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Submission deadline until midnight 30 Nov 2021

What will you learn?

The objective is to provide to talented Master's degree holders the possibility to continue their studies in the doctoral degree program Physics in such specializations which have excellent quality and traditions at the Faculty of Natural Sciences of MU and at cooperating institutions, mainly various institutes of the Czech Academy of Sciences. During his/her doctoral studies the student participates in research as a member of a research team, he/she usually partakes in objective financed research and is led in such a way as to become an independent researcher on concluding the doctoral program. Necessary conditions include the publication activity in prestigious international journals, active participation in meetings of scientific peers and usually a long-term stay abroad. This guarantees the ability to communicate with international research partners in English resp. other languages. Our aim is is to educate the students so that they are able to independently work at universities and research institutes in the Czech Republic as well as anywhere else in the world.

Career opportunities

The Physics PhD graduate becomes a member of a research team during the course of his/her studies, usually participates in objective-funded research and is led in such a way as to become an independent creative scientist. A long-term stay abroad is a common part of his/her studies and guarantees his/her ability to communicate in English and/or other languages with scientific peers. The graduate is able to do research and teach at universities and scientific research centers in the Czech Republic as well as anywhere else in the world. His/her knowledge, logical thinking, scientific world view and foreign language capabilities enable him/her to work in other areas as well: quantitative analyst, data scientist, consultant etc.


1 Aug – 30 Nov 2021

Submit your application during this period

International applicants for doctoral study (Czech and Slovak Republics applicants not included)

1 Aug – 30 Nov 2021

Submit your application during this period

Submit an application

Study options

Single-subject studies with specialization

In the single-subject studies, the student deepens knowledge in the concrete focus of the degree programme and chooses one specialization. The specialization is stated in the university diploma.

Dissertation topics

Specialization: Astrophysics

Study of cosmic ray influence on detection capabilities of satellite experiments for high-energy astrophysics
Supervisor: Mgr. Filip Münz, PhD.

Cosmic-ray (CR) background influences strongly noise level of most astrophysical instruments on orbit. In small-scale missions (cubesats) it can be monitored and partly shielded, in observatories equipped with optics low-energy part of particle spectra gets concentrated and should be treated with more sophisticated way as e.g. magnetic diversion. With example of future Athena X-ray observatory whose magnetic divertor is being developed in Brno, this thesis should contribute to understanding of functioning of this essential part of the instrument using CR tracking tools (e.g. Geant4 package). Similar approach could be used to study detection capabilities of cubesats for current and future constellation mission for monitoring of gamma-ray bursts. When possible, these studies should be complemented with lab tests of prototypes of respective instrument parts.


Literatura: Gabor Galgoczi, Jakub Řípa et al: Simulations of expected signal and background of gamma-ray sources by large field-of-view detectors aboard CubeSats,
Gabor Galgoczi, Riccardo Campana et al: Software toolkit to simulate activation background for high energy detectors onboard satellites, SPIE proceedings 11444 (2020), doi: 10.1117/12.2560829


Mgr. Filip Münz, PhD.

Study of multiple stellar systems
Supervisor: doc. RNDr. Miloslav Zejda, Ph.D.

Vícenásobně zákrytové hvězdné soustavy představují relativně novou třídu objektů, která se nabízí jako významný zdroj informací o hvězdných systémech. Zatím je známo poměrně málo takových soustav a to zejména v severní části hvězdné oblohy.

Cílem práce bude za pomoci dat z přehlídkových projektů, nově zejména TESS, vyhledávat další minimálně dvojzákrytové soustavy a sestavit jejich katalog. Na takto získaném vzorku hvězdných soustav bude studovat obecné vlastnosti těchto soustav, například četnost určitých poměrů oběžných period složek systému.

U alespoň jedné vybrané soustavy doplní případně sesbíraná data o vlastní fotometrická a spektroskopická pozorování a provede detailní analýzu systému s určením parametrů jednotlivých složek.


doc. RNDr. Miloslav Zejda, Ph.D.

Understanding the physics of hot galactic atmospheres
Supervisor: doc. Mgr. Norbert Werner, Ph.D.

Most galaxies comparable to or larger than the mass of the Milky Way host hot, X-ray emitting atmospheres. The crucial role of these atmospheres for the formation and evolution of individual massive galaxies is just beginning to be appreciated. About half of the yet unseen warm-hot diffuse matter in the local Universe may lie in such extended galactic atmospheres, which are inextricably linked to their host galaxies through a complex story of accretion and feedback processes, such as energy and momentum input from supernovae, and jets and winds of accreting supermassive black holes, also called active galactic nuclei.
Using novel data analysis techniques, the student will explore X-ray data complemented by other multi-wavelength observations to study hot galactic atmospheres and their interaction with the central AGN.


doc. Mgr. Norbert Werner, Ph.D.

Specialization: Biophysics

Protein Affinity and Selectivity to Cellular Membranes
Supervisor: doc. RNDr. Robert Vácha, PhD.
OBJECTIVES: The aim is to elucidate the relationship between protein sequence and preferred composition and curvature of human membranes,i.e., find peptide motifs that are selective to specific membranes in cells (plasma membrane, endoplasmic reticulum, Golgi apparatus, mitochondria, etc.). The obtained understanding will be used for the development of new protein biomarkers, sensors, scaffolds, and drugs.

DESCRIPTION: The control of biological membrane shape and composition is vital to eukaryotic life. Despite a continuous exchange of material, organelles maintain a precise combination and organization of membrane lipids, which is crucial for their function and the recruitment of many peripheral proteins. Membrane shape thus enables the cell to organize proteins and their functions in space and time, without which serious diseases can occur. Moreover, membrane curvature and lipid content can be specific to cancer cells, bacteria, and enveloped virus coatings, which could be utilized for selective targeting. We will develop a new method, using which we will elucidate the relationship between the protein sequence and the preferred membrane. The relationship will lay the foundations for the design of new protein motifs sensitive to membranes with a specific curvature and composition. Student(s) will master tools of computer simulations, in particular, molecular dynamics techniques and methods to calculate free energies. Moreover, he/she will learn the advantages and disadvantages of various protein and membrane parameterizations, including all-atom and coarse-grained models.

EXAMPLES of potential projects: * Determination of helical motifs for specific membrane compositions * Development of implicit membrane model for fast determination of protein-membrane affinity * Helical peptides and their sensitivity for membrane curvature


PLEASE NOTE: before the formal application process, all interested candidates should contact Robert Vacha (

doc. RNDr. Robert Vácha, PhD.

Structural dynamics, function and evolution of RNA and DNA. From the origin of life to modern biochemistry.
Supervisor: prof. RNDr. Jiří Šponer, DrSc.

Our scientific goal is understanding of the most basic principles of structural dynamics, function and evolution of DNA and RNA.

To achieve our goal, we use a wide portfolio of theoretical/computational approaches. Our research is closely related to experiments, mostly via extensive collaborations, though in the prebiotic chemistry we have in house experiments. We offer thesis essentially on any topic that is currently active in the laboratory. You can get the most up-to-date idea about our current research from the WOS or SCOPUS databases, where you can find all our publications (Sponer, J.), see all our collaborators, etc. The laboratory is at the Institute of Biophysics, Czech Academy Sciences, Kralovopolska 135, where we have a powerfull set of high-perfomance computer clusters dedicated exclusively to our group

Our methods are:
  • Classical Molecular Dynamics (MD) simulations. Besides standard simulations, we have years of experience in using all classes of enhanced-sampling techniques. We play also a prominent role in development of DNA/RNA simulation force fields and our versions are used world-wide
  • Quantum-chemical (QM) method. We have full spectrum of methods, ranging from ultra-accurate computations of model systems, through large-scale QM studies on biomolecular building blocks with hundreds of atoms up to sophisticated methods that are used in studies of excited states and photochemistry; the later technique is especially relevant to study the origin of life chemistry under UV light. Again, please see the papers we have published in last years.
  • Hybrid quantum-classical (QM/MM) methods, quantum molecular dynamics
  • Structural bioinformatics
Specific experiments are possible in the field of prebiotic chemistry in collaborating laboratories. Modern computations are extensively combined with many experimental techniques (NMR, X-Ray, high-energy lasers, biochemical techniques) mostly via numerous collaborations. We collaborate with 30 foreign and Czech laboratories. We publish about 20 papers annually and belong to the most cited Czech research groups. We currently work in several mutually interrelated research areas, which are open for the students as PhD topics.
  • RNA structural dynamics, folding and catalysis
  • Protein-RNA (or DNA) complexes. We try to go beyond the ensemble-averaged picture of experimental methods in order to understand how rarely accessed dynamical conformations invisible to experiments allow to separate affinity for reactivity or selectivity.
  • DNA, with focus on G-quadruplexes, specifically advanced studies of quadruplex folding mechanisms
  • Diverse types of quantum-chemical studies on nucleic acids systems
  • Origin of life (prebiotic chemistry), i.e., creation of the simplest chemical life on our planet (or anywhere else in the Universe), with a specific attention paid to the formamide pathway to template-free synthesis of the first RNA molecules. This specific project includes also in house experimental research.

Besides studies of specific systems, we are also involved extensively in method testing/development, mainly in the field of parametrization of molecular mechanical force fields for DNA

NOTE: before initiating the formal application process to doctoral studies, all interested candidates are required to contact Prof. Jiri Sponer ( for an informal discussion.

Laboratory web page

List of publications

prof. RNDr. Jiří Šponer, DrSc.

Understanding antimicrobial peptides
Supervisor: doc. RNDr. Robert Vácha, PhD.
OBJECTIVES: The aim is to elucidate the relationship between molecular properties of amphiphilic peptides and their ability to translocate and form transmembrane pores in membranes with various lipid compositions. The obtained understanding will be used for the development of new antimicrobial peptides, which can serve as a new type of antibiotic drugs.

DESCRIPTION: Antibiotic-resistant bacteria cause more than 700 000 deaths per year, and the forecast is 10 million per year in 2050. Moreover, emerging strains of bacteria resistant to all available antibiotics may lead to a global post-antibiotic era. Because of this threat, the WHO and the UN are encouraging the research and development of new treatments. Antimicrobial peptides are promising candidates for such new treatments. We will study the molecular mechanism of action of antimicrobial peptides and determine the critical peptide properties required for membrane disruption via the formation of transmembrane pores and spontaneous peptide translocation across membranes. Based on the obtained insight, we will design new peptides and test their abilities. The most effective peptides will be evaluated for antimicrobial activity and human cell toxicity using growth inhibition and hemolytic assays, respectively. Student(s) will master tools of computer simulations, in particular, molecular dynamics techniques and methods to calculate free energies. Moreover, he/she will learn the advantages and disadvantages of various protein and membrane parameterizations, including all-atom and coarse-grained models. The simulations will be complemented by in vitro experiments using fluorescent techniques.

EXAMPLES of potential projects: * Antimicrobial peptides and formation of membrane pores * Synergistic mechanisms between antimicrobial peptides * Membrane disruption by antimicrobial peptides in non-equilibrium conditions

MORE INFORMATION about the group:

PLEASE NOTE: before the formal application process, all interested candidates should contact Robert Vacha (

doc. RNDr. Robert Vácha, PhD.

Specialization: Condensed Matter Physics

Structural and electronic investigations of topological insulator thin films
Supervisor: Mgr. Ondřej Caha, Ph.D.
Topological insulators have a unique electronic band structure of surface states. These states have spin-momentum locked dispersion caused by time-reversal symmetry or mirror symmetry for topological insulators and topological crystalline insulators, respectively. The time-reversal symmetry can be broken by the magnetic field; thus, ferromagnetically doped topological insulators are of great scientific interest for the possible electronic and spintronic application. The other materials to be studied are thin films and quantum wells of topological crystalline insulators. The quantum well changes the electronic structure of the topological surface states due to changing the inversion symmetry protecting the topological surface states.

The PhD candidate is expected to join our research in one of the following research activities:

  • Structural analysis of thin films: Laboratory x-ray diffraction measurements and data analysis. Preparation of lamellae for HRTEM structural analysis.
  • Electronic characterization of the topological insulators: transport measurements at low temperatures
  • Participation in synchrotron-based experiments: ARPES, XAS, XMCD.
  • Data evaluation and computer simulations necessary to evaluate the experimental results.

Required Skills and Qualifications:

  • Master’s degree in Condensed Matter Physics.
  • Experience in en experimental laboratory, preferably in Solid State Physics.
  • Good communication skills (oral and written) in English.
  • Commitment to complete the PhD studies.


  1. E. D. L. Rienks et al., Nature 576, 423-428 (2019).
  2. G. Springholz et al., submitted to Advanced Functional materials.

PLEASE NOTE: before the formal application process, all interested candidates should contact dr. Caha at and provide curriculum vitae, cover letter with a concise summary of previous research activities, and contacts of two persons who might provide references



Mgr. Ondřej Caha, Ph.D.

Specialization: General Physics

No topics currently listed.

Specialization: Plasma Physics

Advanced spectroscopic analysis of transient non-equilibrium plasma
Supervisor: doc. Mgr. Tomáš Hoder, Ph.D.

Problematika obsazování kvantových stavů molekul a atomů v přechodném nerovnovážném plazmatu je jednou z fundamentálních výzev současné plazmové fyziky. Populace a relaxace distribucí rotačních, vibračních a elektronových kvantových stavů probíhá v extrémně krátkých časových intervalech a jejich mikroskopické zákonitosti jsou stále otevřeným problémem. Doktorský/á student/ka bude analyzovat vybrané stavy a podmínky v plazmatu pomocí pokročilých metod (např. emisní či laserové spektroskopie). Cílem práce bude přispět k objasnění iniciace plazmo-chemických procesů a také vlivu těchto procesů na studované plazma.


doc. Mgr. Tomáš Hoder, Ph.D.

Development of multifuncional thin films using plasma assisted chemical vapor deposition methods
Supervisor: doc. RNDr. Vilma Buršíková, Ph.D.

Současné období pandemie ukázalo na zvýšený požadavek na vývoj metod pro úpravu povrchových vlastností materiálů, např. pro přípravu antibakteriálních a antivirových povrchů nejen pro zdravotnické materiály, ale i pro obalovou techniku a další často dotýkané povrchy (kliky, vypínače, apod.). Nanočástice stříbra, ale i některých dalších kovů (měď, zlato, titan) jsou známé pro jejich antibakteriální i antivirové vlastnosti. Tématem navržené disertační práce bude vyvinout technologii kovem dopovaných organosilikonových tenkých vrstev použitím metody plazmatem aktivované depozice z plynné fáze. Pro zabudování kovů budou odzkoušeny 2 metody: (1) depozice ze směsí organosilikonových a organometalických prekurzorů a (2) příprava organosilikonových vrstev v prachovém plazmatu dodáním nanočástic různých kovů s antibakteriálními vlastnostmi do plazmatu. V případě druhém bude nutné vyřešit dodání částic do plazmatu.
Pro přípravu shora uvedených vrstev je velmi důležitý jejich multifunkční charakter, kromě antibakteriálních vlastností musí splňovat několik dalších důležitých vlastností, jako jsou dobrá adheze k substrátu, otěruvzdornost, elasticita (zejména v případě flexibilních substrátů), transparentnost (v případě obalových materiálů). Požadavek na kvalitu struktury vrstev (dopant se nesmí uvolňovat z povrchu) bude rovněž zvýšená, vrstva musí zachovat povrchové i objemové vlastnosti a musí být odolný vůči běžným čisticím postupům.
V rámci práce budou studovány vlastnosti tenkých vrstev i v závislosti na druhu substrátu na který jsou tenké vrstvy nanášeny (u plazmatem asistované depozice může mít substrát významný vliv). Bude kladen důraz na studium vlivu záporného stejnosměrného předpětí na substrátu na vlastnosti nadeponovaných vrstev. V práci se bude věnovat i studiu časového vývoje předpětí a jeho vliv na hloubkový profil mechanických, strukturních a dalších fyzikálních a chemických vlastností vrstev.
V první části disertační práce se budou vyvíjet metody pro přípravu různých typů vrstev ze směsí organosilikonů anebo organosilazanů s nosnými plyny (např. Ar, O2, N2O, atd.) aby bylo možné vytypovat vhodné typy vrstev pro následné dopování kovovými prvky.
Pro úspěšné řešení tohoto tématu bude velice důležitá důkladná charakterizace tenkých vrstev, jako jsou měření mechanických (nanoindentace, vrypové a nanootěrové zkoušky), povrchových (topografie pomocí AFM, konfokální mikroskopie, studium volné povrchové energie), strukturních a chemických vlastností vrstev (FTIR, XPS, Raman, SEM, TEM, RBS/ERDA atd.). Většina těchto technik je k dispozici na pracovišti ÚFE, TEM můžeme řešit ve spolupráci s ÚFM anebo s CEITEC, RBS/ERDA ve spolupráci s ÚJF (Řež u Prahy). Antibakteriální testy pak můžeme řešit ve spolupráci s FCH VUT, TUL Liberec anebo Univerzitou Tomáše Bati ve Zlíně.
Materiálně je řešení tématu v současné době zabezpečený projektem GAČR 19-15240S.


doc. RNDr. Vilma Buršíková, Ph.D.

Dusty plasma diagnostics
Supervisor: doc. Mgr. Pavel Dvořák, Ph.D.

V reaktivním plazmatu mohou samovolně vznikat mikro a makroskopické částice, které ovlivňují plazma i vlastnosti případných materiálů deponovaných z plazmatu. V rámci této dizertační práce studujte plazma nízkotlakého kapacitně vázaného výboje, ve kterém vznikají prachové částice. Zvolte vhodné diagnostické metody a sestavte potřebná diagnostická zařízení. Zprovozněte monitorování růstu prachu v plazmatu, zjistěte a vysvětlete souvislosti mezi přítomností prachu a vlastnostmi plazmatu. Přístupné diagnostické metody zahrnují zejména elektrická měření (VA charakteristika, sondové metody), optické a laserové metody.


doc. Mgr. Pavel Dvořák, Ph.D.

Laser-based diagnostics of nonequilibrium plasma
Supervisor: doc. Mgr. Pavel Dvořák, Ph.D.

Laserová diagnostika zahrnuje řadu metod, které souhrnně umožňují získat poměrně komplexní informaci o studovaném plazmatu. Mezi laserové metody vhodné pro studium plazmatu patří fluorescenční metody (vč. fluorescence iniciované vícefotonovou absorpcí), Ramanův rozptyl zahrnující vibrační i rotační přenos energie, jenž může existovat ve spontánní i stimulavané variantě, Thomsnův rozptyl umožňující studovat volné elektrony, Rayleigho rozptyl a generace druhé harmonické frekvence laserového záření vlivem elektrického pole. Úkolem této dizertační práce je studium nerovnovážného plazmatu pomocí laserové diagnostiky s důrazem na metody využívající rozptyl laserového záření. Součástí práce je realizace optických experimentů, kvantitativní vyhodnocení měřených dat a studium procesů probíhajících v plazmatu.


doc. Mgr. Pavel Dvořák, Ph.D.

Plasma engineering of nanostructured coatings for flexible energy-harvesting and -storage systems
Supervisor: doc. RNDr. Tomáš Homola, PhD.

The novel emerging field of flexible and printed electronics has attracted increased attention because of its potential to enable low-cost and high-throughput manufacturing of electronics on cheap plastic substrates for various applications including photovoltaics. However, this segment is still far away from commercialization because the cutting edge materials and manufacturing steps are not compatible with thermally sensitive flexible materials.

The PhD. work will focus on low-temperature plasma engineering of novel nanostructured nanomaterials as tungsten oxide, iron oxides, titanium dioxide, molybdenum disulfide, etc ... and their application in various energy-harvesting, -storage systems and sensing devices. The topic and tasks in the laboratory are strongly oriented towards the industrial segment.

Possibility to spend 6 months on an internship in a high-tech company in Singapore working on PhD. topic.

The exacttopic and tasks will be defined later according to applicant preference: perovskite solar cells, tandem solar cells, supercapacitors, etc ...

Keywords: State-of-the-art plasma generators, coating deposition methods (i.e. ink-jet printing), plasma treatment, advanced surfaces, nano-coatings, roll-to-roll manufacturing, flexible and printed electronics, surface characterization (AFM, XPS, SEM, etc.).


More information:

Relevant literature:

T. Homola, J. Pospíšil, R. Krumpolec, P. Souček, P. Dzik, M. Weiter, et al., Atmospheric dry hydrogen plasma reduction of inkjet-printed flexible graphene oxide surfaces, ChemSusChem. 11 (2018) 941–947. doi:10.1002/cssc.201702139.

T. Homola, P. Dzik, M. Veselý, J. Kelar, M. Černák, M. Weiter, Fast and low-temperature (70 C) mineralization of inkjet printed mesoporous TiO2 photoanodes using ambient air plasma, ACS Appl. Mater. Interfaces. 8 (2016) 33562–33571. doi:10.1021/acsami.6b09556.


doc. RNDr. Tomáš Homola, PhD.

Specialization: Theoretical Physics

No topics currently listed.

Specialization: Wave and Particle Optics

No topics currently listed.

Study information

Provided by Faculty of Science
Type of studies Doctoral
Mode full-time Yes
combined Yes
Study options single-subject studies No
single-subject studies with specialization Yes
major/minor studies No
Standard length of studies 4 years
Language of instruction Czech
Collaborating institutions
  • The Czech Academy of Sciences
  • Astronomický ústav AV ČR
  • Biofyzikální ústav AV ČR
  • Ústav fyziky materiálů AV ČR
  • Ústav přístrojové techniky AV ČR
Doctoral board and doctoral committees

Do you have any questions?
Send us an e-mail to

prof. Rikard von Unge, Ph.D.



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