Evolution of the genus Ornithogalum
Supervisor: RNDr. Michal Hroneš, Ph.D.
Hybridization and polyploidy represent the main mechanisms of angiosperm evolution. Plants with lower ploidy levels and small genome sizes are generally used as model species for studying both of these phenomena. On the contrary, species with large genomes or high ploidy levels, such as Monocot geophytes, are usually neglected, although they constitute a significant part of angiosperm diversity. The aim of the project is to investigate the influence of ploidy level and hybridization on selected traits (morphology, genetic diversity, phenology, ecology, etc.) of several species of the genus Ornithogalum. The selected model includes diploid-polyploid complexes with high ploidy levels (up to 7x) and species with medium to large genomes. The project will involve a range of biosystematic methods (morphometric analysis, flow cytometry, molecular methods, etc.), fieldwork, common-garden experiments, laboratory work, and processing of various types of data.

Population genomics, taxonomy and phylogeography of selected representatives of the genus Lactuca
Supervisor: RNDr. Miloslav Kitner, Ph.D.
Classical tools of population genetics (Sanger sequencing, microsatellites) do not provide sufficiently sensitive outputs for detecting the fine genetic structure in populations of wild lettuces. Limited variability is also a problem when solving problems related to the taxonomy of closely related taxa of the genus Lactuca. Whole-genome genotyping eliminates these shortcomings and presents new methodological tools for studying wild lettuce. These approaches can identify cryptic lineages within species on a fine scale and contribute to understanding the probable direction of spread of these lineages in the past. The subject of the PhD project is the bioinformatic processing of the outputs of three sub-projects of whole-genome genotyping of populations of selected taxa of wild Lactuca species implemented using the DArTseq method for the following purposes:
- Population genomic study of prickly lettuce (L. serriola) focused on identifying source populations of L. serriola introduced from Europe to the North American continent, their genetic variability and describing the further spread of the species in North and South America.
- Taxonomic study of species related to L. virosa (L. virosa, L. georgica, L. livida etc. - "Lactuca virosa complex").
- Taxonomic study of a wider range of representatives of the genus Lactuca.

Population dynamics in small rodents in a dynamical landscape
Supervisor: prof. MVDr. Emil Tkadlec, CSc.

Landscape epidemiology of tick-borne pathogens)
Supervisor: doc. RNDr. Tomáš Václavík, Ph.D.

Field size and farmland biodiversity in high-intensity agricultural landscapes
Supervisor: doc. RNDr. Tomáš Václavík, Ph.D.

Response of soil ground dwelling invertebrates to changes in agricultural landscape management
Supervisor: doc. RNDr. Mgr. Ivan Hadrián Tuf, Ph.D.

Terrestrial isopods outside soil environment – their activity on walls and trees
Supervisor: doc. RNDr. Mgr. Ivan Hadrián Tuf, Ph.D.

Indicators of soil quality in connection with its degradation, especially by erosion processes
Supervisor: prof. Dr. Ing. Bořivoj Šarapatka, CSc.

Land use optimization from the point of view of erosion and biodiversity of the landscape
Supervisor: prof. Dr. Ing. Bořivoj Šarapatka, CSc.
Consultant: Ing. Marek Bednář, Ph.D.

Impact of Heavy Machinery on Fluvial Ecosystems: Restoration Measures for Degraded Habitats of Rheophilic Fish in Trout Zones
Supervisor: doc. RNDr. Martin Rulík, Ph.D.

Importance of water bodies in the landscape methane Exchange
Supervisor: doc. RNDr. Martin Rulík, Ph.D.

Eligible for Fischer stipend

Multi-phytohormone analysis in different Ri plants
Supervisor: prof. Mgr. Ondřej Novák, PhD.

Study of plant morphogenesis at the (sub)cellular level
Supervisor: prof. Mgr. Ondřej Novák, PhD.

Natural products and their derivatives with anthelmintic aktivity
Supervisor: doc. RNDr. Jiří Pospíšil, Ph.D.

Synergistic and antagonistic effects of small organic compounds of natural origin on plant growth
Supervisor: doc. RNDr. Jiří Pospíšil, Ph.D.

Natural products: synthesis and study of their synergic interactions in living systems
Supervisor: doc. RNDr. Jiří Pospíšil, Ph.D.

Studium metabolismu methioninu a příbuzných sloučenin v rostlinách
Supervisor: Mgr. Michal Karady, PhD.

Uncovering subcellular pathways for phytohormone homeostasis in land plants
Supervisor: Federica Brunoni Ph.D.

Protein-protein interactions as target for pharmacological modulation of AhR signaling
Supervisor: prof. RNDr. Zdeněk Dvořák DrSc., Ph.D.

Negative allosteric modulation of AhR receptor in the therapy of inflammatory and neoplastic pathologies
Supervisor: prof. RNDr. Zdeněk Dvořák DrSc., Ph.D.

Comprehensive analysis of fruit tree genomes
Supervisor: Mgr. Jan Šafář, Ph.D.

Analysis of parental conflict in the development of cultivated barely
Supervisor: doc. Mgr. Aleš Pečinka, Ph.D.

Genome structure and its impact on fertility and stability of natural and synthetic plant hybrids
Supervisor: Mgr. Eva Hřibová, Ph.D.

Systematics and Ecology of Ants of Melanesia
Supervisor: Mgr. Milan Janda, Ph.D.

Systematics and phylogeny of selected groups of Central American herpetofauna
Supervisor: Doc. RNDr. Mlan Veselý, Ph.D.

Optical detecting systems for cosmic radiation – selected questions
Supervisor: prof. Miroslav Hrabovský, DrSc.
The topic is concentrated on the study of current optical detectors of cosmic radiation, participation in some of current international scientific projects of cosmic-ray research and participation at the research of new particular types of optical detectors of cosmic radiation, including participation in the scientific part of a related international collaboration.

Analysis of characteristics of parametric down-conversion
Supervisor: prof. RNDr. Ondřej Haderka, Ph.D.. / prof. RNDr. Jan Peřina Ph.D.
Simulation and testing of spontaneous parametric down-conversion, correlation measurement using photon-counting techniques as well as by classical intensity measurement.

Photocount statistics and its measurement in nonlinear optical processes
Supervisor: prof. RNDr. Jan Peřina Ph.D.
Theoretical models of photocount statistics arising in different nonlinear optical processes will be studied. Special attention will be paid to parametric processes. Characteristics of the obtained fields will be discussed with respect to measurement.

Characteristics of parametric processes in nonlinear periodically-poled media
Supervisor: doc. RNDr. Jan Soubusta, Ph.D.
Space beam properties. Study of efficiency of various processes. Optimization of generation of frequency down-conversion.

Testing modern materials using optical spectroscopic methods
Supervisor: doc. RNDr. Jan Soubusta, Ph.D.
Measurement of absorbance, fluorescent and time-resolved fluorescent spectra of carbon, metal and metal-oxide nanostructures. Development of appropriate methods.

Damage of materials induced by nanosecond particle bunches
Supervisor: prof. Jan Řídký, DrSc.
Laser-driven particle-acceleration experiments produce high luminosity particle bunches of nanosecond lengths. The aim of the thesis is to inspect mechanisms of damage induced in materials due to the interaction with such a short-time bunched particles.

Quantum correlations in multi-mode optical fields generated in the process of spontaneous parametric down-conversion
Supervisor: prof. RNDr. Jan Peřina Ph.D.
Consultant: prof. RNDr. Ondřej Haderka, Ph.D.
Quantum correlations in photon numbers of multi-mode optical fields originating in the process of spontaneous parametric down-conversion, that generates photons in pairs, and prepared by further manipulations (e.g. postselection) will be studied. Quantification of the quantumness of such correlations, striking features of these correlations as they exhibit in physically interesting quantities and their application potential will be addressed. Theoretical models appropriate for these fields will be developed and compared witht he experimental data, This will allow us  to determie the practical potential of these  fields in various applications including metrology. The topic may be extended to include the experimental part.

Noclassical properties of simple PT-symmetric quantum systems described using methods of quantum statistical physics
Supervisor: prof. RNDr. Jan Peřina Ph.D.
Simple quantum PT-symmetric and generalized systems like two- and more-level atoms and multi-mode optical bosonic systems will be studied from the point of view of their nonclassical properties. The analyzed systems will be described by Liouvillians and attention will be paid to their asymptotic behavior. Exceptional points are the striking features of PT-symmetric systems. At these points, the system behavior qualitatively changes, which may be used, e.g., for increasing sensitivity of quantum measurements. We will identify the exceptional points of analyzed systems including their degeneracies and study the behavior of system nonclassicality close to these points. We will look for suitable applications that expoint the striking properties  of the analyzed systems.

Exclusive processes as a road to New Physics
Supervisor: Mgr. Marek Taševský, PhD. DSc.
Consultant: RNDr. Karel Černý, PhD.
Standard model is extremely successful in describing interactions of elementary particles, nevertheless there are areas that it is not able to explain, that's what we call New Physics. Signals of New Physics are also seen in the so-called exclusive processes. They occur scarcely nevertheless background to them is well under control. The student will get familiar with forward and diffraction physics at large experiments on large colliders of particles, and also with detection techniques and generating artificial (Monte Carlo) events. Emphasis on the former or latter will be decided upon with the supervisor. Stays at CERN are foreseen.

Study of processes of diffractive production at the LHC.
Supervisor: RNDr. Karel Černý, PhD.
Diffractive processes in proton-proton or proton-nucleus collisions, as observed or expected to be seen at the LHC, represent a unique kinematic domain of interactions. Particles in the initial state can survive the interaction without altering their additive quantum numbers, while the inelastically transferred energy in the collision gives rise to a system of secondary particles, similar to what occurs in non-diffractive interactions. The kinematics of the final state in diffraction processes include original particles scattered at small angles, retaining a significant fraction of their initial momentum. This signature allows for the experimental identification and separation of diffraction processes.  The ATLAS experiment at the LHC has collected and will continue to collect data enabling the study of diffraction processes. An important aspect of LHC data analysis is the examination of simulated data produced using collision event generators based on the Monte Carlo method. These generators perform the integration of theoretical cross-sections and random generation of collision events.  Work on the development of generators for diffraction processes has been relatively limited in recent years, presenting an opportunity to make significant contributions and stimulate progress in this field.

Collective measurements for quantum communications
Supervisor: doc. Mgr. Karel Lemr, Ph.D.
Collective measurements are quantum measurements carried out simultaneously on multiple copies of the quantum state under investigation. They have been shown to be an invaluable tool for efficiently detecting and quantifying several key properties of quantum states, such as different entanglement measures or stronger quantum correlations. At the same time, collective measurements can be easily implemented in quantum communications networks, making them a key tool for the operation of prospective large-scale quantum networks connecting multiple users. Thus, the study of collective measurements promises interesting fundamental insights as well as results applicable to practical quantum communications.

Fisher information in classical and quantum optics
Supervisor: doc. RNDr. Pavel Pavlíček, Ph.D.
Fisher information is a quantity that allows the calculation of the uncertainty with which the value of a parameter can be determined. In classical and quantum optics, it is used to calculate the uncertainty with which the value of the phase in a Mach-Zehnder interferometer can be determined. Calculations of measurement uncertainty for different types of light will be performed. The results obtained using classical and quantum methods will be compared with each other.

Characteristics of Low-Photon Detectors for Next-Generation Neutrino Experiments
Supervisor: Mgr. Jiří Kvita, Ph.D.
The Water Cherenkov Test Experiment (WCTE) is an ongoing experiment on a secondary particle beam at CERN. Its purpose is to test technologies for the upcoming neutrino experiment Hyper-Kamiokande (Hyper-K) and measure certain particle cross-sections, such as those of muons and pions, as they pass through matter.
The test beam campaigns focused both on monitoring the composition of the beam using aerogel Cherenkov detectors and time-of-flight scintillation detectors—with the use of photomultipliers, digital readout, and subsequent data processing—and on testing multi-PMT modules for the IWCD (Intermediate Water Cherenkov Detector) and the Hyper-K experiment itself. The latter is scheduled for assembly in 2028 and will begin collecting calibration and physics data.
For its physics program, simulations and feasibility studies will be crucial, along with work on reconstructing the kinematics of particles producing Cherenkov signals and separating the signal from background.
The student will contribute to testing photomultipliers for the IWCD and Hyper-K detectors in the Joint Laboratory of Optics and will also have the opportunity to actively participate in the analysis of existing data of 2025 from the WCTE experiment. They will become familiar with tools for data analysis in high-energy physics using a small-scale version of the detector for future neutrino observatories and will engage in construction, simulations, and possibly analysis of available data from the Hyper-K experiment.

Simulation and Data Analysis for the WCTE and Hyper-Kamiokande Experiments
Supervisor: Mgr. Jiří Kvita, Ph.D.
The Water Cherenkov Test Experiment (WCTE) is an ongoing experiment on a secondary particle beam at CERN. Its purpose is to test technologies for the upcoming neutrino experiment Hyper-Kamiokande (Hyper-K) and measure certain particle cross-sections, such as those of muons and pions, as they pass through matter.
The test beam campaigns focused on monitoring the composition of the beam using aerogel Cherenkov detectors and time-of-flight scintillation detectors—with the use of photomultipliers, digital readout, and subsequent data processing—as well as testing multi-PMT modules for the IWCD (Intermediate Water Cherenkov Detector) and Hyper-K experiments. The Hyper-K experiment is scheduled for assembly in 2028 and will begin collecting calibration and physics data.
For its physics program, simulations and feasibility studies will be crucial, along with work on reconstructing the kinematics of particles producing Cherenkov signals and separating signal from noise.
The student will have the opportunity to contribute to simulations of the WCTE and Hyper-Kamiokande experiments using the WCSim program based on the Geant4 toolkit. Additionally, he/she will use available reconstruction tools, such as likelihood-based methods (fitQun) or machine learning approaches (WatChMaL), to analyze data from 2025 from the  WCTE experiment.
The student will gain experience with data analysis tools in high-energy physics using a small-scale version of the detector for future neutrino observatories and will also engage in construction, simulations, and potentially analysis of available data from the Hyper-K experiment.

Exploring the interplay between cell senescence and melanin regulation
Supervisor: doc. Ankush Prasad, Ph.D.

Ultra-weak photon emission in animal cells
Supervisor: Prof. RNDr. Pavel Pospíšil, Ph.D.

Detection of voice disorders from clinical high-speed videokymographic videos and electroglottographic signals with the help of machine learning
Supervisor: prof. RNDr. Jan Švec, Ph.D. et Ph.D.

Studies of voice production using biological models
Supervisor: prof. RNDr. Jan Švec, Ph.D. et Ph.D.

Studies of voice production using mathematical-physical models
Supervisor: prof. RNDr. Jan Švec, Ph.D. et Ph.D.

Analysis of characteristics of parametric down-conversion
Supervisor: prof. RNDr. Ondřej Haderka, Ph.D.. / prof. RNDr. Jan Peřina Ph.D.
Simulation and testing of spontaneous parametric down-conversion, correlation measurement using photon-counting techniques as well as by classical intensity measurement.

Photocount statistics and its measurement in nonlinear optical processes
Supervisor: prof. RNDr. Jan Peřina Ph.D.
Theoretical models of photocount statistics arising in different nonlinear optical processes will be studied. Special attention will be paid to parametric processes. Characteristics of the obtained fields will be discussed with respect to measurement.

Characteristics of parametric processes in nonlinear periodically-poled media
Supervisor: doc. RNDr. Jan Soubusta, Ph.D.
Space beam properties. Study of efficiency of various processes. Optimization of generation of frequency down-conversion.

Testing modern materials using optical spectroscopic methods
Supervisor: doc. RNDr. Jan Soubusta, Ph.D.
Measurement of absorbance, fluorescent and time-resolved fluorescent spectra of carbon, metal and metal-oxide nanostructures. Development of appropriate methods.

Quantum correlations in multi-mode optical fields generated in the process of spontaneous parametric down-conversion
Supervisor: prof. RNDr. Jan Peřina Ph.D.
Consultant: prof. RNDr. Ondřej Haderka, Ph.D.
Quantum correlations in photon numbers of multi-mode optical fields originating in the process of spontaneous parametric down-conversion, that generates photons in pairs, and prepared by further manipulations (e.g. postselection) will be studied. Quantification of the quantumness of such correlations, striking features of these correlations as they exhibit in physically interesting quantities and their application potential will be addressed. Theoretical models appropriate for these fields will be developed and compared witht he experimental data, This will allow us  to determie the practical potential of these  fields in various applications including metrology. The topic may be extended to include the experimental part.

Noclassical properties of simple PT-symmetric quantum systems described using methods of quantum statistical physics
Supervisor: prof. RNDr. Jan Peřina Ph.D.
Simple quantum PT-symmetric and generalized systems like two- and more-level atoms and multi-mode optical bosonic systems will be studied from the point of view of their nonclassical properties. The analyzed systems will be described by Liouvillians and attention will be paid to their asymptotic behavior. Exceptional points are the striking features of PT-symmetric systems. At these points, the system behavior qualitatively changes, which may be used, e.g., for increasing sensitivity of quantum measurements. We will identify the exceptional points of analyzed systems including their degeneracies and study the behavior of system nonclassicality close to these points. We will look for suitable applications that expoint the striking properties  of the analyzed systems.

Collective measurements for quantum communications
Supervisor: doc. Mgr. Karel Lemr, Ph.D.
Collective measurements are quantum measurements carried out simultaneously on multiple copies of the quantum state under investigation. They have been shown to be an invaluable tool for efficiently detecting and quantifying several key properties of quantum states, such as different entanglement measures or stronger quantum correlations. At the same time, collective measurements can be easily implemented in quantum communications networks, making them a key tool for the operation of prospective large-scale quantum networks connecting multiple users. Thus, the study of collective measurements promises interesting fundamental insights as well as results applicable to practical quantum communications.

Fisher information in classical and quantum optics
Supervisor: doc. RNDr. Pavel Pavlíček, Ph.D.
Fisher information is a quantity that allows the calculation of the uncertainty with which the value of a parameter can be determined. In classical and quantum optics, it is used to calculate the uncertainty with which the value of the phase in a Mach-Zehnder interferometer can be determined. Calculations of measurement uncertainty for different types of light will be performed. The results obtained using classical and quantum methods will be compared with each other.

Nonlinear interactions between microwave cavity modes
Supervisor: Mgr. Ondřej Černotík, Ph.D.
Superconducting quantum devices exhibit strong nonlinearity enabled by the Josephson effect, allowing a range of applications in quantum technologies. Particularly interesting is the possibility of full quantum control of a linear microwave mode controlled using a nonlinear superconducting circuit.

Optimization of the UV Raman spectrometer with excitation wavelength in the range 207 – 250 nm
Supervisor: RNDr. Josef Kapitán, Ph. D.
Resonance enhancement is one way to increase sensitivity of Raman spectroscopy as an analytical technique used in many applications, one of which is the study of the structure of peptides and proteins. A very active and open topic in recent years is also the study of the properties of chiral molecules using resonance Raman optical activity. The dissertation thesis will focus on the optimization of the Raman spectrometer with excitation wavelengths in the range of 207-250 nm, especially with regard to the expansion of the spectrometer for precise polarization measurements. The developed equipment will become the basis for experiments in the field of Raman spectroscopy and Raman optical activity, both in applied (study of conformational and dynamic behavior of biomolecules in solution) and fundamental research (study of electron and vibrational molecular structure).

Realization of photonic interface between trapped ions and levitated nanoparticles
Supervisor: Mgr. Lukáš Slodička, Ph.D.

Critical quantum non-Gaussian effects in bosonic systems
Supervisor: prof. Mgr. Radim Filip, Ph.D.
As part of the dissertation, the doctoral student will investigate the principles and use of fundamental currently achievable hybrid interactions in experiments with trapped cooled ions and molecules, superconducting and electromechanical systems and levitating nanoparticles for the preparation, control, detection and identification of critical quantum non-Gaussian effects, quantum phase transitions and their applications in quantum sensing and simulations. The goal of the work will be to propose new theoretical methods and concepts of the first suitable experimental tests and subsequently contribute to the analysis of data from the experiments.

Quantum non-Gaussian opto-spin-electro-mechanics
Supervisor: prof. Mgr. Radim Filip, Ph.D.
As part of the dissertation, the doctoral student will investigate the principle use of highly nonlinear hybrid quantum interactions currently achievable in trapped cooled ions and quantum electrodynamics with atoms and solid state emitters and, also, similar microwave superconducting systems, both in free space and in optical a microwave resonators and waveguides. The thesis will aim to propose a methodology for generating quantum non-Gaussian states and their first suitable experimental tests in such complex hybrid systems towards applications in quantum sensing, communication, and, potentially, distributed quantum computation.

Quantum control of large-scale qubit and oscillator states
Supervisor: prof. Mgr. Radim Filip, Ph.D.
As part of the dissertation, the doctoral student will investigate the principle and use of hybrid quantum interactions currently achievable with atomic, molecular, nanoscopic and superconducting systems to construct new large-scale states of quantum bits and oscillators and investigate their applications in quantum sensing, simulations and quantum computing using modern optimisation methods. The work will aim to propose a methodology for constructing hybrid circuits and their first suitable experimental tests with trapped cooled ions and molecules, superconducting and electromechanical systems and levitating nanoparticles.

Changes in ions' internal energy during ion mobility separation
Supervisor: prof. RNDr. Karel Lemr, Ph.D.

Identification of components of art paintings by desorption ionization and mass spectrometry with ion mobility
Supervisor: prof. RNDr. Karel Lemr, Ph.D.

Mechanism of desorption and ionization in desorption nanoelectrospray
Supervisor: prof. RNDr. Karel Lemr, Ph.D.

New applications of ion chromatography
Supervisor: doc. RNDr. Petr Bednář, Ph.D.

Microanalytical procedures in metabolomics
Supervisor: doc. RNDr. Petr Bednář, Ph.D.

New methods for chemical analysis in archeology and cultural heritage research
Supervisor: doc. RNDr. Petr Bednář, Ph.D.

Secondary metabolism of intracellular pathogens
Supervisor: prof. Ing. Vladimír Havlíček, Dr.

Central Nervous System diagnostics
Supervisor: prof. Ing. Vladimír Havlíček, Dr.

Characterization of nanoobjects by capillary electrophoresis
Supervisor: doc. RNDr. Jan Petr, Ph.D.

Metrological aspects of microplastics analysis
Supervisor: doc. Ing. David Milde, Ph.D.

Utilization of ICP-MS for elemental analysis of bilogical and clinical samples
Supervisor: doc. Ing. David Milde, Ph.D.

Specific Extractions of active subsatnces and products of their transformations
Supervisor: doc. RNDr. Petr Barták, Ph.D.

More effective single-molecule magnets based on lanthanide complexes with macrocyclic ligands
Supervisor: RNDr. Bohuslav Drahoš, Ph.D.

Complexes of macrocyclic ligands applicable in the field of theranostics
Supervisor: RNDr. Bohuslav Drahoš, Ph.D.

Continuous flow chemistry – a tool for efficient synthesis of macrocyclic ligands and metal complexes suitable for molecular magnetism
Supervisor: RNDr. Bohuslav Drahoš, Ph.D.

Flow reactor assisted continuous conversion of biomass into value-added products: Process design and scale-up
Supervisor: RNDr. Bohuslav Drahoš, Ph.D.
Consultant: Subodh Kumar, Ph.D.

Coordination compounds of f-elements with radical ligands
Supervisor: doc. Ing. Radovan Herchel, Ph.D.

Chiral molecular nanomagnets for magneto-optical phenomena
Supervisor: doc. Ing. Radovan Herchel, Ph.D.
Consultant: Mgr. Kamil Kotrle, Ph.D.

Preparation of biologically active complexes with benzimidazoles and benzazoles
Supervisor: prof. RNDr. Pavel Kopel, Ph.D.

Antibacterial and antiinflammatory properties of gold and silver complexes and nanoparticles
Supervisor: prof. RNDr. Pavel Kopel, Ph.D.

Nanotransporters of potential drugs based on coordination compounds
Supervisor: prof. RNDr. Pavel Kopel, Ph.D.

Development of hybrid plasmonic photocatalysts for the conversion of carbon dioxide into value added chemicals
Supervisor: prof. RNDr. Pavel Kopel, Ph.D.
Consultant: Subodh Kumar, Ph.D.

Design and synthesis of nanocatalysts for biomass transformation into value added chemicals
Supervisor: prof. RNDr. Pavel Kopel, Ph.D.
Consultant: Subodh Kumar, Ph.D.

Passivation of black phosphorous with single-molecule magnets
Supervisor: doc. Ing. Ivan Nemec, Ph.D.

Semi-coordination in single-molecule magnets
Supervisor: doc. Ing. Ivan Nemec, Ph.D.

Multicomponent coordination compounds of platinum metals for biological applications
Supervisor: doc. Mgr. Pavel Štarha, Ph.D.

Liposomal formulation of bioactive coordination compounds for polypharmacology
Supervisor: doc. Mgr. Pavel Štarha, Ph.D.

Photoactivatable coordination compounds for biological applications
Supervisor: doc. Mgr. Pavel Štarha, Ph.D.

Platinum metal complexes for medicinal chemistry and catalysis
Supervisor: doc. Mgr. Pavel Štarha, Ph.D.
Consultant: Mgr. Ondřej Bárta, Ph.D.

Anticancer heterometallic coordination compounds
Supervisor: doc. Mgr. Pavel Štarha, Ph.D.

Heterogenization of the Metal Complexes for the Conversion of CO2 into Industrially Important Chemicals
Supervisor: doc. Mgr. Pavel Štarha, Ph.D.
Consultant: Subodh Kumar, Ph.D.

Modulation of physicochemical properties of multiple nanoemulsions for controlled delivery of active substances
Supervisor: prof. Ing. Lubomír Lapčík, Ph.D.
The aim of the thesis is detailed understanding and quantification of self-organization processes of multiple O/W/O and W/O/W nanoemulsions based on micellar systems of polysaccharides stabilized by phospholipids. The work will be focused on the self-preparation of these systems, the mechanism of their stabilization, deposition and solidification in polymer films with respect to their final functional application in the packaging industry, studying the possibility of their preparation and processing in technical practice. Characterization of their microstructure and macrostructural arrangement, the influence of preparation and processing technology on the resulting physicochemical and material properties of these systems will be carried out.
Contribution:
In the theoretical field, gaining knowledge between nano/micro structure and 3D hierarchy of colloidal systems with respect to their selected functional properties.
In the practical field - deepening the experience of the Institute staff and students with the processes affecting the formation and arrangement of multidimensional nanostructured systems. Experimental facilities: existing facilities are sufficient.

Design and synthesis of novel heterocyclic compounds with potent antimicrobial activity
Supervisor: Doc. RNDr. Lucie Brulíková, Ph.D.
The increasing prevalence of microbial infections and the emergence of resistance to the currently available antimicrobial drugs requires the development of new chemical entities with an alternative mechanism of action to existing therapeutics directed toward unknown targets. The main goal of the thesis will be the design, synthesis and biological activity studies of novel antibacterial and antiparasitic agents. This work will cover the novel compounds design based on the molecular docking studies, their synthesis and optimisation of reaction sequences. Further, this project deals with biological testing. Moreover, these studies will be complemented with enzymatic assays. Final compounds will be further modified according to biological activity testing. Alternatively, a new pharmacophore will be investigated.

Axially Chiral Heterocyclic Compounds with Potential Application in the Area of Organocatalysis, Chiral Derivatization Agents, and Inhibition of Protein Kinases
Supervisor: doc. RNDr. Petr Cankař, Ph.D.
Axial chirality of organic compounds is often described for the ortho-substituted biaryl compounds, where is a single bond joining both aryls with restricted rotation. This bond lies on the chiral axis. In case, the energy barrier of restricted rotation is sufficiently high, it is possible to synthesize and isolate atropisomers for a variety of practical applications. Initially, the attention to atropisomerism was inadequate, since the first isolated atropisomers were not sufficiently stable for practical use. In the recent 20 years, there is a renaissance of the use of axial chirality for organic compounds; especially in organocatalysis and also medicinal chemistry in the last decade. The main reasons are novel opportunities in the spatial arrangement of molecules.
The goal of the Ph.D. thesis will be the synthesis and study of axially chiral heterocyclic compounds, which allow novel various spatial interactions by functional groups and heterocyclic systems for stereoselective organocatalysis or inhibition of protein kinases. Alternatively, another research area can be the use of axially chiral compounds as derivatizing agents for the analysis of stereoisomers and their mixtures.

Tunable non-covalent interaction-based catalysts for stereoselective reactions of iminium and oxonium intermediates
Supervisor: doc. RNDr. Jiří Pospíšil, Ph.D.
Anion-binding catalysis is a fast-growing but very challenging field of organic asymmetric synthesis. The principle of such transformation is fairly simple: the chiral catalyst scavenge/recognizes the anion (generally the chloride anion) and then exerts precise geometric control on the prochiral reaction site. However, the selectivity of the transformation does not rely on interactions with the variable substituents on the substrate. Criteria seem simple, but are not easy to fulfil, and so it is not surprising that only a few so-called 'privileged' molecular scaffolds can meet them. In our proposal, we introduce the novel molecular scaffold for asymmetric catalysis that has not been evaluated before, 1,3-diazetidin-2-one (DAZDO), as a new privileged molecular scaffold for asymmetric catalysis. To prove our concept, we developed DAZDO catalysts that are able to generate oxonium and iminium intermediates in situ and allow them to react with various C-nucleophiles with high stereoselection. Our concept and catalysts will be applied to the total synthesis of selected natural products. Aims of the project: (1) to develop a new generation of anion-binding organocatalysts based on the diazetidinone molecular skeleton (DAZDO); (2) to demonstrate the use of DAZDO catalysts in the context of natural product synthesis (stereoselective addition of C-nucleophiles to iminium and oxonium cyclic intermediates).

Tunable organocatalysts based on Lewis acid-enhanced non-covalent interactions
Supervisor: doc. RNDr. Jiří Pospíšil, Ph.D.
Hydrogen bond-donating (HBD) organocatalysts have recently gained a privileged place in the field of asymmetric synthesis. The activation of the substrates by HBD catalysts is based on multiple weak interactions, and therefore the concept of 'more, better' is applied. The common way to overcome such drawback is to develop catalysts that can form stronger HBD interactions or to multiply the number of them. However, recent advances in the description of substrate activation by catalyst, which introduced the Pauli repulsion-lowering concept, raised the possibility of a new method to overcome such a drawback. We introduce a novel molecular scaffold for asymmetric catalysis that has not been evaluated before and explore the use of the concept of Pauli repulsion-lowering activation. Our TCRP catalyst is built up around the thiourea HBD bidentate catalyst system, but further explores fine-tuning of the HBD abilities via the adjacent aryl groups and coordinated Lewis acid metal. TCRP catalysts are modular, allow fine-tuning of HBD abilities, and have a readily available source of chirality. We expect that the TCRP scaffold will become a new privileged scaffold in catalyst design. Goals of the project: (1) to develop organocatalysts based on non-covalent interactions enhanced by Lewis acid and the principle of Pauli repulsion-lowering (TCRP); (2) Demonstrate the use of TCRP catalysts in the context of organic synthesis (cycloaddition, epoxide opening, spirocyclization).

Synergy effects between polyketide natural products and peptides – total synthesis of polyketide natural products and their biological evaluation
Supervisor: doc. RNDr. Jiří Pospíšil, Ph.D.
The synergistic pharmacological effect of various drugs and/or natural products is a very important topic of pharmacology today. In many cases, clinicians observe synergistic effects when using a mixture of prescribed drugs with different modes of action and/or designed to treat various, often non-related illnesses. Such observations are in most cases based on empirical bases, and no relevant scientific follow-up is made to determine what happens in the human body. However, since recently, several natural drugs with expected/observed biological activity, eg, against bacteria or fungi, were used in the presence of certified drugs with known mode of action and the synergy effect was examined in detail. In this project, we are interested in two main goals: 1) total synthesis of selected natural products of polyketide origin; 2) to study the possible synergy effect between selected polyketides (either of natural or unnatural origin) and known polyaminoacid-based drugs (e.g. antibiotic drugs).

Synthesis and study of nitrogenous heterocycles as ligands for various biological targets
Supervisor: doc. RNDr. Miroslav Soural Ph.D.
Nitrogenous heterocycles represent a very important group of organic compounds. They form a common structural motif in a number of natural or synthetic, biologically active substances. Approximately 60% of drugs that have been approved for clinical use to date contain a nitrogen heterocycle in their structure. For this reason, nitrogenous heterocycles are an attractive chemotype in the field of medicinal chemistry. A number of heterocyclic derivatives have been prepared that exhibit a variety of biological effects, such as antibiotic, antibacterial, antifungal, antitumor, antiviral, analgesic, etc. If the biological target is known, a rational design of new analogues is possible to find analogues more advantageous pharmacological properties, e.g. higher activity, selectivity and metabolic stability. The aim of the dissertation is to search for new heterocyclic drugs based on standard procedures: 1) biological target selection and structural design of potential ligand (typically using scaffold hopping approach or molecular docking), 2) development and optimization of synthetic method to prepare target scaffold , 3) preparation of a series of substituted derivatives to study the structure-activity relationships, 4) primary testing and evaluation of SAR, 5) further rational structure modifications using the information obtained, leading to advanced derivatives and their pharmacological evaluation. The specific structural motives will be determined on the basis of the current results of the research group. At present, attention is paid mainly to cytotoxic compounds acting against tumor cells and derivatives oriented to biological targets located in the central nervous system. The biological evaluation is carried out in cooperation with the Department of Experimental Biology, the Institute of Molecular and Translational Medicine and the Jagiellonian University in Krakow.

Modification of pentacyclic triterpenoid molecules in the E and A ring region and study of their anticancer and neuroprotective activity.
Supervisor: doc. RNDr. Milan Urban, Ph.D.
Triterpenoids are natural compounds with a number of biological activities, at our research group we are mainly concerned with compounds with cytotoxic and related anticancer activity. The most active derivatives have IC50 values in the low micromolar to submicromolar range which, in the context of low toxicity, would predispose these molecules to become anticancer therapeutics. Lupane derivatives in particular are highly cytotoxic and have therefore received particular attention. A second area of interest is triterpenes with neuroprotective activity, which show significant protective effects in cellular models of Parkinson's and Alzheimer's disease.The main problem with active triterpenes is their high lipophilicity, low water solubility and associated lack of bioavailability when administered orally. For some neuroprotective compounds, the downside is their excessive cytotoxicity. One possibility to modify these undesirable properties is the preparation of prodrugs. Despite great efforts to find optimal prodrugs, the results of this research have so far been rather partial.
In the framework of this work, new compounds will be prepared mainly by a series of different oxidation reactions, halogenations, cross-couplings, cycloaddition reactions, etc. with the main aim to find molecules with better selective cytotoxic activity or neuroprotective activity than previously prepared derivatives.  For all new derivatives, the values of both biological activities will be measured and based on the results, suitable candidates will be selected for further development in one or the other activity category from which further derivatives will be synthesized with respect to pharmacological parameters, especially solubility, toxicity and bioavailability. For this purpose, previously developed procedures for the preparation of prodrugs will be used, but new alternatives will also be sought. It is anticipated that several series of derivatives will be prepared in the course of the work and will be fully characterised and tested for their biological activities. The results should show the effect of the different modifications and prodrug groups on activity and pharmacological properties, especially bioavailability and metabolism. The work should lead to the formulation of structure-activity relationships. All syntheses will go hand in hand with biological screening and feedback from this testing will guide the direction of syntheses towards optimised molecules suitable for anticancer drug development.

The Statistical Methods for Analysis of Multi-factorial Compositions
Supervisor: Mgr. Kamila Fačevicová Ph.D.
The disseration will be aimed on extension of methods related to the statistical processing of multi-factorial relative-valued data, so-called compositional tables. Since the analysis of such objects is mostly based on logaritmically transformed values, the main part of the thesis will be devoted to the imputation of zeros in the compositional tables, which is a topic that has not been discussed in the statistical literature so far. Additionally, the problems of handling deviating observations and dimension reduction will be of interest.

Functional regression models with complex structure
Supervisor: doc. RNDr. Eva Fišerová Ph.D.
Functional data analysis is a set of methodologies suitable for the analysis of high-dimensional measurements, such as curves or surfaces, which consider data not as a sequence of single measurements taken one after another, but as whole functional entities. Regression models are considered to be functional if the explanatory variable, the dependent variable, or both the explanatory and dependent variables can be treated as functions. The aim of the dissertation is the development of suitable statistical methods and algorithms mainly focused on statistical modelling when the random variables have a complex variation and correlation structure, there are restrictions on regression parameters, or observations are incomplete. The emphasis will be given both on theoretical aspects concerning estimation, uncertainty and statistical inference, as well as practical implementation and computational feasibility.

Bayesian statistics using Bayes spaces
Supervisor: Prof. RNDr. Karel Hron, Ph.D.
Bayesian statistics has enormous application potential in virtually all scientific fields. At the same time, we often encounter the fact that it is used to process data of a relative nature, either in their discrete form (compositional data) or in continuous form (probability density functions), which needs to be taken into account by their proper logratio representation. Moreover, even within the Bayesian estimates themselves, it is necessary to reflect the specific geometric structure of the key components of the Bayesian theorem: prior distributions, likelihood functions and posterior distibutions. In the dissertation we will address all these topics using the methodology of Bayes spaces, which allows an elegant approach to relevant data processing using Bayesian methods as well as the development of Bayesian statistics itself.

Data depth on simplex
Supervisor: doc. Mgr. Ondřej Vencálek Ph.D.
The concept of data depth is the basis for nonparametric statistics in multidimensional space. Unlike the space R1, where there is a natural ordering of values ​​from smallest to largest, in spaces R^d, where d>1, the values ​​are no longer so easily ordered. However, we can order the values ​​(points) at least partially, using the data depth, which determines the degree of centrality of individual points with respect to some probability distribution. Recently, the concept of depth has been studied in other spaces, e.g. in the space of functions or on the sphere. The aim of the work is to propose an extension of the concept of depth for the simplex space, i.e. the space used in compositional data analysis. The possibilities of extending various depth functions, their theoretical properties and computational complexity will be studied.

Physically Informed Machine Learning and Mathematical Equations
Supervisor: RNDr. Rostislav Vodák Ph.D.
The aim of this work is to apply tools of physically informed machine learning to the analysis, modeling, and derivation of mathematical equations that describe various physical phenomena.

Real-time Interactive Atlas in Dashboard Concept for Online Geovisualization of Dynamic Phenomena
Supervisor: Prof. RNDr. Vít Voženílek, CSc.
The aim of this thesis is to design, develop, implement and validate the concept of a dashboard for compilation of interactive atlases. The student will focus on the geovisualization of a selected group of dynamic phenomena and develop the theoretical background and practical guidelines for the effective making and using a new type of web-based thematic atlases. For this purpose, the student will necessarily establish cooperation with selected entities, generating a time series of geodata. Student will focus on visualization and analytical tools for the atlases.

Predictive modeling of landcover/landuse development in GIS
Supervisor: prof. RNDr. Vilém Pechanec, Ph.D.
The aim of the research is to develop algorithms and methodologies for predictive landscape modeling. Landscape predictions, or those of selected components, can be based on user-defined scenarios as well as on scenarios such as Business-as-Usual (BaU) or What-If scenarios. A significant part of the research should focus on advancing methods for creating logically consistent integrated datasets.

Analyzing the Relationships between Social Progress, Economic Growth, and the Environment as Key Dimensions of Sustainable Development
Supervisor: doc. Ing. Mgr. Jaromír Harmáček Ph.D.
The doctoral subject embarks on a comprehensive exploration of the dynamic relationships and interactions among social progress, economic and income growth, and the environment as key dimensions of sustainable development. The thesis can be delved into the complexities, challenges, and opportunities that arise when striving to align these dimensions and navigate the delicate balance required for achieving sustainability.
Using a methodology that incorporate quantitative analyses and draws upon available data sources such as the Global Carbon Atlas for CO2 emissions, Social Progress Imperative for social progress index (SPI), and the World Inequality Database for income distribution data, this research aims to enrich the ongoing dialogue on sustainable development.
At least three papers in academic journals are assumed. The first paper will analyze the relationship between social progress, and economic and income growth, the second will focus on the interactions between social progress and environmental impacts, while the third will examine the association between income growth and environmental impacts. A potential fourth paper (or the dissertation thesis) will try to reconcile the three aspects of sustainable development, possibly in a new composite measure of this concept. The aforementioned papers could be published in journals such as Social Indicators Research, Ecological Indicators, Applied Geography, Population and Environment, etc.

Beyond GDP: Metrics for Well-being, Sustainability, and Equity
Supervisor: doc. Mgr. Miroslav Syrovátka, Ph.D.
The dissertation will analyze and evaluate selected aspects of “Beyond GDP” metrics, focusing on their development, critique, and institutionalization (Barrington-Leigh and Escande, 2018; van den Bergh, 2022). Candidates are encouraged to explore themes within the dual framework of current well-being (Frijters et al., 2024; Syrovátka and Schlossarek, 2019) and future well-being, i.e., sustainability (McLaughlin et al., 2024; Syrovátka, 2020). The latter also offers opportunities to examine cross-cutting issues like environmental inequality and global justice (Chancel, 2022; Gupta et al., 2023). In addition, candidates may engage with integrative frameworks that address both dimensions, such as the Sustainable Development Goals (van Vuuren et al., 2022; Hametner, 2022; Usubiaga-Liaño et al., 2024) or the Safe and Just Space (Fanning et al., 2022; Alleisa & Bakshi, 2023).
Candidates will prepare a research draft in consultation with the supervisor. The draft will outline the overall framework and propose three research questions, with one of them developed in detail. An interdisciplinary approach, combining quantitative analyses of metrics with other appropriate methods, is encouraged. The dissertation will consist of at least three academic papers linked by a commentary, targeting reputable journals such as Ecological Economics, Social Indicators Research, and Global Sustainability.