Studies of Eu- and Yb-induced Reconstructions on the Si(100) Surface

This thesis presents experimental studies of rare earth (RE) metal induced structures on Si(100) surfaces. Two divalent RE metal adsorbates, Eu and Yb, are investigated on nominally flat Si(100) and on vicinal, stepped Si(100) substrates. Several experimental methods have been applied, including scanning tunneling microscopy/spectroscopy (STM/STS), low energy electron diffraction (LEED), synchrotron radiation photoelectron spectroscopy (SR-PES), Auger electron spectroscopy (AES), thermal desorption spectroscopy (TDS), and work function change measurements (Δφ). Two stages can be distinguished in the initial growth of the RE/Si interface: the formation of a two-dimensional (2D) adsorbed layer at submonolayer coverage and the growth of a three-dimensional (3D) silicide phase at higher coverage. The 2D phase is studied for both adsorbates in order to discover whether they produce common reconstructions or reconstructions common to the other RE metals. For studies of the 3D phase Yb is chosen due to its ability to crystallize in a hexagonal AlB2 type lattice, which is the structure of RE silicide nanowires, therefore allowing for the possibility of the growth of one-dimensional (1D) wires. It is found that despite their similar electronic configuration, Eu and Yb do not form similar 2D reconstructions on Si(100). Instead, a wealth of 2D structures is observed and atomic models are proposed for the 2×3-type reconstructions. In addition, adsorbate induced modifications on surface morphology and orientational symmetry are observed. The formation of the Yb silicide phase follows the Stranski-Krastanov growth mode. Nanowires with the hexagonal lattice are observed on the flat Si(100) substrate, and moreover, an unexpectedly large variety of growth directions are revealed. On the vicinal substrate the growth of the silicide phase as 3D islands and wires depends drastically on the growth conditions. The conditions under which wires with high aspect ratio and single orientation parallel to the step edges can be formed are demonstrated.

Unusual bismuth-containing surface layers of III-V compound semiconductors

The understanding and engineering of bismuth (Bi) containing semiconductor surfaces are signi cant in the development of novel semiconductor materials for electronic and optoelectronic devices such as high-e ciency solar cells, lasers and light emitting diodes. For example, a Bi surface layer can be used as a surfactant which oats on a III-V compound-semiconductor surface during the epitaxial growth of IIIV lms. This Bi surfactant layer improves the lm-growth conditions if compared to the growth without the Bi layer. Therefore, detailed knowledge of the properties of the Bi/III-V surfaces is needed. In this thesis, well-de ned surface layers containing Bi have been produced on various III-V semiconductor substrates. The properties of these Bi-induced surfaces have been measured by low-energy electron di raction (LEED), scanning-tunneling microscopy and spectroscopy (STM), and synchrotron-radiation photoelectron spectroscopy. The experimental results have been compared with theoretically calculated results to resolve the atomic structures of the studied surfaces. The main ndings of this research concern the determination of the properties of an unusual Bi-containing (2×1) surface structure, the discovery and characterization of a uniform pattern of Bi nanolines, and the optimization of the preparation conditions for this Bi-nanoline pattern.

Research and development of III-V semiconductor surfaces for improved device interfaces

This thesis is devoted to understanding and improving technologically important III-V compound semiconductor (e.g. GaAs, InAs, and InSb) surfaces and interfaces for devices. The surfaces and interfaces of crystalline III-V materials have a crucial role in the operation of field-effect-transistors (FET) and highefficiency solar-cells, for instance. However, the surfaces are also the most defective part of the semiconductor material and it is essential to decrease the amount of harmful surface or interface defects for the next-generation III-V semiconductor device applications. Any improvement in the crystal ordering at the semiconductor surface reduces the amount of defects and increases the material homogeneity. This is becoming more and more important when the semiconductor device structures decrease to atomic-scale dimensions. Toward that target, the effects of different adsorbates (i.e., Sn, In, and O) on the III-V surface structures and properties have been investigated in this work. Furthermore, novel thin-films have been synthesized, which show beneficial properties regarding the passivation of the reactive III-V surfaces. The work comprises ultra-high-vacuum (UHV) environment for the controlled fabrication of atomically ordered III-V(100) surfaces. The surface sensitive experimental methods [low energy electron diffraction (LEED), scanning tunneling microscopy/spectroscopy (STM/STS), and synchrotron radiation photoelectron spectroscopy (SRPES)] and computational density-functionaltheory (DFT) calculations are utilized for elucidating the atomic and electronic properties of the crucial III-V surfaces. The basic research results are also transferred to actual device tests by fabricating metal-oxide-semiconductor capacitors and utilizing the interface sensitive measurement techniques [capacitance voltage (CV) profiling, and photoluminescence (PL) spectroscopy] for the characterization. This part of the thesis includes the instrumentation of home-made UHV-compatible atomic-layer-deposition (ALD) reactor for growing good quality insulator layers. The results of this thesis elucidate the atomic structures of technologically promising Sn- and In-stabilized III-V compound semiconductor surfaces. It is shown that the Sn adsorbate induces an atomic structure with (1×2)/(1×4) surface symmetry which is characterized by Sn-group III dimers. Furthermore, the stability of peculiar ζa structure is demonstrated for the GaAs(100)-In surface. The beneficial effects of these surface structures regarding the crucial III-V oxide interface are demonstrated. Namely, it is found that it is possible to passivate the III-V surface by a careful atomic-scale engineering of the III-V surface prior to the gate-dielectric deposition. The thin (1×2)/(1×4)-Sn layer is found to catalyze the removal of harmful amorphous III-V oxides. Also, novel crystalline III-V-oxide structures are synthesized and it is shown that these structures improve the device characteristics. The finding of crystalline oxide structures is exploited by solving the atomic structure of InSb(100)(1×2) and elucidating the electronic structure of oxidized InSb(100) for the first time.

Development of Raman microscopy methods for polymer coatings of polyfilms

Työn tavoitteena oli tutkia Raman-spektrometrin soveltuvuutta muovipäällystettyjen kartonkien syvyyssuuntaisiin mittauksiin. Lisäksi pyrittiin selvittämään voidaanko kiteisyyttä nähdä Raman-laitteistolla. Työn kirjallisessa osassa on selvitetty Raman-laitteiston teknisiä ominaisuuksia. Kokeellinen osa suoritettiin Lappeenrannan teknillisessä yliopistossa Membraanitekniikan ja teknillisen polymeerikemian laboratoriossa. Työssä käytettiin Horiban Jobin Yvon¿in valmistamaa konfokaalista Raman-spektrometri-laitteistoa (LabRam). Syvyyssuuntaisissa mittauksissa käytettiin apuna motorisoitua x-, y- ja z-suuntaan liikkuvaa tasoa. Mittaukset suoritettiin pistemäisesti tietyllä askelvälillä fokusoimalla näytteen pinnasta sisällepäin. Syvyysprofilointimittaukset aloitettiinmäärittelemällä laitteiston syvyysresoluutio eri konfokaalireikäkoolla. Lisäksityössä tehtiin syvyysprofilointimittauksia sekä läpinäkyvillä monikerrosmuoveilla että muovipäällystetyillä kartongeilla. Työssä mitatut muovipäällysteet sisälsivät pääasiassa polyeteeniä. Tulokset osoittivat, että Raman laitteistolla voidaan havainnoida Raman-aktiiviset ryhmät näytteen eri kerroksista. Lisäksi polyeteenin kiteisyysaste voidaan havaita tietyillä aallonpituuksilla.

Combining Near-Field and Far-Field Microscopy: A new method for nanoscale super-resolution imaging

Lähikenttä- ja kaukokenttämikroskopian yhdistäminen: Uusi korkearesoluutioinen menetelmä nanokuvantamiseen. Osteoporoosi on sairaus, jossa luun uudistumisprosessi ei ole enää tasapainossa. Uuden luun muodostuminen on hitaampaa johtuen osteoblastien laskeneesta aktiivisuudesta. Yksi keino estää osteoporoosin syntyä on estää osteoklastien sitoutuminen luun pinnalle, jolloin ne eivät aloita luun syömisprosessia. Tämän Pro gradu -tutkielman tarkoituksena on luoda uusi työkalu osteoklastien sitoutumisen tutkimiseen samanaikaisesti fluoresenssi- ja atomivoimamikroskoopilla. Tätä tarkoitusta varten yhdistettiin atomivoimamikroskooppi sekä STED mikroskooppi. Kirjallisuuskatsauksessa käydään läpi yksityiskohtaisesti molempien mikroskooppitekniikoiden teoriat. Kokeellisessa osiossa esitetään käytetyt metodit ja alustavat tulokset uudella systeemillä. Lisäksi keskustellaan lyhyesti kuvan analysoinnista ImageJohjelmalla. Konfokaalisen fluoresenssimikroskoopin ja atomivoimamikroskoopin yhdistelmä on keksitty jo aikaisemmin, mutta tavallisen konfokaalimikroskoopin erottelukyvyn raja on noin 200 nanometriä johtuen valon diffraktioluonteesta. Yksityiskohdat eivät erotu, jos ne ovat pienempiä kuin puolet käytettävästä aallonpituudesta. STED mikroskooppi mahdollistaa fluoresenssikuvien taltioimisen solunsisäisistä prosesseista 50 nanometrin lateraalisella erotuskyvyllä ja atomivoimamikroskooppi antaa topografista tietoa näytteestä nanometrien erotuskyvyllä. Biologisia näytteitä kuvannettaessa atomivoimamikroskoopin erotuskyky kuitenkin huononee ja yleensä saavutetaan 30-50 nanometrin erotuskyky. Kuvien kerrostaminen vaatii vertauspisteitä ja tätä varten käytettiin atomivoimamikroskoopin kärjen tunnistamista ja referenssipartikkeleita. Kuva-analysointi suoritettiin ImageJ-kuvankäsittelyohjelmalla. Tuloksista nähdään, että referenssipartikkelit ovat hyviä, mutta niiden sijoittaminen tarkasti tietylle kohdealueelle on hankalaa nanoskaalassa. Tästä johtuen kärjen havaitseminen fluoresenssikuvassa on parempi metodi. Atomivoimamikroskoopin kärki voidaan päällystää fluoresoivalla aineella, mutta tämä lisää kärjen aiheuttamaa konvoluutiota mittausdataan. Myös valon takaisinsirontaa kärjestä voidaan tutkia, jolloin konvoluutio ei lisäänny. Ensimmäisten kuvien kerrostamisessa käytettiin hyväksi fluoresoivalla aineella päällystettyä kärkeä ja lopputuloksessa oli vain 50 nanometrin yhteensopimattomuus fluoresenssi- ja topografiakuvan kanssa. STED mikroskoopin avulla nähdään leimattujen proteiinien tarkat sijainnit tiettynä ajankohtana elävän solun sisällä. Samaan aikaan pystytään kuvantamaan solun fyysisiä muotoja tai mitata adheesiovoimia atomivoimamikroskoopilla. Lisäksi voidaan käyttää funktinalisoitua kärkeä, jolla voidaan laukaista signalointitapahtumia solun ja soluväliaineen välillä. Sitoutuminen soluväliaineeseen voidaan rekisteröidä samoin kuin adheesiomediaattorien sijainnit sitoutumisalueella. Nämä dynaamiset havainnot tuottavat uutta informaatiota solun signaloinnista, kun osteoklasti kiinnittyy luun pintaan. Tämä teknologia tarjoaa uuden näkökulman monimutkaisiin signalointiprosesseihin nanoskaalassa ja tulee ratkaisemaan lukemattoman määrän biologisia ongelmia.

Kelvin Probe Force Microscopy (KPFM) characterization of lanthanum lutetium oxide high-k dielectric thin films

Lanthanum lutetium oxide (LaLuO3) thin films were investigated considering their perspective application for industrial microelectronics. Scanning probe microscopy (SPM) techniques permitted to visualize the surface topography and study the electric properties. This work compared both the material properties (charge behavior for samples of 6 nm and 25 nm width) and the applied SPM modes. Particularly, Kelvin probe force microscopy (KPFM) was applied to characterize local potential difference with high lateral resolution. Measurements showed the difference in morphology, chargeability and charge dissipation time for both samples. The polarity effect was detected for this material for the first time. Lateral spreading of the charged spots indicate the diffusive mechanism to be predominant in charge dissipation. This allowed to estimate the diffusion coefficient and mobility. Using simple electrostatic model it was found that charge is partly leaking into the interface oxide layer.

Developing Bioimage Informatics – from Microscopy to Software Solutions – with alpha2beta1 Integrin as a Case Study

Biokuvainformatiikan kehittäminen – mikroskopiasta ohjelmistoratkaisuihin – sovellusesimerkkinä α2β1-integriini Kun ihmisen genomi saatiin sekvensoitua vuonna 2003, biotieteiden päätehtäväksi tuli selvittää eri geenien tehtävät, ja erilaisista biokuvantamistekniikoista tuli keskeisiä tutkimusmenetelmiä. Teknologiset kehitysaskeleet johtivat erityisesti fluoresenssipohjaisten valomikroskopiatekniikoiden suosion räjähdysmäiseen kasvuun, mutta mikroskopian tuli muuntua kvalitatiivisesta tieteestä kvantitatiiviseksi. Tämä muutos synnytti uuden tieteenalan, biokuvainformatiikan, jonka on sanottu mahdollisesti mullistavan biotieteet. Tämä väitöskirja esittelee laajan, poikkitieteellisen työkokonaisuuden biokuvainformatiikan alalta. Väitöskirjan ensimmäinen tavoite oli kehittää protokollia elävien solujen neliulotteiseen konfokaalimikroskopiaan, joka oli yksi nopeimmin kasvavista biokuvantamismenetelmistä. Ihmisen kollageenireseptori α2β1-integriini, joka on tärkeä molekyyli monissa fysiologisissa ja patologisissa prosesseissa, oli sovellusesimerkkinä. Työssä saavutettiin selkeitä visualisointeja integriinien liikkeistä, yhteenkeräytymisestä ja solun sisään siirtymisestä, mutta työkaluja kuvainformaation kvantitatiiviseen analysointiin ei ollut. Väitöskirjan toiseksi tavoitteeksi tulikin tällaiseen analysointiin soveltuvan tietokoneohjelmiston kehittäminen. Samaan aikaan syntyi biokuvainformatiikka, ja kipeimmin uudella alalla kaivattiin erikoistuneita tietokoneohjelmistoja. Tämän väitöskirjatyön tärkeimmäksi tulokseksi muodostui näin ollen BioImageXD, uudenlainen avoimen lähdekoodin ohjelmisto moniulotteisten biokuvien visualisointiin, prosessointiin ja analysointiin. BioImageXD kasvoi yhdeksi alansa suurimmista ja monipuolisimmista. Se julkaistiin Nature Methods -lehden biokuvainformatiikkaa käsittelevässä erikoisnumerossa, ja siitä tuli tunnettu ja laajalti käytetty. Väitöskirjan kolmas tavoite oli soveltaa kehitettyjä menetelmiä johonkin käytännönläheisempään. Tehtiin keinotekoisia piidioksidinanopartikkeleita, joissa oli "osoitelappuina" α2β1-integriinin tunnistavia vasta-aineita. BioImageXD:n avulla osoitettiin, että nanopartikkeleilla on potentiaalia lääkkeiden täsmäohjaussovelluksissa. Tämän väitöskirjatyön yksi perimmäinen tavoite oli edistää uutta ja tuntematonta biokuvainformatiikan tieteenalaa, ja tämä tavoite saavutettiin erityisesti BioImageXD:n ja sen lukuisten julkaistujen sovellusten kautta. Väitöskirjatyöllä on merkittävää potentiaalia tulevaisuudessa, mutta biokuvainformatiikalla on vakavia haasteita. Ala on liian monimutkainen keskimääräisen biolääketieteen tutkijan hallittavaksi, ja alan keskeisin elementti, avoimen lähdekoodin ohjelmistokehitystyö, on aliarvostettu. Näihin seikkoihin tarvitaan useita parannuksia,

Resonant tunneling effects in semiconductor heterostructures

The thesis is devoted to a theoretical study of resonant tunneling phenomena in semiconductor heterostructures and nanostructures. It considers several problems relevant to modern solid state physics. Namely these are tunneling between 2D electron layers with spin-orbit interaction, tunnel injection into molecular solid material, resonant tunnel coupling of a bound state with continuum and resonant indirect exchange interaction mediated by a remote conducting channel. A manifestation of spin-orbit interaction in the tunneling between two 2D electron layers is considered. General expression is obtained for the tunneling current with account of Rashba and Dresselhaus types of spin-orbit interaction and elastic scattering. It is demonstrated that the tunneling conductance is very sensitive to relation between Rashba and Dresselhaus contributions and opens possibility to determine the spin-orbit interaction parameters and electron quantum lifetime in direct tunneling experiments with no external magnetic field applied. A microscopic mechanism of hole injection from metallic electrode into organic molecular solid (OMS) in high electric field is proposed for the case when the molecules ionization energy exceeds work function of the metal. It is shown that the main contribution to the injection current comes from direct isoenergetic transitions from localized states in OMS to empty states in the metal. Strong dependence of the injection current on applied voltage originates from variation of the number of empty states available in the metal rather than from distortion of the interface barrier. A theory of tunnel coupling between an impurity bound state and the 2D delocalized states in the quantum well (QW) is developed. The problem is formulated in terms of Anderson-Fano model as configuration interaction between the carrier bound state at the impurity and the continuum of delocalized states in the QW. An effect of this interaction on the interband optical transitions in the QW is analyzed. The results are discussed regarding the series of experiments on the GaAs structures with a -Mn layer. A new mechanism of ferromagnetism in diluted magnetic semiconductor heterosructures is considered, namely the resonant enhancement of indirect exchange interaction between paramagnetic centers via a spatially separated conducting channel. The underlying physical model is similar to the Ruderman-Kittel-Kasuya-Yosida (RKKY) interaction; however, an important difference relevant to the low-dimensional structures is a resonant hybridization of a bound state at the paramagnetic ion with the continuum of delocalized states in the conducting channel. An approach is developed, which unlike RKKY is not based on the perturbation theory and demonstrates that the resonant hybridization leads to a strong enhancement of the indirect exchange. This finding is discussed in the context of the known experimental data supporting the phenomenon.

Atomic Force Microscopy Investigation of NI Particles Deposited on Porous Silicon

In this thesis properties and influence of modification techniques of porous silicon were studied by Atomic Force Microscope (AFM). This device permits to visualize the surface topography and to study properties of the samples on atomic scale, which was necessary for recent investigation. Samples of porous silicon were obtained by electrochemical etching. Nickel particles were deposited by two methods: electrochemical deposition and extracting from NiCl2 ethanol solution. Sample growth was conducted in Saint-Petersburg State Electrotechnical University, LETI. Kelvin probe force microscopy (KPFM) and Magnetic force microscopy (MFM) were utilized for detailed information about surface properties of the samples. Measurements showed the difference in morphology correlating with initial growth conditions. Submicron size particles were clearly visible on surfaces of the treated samples. Although their nature was not clarified due to limitations of AFM technique. It is expected that surfaces were covered by nanometer scale Ni particles, which can be verified by implication of RAMAN device.

Ultrastructural changes of Fusobacterium nucleatum as a defense mechanism against human neutrophil peptide-1 - A Transmission Electron Microscopy (TEM) study

Aims: The aim of this work was to assess the ultrastructural changes, cellular proliferation, and the biofilm formation ability of F. nucleatum as defense mechanisms against the effect of HNP-1. Materials and methods: The type strain of F. nucleatum (ssp. nucleatum ATCC 25586) and two clinical strains (ssp. polymorphum AHN 9910 and ssp. nucleatum AHN 9508) were cultured and incubated with four different test concentrations of recombinant HNP-1 (1, 5, 10 and 20 µg/ml) and one control group (0 µg/ml). Bacterial pellets from each concentration were processed for TEM imaging. Planktonic growth was assessed and colony forming units (CFU) were measured to determine the cellular proliferation. Scrambled HNP-1 was used for confirmation. Results: TEM analyses revealed a decrease in the outer membrane surface corrugations and roughness of the strain AHN 9508 with increasing HNP-1 concentrations. In higher concentrations of HNP-1, the strain AHN 9910 showed thicker outer membranes with a number of associated rough vesicles attached to the outer surface. For ATCC 25586, the treated bacterial cells contained higher numbers of intracellular granules with increasing the peptide concentration. Planktonic growth of the two clinical strains were significantly enhanced (P<0.001) with gradually increased concentrations of HNP-1. None of the planktonic growth results of the 3 strains incubated with the scrambled HNP-1 was statistically significant. HNP-1 decreased the biofilm formation of the two clinical strains, AHN 9910 and 9508, significantly (P<0.01 and P<0.001; respectively). Conclusions: The present in vitro study demonstrates that F. nucleatum has the ability to withstand the lethal effects of HNP-1 even at concentrations simulating the diseased periodontium in vivo. The increase in planktonic growth could act as defense mechanisms of F. nucleatum against HNP-1.

Developing correlative Optical-Photoacustic microscopy for high-resolution in vivo imaging

PhotoAcoustic Imaging (PAI) is a branch in clinical and pre-clinical imaging, that refers to the techniques mapping acoustic signals caused by the absorption of the short laser pulse. This conversion of electromagnetic energy of the light to the mechanical (acoustic) energy is usually called photoacoustic effect. PAI, by combining optical excitation with acoustical detection, is able to preserve the diffraction limited spatial resolution. At the same time, the penetration depth is extended beyond the diffusive limit. The Laser-Scanning PhotoAcoustic Microscope system (LS-PAM) has been developed, that offers the axial resolution of 7.75 µm with the lateral resolution better than 10 µm. The first in vivo imaging experiments were carried out. Thus, in vivo label-free imaging of the mouse ear was performed. The principle possibility to image vessels located in deep layers of the mouse skin was shown. As well as that, a gold printing sample, vasculature of the Chick Chorioallantoic Membrane Assay, Drosophila larvae were imaged by PAI. During the experimental work, a totally new application of PAM was found, in which the acoustic waves, generated by incident light can be used for further imaging of another sample. In order to enhance the performance of the presented system two main recommendation can be offered. First, the current system should be transformed into reflection-mode setup system. Second, a more powerful source of light with the sufficient repetition rate should be introduced into the system.

The solutions and tunneling properties for a linear potential and an inverted harmonic oscillator in an infinite well

In this work we look at two different 1-dimensional quantum systems. The potentials for these systems are a linear potential in an infinite well and an inverted harmonic oscillator in an infinite well. We will solve the Schrödinger equation for both of these systems and get the energy eigenvalues and eigenfunctions. The solutions are obtained by using the boundary conditions and numerical methods. The motivation for our study comes from experimental background. For the linear potential we have two different boundary conditions. The first one is the so called normal boundary condition in which the wave function goes to zero on the edge of the well. The second condition is called derivative boundary condition in which the derivative of the wave function goes to zero on the edge of the well. The actual solutions are Airy functions. In the case of the inverted oscillator the solutions are parabolic cylinder functions and they are solved only using the normal boundary condition. Both of the potentials are compared with the particle in a box solutions. We will also present figures and tables from which we can see how the solutions look like. The similarities and differences with the particle in a box solution are also shown visually. The figures and calculations are done using mathematical software. We will also compare the linear potential to a case where the infinite wall is only on the left side. For this case we will also show graphical information of the different properties. With the inverted harmonic oscillator we will take a closer look at the quantum mechanical tunneling. We present some of the history of the quantum tunneling theory, its developers and finally we show the Feynman path integral theory. This theory enables us to get the instanton solutions. The instanton solutions are a way to look at the tunneling properties of the quantum system. The results are compared with the solutions of the double-well potential which is very similar to our case as a quantum system. The solutions are obtained using the same methods which makes the comparison relatively easy. All in all we consider and go through some of the stages of the quantum theory. We also look at the different ways to interpret the theory. We also present the special functions that are needed in our solutions, and look at the properties and different relations to other special functions. It is essential to notice that it is possible to use different mathematical formalisms to get the desired result. The quantum theory has been built for over one hundred years and it has different approaches. Different aspects make it possible to look at different things.

Development of 3D super-resolution tomographic STED microscopy and its application to studies on bone resorption

In this doctoral thesis, a tomographic STED microscopy technique for 3D super-resolution imaging was developed and utilized to observebone remodeling processes. To improve upon existing methods, wehave used a tomographic approach using a commercially available stimulated emission depletion (STED) microscope. A certain region of interest (ROI) was observed at two oblique angles: one at a standard inverted configuration from below (bottom view) and another from the side (side view) via a micro-mirror positioned close to the ROI. The two viewing angles were reconstructed into a final tomogram. The technique, named as tomographic STED microscopy, was able to achieve an axial resolution of approximately 70 nm on microtubule structures in a fixed biological specimen. High resolution imaging of osteoclasts (OCs) that are actively resorbing bone was achieved by creating an optically transparent coating on a microscope coverglass that imitates a fractured bone surface. 2D super-resolution STED microscopy on the bone layer showed approximately 60 nm of lateral resolution on a resorption associated organelle allowing these structures to be imaged with super-resolution microscopy for the first time. The developed tomographic STED microscopy technique was further applied to study resorption mechanisms of OCs cultured on the bone coating. The technique revealed actin cytoskeleton with specific structures, comet-tails, some of which were facing upwards and some others were facing downwards. This, in our opinion, indicated that during bone resorption, an involvement of the actin cytoskeleton in vesicular exocytosis and endocytosis is present. The application of tomographic STED microscopy in bone biology demonstrated that 3D super-resolution techniques can provide new insights into biological 3D nano-structures that are beyond the diffraction-limit when the optical constraints of super-resolution imaging are carefully taken into account.

The solutions and tunneling properties for a linear potential and an inverted harmonic oscillator in an infinite well

In this work we look at two different 1-dimensional quantum systems. The potentials for these systems are a linear potential in an infinite well and an inverted harmonic oscillator in an infinite well. We will solve the Schrödinger equation for both of these systems and get the energy eigenvalues and eigenfunctions. The solutions are obtained by using the boundary conditions and numerical methods. The motivation for our study comes from experimental background. For the linear potential we have two different boundary conditions. The first one is the so called normal boundary condition in which the wave function goes to zero on the edge of the well. The second condition is called derivative boundary condition in which the derivative of the wave function goes to zero on the edge of the well. The actual solutions are Airy functions. In the case of the inverted oscillator the solutions are parabolic cylinder functions and they are solved only using the normal boundary condition. Both of the potentials are compared with the particle in a box solutions. We will also present figures and tables from which we can see how the solutions look like. The similarities and differences with the particle in a box solution are also shown visually. The figures and calculations are done using mathematical software. We will also compare the linear potential to a case where the infinite wall is only on the left side. For this case we will also show graphical information of the different properties. With the inverted harmonic oscillator we will take a closer look at the quantum mechanical tunneling. We present some of the history of the quantum tunneling theory, its developers and finally we show the Feynman path integral theory. This theory enables us to get the instanton solutions. The instanton solutions are a way to look at the tunneling properties of the quantum system. The results are compared with the solutions of the double-well potential which is very similar to our case as a quantum system. The solutions are obtained using the same methods which makes the comparison relatively easy. All in all we consider and go through some of the stages of the quantum theory. We also look at the different ways to interpret the theory. We also present the special functions that are needed in our solutions, and look at the properties and different relations to other special functions. It is essential to notice that it is possible to use different mathematical formalisms to get the desired result. The quantum theory has been built for over one hundred years and it has different approaches. Different aspects make it possible to look at different things.

Bioimage informatics in STED super-resolution microscopy

Optical microscopy is living its renaissance. The diffraction limit, although still physically true, plays a minor role in the achievable resolution in far-field fluorescence microscopy. Super-resolution techniques enable fluorescence microscopy at nearly molecular resolution. Modern (super-resolution) microscopy methods rely strongly on software. Software tools are needed all the way from data acquisition, data storage, image reconstruction, restoration and alignment, to quantitative image analysis and image visualization. These tools play a key role in all aspects of microscopy today – and their importance in the coming years is certainly going to increase, when microscopy little-by-little transitions from single cells into more complex and even living model systems. In this thesis, a series of bioimage informatics software tools are introduced for STED super-resolution microscopy. Tomographic reconstruction software, coupled with a novel image acquisition method STED< is shown to enable axial (3D) super-resolution imaging in a standard 2D-STED microscope. Software tools are introduced for STED super-resolution correlative imaging with transmission electron microscopes or atomic force microscopes. A novel method for automatically ranking image quality within microscope image datasets is introduced, and it is utilized to for example select the best images in a STED microscope image dataset.