The thesis deals with a new versatile strategy which is aimed to heat up rapidly the nanostructures with the help of a focused light beam utilizing localized plasmons (collective oscillation of electrons). By local heating, the growth of the semiconductor nanowires can be initiated and controlled at any arbitrarily prespecified location down to the single nanostructure level in a chamber at room-temperature. The aim of the work is to study electromagnetic field in the selected structures, especially in metal nanospheres by using numeric calculations and computations of the thermal field in the vicinity of these illuminated nanostructures. Electromagnetic phenomena is simulated in Lumerical and the temperature field in COMSOL.

This diploma thesis focuses on the preparation of the liposomes, containing lipids with gadolinium, which are used for a contrast magnetic resonance imaging. The liposomes were prepared by the lipid film hydration followed by an extrusion and also by a new nanofluid mixing method on the NanoAssemblr Benchtop. The preparation technology has been optimized for parameters such as the composition of lipids, the flow rate ratio and total flow rate. The method of modification of the liposomes surface by gadolinium complexes has been developed. This method is using a conjugation reaction between the lipids containing cyanuric acid and Gd-DOTA. Prepared Gd-liposomes, which contain gadolinium, were complexly defined by the characterization techniques of DLS and NTA. The morphology of liposomes was observed by TEM and cryo-TEM. Methods for the determination of phospholipid content (Stewart test) and residual water in the lyophylisates of liposomes (Karl-Fischer titration) were used. Gadolinium in liposomal preparations was determined by ICP-OES. Using MR, the concept of gadolinium liposomes was verified and designed for MRI imaging of thrombi. The concept describing the mechanism of liposomes formation based on the experimentally proven existence of a phospholipid bilayer fragment has been developed. This concept is based on the experimentally proven existence of a phospholipid bilayer fragment.

This master’s thesis deals with problematic of correlates finding of heart rate changes in fMRI data. The first part describes principle of fMRI, creation of BOLD signal, data acquisition, their pre-processing and analysis. The next part describes heart rate variability and its impact on fMRI data. The following section is dedicated to pre-processing of heart rate time series to the form, which can be used in correlates finding of heart rate variability and fMRI data with generalized linear model. The process of statistical testing and its result with discussion can be found in the last part of this thesis.

Title: NMR Study of Oligonucleotide Structures Author: Václav Římal Department: Department of Low-Temperature Physics Supervisor: Prof. RNDr. Helena Štěpánková, CSc., Department of Low- Temperature Physics Abstract: The dynamics of nucleic acids plays a fundamental role in the interactions with proteins. Some processes are governed by changes in DNA stability and flexibility caused by sequence alterations or chemical modifications without substantial structural impact. We employed line-shape analysis of variable-temperature 1H NMR spectra to deeply investigate the melting transition of DNA structures. We observed a significant influence of the sequence beyond the nearest neighbours on chemical shifts and thermodynamics of the double helix. The CpG motif is especially sensitive to its distant surroundings and for a particular oligonucleotide it was even found to undergo an unexpected local conformational transition. A strong cooperativity in the duplex dis- ruption was witnessed by both the equilibrium and kinetic aspects as well as by distant effects of cytosine methylation. We propose a two-state melt- ing scheme also for a fragment of a transcription element proved here to fold as a hairpin with a six-membered loop. In addition, we describe the properties of self-assemblies of riboguanosine and...

Title Complex preoperative brain tumor imaging Abstract The differentiation of glioblastoma, metastases and brain lymphoma using modern diagnostic imaging methods has a major impact on the strategy of further diagnostic examinations and treatment. In a group of 67 patients with glioblastoma and 31 with cerebral metastasis, the ability to differentiate them according to the evaluation of perfusion parameters changes in peritumoral white matter by T1 dynamic post-contrast magnetic resonance imaging was verified, with the positive predictive value in glioblastoma detection up to 91%. In a group of 36 brain lymphoma patients the importance of imaging submodalities and contribution of a complex magnetic resonance imaging protocol to detect lymphoma up to 80% were evaluated. Key words brain, glioblastoma, lymphoma, magnetic resonance imaging, neoplasm metastasis

Title: Multifunctional biomolecular assemblies for parallelized analysis of biomolecular interactions Author: Markéta Bocková Department / Institute: Institute of Physics, Charles University Supervisor of the doctoral thesis: Prof. Jiří Homola, Ph.D., DSc., Institute of Photonics and Electronics, The Czech Academy of Sciences Abstract: Surface plasmon resonance (SPR) biosensors represent the most advanced optical method for the direct, real-time monitoring of biomolecular interactions without the need for labelling. This doctoral thesis aims to advance the SPR biosensor method and to expand its utility in the investigation of biomolecular interactions. This encompasses activities on two major fronts of SPR biosensor research - immobilization methods and biosensing methodologies. Methods for the immobilization of biomolecules were researched with the aim of enabling the immobilization of a broad range of biomolecules on the SPR biosensor surface in a spatially controlled manner. The development of novel biosensing methodologies was pursued in order to address the current limitations of SPR biosensors associated with non-specific adsorption and limited analyte transport, and thus to improve the accuracy and robustness of SPR biosensor measurements. Finally, advances in the development of immobilization...

This thesis is focused on study of blood flow through the descending aorta using mag- netic resonance imaging and computational hemodynamics. This combination enables simulations of blood flow in patient specific geometries and under various circumstances such as higher heart rate, velocity or blood pressure. The theoretical part describes the governing equations of the blood flow and possible choices of boundary conditions. The weak formulation and discretization in space and time, which leads to the finite element approximation, is presented. The magnetic resonance data is presented in the second part. The process of segmenta- tion is described together with the preparation of the velocity data for comparison with simulation results. Limitations of magnetic resonance imaging are also presented. The developed methodology is one of the contributions of this thesis. The qualitative and quantitative comparison of simulation results and the magnetic res- onance velocity data is presented in the third part. The main result of the thesis is in the comparison of the flow under different wall boundary conditions. The most important finding is that the best fit for the data is the free-slip wall boundary condition, which is the opposite of commonly used no-slip wall boundary condition. 1

Introduction: The main goal of our work was to compare the diagnostic accuracy of ultrasound examination and magnetic resonance imaging (MRI) in the assessment of deep endometriosis in the pelvis. Our second aim was to establish a learning curve of a sonographer and a radiologists (non-experts). As an introduction to the subject we have published 3 reviews on the diagnosis and one narrative review on the classification systems in the evaluation of endometriosis has been submitted for publication. Methodology: Reviews were written as narrative reviews based on PubMed search and scientific societies recommendations. We have offered participation to all patients in the endometriosis centre with high suspicion of deep endometriosis, who then underwent examination by ultrasound and MRI by expert and non-expert before their surgical treatment, all findings described according to the consensus IDEA (international Deep Endometriosis Analysis group, 2016). Surgical and histological findings were used as a reference standard. Learning curve was defined as an improvement in accuracy in three blocks, into which the patients were assigned in the chronological order. Results of the scientific studies: From 07/2016 to 02/2018 the participation was offered to 111 patients, 51 underwent both imaging examinations...

(AJ) The three aims of the work were as follows: 1. Comparison of prostate magnetic resonance (MR) examination results from 1.5 T and 3 T scanners in patients with prostate carcinoma (PCa). MR findings of 103 patients (ages 44-72 years) were compared with histopathological results after radical prostatectomy. The work was focused on the accuracy of predicting local cancer staging and determining prostate tumour location. Patients were divided into three groups (A, B and C) based on the type of MR scanner and protocol used. Patient groups A and B were examined in 1.5T and 3T MR scanners equipped with surface coils in the identical multiparametric MR imaging protocol included dynamic contrast examination (DCE). Patient group C was examined in a 3T MR scanner without DCE. The highest accuracy of predicting the stage of PCa was seen in patients examined in 3 T MR scanner with DCE included in the protocol, however, no significant differences were seen between results from 1.5 T and 3.T MR scanners. No significant difference was also found in the accuracy of determining the location of prostate tumour between 1.5 T and 3T MR examinations, however, there were significant differences between sequences used, with the highest accuracy attained by using a combination of T2 weighted sequences and diffusion...

In the present theses we study spectral and resonance properties of quantum graphs. First, we consider graphs with rationally related lengths of the edges. In particular examples we study trajectories of resonances which arise if the ratio of the lengths of the edges is perturbed. We prove that the number of resonances under this perturbation is locally conserved. The main part is devoted to asymptotics of the number of resonances. We find a criterion how to distinguish graphs with non-Weyl asymptotics (i.e. constant in the leading term is smaller than expected). Furthermore, due to explicit construction of unitary equivalent operators we explain the non-Weyl behaviour. If the graph is placed into a magnetic field, the Weyl/non-Weyl characteristic of asymptotical behaviour does not change. On the other hand, one can turn a non-Weyl graph into another non-Weyl graph with different "effective size". In the final part of the theses, we describe equivalence between radial tree graphs and the set of halfline Hamiltonians and use this result for proving the absence of the absolutely continuous spectra for a class of sparse tree graphs.