Doctoral Studies

Biophysics - Field

Brief description of field

 

The doctoral studies of Biophysics are offered to the graduates of MSc. studies in Physics and Biophysics finished at Mathematic-Physical and Science Faculties of Universities, including Technical universities in the field of biomedical engineering. It covers a broad spectrum of the problems of general and applied biophysics with special impetus on biophysics of macromolecules, biophysics of membranes and bioelectric phenomena, studies on the structure of the cell (cellular biophysics), photosynthesis, application of modern methods of microscopy, biophysical effects of ionising and non-ionising radiation, effects of magnetic fields etc. It also encompasses the problems of interdisciplinary character: nanotechnology in biomedical research, principles of imaging methods in medicine, analysis of image information or modelling of biological processes on molecular, cellular and system levels. Studies of these themes can be also oriented on the application of obtained results in industrial practice like production of scientific instrumentation or biotechnologies etc. The whole study and doctoral thesis can be focused on biological or physical problems, but it must contain a synthesis of biological and physical way of thinking, i.e. a well-defined biophysical theme. Theses oriented on history of Science or Science popularisation are excluded. Fully theoretical theses will be accepted only exceptionally after agreement of the field board.

Collaborating bodies or facilities

To maintain a high-quality research in the field and to fulfil the requirements on the graduates it is supposed a collaboration of the Faculty of Science with the Faculty of Medicine of the Masaryk University (MU), the CEITEC institute of MU and some other institutions (due to their specialists working as supervisors or members of the field board):

  1. Mendel University in Brno
  2. Veterinary and Pharmacy University in Brno,
  3. Institute of Biophysics, Czech Academy of Sciences, Brno, 
  4. Institute of Scientific Instruments, Czech Academy of Sciences, Brno,

 

Profile of a typical graduate

The graduate has a deep knowledge namely in the field of general and molecular biophysics. He or she can solve experimental biophysical problems autonomously in a creative way, is also able to formulate hypotheses which can be mathematically (statistically) assessed and biophysically interpreted. The graduate is a qualified creative researcher able to become an outstanding scientist. He or she can be employed in scientific institutes, universities of all kinds as well as in other institutions dealing with complex biophysical problems anchored in general and molecular biophysics with possible overlaps in medical or e.g. agricultural sciences.

Requirements for applicants

 (A) Special requirements: 

  1. A good orientation in the topics of the basic university course on general physics and main fields of biophysics.
  2. Mastering of the mathematical methods adequate for solution of problems solved in the above-mentioned courses. 

The thematic areas necessary for the entrance interview (specified according to the planned theme of dissertation thesis, including basic problems in the field of molecular biology, cellular biology, physiology etc.): 

  1. Physical system and its description. 
  2. Physical fields and their description. 
  3. Periodical processes. 
  4. The role of experiments in biophysics, key experiments. 
  5. Structure of atom and electron shell.
  6. Structure of biopolymers.
  7. Biomembrane and its basic properties, membrane potential
  8. Structure of the cell.
  9. Basic characteristics of energetic metabolism.

(B) Language requirements:

  • Reading of a scientific text from the field of biophysics related to the theme of dissertation thesis in English, understanding the text and discussion about its content in English. 

(C) Other requirements:

  •  Motivation discussion about the theme of dissertation thesis.

Evaluation of the entrance interview and conditions necessary for enrolment:

  • Part (A) … gaining 40 points of 60 possible
  • Part (B) … gaining 20 points of 40 possible
  • Part (C) … no points

Study requirements and completion of studies

The standard duration of the studies is 4 years, minimum number of credits obtained is 240.  The studies are not combined (part-time) as a rule. The study is finished (§47/4 law of University studies and the Study and Examination Regulations of the Masaryk University – SER) by (1) state doctoral exam (2) defence of thesis.

The studies obey an Individual study plan (see further) and the relevant paragraphs of SER (namely paragraph 4). The attendance to lectures etc. obeys the paragraph 9 of SER with some exceptions:   

- attendance to scientific seminars of the department (which is the workplace of the supervisor or consultant) or some other departments if it is recommended by the supervisor is compulsory during the whole studies, 

- the attendance to the subject “Help in teaching” is compulsory in the extent specified by the supervisor,

- the attendance to the seminars and presentations serving for the evaluation of students is compulsory,

- the attendance to some other, namely experimental subjects important from the point of view of the thesis topics, to the lectures given by visiting professors and specialists in the fields close to the dissertation thesis etc. are also compulsory in the extent specified by the supervisor.

 

Individual study plan (ISP)

The individual study plan is compiled by the student together with the supervisor. It reflects the thesis topics. According to ISP the doctoral student attends the subjects directly connected with the thesis topics, and the subjects forming his or her profile as a real upgrade of the MSc studies (see below the model ISP): 

  1. Profile subjects of A-type: lectures and seminars, held at the department of the supervisor, oriented on physical, biophysical, physico-chemical and biological problems which goal is to extend the biophysical education and to facilitate a qualified approach to solution of biophysical problems connected with the thesis topics.
  2. Profile subjects of B-type: specialised seminars and consultations held at some other departments.
  3. Stays at a Czech or foreign institutions if necessary for the processing of the dissertation thesis.
  4. Teaching activity of the student in courses of BSc. or MSc. studies to acquire practical experience in formulation and solution of biophysical problems on the adequate levels (the subject “Help in teaching”).
  5. Subjects connected with the language competences or demonstrating these competences, competences to statistical evaluation of measurement results. To the ethics of biomedical experiments etc. specified considering the topics of thesis.
  6. Compilation of the dissertation thesis, studying relevant literature, writing scientific papers and presentations.

 

State doctoral exam – content and extent, required knowledge

Conditions for application to sit the state doctoral exam:

  1. To obtain at least half of the minimum credit number of the whole studies.
  2. To pass through all the compulsory and optional compulsory subjects in ISP for the first four semesters (including the directly connected to the dissertation thesis as specified by the supervisor).
  3. Successful fulfilment of all language requirements according the paragraph 30/4/c of SER (English language).
  4. Submission of theses of dissertation thesis and the list of all publications as an attachment to the state doctoral exam application. 

The state doctoral exam verifies the extent and depth of the student knowledge in the field of general biophysics (resp. molecular, cellular or biomedically oriented) in connection with the dissertation thesis topics and his or her ability to solve in a creative way the problems (namely of experimental character) starting with their biophysical formulations up to the interpretation conclusions. In harmony with that, the exam question areas thematically close to the studied problem and ISP are formulated for individual students in the way to form a real upgrade of MSc. studies.    

Basic question areas of the state exam: 

  1. Molecular structure of living matter and methods how to study it on molecular level.
  2. Conformational changes of biomacromolecules and methods how to study them. 
  3. Biophysics of biological membranes. 
  4. Cell structure and an overview of methods of microscopy suitable for its study. 
  5. Interactions of non-ionising radiation with living matter. 
  6. Interactions of ionising radiation with living matter.
  7. Biophysics of biological systems and subsystems according to the dissertation topics.

The state doctoral exam encompasses also the student presentation about the problems and stage of compilation of the thesis which is presented at the beginning of the state doctoral exam. Duration of this presentation should be about 20 min. and it is followed by discussion. The list of specified questions on the above areas 1. to 7. are submitted to the student at least 4 weeks before the exam, based on paragraph 32 of SER.

The requirements for the doctoral thesis 

The thesis must deal with (till present time) non-solved or insufficiently solved problems in the field of biophysics. It is supposed that it contains a thorough biophysical (i.e. physical and biological) formulation of the problems and their solution including application in practice or practically oriented research. The focus of the thesis is a solution of the biophysical problems with original results obtained from real systems or their mathematical models. The application for the defence contains also the list of publications which reflect the specifics, standards and publication habits in the respective area of biophysics. An absolute condition is to have at least one first-author article with IF which is published already or accepted for publication (confirmed by the editor). It is recommended to publish the dissertation results in the journals listed in the 1st or 2nd quartile of the impact level in given branch of biophysics. The application has following attachments

  1. Three printed copies of the thesis,
  2. List of the applicant publications, including conference abstracts,
  3. The paper or manuscript of the paper accepted for publication which characterises best the original results of the dissertation.

Examples of the dissertation thesis topics

The examples were submitted by experienced researchers in the field of biophysics.   

Topics: Sensitivity of proteins to the composition of membranes

Problem: Control of the composition and shape of biological membranes is vitally important not only for eukaryotic cells. The organelles maintain a correct distribution of lipids despite of constant exchange of substances. It is necessary for a right organisation and function of membrane proteins which can be so controlled in time by the cell. The composition of membranes is also specific in tumour cells, bacteria and viruses with lipid envelopes which can be utilised for targeted and specific therapy. The goal of this project is to study the effect of membrane composition on the interactions of selected proteins.  
The student will acquire some knowledge about Linux, computer simulations and molecular modelling. The research will be done by means of computer simulations using the method of Molecular Dynamics and the advanced methods of phospholipid membrane analysis. 
Process: compilation of the recherche, studying the literature and simulation methods, simulation experiments, analysis of the data acquired, evaluation and discussion of results, finishing the thesis.

Literature:

[1] Amaro, M.; Sachl, R.; Aydogan, G.; Mikhalyov, I.I.; Vácha, R.; Hof, M.: Angewandte Chemie International Edition 2016, 55, 1-6
[2] van Meer, G.; Voelker ,D.R.; Feigenson ,G. W. :Nature Reviews Molecular Cell Biology 2008, 9, 112–124
[3] Bigay, J.; Antonny, B: Developmental Cell 2012, 23
[4] Doucet, C.M.; Esmery, N.; de Saint-Jean, M.; Antonny, B.: PLoS ONE 2015, 10(9): e0137965
[5] Antonny, B.: Annual Reviews Biochemistry 2011, 80, 101–23
[6] Drin, G.; Casella, J.-F.; Gautier, R.; Boehmer, T.; Schwartz, T. U.; Antonny, B.: Nature Structural and Molecular Biology 2007, 14, 138–146

Supervisor: Doc. RNDr. Robert Vácha, PhD

Topics: Study on structural and elastic properties of DNA mutation motifs by means of computational methods.

Mutation motifs are short specific DNA sequences which are characterised by high mutability (the so called hot spots) or by low mutability (the so called cold spots). The knowledge of these motifs and their properties is important for understanding of repair mechanisms of DNA in the cell. The goal of this dissertation will be the study on structural and elastic properties of selected DNA mutation motifs identified in the genes associated with hereditary diseases. For the selected motifs and various combinations of “mismatches” will be constructed 3D models of DNA double helix in silico. Their deformability (flexibility) will be followed by means of various mechanistic approaches which is probably the main factor in repair mechanisms of erroneous pairing of bases (mismatch repair).

Literature:

  • Cooper et al., Human Genomics, 2010, 4, 406–410. Methylation-mediated deamination of 5-methylcytosine appears to give rise to mutations causing human inherited disease in CpNpG trinucleotides, as well as in CpG dinucleotides.
  • Cooper et al., Human Mutation, 2011, 32, 1075–1099. On the Sequence-Directed Nature of Human Gene Mutation: The Role of Genomic Architecture and the Local DNA Sequence Environment in Mediating Gene Mutations Underlying Human Inherited Disease
  • Warren et al., Molecular Cell, 2007, 26, 579-592. Structure of the Human MutSa DNA Lesion Recognition Complex Arnheim and Calabrese, Nature Reviews, 2009, 10, 478-488, Understanding what determines
  • the frequency and pattern of human germline mutations Molecular Modelling: Principles and Applications (2nd Edition), Andrew Leach.

Supervisor: Mgr. Kamila Réblová, PhD

Topics: Metallic nanoparticles as a risk factor of ultrasound therapy and diagnostics – an in vitro study.

The increasing rate of usage and growing variability of nanoparticles which mechanical properties are very different in comparison with other nanostructures, can result in a risk in application of therapeutic and diagnostic ultrasound in medicine. The silver nanoparticles, for example, can enter the tissues from material for covering wounds, which are used in surgery, and the affected tissue can be examined by ultrasound later. Ultrasound causes oscillations of tissues and nanoparticles with different amplitudes which can result in increased penetration of nanoparticles into the cells and hence increase of their cytotoxicity. Similar effects can be expected also in some other nanoparticles exposed to various frequencies of therapeutic ultrasound including the applications of ultrasonic scalpel. Another endangered tissue can be also the gingiva exposed to ultrasound during plaque removal because there cannot be excluded also presence of very small metallic particles coming from decaying amalgam. In the dissertation, the penetration of metallic nanoparticles into cultured non-tumour cells will be studied in the field of high- and low-frequency ultrasound produced by common sources used in medicine. Evaluation of the samples will be done by microscopic methods as well as by means of chemical analysis of the cells after the sonication.

Literature:

  • BERNARD, V. et al. AgCu Bimetallic Nanoparticles under Effect of Low Intensity Ultrasound: The Cell Viability Study In Vitro. Journal of Cancer Research, 2014, p. 1-6.
  • BERNARD, V. et al. Combined effect of silver nanoparticles and therapeutical ultrasound on ovarian carcinoma cells A2780. Journal of Applied Biomedicine 12, 2014, p. 137-145.
  • Capco et al. Nanometerial, impacts on cell biology and medicine. Springer, Dordrecht, 2014, 276 pp.

Supervisor: Prof. RNDr. Vojtěch Mornstein, CSc.

Individual study plan

The ISP prepares the student together with the supervisor. It is submitted before the enrolment in the next study year. The ISP contains the following compulsory items:

  •  Preparation of thesis: 
  • Credit value of the subject “Preparation of thesis” is minimally 130 credits (standard range is one half to two thirds of minimum credit value of the whole study, i.e. 120 to 160 credits).
  •  Study of literature: The student can obtain during the first four semesters max. 15 credits. The subject is completed by a colloquium (examined by the supervisor or a teacher nominated by the head of the field council/board) or by giving credits. Enrolment is possible also in later semesters of the study.                                                                                                          
  • Help in teaching: Student can obtain during the first four semesters min. 6 and max. 18 credits, enrolment is possible also in later semesters. Help in teaching in the extent of 2 contact hours per week has a value of 3 credits. The subject is completed by giving credits by the supervisor or by the guarantee of the subject taught.                                                                                                               
  • Writing of a publication: Student can obtain 15 to 20 credits totally. The paper published after agreement of the supervisor in a national peer-reviewed journal or proceedings – 2 to 5 credits, in an international journal or proceedings with IF – 10 credits. In each case it must be a peer-reviewed journal or proceedings.
  • Language (and other) competences: Student can have during the study (recommended in the first four semesters) the respective subjects in two semesters, e.g. a subject completed by giving two credits, a subject completed by an exam for 4 credits, totally 6 credits (evaluated by the language teacher); eventually it can be only showing the competence at a written and oral exam without visiting the course for 6 credits (evaluated by the language teacher), or alternatively by writing a publication in English (3 credits) or by an English lecture (3 credits), evaluation is done by the supervisor in this case.
  • Stay: Student can obtain after agreement of the supervisor for one month 10 credits. The result of the stay is confirmed by an official authority of the institution in which the stay was done.                                                     
  • Profile subjects A-type: Student can obtain 10 to 15 credits during the whole study. 
  • Profile subjects B-type: Student can obtain 25 to 30 credits during the whole study. 

Summary table and schedule for individual semesters (an example)

z – credits given, zk – exam, k - colloquium

Study duty

credits

completion

Preparation of thesis

130

z

Study of literature

15

z, k

Help in teaching

12

z

Writing of publication

20

z

Language competences*

6

z, zk

Profile subjects A-type

15

k, zk, z

Profile subjects B-type

30

 

Optional subjects, stays

12

k, zk, z

Total

240

 

 *See also paragraph 5. about the ISP

1st semester

credits

completion

Preparation of thesis

5

z

Study of literature

6

z, k

Help in teaching

3

z

Writing of publication

-

 

Language competences

-

 

Profile subjects A-type

6

k, zk, z

Profile subjects B-type–department seminars

2

z

Profile subjects B-type– other

6

k, zk, z

Optional subjects, stays

2

k, zk, z

Total

30

 

 

2nd semester

credits

completion

Preparation of thesis

10

z

Study of literature

4

z, k

Help in teaching

3

z

Writing of publication

-

 

Language competences

-

 

Profile subjects A-type

5

k, zk, z

Profile subjects B-type–department seminars

2

z

Profile subjects B-type– other

4

k, zk, z

Optional subjects, stays

2

k, zk, z

Total

30

 

 

3rd semester

credits

completion

Preparation of thesis

10

z

Study of literature

3

z, k

Help in teaching

3

z

Writing of publication

-

 

Language competences

2

z, zk

Profile subjects A-type

4

k, zk, z

Profile subjects B-type–department seminars

2

z

Profile subjects B-type– other

4

k, zk, z

Optional subjects, stays

2

k, zk, z

Total

30

 

 

4th semester

credits

completion

Preparation of thesis

13

z

Study of literature

2

z, k

Help in teaching

3

z

Writing of publication

4

z

Language competences

4

z, zk

Profile subjects A-type

-

 

Profile subjects B-type–department seminars

2

z

Profile subjects B-type– other

-

 

Optional subjects, stays

2

k, zk, z

Total

30

 

 

5th semester

credits

completion

Preparation of thesis

20

z

Study of literature

-

 

Help in teaching

-

 

Writing of publication

6

z

Language competences

-

 

Profile subjects A-type

-

 

Profile subjects B-type–department seminars

2

z

Profile subjects B-type– other

-

 

Optional subjects, stays

2

k, zk, z

Total

30

 

 

6th semester

credits

completion

Preparation of thesis

26

z

Study of literature

-

 

Help in teaching

-

 

Writing of publication

-

 

Language competences

-

 

Profile subjects A-type

-

 

Profile subjects B-type–department seminars

2

z

Profile subjects B-type– other

-

 

Optional subjects, stays

2

k, zk, z

Total

30

 

 

7th semester

credits

completion

Preparation of thesis

24

z

Study of literature

-

 

Help in teaching

-

 

Writing of publication

4

z

Language competences

-

 

Profile subjects A-type

-

 

Profile subjects B-type–department seminars

2

z

Profile subjects B-type– other

-

 

Optional subjects, stays

-

 

Total

30

 

 

8th semester

credits

completion

Preparation of thesis

22

z

Study of literature

-

 

Help in teaching

-

 

Writing of publication

6

z

Language competences

-

 

Profile subjects A-type

-

 

Profile subjects B-type–department seminars

2

z

Profile subjects B-type– other

-

 

Optional subjects, stays

-

 

Total

30

 

List of members of doctoral committee

List of supervisors

Commission for state doctoral exams and defenses

List of current doctoral topics

Department pages


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