study programme

Biophysical Chemistry

Original title in Czech: Biofyzikální chemieFaculty: FCHAbbreviation: DKCP_BCHAcad. year: 2020/2021

Type of study programme: Doctoral

Study programme code: P0533D110004

Degree awarded: Ph.D.

Language of instruction: Czech

Accreditation: 8.10.2019 - 8.10.2029

Mode of study

Combined study

Standard study length

4 years

Programme supervisor

Degree Programme Board

Fields of education

Area Topic Share [%]
100

Issued topics of Doctoral Study Program

  1. Analysis of DNA binding proteins with a focus on their interaction with local DNA structures

    Local DNA structures play an important role in basic cellular processes such as replication and transcription. Recently, the presence of G-quadruplexes in DNA has been shown to be important for regulation in the cell, but also in the regulation of the life cycle of various viruses (HIV, HSV, EBV). These local structures are recognized by a variety of proteins. In this dissertation thesis, protein interactions with local DNA structures will be studied with a focus to cruciforms and quadruplex DNA. Physical, biochemical and molecular biological methods including the isogenic yeast system will be used to study the recognition of target structural motifs in the gene promoter region. Microscopic methods including confocal microscopy will also be used to study localization and interactions in cellular systems.

    Tutor: Brázda Václav, doc. Mgr., Ph.D.

  2. Biodegradable composites with specific adhesive properties

    This work is focused on the preparation of biocomposites based on starch and other lignocellulosic substances. Important will be not only the ability of biodegradation of the designed composites but especially their sufficient thermal and mechanical stability even under more demanding conditions such as elevated temperature and humidity. Thermoplastics, as well as thermosets, will be designed and prepared. The aim will be to achieve high adhesion between the prepared materials with metals or glass.

    Tutor: Kovalčík Adriána, doc. Ing., Ph.D.

  3. Biomedical applications of non-equilibrium plasma

    Low temperature plasma generated by plasma jet systems has a significant potential in biomedical applications focused on sterilisation or wound healing stimulation. The aim of the work is evaluation of plasma effects at various conditions on real biological materials (microorganisms, skin cells, etc.).

    Tutor: Krčma František, doc. RNDr., Ph.D.

  4. Biomedical applications of plasma systems

    Low temperature plasma generated by plasma jet systems has a significant potential in biomedical applications focused on sterilisation or wound healing stimulation. The aim of the work is evaluation of plasma effects at various conditions on real biological materials (microorganisms, skin cells, etc.).

    Tutor: Kozáková Zdenka, doc. Ing., Ph.D.

  5. Biotechnological preparation of proteins important in food industry and medicine

    Tutor: Brázda Václav, doc. Mgr., Ph.D.

  6. Development of bioelectronic devices based on organic semiconductors

    The thesis is focused on the study of the relationship between the structure of materials for use in bioelectronic devices and their optical, optoelectric and electrical properties. The biocompatibility of these materials and the effect of their modification will be also studied. A typical device will be sensor of living cells physiological functions and platform for influencing cell behavior. The study will include preparation of model devices and their characterization.

    Tutor: Vala Martin, doc. Mgr., Ph.D.

  7. Effect of soil conditioners on the soil physico-chemical and microbiological characteristics

    Definition and optimization of a set of physico-chemical and (micro)biological methods and procedures suitbale for evaluation of the effect of soil conditioners (biochar, hydrosorbent, lignite and others) on the basic soil and soil organic matter characteristics. Determination of the specific action of selected conditioners on soil properties, of conditioners optimum application form and dosage in relation to their exploitation in future conventional agriculture.

    Tutor: Klučáková Martina, prof. Ing., Ph.D.

  8. Encapsulation of microorganisms for application in food industry, agriculture and medicine

    This Ph.D. thesis focuses on utilization of hydrogel matrices based on selected biopolymers for encapsulation of industrially relevant microorganisms for their application in food industry and agriculture. Apart from hydrogel-forming components, the matrices will be also functionalized by selected components providing desirable transport, mechanical and other additional properties. The focus will be directed on development and optimization of preparation protocol for hydrogel matrices, viability, physiological state and stability of entrapped microbial cells as well as rheological and other chemico-mechanical properties of prepared matrices.

    Tutor: Obruča Stanislav, doc. Ing., Ph.D.

  9. Fluorescence spectroscopy in the study of properties of associative colloidal systems

    This work is focused on the use of stationary, time resolved and microscopic fluorescence techniques in research of physical properties of associative colloids. The information obtained will be correlated with technological parameters of associative colloids such as solubilization and solubilization capacity, stability, size distribution, etc. The study will acquire not only skills in various techniques of fluorescence spectroscopy, but also in comparative techniques such as light scattering techniques.

    Tutor: Mravec Filip, doc. Ing., Ph.D.

  10. Fractionation and valorization of waste streams of food industry

    The aim of this PhD thesis is to in detail characterize selected waste streams of food industry, identify the most valuable minor fractions and suggest strategies for their sequential isolation using separation techniques such as extraction, adsorption or preparative chromatography. Furthermore, the major residual fraction will be valorized employing approaches of microbial biotechnology.

    Tutor: Obruča Stanislav, doc. Ing., Ph.D.

  11. Hydration of biocolloids

    Study of hydration of several biocolloids (e.g. chitosan, hyaluronic acid, humic substances) by means of several methods chosen on the basis of students' review, study of phenomenons related to interactions of biocolloids with water and aqueous solutions (dissolving, dissociation).

    Tutor: Klučáková Martina, prof. Ing., Ph.D.

  12. Hydrocolloids based on aminoclay

    This topic is focused on the study of the interaction of aminoclays with biopolymers and biologically active substances, especially selected drugs. The stability and preservation of biological activity of the present compounds will be monitored. Stability and other properties will be studied with respect to the various forms of administration of such complexes into living organisms by appropriate choice of conditions. Part of this topic is to master the synthesis and purification of aminoclay and to prove successful binding of active substances and biopolymers by appropriately selected methods. It is also necessary to discuss the changes in the biocompatibility of such a complex and the bioavailability of the active substance.

    Tutor: Mravec Filip, doc. Ing., Ph.D.

  13. Characterisation and application of plasma activated water

    Nowadays, plasma activated water is a hot topic both in biomedical applications thanks to its high oxidation and sterilisation potential, and in agriculture as an alternative method of fertilisation due to the enhanced amount of nitrogen species. The aim of the work is characterisation of plasma activated water prepared by various plasma systems from the viewpoint of physical, chemical as well as biological or ecotoxicological parameters, and evaluation of its utilisation in praxis.

    Tutor: Kozáková Zdenka, doc. Ing., Ph.D.

  14. Mechanical properties of biohydrogels on the macro- and microlevel

    Study of rheological properties of hydrogels relevant in biological applications, especially models of or real extracellular matrices. These properties will be studied by the techniques of both traditional rheometry and microrheology, links and differences between rheological data on the macro- and microlevel will be analyzed. The ultimate goal is to gain knowledge on causes of differences in the mechanical properties on both levels and their consequences for the functioning of biological environment.

    Tutor: Pekař Miloslav, prof. Ing., CSc.

  15. Mobility and reactivity of pharmaceuticals in soil ecosystems

    Study of interactions of hormones and drugs with soil organic matter, stability of formed complexes. Study of transport of hormones and drugs in model and real soils. Study of relationships between reactivity, mobility and bio-availability of pharmaceuticals.

    Tutor: Klučáková Martina, prof. Ing., Ph.D.

  16. Modelling of transport phenomena in biological environment

    Modelling of nano- and microparticles diffusion in simulated biological environment, especially in hydrogels. Thesis tasks will be solved using COMSOL packet. The tasks include also construction of realistic structural model of the environment and modelling support of microrheological experiments in hydrogels.

    Tutor: Pekař Miloslav, prof. Ing., CSc.

  17. Plasma polymerization of layers for biomedical applications

    Preparation of layers in the atmospheric pressure discharges. Optimization of deposition conditions (monomer flow, substrate temperature ...). Characterization of layers by physical and biological tests.

    Tutor: Mazánková Věra, doc. Mgr., Ph.D.

  18. Plasma processing of nanofibers targeted to bioapplications

    The goal of this thesis is to understand and control biocompatibility, bioactivity and antibacterial properties of polycaprolactone nanofibrous mats modified by metal ion implantation, deposition of metal-containing films and by plasma polymerization enabling immobilization of antifungal and antibacterial drugs, and ECM proteins.

    Tutor: Zajíčková Lenka, doc. Mgr., Ph.D.

  19. Preparation and application of complex microbial and plant extracts in food and cosmetics

    This thesis is focused on preparation and characterization of natural microbial, algal and plynt extracts. The main goal is to evaluate a complex biological effect of these extracts and their mixtures and application potential to some food and cosmetic products. Extracts will be stabilized by encapsulation into different types of organic micr- and nanoparticles and fibres. Characterization of application forms will be performed by microscopy, chromatography and spectoscopy. As a part of thesis development of methods for analysis of active substances as well as testing biological effects and safety (EFSA rules) will be solved. Long-term stability in model and real foods and model physiological conditions will be evaluated. Cytotoxicity and biocompatibility will be studied using cell cultures.

    Tutor: Márová Ivana, prof. RNDr., CSc.

  20. Soil hydrocolloids

    Isolation of sol and gel fractions from real soil samples, their physico-chemical characterization with a special focus on the real existence oh the humic supramolecular structures in the sol fraction. The ultimate goal is to obtain new data for the ongoing discussion on the character of humic substances in real environment and to compare obtained characteristics with those which were historically obtained after the laboratory isolation of humic acids from natural matrices.

    Tutor: Pekař Miloslav, prof. Ing., CSc.

  21. Study of phenolics and hemicelluloses obtained by enzymatic hydrolysis of food waste

    Food waste-based on lignocellulose contains phenolic, hemicellulose and cellulose components. It is known that cellulose and hemicelluloses can be converted to reducing sugars by chemical or enzymatic hydrolysis. The resulting reducing sugars can be used for the fermentation production of various substances, for example, ethanol or polyhydroxyalkanoates. However, the issue is that phenolics often toxic to microorganisms used for fermentation processes are also released during hydrolysis. The dissertation thesis focuses on the use of enzymatic hydrolysis of lignocellulosic food waste with the aim of valorization of all the substances mentioned above. Different types of enzymes will be produced and tested. An essential point of the work will be to propose an effective method of separation of phenolic substances from hemicellulose and cellulose components in order to prevent a significant decrease in the concentration of reducing sugars. The assumption is that the composition of the food waste affects the success of the separation. Another aim of this work is to evaluate the antioxidant and antimicrobial effect of isolated phenolic compounds and their application as active additives for polymers.

    Tutor: Kovalčík Adriána, doc. Ing., Ph.D.

  22. The use of electron microscopy for analysis of microorganisms relevant for food science and biotechnology

    The aim of this PhD thesis is to develop methodology for structural characterization of microorganisms relevant for food science and biotechnology, which will be based on the use of advanced electron microscopic techniques. The main task will be the optimization of preparation of samples for high-resolution electron microscopy (SEM, cryo-SEM, FIB-SEM and TEM), which will include chemical and cryogenic methods. Also, the aim is to image the samples using electron microscopes, analyze and interpret the results, which will contribute for example to deeper knowledge of production of intracellular polymers.

    Tutor: Obruča Stanislav, doc. Ing., Ph.D.

  23. Use of microalgae to biotechnological production of some biomolecules.

    This thesis is focused on the study of application potential of some autotrophic and heterotrophic algae to economically and ecologically efficient production of enriched biomass and metabolites to fortification of feeds, feeds and food supplements. Microalgae will be used to production of biomass with high content of PUFA, provitamins, glucans and other metabolites. As a part of this work optimization of technology and fermentation strategy will be developed and isolation processes will be optimized. Production characteristics of microalgae will be compared with some yeasts. Safety and biological activity of algal produts will be tested using cell cultures.

    Tutor: Márová Ivana, prof. RNDr., CSc.

  24. Use of waste from the food industry in the form of fertilizer to increase the yield and quality of food raw materials

    The main goal of this work is to use waste material, mainly from coffee processing and grain processing, in the form of fertilizer. The work will deal with the pre-treatment of the input material and subsequent further treatment steps, which should lead to the preparation of fertilizer containing additives to improve soil quality, together with the increase of yield and quality of basic cultivated food raw materials on the soil with applied fertilizer. Analytical methods HPLC, ICP-OES and many other physicochemical methods will be used. These methods will be used not only to characterize the prepared fertilizer, but also to evaluate the effects of the prepared fertilizer on soil condition and on crops.

    Tutor: Diviš Pavel, doc. Ing., Ph.D.

Course structure diagram with ECTS credits

1. year of study, winter semester
AbbreviationTitleL.Cr.Com.Compl.Hod. rozsahGr.Op.
DC_BCHBMBiophysics and Biochemistry of Microorganismscs0Compulsory-optionalCol1yes
1. year of study, both semester
AbbreviationTitleL.Cr.Com.Compl.Hod. rozsahGr.Op.
DC_BFCHBiophysical Chemistrycs0CompulsoryColyes
DC_BIOBioengineeringcs0Compulsory-optionalCol1yes
DC_F3DPhotochemistry and 3D printcs0Compulsory-optionalCol1yes
DC_ICHPAdvanced Immunochemistry cs0Compulsory-optionalCol1yes
DC_MTMaterial technology for the biophysical and medical applicationscs0Compulsory-optionalCol1yes
DC_BCHAdvanced Biochemistrycs0Compulsory-optionalCol1no
DC_KPDAdvanced Colloid Chemistrycs0Compulsory-optionalCol1yes
DC_PFTAdvanced fluorescence techniquescs0Compulsory-optionalCol1yes
DC_PTTAdvanced techniques of thermal analysiscs0Compulsory-optionalCol1yes
DC_SMBSpecial molecular biotechnologycs0Compulsory-optionalCol1yes
DC_STISpecial techniques of instrumental analysiscs0Compulsory-optionalCol1yes
All the groups of optional courses
Gr. Min. courses Courses
1 2 DC_BCHBM, DC_BIO, DC_F3D, DC_ICHP, DC_MT, DC_BCH, DC_KPD, DC_PFT, DC_PTT, DC_SMB, DC_STI