Physics education (TVFd)
Adaptation of Young Physicists Tournament problems for upper secondary school level.
Each year there are interesting and unconventional problems solved within the Young Physicists Tournament (YPT). Students solving these problems develop their knowledge and inquiry abilities. There is a limited number of schools involved into the competition within afternoon activities. The problems as solved by students who present and discuss their research project changing the roles of presenter, opponent and reviewer. This system offers great opportunities to implement some elements also in regular physics education. The main goal of the thesis is to implement selected YPT into upper secondary school level in the form of laboratory exercises. The PhD student is expected to select problems for specific topics that are suitable for development of inquiry skills, adapt them into the guided inquiry level and design educational materials both for students and teachers. Consequently, the pedagogical research will be designed to test the developed activities and materials at schools.
doc. RNDr. Marián Kireš, PhD.
prof. RNDr. Peter Kollár, DrSc.
Physics education (TVFdAj)
Adaptation of Young Physicists Tournament problems for upper secondary school level.
Each year there are interesting and unconventional problems solved within the Young Physicists Tournament (YPT). Students solving these problems develop their knowledge and inquiry abilities. There is a limited number of schools involved into the competition within afternoon activities. The problems as solved by students who present and discuss their research project changing the roles of presenter, opponent and reviewer. This system offers great opportunities to implement some elements also in regular physics education. The main goal of the thesis is to implement selected YPT into upper secondary school level in the form of laboratory exercises. The PhD student is expected to select problems for specific topics that are suitable for development of inquiry skills, adapt them into the guided inquiry level and design educational materials both for students and teachers. Consequently, the pedagogical research will be designed to test the developed activities and materials at schools.
[1] HENDL, J. 2008. Kvalitativní výzkum: základní teorie, metody a aplikace. Praha 2008, 2. vydanie, 408 s. ISBN 978-80-7367-485-4. [2] KLUIBER, Z. 2005. Tvůrčí náboj úloh turnaje mladých fyziků. Ed. Scio me multa nescire, č. 28. MAFY Hradec Králové 2005. [3] Martchenko, I.: Preparation to the Young physicist`s tournament, [online]. Dostupné na internete: <www.iypt.org>. [4] MURCIA, K. 2008. Re-thinking the Development of Scientific Literacy Through a Rope Metaphor. In: Research in Science Education. Vol. 39, 2008, No. 2
doc. RNDr. Marián Kireš, PhD.
prof. RNDr. Peter Kollár, DrSc.
Physics education (TVFdAj)
AI tools in innovative physics education.
Artificial Intelligence (AI) tools, especially chatbots based on advanced large-scale neural language models such as ChatGPT, Bard, or Claud, earned significant attention in 2023 across various human activity sectors, including physics education and STEM subjects, due to their impressive capabilities. This dissertation will focus on an in-depth analysis of the current state, impact, dynamic development, and potential of these technologies within the context of innovative physics education. It will explore the possibilities of integrating AI into curricula and teaching methods, aiming to prepare exemplary educational activities supported by AI in a selected area of physics, along with methodological guidelines for their effective use. The empirical mixed methods research will be oriented towards analyzing the impact of these technologies on motivation and teaching efficiency at secondary and tertiary education levels. The work should also evaluate new perspectives on using AI, which could significantly enrich and transform current pedagogical practices in physics education.
The main goal of this dissertation is to theoretically and empirically evaluate the impact and potential of AI tools on improving physics education. Achieving this goal should be realized through integrating AI into physics curricula, creating corresponding educational activities supported by AI, and verifying and analyzing their impact on motivation and efficiency in secondary and tertiary education.
[1] J. W. Creswell and V. L. P. Clark, Designing and Conducting Mixed Methods Research, 3rd ed. London: SAGE Publications, Inc, 2017. ISBN 978-1-483346-98-4 [2] W. Daher, H. Diab, and A. Rayan, “Artificial Intelligence Generative Tools and Conceptual Knowledge in Problem Solving in Chemistry,” Information, vol. 14, no. 7, Art. no. 7, 2023 [3] M. N. Dahlkemper, S. Z. Lahme, and P. Klein, “How do physics students evaluate artificial intelligence responses on comprehension questions? A study on the perceived scientific accuracy and linguistic quality of ChatGPT,” Phys. Rev. Phys. Educ. Res., vol. 19, no. 1, p. 010142, 2023 [4] A. Al-Marzouqi (ed.) rt al., Artificial Intelligence in Education: The Power and Dangers of ChatGPT in the Classroom. Springer, 2024. ISBN 978-3-031-52280-2. [5] G. Kortemeyer, “Toward AI grading of student problem solutions in introductory physics: A feasibility study,” Phys. Rev. Phys. Educ. Res., vol. 19, no. 2, p. 020163, 2023 [6] W. Xu and F. Ouyang, "The Application of AI Technologies in STEM Education: A Systematic Review from 2011 to 2021," International Journal of STEM Education, vol. 9, no. 1, p. 59, 2022.
doc. RNDr. Jozef Hanč, PhD.
Physics (FdAj)
Application of spin models in spatial data prediction
The research will be devoted to the use of appropriately defined spin models for the prediction of missing values in predominantly massive space-time data, e.g. from remote sensing of the Earth. Traditional prediction methods are not suitable for such data, mainly due to high computational complexity as well as other limitations [1]. Recent research has shown that prediction methods, based for example on the application of a simply modified planar rotator spin model [2,3] and its generalized version [4], can be computationally much more efficient. The potential of spin models lies in the ability to model various types of time-space correlations using short-range inter-spin interactions along with global external effects. The proposed research aims to develop strategies for the development of efficient prediction methods that would be flexible and suitable for automatic processing using massively parallel algorithms implemented on graphics processors (GPUs).
1. N. Cressie and C.K. Wikle, Statistics for spatio-temporal data. John Wiley & Sons, 2015. 2. M. Žukovič and D.T. Hristopulos, Gibbs Markov random fields with continuous values based on the modified planar rotator model, Phys. Rev. E 98 062135 (2018). 3. M. Žukovič, M. Borovský, M. Lach and D.T. Hristopulos, GPU-Accelerated Simulation of Massive Spatial Data Based on the Modified Planar Rotator Model, Mathematical Geosciences 52 123 (2020). 4. M. Žukovič and D.T. Hristopulos, Spatial data modeling by means of Gibbs Markov random fields based on a generalized planar rotator model, Physica A 612 128509 (2023).
prof. RNDr. Milan Žukovič, PhD.
Physics education (TVFdAj)
Blended learning in astronomy education at the gymnasium
In elementary school, the concept of teaching astronomy is elaborated in the form of a separate optional subject. In teaching the subject of physics, teachers have the opportunity to include astronomical topics in connection with traditional thematic units. From the point of view of the educational standard, the follow-up high school study lacks the processing of astronomical topics as well as the support of teachers in the form of topics for educational activities. Considering the growing share of non-formal and informal education and the availability of high-quality information resources, the mentioned issue appears to be suitable for making it accessible through the method of blended learning. Our intention will be to introduce astrophysics content into the teaching of physics in the form of a separate thematic unit. In the hybrid educational space, we will use action research to verify the effectiveness of the teaching method and the impact on the development of selected student skills and knowledge. We will implement proven methods in the upcoming physics course as part of the study program of STEM classes at the gymnasium.
1. To map the state of astronomical education and blended learning at the level of high school students. 2. Design and pilot test of educational activities for hybrid education using the action research method.
[1] Dan MacIsaac; Astrophysics Lessons for High School Physics Students. Phys. Teach. 1 September 2023; 61 (6): 544. https://doi.org/10.1119/10.0020780 [2] Boyd, Nora. (2023). Laboratory Astrophysics: Lessons for Epistemology of Astrophysics. 10.1007/978-3-031-26618-8_2. [3] Fitzgerald MT, Hollow R, Rebull LM, Danaia L, McKinnon DH. A Review of High School Level Astronomy Student Research Projects Over the Last Two Decades. Publications of the Astronomical Society of Australia. 2014;31:e037. doi:10.1017/pasa.2014.30 [4] Kapusta, Joseph & Gale, Charles. (2023). Astrophysics and cosmology. 10.1017/9781009401968.017.
doc. RNDr. Marián Kireš, PhD.
doc. RNDr. Rudolf Gális, PhD.
Physics of Condensed Matter (FKLdAj)
Calorimetry of superconductors
Since the discovery of the two-gap superconductivity in MgB2, further examples of this already exceptional characteristic have been continuously investigated. In addition, the study of competing orders in superconductors, where superconductivity coexists or competes with, for example, magnetic order or charge density waves, is an interesting topic at present. The aim of this thesis is to study selected superconductors by various calorimetric methods, mainly by ac-microcalorimetry. In particular, the work will focus on superconductors with competing order parameters, namely the measurement of their heat capacity at different temperatures and magnetic fields. The aim will be to determine from the measured data the basic characteristics of the studied superconductor such as its critical temperature, strength of Cooper pair coupling, type of pairing, critical magnetic fields, anisotropy of superconducting properties, etc. To do this, it will be necessary to learn the basics of ac microcalorimetry technique, preparation and implementation of experiments, processing and interpretation of measured data, presentation of results at domestic and foreign conferences and publication of original results in foreign scientific journals.
The aim of this thesis is to study selected superconductors by various calorimetric methods, mainly by ac-microcalorimetry. In particular, the work will focus on superconductors with competing ordering parameters, namely the measurement of their heat capacity at different temperatures and magnetic fields.
[1] M. Tinkham, Introduction to superconductivity, McGraw-Hill, Inc., New York, 1996. [2] Yaakov Kraftmakher, Modulation Calorimetry: Theory And Applications, Springer-Verlag, 2004. [3] A. Tari, The Specific Heat of Matter at Low Temperatures, Imperial College Press, London, 2003.
RNDr. Jozef Kačmarčík, PhD.
Zuzana Vargaeštoková
Physics (FdAj)
Cosmic ray trajectory in the Earth's magnetosphere model development
Cosmic ray trajectories simulations are a tool for describing the radiation situation in the Earth's magnetosphere. They are connected to several research topics from the radiation situation in the magnetosphere, space weather topics, through the influence of cosmic radiation on the formation of clouds and the wider influence on the climate to the investigation of the accuracy of the dating method of radioactive carbon C14. The aim of the work is to improve the current models for calculating the trajectory of cosmic rays in the magnetosphere and to use them to investigate selected problems associated with cosmic rays in the Earth's magnetosphere. Selected topics include the development of a model enabling the simulation of cosmic radiation intensities during geomagnetic storms, the search for an optimal methodology for investigating the influence of cosmic radiation on cloud formation, and determining the influence of the crustal geomagnetic field on the energy thresholds of cosmic radiation on the Earth's surface and in the magnetosphere.
The aim of the work is to improve the current models for calculating the trajectory of cosmic rays in the magnetosphere and to use them to investigate selected problems associated with cosmic rays in the Earth's magnetosphere.
1. Gecášek D, Bobík P, Genči J, Villim J, Vaško M, COR system: a tool to evaluate cosmic ray trajectories in the Earth's magnetosphere, Advances in Space Research, 2022, ISSN 0273-1177, https://doi.org/10.1016/j.asr.2022.06.001 2. Boella G., Boschini M. J., Gervasi M., Grandi D., Pensotti S., Rancoita P. G., Bobik P., Kudela K., Evaluation of the flux of CR nuclei inside the magnetosphere, Astroparticle, Particle and Space Physics, Detectors and Medical Physics Applications. Proceedings of the 10th Conference. Held 8-12 October 2007 in Villa Olmo, Como, Italy, Published by World Scientific Publishing Co. Pte. Ltd., 2008. ISBN #9789812819093, pp. 875-880, 2008 3, Kudela K., Bobik P., Long-Term Variations of Geomagnetic Rigidity Cutoffs, Solar Physics, Volume 224, Issue 1-2, pp. 423-431, 2004
RNDr. Pavol Bobík, PhD.
Biophysics (BFdAj)
Deciphering the mechanisms of pathological IgG aggregation in oncohematological diseases
This PhD project offers a unique opportunity to delve into the molecular intricacies of oncohematological diseases like multiple myeloma and light chain amyloidosis. These conditions, marked by the aggregation of pathological immunoglobulin G (IgG) light chains, lead to severe health complications and are currently classified as incurable. You will employ a range of structural and biophysical techniques to study these processes ex vivo, gaining insights into the complex mechanisms at play in these diseases. Your work will contribute to a deeper understanding of the aggregation mechanisms of pathological IgGs, potentially leading to new therapeutic strategies for these challenging conditions. As a PhD candidate, you will be actively involved in experimental design, data collection, and analysis. You will also examine the role of chaperone domains as potential binders and therapeutic agents. This project presents a significant opportunity to contribute to a field of high medical importance.
1) Investigate the biological and biochemical factors contributing to the aggregation of pathological IgG light chains. 2) Explore the interactions between serum proteins, lipid vesicles, and cell surface properties that catalyze or drive this aggregation process. 3) Examine the application of chaperone domains as potential disaggregation drugs.
1. Džupponová V, Žoldák G. Aggregation mechanism and branched 3D morphologies of pathological human light chain proteins under reducing conditions. Colloids Surf B Biointerfaces. 2023 Jan;221:112983. doi: 10.1016/j.colsurfb.2022.112983. 2. Džupponová V, Žoldák G. Salt-dependent passive adsorption of IgG1κ-type monoclonal antibodies on hydrophobic microparticles. Biophys Chem. 2021 Aug;275:106609. doi: 10.1016/j.bpc.2021.106609. 3. Džupponová V, Huntošová V, Žoldák G. A kinetic coupling between protein unfolding and aggregation controls time-dependent solubility of the human myeloma antibody light chain. Protein Sci. 2020 Dec;29(12):2408-2421. doi: 10.1002/pro.3968. 4. Nemergut M, Pluskal D, Horackova J, Sustrova T, Tulis J, Barta T, Baatallah R, Gagnot G, Novakova V, Majerova M, Sedlackova K, Marques SM, Toul M, Damborsky J, Prokop Z, Bednar D, Janin YL, Marek M. Illuminating the mechanism and allosteric behavior of NanoLuc luciferase. Nat Commun. 2023 Nov 29;14(1):7864. doi: 10.1038/s41467-023-43403-y.
doc. RNDr. Gabriel Žoldák, DrSc.
RNDr. Michal Nemergut, PhD.
Advanced Materials (PMd)
Deformation and fracture characteristics of ceramic materials at micro/nano level
A theme of dissertation thesis is aimed to relatively new prospective direction of materials research – nanomechanical testing. The origin of most methods is based on nanoindentation testing, novel nano- and micromechanical methods including compression, tension and bending tests as well as fatigue, creep and fracture experiments performed on a very local scale or on small specimens have been applied to determine mechanical and properties and investigation of the effects of size and crystal orientation on the strength and plasticity of materials. Analyzing these behaviour it is possible to acquire new knowledge of fundamental research on deformation mechanisms in advanced ceramics materials, which would be the main expected contribution of dissertation thesis. We are also expected to contribute to the development of new nano-micro-scale testing methods.
A theme of dissertation thesis is aimed to relatively new prospective direction of materials research – nanomechanical testing.
Current journal literature.
prof. RNDr. Ján Dusza, DrSc.
MSc. Tamás Csanádi, PhD.
Advanced Materials (PMdAj)
Deformation and fracture characteristics of ceramic materials at micro/nano level
A theme of dissertation thesis is aimed to relatively new prospective direction of materials research – nanomechanical testing. The origin of most methods is based on nanoindentation testing, novel nano- and micromechanical methods including compression, tension and bending tests as well as fatigue, creep and fracture experiments performed on a very local scale or on small specimens have been applied to determine mechanical and properties and investigation of the effects of size and crystal orientation on the strength and plasticity of materials. Analyzing these behaviour it is possible to acquire new knowledge of fundamental research on deformation mechanisms in advanced ceramics materials, which would be the main expected contribution of dissertation thesis. We are also expected to contribute to the development of new nano-micro-scale testing methods.
A theme of dissertation thesis is aimed to relatively new prospective direction of materials research – nanomechanical testing.
Current journal literature.
prof. RNDr. Ján Dusza, DrSc.
MSc. Tamás Csanádi, PhD.
Physics (FdAj)
Design and implementation of particle based model of compressible fluids
The main focus of the PhD research project is to create a multiscale model of compressible liquid flow (including possible non-Newtonian liquids) with possible embedded fiducial or biological particles, based on particle formalisms as an alternative to the more usual CFD (OpenFoam, as our UOX partner already does). The purpose of such simulations is to provide synthetic data for AI training to interpret fast XMPH experiments (acronym for X-ray multiprojection holography), including flow regimes involving cavitation and turbulence phenomena. This particle model will be used for the reconstruction of data from fast dynamics experiments (sampling rate up to 4.5 MHz), taking advantage of the unique experimental prototype built by the Horizon EU MHz Tomoscopy project (grant agreement No. 101046448), as well as the follow-up fluidics research projects (in preparation). Our partners are EuXFEL (DE), DESY (DE), SUNA GmBH (DE), University of Oxford (GB), Lund University (SE), Tohoku University (JPN), DTU (DK), TUHH (DE), Stockholm University (SE), Iasu University (RO) but also others. The PhD project will require intensive cooperation with project partners due to multidisciplinarity. The scope of the work is also suitable for several (2-3) PhD students. Possibility of bilateral/multilateral studies (dual PhD diplomas) or industrial PhD.
creation of coarse grain multiscale model of compressiblefluids including elastic biological particles for training of AI reconstruction of our XMPH experiments.
[1] Vagovič, P., Sato, T., Mikeš, L., Mills, G., Graceffa, R., Mattsson, F., Villanueva-Perez, P., Ershov, A., Faragó, T., Uličný, J., et al. (2019). Megahertz x-ray microscopy at x-ray free-electron laser and synchrotron sources. Optica, OPTICA 6, 1106–1109. [2] Hrivňak, S., Hovan, A., Uličný, J., and Vagovič, P. (2018). Phase retrieval for arbitrary Fresnel-like linear shift-invariant imaging systems suitable for tomography. Biomed Opt Express 9, 4390–4400., Hrivňak, S., Uličný, J., Mikeš, L., Cecilia, A., Hamann, E., Baumbach, T., Švéda, L., Zápražný, Z., Korytár, D., Gimenez-Navarro, E., et al. (2016). Single- distance phase retrieval algorithm for Bragg Magnifier microscope. Opt Express 24, 27753–27762. [4] Buakor, K.; Zhang, Y.; Birnšteinová, Š.; Bellucci, V.; Sato, T.; Kirkwood, H.; Mancuso, A. P.; Vagovic, P.; Villanueva-Perez, P. Shot-to-Shot Flat-Field Correction at X-Ray Free-Electron Lasers. Opt. Express 2022, 30 (7), 10633. [4] Han, H.; Round, E.; Schubert, R.; Gül, Y.; Makroczyová, J.; Meza, D.; Heuser, P.; Aepfel-bacher, M.; Barák, I.; Betzel, C.; Fromme, P.; Kursula, I.; Nissen, P.; Tereschenko, E.; Schulz, J.; Uetrecht, C.; Ulicný, J.; Wilmanns, M.; Hajdu, J.; Lamzin, V. S.; Lorenzen, K. The XBI BioLab for Life Science Experiments at the European XFEL. J Appl Crystallogr 2021, 54 (1), 7–21. [5] Project: 101046448 — MHz-TOMOSCOPY — HORIZON-EIC-2021- PATHFINDEROPEN-01 , https://www.tomoscopy.eu [6] Soyama, H.; Liang, X.; Yashiro, W.; Kajiwara, K.; Asimakopoulou, E. M.; Bellucci, V.; Birnsteinova, S.; Giovanetti, G.; Kim, C.; Kirkwood, H. J.; Koliyadu, J. C. P.; Letrun, R.; Zhang, Y.; Uličný, J.; Bean, R.; Mancuso, A. P.; Villanueva-Perez, P.; Sato, T.; Vagovič, P.; Eakins, D.; Korsunsky, A. M. Revealing the Origins of Vortex Cavitation in a Venturi Tube by High Speed X-Ray Imaging. Ultrasonics Sonochemistry 2023, 101, 106715. https://doi.org/10.1016/j.ultsonch.2023.106715. [7] Zhang, Y.; Yao, Z.; Ritschel, T.; Villanueva‐Perez, P. ONIX: An X‐ray Deep‐learning Tool for 3D Reconstructions from Sparse Views. Applied Research 2023, e202300016. https://doi.org/10.1002/appl.202300016.
doc. RNDr. Jozef Uličný, CSc.
Aatto Laaksonen
Biophysics (BFdAj)
Designing stable chaperone platforms: from evolution to innovation
Join my research group in an exciting venture to develop new molecular platforms for detection and therapy, leveraging the potential of chaperone domains. This PhD project is at the forefront of molecular innovation, focusing on stabilizing these platforms for library construction and therapeutic applications. Your work will contribute to the development of novel molecular platforms with potential applications in detection and therapy, bridging the gap between basic molecular biology and applied biomedical research. As a PhD candidate, you will be actively involved in experimental design, data collection, analysis, and interpretation. You will have the opportunity to work with advanced technologies and contribute significantly to a rapidly evolving field. You will employ a range of cutting-edge techniques including evolutionary analysis, protein crystallization, and structural characterization using the SOLEIL synchrotron.
1) Explore natural hyperstable chaperone domains and identify stabilization hotspots through comparative evolutionary analysis. 2) Investigate mesophilic and psychrophilic variants of chaperone domains from bacteria adapted to low-temperature environments. 3) Conduct functional analysis and crystallization of new chaperone domains and variants.
1. Džupponová V, Žoldák G. Aggregation mechanism and branched 3D morphologies of pathological human light chain proteins under reducing conditions. Colloids Surf B Biointerfaces. 2023 Jan;221:112983. doi: 10.1016/j.colsurfb.2022.112983. 2. Džupponová V, Žoldák G. Salt-dependent passive adsorption of IgG1κ-type monoclonal antibodies on hydrophobic microparticles. Biophys Chem. 2021 Aug;275:106609. doi: 10.1016/j.bpc.2021.106609. 3. Džupponová V, Huntošová V, Žoldák G. A kinetic coupling between protein unfolding and aggregation controls time-dependent solubility of the human myeloma antibody light chain. Protein Sci. 2020 Dec;29(12):2408-2421. doi: 10.1002/pro.3968. 4. Nemergut M, Pluskal D, Horackova J, Sustrova T, Tulis J, Barta T, Baatallah R, Gagnot G, Novakova V, Majerova M, Sedlackova K, Marques SM, Toul M, Damborsky J, Prokop Z, Bednar D, Janin YL, Marek M. Illuminating the mechanism and allosteric behavior of NanoLuc luciferase. Nat Commun. 2023 Nov 29;14(1):7864. doi: 10.1038/s41467-023-43403-y.
doc. RNDr. Gabriel Žoldák, DrSc.
RNDr. Michal Nemergut, PhD.
Biophysics (BFd)
Singlet oxygen measurements in biological systems
Photodynamic therapy of cancer is based on the cytotoxic effect of singlet oxygen. Singlet oxygen is generated by energy transfer between photo-activated drug molecules (photosensitizers) and molecular oxygen. The range of singlet oxygen cytotoxic activity is determined by its diffusion rate and lifetime. Previous research in this area has not clarified the value of singlet oxygen lifetime in cells. The main objective of the PhD work is to improve the experimental apparatus for measuring the lifetime of singlet oxygen in cells and to obtain an answer to this key issue of photodynamic therapy. As part of the work, we will also focus on the characterization of new photosensitizers in terms of singlet oxygen production.
- To improve the sensitivity of the equipment for the simultaneous measurement of singlet oxygen phosphorescence and transient absorption of photosensitizers. - To determine the kinetics of singlet oxygen formation and decay during pulsed excitation of photosensitizers in cells. - To determine the efficiency of singlet oxygen formation using new and existing photoactive molecules.
da Silva, E. F. F., B. W. Pedersen, T. Breitenbach, R. Toftegaard, M. K. Kuimova, L. G. Arnaut and P. R. Ogilby (2012) Irradiation- and Sensitizer-Dependent Changes in the Lifetime of Intracellular Singlet Oxygen Produced in a Photosensitized Process. J. Phys. Chem. B. 116, 445-461. P. R. Ogilby (2010) Singlet oxygen: there is indeed something new under the sun. Chem. Soc. Rev. 39, 3181–3209.
doc. Mgr. Gregor Bánó, PhD.
Mgr. Andrej Hovan, PhD.
Biophysics (BFdAj)
Development of cellular model platforms to study IgG light chain toxicity of oncohematological diseases
Embark on a groundbreaking PhD project that aims to advance our understanding of oncohematological diseases, particularly multiple myeloma and its associated IgG light chain variants. This research is crucial for unraveling the mechanisms behind the tissue-specific toxicity of these pathological forms. You will utilize a blend of cellular biology, bioengineering, and biotechnology techniques in developing these platforms, enabling a detailed analysis of variant-specific toxic effects. This research holds the potential to significantly enhance our understanding of the tissue-specific toxicity of IgG light chain variants in multiple myeloma, opening pathways to more effective treatments. As a PhD candidate, you will be at the forefront of this innovative research, collaborating with esteemed international researchers, including Dr. Magdaléna Harakalová from the Circulatory Health Research Centre in Utrecht, Netherlands. This partnership offers a rich environment for scientific growth and international networking.
1) Develop innovative cellular platforms to assess the toxicity of various pathological IgG light chain variants found in different patients. 2) Design of an analytical chip for various cellular platforms. 3) Progress from the creation of bio-chips using prokaryotic cells to eukaryotic cells, and potentially to tissue-on-chip prototypes.
1. Džupponová V, Žoldák G. Aggregation mechanism and branched 3D morphologies of pathological human light chain proteins under reducing conditions. Colloids Surf B Biointerfaces. 2023 Jan;221:112983. doi: 10.1016/j.colsurfb.2022.112983. 2. Džupponová V, Žoldák G. Salt-dependent passive adsorption of IgG1κ-type monoclonal antibodies on hydrophobic microparticles. Biophys Chem. 2021 Aug;275:106609. doi: 10.1016/j.bpc.2021.106609. 3. Džupponová V, Huntošová V, Žoldák G. A kinetic coupling between protein unfolding and aggregation controls time-dependent solubility of the human myeloma antibody light chain. Protein Sci. 2020 Dec;29(12):2408-2421. doi: 10.1002/pro.3968. 4. Nemergut M, Pluskal D, Horackova J, Sustrova T, Tulis J, Barta T, Baatallah R, Gagnot G, Novakova V, Majerova M, Sedlackova K, Marques SM, Toul M, Damborsky J, Prokop Z, Bednar D, Janin YL, Marek M. Illuminating the mechanism and allosteric behavior of NanoLuc luciferase. Nat Commun. 2023 Nov 29;14(1):7864. doi: 10.1038/s41467-023-43403-y.
doc. RNDr. Gabriel Žoldák, DrSc.
RNDr. Michal Nemergut, PhD.
Advanced Materials (PMdAj)
Development of high – entropy ceramics: modelling, processing, characterization and testing
The dissertation work is focused on the development and characterization of High – Entropy Structural Ceramics with improved room and high/ultra-high temperature properties suitable for extreme operating conditions in different areas of industry. Systems based on ternary carbides and nitrides mixed in equimolar concentrations to reach the maximum molar configurational entropy with structural order and chemical disorder will be developed applying advanced modelling methods - numerical simulation, machine learning, etc., processing routes as high – energy milling, spark plasma sintering or hot – pressing. The developed systems will be tested using advanced methods as micro/nano – mechanical tests, tribology, strength/toughness tests, thermal shock, oxidation, ablation tests, etc. and characterized by SEM, EBSD, TEM/HREM, AFM etc. The proposed dissertation work will put forward a systematic study of high-entropy ceramics based on ternary carbides and nitrides in in the wide range and so completely, that new original results in this field of material science can be expected.
The proposed dissertation work will put forward a systematic study of high-entropy ceramics based on ternary carbides and nitrides in in the wide range and so completely, that new original results in this field of material science can be expected.
Current journal literature.
prof. RNDr. Ján Dusza, DrSc.
MSc. Tamás Csanádi, PhD.
Advanced Materials (PMdAj)
Development of novel electrospun ceramic nanofibres for special technical applications
Dissertation thesis is oriented to nanofibers systems prepared by relatively novel, low-cost and productive method – needle-less electrospinning, which are expected to have a great potential in the field of solar cell applications, gas sensors, varistors and other special technical applications. The expected contribution of the thesis is to study and explain the relationship between the preparation conditions, the microstructure formation and the selected functional properties of the developed nanofibers and it has all the prerequisites to shift the knowledge about the preparation of the nanofibers towards the real production possibilities. The aim of the thesis is to predict the application possibilities of the studied materials on the basis of the obtained results.
The aim of the thesis is to predict the application possibilities of the studied materials on the basis of the obtained results.
Current journal literature.
prof. RNDr. Ján Dusza, DrSc.
Ing. Eva Múdra, PhD.
Advanced Materials (PMdAj)
Development of novel entropy-stabilized ultra-high temperature ceramics with superior strength and plasticity
The topic of the dissertation work is very timely and challenging in materials science and is about the development of damage-tolerant and strong heat-resistant ceramics for hypersonic and space applications. These materials are the so-called ultra-high temperature ceramics (UHTCs), as the only group of materials that can withstand temperatures exceeding 2000°C in oxidizing atmospheres, and are used for example in thermal protecting layers of spacecraft. Since only about a dozen UHTCs exist (e.g. HfC, ZrB2) and those are brittle at low temperatures (room temperature), the dissertation work focuses on the development of novel materials in the form of entropy-stabilized UHTCs, consisting of at least four different transition metals in the crystal lattice, with improved plasticity/deformability and strength. The topic includes material design, synthesis, structural characterization (e.g. XRD, SEM, EBSD) and mechanical testing from nano to macro scale, all of which the doctoral student gets familiarised with. However, the main task will be micro/nanomechanical testing (e.g. nanoindentation, micropillar compression) of grains and grain boundaries using a state-of-the-art nanoindenter device. The knowledge gathered from the deformation behaviour of grains will be used to design new entropy-stabilized compositions with superior strength and plasticity, accomplishing original and high-impact results.
The topic of the dissertation work is very timely and challenging in materials science and is about the development of damage-tolerant and strong heat-resistant ceramics for hypersonic and space applications.
Current journal literature.
MSc. Tamás Csanádi, PhD.
Physics education (TVFdAj)
Development the skill of argumentation in the conceptual physics course
The student's understanding of physics concepts and phenomenon can be verified through qualitative tasks and their physics interpretation. The ability to appropriately use the most important arguments, to correctly organize them into a comprehensive explanation of a physics concept or phenomenon are signs of the skill of arguing. The content of conceptual physics courses will be analyzed as part of the dissertation. The doctoral student will process a thematically sorted set of qualitative tasks and their clarification at the level of high school physics. For physics teachers, he will create a education course, which will provide basic starting points and materials for the application of qualitative tasks in the teaching of physics at the secondary school. The development of the ability to argue and the level of the student's conceptual understanding of selected physical terms and phenomena will be investigated on a selected sample of high school students.
1. Map the approach to creating the content of conceptual physics courses and the teaching methods used in their implementation. 2. Process a thematically sorted set of qualitative tasks and their clarification at the level of high school physics. 3. Create and implement a course of continuous education for physics teachers focused on teaching conceptual physics in high school. 4. On a selected sample of high school students, examine the development of students' argumentative skills and the level of students' conceptual understanding.
[1] Taşlıdere, Erdal & Eryilmaz, Ali. (2009). Alternative to Traditional Physics Instruction: Effectiveness of Conceptual Physics Approach. Eurasian Journal of Educational Research (EJER). 9. 109-128. [2] Aina, Jacob. (2017). Investigating the Conceptual Understanding of Physics through an Interactive Lecture- Engagement. Cumhuriyet International Journal of Education-CIJE. 6. 82-96. [3] Price, Edward & Goldberg, Fred & Robinson, Steve & McKean, Michael. (2016). Validity of peer grading using Calibrated Peer Review in a guided-inquiry, conceptual physics course. Physical Review Physics Education Research. 12. 10.1103/PhysRevPhysEducRes.12.020145. [4] Walker, Jearl. (2023). The Flying Circus of Physics, 2nd ed.
doc. RNDr. Marián Kireš, PhD.
Biophysics (BFd)
Designing stable chaperone platforms: from evolution to innovation
Join my research group in an exciting venture to develop new molecular platforms for detection and therapy, leveraging the potential of chaperone domains. This PhD project is at the forefront of molecular innovation, focusing on stabilizing these platforms for library construction and therapeutic applications. Your work will contribute to the development of novel molecular platforms with potential applications in detection and therapy, bridging the gap between basic molecular biology and applied biomedical research. As a PhD candidate, you will be actively involved in experimental design, data collection, analysis, and interpretation. You will have the opportunity to work with advanced technologies and contribute significantly to a rapidly evolving field. You will employ a range of cutting-edge techniques including evolutionary analysis, protein crystallization, and structural characterization using the SOLEIL synchrotron.
1) Explore natural hyperstable chaperone domains and identify stabilization hotspots through comparative evolutionary analysis. 2) Investigate mesophilic and psychrophilic variants of chaperone domains from bacteria adapted to low-temperature environments. 3) Conduct functional analysis and crystallization of new chaperone domains and variants.
1. Džupponová V, Žoldák G. Aggregation mechanism and branched 3D morphologies of pathological human light chain proteins under reducing conditions. Colloids Surf B Biointerfaces. 2023 Jan;221:112983. doi: 10.1016/j.colsurfb.2022.112983. 2. Džupponová V, Žoldák G. Salt-dependent passive adsorption of IgG1κ-type monoclonal antibodies on hydrophobic microparticles. Biophys Chem. 2021 Aug;275:106609. doi: 10.1016/j.bpc.2021.106609. 3. Džupponová V, Huntošová V, Žoldák G. A kinetic coupling between protein unfolding and aggregation controls time-dependent solubility of the human myeloma antibody light chain. Protein Sci. 2020 Dec;29(12):2408-2421. doi: 10.1002/pro.3968. 4. Nemergut M, Pluskal D, Horackova J, Sustrova T, Tulis J, Barta T, Baatallah R, Gagnot G, Novakova V, Majerova M, Sedlackova K, Marques SM, Toul M, Damborsky J, Prokop Z, Bednar D, Janin YL, Marek M. Illuminating the mechanism and allosteric behavior of NanoLuc luciferase. Nat Commun. 2023 Nov 29;14(1):7864. doi: 10.1038/s41467-023-43403-y.
doc. RNDr. Gabriel Žoldák, DrSc.
RNDr. Michal Nemergut, PhD.
Physics of Condensed Matter (FKLdAj)
Experimental study of anisotropy in thermal conductivity in two-dimensional systems and thermal conductivity in amorphous systems
Thermal conductivity plays an important role in many applications. The systems with the two-dimensional lattice structure are characterized by high anisotropy due to the different ways of heat transport (in-plane or perpendicular to the planes). The aim of this work will be the experimental study of the anisotropy in the thermal conductivity in the selected two-dimensional systems or thin layers. In the case of amorphous materials, thermal conductivity is characterized by universal anomalous behavior at low temperatures. This part will aim to investigate the possible origin of the mentioned anomaly. The work will have mainly experimental characters. The analysis of the experimental data will be realized using several software packages. The physical mechanism of the heat transfer will be described for the given system and heat transfer orientation. Additional supporting measurements, such as heat capacity or magnetic properties, will be realized if necessary.
Thermal conductivity plays an important role in many applications. The systems with the two-dimensional lattice structure are characterized by high anisotropy due to the different ways of heat transport (in-plane or perpendicular to the planes). The aim of this work will be the experimental study of the anisotropy in the thermal conductivity in the selected two-dimensional systems or thin layers. In the case of amorphous materials, thermal conductivity is characterized by universal anomalous behavior at low temperatures. This part will aim to investigate the possible origin of the mentioned anomaly. The work will have mainly experimental characters. The analysis of the experimental data will be realized using several software packages. The physical mechanism of the heat transfer will be described for the given system and heat transfer orientation. Additional supporting measurements, such as heat capacity or magnetic properties, will be realized if necessary.
1. K. Shrestha, and K. Gofryk, Rev. Sci. Instrum. 89, 043905 (2018). 2. David G. Cahill, Rev. Sci. Instrum. 61, 802 (1990). 3. R. McKinney, P. Gorai, E. S. Toberer, V. Stevanovicc, Chem. Mater. 31, 2048–2057 (2019). 4. Miguel A Ramos, Low-Temperature Thermal and Vibrational Properties of Disordered Solids A Half-Century of Universal “Anomalies” of Glasses, World Scientific (2022).
RNDr. Vladimír Tkáč, PhD.
prof. Ing. Martin Orendáč, DrSc.
Physics of Condensed Matter (FKLd)
Experimental study of anisotropy in thermal conductivity in two-dimensional systems and thermal conductivity in amorphous systems
Thermal conductivity plays an important role in many applications. The systems with the two-dimensional lattice structure are characterized by high anisotropy due to the different ways of heat transport (in-plane or perpendicular to the planes). The aim of this work will be the experimental study of the anisotropy in the thermal conductivity in the selected two-dimensional systems or thin layers. In the case of amorphous materials, thermal conductivity is characterized by universal anomalous behavior at low temperatures. This part will aim to investigate the possible origin of the mentioned anomaly. The work will have mainly experimental characters. The analysis of the experimental data will be realized using several software packages. The physical mechanism of the heat transfer will be described for the given system and heat transfer orientation. Additional supporting measurements, such as heat capacity or magnetic properties, will be realized if necessary.
Thermal conductivity plays an important role in many applications. The systems with the two-dimensional lattice structure are characterized by high anisotropy due to the different ways of heat transport (in-plane or perpendicular to the planes). The aim of this work will be the experimental study of the anisotropy in the thermal conductivity in the selected two-dimensional systems or thin layers. In the case of amorphous materials, thermal conductivity is characterized by universal anomalous behavior at low temperatures. This part will aim to investigate the possible origin of the mentioned anomaly. The work will have mainly experimental characters. The analysis of the experimental data will be realized using several software packages. The physical mechanism of the heat transfer will be described for the given system and heat transfer orientation. Additional supporting measurements, such as heat capacity or magnetic properties, will be realized if necessary.
1. K. Shrestha, and K. Gofryk, Rev. Sci. Instrum. 89, 043905 (2018). 2. David G. Cahill, Rev. Sci. Instrum. 61, 802 (1990). 3. R. McKinney, P. Gorai, E. S. Toberer, V. Stevanovicc, Chem. Mater. 31, 2048–2057 (2019). 4. Miguel A Ramos, Low-Temperature Thermal and Vibrational Properties of Disordered Solids A Half-Century of Universal “Anomalies” of Glasses, World Scientific (2022).
RNDr. Vladimír Tkáč, PhD.
prof. Ing. Martin Orendáč, DrSc.
Physics (FdAj)
Exploring of discrete gravity, black hole paradox and also quantum phenomena for various kinds of cosmological objects as well as nanostructures
Interpretation of emerging spaces using a new geometric/topological approach introduced by PNDP-manifolds, i.e., particular kind of the Einstein sequential warped-product manifold, which allow to cover a wider variety of exact solutions of Einstein's field equation from a differential geometric point of view, without complicating the calculations comparing to the Einstein warped-product manifolds. We will seek to shed light on the underlying physics beyond the Standard model, also by the examination how discrete gravitational effects would affect the motion of spin or spinless particles in a gravitational fields. By exploring these concepts, we hope to provide valuable insights into the nature of dimensions and their impact on gravity and fundamental forces, thus addressing existing inconsistencies in current cosmological models as well as nanostructures.
The aim of thesis will be to shed light on the underlying physics beyond the Standard model, also by the examination how discrete gravitational effects would affect the motion of spin or spinless particles in a gravitational fields.
[1] PINČÁK, Richard** - PIGAZZINI, Alexander - JAFARI, Saeid - OZEL, Cenap. Discrete Gravity in Emergent Space Theory: Hidden Conical Defects and Teleparallel Gravity. In Universe, 2023, vol. 9, no. 1, art. no. 31. [2] PINČÁK, Richard** - PIGAZZINI, Alexander - JAFARI, Saeid - OZEL, Cenap - DEBENEDICTIS, Andrew. A topological approach for emerging D-branes and its implications for gravity. In International Journal of Geometric Methods in Modern Physics, 2021, vol. 18, no. 14, art. no. 2150227. [3] PINČÁK, Richard** - PIGAZZINI, Alexander - JAFARI, Saeid - OZEL, Cenap. The “Emerging” Reality from “Hidden” Spaces. In Universe, 2021, vol. 7, no. 3, art. no. 75.
RNDr. Richard Pinčák, PhD.
RNDr. Michal Pudlák, CSc.
Biophysics (BFdAj)
Exploring the frontiers of protein dynamics: from crystallography to ultrafast spectroscopy
Join our cutting-edge research project aimed at unraveling the intricate world of protein structures and dynamics. This PhD opportunity will immerse you in the fascinating realm of protein crystallography and advanced spectroscopic techniques. You will be at the forefront of employing state-of-the-art methodologies to delve into protein-ligand interactions, protein quakes, and crucial enzymatic processes like proton and electron transfers. As a PhD candidate, you will be instrumental in conducting these sophisticated experiments, analyzing data, and contributing to the field's knowledge. This project offers a unique interdisciplinary and international experience between Košice(SK)•Prague(CZ)•Paris, (FR), bridging the gap between structural biology, biophysics, and chemistry. Your research could pave the way for groundbreaking advancements in understanding protein mechanisms, potentially leading to novel therapeutic approaches.
1) Determine the three-dimensional structures of novel protein domains, including new chaperone domains of Hsp70. 2) Investigate human pathological immunoglobulin light chains in complex with emerging therapeutics. 3) Apply ultrafast optical spectroscopies and time-resolved X-ray techniques to study enzyme catalysis and other dynamic processes.
1. Džupponová V, Žoldák G. Aggregation mechanism and branched 3D morphologies of pathological human light chain proteins under reducing conditions. Colloids Surf B Biointerfaces. 2023 Jan;221:112983. doi: 10.1016/j.colsurfb.2022.112983. 2. Džupponová V, Žoldák G. Salt-dependent passive adsorption of IgG1κ-type monoclonal antibodies on hydrophobic microparticles. Biophys Chem. 2021 Aug;275:106609. doi: 10.1016/j.bpc.2021.106609. 3. Džupponová V, Huntošová V, Žoldák G. A kinetic coupling between protein unfolding and aggregation controls time-dependent solubility of the human myeloma antibody light chain. Protein Sci. 2020 Dec;29(12):2408-2421. doi: 10.1002/pro.3968. 4. Nemergut M, Pluskal D, Horackova J, Sustrova T, Tulis J, Barta T, Baatallah R, Gagnot G, Novakova V, Majerova M, Sedlackova K, Marques SM, Toul M, Damborsky J, Prokop Z, Bednar D, Janin YL, Marek M. Illuminating the mechanism and allosteric behavior of NanoLuc luciferase. Nat Commun. 2023 Nov 29;14(1):7864. doi: 10.1038/s41467-023-43403-y.
doc. RNDr. Gabriel Žoldák, DrSc.
RNDr. Michal Nemergut, PhD.
Advanced Materials (PMdAj)
FEM of micromechanil tests of hard coatings
The work is focused on a detail study of the processes of stress and deformation states during instrumented nanoindentation, scratch and tribological tests in the coated composite systems using finite element modelling (FEM) externded FEM (xFEM) and Cohesive Zone Model (CZM) methods and subsequent experimental verification. The work will be performed on thin coatings on substrates with different mechanical properties. The aim is to understand the details of damage mechanisms in coatings in dependence on the loading conditions as well as the optimization of the conditions for the measurement of the mechanical properties and tribological properties of the studied coatings.
Detail study of the stress and deformation states during instrumented nanoindentation, scratch and tribological tests in the composite systems coating/substrate using finite element modelling (FEM)
1. A.K. Bhattacharya, W.D. Nix, Finite element simulation of indentation experiments, Int. J. Solids Structures 24 (1988) 881-891. doi: 10.1016/0020-7683(88)90039-X 2. H. ur Rehman, F. Ahmed, Ch. Schmid, J. Schaufler, K. Durst, Study on the deformation mechanics of hard brittle coatings on ductile substrates using in situ tensile testing and cohesive zone modelling, Surf. Coat Technol. 207 (2012)163-169. doi: 10.1016/j.surfcoat.2012.06.049 3. Sun, T. Bell, S. Zheng, Finite element analysis of the critical ratio of coating thickness to indentation depth for coating property measurements by nanoindentation, Thin Solid Films 258 (1995) 198-204. doi: 10.1016/0040-6090(94)06357-5 4. T, Csanádi, D. Németh, F. Lofaj, Mechanical Properties of Hard W-C Coating on Steel Substrate Deduced from Nanoindentation and Finite Element Modeling, Exp. Mechanics 57 (2017) 1057 – 1069. Doi: 10.1007/s11340-016-0190-x
doc. RNDr. František Lofaj, DrSc.
Physics education (TVFdAj)
Formative assessment in physics teaching at secondary school
Formative assessment is one of the most effective educational interventions to influence students´ achievements in their process of learning. Formative assessment is aimed at providing feedback to assist students´ learning. The main thesis goal is to analyse available formative assessment tools and consider their implementation to support learning in physics. The PhD student is expected to design a set of formative assessment tools for inquiry activities that will be consistently implemented into the inquiry-based learning scenario in order to develop understanding as well as inquiry skills so that learners assume more responsibility and become more independent in their own learning. The effectivity of the designed model will be evaluated by pedagogical research.
1. Analyze methods, strategies, and assessment tools used in secondary school teaching with an emphasis on formative assessment. 2. Assess the possibilities of implementing formative assessment tools into physics teaching at the secondary school level. 3. Propose a set of formative assessment tools for inquiry-based activities, which will be purposefully and systematically integrated into the structure of inquiry-oriented teaching. 4. Verify the effectiveness of the proposed model through educational research
[1] Black, P. & WIiliam, P. 1998. Assessment and classroom learning, Assessment in Education: Principles, Policy & Practice, 5(1), 7-74, https://doi.org/10.1080/0969595980050102 [2] Etkina, E., Karelina, A., Murthy, S. & Ruibal-Villasenor, M. 2009. Using action research to improve learning and formative assessment to conduct research, Phys. Rev. St Phys. Educ. Res. 5, 010109 [3] Harlen, W. 2013. Assessment & Inquiry-Based Science Education: Issues in Policy and Practice. Global Network of Science Academies (IAP) Science Education Programme (SEP), available at https://www.interacademies.org/sites/default/files/publication/ibse_assessment_guide_iap_sep_0.pdf
doc. RNDr. Zuzana Ješková, PhD.
Physics education (TVFd)
Formative assessment in physics teaching at secondary school
Formative assessment is one of the most effective educational interventions to influence students´ achievements in their process of learning. Formative assessment is aimed at providing feedback to assist students´ learning. The main thesis goal is to analyse available formative assessment tools and consider their implementation to support learning in physics. The PhD student is expected to design a set of formative assessment tools for inquiry activities that will be consistently implemented into the inquiry-based learning scenario in order to develop understanding as well as inquiry skills so that learners assume more responsibility and become more independent in their own learning. The effectivity of the designed model will be evaluated by pedagogical research.
1. Analyze methods, strategies, and assessment tools used in secondary school teaching with an emphasis on formative assessment. 2. Assess the possibilities of implementing formative assessment tools into physics teaching at the secondary school level. 3. Propose a set of formative assessment tools for inquiry-based activities, which will be purposefully and systematically integrated into the structure of inquiry-oriented teaching. 4. Verify the effectiveness of the proposed model through educational research
[1] Black, P. & WIiliam, P. 1998. Assessment and classroom learning, Assessment in Education: Principles, Policy & Practice, 5(1), 7-74, https://doi.org/10.1080/0969595980050102 [2] Etkina, E., Karelina, A., Murthy, S. & Ruibal-Villasenor, M. 2009. Using action research to improve learning and formative assessment to conduct research, Phys. Rev. St Phys. Educ. Res. 5, 010109 [3] Harlen, W. 2013. Assessment & Inquiry-Based Science Education: Issues in Policy and Practice. Global Network of Science Academies (IAP) Science Education Programme (SEP), available at https://www.interacademies.org/sites/default/files/publication/ibse_assessment_guide_iap_sep_0.pdf
doc. RNDr. Zuzana Ješková, PhD.
Biophysics (BFd)
Hypericin, a potential Bcl2 proteins regulator, and its effect on cancer cells apoptosis and autophagy.
Members of the Bcl2 family of proteins are key regulators of apoptosis. The intricate network of protein-protein interactions between multi BH domain anti- and pro-apoptotic Bcl2 proteins, and/or BH3-only proteins control cell survival or death via regulation of mitochondria function and fission/fusion processes. The BH3-only proteins has been shown to fulfill role of either sensitizer or direct activator of pro-apoptotic Bax and Bak. The importance of interaction between pro-survival Bcl2 proteins and BH3 motifs of either pro-apoptotic or BH3 only proteins for cell death or survival decisions makes this interaction an appealing target for cancer therapy and at the present, more than 20 small molecule inhibitors of pro-survival Bcl2 proteins, termed as BH3 mimetics, were explored. We have shown evidence that Hypericin (Hyp) may be another naturally occurring BH3 mimetic. The goal of this study will focus on Hyp interaction with anti-apoptotic Bcl2, BclXL and Mcl1 in apoptosis and autophagy pathways in cancer cells. We will use interdisciplinary approach of confocal fluorescent microscopy, molecular biology and spectroscopy.
To study Hyp interaction with anti-apoptotic Bcl2, BclXL and Mcl1 in apoptosis and autophagy pathways in cancer cells.
1. Llambi, Moldoveanu et al. (2011) Molecular Cell 44(4): 517-531 2. Certo, Del Gaizo Moore et al. (2006) Cancer Cell 9(5): 351-365. 3. Vogler (2014) Adv Med 2014: 943648. 4. Correia, Lee et al. (2015) Biochimica et Biophysica Acta 1853(7): 1658-1671. 5. Gong, Khong et al. (2016) Journal of Biological Chemistry 285(33): 25570-25581. 6. Doroshenko A., Tomkova S., Kozar T., and Stroffekova K. (2022) Hypericin, a potential new BH3 mimetic. Front. Pharmacol. 13:991554, doi: 10.3389/fphar.2022.991554 7. Doroshenko A., Tomkova S., Kozar T., and Stroffekova K. (2022) Hypericin, a potential new BH3 mimetic. Front. Pharmacol. 13:991554, doi: 10.3389/fphar.2022.991554 8. Stroffekova K., Tomkova S., Huntosova V. and T. Kozar, (2019) Importance of Hypericin-Bcl2 interactions for biological effects at subcellular levels. Photodiagnosis and Photodynamic Therapy 28 (2019) 38-52 9. Huntosova, V., M. Novotova, et al. (2017). "Assessing light-independent effects of hypericin on cell viability, ultrastructure and metabolism in human glioma and endothelial cells." Toxicol In Vitro 40: 184-195. 10. Huntosova, V. and K. Stroffekova (2016). "Hypericin in the Dark: Foe or Ally in Photodynamic Therapy?" Cancers (Basel) 8(10).
doc. RNDr. Katarína Štroffeková, PhD.
Physics education (TVFdAj)
Interactive methods and technologies in teaching physics of the microworld
The thesis is focused on physic education research in the new curriculum (content and approaches) in teaching physics using the latest interactive teaching methods and digital technology. The new curriculum should more reflect the current scientific knowledge and technological progress as traditional. At the same time, it should provide the necessary foundation for future natural scientists and engineers, who will be working on such problems as the design of new conductive materials, data storage of high density and access speed, new communications technologies, nanoscience and nanotechnology, alternative energy sources, quantum computers, computer drug design, and modelling of complex systems involving extreme climatic and geophysical phenomena. The work of a Ph.D. student will be concentrated on a study, selection, and preparation of educational activities in physics of the microworld, supported by experiments. The main goal will be the research dealing with the implementation of the new content in the micro-world physics in the school curriculum with subsequent analysis of the impact and effectiveness of selected methods and technologies. The applicant must have some experience in Jupyter technology, Geogebra modelling, and fundamentals of modern physics, especially Feynman’s spacetime approach to quantum physics and Einstein’s theory of relativity.
The work of a Ph.D. student will be concentrated on a study, selection, and preparation of educational activities in physics of the microworld, supported by experiments. The main goal will be the research dealing with the implementation of the new content in the micro-world physics in the school curriculum with subsequent analysis of the impact and effectiveness of selected methods and technologies.
[1] R. Chabay and B. Sherwood, Matter & Interactions. 4th ed. New York, NY, USA: Wiley, 2020. ISBN 978-1-119-08081-7. [2] M. G. Jones, Nanoscale Science: Activities for Grades 6-12. Arlington, VA, USA: NSTA Press, 2007. ISBN 978-1-933531-05-2. [3] T. A. Moore, Six Ideas that Shaped Physics: Units C, N, E, T, R, Q. 3rd ed., Vols. 1–6. Boston, MA, USA: McGraw-Hill Education, 2022. ISBN: 978-1-26-488144-4. [4] C. Hughes, J. Isaacson, A. Perry, R. F. Sun and J. Turner, Quantum Computing for the Quantum Curious. London, UK: Springer International Publishing, 2021. ISBN: 978-3-030-61600-7. [5] D. Prutchi, Exploring Quantum Physics through Hands-on Projects. John Wiley & Sons, 2012. ISBN 978-1-118-14066-6.
doc. RNDr. Jozef Hanč, PhD.
Physics education (TVFd)
Interactive methods and technologies in teaching physics of the microworld
The thesis is focused on physic education research in the new curriculum (content and approaches) in teaching physics using the latest interactive teaching methods and digital technology. The new curriculum should more reflect the current scientific knowledge and technological progress as traditional. At the same time, it should provide the necessary foundation for future natural scientists and engineers, who will be working on such problems as the design of new conductive materials, data storage of high density and access speed, new communications technologies, nanoscience and nanotechnology, alternative energy sources, quantum computers, computer drug design, and modelling of complex systems involving extreme climatic and geophysical phenomena. The work of a Ph.D. student will be concentrated on a study, selection, and preparation of educational activities in physics of the microworld, supported by experiments. The main goal will be the research dealing with the implementation of the new content in the micro-world physics in the school curriculum with subsequent analysis of the impact and effectiveness of selected methods and technologies. The applicant must have some experience in Jupyter technology, Geogebra modelling, and fundamentals of modern physics, especially Feynman’s spacetime approach to quantum physics and Einstein’s theory of relativity.
The work of a Ph.D. student will be concentrated on a study, selection, and preparation of educational activities in physics of the microworld, supported by experiments. The main goal will be the research dealing with the implementation of the new content in the micro-world physics in the school curriculum with subsequent analysis of the impact and effectiveness of selected methods and technologies.
[1] R. Chabay and B. Sherwood, Matter & Interactions. 4th ed. New York, NY, USA: Wiley, 2020. ISBN 978-1-119-08081-7. [2] M. G. Jones, Nanoscale Science: Activities for Grades 6-12. Arlington, VA, USA: NSTA Press, 2007. ISBN 978-1-933531-05-2. [3] T. A. Moore, Six Ideas that Shaped Physics: Units C, N, E, T, R, Q. 3rd ed., Vols. 1–6. Boston, MA, USA: McGraw-Hill Education, 2022. ISBN: 978-1-26-488144-4. [4] C. Hughes, J. Isaacson, A. Perry, R. F. Sun and J. Turner, Quantum Computing for the Quantum Curious. London, UK: Springer International Publishing, 2021. ISBN: 978-3-030-61600-7. [5] D. Prutchi, Exploring Quantum Physics through Hands-on Projects. John Wiley & Sons, 2012. ISBN 978-1-118-14066-6.
doc. RNDr. Jozef Hanč, PhD.
Physics of Condensed Matter (FKLd)
Calorimetry of superconductors
Since the discovery of the two-gap superconductivity in MgB2, further examples of this already exceptional characteristic have been continuously investigated. In addition, the study of competing orders in superconductors, where superconductivity coexists or competes with, for example, magnetic order or charge density waves, is an interesting topic at present. The aim of this thesis is to study selected superconductors by various calorimetric methods, mainly by ac-microcalorimetry. In particular, the work will focus on superconductors with competing order parameters, namely the measurement of their heat capacity at different temperatures and magnetic fields. The aim will be to determine from the measured data the basic characteristics of the studied superconductor such as its critical temperature, strength of Cooper pair coupling, type of pairing, critical magnetic fields, anisotropy of superconducting properties, etc. To do this, it will be necessary to learn the basics of ac microcalorimetry technique, preparation and implementation of experiments, processing and interpretation of measured data, presentation of results at domestic and foreign conferences and publication of original results in foreign scientific journals.
The aim of this thesis is to study selected superconductors by various calorimetric methods, mainly by ac-microcalorimetry. In particular, the work will focus on superconductors with competing ordering parameters, namely the measurement of their heat capacity at different temperatures and magnetic fields.
[1] M. Tinkham, Introduction to superconductivity, McGraw-Hill, Inc., New York, 1996. [2] Yaakov Kraftmakher, Modulation Calorimetry: Theory And Applications, Springer-Verlag, 2004. [3] A. Tari, The Specific Heat of Matter at Low Temperatures, Imperial College Press, London, 2003.
RNDr. Jozef Kačmarčík, PhD.
Zuzana Vargaeštoková
Physics of Condensed Matter (FKLd)
Quantum materials under extreme conditions
Quantum materials, such as frustrated magnets, topological insulators, strongly correlated metals or exotic superconductors, are highlights in the theoretical and experimental study of solids and are beginning to be used in applications connected with quantum technologies. Understanding the ground state of these systems requires their investigation under extreme conditions, i.e. at very low temperatures, high magnetic fields or pressures. Specifically, the dissertation would deal with the study of the influence of a high magnetic field and hydrostatic pressure on the thermal, transport and magnetic properties of selected tetra-, hexa- and dodecaborides at kelvin to millikelvin temperatures.
The study of the influence of a high magnetic field and hydrostatic pressure on the thermal, transport and magnetic properties of selected tetra-, hexa- and dodecaborides at kelvin to millikelvin temperatures.
[1] KITTEL Ch., Úvod do fyziky pevných látek, Academia, Praha, 1985 [2] GABÁNI S. et al., Magnetism and superconductivity of rare earth borides, Journal of Alloys and Compounds 821 (2020), 153201 [3] GABÁNI S. a kol., Fyzika a technika vysokých tlakov II., skriptá, ÚEF SAV Košice, 2016
doc. RNDr. Slavomír Gabáni, PhD.
RNDr. Matúš Orendáč, PhD.
Physics of Condensed Matter (FKLdAj)
Magnetic and thermal studies of the soft magnetic composites
The study is oriented on the preparation and the investigation of the iron based magnetic composite materials. Due to their unique properties, soft magnetic composites have been used in recent years, for example, in electric motors and power electronics. The warming in the working condition can change the magnetic properties of the material, which makes it necessary to consider the temperature effect in the process of core loss prediction. Therefore, the thermal analysis of the magnetic materials will be one of the important issues in motor design, especially for high-speed motors. Composite materials will be prepared by pressing under different physical conditions. The hysteresis loops and their magnetic losses, the electrical resistivity and wideband complex permeability will be studied on prepared materials in a temperature range close to operating temperatures in practice. The aim of the study is the knowledge of temperature behaviour and the optimization of preparation process of soft magnetic materials with required soft magnetic properties at middle-frequencies.
The study of the physical properties of soft magnetic composites, their preparation and thermal treatment. The learning of the magnetic measurements methods. Preparation of the Fe based composite materials with inorganic or organic nonconductive binder. Setting up the method for temperature investigation of the electro-magnetic properties of the prepared samples in the temperature range close to operating temperatures in practice. Optimization of the preparation process for the soft magnetic materials with required magnetic properties in studied temperature interval at middle-frequencies.
1. R. M. Bozorth, Ferromagnetism, third edition (IEEE Press, Piscataway, NJ), 1993. 2. S. Chikazumi, Physics of Ferromagnetism, Oxford University press, 1997 3. scientific publications on the subject of soft magnetic composites
doc. RNDr. Ján Füzer, PhD.
Physics of Condensed Matter (FKLdAj)
Magnetic field induced phase transitions in quantum magnets based on the metal-organic systems.
Magnetic quantum systems are characterized by the presence of quantum fluctuations. In general, their intensity increases with reducing spin value, decreasing lattice dimension, the presence of geometric frustration, or a suitable combination of physical parameters leading to a formation of the singlet (non-magnetic) ground state. By applying a magnetic field, the effect of quantum fluctuations can be suppressed and, depending on the system, the field can simulate an easy-plane type spin anisotropy and can induce a Berezinskii–Kosterlitz–Thouless topological phase transition [1]. In the case of singlet states (e.g. spin systems with a large degree of easy plane single-ion anisotropy or various dimerized spin lattices), phase transitions to a special magnetically ordered state appear and the stabilization of the corresponding magnetic ground state occurs only in a narrow interval of magnetic fields [2]. The mentioned phenomena will be studied on selected low-dimensional materials with an assumed singlet state with a different degree of dimerization of the spin lattice as well as with a different distribution of spin dimers (e.g. type of lattice, confined geometry, etc.), since these parameters guarantee both the variability of the field intervals and the variability of the magnetic ordered phases. For this purpose, the study of magneto-structural correlations involving the measurement and analysis of exp. specific heat, susceptibility, magnetization data as well as several types of spectroscopic measurements will be performed. In cooperation with theoreticians, it will be possible to characterize the studied systems as materials from first principles, and subsequent testing of such calculations with available theoretical models will be carried out. [1] D. Opherden et al, Phys. Rev. Lett. 130 086704 (2023). [2] S. Calder et al, Phys. Rev. Mater. 7 124408 (2023)
To become familiar with the quantum phenomena in magnetic insulators induced by a magnetic field, spatial anisotropy and spin-orbital coupling. Familiarize yourself with the basic experimental methodologies and software necessary for the study. On selected systems based on metal-organic compounds, study the formation of magnetic phases induced by a magnetic field and quantum and thermal fluctuations. On the basis of data analysis and acquired knowledge, to understand the origin of observed phenomena in quantum magnets.
[1] D. Opherden et al, Phys. Rev. Lett. 130, 086704 (2023). [2] S. Calder et al, Phys. Rev. Mater. 7, 124408 (2023) [3] U. Scholllwock et al, Quantum Magnetism, Springer 2004
doc. RNDr. Alžbeta Orendáčová, DrSc.
RNDr. Róbert Tarasenko, PhD.
Physics of Condensed Matter (FKLd)
Magnetic and thermal studies of the soft magnetic composites
The study is oriented on the preparation and the investigation of the iron based magnetic composite materials. Due to their unique properties, soft magnetic composites have been used in recent years, for example, in electric motors and power electronics. The warming in the working condition can change the magnetic properties of the material, which makes it necessary to consider the temperature effect in the process of core loss prediction. Therefore, the thermal analysis of the magnetic materials will be one of the important issues in motor design, especially for high-speed motors. Composite materials will be prepared by pressing under different physical conditions. The hysteresis loops and their magnetic losses, the electrical resistivity and wideband complex permeability will be studied on prepared materials in a temperature range close to operating temperatures in practice. The aim of the study is the knowledge of temperature behaviour and the optimization of preparation process of soft magnetic materials with required soft magnetic properties at middle-frequencies.
The study of the physical properties of soft magnetic composites, their preparation and thermal treatment. The learning of the magnetic measurements methods. Preparation of the Fe based composite materials with inorganic or organic nonconductive binder. Setting up the method for temperature investigation of the electro-magnetic properties of the prepared samples in the temperature range close to operating temperatures in practice. Optimization of the preparation process for the soft magnetic materials with required magnetic properties in studied temperature interval at middle-frequencies.
1. R. M. Bozorth, Ferromagnetism, third edition (IEEE Press, Piscataway, NJ), 1993. 2. S. Chikazumi, Physics of Ferromagnetism, Oxford University press, 1997 3. scientific publications on the subject of soft magnetic composites
doc. RNDr. Ján Füzer, PhD.
Advanced Materials (PMd)
Soft magnetic nanocrystalline alloys metals prepared by unconventional thermal processing techniques.
The PhD thesis is focused on the employment of unconventional techniques of thermal processing in order to tailor the structural and magnetic properties of nanocrystalline alloys based on 3-d metals. We plan to use facility for ultra-rapid annealing of thin metallic ribbons constructed recently at IEP SAS. In this facility, the annealed samples are clamped between pair of the pre-heated massive Cu-blocks and typical annealing times take few seconds. High heating rates and much shorter processing times as compared to conventional annealing allow extend the composition interval where the annealed samples are still capable to form nanocrystalline structure. The other technique of thermal processing in this work is the annealing in a presence of high magnetic fields. We plan to perform a detailed study of structural and magnetic properties of selected alloy systems. The main goal of thesis is improvement of functional properties of studied materials for potential technical applications.
The main goal of thesis is improvement of functional properties of studied materials for potential technical applications.
current journal literature
RNDr. Ivan Škorvánek, CSc.
Ing. Branislav Kunca, PhD.
Physics of Condensed Matter (FKLd)
Magnetic field induced phase transitions in quantum magnets based on the metal-organic systems.
Magnetic quantum systems are characterized by the presence of quantum fluctuations. In general, their intensity increases with reducing spin value, decreasing lattice dimension, the presence of geometric frustration, or a suitable combination of physical parameters leading to a formation of the singlet (non-magnetic) ground state. By applying a magnetic field, the effect of quantum fluctuations can be suppressed and, depending on the system, the field can simulate an easy-plane type spin anisotropy and can induce a Berezinskii–Kosterlitz–Thouless topological phase transition [1]. In the case of singlet states (e.g. spin systems with a large degree of easy plane single-ion anisotropy or various dimerized spin lattices), phase transitions to a special magnetically ordered state appear and the stabilization of the corresponding magnetic ground state occurs only in a narrow interval of magnetic fields [2]. The mentioned phenomena will be studied on selected low-dimensional materials with an assumed singlet state with a different degree of dimerization of the spin lattice as well as with a different distribution of spin dimers (e.g. type of lattice, confined geometry, etc.), since these parameters guarantee both the variability of the field intervals and the variability of the magnetic ordered phases. For this purpose, the study of magneto-structural correlations involving the measurement and analysis of exp. specific heat, susceptibility, magnetization data as well as several types of spectroscopic measurements will be performed. In cooperation with theoreticians, it will be possible to characterize the studied systems as materials from first principles, and subsequent testing of such calculations with available theoretical models will be carried out. [1] D. Opherden et al, Phys. Rev. Lett. 130 086704 (2023). [2] S. Calder et al, Phys. Rev. Mater. 7 124408 (2023)
To become familiar with the quantum phenomena in magnetic insulators induced by a magnetic field, spatial anisotropy and spin-orbital coupling. Familiarize yourself with the basic experimental methodologies and software necessary for the study. On selected systems based on metal-organic compounds, study the formation of magnetic phases induced by a magnetic field and quantum and thermal fluctuations. On the basis of data analysis and acquired knowledge, to understand the origin of observed phenomena in quantum magnets.
[1] D. Opherden et al, Phys. Rev. Lett. 130, 086704 (2023). [2] S. Calder et al, Phys. Rev. Mater. 7, 124408 (2023) [3] U. Scholllwock et al, Quantum Magnetism, Springer 2004
doc. RNDr. Alžbeta Orendáčová, DrSc.
RNDr. Róbert Tarasenko, PhD.
Physics (FdAj)
Magnetocaloric and barocaloric features of selected magnetic insulators
The main goal of the doctoral research project is a detailed theoretical analysis of the magnetocaloric and barocaloric effects of selected magnetic insulators, which will be modeled using basic lattice-statistical models such as the Ising model, Heisenberg model, Ising-Heisenberg model, or XY model. Geometrically frustrated magnetic materials, which do not order up to the lowest achievable temperatures, exhibit enhanced magnetocaloric effects, making them superior to commercially used paramagnetic salts for low-temperature cooling. The geometric spin frustration often leads to anomalous magnetization curves involving discontinuous jumps between fractional magnetization plateaus, providing another interesting platform for efficient adiabatic cooling due to substantial changes in the magnetization. Also, magnetic materials satisfying local conservation laws due to a destructive quantum interference will be in focus, as their fundamental magnetic and thermodynamic properties (including magnetocaloric and barocaloric effects) are a direct consequence of the local geometry of cells capturing bound magnons. The doctoral candidate's task will be to explore how temperature-, magnetic-field-, and/or pressure-driven phase transitions can support enhanced magnetocaloric or barocaloric effects, with particular emphasis on low-temperature cooling. One of the main objectives is to find optimal conditions for the highest efficiency of magnetic cooling achievable by considering various thermodynamic cycles (e.g., Carnot, Ericsson, Brayton, etc.) of selected magnetic insulators.
1. M.E. Zhitomirsky, “Enhanced magnetocaloric effect in frustrated magnets”, Phys. Rev. B 67, 104421 (2003). DOI: 10.1103/PhysRevB.67.104421 2. F. Heidrich-Meisner et al., “Universal emergence of the one-third plateau in the magnetization process of frustrated quantum spin chains”, Phys. Rev. B 75, 064413 (2007). DOI: 10.1103/PhysRevB.75.064413 3. Ch. Aronica et al., Cubane Variations: Syntheses, Structures, and Magnetic Property Analyses of Lanthanide(III)-Copper(II) Architectures with Controlled Nuclearities, Inorg. Chem. 46, 6108 (2007). DOI: 10.1021/ic700645q
doc. RNDr. Jozef Strečka, PhD.
Physics (Fd)
Magnetocaloric and barocaloric features of selected magnetic insulators
The main goal of the doctoral research project is a detailed theoretical analysis of the magnetocaloric and barocaloric effects of selected magnetic insulators, which will be modeled using basic lattice-statistical models such as the Ising model, Heisenberg model, Ising-Heisenberg model, or XY model. Geometrically frustrated magnetic materials, which do not order up to the lowest achievable temperatures, exhibit enhanced magnetocaloric effects, making them superior to commercially used paramagnetic salts for low-temperature cooling. The geometric spin frustration often leads to anomalous magnetization curves involving discontinuous jumps between fractional magnetization plateaus, providing another interesting platform for efficient adiabatic cooling due to substantial changes in the magnetization. Also, magnetic materials satisfying local conservation laws due to a destructive quantum interference will be in focus, as their fundamental magnetic and thermodynamic properties (including magnetocaloric and barocaloric effects) are a direct consequence of the local geometry of cells capturing bound magnons. The doctoral candidate's task will be to explore how temperature-, magnetic-field-, and/or pressure-driven phase transitions can support enhanced magnetocaloric or barocaloric effects, with particular emphasis on low-temperature cooling. One of the main objectives is to find optimal conditions for the highest efficiency of magnetic cooling achievable by considering various thermodynamic cycles (e.g., Carnot, Ericsson, Brayton, etc.) of selected magnetic insulators.
1. M.E. Zhitomirsky, “Enhanced magnetocaloric effect in frustrated magnets”, Phys. Rev. B 67, 104421 (2003). DOI: 10.1103/PhysRevB.67.104421 2. F. Heidrich-Meisner et al., “Universal emergence of the one-third plateau in the magnetization process of frustrated quantum spin chains”, Phys. Rev. B 75, 064413 (2007). DOI: 10.1103/PhysRevB.75.064413 3. Ch. Aronica et al., Cubane Variations: Syntheses, Structures, and Magnetic Property Analyses of Lanthanide(III)-Copper(II) Architectures with Controlled Nuclearities, Inorg. Chem. 46, 6108 (2007). DOI: 10.1021/ic700645q
doc. RNDr. Jozef Strečka, PhD.
Advanced Materials (PMd)
FEM of micromechanil tests of hard coatings
The work is focused on a detail study of the processes of stress and deformation states during instrumented nanoindentation, scratch and tribological tests in the coated composite systems using finite element modelling (FEM) externded FEM (xFEM) and Cohesive Zone Model (CZM) methods and subsequent experimental verification. The work will be performed on thin coatings on substrates with different mechanical properties. The aim is to understand the details of damage mechanisms in coatings in dependence on the loading conditions as well as the optimization of the conditions for the measurement of the mechanical properties and tribological properties of the studied coatings.
Detail study of the stress and deformation states during instrumented nanoindentation, scratch and tribological tests in the composite systems coating/substrate using finite element modelling (FEM)
1. A.K. Bhattacharya, W.D. Nix, Finite element simulation of indentation experiments, Int. J. Solids Structures 24 (1988) 881-891. doi: 10.1016/0020-7683(88)90039-X 2. H. ur Rehman, F. Ahmed, Ch. Schmid, J. Schaufler, K. Durst, Study on the deformation mechanics of hard brittle coatings on ductile substrates using in situ tensile testing and cohesive zone modelling, Surf. Coat Technol. 207 (2012)163-169. doi: 10.1016/j.surfcoat.2012.06.049 3. Sun, T. Bell, S. Zheng, Finite element analysis of the critical ratio of coating thickness to indentation depth for coating property measurements by nanoindentation, Thin Solid Films 258 (1995) 198-204. doi: 10.1016/0040-6090(94)06357-5 4. T, Csanádi, D. Németh, F. Lofaj, Mechanical Properties of Hard W-C Coating on Steel Substrate Deduced from Nanoindentation and Finite Element Modeling, Exp. Mechanics 57 (2017) 1057 – 1069. Doi: 10.1007/s11340-016-0190-x
doc. RNDr. František Lofaj, DrSc.
Physics education (TVFdAj)
Mobile technologies in physics teaching and learning
Mobile technologies, with their wide availability, have great potential for educational purposes. Existing specific applications designed for measuring various physical quantities open up new possibilities to support inquiry-based education, which primarily focuses on experimentation in physics teaching. The task of the doctoral candidate will be to explore available mobile technologies suitable for teaching physics and the possibilities of using mobile technologies in terms of their suitability for fulfilling the goals of physics education, as well as to propose a methodology for implementation into teaching. The main goal of this work will be to study how the integration of mobile technologies affects various aspects of physics education, such as student motivation, conceptual understanding of physical phenomena, and the development of inquiry skills. Meaningful use of mobile technologies in supporting experimental student activities will be verified by a pedagogical experiment.
1. to explore available mobile technologies suitable for teaching physics, primarily in the area of experimentation and measuring physical quantities. 2. to compare the potential of mobile technologies in the field of experimentation with other available means focused on measuring physical quantities. 3. to propose a methodology for implementing mobile technologies into teaching. 4. to verify the meaningful use of mobile technologies in supporting experimental student activities through a pedagogical experiment.
[1] Becker, S. , Klein, P., Gößling, A. and Kuhn, J. (2020) Using mobile devices to enhance inquiry-based learning processes, Learning and Instruction, 69, 101350 [2] Crompton, H., & Burke, D. (2018). The use of mobile learning in science: A systematic review. Journal of Science Education and Technology, 27(2), 133-149. [3] Ranellucci, J., Hall, C., & Hall, S. (2019). Using Mobile Technology to Improve Student Learning in an Introductory Physics Course. American Journal of Physics, 87(4), 293-299. [4] Kaps, A. et al. 2021 Implementation of smartphone-based experimental exercises for physics courses at universities, Phys. Educ. 56 035004 [5] Diković, L., & Milovanović, M. (2019). The Role of Mobile Learning in Physics Education. International Journal of Emerging Technologies in Learning (iJET), 14(11), 91-106. [6] Tlili, A., Essalmi, F., Jemni, M., & Kinshuk (2017). Empirical studies on the use of mobile technology in science education: A systematic review. Educational Technology & Society, 20(2), 91-102. [7] Gonzalez, M. et al. (2015) Teaching and Learning Physics with Smartphones, Journal on Cases on Information Technology 17(1) [8] Rath, G. (2019) Mobile phones in physics teaching – an overview of development and research activities, IOP Conf. Series: Journal of Physics: Conf. Series 1286 (2019) 012050
doc. RNDr. Zuzana Ješková, PhD.
Physics education (TVFd)
Mobile technologies in physics teaching and learning
Mobile technologies, with their wide availability, have great potential for educational purposes. Existing specific applications designed for measuring various physical quantities open up new possibilities to support inquiry-based education, which primarily focuses on experimentation in physics teaching. The task of the doctoral candidate will be to explore available mobile technologies suitable for teaching physics and the possibilities of using mobile technologies in terms of their suitability for fulfilling the goals of physics education, as well as to propose a methodology for implementation into teaching. The main goal of this work will be to study how the integration of mobile technologies affects various aspects of physics education, such as student motivation, conceptual understanding of physical phenomena, and the development of inquiry skills. Meaningful use of mobile technologies in supporting experimental student activities will be verified by a pedagogical experiment.
1. to explore available mobile technologies suitable for teaching physics, primarily in the area of experimentation and measuring physical quantities. 2. to compare the potential of mobile technologies in the field of experimentation with other available means focused on measuring physical quantities. 3. to propose a methodology for implementing mobile technologies into teaching. 4. to verify the meaningful use of mobile technologies in supporting experimental student activities through a pedagogical experiment.
[1] Becker, S. , Klein, P., Gößling, A. and Kuhn, J. (2020) Using mobile devices to enhance inquiry-based learning processes, Learning and Instruction, 69, 101350 [2] Crompton, H., & Burke, D. (2018). The use of mobile learning in science: A systematic review. Journal of Science Education and Technology, 27(2), 133-149. [3] Ranellucci, J., Hall, C., & Hall, S. (2019). Using Mobile Technology to Improve Student Learning in an Introductory Physics Course. American Journal of Physics, 87(4), 293-299. [4] Kaps, A. et al. 2021 Implementation of smartphone-based experimental exercises for physics courses at universities, Phys. Educ. 56 035004 [5] Diković, L., & Milovanović, M. (2019). The Role of Mobile Learning in Physics Education. International Journal of Emerging Technologies in Learning (iJET), 14(11), 91-106. [6] Tlili, A., Essalmi, F., Jemni, M., & Kinshuk (2017). Empirical studies on the use of mobile technology in science education: A systematic review. Educational Technology & Society, 20(2), 91-102. [7] Gonzalez, M. et al. (2015) Teaching and Learning Physics with Smartphones, Journal on Cases on Information Technology 17(1) [8] Rath, G. (2019) Mobile phones in physics teaching – an overview of development and research activities, IOP Conf. Series: Journal of Physics: Conf. Series 1286 (2019) 012050
doc. RNDr. Zuzana Ješková, PhD.
Physics education (TVFdAj)
Model of teaching University General physics course
At University level there are mostly traditional teaching methods based on lectures used. However, after the implementation of curriculum reform there is a significant decrease in the level of knowledge and skills of students entering University. The current situation calls for changes in education, concerning the first physics courses that students take part, in particular. These changes should lead to higher students´ engagement in their own learning by implementing interactive methods even during the lectures shifting the traditional way of teaching to more active learning environment. The thesis is aimed at the analysis of students’ level of understanding and skills before they start their University study, development of activities based on interactive approach, their implementation and analysis of their efficiency.
1. Analyze available interactive methods suitable primarily for teaching physics at the university level. 2. Evaluate and select appropriate interactive methods for teaching the General Physics course at the University. 3. Prepare a series of activities for systematic implementation into the teaching of the General Physics course, both for lecture-based instruction and to support the conduct of practical exercises. 4. Verify the developed teaching model for the General Physics course through a pedagogical experiment.
[1] Proceedings ICPE-EPEC 2013 conference, August 5-9, 2013, Prague, Czech republic, Amsterdam, Active learning in a changing world of new technologies, Charles University in Prague, MATFYZPRESS publisher, Prague 2013, available on <http://www.icpe2013.org/proceedings> [2] Thornton, R., Sokoloff, D. Interactive Lecture Demonstrations, Active learning in Introductory Physics, 2004 John Wiley and Sons [3] Redish, F., J. Research-Based Reform of University Physics, available on <http://per-central.org/per_reviews/media/volume1/> [4] Beichner, R., J., et al. ThHe Student-Centered Activities for Large Enrollment Undergraduate Programs (SCALE-UP) Project, available on http://www.per-central.org/document/ServeFile.cfm?ID=4517 [5] Redish, E,F., Teaching Physics with the Physics Suite, 2003 John Wiley and Sons [6] Laws, P. et al. Physics with Video Analysis, published by Vernier Software and Technology, 2009, ISBN-978-1-929075-11-9
doc. RNDr. Zuzana Ješková, PhD.
Physics education (TVFd)
Model of teaching University General physics course
At University level there are mostly traditional teaching methods based on lectures used. However, after the implementation of curriculum reform there is a significant decrease in the level of knowledge and skills of students entering University. The current situation calls for changes in education, concerning the first physics courses that students take part, in particular. These changes should lead to higher students´ engagement in their own learning by implementing interactive methods even during the lectures shifting the traditional way of teaching to more active learning environment. The thesis is aimed at the analysis of students’ level of understanding and skills before they start their University study, development of activities based on interactive approach, their implementation and analysis of their efficiency.
1. Analyze available interactive methods suitable primarily for teaching physics at the university level. 2. Evaluate and select appropriate interactive methods for teaching the General Physics course at the University. 3. Prepare a series of activities for systematic implementation into the teaching of the General Physics course, both for lecture-based instruction and to support the conduct of practical exercises. 4. Verify the developed teaching model for the General Physics course through a pedagogical experiment.
[1] Proceedings ICPE-EPEC 2013 conference, August 5-9, 2013, Prague, Czech republic, Amsterdam, Active learning in a changing world of new technologies, Charles University in Prague, MATFYZPRESS publisher, Prague 2013, available on <http://www.icpe2013.org/proceedings> [2] Thornton, R., Sokoloff, D. Interactive Lecture Demonstrations, Active learning in Introductory Physics, 2004 John Wiley and Sons [3] Redish, F., J. Research-Based Reform of University Physics, available on <http://per-central.org/per_reviews/media/volume1/> [4] Beichner, R., J., et al. ThHe Student-Centered Activities for Large Enrollment Undergraduate Programs (SCALE-UP) Project, available on http://www.per-central.org/document/ServeFile.cfm?ID=4517 [5] Redish, E,F., Teaching Physics with the Physics Suite, 2003 John Wiley and Sons [6] Laws, P. et al. Physics with Video Analysis, published by Vernier Software and Technology, 2009, ISBN-978-1-929075-11-9
doc. RNDr. Zuzana Ješková, PhD.
Advanced Materials (PMdAj)
Modelling of phase diagrams and thermodynamic properties of the systems for high temperature applications
The work will be focused on the study of phases, phase equilibria and phase diagrams in the systems for high-temperature applications. The aim is to refine the uncertainty of phase diagrams and to investigate unknown parts of selected systems by experimental methods of differential thermal analysis, X-ray diffraction and electron microscopy and subsequently to model their phase diagrams and thermodynamic properties using the semi-empirical Calphad-method. The subjects of the study are ternary systems containing mainly refractory metals and boron as the basis of materials potentially suitable for high-temperature use. The results of the thesis will allow extending the possibility of designing new materials for high-temperature use by computational methods without the need for time-consuming experimental testing.
The aim is to refine the uncertainty of phase diagrams and to investigate unknown parts of selected systems by experimental methods of differential thermal analysis, X-ray diffraction and electron microscopy and subsequently to model their phase diagrams and thermodynamic properties using the semi-empirical Calphad-method.
current scientific literature
RNDr. Viera Homolová, PhD.
Advanced Materials (PMd)
Modelling of phase diagrams and thermodynamic properties of the systems for high temperature applications
The work will be focused on the study of phases, phase equilibria and phase diagrams in the systems for high-temperature applications. The aim is to refine the uncertainty of phase diagrams and to investigate unknown parts of selected systems by experimental methods of differential thermal analysis, X-ray diffraction and electron microscopy and subsequently to model their phase diagrams and thermodynamic properties using the semi-empirical Calphad-method. The subjects of the study are ternary systems containing mainly refractory metals and boron as the basis of materials potentially suitable for high-temperature use. The results of the thesis will allow extending the possibility of designing new materials for high-temperature use by computational methods without the need for time-consuming experimental testing.
The aim is to refine the uncertainty of phase diagrams and to investigate unknown parts of selected systems by experimental methods of differential thermal analysis, X-ray diffraction and electron microscopy and subsequently to model their phase diagrams and thermodynamic properties using the semi-empirical Calphad-method.
current scientific literature
RNDr. Viera Homolová, PhD.
Biophysics (BFd)
Modelling the mechanism of changes in allosteric regulation of ryanodine receptor function evoked by pathogenic mutations
Ryanodine receptors (RyR) are membrane ion channels responsible for the control of excitation-contraction coupling in skeletal (RyR1) as well as cardiac muscle cells (RyR2). Pathogenic RyR mutations in several genetic diseases lead to dysregulation of channel activity by Ca2+ and Mg2+ ions. The aim is to elucidate the effect of selected pathogenic mutations on the regulation of RyR channel activity by Ca2+ and Mg2+ ions, using allosteric models of channel gating. The topic is a continuation of investigations in the group of Ing. A. Zahradníková, DrSc. [1, 2].
1. Using methods of statistical thermodynamics, to develop an equilibrium model of allosteric regulation of RyR activity by its most important modulators and to verify model predictions using literature data on RyR activity under different conditions. 2. Using mathematical modelling, to determine the effect of RyR activators and inhibitors on the kinetics of RyR gating. 3. To develop a model explaining the effect of selected pathogenic RyR mutations on RyR activity using a realistic model of RyR gating.
[1] Iaparov B, Baglaeva I, Zahradník I, Zahradníková A. Magnesium Ions Moderate Calcium-Induced Calcium Release in Cardiac Calcium Release Sites by Binding to Ryanodine Receptor Activation and Inhibition Sites. Front Physiol. 12:805956, 2022. doi: 10.3389/fphys.2021.805956. [2] Colquhoun D, Hawkes AG, Sakmann B, Neher E. The principles of the stochastic interpretation of ion-channel mechanisms. In: Single-channel recording. Plenum, New York. 135-175, 1983. [3] D. Colquhoun, F. J. Sigworth, B. Sakmann and E. Neher. In Single-channel recording. Plenum, New York. 191-263, 1983. [4] Cannell MB, Kong CHT, Imtiaz MS, Laver DR. Control of sarcoplasmic reticulum Ca2+ release by stochastic RyR gating within a 3D model of the cardiac dyad and importance of induction decay for CICR termination. Biophys J. 104:2149-59, 2013. doi: 10.1016/j.bpj.2013.03.058.
Ing. Miloslav Karhánek, PhD.
Biophysics (BFd)
Modulation of protein amyloid aggregation – insight into molecular mechanisms of amyloid formation and inhibition
Amyloid structures of poly/peptides have been associated with diseases such as Alzheimer's disease, systematic amyloidoses, diabetes mellitus and others. Recently, it has been found that amyloids are important for many essential processes in organisms - from bacteria to humans. The aim of this work is to contribute to a better understanding of the mechanisms of the formation and inhibition of protein amyloid aggregation through their modulation by various substances (inorganic and organic molecules, biomolecules, nanoparticles). Based on this, it is possible to better understand the pathological and physiological effects of amyloid structures at the molecular level. Various physico-chemical methods will be used, mainly spectroscopic, calorimetric, chromatographic techniques and atomic force microscopy.
1. Characterization of protein conformers associated with the formation of amyloid structures 2. Modulation of amyloid fibrillization using various substances (inorganic and organic molecules, biomolecules, nanoparticles). 3. Elucidation of the effect of effective modulators on amyloid structures
1. Amyloid fibrils and Prefibrillar Aggregates: Molecular and Biological Properties. Edited by D. E. Otzen, Wiley-VCH and Co., 2013, ISBN: 978-3-527-33200-7 2. Eichner T. and Radford, A. E., A diversity of Assembly Mechanisms of a generic amyloid fold, Molecular Cell, 2011, 43, 1(8), 8 – 18. 3. Fändlich, M., Oligomeric Intermediates in Amyloid Formation: Structure Determination and Mechanism of Toxicity, Journal of Molecular Biology, 2012, 421, 427 - 440 4. scientific reports
doc. RNDr. Zuzana Gažová, CSc.
Biophysics (BFd)
Deciphering the mechanisms of pathological IgG aggregation in oncohematological diseases
This PhD project offers a unique opportunity to delve into the molecular intricacies of oncohematological diseases like multiple myeloma and light chain amyloidosis. These conditions, marked by the aggregation of pathological immunoglobulin G (IgG) light chains, lead to severe health complications and are currently classified as incurable. You will employ a range of structural and biophysical techniques to study these processes ex vivo, gaining insights into the complex mechanisms at play in these diseases. Your work will contribute to a deeper understanding of the aggregation mechanisms of pathological IgGs, potentially leading to new therapeutic strategies for these challenging conditions. As a PhD candidate, you will be actively involved in experimental design, data collection, and analysis. You will also examine the role of chaperone domains as potential binders and therapeutic agents. This project presents a significant opportunity to contribute to a field of high medical importance.
1) Investigate the biological and biochemical factors contributing to the aggregation of pathological IgG light chains. 2) Explore the interactions between serum proteins, lipid vesicles, and cell surface properties that catalyze or drive this aggregation process. 3) Examine the application of chaperone domains as potential disaggregation drugs.
1. Džupponová V, Žoldák G. Aggregation mechanism and branched 3D morphologies of pathological human light chain proteins under reducing conditions. Colloids Surf B Biointerfaces. 2023 Jan;221:112983. doi: 10.1016/j.colsurfb.2022.112983. 2. Džupponová V, Žoldák G. Salt-dependent passive adsorption of IgG1κ-type monoclonal antibodies on hydrophobic microparticles. Biophys Chem. 2021 Aug;275:106609. doi: 10.1016/j.bpc.2021.106609. 3. Džupponová V, Huntošová V, Žoldák G. A kinetic coupling between protein unfolding and aggregation controls time-dependent solubility of the human myeloma antibody light chain. Protein Sci. 2020 Dec;29(12):2408-2421. doi: 10.1002/pro.3968. 4. Nemergut M, Pluskal D, Horackova J, Sustrova T, Tulis J, Barta T, Baatallah R, Gagnot G, Novakova V, Majerova M, Sedlackova K, Marques SM, Toul M, Damborsky J, Prokop Z, Bednar D, Janin YL, Marek M. Illuminating the mechanism and allosteric behavior of NanoLuc luciferase. Nat Commun. 2023 Nov 29;14(1):7864. doi: 10.1038/s41467-023-43403-y.
doc. RNDr. Gabriel Žoldák, DrSc.
RNDr. Michal Nemergut, PhD.
Advanced Materials (PMdAj)
Multifunctional magnetic nanomaterials for use in medicine
Most biological processes take place at the nanoscale, and this gives us the opportunity to understand these processes and create new materials due to technical progress. Magnetic nanomaterials have considerable potential for use in medicine, e.g. in the distribution of the drug to the affected areas, in imaging, and in therapy. The main goal of the dissertation is not only the preparation of new magnetic nanomaterials, the binding of biologically active substances and the study of their physicochemical properties such as size, shape, structure, surface charge, magnetic properties, but also the investigation of their suitability for use in the field of magnetic resonance diagnostics and the treatment of diseases e.g. by magnetic hyperthermia.
The main goal of the dissertation is not only the preparation of new magnetic nanomaterials, the binding of biologically active substances and the study of their physicochemical properties such as size, shape, structure, surface charge, magnetic properties, but also the investigation of their suitability for use in the field of magnetic resonance diagnostics and the treatment of diseases e.g. by magnetic hyperthermia.
Current journal literature.
Ing. Vlasta Závišová, PhD.
RNDr. Martina Kubovčíková, PhD.
Advanced Materials (PMd)
Multifunctional magnetic nanomaterials for use in medicine
Most biological processes take place at the nanoscale, and this gives us the opportunity to understand these processes and create new materials due to technical progress. Magnetic nanomaterials have considerable potential for use in medicine, e.g. in the distribution of the drug to the affected areas, in imaging, and in therapy. The main goal of the dissertation is not only the preparation of new magnetic nanomaterials, the binding of biologically active substances and the study of their physicochemical properties such as size, shape, structure, surface charge, magnetic properties, but also the investigation of their suitability for use in the field of magnetic resonance diagnostics and the treatment of diseases e.g. by magnetic hyperthermia.
The main goal of the dissertation is not only the preparation of new magnetic nanomaterials, the binding of biologically active substances and the study of their physicochemical properties such as size, shape, structure, surface charge, magnetic properties, but also the investigation of their suitability for use in the field of magnetic resonance diagnostics and the treatment of diseases e.g. by magnetic hyperthermia.
Current journal literature.
Ing. Vlasta Závišová, PhD.
RNDr. Martina Kubovčíková, PhD.
Advanced Materials (PMdAj)
Nanomaterials for medical application – functionalization and physicochemical characterization of magnetic nanoparticles based on iron oxides
The aim of the work will be to manage the technology of preparation of magnetic colloidal suspensions based on iron oxide nanoparticles, to functionalize the surface of nanoparticles with biologically active substances in order to minimize their toxicity and ensure their biocompatibility and stability in biological media. Further, to characterize the prepared magnetic nanomaterials in terms of size distribution, morphology, structure, stability, surface and magnetic properties using various techniques. At the same time, their effect on contrast in magnetic resonance imaging (MRI) will be investigated. The amount of heat generated after the application of magnetic hyperthermia will be also measured on the prepared samples, depending on the intensity and frequency of the alternating magnetic field. The results of the study can be used for targeted drug delivery, for the detection of tumour cells, which in combination with hyperthermia and MRI can represent a significant advance in the detection and treatment of cancer.
The aim of the work will be to manage the technology of preparation of magnetic colloidal suspensions based on iron oxide nanoparticles, to functionalize the surface of nanoparticles with biologically active substances in order to minimize their toxicity and ensure their biocompatibility and stability in biological media.
Current journal literature.
Ing. Martina Koneracká, CSc.
doc. Mgr. Iryna Antal, Ph.D.
Advanced Materials (PMd)
Nanomaterials for medical application – functionalization and physicochemical characterization of magnetic nanoparticles based on iron oxides
The aim of the work will be to manage the technology of preparation of magnetic colloidal suspensions based on iron oxide nanoparticles, to functionalize the surface of nanoparticles with biologically active substances in order to minimize their toxicity and ensure their biocompatibility and stability in biological media. Further, to characterize the prepared magnetic nanomaterials in terms of size distribution, morphology, structure, stability, surface and magnetic properties using various techniques. At the same time, their effect on contrast in magnetic resonance imaging (MRI) will be investigated. The amount of heat generated after the application of magnetic hyperthermia will be also measured on the prepared samples, depending on the intensity and frequency of the alternating magnetic field. The results of the study can be used for targeted drug delivery, for the detection of tumour cells, which in combination with hyperthermia and MRI can represent a significant advance in the detection and treatment of cancer.
The aim of the work will be to manage the technology of preparation of magnetic colloidal suspensions based on iron oxide nanoparticles, to functionalize the surface of nanoparticles with biologically active substances in order to minimize their toxicity and ensure their biocompatibility and stability in biological media.
Current journal literature.
Ing. Martina Koneracká, CSc.
doc. Mgr. Iryna Antal, Ph.D.
Physics education (TVFd)
AI tools in innovative physics education.
Artificial Intelligence (AI) tools, especially chatbots based on advanced large-scale neural language models such as ChatGPT, Bard, or Claud, earned significant attention in 2023 across various human activity sectors, including physics education and STEM subjects, due to their impressive capabilities. This dissertation will focus on an in-depth analysis of the current state, impact, dynamic development, and potential of these technologies within the context of innovative physics education. It will explore the possibilities of integrating AI into curricula and teaching methods, aiming to prepare exemplary educational activities supported by AI in a selected area of physics, along with methodological guidelines for their effective use. The empirical mixed methods research will be oriented towards analyzing the impact of these technologies on motivation and teaching efficiency at secondary and tertiary education levels. The work should also evaluate new perspectives on using AI, which could significantly enrich and transform current pedagogical practices in physics education.
The main goal of this dissertation is to theoretically and empirically evaluate the impact and potential of AI tools on improving physics education. Achieving this goal should be realized through integrating AI into physics curricula, creating corresponding educational activities supported by AI, and verifying and analyzing their impact on motivation and efficiency in secondary and tertiary education.
[1] J. W. Creswell and V. L. P. Clark, Designing and Conducting Mixed Methods Research, 3rd ed. London: SAGE Publications, Inc, 2017. ISBN 978-1-483346-98-4 [2] W. Daher, H. Diab, and A. Rayan, “Artificial Intelligence Generative Tools and Conceptual Knowledge in Problem Solving in Chemistry,” Information, vol. 14, no. 7, Art. no. 7, 2023 [3] M. N. Dahlkemper, S. Z. Lahme, and P. Klein, “How do physics students evaluate artificial intelligence responses on comprehension questions? A study on the perceived scientific accuracy and linguistic quality of ChatGPT,” Phys. Rev. Phys. Educ. Res., vol. 19, no. 1, p. 010142, 2023 [4] A. Al-Marzouqi (ed.) rt al., Artificial Intelligence in Education: The Power and Dangers of ChatGPT in the Classroom. Springer, 2024. ISBN 978-3-031-52280-2. [5] G. Kortemeyer, “Toward AI grading of student problem solutions in introductory physics: A feasibility study,” Phys. Rev. Phys. Educ. Res., vol. 19, no. 2, p. 020163, 2023 [6] W. Xu and F. Ouyang, "The Application of AI Technologies in STEM Education: A Systematic Review from 2011 to 2021," International Journal of STEM Education, vol. 9, no. 1, p. 59, 2022.
doc. RNDr. Jozef Hanč, PhD.
Physics (Fd)
Design and implementation of particle based model of compressible fluids
The main focus of the PhD research project is to create a multiscale model of compressible liquid flow (including possible non-Newtonian liquids) with possible embedded fiducial or biological particles, based on particle formalisms as an alternative to the more usual CFD (OpenFoam, as our UOX partner already does). The purpose of such simulations is to provide synthetic data for AI training to interpret fast XMPH experiments (acronym for X-ray multiprojection holography), including flow regimes involving cavitation and turbulence phenomena. This particle model will be used for the reconstruction of data from fast dynamics experiments (sampling rate up to 4.5 MHz), taking advantage of the unique experimental prototype built by the Horizon EU MHz Tomoscopy project (grant agreement No. 101046448), as well as the follow-up fluidics research projects (in preparation). Our partners are EuXFEL (DE), DESY (DE), SUNA GmBH (DE), University of Oxford (GB), Lund University (SE), Tohoku University (JPN), DTU (DK), TUHH (DE), Stockholm University (SE), Iasu University (RO) but also others. The PhD project will require intensive cooperation with project partners due to multidisciplinarity. The scope of the work is also suitable for several (2-3) PhD students. Possibility of bilateral/multilateral studies (dual PhD diplomas) or industrial PhD.
creation of coarse grain multiscale model of compressiblefluids including elastic biological particles for training of AI reconstruction of our XMPH experiments.
[1] Vagovič, P., Sato, T., Mikeš, L., Mills, G., Graceffa, R., Mattsson, F., Villanueva-Perez, P., Ershov, A., Faragó, T., Uličný, J., et al. (2019). Megahertz x-ray microscopy at x-ray free-electron laser and synchrotron sources. Optica, OPTICA 6, 1106–1109. [2] Hrivňak, S., Hovan, A., Uličný, J., and Vagovič, P. (2018). Phase retrieval for arbitrary Fresnel-like linear shift-invariant imaging systems suitable for tomography. Biomed Opt Express 9, 4390–4400., Hrivňak, S., Uličný, J., Mikeš, L., Cecilia, A., Hamann, E., Baumbach, T., Švéda, L., Zápražný, Z., Korytár, D., Gimenez-Navarro, E., et al. (2016). Single- distance phase retrieval algorithm for Bragg Magnifier microscope. Opt Express 24, 27753–27762. [4] Buakor, K.; Zhang, Y.; Birnšteinová, Š.; Bellucci, V.; Sato, T.; Kirkwood, H.; Mancuso, A. P.; Vagovic, P.; Villanueva-Perez, P. Shot-to-Shot Flat-Field Correction at X-Ray Free-Electron Lasers. Opt. Express 2022, 30 (7), 10633. [4] Han, H.; Round, E.; Schubert, R.; Gül, Y.; Makroczyová, J.; Meza, D.; Heuser, P.; Aepfel-bacher, M.; Barák, I.; Betzel, C.; Fromme, P.; Kursula, I.; Nissen, P.; Tereschenko, E.; Schulz, J.; Uetrecht, C.; Ulicný, J.; Wilmanns, M.; Hajdu, J.; Lamzin, V. S.; Lorenzen, K. The XBI BioLab for Life Science Experiments at the European XFEL. J Appl Crystallogr 2021, 54 (1), 7–21. [5] Project: 101046448 — MHz-TOMOSCOPY — HORIZON-EIC-2021- PATHFINDEROPEN-01 , https://www.tomoscopy.eu [6] Soyama, H.; Liang, X.; Yashiro, W.; Kajiwara, K.; Asimakopoulou, E. M.; Bellucci, V.; Birnsteinova, S.; Giovanetti, G.; Kim, C.; Kirkwood, H. J.; Koliyadu, J. C. P.; Letrun, R.; Zhang, Y.; Uličný, J.; Bean, R.; Mancuso, A. P.; Villanueva-Perez, P.; Sato, T.; Vagovič, P.; Eakins, D.; Korsunsky, A. M. Revealing the Origins of Vortex Cavitation in a Venturi Tube by High Speed X-Ray Imaging. Ultrasonics Sonochemistry 2023, 101, 106715. https://doi.org/10.1016/j.ultsonch.2023.106715. [7] Zhang, Y.; Yao, Z.; Ritschel, T.; Villanueva‐Perez, P. ONIX: An X‐ray Deep‐learning Tool for 3D Reconstructions from Sparse Views. Applied Research 2023, e202300016. https://doi.org/10.1002/appl.202300016.
doc. RNDr. Jozef Uličný, CSc.
Aatto Laaksonen
Physics of Condensed Matter (FKLdAj)
New superconductors based on high-entropy alloys
High-entropy alloys (HEAs) represent a relatively new class of materials, which has recently been the subject of considerable interest in both basic and applied research. These alloys consist of several constituent elements (4 - 6), while individual elements occupy lattice positions with a high degree of disorder, i.e. with high configurational entropy. Superconductivity of HEAs, with transition temperature Tc up to approx. 10 K and a critical magnetic field up to approx. 20 T, is very stable and resistant to various chemical and mechanical influences. The topic of the proposed dissertation will be the preparation and research of the properties of new superconductors based on HEAs. These will include HEAs, which will incorporate light elements, e.g. nitrogen, carbon or hydrogen, which will lead to changes in their superconducting properties. In addition, the influence of pressure and thickness of HEAs thin films on their superconducting parameters will also be investigated. Under the guidance of the supervisor, the student will participate in the preparation and characterization of samples, experimental research, data analysis and presentation of the achieved results.
The aim of the proposed dissertation will be the preparation and research of the properties of new superconductors based on high-entropy alloys.
1. G. Pristáš, G.C. Gruber, M. Orendáč, J. Bačkai, J. Kačmarčík, F. Košuth, S. Gabáni, P. Szabó, Ch. Mitterer, K. Flachbart: Multiple transition temperature enhancement in superconducting TiNbMoTaW high entropy alloy films through tailored N incorporation, Acta Materialia 262 (2024) 119428. 2. G. Pristáš, J. Bačkai, Mat. Orendáč, S. Gabáni, F. Košuth, M. Kuzmiak, P. Szabó, E. Gažo, R. Franz, S. Hirn, G. C. Gruber, Ch. Mitterer, S. Vorobiov, K. Flachbart: Superconductivity in medium- and high-entropy alloy thin films: Impact of thickness and external pressure, Physical Review B 107 (2023) 024505.
RNDr. Gabriel Pristáš, PhD.
doc. RNDr. Karol Flachbart, DrSc.
Advanced Materials (PMd)
Novel hybrid 2D magnets based on layered double hydroxides
Layered double hydroxides (LDH) are natural 2D materials with the unique flexibility of chemical composition. LDH are composed of the M2+-M3+ mixed metal layers where the metal cations are surrounded by the edge-linked hydroxide octahedra. The positive charge of the metal layers is compensated by anions intercalated in between. More than one type of anions can be intercalated and exchanged with other anionic species, which are different in their composition, size, and charge. LDH compositions with M2+= Co, Ni and/or M3+= Fe, Cr, Mn demonstrate magnetic ordering at low temperatures. The magnetic properties of those LDH depend on the cation content and ratio as well as the interlayer distance. Moreover, these properties are morphology-dependent and can be tuned via controlled synthesis and formation of arranged layers of crystallites. Such features make the magnetic LDH very attractive for experimental modelling of effects in 2D magnetic systems including quantum magnets. Besides, they can be used to develop hybrid magnets and related materials for practical use. The main objective of this PhD research is to prepare and study of crystal structure, morphology and magnetic behaviour of new magnetic LDH intercalated with functional species such as molecular magnets. During the PhD research, a candidate will acquire the following practical skills: preparation of LDH using coprecipitation, hydrothermal synthesis, anion exchange as well as operating an X-ray powder diffractometer including in-situ measurement in non-ambient conditions, sampling and operating scanning and transmission electron microscopes, operating SQUID magnetometers.
The main objective of this PhD research is to prepare and study of crystal structure, morphology and magnetic behaviour of new magnetic LDH intercalated with functional species such as molecular magnets.
Current journal literature.
doc. RNDr. Erik Čižmár, PhD.
Biophysics (BFd)
Exploring the frontiers of protein dynamics: from crystallography to ultrafast spectroscopy
Join our cutting-edge research project aimed at unraveling the intricate world of protein structures and dynamics. This PhD opportunity will immerse you in the fascinating realm of protein crystallography and advanced spectroscopic techniques. You will be at the forefront of employing state-of-the-art methodologies to delve into protein-ligand interactions, protein quakes, and crucial enzymatic processes like proton and electron transfers. As a PhD candidate, you will be instrumental in conducting these sophisticated experiments, analyzing data, and contributing to the field's knowledge. This project offers a unique interdisciplinary and international experience between Košice(SK)•Prague(CZ)•Paris, (FR), bridging the gap between structural biology, biophysics, and chemistry. Your research could pave the way for groundbreaking advancements in understanding protein mechanisms, potentially leading to novel therapeutic approaches.
1) Determine the three-dimensional structures of novel protein domains, including new chaperone domains of Hsp70. 2) Investigate human pathological immunoglobulin light chains in complex with emerging therapeutics. 3) Apply ultrafast optical spectroscopies and time-resolved X-ray techniques to study enzyme catalysis and other dynamic processes.
1. Džupponová V, Žoldák G. Aggregation mechanism and branched 3D morphologies of pathological human light chain proteins under reducing conditions. Colloids Surf B Biointerfaces. 2023 Jan;221:112983. doi: 10.1016/j.colsurfb.2022.112983. 2. Džupponová V, Žoldák G. Salt-dependent passive adsorption of IgG1κ-type monoclonal antibodies on hydrophobic microparticles. Biophys Chem. 2021 Aug;275:106609. doi: 10.1016/j.bpc.2021.106609. 3. Džupponová V, Huntošová V, Žoldák G. A kinetic coupling between protein unfolding and aggregation controls time-dependent solubility of the human myeloma antibody light chain. Protein Sci. 2020 Dec;29(12):2408-2421. doi: 10.1002/pro.3968. 4. Nemergut M, Pluskal D, Horackova J, Sustrova T, Tulis J, Barta T, Baatallah R, Gagnot G, Novakova V, Majerova M, Sedlackova K, Marques SM, Toul M, Damborsky J, Prokop Z, Bednar D, Janin YL, Marek M. Illuminating the mechanism and allosteric behavior of NanoLuc luciferase. Nat Commun. 2023 Nov 29;14(1):7864. doi: 10.1038/s41467-023-43403-y.
doc. RNDr. Gabriel Žoldák, DrSc.
RNDr. Michal Nemergut, PhD.
Physics of Condensed Matter (FKLd)
New superconductors based on high-entropy alloys
High-entropy alloys (HEAs) represent a relatively new class of materials, which has recently been the subject of considerable interest in both basic and applied research. These alloys consist of several constituent elements (4 - 6), while individual elements occupy lattice positions with a high degree of disorder, i.e. with high configurational entropy. Superconductivity of HEAs, with transition temperature Tc up to approx. 10 K and a critical magnetic field up to approx. 20 T, is very stable and resistant to various chemical and mechanical influences. The topic of the proposed dissertation will be the preparation and research of the properties of new superconductors based on HEAs. These will include HEAs, which will incorporate light elements, e.g. nitrogen, carbon or hydrogen, which will lead to changes in their superconducting properties. In addition, the influence of pressure and thickness of HEAs thin films on their superconducting parameters will also be investigated. Under the guidance of the supervisor, the student will participate in the preparation and characterization of samples, experimental research, data analysis and presentation of the achieved results.
The aim of the proposed dissertation will be the preparation and research of the properties of new superconductors based on high-entropy alloys.
1. G. Pristáš, G.C. Gruber, M. Orendáč, J. Bačkai, J. Kačmarčík, F. Košuth, S. Gabáni, P. Szabó, Ch. Mitterer, K. Flachbart: Multiple transition temperature enhancement in superconducting TiNbMoTaW high entropy alloy films through tailored N incorporation, Acta Materialia 262 (2024) 119428. 2. G. Pristáš, J. Bačkai, Mat. Orendáč, S. Gabáni, F. Košuth, M. Kuzmiak, P. Szabó, E. Gažo, R. Franz, S. Hirn, G. C. Gruber, Ch. Mitterer, S. Vorobiov, K. Flachbart: Superconductivity in medium- and high-entropy alloy thin films: Impact of thickness and external pressure, Physical Review B 107 (2023) 024505.
RNDr. Gabriel Pristáš, PhD.
doc. RNDr. Karol Flachbart, DrSc.
Advanced Materials (PMdAj)
Novel hybrid 2D magnets based on layered double hydroxides
Layered double hydroxides (LDH) are natural 2D materials with the unique flexibility of chemical composition. LDH are composed of the M2+-M3+ mixed metal layers where the metal cations are surrounded by the edge-linked hydroxide octahedra. The positive charge of the metal layers is compensated by anions intercalated in between. More than one type of anions can be intercalated and exchanged with other anionic species, which are different in their composition, size, and charge. LDH compositions with M2+= Co, Ni and/or M3+= Fe, Cr, Mn demonstrate magnetic ordering at low temperatures. The magnetic properties of those LDH depend on the cation content and ratio as well as the interlayer distance. Moreover, these properties are morphology-dependent and can be tuned via controlled synthesis and formation of arranged layers of crystallites. Such features make the magnetic LDH very attractive for experimental modelling of effects in 2D magnetic systems including quantum magnets. Besides, they can be used to develop hybrid magnets and related materials for practical use. The main objective of this PhD research is to prepare and study of crystal structure, morphology and magnetic behaviour of new magnetic LDH intercalated with functional species such as molecular magnets. During the PhD research, a candidate will acquire the following practical skills: preparation of LDH using coprecipitation, hydrothermal synthesis, anion exchange as well as operating an X-ray powder diffractometer including in-situ measurement in non-ambient conditions, sampling and operating scanning and transmission electron microscopes, operating SQUID magnetometers.
The main objective of this PhD research is to prepare and study of crystal structure, morphology and magnetic behaviour of new magnetic LDH intercalated with functional species such as molecular magnets.
Current journal literature.
doc. RNDr. Erik Čižmár, PhD.
Advanced Materials (PMdAj)
Optical emission and electron spectroscopy of reactive sputtering and of the multicomponent ceramic coatings
The advanced ceramic coatings for ultrahigh temperature applications consist of high melting point and heavy (Zr, Hf, Ru, W..) metallic elements strongly bonded with light elements (boron, nitrogen, oxygen, carbon with hydrogen) which result in difficulties in quantitative analysis when using conventional chemical methods. Usually, a combination of several analytical methods is necessary to obtain quantitative characterization of both light and heavy elements at the same time in the resulting compounds. However, the control of the coating composition requires also the control of the plasma composition during the deposition. Thus, the in situ methods of plasma composition should be combined with the methods applied to the coatings to determine the relationships controlling their chemistry, structure and properties. The work should employ both in-situ optical emission spectroscopy for the plasma control with the ex-situ glow discharge optical emission spectrocopy (GDOES), Raman spectroscopy as well as energy and wavelength disperse electron spectroscopy (and potentially also X-ray Photoelectron Spectroscopy (XPS) and Secondary Ion Mass Spectrocopy (SIMS)) methods on the carbide and boride based coatings for quantification of their chemistry to establish the correlations between the plasma characteristics and their structure and properties. The plasma study will be performed on the existing iPVD systems using OES system (Avantes, The Netherlands) and Raman microscope (XploRa, Horiba, France), GDOES (GD2, Horiba, France) as well as on the EDS and WDS (Oxford, UK) attached to the scanning electron microscopes. The introduction of new XPS and SIMS facilities is also anticipated.
Investigation of the relationships among the plasma characteristics and chemical composition and eventually, also structure and properties of the multicomponent ceramic coatings by means of in situ optical emission spectroscopy for the plasma control with the ex-situ glow discharge optical emission spectrocopy (GDOES), Raman spectroscopy as well as energy and wavelength disperse electron spectroscopy.
1. D.M. Mattox, Handbook of Physical Vapor Deposition (PVD) processing, Mattox D.M., Noyes Publ., New Jersey, 1998. 2. N. Britun, T. Minea, S. Konstantinidis, R. Snyders, Plasma diagnostics for understanding the plasma-surface interactions in HIPIMS discharges” a review, J. Phys. D: Appl. Phys., 47 (2014) 224001. doi: 10.1088/0022-3727/47/22/224001 3. F. Lofaj, M. Kabátová, J. Dobrovodský, G. Cempura, Hydrogenation and hybridization in hard W-C:H coatings prepared by hybrid PVD-PECVD method with methane and acetylene, Int. J. Ref. Met. Hard Mat., 88 (2020), 105211. https://doi.org/10.1016/j.ijrmhm.2020.105211
doc. RNDr. František Lofaj, DrSc.
Advanced Materials (PMd)
Optical emission and electron spectroscopy of reactive sputtering and of the multicomponent ceramic coatings
The advanced ceramic coatings for ultrahigh temperature applications consist of high melting point and heavy (Zr, Hf, Ru, W..) metallic elements strongly bonded with light elements (boron, nitrogen, oxygen, carbon with hydrogen) which result in difficulties in quantitative analysis when using conventional chemical methods. Usually, a combination of several analytical methods is necessary to obtain quantitative characterization of both light and heavy elements at the same time in the resulting compounds. However, the control of the coating composition requires also the control of the plasma composition during the deposition. Thus, the in situ methods of plasma composition should be combined with the methods applied to the coatings to determine the relationships controlling their chemistry, structure and properties. The work should employ both in-situ optical emission spectroscopy for the plasma control with the ex-situ glow discharge optical emission spectrocopy (GDOES), Raman spectroscopy as well as energy and wavelength disperse electron spectroscopy (and potentially also X-ray Photoelectron Spectroscopy (XPS) and Secondary Ion Mass Spectrocopy (SIMS)) methods on the carbide and boride based coatings for quantification of their chemistry to establish the correlations between the plasma characteristics and their structure and properties. The plasma study will be performed on the existing iPVD systems using OES system (Avantes, The Netherlands) and Raman microscope (XploRa, Horiba, France), GDOES (GD2, Horiba, France) as well as on the EDS and WDS (Oxford, UK) attached to the scanning electron microscopes. The introduction of new XPS and SIMS facilities is also anticipated.
Investigation of the relationships among the plasma characteristics and chemical composition and eventually, also structure and properties of the multicomponent ceramic coatings by means of in situ optical emission spectroscopy for the plasma control with the ex-situ glow discharge optical emission spectrocopy (GDOES), Raman spectroscopy as well as energy and wavelength disperse electron spectroscopy.
1. D.M. Mattox, Handbook of Physical Vapor Deposition (PVD) processing, Mattox D.M., Noyes Publ., New Jersey, 1998. 2. N. Britun, T. Minea, S. Konstantinidis, R. Snyders, Plasma diagnostics for understanding the plasma-surface interactions in HIPIMS discharges” a review, J. Phys. D: Appl. Phys., 47 (2014) 224001. doi: 10.1088/0022-3727/47/22/224001 3. F. Lofaj, M. Kabátová, J. Dobrovodský, G. Cempura, Hydrogenation and hybridization in hard W-C:H coatings prepared by hybrid PVD-PECVD method with methane and acetylene, Int. J. Ref. Met. Hard Mat., 88 (2020), 105211. https://doi.org/10.1016/j.ijrmhm.2020.105211
doc. RNDr. František Lofaj, DrSc.
Biophysics (BFd)
Amyloid Paradigm: From Pathological Structures to Functional Bionanomaterials
Amyloids represent a class of robust, highly ordered structures that can be formed by many natural or artificially designed peptides and proteins. Traditionally, amyloids are linked with neurodegeneration and numerous other diseases, including Alzheimer's, Parkinson's, Huntington's diseases, and spongiform encephalopathies. On the other hand, many living organisms make use of diverse amyloid proteins as functional building blocks to fulfill a variety of physiological applications. This fact, along with the intrinsic self-assembly and outstanding material properties of amyloids, has prompted significant research in the synthetic design of functional amyloids to form diverse nanoarchitecture, molecular materials, and hybrid or composite materials. Within the doctoral research, the implication of oxidative stress and apoptosis in amyloid aggregation will be examined, i.e., the study of the structural and functional consequences of the interaction of protein/protein amyloid structures with various types of substances, including multifunctional composites, will be conducted. The second goal will be the preparation of multifunctional bioconjugates based on functional amyloid proteins, which can be used for binding and release of biologically active agents, formation of multiple protein arrangements for efficient enzymatic cascades, or even as the promising carriers for targeted drug delivery with controllable release.
1.Preparation of protein amyloid structures. Ia - preparation of pathological amyloid structures Ib - preparation of functional amyloid structures 2.The role of oxidative stress in the process of amyloidogenesis. 3.Preparation of bioconjugates/multicomposites based on amyloid proteins IIIa - Preparation and characterization of unmodified protein fibrils IIIb - DNA-functionalization of fibrils IIIc - Study of self-assembly of DNA-protein conjugates and DNA-directed self-assembly of hybrid fibrils using several biophysical and biochemical techniques
Naleway, S.E., Porter, M.M., McKittrick, J., Meyers, M.A. (2015) Advanced Materials 27, 5455-5476 Knowles, T.P.J., Buehler, M.J. (2011) Nature Nanotechnology 6, 469-479 Das, A., Shah, M., and Saraogi, I. (2022). ACS Bio Med. Chem. Au 0, 205–221 Humenik, M., Scheibel, T. (2014) ACS Nano 8, 1342-1349 Humenik, M., Preiß, T., Gödrich, S, et al. (2020) Materials Today Bio, 6, 100045
Ing. RNDr. Katarína Šipošová, PhD.
RNDr. Veronika Huntošová, PhD.
Advanced Materials (PMdAj)
PEM electrolyzer with new catalysts for hydrogen evolution reaction
Proton exchange membrane (PEM) electrolyzers, using only renewable energy and water, are a promising tool for green hydrogen production. The production process call electrolysis and it includes two half-reactions of water decomposition: reduction of hydrogen and oxidation of oxygen. A PEM electrolyzer can quickly respond to fluctuations typical of renewable energy production, making this technology ideal for balancing the grid and energy deficits. In order for the PEM electrolysis of water to become capable of competition to fossil fuel and produce hydrogen as the fuel of the future, it is necessary to make its individual components cheaper. Catalysts in PEM electrolysis are represented by platinum metals, which represent a limitation in terms of price and scarcity. Therefore, the dissertation will be focused on the preparation of cheap electrocatalysts based on chalcogenides and phosphides, which can be directly placed in PEM electrolyzers. The effectiveness and efficiency of the newly assembled PEM customs will be monitored.
Preparation of a PEM cell with electrocatalysts based on chalcogenides and phosphides for efficient production of hydrogen as the fuel of the future.
Strecková M. et al, Nanoarchitectonics of binary transition metal phosphides embedded in carbon fibers as a bifunctional electrocatalysts for electrolytic water splitting, Journal of Alloys and CompoundsVolume 92325 November 2022 Durovic M. et al, Efficient cathode for the hydrogen evolution reaction in alkaline membrane water electrolysis based on NiCoP embedded in carbon fibres, Journal of Power Sources, Volume 5561 February 2023
RNDr. Magdaléna Strečková, PhD.
Advanced Materials (PMd)
PEM electrolyzer with new catalysts for hydrogen evolution reaction
Proton exchange membrane (PEM) electrolyzers, using only renewable energy and water, are a promising tool for green hydrogen production. The production process call electrolysis and it includes two half-reactions of water decomposition: reduction of hydrogen and oxidation of oxygen. A PEM electrolyzer can quickly respond to fluctuations typical of renewable energy production, making this technology ideal for balancing the grid and energy deficits. In order for the PEM electrolysis of water to become capable of competition to fossil fuel and produce hydrogen as the fuel of the future, it is necessary to make its individual components cheaper. Catalysts in PEM electrolysis are represented by platinum metals, which represent a limitation in terms of price and scarcity. Therefore, the dissertation will be focused on the preparation of cheap electrocatalysts based on chalcogenides and phosphides, which can be directly placed in PEM electrolyzers. The effectiveness and efficiency of the newly assembled PEM customs will be monitored.
Preparation of a PEM cell with electrocatalysts based on chalcogenides and phosphides for efficient production of hydrogen as the fuel of the future.
Strecková M. et al, Nanoarchitectonics of binary transition metal phosphides embedded in carbon fibers as a bifunctional electrocatalysts for electrolytic water splitting, Journal of Alloys and CompoundsVolume 92325 November 2022 Durovic M. et al, Efficient cathode for the hydrogen evolution reaction in alkaline membrane water electrolysis based on NiCoP embedded in carbon fibres, Journal of Power Sources, Volume 5561 February 2023
RNDr. Magdaléna Strečková, PhD.
Biophysics (BFd)
The comparison of cell responses to external stimuli in 2D and 3D cellular models of neurodegenerative diseases.
The etiology of the most neurodegenerations is not clear, however, interactions between genetic and environmental factors, lifestyles and dietary factors were shown to play a role in Parkinson (PD) or Alzheimer (AD) disease and ALS (amyotrophic lateral sclerosis). Long-term/low dose exposure to metals, pesticides, solvents, and petrochemicals were indicated as environment risk factors in PD, AD and ALS. PD was positively associated with two groups of pesticides, including rotenone (ROT) and paraquat (PAR), defined by mechanisms that impair mitochondrial function and those that increase oxida¬tive stress further supporting a role for these mechanisms in PD pathophysiology. ROT induced PD models in vitro and in vivo display clinical symptoms of Parkinsons such as loss of dopaminergic neurons, increased oxida¬tive stress, and aggregates of alpha-synuclein (Lewy body inclusions). This study will focus on comparison of cell responses to oxidative stress, Ca2+ signaling and alpha-synuclein changes in 2D and 3D cellular structures. The research will use an interdisciplinary approach using fluorescent microscopy, AFM, biochemistry, spectroscopy and molecular biology.
Determination of differences between 2D and 3D PD models in cellular response to stress signals.
1. Baltazar et al. (2014) Toxicology Letters 230 85– 2. Tanner et al. (2011) Environmental Health Perspectives 119 (6) 3. Johnson & Bobrovskaya (2015) NeuroToxicology 46 (2015) 101–116 4. Henderson, T.A. and L.D. Morries, Neuropsych. Dis. and Treat. (2015) 11: p. 2191-2208 5. Johnstone, D.M. et al. (2016) Frontiers in Neuroscience, 9. 6. Tang, X., et al. (2014) Front Physiol, 5: p. 175. 7. Yang et al (2018) Experimental Neurology 299 86–96. 8. Stroffekova, K; Kolesarova, S and Tomkova, S (2021 EUR. BIOPHYS. J. WITH BIOPHYS. LETT. 50 (SUPPL 1)
doc. RNDr. Katarína Štroffeková, PhD.
RNDr. Zuzana Bednáriková, PhD.
Advanced Materials (PMd)
Surface deformation of magnetic magnetic domain walls in thin wires
Cylindrical topography of ferromagnetic samples is one of the crucial factors that contributes to a high domain wall velocity. In our work, we will focus on time-resolved observation of a surface domain wall shape in thin wires. We will employ a novel experimental setup based on Magneto-optical Kerr effect (MOKE), that will be extended by an option to observe multiple domain walls simultaneously. Student will participate on design of excitation coils and simulations of magnetic fields. Observations of a surface domain wall deformation will be carried out on samples differing by magnetic anisotropies.
The aim of this work is to make a new magnetooptical observations of wires with non plana topography.
1. HUBERT, Alex; SCHÄFER, Rudolf. Magnetic domains: the analysis of magnetic microstructures. Springer Science & Business Media, 2008. 2. HAJKO ,Vladimír; POTOCKÝ, Ladislav; ZENTKO, Anton. Magnetizačné procesy. Bratislava : Alfa, 1982. 3. VIŠŇOVSKÝ, Štefan. Optics in magnetic multilayers and nanostructures. Crc Press, 2018. 4. CHEN, C. W. Magnetism and metallurgy of soft magnetic materials Dover Pub. Inc., New York, 1986.
RNDr. Kornel Richter, PhD.
Physics of Condensed Matter (FKLdAj)
Preparation and characterization of van der Waals heterostructures with novel quantum properties
Van der Waals heterostructures allow for the combination of materials that don't normally interact. They are made up of two-dimensional layers of different materials held together by weak van der Waals forces, allowing for the formation of unique structures with unique properties. This opens a range of possibilities to explore novel quantum effects and the design of new quantum devices. We will focus on the preparation of heterostructures comprised of superconducting and topologically non-trivial layers by our novel fabrication technique that enables the assembly and deterministic placement of van der Waals heterostructures in a glovebox. Subsequently, the heterostructures will be transferred into our ultra-high vacuum system without being exposed to air. There we will explore their electronic properties utilizing our state-of-the-art low temperature scanning tunneling microscope.
We will focus on the preparation of heterostructures comprised of superconducting and topologically non-trivial layers by our novel fabrication technique that enables the assembly and deterministic placement of van der Waals heterostructures in a glovebox. Subsequently, the heterostructures will be transferred into our ultra-high vacuum system without being exposed to air. There we will explore their electronic properties utilizing our state-of-the-art low temperature scanning tunneling microscope.
Lupke, F. et al. Proximity-induced superconducting gap in the quantum spin Hall edge state of monolayer WTe2. Nat. Phys. 16, 526–530 (2020) Fu, L. & Kane, C. L. Superconducting proximity effect and Majorana fermions at the surface of a topological insulator. Phys. Rev. Lett. 100, 096407 (2008). Kezilebieke, S. et al. Topological superconductivity in a van der waals heterostructure. Nature 588, 424–428 (2020).
Mgr. Tomáš Samuely, PhD., univerzitný docent
Mgr. Dominik Volavka
Advanced Materials (PMdAj)
Preparation and the study of the soft magnetic composites with ferrite as an insulation part
The study is oriented on the preparation and the investigation of magnetic composite materials based on the Fe particles coated by ferrite. Due to their unique properties, soft magnetic composites have been used in recent years, for example, in electric motors and power electronics. Potential advantage of soft magnetic ferrites when used as electro insulating layer instead of other insulations is their ferrimagnetic behaviour, improving the magnetic interaction between the ferromagnetic powder particles in the final composite. Composite materials will be prepared by pressing under different physical conditions. The hysteresis loops and their energy losses, the electrical resistivity and wideband complex permeability will be studied on prepared materials. The aim is the optimization of preparation process (composition, method of preparation of hybrid powder material, pressing parameters, annealing parameters) of soft magnetic materials with required magnetic properties at middle-frequencies.
The study of the physical properties of soft magnetic composites, their preparation and thermal treatment. The learning of the magnetic measurements methods. Preparation of the Fe based composite materials with ferrite as a nonconductive binder. Setting up the method for preparation of ferro/ferrit hybrid composite and the optimization of the preparation process for the soft magnetic materials with required magnetic properties in studied frequency interval.
1. R. M. Bozorth, Ferromagnetism, third edition (IEEE Press, Piscataway, NJ), 1993. 2. S. Chikazumi, Physics of Ferromagnetism, Oxford University press, 1997 3. scientific publications on the subject of soft magnetic composites.
doc. RNDr. Ján Füzer, PhD.
Advanced Materials (PMdAj)
Preparation of compacted and composite soft magnetic materials for low frequency applications
The work is oriented to the investigation of the influence of technological procedures and dielectrics at the preparation of compacted and composite materials on their magnetic properties at magnetization reversal process in alternating magnetic fields in the range of low frequencies in a wide range of maximum magnetic inductions. The ferromagnetic component will be based on iron and nickel and the insulating binder are inorganic materials. The goal is also to compare the magnetic properties of the prepared materials with conventional ones used under similar physical conditions.
1. R. M. Bozorth Ferromagnetism, third edition (IEEE Press, Piscataway, NJ), 1993 2. H. Shokrollahi, K. Janghorban J. Mater. Proc. Technol. 189 (2007) 1 3. E. A. Périgo, B. Weidenfeller, P. Kollár, J. Füzer, Applied Physics Reviews 5, 031301 (2018);
prof. RNDr. Peter Kollár, DrSc.
Physics of Condensed Matter (FKLd)
Preparation and characterization of van der Waals heterostructures with novel quantum properties
Van der Waals heterostructures allow for the combination of materials that don't normally interact. They are made up of two-dimensional layers of different materials held together by weak van der Waals forces, allowing for the formation of unique structures with unique properties. This opens a range of possibilities to explore novel quantum effects and the design of new quantum devices. We will focus on the preparation of heterostructures comprised of superconducting and topologically non-trivial layers by our novel fabrication technique that enables the assembly and deterministic placement of van der Waals heterostructures in a glovebox. Subsequently, the heterostructures will be transferred into our ultra-high vacuum system without being exposed to air. There we will explore their electronic properties utilizing our state-of-the-art low temperature scanning tunneling microscope.
We will focus on the preparation of heterostructures comprised of superconducting and topologically non-trivial layers by our novel fabrication technique that enables the assembly and deterministic placement of van der Waals heterostructures in a glovebox. Subsequently, the heterostructures will be transferred into our ultra-high vacuum system without being exposed to air. There we will explore their electronic properties utilizing our state-of-the-art low temperature scanning tunneling microscope.
Lupke, F. et al. Proximity-induced superconducting gap in the quantum spin Hall edge state of monolayer WTe2. Nat. Phys. 16, 526–530 (2020) Fu, L. & Kane, C. L. Superconducting proximity effect and Majorana fermions at the surface of a topological insulator. Phys. Rev. Lett. 100, 096407 (2008). Kezilebieke, S. et al. Topological superconductivity in a van der waals heterostructure. Nature 588, 424–428 (2020).
Mgr. Tomáš Samuely, PhD., univerzitný docent
Mgr. Dominik Volavka
Advanced Materials (PMd)
Preparation and the study of the soft magnetic composites with ferrite as an insulation part
The study is oriented on the preparation and the investigation of magnetic composite materials based on the Fe particles coated by ferrite. Due to their unique properties, soft magnetic composites have been used in recent years, for example, in electric motors and power electronics. Potential advantage of soft magnetic ferrites when used as electro insulating layer instead of other insulations is their ferrimagnetic behaviour, improving the magnetic interaction between the ferromagnetic powder particles in the final composite. Composite materials will be prepared by pressing under different physical conditions. The hysteresis loops and their energy losses, the electrical resistivity and wideband complex permeability will be studied on prepared materials. The aim is the optimization of preparation process (composition, method of preparation of hybrid powder material, pressing parameters, annealing parameters) of soft magnetic materials with required magnetic properties at middle-frequencies.
The study of the physical properties of soft magnetic composites, their preparation and thermal treatment. The learning of the magnetic measurements methods. Preparation of the Fe based composite materials with ferrite as a nonconductive binder. Setting up the method for preparation of ferro/ferrit hybrid composite and the optimization of the preparation process for the soft magnetic materials with required magnetic properties in studied frequency interval.
1. R. M. Bozorth, Ferromagnetism, third edition (IEEE Press, Piscataway, NJ), 1993. 2. S. Chikazumi, Physics of Ferromagnetism, Oxford University press, 1997 3. scientific publications on the subject of soft magnetic composites.
doc. RNDr. Ján Füzer, PhD.
Biophysics (BFd)
Preparation and realisation of flow-imaging experiments involving individual biological particles and/or their dynamics – customization of multiprojection experiment and its 4D reconstruction
The imaging of individual biological particles with high temporal and spatial resolution has multiple pitfalls, and individual imaging modalities have specific limits. For imaging in a hard X-ray area, the limit is the size and time profile of available photon budget, as well as the quality of the optics, the key advantage is the ability to display arbitrary materials and environments. The high repeating frequency of modern free-electron lasers or synchrotrons with a sufficient photon budget makes it possible to reconstruct in principle the 4D dynamics of optically opaque objects of interest in fundamental science but also in applications. In our experiments on EuXFEL but also on 3rd generation synchrotron sources, we managed to demonstrate the technical feasibility of such 4D multi-projection imaging with submicrometer resolution and megahertz sampling rates. The PhD project is an integral part of a longer-term project of multi-projection X-ray MHz microscopy built on EuXFEL by an international consortium, awarded by the prestigious EU's EIC Horizon Europe project. The longer-term aim is to take advantage of the experience obtained by constructing a prototype of multi-projection X-ray microscopy for a specific design of the experiment for imaging biological particles in a stream and demonstrating its feasibility in pilot measurements. In addition to biological particles, the use of microscopic calibration particles designed theoretically and printed by 3D printers in partner institutions is also envisaged. The main role of the PhD candidate will be the generation of synthetic data by multiscale dynamics techniques, the numerical simulation of an imaging experiment and the use of machine learning techniques to recognize useful behavioral patterns and to accelerate the interpretation of projections in high-throughput experiments. This approach is required by transition from direct imaging techniques to lensless imaging, where 4D reconstruction requires the design/modification of existing reconstruction algorithms] to solve the inverse problem for extreme dataflows generated by multiprojection experiments.
The aim of the PhD topic is to generate synthetic data using multiscale dynamics techniques, numerical simulation of an imaging experiment, and to create machine learning technique procedures to recognize useful behavioral patterns and accelerate the interpretation of projections in high-throughput experiments. The specificity of the approach lies in the transition from direct imaging techniques to lensless imaging, where 4D reconstruction requires design/modification of existing reconstruction algorithms to solve the inverse problem.
1. Vagovič, P., Sato, T., Mikeš, L., Mills, G., Graceffa, R., Mattsson, F., Villanueva-Perez, P., Ershov, A., Faragó, T., Uličný, J., et al. (2019). Megahertz x-ray microscopy at x-ray free-electron laser and synchrotron sources. Optica, OPTICA 6, 1106–1109. 2. Perepelytsya, S., Uličný, J., Laaksonen, A., and Mocci, F. (2019). Pattern preferences of DNA nucleotide motifs by polyamines putrescine2+, spermidine3+ and spermine4+. Nucleic Acids Res 47, 6084–6097. 3. Rebič, M., Mocci, F., Laaksonen, A., and Uličný, J. (2015). Multiscale simulations of human telo-meric G-quadruplex DNA. J Phys Chem B 119, 105–113. 4. Hrivňak, S., Hovan, A., Uličný, J., and Vagovič, P. (2018). Phase retrieval for arbitrary Fresnel-like linear shift-invariant imaging systems suitable for tomography. Biomed Opt Express 9, 4390–4400., 5. Hrivňak, S., Uličný, J., Mikeš, L., Cecilia, A., Hamann, E., Baumbach, T., Švéda, L., Zápražný, Z., Korytár, D., Gimenez-Navarro, E., et al. (2016). Single-distance phase retrieval algorithm for Bragg Magnifier microscope. Opt Express 24, 27753–27762. 6. Buakor, K.; Zhang, Y.; Birnšteinová, Š.; Bellucci, V.; Sato, T.; Kirkwood, H.; Mancuso, A. P.; Vagovic, P.; Villanueva-Perez, P. Shot-to-Shot Flat-Field Correction at X-Ray Free-Electron Lasers. Opt. Express 2022, 30 (7), 10633. 7. Han, H.; Round, E.; Schubert, R.; Gül, Y.; Makroczyová, J.; Meza, D.; Heuser, P.; Aepfel-bacher, M.; Barák, I.; Betzel, C.; Fromme, P.; Kursula, I.; Nissen, P.; Tereschenko, E.; Schulz, J.; Uetrecht, C.; Ulicný, J.; Wilmanns, M.; Hajdu, J.; Lamzin, V. S.; Lorenzen, K. The XBI BioLab for Life Science Experiments at the European XFEL. J Appl Crystallogr 2021, 54 (1), 7–21. 8. Project: 101046448 — MHz-TOMOSCOPY — HORIZON-EIC-2021- PATHFINDEROPEN-01 , https://www.tomoscop
doc. RNDr. Jozef Uličný, CSc.
Dr. Patrik Vagovič, PhD.
Advanced Materials (PMd)
Preparation of compacted and composite soft magnetic materials for low frequency applications
The work is oriented to the investigation of the influence of technological procedures and dielectrics at the preparation of compacted and composite materials on their magnetic properties at magnetization reversal process in alternating magnetic fields in the range of low frequencies in a wide range of maximum magnetic inductions. The ferromagnetic component will be based on iron and nickel and the insulating binder are inorganic materials. The goal is also to compare the magnetic properties of the prepared materials with conventional ones used under similar physical conditions.
1. R. M. Bozorth Ferromagnetism, third edition (IEEE Press, Piscataway, NJ), 1993 2. H. Shokrollahi, K. Janghorban J. Mater. Proc. Technol. 189 (2007) 1 3. E. A. Périgo, B. Weidenfeller, P. Kollár, J. Füzer, Applied Physics Reviews 5, 031301 (2018);
prof. RNDr. Peter Kollár, DrSc.
Biophysics (BFd)
Intrinsically disordered proteins in Alzheimer´s disease and other amyloidoses.
The prevalence of neurodegenerative conditions like Alzheimer's disease (AD) continues to rise with aging of human population. These diseases often result from impaired protein synthesis, leading to the accumulation of misfolded proteins in the brain. The proteins aggregate into amyloid structures rich in β-sheets throughout various brain regions. Despite their widespread impact, the precise mechanisms driving amyloid formation remain poorly understood, and effective treatments remain elusive. This research endeavors to elucidate the mechanisms underpinning amyloid aggregation in intrinsically disordered proteins (IDPs) associated with AD and other amyloid-related diseases. Employing biophysical methodologies, we aim to study the pathways involved in amyloid aggregate formation. Furthermore, we will systematically explore potential interaction partners to counteract amyloid aggregation of IDPs, offering promising therapeutic intervention in these debilitating diseases.
1. Study of the mechanisms of amyloid aggregation of poly/peptides, which are related to Alheimer´s disease and other amyloidosis 2. Identification of substances able to reduce amount of amyloid structures 3. Elucidation of the relationship between the structure and anti-amyloid activity of substances
1. Knowles T- et al., The amyloid state and its association with protein misfolding disease, Nature Reviews Molecular Cell Biology, 2014, 15, 384 – 396. 2. Matthew G. Iadanza et al., A new era for understanding amyloid structures and disease, Nature Reviews Molecular Cell Biology, 2018, 19, 755 – 773 3. Amyloidosis: History and Perspectives., Ed. By J. S. Harrison, IntechOpen, London, UK, 2022, Online ISBN: 978-1-83969-298-7 4. Scientific articles
doc. RNDr. Zuzana Gažová, CSc.
Physics education (TVFd)
Professional development of the physics teacher as a tool for eliminating burnout syndrome
Burnout syndrome is caused by chronic stress and mental strain that have not been successfully managed. In teachers, it is caused by professional situations associated with unreasonable demands, problems, frustration, conflicts and deprivation. Its most common symptom is emotional and cognitive wear and tear, exhaustion, general fatigue associated with a decrease in work performance. It manifests itself in stereotypes, lack of interest in an active approach to the educational process and ultimately inefficiency in the development of the pupil's personality. High demands are placed on a physics teacher, as one of the science subjects in which a long-term decline in science literacy has been reported. One of the possibilities of eliminating the burnout syndrome is the continuous education of teachers. Professional development programs for teachers, which are on the rise in recent years, have a predisposition to be a tool for eliminating the burnout syndrome. The dissertation is focused on analyzing the burnout syndrome of physics teachers in the context of their professional development, on determining the current level of burnout syndrome of physics teachers through the MBI-ED questionnaire (Maslach Burnout Inventory – Educators Survey), on identifying correlations between the burnout syndrome and completed professional development programs for teachers of physics, as well as the proposal of a specific program of professional development for teachers focused on the possibilities of eliminating burnout syndrome.
1. To analyze the burnout syndrome of physics teachers in the context of their professional development. 2. To find out the current level of burnout syndrome of physics teachers through the MBI-ED questionnaire (Maslach Burnout Inventory – Educators Survey). 3. To identify the correlation between burnout syndrome and completed professional development programs for physics teachers. 4. Design and pilot-validate a teacher's professional development program focused on the possibilities of eliminating burnout syndrome.
[1] Bianchi, R., Schonfeld, I. S., & Laurent, E. (2017). Is it Time to Characterize Burnout as a Depressive Syndrome? European Psychiatry, 41(1), 141, https://doi.org/10.1016/j.eurpsy.2017.01.1976 [2] Özer, N., & Beycioglu, K. (2010). The relationship between teacher professional development and burnout. Procedia – Social and Behavioral Sciences, 2(2), 4928–4932. DOI:10.1016/j.sbspro.2010.03.797 [3] Safari, I., Davaribina, M., & Khoshnevis, I. (2020). The Influence of EFL Teachers’ Self-Efficacy, Job Satisfaction and Reflective Thinking on their Professional Development: A Structural Equation Modeling. Journal on Efficiency and Responsibility in Education and Science, 13(1), 27–40. https://doi.org/10.7160/eriesj.2020.130103 [4] Petlák, E., & Baranovská, A. (2016). Stres v práci učiteľa a syndróm vyhorenia. Bratislava: Wolters Kluwer. [5] Burisch, M. (2014). Das Burnout-Syndrom: Theorie der inneren Erschöpfung – Zahlreiche Fallbeispiele – Hilfen zur Selbsthilfe. Verlag: Springer Berlin Heidelberg.
doc. PaedDr. Renáta Orosová, PhD.
doc. RNDr. Marián Kireš, PhD.
Physics education (TVFdAj)
Professional development of the physics teacher as a tool for eliminating burnout syndrome
Burnout syndrome is caused by chronic stress and mental strain that have not been successfully managed. In teachers, it is caused by professional situations associated with unreasonable demands, problems, frustration, conflicts and deprivation. Its most common symptom is emotional and cognitive wear and tear, exhaustion, general fatigue associated with a decrease in work performance. It manifests itself in stereotypes, lack of interest in an active approach to the educational process and ultimately inefficiency in the development of the pupil's personality. High demands are placed on a physics teacher, as one of the science subjects in which a long-term decline in science literacy has been reported. One of the possibilities of eliminating the burnout syndrome is the continuous education of teachers. Professional development programs for teachers, which are on the rise in recent years, have a predisposition to be a tool for eliminating the burnout syndrome. The dissertation is focused on analyzing the burnout syndrome of physics teachers in the context of their professional development, on determining the current level of burnout syndrome of physics teachers through the MBI-ED questionnaire (Maslach Burnout Inventory – Educators Survey), on identifying correlations between the burnout syndrome and completed professional development programs for teachers of physics, as well as the proposal of a specific program of professional development for teachers focused on the possibilities of eliminating burnout syndrome.
1. To analyze the burnout syndrome of physics teachers in the context of their professional development. 2. To find out the current level of burnout syndrome of physics teachers through the MBI-ED questionnaire (Maslach Burnout Inventory – Educators Survey). 3. To identify the correlation between burnout syndrome and completed professional development programs for physics teachers. 4. Design and pilot-validate a teacher's professional development program focused on the possibilities of eliminating burnout syndrome.
[1] Bianchi, R., Schonfeld, I. S., & Laurent, E. (2017). Is it Time to Characterize Burnout as a Depressive Syndrome? European Psychiatry, 41(1), 141, https://doi.org/10.1016/j.eurpsy.2017.01.1976 [2] Özer, N., & Beycioglu, K. (2010). The relationship between teacher professional development and burnout. Procedia – Social and Behavioral Sciences, 2(2), 4928–4932. DOI:10.1016/j.sbspro.2010.03.797 [3] Safari, I., Davaribina, M., & Khoshnevis, I. (2020). The Influence of EFL Teachers’ Self-Efficacy, Job Satisfaction and Reflective Thinking on their Professional Development: A Structural Equation Modeling. Journal on Efficiency and Responsibility in Education and Science, 13(1), 27–40. https://doi.org/10.7160/eriesj.2020.130103 [4] Petlák, E., & Baranovská, A. (2016). Stres v práci učiteľa a syndróm vyhorenia. Bratislava: Wolters Kluwer. [5] Burisch, M. (2014). Das Burnout-Syndrom: Theorie der inneren Erschöpfung – Zahlreiche Fallbeispiele – Hilfen zur Selbsthilfe. Verlag: Springer Berlin Heidelberg.
doc. PaedDr. Renáta Orosová, PhD.
doc. RNDr. Marián Kireš, PhD.
Physics of Condensed Matter (FKLdAj)
Quantum materials under extreme conditions
Quantum materials, such as frustrated magnets, topological insulators, strongly correlated metals or exotic superconductors, are highlights in the theoretical and experimental study of solids and are beginning to be used in applications connected with quantum technologies. Understanding the ground state of these systems requires their investigation under extreme conditions, i.e. at very low temperatures, high magnetic fields or pressures. Specifically, the dissertation would deal with the study of the influence of a high magnetic field and hydrostatic pressure on the thermal, transport and magnetic properties of selected tetra-, hexa- and dodecaborides at kelvin to millikelvin temperatures.
The study of the influence of a high magnetic field and hydrostatic pressure on the thermal, transport and magnetic properties of selected tetra-, hexa- and dodecaborides at kelvin to millikelvin temperatures.
[1] KITTEL Ch., Úvod do fyziky pevných látek, Academia, Praha, 1985 [2] GABÁNI S. et al., Magnetism and superconductivity of rare earth borides, Journal of Alloys and Compounds 821 (2020), 153201 [3] GABÁNI S. a kol., Fyzika a technika vysokých tlakov II., skriptá, ÚEF SAV Košice, 2016
doc. RNDr. Slavomír Gabáni, PhD.
RNDr. Matúš Orendáč, PhD.
Advanced Materials (PMdAj)
Reactive sputtering of the compositionally complex ceramic coatings
The development of magnetron sputtering is oriented toward technologies with high ionization degree of the sputtered material which provides better control of the deposition process as well as better coating properties. The most famous ionized PVD is the High Power Impulse Magnetron Sputtering (HiPIMS) and the relatively new technology High Target Utilization Sputtering (HiTUS) also belongs among these methods. High degree of ionization is achieved in the case of HiPIMS by very short duty cycle impulses with extremely high power density whereas in HiTUS by the power at an independent plasma source. The work should focus on the optimization of the deposition parameters of hard multicomponent carbide, boride and nitride coatings from the viewpoint of the control of their elastic and plastic properties by means of determination of dependencies among the deposition parameters, plasma characteristics, coating structures and their mechanical and tribological properties. The work will be performed on the iPVD systems Cryofox Discovery (Polyteknik, Denmark) and HiTUS C500 (PQL, UK) in combination with the electron microscopy observations (SEM, TEM) and measurements of mechanical properties.
Investigation of the influence of the deposition parameters of hard multicomponent carbide, boride and nitride coatings on their mechanical and tribological properties.
1. D.M. Mattox, Physical sputtering and sputter deposition (sputtering), pp. 343-405 in Handbook of Physical Vapor Deposition (PVD) processing, Mattox D.M., Noyes Publ., New Jersey, 1998. 2. B. Cantor, I.T.H. Chang, P. Knight, A.J.B. Vincent, Microstructural development in equiatomic multicomponent alloys (2004) Mater. Sci. Eng. A, 375-377 (1-2 SPEC. ISS.), pp. 213-218. doi: 10.1016/j.msea.2003.10.257 3. E. Lewin, E. Multi-component and high-entropy nitride coatings - A promising field in need of a novel approach J. Appl. Phys. 127, 160901 (2020); doi: 10.1063/1.5144154 4. F. Lofaj, L. Kvetková, T. Roch, J. Dobrovodský, V. Girman, M. Kabátová, M. Beňo, Reactive HiTUS TiNbVTaZrHf-Nx coatings: structure, composition and mechanical properties, Materials 16 (2) (2023) 563. https://doi.org/10.3390/ma16020563
doc. RNDr. František Lofaj, DrSc.
Physics (FdAj)
Renormalization group study of out-of-equilibrium statistical systems
An important area of theoretical physics consists of models of non-equilibrium systems. Recently, much attention has been paid to active matter models and theoretically related active admixture models. Promising theoretical approaches for their quantitative description are based on the use of various renormalization group methods. For technical reasons, most works focus on the simplest one-loop approximation. For obvious reasons, it would be necessary to elaborate new and efficient analytical and numerical algorithms for the computation of scaling indices and control parameters of the considered models in higher orders of failure theory. Therefore, the main goal of the dissertation will be to elaborate universal approaches to compute, in particular, two-loop Feynman diagrams and to apply them in the determination of anomalous indices for different universality classes describing the large-scale behavior of the statistical correlations of the fields under study. In addition to a good knowledge of the fundamentals of modern physics, the PhD student will be required to have a working knowledge of modern programming languages.
Solve actual problems of non-equilibrium phase transitions in various models of active matter and active admixture by methods of quantum field theory and renormalization group methods.
Adzhemyan, L.T.; Antonov, N.V.; Vasiliev, A.N. Field theoretic renormalization group in fully developed turbulence; CRC Press, 1999. Active Matter and Nonequilibrium Statistical Physics: Lecture Notes of the Les Houches Summer School: Volume 112, (Oxford Academic, 2022) M. C. Marchetti, J. F. Joanny, S. Ramaswamy, T. B. Liverpool, J. Prost, M. Rao, and R. A. Simha, Rev. Mod. Phys. 85, 1143 (2013). A. Cavagna, I. Giardina, and T. S. Grigera, Phys. Rep. 728, 1 (2018). J. Zinn Justin, Quantum Field Theory and Critical Phenomena, (Oxford Univers Press, 1989) A. N. Vasil’ev The Field Theoretic Renormalization Group in Critical Behavior Theory and Stochastic Dynamics, Boca Raton:Chapman & Hall/CRC (2004)
RNDr. Tomáš Lučivjanský, PhD., univerzitný docent
prof. RNDr. Michal Hnatič, DrSc.
Physics education (TVFd)
Development the skill of argumentation in the conceptual physics course
The student's understanding of physics concepts and phenomenon can be verified through qualitative tasks and their physics interpretation. The ability to appropriately use the most important arguments, to correctly organize them into a comprehensive explanation of a physics concept or phenomenon are signs of the skill of arguing. The content of conceptual physics courses will be analyzed as part of the dissertation. The doctoral student will process a thematically sorted set of qualitative tasks and their clarification at the level of high school physics. For physics teachers, he will create a education course, which will provide basic starting points and materials for the application of qualitative tasks in the teaching of physics at the secondary school. The development of the ability to argue and the level of the student's conceptual understanding of selected physical terms and phenomena will be investigated on a selected sample of high school students.
1. Map the approach to creating the content of conceptual physics courses and the teaching methods used in their implementation. 2. Process a thematically sorted set of qualitative tasks and their clarification at the level of high school physics. 3. Create and implement a course of continuous education for physics teachers focused on teaching conceptual physics in high school. 4. On a selected sample of high school students, examine the development of students' argumentative skills and the level of students' conceptual understanding.
[1] Taşlıdere, Erdal & Eryilmaz, Ali. (2009). Alternative to Traditional Physics Instruction: Effectiveness of Conceptual Physics Approach. Eurasian Journal of Educational Research (EJER). 9. 109-128. [2] Aina, Jacob. (2017). Investigating the Conceptual Understanding of Physics through an Interactive Lecture- Engagement. Cumhuriyet International Journal of Education-CIJE. 6. 82-96. [3] Price, Edward & Goldberg, Fred & Robinson, Steve & McKean, Michael. (2016). Validity of peer grading using Calibrated Peer Review in a guided-inquiry, conceptual physics course. Physical Review Physics Education Research. 12. 10.1103/PhysRevPhysEducRes.12.020145. [4] Walker, Jearl. (2023). The Flying Circus of Physics, 2nd ed.
doc. RNDr. Marián Kireš, PhD.
Physics (Fd)
Exploring of discrete gravity, black hole paradox and also quantum phenomena for various kinds of cosmological objects as well as nanostructures
Interpretation of emerging spaces using a new geometric/topological approach introduced by PNDP-manifolds, i.e., particular kind of the Einstein sequential warped-product manifold, which allow to cover a wider variety of exact solutions of Einstein's field equation from a differential geometric point of view, without complicating the calculations comparing to the Einstein warped-product manifolds. We will seek to shed light on the underlying physics beyond the Standard model, also by the examination how discrete gravitational effects would affect the motion of spin or spinless particles in a gravitational fields. By exploring these concepts, we hope to provide valuable insights into the nature of dimensions and their impact on gravity and fundamental forces, thus addressing existing inconsistencies in current cosmological models as well as nanostructures.
The aim of thesis will be to shed light on the underlying physics beyond the Standard model, also by the examination how discrete gravitational effects would affect the motion of spin or spinless particles in a gravitational fields.
[1] PINČÁK, Richard** - PIGAZZINI, Alexander - JAFARI, Saeid - OZEL, Cenap. Discrete Gravity in Emergent Space Theory: Hidden Conical Defects and Teleparallel Gravity. In Universe, 2023, vol. 9, no. 1, art. no. 31. [2] PINČÁK, Richard** - PIGAZZINI, Alexander - JAFARI, Saeid - OZEL, Cenap - DEBENEDICTIS, Andrew. A topological approach for emerging D-branes and its implications for gravity. In International Journal of Geometric Methods in Modern Physics, 2021, vol. 18, no. 14, art. no. 2150227. [3] PINČÁK, Richard** - PIGAZZINI, Alexander - JAFARI, Saeid - OZEL, Cenap. The “Emerging” Reality from “Hidden” Spaces. In Universe, 2021, vol. 7, no. 3, art. no. 75.
RNDr. Richard Pinčák, PhD.
RNDr. Michal Pudlák, CSc.
Biophysics (BFd)
Investigation of the signalling pathways active in an immunotherapy and photodynamic therapy
The application of light plays an important role in the process of regeneration, photodiagnostics and treatment of cancer. It is often a non-invasive form of therapy that is well tolerated by patients. Depending on the wavelength of the radiation source used, the light dose and the concentration of the drug, it is possible to achieve cell regeneration as well as cell death. Passive immunotherapy by antiproliferative antibodies targeting cell surface receptors has been applied successfully to treat leukemias and solid tumors such as breast cancer. In several cases such therapies are inefficient because the cancer cell develops intracellular signaling pathways evading inhibition by antibodies. In such hard-to-treat cases receptors can still be used as therapeutical targets but the targeting antibody must deliver an agent that actively kills the targeted cell; e.g. a nanoparticle with a photodynamic agent can be used. The role of the doctoral student will be to identify the mechanism of action of immunotherapy and photodynamic therapy with respect to the endomembrane system, cell metabolism and signalling molecules leading to cell regeneration or death. The student will use the methods of fluorescence spectroscopy, microscopy (confocal fluorescence microscopy and FLIM), bioimaging, flow cytometry, immunolabeling, western blot and PCR to perform the tasks within the dissertation project. The cell cultures in 2D and 3D, and a preclinical model of the avian chorioallantoic membrane will be used in the study. Within the project, the student will actively cooperate with other laboratories in Slovakia and abroad.
To describe the signaling in the tumor cell leading to cell death activated by photodynamic therapy and to determine its role in immunotherapy.
peer-reviewed publications Correia, J. H., Rodrigues, J. A., Pimenta, S., Dong, T., & Yang, Z. (2021). Photodynamic therapy review: principles, photosensitizers, applications, and future directions. Pharmaceutics, 13(9), 1332. Dzurová, L., Petrovajova, D., Nadova, Z., Huntosova, V., Miskovsky, P., & Stroffekova, K. (2014). The role of anti-apoptotic protein kinase Cα in response to hypericin photodynamic therapy in U-87 MG cells. Photodiagnosis and photodynamic therapy, 11(2), 213-226. Huntosova, V., Nadova, Z., Dzurova, L., Jakusova, V., Sureau, F., & Miskovsky, P. (2012). Cell death response of U87 glioma cells on hypericin photoactivation is mediated by dynamics of hypericin subcellular distribution and its aggregation in cellular organelles. Photochemical & Photobiological Sciences, 11(9), 1428-1436. Mansoori, B., Mohammadi, A., Doustvandi, M. A., Mohammadnejad, F., Kamari, F., Gjerstorff, M. F., ... & Hamblin, M. R. (2019). Photodynamic therapy for cancer: Role of natural products. Photodiagnosis and photodynamic therapy, 26, 395-404. Misuth, M., Horvath, D., Miskovsky, P., & Huntosova, V. (2017). Synergism between PKCδ regulators hypericin and rottlerin enhances apoptosis in U87 MG glioma cells after light stimulation. Photodiagnosis and Photodynamic Therapy, 18, 267-274.
RNDr. Veronika Huntošová, PhD.
Advanced Materials (PMdAj)
Soft magnetic nanocrystalline alloys metals prepared by unconventional thermal processing techniques.
The PhD thesis is focused on the employment of unconventional techniques of thermal processing in order to tailor the structural and magnetic properties of nanocrystalline alloys based on 3-d metals. We plan to use facility for ultra-rapid annealing of thin metallic ribbons constructed recently at IEP SAS. In this facility, the annealed samples are clamped between pair of the pre-heated massive Cu-blocks and typical annealing times take few seconds. High heating rates and much shorter processing times as compared to conventional annealing allow extend the composition interval where the annealed samples are still capable to form nanocrystalline structure. The other technique of thermal processing in this work is the annealing in a presence of high magnetic fields. We plan to perform a detailed study of structural and magnetic properties of selected alloy systems. The main goal of thesis is improvement of functional properties of studied materials for potential technical applications.
The main goal of thesis is improvement of functional properties of studied materials for potential technical applications.
current journal literature
RNDr. Ivan Škorvánek, CSc.
Ing. Branislav Kunca, PhD.
Biophysics (BFd)
Protein stability and aggregation in biocompatible organic solvents
The identification of effective solvents capable of modulating protein stability and aggregation is of great importance for various applications in biotechnology or medicine. The production and long-term storage of proteins requires setting appropriate environmental conditions that preserve the native structure of the proteins and prevent their aggregation. Similarly, the formation of a special type of ordered aggregates - amyloid fibrils, is modulated by external conditions. Amyloid aggregates represent new potential biomaterials due to their unique properties. Therefore, finding conditions capable of inducing the formation of defined amyloid aggregates is of interest. This work aims to study the effect of special solvents - ionic liquids and deep eutectic mixtures – on the stability, kinetics of amyloid aggregation, and morphology of amyloid fibrils of various proteins (lysozyme, insulin). The objective is to determine the relationship between solvent’s composition and physicochemical properties and their ability to stabilize/destabilize protein structure and inhibit/accelerate amyloid aggregation to find solvents capable of stabilizing studied proteins or inducing amyloid aggregate formation with defined morphology. Spectroscopic (UV-VIS, CD, FTIR) and calorimetric (DSC, ITC) methods, as well as atomic force microscopy (AFM) and computer image analysis methods, will be used.
1. Characterization of structural changes of model proteins in the presence of ionic liquids and deep eutectic solvents 2. Identification of solvents capable of inducing or inhibiting amyloid fibril formation - determination of their effect on the kinetics of amyloid aggregation 3. Elucidation of the role of solvent components in the formation of morphologically different fibrils
1.Schindl, A., Hagen, M.L., Muzammal, S., Gunasekera, H.A., Croft A.K.: Proteins in Ionic Liquids: Reactions, Applications, and Futures, Front. Chem., 24 May 2019, Volume 7 - 2019. 2.2. Takekiyo T., Yoshimura Y.:Suppression and dissolution of amyloid aggregates using ionic liquids. Biophys Rev. 2018 Jun; 10(3): 853–860. 3.Silva N.H., Pinto, R.J., Freire, C.R., Marrucho, I.M.:Production of lysozyme nanofibers using deep eutectic solvent aqueous solutions.Coloid. Surf.B: Biointerfaces, 2016, 147, 36-44.
RNDr. Diana Fedunová, PhD.
Advanced Materials (PMd)
The structure determination of metallic glasses by X-ray, synchrotron based scattering and spectroscopic techniques and image techniques at XFEL
The thesis will deal with the preparation and structure observation of (Fe, Ni, Cu)-(Hf,Ta,W)-based metallic glasses in the form of ribbons and rods by melt-spinning technique and the copper mould casting method. The glassy structure of the as-prepared alloys will be investigated by synchrotron based scattering and spectroscopic techniques, namely high-energy X-ray diffraction (HEXRD), anomalous X-ray diffraction (AXRD) and X-ray absorption spectroscopy (XAS). Structure of the samples also will be checked by TEM and MID beamline at XFEL in Hamburg.
Main goal of the thesis is to handle various experimental techniques for structural determination of amorphous metallic glasses
Current journals from Mat. Sci.
prof. RNDr. Pavol Sovák, CSc.
RNDr. Jozef Bednarčík, PhD., univerzitný docent
Advanced Materials (PMdAj)
Structural study of disordered and quasi-ordered metallic alloys using electron and XRD scattering.
Phase transitions of solids from the disordered state to complex structures ordering are subject of modern research. The relationship between initial and final structure state play an important role at forming of the new structures having advanced physical and chemical properties. The variations of external conditions, e.g. strong magnetic fields or extremal temperature changes, can substantially affect the final properties of solids as well. The main highlight of dissertation thesis will be the study of atomic structure and stability of inducted phases of promising advanced materials in relation to their properties, employing electron and X-ray diffraction techniques. The experimental approach, using transmission electron microscope JEOL 2100F UHR, will be emphasized. However, for successful completing of dissertation thesis, it will be necessary to carry out experiments at electron microscopy centres and synchrotron facility abroad.
1.) Preparation of master alloys and bulk metallic glasses. 2.) Thermo-mechanical processing and testing of mechanical and physical properties of bulk metallic glasses. 3.) Local atomic structure investigation of amorphous phases and its correlation to physical and mechanical properties. 4.) Study of amorphization and crystallization processes and related thermo-mechanically induced phase transformations in crystalline phases.
Williams D. B. and Crater C. B.: Transmission electron microscopy. 2nd ed., Springer Science, 2009, ISBN 978-0-387-76500-6. Inoue A. and Suryanarayana C.: Bulk metallic glasses. CRC Press, Talyor and Francis Group, 2011, ISBN-13: 978-1-4200-8597-6 Miller M. and Liaw P.: Bulk metallic glasses: An overview. Springer Science, 2008, ISBN 978-0-387-48920-9. Als-Nielsen J. and McMorrow D.: Elements of Modern X-ray Physics. 2nd ed., John Wiley & Sons Ltd, 2011, ISBN 978-0-470-97395-0
Ing. Vladimír Girman, PhD.
prof. RNDr. Pavol Sovák, CSc.
Advanced Materials (PMdAj)
Structure and properties of lead-free ferroelectric ceramics
The dissertation will be focused on the research and development of advanced electroceramics, derived from lead-free perovskite-structured ferroelectrics. In course of dissertation work, theoretical and experimental approaches will be employed including material processing, X-ray diffraction and the Rietveld refinement method, scanning and transmission electron microscopy, and characterization of specific electro-physical properties of functional ceramics. For analytical assessment of the macroscopic properties with respect to the chemical and structural nature of electroceramics, an extended technique of dielectric spectroscopy will be adopted to study ferroelectric phase transitions.
The dissertation will be focused on the research and development of advanced electroceramics, derived from lead-free perovskite-structured ferroelectrics. In course of dissertation work, theoretical and experimental approaches will be employed including material processing, X-ray diffraction and the Rietveld refinement method, scanning and transmission electron microscopy, and characterization of specific electro-physical properties of functional ceramics.
Current journal literature.
RNDr. Vladimír Kovaľ, DrSc.
Physics (FdAj)
Study of angular substructures of particles produced in heavy ion collisions
An important aim of nucleus collisions investigation at high energies is to search for a phenomena connecting with large densities obtained in such collisions. As an example, the transition from the QGP (quark - gluon plasma) back to the normal hadronic phase is predicted to contribute to fluctuations in the number of produced particles in local regions of phase space. Using unique method collisions of proton-proton and heavy-ion collisions at momenta between 1 AGeV/c and 160 AGeV/c will be analyzed. The methods of transverse momentum, principal vectors, azimuthal correlation functions, Fourier expansion of azimuthal angle distributions and other methods will be applied. Experimental results will be compared with model calculations.
current scientific literature
doc. RNDr. Adela Kravčáková, PhD.
RNDr. Martin Vaľa, PhD.
Advanced Materials (PMdAj)
Study of magnetic and thermal properties of high-entropy functional alloys
The main idea of the dissertation thesis is to find a suitable chemical composition that will meet the criteria for high-entropic functional alloys. Appropriately chosen composition of individual chemical elements leads to the preparation of such materials, focusing on selected physical properties. We will focus on combining elements belonging to the group of half Heusler alloys with the stoichiometric formula XYZ, where X and Y represent a transition element and Z an element from the p block. The preparation of samples in the form of strips and microwires using the Taylor-Ulitovsky method seems very advantageous for the materials we want to deal with. Part of the work is also the design of possible cooling technology and its implementation in technical practice.
The main aim of the dissertation thesis is to research high-entropy alloys as thermoelectric materials. The work will be devoted to finding a suitable composition that will meet the criteria for high-entropy alloys and simultaneously belong to the group of thermoelectric materials. We will focus on combining elements from the group of half Heusler alloys with the stoichiometric formula XYZ, where X and Y represent the transition element and Z is the element from the p block.
[1] S. Skipidarov, M. Nikitin (Eds.): Novel Thermoelectric Materials and Device Design Concepts, Springer 2019, ISBN: 978-3-030-12056-6 [2] H. Fukuyama, Y. Waseda (Eds): High-Temperature Measurements of Materials, Springer 2009, ISBN: 978-3-540-85917 [3] P. Sharma, V. K. Dwivedi, S. P. Dwivedi: Development of high entropy alloys: A review, Materials Today: Proceedings 43, 2021, 502-509
prof. RNDr. Rastislav Varga, DrSc.
Ing. RNDr. Andrea Džubinská, PhD.
Advanced Materials (PMdAj)
Study of shape memory effect stability in Ni2FeGa microwires
The ferromagnetic Heusler alloy Ni2FeGa has broad application potential in sensors and actuators due to the combination of its magnetic properties and the existence of the shape memory phenomenon (SMP). The temperature range of the thermo-elastic phase transformation of the SMP can be controlled by varying the chemical composition of the alloy, more precisely by the changing atomic configuration of the ordered parent phase. While the equilibrium chemical composition of the ordered phase has a transformation temperature of around 50 K, it is possible to shift the transformation above the temperature of 300 K by supersaturating the ordered phase. The pilot experiment showed that the alloy in the form of microwires has, due to its thickness (< 30 m), a unique resistance to cyclic transition through the temperature phase transformation region. Changes in material structure and properties were not observed after more than 106 cycles. The topic of the dissertation is focused on the study of the Heusler alloy shape memory effect and the properties concerning their structure and the form of the prepared alloy. The work is focused on determining the thermal and mechanical stability of the ordered parent phase and justifying the effects on the transformation temperature of the produced microwires.
The topic of the dissertation is focused on the study of the Heusler alloy shape memory effect and the properties concerning their structure and the form of the prepared alloy. The work is focused on determining the thermal and mechanical stability of the ordered parent phase and justifying the effects on the transformation temperature of the produced microwires.
Current journal literature.
doc. Ing. Ondrej Milkovič, PhD.
prof. RNDr. Rastislav Varga, DrSc.
Physics (FdAj)
Study of space weather influence on Earth’s interface to space
The Earth’s interface region to space is located at altitudes of 80-300 km. It is a dynamic environment constantly influenced by solar radiation and space weather from above and atmospheric processes from below. The main objective is to study these dynamics, especially with a focus on identifying the influence of space weather phenomena. For this purpose the following data will be used: optical observations of airglow from satellite missions and ground-based all-sky cameras and photometers; measurements of ionosphere parameters from GNSS receivers and radio systems based on the Doppler shift principle; space weather data describing the solar activity, the solar wind, the interplanetary magnetic field, and disturbances in the geomagnetic field. The work will be dedicated to detailed case studies of specific events as well as to a general data-driven approach using machine learning techniques. The obtained knowledge will contribute to a better understanding of the consequences of space weather on the interface region, which significantly affects the communication and operation of satellites and is therefore crucial for the entire society.
The main objective is to study dynamics of Earth’s interface to space, especially with a focus on identifying the influence of space weather phenomena.
Space Physics, Ch. T. Russell, J. G. Luhmann, and R. J. Strangeway, Cambridge Univ. Press, 2016. Machine Learning Techniques for Space Weather, E. Camporeale, S. Wing, J. Johnson, Elsevier, 2018 Space Physics and Aeronomy, Y. Zhang, L. J. Paxton, American Geophysical Union, 2021
RNDr. Šimon Mackovjak, PhD.
Ing. Ján Kubančák, PhD.
Physics (FdAj)
Study of strange particles production in high multiplicity proton-proton collisions in ALICE experiment at CERN LHC
A recent hardware and software upgrade of the ALICE experiment allowed in 2022 to increase the actual statistics of the proton-proton collisions (obtained in 2009-2018) more than 300 times. The data taking is planned until 2025 with a further rapid statistical increase. The increase offers new opportunities of studying rare processes in pp collisions or in heavy ion collisions. One of the open problems in this field is an origin of the enhanced production of the strange and multi-strange particles with respect to non-strange particle production in high multiplicity pp collisions [1]. It is still unknown whether the strangeness enhancement dependency as a function of multiplicity in pp collisions will follow the similar trend in peripheral heavy ion collisions or it will be significantly different. The thesis will focus on studying strange particle production in high multiplicity proton-proton collisions collected with unprecedented statistics in Run3 (2022-2025) at the LHC. [1] ALICE Collaboration., Adam, J., Adamová, D. et al. Enhanced production of multi-strange hadrons in high-multiplicity proton–proton collisions. Nature Phys 13, 535–539 (2017). https://doi.org/10.1038/nphys4111
Recent publications
doc. RNDr. Marek Bombara, PhD.
Advanced Materials (PMdAj)
Study of the crystallization kinetics of Fe-based amorphous precursors
Kinetics of phase transformations of the first order is without doubt the most intensively studied subject in the field of materials science. The main reason for such increased interest is the fact, that it represents a powerful tool to modify microstructure of studied materials and thus tailor their properties. Understanding the kinetics of a phase transformation and the associated change of microstructure is a prerequisite to utilize this tool to its full extent. Rapid quenching of a melt represents typical example of highly non steady state process which results in formation of metastable materials such as metallic glasses. Amorphous structure characteristic for a liquid state is preserved in solid state by rapid quenching. As a result of their unique structure, which is characterized by short-range order, metallic glasses exhibit excellent magnetic and mechanical properties. In case of magnetic properties metallic glasses exhibit very low values of coercivity, magnetostriction and loses which are complemented by very high values of permeability. One of the main goals of the proposed dissertation will be a detailed study of the kinetics of the crystallization process of the Fe-based amorphous precursor. Emphasis will be placed on optimizing the resulting microstructure to improve the resulting magnetic properties. In addition to standard laboratory methods such as DSC, SEM, TEM, XRD, MSB, modern methods using synchrotron radiation scattering will be used during the study.
One of the main goals of the proposed dissertation will be a detailed study of the kinetics of the crystallization process of the Fe-based amorphous precursor. Emphasis will be placed on optimizing the resulting microstructure to improve the resulting magnetic properties.
relevant scientific literature
RNDr. Jozef Bednarčík, PhD., univerzitný docent
Physics of Condensed Matter (FKLd)
Substitutional compounds of novel multiferroic functional materials with distorted perovskite structure
Transition metal oxides with a distorted perovskite structure are intensively studied both because of the strong correlation between orbital, electric, spin and lattice degrees of freedom, as well as because of their high application potential (cathodes for fuel cells, sensors for the detection of various gases, electronic components with strong magnetoelectric coupling etc.) of these materials. 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 an emphasis on magnetism, multiferroicity, specific heat; and subsequently optimize properties by substitution. Various physical and chemical methods will be used, mainly the float zone method and wet chemistry routes for sample preparation and DC/AC magnetometry, calorimetric methods and dielectric experiments for sample characterization.
Preparation of novel materials with distorted perovskite structure; study of magnetism
[1] A. M. Glazer, The Classification of Tilted Octahedra in Perovskites, Acta Crystographica B 28 (1972), 3384 - 3392 [2] K. Miura, M. Azuma and H. Funakubo, Electronic and Structural Properties of ABO3: Role of the B-O Coulomb Repulsions for Ferroelectricity, Materials 4 (2011), 260 - 273 [3] M. Mihalik et al., Magnetic Properties of NdMn1-xFexO3+δ (0≤x≤0.3) System, Journal of Magnetism and Magnetic Materials 345 (2013), 125-133 [4] M. Mihalik et al.., Magnetic Phase Diagram of the TbMn1-xFexO3 Solid Solution System, Physica B 506 (2017), 163-167 [5] R. Vilarinho et al., Understanding the Magnetic Dynamics and Magnetostructural Coupling in the Paramagnetic Phase of TbMnO3 by Muon-Spin Spectroscopy, Physical Review B 108 (2023), 174401
RNDr. Matúš Mihalik, PhD.
RNDr. Marián Mihálik, CSc.
Physics of Condensed Matter (FKLdAj)
Substitutional compounds of novel multiferroic functional materials with distorted perovskite structure
Transition metal oxides with a distorted perovskite structure are intensively studied both because of the strong correlation between orbital, electric, spin and lattice degrees of freedom, as well as because of their high application potential (cathodes for fuel cells, sensors for the detection of various gases, electronic components with strong magnetoelectric coupling etc.) of these materials. 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 an emphasis on magnetism, multiferroicity, specific heat; and subsequently optimize properties by substitution. Various physical and chemical methods will be used, mainly the float zone method and wet chemistry routes for sample preparation and DC/AC magnetometry, calorimetric methods and dielectric experiments for sample characterization.
Preparation of novel materials with distorted perovskite structure; study of magnetism
[1] A. M. Glazer, The Classification of Tilted Octahedra in Perovskites, Acta Crystographica B 28 (1972), 3384 - 3392 [2] K. Miura, M. Azuma and H. Funakubo, Electronic and Structural Properties of ABO3: Role of the B-O Coulomb Repulsions for Ferroelectricity, Materials 4 (2011), 260 - 273 [3] M. Mihalik et al., Magnetic Properties of NdMn1-xFexO3+δ (0≤x≤0.3) System, Journal of Magnetism and Magnetic Materials 345 (2013), 125-133 [4] M. Mihalik et al.., Magnetic Phase Diagram of the TbMn1-xFexO3 Solid Solution System, Physica B 506 (2017), 163-167 [5] R. Vilarinho et al., Understanding the Magnetic Dynamics and Magnetostructural Coupling in the Paramagnetic Phase of TbMnO3 by Muon-Spin Spectroscopy, Physical Review B 108 (2023), 174401
RNDr. Matúš Mihalik, PhD.
RNDr. Marián Mihálik, CSc.
Physics of Condensed Matter (FKLdAj)
Super spin-glass in restricted geometry.
Transition to spin glass, or super spin-glass state represents unique phase transition, for which autocorrelation function represents the order parameter. In addition, for both states relaxation phenomena in extremely wide time scale ranging from 10-8 to 1010s coexist. The thesis will be focused on preparation, structural characterization, and investigation of magnetic properties of artificial assemblies containing magnetic ions, or magnetic nanoparticles as magnetic entities and selected matrices for their displacement. Matrices based on artificial clay (e. g. smectite) will be adopted for magnetic ions, whereas litographic and electrodeposition techniques will be used to produce the desired spatial arrangement of magnetic nanoparticles. The aim of the thesis is to investigate conditions of the formation of the spin glass and super spin-glass state with respect to spatial anisotropy of dipolar coupling, ratio of magnitudes of energy barrier and effective magnetic interaction, dimensions of clusters and intercluster distances as well as attempts to create super spin-glass state in assemblies with magnetic dimensionality smaller than 3. Student will be focused on the preparation of the aforementioned assemblies, their structural characterization and investigation on their magnetic response using appropriate measuring protocols. She/he will analyze the data using commercial software packages, effort will be developed to simulate the influence of the selected assemblies on the distribution of magnitudes of dipolar coupling in nanoparticle systems.
The goal of the submited thesis is to clarify the conditions for the formation of spin glass and superspin glass in assemblies with restricted geometry focusing on magnetic low-dimensionality, critical ratio of the magnitudes of energy barrier and effective magnetic interactions, as well as finite size effects.
Scientific publications relevant to the topic of the thesis.
prof. Ing. Martin Orendáč, DrSc.
Dr. Serhii Vorobiov, PhD.
Physics of Condensed Matter (FKLd)
Super spin-glass in restricted geometry.
Transition to spin glass, or super spin-glass state represents unique phase transition, for which autocorrelation function represents the order parameter. In addition, for both states relaxation phenomena in extremely wide time scale ranging from 10-8 to 1010s coexist. The thesis will be focused on preparation, structural characterization, and investigation of magnetic properties of artificial assemblies containing magnetic ions, or magnetic nanoparticles as magnetic entities and selected matrices for their displacement. Matrices based on artificial clay (e. g. smectite) will be adopted for magnetic ions, whereas litographic and electrodeposition techniques will be used to produce the desired spatial arrangement of magnetic nanoparticles. The aim of the thesis is to investigate conditions of the formation of the spin glass and super spin-glass state with respect to spatial anisotropy of dipolar coupling, ratio of magnitudes of energy barrier and effective magnetic interaction, dimensions of clusters and intercluster distances as well as attempts to create super spin-glass state in assemblies with magnetic dimensionality smaller than 3. Student will be focused on the preparation of the aforementioned assemblies, their structural characterization and investigation on their magnetic response using appropriate measuring protocols. She/he will analyze the data using commercial software packages, effort will be developed to simulate the influence of the selected assemblies on the distribution of magnitudes of dipolar coupling in nanoparticle systems.
The goal of the submited thesis is to clarify the conditions for the formation of spin glass and superspin glass in assemblies with restricted geometry focusing on magnetic low-dimensionality, critical ratio of the magnitudes of energy barrier and effective magnetic interactions, as well as finite size effects.
Scientific publications relevant to the topic of the thesis.
prof. Ing. Martin Orendáč, DrSc.
Dr. Serhii Vorobiov, PhD.
Advanced Materials (PMdAj)
Surface deformation of magnetic magnetic domain walls in thin wires
Cylindrical topography of ferromagnetic samples is one of the crucial factors that contributes to a high domain wall velocity. In our work, we will focus on time-resolved observation of a surface domain wall shape in thin wires. We will employ a novel experimental setup based on Magneto-optical Kerr effect (MOKE), that will be extended by an option to observe multiple domain walls simultaneously. Student will participate on design of excitation coils and simulations of magnetic fields. Observations of a surface domain wall deformation will be carried out on samples differing by magnetic anisotropies.
The aim of this work is to make a new magnetooptical observations of wires with non plana topography.
1. HUBERT, Alex; SCHÄFER, Rudolf. Magnetic domains: the analysis of magnetic microstructures. Springer Science & Business Media, 2008. 2. HAJKO ,Vladimír; POTOCKÝ, Ladislav; ZENTKO, Anton. Magnetizačné procesy. Bratislava : Alfa, 1982. 3. VIŠŇOVSKÝ, Štefan. Optics in magnetic multilayers and nanostructures. Crc Press, 2018. 4. CHEN, C. W. Magnetism and metallurgy of soft magnetic materials Dover Pub. Inc., New York, 1986.
RNDr. Kornel Richter, PhD.
Biophysics (BFd)
Light robotics
Laser-driven mechanical microstructures, captured and positioned using optical tweezers, can be easily integrated into a microfluidic LOC (lab-on-chip) environment. The vast majority of light-driven microstructures are prepared by two-photon polymerization. The aim of the work is to explore the possibilities of using elastic microstructures in the field of bio-medical applications. Specifically, we will focus on two areas: the use of light-controlled microstructures to measure viscosity and to manipulate living cells.
- To develop and test a mobile micro-viscometer based on stochastic fluctuations of optically trappable microstructures. - To improve light-controlled micro-robots for manipulating living cells and use them (i) to create multicellular structures and (ii) to monitor inter-cellular interactions.
- Z. Song, D. Cheng, L. Zhao: Microfluidics, Wiley-VCH, 2018 - J. Glückstad, Light robotics: Structure-mediated nanobiophotonics, Elsevier, 2017
doc. Mgr. Gregor Bánó, PhD.
Advanced Materials (PMd)
Structure and properties of lead-free ferroelectric ceramics
The dissertation will be focused on the research and development of advanced electroceramics, derived from lead-free perovskite-structured ferroelectrics. In course of dissertation work, theoretical and experimental approaches will be employed including material processing, X-ray diffraction and the Rietveld refinement method, scanning and transmission electron microscopy, and characterization of specific electro-physical properties of functional ceramics. For analytical assessment of the macroscopic properties with respect to the chemical and structural nature of electroceramics, an extended technique of dielectric spectroscopy will be adopted to study ferroelectric phase transitions.
The dissertation will be focused on the research and development of advanced electroceramics, derived from lead-free perovskite-structured ferroelectrics. In course of dissertation work, theoretical and experimental approaches will be employed including material processing, X-ray diffraction and the Rietveld refinement method, scanning and transmission electron microscopy, and characterization of specific electro-physical properties of functional ceramics.
Current journal literature.
RNDr. Vladimír Kovaľ, DrSc.
Advanced Materials (PMd)
Study of the crystallization kinetics of Fe-based amorphous precursors
Kinetics of phase transformations of the first order is without doubt the most intensively studied subject in the field of materials science. The main reason for such increased interest is the fact, that it represents a powerful tool to modify microstructure of studied materials and thus tailor their properties. Understanding the kinetics of a phase transformation and the associated change of microstructure is a prerequisite to utilize this tool to its full extent. Rapid quenching of a melt represents typical example of highly non steady state process which results in formation of metastable materials such as metallic glasses. Amorphous structure characteristic for a liquid state is preserved in solid state by rapid quenching. As a result of their unique structure, which is characterized by short-range order, metallic glasses exhibit excellent magnetic and mechanical properties. In case of magnetic properties metallic glasses exhibit very low values of coercivity, magnetostriction and loses which are complemented by very high values of permeability. One of the main goals of the proposed dissertation will be a detailed study of the kinetics of the crystallization process of the Fe-based amorphous precursor. Emphasis will be placed on optimizing the resulting microstructure to improve the resulting magnetic properties. In addition to standard laboratory methods such as DSC, SEM, TEM, XRD, MSB, modern methods using synchrotron radiation scattering will be used during the study.
One of the main goals of the proposed dissertation will be a detailed study of the kinetics of the crystallization process of the Fe-based amorphous precursor. Emphasis will be placed on optimizing the resulting microstructure to improve the resulting magnetic properties.
relevant scientific literature
RNDr. Jozef Bednarčík, PhD., univerzitný docent
Advanced Materials (PMd)
Study of magnetic and thermal properties of high-entropy functional alloys
The main idea of the dissertation thesis is to find a suitable chemical composition that will meet the criteria for high-entropic functional alloys. Appropriately chosen composition of individual chemical elements leads to the preparation of such materials, focusing on selected physical properties. We will focus on combining elements belonging to the group of half Heusler alloys with the stoichiometric formula XYZ, where X and Y represent a transition element and Z an element from the p block. The preparation of samples in the form of strips and microwires using the Taylor-Ulitovsky method seems very advantageous for the materials we want to deal with. Part of the work is also the design of possible cooling technology and its implementation in technical practice.
The main aim of the dissertation thesis is to research high-entropy alloys as thermoelectric materials. The work will be devoted to finding a suitable composition that will meet the criteria for high-entropy alloys and simultaneously belong to the group of thermoelectric materials. We will focus on combining elements from the group of half Heusler alloys with the stoichiometric formula XYZ, where X and Y represent the transition element and Z is the element from the p block.
[1] S. Skipidarov, M. Nikitin (Eds.): Novel Thermoelectric Materials and Device Design Concepts, Springer 2019, ISBN: 978-3-030-12056-6 [2] H. Fukuyama, Y. Waseda (Eds): High-Temperature Measurements of Materials, Springer 2009, ISBN: 978-3-540-85917 [3] P. Sharma, V. K. Dwivedi, S. P. Dwivedi: Development of high entropy alloys: A review, Materials Today: Proceedings 43, 2021, 502-509
prof. RNDr. Rastislav Varga, DrSc.
Ing. RNDr. Andrea Džubinská, PhD.
Physics (Fd)
Renormalization group study of out-of-equilibrium statistical systems
An important area of theoretical physics consists of models of non-equilibrium systems. Recently, much attention has been paid to active matter models and theoretically related active admixture models. Promising theoretical approaches for their quantitative description are based on the use of various renormalization group methods. For technical reasons, most works focus on the simplest one-loop approximation. For obvious reasons, it would be necessary to elaborate new and efficient analytical and numerical algorithms for the computation of scaling indices and control parameters of the considered models in higher orders of failure theory. Therefore, the main goal of the dissertation will be to elaborate universal approaches to compute, in particular, two-loop Feynman diagrams and to apply them in the determination of anomalous indices for different universality classes describing the large-scale behavior of the statistical correlations of the fields under study. In addition to a good knowledge of the fundamentals of modern physics, the PhD student will be required to have a working knowledge of modern programming languages.
Solve actual problems of non-equilibrium phase transitions in various models of active matter and active admixture by methods of quantum field theory and renormalization group methods.
Adzhemyan, L.T.; Antonov, N.V.; Vasiliev, A.N. Field theoretic renormalization group in fully developed turbulence; CRC Press, 1999. Active Matter and Nonequilibrium Statistical Physics: Lecture Notes of the Les Houches Summer School: Volume 112, (Oxford Academic, 2022) M. C. Marchetti, J. F. Joanny, S. Ramaswamy, T. B. Liverpool, J. Prost, M. Rao, and R. A. Simha, Rev. Mod. Phys. 85, 1143 (2013). A. Cavagna, I. Giardina, and T. S. Grigera, Phys. Rep. 728, 1 (2018). J. Zinn Justin, Quantum Field Theory and Critical Phenomena, (Oxford Univers Press, 1989) A. N. Vasil’ev The Field Theoretic Renormalization Group in Critical Behavior Theory and Stochastic Dynamics, Boca Raton:Chapman & Hall/CRC (2004)
RNDr. Tomáš Lučivjanský, PhD., univerzitný docent
prof. RNDr. Michal Hnatič, DrSc.
Physics (Fd)
Study of angular substructures of particles produced in heavy ion collisions
An important aim of nucleus collisions investigation at high energies is to search for a phenomena connecting with large densities obtained in such collisions. As an example, the transition from the QGP (quark - gluon plasma) back to the normal hadronic phase is predicted to contribute to fluctuations in the number of produced particles in local regions of phase space. Using unique method collisions of proton-proton and heavy-ion collisions at momenta between 1 AGeV/c and 160 AGeV/c will be analyzed. The methods of transverse momentum, principal vectors, azimuthal correlation functions, Fourier expansion of azimuthal angle distributions and other methods will be applied. Experimental results will be compared with model calculations.
doc. RNDr. Adela Kravčáková, PhD.
RNDr. Martin Vaľa, PhD.
Physics (Fd)
Study of strange particles production in high multiplicity proton-proton collisions in ALICE experiment at CERN LHC
A recent hardware and software upgrade of the ALICE experiment allowed in 2022 to increase the actual statistics of the proton-proton collisions (obtained in 2009-2018) more than 300 times. The data taking is planned until 2025 with a further rapid statistical increase. The increase offers new opportunities of studying rare processes in pp collisions or in heavy ion collisions. One of the open problems in this field is an origin of the enhanced production of the strange and multi-strange particles with respect to non-strange particle production in high multiplicity pp collisions [1]. It is still unknown whether the strangeness enhancement dependency as a function of multiplicity in pp collisions will follow the similar trend in peripheral heavy ion collisions or it will be significantly different. The thesis will focus on studying strange particle production in high multiplicity proton-proton collisions collected with unprecedented statistics in Run3 (2022-2025) at the LHC. [1] ALICE Collaboration., Adam, J., Adamová, D. et al. Enhanced production of multi-strange hadrons in high-multiplicity proton–proton collisions. Nature Phys 13, 535–539 (2017). https://doi.org/10.1038/nphys4111
Recent publications
doc. RNDr. Marek Bombara, PhD.
Physics (Fd)
Vector meson production study at ALICE experiment
A PhD student is expected to familiarize themselves with the physical phenomena of the behavior of strongly interacting nuclear matter at extreme energy densities and high temperatures, study the results of previous experiments mainly at RHIC and SPS and their interpretation. They should study the detectors and the trigger system of the experiment, learn how to use simulated cases and programs such as ROOT and Online-Offline Computing System (O2) to determine the detector response from Run 3 data, processing efficiency, establish and verify criteria for the selection of studied particles. They should be able to work in a distributed system such as Hyperloop and compare the results of physical analysis with model results.
1. Cheuk-Yin Wong: Introduction to High-Energy Heavy-Ion Collisions, World Scientific, 1994. 2. Ramona Vogt: Ultrarelativistic Heavy-Ion Collisions, Elsevier Science, 2008. 3. László Pál Csernai: Introduction to Relativistic Heavy Ion Collisions, John Wiley &Sons, Chichester, 1994. 4. Gunnar Lovhoiden: Heavy Ion Collisions at High Energies, Kompendium FYS338(UiB) og FYS374(UiO), August 14, 1996. 5. Donald H. Perkins: Introduction to High Energy Physics, Cambridge University Press, 1972. 6. F. Halzen, A.D. Martin : Quarks and Leptons, John Wiley &Sons, 1984. 7. B. Povh, K. Rith, C. Scholtz, F. Zetsche: Particles and Nuclei, Springer 1995.
RNDr. Martin Vaľa, PhD.
doc. RNDr. Janka Vrláková, PhD.
Advanced Materials (PMd)
Study of shape memory effect stability in Ni2FeGa microwires
The ferromagnetic Heusler alloy Ni2FeGa has broad application potential in sensors and actuators due to the combination of its magnetic properties and the existence of the shape memory phenomenon (SMP). The temperature range of the thermo-elastic phase transformation of the SMP can be controlled by varying the chemical composition of the alloy, more precisely by the changing atomic configuration of the ordered parent phase. While the equilibrium chemical composition of the ordered phase has a transformation temperature of around 50 K, it is possible to shift the transformation above the temperature of 300 K by supersaturating the ordered phase. The pilot experiment showed that the alloy in the form of microwires has, due to its thickness (< 30 m), a unique resistance to cyclic transition through the temperature phase transformation region. Changes in material structure and properties were not observed after more than 106 cycles. The topic of the dissertation is focused on the study of the Heusler alloy shape memory effect and the properties concerning their structure and the form of the prepared alloy. The work is focused on determining the thermal and mechanical stability of the ordered parent phase and justifying the effects on the transformation temperature of the produced microwires.
The topic of the dissertation is focused on the study of the Heusler alloy shape memory effect and the properties concerning their structure and the form of the prepared alloy. The work is focused on determining the thermal and mechanical stability of the ordered parent phase and justifying the effects on the transformation temperature of the produced microwires.
Current journal literature.
doc. Ing. Ondrej Milkovič, PhD.
prof. RNDr. Rastislav Varga, DrSc.
Advanced Materials (PMd)
Structural study of disordered and quasi-ordered metallic alloys using electron and XRD scattering.
Phase transitions of solids from the disordered state to complex structures ordering are subject of modern research. The relationship between initial and final structure state play an important role at forming of the new structures having advanced physical and chemical properties. The variations of external conditions, e.g. strong magnetic fields or extremal temperature changes, can substantially affect the final properties of solids as well. The main highlight of dissertation thesis will be the study of atomic structure and stability of inducted phases of promising advanced materials in relation to their properties, employing electron and X-ray diffraction techniques. The experimental approach, using transmission electron microscope JEOL 2100F UHR, will be emphasized. However, for successful completing of dissertation thesis, it will be necessary to carry out experiments at electron microscopy centres and synchrotron facility abroad.
1.) Preparation of master alloys and bulk metallic glasses. 2.) Thermo-mechanical processing and testing of mechanical and physical properties of bulk metallic glasses. 3.) Local atomic structure investigation of amorphous phases and its correlation to physical and mechanical properties. 4.) Study of amorphization and crystallization processes and related thermo-mechanically induced phase transformations in crystalline phases.
Williams D. B. and Crater C. B.: Transmission electron microscopy. 2nd ed., Springer Science, 2009, ISBN 978-0-387-76500-6. Inoue A. and Suryanarayana C.: Bulk metallic glasses. CRC Press, Talyor and Francis Group, 2011, ISBN-13: 978-1-4200-8597-6 Miller M. and Liaw P.: Bulk metallic glasses: An overview. Springer Science, 2008, ISBN 978-0-387-48920-9. Als-Nielsen J. and McMorrow D.: Elements of Modern X-ray Physics. 2nd ed., John Wiley & Sons Ltd, 2011, ISBN 978-0-470-97395-0
Ing. Vladimír Girman, PhD.
prof. RNDr. Pavol Sovák, CSc.
Physics (Fd)
Study of space weather influence on Earth’s interface to space
The Earth’s interface region to space is located at altitudes of 80-300 km. It is a dynamic environment constantly influenced by solar radiation and space weather from above and atmospheric processes from below. The main objective is to study these dynamics, especially with a focus on identifying the influence of space weather phenomena. For this purpose the following data will be used: optical observations of airglow from satellite missions and ground-based all-sky cameras and photometers; measurements of ionosphere parameters from GNSS receivers and radio systems based on the Doppler shift principle; space weather data describing the solar activity, the solar wind, the interplanetary magnetic field, and disturbances in the geomagnetic field. The work will be dedicated to detailed case studies of specific events as well as to a general data-driven approach using machine learning techniques. The obtained knowledge will contribute to a better understanding of the consequences of space weather on the interface region, which significantly affects the communication and operation of satellites and is therefore crucial for the entire society.
The main objective is to study dynamics of Earth’s interface to space, especially with a focus on identifying the influence of space weather phenomena.
Space Physics, Ch. T. Russell, J. G. Luhmann, and R. J. Strangeway, Cambridge Univ. Press, 2016. Machine Learning Techniques for Space Weather, E. Camporeale, S. Wing, J. Johnson, Elsevier, 2018 Space Physics and Aeronomy, Y. Zhang, L. J. Paxton, American Geophysical Union, 2021
RNDr. Šimon Mackovjak, PhD.
Ing. Ján Kubančák, PhD.
Biophysics (BFd)
Understanding of the structure-stability-cellular internalization relationship of polymeric nanoparticles for targeted drug transport
Nanoparticles formed by the self-assembly of amphiphilic copolymers have gained increased attention as a smart carrier for the improved solubilization and efficient delivery of anticancer agents. Many of those nanoparticles have entered clinical trials and some are in clinic use. To perform high therapeutic efficacy after an intravenous injection of polymeric nano-drug formulation, its stability during circulation in blood compartments is prerequisite for drug delivery. The aim of this thesis is to study and understand the behavior of polymeric nanoparticles under conditions in vivo such as extreme dilutions and interactions with blood proteins (e.g. serum albumin, globulin) and cells. The PhD student will investigate how minor structural changes of copolymer will affect the stability-activity relationship of nanoparticles which may play crucial role in designing effective polymeric nanoparticles for biomedical applications.
The aim of this thesis is to study and understand the behavior of polymeric nanoparticles under conditions in vivo such as extreme dilutions and interactions with blood proteins (e.g. serum albumin, globulin) and cells.
1. Datta S.*, Huntosova V.*, Jutkova A., Seliga R., Kronek J., Tomkova A., Lenkavska L., Macajova M., Bilcik B., Kundekova B., Cavarga I., Pavlova E., Sloufl M., Miskovsky P., Jancura D.: Influence of hydrophobic side-chain length in amphiphilic gradient copoly(2-oxazoline)s on the therapeutics loading, stability, cellular uptake and pharmacokinetics of nano-formulation with curcumin. Pharmaceutics 14, 2576 (2022) 2. Huntosova V.*, Datta S., Lenkavska L., Macajova M., Bilcik B., Kundekova B., Cavarga I., Kronek J., Jutkova A., Miskovsky P., Jancura D.: Alkyl Chain Length in Poly(2-oxazoline)-Based Amphiphilic Gradient Copolymers Regulates the Delivery of Hydrophobic Molecules: A Case of the Biodistribution and the Photodynamic Activity of the Photosensitizer Hypericin. Biomacromolecules, 22: 4199-4216 (2021)
prof. RNDr. Pavol Miškovský, DrSc.
Dr. Shubhashis Datta, PhD.
Physics (Fd)
Theoretical investigation of localized magnetic systems with magnetoelastic coupling
Most of the present theoretical works in the field of localized magnetic systems investigate simple theoretical models that ignore both the magnetostriction phenomena and the thermal expansion of materials. However, these effects are always present in all real magnetic systems, and they can significantly influence almost all of their thermodynamic properties. Owing to this fact, the main goal of the proposed research program is to investigate several theoretical models of localized magnetic systems that will include excepting the magnetic energy also the lattice energy. For this purpose, we will combine various static crystal potentials with anharmonic Einstein or Debye vibrations theories, and the magnetic part of the energy will be included using the generalized Ising or Heisenberg models with distance/volume-dependent exchange interactions. We will pay special attention to magnetic systems with a negative thermal lattice expansion. Such an approach will open a novel view of the magnetism of crystalline insulators and may lead to the prediction of many original and interesting physical phenomena.
The aim of the dissertation is a theoretical study of the thermodynamic properties of localized magnetic models with magnetoelastic coupling.
1. M. Rončík, T. Balcerzak, K. Szalowski and M. Jaščur, Mean-field theory of the spin-1/2 transverse field Ising model with a negative thermal expansion, Journal of Physics: Condensed Matter 34 (2022) 485802 (9pp). 2. M. Jaščur, M. Rončík, T. Balcerzak, and K. Szalowski, A novel critical behavior of the spin-1 Blume–Capel model with a distance-dependent nearest-neighbor exchange interaction and magneto-elastic coupling, Journal of Physics: Condensed Matter 32 (2020) 335801 (11pp).
prof. RNDr. Michal Jaščur, CSc.
Biophysics (BFd)
Theoretical study of possible mechanisms of allosteric activation of calcium pump SERCA
Recent knowledge pointed out importance of disrupted calcium signaling in many pathological processes. A key role in the maintaining calcium homeostasis is ensured by calcium ATPase of sarco/endoplasmic reticulum SERCA, which pumps calcium ions from cytoplasm into lumen. The activity of SERCA, which can be decreased under pathological conditions, can be enhanced by activators. Their mechanism of action, so far unknown, could be based on the interference with the modulation effects of ATP. The main goal of the dissertation will be to contribute to a knowledge on modulation effects of ATP and mechanisms of allosteric activation of SERCA by means of molecular modeling and molecular dynamics methods. The work demands previous experience with the methods mentioned above as well as with high performance computing.
The main goal of the dissertation will be to contribute to a knowledge on modulation effects of ATP and mechanisms of allosteric activation of SERCA by means of molecular modeling and molecular dynamics methods.
Rodríguez, Yoel - Májeková, Magdaléna**. Structural Changes of Sarco/Endoplasmic Reticulum Ca2+-ATPase Induced by Rutin Arachidonate: A Molecular Dynamics Study. In Biomolecules : Open Access Journal, 2020, 10, no. 2, art. no. 214. https://doi.org/10.3390/biom10020214 Clausen, J.D.; McIntosh, D.B.; Woolley, D.G.; Andersen, J.P. Modulatory ATP Binding Affinity in Intermediate States of E2P Dephosphorylation of Sarcoplasmic Reticulum Ca2+-ATPase. Journal of Biological Chemistry 2011, 286, 11792–11802, doi:10.1074/jbc.M110.206094
RNDr. Magdaléna Májeková, PhD.
Physics (Fd)
Theoretical study of skyrmion states in frustrated antiferromagnetics
An antisymmetric Dzyaloshinskii-Moriya spin exchange interaction (DMI) can lead to the formation of twisted magnetic structures. These have attracted much interest mainly after the experimental observation of nontrivial magnetic configurations, called magnetic skyrmion lattices, which have potential technological applications [1]. In ferromagnetic (FM) systems, the skyrmion phase arises from the competition between FM interactions and DMI and it is stabilized by a magnetic field and thermal fluctuations. A similar antiferromagnetic (AFM) skyrmion phase has been discovered in the frustrated classical AFM triangular-lattice Heisenberg model in the field not only with DMI [2] but also without DMI due to further neighbor exchange interactions [3]. It has been shown that magnetic frustration can improve stability of the skyrmion phase [4] and that the usage of AFMs in skyrmion-based devices has certain advantages over the implementation of FM magnets [5]. The goal of the proposed research is theoretical search for suitable candidates among frustrated AFMs that would display skyrmion phases with physically and technologically interesting properties.
prof. RNDr. Milan Žukovič, PhD.
Biophysics (BFd)
Thermodynamic properties of catalytic center of respiratory heme-copper oxidases
Most of the biological oxygen consumption is catalyzed by one family of respiratory oxidases, called heme-copper oxidases. This class of oxidases are essential for cellular respiration and energy supply in aerobic organisms. Oxidases form part of the organized respiratory chain of the enzymes located in the inner mitochondrial membrane of eukaryotes or plasma membrane of many prokaryotes. In this chain, a flow of electrons takes place parallel to the membrane plane. This electron transfer provides the energy supply for an endergonic proton transfer across the membrane. The overall reaction is a transformation of potential energy of electrons into transmembrane proton gradient. The gradient is, however, formed by two different molecular mechanisms, one of which is a proton pumping. In spite a crucial importance of pumping in the cellular energy transformation, the mechanism of linkage of electron flow with a proton pumping has not been precisely established, yet. Nevertheless, it has been identified that proton pumping occurs in two types of enzymes of the respiratory chain, one of which are terminal oxidases. Heme-copper oxidases catalyze the reduction of O2 to H2O at the catalytic center build of heme and copper ion. A large class of heme-copper oxidases are cytochrome c oxidases (CcO) that utilize for reduction of O2 electrons supplied by cytochrome c. Published data suggest that proton pumping has to be linked with the redox transitions at this heme-copper center. In spite clear catalytic importance of the heme-copper center, its thermodynamic properties, which determination is fundamental for explaining of any mechanism of proton pumping, have not been thoroughly determined. In this thesis, it is planned to acquire the thermodynamic properties for heme and copper of the catalytic center of CcO with a special attention to the dependence of the redox potentials of these centers to the pH. For this goal, the purified CcO from bovine heart will be used. It is planned, to employ several experimental techniques, e.g. UV-Vis absorption spectroscopy, magnetic circular dichroism and electron paramagnetic spectroscopy, to get the complex thermodynamic characterization of the catalytic center of CcO.
The main goal of the thesis is to acquire the thermodynamic properties for heme and copper of the catalytic center of CcO with a special attention to the dependence of the redox potentials of these centers to the pH. For this goal, the purified CcO from bovine heart will be used. It is planned, to employ several experimental techniques, e.g. UV-Vis absorption spectroscopy, magnetic circular dichroism and electron paramagnetic spectroscopy, to get the complex thermodynamic characterization of the catalytic center of CcO.
1. D. Nicholls and S. Fergusson. Bioenergetics 4, Academic Press, 2013. 2. M. Wikström (Ed.). Biophysical and Structural Aspects of Bioenergetics, The Royal Society of Chemistry, 2005. 3. D. Harris. Bioenergetics at a Glance, Blackwell Science Ltd., 1995. 4. S. Pappa, F. Guerrini, J. Tager (Eds.). Frontiers of Cellular Bioenergetics, Kluwer Academic, 1999. 5. V. Saks (Ed.). Molecular System Bioenergetics, Wiley-VCH Verlag GmbH & Co., 2007.
doc. Mgr. Daniel Jancura, PhD.
RNDr. Marián Fabián, CSc.
Advanced Materials (PMdAj)
The development of functional nanomaterials using electrochemical deposition
The work's main aim is to study functional nanomaterials prepared using electrochemical deposition in the form of nanowires. Based on the study of scientific literature, select suitable multi-element alloys with outstanding physical properties and investigate the possibilities of their preparation. The prepared materials should then be characterized by available analytical methods in order to analyze their structural, magnetic and other physical properties.
The goal of the work is the development of Heusler nanowires with outstanding physical properties suitable for bioapplications.
1. M. Varga, L. Galdun, P. Diko, K. Saksl, R. Varga, Analysis of magnetocaloric effect in parallel Ni-Mn-Ga Heusler alloy nanowires J. Alloys Compd., 944 (2023) 169196. 2. L. Galdun, P. Szabo, V. Vega, E. D. Barriga-Castro, R. Mendoza-Reséndez, C. Luna, J. Kovac, O. Milkovic, R. Varga, V. M. Prida, High Spin Polarisation in Co2FeSn Heusler Nanowires for Spintronics, ACS Appl. Nano Mater., 3, 8, (2020) 7438-7445. 3. T. Graf, C. Felser, S. S. P. Parkin, Simple Rules for the Understanding of Heusler Compounds. Prog. Solid State Chem., 39, (2011), 1−50.
prof. RNDr. Rastislav Varga, DrSc.
RNDr. Ladislav Galdun, PhD.
Physics of Condensed Matter (FKLdAj)
The effect of oxygen content on the functionality of RMnO3 materials with a perovskite structure
Orthorhombic RMnO3 materials with a perovskite structure show functional properties associated e.g. with strong magneto-electric coupling (multiferroic materials) due to the great variability of structural parameters and the variety of types of magnetic arrangement in these materials. In the work [1] we showed the possibility of creating vacancies in the oxygen crystal positions, which opened the question to what extent the targeted variation of these vacancies will affect the functional properties associated with the magnetic arrangement. In the paper [2] we showed the impact of the preparation conditions of the multiferric material GdMnO3 in the atmosphere of air, Ar or O2 on the magnetic phase transition associated with the generation of a strong magneto-electric coupling. The topic of the doctoral study is to find out to what extent the defective structure created in this way and the oxygen content affect the functionality of these materials from the point of view of magnetic and electrical properties. Successful completion of the doctoral studies requires mastering the preparation of suitable materials in the form of nanopowders, ceramics and crystals, as well as their characterization from the point of view of structure, magnetic and electrical properties.
The goal of the doctoral study is to find out to what extent the possibility of creating vacancies in oxygen crystal positions and the oxygen content in selected materials with a perovskite structure influence the functionality of these materials from the point of view of magnetic and electrical properties.
1. Matúš Mihalik, K. Csach, V. Kavečanský, Marian Mihalik: Cooperative Jahn-Teller effect in NdMn1-xFexO3+delta (0 ≤ x ≤ 0.2), Journal of Alloys and Compounds, 857 (2021) 157612 2. Matúš Mihalik, A. Pacanowska, M. Orendáč, K. Csach, M. Fitta, Marian Mihalik, Vacancy-driven magnetism of GdMnO3+delta multiferroic compound, Journal of Magnetism and Magnetic Materials 587 (2023) 171221
RNDr. Marián Mihálik, CSc.
RNDr. Matúš Mihalik, PhD.
Advanced Materials (PMdAj)
The structure determination of metallic glasses by X-ray, synchrotron based scattering and spectroscopic techniques and image techniques at XFEL
The thesis will deal with the preparation and structure observation of (Fe, Ni, Cu)-(Hf,Ta,W)-based metallic glasses in the form of ribbons and rods by melt-spinning technique and the copper mould casting method. The glassy structure of the as-prepared alloys will be investigated by synchrotron based scattering and spectroscopic techniques, namely high-energy X-ray diffraction (HEXRD), anomalous X-ray diffraction (AXRD) and X-ray absorption spectroscopy (XAS). Structure of the samples also will be checked by TEM and MID beamline at XFEL in Hamburg.
Main goal of the thesis is to handle various experimental techniques for structural determination of amorphous metallic glasses
Current journals from Mat. Sci.
prof. RNDr. Pavol Sovák, CSc.
RNDr. Jozef Bednarčík, PhD., univerzitný docent
Physics (FdAj)
Theoretical investigation of localized magnetic systems with magnetoelastic coupling
Most of the present theoretical works in the field of localized magnetic systems investigate simple theoretical models that ignore both the magnetostriction phenomena and the thermal expansion of materials. However, these effects are always present in all real magnetic systems, and they can significantly influence almost all of their thermodynamic properties. Owing to this fact, the main goal of the proposed research program is to investigate several theoretical models of localized magnetic systems that will include excepting the magnetic energy also the lattice energy. For this purpose, we will combine various static crystal potentials with anharmonic Einstein or Debye vibrations theories, and the magnetic part of the energy will be included using the generalized Ising or Heisenberg models with distance/volume-dependent exchange interactions. We will pay special attention to magnetic systems with a negative thermal lattice expansion. Such an approach will open a novel view of the magnetism of crystalline insulators and may lead to the prediction of many original and interesting physical phenomena.
The aim of the dissertation is a theoretical study of the thermodynamic properties of localized magnetic models with magnetoelastic coupling.
1. M. Rončík, T. Balcerzak, K. Szalowski and M. Jaščur, Mean-field theory of the spin-1/2 transverse field Ising model with a negative thermal expansion, Journal of Physics: Condensed Matter 34 (2022) 485802 (9pp). 2. M. Jaščur, M. Rončík, T. Balcerzak, and K. Szalowski, A novel critical behavior of the spin-1 Blume–Capel model with a distance-dependent nearest-neighbor exchange interaction and magneto-elastic coupling, Journal of Physics: Condensed Matter 32 (2020) 335801 (11pp).
prof. RNDr. Michal Jaščur, CSc.
Physics (FdAj)
Theoretical study of skyrmion states in frustrated antiferromagnetics
An antisymmetric Dzyaloshinskii-Moriya spin exchange interaction (DMI) can lead to the formation of twisted magnetic structures. These have attracted much interest mainly after the experimental observation of nontrivial magnetic configurations, called magnetic skyrmion lattices, which have potential technological applications [1]. In ferromagnetic (FM) systems, the skyrmion phase arises from the competition between FM interactions and DMI and it is stabilized by a magnetic field and thermal fluctuations. A similar antiferromagnetic (AFM) skyrmion phase has been discovered in the frustrated classical AFM triangular-lattice Heisenberg model in the field not only with DMI [2] but also without DMI due to further neighbor exchange interactions [3]. It has been shown that magnetic frustration can improve stability of the skyrmion phase [4] and that the usage of AFMs in skyrmion-based devices has certain advantages over the implementation of FM magnets [5]. The goal of the proposed research is theoretical search for suitable candidates among frustrated AFMs that would display skyrmion phases with physically and technologically interesting properties.
1. N. Romming, C. Hanneken, M. Menzel, J. E. Bickel, B.Wolter, K. von Bergmann, A. Kubetzka, and R. Wiesendanger, Science 341, 636 (2013). 2. H. D. Rosales, D. C. Cabra, and Pierre Pujol, Phys. Rev. B. 92, 214439 (2015) 3. T. Okubo, S. Chung and H. Kawamura, Phys. Rev. Lett. 108, 017206 (2012). 4. H. Y. Yuan, O. Gomonay, and Mathias Kläui, Phys. Rev. B 96, 134415 (2017). 5. J. Barker, O. A. Tretiakov, Phys. Rev. Lett. 116, 147203 (2016); W. Legrand et al., Nature materials 19, 34 (2020).
prof. RNDr. Milan Žukovič, PhD.
Physics (FdAj)
Vector meson production study at ALICE experiment
A PhD student is expected to familiarize themselves with the physical phenomena of the behavior of strongly interacting nuclear matter at extreme energy densities and high temperatures, study the results of previous experiments mainly at RHIC and SPS and their interpretation. They should study the detectors and the trigger system of the experiment, learn how to use simulated cases and programs such as ROOT and Online-Offline Computing System (O2) to determine the detector response from Run 3 data, processing efficiency, establish and verify criteria for the selection of studied particles. They should be able to work in a distributed system such as Hyperloop and compare the results of physical analysis with model results.
1. Cheuk-Yin Wong: Introduction to High-Energy Heavy-Ion Collisions, World Scientific, 1994. 2. Ramona Vogt: Ultrarelativistic Heavy-Ion Collisions, Elsevier Science, 2008. 3. László Pál Csernai: Introduction to Relativistic Heavy Ion Collisions, John Wiley &Sons, Chichester, 1994. 4. Gunnar Lovhoiden: Heavy Ion Collisions at High Energies, Kompendium FYS338(UiB) og FYS374(UiO), August 14, 1996. 5. Donald H. Perkins: Introduction to High Energy Physics, Cambridge University Press, 1972. 6. F. Halzen, A.D. Martin : Quarks and Leptons, John Wiley &Sons, 1984. 7. B. Povh, K. Rith, C. Scholtz, F. Zetsche: Particles and Nuclei, Springer 1995.
RNDr. Martin Vaľa, PhD.
doc. RNDr. Janka Vrláková, PhD.
Physics of Condensed Matter (FKLd); Physics of Condensed Matter (FKLd)
The effect of oxygen content on the functionality of RMnO3 materials with a perovskite structure
Orthorhombic RMnO3 materials with a perovskite structure show functional properties associated e.g. with strong magneto-electric coupling (multiferroic materials) due to the great variability of structural parameters and the variety of types of magnetic arrangement in these materials. In the work [1] we showed the possibility of creating vacancies in the oxygen crystal positions, which opened the question to what extent the targeted variation of these vacancies will affect the functional properties associated with the magnetic arrangement. In the paper [2] we showed the impact of the preparation conditions of the multiferric material GdMnO3 in the atmosphere of air, Ar or O2 on the magnetic phase transition associated with the generation of a strong magneto-electric coupling. The topic of the doctoral study is to find out to what extent the defective structure created in this way and the oxygen content affect the functionality of these materials from the point of view of magnetic and electrical properties. Successful completion of the doctoral studies requires mastering the preparation of suitable materials in the form of nanopowders, ceramics and crystals, as well as their characterization from the point of view of structure, magnetic and electrical properties.
The goal of the doctoral study is to find out to what extent the possibility of creating vacancies in oxygen crystal positions and the oxygen content in selected materials with a perovskite structure influence the functionality of these materials from the point of view of magnetic and electrical properties.
1. Matúš Mihalik, K. Csach, V. Kavečanský, Marian Mihalik: Cooperative Jahn-Teller effect in NdMn1-xFexO3+delta (0 ≤ x ≤ 0.2), Journal of Alloys and Compounds, 857 (2021) 157612 2. Matúš Mihalik, A. Pacanowska, M. Orendáč, K. Csach, M. Fitta, Marian Mihalik, Vacancy-driven magnetism of GdMnO3+delta multiferroic compound, Journal of Magnetism and Magnetic Materials 587 (2023) 171221
RNDr. Marián Mihálik, CSc.
RNDr. Matúš Mihalik, PhD.
Advanced Materials (PMde)
Effect of the presence of atomic hydrogen on the properties of selected steels
In many cases, metallic materials are exposed to hydrogen during their manufacture and use. During the manufacture and surface treatment of materials, hydrogen can bind to other structural components and cause the material to embrittle by improper technological processes. In addition, materials are exposed to hydrogen during use and operation, which can also cause critical damage to the material in the long term. The term hydrogen embrittlement refers to the degradation of a material due to the presence of hydrogen. There are still unanswered questions about the kinetics of the process, and no rigorous model or mechanism has been developed to determine exactly where, when and under what conditions hydrogen embrittlement occurs in steel. Hydrogen in steel causes hardening but also a significant decrease in ductility and toughness. Deterioration of mechanical properties and unexpected fracture and cracking occurs in steels exposed to even slightly aggressive environments such as moist air or hydrogen gas at low pressure. Also, a small amount of hydrogen already enters the steel during the production process. It is therefore in the interest of improving the safety and reliability of machinery and machine components to understand and overcome the effects of hydrogen. In order to test and improve steels that will be exposed to a hydrogen environment, it is necessary to simulate realistic conditions under laboratory conditions. The main objective of the work is to describe the methods by which hydrogen is introduced into steels, to induce embrittlement and to analyse fracture surfaces. On the basis of the experiments, the characteristics of the materials in question are measured, allowing the selection of the most suitable material for the necessary application in practice. It is also possible to test different alloys or additives that would reduce the effects of hydrogen or coatings that would reduce or completely stop the ingress of hydrogen into the material. Hydrogenation and subsequent mechanical testing of induced steels is not common as it requires precise and expensive equipment, is time consuming and also dangerous as hydrogen is highly reactive and explosive. Currently, there are several theories (mechanisms) of hydrogen embrittlement of steels that describe the causes of material degradation by hydrogen. However, these theories are not universally valid; individual accounts have been developed and describe hydrogen embrittlement only for specific conditions and may fail in their descriptions under others.
The aim of this work is to investigate the effect of atomic hydrogen in the steel structure after cathodic induction and to determine when the presence of hydrogen is still safe.
Qian Liu and Andrej Atren, A critical review of the influence of hydrogen on the mechanical properties of medium-strength steels, rros Rev 2013; 31(3-6): 85–103
Mgr. Vladimír Komanický, PhD., univerzitný docent
Biophysics (BFd)
The effect of selected pesticides on the genetic material of cells
The use of pesticides is a persistent ecological problem, so it is necessary to study their action at different levels of living organisms. At present, many scientific institutions deal with the effect of these toxic substances from several perspectives, for example from the point of view of their genetic action or effects on the formation of free radicals in tissues. The dissertation project is focused on investigating the interactions of pesticide molecules with the genetic material of eukaryotic cells, which will be in the first stage of linear and circular DNA. Another target are histones - small basic proteins that form the nucleus of nucleosomes located in the cell nucleus. The nucleosome nucleus consists of the so-called histone octamer, enveloped by circular DNA, which we will focus on after obtaining the results from the previous study. The task of the PhD student will be to determine by biophysical, physico-chemical and thermodynamic methods the mode and strength of interaction between pesticide molecules and the above-mentioned objects. The project will use spectrophotometric methods such as absorption, fluorescence, infrared spectroscopy, spatial spectra, optical dichroism, calorimetry and, in cooperation with the Institute of Genetics, genet
The dissertation project is focused on investigating the interactions of pesticide molecules with the genetic material of eukaryotic cells, which will be in the first stage of linear and circular DNA. Another target are histones - small basic proteins that form the nucleus of nucleosomes located in the cell nucleus. The nucleosome nucleus consists of the so-called histone octamer, enveloped by circular DNA, which we will focus on after obtaining the results from the previous study. The task of the PhD student will be to determine by biophysical, physico-chemical and thermodynamic methods the mode and strength of interaction between pesticide molecules and the above-mentioned objects.
LAKOWICZ, Joseph R. Introduction to fluorescence. In: Principles of fluorescence spectroscopy. Springer, Boston, MA, 1999. p. 1-23. GALDÍKOVÁ, Martina, et al. The effect of thiacloprid formulation on DNA/chromosome damage and changes in GST activity in bovine peripheral lymphocytes. Journal of Environmental Science and Health, Part B, 2015, 50.10: 698-707. RATHNAYAKE, P. V. G. M., et al. Trends in the binding of cell penetrating peptides to siRNA: A molecular docking study. Journal of Biophysics, 2017, 2017. GHOLIVAND, M. B., et al. DNA-binding study of anthraquinone derivatives using chemometrics methods. European journal of medicinal chemistry, 2011, 46.7: 2630-2638. VEREBOVÁ, Valéria, et al. Anthraquinones quinizarin and danthron unwind negatively supercoiled DNA and lengthen linear DNA. Biochemical and biophysical research communications, 2014, 444.1: 50-55.
doc. RNDr. Jana Staničová, PhD.
Biophysics (BFd)
The use of protein evolution methods in modifying the properties of proteins and enzymes
Directed protein evolution methods offer an efficient way to change the properties of proteins on a local as well as global level. The ambition of this project is to change the local properties of enzymes such as specificity, affinity and catalytic properties and to change global properties such as protein solubility. The object of this project will be selected enzymes from the family of haloalkane dehalogenases (HLDs) and the -opioid receptor, an integral protein from the family of G-protein coupled receptors (GPCR). HLDs are microbial enzymes that catalyze the splitting of the carbon-halogen bond and participate in the conversion of toxic halogenated hydrocarbons into less toxic compounds – alcohols. These enzymes therefore have great potential in bioremediation of toxic environmental pollutants, decontamination of chemical warfare agents, biomonitoring of pollutants in the environment and, thanks to their specific reaction, also in protein labeling during cell imaging. GPCRs are cell surface receptors that mediate responses to many endogenous signaling molecules as well as exogenous signals. GPCRs belong to the center of interest of the pharmaceutical industry, since more than 50% of drugs used today act on GPCRs. Improving the specified specific properties of these proteins would significantly help the understanding of the functionality of these proteins and their practical use. This project assumes the mastery of several biophysical, biochemical and molecular biological methods.
Using the methods of controlled protein evolution, to improve the specific properties of selected enzymes and proteins.
1. Könning D, Kolmar H. Beyond antibody engineering: directed evolution of alternative binding scaffolds and enzymes using yeast surface display. Microb Cell Fact. 2018 Feb 26;17(1):32. doi: 10.1186/s12934-018-0881-3. 2. Rosenfeld L, Heyne M, Shifman JM, Papo N. Protein Engineering by Combined Computational and In Vitro Evolution Approaches. Trends Biochem Sci. 2016 May;41(5):421-433. doi: 10.1016/j.tibs.2016.03.002. 3. Plückthun A. Ribosome display: a perspective. Methods Mol Biol. 2012;805:3-28. doi: 10.1007/978-1-61779-379-0_1. 4. Yan X, Xu Z. Ribosome-display technology: applications for directed evolution of functional proteins. Drug Discov Today. 2006 Oct;11(19-20):911-6. doi: 10.1016/j.drudis.2006.08.012. 5. Publications in scientific journals.
prof. RNDr. Erik Sedlák, DrSc.
Mgr. Mária Tomková, PhD.
Biophysics (BFd)
The use of modern methods of biophotonics for the study of the dynamics of the relationship of cellular structures in Wolfram syndrome
The use of light in the investigation, diagnosis and therapy of diseases is growing rapidly underlined by unique properties of light radiation, the availability of high-performance light sources and detectors for its detection. In this regard, light microscopy represents an important area of application of these principles. In the work, we will use the up-to-date methods of confocal microscopy and super-resolution microscopy for the research of the structure and function of cells, their organelles and specific proteins to study rare disease Wolfram syndrome.
Use of up-to-date methods of confocal microscopy and super-resolution microscopy for the research of the structure and function of cells, their organelles and specific proteins to study rare disease Wolfram syndrome.
1. Understanding Biophotonics Fundamentals, Advances, and Applications. K. Tsia et al., 2015 2. Super-Resolution Microscopy: A Practical Guide. U.J. Birk, 2017 3. Calcium Signaling and Contractility in Cardiac Myocyte of Wolframin Deficient Rats. Cagalinec et al., 2019
RNDr. Michal Cagalinec, PhD.
Physics (Fd)
Application of spin models in spatial data prediction
The research will be devoted to the use of appropriately defined spin models for the prediction of missing values in predominantly massive space-time data, e.g. from remote sensing of the Earth. Traditional prediction methods are not suitable for such data, mainly due to high computational complexity as well as other limitations [1]. Recent research has shown that prediction methods, based for example on the application of a simply modified planar rotator spin model [2,3] and its generalized version [4], can be computationally much more efficient. The potential of spin models lies in the ability to model various types of time-space correlations using short-range inter-spin interactions along with global external effects. The proposed research aims to develop strategies for the development of efficient prediction methods that would be flexible and suitable for automatic processing using massively parallel algorithms implemented on graphics processors (GPUs).
1. N. Cressie and C.K. Wikle, Statistics for spatio-temporal data. John Wiley & Sons, 2015. 2. M. Žukovič and D.T. Hristopulos, Gibbs Markov random fields with continuous values based on the modified planar rotator model, Phys. Rev. E 98 062135 (2018). 3. M. Žukovič, M. Borovský, M. Lach and D.T. Hristopulos, GPU-Accelerated Simulation of Massive Spatial Data Based on the Modified Planar Rotator Model, Mathematical Geosciences 52 123 (2020). 4. M. Žukovič and D.T. Hristopulos, Spatial data modeling by means of Gibbs Markov random fields based on a generalized planar rotator model, Physica A 612 128509 (2023).
prof. RNDr. Milan Žukovič, PhD.
Biophysics (BFd)
Development of cellular model platforms to study IgG light chain toxicity of oncohematological diseases
Embark on a groundbreaking PhD project that aims to advance our understanding of oncohematological diseases, particularly multiple myeloma and its associated IgG light chain variants. This research is crucial for unraveling the mechanisms behind the tissue-specific toxicity of these pathological forms. You will utilize a blend of cellular biology, bioengineering, and biotechnology techniques in developing these platforms, enabling a detailed analysis of variant-specific toxic effects. This research holds the potential to significantly enhance our understanding of the tissue-specific toxicity of IgG light chain variants in multiple myeloma, opening pathways to more effective treatments. As a PhD candidate, you will be at the forefront of this innovative research, collaborating with esteemed international researchers, including Dr. Magdaléna Harakalová from the Circulatory Health Research Centre in Utrecht, Netherlands. This partnership offers a rich environment for scientific growth and international networking.
1) Develop innovative cellular platforms to assess the toxicity of various pathological IgG light chain variants found in different patients. 2) Design of an analytical chip for various cellular platforms. 3) Progress from the creation of bio-chips using prokaryotic cells to eukaryotic cells, and potentially to tissue-on-chip prototypes.
1. Džupponová V, Žoldák G. Aggregation mechanism and branched 3D morphologies of pathological human light chain proteins under reducing conditions. Colloids Surf B Biointerfaces. 2023 Jan;221:112983. doi: 10.1016/j.colsurfb.2022.112983. 2. Džupponová V, Žoldák G. Salt-dependent passive adsorption of IgG1κ-type monoclonal antibodies on hydrophobic microparticles. Biophys Chem. 2021 Aug;275:106609. doi: 10.1016/j.bpc.2021.106609. 3. Džupponová V, Huntošová V, Žoldák G. A kinetic coupling between protein unfolding and aggregation controls time-dependent solubility of the human myeloma antibody light chain. Protein Sci. 2020 Dec;29(12):2408-2421. doi: 10.1002/pro.3968. 4. Nemergut M, Pluskal D, Horackova J, Sustrova T, Tulis J, Barta T, Baatallah R, Gagnot G, Novakova V, Majerova M, Sedlackova K, Marques SM, Toul M, Damborsky J, Prokop Z, Bednar D, Janin YL, Marek M. Illuminating the mechanism and allosteric behavior of NanoLuc luciferase. Nat Commun. 2023 Nov 29;14(1):7864. doi: 10.1038/s41467-023-43403-y.
doc. RNDr. Gabriel Žoldák, DrSc.
RNDr. Michal Nemergut, PhD.
Advanced Materials (PMd)
The development of functional nanomaterials using electrochemical deposition
The work's main aim is to study functional nanomaterials prepared using electrochemical deposition in the form of nanowires. Based on the study of scientific literature, select suitable multi-element alloys with outstanding physical properties and investigate the possibilities of their preparation. The prepared materials should then be characterized by available analytical methods in order to analyze their structural, magnetic and other physical properties.
The goal of the work is the development of Heusler nanowires with outstanding physical properties suitable for bioapplications.
1. M. Varga, L. Galdun, P. Diko, K. Saksl, R. Varga, Analysis of magnetocaloric effect in parallel Ni-Mn-Ga Heusler alloy nanowires J. Alloys Compd., 944 (2023) 169196. 2. L. Galdun, P. Szabo, V. Vega, E. D. Barriga-Castro, R. Mendoza-Reséndez, C. Luna, J. Kovac, O. Milkovic, R. Varga, V. M. Prida, High Spin Polarisation in Co2FeSn Heusler Nanowires for Spintronics, ACS Appl. Nano Mater., 3, 8, (2020) 7438-7445. 3. T. Graf, C. Felser, S. S. P. Parkin, Simple Rules for the Understanding of Heusler Compounds. Prog. Solid State Chem., 39, (2011), 1−50.
prof. RNDr. Rastislav Varga, DrSc.
RNDr. Ladislav Galdun, PhD.
Advanced Materials (PMd)
Development of novel electrospun ceramic nanofibres for special technical applications
Dissertation thesis is oriented to nanofibers systems prepared by relatively novel, low-cost and productive method – needle-less electrospinning, which are expected to have a great potential in the field of solar cell applications, gas sensors, varistors and other special technical applications. The expected contribution of the thesis is to study and explain the relationship between the preparation conditions, the microstructure formation and the selected functional properties of the developed nanofibers and it has all the prerequisites to shift the knowledge about the preparation of the nanofibers towards the real production possibilities. The aim of the thesis is to predict the application possibilities of the studied materials on the basis of the obtained results.
The aim of the thesis is to predict the application possibilities of the studied materials on the basis of the obtained results.
Current journal literature.
prof. RNDr. Ján Dusza, DrSc.
Ing. Eva Múdra, PhD.
Advanced Materials (PMd)
Reactive sputtering of the compositionally complex ceramic coatings
The development of magnetron sputtering is oriented toward technologies with high ionization degree of the sputtered material which provides better control of the deposition process as well as better coating properties. The most famous ionized PVD is the High Power Impulse Magnetron Sputtering (HiPIMS) and the relatively new technology High Target Utilization Sputtering (HiTUS) also belongs among these methods. High degree of ionization is achieved in the case of HiPIMS by very short duty cycle impulses with extremely high power density whereas in HiTUS by the power at an independent plasma source. The work should focus on the optimization of the deposition parameters of hard multicomponent carbide, boride and nitride coatings from the viewpoint of the control of their elastic and plastic properties by means of determination of dependencies among the deposition parameters, plasma characteristics, coating structures and their mechanical and tribological properties. The work will be performed on the iPVD systems Cryofox Discovery (Polyteknik, Denmark) and HiTUS C500 (PQL, UK) in combination with the electron microscopy observations (SEM, TEM) and measurements of mechanical properties.
Investigation of the influence of the deposition parameters of hard multicomponent carbide, boride and nitride coatings on their mechanical and tribological properties.
1. D.M. Mattox, Physical sputtering and sputter deposition (sputtering), pp. 343-405 in Handbook of Physical Vapor Deposition (PVD) processing, Mattox D.M., Noyes Publ., New Jersey, 1998. 2. B. Cantor, I.T.H. Chang, P. Knight, A.J.B. Vincent, Microstructural development in equiatomic multicomponent alloys (2004) Mater. Sci. Eng. A, 375-377 (1-2 SPEC. ISS.), pp. 213-218. doi: 10.1016/j.msea.2003.10.257 3. E. Lewin, E. Multi-component and high-entropy nitride coatings - A promising field in need of a novel approach J. Appl. Phys. 127, 160901 (2020); doi: 10.1063/1.5144154 4. F. Lofaj, L. Kvetková, T. Roch, J. Dobrovodský, V. Girman, M. Kabátová, M. Beňo, Reactive HiTUS TiNbVTaZrHf-Nx coatings: structure, composition and mechanical properties, Materials 16 (2) (2023) 563. https://doi.org/10.3390/ma16020563
doc. RNDr. František Lofaj, DrSc.
Physics (Fd)
Cosmic ray trajectory in the Earth's magnetosphere model development
Cosmic ray trajectories simulations are a tool for describing the radiation situation in the Earth's magnetosphere. They are connected to several research topics from the radiation situation in the magnetosphere, space weather topics, through the influence of cosmic radiation on the formation of clouds and the wider influence on the climate to the investigation of the accuracy of the dating method of radioactive carbon C14. The aim of the work is to improve the current models for calculating the trajectory of cosmic rays in the magnetosphere and to use them to investigate selected problems associated with cosmic rays in the Earth's magnetosphere. Selected topics include the development of a model enabling the simulation of cosmic radiation intensities during geomagnetic storms, the search for an optimal methodology for investigating the influence of cosmic radiation on cloud formation, and determining the influence of the crustal geomagnetic field on the energy thresholds of cosmic radiation on the Earth's surface and in the magnetosphere.
RNDr. Pavol Bobík, PhD.
Advanced Materials (PMd)
Development of novel entropy-stabilized ultra-high temperature ceramics with superior strength and plasticity
The topic of the dissertation work is very timely and challenging in materials science and is about the development of damage-tolerant and strong heat-resistant ceramics for hypersonic and space applications. These materials are the so-called ultra-high temperature ceramics (UHTCs), as the only group of materials that can withstand temperatures exceeding 2000°C in oxidizing atmospheres, and are used for example in thermal protecting layers of spacecraft. Since only about a dozen UHTCs exist (e.g. HfC, ZrB2) and those are brittle at low temperatures (room temperature), the dissertation work focuses on the development of novel materials in the form of entropy-stabilized UHTCs, consisting of at least four different transition metals in the crystal lattice, with improved plasticity/deformability and strength. The topic includes material design, synthesis, structural characterization (e.g. XRD, SEM, EBSD) and mechanical testing from nano to macro scale, all of which the doctoral student gets familiarised with. However, the main task will be micro/nanomechanical testing (e.g. nanoindentation, micropillar compression) of grains and grain boundaries using a state-of-the-art nanoindenter device. The knowledge gathered from the deformation behaviour of grains will be used to design new entropy-stabilized compositions with superior strength and plasticity, accomplishing original and high-impact results.
The topic of the dissertation work is very timely and challenging in materials science and is about the development of damage-tolerant and strong heat-resistant ceramics for hypersonic and space applications.
Current journal literature.
MSc. Tamás Csanádi, PhD.
Biophysics (BFd)
Development of new thrombolytics by methods of directed protein evolution
Increasing the efficiency and specificity of thrombolytics represents a complex problem in the field of protein engineering. Directed protein evolution methods, such as ribosome and yeast display, offer a robust alternative to classical protein engineering approaches. In this project, we will focus on improving the critical conformational and functional properties of thrombolytics based on staphylokinase, a bacterial protein obtained from Staphylococcus aureus, which are already used in clinical practice. The topic of the dissertation will be the selection of staphylokinase variants with improved properties by methods of ribosome and yeast display. Conformational and functional properties of the selected proteins will be characterized by biophysical methods including absorption spectroscopy, fluorescence, circular dichroism, differential scanning chlorimetry and corresponding functional tests. The goal of the work will be the development of an improved staphylokinase-based thrombolytic with use in clinical practice.
Improvement of conformational and functional properties of staphylokinase by methods of directed protein evolution.
1. Toul M, Mican J, Slonkova V, Nikitin D, Marek M, Bednar D, Damborsky J, Prokop Z. Hidden Potential of Highly Efficient and Widely Accessible Thrombolytic Staphylokinase. Stroke. 2022 Oct;53(10):3235-3237. doi: 10.1161/STROKEAHA.122.040219. 2. Nikitin D, Mican J, Toul M, Bednar D, Peskova M, Kittova P, Thalerova S, Vitecek J, Damborsky J, Mikulik R, Fleishman SJ, Prokop Z, Marek M. Computer-aided engineering of staphylokinase toward enhanced affinity and selectivity for plasmin. Comput Struct Biotechnol J. 2022 Mar 12;20:1366-1377. doi: 10.1016/j.csbj.2022.03.004. 3. Abdul Rahim P, Rengaswamy D. Fibrinolytic Enzyme - An Overview. Curr Pharm Biotechnol. 2022;23(11):1336-1345. doi: 10.2174/1389201023666220104143113. 4. Nedaeinia R, Faraji H, Javanmard SH, Ferns GA, Ghayour-Mobarhan M, Goli M, Mashkani B, Nedaeinia M, Haghighi MHH, Ranjbar M. Bacterial staphylokinase as a promising third-generation drug in the treatment for vascular occlusion. Mol Biol Rep. 2020 Jan;47(1):819-841. doi: 10.1007/s11033-019-05167-x. 5. Publications in scientific journals.
prof. RNDr. Erik Sedlák, DrSc.
Mgr. Mária Tomková, PhD.
Biophysics (BFd)
Development of efficient genetically encoded photosensitizers based on selected flavoproteins
Genetically encoded photosensitizers (GKFs) have a critical advantage over traditional small molecule photosensitizers used in photodynamic therapy in the ability to selectively distribute to diseased tissue. However, a significant functional limit of GKF compared to small photosensitizers is a significant reduction in the efficiency of singlet oxygen production of the protein-bound photosensitizer. In this project, we will use our recently developed GKF singlet oxygen production enhancement design in combination with a high-throughput method for analyzing efficient singlet oxygen producers at the clone level to develop efficient GKFs. We will test our approach on selected flavoproteins. This project assumes the mastery of several biophysical, biochemical and molecular biological methods.
Increase in singlet oxygen production in selected flavoproteins.
1. Jang J, Woolley GA. Directed evolution approaches for optogenetic tool development. Biochem Soc Trans. 2021 Dec 17;49(6):2737-2748. doi: 10.1042/BST20210700. 2. Westberg M, Etzerodt M, Ogilby PR. Rational design of genetically encoded singlet oxygen photosensitizing proteins. Curr Opin Struct Biol. 2019 Aug;57:56-62. doi: 10.1016/j.sbi.2019.01.025. 3. Ogilby PR. Singlet oxygen: there is indeed something new under the sun. Chem Soc Rev. 2010 Aug;39(8):3181-209. doi: 10.1039/b926014p. 4. Petrenčáková M, Filandr F, Hovan A, Yassaghi G, Man P, Kožár T, Schwer MS, Jancura D, Plückthun A, Novák P, Miškovský P, Bánó G, Sedlák E. Photoinduced damage of AsLOV2 domain is accompanied by increased singlet oxygen production due to flavin dissociation. Sci Rep. 2020 Mar 5;10(1):4119. doi: 10.1038/s41598-020-60861-2. 5. Publications in scientific journals
prof. RNDr. Erik Sedlák, DrSc.
Mgr. Ľuboš Ambro, PhD.
Advanced Materials (PMd)
Development of high – entropy ceramics: modelling, processing, characterization and testing
The dissertation work is focused on the development and characterization of High – Entropy Structural Ceramics with improved room and high/ultra-high temperature properties suitable for extreme operating conditions in different areas of industry. Systems based on ternary carbides and nitrides mixed in equimolar concentrations to reach the maximum molar configurational entropy with structural order and chemical disorder will be developed applying advanced modelling methods - numerical simulation, machine learning, etc., processing routes as high – energy milling, spark plasma sintering or hot – pressing. The developed systems will be tested using advanced methods as micro/nano – mechanical tests, tribology, strength/toughness tests, thermal shock, oxidation, ablation tests, etc. and characterized by SEM, EBSD, TEM/HREM, AFM etc. The proposed dissertation work will put forward a systematic study of high-entropy ceramics based on ternary carbides and nitrides in in the wide range and so completely, that new original results in this field of material science can be expected.
The proposed dissertation work will put forward a systematic study of high-entropy ceramics based on ternary carbides and nitrides in in the wide range and so completely, that new original results in this field of material science can be expected.
Current journal literature.
prof. RNDr. Ján Dusza, DrSc.
MSc. Tamás Csanádi, PhD.
Biophysics (BFd)
Changes of allosteric regulation of the ryanodine receptor evoked by pathogenic mutations studied using molecular simulation
Ryanodine receptors (RyR) are ion channels responsible for the control of excitation-contraction coupling in skeletal (RyR1) as well as cardiac muscle (RyR2). Many pathogenic RyR mutations lead to dysregulation of channel activity by Ca2+ and Mg2+ ions, causing arrhythmias and malignant hyperthermia. For developing effective therapies it is important to elucidate the molecular mechanisms, which is however difficult to achieve experimentally. The aim is therefore to assess the effect of selected pathogenic mutations on the allosteric refulation pathways in the known molecular structure of RyR, using in silico molecular simulation. The topic is a continuation of investigations in the group of Ing. A. Zahradníková, DrSc.
1. Using the data from the RCSB database, to create models of the RyR1 and RyR2 receptor core in various gating states and to examine the dynamics of selected intra- and interdomain interactions in the core. 2. To evaluate the most important allosteric pathways between activation and inhibition sites of the RyR and its gating region in different RyR1 and RyR2 gating states, using snapshots from molecular simulations and public servers such as OHM. 3. To explore the effect of selected pathogenic RyR1 and RyR2 mutations on the dynamics of intra- and interdomain interactions and the allosteric pathways.
[1] A. R. Nayak and M. Samso. Ca(2+) inactivation of the mammalian ryanodine receptor type 1 in a lipidic environment revealed by cryo-EM. Elife 11: e75568, 2022 [2] W. Zheng and H. Wen. Investigating dual Ca(2+) modulation of the ryanodine receptor 1 by molecular dynamics simulation. Proteins 88: 1528-1539, 2020 [3] V. R. Chirasani, K. I. Popov, G. Meissner, and N. V. Dokholyan. Mapping co-regulatory interactions among ligand-binding sites in ryanodine receptor 1. Proteins 90: 385-394, 2022
Ing. Miloslav Karhánek, PhD.
Physics education (TVFd)
Blended learning in astronomy education at the gymnasium
In elementary school, the concept of teaching astronomy is elaborated in the form of a separate optional subject. In teaching the subject of physics, teachers have the opportunity to include astronomical topics in connection with traditional thematic units. From the point of view of the educational standard, the follow-up high school study lacks the processing of astronomical topics as well as the support of teachers in the form of topics for educational activities. Considering the growing share of non-formal and informal education and the availability of high-quality information resources, the mentioned issue appears to be suitable for making it accessible through the method of blended learning. Our intention will be to introduce astrophysics content into the teaching of physics in the form of a separate thematic unit. In the hybrid educational space, we will use action research to verify the effectiveness of the teaching method and the impact on the development of selected student skills and knowledge. We will implement proven methods in the upcoming physics course as part of the study program of STEM classes at the gymnasium.
1. To map the state of astronomical education and blended learning at the level of high school students. 2. Design and pilot test of educational activities for hybrid education using the action research method.
[1] Dan MacIsaac; Astrophysics Lessons for High School Physics Students. Phys. Teach. 1 September 2023; 61 (6): 544. https://doi.org/10.1119/10.0020780 [2] Boyd, Nora. (2023). Laboratory Astrophysics: Lessons for Epistemology of Astrophysics. 10.1007/978-3-031-26618-8_2. [3] Fitzgerald MT, Hollow R, Rebull LM, Danaia L, McKinnon DH. A Review of High School Level Astronomy Student Research Projects Over the Last Two Decades. Publications of the Astronomical Society of Australia. 2014;31:e037. doi:10.1017/pasa.2014.30 [4] Kapusta, Joseph & Gale, Charles. (2023). Astrophysics and cosmology. 10.1017/9781009401968.017.
doc. RNDr. Marián Kireš, PhD.
doc. RNDr. Rudolf Gális, PhD.