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Last update: Hladíková Jana (04.01.2018)
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Last update: Hladíková Jana (04.01.2018)
Students will:
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Last update: Svozil Daniel prof. Mgr. Ph.D. (29.10.2018)
R: I. Nezbeda, J. Kolafa, M. Kotrla, Úvod do molekulárních simulací – Metody Monte Carlo a molekulární dynamiky, Univerzita Karlova, Praha 2002 R: T. Schlick, Molecular Modeling and Simulation, Springer 2010 A: D. Frenkel, B. Smit, Understanding Molecular Simulation, Academic Press 2002 A: J. Šponer, F. Lankaš (eds.), Computational Studies of RNA and DNA, Springer 2006 |
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Last update: Lankaš Filip doc. Ing. Ph.D. (16.02.2018)
Online materials for the course. |
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Last update: Lankaš Filip doc. Ing. Ph.D. (16.02.2018)
Solving homework exercises. |
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Last update: Lankaš Filip doc. Ing. Ph.D. (26.10.2018)
1. Introduction. Length and time scales in biomolecular modelling 2. Probability 3. Random variables 4. Characteristics of random variables 5. Probability distribution 6. Normal distribution 7. Stochastic processes 8. Langevin equation 9. Brownian motion 10. Brownian dynamics simulations 11. Application I: Diffusion-controlled protein-ligand binding 12. Application II: Dynamics of nucleosomes and of the chromatin fibre 13. Application III: Movement and interactions of biomolecules in the cell 14. Application IV: Bownian simulations of DNA and RNA nanostructures |
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Last update: Lankaš Filip doc. Ing. Ph.D. (16.02.2018)
Basic courses in mathematics, physical chemistry, biochemistry and molecular modelling. |
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Last update: Lankaš Filip doc. Ing. Ph.D. (16.02.2018)
A necessary prerequisite to get the credit is active participation at lectures and exercices. The exam is in oral form. |
Teaching methods | ||||
Activity | Credits | Hours | ||
Účast na přednáškách | 1 | 28 | ||
Příprava na přednášky, semináře, laboratoře, exkurzi nebo praxi | 0.5 | 14 | ||
Příprava na zkoušku a její absolvování | 2 | 56 | ||
Účast na seminářích | 0.5 | 14 | ||
4 / 4 | 112 / 112 |