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At least 73 records · Page 4

Computer-based video digitizer analysis of surface extension in maize roots: kinetics of growth rate changes during gravitropism

We used a video digitizer system to measure surface extension and curvature in gravistimulated primary roots of maize (Zea mays L.). Downward curvature began about 25 +/- 7 min after gravistimulation and resulted from a combination of enhanced growth along the upper surface and reduced growth along the lower surface relative to growth in vertically oriented controls. The roots curved at a rate of 1.4 +/- 0.5 degrees min-1 but the pattern of curvature varied somewhat. In about 35% of the samples the roots curved steadily downward and the rate of curvature slowed as the root neared 90 degrees. A final angle of about 90 degrees was reached 110 +/- 35 min after the start of gravistimulation. In about 65% of the samples there was a period of backward curvature (partial reversal of curvature) during the response. In some cases (about 15% of those showing a period of reverse bending) this period of backward curvature occurred before the root reached 90 degrees. Following transient backward curvature, downward curvature resumed and the root approached a final angle of about 90 degrees. In about 65% of the roots showing a period of reverse curvature, the roots curved steadily past the vertical, reaching maximum curvature about 205 +/- 65 min after gravistimulation. The direction of curvature then reversed back toward the vertical. After one or two oscillations about the vertical the roots obtained a vertical orientation and the distribution of growth within the root tip became the same as that prior to gravistimulation. The period of transient backward curvature coincided with and was evidently caused by enhancement of growth along the concave and inhibition of growth along the convex side of the curve, a pattern opposite to that prevailing in the earlier stages of downward curvature. There were periods during the gravitropic response when the normally unimodal growth-rate distribution within the elongation zone became bimodal with two peaks of rapid elongation separated by a region of reduced elongation rate. This occurred at different times on the convex and concave sides of the graviresponding root. During the period of steady downward curvature the elongation zone along the convex side extended farther toward the tip than in the vertical control. During the period of reduced rate of curvature, the zone of elongation extended farther toward the tip along the concave side of the root. The data show that the gravitropic response pattern varies with time and involves changes in localized elongation rates as well as changes in the length and position of the elongation zone. Models of root gravitropic curvature based on simple unimodal inhibition of growth along the lower side cannot account for these complex growth patterns.

NASA Discipline Plant Biology↗

Prediction of hydration energies of adsorbates at Pt(111) and liquid water interfaces using machine learning

Aqueous phase heterogeneous catalysis is important to various industrial processes, including biomass conversion, Fischer–Tropsch synthesis, and electrocatalysis. Accurate calculation of solvation thermodynamic properties is essential for modeling the performance of catalysts for these processes. Explicit solvation methods employing multiscale modeling, e.g., involving density functional theory and molecular dynamics have emerged for this purpose. Although accurate, these methods are computationally intensive. This study introduces machine learning (ML) models to predict solvation thermodynamics for adsorbates on a Pt(111) surface, aiming to enhance computational efficiency without compromising accuracy. In particular, ML models are developed using a combination of molecular descriptors and fingerprints and trained on previously published water–adsorbate interaction energies, energies of solvation, and free energies of solvation of adsorbates bound to Pt(111). These models achieve root mean square error values of 0.09 eV for interaction energies, 0.04 eV for energies of solvation, and 0.06 eV for free energies of solvation, demonstrating accuracy within the standard error of multiscale modeling. Feature importance analysis reveals that hydrogen bonding, van der Waals interactions, and solvent density, together with the properties of the adsorbate, are critical factors influencing solvation thermodynamics. Furthermore, these findings suggest that ML models can provide rapid and reliable predictions of solvation properties. This approach not only reduces computational costs but also offers insights into the solvation characteristics of adsorbates at Pt(111)–water interfaces.

Adsorption↗

Development of Standardized Lunar Regolith Simulant Materials

Lunar exploration requires studies using standardized testing procedures. Previous lunar simulants focused on physical aspects of the lunar regolith. Renewed lunar exploration requires standardized lunar regolith simulant (SLRS) materials that simulate the physical, chemical, and mineralogical properties of the regolith [l]. A root simulant models an end-member, and a derivative is formed by addition of material [2]. The 2005 Workshop recommended a low-Ti mare basalt and a high-Ca highland anorthosite set of roots. Derivatives involve addition of ilmenite and glassy agglutinates [3]. An ideal SLRS material is homogeneous. Geochemical standards are finely-ground to reduce chemical variability, but lunar simulants have a grain size variation and mineralogy that must match the lunar regolith. The simulant homogeneity is monitored using major, minor, and trace element data of progressively smaller samples compared to bulk material. Both chemical and geotechnical properties depend on the contrast from grain to grain. The variability of simulant material is an inherent property that must be taken into account. Simulant production requires monitoring of adherence to simulant requirements and homogeneity during production. Quality control establishes a traceability to a master set of reference standards.

Carpenter, P.↗

Evaluation of Linear, Inviscid, Viscous, and Reduced-Order Modeling Aeroelastic Solutions of the AGARD 445.6 Wing Using Root Locus Analysis

Reduced-order modeling (ROM) methods are applied to the CFD-based aeroelastic analysis of the AGARD 445.6 wing in order to gain insight regarding well-known discrepancies between the aeroelastic analyses and the experimental results. The results presented include aeroelastic solutions using the inviscid CAP-TSD code and the FUN3D code (Euler and Navier-Stokes). Full CFD aeroelastic solutions and ROM aeroelastic solutions, computed at several Mach numbers, are presented in the form of root locus plots in order to better reveal the aeroelastic root migrations with increasing dynamic pressure. Important conclusions are drawn from these results including the ability of the linear CAP-TSD code to accurately predict the entire experimental flutter boundary (repeat of analyses performed in the 1980's), that the Euler solutions at supersonic conditions indicate that the third mode is always unstable, and that the FUN3D Navier-Stokes solutions stabilize the unstable third mode seen in the Euler solutions.

Silva, Walter A.↗

Discerning the thermodynamic feasibility of the spontaneous coexistence of multiple functional vegetation groups

Can the Second Law of Thermodynamics explain why ecosystems naturally organize into a complex structure composed of multiple vegetation species and functional groups? Ecosystem structure, which refers to the number and type of plant functional groups, is the result of self-organization, or the spontaneous emergence of order from random fluctuations. By considering ecosystems as open thermodynamic systems, we model and study these fluctuations of throughput signatures on short timescales to determine the drivers and characteristics of ecosystem structure. This diagnostic approach allows us to use fluxes of energy and entropy to calculate an ecosystem’s estimated work and understand the thermodynamic behavior of the system. We use a multi-layer canopy-root-soil model to calculate the energy and entropy fluxes of different scenarios for field sites across various climates. At each site, scenarios comprised of native individual plant functional groups and a coexisting multi-group composition scenario including all functional groups observed at the site are compared. Ecosystem-scale calculations demonstrate that entropy fluxes and work efficiency—the work performed for the amount of radiation entering the ecosystem—are greatest in the multi-group scenario when its leaf area is significantly larger than each of its individual functional groups. Thus, we conclude that ecosystems self-organize towards the vegetation structure with the greatest outgoing entropy flux and work efficiency, resulting in the coexistence of multiple functional groups and performing the maximum amount of work within the constraints of locally available energy, water, and nutrients.

54 ENVIRONMENTAL SCIENCES↗

Orion Multi-Purpose Crew Vehicle Solving and Mitigating the Two Main Cluster Pendulum Problem

The Orion Multi-purpose Crew Vehicle (MPCV) Orion spacecraft will return humans from beyond earth's orbit, including Mars and will be required to land 20,000 pounds of mass safely in the ocean. The parachute system nominally lands under 3 main parachutes, but the system is designed to be fault tolerant and land under 2 main parachutes. During several of the parachute development tests, it was observed that a pendulum, or swinging, motion could develop while the Crew Module (CM) was descending under two parachutes. This pendulum effect had not been previously predicted by modeling. Landing impact analysis showed that the landing loads would double in some places across the spacecraft. The CM structural design limits would be exceeded upon landing if this pendulum motion were to occur. The Orion descent and landing team was faced with potentially millions of dollars in structural modifications and a severe mass increase. A multidisciplinary team was formed to determine root cause, model the pendulum motion, study alternate canopy planforms and assess alternate operational vehicle controls & operations providing mitigation options resulting in a reliability level deemed safe for human spaceflight. The problem and solution is a balance of risk to a known solution versus a chance to improve the landing performance for the next human-rated spacecraft.

Ali, Yasmin↗

Self-induced spin-orbit torques in metallic ferromagnets

Herein we present a phenomenological theory of spin-orbit torques in a metallic ferromagnet with spin-relaxing boundaries. The model is rooted in the coupled diffusion of charge and spin in the bulk of the ferromagnet, where we account for the anomalous Hall effects as well as the anisotropic magnetoresistance in the corresponding constitutive relations for both charge and spin sectors. The diffusion equations are supplemented with suitable boundary conditions reflecting the spin-sink capacity of the environment. In inversion-asymmetric heterostructures, the uncompensated spin accumulation exerts a dissipative torque on the order parameter, giving rise to a current-dependent linewidth in the ferromagnetic resonance with a characteristic angular dependence. We compare our model to recent spin-torque ferromagnetic resonance measurements, illustrating how rich self-induced spin-torque phenomenology can arise even in simple magnetic structures.

36 MATERIALS SCIENCE↗

From 2D to 4D: a containerized workflow and browser to explore dynamic chromatin architecture

Background Characterizing the physical organization of the genome is essential for understanding long-range gene regulation, chromatin compartmentalization, and epigenetic accessibility. Hi-C experiments generate two-dimensional (2D) genome-wide contact maps of chromatin interactions by capturing the spatial proximity between genomic loci, which reveal interaction frequencies but lack the spatial resolution needed to interpret the three-dimensional (3D) genome structure(s). Emerging evidence suggests that epigenetic regulation is closely linked to 3D genome architecture, and that structural changes over time (4D) drive key biological processes in development, disease, and environmental response. Thus, integrating 3D structure with functional data is critical for a more complete understanding of genome regulation. Previous work, most notably the 4DHiC chromosome modeling framework, has shown that physical multi-dimensional modeling approaches rooted in polymer physics and molecular dynamics can resolve these structures at biologically meaningful resolutions by integrating temporal Hi-C data with physical constraints to uncover dynamic chromosome reorganization. Thus, molecular dynamics simulations, constrained by Hi-C contact matrices, can resolve fine-scale structural changes and reveal functionally significant transitions in chromatin conformation. Results Herein, we present the 4D Genome Browser Workflow (4DGBWorkflow) and the 4D Genome Browser (4DGB). The algorithm is based on the 4DHiC method, and the containerized tool is an end-to-end workflow that can transform, filter, and view 4D epigenomics and chromatin datasets, allowing non-specialists to apply three-dimensional modeling principles to diverse datasets and experimental conditions. The software executes on a laptop running macOS, Linux or Windows. From input Hi-C files (.hic), the 4DGBWorkflow produces 3D reconstructions of chromosomes, integrates the reconstruction with track data (e.g., epigenetic marks, transcriptome profiles), and provides comparative visualization of the results in a single workflow. Conclusions The 4DGBWorkflow and 4D Genome Browser are open-source tools for comparative analysis and visualization of 4D chromosome datasets, including chromatin architecture and epigenomic signals. Automatic integration of Hi-C data with molecular dynamics democratizes the construction of time resolved 3D genome structures, simplifying complex simulations and data integration schemes.

3D Genome Browser↗

The Uncertainty of Biomass Estimates from Modeled ICESat-2 Returns Across a Boreal Forest Gradient

The Forest Light (FLIGHT) radiative transfer model was used to examine the uncertainty of vegetation structure measurements from NASA's planned ICESat-2 photon counting light detection and ranging (LiDAR) instrument across a synthetic Larix forest gradient in the taiga-tundra ecotone. The simulations demonstrate how measurements from the planned spaceborne mission, which differ from those of previous LiDAR systems, may perform across a boreal forest to non-forest structure gradient in globally important ecological region of northern Siberia. We used a modified version of FLIGHT to simulate the acquisition parameters of ICESat-2. Modeled returns were analyzed from collections of sequential footprints along LiDAR tracks (link-scales) of lengths ranging from 20 m-90 m. These link-scales traversed synthetic forest stands that were initialized with parameters drawn from field surveys in Siberian Larix forests. LiDAR returns from vegetation were compiled for 100 simulated LiDAR collections for each 10 Mg · ha(exp -1) interval in the 0-100 Mg · ha(exp -1) above-ground biomass density (AGB) forest gradient. Canopy height metrics were computed and AGB was inferred from empirical models. The root mean square error (RMSE) and RMSE uncertainty associated with the distribution of inferred AGB within each AGB interval across the gradient was examined. Simulation results of the bright daylight and low vegetation reflectivity conditions for collecting photon counting LiDAR with no topographic relief show that 1-2 photons are returned for 79%-88% of LiDAR shots. Signal photons account for approximately 67% of all LiDAR returns, while approximately 50% of shots result in 1 signal photon returned. The proportion of these signal photon returns do not differ significantly (p greater than 0.05) for AGB intervals greater than 20 Mg · ha(exp -1). The 50m link-scale approximates the finest horizontal resolution (length) at which photon counting LiDAR collection provides strong model fits and minimizes forest structure uncertainty in the synthetic Larix stands. At this link-scale AGB greater than 20 Mg · ha(exp -1) has AGB error from 20-50% at the 95% confidence level. These results suggest that the theoretical sensitivity of ICESat-2 photon counting LiDAR measurements alone lack the ability to consistently discern differences in inferred AGB at 10 Mg · ha(exp -1) intervals in sparse forests characteristic of the taiga-tundra ecotone.

LiDAR↗

Earth System Model Simulations of Ameriflux sites using dynamic roots and dynamic leaf to root allocation

This data package contains point-scale Earth System Model simulations run with DOE's E3SM Model. The package includes four sets of simulations, one set of simulations run in the default configuration, a second set of simulations run with the dynamic root module enabled, the third set with dynamic leaf to fine root allocation, and the fourth with the combination of dynamic roots and dynamic allocation. These simulations were run in point mode a Ameriflux sites, US-MMS, US-Moz, US-Syv, and US-NR1. These datasets can be used to assess the impact that dynamic roots have on Land Surface fluxes such as carbon and water. The simulations were run with atmospheric forcing from the Global Soil Wetness Project. We provide specifically here Gross Primary Production, Transpiration, relative root fraction per soil layer as well as Air Temperature, Precipitation and all the parameterizations used for the simulations. Our purpose for generating and analyzing these simulations was to assess the role that root dynamics and foraging for water has in the recovery timescale of ecosystems following climate perturbation. All data provided are in the "netcdf" format using standard CF-1 (Climate and Forecast) Convention. The data are all machine readable using various software platforms including Matlab, NCO, Panoply and R.

54 ENVIRONMENTAL SCIENCES↗

Enhancement of magnetic domain wall velocity via resonant dissipation of standing wave modes of domain wall structure with perpendicular magnetic anisotropy

The dynamic behaviors of magnetic domain walls have significant implications for developing advanced spintronic devices. In this study, we investigate the intriguing resonance phenomenon within the magnetic domain wall structure, focusing on the dissipation mechanism and its impact on domain wall dynamic motion. By applying a static external magnetic field, we observe a remarkable amplification of domain wall velocity through the resonant excitations of the flexure modes. The resonance of the flexure mode exerts an indirect influence on the domain wall velocity through energy dissipation, leading to a significant enhancement from the predictions of the one-dimensional Walker model. We establish a robust model platform rooted in energy dissipation allows comprehensive understanding the dramatic enhancement of domain wall velocity observed during width-directional flexure mode resonance. By directly quantifying energy dissipation, our approach provides highly effective and accurate estimates of domain wall velocity, surpassing previous methods that focus solely on the instantaneous dynamics of the domain wall structure. These findings offer crucial insights into the fundamental mechanisms governing the dynamics of domain walls and other magnetic systems, such as magnetic skyrmions, bubbles, and magnetic vortices, paving the way for development and optimization of next-generation spintronic devices.

Collective dynamics↗

De Novo Design of High‐Affinity Miniprotein Binders Targeting Francisella Tularensis Virulence Factor

Abstract Francisella tularensis poses considerable public health risk due to its high infectivity and potential for bioterrorism. Francisella‐like lipoprotein (Flpp3), a key virulence factor unique to Francisella, plays critical roles in infection and immune evasion, making it a promising target for therapeutic development. However, the lack of well‐defined binding pockets and structural information on native interactions has hindered structure‐guided ligand discovery against Flpp3. Here, we used a combination of physics‐based and deep‐learning methods to design high‐affinity miniprotein binders targeting two distinct sites on Flpp3. We identified four binders for site I with binding affinities ranging between 24–110 nM. For the second site, an initial binder showed a dissociation constant ( K D ) of 81 nM, and subsequent site saturation mutagenesis yielded variants with sub‐nanomolar affinities. Circular dichroism confirmed the topology of designed miniproteins. The X‐ray crystal structure of Flpp3 in complex with a site I binder is nearly identical to the design model (Cα root‐mean‐square deviation (RMSD): 0.9 Å). These designed miniproteins provide research tools to explore the roles of Flpp3 in tularemia and should enable the development of new therapeutic candidates.

Gokce‐Alpkilic, Gizem [Molecular Engineering and S↗

Use of Satellite, Surface Observations and Numerical Weather Prediction Model Data to Improve Cloud Base Height and Cloud Base Vertical Velocity Estimation

Cloud base height (CBH) and cloud base vertical velocity (CBVV) are important variables that impact the overall climate in a region as they influence the formulation, longevity, and evolution of clouds. Retrieval of both parameters have long used ground instrumentation (e.g., Doppler lidar (DL), ground base radar); however, retrieving CBH from satellites is particularly challenging given that space-based instruments only observe cloud tops. In this manuscript, CBH is retrieved using a multi-linear regression equation, while CBVV used a random forests model. Both retrievals combine satellite and numerical weather prediction data. The satellite data used are the Visible Infrared Imaging Radiometer Suite imagery, while measurements of CBH and CBVV include DL and radiosonde data at the Southern Great Plains (SGP) Atmospheric Radiation Measurement observatory. Data from 83 summer days (May-August) in 2018–2021 featuring cumulus clouds forced by solar heating were examined and used to train the models, with years 2022–2023 used for validation. Various spatial domains were defined with one large (2.4° longitude by 2.0° latitude) SGP domain being split into smaller sections (smallest being 0.99° and 0.61° longitude and latitude respectably). CBH and CBVV values obtained from the DL as compared to the models show root mean square errors between 150 and 200 m, with CBVV values between 0.45 and 1 ms -1 . Finally, it was found that the CBH formulation performs well over all domains, while the CBVV retrievals become less accurate due to more turbulence being introduced into the observations as the number of DL stations decreases in the smaller domains.

54 ENVIRONMENTAL SCIENCES↗

Natural variation in growth and yield to waterlogging across climate-diverse pennycress accessions

Many winter annual crops, such as pennycress ( Thlaspi arvense L.), are subjected to heavy precipitation events during their growing season. Therefore, it is essential to identify pennycress accessions with natural variation in flooding resilience. We used climate modeling data to assess spring soil moisture levels in the geographic origins of 471 natural pennycress accessions. We selected 34 accessions with variation in predicted soil moisture and tested survivability under prolonged waterlogging at the rosette stage. It took seven weeks for the first accessions to die, indicating that pennycress is hardy to prolonged waterlogging at the vegetative stage. Furthermore, we chose ‘susceptible’ and ‘tolerant’ accessions to waterlog for one week at the reproductive stage, the growth stage aligned with spring rainfall. Six accessions had significantly reduced seed weight at maturity and two had minimal impacts on growth and seed yield after waterlogging and can be further explored for adaptive traits.

59 BASIC BIOLOGICAL SCIENCES↗

High-frequency and Vertical Variations of Soil Moisture and their Impact on Ecosystem Dynamics

The vertical distribution of subsurface moisture is a major control on ecosystem dynamics and climate. The Mediterranean climate of California, with wet winters and dry summers, provides a testbed for understanding how transpiration is sustained through extended dry periods. The project developed and tested a new subsurface hydrology model that includes a parameterization of stochastic hydraulic conductivity to capture fracture flow, a diagnostic model of rooting profile that depends on the subsurface hydrology, and a representation of hydraulic redistribution by plant roots. A sensitivity study shows that it is plants with rooting depths >8 m that could access the subsurface moisture. The insight is applied to understand differential tree mortality during the 2012-2016 drought in California. The analysis shows that greater mortality trees on plutonic rocks than on sedimentary rocks. The study demonstrates, for the first time, the importance of lithology for the distribution and health of ecosystems.

54 ENVIRONMENTAL SCIENCES↗

An Experimental Study of the Flowfield on a Semispan Rectangular Wing with a Simulated Glaze Ice Accretion

Wind tunnel experiments were conducted in order to study the effect of a simulated glaze ice accretion on the flowfield of a semispan, reflection-plane, rectangular wing at Re = 1.5 million and M = 0.12. A laser Doppler velocimeter was used to map the flowfield on the upper surface of the model in both the clean and iced configurations at alpha = 0, 4, and 8 degrees angle of attack. At low angles of attack, the massive separation bubble aft of the leading edge ice horn was found to behave in a manner similar to laminar separation bubbles. At alpha = 0 and 4 degrees, the locations of transition and reattachment, as deduced from momentum thickness distributions, were found to be in good agreement with transition and reattachment locations in laminar separation bubbles. These values at y/b = 0.470, the centerline measurement location, matched well with data obtained on a similar but two dimensional model. The measured velocity profiles on the iced wing compared reasonably with the predicted profiles from Navier-Stokes computations. The iced-induced separation bubble was also found to have features similar to the recirculating region aft of rearward-facing steps. At alpha = 0 degrees and 4 degrees, reverse flow magnitudes and turbulence intensity levels were typical of those found in the recirculating region aft of rearward-facing steps. The calculated separation streamline aft of the ice horn at alpha = 4 degrees, y/b = 0.470 coincided with the locus of the maximum Reynolds normal stress. The maximum Reynolds normal stress peaked at two locations along the separation streamline. The location of the first peak-value coincided with the transition location, as deduced from the momentum thickness distributions. The location of the second peak was just upstream of reattachment, in good agreement with measurements of flows over similar obstacles. The intermittency factor in the vicinity of reattachment at alpha = 4 degrees, y/b = 0.470, revealed the time-dependent nature of the reattachment process. The size and extent of the separation bubble were found to be a function of angle of attack and the spanwise location. Three dimensional effects were found to be strongest at alpha = 8 degrees. The calculated separation and stagnation streamlines were found to vary little with spanwise location at alpha = 0 degrees. The calculated separation streamlines at alpha = 4 degrees revealed that the bubble was largest near the centerline measurement plane, whereas the tip-induced vortex flow and the model root-tunnel wall boundary-layer interaction reduced the size of the bubble. These effects were found to be most dramatic at alpha = 8 degrees.

Khodadoust, Abdollah↗

Constitutive and life modeling of single crystal blade alloys for root attachment analysis

Work to develop fatigue life prediction and constitutive models for uncoated attachment regions of single crystal gas turbine blades is described. At temperatures relevant to attachment regions, deformation is dominated by slip on crystallographic planes. However, fatigue crack initiation and early crack growth are not always observed to be crystallographic. The influence of natural occurring microporosity will be investigated by testing both hot isostatically pressed and conventionally cast PWA 1480 single crystal specimens. Several differnt specimen configurations and orientations relative to the natural crystal axes are being tested to investigate the influence of notch acuity and the material's anisotropy. Global and slip system stresses in the notched regions were determined from three dimensional stress analyses and will be used to develop fatigue life prediction models consistent with the observed lives and crack characteristics.

Meyer, T. G.↗