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Lecturer:
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Teaching Division:
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Theoretical Chemistry and Crystallography
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Educational and
professional goals:
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Learning practical skills in molecular modeling using basic techniques of molecular modeling supported by the Internet services. Designing and practical implementations of typical task of classical molecular mechanics.
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Course description:
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Writing and implementation of a program simulating the Lennard-Jones liquid. Analysis of the finite-size effects. Tests of the MD algorithms of various orders. MD with a heat bath - Brownian dynamics, a comparison with canonical MD. Statistical tests of the random number generators. Comparison of various Monte Carlo schemes for the lattice gas polymer chain models. Modeling of phase transitions (In the Ising model or collapse transition in polymers). Computing thermodynamic quantities. Modeling of biomolecules using commercial packages Sybyl or Insight. Visualization and analysis of simulation results. Protein modeling supported by sparse experimental data. Final assignment combines elements of the above modeling techniques.
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Required background:
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Basic courses in physical chemistry, statistical thermodynamics. Basic knowledge of polymer and biopolymer structures. Programming in FORTRAN, C or C++.
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Form of assessment:
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Assignments.
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Remarks:
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Suggested for perspective students of Laboratory of Theory of Biopolymers.
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