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At least 127 records · Page 7

Tailoring poplar lignin without yield penalty by combining a null and haploinsufficient CINNAMOYL-CoA REDUCTASE2 allele

Lignin causes lignocellulosic biomass recalcitrance to enzymatic hydrolysis. Engineered low-lignin plants have reduced recalcitrance but often exhibit yield penalties, offsetting their gains in fermentable sugar yield. Here, CRISPR/Cas9-generated CCR2(–/*) line 12 poplars have one knockout CCR2 allele while the other contains a 3-bp deletion, resulting in a 114I115A-to-114T conversion in the corresponding protein. Despite having 10% less lignin, CCR2(–/*) line 12 grows normally. On a plant basis, the saccharification efficiency of CCR2(–/*) line 12 is increased by 25–41%, depending on the pretreatment. Analysis of monoallelic CCR2 knockout lines shows that the reduced lignin amount in CCR2(–/*) line 12 is due to the combination of a null and the specific haploinsufficient CCR2 allele. Analysis of another CCR2(–/*) line shows that depending on the specific CCR2 amino-acid change, lignin amount and growth can be affected to different extents. Furthermore, our findings open up new possibilities for stably fine-tuning residual gene function in planta.

59 BASIC BIOLOGICAL SCIENCES↗

Analysis and visualization of energy densities. II. Insights from linear-response time-dependent density functional theory calculations

Inspired by the analysis of Kohn–Sham energy densities by Nakai and coworkers, we extended the energy density analysis to linear-response time-dependent density functional theory (LR-TDDFT) calculations. Using ethylene–tetrafluoroethylene and oxyluciferin–water complexes as examples, distinctive distribution patterns were demonstrated for the excitation energy densities of local excitations (within a molecular fragment) and charge-transfer excitations (between molecular fragments). It also provided a simple way to compute the effective energy of both hot carriers (particle and hole) from charge-transfer excitations via an integration of the excitation energy density over the donor and acceptor grid points.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

A review on recent machine learning applications for imaging mass spectrometry studies

Imaging mass spectrometry (IMS) is a powerful analytical technique widely used in biology, chemistry, and materials science fields that continue to expand. IMS provides a qualitative compositional analysis and spatial mapping with high chemical specificity. The spatial mapping information can be 2D or 3D depending on the analysis technique employed. Due to the combination of complex mass spectra coupled with spatial information, large high-dimensional datasets (hyperspectral) are often produced. Therefore, the use of automated computational methods for an exploratory analysis is highly beneficial. The fast-paced development of artificial intelligence (AI) and machine learning (ML) tools has received significant attention in recent years. These tools, in principle, can enable the unification of data collection and analysis into a single pipeline to make sampling and analysis decisions on the go. There are various ML approaches that have been applied to IMS data over the last decade. Here, in this review, we discuss recent examples of the common unsupervised (principal component analysis, non-negative matrix factorization, k-means clustering, uniform manifold approximation and projection), supervised (random forest, logistic regression, XGboost, support vector machine), and other methods applied to various IMS datasets in the past five years. The information from this review will be useful for specialists from both IMS and ML fields since it summarizes current and representative studies of computational ML-based exploratory methods for IMS.

47 OTHER INSTRUMENTATION↗

Evidence for Rashba magnetism in ultrathin ferromagnet–heavy metal bilayers

Here, we show that ultrathin transition ferromagnet–heavy metal bilayers exhibit anomalous temperature- and electric bias-dependent behaviors near the Curie temperature, inconsistent with the usual Weiss magnetism. Characterization by several complementary techniques and analysis of the dependence on composition reveal that these effects originate from the interplay between interfacial spin-orbit interaction and magnetism, resulting in the emergence of a state with distinct magnetic and magnetoelectronic properties that can be described in the framework of the Rashba model as Rashba magnetism. Our findings open a route for the characterization and control of interfacial spin-orbit phenomena for efficient spin-orbitronic devices.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Nanoscale Compositional Mapping of Commercial LiNi 0.8 Co 0.15 Al 0.05 O 2 Cathodes Using Atom Probe Tomography

Nickel-rich cathodes provide improved specific capacity that lead to higher gravimetric energy density, critical for electric vehicles. However, poor long-term capacity retention at elevated temperatures/high C-rates (the rate of charge and discharge on a battery) stem from material issues: surface phase changes, corrosive side reactions with the electrolyte, ion dissolution and propagation of cracks. Introducing dopants, developing nanoscale surface coatings and graded core-shell structures have all improved the electrochemical performance of nickel-rich cathodes. However, a material level understanding on the effect of Li composition and distribution in Ni-rich cathodes is limited, due to a lack of characterization methods available that can directly image Li at the nanoscale. Hence, it is critical to establish methods such as atom probe tomography (APT), having both nanometer scale spatial resolution and high compositional sensitivity to quantitatively analyze battery cathodes. To fully realize its potential as a method for quantitative compositional analysis of commercial Li-ion batteries, we provide a comprehensive description of the challenges in sample preparation and analyze the dependency of the analysis parameters, specifically laser pulse energy on the measured stoichiometry of elements in a high Ni content cathode material; LiNi 0.8 Co 0.15 Al 0.05 O 2 (NCA). In this work, our findings show the stoichiometry variations cannot be explained by charge state ratios or Ga implantation damage alone during FIB preparation, indicating that additional factors such as crystallographic orientation may need to be considered to achieve quantitative nanoscale compositional analysis of such battery cathodes using APT.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

The First Detection of an Earthquake From a Balloon Using Its Acoustic Signature

Extreme temperature and pressure conditions on the surface of Venus present formidable technological challenges against performing ground-based seismology. Efficient coupling between the Venusian atmosphere and the solid planet theoretically allows the study of seismically generated acoustic waves using balloons in the upper atmosphere, where conditions are far more clement. However, earthquake detection from a balloon has never been demonstrated. We present the first detection of an earthquake from a balloon-borne microbarometer near Ridgecrest, CA in July 2019 and include a detailed analysis of the dependence of seismic infrasound, as measured from a balloon on earthquake source parameters, topography, and crustal and atmospheric structure. Our comprehensive analysis of seismo-acoustic phenomenology demonstrates that seismic activity is detectable from a high-altitude platform on Earth, and that Rayleigh wave-induced infrasound can be used to constrain subsurface velocities, paving the way for the detection and characterization of such signals on Venus.

58 GEOSCIENCES↗

Investigation of thermal hydraulic behavior of the High Temperature Test Facility's lower plenum via large eddy simulation

A high-fidelity computational fluid dynamics (CFD) analysis was performed using the Large Eddy Simulation (LES) model for the lower plenum of the High–Temperature Test Facility (HTTF), a ¼ scale test facility of the modular high temperature gas-cooled reactor (MHTGR) managed by Oregon State University. In most next–generation nuclear reactors, thermal stress due to thermal striping is one of the risks to be curiously considered. This is also true for HTGRs, especially since the exhaust helium gas temperature is high. In order to evaluate these risks and performance, organizations in the United States led by the OECD NEA are conducting a thermal hydraulic code benchmark for HTGR, and the test facility used for this benchmark is HTTF. HTTF can perform experiments in both normal and accident situations and provide high-quality experimental data. However, it is difficult to provide sufficient data for benchmarking through experiments, and there is a problem with the reliability of CFD analysis results based on Reynolds–averaged Navier–Stokes to analyze thermal hydraulic behavior without verification. To solve this problem, high-fidelity 3-D CFD analysis was performed using the LES model for HTTF. It was also verified that the LES model can properly simulate this jet mixing phenomenon via a unit cell test that provides experimental information. As a result of CFD analysis, the lower the dependency of the sub-grid scale model, the closer to the actual analysis result. In the case of unit cell test CFD analysis and HTTF CFD analysis, the volume-averaged sub-grid scale model dependency was calculated to be 13.0% and 9.16%, respectively. As a result of HTTF analysis, quantitative data of the fluid inside the HTTF lower plenum was provided in this paper. As a result of qualitative analysis, the temperature was highest at the center of the lower plenum, while the temperature fluctuation was highest near the edge of the lower plenum wall. The power spectral density of temperature was analyzed via fast Fourier transform (FFT) for specific points on the center and side of the lower plenum. FFT results did not reveal specific frequency-dominant temperature fluctuations in the center part. It was confirmed that the temperature power spectral density (PSD) at the top increased from the center to the wake. The vortex was visualized using the well-known scalar Q-criterion, and as a result, the closer to the outlet duct, the greater the influence of the mainstream, so that the inflow jet vortex was dissipated and mixed at the top of the lower plenum. Additionally, FFT analysis was performed on the support structure near the corner of the lower plenum with large temperature fluctuations, and as a result, it was confirmed that the temperature fluctuation of the flow did not have a significant effect near the corner wall. In addition, the vortices generated from the lower plenum to the outlet duct were identified in this paper. It is considered that the quantitative and qualitative results presented in this paper will serve as reference data for the benchmark.

97 MATHEMATICS AND COMPUTING↗

Fiducial-cosmology-dependent systematics for the DESI 2024 BAO analysis

When measuring the Baryon Acoustic Oscillations (BAO) scale from galaxy surveys, one typically assumes a fiducial cosmology when converting redshift measurements into comoving distances and also when defining input parameters for the reconstruction algorithm. A parameterised template for the model to be fitted is also created based on a (possibly different) fiducial cosmology. This model reliance can be considered a form of data compression, and the data is then analysed allowing that the true answer is different from the fiducial cosmology assumed. In this study, we evaluate the impact of the fiducial cosmology assumed in the BAO analysis of the Dark Energy Spectroscopic Instrument (DESI) survey Data Release 1 (DR1) on the final measurements in DESI 2024 III. We utilise a suite of mock galaxy catalogues with survey realism that mirrors the DESI DR1 tracers: the bright galaxy sample (BGS), the luminous red galaxies (LRG), the emission line galaxies (ELG) and the quasars (QSO), spanning a redshift range from 0.1 to 2.1. We compare the four secondary AbacusSummit cosmologies against DESI's fiducial cosmology (Planck 2018). The secondary cosmologies explored include a lower cold dark matter density, a thawing dark energy universe, a higher number of effective species, and a lower amplitude of matter clustering. The mocks are processed through the BAO pipeline by consistently iterating the grid, template, and reconstruction reference cosmologies. We determine a conservative systematic contribution to the error of 0.1% for both the isotropic and anisotropic dilation parameters αiso and αAP. We then directly test the impact of the fiducial cosmology on DESI DR1 data.

79 ASTRONOMY AND ASTROPHYSICS↗

Multiscale Richtmyer-Meshkov instability experiments to isolate the strain rate dependence of strength

Theoretical analysis of Richtmyer-Meshkov instability (RMI) experiments for solid strength shows that the strain rate for a given shock should be inversely proportional to the length scale of the sine wave perturbations when η 0 k , the nondimensional amplitude to wavelength ratio, is held fixed. To isolate the effect of strain rate on strength, free-surface RMI specimens of annealed copper were prepared with three perturbation regions with the same η 0 k but different length scales, characterized by the wavelength λ varying by a factor of 4.9 from 65 to 130 to 320 µ m . Three such targets with different fixed η 0 k ′ s were impacted to a shock pressure of 25 GPa, and the instability evolution was measured with photon Doppler velocimetry. Strengths estimated by comparing hydrocode simulation to the data increased from 700 to 1200 MPa as λ decreased. The different η 0 k targets exercised increasing amounts of plastic strain yet showed no evidence of strain hardening. Physical regime sensitivity analysis determined that for 320 − 65 µ m wavelength perturbations, the effective strain rates increased from 8.7 × 10 6 to 3.3 × 10 7 s − 1 , a factor of 3.8. Thus, the predicted strain rate scaling was mostly achieved but slightly suppressed by increased strength at higher rates. The RMI strength estimates were plotted against constitutive testing data on copper from the literature to show striking evidence of the strength upturn at higher strain rates. Published by the American Physical Society 2024

36 MATERIALS SCIENCE↗

Demographic analysis of invasible habitat fraction identifies context‐dependent roles of resource availability and biotic resistance in determining invasion success

Abstract Theories of plant invasions predict that plant communities should be more easily invaded when resources increase and/or competition decreases. We tested this with an experimentally introduced plant population by manipulating precipitation and resident community biomass. We used a spatially explicit demographic approach to develop a new population‐level metric of invasibility that quantifies the invasible habitat fraction (IHF) across the landscape. The existing community was essentially uninvasible (median IHF ≈ 0%), but experimental manipulations greatly increased the range of outcomes, with maximum observed IHF values over 50%. However, changes in invasibility were often context‐dependent, resulting in some outcomes that aligned with existing theory, and others that were not readily predicted. Moreover, variation in invasibility was often driven by specific sets of invader demographic vital rates. Removing competitors revealed the capacity for strong biotic resistance, but this interacted with precipitation such that little biotic resistance was detected under drought conditions. Adding precipitation typically had little positive effect on invasibility, and moderate drought relief led to relatively high invasibility. However, the latter was driven to a large extent by interactions with mammal herbivory that otherwise inhibited invasion in one year. Synthesis . Our findings show that interactions between abiotic and biotic factors, as well as legacy effects, can strongly mediate invasibility. This study also highlights the importance of incorporating spatial heterogeneity into population‐level assessments of invasion, as initial population declines do not necessarily indicate resistance to invasion.

Griffith, Alden B.↗

Creb5 controls its own expression and directly induces the joint interzone regulatory program

Prior studies have indicated that the transcription factor Creb5 is expressed in the joint interzone, which contains the progenitors for all synovial joint tissues in both mouse and human embryos. In the absence of Creb5 function, most synovial joint interzones fail to form and the cartilage templates in the long bones remain fused. This earlier work did not clarify whether Creb5 initiates a cascade of signaling molecules, such as growth and differentiation factor 5 (Gdf5) and Wnt-family members, that in turn induce the formation of the joint interzone, or instead directly activates the expression of joint interzone markers. In the present study, an integrative analysis of the transcriptome, chromatin accessibility, and Creb5-occupancy in joint progenitors revealed that Creb5 directly binds to both its own two promoters and to the regulatory regions of Gdf5 and Sfrp2, each of whose expression in the joint interzone is Creb5-dependent. Functional enhancer analysis indicated that Creb5 binding sites in either the two Creb5 promoters, or in Gdf5 and Sfrp2 regulatory elements are necessary for these sequences to drive transgene expression in the developing synovial joints. While Creb5 directly drives Gdf5 and Sfrp2 expression in the inner joint interzone, Creb5 activates Barx1 expression specifically in the outer joint interzone. Our findings indicate that Creb5 initiates a regulatory network that both promotes the formation of synovial joints, and subsequently activates distinct transcriptional targets in the inner versus the outer regions of the joint interzone, thus regionalizing gene expression in the developing joint.

Zhang, Cheng-Hai↗

Pseudoelastic deformation in Mo-based refractory multi-principal element alloys

Phase diagrams supported by density functional theory methods can be crucial for designing high-entropy alloys that are subset of multi-principal-element alloys. We present phase and property analysis of quinary (MoW) x Zr y (TaTi) 1-x-y refractory high-entropy alloys from combined Calculation of Phase Diagram (CALPHAD) and density-functional theory results, supplemented by molecular dynamics simulations. Both CALPHAD and density-functional theory analysis of phase stability indicates a Mo-W-rich region of this quinary has a stable single-phase body-centered-cubic structure. We report first quinary composition from Mo-W-Ta-Ti-Zr family of alloy with pseudo-elastic behavior, i.e., hysteresis in stress-strain. Our analysis shows that only Mo-W-rich compositions of Mo-W-Ta-Ti-Zr, i.e., Mo+W, show reproducible hysteresis in stress-strain responsible for pseudo-elastic behavior. The (MoW) 85 Zr 7.5 (TaTi) 7.5 was down-selected based on temperature-dependent phase diagram analysis and molecular dynamics simulations predicted elastic behavior that reveals twinning-assisted pseudoelastic behavior. While mostly unexplored in body-centered-cubic crystals, twinning is a fundamental deformation mechanism that competes against dislocation slip in crystalline solids. Furthermore, this alloy shows identical cyclic deformation characteristics during uniaxial < 100 > loading, i.e., the pseudoelasticity is isotropic in loading direction. Additionally, a temperature increase from 77 to 1,500 K enhances the elastic strain recovery in load-unload cycles, offering possibly control to tune the pseudoelastic behavior.

36 MATERIALS SCIENCE↗

Galaxy mergers in eagle do not induce a significant amount of black hole growth yet do increase the rate of luminous AGN

ABSTRACT We investigate the connection between galaxy–galaxy mergers and enhanced black hole (BH) growth using the cosmological hydrodynamical eagle simulation. We do this via three methods of analysis, investigating: the merger fraction of AGN, the AGN fraction of merging systems, and the AGN fraction of galaxies with close companions. In each case, we find an increased abundance of AGN within merging systems relative to control samples of inactive or isolated galaxies (by up to a factor of ≈3 depending on the analysis method used), confirming that mergers are enhancing BH accretion rates for at least a subset of the galaxy population. The greatest excess of AGN triggered via a merger are found in lower mass (M* ∼ 1010 M⊙) gas rich (fgas > 0.2) central galaxies with lower mass BHs (MBH ∼ 107 M⊙) at lower redshifts (z < 1). We find no enhancement of AGN triggered via mergers in more massive galaxies (M* ≳ 1011 M⊙). The enhancement of AGN is not uniform throughout the phases of a merger, and instead peaks within the early remnants of merging systems (typically lagging ≈300 Myr post-coalescence of the two galaxies at z = 0.5). We argue that neither major ($M_{\mathrm{*,1}} / M_{\mathrm{*,2}} \ge \frac{1}{4}$) nor minor mergers ($\frac{1}{10} \lt M_{\mathrm{*,1}} / M_{\mathrm{*,2}} \lt \frac{1}{4}$) are statistically relevant for enhancing BH masses globally. Whilst at all redshifts the galaxies experiencing a merger have accretion rates that are on average 2–3 times that of isolated galaxies, the majority of mass that is accreted on to BHs occurs outside the periods of a merger. We compute that on average no more than 15 per cent of a BHs final day mass comes from the enhanced accretion rates triggered via a merger.

McAlpine, Stuart↗

Safety Risk Reliability Model Library

SR2ML is a software package which contains a set of safety and reliability models designed to be interfaced with the INL developed RAVEN code. These models can be employed to perform both static and dynamic system risk analysis and determine risk importance of specific elements of the considered system. Two classes of reliability models have been developed; the first class includes all classical reliability models (Fault-Trees, Event-Trees, Markov models and Reliability Block Diagrams) which have been extended to deal not only with Boolean logic values but also time dependent values. The second class includes several components aging models. Models of these two classes are designed to be included in a RAVEN ensemble model to perform time dependent system reliability analysis (dynamic analysis). Similarly, these models can be interfaced with system analysis codes to determine failure time of systems and evaluate accident progression (static analysis).

Wang, Congjian↗

Giant resonances in topological spin Hall effect due to electron-skyrmion scattering in two-dimensional Rashba spin-orbit ferromagnets

Here we study a topological spin Hall effect where conduction electrons are scattered by Néel-type skyrmions in two-dimensional Rashba spin-orbit ferromagnets. We find the resonance structures in direct and Hall electric conductivities. The resonances strongly depend on the skyrmion size, the Rashba spin-orbit coupling vector value, and the relative direction between magnetization and Rashba vectors. The antiparallel arrangement of the Rashba spin-orbit coupling vector with respect to the magnetization determines the resonance structure and increases the direct conductivity by about two orders of magnitude. For the parallel arrangement the electric conductivities decrease by one to three orders of magnitude and the Hall conductivity changes the sign. The Rashba spin-orbit coupling also modifies electron bands depending on the ratio ε R /J, where ε R is Rashba energy and J is an exchange integral between conduction and localized electrons. If ε R /J ≤ 1, each energy band has the single minimum while for ε R /J > 1 the lower band has the “Mexican-hat” shape with the maximum at k = 0. We focus on the dependencies of direct and Hall electric conductivities on Fermi energy, ε F , skyrmion sizes, and Rashba spin-orbit coupling constant values and its relative direction with the magnetization. Analyzing both types of the energy bands, in general, we find two types of resonances: at the minimum of the upper band and behaviors, we employ the scattering pattern analysis. The resonance dependencies on skyrmion sizes and Rashba, a spin-orbit coupling contestant, can be qualitatively explained in terms of the Ramsauer-Townsend scattering of the upper band electrons by the skyrmion quantum well. The resonance properties can be used in spin transistors. To discover the resonances it is necessary to know the specific range of the parameters. At some values of the parameters the electric conductivity changes by about two orders of magnitude in the narrow range of ε F (< 0.01 eV). To detect the resonances it is also important to identify the relative direction of the Rashba spin-orbit coupling vector with respect to the magnetization.

36 MATERIALS SCIENCE↗