This diploma thesis is focused on investigation of metallic thin films and nanostructures using scanning probe microscopy. Magnetic properties of these objects are studied by magnetic force microscopy, which is modification of scanning probe microscopy. In the theoretical part basic principles of scanning probe microscopy and magnetic force microscopy are summarized, and also principle of creation of magnetic domains and some special properties of ferromagnetic and antiferromagnetic materials. Further, two techniques of fabricating nanostructures are described. Experimental part is focused on imaging and simulating of magnetic domains. Further, exchange bias is revealed. This phenomenon is present in systems composed from ferromagnetic and antiferromagnetic materials. One part of this diploma thesis is also focused on discussion of problems with magnetic force microscopy.

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Background: The hippocampus and corpus callosum have been shown to be vulnerable in head injury. Various neuroimaging modalities and quantitative measurement techniques have been employed to investigate pathological changes in these structures. Cognitive and behavioural deficiencies have also been well documented in head injury. Aims: The aim of this research project was to investigate structural changes in the hippocampus and corpus callosum. Two different quantitative methods were used to measure physical changes and neuropsychological assessment was performed to determine cognitive and behavioural deficit. It was also intended to investigate the relationship between structural change and neuropsychology at 1 and 6 months post injury. Method: Forty-seven patients with head injury (ranging from mild to severe) had undergone a battery of neuropsychological tests and an MRI scan at 1 and 6 months post injury. T1-weighted MRI scans were obtained and analysis of hippocampus and corpus callosum was performed using region-of-interest techniques and voxel-based morphometry which also included comparison to 18 healthy volunteers. The patients completed neuropsychological assessment at 1 and 6 months post injury and data obtained was analysed with respect to each assessment and with structural data to determine cognitive decline and correlation with neuroanatomy. Results: Voxel-based morphometry illustrated reduced whole scan signal differences between patients and controls and changes in patients between 1 and 6 months post injury. Reduced grey matter concentration was also found using voxel-based morphometry and segmented images between patients and controls. A number of neuropsychological aspects were related to injury severity and correlations with neuroanatomy were present. Voxel-based morphometry provided a greater number of associations than region-of-interest analysis. No longitudinal changes were found in the hippocampus or corpus callosum using region-of-interest methodology or voxel-based morphometry. Conclusions: Decreased grey matter concentration identified with voxel-based morphometry illustrated that structural deficit was present in the head injured patients and does not change between 1 and 6 months. Voxel-based morphometry appears more sensitive for detecting structural changes after head injury than region- of-interest methods. Although the majority of patients had suffered mild head injury, cognitive and neurobehavioural deficits were evidenced by a substantial number of patients reporting increased anxiety and depression levels. Also, the findings of relationships between reduced grey matter concentration and cognitive test scores are indicative of the effects of diffuse brain damage in the patient group.

This PhD study focusses on the use of MEdium Resolution Imaging Spectrometer (MERIS) data for reliable and quantitative water-quality assessment of optically-complex waters (lake, brackish and coastal waters). The thesis is divided into two parts: A. intercalibration of reflectance measurements in different optically-complex water bodies (Paper I), and validation of various satellite processing algorithms for the coastal zone (Paper II). B. Applications: the use of MERIS data in integrated coastal zone management mostly using Himmerfjärden bay as an example. Himmerfjärden bay is one of the most frequently monitored coastal areas in the world and it is also the recipient of a large urban sewage treatment plant, where a number of full-scale nutrient management experiments have been conducted to evaluate the ecological changes due to changes in nutrient schemes in the sewage plant. Paper I describes the development and assessment of a new hyperspectral handheld radiometer for in situ sampling and validation of remote sensing reflectance.  The instrument is assessed in comparison with readily available radiometers that are commonly used in validation. Paper II has a focus on the validation of level 2 reflectance and water products derived from MERIS data. It highlights the importance of calibration and validation activities, and the current accuracy and limitations of satellite products in the coastal zone.  Bio-optical in situ data is highlighted as one of the key components for assessing the reliability of current and future satellite missions. Besides suspended particulate matter (SPM), the standard MERIS products have shown to be insufficient to assure data quality retrieval for Baltic Sea waters. Alternative processors and methods such as those assessed and developed in this thesis therefore will have to be put in place in order to secure the success of future operational missions, such as Sentinel-3. The two presented manuscripts in the applied part B of the thesis (paper III and IV), showed examples on the combined use of in situ measurements with optical remote sensing to support water quality monitoring programs by using turbidity and suspended particulate matter as coastal indicators (manuscript III). The article also provides  a new turbidity algorithm for the Baltic Sea and a robust and cost-efficient method for research and management.  A novel approach to improve the quality of the satellite-derived products in the coastal zone was demonstrated in manuscript IV. The analysis included, the correction for adjacency effects from land and an improved pixel quality screening.  The thesis provides the first detailed spatio-temporal description of the evolution of phytoplankton blooms in Himmerfjärden bay  using quality-assured MERIS data, thus forwarding our understanding of ecological processes in in Swedish coastal waters. It must be noted that monitoring from space is not a trivial matter in these optically-complex waters dominated by the absorption of coloured dissolved organic matter (CDOM). These types of coastal waters are especially challenging for quantitative assessment from space due to their low reflectance.  Papers III and IV thus also provide tools for a more versatile use in other coastal waters that are not as optically-complex as the highly absorbing Baltic Sea waters. The benefits of the increased spatial-temporal data coverage by optical remote sensing were presented, and also compared to in situ sampling methods (using chlorophyll-a as indicator). / <p>Research funders:</p><p>European Space Agency (ESA, contract no.21524/08/I-OL)</p><p>NordForsk funding: Nord AquaRemS Ref. no. 80106</p><p>NordForsk funding:  NordBaltRemS Ref.no. 42041</p><p>At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 3: Manuscript. Paper 4: Manuscript.</p>

Η ΒΥΠ διαθέτει αντίτυπο της διατριβής σε έντυπη μορφή στο βιβλιοστάσιο διδακτορικών διατριβών που βρίσκεται στο ισόγειο του κτιρίου της. / Στα βακτήρια, η μεγάλη ριβοσωματική υπομονάδα αποτελείται από δύο είδη RNA, το 23S και το 5S rRNA, καθώς και 33 πρωτεΐνες. Ο σχηματισμός του πεπτιδικού δεσμού και η απελευθέρωση της πεπτιδικής αλυσίδας επιτελούνται στη μεγάλη υπομονάδα, όπου εδράζεται το καταλυτικό κέντρο της πεπτιδυλοτρανσφεράσης (PTase). Εκτός αυτού, η μεγάλη υπομονάδα περιλαμβάνει το κέντρο προσδέσεως των μεταφραστικών παραγόντων, το οποίο πυροδοτεί τη GTPase δραστηριότητα των G-πρωτεϊνικών παραγόντων, που εμπλέκονται στη μετατόπιση των υποστρωμάτων και άλλες ριβοσωματικές λειτουργίες. Έχει υποτεθεί ότι το 5S rRNA παίζει ουσιώδη ρόλο στη συγκρότηση του κέντρου της PTase και στη μετάδοση σημάτων μεταξύ του καταλυτικού κέντρου και των ριβοσωματικών συστατικών που διεκπεραιώνουν τη μετατόπιση των υποστρωμάτων. Το ιοντικό περιβάλλον φαίνεται να επηρεάζει καθοριστικά τη διαμόρφωση του 5S rRNA. Για παράδειγμα, έχει βρεθεί ότι οι πολυαμίνες δεσμεύονται εκλεκτικά στο 5S rRNA και επηρεάζουν τη δραστικότητα του έναντι του διμεθυλο-θεϊκού, ενός αντιδραστηρίου-ιχνηθέτη της τριτοταγούς δομής του RNA. Αρχικά ελέγξαμε αν υπάρχουν εξειδικευμένες θέσεις πρόσδεσης των πολυαμινών στο 5S rRNA. Στη συνέχεια, με σκοπό να ελέγξουμε αν η πρόσδεση των πολυαμινών επηρεάζει τη λειτουργία του 5S rRNA, 70S ριβοσώματα προγραμματισμένα με πολύ-ουριδυλικό σχηματίσθηκαν από 50S υπομονάδες, ολικά ή εκλεκτικά φωτοσημασμένες με ένα φωτοδραστικό ανάλογο της σπερμίνης και από 30S ακατέργαστες υπομονάδες. Αυτά τα ριβοσώματα είχαν την ικανότητα να δεσμεύουν AcPhe-tRNA ελαφρώς ισχυρότερα, σε σύγκριση με ριβοσώματα συγκροτημένα από φυσικά συστατικά, μη περιέχοντα πολυαμίνες. Το γεγονός αυτό υποδηλώνει ότι η πρόσδεση πολυαμινών στο 5S rRNA επηρεάζει, σε μικρό βαθμό, τη λειτουργία του παράγοντα επιμήκυνσης EF-Tu. Συζευγμένα, όμως, τα εν λόγω ριβοσώματα με tRNAPhe στην Ε-θέση και AcPhe-tRNAστην Ρ-θέση, επέδειξαν ισχυρότερη καταλυτική δραστικότητα και αυξημένη ικανότητα για μετατόπιση των υποστρωμάτων. Τα αποτελέσματα αυτά εισηγούνται σημαντική εμπλοκή των πολυαμινών στο λειτουργικό ρόλο του 5S rRNA κατά την κατάλυση και μετατόπιση των υποστρωμάτων. / In bacteria, the large ribosomal subunit comprises two RNA species, 23S and 5S rRNA, and 33 proteins. Peptide bond formation and peptide release are catalyzed by the large subunit, where the peptidyltransferase (PTase) center is located. In addition to this center, which triggers the GTPase activities of G-protein factors involved in translocation and other ribosomal functions. It has been hypothesized that 5S rRNA plays essential role in assembling the PTase center and mediating signal transmissions between this center and the translocation machinery. Furthermore, the ionic environment seems to affect the conformation of 5S rRNA. For instance, polyamines have been found to bind specifically to 5S rRNA and influence the 5S rRNA reactivity towards dimethyl-sulfate (DMS), a chemical probe of RNA tertiary structure. Initially we examined whether there are specific sites for binding of polyamines. To test whether the binding of polyamines influence the function of 5S rRNA poly(U)-programmed 70S ribosomes were reconstituted from 50S subunits, totally or specifically photolabelled in their 5S rRNA with a photoreactive analogue of spermine, and native 30S subunits. These ribosomes were found to enzymatically bind AcPhe-tRNA better than ribosomes reconstituted from native components. This means, that furnishing 5S rRNA with spermine slightly influences the elongation factor EF-Tu function. However, equipped with tRNAPhe at the A-site and AcPhe-tRNA at the P-site, these ribosomes exhibited higher catalytic activity and enhanced tRNA translocation efficiency. These results suggest an essential impact of polyamines on the functional role of 5S rRNA in catalysis and translocation of translation substrates.

Most biological experiments are performed on an ensemble of cells under the assumption that all cells are identical. However, recent evidence from single cells studies reveals that this assumption is incorrect. Individual cells within the same generation may differ dramatically, and these differences have important consequences for the health and function of the entire living body. I have used Scanning Ion Conductance Microscopy (SICM) for imaging and analysis of topographical change of single cell membrane, which is difficult to be revealed by optical microscopes. Morphological change in the fixed and live HeLa cell membrane during endocytosis of conjugated polymer nanoparticles was studied. Results demonstrated SICM is a powerful tool to study the interaction between nanoparticle and cell membrane during internalization of nanoparticles through the membrane. This research can improve our fundamental understanding of cellular behavior and will be helpful for drug delivery applications. Based on conventional SICM, we have developed a novel method to simultaneous map the topography and potential distributions of the single living cells membranes. At the first step, multifunctional nanopipettes (nanopore/nanoelectrode) have been fabricated and characterized. To demonstrate the potential sensing capability and understand the mechanism, I measured the ionic current and local electric potential change during translocation of 40 nm charged gold nanoparticles. Our results reveal the capability of the multifunctional probe for the highly sensitive detection of the ionic current and local electrical potential changes during the translocation of the charged entity through the nanopore. From the potential change, we revealed the dynamic assembly of GNPs before entering the nanopore. The experimental results are also nicely explained by the finite element method based numerical simulation results. At the second step, I have measured the surface potential of living cell membrane at selected locations. Very recently, I have obtained results to show that we can map the extracellular membrane potential distribution of the complicated living cell membrane with sub-micron spatial resolution.This new imaging technique can help biologist to explore the extracellular potential distribution of varieties of cells quantitatively.These studies will have impacts on several biomedical applications such as regenerative repair and cancer treatment.

High pressure on the development of new magnetic materials and their miniaturization also emphasizes the development of new analytical techniques. This diploma thesis deals with the development and demonstration of correlated magnetic force and electron microscopy, which is a promising tool for the characterization of magnetic nanomaterials. The first part of this thesis describes the fundamental physics of micromagnetism with a focus on cylindrical nanofibers. The following pages describe optic, probe, electron, and synchrotron methods for mapping the magnetic properties of materials. The next part describes magnetic domain wall motion in cylindrical nanowires performed as a part of a more extensive material study. The last part of the thesis describes the development of correlated magnetic force and electron microscopy on LiteScope device. A production of magnetic probes was designed and successfully tested. Probes were fabricated by focused electron beam-induced deposition from the Co2(CO)8 precursor. Further, the developed correlated microscopy is demonstrated on a multilayer PtCo sample, magnetic cylindrical nanofibers, NiFe vortex structures, and FeRh metamagnetic nano-islands.

This thesis deals with the use of Atomic Force Microscopy (AFM) and Kelvin Probe Force Microscopy (KPFM) in solar cells production. Both techniques measure surface properties using interactions between surface and tip that progressively scans entire surface of the sample. Atomic force microscopy allows three dimensional imaging of surface structure. Kelvin probe force microscopy is used to measure the contact potential difference on the sample surface. There are described experimental measurements of monocrystalline and multicrystalline substrates after various etching processes using AFM. By using KPFM the contact potential difference was measured on dielectric layers PSG, SiOX, SiNX and Al2O3 and on selective emitter structures. All experiments described in this work were carried out at the Solartec Ltd. workplace and they completely correspond with the actual technology of crystalline solar cells production.

This diploma thesis deals with the preparation of the very thin films and their investigation by scanning probe microscopy methods. The ultrathin films of Pt on Pt(111) were created by pulsed laser deposition and the ultrathin films of Co on Pt(111) were deposited by thermal evaporation. The coverage of the substrate was much smaller than one monolayer (in order of hundredths of monolayer). The nucleation theory was verified by these experiments using so-called Onset method. Further graphene sheets were prepared on layer of Si/SiO2 by the mechanical exfoliation from the graphite crystal. The fabricated graphene sheets were studied by micro-Raman spectroscopy, microreflectometry, atomic force microscopy and similar techniques. These methods proved the thinnest graphite layers were consisted of two graphene monolayers.

This thesis deals with analysis of flow inside integral SPM sampler. Flowing is described for one-phase flow and multi-phase flow (water-solid particles) approaches. Results of computational modeling and experimental modeling are compared. Experimental box was constructed and its construction is noticed. Methods of used computational and experimental modeling are described. Optimal computational model is recommended. The theme of this thesis was chosen in co-operation with Czech Geological Survey whitin the frame of project MŽP „SP/1b7/156/07“.