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At least 865 records · Page 48

Venus Global Reference Atmospheric Model Status and Planned Updates

The Venus Global Reference Atmospheric Model (Venus-GRAM) was originally developed in 2004 under funding from NASA's In Space Propulsion (ISP) Aerocapture Project to support mission studies at the planet. Many proposals, including NASA New Frontiers and Discovery, as well as other studies have used Venus-GRAM to design missions and assess system robustness. After Venus-GRAM's release in 2005, several missions to Venus have generated a wealth of additional atmospheric data, yet few model updates have been made to Venus-GRAM. This paper serves to address three areas: (1) to present the current status of Venus-GRAM, (2) to identify new sources of data and other upgrades that need to be incorporated to maintain Venus-GRAM credibility and (3) to identify additional Venus-GRAM options and features that could be included to increase its capability. This effort will de-pend on understanding the needs of the user community, obtaining new modeling data and establishing a dedicated funding source to support continual up-grades. This paper is intended to initiate discussion that can result in an upgraded and validated Venus-GRAM being available to future studies and NASA proposals.

Justh, H. L.↗

Venus Global Reference Atmospheric Model Status and Planned Updates

The Venus Global Reference Atmospheric Model (Venus-GRAM) was originally developed in 2004 under funding from NASA's In Space Propulsion (ISP) Aerocapture Project to support mission studies at the planet. Many proposals, including NASA New Frontiers and Discovery, as well as other studies have used Venus-GRAM to design missions and assess system robustness. After Venus-GRAM's release in 2005, several missions to Venus have generated a wealth of additional atmospheric data, yet few model updates have been made to Venus-GRAM. This paper serves to address three areas: (1) to present the current status of Venus-GRAM, (2) to identify new sources of data and other upgrades that need to be incorporated to maintain Venus-GRAM credibility and (3) to identify additional Venus-GRAM options and features that could be included to increase its capability. This effort will de-pend on understanding the needs of the user community, obtaining new modeling data and establishing a dedicated funding source to support continual up-grades. This paper is intended to initiate discussion that can result in an upgraded and validated Venus-GRAM being available to future studies and NASA proposals.

Justh, H. L.↗

Drug discovery efforts at George Mason University

With over 39,000 students, and research expenditures in excess of $200 million, George Mason University (GMU) is the largest R1 (Carnegie Classification of very high research activity) university in Virginia. Mason scientists have been involved in the discovery and development of novel diagnostics and therapeutics in areas as diverse as infectious diseases and cancer. Below are highlights of the efforts being led by Mason researchers in the drug discovery arena. To enable targeted cellular delivery, and non-biomedical applications, Veneziano and colleagues have developed a synthesis strategy that enables the design of self-assembling DNA nanoparticles (DNA origami) with prescribed shape and size in the 10 to 100 nm range. The nanoparticles can be loaded with molecules of interest such as drugs, proteins and peptides, and are a promising new addition to the drug delivery platforms currently in use. The investigators also recently used the DNA origami nanoparticles to fine tune the spatial presentation of immunogens to study the impact on B cell activation. These studies are an important step towards the rational design of vaccines for a variety of infectious agents. To elucidate the parameters for optimizing the delivery efficiency of lipid nanoparticles (LNPs), Buschmann, Paige and colleagues have devised methods for predicting and experimentally validating the pKa of LNPs based on the structure of the ionizable lipids used to formulate the LNPs. These studies may pave the way for the development of new LNP delivery vehicles that have reduced systemic distribution and improved endosomal release of their cargo post administration. To better understand protein-protein interactions and identify potential drug targets that disrupt such interactions, Luchini and colleagues have developed a methodology that identifies contact points between proteins using small molecule dyes. The dye molecules noncovalently bind to the accessible surfaces of a protein complex with very high affinity, but are excluded from contact regions. When the complex is denatured and digested with trypsin, the exposed regions covered by the dye do not get cleaved by the enzyme, whereas the contact points are digested. The resulting fragments can then be identified using mass spectrometry. The data generated can serve as the basis for designing small molecules and peptides that can disrupt the formation of protein complexes involved in disease processes. For example, using peptides based on the interleukin 1 receptor accessory protein (IL-1RAcP), Luchini, Liotta, Paige and colleagues disrupted the formation of IL-1/IL-R/IL-1RAcP complex and demonstrated that the inhibition of complex formation reduced the inflammatory response to IL-1B. Working on the discovery of novel antimicrobial agents, Bishop, van Hoek and colleagues have discovered a number of antimicrobial peptides from reptiles and other species. DRGN-1, is a synthetic peptide based on a histone H1-derived peptide that they had identified from Komodo Dragon plasma. DRGN-1 was shown to disrupt bacterial biofilms and promote wound healing in an animal model. The peptide, along with others, is being developed and tested in preclinical studies. Other research by van Hoek and colleagues focuses on in silico antimicrobial peptide discovery, screening of small molecules for antibacterial properties, as well as assessment of diffusible signal factors (DFS) as future therapeutics. The above examples provide insight into the cutting-edge studies undertaken by GMU scientists to develop novel methodologies and platform technologies important to drug discovery.

59 BASIC BIOLOGICAL SCIENCES↗

Genomic Language model for Annotation of Repetitive Elements (GLARE) v1.0

GLARE (Genomic Language model for Annotation of Repetitive Elements) is a tool that classifies transposable elements (TEs)—the mobile, repetitive DNA sequences that make up large fractions of eukaryotic genomes. GLARE fine-tunes the NTv3-650M genomic language model on a harmonized collection of curated TE sequences from the PanTEon and Repbase reference databases, assigning each input sequence to one of 11 orders and 32 superfamilies in a Wicker-compatible taxonomy. Features. From nucleotide FASTA input, GLARE outputs per-sequence predictions, class summaries, composition figures, and an annotated FASTA. It provides calibrated confidence scores with optional abstention and runs on CPU or GPU. Uses. GLARE serves as a classification component in genome-annotation pipelines, downstream of TE discovery, supporting genome annotation and comparative and evolutionary genomics. Advantages. GLARE is the first repeat-element classifier to leverage a pretrained genomic language model. Combined with multi-database training, this approach outperformed all nine classifiers in the PanTEon benchmark, generalized better to unseen taxonomic clades, and remained robust to sequence orientation—a common failure mode of existing tools.

Bruna, Tomas [Lawrence Berkeley National Laborator↗

Machine Learning-Enabled Image Classification for Automated Electron Microscopy

Abstract Traditionally, materials discovery has been driven more by evidence and intuition than by systematic design. However, the advent of “big data” and an exponential increase in computational power have reshaped the landscape. Today, we use simulations, artificial intelligence (AI), and machine learning (ML) to predict materials characteristics, which dramatically accelerates the discovery of novel materials. For instance, combinatorial megalibraries, where millions of distinct nanoparticles are created on a single chip, have spurred the need for automated characterization tools. This paper presents an ML model specifically developed to perform real-time binary classification of grayscale high-angle annular dark-field images of nanoparticles sourced from these megalibraries. Given the high costs associated with downstream processing errors, a primary requirement for our model was to minimize false positives while maintaining efficacy on unseen images. We elaborate on the computational challenges and our solutions, including managing memory constraints, optimizing training time, and utilizing Neural Architecture Search tools. The final model outperformed our expectations, achieving over 95% precision and a weighted F-score of more than 90% on our test data set. This paper discusses the development, challenges, and successful outcomes of this significant advancement in the application of AI and ML to materials discovery.

Materials Science↗

Contributions of GRACE to Climate Monitoring

The NASA/German Gravity Recovery and Climate Experiment (GRACE) was launched in March 2002. Rather than looking downward, GRACE continuously monitors the locations of and precise distance between twin satellites which orbit in tandem about 200 km apart. Variations in mass near Earth's surface cause heterogeneities in its gravity field, which in turn affect the orbits of satellites. Thus scientists can use GRACE data to map Earth's gravity field with enough accuracy to discern month to month changes caused by ocean circulation and redistribution of water stored on and in the land. Other gravitational influences, such as atmospheric circulation, post-glacial rebound, and solid earth movements are either independently determined and removed or are negligible on a monthly to sub-decadal timescale. Despite its coarse spatial (>150,000 sq km at mid-latitudes) and temporal (approx monthly) resolutions, GRACE has enabled significant advancements in the oceanic, hydrologic, and cryospheric science, and has great potential for climate monitoring, because it is the only global observing system able to measure ocean bottom pressures, total terrestrial water storage, and ice mass changes. The best known GRACE results are estimates of Greenland and Antarctic ice sheet loss rates. Previously, scientists had estimated ice mass losses using ground and satellite based altimetry and surface mass balance estimates based on snowfall accumulation and glacier discharge. While such measurements are still very useful for their spatial detail, they are imperfectly correlated with large-scale ice mass changes, due to snow and ice compaction and incomplete spatial coverage. GRACE enables scientists to generate monthly time series of Greenland and Antarctic ice mass, which have confirmed the shrinking of the polar ice sheets, one of the most obvious and indisputable manifestations of climate change. Further, GRACE has located and quantified hot spots of ice loss in southeastern Greenland and western Antarctica. For 2002 to present, the rate of ice mass loss has been 200 to 300 GT/yr in Greenland and 70 to 210 GT/yr in Antarctica, and some scientists are suggesting that the rates are accelerating. Similarly, GRACE has been used to monitor mass changes in alpine glaciers. Tamisiea et al. first characterized glacier melt along the southern coast of Alaska, more recently estimated to be occurring at a rate of 84 GT/yr. Chen et al. estimated that Patagonian glaciers are melting at a rate of 28 GT/yr, and estimated that the high mountains of central Asia lose ice at a rate of 47 GT/yr. Tapley et al. and Wahr et al. presented the first GRACE based estimates of changes in column-integrated terrestrial water storage (TWS; the sum of ground-water, soil moisture, surface waters, snow, ice, and water stored in vegetation) at continental scales. Since then, dozens of studies have shown that GRACE based estimates of regional to continental scale TWS variations agree with independent information, and some innovative uses of GRACE data have been developed. Rodell et al. (2004) and Swenson and Wahr (2006) demonstrated that by combining GRACE derived terrestrial water storage changes with observations of precipitation and runoff in a river basin scale water budget, it was possible to produce new estimates of evapotranspiration and atmospheric moisture convergence, essential climate variables that are difficult to estimate accurately. Similarly, GRACE has been used to constrain estimates of global river discharge and the contribution of changes in TWS to sea level rise. Crowley et al. observed a negative correlation between interannual TWS anomalies in the Amazon and the Congo River basin. Yeh et al. and Rodell et al. estimated regionally averaged groundwater storage variations based on GRACE and auxiliary observations. Rodell et al. and Tiwari et al. applied that method to quantify massive groundwater depletion in northern India caused by over reliance on aquifers for irration, and Famiglietti et al. found a similar situation in California's Central Valley. Zaitchik et al. and Lo et al. described approaches to use GRACE to constrain hydrological models, enabling integration of GRACE data with other observations and achieving much higher spatial and temporal resolutions than GRACE alone. Such approaches are now supporting applications including drought and water resources monitoring. Oceanography has likewise benefitted from the independent nature of GRACE observations. One application is measurement of the mass component of sea level rise, which complements radar altimetry and in situ measurements. GRACE also measures ocean bottom pressures (OBP), which help to refine understanding and modeling of ocean circulation and the ocean's fresh water budget, among other things. For example, Hayakawa et al. showed that GRACE observes OBP patterns absent from the background models of oceanic variability. Morison et al. used GRACE to describe important decadal scale shifts in circulation and an ongoing trend of freshening of the western Arctic, important indicators of climate variability. The research of Song and Zlotnicki and Chambers and Willis on GRACE-derived ocean bottom pressures in the sub-polar gyre led to the discovery of an ENSO teleconnection and a long-term change in OBP in the North Pacific sub-polar gyre that was not predicted by an ocean model. Further, Chambers and Willis were able to identify an internal redistribution of mass between Atlantic and Pacific Oceans lasting at least six years, which was not predicted by ocean models and was the first direct evidence of sustained mass transport from one ocean basin to another on periods longer than a year. Boening et al. observed a record increase in OBP over part of the southeastern Pacific in late 2009 and early 2010, primarily caused by wind stress curl associated with a strong and persistent anticyclone and likely related to the concurrent Central Pacific El Nino. GRACE has far surpassed its 5-year design lifetime, but it will likely succumb to the aging of batteries and instrument systems sometime in the next few years. NASA has begun initial development of a follow-on to GRACE with very similar design, which could launch as soon as 2016 and would provide continuity in the data record while improving resolution slightly. Higher resolution time variable gravity missions are also on the drawing board .

Rodell, Matthew↗

Extensive Attention Mechanisms in Graph Neural Networks for Materials Discovery

We present our research where attention mechanism is extensively applied to various aspects of graph neural net- works for predicting materials properties. As a result, surrogate models can not only replace costly simulations for materials screening but also formulate hypotheses and insights to guide further design exploration. We predict formation energy of the Materials Project and gas adsorption of crystalline adsorbents, and demonstrate the superior performance of our graph neural networks. Moreover, attention reveals important substructures that the machine learning models deem important for a material to achieve desired target properties. Our model is based solely on standard structural input files containing atomistic descriptions of the adsorbent material candidates. We construct novel methodological extensions to match the prediction accuracy of state-of-the-art models some of which were built with hundreds of features at much higher computational cost. We show that sophisticated neural networks can obviate the need for elaborate feature engineering. Our approach can be more broadly applied to optimize gas capture processes at industrial scale.

Cong, Guojing↗

MuSIKAL: Multiphysics Simulations and Knowledge Discovery through AI/ML Technologies

Under the MuSiKAL project, we developed a framework for a coastal digital twin (DT) platform capable of integrating diverse data resources, configuring multiscale model simulations, performing SciML‐accelerated predictions, with applications primarily driven by storm surge and heavily rainfall events impacting the Gulf Coast of the U.S.

54 ENVIRONMENTAL SCIENCES↗

The discovery of an O subdwarf in the globular cluster NGC 6712

Spectral data for C49 in the globular cluster NGC 6712 are examined with reference to evolutionary models for low-mass stars that are contracting into white dwarfs. The spectrum of this star is found to be almost identical to that of the first sdO star found in a globular cluster, star A in NGC 6397. Analysis of the spectral data using nonlocal thermodynamic equilibrium models gives surface parameters T not less than 50,000 K, log g = 5.5 plus or minus 0.5, and N(He)/N(H) approximately equal to 0.1. The results are consistent with the models considered.

Remillard, R. A.↗

Photometric and spectroscopic observations of SN 1990E in NGC 1035 - Observational constraints for models of type II supernovae

We present 126 photometric and 30 spectral observations of SN 1990E spanning from 12 days before B maximum to 600 days past discovery. These observations show that SN 1990E was of type II-P, displaying hydrogen in its spectrum, and the characteristic plateau in its light curve. SN 1990E is one of the few SNe II which has been well observed before maximum light, and we present evidence that this SN was discovered very soon after its explosion. In the earliest spectra we identify, for the first time, several N II lines. We present a new technique for measuring extinction to SNe II based on the evolution of absorption lines, and use this method to estimate the extinction to SN 1990E, A(V) = 1.5 +/- 0.3 mag. From our photometric data we have constructed a bolometric light curve for SN 1990E and show that, even at the earliest times, the bolometric luminosity was failing rapidly. We use the late-time bolometric light curve to show that SN 1990E trapped a majority of the gamma rays produced by the radioactive decay of Co-56, and estimate that SN 1990E ejected an amount of Ni-56 virtually identical to that of SN 1987A.

Schmidt, Brian P.↗

TOI-1235 b: A Keystone Super-Earth for Testing Radius Valley Emergence Models around Early M Dwarfs

Small planets on close-in orbits tend to exhibit envelope mass fractions of either effectively zero or up to a few percent depending on their size and orbital period. Models of thermally driven atmospheric mass loss and of terrestrial planet formation in a gas-poor environment make distinct predictions regarding the location of this rocky/nonrocky transition in period–radius space. Here we present the confirmation of TOI-1235 b (P = 3.44 days, r(p)=1.738 (+0.087, -0.076) Rꚛ), a planet whose size and period are intermediate between the competing model predictions, thus making the system an important test case for emergence models of the rocky/nonrocky transition around early M dwarfs (R(s) = 0.630 ± 0.015 Rꙩ, M(s) = 0.640 ± 0.016 Mꙩ}$). We confirm the TESS planet discovery using reconnaissance spectroscopy, ground-based photometry, high-resolution imaging, and a set of 38 precise radial velocities (RVs) from HARPS-N and HIRES. We measure a planet mass of 6.91 (+0.75, -0.85) Mꚛ, which implies an iron core mass fraction of 20 (+15,-12)% in the absence of a gaseous envelope. The bulk composition of TOI-1235 b is therefore consistent with being Earth-like, and we constrain an H/He envelope mass fraction to be <0.5% at 90% confidence. Our results are consistent with model predictions from thermally driven atmospheric mass loss but not with gas-poor formation, suggesting that the former class of processes remains efficient at sculpting close-in planets around early M dwarfs. Our RV analysis also reveals a strong periodicity close to the first harmonic of the photometrically determined stellar rotation period that we treat as stellar activity, despite other lines of evidence favoring a planetary origin P= 21.8(+0.9, _0.8) days, m(p)sin i= 13.0 (+3.8,-5.3) Mꚛ) that cannot be firmly ruled out by our data.

Ryan Cloutier↗

Machine Learning Prediction of the Critical Cooling Rate for Metallic Glasses from Expanded Datasets and Elemental Features

In this study, we use a random forest (RF) model to predict the critical cooling rate (R C ) for glass formation of various alloys from features of their constituent elements. The RF model was trained on a database that integrates multiple sources of direct and indirect R C data for metallic glasses to expand the directly measured R C database of less than 100 values to a training set of over 2000 values. The model error on 5-fold cross-validation (CV) is 0.66 orders of magnitude in K/s. The error on leave-out-one-group CV on alloy system groups is 0.59 log units in K/s when the target alloy constituents appear more than 500 times in training data. Using this model, we make predictions for the set of compositions with melt-spun glasses in the database and for the full set of quaternary alloys that have constituents which appear more than 500 times in training data. These predictions identify a number of potential new bulk metallic glass systems for future study, but the model is most useful for the identification of alloy systems likely to contain good glass formers rather than detailed discovery of bulk glass composition regions within known glassy systems.

36 MATERIALS SCIENCE↗

Diazotrophic Bacteria and Their Mechanisms to Interact and Benefit Cereals

Plant-growth-promoting bacteria (PGPB) stimulate plant growth through diverse mechanisms. In addition to biological nitrogen fixation, diazotrophic PGPB can improve nutrient uptake efficiency from the soil, produce and release phytohormones to the host, and confer resistance against pathogens. The genetic determinants that drive the success of biological nitrogen fixation in nonlegume plants are understudied. These determinants include recognition and signaling pathways, bacterial colonization, and genotype specificity between host and bacteria. This review presents recent discoveries of how nitrogen-fixing PGPB interact with cereals and promote plant growth. We suggest adopting an experimental model system, such as the Setaria–diazotrophic bacteria association, as a reliable way to better understand the associated mechanisms and, ultimately, increase the use of PGPB inoculants for sustainable agriculture. [Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .

Biochemistry & Molecular Biology↗

Platform Of Optimal Experiment Management

The platform of optimal experiment management, POEM, powered with automated machine learning to accelerate the discovery of optimal solutions, and automatically guide the design of experiments to be evaluated. POEM currently supports 1) random model explorations for experiment design, 2) sparse grid model explorations with Gaussian Polynomial Chaos surrogate model to accelerate experiment design ,3) time-dependent model sensitivity and uncertainty analysis to identify the importance features for experiment design, 4) model calibrations via Bayesian inference to integrate experiments to improve model performance, and 5) Bayesian optimization for optimal experimental design. In addition, POEM aims to simplify the process of experimental design for users, enabling them to analyze the data with minimal human intervention, and improving the technological output from research activities.

Wang, Congjian [Idaho National Laboratory (INL), I↗

Defect diffusion graph neural networks (d2gnn)

SAND2025-01004O Defect Diffusion Graph Neural Networks (d2gnn) is a software tool that assists in the discovery of new materials for high-temperature, clean-energy applications. It uses advanced graph neural networks to model the relationship between material structures and their defect properties. The application helps predict how materials will behave under different conditions and accelerates the development of innovative materials. Sandia National Laboratories is a multimission laboratory managed and operated by National Technology & Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International Inc., for the U.S. Department of Energy’s National Nuclear Security Administration under contract DE-NA0003525.

Witman, Matthew [Sandia National Lab. (SNL-CA), Li↗

Cortical Proteins and Individual Differences in Cognitive Resilience in Older Adults

Background and objectives: Cognitive resilience is a well-recognized concept, but knowledge gaps about its underlying mechanisms have made it difficult to develop instruments that identify older adults with high or low resilience. We tested whether aggregating cortical peptides associated with cognitive resilience into an index can identify adults with higher or lower cognitive resilience. Methods: We used data from 1,192 older decedents, including annual clinical testing, indices of 10 Alzheimer disease (AD) and related dementia (ADRD) pathologies, and 226 proteotypic peptides measured in the dorsal lateral prefrontal cortex. We used linear mixed-effects models to identify peptides that were related to cognitive resilience (i.e., cognitive decline not explained by ADRD pathologies [false discovery rate <0.05]). We aggregated the expression levels of these resilience peptides into a person-specific cognitive resilience index and examined its association with AD clinical and pathologic phenotypes. Results: We constructed a resilience index from 52 of 226 peptides related to cognitive resilience. A higher index was associated with slower cognitive decline (estimate 0.05, SE 0.003, p < 0.001) and slower motor decline (estimate 0.005, SE 0.001, p < 0.001). Most resilience peptides (70%) were specific to cognitive decline, but 30% also provided resilience for motor decline. A higher index was also related to a lower burden of AD pathologies (odds ratio [OR] 0.41, SE 0.01, p < 0.001) and modified the association of AD pathology with cognition in that a higher index modified the negative effects of AD pathology on AD dementia proximate to death (OR 0.70, SE 0.14, p = 0.010). Up to 90% of cognitive resilience peptides were related to AD pathologic phenotypes. Discussion: Cortical proteins may provide some degree of cognitive resilience. These multifunctional proteins also seem to provide resilience to other AD clinical phenotypes and have independent associations with ADRD pathologies. Resilience proteins may be high-value therapeutic targets for drug discovery of interventions that maintain brain health in aging adults via multiple pathways.

60 APPLIED LIFE SCIENCES↗

High Precision Penning Trap Measurements of beta-decay Q-values for Neutrino Physics

The 2015 Nobel Prize in physics was awarded to Takaaki Kajita and Arthur B. McDonald “for the discovery of neutrino oscillations, which shows that neutrinos have mass”. This fact has wide reaching implications for the standard model of particle physics, nuclear physics, and cosmology. However, important fundamental questions remain: What is the absolute neutrino mass scale? Is the neutrino a Majorana or a Dirac particle? A number of large-scale experiments are underway or are being developed to attempt to answer these questions. Two classes of experiments are direct neutrino mass determination experiments, and searches for neutrinoless double betadecay. This work aimed to aid these experiments via high-precision Q value determinations for the relevant isotopes using Penning trap mass spectrometry (PTMS).

42 ENGINEERING↗