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Description of the study programme
The name of the university:
Pavol Jozef Šafárik University in Košice
The seat of the university:
Šrobárova 2, 04180 Košice
The name of the faculty:
Faculty of Science
The seat of the faculty:
Šrobárova 2, 040 01 Košice
Institution body for approving the study programme:
Board for Internal Quality Verification at UPJŠ in Košice
1. - Basic information about the study programme
a) - Name of the study program and its number according to the register of study programmes.
BFd, Biophysics, 12270
b) - Degree of higher education and ISCED-F education degree code.
III. degree – PhD., ISCED-F: 864
c) - Place(s) of delivery of the study programme.
The Pavol Jozef Šafárik University in Košice (hereinafter UPJŠ), Košice
d) - Name and number of the field of study in which higher education is obtained by completing the study programme, or a combination of two fields of study in which higher education is obtained by completing the study programme, ISCED-F codes of the field/fields.
13 - Physics, ISCED-F: 0533
e) - Type of the study programme: academically oriented, professionally oriented; translation, translation combination study programme (listing the specializations); teaching, teaching combination study programme (listing the specializations); artistic, engineering, doctoral, preparation for regulated profession, joint study programme, interdisciplinary studies.
academically oriented
f) - Awarded academic degree after the name
PhD.
g) - Form of study.
Full-Time
i) - Language or languages in which the study programme is delivered.
Slovak, English
j) - Standard length of the study expressed in academic years.
4
k) - Capacity of the study programme (planned number of students), the actual number of applicants and students.
4, 5, 12
2. - Graduate profile and learning objectives
a) - The institution defines the learning objectives of the study programme such as student's abilities at the time of completion of the programme and the main learning outcomes.

The aim of the education in the PhD. programme Biophysics is to prepare highly educated graduates with a wide range of knowledge, skills, and specific abilities in the field of biophysics and its related disciplines. The acquired knowledge, abilities, and skills correspond to the level 8 of the knowledge, skills, and competencies according to the National Qualification Framework of the Slovak Republic, The qualifying framework in the European area of ​​higher education.

A graduate in the PhD. study program in biophysics masters the following knowledge and skills:

  • the scientific methods of biophysics that can be applied in a creative way to solve a wide range of problems in the field of bio-sciences (physiology, molecular biology, biochemistry, pharmacology and theoretical medicine, theoretical biology and medicine, immunology, bioinformatics)
  • the methods and practical applications of the up-to-date interdisciplinary sciences e.g. biomedicine, biology, nanotechnology and bioinformatics technologies
  • ability to bring the original and creative solutions of the scientific problems, formulate the problem, publish the results of scientific research, work in interdisciplinary collectives, participate in the scientific projects and the international scientific cooperation enabling involvement in scientific programs within the European Research Area as well as conditioning the further development of the field of study, and cooperate with the industrial partners.
  • during the PhD. study a student also acquires social, ethical, environmental, and legal aspects of the scientific work.

In addition to the mentioned knowledge and abilities, the graduates in the PhD study programme Biophysics will acquire specialized knowledge, abilities, and skills – that can bring creative solutions to complex problems in the fields of:

  • molecular and cell biophysics
  • molecular spectroscopy and molecular physics
  • computer modelling of biological and other complex systems
  • quantum chemistry and chemical physics
  • photophysics, photochemistry, photobiology, biochemistry, molecular biology, pharmacology, nanotechnology, and bioinformatics

The learning objectives in this study programme are achieved through measurable learning outputs. The rules of the doctoral study at UPJŠ define a basic framework for the cumulation of credits in the education and scientific parts of the study, so a highly professional nature of the study is guaranteed. Specific knowledge, skills, and competencies that students acquire by completing individual educational activities are sufficiently detailed in the information letters of the subjects of the study programme.

b) - The institution indicates the professions for which the graduate is prepared at the time of completion and the potential of the study programme from the point of view of graduate's employability.

The professions for which the graduates are prepared after completion of the PhD. study programme Biophysics are as follows:

211 Specialists in the field of physical and natural sciences

2111009 Physicist of dosimetry

2111007 Physicist in thermodynamics, acoustics, optics

2113004 Physical chemist

2113001 Chemist of quantum chemistry

2131007 Biochemist, biophysicist

2310001 Professor

2310002 Associate professor

2310003 Assistant professor

2310004 University assistant

2310005 University lecturer

2310006 Visiting professor

2511999 System analyst n.e.c

c) - Relevant external stakeholders who have provided the statement or a favorable opinion on the compliance of the acquired qualification with the sector-specific requirements for the profession.
  • ÚEF SAS (letter of support sent by the director of ÚEF SAS Košice - doc. RNDr. Zuzana Gažová, CSc.) https://wwwnew.saske.sk/uef/
  • Slovak Biophysical Society (letter of support sent by SKBS president - Prof. RNDr. Alžbeta Marček-Chorvátová, DrSc.) https://skbs.sk/
  • JUHAPHARM s.r.o. (a supportive opinion was expressed by the director of the company - Ing., JUDr. Michal Juhás, see minutes from the meeting of the Council of the Study Program), https://juhapharm.sk/
3. - Employability
a) - Evaluation of the study programme graduates employability.

The employability of the graduates of the PhD study programme in Biophysics is monitored using questionnaire surveys on the employability of the university graduates. The aim of the surveys is to improve the link between the profile of the graduates and various employers requirements resulting in the improving of the position of the graduates in the labour market. UPJŠ maintains contact with alumni through the Alumni Club - Alumni Space.

The graduates of the PhD. study programme in Biophysics are employable as scientific researchers which have all the prerequisites to grow professionally in the various positions in the fields of biophysics, biochemistry, molecular biology and biomedical physics. It is possible to expect their employment also in managerial positions in industrial sector.

b) - If applicable, indicate the successful graduates of the study programme.

RNDr. Veronika Huntošová, PhD. - researcher, CIB, TIP UPJŠ in Košice, previously a postdoctoral fellow at Swiss Fed Inst Technol Lausanne EPFL, Switzerland www.upjs.sk

RNDr. Silvia Kočanová, PhD. - researcher, Département de Biologie et Géosciences, Paul Sabatier University, Toulouse III, France sk.linkedin.com

RNDr. Štefan Bálint, PhD. - Research Fellow, The Kennedy Institute of Rheumatology, University of Oxford, Great Britain uk.linkedin.com

RNDr. Slávka Kaščáková, PhD. - researcher, University Paris Sud XI, Villejuif, France

RNDr. Jozef Hritz, PhD. – independent researcher, CEITEC Brno, Czech Republic www.muni.cz

RNDr. Martin Savko, PhD. - Scientist, Protein Crystallography, Synchrotron Soleil, Gif-sur-Yvette, France www.synchrotron-soleil.fr

RNDr. Tomáš Tokár, PhD. - Researcher, Krembil Research Institute, University Health Network, Toronto, ON, Canada

RNDr. Matúš Rebič, PhD. - developer of dedicated medical devices, GlobalLogic, Košice sk.linkedin.com

RNDr. Stanislav Hrivňak, PhD. - researcher, development, and use of neural networks for biomedicine and diagnostics, GlobalLogic, Košice, has a profile in the Forbes 30 under 30 list in 2019, winner of Falling Walls Lab Slovakia in 2017 sk.linkedin.com

RNDr. Michal Nemergut, PhD. - postdoctoral fellow, CEITEC Brno, Czech Republic www.upjs.sk

RNDr. Jaroslava Joniová, PhD. - researcher, Swiss Fed Inst Technol Lausanne EPFL, Switzerland sk.linkedin.com

RNDr. Martina Petrenčákova, PhD. - development worker, Medical Pharma Services, Switzerland sk.linkedin.com

c) - Evaluation of the study programme quality by employers (feedback).

The quality of the PhD. study programme in Biophysics was discussed and evaluated during the meeting of the Council of the study program, held on 29th September 2021.

The opinion of the representatives of the employers about the quality of the study programme is part of the Minutes of the meeting.

4. - Structure and content of the study programme
a) - The institution describes the rules for the design of study plans within the study programme.

The rules for the design of study plans are governed by the Study Regulations, which define the student's workload, evaluation, control stages of the study, the method of completing the study and other requirements. Responsibility for the content of the study and the correct course of the quality evaluation is defined by:


b) - The institution compiles the recommended study plans for individual study paths.

An overview of the study programmes provided by UPJŠ, including links to the teachers' websites with contacts, is available at: https://studijne-programy.upjs.sk/en/

In the PhD. study program Biophysics, the professional profile of a graduate is fundamentally formed by compulsory and compulsory optional subjects. These subjects, together with the scientific research focus of the dissertation, define the profile of a graduate in such a way that the practical requirements for his/her employability, especially in education and research areas, are met. In addition to basic professional profiling, the graduates acquire additional knowledge and skills in the field of information technology and computer science, important for employment outside the academic sphere.

All relevant information on subjects, such as educational outcomes and related criteria and rules for their evaluation, prerequisites, co-requisites, types of educational activities and methods by which educational activities are carried out, syllabi, scope and teachers are listed in the information sheets of the subjects that are available in electronic form in the academic information system AiS2, see https://studijne-programy.upjs.sk/en/study-program/BFd.

Guidance and control of creative scientific research activity are primarily the responsibility of the supervisors of the dissertation thesis.

The place of teaching and scientific activities within the PhD. study program in Biophysics is the UPJŠ in Košice.

c) - The study plan generally states:

All data and information about the PhD. study programme in Biophysics are listed in the study plan, which is generated from AIS2 and forms part of the submitted documentation

d) - The institution states the number of credits, the achievement of which is a condition for proper completion of studies and other requirements that the student must meet within the study programme and for its proper completion, including the requirements for state examinations, rules for re-study and rules for the extension, interruption of study.
The rules for a proper completion of the study programmes at UPJŠ, control stages of studies and rules for repeating studies, extending studies, or interrupting studies are noted in the PhD Study Regulations at the Pavol Jozef Šafárik University in Košice (https://www.upjs.sk/public/media/2062/phd-study-regulations-upjs-2019.pdf). The study schedule also regulates the organization of state exams. Specific conditions for passing the state exams for the PhD. study programme in Biophysics are available in the study plan. • A student properly completes the doctoral studies by completing the study according to the relevant study program. The length of the study may not exceed the standard period of study by more than two years. • The condition for proper completion of the study in this study program is successful completion of all subjects in the composition prescribed in the study plan for the specialization, successful completion of the dissertation examination and successful defence of the dissertation. For all activities (study, scientific work, dissertation exam, dissertation defence and complementary activities), a student must achieve a minimum of 240 credits during the study. • A student is obliged to take the dissertation exam no later than 24 months and in external form within 36 months from the beginning of the study. Only a student who has fulfilled the following conditions is admitted to the dissertation exam: • complete all compulsory subjects, as well as other subjects and evaluated activities of the study program in the prescribed composition and achieved at least 90 credits. • prepare and submit the written work for the dissertation exam on time. • A student who has received a positive recommendation from the supervisor and has achieved at least 210 credits is admitted to the defence of the dissertation, while he/she must have at least 60 credits for the study part and 120 credits for the scientific part according to the specialization of the study program. The student is obliged to obtain at least another 30 credits for complementary activities specified in detail in the study program. • Specific deadlines for fulfilling these obligations are updated centrally at the faculty level and published in the schedule of the current school year. Fulfilment of all conditions for the completion of the study is consistently recorded in the AiS2 electronic system and checked by the relevant clerk of the Study Department of the Faculty of Science, UPJŠ.
e) - For individual study plans, the institution states the requirements for completing the individual parts of the study programme and the student's progress within the study programme in the given structure:

The following requirements are valid for completing the PhD. study programme in Biophysics:

number of credits for compulsory subjects required for proper graduation: 38

the minimum number of credits for mandatory optional subjects required for proper graduation: 17

minimum number of credits for optional subjects required for proper graduation: 5

the minimum number of credits for the scientific part required for proper graduation: 120

minimum number of credits for other activities required for proper graduation: 30

number of credits required for proper graduation for the dissertation exam: 20

number of credits required for the proper completion of studies for the defence of the dissertation: 30


f) - The institution describes the rules for verification of learning outcomes, students assessment and the possibilities of appealing against the assessment.

Verification of the methods and objectivity of student evaluations is governed by the Rules of the Internal Quality Assurance and Verification System at Pavol Jozef Šafárik University in Košice

  • Examination of the student's suggestions is governed by:
  • Law no. 269/2018 Coll. on quality assurance in higher education,
  • The Law on Complaints,
  • Rector's Decision No. 13/2017 on the handling of complaints,
  • PhD Study Regulations of doctoral studies at UPJŠ in Košice.

Additional information is available on the website: Study programmes.

g) - Conditions for recognition of studies or a part of studies.

The rules for the recognition of studies or parts thereof are regulated by the PhD Study Regulations at the Pavol Jozef Šafárik University in Košice. Further information is publicly available at university website Study Programmes.


h) - The institution states the topics of final theses of the study programme (or a link to the list).

The topics of the PhD. theses are registered centrally in the academic information system AiS2:

doc. Mgr. Gregor Bánó, PhD., gregor.bano@upjs.sk:

Microstructures for biomedical lab-on-chip applications

doc. Mgr. Daniel Jancura, PhD., daniel.jancura@upjs.sk:

The coupling mechanism of electron and proton transport in cytochrome c oxidase

RNDr. Zuzana Jurašeková, PhD., zuzana.jurasekova@upjs.sk:

Development of nanosensors based on plasmon-enhanced optical spectroscopy for sensitive and selective detection of organic molecules in the environment and industry

doc. RNDr. Katarína Štroffeková, CSc., katarina.stroffekova@upjs.sk:

Hypericin as a potential regulator of Bcl2 proteins and its effect on tumour cell apoptosis and autophagy

doc. RNDr. Erik Sedlák, DrSc., erik.sedlak@upjs.sk:

Development of efficient genetically encoded photosensitizers

Use of ribosome display in enzyme development

RNDr. Marián Fabián, CSc., marian.fabian@upjs.sk:

Chemical structure of feryl intermediates in respiratory oxidases

RNDr. Gabriel Žoldák, PhD., gabriel.zoldak@upjs.sk:

In silico engineering of complex biophysical properties of proteins

Molecular mechanism of colloidal stability of immunoglobulins

i) - The institution describes or refers to:

Rules for the assignment, processing, opposition, defence and evaluation of final theses in the study programme are stated in section Dissertation thesis defence of PhD Study Regulations at UPJŠ.

International mobility of students and staff is an essential area of ​​the university's international activities. All information is available at the university website part International Relations.

The Rules of the Internal quality assurance and verification system at UPJŠ in Košice declare compliance with the general principles and rules of ethical behaviour - UPJŠ Code of Ethics and UPJŠ Student Code of Ethics, to which the Principles of good practice of scientific publishing (Rector's Decree No. 8/2021) and Rules for assessing plagiarism (Rector’s Decision No. 21/2021) are closely linked.

The following support services are available to students by University Counselling Centre (hereinafter UNIPOC), including students with special needs (Rector's Decree No. 19/2018):

  • Counseling: psychological, social, legal, courier
  • Career services and Career Club
  • Support for students with special needs:
  • Technical support (special devices and tools)
  • IT consulting - assistance and support in the use of IT resources; AiS2 setup consultancy for visually impaired students; PC settings for visually impaired students
  • Library services adjusted to the special needs of students
  • Erasmus+: a UPJŠ student with special needs has the opportunity to apply for a grant to cover expenses related to special needs during the implementation of mobility abroad; more information at the university page International Relations.

The examination of complaints by the student is governed by the Rules of the Internal Quality Assurance and Verification System, the Law on Complaints, the Rector's Decision on Handling Complaints and the PhD Study Regulations. Verification of the methods and objectivity of awarding students is governed by the Rules of the Internal Quality Assurance and Verification System of education, scientific, research, development, artistic or other creative and supportive activities at Pavol Jozef Šafárik University in Košice.


5. - Course information sheets of the study programme
In the structure according to Decree no. 614/2002 Coll.

The information sheets are available in the monitoring panel of the PhD. study program in Biophysics in the Academic Information System AiS2.

They are available to the public in the Register of study programs https://studijne-programy.upjs.sk/en/program/BFd

6. - Current academic year plan and current schedule
(or hyperlink).

The current university schedule of the academic year is available on the UPJŠ website in the information section for students (https://www.upjs.sk/studium/) and the section on meeting standards for the study programmes (https://www.upjs.sk/en/information/current-students/).

The faculty's current schedule for the academic year is available on the PF UPJŠ website in the section https://www.upjs.sk/en/faculty-of-science/foreign-students/.

7. - Persons responsible for the study programme
a) - A person responsible for the delivery, development, and quality of the study programme (indicating the position and contact details).

prof. RNDr. Pavol Miškovský, DrSc., professor, director of TIP UPJŠ, pavol.miskovsky@upjs.sk, https://www.upjs.sk/UPJS/zamestnanec/pavol.miskovsky/, https://www.portalvs.sk/regzam /detail/15268

b) - List of persons responsible for the profile courses of the study programme with the assignment to the course and provided with a link to the central Register of university staff and with contact details (they may also be listed in the study plan).

prof. RNDr. Pavol Miškovský, DrSc./OZŠP/,

Biophotonics, Cell Biology,

pavol.miskovsky@upjs.sk, https://www.portalvs.sk/regzam/detail/15268

 

doc. RNDr. Jozef Uličný, CSc./OZPP/,

Molecular simulations, Simulations and optimizations of complex biosystems

jozef.ulicny@upjs.sk, https://www.portalvs.sk/regzam/detail/15281

 

doc. Mgr. Daniel Jancura, PhD./OZPP/,

Molecular biophysics II, Bioenergetics II, Biological thermodynamics,

daniel.jancura@upjs.sk, https://www.portalvs.sk/regzam/detail/15310

 

doc. RNDr. Katarína Štroffeková, CSc./OZPP/,

Cell biophysics II,

katarina.stroffekova@upjs.sk, https://www.portalvs.sk/regzam/detail/14817

 

doc. Mgr. Gregor Bánó, PhD./OZPP/,

Photonics II,

gregor.bano@upjs.sk, https://www.portalvs.sk/regzam/detail/15381

 

RNDr. Michal Cagalinec, PhD.,

Bioenergetics II, Biophotonics, Cell biophysics II, Cell biology, Molecular biophysics II,

Extern Biomedical Center SAS Bratislava,

michal.cagalinec@savba.sk, http://confolab.sav.sk/ovsb/pracovnici/vyskumnici/rndr-michal-cagalinec-phd/

 

Ing. Alexandra Zahradníková, DrSc.,

Biophotonics, Cell biophysics II, Cell biology, Molecular biophysics II,

extern Biomedical Center SAS Bratislava,

alexandra.zahradnikova@savba.sk, http://confolab.sav.sk/ovsb/pracovnici/vyskumnici/ing-alexandra-zahradnikova-drsc/

 

RNDr. Branislav Brutovský, CSc.,

Simulations and optimization of complex biosystems,

branislav.brutovsky@upjs.sk, https://www.portalvs.sk/regzam/detail/14843

 

doc. RNDr. Erik Sedlák, DrSc.,

Biological thermodynamics, Protein engineering,

erik.sedlak@upjs.sk, https://www.portalvs.sk/regzam/detail/15371

 

doc. RNDr. Gabriel Žoldák, PhD.,

Protein engineering,

gabriel.zoldak@upjs.sk, https://www.portalvs.sk/regzam/detail/29213

 

RNDr. Zuzana Naďová, PhD.,

Cell biology,

zuzana.nadova@upjs.sk, https://www.portalvs.sk/regzam/detail/15380

 

RNDr. Veronika Huntošová, PhD.,

Cell biology,

veronika.huntosova@upjs.sk, https://www.portalvs.sk/regzam/detail/21857

 

RNDr. Magdaléna Májeková, PhD.,

Molecular simulations,

extern Center of experimental medicine SAV Bratislava,

magdalena.majekova@savba.sk, https://www.sav.sk/?lang=sk&doc=user-org-user&user_no=209

 

RNDr. Marta Gaburjáková, PhD.,

Molecular biophysics II,

extern at the Center for Biosciences SAS Bratislava

marta.gaburjakova@savba.sk, https://www.sav.sk/?lang=sk&doc=user-org-user&user_no=2061

 

RNDr. Marian Fabian, CSc.,

Bioenergetics II,

marian.fabian@upjs.sk, https://www.portalvs.sk/regzam/detail/21089

 

RNDr. Zuzana Sumbalová, PhD.,

Bioenergetics II,

extern III. internal clinic of the Faculty of Medicine of the UK and the University of Bratislava

zuzana.sumbalova@fmed.uniba.sk, https://uniba.sk/nc/ludia/sumbalova1

c) - Reference to the research/art/teacher profiles of persons responsible for the profile courses of the study programme.

Research/art/teacher profiles of the persons responsible for profile subjects are available in the monitoring panel of the PhD. study program in Biophysics in the Academic Information System AiS2.

Data from research/art/teacher profiles are also included in the official personal pages of employees, which have a URL in the form: https://www.upjs.sk/PF/zamestnanec/name.surname/

The list of current teachers and their research/art/teacher profiles are also available from the public register of the study programmes https://studijne-programy.upjs.sk/en/program/BFd.

d) - List of teachers of the study programme with the assignment to the course and provided with a link to the central Register of university staff and with contact details (may be a part of the study plan).

prof. RNDr. Pavol Miškovský, DrSc.,

Biophotonics, Surface-enhanced spectroscopy, Cell biology

pavol.miskovsky@upjs.sk, https://www.portalvs.sk/regzam/detail/15268


doc. RNDr. Jozef Uličný, CSc.,

Molecular simulations, Simulations and optimization of complex biosystems, Systems and synthetic biology,

jozef.ulicny@upjs.sk, https://www.portalvs.sk/regzam/detail/15281

 

doc. Mgr. Daniel Jancura, PhD.,

Molecular biophysics II, Bioenergetics II, Biological thermodynamics,

daniel.jancura@upjs.sk, https://www.portalvs.sk/regzam/detail/15310

 

doc. RNDr. Katarína Štroffeková, CSc.,

Cell Biophysics II, Molecular biology methods, Biophysical seminar,

katarina.stroffekova@upjs.sk, https://www.portalvs.sk/regzam/detail/14817

 

doc. Mgr. Gregor Bánó, PhD.,

Photonics II,

gregor.bano@upjs.sk, https://www.portalvs.sk/regzam/detail/15381

 

RNDr. Branislav Brutovský, CSc.,

Simulations and optimization of complex biosystems,

branislav.brutovsky@upjs.sk, https://www.portalvs.sk/regzam/detail/14843

 

RNDr. Zuzana Naďová, PhD.,

Cell biology,

zuzana.nadova@upjs.sk, https://www.portalvs.sk/regzam/detail/15380

 

RNDr. Zuzana Jurašeková, PhD.,

Surface-Enhanced spectroscopy,

zuzana.jurasekova@upjs.sk, https://www.portalvs.sk/regzam/detail/14900

 

doc. RNDr. Erik Sedlák, DrSc.,

Biological thermodynamics, Methods of molecular biology, Protein engineering,

erik.sedlak@upjs.sk, https://www.portalvs.sk/regzam/detail/15371

 

doc. RNDr. Gabriel Žoldák, PhD.,

Analysis of experimental data in biophysics, protein engineering,

gabriel.zoldak@upjs.sk, https://www.portalvs.sk/regzam/detail/29213

 

RNDr. Marián Fabián, CSc.,

Bioenergetics II,

marian.fabian@upjs.sk, https://www.portalvs.sk/regzam/detail/21089

 

RNDr. Veronika Huntošová, PhD.,

Cell biology,

veronika.huntosova@upjs.sk, https://www.portalvs.sk/regzam/detail/21857

 

Ing. Alexandra Zahradníková, DrSc.,

Biophotonics, Cell biophysics II, Cell biology, Methods of molecular biology, Molecular biophysics of cells, Molecular biophysics II, Special methods of biophysics I, Special methods of biophysics II,

extern Biomedical Center SAS Bratislava,

alexandra.zahradnikova@savba.sk, http://confolab.sav.sk/ovsb/pracovnici/vyskumnici/ing-alexandra-zahradnikova-drsc/

 

RNDr. Alexandra Zahradníková, PhD.,

Molecular biophysics of cells, Special methods of biophysics II, Basic laboratory techniques, Basics of good laboratory practice,

extern Biomedical Center SAS Bratislava,

saschia.zahradnikova@savba.sk, http://confolab.sav.sk/ovsb/pracovnici/vyskumnici/rndr-alexandra-zahradnikova-ml-phd/

 

RNDr. Michal Cagalinec, PhD.,

Bioenergetics II, Biophotonics, Cell biophysics II, Biophysical seminar I-IV, Cell biology, Molecular biophysics of cells, Molecular biophysics II, Special methods of biophysics II,

extern Biomedical Center SAS Bratislava,

michal.cagalinec@savba.sk, http://confolab.sav.sk/ovsb/pracovnici/vyskumnici/rndr-michal-cagalinec-phd/

 

RNDr. Marta Gaburjáková, PhD.,

Molecular biophysics II, Special methods of biophysics I, Fundamentals of scientific ethics,

extern at the Center for Biosciences SAS Bratislava

marta.gaburjakova@savba.sk, https://www.sav.sk/?lang=sk&doc=user-org-user&user_no=2061

 

RNDr. Jana Gaburjáková, PhD.,

Special methods of biophysics I,

extern Center of Biosciences SAS Bratislava,

jana.gaburjakova@savba.sk, https://www.sav.sk/?lang=sk&doc=user-org-user&user_no=1404

 

RNDr. Magdaléna Májeková, PhD.,

Molecular simulations,

extern Center of experimental medicine SAV Bratislava,

magdalena.majekova@savba.sk, https://www.sav.sk/?lang=sk&doc=user-org-user&user_no=209

 

doc. RNDr. Zuzana Gažová, DrSc.,

Experimental methods of studying proteins, Selected chapters from biophysics - conformational disorders of proteins,

extern at the Institute of Experimental Physics SAS Košice,

gazova@saske.sk, https://www.sav.sk/?lang=sk&doc=user-org-user&user_no=5425

 

RNDr. Diana Fedunová, PhD.,

Experimental methods of studying proteins, Selected chapters from biophysics - conformational disorders of proteins,

extern at the Institute of Experimental Physics SAS Košice,

fedunova@saske.sk, https://www.sav.sk/?lang=sk&doc=user-org-user&user_no=4337

 

MUDr. Andrey Musatov, DrSc.,

Molecular mechanisms of oxidative stress in cells,

extern at the Institute of Experimental Physics SAS Košice,

musatov@saske.sk, https://www.sav.sk/?lang=sk&doc=user-org-user&user_no=8816

 

doc. Ing. Zoltán Tomori, CSc.,

Collection and processing of images in microscopy,

extern at the Institute of Experimental Physics SAS Košice,

tomori@saske.sk, https://www.sav.sk/?lang=sk&doc=user-org-user&user_no=4060

 

RNDr. Zuzana Sumbalová, PhD.,

Bioenergetics II,

extern III. internal clinic of the Faculty of Medicine of the UK and the University of Bratislava

zuzana.sumbalova@fmed.uniba.sk, https://uniba.sk/nc/ludia/sumbalova1

 

doc. PaedDr. Renáta Orosová, PhD.,

Pedagogy for university teachers

renata.orosova@upjs.sk, https://www.portalvs.sk/regzam/detail/15382

 

PhDr. Anna Janovská, PhD.,

Psychology for university teachers

anna.janovska@upjs.sk, https://www.portalvs.sk/regzam/detail/6858

 

PhDr. Helena Petruňová, CSc.,

English professional language for doctoral students 1, English language for doctoral students 2

helena.petrunova@upjs.sk, https://www.portalvs.sk/regzam/detail/15418

 

Mgr. Zuzana Kolaříková, PhD., English professional language for doctoral students 1, English language for doctoral students 2

zuzana.kolarikova@upjs.sk, https://www.portalvs.sk/regzam/detail/15420

e) - List of the supervisors of final theses with the assignment to topics (indicating the contact details).

doc. Mgr. Gregor Bánó, PhD., gregor.bano@upjs.sk:

Microstructures for biomedical "lab-on-chip" applications

 

doc. Mgr. Daniel Jancura, PhD., daniel.jancura@upjs.sk:

The coupling mechanism of electron and proton transport in cytochrome c oxidase

 

RNDr. Zuzana Jurašeková, PhD., zuzana.jurasekova@upjs.sk:

Development of nanosensors based on plasmon-enhanced optical spectroscopy for sensitive and selective detection of organic molecules in the environment and industry

 

doc. RNDr. Katarína Štroffeková, CSc., katarina.stroffekova@upjs.sk:

Hypericin as a potential regulator of Bcl2 proteins and its influence on apoptosis and autophagy of tumour cells

 

doc. RNDr. Erik Sedlák, DrSc., erik.sedlak@upjs.sk:

Development of effective genetically encoded photosensitizers

Use of ribosome display in enzyme development

 

RNDr. Marián Fabián, CSc., marian.fabian@upjs.sk:

Chemical structure of ferryl intermediates in respiratory oxidases

 

RNDr. Gabriel Žoldák, PhD., gabriel.zoldak@upjs.sk:

In silico engineering of complex biophysical properties of proteins

Molecular mechanism of colloidal stability of immunoglobulins

f) - Reference to the research/art/teacher profiles of the supervisors of final theses.

Information from research/art/teacher profiles is included in the official personal web- pages of the employees, whose URL is in the form https://www.upjs.sk/en/PF/zamestnanec/name.surname/

Research/art/teacher profiles are publicly available in the overview of the PhD. study programme in Biophysics (https://studijne-programy.upjs.sk/en/program/BFd).


g) - Student representatives representing the interests of students of the study programme (name and contact details).

Mgr. Veronika Džupponová, student 3BFd veronika.dzupponova@student.upjs.sk

Mgr. Veronika Dzurillová, student 3BFd veronika.dzurillova@student.upjs.sk

h) - Study advisor of the study programme (indicating contact details and information on the access to counseling and on the schedule of consultations).

doc. Mgr. Daniel Jancura, PhD., daniel.jancura@upjs.sk, https://www.upjs.sk/PF/zamestnanec/daniel.jancura/

ÚFV, Jesenná 5, m. no. SJ0O51

- consultations are by personal agreement

i) - Other supporting staff of the study programme – assigned study officer, career counselor, administration, accommodation department, etc. (with contact details).

The PhD. study program in Biophysics is supported through the Study department of the Faculty of Science, UPJŠ in Košice (https://www.upjs.sk/en/faculty-of-science/foreign-students/stud-adm-office/) using the Academic Information System AiS2. Most of the agenda is efficiently handled through the information system, without direct personal interaction with the study department.

The students can also use the services of the UPJŠ University Counselling Center in Košice (UNIPOC), which is a specialized UPJŠ workplace established by the rector of UPJŠ. UNIPOC's mission is to provide free counselling to all UPJŠ students, namely psychological, career, legal and social counselling, and counselling in effective learning. UNIPOC is also in charge of support and care for the students with specific needs. Counselling services can be used by students both in-person and online, in Slovak and English. The purpose of the services provided is to improve the employability of students and graduates in the labour market, act preventively and help with problems that could threaten the successful completion of the studies. More information can be found on the UNIPOC website: https://www.upjs.sk/en/departments/university-counselling-center/.

Students can learn more about the possibilities of employment in the labour market during the UPJŠ Career Day (https://www.upjs.sk/en/departments/university-counselling-center/events/).

The UPJŠ university counselling center in Košice also provides support for students with specific needs: https://www.upjs.sk/en/departments/university-counselling-center/support-for-students-with-special-needs/. ·

UPJŠ in Košice also offers students accommodation and catering services through UPJŠ Student Hostel and Canteens (hereinafter ŠDaJ) or at contractual partners. The accommodation subsystem is part of AiS2, and catering in ŠDaJ is administered by a separate information system that is integrated within UIS UPJŠ.


8. - Spatial, material, and technical provision of the study programme and support
a) - List and characteristics of the study programme classrooms and their technical equipment with the assignment to learning outcomes and courses (laboratories, design and art studios, studios, workshops, interpreting booths, clinics, priest seminaries, science and technology parks, technology incubators, school enterprises, practice centers, training schools, classroom-training facilities, sports halls, swimming pools, sports grounds).

The UPJŠ in Košice provides spatial, material, technical and informational resources for individual study programmes for each location where the study programme takes place, proportionate to the goals and outcomes of education in the study programme. Ensuring a full-fledged infrastructure supporting higher education, creative scientific research and research activity is one of the university's priorities. The constant progress of the university is also reflected in the continuous expansion of the existing infrastructure, the reconstruction of buildings and the introduction of modern information and communication technologies.

The existence of university workplaces is essential to ensure the required quality of selected services, which are characteristic of a respected and materially well-equipped university.

All current information on the quality of PhD study programs at the university can be found at website PhD Portal

Further information:

Students in the PhD. study programme in Biophysics have at their disposal top experimental equipment concentrated in 12 specialized laboratories (http://www.biofyzika.sk):

Laboratory of chemistry

Laboratory of chemical technology

Laboratory of molecular biology

Laboratory of cell cultures

Laboratory of laser spectroscopy

Laboratory of confocal microscopy

Laboratory of biothermodynamics and optical spectroscopy

Laboratory of Raman spectroscopy

Laboratory of protein engineering

Laboratory of biotechnology and cell physiology

Laboratory of flow cytometry

Laboratory of advanced molecular simulations and visualizations

Examples of the specific infrastructure used for the PhD. study program in Biophysics:

The cell biology laboratory is used for the cultivation of cell cultures, which is equipped with a laminar box (TelStar Bio II Advance), a CO2 incubator (Hera Cell), a 96-plate reader (Glomax multidetection system) and a flow cytometer (MACSQuant Analyzer). Fluorescent imaging of cellular structures is captured using a Zeiss LSM 700 confocal system (with excitation at 405, 488, or 555 nm) attached to a Zeiss Aviovert 200M inverted microscope. In a fully equipped laboratory for molecular biology focusing on techniques such as DNA isolation and purification or targeted mutagenesis, there are: centrifuges (Eppendorf 5810R and 5430D), thermal cycler Eppendorf - PCR, electrophoresis (BioRad), ultra-freezer (-86oC) and an incubator for bacteria. The electrophysiological parameters of the cells are monitored using a patch-clamp apparatus, which is composed of a fluorescence microscope (Olympus IX71), a CCD camera (Hamamatsu ORCA R-2), a micromanipulator (MP-285), a patch-clamp amplifier (Axopatch™ 200B) and a digitizer. (Axon Digidata 1440A).

The Molecular Simulation Laboratory offers 8+1 workstations (OSX/Windows7/Linux) with stereoscopic imaging, haptic devices, GPGPU and access to the programs of the Schrodinger, AMBER, Gaussian package as well as Open Source software. The workplace enables simulations in the field of biophysics: from ab initio calculations to molecular mechanics and dynamics, docking and free energy calculations.

The Raman spectroscopy laboratory is equipped with a Renishaw InVia Reflex confocal Raman microspectrometer (excitation lasers 532, 633 and 785 nm) in combination with a pair of Leica DM2500 and Leica DMI3000 B microscopes.

The laboratory of biological thermodynamics is methodically focused on the study of biomacromolecules and their interactions with low molecular weight ligands (e.g. drugs). An isothermal titration calorimeter (MicroCal, ITC-200), a stopped-flow measuring device (Applied Photophysics, SX-20), an absorption and fluorescence spectrophotometer (Shimadzu UV-2401PC and RF -5301PC), Xvivo System (BioSpherix, USA) and Seahorse XF24 analyser.

In the laboratory of laser spectroscopy, there are two own experimental apparatuses. The first of them is a micro-Raman apparatus in combination with optical tweezers, which is equipped with a set of cw lasers (488, 532, 596, 633 and 785 nm) and a spectrograph (Jobin-Yvon iHR550). The second apparatus is focused on the detection of singlet oxygen using excitation by a pulsed Nd:YAG laser (Spectra-Physics - Quanta Ray), which pumps an optical parametric oscillator and/or a dye laser. Singlet oxygen phosphorescence detection is enabled by a photomultiplier (Hamamatsu H10330A-75).

Sample preparation takes place in the chemical laboratory, where centrifuges (Eppendorf 5424 and 5804R), shaker (IKA MS3), scales (OHAUS – Explorer, ExplorerPro, Discovery), mixer with heating (Heidolph Mr-Tec), pH meter (HANNA instrument – ​​HI 9017 and HI3220), dryer (Nüve – FN 055) and combustible safety cabinet (Asecos). An invaluable part of the equipment is an autoclave (Tuttnauer 3150 EL) and a set of devices to produce pure water (Thermo scientific – TKA, TKA Smart2Pure).


b) - Characteristics of the study programme information management (access to study literature according to Course information sheets, access to information databases and other information sources, information technologies, etc.).

Students' access to the study literature is provided by the central university workplace, the UPJŠ University Library in Košice. The main mission of the UPJŠ University Library (UL) as the university's information workplace is to participate on the information basis of teaching and scientific research activities of the employees and students, to create conditions for supporting the educational process and inspiring environment for users. UL fulfils this mission by creatively using information resources and technologies, providing documents, information and consultations, and professional knowledge of staff and facilities to support teaching, education and research. More information on the individual areas provided by the UL  can be found at the following links:

The Šafárik Press publishing house of UPJŠ in Košice participates in spreading awareness of the possibilities of electronic publishing at the university. The Unibook portal provides a permanent repository of electronic documents, an archive of all published publications and at the same time modern possibilities for purchasing books authored by UPJŠ employees via the standard web interface of the e-shop.

The AiS2 Academic Information System is used to support comprehensive education management at all three levels of higher education.

The Centre of Information and Communication Technologies (hereinafter CIaKT) UPJŠ in Košice is a university-wide information workplace that covers the activities of information and communication technologies inside UPJŠ, but also externally in relation to its surroundings. The CIaKT UPJŠ university node is also a regional node of the Slovak Academic Network (SANET).

c) - Characteristics and extent of distance education applied in the study programme with the assignment to courses. Access, manuals of e-learning portals. Procedures for the transition from contact teaching to distance learning.

The standard form of the education for the PhD. study programme in Biophysics is contct teaching. Distance learning for this programme is only implemented in crisis situations, e.g. restrictions related to the COVID-19 pandemic. In such exceptional cases, all teachers switch to distance teaching in accordance with the decision of the Rector of UPJŠ in Košice for the implementation of teleconference lectures (see Rector's Decision No. 22/2020).

Educational activities at UPJŠ in Košice, which are provided via distance learning, are sufficiently supported, and also secured (https://www.upjs.sk/en/university/Internal-system-evaluation-quality/study-programmes/). Information on the distance form of education, an overview of tools with instructions and available university portals can be found on the website for e-learning at UPJŠ (https://www.upjs.sk/elearning/).

d) - Institution partners in providing educational activities for the study programme and the characteristics of their participation.

UPJŠ pays attention to the connection of knowledge with practice. This connection is supported by strong ties with important academic and industrial partners and organizations. The partners are officially associated with Career Club UPJŠ.

UPJŠ is a founding member of IT Valley Košice. The university also cooperates with international partners https://www.upjs.sk/univerzita/cinnost/medzinarodne-vztahy/clenstva/.

Partnerships of the Faculty of Science of UPJŠ in Košice enabling the provision of educational activities in many study programmes. The following parts of UPJŠ are involved in the education process at Faculty of Science:

In ensuring the educational activities in the PhD. study programme Biophysics, the Faculty of Science UPJŠ in Košice cooperates with the Department of Biophysics of The Institute of the experimental physics, SAS, https://websrv.saske.sk/uef/en/


e) - Characteristics of the possibilities for social, sports, cultural, spiritual and social activities.

The development of UPJŠ students is ensured not only by quality education, but also by social, sports, cultural, spiritual and social activities during their studies. An overview of what the university, its workplaces and also the city of Košice (as well as the Official Website of the city of Košice) offer to our students can be found on the university's website, in the part Current students, section Recommendation and Announcements for students: Student Associations and Interest Group or Further information for students.

The offer of events for students organized by the University Counseling Center such as Career Day, Internship Day, Do something!, Learn to live can be found at https://www.upjs.sk/en/departments/university-counselling-center/.

Among the traditional events that are very popular among students are the events as Science Days or Science Fest (https://www.upjs.sk/prirodovedecka-fakulta/sr/siencefest/)

Students can spend time between lectures in the MARK relaxation corner at the Institute of Physic, Faculty of Science, UPJŠ in Košice (https://www.upjs.sk/prirodovedecka-fakulta/15959/) or the Creative Laboratory at the ÚINF PF UPJŠ.

Student Radio Košice - ŠtuRKo (http://sturko.intrak.upjs.sk) takes care of good well-being.

The list of the student organizations operating at UPJŠ in Košice can be found on the website https://www.upjs.sk/studium/studentske-organizacie/.

Interest associations operating at UPJŠ in Košice are listed on the page https://www.upjs.sk/studium/zaujmove-zdruzenia/.

Sports activities for UPJŠ students are provided by the university Institute of physical education and sport (ÚTVŠ). This institute offers the possibility of choosing from 21 types of sports through the Sports activities subject (https://www.upjs.sk/en/departments/institute-of-physical-education/). Students can participate in sport activities not only within a compulsory or optional subjects but also beyond the credit form. In addition to the physical activities offered, students can participate in the university league in 4 sports (futsal, soccer, basketball, and volleyball). Between traditional ÚTVŠ offers belong winter athletic courses (skiing course, survival, cycle tourism course, Tisa river rafting and exercise by the sea). Students for whom the sports activities offered by ÚTVŠ are not enough can also apply for a much wider range of sports offered by TJ Slávia UPJŠ. For students are available 5 gyms, most of which have undergone major renovations in the recent years. The gyms are equipped for the needs of different levels - from beginners to advanced sprtsmen and are regularly supplemented and renovated. In addition, the ÚTVŠ facility has 4 tennis courts and 3 multifunctional concrete playgrounds, which students use primarily for sports games.

The city of Košice offers many cultural and social sports activities for students (https://www.kosice.sk/en).


f) - Possibilities and conditions for participation of the study programme students in mobilities and internships (indicating contact details), application instructions, rules for recognition of this education.

UPJŠ enables and supports education outside the university in domestic and foreign institutions (https://www.upjs.sk/en/departments/institute-of-physical-education/actualities/). Foreign mobility of the students form an essential part of ​​the university's international relations. All important information about mobility and internship opportunities for university students are published on the website International Relations.

Comprehensive information on the offer of the mobility and internships within the Erasmus+ program, including a description of the applicant selection process, is available on the website Erasmus+.

Information about the support for foreign mobility and internships at the Faculty of Science, UPJŠ in Košice, is available at https://www.upjs.sk/en/faculty-of-science/foreign-students/office/.

For mobility administration, the university uses the Academic Information System AiS2 and portal tools created as part of the Erasmus without paper (EWP) project. AiS2 and EWP are gradually integrated into one functional unit.

The conditions for recognition of completed studies are governed by the PhD Study Regulations at UPJŠ.

9. - Required abilities and admission requirements for the study programme applicants
a) - Required abilities and necessary admission requirements.

Graduates of master's studies in the fields of physics, chemistry, biology, and computer science can be admitted to the PhD. study program in Biophysics.

The admission exam is held before the admission committee appointed by the deanof the Faculty of Science, UPJŠ in Košice. The guarantee of the study program is obviously the chairman of at least four-member committee. The other members of the committee are supervisors who assigned the topics of the disertation thesis. The range of the questions is determined by the committee members. Applicants are expected to have mastered the content of the subjects Molecular biophysics I, Cell biophysics I and Experimental methods of biophysics I-III within the scope of the Bachelor’s and Master's degree in Biophysics at the Faculty of Science, UPJŠ in Košice.

Requirements for the admission procedure for doctoral studies at the Faculty of Science, UPJŠ in Košice, are listed on the website https://www.upjs.sk/en/faculty-of-science/potential-students/.


b) - Admission procedures.

The admission procedures are in accordance with the PhD Study Regulations (Rector's Decision No. 14/2021, which determines the Principles of the Admission Procedure for studies at UPJŠ). The principles of the admission procedure define the basic legislative points and general principles according to which a reliable, fair and transparent admission procedure for study programs carried out at UPJŠ in I., II., joint I. and II. as well as in III. degree of higher education. General information on the admission procedure at UPJŠ is published on the university's website in the section Information for prospective students and in the section Internal quality assurance and verification system, Study programs.

c) - Results of the admission process over the last period.

The results of the admission process for the study programs can be found on the website of UPJŠ dedicated to basic quality indicators and monitoring the quality of education at UPJŠ and its components https://www.upjs.sk/en/university/Internal-system-evaluation-quality/indicators/. A detailed structured analysis of the admission procedure is listed in the follow.

AY                 number of applicant  number of admitted applicant   number of enrolled

study                 daily/external                daily/external                         daily/external

2021/2022                            3/0                             3/0                                      3/0

2020/2021                            6/0                             5/0                                      5/0

2019/2020                            10/0                           8/0                                      8/0

2018/2019                            3/0                             3/0                                      3/0

2017/2018                            5/0                             5/0                                      4/0


10. - Feedback on the quality of provided education
a) - Procedures for monitoring and evaluating students' opinions on the study programme quality.

Information on the procedure for monitoring and evaluating student satisfaction at the university is published on the website: https://www.upjs.sk/en/university/Internal-system-evaluation-quality/study-programmes/.

Quality indicators and results of quality monitoring at UPJŠ and its components are publicly available at: https://www.upjs.sk/en/university/Internal-system-evaluation-quality/indicators/.


b) - Results of student feedback and related measures to improve the study programme quality.

The UPJŠ informs about the results of the evaluation of the quality of educational activities on its website https://www.upjs.sk/en/university/Internal-system-evaluation-quality/surveys/.

Specific measures to improve the quality of the study program based on the results of the conducted surveys are listed in the minutes of the study program Council meetings, which are archived in the monitoring panel of the study programme in Biophysics in AiS2.

c) - Results of graduate feedback and related measures to improve the study programme quality.

The UPJŠ in Košice and its faculties conduct questionnaire surveys on the employment of the university graduates with the aim to improve the profile of the graduates, more closely link studies with practice, and improve the position of graduates in the labour market. Information on monitoring alumni feedback is available on the website https://www.upjs.sk/en/university/Internal-system-evaluation-quality/surveys/graduates/.

The currently valid rules, periodicity and methodology of the questionnaire surveys are described on the website https://www.upjs.sk/en/university/Internal-system-evaluation-quality/study-programmes/.

Specific conclusions from the questionnaire surveys carried out at the level of the university, faculty or workplaces for the given study program are documented in the minutes of the study program Council. Minutes are archived in the monitoring panel of the study program in AiS2.

11. - References to other relevant internal regulations and information concerning the study or the study programme student
(e.g study guide, accommodation regulations, fee directive, guidelines for student loans, etc.).

All information on the study programmes, which provide an overview of the relevant internal regulations, fees, and student loans, are available to the public and regularly updated on the website https://www.upjs.sk/en/university/Internal-system-evaluation-quality/study-programmes/ and in the information area for UPJŠ students, which can be found on the website: https://www.upjs.sk/en/information/current-students//.

Specific information for the students at the Faculty of Science, UPJŠ in Košice, are published on the faculty website https://www.upjs.sk/en/faculty-of-science/education/.