Funded projects under the Grant Programme for SAS PhD students in 2025

The incompatibility of general relativity and quantum mechanics motivates the search for a quantum theory of gravity. Rather than attempting to build a complete quantum theory of gravity directly, one can instead ask what features of spacetime are accessible by probes that are simple quantum systems. A central tool in this endeavor is the Unruh-DeWitt detector, modeled as a two-level quantum system coupled locally to a scalar field, which provides an operational window on quantum gravitational effects. It has been shown that a static detector inside a hollow gravitational shell can distinguish global spacetime structure from local flatness on timescales shorter than the light-crossing time of the shell. Building on this foundation, I propose two research directions. The first is to investigate quantum-controlled Unruh-DeWitt detectors with temporal superposition inside hollow shells to explore enhanced sensitivity through quantum interference effects and indefinite causal order. The second is to develop operational criteria for detecting spacetime superpositions by examining detector responses to quantum superpositions of different shell configurations. This project will demonstrate that detector-based phenomenology can reveal quantum features of spacetime that go beyond the reach of classical protocols.

This project aims to construct a new generation of probabilistic models based on support vector machines. The support vector machines are a powerful tool for tackling non-linearity in decision boundaries and have shown strong empirical success in diverse domains. They were originally proposed to solve binary classification problem. Their extension to the multi-class setting is not immediate. There have been multiple non-canonical extensions proposed, both in non-probabilistic as well as in probabilistic setting, when one needs reliable probabilistic predictions. Existing probabilistic extensions are based on calibration or aggregation methods, but these are not yet fully understood and their theoretical guarantees are weak. By rigorous analysis of experiments on benchmark datasets, this project will investigate the circumstances under which novel modeling decisions yield improved calibration, interpretability, and predictive performance.

Transition metal oxides with distorted perovskite structures are heavily studied because their unique structure strongly links their orbital, electric, spin, and lattice properties, leading to diverse and technologically important phenomena like metal-insulator transitions, superconductivity, colossal magnetoresistance, multiferroicity or magnetocaloric effect. The ability to control and tune these interconnected degrees of freedom makes them ideal for developing new materials for advanced electronics and energy applications. The distorted perovskite structure is very tolerant to substitution at individual crystallographic positions, which opens up the possibilities of tuning the physical properties towards a higher application potential of these compounds, as well as the possibilities of a better understanding of the basic physical properties and processes. The goal of the work is to synthesize new solid solutions with the chemical formula RET1-xT'xO3 (RE = rare earth; T, T' = transition metal; 0 ≤ x ≤ 1), to characterize their basic physical properties with a focus on magnetism, multiferroicity, magnetocaloric effect and subsequently optimize their properties by heat treatment. For this purpose, various physical and chemical methods will be used, mainly the preparation of crystals by vertical floating zone method in an optical furnace with subsequent appropriate heat treatment, the characterization of samples by the methods of X-ray diffraction, scanning electron microscopy and thermogravimetry as well as the study of their properties by DC/AC magnetometry and heat capacity. The characterization of samples by X-ray photoelectron spectroscopy and electron-positron annihilation as well as the study of phonon states and dielectric properties in the context of magneto-electric coupling is expected within the framework of international cooperation in broader time horizon.

In multi-class classification problems, classifying an object becomes more challenging as the number of classes increases. One of the simplest techniques to solve 𝑘-class problems is to decompose it into 𝑘(𝑘 − 1)/2 pairs of binary classifiers using the one-vs-one technique. This results in a complete graph with 𝑘 vertices and 𝑘(𝑘−1)/2 edges, where each edge corresponds to a binary classifier. In graph theory, a spanning tree is a well-known example of a sparse graph. Our goal is to develop an algorithm to choose an optimal spanning tree to estimate the posterior probability for each class by coupling pairwise binary classifiers. The main advantage of this approach is that it is computationally much less expensive than existing coupling methods. Moreover, this benefit grows proportionally with the number of classes. For example, on the ImageNet dataset with 1000 classes, classification using a spanning tree would be approximately 500 times faster.

Nanomaterials, and in particular magnetic nanoparticles (MNPs), represent one of the most promising areas of contemporary research in nanomedicine. Owing to their unique physicochemical properties, they can serve as efficient drug carriers designed for targeted delivery. Moreover, they play a key role in magnetic hyperthermia, which is one of the promising therapeutic approach in the treatment of oncological diseases. In addition to MNPs, biodegradable polymer carriers, such as nanospheres based on polylactic acid (PLA), also have an important position in nanomedicine,. The combination of biodegradable polymeric nanospheres and magnetic nanoparticles enables the development of a multifunctional system capable of controlled drug release and localized activation through an external magnetic field. S-nitrosoglutathione (GSNO) will be used as a model drug in this project. GSNO serves as a reservoir and carrier of nitric oxide (NO) within the body and exhibits several biologically significant effects, including antithrombotic, anti-inflammatory, and antioxidant activities. Based on these properties, GSNO is a suitable candidate for evaluating the performance of nanosystems designed for targeted transport and controlled release of therapeutics. The project will be carried out in the following stages: (1) Optimization of the synthesis of biodegradable PLA-based nanospheres (PLA-NS), functionalization of nanospheres, conjugation of GSNO, and subsequent incorporation of magnetic nanoparticles; (2) Optimization of the preparation process of final PLA-NS+GSNO+MNPs nanosystem and its comprehensive physicochemical characterization using DLS, UV-Vis spectroscopy, SEM/TEM/AFM microscopy, FTIR, TGA, and magnetic measurements; (3) In vitro drug release studies and assessment of the hyperthermic properties of the prepared material; (4) In case of satisfactory in vitro results, in vivo application in an animal model (rat) will follow, enabling the monitoring of system distribution and therapeutic efficacy.

Amyloid aggregation refers to the structural transformation of native proteins into highly ordered fibrillar assemblies characterized by a cross-β-sheet secondary structure. Although amyloid fibrils are typically associated with amyloidoses, emerging research highlights their potential beneficial applications, particularly in the food and nutraceutical sectors, where they may serve as bioactive and food protein structures with enhanced nutritional properties. α-lactalbumin (α-LA), a whey-derived protein naturally present in mammalian milk, is a suitable model amyloid protein to study the potential use of amyloids in biotechnological applications. The project aims to identify and optimize conditions that promote the controlled fibrillization of α-LA, leading to the formation of amyloid fibrils and hydrogels. We will also explore their potential applications in the food industry, including as nutritional supplements with improved nutritional value or as carriers and stabilizers of hydrophobic compounds. To assess the stability and digestibility of α-LA hydrogels in the gastrointestinal tract, the prepared hydrogels will be subjected to an in vitro digestion assay in the presence of digestive enzymes. These studies will inform the feasibility of incorporating α-LA hydrogels into next-generation nutraceuticals.

Multiferroic materials, such as RMnO3, are increasingly in the center of scientific interest due to their potential in the field of spintronics and multifunctional devices. The project focuses on how structural changes induced by controlled changes in oxygen content and occupancy of crystal sites affect magnetic ordering and phase transitions. RMnO3 samples will be prepared as single crystals by the vertical floating zone method in an optical furnace under different atmospheric conditions (air, argon, oxygen), which will allow us to study the influence of magnetocrystalline anisotropy on magnetic and electrical properties and the possible coupling between them. Advanced analytical techniques such as X-ray powder diffraction (XRPD), scanning electron microscopy with EDX analysis, thermogravimetry (TG), differential thermal analysis (DTA), iodometric titration, SQUID magnetometry, AC calorimetry and vibrational spectroscopies (Raman, infrared), XPS measurements and electron-positron annihilation will be used to comprehensively study the correlations between structure, magnetic and thermal properties and oxygen content. The expected benefit of the project is a deeper understanding of the oxygen-induced change in magnetic and magnetoelectric behavior in RMnO₃ materials, which may contribute to the development of new functional materials for future electronic applications.

Shape coexistence in atomic nuclei is one of the current topics of fundamental research in nuclear physics. It is a phenomenon where energy states with different deformations are present within the same isotope. Although research in this area has advanced considerably in recent decades, we still do not have enough information to fully understand this phenomenon, so current research focuses on the systematic investigation of the structure of selected isotopes. A closely related topic is the study of isomeric, i.e. long-lived, excited states. One of the interesting areas of the isotope table from this point of view are neutron-deficient nuclei from the vicinity of the closed proton shell Z = 82. For several years, our group has been focusing on the study of such gold isotopes (Z = 79) with an odd number of nucleons. In 2022, the M20 experiment was conducted at the University of Jyväskylä under its lead, which investigated the isotope 179Au and aimed to extend previous results. Two years later, it was followed by the R66 experiment, which focused on heavier isotopes 181,183Au. During the project, we will analyse the measured data from the aforementioned experiments and, in collaboration with the University of Jyväskylä, we plan to carry out similar measurements aimed for 177Ir and possibly other odd-even isotopes of iridium. In 177Ir, which is isotonic to 179Au, the presence of several isomeric states, probably analogous to those in 179Au, has been confirmed. However, the data statistics were not sufficient to obtain much information. The study of iridium isotopes can therefore help us to understand the situation in gold isotopes better. The results of our work will contribute to general research on shape coexistence in this area.

The development of next-generation all-solid-state lithium batteries (ASSLBs) represents a significant breakthrough in energy storage technology, offering high electrochemical performance, improved safety, and greater sustainability, which can help achieve the goal of a carbon-neutral environment, compared to conventional lithium-ion batteries. However, for large-scale applications, it’s still hindered by interfacial resistance between the solid electrolyte and the electrode. It arises from poor physical contact, space-charge buildup, and side reactions, which all make lithium-ion transport less efficient. Reducing this resistance remains the bottleneck challenge for practical ASSLBs. To investigate this problem, we will use the well-established symmetric cell configuration, which allows direct study of interfacial behaviour. In this work, we propose a novel in-situ synthesis of a flexible Polyvinylidene fluoride (PVDF)/Li3InCl6 (LIC) composite as a function of temperature. High-energy laboratory operando wide-angle X-ray scattering (WAXS, Ag-22 keV) will track the structural evolution of the precursors to the final PVDF/LIC composite in real time, while simultaneously performing electrochemical impedance spectroscopy (EIS) to measure ionic transport. Together, it will provide a comprehensive understanding of both the material's structural evolution and its electrochemical dynamics. Our approach directly addresses the reduction of interfacial resistance. Although high-energy ball milling is effective for particle size reduction and homogeneous mixing, the pressures generated during milling are transient and non-uniform, which prevents the formation of continuous and stable interfacial contact. In our unique strategy, the precursors are initially compacted into a pellet under 400 MPa, achieving a highly dense and uniform microstructure. During the synthesis step, a constant load of 50 MPa is applied in combination with heating, providing a uniform static pressure. Under these conditions, PVDF and LIC interact to form a mechanically robust composite with continuous interfacial bonding, effectively eliminating micro voids and ensuring smooth pathways for lithium-ion transport. In this way, even though the electrode is unchanged, the novel synthesis electrolyte layer significantly improves interfacial contact and reduces overall resistance. The fabricated PVDF/LIC film will be tested in a symmetric cell with the configuration Li / LPSCl / PVDF-LIC / LPSCl / Li. The commercial LPSCl layers protect lithium metal and prevent side reactions. This setup allows us to study interfacial stability and ionic transport under realistic conditions. EIS will be used to measure both the bulk and interfacial resistance, as it can clearly separate the resistance from the electrolyte and the electrode interface. By performing EIS at various pressures and overtime, we can track the changes in interfacial resistance, indicating the mechanical and chemical stability of the PVDF/LIC composite. Both materials play important roles: PVDF provides flexibility for better contact, strong film-forming ability for mechanical strength, chemical stability with high-energy cathodes, and a high dielectric constant to promote lithium-ion transport. We chose LIC, as a benchmark halide solid electrolyte for its simple synthesis, strong electrochemical performance, moderate Young’s modulus, oxidative stability, and absence of toxic gas generation, making it highly suitable for practical systems. By combining these materials into a flexible composite, we aim to overcome key interfacial challenges and demonstrate a scalable approach for ASSLBs. The combined operando structural and electrochemical study will not only support this design but also offer insights that can be applied to other solid-state electrolyte systems.

The project is focused on a systematic investigation of a soft magnetic composite material based on iron powder with the addition of 2.5 wt.% mica, deposited onto the surface of iron particles using a resonant acoustic mixer (RAM) during continuous mixing for 24 hours. In this system, mica serves as an electrical insulator between the conductive iron particles. The primary objective of the project is the optimization of heat treatment parameters in order to increase the density and mechanical integrity of the composite while maintaining the electrical insulation function of mica and minimizing the formation of interparticle contacts. For the experimental part, a high-precision horizontal dilatometer DIL L75 (Linseis) will be employed, enabling continuous monitoring of dimensional changes in the samples throughout the entire thermal cycle. The dilatometric data will be correlated with the microstructural characteristics of the studied materials, analyzed by scanning electron microscopy (SEM) in combination with energy-dispersive X-ray spectroscopy (EDS). The methodology will also include measurements of electrical properties (DC resistivity by the four-point probe method), magnetic properties (coercive force in an open magnetic circuit), and elastic properties using the impulse excitation method.

The general aim of the project of the basic oriented type is preparation of bioabsorbable high strength Zn-based material with stable mechanical properties, acceptable corrosion rate and homogeneity, creep and fatigue performance, biological response, and at the same time feasible to be fabricated to thin sections, for the implantology. The anticipated applications of developed materials are inert endovascular stents (ES) and orthopedic internal fixators (OIF). The issue of intrinsic microstructural and mechanical instability significantly limits widespread of bioabsorbable Zn-based materials. The proposed project relies on the encouraging preliminary results of the material study conducted for the model material by our group recently. We introduced particular innovative pure Zn metal matrix composite (MMC) with ultrafine-grained (UFG) structure effectively stabilized by small portion of in-situ formed nanometric ZnO dispersoids, which was manufactured by an attractive, technologically feasible and economical powder metallurgy (PM) approach for the first time. It presented a promising group of novel materials, which has an immense application potential as a candidate for the fabrication of bioabsorbable medical devices. In general, the proposed project intends to comprehend and describe the various scientific phenomena active in this new group of material, in order to optimize i.e., to boost the performance of Zn+ZnO concept MMC, and bring it closer to the anticipated application.

The aim of this project is to develop an optimized system for integrating Phase Change Materials (PCMs) into residential building walls to enhance energy efficiency in the Slovak Republic and the European Union (EU). It combines laboratory testing, simulations, and building monitoring to identify suitable PCM types, 3D-printed encapsulations, and placement strategies tailored to local climates. A novel aspect is the use of additive manufacturing to enable cost-effective, scalable thermal storage. The project will quantify energy savings across seasons, validate models with empirical data, and assess economic feasibility. Outcomes will include technical guidelines to support sustainable building and retrofitting, directly contributing to EU Green Deal targets and national decarbonization goals.

The proposed project focuses on advancing seasonal thermal energy storage (STES) systems for energy self-sufficient buildings through the development of a novel storage tank filled with bio-based phase change materials (Bio-PCM), particularly sugar alcohols such as erythritol. Bio-PCMs provide high latent heat capacity and environmental compatibility, making them a sustainable alternative to conventional storage materials, but their low thermal conductivity limits efficiency. To address this challenge, the research introduces nature-inspired fin geometries designed to enhance heat transfer, accelerate charging and discharging, and improve long-term energy retention. The study will integrate three-dimensional numerical simulations with laboratory-scale experiments on a truncated-cone prototype to validate performance. The expected outcomes include improved reliability and efficiency of STES systems, seamless integration with solar energy infrastructure, and reduced dependence on external energy sources. Ultimately, this research aims to support the transition towards energy-efficient, low-carbon buildings and establish new design guidelines for sustainable TES technologies.

The aim of this project is to grow high-quality epitaxial Ga2O3 films on sapphire using patterned and off-cut substrates. Both can improve crystal quality of grown films. β-Ga2O3 can be grown homoepitaxially on native bulk Ga2O3 substrates and heteroepitaxially on foreign substrates. The main advantage of the former is superior crystal quality; the main disadvantage is the high cost, small size, and availability of native substrates. Although heteroepitaxial growth on sapphire offers affordable substrates, one of the drawbacks is a hexagonal symmetry of sapphire substrates which promotes presence of rotational domains (RD) in β-Ga2O3 and affect the crystal quality [1]. Therefore, by suppressing the rotational domains of β-Ga2O3 we can improve the crystal quality by reducing the number of differently oriented crystals and grain boundaries, which can cause scattering and lower mobility. This can be achieved by using patterned or off-cut sapphire substrates. In this project, we focus on the optimisation of the growth parameters for epitaxial β-Ga2O3 layers on patterned and off-cut substrates using MOCVD. We will use standard c-plane sapphire substrates with varying off-cut angle (up to10°) towards major crystal planes (e.g. m-, a-, r-plane). We will also perform comprehensive structural, morphological, optical, and electrical characterization of grown layers. Results on patterned and off-cut substrates will be correlated with reference samples prepared on standard on-axis c-plane sapphire substrates with off-cut angle of 0°.

Bed load sediment movement is a fundamental process that shapes river landscape and supports ecological health. Understanding these dynamics is critical for effective river management, especially in gravel-bed rivers where sediment transport governs channel stability and response to human impact. A key concept for this analysis is sediment connectivity, the degree to which sediment is transferred through a river system from sources to sinks. Processes such as entrainment, transport, deposition and resuspension are dictated by factors like slope, grain size, discharge and vegetation. This complex interaction produces a pattern of sediment routing that vary dramatically between events and across spatial scales. Quantifying and modelling the channel sediment transport process is critical and remains a scientific challenge, especially in large dynamic catchments. To address these challenges, this research applies to utilise the CASCADE (CAtchment Sediment Connectivity And Delivery) toolbox in MATLAB to analyse sediment dynamics in the Western Carpathians Ondava River catchment, which exhibits dynamic channel forms and coarse sediment pulses in East Slovakia, a gravel-bed river system. However, catchment-scale sediment transport remains poorly quantified. We use precise elevation models - DEMs (reproject, mask vegetation, extract stream network via TopoToolbox), assign grain-size and flow data to reaches, then run CASCADE connectivity modules. The presented model simulates network-scale sediment fluxes (“cascade”) using reach-scale transport formulas. We will integrate high-resolution DEMs, UAV/LiDAR-derived grain size survey, and discharge records into the CASCADE MATLAB toolbox. The study will involve collecting data such as grain size surveys and discharge records, followed by preprocessing, model setup, calibration and validation using the CASCADE toolbox. Sensitivity analysis will explore how different hydrological scenarios (e.g. varying flood magnitudes) affect sediment connectivity. We will compute connectivity metrics (e.g., indices of hillslope channel linkage) and perform sensitivity tests under varying hydrological scenarios (from low flow to extreme floods). Output will include spatial maps of connectivity “hotspots” and sediment source contributions, identification of key sediment sources and sinks, and insights into the impacts of anthropogenic alterations such as dams and land-use changes. Finally, the results will inform river management by identifying key erosion zones and deposition sinks, aiding our analysis will directly integrate catchment planning and the development of more robust transport models improved river management practices and information strategies, and advance the application of the CASCADE toolbox in gravel-bed river system, targeted restoration efforts, and the development of more robust sediment transport models in complex gravel-bed environments.

Grasslands are among the most species-rich habitats. Appropriate management is necessary to preserve their biodiversity and prevent their conversion to other types of ecosystems. In Central Europe, semi-natural grasslands are the most dominant, created mainly due to human activity and subject to controlled management practices to preserve and protect their species richness. Precise monitoring of grassland management practices is essential for the adequate protection of grasslands and for understanding their impact on the ecosystem, as different practices and their intensity have different effects on the conservation of biodiversity and ecosystem services. Remote sensing and satellite and aerial imagery availability have greatly facilitated and refined the monitoring of grasslands. The application of artificial intelligence techniques, particularly Deep Learning methods, offers new possibilities for analysing this data and detecting changes in landscape structure that might otherwise go unnoticed. This project aims to use Deep Learning methods to analyse current and historical aerial images to monitor grasslands, evaluate their management, and track their development over time. To achieve this goal, current digital and historical aerial images will be used, to which various deep learning methods will be applied and compared, making it possible to determine the current state and methods of grassland management and reconstruct their historical development. The project results will include precise information on the current management of grasslands and the historical development of grasslands, contributing to the long-term goals of projects Biodiversa2021-532 and APVV-21-0226.

The submitted project aims to improve the classification of the coraline algae by analyzing the possible use of new methodological procedures and diagnostic features. These are mainly oriented cuts and ultrastructure. Oriented cuts could help us capture more diagnostic features in samples and ultrastructure of calcified cell wall have potential to overcome differencies between classification of fossil coraline algae based on morphology and classification of recent coraline algae based on molecular data, as the first result in the article Auer and Piller (2020) already show to a high level of agreement with the molecular data. This methodological procedures will be tested by comparison of analysis of fossil samples of coraline algae from Central Paratethys (my samples and samples of my supervisor, plus new sampling) and analysis of recent samples of coraline algae from Caribbean Sea (sample from my supervisor).

Colorectal cancer (CRC) is one of the most common malignancies, characterized by high mortality, with the metastatic stage frequently associated with treatment resistance. In recent years, long non-coding RNAs (lncRNAs) have emerged as key players in tumor progression, metastasis regulation, and the maintenance of cancer stem cell populations. In our project, we will focus on two lncRNAs – NRAD1 (LINC00285) and CRNDE (Colorectal Neoplasia Differentially Expressed) – both of which showed increased expression in CRC tumor samples and cancer cell lines compared to healthy tissue. NRAD1 is associated with aldehyde dehydrogenase 1A3 (ALDH1A3) activity, epithelial–mesenchymal transition (EMT), and signaling pathways, including the Wnt/β-catenin and TGF-β pathways. CRNDE is an lncRNA with a well-characterized oncogenic role – promoting proliferation, migration, and chemoresistance through interaction with various miRNAs and epigenetic regulators. We aim to use CRISPR-Cas9 gene editing to generate deletion models of NRAD1 and CRNDE in CRC cell lines, enabling us to investigate their functional roles in cell proliferation, migration, apoptosis, and resistance to chemotherapy. The insights gained from this study could contribute to the identification of novel prognostic markers and therapeutic targets in colorectal cancer.

Pre-mRNA splicing is a crucial step in the regulation of gene expression. In this project, we plan to analyze a selected group of poorly characterized RNA-binding proteins to better understand their roles in splicing regulation in the model organism Schizosaccharomyces pombe. Based on our preliminary findings showing that these proteins form complexes with several splicing factors, we will validate and expand their interaction networks through additional affinity purifications and protein–protein interaction assays. Additionally, we will generate deletion mutants and perform transcriptomic analyses to assess how dysfunction of these RNA-binding proteins affects pre-mRNA splicing. Through this integrated approach, we aim to provide new insights into the molecular mechanisms controlling pre-mRNA splicing and gene expression regulation in S. pombe, with potential relevance to broader eukaryotic biology.

Adipose tissue represents a highly dynamic organ that, in addition to energy storage, plays a key role in thermoregulation and the energy homeostasis of the organism. In response to cold exposure, the activation of non-shivering thermogenesis, a process that occurs in both brown and white adipose tissue, significantly contributes to heat production at the cost of increased energy expenditure. Activation of this metabolic pathway is therefore considered a promising therapeutic approach for preventing and treating obesity. The activity of brown adipocytes and the browning of white adipose tissue are governed by a complex transcriptional regulatory network, whose key components include PR domain-containing 16 (PRDM16), peroxisome proliferator-activated receptor gamma (PPARγ), and peroxisome proliferator-activated receptor gamma coactivator 1-alpha (PGC-1α). However, numerous other transcriptional regulators involved in this process remain unidentified or poorly characterised. In a preliminary functional screening on murine immortalised brown adipocytes (iBAs), we identified several novel transcription factors with the potential to control mitochondrial activity and expression of thermogenic gene markers. Among them, CCAAT/enhancer-binding protein gamma (CEBPγ) showed consistent inhibitory effects on brown adipocyte function. Despite its structural similarity to other CEBP family members, CEBPγ remains largely unstudied in the context of brown adipose tissue function. CEBPγ lacks a canonical activation domain for recruiting transcriptional machinery, suggesting that it regulates gene transcription through its heterodimeric partner/s. This project aims to uncover the molecular mechanism of action and the role of CEBPγ in regulating brown adipocyte thermogenic activity, using genetic gain and loss-of-function studies in iBAs. We will primarily focus on identifying CEBPγ interaction partners and target genes to uncover a novel mechanism regulating brown adipocyte thermogenic activity.

Drug-induced gastrointestinal toxicity (DI-GIT) is a common adverse effect in clinical trials but remains poorly predicted in preclinical testing. Animal models, especially rodents, have limited translational value, with only ~6% of toxicological findings confirmed in humans (Shuler, 2017; Markus et al., 2021). This is due to interspecies differences, microbiome variability, and low-throughput study designs. Conventional in vitro models such as Caco-2 monolayers are widely used but lack critical features of intestinal tissue, including key transporters, metabolic enzymes (e.g., CYP3A4, CYP2C9, CYP2C19), and robust barrier function (Cui et al., 2020). Advanced 3D reconstructed tissues such as EpiIntestinal™ provide physiologically relevant structure and function, with superior correlation to human in vivo absorption (R² = 0.91 vs. 0.71; Ayehunie et al., 2018), while complying with 3Rs principles. This project will systematically compare Caco-2 monoculture, Caco-2/HT-29 co-culture, and EpiIntestinal™ using multi-endpoint profiling (transepithelial electrical resistance - TEER, cytokine release, viability, morphology, glycomic analysis). The novel Intesti-Rank (IR) scoring system, based on responses to five reference drugs and five endpoints, will provide a pilot concept index of predictive performance, which could contribute to more accurate and faster preclinical assessment of drug-induced gastrointestinal toxicity.

Post-traumatic stress disorder (PTSD) is a serious mental disorder that can develop after exposure to extremely stressful and traumatic events. Such events can induce long-term changes in stress-sensitive brain structures such as the hippocampus (HIP) and thus lead to reduced neurogenesis. Impairment in neurogenesis can contribute to the development of affective disorders that are closely linked to PTSD as well as impaired memory processes and fear regulation. Antipsychotics are drugs used for treatment for PTSD. According to published studies, aripiprazole a third-generation antipsychotic drug can exert neuroprotective properties and promote neuronal regeneration and neurogenesis. Given the existence of the gut-brain axis, adverse factors such as stress or poor lifestyle have been linked to the development of several mental diseases. New studies show a link between the imbalanced gut microbiome and PTSD as well. Antipsychotic drugs may alter the composition and diversity of gut bacteria, while the microbiome itself may influence the effectiveness of antipsychotics. Therefore, the aim of this project is to investigate whether administration of aripiprazole and modulation of the gut microbiome by probiotics can influence the negative consequences of PTSD, in particular neurogenesis in the hippocampus and subventricular zone. Obtained results may contribute to a better understanding of the pathophysiology of PTSD and provide new insights into the potential therapeutic strategies.

Intrinsically disordered proteins (IDPs) are distinguished by a dynamic network of interactions between various parts of their molecule, which are much less stable than those in globular proteins. Tau protein, the object of our study, is an IDP that aggregates and propagates pathology in tauopathies - a group of human neurodegenerative diseases. Although the structures of tau aggregates found post mortem in brain have been resolved by cryoelectron microscopy, the structural basis of tau aggregate formation remains incompletely understood. Specifically, the role of transient intramolecular interactions in tau underlying tau pathophysiology has not been elucidated yet. This project aims to identify short-lived intramolecular motifs within tau, which may act as determinants of both physiological and pathophysiological behaviours of tau. To achieve this, we will pursue two complementary strategies. We will characterize crystallized complexes of tau filament core fragments with several filament-specific monoclonal antibodies. In parallel, we will mutate the prototype of filament core, tau297-391 (dGAE), in positions S305 and D387 known to participate in short lived motives, to scrutinize their role in aggregation. This knowledge might contribute to the development of new therapeutic approaches for tauopathies.

Although testicular tumors are rare and highly treatable malignancies, the unexplained rising incidence has been accompanied by an increase in the proportion of patients exhibiting resistance to cisplatin (CisPt), the primary therapeutic agent for this disease. Elucidating the differences between CisPt-sensitive and -resistant cells is therefore critical. It is well established that carcinomas can reprogram their metabolism to survive under the adverse conditions of a chemotherapy-influenced tumor microenvironment. Lipid metabolism, in particular, plays a central role in this adaptation, providing cancer cells with multiple survival advantages. Investigating lipid dynamics, especially through the study of lipid droplets, whose accumulation is frequently observed in chemoresistant cancer cells, offers valuable insights into mechanisms of chemoresistance and may inform the optimization of therapeutic strategies.

Metabolic dysfunction-associated steatotic liver disease (MASLD) affects nearly 40% of the global population, yet no pharmacological therapy is approved. A deeper understanding of the molecular events driving its progression is therefore urgently needed. Activation of hepatic stellate cells is a critical step toward fibrosis and irreversible liver injury. This process is largely governed by TGF-β signaling and mitochondrial dysfunction, particularly altered ATP production and reactive oxygen species (ROS) generation. Our preliminary findings identify GPR180, a membrane receptor involved in energy metabolism, as a potential regulator of both mitochondrial activity and TGF-β signaling in multiple cell types. We hypothesize that GPR180 mediates stellate cell activation and thereby contributes to MASLD progression. Using cultured primary human stellate cells (HHSC), this project will assess how modulation of GPR180 expression affects cell phenotype, such as activation markers expression, extracellular matrix production, cytokine release, mitochondrial function, and TGF-β pathway activity. This project will uncover the role of GPR180 in HHSC activation, which can be applied in development of therapeutic agents in MASLD.

The project is focused on the use of CRISPR/Cas9 systems to modulate the tumor suppressor gene ARID1A at the epigenetic level, whose loss or mutation increases tumor sensitivity to selected targeted therapies. As part of the work, we will design and validate plasmid constructs capable of inhibiting ARID1A gene expression. Their effects will then be compared with natural mutations and gene knockout in pancreatic cancer cell lines. Comprehensive molecular and functional analyses will be conducted to assess the cellular response to selected therapeutic agents. The aim is to determine whether epigenetic modulation can induce a similar therapeutic response as gene loss itself, which could represent a novel approach to personalized cancer therapy.

Small nuclear RNAs (snRNAs) are essential components of the major and minor spliceosomes and play a key role in pre-mRNA splicing. Although RNU genes do not code for proteins, their structural and functional integrity is crucial for the accurate regulation of gene expression. Pathogenic variants in RNU4-2, RNU5A-1, RNU5B-1 and RNU4ATAC genes have predominantly been reported in individuals with neurodevelopmental disorders, often presenting with cognitive deficits, delays in development and psychomotor skills, and, in some cases, additional sensory impairments such as hearing or vision loss. The proposed project will focus on a cohort of approximately 92 probands affected by syndromic hearing loss, in whom previous molecular-biological analyses have failed to identify the underlying cause of the condition. The aim is to explore the presence of pathogenic variants in the snRNA genes RNU4-2, RNU5A-1, RNU5B-1, and RNU4ATAC, which may contribute to complex clinical presentations. Given that whole-exome sequencing lacks adequate coverage of these non-coding regions, we will employ targeted PCR amplification followed by Sanger sequencing to ensure accurate variant detection. Through this approach, the study aims to expand current understanding of genetic variation in syndromic hearing loss and assess the role of spliceosome-associated snRNA genes as potential contributors. The findings may provide novel insights into the molecular basis of these disorders and enhance diagnostic outcomes for patients with previously unexplained genetic aetiologies.

Rheumatoid arthritis (RA) is a chronic autoimmune disease marked by persistent inflammation, progressive joint destruction, and bone resorption. Dysregulation of the receptor activator of nuclear factor kappa-B ligand (RANKL) pathway plays a central role in these processes. Current therapies, although effective, are often limited by adverse effects and incomplete disease control, highlighting the need for novel supportive strategies. This project investigates the potential of α-phellandrene, a natural cyclic monoterpene with anti-inflammatory properties, in the adjuvant arthritis rat model. Its effects will be assessed as monotherapy and in combination with sub-therapeutic methotrexate. The evaluation will include biometric parameters, inflammatory cytokines (IL-6, IL-17A), and plasma RANK/RANKL concentrations measured by ELISA. By exploring both systemic inflammation and bone resorption mechanisms, the study aims to provide new insights into the pharmacological actions of α-phellandrene and its potential role as an adjunct therapy in RA management.

Rheumatoid arthritis (RA) is a chronic autoimmune disorder characterized by persistent synovial inflammation, cartilage degradation, and progressive bone erosion. It presents with painful, swollen joints, morning stiffness, and gradual functional decline. Beyond articular damage, RA is associated with extra-articular complications affecting multiple organ systems, contributing to morbidity, reduced quality of life, and increased mortality. Its pathogenesis is multifactorial, involving genetic predisposition, environmental triggers, and immune dysregulation, with additional factors such as microbial infections or vascular injury also implicated. This complexity underscores the challenge of fully understanding RA and developing effective therapies. This study aims to advance therapeutic strategies for RA and its extra-articular manifestations by investigating the efficacy of crocin and β-cryptoxanthin in an adjuvant-induced arthritis model. Crocin and β-cryptoxanthin will be evaluated both as a monotherapy and in combination with a sub-therapeutic dose of methotrexate (0.3 mg/kg) to assess potential synergistic benefits. Key biochemical and immunological parameters will be assessed, including γ-glutamyl transferase (GGT) activity in spleen and joint tissues, plasma concentrations of interleukin-1β (IL-1β), monocyte chemoattractant protein-1 (MCP-1), and transforming growth factor-β1 (TGF-β1), as well as oxidative stress markers. The findings are expected to provide new insights into the potential of crocin and β-cryptoxanthin as an adjunctive therapy for RA and its systemic complications.

The SERCA calcium pump plays an important role in maintaining calcium homeostasis in cells. One of the endogenous ligands that modulates SERCA activity is ATP. ATP can also bind outside its active site in the cytoplasmic N domain of the enzyme, namely to the so-called modulation sites. To clarify the modulatory effect of ATP, it is important to identify these sites, which will make it easier to clarify the allosteric pathways and the mechanism of action of allosteric activators of SERCA. The aim of the project is therefore to use molecular modeling and molecular dynamics methods to find probable modulation sites for ATP and to determine the effect of ATP binding on the dynamics of the SERCA molecule.

Athletes in contact sports are frequently exposed to collisions, falls and blows to the head that may result in both acute and chronic neurological impairments. Recent evidence suggests that history of suffered head traumas together with high exposure of repetitive head impacts increase the risk of developing various neurodegenerative disorders, such as chronic traumatic encephalopathy or Alzheimer’s disease later in life. The main aim of our study is to explore the molecular processes associated with nonconcussive repetitive head impacts (RHI) in elite female football players. Using a transcriptomic approach, we aim to identify differentially expressed circulating microRNAs (miRNAs) in response to repetitive low-intensity headers and compare the miRNA expression profiles with control athletes without head impacts. Furthermore, integration of miRNA profiles with neuroprotein markers, precise training metrics, cognitive data and the use of state-of-the-art bioinformatic tools will enable detailed understanding of involved signalling pathways after RHI, while controlling for the effect of physical exercise. The outcomes of this project may be highly informative for future design of studies exploring the chronic effects of RHI in exposed populations.

Ryanodine receptor (RyR) is a large intracellular Ca²⁺-release channel essential for excitation–contraction coupling in muscle cells. The skeletal isoform (RyR1) plays a key role in muscle physiology. Many disease-causing mutations in RyR1 perturb its Ca²⁺/Mg²-dependent regulation, leading to serious disorders such as malignant hyperthermia and multiple myopathies. Understanding molecular mechanisms of RyR regulation is crucial for developing targeted therapies, but direct experimental characterization is difficult, given the channel’s size and complexity. In this project, we will use computational structural biology to address the mechanism of selected RyR1 mutations (R4736W, R4736Q, F4733D, G4732E) observed in patients suffering from MH. We will base our models on high-resolution cryo-EM structures of RyR1 and build atomic models of the WT and mutant channel core in different functional states. Extensive all-atom molecular dynamics (MD) simulations will map the key intra- and inter-domain interactions, and reveal how binding at regulatory sites (activating and inhibitory Ca²⁺ sites, ATP binding site) influences the channel pore. These analyses will reveal the network of allosteric couplings that mediate RyR activation and inhibition. We will compare the dynamics of wild-type and mutant RyR1, quantifying how each mutation disrupts the allosteric signaling pathways. The insights gained will clarify the molecular basis of RyR dysregulation and may guide future therapeutic strategies for RyR-related muscle diseases. The project capitalizes on recent advances in computational methods that enable not only bioinformatic and structural analyses of proteins, but also extend the scope of molecular dynamics (MD) simulations to very large systems such as multimeric, membrane-embedded ion channels. It builds on the recent findings of our team that demonstrated a direct connection between the allosteric pathways of the RyR1 core and its ligand-dependent regulation and enabled interpretation of the structural and functional data of mammalian RyR channels on common grounds.

Sporulation is the simplest cell differentiation process, which allows Bacillus subtilis to adapt to changing environmental conditions by producing highly resistant spores. Sporulation is connected with a fascinating process called engulfment, where the mother cell engulfs the forespore, internalizing the latter as a-cell-within-a-cell. Peptidoglycan degradation and synthesizing machinery and SpoIIQ-SpoIIIAH protein complex are crucial parts of engulfment process. SpoIIIAH is expressed in the mother cell and its gene is part of the spoIIIA operon (SpoIIIAA-SpoIIIAH). SpoIIQ is produced in the forespore. SpoIIIAH and SpoIIQ interact through their extracellular domains across the intermembrane space tracking the migration of the engulfing mother cell membrane and stabilizing the double membrane structure. Based on crystal structure, mutations in the interface domain of spoIIQ gene were prepared. It seems from our preliminary results that these site-directed mutations in spoIIQ do not have major effect on sporulation process. Spores are formed efficiently from cells in which the SpoIIQ-SpoIIIAH interaction is disrupted. We hypothesize that the key role of SpoIIQ may be recruitment to the septum other proteins than SpoIIIAH, such SpoIIE from the forespore side and GerM and the other SpoIIIA proteins from the mother cell side. The project's additional goal is to search for other potential interacting partners of SpoIIQ or SpoIIIAH, respectively, involved in the engulfment and sporulation process.

Cardiac arrhythmias are among the leading causes of mortality worldwide, and their onset is often associated with ischemia-reperfusion (I/R) injury. During reperfusion, there is a sharp increase in reactive oxygen species (ROS), leading to oxidative stress and impaired cardiac function. One of the key mechanisms involved is mitochondrial dysfunction, particularly oscillations in the mitochondrial membrane potential (ΔΨm), which are directly linked to the development of arrhythmias. Mitochondrial chloride channels, historically known as IMAC or mCS, play a significant role in this process. These channels modulate ΔΨm, especially under conditions of oxidative stress. Elevated ROS levels induce synchronized depolarizations that promote arrhythmogenesis. Pharmacological interventions targeting these channels—particularly through ligands of the mitochondrial translocator protein (TSPO), such as 4-chlorodiazepam (4Cl-DZP)—have shown cardioprotective effects. TSPO ligands may influence the activity of chloride channels, suggesting their therapeutic potential. Studies have demonstrated that TSPO ligands inhibit these channels at low concentrations. On the other hand, one isoform of the chloride intracellular channels (CLIC) has been localized to the inner mitochondrial membrane, and its inhibition using indanyloxyacetic acid (IAA-94) has been shown to increase the risk of myocardial infarction by reducing the mitochondria’s ability to retain calcium. Multiple findings point to a functional interaction between TSPO and mitochondrial chloride channels, and their modulation represents a promising strategy for preventing reperfusion-induced arrhythmias. The aim of the study is to compare the effects of substances that inhibit mitochondrial chloride channels, specifically the CLIC channel inhibitor IAA-94 with the effects of TSPO ligands on mitochondrial function and morphology.

Furan-based monomers derived from renewable resources such as furfural, 2,5-furandicarboxylic acid, and 5-hydroxymethylfurfural represent a promising class of bio-based alternatives to petroleum-derived monomers. Despite their sustainability and synthetic versatility, the homopolymers of furan-based monomers often suffer from poor solubility and limited tunability in amphiphilicity, which restricts their application in biomedical fields. To overcome these limitations, this project proposes the copolymerization of furan-based monomers with hydrophilic monomers (poly (ethylene glycol) methacrylate, PEGMA 360). According to the literature, this strategy is expected to yield amphiphilic copolymers capable of self-assembling into nanoparticles suitable for drug delivery applications. The hydrophobic segment of the copolymer will form defined domains that serve as a core for the encapsulation hydrophobic drugs, while the hydrophilic part (PEGMA 360) will enhance water solubility, colloidal stability, and biocompatibility.

The proposed project focuses on the modification and functionalization of clay minerals from the smectite group using amino silanes with varying chain lengths and different functional groups. Due to their layered structure and ability to expand the interlayer space, smectites offer significant potential for intercalating various molecules. Additionally, their surface active sites enable easy interaction with other molecules. The main goal of the project is to optimize the preparation of silane-modified smectites for their application as selective adsorbents for dye molecules. The research will investigate the influence of the molecular structure of the organosilane (e.g., chain length, presence of functional groups in the amino silane) on the structural characteristics of smectites and, subsequently, on the adsorption properties of these materials. Optimization of the adsorbent preparation process will include studying the effects of solvent type, pH, and silane amount. In the final stage, the adsorption efficiency of the optimized organoclays for model pollutants (dyes) will be evaluated under controlled conditions. The study aims to establish a relationship between structural changes and adsorption properties, contributing to the development of advanced materials for environmental applications.

Ticks are hematophagous ectoparasites that transmit a wide range of pathogens, including bacteria, viruses, and protozoa, posing significant threats to human and animal health worldwide. Their success as vectors relies on tightly regulated physiological mechanisms that enable blood feeding, off-host survival, and reproduction. In recent years, the geographic expansion of ticks across Europe, driven by climate change, has raised public health concerns by facilitating the spread of tick-borne pathogens into previously unaffected regions. Despite growing ecological and epidemiological knowledge, the molecular regulation of tick physiology remains unexplored. Among the key regulators of physiological and behavioural functions in arthropods are neuropeptides, including RYamide, which has been implicated in nutrient-dependent control of feeding and host-seeking behaviour in insects. Although its role has been described in multiple insect models, no functional or expression data have yet been reported in ticks, leaving its potential involvement in tick physiology entirely unresolved. Since RYamide is expressed in the tick midgut, which is the central site of blood digestion, activation of digestive enzymes, and a reservoir for pathogens, its study may provide novel insights into how digestive regulation is linked to vector competence and the efficiency of pathogen transmission.

In Slovakia, bladder cancer (BC) is diagnosed in approximately 800 new patients each year. BC is often painless, which can make early detection difficult. To diagnose BC, doctors use urine tests, imaging methods (especially ultrasound and CT), and in cases of suspected tumors, cystoscopy with biopsy for histopathological examination. However, to minimize health risks for the patient, it would be beneficial to have non-invasive methods based on liquid biopsy that enable even faster and more reliable diagnosis. Considerable attention is being devoted to the research of BC biomarkers present in blood or urine. In addition to genomic and proteomic markers, glycomic biomarkers are also being studied, as aberrant glycosylation is one of the hallmarks of cancer. The aim of this project is to investigate potential glycan biomarkers of BC using the lectin microarray biochip method. This platform represents a sensitive and high-throughput method for detecting and analyzing changes in protein glycosylation. The project focuses on the development and optimization of the lectin microarray method to enable sensitive, rapid, and selective measurement of protein glycosylation in serum, urine, and tissue samples from BC patients, as well as serum and urine samples from a control group. The resulting glycosylation profiles will be compared within individual patients/controls, and the correlation between glycoprofiles of different sample types will be evaluated. Subsequently, the glycoprofiles of the different sample types will be compared between the group of BC patients and the control group. The obtained results will contribute to evaluating the potential of glycan biomarkers in BC diagnosis and will also lay the foundation for further research in this area.

High-entropy perovskite oxide-based thermoelectric materials (HEPO) have gained significant attention due to their structural flexibility, stability, and potential for sustainable energy applications. However, up to date, most studies have focused on HEPOs containing lead or rare-earth elements, limiting their scalability and sustainability. This project aims to develop novel, lead-free HEPOs with four- and five-component equimolar A-site cations in the ABO₃ structure, while systematically investigating the role of heterovalent Nb⁵⁺ and homovalent Zr⁴⁺ substitutions at the B-site. Two compositions have been identified through literature analysis and structural-property considerations: Ba₀.₂₅Ca₀.₂₅Sr₀.₂₅La₀.₂₅Ti₁₋ₓNbₓO₃ (HEPO1) and Ba₀.₂Ca₀.₂Sr₀.₂La₀.₂Nd₀.₂Ti₁₋ₓZrₓO₃ (HEPO2), with substitution levels of x = 0, 0.005, 0.01, and 0.05. Nb⁵⁺ and Zr⁴⁺ were selected due to their contrasting ionic radii and electronic configurations, which are expected to significantly affect lattice dynamics, microstructure, charge transport, and thermoelectric performance. This work seeks to elucidate the specific role of aliovalent and isovalent substitutions in tuning thermoelectric properties, thereby providing insights for the rational design of environmentally friendly, high-performance HEPOs.

The project addresses the use of agro-industrial processing waste (APPO) — specifically, berry pomace, which is rich in bioactive substances (polyphenols) — as feed, to reduce the environmental impact of endoparasitic infections on small ruminant farms. Infections caused by gastrointestinal nematodes affect a number of factors related to feed efficiency and utilisation, while contributing to increased greenhouse gas emissions, primarily in the form of methane. This project aims to investigate how locally available APPOs, such as berry pomace (e.g., from blueberries), can influence rumen fermentation and methanogenesis, and improve the health of lambs affected by endoparasitic infections. Using alternative sources of polyphenols contained in APPO could also help address the phase-out of anthelmintic drugs (chemotherapeutics). Using APPO could exemplify a circular economy, utilising locally available sources of bioactive substances within an agroecological approach to livestock production.

An escalation in antimicrobial drug resistance among pathogens has driven the need to develop alternative treatment methods. Photodynamic inactivation (PDI) represents a promising antibiotic-free antimicrobial approach that involves the administration of a photosensitising molecule (PS), which, upon activation by light of a specific wavelength, produces cytotoxic reactive oxygen species capable of inducing photodamage in microbial cells. Hydrogels have been demonstrated to be effective as delivery systems for PS in antimicrobial PDI. Despite increasing interest, PS-loaded hydrogels encounter several challenges, including limited light penetration, issues with the solubility, stability, and bioactivity of many PSs under physiological conditions. Moreover, achieving a uniform distribution of PS within hydrogels remains a significant challenge during fabrication. Expandable phyllosilicates are versatile materials capable of intercalating various compounds, thereby modifying their structural and functional properties. Due to their 2D layered structure and high surface area, they are considered ideal host matrices for constructing dye assemblies to enhance photochemical efficiency. This project focuses on developing a dual-carrier hydrogel nanocomposite system, employing smectite and hydrogel as carriers for the PS to enhance stability and better release profile. The smectites, particularly saponites (Sap), are modified with an organic surfactant that serves as the primary carrier for the photosensitising dye molecules. Specifically, this study selects phloxine B and Rose Bengal, which belong to the xanthene dye family, as the photosensitizers. These functionalised silicate particles are subsequently incorporated into hydrogel formulations commonly used in biomedical applications, particularly wound healing, to prepare the composite. This strategy aims to develop a multifunctional, multi-carrier nanocomposite with photoactive and antibiofilm properties, synergising the unique features of phyllosilicate minerals and hydrogels.

Mycobacterium tuberculosis (MTB) possesses a highly impermeable cell wall, made up of the mycolyl-arabinogalactan-peptidoglycan. While clinically relevant tuberculosis drugs, like ethambutol and isoniazid, target the biosynthesis of arabinan polymers and mycolates, respectively, their efficacy is increasingly compromised by the rise of drug-resistant strains. No current drugs target the biosynthesis of the galactan core, the other component of the cell wall. The two galactofuranosyl-transferases GlfT1, and GlfT2 catalyze the biosynthesis of galactans in MTB. While GlfT1 initiates the polymerization by the synthesis of a dimer of two Galf units, GlfT2 transfers additional Galf units from the donor substrate uridine diphosphate α-d-galactofuranose (UDP-Galf) onto a growing galactan chain. Thus, blocking these biological activities by identifying small molecule inhibitors could offer a novel approach to overcome the current limitations in the tuberculosis treatment due to the defensive role of the cell wall. Nevertheless, the development of such inhibitors is challenging due to the high selectivity of these enzymes for its donor substrate UDP-Galf (Figure 1a). Therefore, the understanding of the key interactions along the catalytic process of these enzymes will open new avenues for the identification of strong inhibitors. The main goal of this project is to identify and design potent transition state analogs to inhibit the activity of GlfT2 as potential drugs for the treatment of tuberculosis. In particular, this project will make use of two transition state (TS) structures at the active site of GlfT2 for the extension of the galactan polymer via β-(1→5) and β-(1→6) linkages (figure 1b), characterized via expensive quantum mechanics/molecular mechanics (QM/MM) calculations (Figure 1c), as initial queries for an extensive search of novel molecules. A combined structural and fragment-based screening protocol will be implemented: the TS scaffolds will be decorated with active fragments from curated databases, while the ZINC20 library (>1 billion compounds) will be explored through high-throughput machine-learning–assisted screening. A previous benchmarking with other targets by the fellow has shown to reduce the number of compounds to reachable number for traditional docking approaches in only one month (Figure 1d). Promising candidates will be filtered by ADME/Tox properties and structural features (e.g., absence of heavy metals or undesirable halogens), and the top few million docking poses will be prioritized using consensus scoring and pharmacophore constraints derived from the TSs. The most diverse hits will then undergo clustering (Tanimoto/Morgan fingerprints) to ensure chemical diversity, with the top candidate from each cluster subjected to molecular dynamics simulations and binding energy calculations. Finally, strong binders will be compared to the natural donor substrate (UDP-Galf) via pulling simulations to assess residence time and stability. Only compounds with comparable or superior computational binding profiles will be shortlisted for purchase and experimental testing. By explicitly incorporating transition state information into the screening pipeline, this project provides a systematic strategy for the discovery of selective GlfT2 inhibitors.

Squalene is a lipid with broad applications in medicine, pharmacy, and cosmetics. Traditionally, squalene is obtained from shark liver; however, this source is not sustainable in the long term. Intensive shark fishing significantly contributes to the loss of biodiversity, which has driven research increasingly toward squalene production using microorganisms, particularly yeasts, in which squalene naturally accumulates as an intermediate in the ergosterol biosynthetic pathway. In genetic engineering, the best-studied yeast, Saccharomyces cerevisiae, was initially the most commonly used; however, unconventional yeast species are now increasingly employed in biotechnological production. Although their genetic modification is often more demanding compared to the traditionally used S. cerevisiae, less known yeasts offer several key advantages, such as lipid accumulation, rapid growth, and the ability to utilize waste substrates, all of which critically impact the final production cost of squalene. Our goal is to employ molecular-genetic approaches to modify the metabolism of unconventional yeast species to enhance squalene overproduction. We are particularly focusing on the red yeast Rhodotorula toruloides.

X-ray absorption spectroscopy (XAS) enable to measure the electronic structure of complexes, which has led to advances in the determination of structure and function of catalysts, metalloproteins and coordination complexes. As XAS is becoming more accessible, interest in this technique continues to grow, which motivates the development of robust theoretical methods to interpret and predict the spectra. Traditionally, the electric-dipole approximation—assuming a spatially uniform electromagnetic field—has been employed to predict electronic absorption spectra (EAS), yielding reliable results in many cases. In X-ray regime, however, with wavelengths of comparable size to the molecule, this approximation is often not enough. Recent efforts have extended XAS theory beyond the dipole approximation, both in relativistic and non-relativistic contexts. Still, these developments are limited to closed-shell systems. The present project aims to develop the theoretical formalism required to generalize such methods for open-shell molecules in the relativistic framework. Once stablished, the method will be programmed into the ReSpect software package, providing researchers with a powerful tool to compute and analyze XAS spectra across a significantly broader range of molecular systems.

Meiosis is a specialized form of cell division that reduces the diploid chromosome set by half, enabling the formation of gametes or spores. In Schizosaccharomyces pombe yeast, deletion of the dbl2 gene results in aberrant meiotic DNA segregation, persistence of unresolved recombination intermediates, defective Rad51 recombinase clearance and spindle malfunctions. Similar to dbl2, rdh54 has been suggested to be important for formation and processing of meiotic recombination intermediates. Combined deletion of these genes intensifies segregation defects in both anaphase I and II, possibly caused by a physical tether between chromatids. We hypothesize that the defects are caused by abnormal retention of cohesin complexes on chromatids that act as a mechanical barrier hindering chromosome separation. This project therefore aims to explore the yet uncharacterized role of dbl2 and rdh54 in ensuring proper chromosomal segregation during meiotic progression in S. pombe, to provide broader insight into molecular pathways that safeguard genome stability.

Cartilage regeneration remains a critical biomedical challenge due to the mechanical mismatch between synthetic implants and native tissue, the limited availability and efficacy of cartilage-derived stem cell products, the reliance on invasive surgical procedures, and the difficulty of fully restoring both biological and mechanical function in damaged articular cartilage. Since the dynamic extracellular matrix (ECM) plays a central role in regulating cellular behavior, biomaterials that replicate its viscoelasticity and adaptive mechanics are highly desirable. In this project, we propose the development of injectable, shear-thinning hydrogels that combine dynamic covalent networks with permanent covalent crosslinks. A tannic boronate complex will serve as a fast, reversible “dynamic bridge” within a sulfonated chitosan, allowing independent tuning of the storage and loss moduli through the ratio of dynamic to permanent crosslinks. This strategy is expected to yield hydrogels with biomimetic mechanical properties, excellent injectability, and enhanced biological performance, providing a promising platform for minimally invasive cartilage tissue regeneration.

Honey is a complex natural product containing various phytochemicals that may influence the activity of endogenous enzymes, such as glucose oxidase (GOX), a key enzyme responsible for hydrogen peroxide generation and honey's antibacterial properties. This project aims to elucidate the role of honey phytochemicals in modulating GOX enzymatic activity in honey samples from diverse botanical origins and geographical regions of Slovakia and Armenia. The research will involve comprehensive characterization of GOX enzyme activity and phytochemical composition in honey samples, and will investigate how different experimental conditions influence these molecular interactions.

This project focuses on the design and synthesis of a series of BODIPY dyes with di-, tri-, and policationic structures for the preparation and study of hybrid materials based on saponite, a layered silicate. BODIPY derivatives are renowned for their exceptional photophysical properties, including strong fluorescence, high photostability, and tunable absorption and emission spectra. By introducing cationic and other functional groups, we aim to enhance their interaction with negatively charged saponite nanolayers, leading to stable and well-defined organic–inorganic hybrids. The project will investigate how structural variations in the dye molecules influence their arrangement, optical properties, and stability in the hybrid systems. The anticipated results include a deeper understanding of host–guest interactions in layered materials and the development of novel materials with potential applications in photonics, sensing, and optoelectronics. This research will contribute to the advancement of functional materials science and expand the toolbox of BODIPY-based materials for applied technologies.

Brain injuries and neurodegenerative disorders are major causes of mortality and disability. Regeneration of central nervous system (CNS) in adult mammals is limited largely due to neuroinflammation. On the other hand, the brain of songbirds is able to regenerate after damage. Injury triggers pro-inflammatory cytokine release that activates immune cells for pathogen clearance and tissue repair, and it is followed by anti-inflammatory cytokines that promote recovery. Although often viewed as harmful, neuroinflammation can support neurogenesis under certain conditions. This project will investigate temporal mRNA expression profiles of pro- and anti-inflammatory cytokines after neurotoxic striatal lesions, using songbirds as a model due to their exceptional CNS regenerative capacity.

Title: Developing an approach to mapping green infrastructure in agricultural landscapes and their ecosystem services Annotation: Agricultural landscapes cover extensive or intensively managed areas of Europe and are expected to deliver not only food but also a range of ecological and cultural services. However, landscape homogenization and intensive farming have reduced biodiversity and weakened ecosystem functions. Green infrastructure (GI) — understood as landscape elements such as hedgerows, riparian strips, wetlands, agroforestry systems and flower strips — offers a way to support biodiversity and provide multiple ecosystem services while keeping farmland productive. This one year project will focus on the identification and assessment of GI elements in selected study area of agricultural landscape in Slovakia. The aim is to map these elements, document their presence and spatial arrangement, and evaluate their contributions to selected ecosystem services such as pollination, soil protection, and water regulation. The expected output is an integrated case study that links ecological observations with socio economic insights. This work will contribute to both academic knowledge and contribute to strengthen strategies for sustainable land management under the EU Biodiversity Strategy 2030.

Root hairs are essential for plant survival as they ensure efficient nutrient uptake. Their growth proceeds in a highly polarized manner, requiring tightly regulated remodeling of the cell wall. However, it remains unclear how the key components of the wall – pectins – are deposited and reorganized during this process. Recent findings further suggest that hair expansion may not be strictly restricted to the tip, challenging established views of their “tip growth” mechanism. The main aim of this project is therefore to elucidate pectin dynamics during root hair growth using a novel peptide probe, Lys10, developed in our laboratory. This probe enables the visualization of pectins in living cells and provides a unique opportunity to monitor cell wall remodeling in real time. Such an approach will not only bring a new perspective on the mechanism of root hair growth but also introduce a new methodological toolkit for cell wall research.

Polyploidization plays a crucial role in the evolution of flowering plants. While polyploids are formed relatively frequently in nature, only a small proportion of them becomes evolutionarily successful and lead to polyploid speciation. We hypothesize that polyploid establishment is enhanced in mountainous regions, which will be investigated here using the Erysimum sylvestre species complex from the family of crucifers (Brassicaceae). We will test the monophyletic origin of the complex and analyse two diploid–polyploid species pairs in the Alps and Apennines, with supposedly ancestor–descendant relationships. Flow cytometry will be used to screen for ploidy levels, and a next-generation sequencing method will be used to elucidate the phylogenetic relationships and polyploid origins. We expect that the present case study will shed light on the processes of polyploid speciation not only in this genus but also in the European mountains in general.

European forest ecosystems are becoming increasingly stressed by heat − south-facing and low-altitude forests are the most exposed to these changes. Although heat stress is becoming in-creasingly important, it is less studied than drought stress. This study centres on European beech (Fagus sylvatica) and sessile oak (Quercus petraea), two ecologically dominant though physiologically opposite types in Slovakian forests. We will assess their adaptive mechanisms in response to heat stress with photosynthetic thermotolerance, stomatal characters, and pig-ment content of five study plots across an climatic gradient. This work will deepen what we know about species-specific resilience and plasticity, information that will be critical for forest management in a changing climate.

The planned project is based on current trends in research, which emphasizes interdisciplinary approaches and the use of digital tools to better understand historical events. The main goal of the project is to identify spatial patterns and dynamics of events related to deportations from Slovakia during 1944 and 1945. The thesis examines the influence of geographical aspects on the different phases of the deportations, including organization, progression, and consequences. The project combines interdisciplinary approaches from history, geography, and digital technologies. QGIS software enables the digitization of historical data, georeferencing and visualization of spatial patterns. The project aims to analyze available data on deportees, including data on birthplaces, pre-deportation residence, transport routes and final destinations.

The research project examines the architecture of the Slovak Communist Party's headquarters, buildings designated for the Slovak Socialist Republic's government, and other bodies whose functional program required a high level of political engagement. This is a type of political architecture that emerged in large numbers during the 1970s and 1980s across the entire territory of the former Czechoslovakia. Although these projects were often prestigious commissions for the seats of the party or the state, they were rarely mentioned in professional architectural circles before to 1989. However, the existing communication between central and local power structures concerning the preparation of investment plans and the requirements for the construction of new headquarters, as well as educational and recreational facilities for the party apparatus, allows us to interpret views on the purpose and significance of this specific type of architecture from investor's expert perspective. At the same time, it enables us to confront these perspectives with the designers' ideas and the completed architectural works. The long construction period, as well as the fact that some of these buildings were put into service only in the late 1980s or even after the regime change provide an opportunity to trace the historical development of shifting views on architecture in relation to the dominant political discourse. The aim of the project is therefore to analyze and interpret the reflection of this architecture in the domestic expert environment during the “Normalization era” of its creation and after 1989. Furthermore, attention will be directed to the change of function of these buildings, new construction interventions, and their reception by users, experts, and the public in the new political and economic reality.

The project examines how Slovak poetry of the 1970s and 1980s reflects ecological and civilizational themes. The aim is to adapt ecocritical approaches to Slovak cultural and historical conditions, map contemporary representations of the relationship between humans and nature, and identify texts that can enrich the current environmental discourse. The research includes the systematic collection of poetry collections, critical discursive interpretation, and contextualization with regard to the socio-political environment of the period. The project is the first to systematically address this issue and will offer a new interpretative model that can also be applied in a broader Central European context. The results will contribute to a re-evaluation of the literary canon, enrich literary science, and provide impetus for pedagogy and broader environmental discussion.

The project focuses on the processing and evaluation of qualitative research related to the Hero’s Journey method developed by Paul Rebillot, which remains virtually unknown in the Slovak context despite being a comprehensive and internationally established dramatherapeutic approach. The research aims to examine the aesthetic and dramatic elements of this method and their impact on participants’ personal transformation, as well as their professional development—especially in the fields of helping and artistic professions. The research is based on the doctoral dissertation of the project applicant and employs a qualitative methodology. It includes three types of questionnaires (administered before, immediately after, and several months or years following participation in the Hero’s Journey process), semi-structured interviews, and a focus group. The project involves the analysis of already collected narratives and continued data collection during upcoming Hero’s Journey workshops in 2025–2026. An important component of the project is collaboration with international experts—Manfred and Helga Weule—direct students of Paul Rebillot and also the applicant’s supervisors and trainers in the method. The results will be used in the dissertation and may also be presented at academic events upon project completion. The project responds to the growing need for interdisciplinary research on theatrical language in therapeutic contexts and its practical relevance for professionals working in the helping and creative sectors.

Cross-border transformations have been a long-discussed topic that has not been harmonized for over 30 years, with the exception of cross-border mergers and acquisitions. However, in 2019, a Conversion Directive was adopted to ensure a uniform legal framework for all member states of the European Union and the European Economic Area. The draft Conversion Directive itself contained an article that was intended to introduce in-depth scrutiny to prevent unfair and fraudulent cross-border conversions, but this was removed during the legislative process. However, the Conversion Directive retained recitals that partially refer to this in-depth control, whilst also keeping the pre-conversion control, whereby the authority of the Member State of origin may refuse to issue certificates if the cross-border conversion has abusive or fraudulent objectives. This control represents a compromise between the European Commission's original proposal and the political objectives of the European Parliament. The Slovak legislator transposed the Transformations Directive into a separate Act on Conversions, in which it introduced the possibility of refusing to issue a pre-conversion certificate on the grounds that European Union law is being avoided. The Conversion Directive and the Conversion Act thus use different terminology, which may lead to different interpretations of two concepts that should be identical. This fact may ultimately affect material control in application practice. At the same time, compared to the Czech Republic, the Czech Act on Conversions has retained the original terminology of the Conversion Directive. The main objective of the grant is to examine the reasons for refusing to issue a certificate prior to conversion for abusive and fraudulent purposes under the Czech Act on Conversions and the Conversion Directive, circumventing EU law under the Slovak Conversion Act. The project researcher aims to compare these conclusions with the Czech legal regulation of the Czech Act on Conversions in order to reveal possible overlaps or, conversely, to reveal how these terms differ. At the same time, the project researcher aims to at least partially clarify the powers of a notary when issuing a certificate prior to transformation, in particular the pitfalls in the actual review of transformation documents, the possibility of detecting circumvention of European Union law and the subsequent possibility of refusing to issue a certificate of prior conversion.

This project investigates the psychological mechanisms underlying Russian political migrants’ engagement in collective action, distinguishing between social change-oriented action (e.g., antigovernmental resistance) and solidarity-based action (e.g., solidarity with Ukrainian refugees). We focus on the unique status of Russian political migrants, who are simultaneously oppressed by their home regime, minorities in receiving countries, and citizens of an aggressor state. In this project, we will compare Russian political migrants’ engagement in collective action in two different receiving countries, representing a liberal democratic and an illiberal democratic context (Germany and Serbia, respectively). The research examines the relationship between different forms of national identification, group-based emotions, self-esteem, and participation in collective action. The project consists of two interconnected studies: a qualitative interview study (Study 1) and a quantitative analysis of predictors of collective action (Study 2). This project contributes to the social and political psychology of migration and collective action by offering a nuanced view of identity, emotion, and agency in people navigating exile and oppression in their home country.

The growing polarization of society and the spread of conspiracy theories undermine trust in science and democratic institutions. While motivated reasoning and identity protection play a crucial role in endorsing such beliefs, most existing interventions overlook these mechanisms. This project seeks to fill this gap through an intervention based on moral reframing, presenting information in line with the recipient’s values, drawing on the framework of Moral Foundations Theory. The aim is to test whether such an intervention can reduce endorsement of conspiracy theories, to examine how its effectiveness relates to trust in science and research institutions, and to assess whether providing participants with an opportunity for feedback strengthens trust in scientists and perceptions of ethical integrity. The expected outcome is empirically grounded recommendations for more effective and ethically responsible approaches to studying disinformation and conspiracy theories.

This research project focuses on digital sex work, especially the creation of sexually explicit content through platforms like OnlyFans. The aim of the study is to identify the problems faced by digital sex workers in Slovakia and to examine the power dynamics between the different actors (workers, platforms, the state, and intermediaries). Platform-mediated sex work is neglected in discourses on platform work at the academic and policy levels, which is particularly evident in the recently adopted Platform Work Directive. The project utilizes qualitative methods, namely semi-structured interviews with digital sex workers and expert interviews. Data will be analyzed using reflective thematic analysis. The project’s research design addresses ethical and methodological issues related to the study of sex work arising from marginalization, stigmatization, and criminalization. The project contributes to a growing body of research that places digital sex work within the framework of platform work to enrich the understanding of its key concepts, including autonomy.