Annotation of PhD topics

Nucleic structure prediction and modelling - doc. Mgr. Pavel Banáš, Ph.D.

The topic of the thesis will be studies of prediction and modelling of the 3D structure of the nucleic acids. The work may include development of the structure prediction algorithms, multiscale description of the nucleic acids structure and simulation techniques for sampling of the nucleic acids conformational space. We collaborate with a number of experienced laboratories including groups of prof. G. Bussi, group of prof. Nils G. Walter, etc.

Chemical databases - doc. RNDr. Karel Berka, Ph.D.

In today's age of information technology, it is also time to manage and extract available chemical data. Within the group, we have already developed several databases (www.molmedb.upol.cz, or www.pokusnice.upol.cz), which store specific chemical data and enable basic manipulation and extraction with them. The aim of the work is to expand databases, automate their performance, increase their interoperability (eg by connecting to Wikidata), improve existing data management, but above all use their outputs to solve research questions. Prerequisites and co-requisites:

Molecular Simulations of Biomembrane Systems - doc. RNDr. Karel Berka, Ph.D.

The aim of this research topic is to understand the behavior and nature of the interaction of small molecules and biomacromolecules with biological membranes. A combination of simulation techniques (eg molecular dynamics simulations or quantum chemical calculations) and bioinformatics and cheminformatics approaches - eg identification of substances suitable for encapsulation in liposomes (eg bioRxiv, 05 (11)) will be used to understand and quantify the interactions of molecules with biological membranes. 087742, 2020.) and storing this information in a publicly available database (eg molmedb.upol.cz Database, 2019, baz078, 2019); mode of action of membrane-bound proteins together with the development of necessary structural bioinformatics tools (eg http://mole.upol.cz/ - Nucleic Acids Res, 46 (W1), W368 – W373, 2018., or SecStrAnnotator - bioRxiv, 04 (15 ), 042531, 2020.). We expect close cooperation with colleagues from the European bioinformatics infrastructure ELIXIR, Masaryk University in Brno, Czech Republic; University of Limoges, FR; Uppsala University, SE and University of Chemical Technology in Prague, Czech Republic.

Computer-Aided Drug Design based on Quantum Chemical Calculations - doc. RNDr. Karel Berka, Ph.D.

Modern computer-aided drug design is an attractive interdisciplinary scientific area where physical chemistry, structural biology and informatics meet. The main aim is to discover and improve chemical compounds, ligands, which would bind strongly its molecular target, a certain protein, and thus cure a disease. Theoretical methods can do this more efficiently than experiment, provided their reliability is increased. We have achieved this by developing new approaches to calculate Gibbs free energy of protein-ligand interaction based on quantum chemical methods, which are superior in accuracy to standard methods and successfully applied to tens of systems (ChemPlusChem, 2013. 78(9): p. 921-931; ChemPlusChem, 2020. 85(11): p. 2361.). The topic of this work will be to test the universality of the method in databases of other systems and also an improvement of the methodology. Conzultant: RNDr. Martin Lepšík, Ph.D.(ÚOCHB AV ČR)

Theoretical study of charge transport in nanostructures - 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.

Intermolecular Interactions in Biomolecules - doc. RNDr. Petr Jurečka, Ph.D.

Whereas structure of ribosomal RNA is relatively well known, the interactions that determine and stabilize it are less well studied. Quick development of computational chemistry enables still more accurate modeling of biomolecular interactions. In our work we focus on modeling of weak intermolecular interactions in biomolecules, such as ribosomal RNA or protein-DNA complexes and search for important stabilization motifs of these unique molecular architectures.

Development of Empirical Potentials for Biomolecular Modeling - doc. RNDr. Petr Jurečka, Ph.D.

Development of empirical potentials for molecular dynamics is a necessary condition for progress in the whole area of molecular modeling. A promising method for obtaining high quality empirical parameters has been developed at the Department of Physical Chemistry in Olomouc a few years ago. The newly developed parameters for DNA and RNA simulations are now used worldwide as a part of the most popular simulation package AMBER. In this work we are going to apply our method to dozens of biologically interesting systems, such as unusual DNA structures, protein-DNA complexes and fragments of ribosomal RNA.

Study of the natural antioxidants for their therapeutic applications - prof. Ing. Lubomír Lapčík, Ph.D.

Natural antioxidants play an important role in guarding organisms against cancer illnesses. Those are mainly their antioxidant properties and their use in the organisms. The aim of this research will be comparison of antioxidants extracted from selected types of plant products, mainly with respect to their free radicals trapping capacity. There will be determined basic kinetic parameters of the free radicals trapping by means of the antioxidants action, their identification, thermal and chemical stability in different environments. Requirements: Graduate of the technical or natural science university curricula in the subjects of chemistry, physical chemistry, materials chemistry or technology. Literatura
  1. Simunkova, M., Alwasel, S.H., Alhazza, I.M., Jomova, K., Kollar, V., Rusko, M., Valko, M. Management of oxidative stress and other pathologies in Alzheimer’s disease (2019) Archives of Toxicology, 93 (9), pp. 2491-2513.
  2. Lawson, M., Jomova, K., Poprac, P., Kuca, K., Musílek, K., Valko, M. Free radicals and antioxidants in human disease (2018) Nutritional Antioxidant Therapies: Treatments and Perspectives, pp. 283-305.

Graphene and Graphene Derivatives - 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 the 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, dispersibility etc.), understanding the strength and nature of noncovalent interactions to graphene and graphene derivatives, application of graphene derivatives in sensing, catalysis and energy storage.

Fast and accurate quantum-mechanical methods for computer-aided drug design - doc. RNDr. Jan Rezac, Ph.D.

Application of computational chemistry to biochemical problems such as study of protein-drug interactions requires accurate computational methods scalable to large systems. These contradictory requirements can be reached with approximate quantum-mechanical methods parametrized specifically the description of non-covalent interactions in biomolecules. We have developed a series of corrections for semiempirical quantum-mechanical methods that reach the required accuracy, and are applicable to systems of thousands of atoms, such as whole proteins. Our methods have been successfully applied in computer-aided drug design, where they significantly outperform other commonly used approaches. The topic of this project will be further development of semiempirical QM methods towards better description of interactions and structure of biomolecules. The project requires basic programming skills.

Reference quantum-chemical calculations of non-covalent interactions - doc. RNDr. Jan Rezac, Ph.D.

Accurate quantum-mechanical calculations often serve as a benchmark for the development of more approximate computational methods and for the validation of their accuracy. Our group has a long tradition in the development of benchmark databases of the calculations of non-covalent interactions, and our data sets such as the S66 set became a de facto standard in the field. New datasets published within our project Non-Covalent Interactions Atlas (www.nciatlas.org) are now the world's largest database of the highest-quality benchmark data for non-covalent interactions. The goal of this project is to expand this reference database to additional classes of interactions, with special focus on interactions of organic molecules and biomolecules. The work will also include testing of existing computational methods and possibly their reparametrization on the new data.

Structure and Dynamics of RNA - 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 a 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 non-canonical 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 - prof. RNDr. Jiří Šponer, DrSc.

The topic of the thesis will be the 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, a 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 - 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.

Understanding biology at an atomic resolution - Prof. 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

Annotation of PhD topics in Nanomaterial Chemistry (Guarantor: doc. RNDr. Robert Prucek, Ph.D.)

Theoretical study of charge transport in nanostructures - 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 - 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.

Catalytic activity of metal nanoparticles and their composites for applications in energy production - doc. RNDr. Libor Kvítek, CSc.

Metal based nanomaterials are frequently studied due to the number of their unique properties. Mainly their catalytic activity is important in the chemical industry, which is primarily associated with a high ratio of atoms or molecules on the surface of the particle to its volume. Current developments in the field of nanotechnologies for energy applications are related directly to this high catalytic activity of nanomaterials. In addition to research aimed at development of new power generation systems, either chemically (electrochemical cells) or solar energy conversion, many research teams are also focused on energy conservation in energy-rich compounds. One such reaction that allows the energy to be stored for later use while eliminating some of the unfavorable carbon dioxide emissions is the reduction of this fossil fuel combustion product to produce many organic compounds for reuse in the energy industry or in the chemical industry. Carbon dioxide can be reduced by hydrogen to form a series of hydrocarbons and other organic compounds, typically methanol. This reaction uses similar catalysts as well-known Fischer-Tropsch synthesis which proceeds efficiently with the aid of metal-based catalytic systems. Long-term experience in the research of catalytic activity of metal nanomaterials at laboratories of Department of Physical Chemistry UPOL and RCPTM has recently led to the development of an efficient composite nanocatalyst for this reaction based on copper nanoparticles bound to nanostructured iron oxide. The first tests of this catalyst, in collaboration with the catalytic group of Dr. Vajda at Argonne National Laboratory (Chicago, USA), showed high activity of this catalyst for hydrocarbon production. Further research will be carried out using a PID micro-reactor for study of heterogeneous catalysis in a gaseous reaction system linked to a GC/MS analytical instrument. The main aim of this PhD thema is focus on the research and development of the catalytic system based on nanoparticles of noble metals combined with iron oxide nanoparticles with high catalytic activity for low-temperature (up to 300 ° C) hydrogenation of carbon dioxide to produce energy-rich compounds usable in energetics and chemical industry.

Graphene and Graphene Derivatives - 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 the 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, dispersibility etc.), understanding the strength and nature of noncovalent interactions to graphene and graphene derivatives, application of graphene derivatives in sensing, catalysis and energy storage.

Nanomaterials for biological applications - doc. RNDr. Ales Panacek, Ph.D.

Nanostructured materials are unique due to specific physicochemical properties, which are also reflected in the specific interaction with living organisms, thanks to which nanomaterials exhibit unique biological properties. The useful properties of nanomaterials with biological properties are wide and can be used, for example, in medicine to treat or diagnose diseases, biologically active nanomaterials can be used in industries or environmental applications to remove unwanted biological, especially microbial, contamination. A typical example is silver nanoparticles, which have high antimicrobial activity, which can be used in the treatment of microbial infections, including those caused by highly resistant bacterial strains in which treatment with conventional antibiotics fails. On the other hand, it is necessary to take into account the possible adverse biological effects of nanomaterials in the interaction with biological systems, which may occur precisely due to their unique and unusual biological properties. The study of the mechanism of interaction of nanomaterials with biological systems at various cellular levels and their use for biological and medical applications thus represents a very interesting and diverse field of scientific research.

Nanomaterials for catalytic applications - doc. RNDr. Ales Panacek, Ph.D.

Due to their specific physicochemical properties, noble metal nanoparticles show high chemical activity, in particular high catalytic activity. The catalytic effects are due to the chemical nature of the metals themselves, and in addition the nanoscale and morphology of the particles of these metals can be increased, leading to a huge increase in the surface area of ​​the metal necessary for efficient heterogeneous catalysis. Nanoparticles of group I B metals show high catalytic activity especially in redox reactions, platinum group metals and related metals are then highly effective in reactions involving hydrogen, especially with regard to the synthesis of simple hydrocarbons and their derivatives (eg Fischer-Tropsch synthesis). In the field of catalytic applications, research and development can focus mainly on the synthesis and development of highly catalytically effective nanomaterials based on metals and their compounds applicable e.g. to environmental technologies (e.g. redox reactions and liquidation of pollutants), or in industrial chemistry in many chemicals. processes (ethylene oxide production, Fischer-Tropsch synthesis) or in the field of energy technologies (CO2 reformation to methanol, highly active electrodes for fuel cells). However, practical applications of nanomaterials are often accompanied by aggregate instability of metal nanoparticles or limited possibility of separation after the reaction in real application systems. One way to prevent these side effects is to anchor the metal nanoparticles to selected inert substrates. Examples are natural aluminosilicate materials, metal oxides or magnetic materials such as iron oxides, which further facilitate the magnetic separation of the catalyst after the reaction.

Preparation of nanoparticles and nanocomposites for catalytic applications - doc. RNDr. Robert Prucek, Ph.D.

Current developments in the field of nanotechnologies are moving from the preparation and use of isolated nanoparticles to systems where they are firmly captured on a suitable substrate (colloidal particles, microparticles or macrosystems). Such composites exhibit unique physicochemical properties, different from the nanoparticles themselves. In addition to the increased aggregate stability of nanoparticles, there is often a synergistic effect of improving the physicochemical properties of the mentioned materials (e.g. catalytic activity, optical properties, separation, aggregate stability, etc.). The aim of this work will be research and development in the field of preparation, characterization and application of nanoparticles of precious metals (copper, silver, gold, platinum, palladium, etc.) or their compounds. The research area will focus on the development and optimization of methods for the preparation of nanoparticles and nanocomposites based on these metals and their compounds (in the form of aqueous dispersions, self-organized layers or immobilized particles on carriers such as: SiO2, Al2O3, ZrO2, FexOy, glass, quartz, etc. .) including their characterization (size, morphology, stability, etc.). The mentioned materials will then be studied and tested in terms of their effectiveness for the purposes of heterogeneous catalysis or spectroscopic applications (surface-enhanced Raman spectroscopy). In the field of catalysis, micro or nanoparticles or nanocomposites are used on a very large scale in the field of organic synthesis (Ullmann synthesis, Fischer-Tropsch synthesis, ammonia preparation (Haber-Bosch reaction), hydrogenation or dehydrogenation reaction, Suzuki reaction, etc.), further in the field of very intensively developing areas such as fuel cells, photovoltaics, photocatalysis, photochemical water splitting, catalysts in automobiles for the oxidation of unburned hydrocarbons, carbon monoxide and the reduction of nitrogen oxides. Another important application of these materials is their use in advanced oxidation processes used for remediation technologies used for wastewater treatment and old environmental burdens. A common and common requirement for industrial application is their ability to degrade toxic and often persistent organic pollutants, which resist or directly deactivate the traditionally used biological stage, which forms an integral part of most wastewater treatment plants.

Preparation of nanoparticles and nanocomposites for spectroscopic applications - doc. RNDr. Robert Prucek, Ph.D.

Surface-enhanced Raman spectroscopy is one of the modern analytical techniques for detecting very low concentrations of substances. As a result of the constant development of Raman spectrometers, these instruments are becoming more affordable, and as a result, the number of these instruments is expanding not only in scientific workplaces, but especially in these laboratories to become a common part of commercial laboratories. A very important area where these devices can be found, whether in the form of classic or especially mobile versions, are selected units of the police, fire brigade or army, where these instruments are used to identify flammables, drugs, explosives, etc. Raman spectroscopy has a very significant potential, which predestines it for future expansion into many areas of human activity (rapid and sensitive detection of explosives, drugs, or detection of markers for disease determination, toxicology, forensic analysis, etc.), so the goal will be reproducible preparation of effective reliable, easy-to-use substrates based on silver and gold.