Study programmes
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| Faculty | Study type | Name of the study program | Language of instruction | Study form | ||
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| Faculty of Mathematics and Physics | doctoral | Physics of Plasmas and Ionized Media | Czech | combined |
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| Faculty of Mathematics and Physics | doctoral | Computer Science - Theory of Computing, Discrete Models and Optimization | English | combined |
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| Faculty of Mathematics and Physics | doctoral | Theoretical Physics, Astronomy and Astrophysics | English | combined |
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| Faculty of Mathematics and Physics | doctoral | Physics of Surfaces and Interfaces | English | combined |
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| Faculty of Mathematics and Physics | doctoral | Physics of Condensed Matter and Materials Research | English | combined |
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| Faculty of Mathematics and Physics | doctoral | Physics of nanostructures and nanomaterials | English | combined |
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| Faculty of Mathematics and Physics | doctoral | Algebra, number theory, and mathematical logic | English | combined |
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| Faculty of Mathematics and Physics | doctoral | Computer Science - Visual computing and computer games | English | combined |
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| Faculty of Mathematics and Physics | doctoral | Computational mathematics | English | combined |
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| Faculty of Mathematics and Physics | doctoral | Physics of Plasmas and Ionized Media | English | combined |
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| Faculty of Mathematics and Physics | doctoral | Mathematical analysis | English | combined |
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| Faculty of Mathematics and Physics | doctoral | Computer Science - Software Systems | English | combined |
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| Faculty of Mathematics and Physics | doctoral | Physics of the Earth and Planets | English | combined |
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| Faculty of Mathematics and Physics | doctoral | Theoretical Computer Science and Artificial Intelligence | English | combined |
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| Faculty of Mathematics and Physics | doctoral | Geometry, topology, and global analysis | English | combined |
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| Faculty of Mathematics and Physics | doctoral | Quantum Optics and Optoelectronics | English | combined |
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| Faculty of Mathematics and Physics | doctoral | Probability and statistics, econometrics and financial mathematics | English | combined |
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| Faculty of Mathematics and Physics | doctoral | Computational linguistics | English | combined |
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| Faculty of Mathematics and Physics | doctoral | General Questions of Mathematics and Computer Science | English | combined |
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| Faculty of Mathematics and Physics | doctoral | Atmospheric physics, meteorology and climatology | English | combined |
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| Faculty of Mathematics and Physics | doctoral | Mathematical and computer modeling | English | combined |
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| Faculty of Mathematics and Physics | doctoral | Bioinformatics and computational biology | English | combined |
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| Faculty of Mathematics and Physics | doctoral | Biophysics, Chemical and Macromolecular Physics | English | combined |
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| Faculty of Mathematics and Physics | doctoral | Particle and Nuclear Physics | English | combined |
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| Faculty of Mathematics and Physics | doctoral | Physics Education and General Problems of Physics | English | combined |
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| Faculty of Mathematics and Physics | doctoral | General Questions of Mathematics and Computer Science | Czech | full-time |
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| Faculty of Mathematics and Physics | doctoral | Physics of nanostructures and nanomaterials | Czech | full-time |
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| Faculty of Mathematics and Physics | doctoral | Physics Education and General Problems of Physics | Czech | full-time |
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| Faculty of Mathematics and Physics | doctoral | Computational linguistics | Czech | full-time |
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| Faculty of Mathematics and Physics | doctoral | Mathematical analysis | Czech | full-time |
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| Faculty of Mathematics and Physics | doctoral | Computer Science - Software Systems | Czech | full-time |
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| Faculty of Mathematics and Physics | doctoral | Atmospheric physics, meteorology and climatology | Czech | full-time |
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| Faculty of Mathematics and Physics | doctoral | Mathematical and computer modeling | Czech | full-time |
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| Faculty of Mathematics and Physics | doctoral | Physics of Condensed Matter and Materials Research | Czech | full-time |
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| Faculty of Mathematics and Physics | doctoral | Theoretical Physics, Astronomy and Astrophysics | Czech | full-time |
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| Faculty of Mathematics and Physics | doctoral | Bioinformatics and computational biology | Czech | full-time |
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| Faculty of Mathematics and Physics | doctoral | Physics of the Earth and Planets | Czech | full-time |
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| Faculty of Mathematics and Physics | doctoral | Computer Science - Theory of Computing, Discrete Models and Optimization | Czech | full-time |
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| Faculty of Mathematics and Physics | doctoral | Particle and Nuclear Physics | Czech | full-time |
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| Faculty of Mathematics and Physics | doctoral | Probability and statistics, econometrics and financial mathematics | Czech | full-time |
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| Faculty of Mathematics and Physics | doctoral | Theoretical Computer Science and Artificial Intelligence | Czech | full-time |
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| Faculty of Mathematics and Physics | doctoral | Geometry, topology, and global analysis | Czech | full-time |
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| Faculty of Mathematics and Physics | doctoral | Biophysics, Chemical and Macromolecular Physics | Czech | full-time |
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| Faculty of Mathematics and Physics | doctoral | Quantum Optics and Optoelectronics | Czech | full-time |
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| Faculty of Mathematics and Physics | doctoral | Physics of Surfaces and Interfaces | Czech | full-time |
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| Faculty of Mathematics and Physics | doctoral | Computer Science - Visual computing and computer games | Czech | full-time |
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| Faculty of Mathematics and Physics | doctoral | Computational mathematics | Czech | full-time |
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| Faculty of Mathematics and Physics | doctoral | Algebra, number theory, and mathematical logic | Czech | full-time |
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| Faculty of Mathematics and Physics | doctoral | Physics of Plasmas and Ionized Media | Czech | full-time |
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| Faculty of Mathematics and Physics | doctoral | Bioinformatics and computational biology | English | full-time |
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