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At least 973 records · Page 54

FREDA: A Web Application for the Processing, Analysis, and Visualization of Fourier‐Transform Mass Spectrometry Data

The high-resolution measurement capability of Fourier-transform mass spectrometry (FT-MS) has made it a necessity for exploring the molecular composition of complex organic mixtures, like soil, plant, aquatic, and petroleum samples. This demand has driven a need for informatics tools to explore and analyze FT-MS data in a robust and reproducible manner. FREDA is an interactive web application developed to enable spectrometrists to format, process, and explore their FT-MS data without the need for statistical programming expertise. FREDA was built to explore outputs from a molecular identification tool, like CoreMS, and provide a suite of methods to filter data, compute chemical properties of peaks, statistically compare samples and groups of samples, conduct exploratory data analysis, and download the results with a report detailing all steps conducted. To demonstrate the utility of FREDA, an example analysis was conducted using FT-MS data from a soil microbiology study of samples collected in two different soil depths at the Sphagnum bog forest north of Grand Rapids, Minnesota. Differences between the two depths are observed using Kendrick, Gibbs free energy, and van Krevelen plots. G-tests are used to quantify a significant difference between the groups. All analyses and plotting are conducted using only the FREDA application. FREDA is an open-source and readily available web application that allows users to explore and make statistically valid conclusions about their FT-MS data. The application is available online (https://map.emsl.pnnl.gov/app/freda) with a tutorial web series (https://youtu.be/k5HLE2kNSBY?si=yB6sGoyvzxrFf5MP) and freely accessible code on Github (https://github.com/EMSL-Computing/FREDA).

47 OTHER INSTRUMENTATION↗

Tetragonal Lysozyme Nucleation and Crystal Growth: The Role of the Solution Phase

Lysozyme, and most particularly the tetragonal form of the protein, has become the default standard protein for use in macromolecule crystal nucleation and growth studies. There is a substantial body of experimental evidence, from this and other laboratories, that strongly suggests this proteins crystal nucleation and growth is by addition of associated species that are preformed by standard reversible concentration-driven self association processes in the bulk solution. The evidence includes high resolution AFM studies of the surface packing and of growth unit size at incorporation, fluorescence resonance energy transfer measurements of intermolecular distances in dilute solution, dialysis kinetics, and modeling of the growth rate data. We have developed a selfassociation model for the proteins crystal nucleation and growth. The model accounts for the obtained crystal symmetry, explains the observed surface structures, and shows the importance of the symmetry obtained by self-association in solution to the process as a whole. Further, it indicates that nucleation and crystal growth are not distinct mechanistically, but identical, with the primary difference being the probability that the particle will continue to grow or dissolve. This model also offers a possible mechanism for fluid flow effects on the growth process and how microgravity may affect it. While a single lysozyme molecule is relatively small (M.W. = 14,400), a structured octamer in the 4(sub 3) helix configuration (the proposed average sized growth unit) would have a M.W. = 115,000 and dimensions of 5.6 x 5.6 x 7.6 nm. Direct AFM measurements of growth unit incorporation indicate that units as wide as 11.2 nm and as long as 11.4 nm commonly attach to the crystal. These measurements were made at approximately saturation conditions, and they reflect the sizes of species that both added or desorbed from the crystal surface. The larger and less isotropic the associated species the more likely that it will be oriented to some degree in a flowing boundary layer, even at the low flow velocities measured about macromolecule crystals. Flow-driven effects resulting in misorientation upon addition to and incorporation into the crystal need only be a small fraction of a percentage to significantly affect the resulting crystal. One Earth, concentration gradient driven flow will maintain a high interfacial concentration, i.e., a high level (essentially that of the bulk solution) of solute association at the interface and higher growth rate. Higher growth rates mean an increased probability that misaligned growth units are trapped by subsequent growth layers before they can be desorbed and try again, or that the desorbing species will be smaller than the adsorbing species. In microgravity the extended diffusive boundary layer will lower the interfacial concentration. This results in a net dissociation of aggregated species that diffuse in from the bulk solution, i.e., smaller associated species, which are more likely able to make multiple attempts to correctly bind, yielding higher quality crystals.

Pusey, Marc L.↗

Continuous flow electrophoresis system experiments on shuttle flights STS-6 and STS-7

The development of a space continuous flow electrophoresis system (CFES) is discussed. The objectives of the experiment were: (1) to use a model sample material at a high concentration to evaluate the continuous flow electrophoresis process in the McDonnell Douglass CFES instrument and compare its separation resolution and sample throughput with related devices on Earth, and (2) to expand the basic knowledge of the limitations imposed by fluid flows and particle concentration effects on the electrophoresis process by careful design and evaluation of the space experiment. Hemoglobin and polysaccharide were selected as samples of concentration effects. The results from space show a large band spread of the high concentration of the single species of hemoglobin that was principally due to the mismatch of electrical conductivity between the sample and buffer.

Snyder, Robert S.↗

Using X-Ray Computed Tomography to Image Apollo Drive Tube 73002

The Apollo missions collected 382 kg of rock, regolith, and core samples from six locations on the nearside of the Moon. Today, just over 84% by mass of the Apollo collection remains in pristine condition within the curation facility at Johnson Space Center. Most Apollo samples have been well characterized, however there are several types of samples that have remained wholly or largely unstudied since their return, and/or that have been curated under special conditions. These sample types are: (1) unopened samples sealed under vacuum on the Moon; (2) unopened (but unsealed) drive tubes; (3) Apollo 17 samples frozen shortly after their return; and (4) Apollo 15 samples opened and stored in a helium atmosphere since their return. NASA solicited proposals for the Apollo Next Generation Sample Analysis Program (ANGSA), and 9 teams were selected to study: (1) unsealed, unopened drive tube 73002; (2) sealed, unopened drive tube 73001 (paired with 73002); and (3) a subset of the frozen and He-purged samples [1]. The first sample opened as part of the ANGSA program was drive tube 73002. This was originally a ~30 cm long, 4 cm diameter drive tube collected on a landslide deposit near Lara Crater at the Apollo 17 landing site. It was part of a ~60 cm long double drive tube collected, and the bottom half of the tube (73001) was sealed under vacuum on the Moon [2]. Prior to opening sample 73002, the sample was imaged with a high resolution X-ray Computed Tomography (XCT) scan of the entire tube. Additional XCT scans have been made of “large” clasts removed from the core as part of the dissection process [3]. Here we present the whole tube and close-up XCT data from 73002, and talk about the utility of the scans as part of the curation process, including the potential for future science returns from the high resolutions scans.

R A Zeigler↗

Azimuthally averaged wind and thermodynamic structures of tropical cyclones in global climate models and their sensitivity to horizontal resolution

Characteristics of tropical cyclones (TCs) in global climate models (GCMs) are known to be influenced by details of the model configurations, including horizontal resolution and parameterization schemes. Understanding model-to-model differences in TC characteristics is a prerequisite for reducing uncertainty in future TC activity projections by GCMs. This study performs a process-level examination of TC structures in eight GCM simulations that span a range of horizontal resolutions from 1° to 0.25°. A recently developed set of process-oriented diagnostics is used to examine the azimuthally averaged wind and thermodynamic structures of the GCM-simulated TCs. Results indicate that the inner-core wind structures of simulated TCs are more strongly constrained by the horizontal resolutions of the models than are the thermodynamic structures of those TCs. As expected, the structures of TC circulations become more realistic with smaller horizontal grid spacing, such that the radii of maximum wind (RMW) become smaller, and the maximum vertical velocities occur off the center. However, the RMWs are still too large, especially at higher intensities, and there are rising motions occurring at the storm centers, inconsistently with observations. The distributions of precipitation, moisture, radiative and surface turbulent heat fluxes around TCs are diverse, even across models with similar horizontal resolutions. At the same horizontal resolution, models that produce greater rainfall in the inner-core regions tend to simulate stronger TCs. Further, when TCs are weak, the radial gradient of net column radiative flux convergence is comparable to that of surface turbulent heat fluxes, emphasizing the importance of cloud-radiative feedbacks during the early developmental phases of TCs.

54 ENVIRONMENTAL SCIENCES↗

Multimodal (Non)Linear Optical Nanoimaging and Nanospectroscopy

This article highlights recent advances in linear and nonlinear spectral nanoimaging. The described developments are motivated by the need to characterize molecular and material systems noninvasively with nanometer spatial and femtosecond temporal resolution. Indeed, the ability to image and chemically characterize heterogeneous interfaces with joint nano–femto resolution is a prerequisite to advancing our fundamental understanding of processes as diverse as heterogeneous catalysis, microbial communication, and energy flow in pristine/defect-containing low-dimensional quantum materials, to name a few. We describe pioneering work and recent demonstrations of (non)linear optical nanoimaging and nanospectroscopy, with an emphasis on high spatial resolution measurements conducted under ambient laboratory conditions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Effects of Digitization and JPEG Compression on Land Cover Classification Using Astronaut-Acquired Orbital Photographs

Studies that utilize astronaut-acquired orbital photographs for visual or digital classification require high-quality data to ensure accuracy. The majority of images available must be digitized from film and electronically transferred to scientific users. This study examined the effect of scanning spatial resolution (1200, 2400 pixels per inch [21.2 and 10.6 microns/pixel]), scanning density range option (Auto, Full) and compression ratio (non-lossy [TIFF], and lossy JPEG 10:1, 46:1, 83:1) on digital classification results of an orbital photograph from the NASA - Johnson Space Center archive. Qualitative results suggested that 1200 ppi was acceptable for visual interpretive uses for major land cover types. Moreover, Auto scanning density range was superior to Full density range. Quantitative assessment of the processing steps indicated that, while 2400 ppi scanning spatial resolution resulted in more classified polygons as well as a substantially greater proportion of polygons < 0.2 ha, overall agreement between 1200 ppi and 2400 ppi was quite high. JPEG compression up to approximately 46:1 also did not appear to have a major impact on quantitative classification characteristics. We conclude that both 1200 and 2400 ppi scanning resolutions are acceptable options for this level of land cover classification, as well as a compression ratio at or below approximately 46:1. Auto range density should always be used during scanning because it acquires more of the information from the film. The particular combination of scanning spatial resolution and compression level will require a case-by-case decision and will depend upon memory capabilities, analytical objectives and the spatial properties of the objects in the image.

Robinson, Julie A.↗

High Resolution Imaging Spectrometer (HIRIS): Science and Instrument

The High Resolution Imaging Spectrometer (HIRIS) is a facility instrument slated for flight on the second of the EOS-A series of platforms. HIRIS is designed to acquire 24-km wide, 30-m pixel images in 192 spectral bands simultaneously in the 0.4-2.45-micrometer wavelength region. With pointing mirrors it can sample any place on Earth, except the poles, every two days. HIRIS operates at the intermediate scale between the human and the global and therefore links studies of Earth surface processes to global monitoring carried out by lower-resolution instruments. So far, over 50 science data products from HIRIS images have been identified in the fields of atmospheric gases, clouds, snow and ice, water, vegetation, and rocks and soils. The key attribute of imaging spectrometry that makes it possible to derive quantitative information from the data is the large number of contiguous spectral bands. Therefore spectrum matching techniques can be applied. Such techniques are not possible with present-day, multispectral scanner data.

Goetz, Alexander F. H.↗

On the Use of Fourier Transform Infrared (FT-IR) Spectroscopy and Synthetic Calibration Spectra to Quantify Gas Concentrations in a Fischer-Tropsch Catalyst System

One possible origin of prebiotic organic material is that these compounds were formed via Fischer-Tropsch-type (FTT) reactions of carbon monoxide and hydrogen on silicate and oxide grains in the warm, inner-solar nebula. To investigate this possibility, an experimental system has been built in which the catalytic efficiency of different grain-analog materials can be tested. During such runs, the gas phase above these grain analogs is sampled using Fourier transform infrared (FT-IR) spectroscopy. To provide quantitative estimates of the concentration of these gases, a technique in which high-resolution spectra of the gases are calculated using the high-resolution transmission molecular absorption (HITRAN) database is used. Next, these spectra are processed via a method that mimics the processes giving rise to the instrumental line shape of the FT-IR spectrometer, including apodization, self-apodization, and broadening due to the finite resolution. The result is a very close match between the measured and computed spectra. This technique was tested using four major gases found in the FTT reactions: carbon monoxide, methane, carbon dioxide, and water. For the ranges typical of the FTT reactions, the carbon monoxide results were found to be accurate to within 5% and the remaining gases accurate to within 10%. These spectra can then be used to generate synthetic calibration data, allowing the rapid computation of the gas concentrations in the FTT experiments.

Infrared Spectroscopy↗

Contrasting landform perception with varied radar illumination geometries and at simulated resolutions of Venera and Magellan

The high sensitivity of imaging radars to slope at moderate to low incidence angles enhances the perception of linear topography on images. It reveals broad spatial patterns that are essential to landform mapping and interpretation. As radar responses are strongly directional, the ability to discriminate linear features on images varies with their orientation. Landforms that appear prominent on images where they are transverse to the illumination may be obscure to indistinguishable on images where they are parallel to it. Landform detection is also influenced by the spatial resolution in radar images. Seasat radar images of the Gran Desierto Dunes complex, Sonora, Mexico; the Appalachian Valley and Ridge Province; and accreted terranes in eastern interior Alaska were processed to simulate both Venera 15 and 16 images (1000 to 3000 km resolution) and image data expected from the Magellan mission (120 to 300 m resolution. The Gran Desierto Dunes are not discernable in the Venera simulation, whereas the higher resolution Magellan simulation shows dominant dune patterns produced from differential erosion of the rocks. The Magellan simulation also shows that fluvial processes have dominated erosion and exposure of the folds.

Ford, J. P.↗

Redox Mechanisms and Migration Tendencies in Earth-Abundant 0.7Li 2 MnO 3 ·0.3LiFeO 2 Cathodes: Coupling Spin-Resolved X-ray Absorption Near Edge and X-ray Absorption Fine Structure Spectroscopies

We report the use of iron 1s3p resonant X-ray emission processes to conduct spin-selective, high-energy resolution fluorescence detected X-ray absorption near-edge spectroscopy (HERFD-XANES) on an iron-containing, lithium- and manganese-rich, fully earth-abundant cathode material, Li 1.3 Mn 0.5 Fe 0.2 O 2 (0.7Li 2 MnO 3 ·0.3LiFeO 2 ). Coupling this technique with conventional Mn K-edge XANES and detailed extended X-ray absorption fine structure (EXAFS) analysis from both the Mn and Fe vantage points, we gain fundamental insights into the redox processes and migration tendencies of transition metals in this cathode material at the bulk level. We show that during the first charge, Fe 3+ undergoes oxidation to form Fe 4+ prior to the activation plateau. Toward the end of activation, a significant fraction of the iron is present as tetrahedral Fe 3+ . This observation reveals that iron migration from octahedral to tetrahedral sites and iron reduction are initiated during activation. Upon first discharge from the activated state, a continuous and overlapping reduction of both Fe and Mn is observed, with Fe largely restored back as an octahedrally coordinated Fe 3+ . The manganese local environment gradually changes to a distorted cooperative Jahn–Teller Mn 3+ structure during discharge, with the clear presence of two Mn–O as well as two Mn–Mn correlation distances at 2.0 V. The significant reduction of manganese in the very first discharge is distinctly different from that seen in typical nickel-based lithium-manganese-rich materials but is similar to that observed for pure Li 2 MnO 3 . In conclusion, these findings shed light on key structure–property correlations in the cathode material and point to a causative relationship between the redox mechanisms as well as structural changes endured by the material and relatively poor performance during extended electrochemical cycling.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Virtual Volumetric Additive Manufacturing (VirtualVAM)

Abstract Tomographic volumetric additive manufacturing (VAM) produces arbitrary 3D geometries by exposure of a rotating volume of photopolymer resin to tomographically‐patterned illumination. This enables high speed, layer‐less printing of parts from a wide range of photopolymers not amenable to layer‐by‐layer processes. Since the entire geometry is produced at once over the course of a few seconds to minutes, molecular diffusion length scales become significant to the printing process. Understanding these molecular reaction and diffusion processes is imperative for advancing VAM to a usable technology. These processes are experimentally very difficult to monitor and measure. Herein, VirtualVAM ‐ a simulation framework for modeling the tomographic VAM process, is developed and experimentally validated. VirtualVAM simulates reaction, diffusion, and heat generation processes over the course of a print with single‐voxel resolution. From a few experimentally‐determined input parameters and a set of images for projection, VirtualVAM is able to generate a large spatio‐temporal data set for any given tomographic VAM print. Using VirtualVAM, a number of experimentally‐unattainable aspects of the VAM process are investigated such as single‐voxel conversion profiles, effect of molecular oxygen, and stopping time determination. VirtualVAM also enables the optimization of exposure patterns to further improve contrast between in‐part and out‐of‐part delivered dose.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Machine Learning and Economic Models to Enable Risk-Informed Condition Based Maintenance of a Nuclear Plant Asset

The primary objective of this research is to address challenges in the implementation of risk-informed, condition-based predictive maintenance (PdM), which reduces operating costs while still maintaining the safety and reliability of commercial nuclear power plants (NPPs). To achieve the objective, risk models are being developed by taking advantage of advancements in data analytics, deep learning, machine learning (ML), and artificial intelligence (AI). The notable outcomes presented in the report include ? Development of a ML models using heterogeneous plant process and vibration data collected at different spatial and temporal resolutions from the Salem?s CWS to diagnose a circulating water pump (CWP) failure based on salient fault signatures. The developed diagnostic models are extendable to other faults associated with CWPs and CWP motors given associated fault signatures. ? Development of a natural language processing (NLP) technique to automatically classify the WO data into different categories. The developed NLP technique was validated on independent WO data. This automates the tedious and time-consuming activity of mining and classifying WOs by subject matter experts. ? Estimation of mean time between downtime (i.e., time duration between time instances when 1 or more CWPs are not available) and developed an approach to establish reliability of CWS components using unstructured WO data along with CWS plant process data. ? Formulation of economic model based on Markov chain models. The parameters of associated with the transition rate between different states of Markov chain models were estimated using WO data. The economic model formulation and discussion captures both time-independent and time-dependent parameter variation, leading to risk-informed decision-making.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Unprecedented cloud resolution in a GPU-enabled full-physics atmospheric climate simulation on OLCF’s summit supercomputer

Clouds represent a key uncertainty in future climate projection. While explicit cloud resolution remains beyond our computational grasp for global climate, we can incorporate important cloud effects through a computational middle ground called the Multi-scale Modeling Framework (MMF), also known as Super Parameterization. This algorithmic approach embeds high-resolution Cloud Resolving Models (CRMs) to represent moist convective processes within each grid column in a Global Climate Model (GCM). The MMF code requires no parallel data transfers and provides a self-contained target for acceleration. This study investigates the performance of the Energy Exascale Earth System Model-MMF (E3SM-MMF) code on the OLCF Summit supercomputer at an unprecedented scale of simulation. Hundreds of kernels in the roughly 10K lines of code in the E3SM-MMF CRM were ported to GPUs with OpenACC directives. A high-resolution benchmark using 4600 nodes on Summit demonstrates the computational capability of the GPU-enabled E3SM-MMF code in a full physics climate simulation.

58 GEOSCIENCES↗

Non-averaged single-molecule tertiary structures reveal RNA self-folding through individual-particle cryo-electron tomography

Large-scale and continuous conformational changes in the RNA self-folding process present significant challenges for structural studies, often requiring trade-offs between resolution and observational scope. Here, we utilize individual-particle cryo-electron tomography (IPET) to examine the post-transcriptional self-folding process of designed RNA origami 6-helix bundle with a clasp helix (6HBC). By avoiding selection, classification, averaging, or chemical fixation and optimizing cryo-ET data acquisition parameters, we reconstruct 120 three-dimensional (3D) density maps from 120 individual particles at an electron dose of no more than 168 e - Å -2 , achieving averaged resolutions ranging from 23 to 35 Å, as estimated by Fourier shell correlation (FSC) at 0.5. Each map allows us to identify distinct RNA helices and determine a unique tertiary structure. Statistical analysis of these 120 structures confirms two reported conformations and reveals a range of kinetically trapped, intermediate, and highly compacted states, demonstrating a maturation folding landscape likely driven by helix-helix compaction interactions.

36 MATERIALS SCIENCE↗

Image data processing of earth resources management

The Earth Resources Technology Satellite (ERTS-1) was launched on July 23, 1972. Since that date, the vehicle has been acquiring and transmitting to earth a vast amount of information relating to the earth's resources. Scientific investigators throughout the world have been analyzing photographic products produced from this data with significant results. Recently, there has been a major shift of emphasis from the visual analysis of photo products to the use of sophisticated digital information extraction techniques. Specialized equipment, such as the GE IMAGE 100 System, has been developed that operates directly from Computer Compatible Tapes, (CCT’s), which contain preprocessed digital data acquired from the ERTS spacecraft. Analysis of CCT data avoids the losses in image resolution and quality which are inherent to all photo processing techniques, thereby greatly increasing the utility of ERTS data. Future ground processing systems will turn out fully corrected (radiometric and geometric) digital tapes which will further increase the utility of ERTS data. This paper is presented in two parts: the first part deals with the subject of present and future generations of image processing and information extraction systems under development at the General Electric Company; the second part describes in more detail the design and operation of GE1s interactive multispectral information extraction systems, IMAGE 100, and discusses results of analyses of ERTS data over a number of U.S. sites.

A W DeSio↗

Aerosol‐Jet‐Printable Covalent Organic Framework Colloidal Inks and Temperature‐Sensitive Nanocomposite Films

Abstract With molecularly well‐defined and tailorable 2D structures, covalent organic frameworks (COFs) have emerged as leading material candidates for chemical sensing, storage, separation, and catalysis. In these contexts, the ability to directly and deterministically print COFs into arbitrary geometries will enable rapid optimization and deployment. However, previous attempts to print COFs have been restricted by low spatial resolution and/or post‐deposition polymerization that limits the range of compatible COFs. Here, these limitations are overcome with a pre‐synthesized, solution‐processable colloidal ink that enables aerosol jet printing of COFs with micron‐scale resolution. The ink formulation utilizes the low‐volatility solvent benzonitrile, which is critical to obtaining homogeneous printed COF film morphologies. This ink formulation is also compatible with other colloidal nanomaterials, thus facilitating the integration of COFs into printable nanocomposite films. As a proof‐of‐concept, boronate‐ester COFs are integrated with carbon nanotubes (CNTs) to form printable COF‐CNT nanocomposite films, in which the CNTs enhance charge transport and temperature sensing performance, ultimately resulting in high‐sensitivity temperature sensors that show electrical conductivity variation by 4 orders of magnitude between room temperature and 300 °C. Overall, this work establishes a flexible platform for COF additive manufacturing that will accelerate the incorporation of COFs into technologically significant applications.

2D materials↗

Spatio–Temporal Machine Learning for Regional to Continental Scale Terrestrial Hydrology

Integrated hydrologic models can simulate coupled surface and subsurface processes but are computationally expensive to run at high resolutions over large domains. Here we develop a novel deep learning model to emulate subsurface flows simulated by the integrated ParFlow–CLM model across the contiguous US. We compare convolutional neural networks like ResNet and UNet run autoregressively against our novel architecture called the Forced SpatioTemporal RNN (FSTR). The FSTR model incorporates separate encoding of initial conditions, static parameters, and meteorological forcings, which are fused in a recurrent loop to produce spatiotemporal predictions of groundwater. We evaluate the model architectures on their ability to reproduce 4D pressure heads, water table depths, and surface soil moisture over the contiguous US at 1 km resolution and daily time steps over the course of a full water year. The FSTR model shows superior performance to the baseline models, producing stable simulations that capture both seasonal and event–scale dynamics across a wide array of hydroclimatic regimes. The emulators provide over 1,000× speedup compared to the original physical model, which will enable new capabilities like uncertainty quantification and data assimilation for integrated hydrologic modeling that were not previously possible. Our results demonstrate the promise of using specialized deep learning architectures like FSTR for emulating complex process–based models without sacrificing fidelity.

54 ENVIRONMENTAL SCIENCES↗