Study plan

Formal requirements for state doctoral examination are specified in MU Study and examination regulations (section 32). In a doctoral state examination the students have to demonstrate primarily a good orientation in the fields involving the scientific problem investigated in the doctoral thesis. They should prove the ability to communicate and discuss in their respective field and the ability to apply in a creative way their knowledge for the solution of specific problems. As a rule, the examination has the character of a discussion between the committee members and the candidate, in which the candidate has, on the one hand, to prove the ability to be deeply oriented in the area of problems for which he or she has specialized and, on the other hand, to demonstrate their general range of knowledge extending also into related fields.

The state doctoral examination is composed of two mandatory exams:
Biomolecular chemistry
Bioinformatics
and one optional exam out of the following:
Biophysics
Molecular biology and genetics
Biochemistry
Physical chemistry

Prior to the examination, the students will receive, by means of their supervisors or the respective doctoral committee, lists of the topics to be discussed.

When the student fulfils all of his or her study requirements according to the individual study plan and Study and Examination Regulations, he may submit an application to take the state doctoral exam and defend his dissertation work. The student may take the exam and thesis defence at the same time or independently at different times.

Studies are concluded with a state doctoral examination, and defense of doctoral dissertation work. Studies take place according to an individual study plan, which determines the time schedule for classes, academic and research work on the dissertation thesis, and possible study stays at other institutions including those abroad, the extent of participation in teaching activities, the dates of course exams, and other requirements. Annual individual study plans are assembled by the doctoral candidate in consultation with his supervisor.

In creating and fulfilling the study plan, each student must adhere to the following rules and conditions:

Study requirements:
Until end of 4. semester students are obliged to enroll courses expanding and deepening the student's knowledge in the field of his/her dissertation thesis and possibly other courses expanding his soft skill competences. Students enroll courses offered at the Faculty of Science and other faculties of Masaryk University, and which the student did not take during his bachelor’s and master's studies. The suitability of a subject for doctoral studies is determined by supervisor. Upon the proposal of his supervisor, the student can also enroll some of that courses at universities other than MU (in accordance with regulations of Faculty of Science MU).
Each semester (of presentation form of study) students are obliged to complete NCBR seminar CC060 (spring term) and CB060 (autumn term).
At the beginning of each academic year, the student must attend a required two-hour bloc lecture C7777 Working with Chemical Substances. Attendance is mandatory only for students whose work require manipulation with chemical substances.
Undergraduate teaching duties (till end of 4. semester). Students participate in teaching of practical courses in Bachelor and Master degree programmes and possibly participate in supervision of bachelor theses. The extent of teaching duties of a student does not exceed 150 hours.
Student must successfully finish of all parts of the state doctoral examination.

Research requirements:
Systematic creative scientific work on the topic of the dissertation thesis (workload min. 70%).
Presentation of results on NCBR seminar in extent specified by seminar leader (max. once in semester).
Presentation about their dissertation progress before Doctoral board within „PhD days“.
Presentation of results on international scientific event in English language.
Students have to make a stay abroad for at least 1 months or participate in international creative project with results published or presented abroad or participate directly in international cooperation. This duty must be done until end of standard period of study.
Publication of results in international journal (workload 10%). At least one publication in peer-reviewed journal with impact factor (IF) above median in journal category where the student is the first author is required or at least 2 first authorship publications in journals with IF below median. Exception from this requirements need to be approved by Doctoral board.
Preparation of doctoral dissertation work and defense of doctoral dissertation.

Suggested theses topics for newly accredited programme Biomolecular chemistry and bioinformatics:
Chemoinformatical methods for prediction of physico-chemical properties of molecules
Protein-small molecule interactions studied by computer simulations and modeling
Structure-specific nucleases as therapeutic targets
Study of RecQ helicases associated with genomic instability syndromes
Advanced carriers for platinum drugs and prodrugs
Structure and ion transport in modified DNA quadruplexes
Development of novel paramagnetic metallodrugs
Studies of protein - nucleic acids complexes
Structure, dynamics, chemistry and evolution of nucleic acids. From prebiotic reactions to protein/RNA complexes
Studies of quadruplex nucleic acids
Structural and functional studies of RNA-binding proteins involved in RNA metabolism
Protein sensitivity of membrane composition
RNA surveillance in human pathogens
The role of noncoding RNAs in gene expression regulation
NMR Methods for structure determination of excited protein states
Protein channels, tunnels, and cavities - discovery, analysis, comparison, applications
Characterization of structure and dynamics of specific subunits and sigma factors of RNA polymerase from Bacillus subtilis
How did the DNA genome evolve from RNA?
Integrative structural biology of 3’UTRs