Study

Why to choose Faculty of Science?

The Faculty of Science of Palacký University in Olomouc is a research-based faculty that offers Bachelor’s, Master’s, and Doctoral studies invarious branches of Mathematics and Computer Science, Physics, Chemistry, Biology and Ecology, and Earth Sciences. Currently there are approximately the Faculty 4,000 students and 900 employees at the Faculty.

Palacký University is an inalienable part of Olomouc, which has been listed as one of Europe’s hidden treasures by the Lonely Planet guide. Olomouc with approximately 100,000 inhabitants deserves the label "university city", since there are more than 24,000 students living here during the academic year. The tradition of the second oldest University in the Czech Republic dates back to 1573. Nowadays it represents a modern educational and research institution offering a wide range of study fields at eight faculties.

Degree Programmes in English

Master Study Programmes

Standard follow-up Master study programmes last two years. Students are required to take courses and examinations, present seminars, annual progress reports, pursue research governed by respective supervisors. Results of the research are compiled in master thesis. Students prepare for the State Examination, which tests the range and quality of the student’s abilities in respective field of study and the potential to acquire and creatively implement the knowledge. After successful defense of the master thesis and passing the State Examination, the student will be awarded a Master´s Degree.

Doctoral Study Programmes

Standard Ph.D. study programmes last four years. Students are required to take courses and examinations, present seminars, annual progress reports, pursue research and publish their data in scientific journals according to their individual study plans governed by respective supervisors. Results of the research are compiled in Ph.D. thesis. Students prepare for the State Doctoral Examination, which tests the range and quality of the student's abilities in respective field of study and the potential to acquire and creatively implement the knowledge. After successful defense of the doctoral thesis and passing the State Doctoral Examination, the student will be awarded the degree Ph.D.

Fields of Study

Study Programme Applied Mathematics
Field of Study Applied Mathematics

Study Programme Biochemistry
Field of Study Biochemistry

Study Programme Biology
Fields of Study Botany – NOT OPEN, Zoology, Molecular and Cell Biology, Experimental Biology

Study Programme Chemistry
Fields of Study Analytical Chemistry, Inorganic Chemistry – NOT OPEN, Organic Chemistry, Physical Chemistry

Study Programme Computer Science
Fields of Study Computer Science

Study Programme Ecology and Environmental Protection
Field of Study Ecology – NOT OPEN

Study Programme Geography
Fields of Study Geoinformatics and Cartography, International Development Studies

Study Programme Geology
Field of Study Geological Sciences

Study Programme Mathematics
Fields of Study Algebra and Geometry, Mathematical Analysis

Study Programme Physics
Fields of Study Applied Physics, Biophysics, General Physics and Mathematical Physics – NOT OPEN, Optics and Optoelectronics

Thesis topics

Applied Mathematics

Field od Study Applied Mathematics

Logratio approach to symbolic data analysis
Supervisor: Doc. RNDr. Karel Hron Ph.D.
Symbolic data analysis in compositional context means statistical processing of data sets representing several compositions simultaneously. Aim of the dissertation thesis is to propose symbolic extensions of basic statistical methods for compositional data analysis using the logratio methodology and including applications to real data.

Regression models with complex structure
Supervisor: doc. RNDr. Eva Fišerová, Ph.D.
Regression models are typically used to understand better the relationships between different dependent (target) and explanatory variables. The aim of the dissertation is the development of suitable statistical methods and algorithms mainly focused on statistical modelling for small and high dimensional data sets when variables exhibit a complex variation structure. The emphasis will be given both on theoretical aspects concerning estimation, uncertainty and statistical inference, as well as practical implementation and computational feasibility.

Biochemistry

Field of Study Biochemistry

Molecular approaches for the large-scale production of recombinant proteins in the barley endosperm
Supervisor: RNDr. Ondřej Plíhal, Ph.D.
Plants can be used as an inexpensive and safe production platform for the synthesis of valuable active compounds with application in human or veterinary medicine. There are number of different platforms based on transient or stable expression systems in a range of plant species from dicots to monocots. In contrast to transient expression system, stably transformed plant lines provide several benefits such as the possibility to easily scale up the production, which in turn leads to more economical and sustainable large-scale molecular pharming. Grain crops are especially valuable in this respect due to their ability to store recombinant proteins in seeds. The main aim of the project is to optimize high-capacity production procedure and purification protocol for the isolation of recombinant proteins in barley grain. Towards this end, several production strategies will be tested including bioencapsulation of recombinant proteins, protein tagging (MBP, elastin-type proteins, His tag, N-terminal gamma-zein domain, DAMP4 peptide, etc.) and targeted accumulation of recombinant proteins in protein storage vacuoles. Protein expression will be first tested in the transient expression systems (Arabidopsis, tobacco), and subsequently selected constructs will be used for stable barley transformation. Finally, the isolation of the recombinant protein will be optimized using combination of the affinity chromatography and/or simplified method for one-step purification on HPLC.

Biology

Field of Study Experimental Biology

Role of blue light photoreceptors in plant sensitivity to abiotic stres
Supervisor: Doc. RNDr. Martin Fellner, Ph.D.
The project deals with problems how blue light influence responses of plants to tolerate abiotic stress (salt, osmotic, water, or temperature stress). We previously revealed that phototropin mutants in Arabidopsis are highly tolerant to osmotic stress. Similarly, tomato mutant 7B-1 affected in phototropin signaling pathway shows blue light-specific tolerance to salt and osmotic stress. The aim of the project is to find out mechanisms by which blue light and its specific receptors, such as phototropins and cryptochromes, are involved in plant responses to various abiotic stresses. To investigate link between blue light and stress signaling, student will be responsible for physiological, molecular and biochemical experiments on various mutants with defects in blue light perception.

Radiometric and telemetric methods of field plant growth analysis
Supervisor: Mgr. Karel Doležal, Dr.

Validation of methods of non-invasive plant phenotyping using classical physiological approaches
Supervisor: Dr. Nuria De Diego

Field of Study Molecular and Cell Biology

Functional analysis of genes involved in flowering of grains
Supervisor: RNDr. Jan Šafář, Ph.D.
Initiation of flowering is one of the most important process in the plant life with impact on the yield and grain quality in crops. A topic of the PhD study focuses on deciphering of molecular mechanisms underlying vernalization and photoperiod pathways. Sensing of prolonged cold period for expression of VRN1 gene of bread wheat winter varieties will be studied comprehensively (e.g. gene expression profile, histone methylation status). Moreover, identification of proteins involved in VRN1 regulation will be performed. Functional analysis of the promoter and the first intron of the gene will be carried out using genome editing (CRISPR/Cas9) protocol and validated by plant transformation.

Identification of genes involved in repair of toxic DNA-protein bonds in Arabidopsis thaliana
Supervisor: priv.doz. RNDr. Aleš Pečinka, Ph.D.
DNA molecule is constantly damaged by endogenous and exogenous factors. Depending on the type of damage, dedicated repair pathways are activated and fix the lesion. Lack of DNA damage repair leads to the accumulation of mutations, reduced fitness and fertility, lower yield and development of diseases. The aim of this Ph.D. project is to identify and characterize largely unknown DNA-protein crosslink (DPCs) repair pathway by forward directed genetic screen in the model plant Arabidopsis thaliana. The mutated genes will be identified using mapping by sequencing and characterized by mix of genetic, molecular and biochemical methods. This project has a strong potential to characterize genes with currently unknown functions, and being important for maintenance of plant genome integrity during plant development and in response to genomic stress.

Role of intestinal microbiota metabolites in regulation of xenoprotective signaling pathways
Supervisor: prof. RNDr. Zdeněk Dvořák, DrSc., Ph.D.
Intestinal microbiota was demonstrated to produce plethora of products and intermediates, which display pathological effects, but have also important physiological roles in human. Hence, a functional intestine to liver and intestine to brain cross-talks, involving signaling molecules produced by intestinal microbiota were established. In the proposed PhD topic, the effects of intestinal microbiota-derived compounds, including indole-based and short fatty acids, on the expression and functions of xenoprotective genes will be examined.

Modulation of xenobiotic signaling pathways by indole derivatives
Supervisor: prof. RNDr. Zdeněk Dvořák, DrSc., Ph.D.
Indole-based compounds were demonstrated to activate aryl hydrocarbon receptor AhR, which is a master regulator of xenobiotics metabolism, but also plays many physiological roles. These indoles include endogenous (kynurenines, melatonines, 5HT), microbiota-produced (skatole, indolyl-3-acetic acid, indolyl-3-propionic acid) and synthetic indoles (methyl indoles). The goal of the proposed PhD topic is to study mechanistic aspects of interaction between different indoles and AhR-regulated pathways in human cells.

Studies of chromosome B in corn and related species
Supervisor: Mgr. Jan Bartoš, Ph.D.
B chromosomes are supernumerary non-essential chromosomes that are present in about 15% of all eukaryotes. They have been discovered in many species among plants, animals and fungi. Due to their dispensable nature, in a given species, B chromosomes can be either present or absent among different individuals and even different tissues. B chromosomes have low or no obvious impact on the phenotype in many species when present in few copies, and were therefore for a long time considered to not carry functional genes. Among the most studied B chromosomes belong B chromosomes of maize, which were discovered in the early 1920s. Analysis of the inheritance of the B chromosomes revealed their ability to accumulate in progeny through non-disjunction at the second pollen division and preferential fertilization of maize eggs with sperms that contain B chromosomes. Advances in sequencing technologies and assembling algorithms have enabled us to establish sequence of maize B chromosomes. The objective of the project is to study structure and behaviour of B chromosomes, characterize their gene content as well as repetitive elements. Further, origin and evolution of B chromosome(s) will be targeted.

 

Field of Study Zoology

The evolution of parental strategies in birds
Supervisor: Doc. Mgr. Vladimír Remeš Ph.D.
Parents differ in how much they invest in reproduction, and males and females provide strikingly different contribution among bird species. You will analyze male and female parental behavior in birds to try and reveal ecological factors that shape sex-specific parental strategies. You will use large-scale data from literature and metaanalyses together with advanced phylogenetic comparative methods to reveal mechanisms shaping parental care, mating systems and offspring performance across avian species.

Diversification, species coexistence and trait evolution
Supervisor: Doc. Mgr. Vladimír Remeš Ph.D.
Diversifying clades fill ecological space and due to secondary sympatry build-up local diversity. This secondary sympatry then affects the evolution of morphological, physiological and signaling traits. You will use large-scale data from literature, citizen science projects, museums, and fieldwork to reveal mechanisms allowing secondary sympatry and subsequent build-up of regional and local diversity.

Physics

Field of Study Applied Physics


Acoustic wave analysis for exploring the physical properties of surfaces Supervisor: prof. Miroslav Hrabovský, DrSc.Mgr. Radim Čtvrtlík, Ph.D. Acoustic waves emitted during the mechanical tests at the nano-micro scale are a rich source of information about the deformation behavior of the tested material. Analysis of acoustic emissions provides a better understanding and more complex interpretation of the results obtained by the nanoindentation and scratch test. The topic encompasses an experimental testing of local mechanical and tribological properties of surfaces and a theoretical and experimental analysis of acoustic emission signals. In particular, the adaptation of classical macroscopic acoustic emission approaches to micro scale for exploration the formation of micro cracks, delamination or phase transformations of thin films, coatings, and micro objects.

Analysis of cosmic ray events at the highest energy
Supervisor: prof. Miroslav Hrabovský, DrSc.
RNDr. Petr Trávníček, Ph.D., Ing. Jakub Vícha
Pierre Auger Observatory is the largest experimental apparatus in the field of astroparticle physics. Particles with energies larger than that of the LHC beams are detected by the array covering 3000 square kilometres in the Argentinian pampa. These cosmic particles originate in yet unknown sources in the Universe. The Aim of the Observatory is to measure the energy spectrum, direction of the incoming particles and answer the question about their chemical composition. New analysis techniques at the Observatory will be developed by the student as well as new emerging detection techniques of cosmic rays will be investigated.

Analysis of characteristics of parametric down-conversion
Supervisor: doc. RNDr. Ondřej Haderka, Ph.D.
doc. 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: doc. 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.

Photon-pair generation in metal-dielectric photonic structures
Supervisor: doc. RNDr. Jan Peřina, Ph.D.
Properties of photon pairs in metal-dielectric layers will be studied, especially spectral and timing characteristics and quantum correlations of the photons in a pair. Special attention will be devoted to intense generation of pairs in metal layers.

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.

Quantum information processing with correlated photon pairs
Supervisor: doc. RNDr. Jan Soubusta, Ph.D.
Arrangement, processing and detection of special light states of single photon level. An interference of the second and fourth order is utilized in the experiments.

Quantum and classical machine learning for quantum information protocols
Supervisor: doc. Mgr. Karel Lemr, Ph.D.
Within the scope of this topic the student will combine two modern research fields: machine learning algorithms and quantum information processing. Both purely theoretical and experimental approaches are possible, and the specific studied problems will reflect this choice.

Modern methods of evaluation of optical elements
Supervisor: prof. Miroslav Hrabovský, DrSc.
The topic is focused on the development and application of selected optical topographic methods or their combinations on non-standard large-scale surfaces as control methods for assessing the quality of these areas and for correlation research between the technological process and the qualitative and quantitative product parameters. Furthermore, it is assumed that the research findings will be applied directly to available optical production technologies, especially new generation ones. This topic is chosen broadly due to the fact that the theme will be concretized to the expected customer according to actual necessity of solving this problem in the Joint Laboratory of Optics of Palacky University and Institute of Physics of the Czech Academy of Sciences, possibly in cooperation with foreign partners and in accordance with the student's individual orientation and abilities.

Design and construction of devices for quantum information processing
Supervisor: doc. Mgr. Karel Lemr, Ph.D.
Ph.D. student will work in the field of quantum information processing on the platform of linear optics. The task consists of proposing schemes for devices implementing quantum information protocols. Subsequently these devices should be experimentally constructed in the laboratory.

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.

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.

Fibre-optic gates for quantum information processing
Supervisor: Mgr. Antonín Černoch, Ph.D.
Design and experimental activation of optical arrangements used for processing of the light states of single photon level. Devices built with fibre optics are implemented in applications more easily in comparison with bulk optics.

Influence of deposition conditions on the physical properties of thin layers on optical elements
Supervisor: Mgr. Libor Nožka, Ph.D.
The topic of Ph.D. work deals with study of characteristics of thin protective layers made of SiO2, TiO2, and HfO2 deposited onto optics elements. A deep description of these characteristics as a function of deposition process settings is the main goal. Following properties are of the main interest: structure of deposited layers, degree of crystallization, hardness and resistance to abrasion, transmittance in UV/VIS region etc. An impact of the annealing in a protective atmosphere on layers quality is another goal of the research.

Study of Heavy Particles Production and Properties with the ATLAS Experiment
Supervisor: Mgr. Jiří Kvita, Ph.D.
The ATLAS experiment at CERN is a multipurpose detector in high energy physics allowing to probe properties of exotic particles determining the symmetries breaking in particle physics as well affecting the evolution of the Universe. Measuring spectra of these particles can constrain current underlying theories or find hints of new physics beyond the Standard model. Of particular interest is the top quark, whose large mass can signalize a special role in the mechanism of the electroweak symmetry breaking or a special coupling to the recently discovered Higgs boson. By analyzing objects in final states consistent with the top pairs production and by measuring their spectra and fully correcting the detector resolution effects, the scientific community is provided by unique data on physics at the edge of current energy frontier, with implications for future theories and colliders. The goal of the thesis is to take an active part high energy physics measurements of heavy particles produced in proton-proton or ion-ion collisions, or even in cosmic ray events recorded by the ATLAS detector.

Field of Study Biophysics

Singlet oxygen signaling in plants
Supervisor: doc. RNDr. Pavel Pospíšil, Ph.D.
Singlet oxygen formed by energy transfer from triplet chlorophyll to molecular oxygen serves as signaling molecule in acclimation and programmed cell death. Role of singlet oxygen in regulation of phytohormone synthesis associated with gene expression will be studied during photooxidative stress in Arabidopsis thaliana.

Bimetallic and trimetallic nanoclusters: syntheses, physico-chemical and biological properties
Supervisor: doc. RNDr. Karolína Machalová Šišková, Ph.D.
Composite nanomaterials consisting of a biocompatible organic component and a functional inorganic component are frequently investigated and in several cases already employed in praxis, e.g. in catalysis and/or imaging. Nanoclusters containing tens to hundreds of noble metal atoms are sort of a size interconnection between atoms and nanoparticles; their properties are considered as molecule-like. The aim of this PhD thesis is the experimental preparation of new bimetallic and trimetallic nanoclusters, their characterization and testing of their interactions with cells.

Biomechanics and acoustics of human voice production
Supervisor: RNDr. Jan Švec, Ph.D. et Ph.D.
The production of human voice involves complex biomechanical processes leading towards the vibration of the vocal folds, and acoustic processes resulting in production of the final sound of human voice.  This PhD project will aim at uncovering the basic mechanisms involved in the vibration of the vocal folds and in the final voice production.  Experiments on excised larynges will be used to determine the resonance properties of the vocal folds and to relate them to the fundamental frequency of the self-sustained vocal fold vibrations.  The vocal fold vibrations will be captured by a high-speed camera and will be analyzed to obtain the details of the vibration characteristics. The characteristics will be compared to the behavior of physical and mathematical models of the vocal folds connected to the vocal tract. The changes of vibration characteristics due to changes of material properties of the vocal folds caused by physiologic and pathologic processes will be investigated in order to help clinicians in diagnosing voice problems more specifically.

Field of Study Optics and Optoelectronics

Experimental quantum optics and optical quantum information processing
Supervisor: RNDr. Miroslav Ježek, Ph.D.
Department of Optics at Palacky University Olomouc is a stimulating and collaborative environment with research groups focused on quantum information processing, quantum devices, and imaging. We are looking for a highly-motivated student to pursue experiments in the exciting field of quantum optics with applications in communications, computing, and metrology. Your work in our team will involve many aspects of quantum optics and quantum technology: multi-photon and multi-qubit systems, entanglement, quantum simulations, generation and detection of light at the quantum level, quantum networks, light-matter interactions in the quantum regime, and quantum memories. You will also collaborate with our international partners, e.g. towards developing novel solid state sources for quantum communication networks. The successful candidate will have the opportunity to learn new experimental techniques (QO, AMO, cryogenics, electronics, signal processing) and understand the underlying principles of various quantum systems and their interactions.

Characterization and utilization of the spatial degrees of freedom of light
Supervisor: prof. Mgr. Jaroslav Řeháček, Ph.D
Spatial degrees of freedom of light will be mastered for the purpose of metrology and information processing. Optical beams with phase singularities - optical vortices - will be adopted for the theoretical analysis and experimental realization of high-dimensional quantum states of the orbital momentum of a photon. Optimal methods of characterizing spatial degrees of freedom of light will be proposed and the information content of vortex beams will be analyzed. New theoretical and experimental techniques will find applications in optical processing of information, preparation of special states of light, coding and transmission of information, metrology, quantum tomography, and quantum information.

Quantum communication and optically connected quantum operations
Supervisor: prof. Mgr. Radim Filip, Ph.D.
The goal is to upgrade quantum communication toolbox and methods of quantum key distribution from purely optical experiments to hybrid quantum experiments with cold atomic, mechanical and electrical oscillators and study their mutual interaction and secure correlations in a network architecture. Simultaneously, free space quantum communication and operations including connection with the satellites will be included. The prerequisites are Master Degree in Physics, Applied Mathematics or equivalent, and fluency in English. The PhD student will participate in ESA project.

Quantum metrology and information processing with atomic systems
Supervisor: prof. RNDr. Tomáš Opatrný, Dr.
Recent experiments with cold atomic samples reveal many interesting phenomena with potential applications in metrology and in quantum information processing. Among them, e.g., spin squeezed states of atoms in optical resonators and interferometers, or Rydberg-dressed states, are especially promising. Questions how light can control behavior of atoms, and vice versa, will be addressed. Theoretical research focused on finding new schemes and protocols based on both numerical simulations and analytical calculations will be pursued with the goal of finding interesting applications to be tested in experimental labs worldwide.

Quantum nonlinear interactions with atoms and mechanical oscillators
Supervisor: prof. Mgr. Radim Filip, Ph.D.
The goal is to develop feasible quantum highly nonlinear interactions for the oscillating collective spin of atomic or solid-state ensembles and mechanical oscillators controlled by nonlinear squeezed quantum states of light and couple these nonlinear systems optically together. As a first step, feasible evaluation of quantum non-Gaussian entangled states of the oscillators will be proposed. The prerequisites are Master Degree in Physics, Applied Mathematics or equivalent, and fluency in English. The PhD student will participate in the Czech Science Foundation project or the EU QUANTERA project.

Quantum operations with superconducting electric circuits
Supervisor: prof. Mgr. Radim Filip, Ph.D.
The goal is to extend toolbox of existing quantum operations with microwave superconducting electric circuits and transmons to the highly nonlinear interaction between many oscillators. The interactions will be used to generate and study complex highly nonclassical states of oscillators and applied to analog quantum simulation. The prerequisites are Master Degree in Physics, Applied Mathematics or equivalent, and fluency in English. The PhD student will participate in collaboration with Yale University.

Linear optics quantum information processing
Supervisor: doc. Mgr. Jaromír Fiurášek, Ph.D.
The goal of the thesis is to theoretically develop, optimize and experimentally demonstrate novel schemes and protocols for quantum information processing with linear optics. The proposed schemes and devices will exploit hybrid encoding of qubits into several different degrees of freedom of single photons such as polarization or optical path, and manipulation of these qubits with bulk optics as well as with fiber-based setups. Main focus will be on small-scale quantum processors for quantum communication networks where efficient long-distance distribution of quantum states requires advanced techniques such as entanglement distillation and quantum repeaters. Another very promising research direction is to exploit linear optics as an ecellent testbed for design, verification and optimization of various quantum protocols destined for other physical platforms.

Monogamy based measures of quantum correlations
Supervisor: doc. Mgr. Ladislav Mišta, Ph.D.
The question of existence of computable and operationally meaningful measures of quantum entanglement is an open problem in current quantum-information theory. The thesis focuses on analysis of the entanglement measures for an important class of Gaussian states. The goal of the thesis is development of the theory of a quantifier of Gaussian entanglement called Gaussian intrinsic entanglement (GIE), which we introduced recently, and which compromises between computability and operational significance. We will investigate properties of GIE, its computability for new Gaussian states and its relation to other Gaussian measures. Next, we will explore relation of GIE to its quantum generalization known as Gaussian squashed entanglement. Since GIE is operationally associated to the classical secret key generation from common randomness, we will also analyze relation of GIE to Gaussian quantum key distribution. Finally, we will perform multipartite and non-Gaussian generalization of GIE to evaluate it for Gaussian bound entangled state and to probe its extremality on Gaussian states.

Advanced quantum detection and estimation methods in optical metrology
Supervisor: prof. Mgr. Jaroslav Řeháček, Ph.D.
Fundamental limits of imaging and metrology will be investigated. Inspired by the quantum theories of detection and estimation, the novel theoretical and experimental sensing protocols and estimation techniques will test the ultimate resolutions compatible with the laws of physics. Improved resolution in imaging and metrology are required for future applications in basic research as well as in observational astronomy, spectroscopy, microscopy imaging of biological samples, calibration of UV sources used in photo-litography and improved wafer inspection.

Stochastic and quantum thermodynamics of nanomechanical objects
Supervisor: prof. Mgr. Radim Filip, Ph.D.
The goal is to use already developed highly nonlinear stochastic and quantum motion of nanomechanical objects to study thermally driven nanoscopic engines producing low-noise oscillations and individual quanta of energy. The primary focus will be on the development of engines with optically and magnetically levitating nanoparticles. The prerequisites are Master Degree in Physics, Applied Mathematics or equivalent, and fluency in English. The PhD student will participate in EU QUANTERA project.

Tomography for quantum and classical information processing
Supervisor: prof. RNDr. Zdeněk Hradil, CSc.
Quantum tomography is a method inspired by quantum-state estimation for inferring the quantities, which cannot be measured directly. The program will consider the analogies between optics, quantum mechanics and information in order to assess the inferred  parameters as well as their resolution. Attention will be paid to the realistic  experimental  schemes such as wave front sensing, heterodyne detection or advanced schemes for digital image processing.  As a part of the research program, the overall  performance and possible optimal schemes for improvingf the reconstruction will be considered.

Geography

Field of Study Geoinformatics and Cartography

Analysis methods of artificial intelligence in spatial data mining
Supervisor: Doc. Ing. Zdena Dobešová, Ph.D.
Methods of artificial intelligence like clustering, similarity search or decision tree discovered in spatial data new knowledge and help predict the behaviour in space and time. The research and application of classic machine learning algorithms on the spatial-temporal data is new approach how research geographically located data. Mainly time and spatial prediction of phenomena bring new useful knowledge from existing data. The aim of work is description, selection and application of data mining methods for suitable spatial data.

Analysis of concepts, contents and use of school atlases in terms of Bloom's taxonomy
Supervisor: prof. RNDr. Vít Voženílek, CSc.
The research aim is to design, perform and proceed the analyses of concepts, contents and use of school atlases regarding Bloom's taxonomy. It involves testing a comparison of the reading of the school atlases map by the teacher and his pupil. The series of the test will be designed according to Bloom’s taxonomy. They, in collaboration with a psychologist, will be based on eye-tracking methods to find out if the teacher reads maps in the school atlas as well as his pupils. The test will include the maps from school atlases and will assemble appropriate questions on basic types of geographic tasks (according to Bloom).

Dynamic models of carbon sequestration in the landscape
Supervisor: Doc. RNDr. Vilém Pechanec, Ph.D.
The aim of the research is to design and test the appropriate process (series of algorithms) of the carbon stock calculation in two basic fields (aboveground and underground biomass). The student will perform practical testing of available tools (e.g. YASSO, Century 4.0, InVEST) and then focus on optimizing the process.The studied detail is a landscape scale, and the procedure will be based on geodata that has a defined update cycle. Multi-spectral data (Sentinel) procedures and sensors providing repeat data available for the Czech Republic will be preferred.

Geoinformatic alternatives for monitoring and modelling of water-retention function of the landscape
Supervisor: Doc. RNDr. Vilém Pechanec, Ph.D.
The aim of the research is to analyse landscape retention using GIS tools. The student will test tools for calculating the retention function in several selected GIS products (e.g. InVEST, Watem/SEDEM, TerrSet, ArcGIS). The results of the analysis will be evaluated in two levels. At the technological level, the student compares the algorithms used, how they are implemented, and the complexity of pre-processing, and incorporating the tool into a wider workflow analysis. In the application level, the results will be interpreted from the point of view of landscape ecology.

Cognitive research in visual analytics
Supervisor: prof. RNDr. Vít Voženílek, CSc.
The aim of the PhD research is to examine various approaches for method of cognitive aspects in visual analytics related to thematic maps and atlases. There are mainly: typology of spatial decision problems; advances in geovisualization and geovisual analytics technology; support of spatial decision support processes; development of standards and benchmarks in geovisual analytics; challenges in system design, adoption, and use; applied geovisualization and geovisual analytics (including areas such as climate change, crisis management, food and water security, epidemiology, etc.).

Spatial models of landscape response under the influence of climate change
Supervisor: Doc. RNDr. Vilém Pechanec, Ph.D.
The aim of the research is to test and compare models that are able to capture, evaluate or predict landscape changes caused by climate change (e.g. EcoCrop, CCAM, GLOBIO, EUROMOVE, TerrSet). The studied detail is a landscape scale and the subject of interest is changes in the distribution of plant species, loss of biodiversity, changes in the fulfilment of ecosystem functions. The planned outcome is the prediction model valid for the Czech Republic.

Visual programming for spatial data processing
Supervisor: Doc. Ing. Zdena Dobešová, Ph.D.
Visual programming in GIS is a straightforward method of designing spatial data processing workflows in a graphical form. . The aim of work is research of cognition and functional aspects of visual languages. Improvements of graphical notation and functionality of visual languages have potential for wider usability of workflows in GIS.

Geology

Field of Study Geological Sciences

Sedimentary budget and anthorpogenic contamination of dam reservoirs in selected river catchment
Supervisor: prof. Mgr. Ondřej Bábek, Dr.
Sedimentary infill of dammed reservoirs represents an important environmental and economic issue due to the costs related to dredging and risks of anthropogenic contamination of reservoir sediments. Simple prediction infill models are difficult to achieve due to a high number of factors that influence the sediment accumulation rates. Site-specific data such as erosion rates in the river catchment, grain size characteristics of the sediment load and the bottom morphology are usually needed in such an effort while, in general, little is known about the depositional architecture of reservoir lakes sediments. Chains of dam reservoirs along river courses such as the Váh River dam cascade, offer a unique case to study the effects of damming on river sediment transport and silting of dam reservoirs. This project will focus on stratigraphic and petrologic analysis of sedimentary depositional record several dams of the Váh River cascade. The project aim will be modelling of dam reservoir filling and evaluating the role of internal controls (bottom topography, size, pelagic production) and external, mainly anthropogenic controls (upstream damming, river regulation) on dam sedimentation. The project will be based on bathymetric mapping of reservoir bottom, geophysical imaging of sediment architecture using ground penetrating radar (GPR), analysis of sediment grain size and geochemistry based on sediment cores and analysis of sediment accumulation rates using 137Cs dating. Results will be published in peer-reviewed journals (WoS). Suitable candidates typically have a MSc. degree in geology / physical geography with excellent results and previous experience with work in the field (Bc., MSc. thesis in sedimentary geology or geomorphology). Good written and spoken English is required. Previous experience with scientific publishing is advantage.

The origin and genesis of fluids in the karst at Hranice na Moravě
Supervisor: prof. Ing. Ondřej Šráček Ph.D., M.Sc.
The karst in Hranice na Moravě is an exceptional structure in the Devonian carbonates. There is a deepest flooded abyss in Czech Republic and Teplické Caves with emanations of CO2. However, the information about the origin and genesis of fluids in the karstic area is only limited and suggests that at least a part of gases might be of a mantle origin. The project aims to integrate the geological and tectonic data in the area with analyses of water chemistry and stable isotopes 2H, 18O, 13C, 34S and radioactive 14C. The output of the project should be a model of the genesis of fluids and determination of their recharge area. This should contribute to the better protection of thermal waters exploited in the Teplice nad Bečvou Spa. Candidates should have a MSc. degree in geology / physical geography with previous experience in hydrogeochemistry, isotopic chemistry and geochemical modeling. Good level of written and spoken English is required.

Chemistry

Field of Study Analytical Chemistry

Chemical microanalysis of plant material
Supervisor: doc. RNDr. Petr Bednář, Ph.D.
Analysis of chemical composition of plants tissues has an irreplaceable role for understanding of plant life that is important for biology, agriculture, food science and industry. Plant tissues are heterogeneous and contain a number of different types of cells with different functions. The aim of this topic is the development of instrumental methods for chemical analysis of very small parts of plant tissues and cell layers with particular functions or even analysis of selected cells. In the frame of this topic, potential of various imaging techniques as well as procedures for manipulation with plant micro-samples and their consequent chemical characterization will be studied.

Intraoperative mass spectrometry in burn surgery
Supervisor: prof. Ing. Vladimír Havlíček, Dr.
Based on collaboration with Faculty hospital Kralovske Vinohrady, see https://www.fnkv.cz/klinika-popaleninove-mediciny-o-klinice.php (MUDr. Robert Zajíček and MUDr. Šuca) and Dr Julia Balog, Computational and Systems Medicine, Department of Surgery and Cancer Imperial College London, 5th floor lab block, room 5L16/17, Charing Cross Hospital, London W6 8RD. The development, construction and clinical application of a tangential knife (REIMS: rapid evaporation ionization mass spectrometry) for online characterization of human tissues. The aim is to quantitatively distinguish between the necrosis and potentially vital tissue types. The work will be combined with multimodal imaging approaches, especially with MSI and optical scans. It will be accomplished on FTICR and nano-HPLC-IM-QTof spectrometers exclusively.

The diagnostics of infectious diseases by metabolomics approaches
Supervisor: prof. Ing. Vladimír Havlíček, Dr.
Collaboration with the Institute of experimental medicine in Prague and other Czech leading hospitals. International partners are University College London, Centre for Clinical Microbiology (Emmanuel Wey), Medicinal University in Vienna (Goran Mitulovic) and Medicinal University in Innsbruck (Michaela Lackner). The goal is to develop a non-invasive diagnostic tool useful for infections caused by Pseudomonas aeruginosa (see the similar literature below) and other BSL-2 pathogens. The work will be accomplished on a rat model. Analysis of human samples (urine, serum, tissues) is also expected.
Literature: Luptakova D, Pluhacek T, Petrik M, Novak J, Palyzova A, Sokolova L, Skriba A, Sediva B, Lemr K, Havlicek V. 2017. Non-invasive and invasive diagnoses of aspergillosis in a rat model by mass spectrometry. Scientific Reports 7:16523.

Field of Study Physical Chemistry

Graphene and Graphene Derivatives
Supervisor: prof. RNDr. Michal Otyepka, Ph.D.
Graphene is without any doubt an extraordinary material. Some of its properties (hydrophobicity, zero band-gap, low chemical reactivity), however, limit its application potential, e.g., in electronics and biosensing. We seek for new preparation routes for tailored graphene modifications. The modification can be achieved via covalent as well as noncovalent approaches (Chem. Rev., 112(11), 6156-6214, 2012). The framework topic focuses on development of alternative routes for synthesis of graphene derivatives, on understanding of mechanism of chemistries of carbon 2D materials and understanding of physical-chemical properties of graphene derivatives. The aims will be fulfilled via experimental (synthesis, characterization via e.g., HRTEM, SEM, AFM, XPS, and sensing, and (electro)catalytic applications) or computational (DFT, advanced DFT and post-HF) methods and simulation (all-atom and coarse-grained molecular dynamics simulations) techniques. The particular topics will be focused on design, synthesis, and characterization of new graphene derivatives with tailored properties (e.g., magnetic, electronic, dispersability etc.), understanding on the strength and nature of noncovalnet interactions to graphene and graphene derivatives etc. The topic is supported by ERC grant.

Advanced nanomaterials for heterogeneous catalysis, photocatalysis and electrocatalysis
Supervisor: prof. RNDr. Radek Zbořil, Ph.D.
Nanomaterials offer a great application potential in catalytic reactions due to the small size and a high fraction of surface atoms enabling to achieve higher rate constants and better selectivity compared to microcrystalline counterparts. Their efficiency would be further enhanced by combination of various nano-species creating so called hybrid or integrated catalysts. The aim of this research topic is the development of such hybrid nanoarchitectures including core-shell nanostructures, magnetically separable catalysts, micro-mesoporous hybrids and N-doped carbon systems and their applications in selected organic, photocatalytic and electrocatalytic reactions.

Hybrid nanostructures for photoelectrochemical water splitting
Supervisor: prof. RNDr. Radek Zbořil, Ph.D.
Solar-powered water splitting is a central technology for the realization of a sustainable economy based on clean and renewable energy vectors such as hydrogen (H2). The overall reaction (2H2O → 2H2 + O2) is endothermic (E = 1.23 V vs RHE) and consists of two half reactions: 2H+ + 2e– → H2 (HER, E°red = 0.0 V) and 2H2O + 4h<sup+< sup=""> → O2 + 4H+ (OER, E°ox = 1.23 V). Adopted semiconductors should ideally absorb photons with energies higher than 1.23 eV and feature conduction band (ECB) and valence band (EVB) edges that straddleE°red and E°ox, respectively. However, though CB and VB may have appropriate energies, unavoidable potential losses and kinetic overpotentials imply that 1.6–2.4 eV is the actual energy necessary to sustain the overall water splitting. Such a severe thermodynamic and kinetic restriction explains why a semiconductor able to efficiently drive the overall reaction has yet to be identified. Transition metal oxides rarely meet the criteria of an Eg suitable for sunlight activation, or of favorable band edges relative to E°red and E°ox. Thus, the well renowned earth abundant materials potentially stable in the long-term, such as TiO2, α-Fe2O3, WO3, BiVO4, etc. still represent the most viable option for PEC applications. However, the intrinsic limitations of these materials still have to be addressed. There are several viable options to increase the PEC water splitting efficiency including (i) 1D material nanostructuring, to overcome the short hole diffusion length and prevent the photogenerated charge recombination; (ii) engineering of multi-component hybrid nanostructures and (iii) the use of co-catalysts/sensitizers, to enhance structural stability and extend the spectral range of light absorption, pointing to improve the efficiencies in PEC processes. The framework of this PhD program is based on developing a new class of multicomponent hybrid systems composed of a central semiconductor (CS), most likely TiO2, α-Fe2O3, ZnO and WO3, with controlled shape and dimensionality (e.g., 1D-nanotubes, 2D-ultrathin films). The key-approach is represented by the simultaneous and synergistic combination of strategies (nanostructuring, co-catalyst deposition, surface sensitization) usually studied and developed independently. Therefore, the nanostructured CSs will be coupled to counterparts with specific functionalities (extended visible light absorption, remarkable efficiency in charge transfer, enhanced carrier mobility) and the effective interaction of the single components will significantly benefit the PEC efficiency of the composite system. </sup+<>

Noncovalent interactions at metallic and non-metallic surfaces: qauntum mechanical study
Supervisor: prof. Ing. Pavel Hobza, DrSc., FRSC
Noncovalent interactions of small and medium-sized molecules on metallic and non-metallic surfaces will be studied by using nonempirical and semiempirical quantum mechanical methods. Besides structure and geometry of complexes formed also total stabilization energy as well as its components will be investigated. Attention will be paid to eletric and magnetic properties of molecules adsorbed and thier complexes with the surfaces. The study will be based on cluster model as well as on infinitive surface model based on periodic boundary conditions.

Molecular Simulations of Biomembrane Systems
Supervisor: doc. RNDr. Karel Berka, Ph.D.
The aim of this research topic is to understand behavior and the nature of interaction of small molecules as well as biomacromolecules with biological membranes. A combination of simulation techniques (e.g. all atomic and coarse-grained molecular dynamics simulations or quantum chemical calculations) and bioinformatics and cheminformatics approaches will be used to understand and quantify interactions of molecules with biological membranes - e.g. penetration and partitioning of small molecules into the individual membranes (Pharmacol. Res., 111, 471–486, 2016; Langmuir, 30(46), 13942-13948, 2014) and storage of such information in publicly available database; mode of action of membrane-bound proteins - e.g. interplay between cytochromes P450 and other metabolic enzymes (Drug. Metab. Dispos., 44(4), 576-590, 2016) including studies of molecular pathways within structure of those membrane proteins (J. Chem. Theory Comput., 12(4), 2101–2109, 2016) together with development of necessary structural bioinformatics tools (e.g. http://mole.upol.cz/ - Nucleic Acids Res., 40(W1), W222-W227, 2012). We expect a tight cooperation with colleagues from European bioinformatics infrastructure ELIXIR, Masaryk University, Czech Republic, Procter & Gamble company, USA, Université de Limoges, France, and Friedrich-Alexander Universität Erlangen-Nürnberg, Germany.

Magnetism of 2D systems
Supervisor: doc. Mgr. Jiří Tuček, Ph.D.
The long-term challenge of the scientific community is to develop metal-free magnetic systems based on carbon. However, so far, magnetism self-sustainable at higher temperatures (up to room temperature) has not been reported for any sp-based material including all carbon allotropes. The most promising results have been achieved with 2D graphene and its derivatives, which would exhibit low-temperature magnetism after appropriate chemical treatment. Among carbon nanoallotropes, graphene has been identified as the most promising candidate to show interesting self-sustainable magnetic features once defects are introduced. The defects include local topology perturbations, vacancies, non-carbon atoms in the graphene lattice, adatoms (i.e., atoms added to the surface of the graphene sheet), mixed sp2/sp3 hybridization (i.e., suitable sp2/sp3 ratio), and zigzag-type edges (i.e., confinement-related phenomena). The imprinting of self-sustainable magnetism at room temperature to graphene and/or its derivatives is widely recognized as a key challenge for the further development of 2D carbon-based materials with a huge potential in spintronics devices, biomedicine, environmental technologies etc. The goal of this PhD topic is viewed in finding, both experimentally and theoretically, the optimal combination of defects of various natures towards generation of magnetic centers, promotion of their communication and, at the same time, preservation of the role of conduction electrons. The issue of imprinting self-sustainable magnetism will be also addressed for systems analogous to graphene such as MoS2, WS2, etc.

Structure and Dynamics of RNA
Supervisor: prof. RNDr. Jiří Šponer, DrSc.
The topic of the thesis will be studies of selected RNA molecules (ribosomal RNA motifs, protein-RNA complexes, ribozymes, riboswitches, selected from systems presently studied in our laboratory as well as in collaborating laboratories) using methods of classical molecular dynamics simulations, bioinformatics and quantum-chemistry. RNA presently belongs to the most widely studied biomolecules. Functional RNA molecules are fascinating 3D architectures and computational chemistry is one of the basic tools in their characterization, as can be documented also by number of our preceding studies in the field (see, e.g., the WOS database). Computer simulations can obtain new information for example about the role of noncanonical base pairs in RNA structure and evolution, and can substantially complement information obtained by X-ray crystallography, NMR and bioinformatics. The work may include either studies of specific systems or tasks oriented more towards method testing and development. We collaborate with a number of experienced laboratories across the world, including F.H.T. Allain, G. Bussi, N.B. Leontis, N.G. Walter, M. Nowotny, and others.

Origin of Life Theory – Studies of Prebiotic Chemical Reactions
Supervisor: prof. RNDr. Jiří Šponer, DrSc.
The topic of the thesis will be origin of life theory, which is a complex research area ranging from the evolution of planetary systems through prebiotic synthesis of basic components of the living materials up to simple protocells. Theoretical quantum-chemical (QM) methods can be efficiently applied to studies of prebiotic chemical reactions. The main advantage of QM methods is their capability to describe processes which in some cases cannot be fully satisfactorily understood by means of experiments. Presently, we are involved in studies related for example to the formamide pathway to the origin of life, non-templated synthesis of the first RNAs from the cyclic nucleotides, role of photochemical processes in prebiotic chemistry, QM molecular dynamics simulations, high energy impact chemistry and some other topics. The dissertation is suitable for students who are interested in application of modern QM methods and have a feeling for chemical reactions. Because it is a very difficult topic, specific research goal can be proposed only after careful assessment of the capabilities of the applicant. We closely collaborate with other experimental and theoretical laboratories, e.g. E. Di Mauro, R. Salladino, M. Ferus, M. Saitta, J.D. Sutherland and some others.

Multiscale Modeling of Nucleic Acids
Supervisor: prof. RNDr. Jiří Šponer, DrSc.
Nucleic acids (RNA and DNA) belong to the most important biomacromolecules. Studies of structure and dynamics of nucleic acids represent an important task of modern life sciences. Due to fast development of hardware and software, computational and theoretical approaches are frequently used in nucleic acids studies and represent a respected counterpart of experimental techniques. This PhD project will be based on integrated interdisciplinary utilization of a broad spectrum of computational methods (multi-scale modelling) ranging from state-of-the-art quantum-chemical (QM) approaches through modern explicit solvent molecular dynamics (MD) simulation methods up to bioinformatics. Cooperation with established experimental laboratories will provide necessary experimental feedback. State-of-the-art computational facilities are available not only in our laboratory but also in cooperating laboratories abroad. The exact topic will be specified based on the discussion with the applicant and her/his scientific interests and capabilities. Currently available specific themes include for example multiscale studies of protein-RNA complexes, RNA catalysis, structural dynamics and folding of quadruplex DNA and large-scale QM studies of complete nucleic acids building blocks.

Advanced Nanomaterials: Synthesis and Applications in Catalysis, Organic Transformations, Photo (electro) catalysis
Supervisor: doc. Manoj B. Gawande, Ph.D.
Nanoparticles are regarded as attractive candidates for heterogeneous catalysis in various imperative catalytic processes as they are now easy to synthesize with a desired size, structure, morphology and composition. Keeping in mind the current environmental sustainability concerns, it is important to design inexpensive and benign nanocatalysts for organic transformations/catalytic processess. Over the last decade, a variety of new types of nanocatalysts have been investigated, including well-defined Morphology Depdendent Catalysts, Single-atom catalysts, Core–shell and yolk–shell nanocatalysts, Silica-based hybrid catalysts, 2 D graphene-based materials and 2D single metal or mixed metal ionic nanocatalysts. The ascent of these complex nanomaterials over the last few years has enabled chemists to understand traditional catalysts from a new perspective. The aim of these hot research areas is to desinged the materials based on highly important targated catalytic, organic transformations and Photo (electro) catalysis applications.

Theoretical study of charge transport in nanostructures
Supervisor: Doc. Ing. Pavel Jelínek, Ph.D.
Possibility to actively control charge states on atomic scale in nanostructures opens new horizons in the field of nanoelectronics. To get more insight into processes of charge transfer on atomic scale requires new theoretical approaches. The aim of this work is to employ the density functional theory and its application on selected cases charge transport in nanostructures. Theoretical simulations will be performed in close collaboration with ongoing experimental measurements. Development of computational methods is expected.

Chemical and physical properties of molecular nanostructures on surfaces investigated by means of scanning probe microscopy
Supervisor: Doc. Ing. Pavel Jelínek, Ph.D.
The current development of the scanning microscopes working in ultrahigh vacuum allows high-resolution measurements of atomic force and tunneling currents on individual atoms or molecules deposited on the surface of solids. Simultaneous measurement of the atomic force and tunneling current opens up completely new possibilities for the characterization of single molecules or molecular nanostructures on solid surfaces. The candidate will learn to work with atomic force microscope and scanning tunneling microscope in ultra-high vacuum. The aim of this work is carried out high-resolution measurements of the atomic and electronic structure of selected molecules deposited on solid surfaces. The main objective is to study chemical and physical properties of the molecular nanostructure by means of scanning probe microscopy.

Understanding biology at an atomic resolution
Supervisor: Dr. Patrick Trouillas
Interaction of new materials and new chemical derivatives with biological systems is of crucial importance in many research fields related to healthcare. The today and tomorrow’s challenges lie in rationalization of these interactions with an atomistic resolution. The gamut of theoretical chemistry methods allows achievement of that outcome, with increasingly precise accuracy. We propose a series of research topics focusing on noncovalent interaction between π-conjugated systems, interaction with lipid bilayers membranes and interactions with proteins.

Field of Study Organic Chemistry

Molecular system for multiple detection of enzymes inside the cells
Supervisor: Prof. RNDr. Jan Hlaváč Ph.D.
Regulation of biochemical processes inside a cell is intensively studied area of chemical biology with aim to elucidate relationship between (de)activation of various proteins and cells transformation or apoptosis. The elucidation of this relationship belongs to crucial knowledge in mosaic of factors causing a start of various diseases, mechanism of drugs action, resistance to therapy or e.g. self-regulation processes of cells to prevent a disease development. The project is focused on development of molecular systems for simultaneous/sequential detection of relevant enzymes inside the cells. The system will be constructed from peptide linkers for specific interaction with the enzymes and several fluorescent dyes/quenchers. Interaction of appropriate enzyme with specific linker should cause a change of fluorescence characteristic for its presence. Combination of various changes should be characteristic for presence of more enzymes.

Drug-delivery systems with releasing visualization
Supervisor: Prof. RNDr. Jan Hlaváč Ph.D.
Drug-delivery systems play important role in modern chemotherapy approaches. One of the strategies in treatment of various diseases is based on specific releasing of a drug from a carrier in transformed cell. Visualization of this process is important factor of chemotherapy efficiency evaluation. The project is focused on development of novel systems for delivery of a drug to cancer cells or bacteria with an ability to track the system and visualize the drug releasing. The systems will be based on drug-fluorescent dye conjugate including a linker specifically cleavable inside a cancer cell or bacteria.

Preparation of heterocycles using solid-phase synthesis
Supervisor: Doc. RNDr. Miroslav Soural Ph.D.
Aim of the work is development of synthetic methods applicable for preparation of novel heterocyclic derivatives. Starting from readily available building blocks, multireactive polymer-supported intermediates will be synthesized and subjected to diversity oriented, reagent-based synthesis to obtain different heterocyclic scaffolds. Particular attention will be paid to asymmetric reactions enabling the preapration of heterocycles with directed configuration. Developed protocols will be applicable for simple parallel/combinatorial synthesis of target derivatives.

Preparation of new semisynthetic triterpenes and study of their biological properties
Supervisor: doc. RNDr. Milan Urban, Ph.D.
This thesis will be focused on the synthesis of new bioactive natural compounds - triterpenes in order to improve their antitumor activity and pharmacological properties. The triterpenoid skeleton of lupane, oleanane, ursane or friedeline will be mostly modified by the introduction of heterocycle moieties, secoderivatives will be prepared as well as more oxidized terpenic structures and conjugates with other molecules of interest. The active compounds will then be used for the evaluation of their mechanism of action, prodrugs will be investigated in order to improve their solubility and bioavailability.

Nitrogen-Containing Heterocyclic Compounds: Synthesis, Method Development, Study of Physical-Chemical Properties and Reactivity
Supervisor: doc. RNDr. Petr Cankař, Ph.D.
The PhD thesis will be focused on the synthesis of nitrogen-containing heterocyclic compounds with the potential biological relevance or the development of novel synthetic methods. The prepared compounds will be studied with regard to physical-chemical properties, reactivity, and potential biological activity.

Computer Science

Field of Study Computer Science

Relational data analysis
Supervisor: Prof. RNDr. Radim Bělohlávek Ph.D.,DSc.
Relational data analysis represents a recent direction in data mining. The PhD student will conduct researchin foundations and algorithms for methods of relational data analysis, with particular focus on factorization, clustering, and reduction of dimensionality of relational data.

Cognitive psychology nad relational data
Supervisor: Prof. RNDr. Radim Bělohlávek Ph.D.,DSc.
Cognitive psychology offers a number of interesting concepts and principles regarding people's capability to process and understand data. Most of them has not yet been utilized in processing relational data. The PhD student will attempt to formalize such concepts and principles and utilize them in the design of novel methods of processing and analysis of relational data.

Selected verification problems: algorithms and complexity
Supervisor: Prof. RNDr. Petr Jančar CSc.
In the area of automated verification of behavioural properties of(software and hardware) systems there are various problems whosecomputational complexity has not been sufficiently clarified so far.The aim of proposing this PhD thesis is to attract a student to this area,possibly within a running project of the Czech Grant Agency;the research effort can be directed at a theoretical and/or an experimental part.

Simplifying axiomatic systems
Supervisor: Doc. RNDr. Miroslav Kolařík Ph.D.
The main goal is to solve some concrete open problems from the area of simplification of axiomatic systems. The student is expected to learn the state of the art in the area, including related software tools, and then he implements their own software tool. The tool should be able to derive new identities from a given axiomatic system (given enough time and memory) and thus to find redundant axioms, and to prove that all axioms in a given axiomatic system are independent by constructing models of all but one axiom.

Formal concept analysis
Supervisor: Doc. RNDr. Michal Krupka Ph.D.

Topology in Computer Science
Supervisor: Doc. RNDr. Michal Krupka Ph.D.

Structure of minimal theories in fragments of general logics
Supervisor: Doc. RNDr. Vilém Vychodil Ph.D.
The goal is to study necessary and sufficient conditions of non-redundancy and minimality of finite sets of formulas describing dependencies or constraints in data. The investigation is aimed at formulas appearing in sublanguages of logical frameworks that generalize the classic Boolean logic and includes theoretical research in the areas of complete axiomatizations, decidability, and complexity.

Mathematics

Field of Study Algebra and Geometry

Aggregation operators on lattices and posets
Supervisor: Prof. Mgr. Radomír Halaš Dr.
The work will be focused on certain aspects of aggregation theory on partially ordered sets. One of the main goals is to identify or even characterize finite posets for which the respective clones of aggregation functions are finitely generated. Also description of some special clones of aggregation functions will be the objective of this work.

Special diffeomorphisms of differentiable manifolds
Supervisor: Prof. RNDr. Josef Mikeš DrSc.
This work will deal with Riemannian spaces and spaces with affine connection. We suppose to study general properties of F-planar mappings and also properties of special  spaces that admit these mappings and transformations.

Field of Study Mathematical Analysis

Multivalued boundary value problems
Supervisor: Prof. RNDr. dr hab. Jan Andres, DSc.
The solvability of boundary value problems will be investigated for the first-order and second-order vector differential  inclusions.
In particular, the Neumann boundary value problems will be treated by the methods combining the topological tools (degrees, indices, etc.), jointly with the locally and globally applied Liapunov functions.

Almost-periodic sequences
Supervisor: Prof. RNDr. dr hab. Jan Andres, DSc.
The hierarchy of almost periodic sequences in various metrics, defined by different alternative approaches, will be clarified. A similar classification was already done for continuous functions which can be regarded as a model to be followed, i.e. as a discrete analogy. Almost periodic sequences will be also considered as solutions of difference equations and inclusions.

Singular differential equations on the half-line
Supervisor: Doc. RNDr. Jan Tomeček, Ph.D.
In the Cahn-Hilliard theory, field theory, etc. arise problems leading to ordinary differential equations on the half-line with a time singularity at the origin. The main goal of the thesis is the investigation of solutions of such equations and their behaviour.

Differential equations with state-dependent impulses
Supervisor: Doc. RNDr. Jan Tomeček, Ph.D.
The main goal of the thesis is to obtain new existence results for various problems from the theory of differential equations with impulses, where the intstants of impulses are not a priori known.

What to do before applying for Ph.D. study

  1. Choose your field of study and thesis topic.
  2. Contact your potential supervisor and get the endorsement for your application. Only then you can apply for your application!
  3. Some documents are necessary for application – see below Applications & Deadlines.
  4. Complete our electronic application. Choose only fields of study with English titles.
  5. In order to complete the e-application, you will be asked to pay processing fee 650 Kč (approximately 24 EUR) by credit card. More information in Applications & Deadlines.
    Without the payment, the application will not be considered.
  6. Be aware that tution fee 4000 EUR per academic year is required, however there are several Fischer scholarships (below) for selected topics.

Applications & Deadlines

Applicants for master’s study and doctoral´s programmes conducted in English must fill in an online application.

Application deadline for academic year 2018/2019 is 30 April 2018.

Processing fee 650 Kč (approximately 24 EUR) pay by credit card in your electronic application.
You can also pay to following account:
Bank name: Komercni banka, Olomouc
SWIFT: KOMB-CZ-PP
Account number - IBAN: CZ0901000000191096330227
Account holder: Univerzita Palackeho v Olomouci, Krizkovskeho 8, 771 11 Olomouc
Payment description: your name, FS-PAPL
Reference No.: 3900
A transcript of the bank transfer must accompany the application.
Without the payment, the application will not be considered.

Documents Required for Application

These documents attach to your electronic application (in pdf):

  1. Official transcript and a copy of your certificate/diploma. Should be requested from the colleges and universities attended. For applicants from non-member states of the Hague Conference on International Law (see the list), the documents must be accompanied by an apostille issued by the local Czech Embassy.
  2. Two recommendation letters. These provide an additional source of information about professional and academic level and should be completed by employer or university professor.
  3. Curriculum vitae. Information concerning your life, education, including work, study and research experience. Statement of academic goal indicating why you wish to study in a particular program. Ph.D. applicants are expected to submit a description of their graduate program, diploma thesis, published papers, honours awarded, membership in scientific societies and personal professional goals.
  4. English language proficiency certificate.
  5. Health status certificate (not older than one month). All accepted international students are required to join International Student Medical Expense Plan or show a proof of equivalent coverage of their health insurance.
  6. Diploma recognition

Scholarships

Fischer scholarship for International Students at the Faculty of Science

J. L. Fischer
The Faculty of Science now wishes to invite applicants for the Fischer Ph.D. scholarship to support International scholars. The scholarship is open for 10 outstanding international students in the field of Mathematical Analysis, Algebra and Geometry, Applied Mathematics, Computer Science, Geological Science, Geoinformatics and Cartography, International Development Studies, Biochemistry, Analytical Chemistry, Physical Chemistry, Organic Chemistry, Molecular and Cell Biology, Experimental Biology, Zoology, Applied Physics, Biophysics, Optics and Optoelectronics. The scholarship is available for up to 48 months.

Thesis topics

Scholarship Description:

  • Application Deadline: April 30, 2018.
  • Course Level: The scholarship is available for pursuing the Ph.D. program and it is offered to full-time students.
  • Scholarship Award: The Faculty of Science grants 11000 EUR per academic year (CZK 25000 / month).
  • Nationality: International.
  • Number of Scholarships: up to 10 scholarships  to support International  Scholars
  • Tuition: 4000 EUR is required.
  • On-campus an exclusive single room accommodations for a PhD students (accommodation type is based on availability).

All the above items are covered for up to 48 months based on satisfactory progression

Eligible Countries:

  • This scholarship is open to applicants of all nationalities.

Entrance Requirements:

  • Applicants must have a Master’s Degree in a similar field of study and meet the required English language proficiency for the relevant subject area. 

Application Procedure:

  • The Applicant is strongly advised to contact the perspective supervisor. 
  • Applicants must submit online applications with uploaded documents only. 
  • Diploma and Transcript of Record.
  • Two Recommendation Letters by an employer or a university professor which should provide an additional source of information about the professional and academic level.
  • Curriculum vitae.
  • English language proficiency certificate.
  • A hard copy of the application and any other documents are not required at this stage.
  • Health status certificate (not older than one month).
  • All accepted international students are required to join the International Student Medical Expense Plan or show a proof of equivalent coverage of their health insurance.
  • Diploma must be recognized.
  • The application fee is CZK 650 (non-refundable).

Short-term Courses

Most departments at the Faculty of Science offer courses for foreign students in English. These courses are not exclusively intended for foreigners, exchange students will study alongside Czech students. In case of successful completion of a course, students are awarded ECTS credits. These credits allocated to each course should describe the approximate student workload required to complete them. 30 ECTS credits per semester (4–6 courses) are considered to be the regular workload for an exchange student. After choosing a specific field of study Exchange students may browse the list of courses according to a department or a semester. In case you need more information about study opportunities at the faculty, please contact dana.gronychova@upol.cz.

Summer Schools

Summer School on Development Cooperation (Department of Development and Environmental Studies)

Contacts

Faculty of Science, Palacký University Olomouc

Study Department
17. listopadu 1192/12
771 46 Olomouc
tel.: +420 585 634 010-14
fax: +420 585 225 737
e-mail: studijni.prf@upol.cz

Contact person for foreign students:

Dana Gronychová
dana.gronychová@upol.cz
+420 585 634 058

Room number: 1.005, ground floor next to the reception