Physics

Supervisor: doc. RNDr. Robert Vácha, PhD.

OBJECTIVES: The aim is to elucidate the relationship between protein sequence and preferred composition and curvature of human membranes,i.e., find peptide motifs that are selective to specific membranes in cells (plasma membrane, endoplasmic reticulum, Golgi apparatus, mitochondria, etc.). The obtained understanding will be used for the development of new protein biomarkers, sensors, scaffolds, and drugs.



DESCRIPTION: The control of biological membrane shape and composition is vital to eukaryotic life. Despite a continuous exchange of material, organelles maintain a precise combination and organization of membrane lipids, which is crucial for their function and the recruitment of many peripheral proteins. Membrane shape thus enables the cell to organize proteins and their functions in space and time, without which serious diseases can occur. Moreover, membrane curvature and lipid content can be specific to cancer cells, bacteria, and enveloped virus coatings, which could be utilized for selective targeting. We will develop a new method, using which we will elucidate the relationship between the protein sequence and the preferred membrane. The relationship will lay the foundations for the design of new protein motifs sensitive to membranes with a specific curvature and composition. Student(s) will master tools of computer simulations, in particular, molecular dynamics techniques and methods to calculate free energies. Moreover, he/she will learn the advantages and disadvantages of various protein and membrane parameterizations, including all-atom and coarse-grained models.



EXAMPLES of potential projects: * Determination of helical motifs for specific membrane compositions * Development of implicit membrane model for fast determination of protein-membrane affinity * Helical peptides and their sensitivity for membrane curvature



MORE INFORMATION: vacha.ceitec.cz



PLEASE NOTE: before the formal application process, all interested candidates should contact Robert Vacha (robert.vacha@mail.muni.cz).

Supervisor: prof. RNDr. Jiří Šponer, DrSc.

Our scientific goal is understanding of the most basic principles of structural dynamics, function and evolution of DNA and RNA.

To achieve this goal, we use a wide range of computational and theoretical methods, often with a close collaboration with many experimental laboratories. The best and entirely independent assessment of our research and the available topics can be obtained from the list of our papers, which can be easily found in the WOS and SCOPUS dat.abases (J. Sponer). We do not specify details of exact PhD project in this material, as for any student we offer all topics on which we currently have active research and all methods that we are currently using. Thus we discuss details of each specific PhD project with the individual student based on her/his specific interest and capabilities; selection of an optimal project requires some time

Our methods are:

• Classical Molecular Dynamics (MD) simulations
• Quantum-chemical (QM) method
• Hybrid quantum-classical (QM/MM) methods, quantum molecular dynamics
• Structural bioinformatics

Specific experiments are possible in the field of prebiotic chemistry in collaborating laboratories - need to discussed. Modern computations are extensively combined with many experimental techniques (NMR, X-Ray, high-energy lasers, biochemical techniques) mostly via numerous collaborations. We collaborate with 30 foreign and Czech laboratories. We publish about 20 papers annually and belong to the most cited Czech research groups. See the full list of papers on this web page. We have excellent in-house computer facilities, which are regularly upgraded. We currently work in several mutually interrelated research areas.

• RNA structural dynamics, folding and catalysis
• Protein-RNA complexes
• DNA, with focus on G-quadruplexes
• Diverse types of quantum-chemical studies on nucleic acids systems

Origin of life (prebiotic chemistry), i.e., creation of the simplest chemical life on our planet (or anywhere else in the Universe), with a specific attention paid to the formamide pathway to template-free synthesis of the first RNA molecules. This specific project includes also in house experimental research. Besides studies of specific systems, we are also involved extensively in method testing/development, mainly in the field of parametrization of molecular mechanical force fields for DNA

NOTE: before initiating the formal application process to doctoral studies, all interested candidates are required to contact Prof. Jiri Sponer (sponer@ncbr.muni.cz) for an informal discussion.

Laboratory web page https://www.ibp.cz/en/research/departments/structure-and-dynamics-of-nucleic-acids/info-about-the-department

List of publications https://www.ibp.cz/en/research/departments/structure-and-dynamics-of-nucleic-acids/publications

Supervisor: doc. RNDr. Robert Vácha, PhD.

OBJECTIVES: The aim is to elucidate the relationship between molecular properties of amphiphilic peptides and their ability to translocate and form transmembrane pores in membranes with various lipid compositions. The obtained understanding will be used for the development of new antimicrobial peptides, which can serve as a new type of antibiotic drugs.



DESCRIPTION: Antibiotic-resistant bacteria cause more than 700 000 deaths per year, and the forecast is 10 million per year in 2050. Moreover, emerging strains of bacteria resistant to all available antibiotics may lead to a global post-antibiotic era. Because of this threat, the WHO and the UN are encouraging the research and development of new treatments. Antimicrobial peptides are promising candidates for such new treatments. We will study the molecular mechanism of action of antimicrobial peptides and determine the critical peptide properties required for membrane disruption via the formation of transmembrane pores and spontaneous peptide translocation across membranes. Based on the obtained insight, we will design new peptides and test their abilities. The most effective peptides will be evaluated for antimicrobial activity and human cell toxicity using growth inhibition and hemolytic assays, respectively. Student(s) will master tools of computer simulations, in particular, molecular dynamics techniques and methods to calculate free energies. Moreover, he/she will learn the advantages and disadvantages of various protein and membrane parameterizations, including all-atom and coarse-grained models. The simulations will be complemented by in vitro experiments using fluorescent techniques.



EXAMPLES of potential projects: * Antimicrobial peptides and formation of membrane pores * Synergistic mechanisms between antimicrobial peptides * Membrane disruption by antimicrobial peptides in non-equilibrium conditions



MORE INFORMATION about the group: vacha.ceitec.cz



PLEASE NOTE: before the formal application process, all interested candidates should contact Robert Vacha (robert.vacha@mail.muni.cz).

Supervisor: Hoa Hong NGUYEN, PhD

The aim of the study is to verify the role of oxygen vacancies and defects in introducing room temperature ferromagnetism in various pristine Semiconducting Oxides in nanoscale. By down scaling semiconducting oxides, under appropriate conditions that may create oxygen vacancies/defects, room temperature ferromagnets can be obtained. This may allow one to manipulate the spins and charges simultaneously in the same device. We propose to study the effect of introducing additional carriers and lattice defects on the ferromagnetic properties of thin films of undoped oxides. The investigations will exploit the element selectivity of X-ray magnetic circular dichroism to detect changes in the spin polarization caused by the presence of extra charge carriers due either to x-ray irradiation or to dopant impurities. We expect these studies to shed new light on the mechanisms of d0-Ferromagnetism.

The PhD candidate is expected to join our research in one of the following research activities:

• Preparation of targets and ultrathin films of pristine TiO2 and Ta- or C- doped TiO2 with different dopant concentrations. Perform XRD, VSM or MPMS, XAS, XMCD, and other necessary measurements at different temperatures and fields to characterize the films.
• Preparation of targets and ultrathin films of undoped- SnO2 and C-doped SnO2 ultrathin films on different substrates grown under different annealing conditions. Perform necessary measurements such as XRD, VSM or MPMS, XAS, XMCD, etc. to characterize the films.
• Manipulating oxygen vacancies and defects in a controllable way by means of changing size, conditions, in-situ arrangements.
• Performing possible simulations to guide the experiments.

Required Skills and Qualifications:

• Master’s degree in either Condensed Matter Physics or Chemistry of Solids
• Hands-on experience in experimental laboratories, being familiar with equipment in Physics and/or Chemistry Labs should be preferable
• Good communication skills (oral and written) in English
• High level of commitment to complete the PhD studies

REFERENCES

1. Room temperature ferromagnetism observed in undoped semiconducting and insulating oxide thin films. Nguyen Hoa Hong, Joe Sakai, Nathalie Poirot, and Virginie Brizé, Physical Review B 73, 132404 (2006).
2. Ferromagnetism in C-doped SnO2 thin films. Nguyen Hoa Hong, J.-H. Song, A.T. Raghavender, T. Asaeda, and M. Kurisu, Applied Physics Letters 99, 052505 (2011).
3. Oxygen vacancy induced ferromagnetism in undoped SnO2 thin films. G. S. Chang, J. Forrest, E. Z. Kurmaev, A. N. Morozovska, M. D. Glinchuk, J. A. McLeod, A. Moewes, T. P. Surkova , and Nguyen Hoa Hong, Physical Review B 85, 165319 (2012).
4. “Nano-sized Multifunctional Materials: Synthesis, Properties and Applications”, Edited by Nguyen Hoa Hong, Elsevier 2018, ISBN 978-0-12-813934-9.

PLEASE NOTE: before the formal application process, all interested candidates should contact dr. Nguyen at hong.nguyen@mail.muni.cz and provide curriculum vitae, cover letter with a concise summary of previous research activities, and contacts of two persons who might provide references

MORE INFORMATION:https://www.physics.muni.cz

Supervisor: doc. Mgr. Tomáš Hoder, Ph.D.

Problematika obsazování kvantových stavů molekul a atomů v přechodném nerovnovážném plazmatu je jednou z fundamentálních výzev současné plazmové fyziky. Populace a relaxace distribucí rotačních, vibračních a elektronových kvantových stavů probíhá v extrémně krátkých časových intervalech a jejich mikroskopické zákonitosti jsou stále otevřeným problémem. Doktorský/á student/ka bude analyzovat vybrané stavy a podmínky v plazmatu pomocí pokročilých metod (např. emisní či laserové spektroskopie). Cílem práce bude přispět k objasnění iniciace plazmo-chemických procesů a také vlivu těchto procesů na studované plazma.

Supervisor: doc. RNDr. Vilma Buršíková, Ph.D.

Současné období pandemie ukázalo na zvýšený požadavek na vývoj metod pro úpravu povrchových vlastností materiálů, např. pro přípravu antibakteriálních a antivirových povrchů nejen pro zdravotnické materiály, ale i pro obalovou techniku a další často dotýkané povrchy (kliky, vypínače, apod.). Nanočástice stříbra, ale i některých dalších kovů (měď, zlato, titan) jsou známé pro jejich antibakteriální i antivirové vlastnosti. Tématem navržené disertační práce bude vyvinout technologii kovem dopovaných organosilikonových tenkých vrstev použitím metody plazmatem aktivované depozice z plynné fáze. Pro zabudování kovů budou odzkoušeny 2 metody: (1) depozice ze směsí organosilikonových a organometalických prekurzorů a (2) příprava organosilikonových vrstev v prachovém plazmatu dodáním nanočástic různých kovů s antibakteriálními vlastnostmi do plazmatu. V případě druhém bude nutné vyřešit dodání částic do plazmatu.
Pro přípravu shora uvedených vrstev je velmi důležitý jejich multifunkční charakter, kromě antibakteriálních vlastností musí splňovat několik dalších důležitých vlastností, jako jsou dobrá adheze k substrátu, otěruvzdornost, elasticita (zejména v případě flexibilních substrátů), transparentnost (v případě obalových materiálů). Požadavek na kvalitu struktury vrstev (dopant se nesmí uvolňovat z povrchu) bude rovněž zvýšená, vrstva musí zachovat povrchové i objemové vlastnosti a musí být odolný vůči běžným čisticím postupům.
V rámci práce budou studovány vlastnosti tenkých vrstev i v závislosti na druhu substrátu na který jsou tenké vrstvy nanášeny (u plazmatem asistované depozice může mít substrát významný vliv). Bude kladen důraz na studium vlivu záporného stejnosměrného předpětí na substrátu na vlastnosti nadeponovaných vrstev. V práci se bude věnovat i studiu časového vývoje předpětí a jeho vliv na hloubkový profil mechanických, strukturních a dalších fyzikálních a chemických vlastností vrstev.
V první části disertační práce se budou vyvíjet metody pro přípravu různých typů vrstev ze směsí organosilikonů anebo organosilazanů s nosnými plyny (např. Ar, O2, N2O, atd.) aby bylo možné vytypovat vhodné typy vrstev pro následné dopování kovovými prvky.
Pro úspěšné řešení tohoto tématu bude velice důležitá důkladná charakterizace tenkých vrstev, jako jsou měření mechanických (nanoindentace, vrypové a nanootěrové zkoušky), povrchových (topografie pomocí AFM, konfokální mikroskopie, studium volné povrchové energie), strukturních a chemických vlastností vrstev (FTIR, XPS, Raman, SEM, TEM, RBS/ERDA atd.). Většina těchto technik je k dispozici na pracovišti ÚFE, TEM můžeme řešit ve spolupráci s ÚFM anebo s CEITEC, RBS/ERDA ve spolupráci s ÚJF (Řež u Prahy). Antibakteriální testy pak můžeme řešit ve spolupráci s FCH VUT, TUL Liberec anebo Univerzitou Tomáše Bati ve Zlíně.
Materiálně je řešení tématu v současné době zabezpečený projektem GAČR 19-15240S.

Supervisor: doc. Mgr. Pavel Dvořák, Ph.D.

V reaktivním plazmatu mohou samovolně vznikat mikro a makroskopické částice, které ovlivňují plazma i vlastnosti případných materiálů deponovaných z plazmatu. V rámci této dizertační práce studujte plazma nízkotlakého kapacitně vázaného výboje, ve kterém vznikají prachové částice. Zvolte vhodné diagnostické metody a sestavte potřebná diagnostická zařízení. Zprovozněte monitorování růstu prachu v plazmatu, zjistěte a vysvětlete souvislosti mezi přítomností prachu a vlastnostmi plazmatu. Přístupné diagnostické metody zahrnují zejména elektrická měření (VA charakteristika, sondové metody), optické a laserové metody.

Supervisor: doc. Mgr. Pavel Dvořák, Ph.D.

Laserová diagnostika zahrnuje řadu metod, které souhrnně umožňují získat poměrně komplexní informaci o studovaném plazmatu. Mezi laserové metody vhodné pro studium plazmatu patří fluorescenční metody (vč. fluorescence iniciované vícefotonovou absorpcí), Ramanův rozptyl zahrnující vibrační i rotační přenos energie, jenž může existovat ve spontánní i stimulavané variantě, Thomsnův rozptyl umožňující studovat volné elektrony, Rayleigho rozptyl a generace druhé harmonické frekvence laserového záření vlivem elektrického pole. Úkolem této dizertační práce je studium nerovnovážného plazmatu pomocí laserové diagnostiky s důrazem na metody využívající rozptyl laserového záření. Součástí práce je realizace optických experimentů, kvantitativní vyhodnocení měřených dat a studium procesů probíhajících v plazmatu.

Supervisor: doc. RNDr. Tomáš Homola, PhD.

The novel emerging field of flexible and printed electronics has attracted increased attention because of its potential to enable low-cost and high-throughput manufacturing of electronics on cheap plastic substrates for various applications including photovoltaics. However, this segment is still far away from commercialization because the cutting edge materials and manufacturing steps are not compatible with thermally sensitive flexible materials.

The PhD. work will focus on low-temperature plasma engineering of novel nanostructured nanomaterials as tungsten oxide, iron oxides, titanium dioxide, molybdenum disulfide, etc ... and their application in various energy-harvesting, -storage systems and sensing devices. The topic and tasks in the laboratory are strongly oriented towards the industrial segment.

Possibility to spend 6 months on an internship in a high-tech company in Singapore working on PhD. topic.

The exacttopic and tasks will be defined later according to applicant preference: perovskite solar cells, tandem solar cells, supercapacitors, etc ...

Keywords: State-of-the-art plasma generators, coating deposition methods (i.e. ink-jet printing), plasma treatment, advanced surfaces, nano-coatings, roll-to-roll manufacturing, flexible and printed electronics, surface characterization (AFM, XPS, SEM, etc.).

Notes

More information:

https://plasma.sci.muni.cz/en/for-students/flexible-and-printed-electronics

Relevant literature:

T. Homola, J. Pospíšil, R. Krumpolec, P. Souček, P. Dzik, M. Weiter, et al., Atmospheric dry hydrogen plasma reduction of inkjet-printed flexible graphene oxide surfaces, ChemSusChem. 11 (2018) 941–947. doi:10.1002/cssc.201702139.

T. Homola, P. Dzik, M. Veselý, J. Kelar, M. Černák, M. Weiter, Fast and low-temperature (70 C) mineralization of inkjet printed mesoporous TiO2 photoanodes using ambient air plasma, ACS Appl. Mater. Interfaces. 8 (2016) 33562–33571. doi:10.1021/acsami.6b09556.

Supervisor: doc. Mgr. Dušan Kováčik, Ph.D.

Atmospheric pressure plasma is effective method for surface cleaning, modification and activation of various types of materials [1]. It is well know that the atmospheric non-isothermal plasma treatment is capable to induce the surface modification in only very thin surface layer of material. Diffuse Coplanar Surface Barrier Discharge (DCSBD) generates stable, uniform, diffuse, low-temperature, non-equilibrium atmospheric plasma suitable for fast and effective plasma modification of flat and flexible substrates [2]. As reported, the effective thickness of DCSBD plasma is only 0.3 mm, and thus, it is not suitable for plasma modification of structured and porous materials. However, very recently, we observed a new phenomenon, that DCSBD plasma can modify “thick” samples, of thickness even 0.5 – 2 mm, in a whole volume, when the material is in a form of aerogel.

The dissertation thesis will focus on plasma modification and functionalization of porous materials - powders and aerogels. The effect of atmospheric plasma will be studied on graphene oxide aerogel and carbon nanotubes-graphene hybrid aerogel. The effect of atmospheric pressure plasma, generated by DCSBD and multihollow DBD [3], will be studied at various process parameters (gas flow and type of process gas, sample distance). The functionalization of porous materials will be studied by plasma modification in various gas mixtures as well as by the deposition of thin functional layers prepared by Atomic Layer Deposition [4]. The materials will be studied by means of surface characterization methods (XPS, SEM, AFM), electrical analyses (4-point probe) and thermal and mechanical stability measurements. The dissertation thesis should also try to provide an understanding of plasma – aerogel interaction.


Literature:

[1] J.R. Roth, Industrial Plasma Engineering Volume 1: Principles, IOP Publishing Ltd, 1995.

[2] M. Černák, D. Kováčik, J. Ráhel’, P. St’ahel, A. Zahoranová, J. Kubincová, et al., Generation of a high-density highly non-equilibrium air plasma for high-speed large-area flat surface processing, Plasma Phys. Control. Fusion. 53 (2011) 124031. doi:10.1088/0741-3335/53/12/124031.

[3] R. Krumpolec, V. Richter, M. Zemánek, T. Homola, Multi-hollow surface dielectric barrier discharge for plasma treatment of patterned silicon surfaces, Surfaces and Interfaces. 16 (2019) 181–187. doi:10.1016/j.surfin.2019.01.014.

[4] R. Krumpolec, D.C. Cameron, T. Homola, M. Černák, M. Cernák, Surface chemistry and initial growth of Al2O3 on plasma modified PTFE studied by ALD, Surfaces and Interfaces. 6 (2017) 223–228. doi.org/10.1016/j.surfin.2016.10.005.