Brno University of Technology

Latest additions:
2022-11-27
22:33
Simulations of Photobioreactors from Hydrodynamics and Mass Transfer Point of View
Rebej, Miroslav ; Turek, Vojtěch (oponent) ; Jördening, Alexandra (oponent) ; Jegla, Zdeněk (vedoucí práce)
Simulations of photobioreactors with microalgae-specific cultures is a field that connects microbiology with the multiphase fluid dynamics. With microalgae cultivation, it is necessary to account various phenomena, e.g., multiphase hydrodynamics with water, CO2 bubbles and microalgae, multiphase species mass transfer, radiation transport, light attenuation, growth and culmination of microalgae and their effect on fluid properties. Computational model presented in this doctoral dissertation thesis links multiphase hydrodynamic model and the species mass transfer model. In the thesis, there is an overview of applicable computational models for the given types of photobioreactors. The multiphase hydrodynamic model and the species mass transfer model then draw from this overview. Next, the accuracy of these sub-models was compared with laboratory experiments. As a result, the developed computational model of the photobioreactor can be further extended with other sub-models, i.e., the irradiation model and the biomass growth model.

Detailed record
2022-11-27
22:33
Stress-strain Analysis of Carotid Arteries with Atheroma
Lisický, Ondřej ; Návrat, Tomáš (oponent) ; Vimmr, Jan (oponent) ; Burša, Jiří (vedoucí práce)
Health risks associated with cardiovascular diseases are apparent in many countries' high mortality rates. Atherosclerosis in carotid arteries can cause a stroke and contributes thus in a large extent. Early detection of risky lesions is substantial to prevent an incident. The forces from the blood flow influence a rupture of a vulnerable plaque. The biomechanics of soft tissue is often incorporated with computational modelling as a potential tool to predict the plaque vulnerability for patients who underwent screening. Mechanical characteristics can then be correlated with clinical biomarkers such as crucial plaque dimensions or the presence of some risky component. However, the plaque complexity, together with a small size, influences a proper model creation leading to simplifications with an unknown effect on the mechanical characteristics. To incorporate computational modelling as a potential diagnostic tool, this is to be solved. The thesis is structured into chapters describing state of the art in computational modelling of atherosclerotic tissue. Relevant chapters are completed with a description of the author's contribution with references to the original works. Many possible directions were discovered during the literature review, although their inclusion was possible only partly as it would require more than one thesis. The main topics of interest were: (i) creation of 3D models from imaging and their subsequent use in computational study augmented by other factors, (ii) study of mechanical properties of endarterectomy samples during the study period, (iii) study of full-field strain detection methods for soft biological tissue and (iv) experimental and computational study of residual deformations and stresses of carotid arteries. The results of each part indicated problems related to computational modelling of atherosclerotic tissue, like omission of the arterial wall when the plaque stress-strain analysis is performed, the necessity of a proper understanding of mechanical responses, and its evaluation for more samples. Last but not least a negligible influence of layer-specific residual stresses for carotid plaques.

Detailed record
2022-11-27
22:33
Syntéza a stanovení vlastností čistých fází portlandského slínku a jejich polymorfů
Ravaszová, Simona ; Keppert, Martin (oponent) ; Reitermann, Pavel (oponent) ; Palou, Martin (oponent) ; Dvořák, Karel (vedoucí práce)
V cementářském průmyslu je kvantitativní difrakční analýza v současné době uskutečňována prostřednictvím Rietveldovy analýzy, která je schopna dekódovat různé difrakční linie na difrakčním záznamu za předpokladu, že je dobře znám strukturální model pro každou fázi slínku. Předmětem zkoumání této disertační práce je laboratorní příprava čistých fází jednoho triklinického a dvou monoklinických polymorfů hlavního slínkového minerálu alitu. Monoklinické fáze budou sloužit jako standardy pro kalibraci práškové rentgenové difrakční analýzy. Výsledkem této práce budou detailní postupy přípravy jednotlivých polymorfů alitu a kalibrační vztahy pro jednoznačnou a snazší identifikaci monoklinických polymorfů v reálných slíncích.

Detailed record
2022-11-27
22:33
SPECIÁLNÍ POLYMERNÍ NÁTĚROVÉ A STĚRKOVÉ HMOTY S VYUŽITÍM DRUHOTNÝCH SUROVIN
Žlebek, Tomáš ; Seidlová, Michaela (oponent) ; Bydžovský, Jiří (oponent) ; Ďurica, Tibor (oponent) ; Drochytka, Rostislav (vedoucí práce)
Práce se zabývá vývojem nových polymerních nátěrových a stěrkových hmot – konkrétně epoxidových, polyuretanových a vinylesterových s využitím nebezpečných odpadů ve formě plniv. Neustále se rozšiřují oblasti, které jsou určeny k jejich skládkování a náklady na uložení těchto odpadů jsou vysoké. Jejich užíváním dochází k eliminaci negativních dopadů na životní prostředí, ale i k nezanedbatelným úsporám finančním. V rámci této disertační práce byl vyvíjen vhodný způsob úpravy vybraných nebezpečných odpadů a experimentálně ověřovány možnosti využití takovýchto speciálně připravených plniv do polymerních nátěrových a stěrkových hmot. Tyto nátěry a stěrky jsou určeny především na betonový podklad, ale byla ověřována možnost použití i na kovový podklad, asfalt a cementotřískové desky. Tyto hmoty slouží jako sekundární ochrana konstrukcí před nepříznivými vlivy povětrnostních podmínek. Jako plnivo byly použity druhotné suroviny, kterými byl fluidní filtrový popílek kontaminovaný vlivem denitrifikace spalin a speciálně upravené nebezpečné odpady (solidifikáty). Snahou bylo progresivní využití těchto surovin v co největším množství, aby se v maximální míře omezilo skládkování. Nebezpečné odpady bylo nutné upravit takovým způsobem, aby byla provedena co nejúčinnější solidifikace. Podrobně byl zkoumán účinek solidifikace, dále chování solidifikátu v polymerní matrici, rozložení částic ve struktuře a narušení nátěrů a stěrek vlivem chemického namáhání.

Detailed record
2022-11-20
00:00
Problematika teplotní kompenzace lineárního enkodéru obráběcího centra
Štěpánek, Vojtěch ; Šooš, Ĺubomír (oponent) ; Suchánek, Rostislav (oponent) ; Marek, Jiří (vedoucí práce)
CNC obráběcí stroj je komplexní mechatronický systém, jehož chování je ovlivňováno změnou teplotního gradientu. V dnešní době bychom mohli prohlásit, že za určitých podmínek se jedná o kyber fyzikální systém. Z tohoto pohledu existují dva přístupy řešení této úlohy. Jeden směr řeší celý stroj pomocí vhodné metody jako celku. Modely bývají často velmi složité a jejich spolehlivost bývá diskutabilní. Tato práce se zabývá dekompozicí stroje za pomocí systémového přístupu s tím, že chce nalézt závislosti mezi geometrickou chybou přesnosti najetí do polohy v ose a teplotním gradientem. Pomocí vhodného virtuálního modelu následně predikovat vývoj teplotní chyby a na základě této predikce provádět akční zásahy v řídicím systému obráběcího stroje a tím eliminovat chybu najetí do polohy v ose v maximální možné míře. Jedním ze základních stavebních prvků obráběcího stroje z hlediska polohování je lineární senzor polohy, který figuruje jako přímý zpětnovazební člen regulace polohy v ose. Proto je tato publikace věnována zejména teplotnímu chování lineárního snímače polohy.

Detailed record
2022-11-20
00:00
Studying the properties of molecular photoactive materials via the methods of computational chemistry
Truksa, Jan ; Rapta, Peter (oponent) ; Toman, Petr (oponent) ; Salyk, Ota (vedoucí práce)
In this work, the principles of theoretical density functional theory are briefly discussed first, together with the method of searching for lowest-energy structures of molecules and predicting the spectroscopic and electronic properties. Afterwards, the results of the theoretical analysis of the geometry and electronic structure of two types of molecules is presented, combined with experimental results. First, the alloxazine and lumazine, considered together as flavins, and their derivatives represent molecular materials, while adamantyl substituted polythiophenes represent polymer materials. With respect to the flavins, different basis sets, together with the B3LYP functional, were used to find the best possible fit to experimental absorption spectra. Here, the B3LYP/6-31+G** and B3LYP/aug-cc-PVDZ methods proved to have the best correlation, with correlation coefficients 0.95 and 0.96, respectively, while the def2SVP set reached 0.94. In this context, the B3LYP/6-31+G** method seems to be the most cost-efficient. By measuring the absorption spectra of selected flavins in a mixture of dimethylsulfoxide (DMSO) and water, the spectra of flavin isomers – the alloxazine and isoalloxazine form were gained. The response of these molecules to changes in the concentration of DMSO and water will be the object of further study. For the polythiophenes, the electronic and optical properties were theoretically investigated using model octamers, while the conformations of the adamantylated side chains were considered using trimer molecules, due to a high computational complexity. Here, the methyladamantyl thiophene was found to have a more rigid structure compared to the ethyladamantyl substituted chain, which was later confirmed via crystallographic analysis and atomic force microscopy scans. Crystal structures were confirmed to be present, with lattice parameters comparable to poly(3-hexylthiophene) (P3HT). Inspired by this research, different polymer backbones based on polythiophene were considered for future synthesis. The main recommendation here is to lower the amount of side substituents, so that only one in two or one in three thiophenes bear an adamantylated side chain. Overall, the molecules presented here are interesting candidates for future use in optoelectronics, and the theoretical predictions generally agree with experimental results, although the comparison with experiment is not always trivial, e.g., in the case of the polythiophene side chains.

Detailed record
2022-11-20
00:00
Novel Devices and Materials for Bioelectronics
Ehlich, Jiří ; Achilleas Savva, Ph.D (oponent) ; Cifra,, Michal (oponent) ; Salyk, Ota (vedoucí práce)
This dissertation represents a synthesis of projects I have been working on in the course of my Ph.D. studies. The projects evolve around a wide range of topics, which is the reason for the broad and general title. Projects described it the thesis involve the development of electronic tools which can be applied to several areas of bioelectronics: The first part of the thesis concerns platforms for the study of unique microorganisms capable of direct electron exchange with electronic devices. This involved design, fabrication, and application of such platforms. The second part of the thesis deals with electrical stimulation; its application to stem cells towards their directed differentiation, and fundamental studies of possibly harmful irreversible faradaic reactions happening in the course of broadly used electrical stimulation protocols applied in clinical practice. All the projects share core, common, theoretical, and practical foundation originating in chemical engineering, electrochemistry, and materials science. A unifying feature playing a major factor and appearing throughout all the projects would be a family of oxygen reduction reactions. Oxygen reduction is a necessary half-cell reaction taking place in the developed device studying electroactive microorganisms. Oxygen reduction and subsequent generation of reactive oxygen species might arguably play a significant role in the direct electrical stimulation of stem cells towards their differentiation. Lastly, oxygen reduction reactions were the main irreversible faradaic reactions we have been observing during standard electrical stimulation protocols. The thesis presents summarized theoretical background necessary to understand presented projects. Goals are defined. Results are introduced as a commented list of published scientific publications. Achieved outcomes are summarized and discussed. Also, a perspective into the future is given. Main results can be summarized as follows. First goal was to develop a platform for electrochemical characterization of electroactive microorganisms. The platform was based on 24 or 96-well Microbial Fuel Cell array. After two design iterations a prototype fulfilling all the intended requirements was developed, tested, and proven to be reliably working. Next, a multi-well platform of interdigitated electrodes was fabricated and used for electrical stimulation of stem cells. Unfortunately, the platform turned out to be unreliable and not working properly which resulted in the failed attempt to differentiate stem cells into a specific type of cells. Lastly, we have examined oxygen reduction reactions (ORRs) on electrodes made of typical materials used for neural stimulation electrodes. Oxygen can be reduced either to water or hydrogen peroxide. Both reactions can significantly reduce the quantity of dissolved oxygen near the electrode, creating hypoxic conditions harmful to neurons. Peroxide, meanwhile, can induce toxic reactions or act as a signaling molecule. We have examined the amount of reduced oxygen and produced peroxide by various stimulation protocols using amperometric sensors and compared electro-catalytic activities of studied materials. Main finding is that typical protocols lead to irreversible ORRs. Some electrode materials induce highly hypoxic conditions, others additionally produce hydrogen peroxide into the mM range.

Detailed record
2022-11-20
00:00
Návrh robotické buńky s řídicím systémem Siemens
Junek, Jaroslav ; Lacko, Branislav (oponent) ; Němec, Zdeněk (vedoucí práce)
Tato práce se zabývá návrhem optimalizace pro výrobní proces armatur a paletizace. Tento proces je řízený pomocí PLC a jsou zde pro něj navrhnuty příslušné algoritmy a vizualizace. Dále zkoumá problematika MXAtomation, jako prostředku pro řízení robotu prostřednictvím programovatelného logického automatu.

Detailed record
2022-11-20
00:00
Computer Vision for Autonomous Vehicles
Lečbych, Michal ; Škrabánek, Pavel (oponent) ; Shehadeh, Mhd Ali (vedoucí práce)
Perceptive systems in autonomous cars are a heavily researched topic these days and an essential part of making fully autonomous vehicles possible. First, we make a short summary of the development of such a system, then we explain different approaches to make these systems possible, and we focus on object detection, as this will be the main part of our own created perceptive system. A new model for object detection is implemented, and some additional parts like distance estimation and lane detection are added.

Detailed record
2022-11-20
00:00
Mining of soluble enzymes from genomic databases
Hon, Jiří ; Brejová, Bronislava (oponent) ; Šafránek, David (oponent) ; Zendulka, Jaroslav (vedoucí práce)
Enzymes are proteins accelerating chemical reactions, which makes them attractive targets for both pharmaceutical and industrial applications. The enzyme function is mediated by several essential amino acids which form the optimal chemical environment to catalyse the reaction. In this work, two integrated bioinformatics tools for mining and rational selection of novel soluble enzymes, EnzymeMiner and SoluProt, are presented. EnzymeMiner uses one or more enzyme sequences as input along with a description of essential residues to search the protein database. The description of essential amino acids is used to increase the probability of similar enzymatic function. EnzymeMiner output is a set of annotated database hits. EnzymeMiner integrates taxonomic, environmental, and protein domain annotations to facilitate selection of promising targets for experiments. The main prioritization criterion is solubility predicted by the second tool being presented, SoluProt.  SoluProt is a machine-learning method for the prediction of soluble protein expression in Escherichia coli . The input is a protein sequence and the output is the probability of such protein to be soluble. SoluProt exploits a gradient boosting machine to decide on the output prediction class. The tool was trained on TargetTrack database. When evaluated against a balanced independent test set derived from the NESG database, SoluProt accuracy was 58.5% and its AUC 0.62, slightly exceeding those of a suite of alternative solubility prediction tools. Both EnzymeMiner and SoluProt are frequently used by the protein engineering community to find novel soluble biocatalysts for chemical reactions. These have a great potential to decrease energetic consumption and environmental burden of many industrial chemical processes.

Detailed record