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Variable Projection Method for Semi-Blind Deconvolution with Mixed Gaussian Kernels
I am a summer intern. The thesis includes work I’ve done here this summer with EV40. It is on mathematical methods for deblurring images. It doesn't include any radiographic images or data, its all synthetic examples - Dworaczyk, Jordan T.
Deconvolution strategies for efficient parametric variance estimation in stochastic media transport problems.
Abstract not provided.
Numerical Investigation on the Performance of a Variance Deconvolution Estimator.
Abstract not provided.
A sampling-based approach to solve Sobol' Indices using variance deconvolution for arbitrary uncertainty distributions.
Abstract not provided.
DUAL-PARTICLE DOSEMETER BASED ON ORGANIC SCINTILLATOR
Abstract Traditionally available handheld dosemeters are generally sensitive to only one type of radiation: neutrons or photons. Some dosemeters also rely on very specific attenuation correlations between response and dose, are not scalable in size and multiple dosemeters are required to characterise mixed-particle fields. The research presented here serves as a proof-of-concept for a method to simultaneously measure dose rates from neutrons and photons using a particle discriminating organic scintillation detector without the need for spectral deconvolution. The method was compared with traditional instruments and to simulation. Isotopic photon dose rates measured with this method were within 4% of simulated truth, whereas fission spectrum neutron dose rates were measured within 21%. Measurements of dose rates from both particles agree with simulated truth better than traditional instruments. This new method allows for measurement of dose equivalent from both neutrons and photons with a single instrument and no reliance on spectral deconvolution.
The deep-DRT: A deep neural network approach to deconvolve the distribution of relaxation times from multidimensional electrochemical impedance spectroscopy data
Electrochemical impedance spectroscopy (EIS) is an experimental technique ubiquitously used to study electrochemical systems. However, conventional EIS data interpretation through physical and equivalent circuit models is challenging because physical models are problem-specific, and equivalent circuits are often just lumped-element analogs lacking physical meaning. The distribution of relaxation times (DRT) has emerged as a complementary approach to resolve these issues. One drawback of conventional DRT deconvolution is that the EIS data is understood to be (only) a function of frequency (i.e. 1D data) and deconvolved accordingly. This work proposes a novel deconvolution method based on deep neural networks (DNNs), allowing the analysis of multidimensional EIS spectra to bridge data dependency on both frequencies and experimental conditions. Two particularly appealing traits of the deep-DRT method developed in this article are that neither regularization nor specific spacing on the state variables defining the experiment are required. Finally, leveraging DNN to examine complex EIS spectra and their dependence on experimental conditions, this work opens a new research direction in the area of EIS analysis and DRT deconvolution.
An artificial intelligence’s interpretation of complex high-resolution in situ transmission electron microscopy data
Complicated nano- and atomic-scale processes with sub-angstrom spatial resolution and millisecond time resolution visualized by in situ transmission electron microscopy (TEM) are often highly dynamical and time consuming to analyze and interpret. Here, we report how variational autoencoders (VAEs) can provide an artificial intelligence’s interpretation of high-resolution in situ TEM data by condensing and deconvoluting complicated atomic-scale dynamics into a latent space with reduced dimensionality. We designed a VAE model with high latent dimensions capable of deconvoluting information from complex high-resolution TEM data. We demonstrate how this model, with high latent dimensions trained on atomically resolved TEM images of lead sulfide (PbS) nanocrystals, is able to capture movements and perturbations of periodic lattices in both simulated and real in situ TEM data. Importantly, the VAE model shows the capability of detecting and deconvoluting dynamical nanoscale physical processes, such as the rotation of crystal lattices and intra-particle ripening during the annealing of semiconductor nanocrystals.
Comparison of methodologies used to determine aromatic lignin unit ratios in lignocellulosic biomass
Abstract Background Multiple analytical methods have been developed to determine the ratios of aromatic lignin units, particularly the syringyl/guaiacyl (S/G) ratio, of lignin biopolymers in plant cell walls. Chemical degradation methods such as thioacidolysis produce aromatic lignin units that are released from certain linkages and may induce chemical changes rendering it difficult to distinguish and determine the source of specific aromatic lignin units released, as is the case with nitrobenzene oxidation methodology. NMR methods provide powerful tools used to analyze cell walls for lignin composition and linkage information. Pyrolysis-mass spectrometry methods are also widely used, particularly as high-throughput methodologies. However, the different techniques used to analyze aromatic lignin unit ratios frequently yield different results within and across particular studies, making it difficult to interpret and compare results. This also makes it difficult to obtain meaningful insights relating these measurements to other characteristics of plant cell walls that may impact biomass sustainability and conversion metrics for the production of bio-derived fuels and chemicals. Results The authors compared the S/G lignin unit ratios obtained from thioacidolysis, pyrolysis-molecular beam mass spectrometry (py-MBMS), HSQC liquid-state NMR and solid-state (ss) NMR methodologies of pine, several genotypes of poplar, and corn stover biomass. An underutilized approach to deconvolute ssNMR spectra was implemented to derive S/G ratios. The S/G ratios obtained for the samples did not agree across the different methods, but trends were similar with the most agreement among the py-MBMS, HSQC NMR and deconvoluted ssNMR methods. The relationship between S/G, thioacidolysis yields, and linkage analysis determined by HSQC is also addressed. Conclusions This work demonstrates that different methods using chemical, thermal, and non-destructive NMR techniques to determine native lignin S/G ratios in plant cell walls may yield different results depending on species and linkage abundances. Spectral deconvolution can be applied to many hardwoods with lignin dominated by S and G units, but the results may not be reliable for some woody and grassy species of more diverse lignin composition. HSQC may be a better method for analyzing lignin in those species given the wealth of information provided on additional aromatic moieties and bond linkages. Additionally, trends or correlations in lignin characteristics such as S/G ratios and lignin linkages within the same species such as poplar may not necessarily exhibit the same trends or correlations made across different biomass types. Careful consideration is required when choosing a method to measure S/G ratios and the benefits and shortcomings of each method discussed here are summarized.
RISE: robust iterative surface extension for sub-nanometer X-ray mirror fabrication
Precision optics have been widely required in many advanced technological applications. X-ray mirrors, as an example, serve as the key optical components at synchrotron radiation and free electron laser facilities. They are rectangular silicon or glass substrates where a rectangular Clear Aperture (CA) needs to be polished to sub-nanometer Root Mean Squared (RMS) to keep the imaging capability of the incoming X-ray wavefront at the diffraction limit. The convolutional polishing model requires a CA to be extended with extra data, from which the dwell time is calculated via deconvolution. However, since deconvolution is very sensitive to boundary errors and noise, the existing surface extension methods can hardly fulfill the sub-nanometer requirement. On one hand, the figure errors in a CA were improperly modeled during the extension, leading to continuity issues along the boundary. On the other hand, uncorrectable high-frequency errors and noise were also extended. In this study, we propose a novel Robust Iterative Surface Extension (RISE) method that resolves these problems with a data fitting strategy. RISE models the figure errors in a CA with orthogonal polynomials and ensures that only correctable errors are fit and extended. Combined with boundary conditions, an iterative refinement of dwell time is then proposed to compensate the errors brought by the extension and deconvolution, which drastically reduces the estimated figure error residuals in a CA while the increase of total dwell time is negligible. To our best knowledge, RISE is the first data fitting-based surface extension method and is the first to optimize dwell time based on iterative extension. An experimental verification of RISE is given by fabricating two elliptic cylinders (10 mm × 80 mm CAs) starting from a sphere with a radius of curvature around 173 m using ion beam figuring. The figure errors in the two CAs greatly improved from 204.96 nm RMS and 190.28 nm RMS to 0.62 nm RMS and 0.71 nm RMS, respectively, which proves that RISE is an effective method for sub-nanometer level X-ray mirror fabrication.
Holistic digital gamma-ray spectroscopy methods and instrumentation for high-throughput high-resolution applications
Method of real-time adaptive digital pulse signal processing for high count rate gamma-ray spectroscopy applications includes receiving a preamplifier signal at a pulse deconvolver, the preamplifier signal including resolution deterioration resulting from pulse pile-up. The method further includes generating a deconvoluted signal, by the pulse deconvolver, from the preamplifier signal, the deconvoluted signal having less resolution deterioration as compared to the received preamplifier signal. The method furthermore includes shaping of the deconvoluted signal by a trapezoid filter, the shaping comprising adjusting a shaping parameter of the trapezoid filter for an incoming signal based on a time separation from a subsequent incoming signal.
Using photoelectron spectroscopy to measure resonant inelastic X-ray scattering: a computational investigation
Resonant inelastic X-ray scattering (RIXS) has become an important scientific tool. Nonetheless, conventional high-resolution (few hundred meV or less) RIXS measurements, especially in the soft X-ray range, require low-throughput grating spectrometers, which limits measurement accuracy. Here, the performance of a different method for measuring RIXS, i.e. photoelectron spectrometry for analysis of X-rays (PAX), is computationally investigated. This method transforms the X-ray measurement problem of RIXS to an electron measurement problem, enabling use of high-throughput, compact electron spectrometers. X-rays to be measured are incident on a converter material and the energy distribution of the resultant photoelectrons, the PAX spectrum, is measured with an electron spectrometer. A deconvolution algorithm for analysis of such PAX data is proposed. It is shown that the deconvolution algorithm works well on data recorded with ~0.5 eV resolution. Additional simulations show the potential of PAX for estimation of RIXS features with smaller widths. For simulations using the 3d levels of Ag as a converter material, and with 10 5 simulated detected electrons, it is estimated that features with a few hundred meV width can be accurately estimated in a model RIXS spectrum. For simulations using a sharp Fermi edge to encode RIXS spectra, it is estimated that one can accurately distinguish 100 meV FWHM peaks separated by 45 meV with 10 5 simulated detected electrons that were photoemitted from within 0.4 eV of the Fermi level.
Single-Filament Imaging Mass Spectrometry Lipidomics in Arthrospira platensis
Elucidating intra-organismal biochemical and lipid organization in photosynthetic biological cell factories of filamentous cyanobacteria, i.e., Arthrospira platensis (Spirulina), is important to track physiological response mechanisms during growth. Little is known about the filaments' biochemical organization and cellular structure and no label-free imaging techniques exist that provide molecular mapping. We applied ultra-high resolution mass spectrometry (7T FT-ICR-MS) matrix-assisted laser desorption ionization (MALDI) imaging to immobilized Spirulina filaments to investigate the localization of lipids across distinct physiological regions. We optimized matrix selection and deposition methods with the goal of facilitating high spatial, and intra-filament, resolution using untargeted multivariate statistical spectral deconvolution across MS pixels. Our results demonstrate an improved two step application with an optimized procedure for intra-organismal lipid profiling to improve analyte sensitivity and achieve higher spatial resolution, whereby we evaluate three conventional matrices 2,5-dihydroxybenzoic acid (DHB), a 9:1 ratio of DHB:superDHB (sDHB), 1,5- diaminonaphthalene (DAN) and a 50:50 mix of DHB:sDHB and compare delineation and pixel-based elucidation of intra-filament lipidomics. We identified a total of 1,626 features that could be putatively assigned a lipid-like formula based on database query and 46 unique features, with associated lipid assignments that were significantly distinct in their intra-filament location. MALDI- imaging MS with untargeted statistical spectral deconvolution was used to visualize intra-filament lipidomics organization in Spirulina filaments. Improvements in matrix deposition, including sequential sublimation and pneumatic spraying, increased signal abundance at high spatial resolution and allowed for identification of distinct lipid composition regions. Here in this work outlines a methodology that may be used for micro-ecological untargeted molecular phenotyping.
Degradation of electrical resistivity of tungsten following shielded neutron irradiation
A major challenge for heat transfer in nuclear materials is to ensure thermal mobility after high amounts of neutron irradiation. Tungsten is widely selected as a heat transfer material in fusion reactors. In metals, thermal conductivity is dominated by electrons’ ability to transfer energy. Neutron irradiation generates point defects, clusters, and solid transmutation (e.g.rhenium and osmium in tungsten), which inhibit electron motion. The purpose of this work is to quantify the irradiation-induced change in electron mobility and deconvolute transmutation and microstructural effects on observed changes to electron mobility. Single and polycrystalline tungsten were fast neutron irradiated in the High Flux Isotope Reactor at Oak Ridge National Laboratory to doses between 0.2 and 0.7 displacements per atom (dpa) and temperatures from 500 °C to 1000 °C. Grain growth was observed in all samples. Microstructure and transmutation were quantified. The geometric orientation of samples with elongated grains has been shown to affect electrical resistivity. A mathematical model was developed and used to deconvolute solid-solution transmutation, grain, and temperature-dependent lattice effects on resistivity. At ~0.4 dpa at ~590 °C, the combined resistivity degradation due to voids, vacancies, interstitials, and dislocations is estimated to be greater than the contribution from solid solution Re transmutation, which is greater than the contribution from grain boundaries. At doses of ~0.7 dpa at ~750 °C, solid solution Re contributions are greater than all other effects combined. As a result, this work establishes a basis to predict the effects of irradiation temperature and transmutation on thermal properties of tungsten and highlights the importance of irradiation temperature.
Effects of micrometer-scale surface roughness on thermal infrared emittance spectra of silica glass
Surface roughness is known to decrease thermal infrared (TIR) absorption band intensity, but studies of the effect on geologically relevant samples are relatively limited. To determine the effect of surface roughness (with features smaller than ~2/3 of the wavelength) on TIR spectra, we investigated two glass compositions with prepared roughened surfaces: (1) high purity fused silica and (2) soda-lime glass (73 wt% SiO$_2$). We roughened the surfaces of the glasses by sandblasting and polishing with grit paper. The surfaces were characterized with scanning electron microscopy and stylus profilometry. We then analyzed the roughened glasses with TIR emittance spectroscopy. Micrometer-scale roughness causes a decrease in TIR absorption band intensity, relative to a specular surface. No significant changes in band shape or shifts in wavelength were detected. As roughness increases, empirical results show a logarithmic decrease in TIR absorption band intensity. The logarithmic trends of the two glass compositions are different; empirical roughness calibrations do not translate across different compositions. A linear, least-squares spectral deconvolution using two endmembers, specular and blackbody, predicts model spectra of roughened glass surfaces with relatively low error. This is of consequence to orbital TIR measurements of poorly constrained targets, such as the martian surface, because micrometer-scale roughness is adequately modeled by the addition of a blackbody spectrum to the deconvolution endmember matrix.
High-Field One-Dimensional and Two-Dimensional 27Al Magic-Angle Spinning Nuclear Magnetic Resonance Study of ?-, d-, and ?-Al2O3 Dominated Aluminum Oxides: Toward Understanding the Al Sites in ?-Al2O3
Herein, a detailed analysis was carried out using high-field (19.9 T) 27Al magic-angle spinning (MAS) nuclear magnetic resonance (NMR) on three specially prepared aluminum oxide samples where the ?-, d-, and ?-Al2O3 phases are dominantly expressed through careful control of the synthesis conditions. Specifically, two-dimensional (2D) multiquantum (MQ) MAS 27Al was used to obtain high spectral resolution, which provided a guide for analyzing quantitative 1D 27Al NMR spectra. Six aluminum sites were resolved in the 2D MQ MAS NMR spectra, and seven aluminum sites were required to fit the 1D spectra. A set of octahedral and tetrahedral peaks with well-defined quadrupolar line shapes was observed in the ?-phase dominant sample and was unambiguously assigned to the ?-Al2O3 phase. The distinct line shapes related to the ?-Al2O3 phase provided an opportunity for effectively deconvoluting the more complex spectrum obtained from the d-Al2O3 dominant sample, allowing the peaks/quadrupolar parameters related to the d-Al2O3 phase to be extracted. The results show that the d-Al2O3 phase contains three distinct AlO sites and three distinct AlT sites. This detailed Al site structural information offers a powerful way of analyzing the most complex ?-Al2O3 spectrum. It is found that the ?-Al2O3 phase consists of Al sites with local structures similar to those found in the d-Al2O3 and ?-Al2O3 phases albeit with less ordering. Spin–lattice relaxation time measurement further confirms the disordering of the lattice. Collectively, this study uniquely assigns 27Al features in transition aluminas, offering a simplified method to quantify complex mixtures of aluminum sites in transition alumina samples.
Laue-DIALS: Open-source software for polychromatic x-ray diffraction data
Most x-ray sources are inherently polychromatic. Polychromatic (“pink”) x-rays provide an efficient way to conduct diffraction experiments as many more photons can be used and large regions of reciprocal space can be probed without sample rotation during exposure—ideal conditions for time-resolved applications. Analysis of such data is complicated, however, causing most x-ray facilities to discard >99% of x-ray photons to obtain monochromatic data. Key challenges in analyzing polychromatic diffraction data include lattice searching, indexing and wavelength assignment, correction of measured intensities for wavelength-dependent effects, and deconvolution of harmonics. We recently described an algorithm, Careless, that can perform harmonic deconvolution and correct measured intensities for variation in wavelength when presented with integrated diffraction intensities and assigned wavelengths. Here, we present Laue-DIALS, an open-source software pipeline that indexes and integrates polychromatic diffraction data. Laue-DIALS is based on the dxtbx toolbox, which supports the DIALS software commonly used to process monochromatic data. As such, Laue-DIALS provides many of the same advantages: an open-source, modular, and extensible architecture, providing a robust basis for future development. We present benchmark results showing that Laue-DIALS, together with Careless, provides a suitable approach to the analysis of polychromatic diffraction data, including for time-resolved applications.
Practical considerations in using a binary pseudorandom array for instrument transfer function calibration
Binary pseudo-random array (BPRA) artifacts are useful devices for calibrating the instrument transfer function (ITF) of interferometric microscopes and other optical and non-optical surface and wavefront measurement instruments. The intrinsic white noise character of the power spectral density function of the artifact simplifies the deconvolution of the ITF from the measured power spectral density (PSD). However, resampling of the BPRA intrinsic artifact features with the measurement tool's specific sampling pattern modifies the white noise character of the intrinsic spectrum and needs to be accounted for in the ITF-based data deconvolution process. We have developed an analytic solution to the spectrum of a resampled one- and two- dimensional BPRA. The resultant nominal PSD function is a simple twoparameter cosine function with a period equal to the resampled pixel width. A transfer function model for interferometric microscopes that incorporates this function, along with an ITF that includes aliasing effects and variable numerical aperture (NA), wavelength, and obscuration factor, is used to fit to the BPRA PSDs measured by an interference microscope for a range of objective and zoom lens magnification combinations.