The work is devoted to problems of electron microscopy, focusing on the scintillation detector, which is located in chamber separating the field from different pressures. Using of the CAD and CAE was created 3D model of the detector, which took place on calculations focused to influence of the performance of different types of air pumps at gas flow between the chambers. The results of individual variants are compared in graphic form and evaluated.

Falling technology costs are allowing renewable sources of energy to become increasingly more competitive with fossil fuel-based sources. However, challenges still remain in the widespread deployment of sources like wind and solar due to their intermittent nature and cost-prohibitive storage options. An attractive solution to address these issues is by using renewably derived energy to drive electrolysis reactions that generate useful chemicals and fuels. In order to do this effectively and economically, efficient and durable electrocatalysts are needed for the reactions of interest, such as hydrogen production from water electrolysis. Presently, the best catalysts for this process are noble metals such as platinum, which are expensive and in limited supply. The discovery and mechanistic understanding of earth abundant materials that can also efficiently catalyze these reactions remains a current research focus. Scanning probe microscopy (SPM) techniques can be used to aid in the discovery of these materials, as they are able to investigate catalyst surfaces in situ and at a higher resolution than conventional 3-electrode electroanalytical methods. This dissertation explores the use of two in situ SPM techniques, scanning electrochemical microscopy (SECM) and scanning photocurrent microscopy (SPCM), for evaluating both photocatalytic and electrocatalytic electrochemical systems. Three different studies that use these two techniques were carried out over the duration of my thesis work and are presented in Chapters 2 through 4. After providing an overview of solar fuels and SPM techniques in Chapter 1, Chapter 2 describes the design considerations, implementation and demonstration of a home-built SECM instrument for use with nonlocal continuous line probes (CLPs) that can achieve high areal imaging rates with compressed sensing (CS) image reconstruction. The CLP consists of an electroactive band electrode sandwiched between two insulating layers, where one of the insulating layers needs to be on the same length scale as the band electrode because it determines the average separation distance from the band electrode to the substrate. Similarly, the spatial resolution of the CLP is determined by the thickness of the band and the realizable imaging rate is determined by its width and linear scan rate. Like conventional SECM systems, a combination of linear motors and a bipotentiostat is needed. However, for the CLP-SECM system both linear and rotational motors are needed to scan at different substrate angles to obtain the necessary raw signal to reconstruct the target electrochemical image with CS algorithms. Detailed descriptions of the microscope design, CLP fabrication, and the procedures necessary to carry out the CLP-SECM imaging are given in this chapter. Measurements with this novel CLP-SECM microscope are done with flat platinum disk electrode samples of varying sizes. A substrate-generation-probe-collection mode is used during the SECM linescan measurements to illustrate procedures for position calibration of the system, CLP and substrate cleaning, as well as verifying the sensitivity along the length of the CLP. Finally, linescans over a three disk platinum sample were taken and CS image reconstruction was done, with as few as three linescans, to demonstrate the order of magnitude time advantage of this approach over conventional SECM scanning methods. In Chapter 3, colorimetric imaging studies are done using a pH dye indicator to visualize the plume of electroactive species that is generated during in situ SECM measurements for both conventional and CLP-SECM systems. In SECM, the signal recorded by the probe is facilitated by transport of electroactive species and not by direct contact between the probe and the substrate, which is typical of many scanning probe microscopy (SPM) techniques. One of the complexities with SECM is being able to fully understand the interaction between the electroactive species generated at the substrate and the probe. Thus in order to understand this further, a pH indicator dye is used to visualize pH gradients associated with the hydrogen product plume generated by water electrolysis during in situ SECM measurements. The in situ colorimetric experiments are then used to inform assumptions about the system and validate simulations using finite element modeling software. From this study, we are able to develop quantitative relationships to describe how the plume of electroactive species influences the recorded current at the probe for different probe geometries. Finally, we use this initial study as groundwork for investigating the influence of higher probe scan speeds where convection starts to play a role on the distortion of the signal and plume dynamics, and how it can be corrected using CS post-processing methods. Lastly, SPCM is employed in Chapter 4 to study the optical efficiency losses due to varying size bubbles on a photoelectrode surface. Individual single hydrogen bubbles ranging from 100 µm to 1000 µm were generated on a photoelectrode surface and a laser was used to scan over single isolated bubbles to create localized optical efficiency maps based on photocurrent and external quantum efficiency (EQE). Moreover, a ray-tracing model based on Snell’s law was also constructed to compare to experimental SPCM linescans. This model showed very good agreement to the experimental SPCM linescan results. This investigation showed that larger bubbles lead to higher optical efficiency losses, not only due to higher inactive electrochemically active surface areas (ECSAs) but also due to a larger region of total internal reflection of light from the edge regions of bubbles. A macroscale study over a large photoelectrode surface was also done where the images of the surface were taken while the “sawtooth” was measured under AM1.5 illumination. Consequently, a predictive current−time profile was generated from the single bubble SPCM empirical relationship between bubble size and optical losses and was compared to the experimental measurement. Understanding how bubbles can impact the efficiency of the overall system is important, as bubbles in a system and on an electrode surface increases ohmic resistances, optical losses, and kinetic losses. Overall, this study can be used as a starting point for designing systems, electrolyte, and catalyst surfaces to improve one or more of the aforementioned losses.

After more than a century, there are no analytical solutions for the Navier-Stokes equations to describe complex fluid behavior, and we often resort to different computational methods to find solutions under specific conditions. In particular, to address many biological questions, we need to use techniques which are accurate at the mesoscale regime and computationally efficient, since atomistic simulations are still incredibly computationally costly, and continuum methods based on Navier-Stokes present challenges with complicated moving boundaries, in the presence of fluctuations. Here, we use a novel particle-based coarse-grained method, known as MPCD, to study ciliated swimmers. Using experimentally measured beating patterns, we show how we recapitulate the emergence of metachronal waves (MCW) on planar surfaces, and present new results on curved surfaces. To quantitatively study these waves, we also analyzed their effect on beating intervals, energy fluctuations, and fluid motion. We then extended our model to realistic cellular geometries, using experimentally obtained Basal Bodies locations.\par In the second part of our study, we focused on the intracellular fluid motion, neglecting hydrodynamic interactions. We developed the Digital Confocal Microscopy Suite (DCMS) that can run on multiple platforms using GPUs and can input realistic cell shapes and optical properties of the confocal microscope. It has this ability to simulate both (Fluorescence Recovery After Photobleaching) FRAP and Fluorescence Correlation Spectroscopy (FCS) experiments, as well as the capability to model photo-switching of fluorophores, acquisition photo-bleaching, and reaction-diffusion systems. With this platform, in collaboration with the Vidali Lab, we were able to elucidate the role of boundaries in interpreting FRAP experiments in \textit{moss} and estimate the binding rates of myosin XI.

Thesis advisor: Michael J. Naughton / The nanoscale coaxial cable (nanocoax) has demonstrated sub-diffraction-limited optical confinement in the visible and the near infrared, with the theoretical potential for confinement to scales arbitrarily smaller than the free space wavelength. In the first part of this thesis, I define in clear terms what the diffraction limit is. The conventional resolution formulae used by many are generally only valid in the paraxial limit. I performed a parametric numerical study, employing techniques of Fourier optics, to resolve precisely what that limit should be for nonparaxial (i.e. wide angle) focusing of scalar spherical waves. I also present some novel analytical formulae born out of Debye’s approximation which explain the trends found in the numeric study. These new functional forms remain accurate under wide angle focusing and could materially improve the performance, for example, in high intensity focused ultrasound surgery by further concentrating the power distributed within the point spread function to suppress the side lobes. I also comment of some possible connections to the focusing of electromagnetic waves. In the second part of this thesis I report on a novel fabrication process which yields optically addressable, sub-micron scale, and high aspect ratio metal-insulator-metal nanocoaxes made by atomic layer deposition of Pt and Al2O3. I discuss the observation of optical transmission via the fundamental, TEM-like mode by excitation with a radially polarized optical vortex beam. Also, Laguerre-Gauss beams are shown to overlap well with cylindrical waveguide modes in the nanocoax. My experimental results are based on interrogation with a polarimetric imager and a near-field scanning optical microscope. Various optical apparatus I built during my studies are also reviewed. Numerical simulations were used with uniaxial symmetry to explore 3D adiabatic taper geometries much larger than the wavelength. Finally, I draw some conclusions by assessing the optical performance of the fabricated nanocoaxial structures, and by giving some insights into future directions of investigation. / Thesis (PhD) — Boston College, 2019. / Submitted to: Boston College. Graduate School of Arts and Sciences. / Discipline: Physics.

Physicians are blind to the microscopic tissue structure that defines tissue type and pathologies during procedures. For diagnosis, tissue must be excised, fixed, and processed for histology, which can take anywhere from 20 minutes to days. This need for tissue excision and processing for microscopic visualization delays decision-making and necessitates repeat procedures. Limited sampling can also never fully eliminate the presence of disease. However, advances in optical sectioning techniques such as confocal and two-photon microscopy, which provide isotropic cellular-level resolution in bulk tissues, have obviated the need to physically section and process tissues for histology. Many optical imaging probes have been developed over the last three decades with the goal of demarcating tissue health in situ, either completely eliminating the need for tissue excision and processing for histopathology or guiding biopsy selection to reduce sampling bias. However, these techniques have faced major barriers to routine and widespread clinical use, including small 2D fields of view, limited contrast, slow imaging speeds and bulky laser sources. To address this critical need, SCAPE Microscopy, a light sheet-based microscopy technique recently developed in the Hillman lab, was developed for label-free, real-time, volumetric imaging at the point-of-care. SCAPE allows visualization of both cross-sectional and multilayer en face geometries in parallel and real-time, providing a more comprehensive view of tissue architecture than individual histology slides. Furthermore, tissues can be imaged label-free with structure shown through intrinsic fluorescence or in conjunction with intravenous or topical dyes. SCAPE’s video-rate speeds permit 3D stitching of large tissue areas and can withstand in vivo motion, which typically renders point-scanning techniques impractical. Most importantly, SCAPE is shown to allow 3D visualization of key histoarchitectural markers in human kidney biopsies through both endogenous and exogenous fluorophores. In this thesis work, a benchtop system is used for proof-of-concept imaging; however, miniaturized prototypes more suitable for clinical use are also presented. Further, high-throughput imaging of tissues is a critical but underserved need for bedside biopsy evaluation, as well as large-scale interrogation of structural organization and connectivity in the brain, retina and even whole model organisms. SCAPE provides near giga-voxel per second imaging rates that are well-suited for imaging large-scale ex vivo tissues at isotropic resolution at orders of magnitude faster speeds than point-scanning techniques. To this end, SCAPE was also developed as a versatile imaging platform for structural imaging of large-scale fresh, fixed, cleared and expanded samples for both bedside clinical evaluation and basic science research. It is demonstrated that planar samples of a few millimeters can be fully imaged at cellular resolution in just minutes by combining 3-axis stage-scanning and 3D stitching.

This thesis deals with concepts and solutions in the field of data management in everyday scientific life for image data from microscopy. The focus of the formulated requirements has so far been on published data, which represent only a small subset of the data generated in the scientific process. More and more, everyday research data are moving into the focus of the principles for the management of research data that were formulated early on (FAIR-principles). The adequate management of this mostly multimodal data is a real challenge in terms of its heterogeneity and scope. There is a lack of standardised and established workflows and also the software solutions available so far do not adequately reflect the special requirements of this area. However, the success of any data management process depends heavily on the degree of integration into the daily work routine. Data management must, as far as possible, fit seamlessly into this process. Microscopy data in the scientific process is embedded in pre-processing, which consists of preparatory laboratory work and the analytical evaluation of the microscopy data. In terms of volume, the image data often form the largest part of data generated within this entire research process. In this paper, we focus on concepts and techniques related to the handling and description of this image data and address the necessary basics. The aim is to improve the embedding of the existing data management solution for image data (OMERO) into the everyday scientific work. For this purpose, two independent software extensions for OMERO were implemented within the framework of this thesis: OpenLink and MDEmic. OpenLink simplifies the access to the data stored in the integrated repository in order to feed them into established workflows for further evaluations and enables not only the internal but also the external exchange of data without weakening the advantages of the data repository. The focus of the second implemented software solution, MDEmic, is on the capturing of relevant metadata for microscopy. Through the extended metadata collection, a corresponding linking of the multimodal data by means of a unique description and the corresponding semantic background is aimed at. The configurability of MDEmic is designed to address the currently very dynamic development of underlying concepts and formats. The main goal of MDEmic is to minimise the workload and to automate processes. This provides the scientist with a tool to handle this complex and extensive task of metadata acquisition for microscopic data in a simple way. With the help of the software, semantic and syntactic standardisation can take place without the scientist having to deal with the technical concepts. The generated metadata descriptions are automatically integrated into the image repository and, at the same time, can be transferred by the scientists into formats that are needed when publishing the data.

This thesis describes the design, fabrication, and characterization of the Implantable Fluorescence Imager (IFI): a camera chip with a needle-like form factor designed for imaging neuronal activity in the deep brain. It is fabricated with a complementary metal oxide semiconductor (CMOS) process, allowing for hundreds or thousands of single- photon-sensitive photodetectors to be densely packed onto a device width comparable to a single-channel fiber optic cannula (~100 μm). The IFI uses a combination of spectral and temporal filters as a fluorescence emission filter, and per-pixel Talbot gratings for 3D light-field imaging. The IFI has the potential to overcome the imaging depth limit of multi-photon microscopes imposed by the scattering and absorption of photons in brain tissue, and the resolution limit of noninvasive imaging techniques, such as functional magnetic resonance imaging and photoacoustic imaging. It competes with graded index lens-based miniaturized microscopes in imaging depth, but offers several comparative advantages. First, its cross sectional area is at least an order of magnitude smaller for an equal field of view. Second, the distribution of pixels along its entire length allows the study of multi- layer or multi-region dynamics. Finally, the scalability advantage of silicon integrated circuit technology in system miniaturization and data bandwidth may allow thousands of such imaging shanks to be simultaneously deployed for large-scale volumetric recording.

>Magister Scientiae - MSc / Solid-state reactions of bi-metallic systems can be driven or activated by various external stimuli like pressure, energetic photons, energetic charged particles or heat. For an example, high pressure torsion can be applied to aluminium-copper (Al-Cu) to drive solid-state reaction [1.1]. Oh-ishi et al. [1.1] applied a pressure of 6 GPa to Al and Cu half discs. Following this, x-ray diffraction (XRD) and high-resolution transmission electron microscope (HRTEM) were used to confirm the formation of different intermetallic phases such as Al2Cu and Al4Cu9. One of the first reported case where photons were used to drive solid phase diffusion was reported in 1998 by Ditchfield et al. [1.2]. The study was carried out to study the non-thermal effects of photons illumination on surface diffusion, an important process in microelectronics fabrication. Surface diffusion governs several important steps in microelectronics fabrication including the formation of hemispherical grained silicon used in memory devices [1.2], filling of channels with metals for devices interconnection purposes among others [1.2]. In this study, germanium-indium (Ge-In) on silicon was used because the thermal diffusion of this system was well understood [1.3]. Surface diffusion was measured in ultrahigh vacuum via second harmonic microscopy when the sample was illuminated with pulsed Nd: YAG laser at a wavelength of 1064 nm [1.3]. This study showed conclusively that photons could be used to drive solid-state reactions.

The complex structures of water-soluble wheat arabinoxylans have been mapped along individual molecules, and within populations, using the visualisation of the binding of inactivated enzymes by atomic force microscopy (AFM). It was demonstrated that site-directed mutagenesis (SDM) can be used to produce inactive enzymes as structural probes. For the SDM mutants AFM has been used to compare the binding of different xylanases to arabinoxylans. Xylanase mutant E386A, derived from the Xyn11A enzyme (Neocallimastrix patriciarium), was shown to bind randomly along arabinoxylan molecules. The xylanase binding was also monitored following Aspergillus niger arabinofuranosidase pre-treatment of samples. It was demonstrated that removal of arabinose side chains significantly altered the binding pattern of the inactivated enzyme. Xylanase mutant E246A, derived from the Xyn10A enzyme (Cellvibrio japonicus), was found to show deviations from random binding to the arabinoxylan chains. It is believed that this is due to the effect of a small residual catalytic activity of the enzyme that alters the binding pattern of the probe. Control procedures were developed and assessed to establish that the interactions between the modified xylanases and the arabinoxylans were specific interactions. The experimental data demonstrates the potential for using inactivated enzymes and AFM to probe the structural heterogeneity of individual polysaccharide molecules.

The interaction of emotion and memory is necessary for establishing a cognitive map including current context and past experiences, which is used by prefrontal cortex to regulate the internal state and guide goal directed actions and decision making. The amygdala, hippocampus and anterior cingulate cortex (ACC) play critical roles in these processes, but the organization of pathways between them is largely unknown in primates. This issue was addressed using neural tracers in rhesus monkeys to label the bidirectional pathways between amygdala and hippocampus and the unidirectional pathway from hippocampus to ACC. The amygdala sent a robust projection to hippocampus that formed large and closely spaced dual synapses on spines from the same dendritic segment, suggesting a strong influence. Further, amygdalar axon boutons innervated some disinhibitory calretinin neurons in CA1, suggesting enhanced excitatory influence. In contrast, in CA3 the amygdala pathway innervated calretinin and some of the powerful parvalbumin inhibitory neurons, which may help enhance memory of affective events. The reverse pathway from hippocampus densely and mainly targeted the ventro-medial part of the amygdala, including the basolateral (BL) and paralaminar basolateral (PLBL) nuclei. Hippocampal terminations formed synapses mostly on spines vii of presumed excitatory neurons. Some hippocampal terminations innervated inhibitory neurons in BL and PLBL and showed a rank of preference, by targeting mostly calretinin, and then calbindin and least parvalbumin inhibitory neurons. This pattern of innervation may allow contextual information represented by hippocampus to influence affective processes in the amygdala. The hippocampus sent strong projections to ACC (A32, A24a and A25) and targeted particularly A25, suggesting a role in affective and autonomic regulation. About 90% of hippocampal terminations in A25 innervated excitatory neurons, suggesting strong excitatory effects. The hippocampal pathway had a close relationship with postsynaptic D1 receptors in A25, especially in the deep layers. Dopamine has a strong influence in goal-directed actions, rewards, and attention in prefrontal cortex in primates, and may facilitate contextual information from the hippocampus to A25 to influence emotional regulation. The pathways studied were distinct, and suggest specific roles in emotional memory by the amygdala in hippocampus, in flexible learning and forgetting fear based on context transmitted from hippocampus to the amygdala, and in the synthesis of current context and past experience carried out by the hippocampal pathway to ACC to influence adaptive goal directed behavior. / 2021-09-27T00:00:00Z