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Molecular chemical physics and sensorics
Doctoral Programme,
Faculty of Chemical Engineering
The aim of the doctoral study programme Molecular Chemical Physics and Sensors is to prepare highly qualified specialists in the interdisciplinary fields of molecular chemical physics and sensorics. The main areas of study of this programme are related to knowledge of quantum physics and quantum chemistry, optics, electronics, vacuum physics, spectroscopy, modelling of molecules and molecular processes, and theoretical and experimental methods of studying nanostructures. As part of this study, PhD students will be prepared for independent research work in laboratories as well as for managerial positions at various levels, both in the public institutions and in the private sector. The aim of the doctoral study programme is to deepen and broaden students' knowledge so that they can combine experimental work with computational models and analyze large multivariate datasets with the aim of qualified evaluation of information and formulation of appropriate conclusions. CareersGraduates of the doctoral study programme Molecular Chemical Physics and Sensorics will have both deep theoretical knowledge and extensive experimental experience in chemical-physical disciplines (quantum theory, optics, optoelectronics, spectroscopy, computational chemistry and modelling of molecular and supramolecular systems, etc.). Graduates will be prepared for highly creative work in interdisciplinary teams dealing with molecular chemical physics, sensorics, spectroscopy, computational chemistry and nanostructure research, they will be able to communicate with experts in the field of measurement and control technology, physical and analytical chemistry, computer data evaluation or material research. Graduates will have extensive experience in communicating specialised knowledge in the form of written / electronic texts, especially in English, as well as oral and poster presentations. Programme Details
Ph.D. topics for study year 2026/27Ab initio modeling of charge-carrier mobility in polymorphic of organic semiconductors
AnnotationLarge structural and chemical variability of organic semiconductors raises the need for computational screening of the electronic structure of the bulk phase and related material parameters, such as the band gap or the charge-carrier mobility. The latter property remains rather low for most existing organic semi-conductive materials when compared to the traditional inorganic crystalline platforms of the optoelectronic devices. Understanding relationships among the bulk structure, non-covalent interactions therein, electronic properties, conductivity, and the response of all such properties to temperature and pressure variation will greatly fasten the material research in the field of organic semiconductors. This thesis will employ the established electronic structure methods with periodic boundary conditions, as well as fragment-based ab initio methods to map the cohesion of bulk organic semiconductors with the charge-carrier mobility is both crystalline and amorphous structures of these materials. Ab initio calculations and the Marcus theory will be used as the starting point for a detailed investigation of the impact of local structure variations, due to chemical substitution, thermal motion, or polymorphism on the conductivity of target materials. Predikce struktury proteinů z prvních principů: pohled na skládání proteinů jako na problém intramolekulární solvatace
AnnotationThe research goal is the development and implementation of an ab initio protein structure predictor (tentatively denoted QMLFold). QMLFold will couple an extension of the COSMO-RS solvation theory into 3 D space (this new method is denoted as 3D-COSMO-RS) with ML-based peptide potentials, recently developed in our group, and efficient sampling algorithms. The program should be independent of known protein structures, and as such, it shall be universal and versatile. The machine-learning component inside its algorithm – ‘ML’ in the QMLFold – will only be used to predict the “QM-quality” intramolecular free energies of the short peptide fragments constituting the protein chain. The paradigm-shifting idea behind QMLFold is embodied in the question of whether we can view protein folding as a ‘universal solvation problem’. Or rephrased as: “Can we consider a protein as an ensemble of chemically distinct entities – amino acid side chains, covalently linked by a “poly-glycine” backbone, which are solvated in themselves?” QMLFold may open new horizons in biocatalysis, metal-binding peptides (sensors), and might be a potential game changer in the area that is not amenable to AlphaFold3-like algorithms (medium-sized peptides, intrinsically disordered proteins, or peptides with xeno- amino acids). Ab initio refinement of cocrystal screening methods for active pharmaceutical ingredients
AnnotationModern formulations of drugs often rely on cocrystalline forms the crystal lattice of which is built from multiple chemical species, mainly an active pharmaceutical ingredient and another biocompatible compound being called a coformer in this context. These cocrystalline drug forms often exhibit higher solubility, stability or other beneficial properties when compared to crystals of pure active pharmaceutical ingredients. Since molecular materials tend to crystallize in single-component crystals rather than in cocrystals, the task of finding a suitable coformer for a given active pharmaceutical ingredient may be very tedious and labor demaning. To circumvent the costly experimental trial-and-error attempts, in silico methods can help to preselect a list of possible coformers offering a high probability of forming the cocrystal. Currently available methods focus on screening the electrostatic potential around the assessed molecules and empiric pairing of its maxima and minima for the individual molecules, which enables coformer screening with a fair accuracy for predominantly hydrogen-bonded molecules. This thesis will aim at incorporation of ab initio calculations of molecular interactions that will bring further improvements also for cocrystal screening of larger molecules with prevailing dispersion components of their interactions. Also the impacts of stechiometry variations and of the spatial packing of the molecules in the cocrystal lattice will be newly considered, greatly enlarging the applicability range of the current cocrystal screening procedures. Výpočetní návrh ligandů pro radioterapii
AnnotationTargeted radiotherapy based on metal radionuclide complexes is an important and rapidly developing approach in modern oncology. A key component of such systems is the chelator, which must provide high thermodynamic stability, kinetic inertness under physiological conditions, and an appropriate coordination environment of the metal center. This thesis focuses on the computational design and characterization of chelators based on peptidic ligands/frameworks for complexation of therapeutically relevant radionuclides, in particular 177Lu, 161Tb, 225Ac, and others. Density functional theory (DFT) calculations will be employed to study geometries, binding energies, and electronic properties of the complexes. In addition, paramagnetic NMR parameters will be calculated to support the interpretation of experimental NMR data, providing detailed insight into the structure and solution dynamics of paramagnetic metal complexes. Based on this analysis, new or modified ligand architectures will be proposed to optimize metal–ligand bonding, coordination geometry, and complex stability. The results will be discussed in the context of structure–property relationships relevant to rational radiopharmaceutical ligand design. Practical realizations will be carried out by our foreign collaborators. Molekulový design nových (metalo- and xeno-)peptidových architektur pro biokatalýzu
AnnotationEnzyme redesign or de novo design, often supported by computational algorithms, has matured over the last few decades and various successful examples can be found in the literature. They include changing a single amino acid in a protein to achieve catalytic activity in previously non-catalytic proteins, designing catalytic activity for established protein folds, cofactor preference redesign, or chemomimetic biocatalysis exploiting the synthetic potential of cofactor-dependent enzymes. We will utilize efficient conformational sampling based on the machine-learned quantum mechanical energies in implicit solvent (ML-QM(DFT)/COSMO energies) for the design of new and unprecedented oligopeptides which, after metal insertion, will mimic catalytic sites in the native scaffolds in metalloenzymes. Using the same methods and approaches, we will also explore the same question for peptides composed of xeno- (non-natural) -amino acids to unravel the unknown catalytic potential of metallo-xeno peptides or their small protein counterparts. With this, we may be able to open new horizons in biocatalysis and in the design of metallo-xeno peptides. Příprava a charakterizace kvantově-optických bionanosenzorů
AnnotationPhotoluminescent nanodiamonds represent a novel type of quantum biosensor that exploits changes in luminescent properties in response to external stimuli. Compared to classical sensors, they offer the benefits of high sensitivity and resolution but are often nonspecific. The aim of the project is to chemically functionalize these sensors for specific and sensitive detection in biologically relevant environments. To achieve this, the student will employ covalent surface modifications of nanosensors in a colloidal state and subsequently characterize them. The functionality of the constructed nanosensors will be verified using a quantum confocal microscope with advanced pulse sequences. The outcome of the project will be time-resolved, localized quantum detection of specific molecules. The expected knowledge of the applicant should be at the level of a completed Master's degree in the field of biophysics, chemical physics or physical chemistry. The work will be carried out by the Synthetic Nanochemistry team at the Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences. Radiation damage to DNA, experiment and theory
AnnotationThe project aims to study radiation damage to DNA on individual molecules using DNA origami nanostructures. The methodology developed in our laboratory [Sala et al. J. Phys. Chem. Lett. 2022, 13, 17, 3922] will be used to study the radiosensitization effect of nanoparticles on precisely defined DNA sequences. This basic research is focused on understanding the details of radiation therapy using gold nanoparticles with the potential for better targeting of therapy and development of new theranostic procedures. The student will become familiar with the preparation of DNA origami nanostructures and he/she will participate in experiments with ionizing radiation in collaborating laboratories in the Czech Republic and abroad. A significant part of the project will focus on theoretical modeling of the studied processes, especially using molecular dynamics tools and coarse-grained models. |
Updated: 20.1.2022 16:26, Author: Jan Kříž