Passing the study plan

Requirements for filing an application for admission to the state doctoral dissertation:

- passing of all required and selective courses in the Individual Study Plan (ISP) of the first 4 semesters including those which are connected to the dissertation topic and are marked as such by the advisor
- successful fulfillment of foreign language requirements according to Article 30 §4 c) of the MU study and examination regulations
- submitting the dissertation theses, an eventual list of publications and conference presentations as supplement to the application

The state doctoral examination verifies the extent and depth of the students' general knowledge of biophysics (or molecular resp. cellular or biomedically oriented biophysics) connected with the dissertation topic as well as their ability to creatively solve problems of mostly experimental character, beginning by their biophysical formulation up to the interpretation of the results. The examination topics falling into purview of individual study plans are formulated for the individual examinee accordingly so as to create a higher level of learning over the Master's degree examination.

Basic examination topics:

1. Molecular structure of living matter and the methods of its study on the level of individual molecules
2. Conformational changes in biomacromolecules and the methods of their study
3. Biophysics of processes on biological membranes
4. The structure of a cell and an overview of methods suitable for its study
5. Interaction of non-ionizing radiation with living matter
6. Interaction of ionizing radiation with living matter
7. Biophysics of biological systems and subsystems according to the dissertation topic

A presentation detailing the topic and the state of the solution of the dissertation thesis forms the initial part of the state doctoral examination which is followed up by the discussion. In this part of the state doctoral examination the students present their results in the form of publications in scientific journals and conference proceedings. Specific examination topics are given at least 4 weeks ahead of the examination according to Article 32 § 4 of the MU study and examination regulations.

Doctoral Thesis Requirements
The thesis is focused on the isolation of up to date unsolved or unsatisfactorily solved problems in biophysics. It is assumed that it contains a thorough biophysical (i.e. biological and physical) formulation of those problems and their solution including their possible application in practice or practically oriented research. The core of the thesis is the solution of the biophysical problems of the topic with original results on physical systems or mathematical models.
The application must contain a list of publications corresponding with the publication practices in the field. A necessary condition for admission is an acknowledged impact factor of a first-authored publication already published or accepted for publication (with the editor's confirmation). It is recommended that the journal in which the publication is placed be in the first or second quartile of impact in the given field.

The preparation of the dissertation takes place during the whole duration of the studies and comprises at least 60% of the workload.

During the second semester at the latest the students in concert with their advisors create their Individual Study Plan (ISP) and present it for approval to the PhD comission.

At the end of the 3rd year of study i.e. 6th semester at the latest the student
- have passed all theoretical preparation examinations (obligatory ones and the ones chosen with the advisor in the ISP) comprising approximately 20% of the workload (point 4 of the approved ISP) excepting ongoing seminars
- present the results of their work in English at the Institute seminar (point 5 of the approved ISP)
- prove their foreign language competence (point 6 of the approved ISP)
- discharge their duties connected with their pedagogical development (at most 10% of the workload and point 8 of the approved ISP)

At the end of their studies, ideally during the standard 4 year duration of their studies, i.e. at the end of the 8th semester the students
- present their findings at an international scientific conference (point 3 of the approved ISP)
- undergo the obligatory international research internship at least 1 month in duration
- present their findings in an international scientific journal - 10% of the workload ((point 2 of the approved ISP)
- finish their dissertation thesis and file the application to defend their dissertation thesis (point 1 and 2 of the approved ISP)

The study of microorganisms by advanced microscopic and spectroscopic techniques, Adámková, Kateřina (ongoing thesis). Advisor: Ing. Vladislav Krzyžánek, Ph.D.

Utilization of spectral and time-domain prior knowledge in the quantitative analysis of in vivo magnetic resonance spectroscopy signals, Jablonski, Michal (2018). Advisor: Ing. Zenon Starčuk, CSc. (https://is.muni.cz/th/q184v/).

The utilization of techniques of confocal microscopy and FRAP analysis in the study and dynamics of chromatin, Řezníčková-Podloučková, Petra (2017). Advisor: doc. RNDr. Eva Bártová, Ph.D. (https://is.muni.cz/th/citk9).

Global proteome analysis of temperature perception in Arabidopsis thaliana and its cross-talk with cytokinin signaling pathway at the proteome response level, Skalák, Jan (2016). Advisor: prof. RNDr. Břetislav Brzobohatý, CSc. (https://is.muni.cz/th/xwahp).

Identification and characterisation of proteins regulated by plant hormones cytokines using mass spectrometry, Dyčka, Filip (2012). Advisor: Ing. Janette Bobáľová, CSc. (https://is.muni.cz/th/kz5f3).

Distribution function approach to kinetic study of ligand-receptor interactions by flow cytometry and confocal laser scanning microscopy, Orlova, Darya Yurevna (2012). Advisor: doc. RNDr. Stanislav Kozubek, DrSc. (https://is.muni.cz/th/plpip).