Title	Biochemistry II
Code	ÚCHV/BCH1b/03	Teacher	Potočňák Ivan, Podhradský Dušan
ECTS credits	5	Hrs/week	3/-
Assessment	Examination	Semester	2
T/L method	Lecture
Objective	To teach students about living organisms on the basis of their molecular structure and metabolism.
Content	Introduction to Metabolism; regulation of metabolic pathways. Basic metabolic processes: oxidative phosphorylation, glycolysis, phentose phosphate pathway, citric acid cycle, gluconeogenesis, oxidation of fatty acids, amino acids degradation and the urea cycle. Photosynthesis. Transport through membranes. Lipid metabolism. Amino acid metabolism. Energy metabolism: Integration and Organ specialisation. Nucleotide metabolism. Principle of bioenergetic. Hormones and vitamins.
Prerequisite courses	ÚCHV/BCH1a/03
Recommended reading	Lubert Stryer and col.: Biochemistry 5th edition, W.H.Freeman and Company, New York, 2003 Voet, Voet: Biochemistry 3rd edition, John Wiley & sons, England, 2004

Title	Semester project
Code	ÚFV/SP2/04	Teacher	Miškovský Pavol
ECTS credits	6	Hrs/week	-/6
Assessment	Assessment	Semester	3
T/L method	Practical
Objective	To realise experimental and/or theoretical works within the frame of a chosen theme and to present the results of this work in a consistent way.
Content	Work on a chosen theme for the semester project in the Department of Biophysics.
Recommended reading	The literature will be recommended by supervisors of individual works.

Compulsory elective courses

Title	Nontraditional Optimisation Techniques I
Code	ÚFV/NOT1a/03	Teacher	Horváth Denis, Uličný Jozef, Brutovský Branislav
ECTS credits	5	Hrs/week	2/2
Assessment	Examination	Semester	3
T/L method	Lecture, Practical
Objective	To allow students to learn major optimisation methods.
Content	The classification of optimisation methods. Optimisation function. Multifunction-optimisation. The penalty function. The Barier function. The stochastic and deterministic methods. Gradient methods. The physical picture of gradient optimisation. Blind search and hill climbing methods. Multi-agent evolutionary strategy and meta-optimisation. Genetic algorithms. Quantum mechanical applications of genetic algorithms. Genetic algorithms in variable environments. The training of neural nets as optimisation. Principal component analysis. The prediction of time series.  Monte Carlo techniques and simulated annealing. Optimisation and self-organisation attractor. The self-organised Kohonen nets; neural gas model. Cellular automata models. Agent-based systems. Strategies and demographic games on the lattice. Swarm optimisation.
Recommended reading	J.C.Principe, N.R.Euliano, Neural and Adaptive Systems, John Wiley & Sons. INC., New York, 2000. K.Binder, D.W.Heermann, Monte Carlo Simulation in Statistical Physics, Springer-Verlag, Berlin, 2002.

Title	Fundamentals of Cellular and Molecular Biology
Code	ÚFV/MBB1/03	Teacher	Fabriciová Gabriela, Miškovský Pavol
ECTS credits	5	Hrs/week	3/-
Assessment	Examination	Semester
T/L method	Lecture
Objective	To provide students basic information about the structure and function of cells and genetics processes.
Content	Characteristics of cells, the surface of the cell, biological membranes, cell's organelles, the cell cycle.  Macromolecules of information,  genome of prokaryotes, eukaryotes and viruses, the mechanisms of DNA replication, mechanisms of transcription and transduction, the regulation of gene expression, mutations and mutagenes, experimental methods in molecular biology.
Prerequisite courses	ÚCHV/BCH1b/03
Recommended reading	G. M. Cooper, The cell a molecular approach, ASM Press, Washington 2000 J. D. Watson, molekulární biologie genu, Acadenie, Praha 1982 J. Darnell, H. Lodish, D. Baltimore: Molecular Cell Biology, W. H. Freeman and Co., New York 1990

Title	Modern Trends in Biophysical Methods
Code	ÚFV/EMB1c/04	Teacher	Miškovský Pavol, Uličný Jozef
ECTS credits	5	Hrs/week	3/-
Assessment	Examination	Semester
T/L method	Lecture
Objective	To inform students about state-of the art experimental and theoretical methods in biophysics (different types of microscopy, nanotechnology, methods of genomics, proteomics, etc.). The content of the course will be determined each year.
Content	AFM, SNOM, microspectroscopic methods, modern methods in time-resolved spectroscopy, microcalorimetry, modern methods in the simulation of biological processes.
Prerequisite courses	ÚFV/EMB1b/04

Title	Biophysical Seminar
Code	ÚFV/SBFc/03	Teacher
ECTS credits	1	Hrs/week	-/1
Assessment	Assessment	Semester
T/L method	Practical
Objective	To teach students about individual scientific work within the frame of the year's diploma theses and lead them to the intelligible presentation of their scientific results.
Content	Biophysics Department seminar oriented to the themes of the year's diploma works.
Recommended reading	The literature will be recommended by supervisors of individual works.

Title	Biophysical Seminar
Code	ÚFV/SBFe/03	Teacher
ECTS credits	1	Hrs/week	-/1
Assessment	Assessment	Semester
T/L method	Practical
Objective	To teach students about individual scientific work within the frame of the year's diploma theses and lead them to the intelligible presentation of their scientific results.
Content	Biophysics Department seminar oriented to the themes of the year's diploma works.
Recommended reading	The literature will be recommended by supervisors of individual works.

Title	Enzymology
Code	ÚCHV/ENZ/04	Teacher	Sedlák Erik, Podhradský Dušan, Györyová Katarína
ECTS credits	5	Hrs/week	3/-
Assessment	Examination	Semester
T/L method	Lecture
Objective	To teach students to use the basic equations of enzyme kinetics. To have students develop the ability to determine basic kinetic and thermo-dynamic parameters of enzyme catalyzed reaction.
Content	Introduction. Chemical catalysis: theory of transition state. Enzyme catalysis: types and examples. Cofactors. Active site: lock and key; induced fit. Enzymes: classification. 3D structure of proteins.  Noncovalent interactions. Secondary, tertiary and quaternary structures. Convergent and divergent evolution. Multienzyme complexes. Dynamics of proteins. Ligand binding. Thermodynamics and kinetics. Techniques. Chemical kinetics. Basic equations of enzyme kinetics. Regulations of enzyme activity: examples. Conformational change; allosteric regulation. Regulation of metabolic pathways. Experimental determination of enzyme activity. pH and temperature dependence of enzyme catalysis. Determination of individual rate constants. Stop flow. Enzyme-substrate complementarities and the use of binding energy in enzyme catalysis. Reversible inhibition. Irreversible inhibition. Specificity and control mechanisms. „Moonlighting“ enzymes. Applic-ations of enzymes (organic solvents). Catalytic antibodies. Extremo-philes. Directed selection of enzymes. Enzymatic reactions with multiple substrates.
Recommended reading	Alan Fersht “Structure and Mechanism in Protein Science: A Guide to Enzyme Catalysis and Protein Folding. “ (3rd Ed. W. H. Freeman and Company, 1999) Robert A. Copeland: Enzymes (2nd edition), Wiley-VCH, 2000

Title	Biomolecular  Simulations
Code	ÚFV/BSIM1/03	Teacher	Uličný Jozef
ECTS credits	6	Hrs/week	2/2
Assessment	Examination	Semester
T/L method	Lecture, Practical
Objective	To introduce students to actual problems of biomolecular simulations.
Content	Structural characteristics of biological polymers. Foldamers. Central dogma of molecular biology as flow of biological information. 3D-structure and function of foldamers. Recent view on enzyme mechanisms. Experimental methods of structure determination and their limitations. Empirical force fields and methods of classical molecular dynamics. Molecular dynamics and Monte Carlo methods: algorithms and parallelisation. Ab initio molecular dynamics and hybrid approaches. Computational challenges in biomolecular simulations: simulations of chemical reactions, free energy evaluation, protein folding. Computational complexity, nontraditional approaches and heuristic approaches.

Title	Bioenergetics
Code	ÚFV/BIOE1/02	Teacher	Jancura Daniel, Miškovský Pavol
ECTS credits	3	Hrs/week	2/-
Assessment	Examination	Semester
T/L method	Lecture
Objective	To provide students an introduction to the principles of membrane transport in biological systems and to the fundamental bioenergetic processes in biological organisms with emphasis on the description of the structure and function of the biomacromolecules involving in the processes of the oxidative phosphorylation.
Content	Energy in the biosphere. Phenomenology of bioenergetical processes. Control and regulation in bioenergetics. Chemiosmotic theory. Structure and function of the respiratory chain. Oxidative phosphorylation. The enzymes of the respiratory chain. Structure and function of NADH dehydrogenase (complex I), succinate dehydrogenase (complex II), cytochrome bc1 (complex III) and cytochrome c oxidase (complex IV). Formation of the mitochondrial proton gradient. Photosynthesis-basic informations and mechanisms. Thermodynamics and kinetics of membrane transport. Carriers, pumps and channels in the biological membranes.
Recommended reading	I. Scheffer, Mitochondria, John Wiley & Sons, Inc., 1999 D. Harris, Bioenergetics at a glance, Blackwell Science Ltd., 1995 D. Nicholls, S. Ferguson, Bioenergetics 3, Academic Press, Elsevier Science Ltd., 2002 S. Papa, F. Guerrieri, J. Tager (Eds.), Frontiers of cellular   bioenergetics, Kluwer Academic, 1999 Selected scientific publications.

Title	Laboratory Training II: Optical Spectroscopy Methods
Code	ÚFV/PRb/04	Teacher	Miškovský Pavol
ECTS credits	3	Hrs/week	-/3
Assessment	Assessment	Semester
T/L method	Practical
Objective	To provide students with basic skills for manipulations with the instruments utilised in optical spectroscopy.
Content	Practical training in the frame of the subject "Methods of Optical Spectroscopy". The training includes a practical intoduction to the following experimental techniques: UV-VIS spectroscopy, fluorescence spectroscopy, Raman and IR spectroscopy and CD spectroscopy.
Recommended reading	The actual scientific papers.

Title	Biophysical Seminar
Code	ÚFV/SBFd/03	Teacher
ECTS credits	1	Hrs/week	-/1
Assessment	Assessment	Semester
T/L method	Practical
Objective	To teach students about individual scientific work within the frame of the year's diploma theses and lead them to the intelligible presentation of their scientific results.
Content	Biophysics Department seminar oriented to the themes of the year's diploma works.
Recommended reading	The literature will be recommended by supervisors of individual works.

Title	Nontraditional Optimisation Techniques II
Code	ÚFV/NOT1b/03	Teacher	Horváth Denis, Uličný Jozef, Brutovský Branislav
ECTS credits	5	Hrs/week	2/2
Assessment	Examination	Semester
T/L method	Lecture, Practical
Objective	To teach students applications of optimisation techniques on thestudy and interpretation of complex systems using examples from biology. To introduce students to new paradigms in the area of systems biology.
Content	Complex systems; emergent behavior. Evolutionary theory and memetics. Application of optimisation techniques on complex systems. Application of methods (genetic algorithms, simulated annealing, taboo search) on selected problems of biomolecular simulations. Molecular dynamics; protein folding. Population dynamics, metabolic networks and complexity in bioinformatics.
Recommended reading	The actual scientific papers.

Title	Methods of Structural Analysis
Code	ÚFV/MSA1/03	Teacher	Sovák Pavol
ECTS credits	7	Hrs/week	3/2
Assessment	Examination	Semester
T/L method	Lecture, Practical
Content	Optic microscopy. Electron microscopy: Electron beam instruments, electron optics, electron lenses and deflection systems, transmission electron microscopy (principle and construction). Electron–specimen interactions. Electron diffraction.  Kikuchy lines. Scanning electron microscopy (principle and construcion). Scanning transmission electron microscopy. High Voltage electron microscopy. Electron microprobe analysis: WDX spectrometer, EDX spectrometer, Auger electron spectrometer. self-emission microscopy. Convergent beam diffraction. X-ray diffractometry: Scattering of x-rays, neutrons and neutron scattering, CW-diffractometer, Ewald´s sphere, diffraction on powder samples, The main characteristics of powder diffraction pattern, structure factor, occupation factor, Atomic displacement factor, Peak intensity, shape and symmetry, Sherrer equation. Peak profile, Rietweld method.
Alternate courses	ÚFV/SAK1/99,ÚFV/SAK1/00,ÚFV/RTG1/01
Recommended reading	S. Amelincks, D.van Dyck, J. van Landyut: Electron Microscopy – Principles and Fundamentals, VCH, 1997 M.H. Loretto: Electrom beam analysis of materials. Springer, 2002 Fundamentals of Powder Diffraction and Structural Characterisation of Materials,  Vitalij K. Pecharsky & Peter Y. Zavalij , Kluwer Academic Publishers, 2003 Structure Determination from Powder Diffraction Data, Edited by W.I.F. David, K. Shankland, L.B. McCusker, C. Bärlocher, Oxford University Press, 2006

Title	Biophysical Seminar
Code	ÚFV/SBFf/03	Teacher
ECTS credits	1	Hrs/week	-/1
Assessment	Assessment	Semester
T/L method	Practical
Objective	To teach students about individual scientific work within the frame of the year's diploma theses and lead them to the intelligible presentation of their scientific results.
Content	Biophysics Department seminar oriented to the themes of the year's diploma works.
Recommended reading	The literature will be recommended by supervisors of individual works.

Title	Introduction to Physics of Biomacromolecules
Code	ÚFV/BMM1/05	Teacher	Fabriciová Gabriela, Miškovský Pavol
ECTS credits	3	Hrs/week	2/-
Assessment	Examination	Semester
T/L method	Lecture
Objective	To provide information about the structure and principles of organisation of the biological macromolecules.
Content	Conformations of biological macromolecules. Dynamics of the biopolymers. Hydratation of the biopolymers. Biopolymers as polyelectrolytes.
Alternate courses	ÚFV/BPM1/99,ÚFV/DNA1/99
Recommended reading	C.R.Cantor, P.R. Schimmel: Biophysical Chemistry Part I-III,  Freeman and Co., San Francisco, 1980. H.Frauenfelder, J.Disenhofer, P.G.Wolyns: Simplicity and Complexity in Proteins and Nucleic Acids, Dahlem University Press, 1999. M. Daune: Molecular biophysics, Oxford University press, 2004.

Study programme   Nuclear and Subnuclear Physics

(Full-time master)

Code   Title   ECTS   Credit   Hours/week   Assessment   Recommended Year/Semester

Compulsory courses

ÚFV/DPF1a/00	Diploma Work	2	-/-	Recognition	1/1
KFaDF/DF2p/07	History of Philosophy	4	2/1	Examination	1/1
ÚFV/FJA1/99	Physics of the Nucleus	3	2/-	Examination	1/1
ÚFV/FEC1/04	Elementary Particle Physics	8	4/2	Examination	1/1
ÚFV/KTP1a/03	Quantum Field Theory I	6	3/1	Examination	1/1
FFKF/DF/07	History of Philosophy	4	2/1	Examination	1/1
ÚFV/DPF1b/00	Diploma Thesis	6	-/-	Recognition	1/2
ÚFV/KTP1b/03	Quantum Field Theory II	6	3/1	Examination	1/2
ÚFV/RJF1/99	Relativistic Nuclear Physics	3	2/-	Examination	1/2
ÚFV/EJF1a/04	Experimental Methods of Nuclear Physics	8	4/1	Examination	2/3
ÚFV/DPF1c/03	Diploma Work	8	-/-	Recognition	2/3
ÚFV/DPF1d/03	Diploma Work	30	-/-	Recognition	2/4

Compulsory elective courses

     

ÚFV/TGC1/03	Group Theory, Classification and Structure of Elementary Particles	3	2/-	Examination	1/1
ÚFV/DJB1/07	Programming and Data Processing in HEP	4	2/1	Examination	1/1
ÚFV/SEB1/04	Nuclear Physics Seminar	1	-/1	Assessment	1/1
ÚFV/UMJF/06	Introduction to Experimental Methods in Nuclear Physics	4	2/1	Examination	1/1
ÚFV/JRE1/03	Nuclear Reactions	3	2/-	Examination	1/2
ÚFV/ZMSE/07	Introduction to Simulations and Modelling of Experiments	4	2/1	Examination	1/2
ÚFV/SPJ1/99	Special Practice in Nuclear Physics	3	-/3	Assessment	1/2
ÚFV/SEC1/04	Nuclear Physics Seminar	1	-/1	Assessment	1/2
ÚFV/FPL/03	Plasma Physics	3	2/-	Examination	1/2
ÚFV/KDO1/99	Methods of Clinical Dosimetry	3	2/-	Examination	1/2
ÚFV/AJF1/03	Applied Nuclear Physics	4	3/-	Examination	2/3
ÚFV/KZI1/03	Cosmic Rays	4	2/-	Examination	2/3
ÚFV/SPE1/03	Solid State Spectroscopy	5	3/1	Examination	2/3
ÚFV/SED1/04	Nuclear Physics Seminar	1	-/1	Assessment	2/3
ÚFV/PFC1/03	Selected topics in Elementary Particle Physics	4	2/-	Examination	2/3

Recommended elective courses

ÚINF/NEU1/03	Neural networks	5	2/1	Examination	1/1
ÚFV/TRV1/00	General Theory of Relativity	3	2/-	Examination	1/2
ÚFV/SVKJ/99	Student Scientific Conference	4	-/-	Assessment	1/2
ÚFV/RPJ/03	Term Project	2	-/-	Assessment	1/2
ÚFV/IKTN/03	New Information and Communication Technologies	4	1/2	Examination	2/3

Course units

Compulsory courses

Title	Quantum Field Theory I
Code	ÚFV/KTP1a/03	Teacher	Hnatič Michal
ECTS credits	6	Hrs/week	3/1
Assessment	Examination	Semester	1
T/L method	Lecture, Practical
Objective	To introduce students to quantum field theory.
Content	Relativistic quantum field conception. Particles as quantum fluctuations of the field. Lagrange formalism. Symmetries and conservation laws. Euler-Lagrange equation. The basic fields: scalar, spinor, electro-magnetic and vector. Equations for the classical fields: Klein-Gordon and Dirac, Maxwell, Lagrange and Hamilton operators. The quantisation of the free fields. Basic quantum field commutation and anti-commutation relations.
Alternate courses	ÚFV/KTP1a/99

Title	Physics of the Nucleus
Code	ÚFV/FJA1/99	Teacher	Chalupka Slavko
ECTS credits	3	Hrs/week	2/-
Assessment	Examination	Semester	1
T/L method	Lecture
Content	Basic properties of nucleus. Nuclear masses, binding energy, nuclear stability. Nuclear radius, density distribution of nuclear matter. Nuclear momentum and parity. Spin and magnetic momentum of nuclei. Quadrupole electric momentum. Theory of deuteron. Theory of scattering. Nuclear spin and isospin. Nuclear forces. Tensor character of nuclear forces. Models of atomic nucleus.

Title	Elementary Particle Physics
Code	ÚFV/FEC1/04	Teacher	Martinská Gabriela
ECTS credits	8	Hrs/week	4/2
Assessment	Examination	Semester	1
T/L method	Lecture, Practical
Objective	To provide basic knowledge of particle physics necessary for quantum field theory and quantum chromodynamics.
Content	The basic characteristics of elementary particles and conservation laws. Fundamental interactions (gravitational, weak, electromagnetic and strong forces). Classification of the particles. Determination of the mass, time of life, spin and parity of particles. Dalitz diagram. Leptons, baryons, pseudoscalar mesons. Resonances. Quark model. Symmetries and conservation laws. C-, P- and CP-parity violation. Helicity of the leptons. Neutral K mesons and CP-violation. Weak interaction and its classification. Neutral and charged currents. Cabbibo theory. The Glashow-Weinberg-Salam model. Intermediate W±, Z0 bosons.
Alternate courses	ÚFV/FEC1/03

Title	Quantum Field Theory II
Code	ÚFV/KTP1b/03	Teacher	Hnatič Michal
ECTS credits	6	Hrs/week	3/1
Assessment	Examination	Semester	2
T/L method	Lecture, Practical
Objective	To have students examine selected topics in quantum field theory.
Content	Interacting fields. The principle of symmetry and the form of interactions of quantum fields. Lagrange operator in QED. S–matrix. Wick’s theorems and Feynman diagrams. Perturbative calculation of S - matrix. S-matrix and cross section of the processes. Compton scattering of the proton on electron cross section calculation in QCD frame. Radiation corrections and the divergences of the Feynman graphs. Running coupling constant.
Prerequisite courses	ÚFV/KTP1a/03
Alternate courses	ÚFV/KTP1b/99