CHARLES UNIVERSITY and HASSELT UNIVERSITY / tUL Doctoral dissertation Collagen structures from cell culture to intact tendon ABSTRACT Author: Daniel Hadraba Promoters: Assoc. Prof. Karel Jelen | Charles University Prof. Marcel Ameloot | Hasselt University Co-promoters: Dr. Frantisek Lopot | Charles University Prof. Virginie Bito | Hasselt University Annotation Author: Ing. Mgr. Daniel Hadraba Doctoral thesis title: Collagen structures from cell culture to intact tendon Year: 2010 - 2017 Doctoral program: Doctor of Biomechanics at Charles University Doctor of Biomedical Science at Hasselt University / transnational University Limburg Departments: Dept. Anatomy and Biomechanics | Faculty of Physical Education and Sport | Charles University Dept. Biophysics | Hasselt University Promoters: Assoc. Prof. Karel Jelen | Dept. Anatomy and Biomechanics | Faculty of Physical Education and Sport | Charles University Prof. Marcel Ameloot | Hasselt University / transnational University Limburg Co-promoters: Dr. Frantisek Lopot | Dept. Anatomy and Biomechanics | Faculty of Physical Education and Sport | Charles University Prof. Virginie Bito | Hasselt University / transnational University Limburg Bibliography details: Pages 102 Figures 30 Tables 2 Equations 17 Keywords: tendon, collagen, crimps, orientation, aging,...

Die Nanooptik beschäftigt sich mit der Wechselwirkung von Licht mit Materie, deren charakteristische Dimension im Nanometer Bereich liegt. Insbesondere wenn die Materie aus Metall besteht, zeigen sich interessante, wellenlängenabhängige Unterschiede in der Stärke der Wechselwirkung. Die Ursache dafür sind die kollektiven Moden der quasifreien Ladungsträger, die Plasmonen. Obgleich sich experimentelle Methoden in den letzten Jahren stetig verbessert haben, ist es nach wie vor nur mit erheblichem Aufwand möglich, sich Einblicke in die mikroskopischen Zusammenhänge zu verschaffen. Eine Ergänzung zu den Experimenten bieten theoretische Modelle. Auf Grund der sich mit der Zeit stetig verbesserten Leistung der Rechentechnik, kommen dabei zunehmend numerische Verfahren zum Einsatz. Eines dieser Verfahren ist das Unstetige Galerkin Verfahren, welches in dieser Arbeit auf folgende Fragestellungen der plasmonischen Nanooptik angewandt wurde: • Bei dem unstetigen Galerkin Verfahren werden die zu simulierenden Körper üblicherweise mittels Dreiecke und Tetraeder approximiert. Da die Geometrie der metallischen Systeme einen entscheidenden Einfluss auf die Wechselwirkung hat, wurde untersucht, inwieweit sich durch Einsatz von Elementen mit gekrümmten Flächen die Genauigkeit oder die Geschwindigkeit der Simulation steigern lässt. Es konnte gezeigt werden, dass runde Elemente die Genauigkeit bei gleicher Diskretisierung um bis zu zwei Größenordnungen steigern oder die Rechenzeit bei gleicher Genauigkeit auf ein Sechstel verkürzen können. • Bestrahlt man Metallnanopartikel mit intensiven Laserpulsen, so strahlen diese nicht nur bei der Frequenz des eingestrahlten Lichtes, sondern auch bei der doppelten Frequenz ab. Dieses Phänomen der Frequenzverdopplung (SHG, engl.: „Second-Harmonic-Generation“) ist unter anderem von der Form der Partikel und der Wellenlänge des Pulses abhängig. Da durchstimmbare gepulste Laser sehr teuer sind, wurde untersucht, ob sich mit Hilfe der linearen Partikelspektren Vorhersagen über die Stärke der Frequenzverdopplung machen lassen. Dabei wurde festgestellt, dass die Effizienz der Frequenzverdopplung zunimmt, wenn man die linearen Resonanzen der Partikel auf die SHG- oder Anregungswellenlänge abstimmt. Schafft man es, das plasmonische System so einzustellen, dass sowohl die Anregungswellenlänge, wie auch die SHG- Wellenlänge auf einer linearen Resonanz liegen, so kann die Effizienz der SHG weiter gesteigert werden. / Nanooptics is a discipline dealing with the interaction of light with matter where its characteristic dimensions are defined to be in the range of nanometers. In particular, if the matter consists of metal, i.e. conductive material, interesting wavelength dependent phenomena can be observed, which scale with the strength of the interaction. These phenomena are caused by the formation of collective modes between quasi-free charge carriers resulting in so called plasmons. Although improved experimental methods have evolved over the last few years, insight into the microscopic relationship between light and matter is only achievable with high effort. Supplemental information to experimental findings can be drawn from theoretical models. Due to the constantly improving computational power, numerical methods are progressively more employed. One of these methods is the discontinuous Galerkin method, which was applied to the following problems in plasmonic nanooptics: • Within the discontinuous Galerkin method the simulated objects are usually approximated by triangles or tetrahedrons. Since the geometry of conductive systems has a major impact on the interaction between light and matter, the usability of elements with curved surfaces for the discretisation of the space has been investigated with respect to accuracy and speed of the simulation. In this work, it could be shown that curved elements improve the simulations precision up to two orders of magnitude with the same amount of discretisation compared to linear elements. Related to speed, it has been found that the computational time is reduced by a factor of 6 with a comparable simulation accuracy. • By irradiating metallic nanoparticles with high power laser pulses these particles do not only emit light of the same frequency as the incident electromagnetic wave, but also with the doubled frequency (SHG, second harmonic generation). Among other things, this phenomenon of frequency doubling mainly depends on the geometry of the particle and the wavelength of the pulse. Since tunable pulsed laser sources are very expensive, it has been theoretically investigated if the strength of the frequency doubling can be deduced from the particles linear spectra. By this, it has been discovered that the efficiency of frequency doubling can be improved by adjusting the linear resonances of the particle to the SHG or excitation wavelength. The SHG efficiency can be increased even further, if the plasmonic system is tuned to a point where both the excitation and the SHG wavelength correspond to a linear resonance of the nanoparticle.

Refractive index measurements of the Strontium-Barium-Niobate (SBN) crystals show that none of the known second-harmonic-generation scheme (SHG) can be hold responsible for the SHG in SBN. Based on observations of the SHG experiments carried out with several compositions of the crystals in different setup-geometries a new model of second harmonic generaion was developed. The new SHG model, domain-induced second-harmonic generation (DISHG), which considers that the needle-like domain structure of this material plays an active role in the quasi phase matching of the produced second harmonic light has been experimentally proved using two different experiments. The new SHG process in the SBN crystals is a potential light source of cylindrically polarized light. The easy way of obtaining cylindrically polarized light with the SBN crystal broadens the potential applications for this material. The (DISHG) allows to investigate several properties of the ferroelectric domains. Using SHG measurements it was possible to analyze the development of the domain densities for domains of different sizes during the poling of the crystal. SHG measurements allow us to determine the minimum length of the ferroelectric domains. It was shown that this does not depend on the [Sr]/[Ba] ratio and domains are not getting longer after the sample was poled, except for the case of doped SBN. The ferroelectric-paraelectric phase transition has also been investigated. From the inflection point of the nonlinear susceptibility as function of the temperature the phase transition temperature was determined. The non fully-linear dependence of the phase transition temperature as function of the [Sr]/[Ba] ratio can be explained by a system of three different sublattices at the crystallographic positions of Strontium and Barium atoms.

CHARLES UNIVERSITY and HASSELT UNIVERSITY / tUL Doctoral dissertation Collagen structures from cell culture to intact tendon ABSTRACT Author: Daniel Hadraba Promoters: Assoc. Prof. Karel Jelen | Charles University Prof. Marcel Ameloot | Hasselt University Co-promoters: Dr. Frantisek Lopot | Charles University Prof. Virginie Bito | Hasselt University Annotation Author: Ing. Mgr. Daniel Hadraba Doctoral thesis title: Collagen structures from cell culture to intact tendon Year: 2010 - 2017 Doctoral program: Doctor of Biomechanics at Charles University Doctor of Biomedical Science at Hasselt University / transnational University Limburg Departments: Dept. Anatomy and Biomechanics | Faculty of Physical Education and Sport | Charles University Dept. Biophysics | Hasselt University Promoters: Assoc. Prof. Karel Jelen | Dept. Anatomy and Biomechanics | Faculty of Physical Education and Sport | Charles University Prof. Marcel Ameloot | Hasselt University / transnational University Limburg Co-promoters: Dr. Frantisek Lopot | Dept. Anatomy and Biomechanics | Faculty of Physical Education and Sport | Charles University Prof. Virginie Bito | Hasselt University / transnational University Limburg Bibliography details: Pages 102 Figures 30 Tables 2 Equations 17 Keywords: tendon, collagen, crimps, orientation, aging,...

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Time Dependent Density Functional Theory offers a good accuracy/computational cost ratio among different methods used to predict the electronic structure for molecules of practical interest. The Coupled Electronic Oscillator (CEO) formalism was recently shown to accurately predict Nonlinear Optical (NLO) properties of organic chromophores when combined with Time Dependent Density Functional Theory. Unfortunately, CEO does not lend itself easily to interpretation of the structure activity relationships of chromophores. On the other hand, the Sum Over States formalism in combination with semiempirical wavefunction methods has been used in the past for the design of simplified essential states models. These models can be applied to optimization of NLO properties of interest for applications. Unfortunately, TD-DFT can not be combined directly with SOS because state-to-state transition dipoles are not defined in the linear response TD approach. In this work, a second order CEO approach to TD-DFT is simplified so that properties of double excited states and state-to-state transition dipoles may be expressed through the combination of linear response properties. This approach is termed the a posteriori Tamm-Dancoff approximation (ATDA), and validated against high-level wavefunction theory methods. Sum over States (SOS) and related Two-Photon Transition Matrix formalism are then used to predict Two-Photon Absorption (2PA) profiles and anisotropy, as well as Second Harmonic Generation (SHG) properties. Numerical results for several conjugated molecules are in excellent agreement with CEO and finite field calculations, and reproduce experimental measurements well.

The extracellular matrix (ECM) is a three-dimensional, acellular scaffold of living tissues. Incorporating the ECM into cell culture models is a goal of cell biology studies and requires biocompatible materials that can mimic the ECM. Among such materials are hydrogels: polymeric networks that derive most of their mass from water. With the tuning of their properties, these polymer networks can resemble living tissues. The microarchitectural properties of hydrogels, such as porosity, pore size, fiber length, and surface topology can determine cell plasticity. The adequate characterization of these parameters requires reliable and reproducible methods. However, most methods were historically standardized using other biological specimens, such as 2D cell cultures, biopsies, or even animal models. Therefore, their translation comes with technical limitations when applied to hydrogel-based cell culture systems. In our current work, we have reviewed the most common techniques employed in the characterization of hydrogel microarchitectures. Our review provides a concise description of the underlying principles of each method and summarizes the collective data obtained from cell-free and cell-loaded hydrogels. The advantages and limitations of each technique are discussed, and comparisons are made. The information presented in our current work will be of interest to researchers who employ hydrogels as platforms for cell culture, 3D bioprinting, and other fields within hydrogel-based research.

<p>The thesis consists of two main parts of nonlinear optical instrumentation development. </p> <p>Fluorescence-detected mid-infrared photothermal (F-PTIR) microscopy is demonstrated for sub-diffraction limited mid-infrared microspectroscopy of model systems and applied to probe phase transformations in amorphous solid dispersions. To overcome the diffraction limit in infrared imaging, a highly localized temperature-dependent photothermal effect is an attractive alternative indicator to infrared absorption. Photothermal atomic force microscopy infrared spectroscopy (AFM-IR) achieves nanometer resolution by monitoring heat caused expansion but only restricted on the surface. For 3D imaging, optically detected photothermal infrared (O-PTIR) combines an infrared laser with a visible probe source with to transduce photothermal refractive index changes (e.g., from changes in beam divergence or scattering). The sensitivity of O-PTIR is ultimately limited by the relatively weak dependence of refractive index with temperature, exhibiting changes of ~0.01% per oC. Fluorescence-detected photothermal mid-infrared (F-PTIR) spectroscopy (Fig. 1) is demonstrated herein to support 3D imaging with improved photothermal sensitivity. In F-FTIR, the sensitivity of fluorescence quantum efficiency to temperature change (~1-2% per oC) is used to transduce transient heat flux from localized IR absorption. The infrared spatial resolution of F-FTIR is defined by fluorescence microscopy and the thermal diffusivity of the sample instead of infrared wavelength. Initial F-PTIR proof of concept studies are described for microparticle assemblies of silica gel and polyethylene glycol, followed by applications of F-PTIR for analysis of localized composition within phase-separated domains induced by water vapor exposure of an amorphous solid dispersion (ritonavir in copovidone).</p> <p>Fluorescence recovery while photobleaching (FRWP) is demonstrated as a method for quantitative measurements of rapid diffusion mapping over the microsecond to millisecond time scale. Diffusion measurements are critical for molecular mobility assessment in cell biology, materials science and pharmacology. Fluorescence recovery after photobleaching (FRAP) is a well-known noninvasive optical microscopy method for measuring diffusion coefficients of macromolecules, such as proteins in cells and viscous solutions. However, conventional point-bleach FRAP is challenging to implement with multi-photon excitation and typically only supports diffusion analysis over millisecond time scales due to camera frame rate limitations. FRWP with patterned illumination addresses these limitations of FRAP by probing the fluorescence intensity changes while bleaching a comb pattern within a field of view (FoV). Fast-scanning of an ultrafast excitation beam distributes heat rapidly over multiple adjacent pixels, minimizing local heating effects that could complicate analogous diffusion measurements by point-bleach FRAP with multiphoton excitation. In FRWP, time-scales of the probed diffusion events are defined by a single line-pass time of a resonant scanning-mirror with a period of 125  s. In FRWP, the bleach pattern spans locations across the whole FoV, enabling diffusion mapping through image segmentation. More than a hundred bleaching and recovery events can be recorded during a single 10s measurement. Normal and anomalous diffusion of rhodamine-labeled bovine serum albumin (BSA) molecules was studied as a model system, with applications targeting rapid assessment of therapeutic macromolecule mobility within heterogeneous biological environments.</p>

<p>Space-based global navigation and precision timing systems are critical for modern infrastructure. Atomic clock technology has increased the precision of these systems so that they are viable for military operations, navigation, telecommunications, and finance. Advances in optical atomic clocks, based on optical frequencies, provide an opportunity for even more precise timing. Therefore, developments in chip-scale optical atomic clock technologies could lead to increased and more wide-spread application of this precision timing. One component of the optical atomic clock is the optical frequency comb which serves as an interface between optical and microwave frequencies. This thesis will cover experiments related to these optical frequency combs. A 2$\mu$m fiber laser was developed in order to test second harmonic devices required to stabilize an optical frequency comb. The laser was then employed to measure the operating wavelengths and efficiencies of non-linear devices. In addition, an analysis of the radio frequency instruments used to evaluate microwave outputs was conducted to determine whether a digital signal analyzer (oscilloscope) or an analog electronic spectrum analyzer provides more accurate results for optical frequency comb based experiments.</p>