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DOE OSTI2021

Boosting the signal-to-noise of low-field MRI with deep learning image reconstruction

Recent years have seen a resurgence of interest in inexpensive low magnetic field (< 0.3 T) MRI systems mainly due to advances in magnet, coil and gradient set designs. Most of these advances have focused on improving hardware and signal acquisition strategies, and far less on the use of advanced image reconstruction methods to improve attainable image quality at low field. We describe here the use of our end-to-end deep neural network approach (AUTOMAP) to improve the image quality of highly noise-corrupted low-field MRI data. We compare the performance of this approach to two additional state-of-the-art denoising pipelines. We find that AUTOMAP improves image reconstruction of data acquired on two very different low-field MRI systems: human brain data acquired at 6.5 mT, and plant root data acquired at 47 mT, demonstrating SNR gains above Fourier reconstruction by factors of 1.5- to 4.5-fold, and 3-fold, respectively. In these applications, AUTOMAP outperformed two different contemporary image-based denoising algorithms, and suppressed noise-like spike artifacts in the reconstructed images. The impact of domain-specific training corpora on the reconstruction performance is discussed. The AUTOMAP approach to image reconstruction will enable significant image quality improvements at low-field, especially in highly noise-corrupted environments.

42 ENGINEERING↗

DOE OSTI2021

Limited-angle computed tomography with deep image and physics priors

Computed tomography is a well-established x-ray imaging technique to reconstruct the three-dimensional structure of objects. It has been used extensively in a variety of fields, from diagnostic imaging to materials and biological sciences. One major challenge in some applications, such as in electron or x-ray tomography systems, is that the projections cannot be gathered over all the angles due to the sample holder setup or shape of the sample. This results in an ill-posed problem called the limited angle reconstruction problem. Typical image reconstruction in this setup leads to distortion and artifacts, thereby hindering a quantitative evaluation of the results. To address this challenge, we use a generative model to effectively constrain the solution of a physics-based approach. Our approach is self-training that can iteratively learn the nonlinear mapping from partial projections to the scanned object. Because our approach combines the data likelihood and image prior terms into a single deep network, it is computationally tractable and improves performance through an end-to-end training. We also complement our approach with total-variation regularization to handle high-frequency noise in reconstructions and implement a solver based on alternating direction method of multipliers. We present numerical results for various degrees of missing angle range and noise levels, which demonstrate the effectiveness of the proposed approach.

47 OTHER INSTRUMENTATION↗

DOE OSTI2021

Five-second STEM dislocation tomography for 300 nm thick specimen assisted by deep-learning-based noise filtering

Scanning transmission electron microscopy (STEM) is suitable for visualizing the inside of a relatively thick specimen than the conventional transmission electron microscopy, whose resolution is limited by the chromatic aberration of image forming lenses, and thus, the STEM mode has been employed frequently for computed electron tomography based three-dimensional (3D) structural characterization and combined with analytical methods such as annular dark field imaging or spectroscopies. However, the image quality of STEM is severely suffered by noise or artifacts especially when rapid imaging, in the order of millisecond per frame or faster, is pursued. Here we demonstrate a deep-learning-assisted rapid STEM tomography, which visualizes 3D dislocation arrangement only within five-second acquisition of all the tilt-series images even in a 300 nm thick steel specimen. The developed method offers a new platform for various in situ or operando 3D microanalyses in which dealing with relatively thick specimens or covering media like liquid cells are required.

47 OTHER INSTRUMENTATION↗

DOE OSTI2022

Nanoscale defect evaluation framework combining real-time transmission electron microscopy and integrated machine learning-particle filter estimation

Observation of dynamic processes by transmission electron microscopy (TEM) is an attractive technique to experimentally analyze materials’ nanoscale phenomena and understand the microstructure-properties relationships in nanoscale. Even if spatial and temporal resolutions of real-time TEM increase significantly, it is still difficult to say that the researchers quantitatively evaluate the dynamic behavior of defects. Images in TEM video are a two-dimensional projection of three-dimensional space phenomena, thus missing information must be existed that makes image’s uniquely accurate interpretation challenging. Therefore, even though they are still a clustering high-dimensional data and can be compressed to two-dimensional, conventional statistical methods for analyzing images may not be powerful enough to track nanoscale behavior by removing various artifacts associated with experiment; and automated and unbiased processing tools for such big-data are becoming mission-critical to discover knowledge about unforeseen behavior. We have developed a method to quantitative image analysis framework to resolve these problems, in which machine learning and particle filter estimation are uniquely combined. The quantitative and automated measurement of the dislocation velocity in an Fe-31Mn-3Al-3Si autunitic steel subjected to the tensile deformation was performed to validate the framework, and an intermittent motion of the dislocations was quantitatively analyzed. The framework is successfully classifying, identifying and tracking nanoscale objects; these are not able to be accurately implemented by the conventional mean-path based analysis.

36 MATERIALS SCIENCE↗

DOE OSTI2022

Uncertainty propagation in pore water chemical composition calculation using surrogate models

Performance assessment in deep geological nuclear waste repository systems necessitates an extended knowledge of the pore water chemical conditions prevailing in host-rock formations. In the last two decades, important progress has been made in the experimental characterization and thermodynamic modeling of pore water speciation, but the influence of experimental artifacts and uncertainties of thermodynamic input parameters are seldom evaluated. In this respect, we conducted an uncertainty propagation study in a reference geochemical model describing the pore water chemistry of the Callovian-Oxfordian clay formation. Nineteen model input parameters were perturbed, including those associated to experimental characterization (leached anions, exchanged cations, cation exchange selectivity coefficients) and those associated to generic thermodynamic databases (solubilities). A set of 13 quantities of interest were studied by the use of polynomial chaos expansions built non-intrusively with a least-squares forward stepwise regression approach. Training and validation sets of simulations were carried out using the geochemical speciation code PHREEQC. The statistical results explored the marginal distribution of each quantity of interest, their bivariate correlations as well as their global sensitivity indices. The influence of the assumed distributions for input parameters uncertainties was evaluated by considering two parametric domain sizes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

Deep learning of structural morphology imaged by scanning X-ray diffraction microscopy

Scanning X-ray nanodiffraction microscopy is a powerful technique for spatially resolving nanoscale structural morphologies by diffraction contrast. One of the critical challenges in experimental nanodiffraction data analysis is posed by the convergence angle of nanoscale focusing optics which creates simultaneous dependency of the far-field scattering data on three independent components of the local strain tensor-corresponding to dilation and two potential rigid body rotations of the unit cell. All three components are in principle resolvable through a spatially mapped sample tilt series; however, traditional data analysis is computationally expensive and prone to artifacts. In this study, we implement NanobeamNN, a convolutional neural network specifically tailored to the analysis of scanning probe X-ray microscopy data. NanobeamNN learns lattice strain and rotation angles from simulated diffraction of a focused X-ray nanobeam by an epitaxial thin film and can directly make reasonable predictions on experimental data without the need for additional fine-tuning. We demonstrate that this approach represents a significant advancement in computational speed over conventional methods, as well as a potential improvement in accuracy over the current standard.

Luo, Aileen [Cornell Univ., Ithaca, NY (United Sta↗

DOE OSTI2022

Accelerating error correction in tomographic reconstruction

Abstract Spurred by recent advances in detector technology and X-ray optics, upgrades to scanning-probe-based tomographic imaging have led to an exponential growth in the amount and complexity of experimental data and have created a clear opportunity for tomographic imaging to approach single-atom sensitivity. The improved spatial resolution, however, is highly susceptible to systematic and random experimental errors, such as center of rotation drifts, which may lead to imaging artifacts and prevent reliable data extraction. Here, we present a model-based approach that simultaneously optimizes the reconstructed specimen and sinogram alignment as a single optimization problem for tomographic reconstruction with center of rotation error correction. Our algorithm utilizes an adaptive regularizer that is dynamically adjusted at each alternating iteration step. Furthermore, we describe its implementation in a software package targeting high-throughput workflows for execution on distributed-memory clusters. We demonstrate the performance of our solver on large-scale synthetic problems and show that it is robust to a wide range of noise and experimental drifts with near-ideal throughput.

Ali, Sajid (ORCID:0000000321864636)↗

DOE OSTI2026

Time irreversibility as an indicator of approaching tipping points in Earth subsystems

With shifting environmental trends, many Earth system elements may be poised to undergo critical transitions or ‘tipping’. Reliable anticipation of these tipping elements is vital to inform policy decisions. Many of the current methods for tipping point detection are based on loss of resilience or ‘critical slowdown’ of the system as it approaches a tipping point. However, these methods are prone to false alarms; the detected slowdown may be an artifact of nonstationary noise unrelated to tipping behavior. Here, we explore the efficacy of early warning signs based on a nonequilibrium thermodynamics framework. The model-free detection method relies on the increased intrinsic time-irreversibility due to detailed balance breaking, preceding the onset of tipping or instabilities. We demonstrate that these EWSs are effective for tipping point detection and robust against false alarms due to nonstationary noise, using idealized models for two key elements of the Earth system that are prone to tipping: the Atlantic Meridional Overturning Circulation and Arctic sea-ice loss.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2020

Boosting solid oxide fuel cell performance via electrolyte thickness reduction and cathode infiltration

Increasing the power density and reducing the operating temperature of solid oxide fuel cells (SOFCs) is important for improving commercial viability. Here we discuss two strategies for achieving such improvements in Ni–YSZ supported SOFCs – electrolyte thickness reduction and cathode infiltration. Microstructural and electrochemical results are presented showing the effect of reducing YSZ/GDC electrolyte thickness from 8 to 2.5 μm, and the effect of PrO x infiltration into the LSCF–GDC cathode. Both of these measures are effective, particularly at lower temperatures, leading to an increase in the maximum power density at 650 °C from 0.4 to 0.95 W cm –2 , for example. Electrochemical impedance spectroscopy utilizing subtractive analysis shows that PrO x enhances the cathode charge transfer process. Reducing the electrolyte thickness reduces not only the cell ohmic resistance but also the electrode polarization resistance. Furthermore, the latter effect appears to be an artifact associated with a slight increase in the steam partial pressure at the anode due to minor gas leakage across the thinner electrolyte.

25 ENERGY STORAGE↗

DOE OSTI2021

A near-infrared optical nanosensor for measuring aerobic respiration in microbial systems

We developed a ratiometric oxygen-sensitive nanosensor and demonstrated application in monitoring metabolic oxygen consumption in microbial samples over time. Based on a near-infrared (NIR) emitting oxygen-quenched luminophore, platinum(II) octaethylporphine ketone (PtOEPK), along with a stable dioctadecyl dicarbocyanine reference dye (DiD), this nanosensor system provides an advantageous approach for overcoming imaging issues in biological systems, such as autofluorescence and optical scattering in the visible wavelength region. The dyes are encapsulated within a polymer-based nanoparticle matrix to maintain them at a constant ratio in biological samples, precluding the need for complex synthetic approaches. With this constant ratio of the two dyes, the nanosensor response can be measured as a ratio of their two signals, accounting for nanosensor concentration artifacts in measurements. The nanosensors are reversible, which enabled us to temporally monitor systems in which dissolved oxygen concentrations both increase and decrease. These sensors were applied for the monitoring of oxygen in samples of Saccharomyces cerevisiae (brewing yeast) in a 96-well optical fluorescence plate reader format over 60 h. By mixing the nanosensors directly into the sample well with the yeast, we were able to dynamically track metabolic activity changes over time due to varying cell concentration and exposure to an antimicrobial agent. As a result, this system could be a potential platform for high-throughput screening of various species or variants of microbes with unknown metabolic rates in response to external stimuli (antimicrobials, metabolites, etc.).

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Optimizing the accuracy of viscoelastic characterization with AFM force–distance experiments in the time and frequency domains

Atomic Force Microscopy (AFM) force-distance (FD) experiments have emerged as an attractive alternative to traditional micro-rheology measurement techniques owing to their versatility of use in materials of a wide range of mechanical properties. Here, we show that the range of time dependent behaviour which can reliably be resolved from the typical method of FD inversion (fitting constitutive FD relations to FD data) is inherently restricted by the experimental parameters: sampling frequency, experiment length, and strain rate. Specifically, we demonstrate that violating these restrictions can result in errors in the values of the parameters of the complex modulus. In the case of complex materials, such as cells, whose behaviour is not specifically understood a priori, the physical sensibility of these parameters cannot be assessed and may lead to falsely attributing a physical phenomenon to an artifact of the violation of these restrictions. We use arguments from information theory to understand the nature of these inconsistencies as well as devise limits on the range of mechanical parameters which can be reliably obtained from FD experiments. The results further demonstrate that the nature of these restrictions depends on the domain (time or frequency) used in the inversion process, with the time domain being far more restrictive than the frequency domain. Lastly, we demonstrate how to use these restrictions to better design FD experiments to target specific timescales of a material's behaviour through our analysis of a polydimethylsiloxane (PDMS) polymer sample.

information theory↗

DOE OSTI2024

Finding a needle in a haystack: quantitative HERFD-XRF imaging and HERFD-XANES characterization of trace platinum in gold solidi from the Late Roman and Byzantine Empires

High-Energy Resolution Fluorescence Detection X-Ray Fluorescence (HERFD-XRF) imaging and HERFD X-ray Absorption Near Edge Structure (XANES) spectroscopy are used to quantify and characterize trace platinum (Pt) in gold solidi from the Late Roman and Byzantine Empires. Historically, the elemental analysis of coins has been pivotal in distinguishing authentic artifacts from forgeries, elucidating minting practices, and understanding economic shifts. Notably, a new gold source with high platinum content appeared in the fourth century CE, transforming the Roman economy. Traditional methods struggled to detect platinum due to the overwhelming gold matrix. Here, this study demonstrates the effectiveness of HERFD techniques in resolving this challenge. Three gold solidi, minted between 654 and 659 CE, were analyzed alongside reference gold materials with known Pt concentrations. The HERFD-XRF imaging revealed spatial distributions of platinum, highlighting non-uniformities within the coins. Additionally, HERFD-XANES spectroscopy identified the oxidation states and chemical speciation of platinum. Results demonstrate that platinum in the solidi primarily exists as metallic Pt, with some surface oxidation. The findings align with previous measurements but reveal higher Pt concentrations and significant inhomogeneities. This research confirms the reliability of HERFD methods for quantifying trace elements and provides new insights into the raw material sources and minting techniques of ancient gold coins. The non-destructive nature of this approach allows for extensive analyses, offering valuable data for historical, economic, and archaeological studies. This innovative application of HERFD-XRF imaging and XANES in cultural heritage research underscores the potential for detailed material characterization and conservation, enhancing our understanding of ancient economies and trade patterns.

Van Loon, Lisa L.↗

DOE OSTI2023

BeyondPlanck: VII. Bayesian estimation of gain and absolute calibration for cosmic microwave background experiments

We present a Bayesian calibration algorithm for cosmic microwave background (CMB) observations as implemented within the global end-to-end BEYONDPLANCK framework and applied to the Planck Low Frequency Instrument (LFI) data. Following the most recent Planck analysis, we decomposed the full time-dependent gain into a sum of three nearly orthogonal components: one absolute calibration term, common to all detectors, one time-independent term that can vary between detectors, and one time-dependent component that was allowed to vary between one-hour pointing periods. Each term was then sampled conditionally on all other parameters in the global signal model through Gibbs sampling. The absolute calibration is sampled using only the orbital dipole as a reference source, while the two relative gain components were sampled using the full sky signal, including the orbital and Solar CMB dipoles, CMB fluctuations, and foreground contributions. We discuss various aspects of the data that influence gain estimation, including the dipole-polarization quadrupole degeneracy and processing masks. Comparing our solution to previous pipelines, we find good agreement in general, with relative deviations of -0.67% (-0.84%) for 30 GHz, 0.12% (-0.04%) for 44 GHz and -0.03% (-0.64%) for 70 GHz, compared to Planck PR4 and Planck 2018, respectively. We note that the BEYONDPLANCK calibration was performed globally, which results in better inter-frequency consistency than previous estimates. Additionally, WMAP observations were used actively in the BEYONDPLANCK analysis, which both breaks internal degeneracies in the Planck data set and results in an overall better agreement with WMAP. Finally, we used a Wiener filtering approach to smoothing the gain estimates. We show that this method avoids artifacts in the correlated noise maps as a result of oversmoothing the gain solution, which is difficult to avoid with methods like boxcar smoothing, as Wiener filtering by construction maintains a balance between data fidelity and prior knowledge. Although our presentation and algorithm are currently oriented toward LFI processing, the general procedure is fully generalizable to other experiments, as long as the Solar dipole signal is available to be used for calibration.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2023

Data Reliability in BIM and Performance Analytics: A Survey of Contemporary AECO Practice

As awareness around building energy consumption increases, practitioners are encouraged to consider performance aspects regarding the built environment more closely and find ways to improve its efficiency. Improvements in building information modeling (BIM) and building performance simulation (BPS) tools present opportunities to facilitate information communication with a wider range of stakeholders. The building sector can benefit from the integration of performance informatics; however, there has been limited success in utilizing available technologies that promote data integration and management in favor of enriching our knowledge and understanding of buildings as artifacts of information. This phenomenon was investigated by conducting a survey, together with a review of relevant literature, to depict the relevant challenges and opportunities for the architecture, engineering, construction, and owner-operated (AECO) industry, as it undergoes digital transformation, as well as the working practices that have formed around them. It is argued that the current tools available to practitioners do not support effective data serialization between design and analytics processes, affecting the collaboration between team members. Lastly, a series of functional goals are proposed to support a higher level of reliability in the ways information is mobilized, by rethinking the technologies and methods for organizing information systems.

42 ENGINEERING↗

DOE OSTI2020

Measurement of the angular dependence of the spontaneous Raman scattering in anisotropic crystalline materials using spherical samples: Potassium dihydrogen phosphate as a case example

A specialized experimental configuration was created to allow for more-accurate characterization of the spontaneous Raman scattering properties in anisotropic materials. This need stems from the challenges, arising from the complexity of light propagation, in obtaining accurate measurements of the angular dependence of the Raman scattering cross section in birefringent materials. The nonlinear optical material KH 2 PO 4 (KDP) is used as a model medium. Our report is motivated by the need to improve our understanding and management of transverse stimulated Raman scattering in KDP crystals and its deuterated analog, DKDP, typically used for frequency conversion and polarization control in large-aperture laser systems. Key to this experimental platform is the use of high-quality spherical samples that enable one to measure the Raman scattering cross section in a wide range of geometries using only a single sample. The effect of polarization rotation of both the pump light and the collected Raman signal must be carefully considered in data analysis and can give rise to artifacts, which can, in part, be mitigated by reducing the input and collection cone angles.

47 OTHER INSTRUMENTATION↗

DOE OSTI2020

Effective Hamiltonians derived from equation-of-motion coupled-cluster wave functions: Theory and application to the Hubbard and Heisenberg Hamiltonians

Effective Hamiltonians, which are commonly used for fitting experimental observables, provide a coarse-grained representation of exact many-electron states obtained in quantum chemistry calculations; however, the mapping between the two is not trivial. In this contribution, we apply Bloch’s formalism to equation-of-motion coupled-cluster (EOM-CC) wave functions to rigorously derive effective Hamiltonians in the Bloch’s and des Cloizeaux’ forms. We report the key equations and illustrate the theory by application to systems with two or three unpaired electrons, which give rise to electronic states of covalent and ionic characters. We show that the Hubbard and Heisenberg Hamiltonians can be extracted directly from the so-obtained effective Hamiltonians. By establishing a quantitative connection between many-body states and simple models, the approach facilitates the analysis of the correlated wave functions. We propose a simple diagnostic for assessing the validity of the model space choice based on the overlaps between the target- and model-space states. Finally, artifacts affecting the quality of electronic structure calculations such as spin contamination are also discussed.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2025

Filling data analysis gaps in time-resolved crystallography by machine learning

There is a growing understanding of the structural dynamics of biological molecules fueled by x-ray crystallography experiments. Time-resolved serial femtosecond crystallography (TR-SFX) with x-ray Free Electron Lasers allows the measurement of ultrafast structural changes in proteins. Nevertheless, this technique comes with some limitations. One major challenge is the quality of data from TR-SFX measurements, which often faces issues like data sparsity, partial recording of Bragg reflections, timing errors, and pixel noise. To overcome these difficulties, conventionally, large volumes of data are collected and grouped into a few temporal bins. The data in each bin are then averaged and paired with the mean of their corresponding jittered timestamps. This procedure provides one structure per bin, resulting in a limited number of averaged structures for the entire time interval spanned by the experiment. Therefore, the information on ultrafast structural dynamics at high temporal resolution is lost. This has initiated research for advanced methods of analyzing experimental TR-SFX data beyond the standard binning and averaging method. To address this problem, we use a machine learning algorithm called Nonlinear Laplacian Spectral Analysis (NLSA), which has emerged as a promising technique for studying the dynamics of complex systems. In this work, we demonstrate the power of this algorithm using synthetic x-ray diffraction snapshots from a protein with significant data incompleteness, timing uncertainties, and noise. Our study confirms that NLSA is a suitable approach that effectively mitigates the effects of these artifacts in TR-SFX data and recovers accurate structural dynamics information hidden in such data.

Trujillo, Justin (ORCID:0000000285505360)↗

DOE OSTI2020

On the proper derivation of the Floquet-based quantum classical Liouville equation and surface hopping describing a molecule or material subject to an external field

We investigate different approaches to derive the proper Floquet-based quantum–classical Liouville equation (F-QCLE) for laser-driven electron-nuclear dynamics. The first approach projects the operator form of the standard QCLE onto the diabatic Floquet basis and then transforms to the adiabatic representation. The second approach directly projects the QCLE onto the Floquet adiabatic basis. Both approaches yield a form that is similar to the usual QCLE with two modifications: (1) The electronic degrees of freedom are expanded to infinite dimension and (2) the nuclear motion follows Floquet quasi-energy surfaces. However, the second approach includes an additional cross derivative force due to the dual dependence on time and nuclear motion of the Floquet adiabatic states. Our analysis and numerical tests indicate that this cross derivative force is a fictitious artifact, suggesting that one cannot safely exchange the order of Floquet state projection with adiabatic transformation. Our results are in accord with similar findings by Izmaylov et al., [J. Chem. Phys. 140, 084104 (2014)] who found that transforming to the adiabatic representation must always be the last operation applied, although now we have extended this result to a time-dependent Hamiltonian. Finally, this paper and the proper derivation of the F-QCLE should lay the basis for further improvements of Floquet surface hopping.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗