Doctoral program Biophysics

Responsible person: prof. RNDr. Tomáš Polívka, PhD.; contact: phone 387 776 259; e-mail: tpolivka@jcu.cz


Characteristics

Study program biophysics provides education in research fields at the borders between physics, chemistry and biology. Students are involved in solving problems related to biology and/or chemistry by means of physical methods. The doctoral projects are both theoretical and experimental, and they are dealing either with basic or applied research, depending on particular project and supervisor. During the Ph.D. study, students are guided to carry out independent research, from design and realization of experimental and theoretical approaches, rigorous and correct data analysis to presentation of results. Topics of Ph.D. projects are based on research profiles of individual research groups and cover a broad range of modern biophysical methods from ultrafast optical spectroscopy, single-molecular spectroscopy, X-ray diffraction, molecular dynamics, quantum-chemical and semi-empirical calculations, molecular modeling to advanced techniques of microscopy, including atomic force microscopy and electron microscopy. These methods are applied to various biological systems from molecular level to isolated proteins, whole cells to modeling processes in large ecosystems.

Topics of Ph.D. projects

Ultrafast spectroscopy. Time-resolved spectroscopy with femtosecond time resolution allows monitoring extremely fast processes occurring in various materials. Our projects are at the borders between physics, chemistry and biology, and they focus on studies of excited-state dynamics of molecules, predominantly photosynthetic pigments. We study processes of energy and/or electron transfer in photosynthetic proteins by means of femtosecond time-resolved spectroscopy, but the ultrafast spectroscopy group also develops new methods of ultrafast spectroscopy, such as multi-pulse methods enabling to manipulate populations of excited states or experiments with two-photon excitation.

Contact person: prof. Tomáš Polívka (tpolivka@jcu.cz), www.polivkalab.cz

Studies of photosynthetic processes by means of optical and biochemical methods. Photosynthesis is a complex process requiring interplay of pigments, proteins and lipids for efficient utilization of light energy. Students work on projects analyzing energy transfer efficiency, photoprotection mechanisms, structure-function relationship and other aspects of photosynthetic apparatus components from various photosynthetic organisms by employing a broad range of optical and analytical methods such as steady-state and time-resolved absorption and fluorescence spectroscopies or circular dichroism as well as a diverse set of biochemical analysis methods.

Contact persons: dr. Radek Litvín (rlitvin@prf.jzu.cz), dr. David Bína (bina@umbr.cas.cz)

Atomic Force Microscopy (AFM). AFM enables to image details of surface and/or mechano-elastic properties including their dynamics in living cells, biological membranes, protein complexes, individual proteins, peptides, nucleic acids, organic polymers and their conjugates in both gas and liquid phase. In solid state samples e.g. nanoparticles and nanostructured surfaces, maps of conductivity and capacitance can be additionally imaged. AFM also allows for measurements of forces acting between all the above-mentioned objects down to the level of non-covalent bonds formed between individual molecules.

Contact person: dr. David Kaftan (dkaftan@prf.jcu.cz)

Electron microscopy (EM). Electron microscopy offers projects that combine advanced technologies to localize specific components in cell ultrastructures (TEM) or in surface morphology of biological samples (SEM). The projects also include the preparation of biological specimens for electron and correlative microscopy. In addition, our projects are focused also on cryo-EM structural studies of viral particles and protein complexes. The outcome of cryo-EM is 3D structure reconstruction of the studied objects. Another structure reconstruction method available in our laboratory and useful mainly for larger objects (e.g. cell organelles) is electron tomography.

Contact person: ing. Jana Nebesářová (nebe@paru.cas.cz), dr. Zdeno Gardian (gardian@prf.jcu.cz)

Bio-active nanostructured thin films and surfaces. Students focuses on research and development of thin, functional, nanostructured films that are able to interact with molecular complexes; these are namely surfaces for LMR, SERS, LSPR, SPR sensing; bio-molecule enriched thin films (e.g. films doped by antibiotics); surfaces with functional groups etc. Nanostructured surfaces are typically prepared by plasma-assisted deposition employing PVD (Plasma Vapor Deposition) of PECVD (Plasma Enhanced Chemical Vapor Deposition) techniques.

Contact person: Vítězslav Straňák (stranak@prf.jcu.cz), www.prf.jcu.cz/plasma

Molecular simulations of aqueous solutions and solid-liquid interfaces provide molecular-level understanding of structure, interactions, and dynamics of ions, molecules and biomolecules, leading to deeper understanding of the molecular origin of experimental signals. Both classical molecular dynamics and ab initio calculation, including ab initio dynamics, is used and the computational and experimental results are compared. Currently the focus is on prediction of non-linear optics signals (Sum Frequency Generation, Second Harmonic Generation) and electrokinetic phenomena (electroosmosis, electrophoresis) applied to systems of increasing complexity.

Contact person: assoc. prof. Milan Předota (predota@prf.jcu.cz)

Computational modelling of biomolecules and their interactions with the environment
Students work with computational methods for modelling of biological systems with focus on the analysis of dynamical changes of biomolecules and their interactions with environment. Students will use methods of molecular modelling and quantum chemical calculations in order to study the relationship between structure and function of biomolecules (proteins, nucleic acids) and their interactions with the environment (solvents, ionic liquids). The results of theoretical methods are the directly compared with experimental data.
Contact: Dr. David Řeha (reha@nh.cas.cz), Dr. Babak Minofar (minofar@nh.cas.cz)

Crystallization and protein crystallography aims at preparation of crystals and determination of structures of proteins and protein complexes using X-ray diffraction analysis. Knowledge of the detailed protein structure is essential to understand their function. Students deal with the entire process leading to the determination of the protein structure from the protein isolation and purification by the use of molecular biological and biochemical methods, through its own crystal preparation to X-ray structural analysis. A number of enzymes, viral and other proteins important for biomedicine, pharmacology, biotechnology or biotransformation are available for a detailed study.

Contact person and supervisors: prof. Ivana Kutá Smatanová, Ph.D. (kuta@prf.jcu.cz), Taťána Prudnikova, Ph.D. (prudnikova@prf.jcu.cz), Michal Kutý, Ph.D. (kuty@prf.jcu.cz), https://www.prf.jcu.cz/en/uchbch/research/laboratory-of-structural-chemistry.html

Assembly of viruses – from in vitro models to live cell imaging. Viruses are infectious agents causing many diseases of humans, animals as well as crop plants. Design of antiviral drugs that selectively target key steps in viral life cycle requires detailed knowledge of virus entry, replication and assembly in the host cell. Our interest is in the replication of RNA viruses belonging to Reoviridae family, avian reovirus and human rotavirus. The former causes significant losses for poultry farms while the latter is causative agent of severe diarrhea in children. Both viruses replicate and assemble inside viral inclusion bodies (VIB), also called viroplasms or viral factories, in the host cell cytoplasm. We have established that VIB are dense, liquid separated phases. This project will focus on developing model systems and using combination of biophysical techniques (e.g. live cell interference tomography, super-resolution and Raman microscopy) to study formation and phase transitions of VIB which constitute novel target for antiviral therapies.

Contact: rtuma@prf.jcu.cz, Supervision: Roman Tůma & Tomáš Fessl

Understanding TBEV replication. Tick Borne Encephalitis Virus is a single-stranded RNA virus, which replicates in association with the host Endoplasmatic Reticulum (ER) forming dynamic and well-orchestrated Replication Complex (RC).  Despite its importance, the molecular composition and structure of the RC, as well as the interaction among individual constituents and precise mechanism of RNA replication is still largely unknown. We combine various molecular-biological, biochemical, biophysical and structural techniques to explore the formation and function of RC within membrane bilayer.

Contact: Zdeněk Franta, zfranta@prf.jcu.cz, Supervisors: Zdeněk Franta, Filip Dyčka (fdycka@prf.jcu.cz), Zdeno Gardian (gardian@prf.jcu.cz), Tomáš Fessl (fessl@prf.jcu.cz), Roman Tůma (rtuma@prf.jcu.cz)

Allosteric communication in membrane protein complexes linked to conformational transitions on multiple timescales. Allosterically modulated molecular machines mediate many of the key processes in all forms of life. A general feature of these machines is that they undergo repeated cycles of ATP hydrolysis and switch between various conformational states. The coordinated movements of most molecular machines are achieved by nucleotide binding, hydrolysis (energy conversion) and allosteric control. Consequently, a molecular level understanding of how the essential machines of life work requires invoking and further developing allosteric theory. Membrane proteins have historically been difficult to study from the mechanistic perspective as many of the biophysical and chemical techniques applicable to soluble enzymes fail to deal with either their heterogeneity, dynamics or the complexity of their native environment. Single-molecule fluorescence can resolve all these issues. Here we present research projects to map the full allosteric network regulating processes in membrane protein complexes using a combination of single-molecule, in silico methods and hydrogen-deuterium exchange mass spectrometry.

Supervision: Tomáš Fessl (single molecules), David Řeha (computational techniques), Filip Dyčka (mass spectrometry), Alexey Bondar (membrane proteins) and Roman Tůma (macromolecular complexes).

Some other biophysical topics are offered in collaboration with the Faculty of Fisheries and Protection of Waters.

 Requirements for dissertation thesis

Dissertation thesis in Biophysics must comply with general requirements given by the Dean Provision No. 62. If the dissertation thesis consists of introduction complemented by papers published by the student during the Ph.D. study, the Board of Biophysics further extends this Provision by specific requirements on introduction and conclusion. For such thesis, introduction must be an original text of length at least 20-30 pages (5000-7000 words), excluding figures, tables and references. Introduction must contain overview of the research topic of the thesis, current status of knowledge in the field, description of experimental or theoretical methods (beyond the brief description commonly used in papers), and goals of the dissertation thesis. The thesis also must contain Conclusions that summarize the results of the whole thesis, eventually suggests further possibilities how to exploit results presented in the thesis.

Requirements for the state exam

The Board of Biophysics suggests to take the state exam during the third year of the Ph.D. study. The state exam consists of two parts. The first part tests the students' knowledge from the key courses passed during the study. The second part is directly related to the topic of the thesis.