L.S.Costanzo, Physiology, fourth edition, 2010 Saunders, Inc, Elsevier.
S. Reed, Essential Physiological Biochemistry, 2009 John Wiley & Sons, Ltd.
B. Alberts, Molecular Biology of the Cell, sixth edition, 2002 Garland Science, Taylor & Francis Group. LLC.
Články v časopisoch.
Cellular physiology. Biochemical specialization of intracellular organelles.
Biological membranes, ion channels, membrane pumps.
Cell cycle, cell cycle regulation.
Apoptosis and regulatory mechanisms of apoptosis.
Physiology of specific organs in terms of metabolism. Muscle physiology and muscle contraction. Liver and gallbladder physiology. Kidney physiology.
Endocrine system, importance of internal secretion, mechanism of action of hormones. The second messengers and signal-transduction pathways.
To provide the introduction to the fundamental bioenergetic processes in the biological organisms. The emphasis will be on the description of the structure and function of the biomacromolecules involving in the processes of the oxidative phosphorylation. The principles of the membrane transport in the biological systems will be provide as well.
Literature:
1. D. Nicholls and S. Fergusson. Bioenergetics 4, Academic Press, 2013.
2. M. Wikström (Ed.). Biophysical and structural aspects of bioenergetics, The Royal
Society of Chemistry, 2005.
3. D. Harris. Bioenergetics at a glance, Blackwell Science Ltd., 1995.
4. V. Saks (Ed.). Molecular system bioenergetics, Wiley-VCH, 2007.
5. I. Scheffer. Mitochondria (2nd Edition), John Wiley & Sons, Inc., 2008.
6. A.D.N.J. de Grey. The mitochondrial free radical theory of aging, R.G. Landis
Company, 1999.
7. J.A.M. Smeiting, R.C.A. Sengers and J.M.F. Trijbels. Oxidative phosphorylation in
health and disease, Kluwer Academic/Plenum Publisher, 2004.
8. N.W.C. Cheetham. Introducing biological energetics, Oxford University Press, 2011.
.
Exam
During an exam, a student should be able to demonstrate his/her knowledge from the parts of Bioenergetics which are involved in the brief outline of the course.
English language
Week 1
Areas of interest of bioenergetics, its importance and position in science. Central concept of bioenergetics - chemiosmotic theory. The main sources of energy in living organisms. Processes in biological systems in which energy is consumed. Gibbs free energy. Structure and significance of adenosine triphosphate (ATP). Change in Gibbs energy during ATP hydrolysis. Reasons why ATP plays an important role in bioenergetics.
Week 2
Oxidation-reduction (redox) potential. Determination of redox potential. Influence of pH on redox potential. Relationship between Gibbs energy and redox potential. Ionic electrochemical gradient. The force of proton motion. Equilibrium distribution of ions on the membrane. Nernst potential. Donnan's equilibrium.
Week 3
Glycolysis. Glucose metabolism in different cell types. Glycolytic (Embden-Mayerhoff) path. Preparatory, cleavage and redox phase of glycolysis. Regulation of glycolysis. Regulatory enzymes in glycolysis. Post-glycolytic processes. Citrate (Krebs) cycle. Regulation of the Krebs cycle.
Week 4
Mitochondria - structure and basic functions. Mitochondrial genome. Origin of mitochondria. Respiratory chain in mitochondria. Respiratory chain components. Mechanism of electron transport in the respiratory chain. Proton transport across the inner mitochondrial membrane. Chemiosmotic proton circuit.
Weeks 5-6
NADH dehydrogenase (complex I) - structure and mechanism of functioning. Mechanism of proton pumping in NADH dehydrogenase. NADH dehydrogenase inhibitors. Succinate dehydrogenase (complex II) - structure and catalytic mechanism. Cytochrome c reductase (complex III) - structure. Mechanism of proton pumping in complex III - Q cycle. Cytochrome c oxidase (complex IV) - structure and basic functions. Catalytic mechanism of oxygen reduction and proton pumping in cytochrome c oxidase.
Week 7
ATP synthesis in mitochondria. ATP - synthase (F1- FO ATP-ase) - structure and basic functions. Mechanism of ATP synthesis. Control and regulation of ATP synthesis - thermodynamic and kinetic aspect. Uncoupling of electron transport from ATP formation. ATP synthase inhibitors. Proton transport in other ATP-ases.
Weeks 8-9
Photosynthesis - basic concepts and definitions. Chloroplasts - sites of photosynthesis. Photosystem I and photosystem II - structure and properties. Light phase of photosynthesis. Molecular mechanism of the light phase of photosynthesis. Dark phase of photosynthesis. Calvin cycle. CO2 fixation. Photosynthesis and ATP production. Evolutionary consequences of photosynthesis for the existence of life - the formation of molecular oxygen. Photosynthesis in bacteria.
Week 10
Alternative methods of creating a transmembrane proton gradient. Proton pumps. Bacteriorodopsin - structure and basic mechanisms of function. Primary sodium pumps. Classification of ion transport in biological membranes. ATP-controlled ion pumps.
Week 11
Mitochondrial aging theory. History of mitochondrial aging theory. Oxygen radical formation and oxidative stress in mitochondria. Testable predictions of mitochondrial aging theory. The possibility of extending the lifespan of biological organisms.
Week 12
Evolution of bioenergetics systems. The future of bioenergetics.
To provide the introduction to the fundamental bioenergetic processes in the biological organisms. The emphasis will be on the description of the structure and function of the biomacromolecules involving in the processes of the oxidative phosphorylation. The principles of the membrane transport in the biological systems will be provide as well.
Cvrčková F. Úvod do praktické bioinformatiky. Česko: Academia, 2006. 148 s. ISBN 80-200-1360-1.
Brown, T. A. Genomes 3. 3rd ed. New York : Garland Science Publishing. 2007. 713 p. ISBN 0-8153-4138-5
Nei M, Kuma, S. Molecular Evolution and Phylogenetics. Oxford University Press. 2000. 333 p. ISBN 978-0195135855
Lemey P, Salemi M, Vandamme A-M. The Phylogenetic Handbook: A Practical Approach to Phylogenetic Analysis and Hypothesis Testing / Edition 2. Cambridge University Press. 2009. 750 p. ISBN 978-0521730716
Manuals for used software and online tools
Introduction to bioinformatics - definition and content of the subject, brief history, overview of basic tools for biological data processing.
Biological and biomedical databases I. - search and acquisition data - PubMed, GenBank, SwissProt.
Biological and biomedical databases II. - search and acquisition data - PDB, KEGG, OMIM, REBASE.
Sequence analysis - input/output data formats, analysis of biopolymer sequences with a focus on nucleic acids - analysis of chromatograms, assembly of sequences, use of MEGA tools, Unipro UGENE tools, CAP3 server, data publication in the GenBank database.
Pairwise sequence comparisons - local comparisons, use of blastn, blastp, blastx tools in the analysis of nucleic acid and protein sequences, setting of parameters, biological significance of obtained results.
Analysis of protein sequences - identification of protein motifs and domains, use of CDD and PFAM database.
Searching for open reading frames in nucleic acid sequences - use of various tools (ORFfinder, NEBcutter).
Restriction analysis - use of various tools for searching suitable enzymes for restriction analysis (REBASE, NEBcutter).
Design and verification of primers for PCR analysis - properties of primers, use of various tools (Primer3, Primer-BLAST).
Phylogenetic analysis - comparison of multiple sequences using Clustal, MUSCLE tools, analysis of evolutionary and phylogenetic relatedness of organisms - creation and analysis of phylogenetic trees, use of various construction methods, biological significance of obtained results
Sequencing of the new generation I. - brief overview of massive parallel sequencing methods, output formats of obtained data, use of Unix operating systems in data processing.
Next generation sequencing II. - whole-genome sequencing, de novo sequencing, mapping to the reference sequence.
Next generation sequencing III. - metagenomic analysis of environmental samples
Molecular identification of organisms - global sequence comparisons (EZ Taxon, UNITE database, BOLD system).
attendance at lectures and practicals (at least 80%), continuous evaluation of the performance of tasks, final examination
Introduction to Bionformatics, free accessible biological and biomedical databases, free available bioinformatics tools. Analysis of biopolymers - nucleic acids and proteins. Pairwise sequence comparisons, multiple sequence comparisons, analysis of evolutionary and phylogenetic relatedness of biopolymers, creation and analysis of phylogenetic trees, molecular identification of organisms.
The students will acquire basic knowledge of biological databases, acquisition and analysis of sequencing data, biological approaches in phylogenetic analysis, construction and interpretation of phylogenetic trees and methods for molecular identification of organisms
Written test and final exam in writing and oral form
Week 1 - Composition of biological membranes and their models.
Week 2 - Lipid bilayers characteristics - physical, chemical and mechanical properties.
Week 3 - Membrane microdomains and their function.
Week 4 - Biological membranes function - plasma, organelle and nuclear membrane
Week 5 - Types of transports across membranes.
Week 6 - Membrane proteins - species and their functions
Week 7 - Ion channels
Week 8 - Receptors and cell signaling.
Week 9 - Transmitters and pumps and their function in the cell.
Week 10 - Propagation of signals in the body - electrical and chemical signaling.
Week 11 - Methods for studying membranes and their properties.
Week 12 - Methods to study membrane transport.
Gaining basic knowledge about the biological membranes structure, properties, and their functions. Further, obtaining the knowledge regarding physiological processes in organisms which are dependent on biological membrane functions.
H. Dugas: Bioorganic Chemistry, Wiley, London 1995.
1. Individual work and activity in seminars.
2. Passing a written exam with a success rate of min. 51%.
Slovak language
Teaching is carried out in person or, if necessary, online using the MS Teams or BBB (BigBlueButton) tool. The form of teaching is specified by the teacher at the beginning of the semester, updated continuously.
Metodology of organic chemistry used to understanding of processes in living forms. Mechanism of the basic biochemical processes including proteosynthesis, enzymatic catalysis, nucleic acid chemistry, photosynthesis.
1. BUZKOVÁ, K. 2006. Fitness jóga. Praha: Grada. 167 s.
2. ČECHOVSKÁ, I., MILEROVÁ, H., NOVOTNÁ, V. Aqua-fitness. Praha: Grada. 136 s.
3. EVANS, M ., HUDSON, J., TUCKER, P. 2001. Umění harmonie: meditace, jóga, tai-či, strečink. 192 s.
4. JARKOVSKÁ, H., JARKOVSKÁ, M. 2005. Posilováni s vlastním tělem 417 krát jinak. Praha: Grada. 209 s.
5. KOVAŘÍKOVÁ, K. 2017. Aerobik a fitness. Karolium, 130 s.
Completion: passed
Condition for successful course completion:
- active participation in line with the study rule of procedure and course guidelines
- effective performance of all tasks- aerobics, water exercise, yoga, Pilates and others
Slovak language
Brief outline of the course:
1. Basic aerobics – low impact aerobics, high impact aerobics, basic steps and cuing
2. Basics of aqua fitness
3. Basics of Pilates
4. Health exercises
5. Bodyweight exercises
6. Swimming
7. Relaxing yoga exercises
8. Power yoga
9. Yoga relaxation
10. Final assessment
Students can engage in different sport activities offered by the sea resort – swimming, rafting, volleyball, football, table tennis, tennis and other water sports in particular.
Content standard:
The student demonstrates relevant knowledge and skills in the field, which content is defined in the course syllabus and recommended literature.
Performance standard:
Upon completion of the course students are able to meet the performance standard and:
- perform basic aerobics steps and basics of health exercises,
- conduct verbal and non-verbal communication with clients during exercise,
- organise and manage the process of physical recreation in leisure time
T.E. Creighton: Proteins - structures and molecular properties, 1993, W.H. Freeman and Company - New York.
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.
Successful completion of the exam, which consists of two parts: (i) written and (ii) oral part. The student passes the exam if s/he obtains at least 60% of the points in the written part and at the same time adequately answers the asked questions in the oral part.
1. Introduction. Chemical catalysis – theory of transition state.
2. Enzyme catalysis - types and examples.
3. Cofactors. Active site - lock and key, induced fit. Enzymes - classification.
4. 3D structure of proteins. Noncovalent interactions. Secondary, tertiary and quaternary structures. Convergent and divergent evolution. Multienzyme complexes. Dyanmics of proteins.
5. Ligand binding. Thermodynamics and konetics. Techniques.
6. Chemical kinetics. Basic equations of enzyme kinetics.
7. Regulations of enzyme activity - examples.
8. Conformational change, allosteric regulation. Regulation of metabolic pathways.
9. Experimental determination of enzyme activity. pH and temperature dependence of enzyme catalysis.
10. Determination of individual rate constants. Stop flow. Enzyme-substrate complementarities and the use of binding energy in enzyme catalysis.
11. Reversible inhibition.
12. Irreversible inhibition.
13. Specificity and control mechanisms. „Moonlighting“ enzymes. Applications of enzymes (organic solvents). Catalytic antibodies. Extremophiles. Directed selection of enzymes. Enzymatic reactions with multiple substrates.
Understand the principle of enzyme catalysis. Learn to use the basic equations of enzyme kinetics. Ability to determine the basic kinetic and thermodynamic parameters of the enzyme-catalyzed reaction from experimental measurements.
combination of written and oral examination
Written tests during the semester and final written and oral examination
Week 1 - Using animal models of human disease - why it's important.
Week 2 - Types of animal models - small animals - mice, rats
Week 3 - Types of animal models - primates
Week 4 - Types of animal models - Drosophila insects, Zebra fish
Week 5 - Use of different cell types as models for human diseases.
Week 6 - Transport across cell membranes - diseases caused by disorders of transport across ion channels.
Week 7 - Models of diseases caused by disorders of transport through ion channels - at the level of cells and whole organisms.
Week 8 - Cell metabolism - diseases caused by disorders of metabolic pathways.
Week 9 - Cell metabolism - diseases caused by disorders of metabolic pathways - models at the level of cells and animals.
Week 10 - Auoimmune and degenerative disorders - cell and animal models.
Week 11 - Organoids - as models at the level of organs and tissues.
Week 12 - Molecular models of disease - Artificial intelligence modeling
To get familiar with the models of human diseases used at the cellular and whole organism level.
Mycek & Pogue, "Handbook of Biomedical Fluorescence", Dekker, 2003. R. Splinter & B.A. Hooper, "An introduction to Biomedical Optics", Taylor&Francis, 2007. Lakowicz, “Principles of fluorescence spectroscopy“, Springer 2006. Muzykantov & Torchilin, “Biomedical aspects of drug targeting“, Kluwer Academic Publishers 2002
Presentation, test, oral exam.
The student will be able to present the knowledge acquired in the areas described in the note. Skills acquired in photochemistry and photobiology may be presented in the form of an oral presentation.
Slovak, English
Lectures:
1. tissue optics - basic parameters describing the application of light in the detection of changes in tissue.
2. Detection and application of endogenous and exogenous fluorophores - definition of light sensitive molecule, difference between endo- and exo-fluorophores and intra- and extracellular processes.
3. Photophysics - description of processes active in photoreaction. Formation of reactive oxygen species in solution.
4. photochemistry - chemical changes in fluorophore and environment during photoreaction. The ability to detect these changes in steady state and time resolved measurements.
5. the application of luminescent probes to measure tissue oxygenation, acidification and oxidative stress in tissue by spectroscopic and microscopic techniques.
6. processes of light application in cells - influence of these processes on subcellular organelles.
7. cell death as a consequence of photoreaction - description of selected parameters active in signaling pathways leading to apoptosis, necrosis and autophagy.
8. photodynamic therapy - mechanism and basic principles of treatment at the cellular level.
9. application of protoporfyrin IX in photodetection of tissue oxygenation and cancer detection.
10. Application of phototherapy and photodiagnostics in cancer and non-cancerous diseases in the clinic.
11. Singlet oxygen - production and detection of singlet oxygen, application in practice.
12. Organometallic complexes - photoreaction in solar cells, application in practice.
Training in phototreatment and photodetection using spectrofluorimeters, fluorescence and absorbance readers for detection of metabolic changes in cells, flow cytometer for analysis of oxidative stress in cells, photodynamic therapy in cell cultures and tissues. Simulation of photodynamic therapy in ovo.
Presentation: oral presentation of new trends in photophysics, photochemistry and photobiology.
Introduction to the problems of interaction of light with biological systems, in particular the role of light-activated molecules in biology and medicine. Description of relevant spectral, photochemical, and photobiological concepts used in the field. In addition to basic knowledge of photochemistry and photobiology, students will become familiar with the methods and detection systems used in this field. Applications will be focused on light-activated therapy. Students will be trained in the fundamentals of photodynamic therapy.
BILASOVÁ, V. – ANDREANSKÝ, E.: Epistemológia a metodológia vedy. Prešov: FF PU 2007.
FAJKUS, B.: Filosofie a metodologie vědy. Praha: Academia 2005.
BEDNÁRIKOVÁ, M. Úvod do metodológie vied. Trnavská univerzita: Trnava 2013.
DÉMUTH, A. Filozofické aspekty dejín vedy. Trnavská univerzita: Trnava 2013.
FEYERABEND, P.: Proti metodě. Prel. J. Fiala. Praha: Aurora 2001.
KUHN, T. S.: Štruktúra vedeckých revolúcií. Prel. Ľ. Valentová. Bratislava 1982.
Attendance: A student may have one unexcused absence in seminar at the most. Absence in more than one seminar must be reasoned and substituted by consultations. Conditions of continuous and final control: during the semester a student is continuously checked and assessed according to his/her activity. To be awarded the credits, a student must pass a test from knowledge obtained in the lectures and seminars. Results of the test will make up the final grade.
Slovak
• Falsificationism and critical realism by K. R. Popper.
• Development and critique of the Popper’s concept.
• Understanding the science development in the work by T. S. Kuhn.
• Methodology of scientific research programmes of I. Lakatos.
• Methodological anarchism of P. Feyerabend.
• W.V.O. Quine – the issue of relation between theory and empiricism.
The course is aimed at getting familiar with the basic issues of methodology and philosophy of science. Significant part will be devoted to presenting the main concepts of the philosophy of science in the 20th century and this aim will be achieved by reading the source and interpretive texts.
1. B. E. A. Saleh, M. C. Teich, Fundamentals of Photonics, John-Wiley & Sons 2007 New Jersey
2. W. Demtroder, Laser Spectroscopy, Springer-Verlag 2008 Berlin
Oral exam where the students present theoretical knowledge of topics listed in the course syllabus and demonstrate the ability to find connections between the different areas of photonics and optics.
Slovak language
1. Ray optics.
2. Wave optics.
3. Beam optics.
4. Electromagnetic optics.
5. Polarization optics.
6. Photon optics.
7. Resonator optics.
8. Laser amplifiers.
9. Lasers.
10. Optical devices: acousto-optics.
11. Optical devices: electro-optics.
12. The basics of non-linear optics.
Students completing the course will gain basic knowledge in the field of photonics with a focus on the practical use of optical phenomena for scientific purposes. Students will also get an overview of optical components and equipment that are used in photonic and/or laser experiments.
To acquaint students with based problems of the phase transitions and critical phenomena.
Basic literature:
BOBÁK, A., Phase Transitions and Critical Phenomena, Project 2005/NP1-051 11230100466, European Social Fund, Košice 2007.
STANLEY, H.G.: Introduction to Phase Transitions and Critical Phenomena, Clarendon Press Oxford, 1971.
Other literature:
REICHL, L.E.: A Modern Course in Statistical Physics, University of Texas Press, Austin, 1980.
PLISCHKE, M., BERGERSEN, B.: Equilibrium Statistical Physics, World Scientific, 1994.
KADANOFF, L.P.: Statistical Physics, Statistics, Dynamics and Renormalization, World Scientific, 2000.
To successfully complete the course, the student is required to understand the concept of phase transitions and critical phenomena based on thermodynamics and statistical physics. The successful graduate will be able to apply this apparatus to simpler models of magnetic systems using exact or approximate methods. The condition for obtaining credits is successful completion of the final oral exam. The credit evaluation of the course takes into account the following student workload: direct teaching (2 credits), self-study (1 credit), and assessment (1 credit). The minimum limit for completing the course is to obtain at least 50% of the total score, using the following rating scale: A (90-100%), B (80-89%), C (70-79%), D (60- 69%), E (50-59%), F (0-49%).
1. Slovak,
2. English
The course is realized in the presence form, if necessary remotely in the MS Teams environment.
1. Thermodynamics and phase transitions.
2. Conditions of stability of the equilibrium state of the magnetic system.
3. Phase equilibrium, phase transitions. Clausius-Clapeyron equation.
4. Classical (Ehrenfest) classification of phase transitions: phase transitions of the first and second kind.
5. Landau's description of phase transitions of the second kind.
6. Critical indices, universality. Definition of critical indices for the magnetic system. Thermodynamic relations between critical indices.
7. Basic microscopic models of magnetic phase transitions. Heisenberg and Ising model.
8. Exact solutions of microscopic models: one-dimensional and two-dimensional Ising model.
9. Thermodynamic functions for a one-dimensional Ising model.
10. Some approximate methods of solving the Ising model.
11. Landau's theory of phase transitions.
12. Phases of nuclear matter.
To acquaint students with the basic problems of the theory of phase transitions and critical phenomena and their solutions using the methods of thermodynamics and statistical physics. Emphasis is placed on the study of phase transitions in magnetic systems, through several theoretical models, but the course also covers other areas such as phase transitions in nuclear matter.
BROWN, Terence A. Gene cloning and DNA analysis: an introduction. Wiley-blackwell, 2020.
DALE, Jeremy W.; VON SCHANTZ, Malcolm; PLANT, Nicholas. From Genes to Genomes: Concepts and Applications of DNA Technology. John Wiley & Sons, 2011.
HOWE, Christopher. Gene cloning and manipulation. Cambridge University Press, 2007.
Independent elaboration of a presentation on a topic related to the subject. Completion of exercises. Oral examination
English
Cloning and expression of genes in yeast and animal cells. In vitro amplification techniques for DNA and RNA molecules. In vitro mutagenesis. Biotechnology and genetic engineering. Preparation of biologically active substances and recombinant vaccines.
Obtaining the knowledge on cloning and gene expression in various host systems, their use in biotechnological and biological research. Acquisition of knowledge about more complex and latest genetic methods and procedures and their use in solving specific biological problems.
Attendees will learn actual methods used for computer simulations of molecules. By using practical examples he/she will get hands-on experience with standart methods.
1. Leech: Molecular Modeling: Principles and Applications, Longmann, 1996.
2. M.P. Allen, D.J. Tildesley: Computer Simulation of Liquids, Oxford University Press, 1989.
3. Polák, Zahradník: Kvantová chemie, SNTL/Alfa , 1985.
4. P. W. Atkins, R. S. Friedman: Molecular Quantum Mechanics.Oxford University Press, 1997
Elaboration of the project - characterization of the chosen molecule using methods mentioned in the course. Exam. Written form, including Q/A part allowed due to corona-virus measures.
Born-Oppenheimer approximation. Methods and approaches of classical molecular mechanics. Force fields and force constants for polyatomic simulations. Force fields for biomolecular simulations (CHARMM, AMBER, MM2-4, MMFF, CVFF,...). Independent electron approximation. Hartree-Fock self-consistent field method. Post Hartee-Fock methods. Density functional theory (DFT) - basic principles and implementation. LSDA approximation and gradient corrected methods. Hybrid methods. Wavefunction and electron density analysis. Limits and perspectives of classical and quantum molecular mechanics. Alternativ methods. Ab initio computations and experimental observables. Experimental and computational observables. Molecular dynamics and stochastic methods. Integration algorithms. Car-Parinello dynamics.
Attendees will learn actual methods used for computer simulations of molecules. By using practical examples he/she will get hands-on experience with standart methods.
1. JUNGER, J. et al. Turistika a športy v prírode. Prešov: Fakulta humanitných a prírodných vied PU v Prešove. 2002. 267s. ISBN 80-8068-097-3.
2. PAVLÍČEK, J. Člověk v drsné přírodě. 3. vyd. Praha: Práh. 2002. ISBN 8072520598.
3. WISEMAN, J. SAS: příručka jak přežít. Praha: Svojtka & Co. 2004. 566s. ISBN
8072372807.
Completion: passed
Condition for successful course completion:
- active participation in line with the study rule of procedure and course guidelines,
- effective performance of all the tasks defined in the course syllabus
Slovak language
Brief outline of the course:
1. Principles of conduct and safety in the movement in unfamiliar natural environment
2. Preparation and guidance of a hike tour
3. Objective and subjective danger in the mountains
4. Principles of hygiene and prevention of damage to health in extreme conditions
5. Fire building
6. Movement in the unfamiliar terrain, orientation and navigation
7. Shelters
8. Food preparation and water filtering
9. Rappelling, Tyrolian traverse
10. Transport of an injured person, first aid
Content standard:
The student demonstrates relevant knowledge and skills in the field, which content is defined in the course syllabus and recommended literature.
Performance standard:
Upon completion of the course students are able to meet the performance standard and should:
- acquire knowledge about safe stay and movement in natural environment,
- obtain theoretical knowledge and practical skills to solve extraordinary and demanding situations connected with survival and minimization of damage to health,
- be able to resist and face situations related to overcoming barriers and obstacles in natural environment,
- be able implement the acquired knowledge as an instructor during summer sport camps for children and youth within recreational sport.
- Režňák I. et al., Modern imaging methods in medical diagnostics, Vyd. Osveta, Martin, 1992.
- Jurga Ľ. et al., Basics of Medical Radiology, Script of LF UPJŠ, Košice, 1990.
- Mc Ainsh T.F., Physics in Medicine and Biology, Pergamon Press, Oxford, 1987.
- Huda W., Slone R.M., Review of Radiologic Physics, Lippincot, London, 1995
- Bushberg J.T, et al., The essential physics of imaging, Lippincott Williams, Philadelphia, 2002.
To complete successfully the course, the student has to demonstrate the understanding of the basic notions and the physical principles of medical technology, especially of the diagnostic (imaging). In addition to attending classes, it is necessary for the student to study some specifics (details) of the discussed issues within self-study. The conditions for obtaining credits is, in addition to participation in teaching and passing the final exam, a successful completion of a written test. The minimum limit for passing the exam is to obtain 51% of the total score, which takes into account all required activities. The credit evaluation takes into account the following student workload: direct teaching - 1 credit, self-study of recommended literature - 1 credit, continuous study for the test and evaluation - 1 credit.
Rating scales: A - 91% -100% points, B - 81% -90% points, C - 71% -80% points, D - 61% -70% points, E - 51% -60% points.
Slovak, English
Recommended range of lessons (in hours): Weekly: 2/0
For the period of study: 26/0
Method of study: Teaching is carried out in person, if necessary remotely, in the environment of MS Teams.
Number of ECTS credits: 3
Degree of studz: I. resp. II.
Prerequisites: none
1. Division of medical technology into diagnostic and therapeutic. A brief history of medical technology.
2. Ultrasound diagnostics (USG). Basic terms - used frequencies, wave intensities, acoustic impedance, ultrasound generation, absorption of ultrasonic waves, reflection and refraction of waves, space resolution, focusing of waves. Types of ultrasound imaging: type A and B imaging, creation of a dynamic (real time) image, time imaging (time motion). Some methods of signal processing: digitization, time-dependent signal balancing, etc.
3. Ultrasound diagnostics based on Doppler effect. Systems with unmodulated and modulated carrier waves, examination of blood flow in the organism. Possibilities of ultrasound diagnostics and its advantages. Interaction of ultrasound with tissues (active and passive), principles of ultrasound therapy.
4. Transmission computed tomography (CT). Absorption of X-rays in tissues, evaluation of relationships between the intensity of incident and the intensity of penetrated radiation, image constructions.
5. Construction of a CT equipment, X-ray source, detection system, evaluation and processing of results. Types (generations) of CT devices. Implementation of CT examination and image evaluation. 6. Emission computed tomography (ET). Single-photon emission tomography - selection of suitable radionuclides and evaluation of the distribution of radionuclides in the body.
7. Construction of emission tomograph, benefits and use of emission tomography. Positron emission tomography (PET). Positron emitters, positron - electron annihilation, coincident photon detection. Construction of PET equipment, benefits and use of PET.
8. Thermography - basic concepts. Contact thermography - properties of liquid crystals, detection of changes in surface temperature of an organism. Contactless thermography. Radiation of bodies, detection of infrared radiation, distribution and properties of detectors. Thermograph design, use of thermography in medicine and other areas.
9. Magnetic (resonance) tomography (MR/MT). Principles of nuclear magnetic resonance - magnetic moment of the nucleus, movement (precession) of magnetic moments in magnetic field. Longitudinal and transverse relaxation times, causes of their change. Methods of measuring relaxation times.
10. Acquisition of image information - use of magnetic field gradients, methods of their creation. Design of magnetic tomographs - basic magnet, high frequency coils, shielded rooms, evaluation systems. Possibilities and use of MT, the use of contrast agents.
11. Lasers in medical technology. Principle of laser operation, spontaneous and induced emission, three-level lasers (solid, gas), construction of lasers. Properties of laser radiation and the effect of laser beam on biological objects (tissues). Use of lasers in various fields of medicine.
12. Principles of radiotherapy. Interaction of various ionizing particles (photons, electrons, neutrons, protons) with the environment. Biological effects of ionizing radiation, applied doses, survival curves. New methods of irradiation, the use of Bragg maximum in hadron irradiation therapy, neutron capture therapy. Possibilities of ionizing radiation beam modification.
After completing the lectures, the student will have the knowledge to understand the principles and operation of modern medical devices, such as e.g. ultrasound diagnostics, computed transmission tomography, computed emission (positron) tomography, magnetic (resonance) tomography, radiotherapy and lasers, and to be able to explain the principles and use of the facilities to others. The acquired knowledge should also be a good prerequisite for a possible employment of the student in companies producing or operating modern medical technology.
Y. Song, D. Cheng, L. Zhao, Microfluidics, Wiley-VCH, 2018
J. Gieseler et al., Optical tweezers — from calibration to applications: a tutorial, Advances in Optics and Photonics 13, 74-241 (2021)
Project focused on the construction of optical tweezers and its use for manipulating objects in a microfluidic system.
Slovak, English.
1. Overview of lab-on-chip technologies in biophysical and biomedical applications.
2. Physical basis of fluid flow, microrheology, heat transfer.
3. Instrumentation of microfluidic systems.
4. Basics of optical micromanipulation, sources of laser radiation, design of optical systems, optical imaging.
Project:
5-6. Construction of an optical tweezers apparatus.
7. Design and preparation of a microfluidic system.
8-9. Calibration of optical tweezers stiffness,
10. Measurement of fluid flow rate in microchannels.
11-12. Numerical modeling of fluid flow and microstructure motion using the finite element method (eg COMSOL Multiphysics).
By completing the course, students will gain basic knowledge about the use of microfluidic systems. We will focus on lab-on-chip technologies associated with optical micro-manipulation of biologically relevant samples. Students will build their own experimental equipment, and they will learn how to design and fabricate simple microfluidic chips.
1. JUNGER, J. et al. Turistika a športy v prírode. Prešov: FHPV PU v Prešove. 2002. ISBN 8080680973.
Internetové zdroje:
1. STEJSKAL, T. Vodná turistika. Prešov: PU v Prešove. 1999.
Dostupné na: https://ulozto.sk/tamhle/UkyxQ2lYF8qh/name/Nahrane-7-5-2021-v-14-46-39#!ZGDjBGR2AQtkAzVkAzLkLJWuLwWxZ2ukBRLjnGqSomICMmOyZN==
Completion: passed
Condition for successful course completion:
- active participation in line with the study rule of procedure and course guidelines
- effective performance of all tasks: carrying a canoe, entering and exiting a canoe, righting a canoe, paddling
Slovak language
Brief outline of the course:
1. Assessment of difficulty of waterways
2. Safety rules for rafting
3. Setting up a crew
4. Practical skills training using an empty canoe
5. Canoe lifting and carrying
6. Putting the canoe in the water without a shore contact
7. Getting in the canoe
8. Exiting the canoe
9. Taking the canoe out of the water
10. Steering
a) The pry stroke (on fast waterways)
b) The draw stroke
11. Capsizing
12. Commands
Content standard:
The student demonstrates relevant knowledge and skills in the field, which content is defined in the course syllabus and recommended literature.
Performance standard:
Upon completion of the course students are able to meet the performance standard and:
- implement the acquired knowledge in different situations and practice,
- implement basic skills to manipulate a canoe on a waterway,
- determine the right spot for camping,
- prepare a suitable material and equipment for camping.
EN
Ligand binding to macromolecules, Michaelis-Menten model, Equilibrium thermal denaturation of proteins and nucleic acids, equilibrium chemical denaturation of proteins and nucleic acids, nonequilibrium thermal denaturation of proteins and nucleic acids, protein aggregation, kinetic modeling of biological processes, introduction to machine learning, PCA, LDA, logistic regression, SVM, deep learning and computer vision (convolutional neural networks).
1. preparation and presentation of the selected publication 2. oral examination
Slovak, English
1. Binding of ligands to macromolecules 2. Michaelis-Menten model 3. Equilibrium thermal denaturation of proteins and nucleic acids 4. Equilibrium chemical denaturation of proteins and nucleic acids 5. Non-equilibrium thermal denaturation of proteins and nucleic acids 6. Protein aggregation 7. Kinetic modeling of biological processes 8. Introduction to machine learning 9. Principal Component Analysis 10. Linear discriminant analysis 11. Logistic regression and SVM 12. Deep learning and computer vision (convolutional neural networks)
Introduction to mathematical description of physical models describing experimental measurements of thermal stability, enzyme catalysis, ligand binding. Use of machine learning to solve biological problems.
The course is oriented on modern methods of structural analysis of metals. Main topics are: optic microscopy, electron microscopy (TEM, SEM),electron microprobe analysis and X-ray diffractometry.
1. P.W. Hawkes, J.C.H. Spence, Science of Microscopy, Springer, 2007, ISBN: 10:0-387-25296-7.
2. Vitalij Pecharsky, Peter Zavalij, Fundamentals of Powder Diffraction and Structural characterization of Materials, Publisher: Springer (March 3, 2005)
ISBN-10: 0387241477, ISBN-13: 978-0387241470
3. Jens Als-Nielsen, Des McMorrow, Elements of Modern X-ray Physics, Publisher: Wiley; 2 edition (April 4, 2011),ISBN-10: 0470973943, ISBN-13: 978-0470973943.
4. Current Publications in the field of TEM, REM, X-ray
5. M.D. Graef, M.E. Henry, Structure of Materials, Cambridge Univ. Press, 2012, ISBN:978-1-107-00587-7.
6. S. Amelinckx, D. Dyck, et al, Electron Microscopy - Principle and Fundamentals, VCH, 1997, ISBN: 3-527-29479-1.
ÚFV/SVL/03
For successful completing of the subject student has to show after taking exam adequate knowledge from the area using sophisticated research infrastructure for structural analysis of solids. Content of the subject is focused study of structure analytical methods as TEM, SEM, STEM and X-ray techniques. Credits evaluation takes into account taking part at the lectures - 3credits, study of recommended literature -1credit, working out of experimental protocol from OM and EM -2 credidts and study of recommended literature -2 credits, 2 credits – project, 1 credit – study for 2 written tests (EM and X-ray) - 1 credit. Minimal value to obtain evaluation for is reach 50% of each evaluation (tests and project) points. Point ratio protocol/test EM/TEST X-ray is 40/30/30.
1. English
Lectures can be done at presence form or online using MS Teams. Education form is updated at the begining of the subject. All ppt presentations are accesible in LMS UPJŠ.
1. week:Optic microscopy.
2.- 4. week: Electron microscopy: Electron beam instruments, Electron optics, Electron lences and deflection systems, Transmission electron microscopy - principle and construction. Electron – specimen interactions. Electron diffraction. Kikuchy lines.
5.week (online lecture):Scanning electron microscopy – principle and cnstrucion. Scanning transmission electron microscopy. High Voltage electron microscopy.
6. week (online lecture): Electron microprobe analysis: WDX spectrometer, EDX spectrometer,
7.-8. week (online lecture): Auger electron spectrometer. Self-emision microscopy. Convergent beam diffraction.
9.-10. week (online lecture): 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, 11.-13. week (online lecture): Structure factor, Ocupation factor, Atomic displacement factor, Peak intensity, shape and symmetry, Sherrer equation. Peak profile, Rietweld method. Qualitative phase analysis, parameters of elementary cell, Profile analysis of diffraction peak and interpretation of profile analysis.
Optic microscopy. Electron microscopy: Electron beam instruments, Electron optics, Electron lences and deflection systems, Transmission electron microscopy - principle and construction. Electron – specimen interactions. Electron diffraction. Kikuchy lines. Scanning electron microscopy – principle and cnstrucion. Scanning transmission electron microscopy. High Voltage electron microscopy. Electron microprobe analysis: WDX spectrometer, EDX spectrometer, Auger electron spectrometer. Self-emision 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, Ocupation factor, Atomic displacement factor, Peak intensity, shape and symmetry, Sherrer equation. Peak profile, Rietweld method. Qualitative phase analysis, parameters of elementary cell, Profile analysis of diffraction peak and interpretation of profile analysis.
75/25
Student due to lecrures and experimental work after final exam demonstrates that he/she meets expectations according to the standards of the subject, which is predicted by short content andreferences. Student is able to use modern methods for structural analysis of metals. He has experiences with optic microscopy, electron microscopy (TEM, SEM, STEM),electron microprobe analysis and X-ray diffractometry.
Participation in lectures (also by distance learning).
The lecturer conducting the lecture/seminar will excuse the justified absence of the student (sickness, family reasons, etc.) at a maximum of two lectures/seminars during the semester without the need for a substitute. In the event of longer-term justified absence (e.g. due to sickness), the student must provide evidence of mastery of the missed course content by means of an agreed substitute; oral examination
Cell signaling system. Molecular basis of neoplastic cell transformation leading to development of cancer - oncogenes, tumor suppressing genes, regulatory regions of DNA. Gene mutations and DNA repair mechanisms. Induced pluripotent stem cells.
Current trends and advances in the study of nucleic acids, their biological significance in cell metabolism. Gene therapy. Gene editing. Gene silencing.
The classification of viruses based on genetic material, the effect of physical and chemical factors on viruses. Biochemistry of viruses. Virus replication. Viral oncogenicity. Retroviruses and HIV. Pandemic viruses - Covid, SARS, MERS, Ebola, influenza papillomaviruses.
Prions. Aptamers and nanobioconjugates.
Molecular basis of the manifestation of genetically determined diseases and their detection and diagnostic.
1. H. Friebolin: Basic One- and Two-Dimensional NMR Spectrocopy, 5. Ed., Wiley, 2010.
2. T. D. W. Claridge: High-Resolution NMR Techniques in Organic Chemistry, 5. Ed., Elsevier, 2016.
3. Atta-ur-Rahman, M. I. Choudhary: Solving Problems with NMR spectroscopy, Academic Press 1996.
1. Attendance at lectures and seminars (this also applies to the online form of teaching)
2. Activity at seminars (also applies to the online form of teaching) - theoretical preparation of students for all seminars is required
3. Elaboration of written assignments (20% of the total evaluation) according to the teacher's instructions.
4. Passing the final test (30% of the total evaluation).
5. Exam (written 25% and oral part 25%).
english
Teaching is carried out in person or, if necessary, online using the MS Teams or BBB (BigBlueButton) tool. The form of teaching is specified by the teacher at the beginning of the semester, updated continuously.
1. Advanced 1D NMR methods
a) 13C NMR experiments – APT, DEPT
b) NOE experiments
c) Selective experiments
2. 2D NMR methods
a) Proton-proton correlation through coupling – COSY, TOCSY
b) Proton-proton correlation through space - NOESY
c) Proton-carbon correlation – HSQC/HMQC/HETCOR, HMBC, H2BC, EXSIDE
d) Carbon-carbon correlation - INADEQUATE
The aim of the course is to get acquainted with 1D and 2D NMR methods and the application of the acquired knowledge in solving NMR problems.
To familiarize students with biologically and physically inspired optimization, simulation and prediction techniques. To expand students' creativity and programming skills by applying heuristic techniques in solving applied problems.
Hartmann, A. K., Rieger, H., Optimization Algorithms in Physics, Wiley, 2002
Reeves, C. R., Rowe, J. E., Genetic Algorithms: Principles and perspectives, Kluwer, 2003
Mitchell, M., Complexity. A Guided Tour, Oxford University Press, 2009
Solé, R. V., Phase Transitions, Princeton University Press, 2011
Ilachinski, A., Cellular Automata. A Discrete universe, World Scientific, 2002
Haykin, S., Neural Networks. A Comprehensive Foundation, Prentice-Hall, 1999
Actual literature and data related to problem sets
Monitoring progress in solving applied projects.
Oral examination (50%), results and quality of the
personal presentation of the projects (50%).
Monitoring progress in solving applied projects. From given set of problems, the student must pick 1 to 3 projects and develop functioning implementation of the solution in form of computer program. In case of more challenging problems, collaborative work of students is acceptable, but each student must be able to present her/his individual contribution.
English language is essential for students as "lingua franca" for the latest advancements and applications of optimization techniques.
The subject is taught using direct contact form. Should the epidemiological situation (or other relevant circumstances) mandate, the distant form will be used, preferentially using MS Teams learning environment.
1. Fundamentals terms and definitions of optimization theory. Physical laws as optimization tasks. Variational principle.
2. Model optimization problems. Basic types of objective functions. Classification of optimization methods. Computational scaling of optimization methods. Big O notation. Parallelization, Metcalf's law, Amdahl's bottleneck.
3. Exhaustive search, Gradient-based optimization techniques.
4. Evolutionary algorithms. Canonical Genetic algorithm. Genetic algorithms as Markov processes. Statistical Mechanics description of Genetic Algorithms.
5. Monte Carlo simulation and simulated annealing. Metropolis algorithm and statistics of sampling in solution space.
6. Swarm optimization. Ant algorithms.
7. Cellular Automata and their applications in simulations of complex systems.
8. data structures and representation of solution space and optimization problems. Compression of information and symmetry. Manifolds.
9. Generators. grammars and languages. Genetic programming. AST and operations on AST representation of programs.
10. Fractals. Lindenmayer systems. Life-like and agent-based models.
11. Evolutionary games. Evolution of cooperation.
12. Fundamentals of Neural Networks. Stochastic gradient optimization.
examination (50%), quality of the project (50%)
To familiarize students with biologically and physically inspired optimization, simulation and prediction techniques. To expand students' creativity and programming skills by applying heuristic techniques in solving applied problems.
Upon successful completion of course, student shall possess knowledge about most typical non-traditional optimization techniques, as well as practical experience of solving concrete problems.
examination
By using examples from the biology to learn applications of optimization techniques on study and interpretation of complex systems. Introduction to new paradigms in the area of systems biology.
The actual scientific papers.
Presentation of the project in written form. Oral exam and discussion of the presented project.
Should corona-virus quarantine persist, written report and answer to posed questions suffice.
Complex systems, emergent behavior. Evolutionary theory and memetics. Application of optimization 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.
By using examples from the biology to learn applications of optimization techniques on study and interpretation of complex systems. Introduction to new paradigms in the area of systems biology, including parasite/host coevolution.
To give basic knowledges about modern trends and theoretical methods in description of non-equlibrium phenomena in physics.
1. Landau L.D., Lifshitz E.M.: Teoreticheskaja fizika X: Lifshitz E.M., Pitaevskij L.P.: Fizicheskaja
kinetika, Moskva, Fizmatlit 2002
2. K. Huang: Statistical mechanics, John Wiley and Sons, Inc., New York-London, 1963.
D.N.Zubarev: Neravnovesnaja statisticheskaja termodinamika, Moskva, Nauka, 1971.
A.N.Vasiliev Kvantovopolevaja renormgruppa v teorii kriticeskogo povedenija i stochasticeskoj
dinamike, Sankt-Peterburg, Izd. Peters. Inst. Of. Nuclear physics (1998) 773 (The Field Theoretic
Renormalization Group in Critical Behavior Theory and Stochastic Dynamics, Chapman & Hall
CRS Press Company New York, 2004)
slovak and english
Problems of kinetic theory - formulations of basic tasks. Distribution function. Liouville theorem. Liouville operator. Kinetic Boltzman equation. H-theorem. Maxwell distribution. Transport phenomena. Conservation laws. Derivation of the macroscopic eduqtions in leading and next-to-leading approximation. Hydrodynamic approximation. Set of equations for density, mean velocity and temperature. Derivation of continuity equation, Navier-Stokes equation, heat conductivity equation. Derivation of vicosity and diffusivity coefficients from microscopic description. Stokes laws. Reynolds number. Dynamical derivation of kinetic equation. Liouville (master) equation for N-particle distribution function. Bogolyubov set of equations for distribution functions.
Principle of weakening of statistical correlations. Equation for one-particle distribution function. Brown motion. Langevin equation. Fokker-Planck equation and specific tasks.
To give basic knowledges about modern trends and theoretical methods in description of non-equlibrium phenomena in physics.
1. Alan J. Gottesman and Sally G. Hoskins (2013) CREATE Cornerstone: Introduction to Scientific Thinking, a New Course for STEM-Interested Freshmen, Demystifies Scientific Thinking through Analysis of Scientific Literature CBE—Life Sciences Education; Vol. 12, 59–72, Spring 2013
2. Abdullah C. et al (2015)Critical Analysis of Primary Literature in a Master’s-Level Class: Effects on Self-Efficacy and Science-Process Skills; CBE—Life Sciences Education Vol. 14, 1–13, Fall 2015
3. Price et al 2021 A Detailed Characterization of the Expert Problem-Solving Process in Science and Engineering: Guidance for Teaching and Assessment CBE—Life Sciences Education • 20:ar43, 1–15, Fall 2021
4. Purugganan et al 2004 How to Read a Scientific Article Cain Project for Engineering and Professional Communication, Rice University, 2004
5. Hubbard K. and Dunbar S. 2017 Perceptions of scientific research literature and strategies for reading papers depend on academic career stage PLoS One. 2017; 12(12): e0189753
6. Hoskins S (2019) CREATE a Revolution in Undergraduates’ Understanding of Science: Teach through Close Analysis of Scientific Literature; https://doi.org/10.1162/DAED_a_01764
Publications from top level journals in the field published within last three years. Publications should contain topics regarding the focus of the research in the Department of Biophysics, and also a new approaches or methods.
Presentation of the publication, active and critical participation in discussion regarding the presented results, active attendance at the lectures.
Week 1 - Introduction to the analysis of scientific literature - access, databases and selection of articles.
Week 2 - Methods of evaluating scientific literature - critical thinking, ability to evaluate experimental design and results.
Week 3 - Methods of evaluation of scientific literature - creation of alternative explanations.
Week 4 - Module 1 - selection of 3 articles with the same research subjects but different interpretations; division into working groups
Week 5 - Evaluation and comparison of experimental approaches in articles - analysis of working groups.
Week 6 - Evaluation and comparison of hypotheses, experimental results and discussion in articles - analysis of working groups.
Week 7 - Continuous assessment of students in the evaluation of literature - test
Week 8 - Module 2 - selection of 3 articles with the same research subjects but different interpretations - assignment for individuals
Week 9 - Presentation of student evaluation of articles and discussion
Week 10 - Written evaluation of the article - "per review" process.
Week 11 - Module 3 - Example of processed per review evaluation - discussion.
Week 12 - Final assignment of article evaluation for students.
Students will be able independently work in scientific databases, analyze and interpret results published in the literature.
Amino acids and their physicochemical properties, peptide bond and polypeptide chain, detection of amino acids, peptides and proteins, separation methods, determination of protein size, determination of covalent structure of proteins, synthesis of peptides, biosynthesis of proteins and peptides, determination of secondary and tertiary structure of proteins, posttranslational modifications - enzymatic, posttranslational modifications - non-enzymatic, interactions determining protein properties, conformational changes of proteins, protein folding, protein aggregation, prions, membrane proteins
1. preparation and presentation of the selected publication
2. oral examination
Slovak, English
1. Amino acids and their physicochemical properties
2. Peptide binding and polypeptide chain
3. Detection of amino acids, peptides and proteins
4. Separation methods, determination of protein size
5. Determination of covalent structure of proteins
6. Synthesis of peptides, biosynthesis of proteins and peptides
7. Determination of secondary and tertiary structure of proteins
8. Posttranslational modifications - enzymatic
9. Posttranslational modifications - non-enzymatic
10. Interactions determining the properties of proteins, conformational changes of proteins
11. Protein folding, protein aggregation, prions
12. Membrane proteins
Introduction to proteins, structure and function.
To teach students of the individual scientific work in the frame of the year's and diploma thesis and lead them to the intelligible presentation of the scientific results.
The literature will be recommended by supervisors of the theses.
The active presence on the seminars.
English language
The seminar of the biophysics department oriented to the themes of the year's and diploma works.
To teach students of the individual scientific work in the frame of the year's and diploma thesis and lead them to the intelligible presentation of the scientific results.
To teach students of the individual scientific work in the frame of the year's and diploma thesis and lead them to the intelligible presentation of the scientific results.
The literature will be recommended by supervisors of the theses.
The active presence on the seminars.
English language
The seminar of the biophysics department oriented to the themes of the year's and diploma works.
To teach students of the individual scientific work in the frame of the year's and diploma thesis and lead them to the intelligible presentation of the scientific results.
The literature will be recommended by supervisors of individual works.
Successful completing the course, requires the student to demonstrate adequate level of the assigned tasks set by the project leader at the beginning of the semester to the required extent and at the required level. The assignments are formulated by the teacher at the beginning of the semester, the project leader is usually the supervisor of the final thesis. Tasks include e.g. study of literature in the field, mastering the operation of experimental equipment, sample preparation technology, preparation and implementation of the experiment, processing of the obtained data, or collaborating during the preparation of a scientific publication. Credit evaluation takes into account the time requirements of the student when working on a semester project in the range of 50 hours per semester. Individual activities of the student are evaluated by the project leader, the overall work of the student is evaluated by points on a point scale of 0 - 100 points. The minimum threshold for obtaining a rating is 50% of the rating scale, which is determined as follows: A 100-91% B 90-81% C 80-71% D 70-61% E 60-50% Fx 49-0%.
Subject Semester work I is realized in attendance form. If necessary (e.g. Covid pandemic) it is taught online using software MS Teams, which allows to maintain contact with students even in adverse conditions and also allows to meet the requirements of the subject.
Program for semestral project is prepared individually for each student by supervisor of the project at the beginning of each semester and can be focused on search in literature for a selected area of research, preparation of experiment and its performing, creation of software for data acquisition and analysis, collaboration during preparation of manuscript, presentation of the obtained results for department audience. Supervisor of the project will specify the topic of the project.
After completing the course, the student will acquire knowledge and skills associated with scientific work in the field of biophysics. By actively participating in individual research teams, students will extend their knowledge in the relevant part of biophysics, acquire experimental skills in operating contemporary scientific equipment, study of the literature will improve their language skills. Data processing resp. the creation of original software will improve their computer skills.
The literature will be recommended by supervisors of individual works.
Successful completing the course, requires the student to demonstrate adequate level of the assigned tasks set by the project leader at the beginning of the semester to the required extent and at the required level. The assignments are formulated by the teacher at the beginning of the semester, the project leader is usually the supervisor of the final thesis. Tasks include e.g. study of literature in the field, mastering the operation of experimental equipment, sample preparation technology, preparation and implementation of the experiment, processing of the obtained data, or collaborating during the preparation of a scientific publication. Credit evaluation takes into account the time requirements of the student when working on a semester project in the range of 50 hours per semester. Individual activities of the student are evaluated by the project leader, the overall work of the student is evaluated by points on a point scale of 0 - 100 points. The minimum threshold for obtaining a rating is 50% of the rating scale, which is determined as follows: A 100-91% B 90-81% C 80-71% D 70-61% E 60-50% Fx 49-0%.
Subject Semester work I is realized in attendance form. If necessary (e.g. Covid pandemic) it is taught online using software MS Teams, which allows to maintain contact with students even in adverse conditions and also allows to meet the requirements of the subject.
Program for semestral project is prepared individually for each student by supervisor of the project at the beginning of each semester and can be focused on search in literature for a selected area of research, preparation of experiment and its performing, creation of software for data acquisition and analysis, collaboration during preparation of manuscript, presentation of the obtained results for department audience. Supervisor of the project will specify the topic of the project.
After completing the course, the student will acquire knowledge and skills associated with scientific work in the field of biophysics. By actively participating in individual research teams, students will extend their knowledge in the relevant part of biophysics, acquire experimental skills in operating contemporary scientific equipment, study of the literature will improve their language skills. Data processing resp. the creation of original software will improve their computer skills.
The literature will be recommended by supervisors of individual works.
Successful completing the course, requires the student to demonstrate adequate level of the assigned tasks set by the project leader at the beginning of the semester to the required extent and at the required level. The assignments are formulated by the teacher at the beginning of the semester, the project leader is usually the supervisor of the final thesis. Tasks include e.g. study of literature in the field, mastering the operation of experimental equipment, sample preparation technology, preparation and implementation of the experiment, processing of the obtained data, or collaborating during the preparation of a scientific publication. Credit evaluation takes into account the time requirements of the student when working on a semester project in the range of 50 hours per semester. Individual activities of the student are evaluated by the project leader, the overall work of the student is evaluated by points on a point scale of 0 - 100 points. The minimum threshold for obtaining a rating is 50% of the rating scale, which is determined as follows: A 100-91% B 90-81% C 80-71% D 70-61% E 60-50% Fx 49-0%.
Subject Semester work I is realized in attendance form. If necessary (e.g. Covid pandemic) it is taught online using software MS Teams, which allows to maintain contact with students even in adverse conditions and also allows to meet the requirements of the subject.
Program for semestral project is prepared individually for each student by supervisor of the project at the beginning of each semester and can be focused on search in literature for a selected area of research, preparation of experiment and its performing, creation of software for data acquisition and analysis, collaboration during preparation of manuscript, presentation of the obtained results for department audience. Supervisor of the project will specify the topic of the project.
After completing the course, the student will acquire knowledge and skills associated with scientific work in the field of biophysics. By actively participating in individual research teams, students will extend their knowledge in the relevant part of biophysics, acquire experimental skills in operating contemporary scientific equipment, study of the literature will improve their language skills. Data processing resp. the creation of original software will improve their computer skills.
Students get an overview about the symmetry at the micro- and macrostructure level and about diffraction methods used for the crystal structure determination and they will learn how to use the results of the crystal structure analysis in their own work.
Massa, W.: Crystal structure determination, 2nd edition. Springer 2004.
Clegg, W. et al.: Crystal structure analysis. Principles and practice. Oxford University Press 2009.
Hahn, T.: International tables for crystallography, Vol. A. Kluwer Academic Publishers 2002.
Klug, H.P. & Alexander, L.E.: X-Ray diffraction procedures for polycrystalline and amorphous materials. John Wiley & Sons, Inc. 1970.
2 written tests.
2 written tests during semester and written examination.
The final evaluation is based on the results from the tests (30 %) and written examination (70 %). The student must obtain at least 51% of each test and exam.
The same is valid also for online education.
Slovak and English
Teaching is carried out in person or, if necessary, online using the MS Teams tool. The form of teaching is specified by the teacher at the beginning of the semester, updated continuously.
1. History of crystallography, fundamentals of crystallography.
2. Morphological crystallography: crystal shape, symmetry of crystal shapes, position of the crystal surface in the space, zones, simple crystal forms.
3. Structural crystallography: space lattices, Bravais lattices, unit cell, crystal systems.
4. Point groups and their stereographic projections.
5. Space groups: open symmetry operations, two-dimensional space groups, three-dimensional space groups.
6. The origin and properties of X-rays, continuous and characteristic spectra, absorption and monochromatization of X-rays.
7. Fundamental principles of X-ray diffraction. I. The geometry of diffraction: scattering of X-rays by electrons and atoms, scattering on the nodal line, plane and lattice, distance between lattice planes, the reciprocal lattice, Ewald’s construction.
8. Fundamental principles of X-ray diffraction. II. The intensity of diffraction: scattering by two electrons, the atom formfactor, atom displacement factor, structure factor, structure factor and symmetry, Friedel’s law and independent reflections.
9. Experimental methods. I. Growth, choice and mounting of a single crystal, crystal density determination.
10. Experimental methods. II. Film methods: Laue method, rotation and Weissenberg methods, the precession method, the Debye-Scherrer method. Qualitative analysis of powder sample, indexing of cubic powder sample, determination of the lattice constant of the cubic powder sample.
11. Experimental methods. III. Single-crystal diffractometers, data reduction, other diffraction methods, crystallographic databases.
12. The second stage of structural analysis. Structure solution: Fourier transforms, Patterson method, direct methods, charge flipping. Structure refinement. Interpretation and presentation of results: preparation of tables and structural diagrams.
Macrostructure and microstructure symmetry, individual work with space groups. Theoretical basis of the diffraction experiment. Practical aspects of crystal structure solution. Processing the results of structural analysis. Theoretical basis, practical aspects and possibilities of X-ray powder diffraction analysis, its use at work of a chemist.
30 %
Students get an overview about the symmetry at the micro- and macrostructure level, about principles of difraction and about diffraction methods used for the crystal structure determination and they will learn how to use the results of the crystal structure analysis in their own work.
The final examination is in a written form. The final mark is based on the results from current and final tests.
BENCE, M. et al. 2005. Plávanie. Banská Bystrica: FHV UMB. 198s. ISBN 80-8083-140-8.
[online] Dostupné na: https://www.ff.umb.sk/app/cmsFile.php?disposition=a&ID=571
BUZKOVÁ, K. 2006. Fitness jóga, harmonické cvičení těla I duše. Praha: Grada. ISBN 8024715252.
JARKOVSKÁ, H, JARKOVSKÁ, M. 2005. Posilování s vlastním tělem 417 krát jinak. Praha: Grada. ISBN 9788024757308.
KAČÁNI, L. 2002. Futbal:Tréning hrou. Bratislava: Peter Mačura – PEEM. 278s. ISBN
8089197027.
KRESTA, J. 2009. Futsal.Praha: Grada Publishing, a.s. 112s. ISBN 9788024725345.
LAWRENCE, G. 2019. Power jóga nejen pro sportovce. Brno: CPress. ISBN 9788026427902.
SNER, Wolfgang. 2004. Posilování ve fitness. České Budějovice: Kopp. ISBN 8072322141.
STACKEOVÁ, D. 2014. Fitness programy z pohledu kinantropologie. Praha: Galén. ISBN 9788074921155.
VOMÁČKO, S. BOŠTÍKOVÁ, S. 2003. Lezení na umělých stěnách. Praha: Grada. 129s. ISBN
8024721743.
Min. 80% of active participation in classes.
Slovak language
Brief outline of the course:
The Institute of physical education and sport at the Pavol Jozef Šafárik University offers 20 sports activities aerobics; aikido, basketball, badminton, body-balance, body form, bouldering, floorball, yoga, power yoga, pilates, swimming, fitness, indoor football, SM system, step aerobics, table tennis, chess, volleyball, tabata, cycling.
Additionally, the Institute of physical education and sport at the Pavol Jozef Šafárik University offers winter courses (ski course, survival) and summer courses (aerobics by the sea, rafting on the Tisza River) with an attractive programme, sports competitions with national and international participation.
Sports activities in all their forms prepare university students for their professional and personal life. They have a great impact on physical fitness and performance. Specialization in sports activities enables students to strengthen their relationship towards the selected sport in which they also improve.
BENCE, M. et al. 2005. Plávanie. Banská Bystrica: FHV UMB. 198s. ISBN 80-8083-140-8.
[online] Dostupné na: https://www.ff.umb.sk/app/cmsFile.php?disposition=a&ID=571
BUZKOVÁ, K. 2006. Fitness jóga, harmonické cvičení těla I duše. Praha: Grada. ISBN 8024715252.
JARKOVSKÁ, H, JARKOVSKÁ, M. 2005. Posilování s vlastním tělem 417 krát jinak. Praha: Grada. ISBN 9788024757308.
KAČÁNI, L. 2002. Futbal:Tréning hrou. Bratislava: Peter Mačura – PEEM. 278s. ISBN
8089197027.
KRESTA, J. 2009. Futsal.Praha: Grada Publishing, a.s. 112s. ISBN 9788024725345.
LAWRENCE, G. 2019. Power jóga nejen pro sportovce. Brno: CPress. ISBN 9788026427902.
SNER, Wolfgang. 2004. Posilování ve fitness. České Budějovice: Kopp. ISBN 8072322141.
STACKEOVÁ, D. 2014. Fitness programy z pohledu kinantropologie. Praha: Galén. ISBN 9788074921155.
VOMÁČKO, S. BOŠTÍKOVÁ, S. 2003. Lezení na umělých stěnách. Praha: Grada. 129s. ISBN
8024721743.
active participation in classes - min. 80%.
Slovak language
Brief outline of the course:
The Institute of physical education and sport at the Pavol Jozef Šafárik University offers 20 sports activities aerobics; aikido, basketball, badminton, body-balance, body form, bouldering, floorball, yoga, power yoga, pilates, swimming, fitness, indoor football, SM system, step aerobics, table tennis, chess, volleyball, tabata, cycling.
Additionally, the Institute of physical education and sport at the Pavol Jozef Šafárik University offers winter courses (ski course, survival) and summer courses (aerobics by the sea, rafting on the Tisza River) with an attractive programme, sports competitions with national and international participation.
Sports activities in all their forms prepare university students for their professional and personal life. They have a great impact on physical fitness and performance. Specialization in sports activities enables students to strengthen their relationship towards the selected sport in which they also improve.
BENCE, M. et al. 2005. Plávanie. Banská Bystrica: FHV UMB. 198s. ISBN 80-8083-140-8.
[online] Dostupné na: https://www.ff.umb.sk/app/cmsFile.php?disposition=a&ID=571
BUZKOVÁ, K. 2006. Fitness jóga, harmonické cvičení těla I duše. Praha: Grada. ISBN 8024715252.
JARKOVSKÁ, H, JARKOVSKÁ, M. 2005. Posilování s vlastním tělem 417 krát jinak. Praha: Grada. ISBN 9788024757308.
KAČÁNI, L. 2002. Futbal:Tréning hrou. Bratislava: Peter Mačura – PEEM. 278s. ISBN
8089197027.
KRESTA, J. 2009. Futsal.Praha: Grada Publishing, a.s. 112s. ISBN 9788024725345.
LAWRENCE, G. 2019. Power jóga nejen pro sportovce. Brno: CPress. ISBN 9788026427902.
SNER, Wolfgang. 2004. Posilování ve fitness. České Budějovice: Kopp. ISBN 8072322141.
STACKEOVÁ, D. 2014. Fitness programy z pohledu kinantropologie. Praha: Galén. ISBN 9788074921155.
VOMÁČKO, S. BOŠTÍKOVÁ, S. 2003. Lezení na umělých stěnách. Praha: Grada. 129s. ISBN
8024721743.
min. 80% of active participation in classes
Slovak language
Brief outline of the course:
The Institute of physical education and sport at the Pavol Jozef Šafárik University offers 20 sports activities aerobics; aikido, basketball, badminton, body-balance, body form, bouldering, floorball, yoga, power yoga, pilates, swimming, fitness, indoor football, SM system, step aerobics, table tennis, chess, volleyball, tabata, cycling.
Additionally, the Institute of physical education and sport at the Pavol Jozef Šafárik University offers winter courses (ski course, survival) and summer courses (aerobics by the sea, rafting on the Tisza River) with an attractive programme, sports competitions with national and international participation.
Sports activities in all their forms prepare university students for their professional and personal life. They have a great impact on physical fitness and performance. Specialization in sports activities enables students to strengthen their relationship towards the selected sport in which they also improve.
BENCE, M. et al. 2005. Plávanie. Banská Bystrica: FHV UMB. 198s. ISBN 80-8083-140-8.
[online] Dostupné na: https://www.ff.umb.sk/app/cmsFile.php?disposition=a&ID=571
BUZKOVÁ, K. 2006. Fitness jóga, harmonické cvičení těla I duše. Praha: Grada. ISBN 8024715252.
JARKOVSKÁ, H, JARKOVSKÁ, M. 2005. Posilování s vlastním tělem 417 krát jinak. Praha: Grada. ISBN 9788024757308.
KAČÁNI, L. 2002. Futbal:Tréning hrou. Bratislava: Peter Mačura – PEEM. 278s. ISBN
8089197027.
KRESTA, J. 2009. Futsal.Praha: Grada Publishing, a.s. 112s. ISBN 9788024725345.
LAWRENCE, G. 2019. Power jóga nejen pro sportovce. Brno: CPress. ISBN 9788026427902.
SNER, Wolfgang. 2004. Posilování ve fitness. České Budějovice: Kopp. ISBN 8072322141.
STACKEOVÁ, D. 2014. Fitness programy z pohledu kinantropologie. Praha: Galén. ISBN 9788074921155.
VOMÁČKO, S. BOŠTÍKOVÁ, S. 2003. Lezení na umělých stěnách. Praha: Grada. 129s. ISBN
8024721743.
min. 80% of active participation in classes
Slovak language
Brief outline of the course:
The Institute of physical education and sport at the Pavol Jozef Šafárik University offers 20 sports activities aerobics; aikido, basketball, badminton, body-balance, body form, bouldering, floorball, yoga, power yoga, pilates, swimming, fitness, indoor football, SM system, step aerobics, table tennis, chess, volleyball, tabata, cycling.
Additionally, the Institute of physical education and sport at the Pavol Jozef Šafárik University offers winter courses (ski course, survival) and summer courses (aerobics by the sea, rafting on the Tisza River) with an attractive programme, sports competitions with national and international participation.
Sports activities in all their forms prepare university students for their professional and personal life. They have a great impact on physical fitness and performance. Specialization in sports activities enables students to strengthen their relationship towards the selected sport in which they also improve.
Rekha S. Rajan a Daniel R. Tomal Grant Writing: Practical Strategies for Scholars and Professionals (The Concordia University Leadership Series) Paperback – July 8, 2015 Rowman & Littlefield Publishers ISBN-10: 1475814410
Robert J. Hamper a L. Baugh (Author) Handbook For Writing Proposals, Second Edition Paperback – Illustrated, August 26, 2010 McGraw-Hill Education ISBN-10 007174648X
Anne L. Rothstein Creating Winning Grant Proposals: A Step-by-Step Guide 1st Edition ISBN-13: 978-1462539086; ISBN-10: 1462539084
Vikash Singh, Philipp Mayer Scientific writing: Strategies and tools for students and advisors Biochemistry and Molecular Biology Education 42(5) https://doi.org/10.1002/bmb.20815
Margaret Cargill, Patrick O'Connor Writing Scientific Research Articles: Strategy and Steps, 2nd Edition (2013) ISBN: 978-1-118-57070-8
Hilary Glasman-Deal Science Research Writing For Non-native Speakers Of English Imperial College Press; • World Scientific Publishing Company; December 2009; ISBN: 9781848167209
Schimel Joshua Writing Science : How to Write Papers That Get Cited and Proposals That Get Funded 2012 Oxford University Press ISBN-13: 978-0199760244; ISBN-10: 0199760241
Stephen B. Heard The Scientist's Guide to Writing: How to Write More Easily and Effectively throughout Your Scientific Career Paperback – April 12, 2016; Princeton University Press; ISBN-10 0691170223
Wendy Laura Belcher Writing Your Journal Article in Twelve Weeks, Second Edition: A Guide to Academic Publishing Success (Chicago Guides to Writing, Editing, and Publishing) Second Edition; ISBN-13: 978-0226499918; ISBN-10: 022649991X
Paul J. Silvia How to Write a Lot: A Practical Guide to Productive Academic Writing (2018) Second Edition ISBN-13: 978-1433829734; ISBN-10: 1433829738
Week 1 - Define the need of proposal - first step in creating a comprehensive project plan and proposal is defining your need, or what you want to accomplish.
Week 2 - Identify and Contact Potential Funders - Find an organization that supports the vision or goal you have identified.
Week 3 - Craft the Proposal
Know the preliminary components needed to apply for any grant funding.
Appreciate the importance of communicating grant ideas clearly. Understand the basic construction of a grant and how to address each component.
Understand the budget process and its implications.
Understand the aspects of a general peer review process, what it entails, and what happens after the grant application submission.
Week 4 - Basic Proposal Elements
• Executive Summary/Abstract
• Statement of Need
• Project Description
• Evaluation
• Sustainability
• Budget
Week 5 - Writing your own project according to the assignment
Week 6 - Scientific Writing: Strategies and Tools for Students and Advisors
Week 7 - Stages of writing process – preparing the material for paper, figures, references
Week 8 - Selecting a journal – follow journal manuscript format demands
Week 9 - Structure of the manuscript – Introduction, Material and Methods, Results, Discussion
Week 10 - Drafts of manuscript – final draft – revising grammar, readability and layout.
Week 11 - Writing your own paper – exercise.
1. Podorsak E.B..et al.: Radiation Oncology Physics , IAEA, 2005
2. Khan F. M.: The Physics of Radiation Therapy, Lippincott Williams & Wilkins, 2009
3. Šlampa P., Petera J.: Radiační onkológie, Galen Karolinum Praha 2007
4. Hirohiko T., et al.: Carbon-Ion Radiotherapy, Springer, 2014
5. Bushberg J. T., et al.: The Essential Physics of Medical Imaging, Wolters Kluwer, 2020
6. Lancaster J.L., Hasegawa B.1: Fundamental Mathematics And Physics Of Medical Imaging, CRC Press, 2016
7. Platná legislatíva SR (Zák.č. 87/2018 Z.z., vyhláška MZ SR č. 99/2018 Z.z., vyhláška MZ SR č. 101/2018 Z.z.)
1. Attendance at seminars (also applies to the online form of Teaching). A student's excused absence for a maximum of two seminars will be excused without the need for an alternative term. In the case of long-term justified absence (e.g. due to sick leave), the teacher will assign the student a substitute form of mastering the missed content.
2. Successful completion of the exam.
1. Competencies of medical physicists in radiation oncology, nuclear medicine and radiodiagnostics.
2. Ionizing radiation sources used in medicine - radionuclides and generators.
3. Interactions of photon, electron, proton and heavy ions with matter. Interaction of ionizing radiation with organisms.
4. Ionizing radiation detection and measurement of the absorbed dose in medicine. Quantities and units used in medical dosimetry.
5. Radiofrequency linear accelerators. Proton accelerators and heavy ion accelerators for radiotherapy.
6. Overview of radiation treatment techniques (3D CRT, IMRT, SRS, SABR, TBI, RMM, gating). Imaging methods in radiotherapy.
7. Linear accelerator quality control systems.
8. Physical principles of brachytherapy application.
9. Treatment planning systems for radiotherapy. Information and verification systems in radiation oncology.
10. Imaging methods in radiodiagnostics and nuclear medicine.
11. Radiobiological models for predicting the effect of ionizing radiation.
12. Principles of radiation protection and current legislation.
The course provides students with the theoretical basis for the work of a medical physicist. The student should know the physical principles of application of ionizing radiation in medicine - in radiodiagnostics, nuclear medicine, radiotherapy and the principles of radiation protection.
Lectures: This course is focused on basic concepts of morphology, molecular biology, genetics, genomics, evolution and taxonomy of viruses. Students will receive information about bacteriophages, viruses infecting bacteria as well as viruses causing major human and animal diseases (oncogenic viruses, herpes, coronaviruses, HIV) as well as viruses infecting plant cells and prions. Attantion is also devoted to the pathogenesis and epidemiology of viral infections and laboratory diagnosis of viral infections.
Laboratory classess are designed to master the basic methodological procedures for the identification and enumeration of bacteriophages, as well as the basic procedures used for the detection of viruses infecting eukaryotic cells.
SYLABUS:
• Introduction to the issue and terminology
• Virus morphology
• Life cycle and genetics of viruses
• Life cycle and genetics of viruses II
• Classification and taxonomy of viruses
• Bacteriophages - bacterial viruses
• Viruses causing major human and animal diseases
• Satellites, viroids, prions, viruses infecting plant cells
• Prevention and treatment of viral infections
• Pathogenesis and epidemiology of viral diseases
• Laboratory diagnosis of viral infections
• Evolution of viruses
Virology course will provide in-depth knowledge and understanding the biology, genetics and genomics of viruses.You will become familiar with professional terminology in the field of virology, understand the specifics of the biology of viruses, their multiplication, spreading and how they cause diseases. Through hands-on practical classes, the student will acquire the fundamental skills regarding the characterization and enumeration of bacteriophages.