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NASA NTRS2005

Documentation and Validation of the Goddard Earth Observing System (GEOS) Data Assimilation System, Version 4

This document describes the structure and validation of a frozen version of the Goddard Earth Observing System Data Assimilation System (GEOS DAS): GEOS-4.0.3. Significant features of GEOS-4 include: version 3 of the Community Climate Model (CCM3) with the addition of a finite volume dynamical core; version two of the Community Land Model (CLM2); the Physical-space Statistical Analysis System (PSAS); and an interactive retrieval system (iRET) for assimilating TOVS radiance data. Upon completion of the GEOS-4 validation in December 2003, GEOS-4 became operational on 15 January 2004. Products from GEOS-4 have been used in supporting field campaigns and for reprocessing several years of data for CERES.

Suarez, Max J.↗

NASA NTRS2023

Aura/MLS Observes and SD-WACCM-X Simulates the Seasonality, Quasi-Biennial Oscillation and El Niño-Southern Oscillation of the Migrating Diurnal Tide Driving Upper Mesospheric CO Primarily Through Vertical Advection

This work uses 17 years of upper mesospheric carbon monoxide (CO) and temperature observations by the Microwave Limb Sounder (MLS) on-board the Aura satellite to present and explain the seasonal and interannual variability of the migrating diurnal tide (DW1) component of upper mesospheric CO. This work then compares these observations to simulations by the Specified Dynamics – Whole Atmosphere Community Climate Model with Ionosphere/Thermosphere eXtension (SD-WACCM-X). Results show that, for all seasons, MLS CO local-time perturbations peaks above 85 km and has a latitude structure resembling the (1,1) mode in temperature. On the other hand, SD-WACCM-X DW1 also peaks above 85 km and has a latitude structure resembling the (1,1) mode but it simulates 2 local maximum of the (1,1) mode between 85 km and 92 km. Despite the differences in altitude structure, a tendency analysis and the adiabatic displacement method revealed that, on seasonal and interannual timescales, observed and modelled CO’s (1,1) component can be reproduced solely using vertical advection. It was also found that both observed and modelled CO’s (1,1) component contains interannual oscillations with periodicities close to that of the Quasi-biennial Oscillation and the El Niño–Southern Oscillation. From these results, this work concludes that on seasonal and interannual timescales, the observed and modelled (1,1) mode affects the global structure of upper mesospheric CO primarily through vertical advection.

Cornelius Csar Jude H Salinas↗

NASA NTRS2023

Aura/MLS Observes, and SD-WACCM-X Simulates the Seasonality, Quasi-Biennial Oscillation and El Nino Southern Oscillation of the Migrating Diurnal Tide Driving Upper Mesospheric Co Primarily Through Vertical Advection

This work uses 17 years of upper mesospheric carbon monoxide (CO) and temperature observations by the Microwave Limb Sounder (MLS) on-board the Aura satellite to present and explain the seasonal and interannual variability of the migrating diurnal tide (DW1) component of upper mesospheric CO. This work then compares these observations to simulations by the Specified Dynamics – Whole Atmosphere Community Climate Model with Ionosphere/Thermosphere eXtension (SD-WACCM-X). Results show that, for all seasons, MLS CO local-time perturbations peaks above 85 km and has a latitude structure resembling the (1,1) mode in temperature. On the other hand, SD-WACCM-X DW1 also peaks above 85 km and has a latitude structure resembling the (1,1) mode but it simulates 2 local maximum of the (1,1) mode between 85 km and 92 km. Despite the differences in altitude structure, a tendency analysis and the adiabatic displacement method revealed that, on seasonal and interannual timescales, observed and modelled CO’s (1,1) component can be reproduced solely using vertical advection. It was also found that both observed and modelled CO’s (1,1) component contains interannual oscillations with periodicities close to that of the Quasi-biennial Oscillation and the El Nino Southern Oscillation. From these results, this work concludes that on seasonal and interannual timescales, the observed and modelled (1,1) mode affects the global structure of upper mesospheric CO primarily through vertical advection.

Cornelius Csar Jude H. Salinas↗

DOE OSTI2025

Integrating Ultra-Coarse-Grained Protein Models into Accessible Workflows for Multiscale Molecular Dynamics

To capture protein conformational transitions using molecular dynamics (MD), several simulation resolutions covering different spatial and temporal scales are typically needed. All-atom (AA) simulations provide fine resolution, but are computationally infeasible for large systems over longer durations. Coarse-grained (CG) and ultra-coarse-grained (UCG) models have a lower resolution and computational cost while still being able to conserve essential protein features. Prior work on a Multiscale Machinelearned Modeling Infrastructure (MuMMI) combined both AA and CG simulations to study RAS-RAF protein interactions, leveraging CG models for longer time scales and using AA to investigate unusual conformations in greater detail. However, MuMMI is still resource-intensive, and this study aims to maximize exploration of the protein conformational space while reducing computational cost. In this paper, we build on prior work that integrates UCG models based on heterogeneous elastic network modeling (hENM) into the MuMMI workflow. We demonstrate that UCG models enable accurate sampling of protein conformations, focusing on simulating RAS-RAF protein interactions. Using higher-resolution CG Martini simulation data, we can automatically refine intramolecular interactions in UCG models. We present a scalable Python package that uses fluctuations observed in higher-resolution CG Martini simulations to estimate bond coefficients of the UCG model. We built novel machine learning-based backmapping methods to recover more detailed CG Martini structures from UCG structures, using diffusion models to learn the mapping between scales. Finally, we present UCG-mini-MuMMI, an accessible and less compute-intensive version of MuMMI as a resource for the scientific community. Incorporating UCG models into MD studies is applicable to a broad range of systems and proteins, and our study offers insights into the advantages and limitations of these methods.

Chemical structure↗

DOE OSTI2020

Threat Reduction Research Networks: Fostering Sustainable Collaborations Through Trainings for Genomics for Biosurveillance

Scientific research communities can be represented as heterogeneous or multidimensional networks encompassing multiple types of entities and relationships. These networks might include researchers, institutions, meetings, and publications, connected by relationships like authorship, employment, and attendance. We describe a method for efficiently and flexibly capturing, storing, and extracting information from multidimensional scientific networks using a graph database. The database structure is based on an ontology that captures allowable types of entities and relationships. This allows us to construct a variety of projections of the underlying multidimensional graph through database queries to answer specific research questions. We demonstrate this process through a study of the U.S. Biological Threat Reduction Program (BTRP), which seeks to develop Threat Reduction Networks to build and strengthen a sustainable international community of biosecurity, biosafety, and biosurveillance experts to address shared biological threat reduction challenges. Networks like these create connectional intelligence among researchers and institutions around the world, and are central to the concept of cooperative threat reduction. Our analysis focuses on a series of seven BTRP genome sequencing training workshops, showing how they created a growing network of participants and countries over time, which is also reflected in coauthorship relationships among attendees. By capturing concept and relationship hierarchies, our ontology-based approach allows us to pose general or specific questions about networks within the same framework. This approach can be applied to other research communities or multidimensional social networks to capture, analyze, and visualize different types of interactions and how they change over time.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRSDate not supplied

NASA Life Sciences Portal (NLSP): Supporting Scientific Transparency and Reproducibility

NASA’s Life Sciences Ports (NLSP) serves the scientific community by providing curated data from space life science experiment. The Human Research Program (HRP) with the help of NLSP is currently transforming their life sciences data archive systems and processes to improve compliance with the FAIR principles [1]. Some of these improvements will at the same time support the twin pillars of Open Science [2]: transparency of methods and reproducibility of results. Scientific transparency is marked by the easily intelligible communication of what has been investigated: what were the procedures for collecting sample and the characteristics of samples collected? what kinds of measurements were made, what were the environmental conditions of the measurements? What were the analysis techniques of the collected data? Reproducibility of the results and findings from the investigation requires a high level of transparency for all but the simplest investigations; the slightest deviation in communicating and replicating complex experimental procedures or data analyses can often yield quite different data and even findings, thwarting their validation. One of the ways the NLSP is aiming to improve the communication of scientific information is through the use of ontology-driven metadata. Ontologies are powerful, graph-based knowledge representation structures, which can be leveraged to increase data interoperability, the area of the FAIR principles in which many data systems most lack compliance. Over the past decade, there has been a concerted effort in the biomedical community to develop modular and narrowly focused domain and application-specific ontologies in a common, open-source framework, the Open Biological and Biomedical Ontology (OBO) Foundry [3]. The open sharing and modular nature of this effort promises huge increases in harmonized data sharing for systems that leverage these models. Which is in line with the FAIR Data Principles of Findability, Accessibility, Interoperability, and Reuse for scientific data management and stewardship. 1. Wilkinson, M.D., et al., The FAIR Guiding Principles for scientific data management and stewardship. Sci Data, 2016. 3: p. 160018. 2. National Academies of Sciences, E. and Medicine, Open Science by Design: Realizing a Vision for 21st Century Research. 2018, Washington, DC: The National Academies Press. 232. 3. Smith, B., et al., The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nat Biotechnol, 2007. 25(11): p. 1251-5.

Life Sciences data↗

NASA NTRSDate not supplied

NASA Life Sciences Portal (NLSP): Supporting Scientific Transparency and Reproducibility

Life Sciences data↗

DOE OSTI2025

A Shared Understanding and Paths Forward for Community Benefit Mechanisms: Workshop Summary Report

On October 7-8, 2024, the U.S. Department of Energy's Office of Energy Efficiency and Renewable Energy (EERE) and the National Renewable Energy Laboratory hosted an in-person workshop focused on research needs and strategies for community benefit mechanisms (CBMs) used in the deployment of renewable energy infrastructure. Community benefit mechanisms (such as community benefit agreements, funds, and donations) are used to provide increased benefits and/or mitigate negative impacts of energy development for the communities that are impacted. The workshop aimed to assess the current state of knowledge, tools, practices, and lessons learned, as well as to identify research and other work needed to improve the impact and effective implementation of CBMs. This report describes the purpose and structure of the workshop and summarizes key themes, questions, issues, and ideas that arose from the workshop.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

DOE OSTI2022

Transitions of foliar mycobiota community and transcriptome in response to pathogenic conifer needle interactions

Profiling the host–mycobiota interactions in healthy vs. diseased forest ecosystems helps understand the dynamics of understudied yet increasingly important threats to forest health that are emerging due to climate change. We analyzed the structural and functional changes of the mycobiota and the responses of Pinus contorta in the Lophodermella needle cast pathosystem through metabarcoding and metatranscriptomics. When needles transitioned from asymptomatic to symptomatic, dysbiosis of the mycobiota occurred, but with an enrichment of Lophodermella pathogens. Many pathogenicity-related genes were highly expressed by the mycobiota at the necrotrophic phase, showing an active pathogen response that are absent in asymptomatic needles. This study also revealed that Lophodermella spp. are members of a healthy needle mycobiota that have latent lifestyles suggesting that other pine needle pathogens may have similar biology. Interestingly, Pinus contorta upregulated defense genes in healthy needles, indicating response to fungal recognition, while a variety of biotic and abiotic stresses genes were activated in diseased needles. Further investigation to elucidate the possible antagonistic interplay of other biotic members leading to disease progression and/or suppression is warranted. This study provides insights into microbial interactions in non-model pathosystems and contributes to the development of new forest management strategies against emerging latent pathogens.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Dual function of Candida auris mannosyltransferase, MNT5, in biofilm community protection from antifungal therapy and the host

Screen of mutants from a mannosyltransferase family identified the importance of MNT5 for C. auris biofilm drug resistance and neutrophil evasion. Biochemical analysis of the mnt5∆ mutant matrix and cell wall identified alterations in the mannan structures. Resistance and matrix for mnt5∆ were restored with delivery of wild-type matrix via extracellular vesicles. Analysis of the mnt5∆ cell wall revealed a reduction in mannan and compensatory increase in cell surface glucan and chitin, suggesting a role for MNT5 in mannan masking of pathogen-associated molecular patterns.

Candida auris↗

NASA NTRSDate not supplied

Overview of A Survey Methods Test for the NASA Quesst Community Survey Campaign

In its mission to expand knowledge and improve aviation, NASA conducts research to address sonic boom noise, the prime barrier to overland supersonic flight. NASA is currently preparing for a community survey campaign to assess response to noise from the new X-59 aircraft. During each community survey, a substantial number of observations must be collected over a limited timeframe to generate a dose response relationship. A sample of residents will be recruited in advance to fill out a brief survey each time X-59 flies over, approximately 80 times throughout a month. In preparation NASA conducted a month-long test of survey methods in 2023. A sample of 800 residents was recruited from a simulated fly-over area. Because there were no actual X-59 fly-overs, respondents were asked about their reactions to noise from normal aircraft operations. The respondents chose whether to fill out the survey on the web or via a smartphone application. Evaluating response rates and how they evolved over time was a specific focus of the test. Also, a graduated incentive structure was implemented to keep respondents engaged. Finally, location data was collected from respondents since it will be needed to estimate individual noise exposure from X-59. The results of this survey test will help determine the design of the community survey campaign.

Sonic boom↗

NASA NTRS2000

Highly ordered vertical structure of Synechococcus populations within the one-millimeter-thick photic zone of a hot spring cyanobacterial mat

A variety of contemporary techniques were used to investigate the vertical distribution of thermophilic unicellular cyanobacteria, Synechococcus spp., and their activity within the upper 1-mm-thick photic zone of the mat community found in an alkaline siliceous hot spring in Yellowstone National Park in Wyoming. Detailed measurements were made over a diel cycle at a 61 degrees C site. Net oxygenic photosynthesis measured with oxygen microelectrodes was highest within the uppermost 100- to 200-microm-thick layer until midmorning, but as the day progressed, the peak of net activity shifted to deeper layers, stabilizing at a depth of 300 microm from midday throughout the afternoon. Examination of vertical thin sections by bright-field and autofluorescence microscopy revealed the existence of different populations of Synechococcus which form discrete bands at different vertical positions. Denaturing gradient gel electrophoresis analysis of PCR-amplified 16S rRNA gene segments from horizontal cryosections obtained at 100-microm-thick vertical intervals also suggested vertical stratification of cyanobacterial, green sulfur bacterium-like, and green nonsulfur bacterium-like populations. There was no evidence of diel migration. However, image analysis of vertical thin sections revealed the presence of a narrow band of rod-shaped Synechococcus cells in which the cells assumed an upright position. These upright cells, located 400 to 800 microm below the surface, were observed only in mat samples obtained around noon. In mat samples obtained at other time points, the cells were randomly oriented throughout the mat. These combined observations reveal the existence of a highly ordered structure within the very thin photic zone of this hot spring microbial mat, consisting of morphologically similar Synechococcus populations that are likely to be differentially adapted, some co-occurring with green sulfur bacterium-like populations, and all overlying green nonsulfur bacterium-like populations.

Non-NASA Center↗

DOE OSTI2023

Community Centered Solar Development (CCSD) Case Study Interviews [Slides]

Large-scale solar (LSS, defined here as ground-mounted photovoltaic projects ≥1 MWDC) has grown rapidly in the U.S., accounting for nearly half of new electric generating capacity added to the U.S. grid in 2022. All sources of electricity bring positive and negative impacts to hosting communities and the rapid growth of LSS has increased the urgency to understand those impacts. Yet, information about the potential positive and negative impacts of LSS on host communities, and the factors or drivers leading to support or opposition to a project, is lacking. This information gap limits how project developers, municipalities, and local siting authorities can address community concerns and appropriately align proposed projects to best suit and benefit local communities. As part of Berkeley Lab’s Community-Centered Solar Development (CCSD) project, this research set out to explore deep insights and perceptions from LSS stakeholders that only qualitative data can provide to identify key factors driving project success or threatened failure. Case studies, such as those utilized in this research, are uniquely adept at capturing the subjective experience of individuals and at identifying variables, structures, and interactions between stakeholders. Our case studies included 54 semi-structured interviews across 7 different LSS sites, representing a diversity of geographies, project sizes (MW), site types (i.e., greenfield, agrivoltaic, and brownfield / contaminated sites), zoning jurisdiction types, and more (Table 1). In addition to local residents living in close proximity to these LSS sites, we interviewed other key stakeholders involved in the projects such as developers, decision-makers, utility representatives, landowners, and individuals from community-based organizations. The overarching aim of this case study research was two-fold: (1) to inform subsequent tasks in the CCSD research project (including an upcoming national survey of LSS neighbors), and (2) to provide insights into the following set of research questions: -What are the key positive and negative drivers leading to support and opposition to LSS projects? -To what extent do LSS projects exacerbate or mitigate perceived inequities and marginalization within hosting communities and how can those inequities be mitigated going forward? -What strategies can communities employ to align LSS development with local land-use plans and community needs and values? The research findings and next steps are described in this slide deck report.

14 SOLAR ENERGY↗

DOE OSTI2023

Spatiotemporal Studies of Soluble Inorganic Nanostructures with X‐rays and Neutrons

This Review addresses the use of X-ray and neutron scattering as well as X-ray absorption to describe how inorganic nanostructured materials assemble, evolve, and function in solution. We first provide an overview of techniques and instrumentation (both large user facilities and benchtop). We review recent studies of soluble inorganic nanostructure assembly, covering the disciplines of materials synthesis, processes in nature, nuclear materials, and the widely applicable fundamental processes of hydrophobic interactions and ion pairing. Reviewed studies cover size regimes and length scales ranging from sub-Ångström (coordination chemistry and ion pairing) to several nanometers (molecular clusters, i.e. polyoxometalates, polyoxocations, and metal-organic polyhedra), to the mesoscale (supramolecular assembly processes). Reviewed studies predominantly exploit 1) SAXS/WAXS/SANS (small- and wide-angle X-ray or neutron scattering), 2) PDF (pair-distribution function analysis of X-ray total scattering), and 3) XANES and EXAFS (X-ray absorption near-edge structure and extended X-ray absorption fine structure, respectively). While the scattering techniques provide structural information, X-ray absorption yields the oxidation state in addition to the local coordination. Our goal for this Review is to provide information and inspiration for the inorganic/materials science communities that may benefit from elucidating the role of solution speciation in natural and synthetic processes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

Multifrontal Non-negative Matrix Factorization

Non-negative matrix factorization (Nmf) is an important tool in high-performance large scale data analytics with applications ranging from community detection, recommender system, feature detection and linear and non-linear unmixing. While traditional Nmf works well when the data set is relatively dense, however, it may not extract sufficient structure when the data is extremely sparse. Specifically, traditional Nmf fails to exploit the structured sparsity of the large and sparse data sets resulting in dense factors. We propose a new algorithm for performing Nmf on sparse data that we call multifrontal Nmf (Mf-Nmf) since it borrows several ideas from the multifrontal method for unconstrained factorization (e.g. LU and QR). We also present an efficient shared memory parallel implementation of Mf-Nmf and discuss its performance and scalability. We conduct several experiments on synthetic and realworld datasets and demonstrate the usefulness of the algorithm by comparing it against standard baselines. We obtain a speedup of 1.2x to 19.5x on 24 cores with an average speed up of 10.3x across all the real world datasets.

Sao, Piyush↗

DOE OSTI2024

Atomic-scale investigations of Ti 3 C 2 T x MXene surfaces

The family of two-dimensional (2D) carbides and/or nitrides, also known as MXenes, has generated great excitement within the scientific community and has been proposed for a wide variety of applications since its discovery. Despite this attention, there have been only limited studies of the atomically resolved local electronic and physical structure of MXene surfaces strongly affecting the physicochemical properties of these materials. Here, in this study, we report local structural, spectroscopic, and chemical investigations of the surfaces of Ti 3 C 2 T x flakes using scanning tunneling microscopy and spectroscopy, closely coupled to theoretical studies. Terminal groups are visualized and characterized, along with surface TiO 2 clusters formed upon exposure to air. Fundamental insight into the local electronic and chemical properties associated with different terminal groups on MXenes and their oxidation products is presented.

36 MATERIALS SCIENCE↗

DOE OSTI2024

The present and future of QCD

This White Paper presents an overview of the current status and future perspective of QCD research, based on the community inputs and scientific conclusions from the 2022 Hot and Cold QCD Town Meeting. We present the This White Paper presents an overview of the current status and future perspective of QCD research, based on the community inputs and scientific conclusions from the 2022 Hot and Cold QCD Town Meeting. We present the progress made in the last decade toward a deep understanding of both the fundamental structure of the sub-atomic matter of nucleon and nucleus in cold QCD, and the hot QCD matter in heavy ion collisions. We identify key questions of QCD research and plausible paths to obtaining answers to those questions in the near future, hence defining priorities of our research over the coming decades.progress made in the last decade toward a deep understanding of both the fundamental structure of the sub-atomic matter of nucleon and nucleus in cold QCD, and the hot QCD matter in heavy ion collisions. We identify key questions of QCD research and plausible paths to obtaining answers to those questions in the near future, hence defining priorities of our research over the coming decades.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2021

Database of ab initio L-edge X-ray absorption near edge structure

Abstract The L-edge X-ray Absorption Near Edge Structure (XANES) is widely used in the characterization of transition metal compounds. Here, we report the development of a database of computed L-edge XANES using the multiple scattering theory-based FEFF9 code. The initial release of the database contains more than 140,000 L-edge spectra for more than 22,000 structures generated using a high-throughput computational workflow. The data is disseminated through the Materials Project and addresses a critical need for L-edge XANES spectra among the research community.

42 ENGINEERING↗