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Education |
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1997 |
Ph.D. in Fluid Mechanics and Thermodynamics
Institute of Thermomechanics, Academy of Sciences of the Czech Repuclic, Prague. Thesis: "Thermodynamics of Condensation Waves" (tutor prof. F. Maršík) |
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1991 |
Master (Ing.) in Mathematical Engineering
Faculty of Nuclear Science and Physical Engineering, Czech Institute of Technology, Prague. Graduated with honors |
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Academic positions |
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since 2008 |
J. E. Purkyně Research Fellow, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague |
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2003-2007 |
Assistant, Laboratory of Computation and Visualization in Mathematics and Mechanics, Institute for Mathematics B, Swiss Federal Institute of Technology (EPFL), Lausanne (with prof. J.H. Maddocks) |
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1997-2003 |
Visiting scientist, Dept. of Biophysics of Macromolecules, German Cancer Research Centre (DKFZ), Heidelberg (with prof. J. Langowski) |
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1997-2001 |
Junior researcher, J.Heyrovsky Institute of Physical Chemistry, Prague (with prof. P. Hobza) |
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Research interests |
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Multiscale modelling of biomolecules and biomolecular systems. Performing large-scale atomistic computer simulations and employing methods from statistical mechanics to construct molecular models at different levels of coarse-graining. Applying the models to problems of biological interest.
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Awards |
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2007 |
J.E. Purkyně Fellowship |
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2007 |
Certificate of qualification for University professor of theoretical, physical and analytical chemistry, from French Ministry of Education and Research |
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2006 |
Best poster award, International Society for Quantum Biology and Pharmacology, President's meeting, Strasbourg |
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1996 |
The Špaček Prize for Biomechanics |
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Teaching |
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since 2011 |
Course "Mesoscopic Modelling", Dept. of Physical and Macromolecular Chemistry, Faculty of Sciences, Charles University, Prague. This is a master course also suitable for PhD students. The topics include introduction to probability theory and stochastic processes, Brownian dynamics and its computer implementation, and application to biomolecular modelling. In Czech |
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2004-2007 |
Course "Applied Mathematics" for chemistry and chemical engineering specialization (EPFL, bachelor 3rd semester). In French |
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2005 |
Course of DNA modelling, Free University, Berlin. In English |
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2001 |
Lecturer, Czech-German Summer Academy (Studienstiftung des deutschen Volkes and J. Heyrovsky Institute, Prague). In English |
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2001 |
Lecturer, Summer School of Computational Chemistry, J. Heyrovsky Institute, Academy of Sciences of Czech Republic. In English |
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Students |
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Tomáš Dršata |
Bachelor thesis 2010, master thesis 2012, accepted for PhD studies since winter semester 2012/2013 at the Faculty of Sciences, Charles University, Prague |
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Pavlína Brettlová |
Master thesis 2009, Faculty of Sciences, Charles University, Prague |
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Scientific reporting and editing |
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referee for scientific journals (J. Am. Chem. Soc., Nucleic Acids Res. etc.)
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book editor ("Computational Studies of RNA and DNA", Springer 2006 - with J. Šponer)
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referee for Ph.D. and diploma theses
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Languages |
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English (The Cambridge Certificate of Advanced English, level A)
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French and German (fluent, written and spoken)
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Italian (intermediate level)
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