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    Sommersemester 2012

    Computational Physics:
    Theory and Simulation of Molecular Dynamics

    Prof. G. Stock & Dr. F. Rao

    Tue 12.00 s.t. - 14.00 in SR II
    Fr 10 c.t. -12.00 in SR III

    Wahlpflichtfach 2, BSc, MSc
    includes computer labs

    Table of Contents

    I. Computational Physics

    • Why doing simulations?


    II. Molecular systems

    • Biomolecules
    • Non-covalent interactions
    • Van der Waals forces
    • Electrostatics
    • Water and the hydrophobic effect


    III. Statistical Mechanics

    • Statistical description and probability
    • Equilibrium: the second law of thermodynamics
    • Entropy
    • The partition function
    • Ensembles and thermodynamics potentials


    IV. Molecular Dynamics

    • Monte-Carlo and molecular dynamics
    • The force-field
    • Integration of the equation of motion
    • Sampling methods
    • Analysis
    • Normal mode analysis


    V. Fundamental Stochastic Processes

    • A simple system: the two state model
    • Activation energies
    • Transition state theory: Kramers theory
    • The reaction coordinate
    • Markov processes


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    Material


    Prerequisites:

    basic knowledge of classical-and quantum mechanics

    Literature:




    Molecular Dynamics Seminar

    Prof. G. Stock & Dr. F. Rao

    Mi 16:15 in GMH SR, EG
    Beginn: 02. Mai 2012
    Programm

    Zusätzlich zu den Vorträgen der auswärtigen Sprecher
    sind auch studentische Seminarvorträge möglich (BSc, Diplom, MSc)





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