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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 tasks of classical molecular mechanics.
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Course description:
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The role of molecular modeling in science. Basic techniques of molecular mechanics and their relations with physical experiments. Selected software packages and databases. Molecular dynamics - algorithms and stability of MD. Brownian dynamics. The problem of the finite size of model systems. Force fields in MD. Monte Carlo methods. Various statistical ensembles in MC. Generalized ensemble MC. Replica Exchange MC. Applications of various techniques of molecular modeling to the global energy minimum problem. Studying phase transitions and diffusion - selection of methods and boundary conditions -critical slow down. Mesoscopic and reduced models. Modeling of macromolecules and large biomolecular systems. Ligand docking. Membranes. Reduction of conformational space. Potentials of mean force and statistical potentials. Multiscale modeling. Realtions between Monte Carlo dynamics and classical molecular dynamics.
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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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Exam.
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Remarks:
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Suggested for perspective students of Laboratory of Theory of Biopolymers.
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