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DOE OSTI2020

Characterization and identification of HPC applications at leadership computing facility

High Performance Computing (HPC) is an important method for scientific discovery via large-scale simulation, data analysis, or artificial intelligence. Leadership-class supercomputers are expensive, but essential to run large HPC applications. The Petascale era of supercomputers began in 2008, with the first machines achieving performance in excess of one petaflops, and with the advent of new supercomputers in 2021 (e.g., Aurora, Frontier), the Exascale era will soon begin. However, the high theoretical computing capability (i.e., peak FLOPS) of a machine is not the only meaningful target when designing a supercomputer, as the resources demand of applications varies. A deep understanding of the characterization of applications that run on a leadership supercomputer is one of the most important ways for planning its design, development and operation. In order to improve our understanding of HPC applications, user demands and resource usage characteristics, we perform correlative analysis of various logs for different subsystems of a leadership supercomputer. This analysis reveals surprising, sometimes counter-intuitive patterns, which, in some cases, conflicts with existing assumptions, and have important implications for future system designs as well as supercomputer operations. For example, our analysis shows that while the applications spend significant time on MPI, most applications spend very little time on file I/O. Combined analysis of hardware event logs and task failure logs show that the probability of a hardware FATAL event causing task failure is low. Combined analysis of control system logs and file I/O logs reveals that pure POSIX I/O is used more widely than higher level parallel I/O. Based on holistic insights of the application gained through combined and co-analysis of multiple logs from different perspectives and general intuition, we engineer features to "fingerprint" HPC applications. We use t-SNE (a machine learning technique for dimensionality reduction) to validate the explainability of our features and finally train machine learning models to identify HPC applications or group those with similar characteristic. To the best of our knowledge, this is the first work that combines logs on file I/O, computing, and inter-node communication for insightful analysis of HPC applications in production.

Liu, Zhengchun↗

NASA NTRS1994

Primitive Xe in the atmospheres of Earth and mars

Published data on Xe isotope compositions in primitive carbonaceous meteorites are examined using multidimensional correlation analysis. Distribution of the Xe data in multidimensional data space, except for (129)Xe, can be characterized by a single component, whose isotope composition is identical to 'H plus L minus Xe'. Additional small contributions to the data variations, less than 1 percent of total variations, can be attributed to 'S minus Xe' as well as atmospheric contamination. Isotopic composition of primitive Xe common to the Earth's atmosphere and carbonaceous meteorites are determined with the same assumption as adopted by Pepin and Phinney: primitive Xe is precisely related to fission-free Xe in the Earth's atmosphere by mass fractionation. The determined isotopic composition of primitive Xe is closer to Solar-type Xe, rather than U-Xe (and the primitive Xe estimated from chondrite-achondrite correlation. Hence, the present published data on Xe isotope compositions in meteorites do not seem to require any special component for the primitive Xe common to the Earth's atmosphere and carbonaceous meteorites. Thus Earth's accreting planetesimals would have trapped Xe from the surrounding nebula gases where Xe isotope composition is identical to Solar-type Xe. The trapped Xe was subsequently subject to isotopic fractionation due to gravitational separation as planetesimals grew. Finally fissiogenic Xe from (244)Pu was added to form the present Xe isotope composition of the Earth's atmosphere. The amount of fissiogenic (136)Xe is estimated to be 2.6 percent of the total amount of (136)Xe in the atmosphere, which is about a half of that estimated by Pepin and Phinney (4.65 percent).

Igarashi, G.↗

NASA NTRS1975

Study of noise sources in a subsonic fan using measured blade pressures and acoustic theory

Sources of noise in a 1.4 m (4.6 ft) diameter subsonic tip speed propulsive fan running statically outdoors are studied using a combination of techniques. Signals measured with pressure transducers on a rotor blade are plotted in a format showing the space-time history of inlet distortion. Study of these plots visually and with statistical correlation analysis confirms that the inlet flow contains long, thin eddies of turbulence. Turbulence generated in the boundary layer of the shroud upstream of the rotor tips was not found to be an important noise source. Fan noise is diagnosed by computing narrowband spectra of rotor and stator sound power and comparing these with measured sound power spectra. Rotor noise is computed from spectra of the measured blade pressures and stator noise is computed using the author's stator noise theory. It is concluded that the rotor and stator sources contribute about equally at frequencies in the vicinity of the first three harmonics of blade passing frequency. At higher frequencies, the stator contribution diminishes rapidly and the rotor/inlet turbulence mechanism dominates. Two parametric studies are performed by using the rotor noise calculation procedure which was correlated with test. In the first study, the effects on noise spectrum and directivity are calculated for changes in turbulence properties, rotational Mach number, number of blades, and stagger angle. In the second study the influences of design tip speed and blade number on noise are evaluated.

Hanson, D. B.↗

DOE OSTI2020

Speckle correlation as a monitor of X-ray free-electron laser induced crystal lattice deformation

X-ray free-electron lasers (X-FELs) present new opportunities to study ultrafast lattice dynamics in complex materials. While the unprecedented source brilliance enables high fidelity measurement of structural dynamics, it also raises experimental challenges related to the understanding and control of beam-induced irreversible structural changes in samples that can ultimately impact the interpretation of experimental results. This is also important for designing reliable high performance X-ray optical components. In this work, X-FEL beam-induced lattice alterations are investigated by measuring the shot-to-shot evolution of near-Bragg coherent scattering from a single crystalline germanium sample. It is shown that X-ray photon correlation analysis of sequential speckle patterns measurements can be used to monitor the nature and extent of lattice rearrangements. Additionally, abrupt, irreversible changes are observed following intermittent high-fluence monochromatic X-ray pulses, thus revealing the existence of a threshold response to X-FEL pulse intensity.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

NASA NTRS2004

Crash Simulation of a Vertical Drop Test of a Commuter-Class Aircraft

A finite element model of an ATR42-300 commuter-class aircraft was developed and a crash simulation was executed. Analytical predictions were correlated with data obtained from a 30-ft/s (9.14-m/s) vertical drop test of the aircraft. The purpose of the test was to evaluate the structural response of the aircraft when subjected to a severe, but survivable, impact. The aircraft was configured with seats, dummies, luggage, and other ballast. The wings were filled with 8,700 lb. (3,946 kg) of water to represent the fuel. The finite element model, which consisted of 57,643 nodes and 62,979 elements, was developed from direct measurements of the airframe geometry. The seats, dummies, luggage, fuel, and other ballast were represented using concentrated masses. The model was executed in LS-DYNA, a commercial code for performing explicit transient dynamic simulations. Predictions of structural deformation and selected time-history responses were generated. The simulation was successfully validated through extensive test-analysis correlation.

Jackson, Karen E.↗

DOE OSTI2022

A Novel Method for Preoperative Positioning of Total Ankle Replacement Using 3D Digital Model

Abstract Objective To establish a digital model of the ankle joint through 3D imaging technology and explore the preoperative placement of ankle replacement prostheses. Methods Computed tomography images of intact ankle joints from 54 cases in the outpatient and inpatient departments of our hospital were collected; according to the INBONE® total ankle system surgery process, the surgery model and surgical osteotomy were finished using MIMICS based on computer simulation method. The shortest distance was measured between the center point and the anterior, posterior, medial, and lateral, respectively, to ensure the precise position of the ankle replacement prosthesis by digital simulation surgery. The relationship between the two variables was analyzed by bivariate correlation analysis. Results The dataset of this study included 48 cases of the sub‐data set (26 males and 22 females) and included 27 cases of left ankle and 21 cases of right ankle. The average medial malleolar angle was 18.67°± 2.87°, the average amount of bone resection was 12.13 ± 1.86 cm 3 , the mid‐anterior distance was 1.72 ± 0.19 cm, the mid‐posterior distance was 2.00 ± 0.19 cm, the ratio of mid‐anterior to mid‐posterior was 0.87, the mid‐medial distance was 1.26 ± 0.17 cm, the mid‐lateral distance was 1.19 ± 0.16 cm, and the ratio of mid‐medial to mid‐lateral was 1.06. After osteotomy, the anteroposterior diameter was 3.73 ± 0.32 cm, the transverse diameter was 2.46 ± 0.27 cm, and the ratio of anteroposterior diameter to transverse diameter was 1.53. In the bottom view, the shape after osteotomy is rectangular. The mid‐anterior distance was strongly negatively correlated with age, the mid‐anterior distance and the amount of bone resection, the mid‐medial distance and the amount of bone resection, the mid‐lateral distance and the amount of bone resection, the mid‐lateral distance and the anteroposterior diameter, the anteroposterior diameter and the transverse diameter were all strongly positively correlated. Conclusion The projection point of the lower tibia centerline on the tibial horizontal osteotomy surface is located at a position slightly anterior to the midpoint of the transverse diameter after ankle arthroplasty. The rational positioning of the total ankle replacement is located at both a position slightly anterior to the midpoint of the transverse diameter and midpoint of the anteroposterior diameter, which can be used as a reference method before total ankle arthroplasty surgery.

Wu, Shi‐xun↗

DOE OSTI2021

Discovery and analysis of low-surface-brightness galaxies in the environment of NGC 1052

The environment of NGC 1052 has recently attracted much attention because of the presence of low-surface-brightness galaxies (LSBGs) with apparently “exotic” properties, making it a region of high interest for the detection of new objects. Here, we used public deep photometric data from the Dark Energy Camera Legacy Survey to carry out a comprehensive search for LSBGs over a wide region of 6 × 6 degrees, equivalent to 2 × 2 Mpc at the distance of NGC 1052. We detected 42 LSBGs with r eff > 5 arcsec and μ g (0) > 24 mag arcsec -2 , of which 20 are previously undetected objects. Among all the newly detected objects, RCP 32 stands out with extreme properties: r eff = 23.0 arcsec and $\langle$μ g $\rangle$ eff = 28.6 mag arcsec -2 . This makes RCP 32 one of the lowest surface brightness galaxies ever detected through integrated photometry, located at just 10 arcmin from the extensively studied NGC 1052-DF2. We explored the presence of globular clusters (GCs) in the LSBGs. We marginally detected a GC system in RCP 32, and argue that this LSBG is of great interest for follow-up observations given its extremely low baryon density. After analyzing the distribution of galaxies with available spectroscopy, we identified a large-scale structure of approximately 1 Mpc that is well isolated in redshift space and centered on NGC 1052. The spatial correlation analysis between the LSBGs and this large-scale structure suggests their association. However, when exploring the distribution of effective radius, we find an overpopulation of large LSBGs (r eff > 15 arcsec) located close to the line of sight of NGC 1052. We argue that this is suggestive of a substructure with similar radial velocity in sight projection, but at a closer distance, to which some of these apparently larger LSBGs could be associated. However, possible effects derived from tidal interactions are worthy of further study. Our work expands the catalog of LSBGs with new interesting objects and provides a detailed environmental context for the study of LSBGs in this region.

79 ASTRONOMY AND ASTROPHYSICS↗

NASA NTRS1993

Age and thermochronology of K-feldspars from the Manson Impact Structure

As a contribution to the effort to obtain a precise age for the Manson Impact Structure, we are approaching the problem from a thermo chronological perspective, with the goal of extracting an age from Ar-40/Ar-39 age-spectrum analysis of partially overprinted K-feldspars taken from granitoid clasts. We find that shocked feldspars from Manson generally show a strong overprint in their age spectra, with more than 50 percent of each spectrum being reset. The reset portions of the age spectra correspond to gas lost from very small diffusion domains, and a characteristic of the Manson samples is the very large range in apparent diffusion dimensions that they display, with the smallest domains being some 400 times smaller than the largest domains. It is also noteworthy that the small domains comprise a substantial portion of the volume of the feldspars (50 percent or more). These observations are consistent with the extreme shock experienced by these samples. In detail, the spectra we have measured to date are saddle-shaped and show minimum ages of between 67 and 72 Ma, which we interpret to be maximum estimates for the age of the impact. In the case of one sample (M1-678.3; K-feldspar from a large syenite block located well below the apparent melt-matrix breccia in the M1 borehole), isotope correlation analysis suggests the presence of a non-atmospheric trapped Ar component (Ar-40/Ar-36 of 660 plus or minus 40), and an age of about 65.3 plus or minus 0.5 Ma (2 sigma). Our interpretation of our results is that the shock of impact greatly reduced the diffusion-domain sizes of our samples, making them susceptible to significant Ar loss during heating associated with impact. It appears that while our feldspars were partially open to Ar loss, they equilibrated with a non-atmospheric Ar component, probably related to impact-related degassing of old basement around the impact site.

Zeitler, P. K.↗

DOE OSTI2020

Periodic Narrowband Radio Wave Emissions and Inward Plasma Transport at Saturn's Magnetosphere

The abrupt brightening of an Energetic Neutral Atom (ENA) blob or cloud has been interpreted as plasma injection in the Kronian magnetosphere (termed ENA injection herein). Morphologically, there appears to be two types of abrupt ENA cloud brightening: (1) the brightening of a large cloud usually seen at distances >10–12 R {sub s} (R {sub s} ∼ 60,268 km) in the midnight or postmidnight region; (2) the brightening of a smaller cloud usually seen at distances <10–12 R {sub s} around 21–03 magnetic local time. Among many radio waves observed at Saturn, type 2 ENA injections correlate best with the 5 kHz narrowband (NB) waves. Using Cassini Ion and Neutral Camera (INCA) and Radio and Plasma Wave Science (RPWS) data, we examine the periodicities of the type 2 ENA injections and the 5 kHz NB emissions as well as their cross-correlations, which have been previously used to measure the lag times or phase differences. Because correlational analysis can only establish linear relationships, we also use mutual information to establish linear and nonlinear relationships. On average, the peak of the 5 kHz NB emission lags those of the type 2 ENA injection by about a few minutes to 2 hr. The injection of hot plasma to the inner magnetosphere can lead to temperature anisotropy, which can generate electrostatic upper hybrid waves, which upon encountering the high-density gradient at the outer edge of the Enceladus density torus, can mode convert to Z mode and then to O mode. The 5 kHz NB waves commonly propagate in the O mode.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2025

Dynamics of Thermally Driven Domain Transformation in Ferroelectric Thin Films

An important feature in ultrathin ferroelectric films is the spontaneous formation of nanoscale polarization domain patterns. Epitaxial strain can greatly increase the ferroelectric transition temperature such that films can be in the ferroelectric state during growth. On the other hand, depolarization fields compete with ferroelectricity in ultrathin films, and, consequently, the optimal domain configuration during growth is a moving target. Under these conditions it is readily possible for a grown film to be in a nonequilibrium domain configuration. As the energy landscape in the system is quite complex, the relaxation dynamics by which a system can evolve towards the true equilibrium configuration are also quite interesting. Here, to capture the details of this process we used Bragg-geometry x-ray photon correlation spectroscopy (XPCS), in which x-ray scattering speckle patterns contain the information from the domain arrangements inside the film. With modest heating (∼15⁢0 °C) domain relaxation from 𝑇 (tetragonal) to 𝑀 𝐶 (monoclinic) was observed in BaTiO 3 films grown on ultrathin ferroelectric PbTiO 3 layers. Two-time correlation analysis reveals fascinating details associated with sticking points and reversals in the process.

36 MATERIALS SCIENCE↗

NASA NTRS2010

Relationship Between Satellite-Derived Snow Cover and Snowmelt-Runoff Timing and Stream Power in the Wind River Range, Wyoming

Earlier onset of springtime weather including earlier snowmelt has been documented in the western United States over at least the last 50 years. Because the majority (>70%) of the water supply in the western U.S. comes from snowmelt, analysis of the declining spring snowpack (and shrinking glaciers) has important implications for streamflow management. The amount of water in a snowpack influences stream discharge which can also influence erosion and sediment transport by changing stream power, or the rate at which a stream can do work such as move sediment and erode the stream bed. The focus of this work is the Wind River Range (WRR) in west-central Wyoming. Ten years of Moderate-Resolution Imaging Spectroradiometer (MODIS) snow-cover, cloud- gap-filled (CGF) map products and 30 years of discharge and meteorological station a are studied. Streamflow data from six streams in the WRR drainage basins show lower annual discharge and earlier snowmelt in the decade of the 2000s than in the previous three decades, though no trend of either lower streamflow or earlier snowmelt was observed using MODIS snow-cover maps within the decade of the 2000s. Results show a statistically-significant trend at the 95% confidence level (or higher) of increasing weekly maximum air temperature (for three out of the five meteorological stations studied) in the decade of the 1970s, and also for the 40-year study period. MODIS- derived snow cover (percent of basin covered) measured on 30 April explains over 89% of the variance in discharge for maximum monthly streamflow in the decade of the 2000s using Spearman rank correlation analysis. We also investigated stream power for Bull Lake Creek Above Bull Lake from 1970 to 2009; a statistically-significant trend toward reduced stream power was found (significant at the 90% confidence level). Observed changes in streamflow and stream power may be related to increasing weekly maximum air temperature measured during the 40-year study period. The strong relationship between percent of basin covered and streamflow indicates that MODIS data is useful for predicting streamflow, leading to improved reservoir management.

Hall, Dorothy K.↗

NASA NTRS2010

Relationship Between Satellite-Derived Snow Cover and Snowmelt-Runoff Timing and Stream Power in the Wind River Range, Wyoming

Earlier onset of springtime weather including earlier snowmelt has been documented in the western United States over at least the last 50 years. Because the majority (>70%) of the water supply in the western U.S. comes from snowmelt, analysis of the declining spring snowpack (and shrinking glaciers) has important implications for streamflow management. The amount of water in a snowpack influences stream discharge which can also influence erosion and sediment transport by changing stream power, or the rate at which a stream can do work such as move sediment and erode the stream bed. The focus of this work is the Wind River Range (WRR) in west-central Wyoming. Ten years of Moderate-Resolution Imaging Spectroradiometer (MODIS) snow-cover, cloud- gap-filled (CGF) map products and 30 years of discharge and meteorological station data are studied. Streamflow data from six streams in the WRR drainage basins show lower annual discharge and earlier snowmelt in the decade of the 2000s than in the previous three decades, though no trend of either lower streamflow or earlier snowmelt was observed using MODIS snow-cover maps within the decade of the 2000s. Results show a statistically-significant trend at the 95% confidence level (or higher) of increasing weekly maximum air temperature (for three out of the five meteorological stations studied) in the decade of the 1970s, and also for the 40-year study period. MODIS-derived snow cover (percent of basin covered) measured on 30 April explains over 89% of the variance in discharge for maximum monthly streamflow in the decade of the 2000s using Spearman rank correlation analysis. We also investigated stream power for Bull Lake Creek Above Bull Lake from 1970 to 2009; a statistically-significant end toward reduced stream power was found (significant at the 90% confidence level). Observed changes in streamflow and stream power may be related to increasing weekly maximum air temperature measured during the 40-year study period. The strong relationship between percent of basin covered and streamflow indicates that MODIS data is useful for predicting streamflow, leading to improved reservoir management

Hall, Dorothy K.↗

DOE OSTI2022

High manganese redox variability and manganate predominance in temperate soil profiles as determined by X-ray absorption spectroscopy

Manganese speciation is a key to understanding the fate of contaminants, nutrients, and organic matter in soils. To date, quantification of Mn species in bulk soils has been performed mainly by sequential extraction methods and rarely supported by spectroscopic analysis. In order to obtain quantitative information on the Mn species inventory of soils, we investigated 46 soil horizons (<2-mm fraction, 45.1–2,280 mg/kg Mn) of nine typical Central European soils (Cambisols, Chernozems, Luvisols, Podzol, Stagnosol) by chemical Mn analyses and Mn K-edge X-ray absorption spectroscopy, and related speciation results to major soil properties. Amounts of Mn 2+ , Mn 3+ , and Mn 4+ and the average oxidation state of Mn were evaluated by linear combination fitting (LCF) of X-ray absorption near edge structure (XANES) spectra. Additionally, we used extended X-ray absorption fine structure (EXAFS) spectroscopy to identify and quantify major Mn species. For this, EXAFS spectra of 20 organic and mineral soil samples from five soils (Cambisols, Chernozem, Luvisol) were analyzed by LCF and shell fitting. XANES analyses revealed a high Mn redox variability in organic surface layers, with Mn 2+ being most abundant (≤100%, $\overline{x}$ = 54%), followed by Mn 3+ (≤80%, $\overline{x}$ = 32%) and Mn 4+ (≤55%, $\overline{x}$ = 14%). Mineral soil horizons contained significantly less Mn 2+ (≤56%, $\overline{x}$ = 23%), about equal quantities of Mn 3+ (≤68%, $\overline{x}$ = 31%), and were enriched in Mn 4+ (≤89%, $\overline{x}$ = 46%). EXAFS analyses implied the presence of six major Mn species groups: manganates, organically complexed Mn, Mn(III) oxyhydroxides, silicate-bound Mn, Mn oxides without tunnel- or layer structure, and physisorbed Mn. In litter horizons, Mn was mainly present in organic complexes (58–91%, $\overline{x}$ = 78%) and as physisorbed Mn (≤15%), but individual horizons also comprised manganates, Mn(III) oxyhydroxides, and silicate-bound Mn. Manganates, likely mixtures of phyllomanganates with hexagonal layer symmetry and tectomanganates, dominated in all mineral soil horizons (37–94%, $\overline{x}$ = 67%). Correlation analysis showed that manganates dissolve completely during dithionite-citrate and acid ammonium oxalate extractions, and suggested that Mn 4+ -rich manganates preferentially form under less acidic soil conditions, partly by oxidation of organically complexed Mn(II), and that they are enriched in the soil clay fraction. Mineral soil horizons also contained minor quantities of organically complexed Mn (≤39%, $\overline{x}$ = 11%), silicate-bound Mn (≤30%, $\overline{x}$ = 8%), Mn(III) oxyhydroxides (≤37%, $\overline{x}$ = 7%), Mn oxides without tunnel- or layer structure (≤18%, $\overline{x}$ = 5%), and physisorbed Mn (≤14%, $\overline{x}$ <1%). The detection of Mn(III) oxyhydroxides such as feitknechtite (β-MnOOH) or groutite (α-MnOOH) as well as the spinel hausmannite (Mn 3 O 4 ) in acidic soils is remarkable, since their formation is normally linked to neutral or alkaline pH conditions. Minor contributions of silicate-bound Mn indicate the release of Mn from primary minerals already at early stages of soil formation, and low concentrations of physisorbed Mn suggest that exchangeable Mn is rapidly converted into manganates in oxic soils. In conclusion, the predominance of manganates in mineral soils has far-reaching implications for the functioning of soils and biogeochemical element cycles, as these minerals play an important role in metal binding, plant nutrition, and redox-related processes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

A Standardized Analysis Process Using Digital Image Correlation to Calculate In Situ Cladding Strain from Modified Burst Tests for Fuel Performance Code Validation

Historical data collection on nuclear fuel cladding materials has focused on generating a statistically significant amount of data to assess the material and its failure behavior. Furthermore, data generated to support material model and failure criteria development were previously posttest evaluations, so a large number of tests was required to gain new understanding. A way to expedite this process is to develop techniques capable of generating large, high-fidelity data sets from a single test with lower uncertainty or quantified uncertainty. One such example of this approach is Oak Ridge National Laboratory’s use of modified burst tests (MBTs) to analyze the mechanical behavior and failure conditions of cladding during a simulated reactivity-initiated accident (RIA). Each test incorporates digital image correlation (DIC) analysis techniques that are used to assess the accumulated strain in situ, as well as eventual cladding failure. This work has been fruitful in defining strain-to-failure conditions for materials like silicon carbide (SiC) fiber–reinforced/SiC matrix composite tubes (SiC/SiC), iron-chromium-aluminum (FeCrAl) alloy tubes, and chromium-coated Zircaloy-4 tubes. However, there are numerous DIC software available, including open-source and proprietary software. The different DIC software use various algorithms to process images and calculate displacement values. Using these different software and algorithms can lead to varying results, and perhaps larger-than-expected uncertainties. In the present study, previously published MBT data encompassing a variety of test conditions were reanalyzed with two different DIC software to assess the variance in the calculated strain results. The data consisted of SiC/SiC, FeCrAl, and chromium-coated Zircaloy-4 tubes. Plots of the calculated strains during the transient revealed good agreement between the two DIC software. The average root-mean-square errors between the two software was 0.20% strain, which is slightly larger than a previously reported error value for these tests. In conclusion, this variance in results is low enough that this analysis method can be used for code validation.

Reactivity-initiated accident↗

DOE OSTI2022

Transcriptome and metabolome integration in sugarcane through culm development

Abstract Sugarcane (Saccharum sp.) is a tropical and subtropical C4 plant with a high photosynthetic and carbon assimilation efficiency that stores sucrose. Culm biomass is also composed of bagasse fibre, a by‐product of the sugarcane industry. This high‐yielding grass, high in sucrose and lignocellulosic biomass, is considered an optimal feedstock as an alternative to fossil fuels and to produce a broad range of high‐value biomaterials. The ideal sugarcane production system would optimise the relative production of sugar and these new products. Multi‐omics correlation analysis was used to generate a global view of the essential metabolic pathways identifying critical genes involved in carbon partitioning during different stages of development. This research employed an unprecedented metabolic and transcriptomic dataset of 360 samples from a selection of 1440 culms of 24 genotypes at five different development stages. Chemical composition and metabolome analysis showed an increase through the culm development of lignin, sucrose, carbon, and amino acids such as aspartic acid, serine, alanine, methionine, threonine 3‐cyano‐L‐alanine, and citric acid. Transcriptome analysis revealed functionalities such as transcription, nucleotide transport and metabolism, and the biosynthesis of amino acids that are highly activated during the immature stage and highly down‐regulated during the most mature age.

Perlo, Virginie↗

DOE OSTI2021

Molecular basis for higher affinity of SARS-CoV-2 spike RBD for human ACE2 receptor

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has caused substantially more infections, deaths, and economic disruptions than the 2002-2003 SARSCoV. The key to understanding SARS-CoV-2's higher infectivity lies partly in its host receptor recognition mechanism. Experiments show that the human angiotensin converting enzyme 2 (ACE2) protein, which serves as the primary receptor for both CoVs, binds to the receptor binding domain (RBD) of CoV-2's spike protein stronger than SARS-CoV's spike RBD. The molecular basis for this difference in binding affinity, however, remains unexplained from X-ray structures. To go beyond insights gained from X-ray structures and investigate the role of thermal fluctuations in structure, we employ all-atom molecular dynamics simulations. Microseconds-long simulations reveal that while CoV and CoV-2 spike-ACE2 interfaces have similar conformational binding modes, CoV-2 spike interacts with ACE2 via a larger combinatorics of polar contacts, and on average, makes 45% more polar contacts. Correlation analysis and thermodynamic calculations indicate that these differences in the density and dynamics of polar contacts arise from differences in spatial arrangements of interfacial residues, and dynamical coupling between interfacial and non-interfacial residues. Furthermore, these results recommend that ongoing efforts to design spike-ACE2 peptide blockers will benefit from incorporating dynamical information as well as allosteric coupling effects.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2026

Evaluating ecosystem water use efficiency under drought stress: a case study of the Helan Mountain region, northwest China

Context Water use efficiency (WUE) is a fundamental ecological indicator links carbon assimilation and water loss in terrestrial ecosystems. Understanding its responses to drought stress is essential for adaptive ecosystem management, particularly in climate-sensitive mountain landscapes. Objectives This study aimed to investigate drought-driven variations in WUE across major vegetation types in the Helan Mountain region of Northwest China. Specifically, we sought to identify dominant ecological drivers of WUE variability and to disentangle their relative importance and causal pathways. Methods We quantified WUE using the Moderate Resolution Imaging Spectroradiometer (MODIS) products and the Drought Severity Index (DSI) data from 2001 to 2020. To examine WUE – drought relationships across contrasting vegetation types, we employed a spatially explicit analytical framework integrating Random Forest (RF) modeling, partial correlation analysis, and structural equation modeling (SEM). Results Regional WUE exhibited relatively stable interannual dynamics, yet pronounced spatial heterogeneity that was strongly modulated by drought conditions. Vegetation properties, particularly Leaf Area Index (LAI) and Normalized Difference Vegetation Index (NDVI), emerged as the dominant determinants of WUE, with NDVI alone explaining over 20% of its spatial variance in forest and grassland during non-drought periods. SEM analyses revealed that climate forcing influenced WUE mainly through indirect pathways mediated by soil moisture availability and vegetation structural dynamics, rather than through direct climatic controls. Among all regulating factors, LAI acted as the central control node governing ecosystem carbon–water coupling. In contrast, short-term climatic stress, especially atmospheric demand and drought duration, exerted weak or negative direct effects on WUE. Ecosystem-specific responses were observed, with croplands mainly regulated by soil water availability, whereas forests and grasslands showed more sensitive to atmospheric drought stress. Together, these results reveal a hierarchical control framework where soil–vegetation interactions mediate climate impacts on WUE, driving strong spatial heterogeneity in drought responses across mountain landscapes. Conclusions Our findings highlight the pivotal role of indirect drought effects mediated by vegetation and soil processes in shaping ecosystem WUE. The identified soil–vegetation–climate regulatory hierarchy provides mechanistic insight into landscape–scale drought sensitivity and supports integrated modeling approaches for evaluating ecosystem resilience and sustainable management in arid mountain regions.

China↗

DOE OSTI2023

Influence of graphite geography on the yield of mechanically exfoliated few-layer graphene

Some of graphene's exciting properties that inspired countless studies over the last two decades are exclusive to defect-free, few-layer graphene (FLG, ≤4 layers) produced by mechanical exfoliation. Despite graphite exfoliation having been thoroughly studied, the influence of the graphite source on the successful exfoliation of FLG remains unexplored. Here, in this work, we examine the physicochemical properties and exfoliation performance of various graphite types (e.g., natural crystalline flake, natural vein, and synthetic) from around the globe (e.g., Alaska, Tanzania, China, etc.). We first established a normalization method for the facile comparison of FLG (Φ) yields between separately exfoliated graphites. Using this approach, we find that the relative yield of FLG ranges from 0% to 22% across graphite types, with regular natural crystalline flakes (NCF-R) performing the best overall (Φ NCF-R = 16% ± 5%). FLG yield was also found to depend on source geography, evidenced by Φ NCF-R ranging from 8% to 22% for NCF-R sourced from Alabama and Canada, respectively. We employed machine learning and Pearson correlation analysis to determine the graphite characteristics that govern FLG yield. Graphite source-dependent properties such as graphite surface area and mineral impurities, including aluminum and calcium, were found to be critically important. Our findings highlight the importance of the graphite source when trying to maximize the yield of mechanically exfoliated FLG and represent an important step toward producing higher quantities of defect-free FLG for graphene-based research.

42 ENGINEERING↗