: Heyda Jan RNDr. Mgr. Ph.D. (29.05.2018)