Course: Advanced simulations in many body physics

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Course title Advanced simulations in many body physics
Course code UFY/SIM2
Organizational form of instruction Lecture + Lesson
Level of course Master
Year of study not specified
Frequency of the course In each academic year, in the summer semester.
Semester Summer
Number of ECTS credits 5
Language of instruction Czech
Status of course Compulsory-optional, Optional
Form of instruction unspecified
Work placements unspecified
Recommended optional programme components None
Lecturer(s)
  • Předota Milan, doc. RNDr. Ph.D.
Course content
Content of lectures: Advanced techniques Non-Boltzmann sampling of configurational space, Nosé thermostat in MD. Simulations of charged and molecular systems Reaction field method and Ewald summation, simulations of rigid molecules, simulations of molecules with internal degrees of freedom, dynamics with constraints. Phase transitions and critical phenomena Calculation of entropic properties, measurement of chemical potential, thermodynamics integration method, Gibbs ensemble, determination of phase equilibria, determination of critical temperature. Nonequilibrium systems close to equilibrium Methodology of simulations of nonequilibrium effects, kinetic coefficients, time correlation functions, Einstein's formula, nonequilibrium MD, kinetic MC - choice of kinetics, time in kinetic MC Content of practicals: Solving of simulation tasks in accord with the content of the lectures.

Learning activities and teaching methods
Monologic (reading, lecture, briefing), Demonstration, Activating (simulations, games, drama)
  • Preparation for classes - 10 hours per semester
  • Preparation for exam - 10 hours per semester
  • Class attendance - 28 hours per semester
Learning outcomes
Advanced Monte Carlo and molecular dynamics methods, applications to charged and molecular systems, nonequilibrium systems, determination of phase equilibria.
Theoretical basics of advanced simulation techniques, ability to perform non-equilibrium simulations in software Gromacs
Prerequisites
Completion of either course UFY/SIM1 or UFY/PFM

Assessment methods and criteria
Oral examination, Student performance assessment

To acquaint students with advanced molecular dynamics and methods for efficient sampling (metadynamics, potential of mean force calculations), non-equilibrium simulations.
Recommended literature
  • D. Frenkel, B. Smit, Understanding Molecular Simulation.
  • I. Nezbeda, J. Kolafa, M. Kotrla, Úvod do počítačových simulací: Metody Monte Carlo a molekuární dynamiky, Karolinum 2003..


Study plans that include the course
Faculty Study plan (Version) Category of Branch/Specialization Recommended year of study Recommended semester
Faculty: Faculty of Science Study plan (Version): Biophysics (1) Category: Physics courses - Recommended year of study:-, Recommended semester: Summer