Full-time study

4 years

prof. RNDr. Tomáš Šikola, CSc.

Chairman :
prof. RNDr. Tomáš Šikola, CSc.
Councillor internal :
prof. Ing. Ivan Křupka, Ph.D.
doc. Mgr. Vlastimil Křápek, Ph.D.
prof. RNDr. Radim Chmelík, Ph.D.
prof. RNDr. Petr Dub, CSc.
prof. RNDr. Pavel Šandera, CSc.
Councillor external :
prof. Mgr. Dominik Munzar, Dr.
prof. RNDr. Pavel Zemánek, Ph.D.
RNDr. Antonín Fejfar, CSc.

The aim of the doctoral study in the proposed programme is to prepare highly educated experts in the field of physical engineering and nanotechnology with sufficient foreign experience, who will be able to perform independent creative, scientific and research activities in academia or applications in our country and abroad. The study is based on the doctoral students' own creative and research work at the level standardly required at foreign workplaces in the areas of research carried out at the training workplace and supported by national and international projects. These are the following areas of applied physics: physics of surfaces and nanostructures, light and particle optics and microscopy, construction of physical instruments and equipment, micromechanics of materials.

The graduate has knowledge, skills and competencies for their own creative activities in some of the areas in which the research activities of the training workplace are carried out. These are applications of physics especially in the field of physics of surfaces and nanostructures, two-dimensional materials, nanoelectronics, nanophotonics, micromagnetism and spintronics, biophotonics, advanced light microscopy and spectroscopy, electron microscopy, laser nanometrology and spectroscopy, computer controlled X-ray micro and nanotomography, micro and development of technological and analytical equipment and methods for micro/nanotechnologies. The possibility of using the personnel and material background provided by the CEITEC research infrastructure as well as extensive cooperation with important foreign workplaces contributes to the high level of education. This guarantees that the graduate is able to present the results of their work orally and in writing and discuss them in English. Due to high professional competencies and flexibility, graduates find employment both in universities and other research institutions in our country and abroad, and in high-tech companies in the positions of researchers, developers, designers or team leaders.

Due to their high professional competencies and flexibility, graduates find employment in the field of basic and applied research at universities and other research institutions in our country and abroad, as well as in high-tech companies in the positions of researchers, developers, designers and team leaders.

See applicable regulations, DEAN’S GUIDELINE Rules for the organization of studies at FME (supplement to BUT Study and Examination Rules)

The rules and conditions of study programmes are determined by:
BUT STUDY AND EXAMINATION RULES
BUT STUDY PROGRAMME STANDARDS,
STUDY AND EXAMINATION RULES of Brno University of Technology (USING "ECTS"),
DEAN’S GUIDELINE Rules for the organization of studies at FME (supplement to BUT Study and Examination Rules)
DEAN´S GUIDELINE Rules of Procedure of Doctoral Board of FME Study Programmes
Students in doctoral programmes do not follow the credit system. The grades “Passed” and “Failed” are used to grade examinations, doctoral state examination is graded “Passed” or “Failed”.

Brno University of Technology acknowledges the need for equal access to higher education. There is no direct or indirect discrimination during the admission procedure or the study period. Students with specific educational needs (learning disabilities, physical and sensory handicap, chronic somatic diseases, autism spectrum disorders, impaired communication abilities, mental illness) can find help and counselling at Lifelong Learning Institute of Brno University of Technology. This issue is dealt with in detail in Rector's Guideline No. 11/2017 "Applicants and Students with Specific Needs at BUT". Furthermore, in Rector's Guideline No 71/2017 "Accommodation and Social Scholarship“ students can find information on a system of social scholarships.

The presented doctoral study programme represents the highest level of education in the field of physical engineering and nanotechnology. Follows the academic and bachelor's and subsequent master's degree programme of "Physical Engineering and Nanotechnology", which are carried out at FME BUT.

1. round (applications submitted from 01.04.2026 to 31.05.2026)

1. Advanced Cryogenic Technologies for Electron Microscopy and Their Applications in the Research of Biodegradable Materials and Microorganisms

   The thesis focuses on the utilization of advanced cryogenic technologies developed at the Institute of Scientific Instruments (ISI) to convert standard electron microscopes into fully functional cryo-EM systems, and their subsequent application in the research of eco-friendly biodegradable materials and biotechnologically significant microorganisms. The work emphasizes the experimental application of established cryogenic adaptations for the Magellan SEM, Helios FIB-SEM, and the ACE 600 preparation system, including a specialized cryogenic sample holder with unlimited rotation designed for cryo-electron tomography.

   A core component of the research involves the development and optimization of cryogenic sample preparation methodologies. This includes the vitrification of biodegradable polymers, bioplastics, microorganisms, and other soft matter samples using high-pressure freezing (HPF), plunge freezing, and freeze-fracturing techniques. Freeze-fracturing is employed as a key method for revealing the internal structures of materials that transition into a brittle state at temperatures near 4 K, allowing for the creation of clean fracture surfaces without plastic deformation.

   The scope of the thesis further includes the study of vitrification physics, simulations of high-pressure freezing processes, and the analysis of ultra-low temperatures' impact on suppressing radiation damage and improving imaging stability.

   The primary output of the work will be experimentally verified cryogenic instrumentation and standardized preparation methodologies for biological and biodegradable samples in cryo-EM. These will be accompanied by new structural insights obtained through advanced cryogenic electron microscopy methods. The results will be particularly valuable in the fields of biomedicine, cryobiology, and the research of soft biological materials and polymers.

   Supervisor: Krzyžánek Vladislav, Ing., Ph.D.

2. Biosensors based on graphene and related 2D materials

   Classical biochemical tests in vitro are currently replaced by bioelectronic sensors that excel in their speed, reusability and minimal dimensions. One of the most promising materials in this area is graphene, which has a high sensitivity to the presence of adsorbed molecules and is biocompatible at the same time. The subject of the doctoral thesis will be development and production of biosensors based on graphene and related two-dimensional materials. In the thesis, it will be necessary to master the general physical principles of sensors, problems of field-controlled transistors with electrolytic gate and functionalization to achieve selective sensor response. A suitable applicant is a graduate of a Master's degree in Physical Engineering, Electrical Engineering or Biochemistry. Aims: 1) Managing physical principles of biosensors, their theoretical and experimental aspects. 2) Design and manufacture of a sensor based on a field-controlled transistor with an electrolytic gate. 3) Functionalization of sensor for specific biological and chemical reaction 4) Sensor response testing on selected biological materials. 5) Adequate publishing output and presentation of results at the international conference. Literature: Schedin, F.; Geim, A. K; Morozov, S. V.; Hill, E. W.; Blake, P.; Katsnelson, M. I; Novoselov, K. S., Detection of individual gas molecules adsorbed on graphene. Nature Materials 2007, 6, 652. Justino, C. I. L.; Gomes, A. R.; Freitas, A. C.; Duarte, A. C.; Rocha-Santos T. A. P., Graphene based sensors and biosensors. Trends in Analytical Chemistry 2017, 91, 53. Kaisti, M., Detection principles of biological and chemical FET sensors. Biosensors and Bioelectronics 2017, 98, 437. Wangyang, F.; Lingyan, F.; Panaitov, G.; Kireev, D.; Mayer, D.; Offenhausser, A.; Krause, H.-J., Biosensing near the neutrality point of graphene. Science Advances 2017, 3, 10, e1701247. Wangyang, F.; Lingyan, F.; Panaitov, G.; Kireev, D.; Mayer, D.; Offenhausser, A.; Krause, H.-J., Electrolyte-Gated Graphene Ambipolar Frequency Multipliers for Biochemical Sensing 2016, 16, 4, 2295.

   Supervisor: Bartošík Miroslav, doc. Ing., Ph.D.

3. Fabrication of advanced low-dimensional materials for nanoelectronics and nanophotonics

   In recent decades, many materials have been discovered whose electronic properties significantly surpass those currently used, and this has already been demonstrated in practice (e.g., sub-60 mV/decade switching in transistors based on 2D materials, single-electron transistors, topological semimetals for interconnects, etc.). However, in the vast majority of cases, device fabrication has relied on methods that are not scalable to industrial production. Therefore, research and development of advanced material synthesis techniques suitable for electronic and photonic applications and compatible with large-scale device fabrication remain a major challenge.

   Our research group possesses extensive know-how in the preparation of low-dimensional materials, including their subsequent characterization. The aim of this Ph.D. project will be to study the growth modes of advanced low-dimensional materials, with a particular focus on 2D materials (such as transition metal dichalcogenides, phosphides, etc.) and growth by intercalation in the van der Waals gap, and to investigate their properties using advanced microscopy and spectroscopy techniques, including in situ approaches. The PhD work will involve participation in instrumentation development and experimental work on several selected material systems. The ultimate goal is to understand the growth mechanisms of these materials and, based on this understanding, to identify suitable strategies for their controlled synthesis.

   Supervisor: Kolíbal Miroslav, prof. Ing., Ph.D.

4. Integrated photonic structures with bound states in the continuum

   Bound states in the continuum (BICs) represent a theoretically interesting way of field localization, which contradicts the conventional wisdom of bound states with energies solely outside the continuum of free states. BICs offer several interesting applications; for example, in photonics, BICs enable development of sensitive nanostructures with significant reduction of radiation leakage [1,2]. The study will focus on theoretical analysis and physical understanding of BICs in periodic nanophotonic systems, such as photonic crystals or metasurfaces, which can be used, e.g., for advanced biosensing [3]. The student will explore the existence and properties of the BICs in a selected class of the systems. Critical assessment of the benefits of the BICs in comparison with more traditional techniques from the point of view of potential sensing applications will be carried out. The study will rely heavily on numerical analysis.

   [1] K. Koshelev, A. Bogdanov, and Y. Kivshar, “Engineering with Bound States in the Continuum,” Opt. Photonics News, vol. 31, no. 1, p. 38, 2020

   [2] S. I. Azzam and A. V. Kildishev, “Photonic Bound States in the Continuum: From Basics to Applications,” Adv. Opt. Mater., vol. 9, no. 1, pp. 16–24, 2021

   [3] M. L. Tseng, Y. Jahani, A. Leitis, and H. Altug, “Dielectric Metasurfaces Enabling Advanced Optical Biosensors,” ACS Photonics, vol. 8, no. 1, pp. 47–60, 2021.

   Supervisor: Petráček Jiří, prof. RNDr., Dr.

5. Mapping plasmonic modes

   Localized surface plasmons (LSP) generated in metal nanoparticles (plasmonic antennas) can exhibit various modes differing in energy, charge distribution (dipoles vs. multipoles) and radiation capability (bright and dark modes). One of the most effective methods enabling generation and characterization - mapping of these modes at the single antenna level is Electron Energy Loss Spectroscopy (EELS) provided by High-resolution Scanning Transmission Electron Microscopy (HR STEM). The PhD study will be aimed at application of HR STEM-EELS for mapping the modes of LSP in plasmonic antennas. The emphasis will be especially put at a study of hybridized modes of coupled antenna structures and/or strong coupling effects between modes in plasmonic antennas and excitations in their surrounding environments. These excitations will be polaritons in quantum nanodots localized nearby antennas (the visible range) and/or phonons in absorbing antenna substrate membranes (IR – mid IR). In the former case, the experiment will be carried out by HR STEM-EELS at CEITEC Nano infrastructure (Titan), in the latter case, by Nion Ultra STEM available at some laboratories abroad (e.g. Oak Ridge national laboratory).

   Supervisor: Šikola Tomáš, prof. RNDr., CSc.

6. Modeling of Functional Properties of Nanostructures for Plasmonics

   The topic includes the theoretical description of the optical response of metallic nanostructures and metasurfaces for applications in plasmonics and nanophotonics. Used calculation tools will be represented by both analytical methods (e.g. optical properties of layered systems illuminated by a monochromatic plane wave, decomposition of the optical response of nanoparticles into the normal or quasinormal modes, mathematics used in diffraction optics) and numerical methods by using available software packages (e.g. based on a finite-difference time-domain method, a finite-element frequency-domain method, rigorous coupled-wave analysis) or, possibly, by using home-made computational algorithms. The results will be used for the qualitative- and quantitative interpretation of experimental data.

   Supervisor: Kalousek Radek, doc. Ing., Ph.D.

7. Quantum-Mechanical Calculations Based on Density Functional Theory (DFT) Supported by Machine Learning for Two-Dimensional Materials

   Graphene is one of the most important nanomaterials due to its exceptionally high charge carrier mobility, outstanding mechanical strength, and two-dimensional structure. However, its zero band gap limits its practical application in electronic devices. One promising approach to tailoring this property is the hydrogenation or oxidation of graphene, which enables band gap opening, modification of magnetic properties, and control of surface reactivity. As a result, hydrogenated graphene emerges as a перспектив material for applications in transistors, sensors, and memory devices.

   The investigation of these phenomena requires reliable and accurate computational approaches. Density Functional Theory (DFT) methods provide detailed insight into the electronic structure and stability of various chemical configurations. Modern implementations in the VASP 6.0 software further incorporate machine-learned force fields (ML-FF), which significantly accelerate molecular dynamics simulations while maintaining higher accuracy than classical empirical potentials. This enables efficient modeling of graphene hydrogenation dynamics while simultaneously analyzing the electronic properties of the most stable structures.

   Literature:

   Timmerman, L. R., et al. (2024). Overcoming chemical complexity in molecular dynamics using on-the-fly machine learned force fields, Journal of Chemical Theory and Computation.

   Soong, Y. C., et al. (2025). Mechanism of the electrochemical hydrogenation of graphene, Nature Communications.

   Elhaes, H., et al. (2025). Investigating the electronic properties of graphene oxide and its non-covalent interactions, Scientific Reports.

   Supervisor: Bartošík Miroslav, doc. Ing., Ph.D.

8. Study of catalytic reactions in real time

   The doctoral thesis will deal with research in the field of catalytic reactions using analytical methods capable of monitoring reactions in real-time. The reactions will be studied by various analytical methods such as UHV-SEM, E-SEM, MS, SIMS etc. aiming to better understand the mechanism of catalytic reactions on different types of surfaces (crystals, nanoparticles) and in a wide range of reaction pressures. In the first phase, the oxidation of carbon monoxide and subsequently other oxidation or reduction reactions important in technical practice will be studied. The work will also include the development of new methods and devices enabling real-time observation under various experimental conditions.

   Supervisor: Bábor Petr, doc. Ing., Ph.D.

9. System-Independent Data Library Transfer for LIBS Applications in Geosciences

   Laser-Induced Breakdown Spectroscopy (LIBS) is widely used in geological applications for rapid material analysis employing compact and robust systems. However, one of the main obstacles to its broader practical deployment is the limited transferability of spectral libraries and calibration models between different LIBS instruments. Variations in laser parameters, optical configurations, spectral resolution, detection systems, and experimental conditions introduce systematic differences in the measured data, preventing the direct sharing of libraries across platforms.

   The aim of this project is to develop a systematic approach for transferring LIBS data libraries between different analytical platforms without the need for direct recalibration of individual instruments. The work will be based on machine learning methods, particularly representation learning techniques such as autoencoders and related architectures, as well as approaches inspired by domain adaptation. These methods enable the transformation of spectral data into a latent space that preserves chemically relevant information while suppressing systematic instrument-specific variations.

   The research will focus on the design, training, and validation of models capable of mapping spectra acquired from different LIBS systems into a shared, instrument-independent space. Special emphasis will be placed on maintaining physical interpretability, robustness to variations in experimental conditions, and long-term model stability. The methodology will be tested on geological datasets comprising various rock and mineral types, and the transfer performance will be evaluated in terms of classification accuracy, quantitative analysis, and generalization to previously unseen systems.

   The outcome of the project will be a general framework for instrument-independent transfer of LIBS spectral libraries, enabling efficient data sharing, reduced recalibration requirements, and improved reproducibility of LIBS analyses in geoscientific applications. This approach has the potential to significantly enhance the broader adoption of LIBS in both laboratory and field environments.

   Supervisor: Pořízka Pavel, doc. Ing., Ph.D.

10. Two-Dimensional Nanoelectronics Based on Hydrogenated and Oxidized Graphene

    Graphene, owing to its exceptionally high charge carrier mobility, tunable carrier type via external electric fields, long spin coherence times, and low electronic noise, represents a highly promising material for applications in both classical and quantum electronics. It has already demonstrated potential in high-frequency transistors, photodetectors, chemical and biological sensors, and may play a significant role in future quantum information technologies.

    For practical implementation in nanoelectronic devices, graphene must be laterally patterned with nanometer-scale resolution. Conventional optical lithography lacks the required spatial resolution, while electron-beam lithography may adversely affect insulating substrates (e.g., SiO₂ or hBN) due to electron irradiation damage.

    The aim of this doctoral project is to experimentally and theoretically investigate lateral graphene patterning using local anodic oxidation and local cathodic hydrogenation (LAO/LCH) performed by atomic force microscopy (AFM). This approach offers the potential for nanometer-scale resolution while minimizing damage to the substrate and surrounding structures.

    Special attention will be devoted to the investigation of the insulating properties of hydrogenated barriers, their structural stability, and their impact on charge transport characteristics in graphene-based nanoelectronic devices. The central research question is whether this technique enables the fabrication of sufficiently insulating and stable nanostructures suitable for applications in two-dimensional nanoelectronics.

    Literature:

    BYUN, I. S., D. Y. LEE, M. H. PARK, H. C. SHIN, J. J. SONG, S. LEE, K. H. KIM a J. D. LEE, 2011. Nanoscale lithography on monolayer graphene using hydrogenation and oxidation. ACS Nano. 5(9), 6417–6424. DOI: 10.1021/nn201601m.

    Supervisor: Bartošík Miroslav, doc. Ing., Ph.D.