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DOE OSTI2018

Probing charge transfer dynamics in a single iron tetraphenylporphyrin dyad adsorbed on an insulating surface

Although the dynamics of charge transfer (CT) processes can be probed with ultimate lifetime resolution, the inability to control CT at the nanoscale is one of the most important roadblocks to revealing some of its deep fundamental aspects. In this work, we present an investigation of CT dynamics in a single iron tetraphenylporphyrin (Fe-TPP) donor/acceptor dyad adsorbed on a CaF 2 /Si(100) insulating surface. The tip of a scanning tunneling microscope (STM) is used to create local ionic states in one fragment of the dyad. The CT process is monitored by imaging subsequent changes in the neighbor acceptor molecule and its efficiency is mapped, revealing the influence of the initial excited state in the donor molecule. In the validation of the experiments, simulations based on density functional theory show that holes have a higher donor–acceptor CT rate compared to electrons and highlight a noticeable initial state dependence on the CT process. We leverage the unprecedented spatial resolution achieved in our experiments to show that the CT process in the dyad is governed via molecule–molecule coherent tunneling with negligible surface-mediated character.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

DOE OSTI2021

Uranium Oxide Synthetic Pathway Discernment through Unsupervised Morphological Analysis

We present a novel unsupervised machine learning method for quantitative representation of scanning electron micrographs and its applications and performance for nuclear forensic analysis of uranium ore concentrates. The method uses a vector quantizing variational autoencoder followed by a histogram operation to encode a micrograph into a single dimensional representation, called the latent vector. The method requires no extant labeling of the data and can be applied over large datasets of micrographs with minimal human interaction. The representations generated are broadly descriptive of each micrograph and the microstructure of the material imaged. In the case of uranium ore concentrate analysis, the representations were amenable to processing reagent and ore concentrate species classification with accuracy of 81:8%, which is competitive with state-of-the-art supervised networks. The representations were also used to classify previously unseen processing routes, were able to classify imaging parameters such as magnification (to 76:0% accuracy), were able to classify fine grained process parameters such as calcining temperature (to 74:4% accuracy), and their informatic properties indicate that they are generally descriptive of the image represented. This method can be applied across microstructure analysis fields to perform quantitative analysis without the need for labor intensive and possibly biased human analysis.

Scanning Electron Microscopy, Vector Quantizing Va↗

DOE OSTI2023

PhytoOracle: Scalable, modular phenomics data processing pipelines

As phenomics data volume and dimensionality increase due to advancements in sensor technology, there is an urgent need to develop and implement scalable data processing pipelines. Current phenomics data processing pipelines lack modularity, extensibility, and processing distribution across sensor modalities and phenotyping platforms. To address these challenges, we developed PhytoOracle (PO), a suite of modular, scalable pipelines for processing large volumes of field phenomics RGB, thermal, PSII chlorophyll fluorescence 2D images, and 3D point clouds. PhytoOracle aims to ( i ) improve data processing efficiency; ( ii ) provide an extensible, reproducible computing framework; and ( iii ) enable data fusion of multi-modal phenomics data. PhytoOracle integrates open-source distributed computing frameworks for parallel processing on high-performance computing, cloud, and local computing environments. Each pipeline component is available as a standalone container, providing transferability, extensibility, and reproducibility. The PO pipeline extracts and associates individual plant traits across sensor modalities and collection time points, representing a unique multi-system approach to addressing the genotype-phenotype gap. To date, PO supports lettuce and sorghum phenotypic trait extraction, with a goal of widening the range of supported species in the future. At the maximum number of cores tested in this study (1,024 cores), PO processing times were: 235 minutes for 9,270 RGB images (140.7 GB), 235 minutes for 9,270 thermal images (5.4 GB), and 13 minutes for 39,678 PSII images (86.2 GB). These processing times represent end-to-end processing, from raw data to fully processed numerical phenotypic trait data. Repeatability values of 0.39-0.95 (bounding area), 0.81-0.95 (axis-aligned bounding volume), 0.79-0.94 (oriented bounding volume), 0.83-0.95 (plant height), and 0.81-0.95 (number of points) were observed in Field Scanalyzer data. We also show the ability of PO to process drone data with a repeatability of 0.55-0.95 (bounding area).

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Octave bandwidth photonic fishnet-achromatic-metalens

Planar structured interfaces, also known as metasurfaces, are continuously attracting interest owing to their ability to manipulate fundamental attributes of light, including angular momentum, phase, or polarization. However, chromatic aberration, limiting broadband operation, has remained a challenge for metasurfaces-based optical components and imagers. The limitation stems from the intrinsic dispersion of existing materials and design principles. Here we report and experimentally demonstrate polarization-independent fishnet-achromatic-metalenses with measured average efficiencies over 70% in the continuous band from the visible (640 nm) to the infrared (1200 nm). Results of the scalable platform are enabling for applications requiring broad bandwidth and high efficiency including energy harvesting, virtual reality and information processing devices, or medical imaging.

36 MATERIALS SCIENCE↗

DOE OSTI2017

Processing of Ice Cloud In Situ Data Collected by Bulk Water, Scattering, and Imaging Probes: Fundamentals, Uncertainties, and Efforts toward Consistency

Abstract In situ observations of cloud properties made by airborne probes play a critical role in ice cloud research through their role in process studies, parameterization development, and evaluation of simulations and remote sensing retrievals. To determine how cloud properties vary with environmental conditions, in situ data collected during different field projects processed by different groups must be used. However, because of the diverse algorithms and codes that are used to process measurements, it can be challenging to compare the results. Therefore it is vital to understand both the limitations of specific probes and uncertainties introduced by processing algorithms. Since there is currently no universally accepted framework regarding how in situ measurements should be processed, there is a need for a general reference that describes the most commonly applied algorithms along with their strengths and weaknesses. Methods used to process data from bulk water probes, single-particle light-scattering spectrometers and cloud-imaging probes are reviewed herein, with emphasis on measurements of the ice phase. Particular attention is paid to how uncertainties, caveats, and assumptions in processing algorithms affect derived products since there is currently no consensus on the optimal way of analyzing data. Recommendations for improving the analysis and interpretation of in situ data include the following: establishment of a common reference library of individual processing algorithms, better documentation of assumptions used in these algorithms, development and maintenance of sustainable community software for processing in situ observations, and more studies that compare different algorithms with the same benchmark datasets.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2024

Integrating the PanDA Workload Management System with the Vera C. Rubin Observatory

The Vera C. Rubin Observatory will produce an unprecedented astronomical data set for studies of the deep and dynamic universe. Its Legacy Survey of Space and Time (LSST) will image the entire southern sky every three to four days and produce tens of petabytes of raw image data and associated calibration data over the course of the experiment’s run. More than 20 terabytes of data must be stored every night, and annual campaigns to reprocess the entire dataset since the beginning of the survey will be conducted over ten years. The Production and Distributed Analysis (PanDA) system was evaluated by the Rubin Observatory Data Management team and selected to serve the Observatory’s needs due to its demonstrated scalability and flexibility over the years, for its Directed Acyclic Graph (DAG) support, its support for multi-site processing, and its highly scalable complex workflows via the intelligent Data Delivery Service (iDDS). PanDA is also being evaluated for prompt processing where data must be processed within 60 seconds after image capture. This paper will briefly describe the Rubin Data Management system and its Data Facilities (DFs). Finally, it will describe in depth the work performed in order to integrate the PanDA system with the Rubin Observatory to be able to run the Rubin Science Pipelines using PanDA.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2020

Early High-contrast Imaging Results with Keck/NIRC2-PWFS: The SR 21 Disk

High-contrast imaging of exoplanets and protoplanetary disks depends on wave front sensing and correction made by adaptive optics instruments. Classically, wave front sensing has been conducted at optical wavelengths, which made high-contrast imaging of red targets such as M-type stars or extincted T Tauri stars challenging. Keck/NIRC2 has combined near-infrared (NIR) detector technology with the pyramid wave front sensor (PWFS). With this new module we observed SR 21, a young star that is brighter at NIR wavelengths than at optical wavelengths. Compared with the archival data of SR 21 taken with the optical wave front sensing we achieved ~20% better Strehl ratio in similar natural seeing conditions. Further post-processing utilizing angular differential imaging and reference-star differential imaging confirmed the spiral feature reported by the Very Large Telescope/Spectro-Polarimetric High-contrast Exoplanet REsearch instrument polarimetric observation, which is the first detection of the SR 21 spiral in total intensity at L' band. We also compared the contrast limit of our result (10 -4 at 0.'4 and 2 × 10 -5 at 1.'0) with the archival data that were taken with optical wave front sensing and confirmed the improvement, particularly at ≤0.'5. Our observation demonstrates that the NIR PWFS improves AO performance and will provide more opportunities for red targets in the future.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2026

New perspectives on materials and device dynamics using time-resolved full-field diffraction X-ray imaging

Understanding how materials evolve during synthesis, processing, or device operation requires experimental access to structural dynamics across wide ranges of length and time scales, often in bulk samples or even within packaged devices. Time-resolved full-field diffraction X-ray microscopy has recently emerged as a powerful way to meet this need by combining the penetration and structural sensitivity of X-ray diffraction with objective-lens-based magnification, sensitive high-resolution X-ray imaging detectors, and pump-probe and real-time imaging strategies. Advances in full-field X-ray diffraction microscopy, often termed dark-field X-ray microscopy (DFXM), enable simultaneous imaging of extended fields of view while retaining crystallographic selectivity. Time-resolved DFXM promises to enable advances in materials processing and dynamics, electrochemical and photochemical processes, and the design of electronic devices. This Perspective summarizes the key instrumental concepts that define the performance of these methods, including the choice of imaging optics, detector considerations, and the impact of source time structure at synchrotron light sources and X-ray free-electron lasers (XFELs). We discuss the simultaneous use of complementary imaging modes that are increasingly used in practice. The early demonstrations of the potential of time-resolved DFXM include real-time defect and grain-boundary dynamics during metal annealing, stroboscopic imaging of functional devices with high strain sensitivity, and ultrafast pump-probe implementations at XFELs that directly visualize acoustic-wave propagation and energy dissipation in bulk crystals.

Dark-field X-ray microscopy↗

DOE OSTI2018

Unsupervised learning about 4D features of microparticle motion

Material clusters of different sizes are known to exist in high-temperature plasmas due to plasma-wall interactions. The facts that these clusters, ranging from sub-microns to above mm in size, can move from one location to another quickly and that there are a lot of them make high-speed imaging and tracking one of the best, effective, and sometimes only diagnostic. An unsupervised machine learning technique based on deconvolutional neural networks is developed to analyze two-camera videos of high-temperature microparticles generated from exploding wires. The neural network utilizes a locally competitive algorithm to infer representations and optimize a dictionary composed of kernels, or basis vectors, for image analysis. Our primary goal is to use this method for feature recognition and prediction of the time-dependent three-dimensional (or “4D”) microparticle motion. Features equivalent to local velocity vectors have been identified as the dictionary kernels or “building blocks” of the scene. The dictionary elements from the left and right camera views are found to be strongly correlated and satisfy the projection geometrical constraints. The results show that unsupervised machine learning techniques are promising approaches to process large sets of images for high-temperature plasmas and other scientific experiments. In conclusion, machine learning techniques can be useful to handle the large amount of data and therefore aid the understanding of plasma-wall interaction.

47 OTHER INSTRUMENTATION↗

DOE OSTI2022

A Scalable Pipeline for Gigapixel Whole Slide Imaging Analysis on Leadership Class HPC Systems

Whole Slide Imaging (WSI) captures microscopic details of a patient's histopathological features at multiple res-olutions organized across different levels. Images produced by WSI are gigapixel-sized, and saving a single image in memory requires a few gigabytes which is scarce since a complicated model occupies tens of gigabytes. Performing a simple met-ric operation on these large images is also expensive. High-performance computing (HPC) can help us quickly analyze such large images using distributed training of complex deep learning models. One popular approach in analyzing these images is to divide a WSI image into smaller tiles (patches) and then train a simpler model with these reduced-sized but large numbers of patches. However, we need to solve three pre-processing challenges efficiently for pursuing this patch-based approach. 1) Creating small patches from a high-resolution image can result in a high number (hundreds of thousands per image) of patches. Storing and processing these images can be challenging due to a large number of I/O and arithmetic operations. To reduce I/Oand memory accesses, an optimal balance between the size and number of patches must exist to reduce I/O and memory accesses. 2) WSI images may have tiny annotated regions for cancer tissue and a significant portion with normal and fatty tissues; correct patch sampling should avoid dataset imbalance. 3) storing and retrieving many patches to and from disk storage might incur I/O latency while training a deep learning model. An efficient distributed data loader should reduce I/O latency during the training and inference steps. This paper explores these three challenges and provides empirical and algorithmic solutions deployed on the Summit supercomputer hosted at the Oak Ridge Leadership Computing Facility.

Dash, Sajal↗

DOE OSTI2019

Physical processes affecting the survival of microbiological systems in laser printing of gel droplets

We consider laser printing of gel microdroplets – a promising method for microbiology, biotechnology and medicine. In the printing process, small volumes of gel containing living microorganisms are transferred as a result of cavitation caused by the absorption of a short laser pulse in a metal film. However, in such a transfer, certain physical factors arise that can lead to damage and death of biological material. These factors include elevated temperature and pressure, high radiation intensity and some others. Experimental estimates of these parameters are conducted, based on measurements of the acoustic response of laser printing, electron microscopy of the affected areas and the results of high-speed imaging of the transfer process. It is shown that these factors are not a significant limitation for the technology being developed. Laser printing is performed by exposing a metal film to laser pulses with an energy of 5 – 30 μJ and a duration of 8 – 14 ns, the laser beam diameter being 30 μm. (laser applications and other topics in quantum electronics)

60 APPLIED LIFE SCIENCES↗

DOE OSTI2021

Improving the astrometric solution of the Hyper Suprime-Cam with anisotropic Gaussian processes

Context. We study astrometric residuals from a simultaneous fit of Hyper Suprime-Cam images. Aims. We aim to characterize these residuals and study the extent to which they are dominated by atmospheric contributions for bright sources. Methods. We used Gaussian process interpolation with a correlation function (kernel) measured from the data to smooth and correct the observed astrometric residual field. Results. We find that a Gaussian process interpolation with a von Kármán kernel allows us to reduce the covariances of astrometric residuals for nearby sources by about one order of magnitude, from 30 mas 2 to 3 mas 2 at angular scales of ~1 arcmin. This also allows us to halve the rms residuals. Those reductions using Gaussian process interpolation are similar to recent result published with the Dark Energy Survey dataset. We are then able to detect the small static astrometric residuals due to the Hyper Suprime-Cam sensors effects. We discuss how the Gaussian process interpolation of astrometric residuals impacts galaxy shape measurements, particularly in the context of cosmic shear analyses at the Rubin Observatory Legacy Survey of Space and Time.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2024

Using double pulse laser ablation in air to enhance the strength of laser-driven shocks

In the process of multi-pulse laser ablation, inter-pulse delay time, Δ t , is known to be an important parameter for maximizing ablation efficiency as well as impulse imparted to the target. In this work, using photon Doppler velocimetry, we show that for single pairs of colinear pulses (1064 nm, 8 ns, ∼ 60 J cm -2 per pulse) in air, the peak free surface velocity of the back surface of an aluminum target (125 µm thick) is increased, by a factor of nearly 3, when Δ t = 10 microseconds, compared with both pulses arriving simultaneously (Δ t = 0). Fast imaging of the ablation process suggests this enhancement is due to rarefaction of the contiguous air in the passage of the leading shock produced by ablation, which then in turn allows a larger fraction of the energy of the second pulse to reach the target surface. This interpretation is strengthened by additional experiments in which the two pulses do not overlap on the target surface, but the shock strength is nevertheless enhanced. Given a fixed energy budget this work suggests a prescription for maximizing laser-driven shock strength by judicious choice of inter-pulse delay.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2017

What Lies Beneath Can Be Imaged

The Hanford Site was quickly established to help end World War II, making history for producing the plutonium used in the world’s first nuclear weapons. Throughout the Cold War years, Hanford employees produced plutonium for most of the more than 60,000 weapons in the U.S. nuclear arsenal stockpile. Today, the once highly active nuclear reactors are shut down. And the mission at Hanford turned full-circle as scientists, engineers and specialists work to clean up our nation’s most contaminated nuclear site. PNNL Computational Geophysicist Tim Johnson is helping decision-makers understand the complexity and breadth of the contamination in soils at Hanford. Tim and others are applying remote, high-resolution geophysical imaging to determine the extent of contamination in the soil below the surface and understand the processes controlling its movement. They also provide real-time imaging of remediation processes that are working to limit the movement of contaminants below the surface and toward water resources. Geophysical imaging simply means that PNNL scientists are combining the techniques of geology, physics, mathematics and chemistry with supercomputer modeling to create three-dimensional images of the waste and its movement. These real-time, remote images are essential in reducing the uncertainty associated with cleanup costs and remediation technologies.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2020

Foliar functional traits from imaging spectroscopy across biomes in eastern North America

Summary Foliar functional traits are widely used to characterize leaf and canopy properties that drive ecosystem processes and to infer physiological processes in Earth system models. Imaging spectroscopy provides great potential to map foliar traits to characterize continuous functional variation and diversity, but few studies have demonstrated consistent methods for mapping multiple traits across biomes. With airborne imaging spectroscopy data and field data from 19 sites, we developed trait models using partial least squares regression, and mapped 26 foliar traits in seven NEON (National Ecological Observatory Network) ecoregions (domains) including temperate and subtropical forests and grasslands of eastern North America. Model validation accuracy varied among traits (normalized root mean squared error, 9.1–19.4%; coefficient of determination, 0.28–0.82), with phenolic concentration, leaf mass per area and equivalent water thickness performing best across domains. Across all trait maps, 90% of vegetated pixels had reasonable values for one trait, and 28–81% provided high confidence for multiple traits concurrently. Maps of 26 traits and their uncertainties for eastern US NEON sites are available for download, and are being expanded to the western United States and tundra/boreal zone. These data enable better understanding of trait variations and relationships over large areas, calibration of ecosystem models, and assessment of continental‐scale functional diversity.

Wang, Zhihui↗

DOE OSTI2022

High-Magnification Faraday Rotation Imaging and Analysis of X-pinch Implosion Dynamics

An X-pinch load driven by an intense current pulse (>100 kA in ~100 ns) can result in the formation of a small radius, runaway compressional micro-pinch. A micro-pinch is characterized by a hot (>1 keV), current-driven (>100 kA), high-density plasma column (near solid density) with a small neck diameter (1–10 μm), a short axial extent (<1 mm), and a short duration (.1 ns). With material pressures often well into the multi-Mbar regime, a micro-pinch plasma often radiates an intense, sub-ns burst of sub-keV to multi-keV x-rays. A low-density coronal plasma immediately surrounding the dense plasma neck could potentially shunt current away from the neck and thus reduce the magnetic drive pressure applied to the neck. To study the current distribution in the coronal plasma throughout the implosion process, a Faraday rotation imaging diagnostic (1064 nm) capable of producing simultaneous high-magnification polarimetric and interferometric images has been developed for the 1-MA, 100-ns MAIZE facility at the University of Michigan. Designed with a variable magnification (1–10×), this diagnostic achieves a spatial resolution of approximately 35 μm, which is useful for resolving the ~100-μm-scale coronal plasma region immediately surrounding the dense core. Combined with the corresponding interferogram, which provides the radial density distribution in the low-density coronal plasma, the measured rotation can be used to diagnose the delivery of the driver current, and thus the magnetic drive pressure, to the micro-pinch plasma as it approaches minimal radius. Using this technique on MAIZE, we have measured

Dowhan, G. V.↗

DOE OSTI2017

Asymmetry in serial femtosecond crystallography data

Serial crystallography is an increasingly important approach to protein crystallography that exploits both X-ray free-electron laser (XFEL) and synchrotron radiation. Serial crystallography recovers complete X-ray diffraction data by processing and merging diffraction images from thousands of randomly oriented non-uniform microcrystals, of which all observations are partial Bragg reflections. Random fluctuations in the XFEL pulse energy spectrum, variations in the size and shape of microcrystals, integrating over millions of weak partial observations and instabilities in the XFEL beam position lead to new types of experimental errors. The quality of Bragg intensity estimates deriving from serial crystallography is therefore contingent upon assumptions made while modeling these data. Here it is observed that serial femtosecond crystallography (SFX) Bragg reflections do not follow a unimodal Gaussian distribution and it is recommended that an idealized assumption of single Gaussian peak profiles be relaxed to incorporate apparent asymmetries when processing SFX data. The phenomenon is illustrated by re-analyzing data collected from microcrystals of the Blastochloris viridis photosynthetic reaction center and comparing these intensity observations with conventional synchrotron data. The results show that skewness in the SFX observations captures the essence of the Wilson plot and an empirical treatment is suggested that can help to separate the diffraction Bragg intensity from the background.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2018

Directional Software Algorithms and Sensor Evaluations

This report evaluates the relative performance of two directional gamma-ray spectrometers and processing algorithms that are used to construct images and spatially resolved spectra. Polaris, which was developed by H3D Inc., uses 18 pixelated CZT crystals to construct gamma-ray images in either Compton camera(CC) or coded aperture (CA) mode. The other sensor that is referenced in this report incorporates a commercial high-purity germanium based imager, called GeGI, with a coded aperture mask and processing software developed by Oak Ridge National Laboratory (ORNL). H3D and the University of Michigan provided several algorithms that can be used to process data collected by Polaris in CC mode. This evaluation compares the performance of these algorithms with a Directional Unfolded Source Term (DUST) approach developed by Sandia National Laboratories (SNL). DUST differs from the other algorithms because its primary objective is synthesis of spatially-resolved gamma ray spectra as opposed to image reconstruction.

97 MATHEMATICS AND COMPUTING↗