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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

Model Data Archive Associated with Manuscript "Fire-altered Carbon Pools Create Disturbance Memory in Stream Dissolved Organic Carbon"

This data package supports the publication “Fire-altered Carbon Pools Create Disturbance Memory in Stream Dissolved Organic Carbon” by Li et al. (2026). The package contains processed model inputs, configuration files, restart files, simulation outputs, scripts, and visualization products used to evaluate post-fire dissolved organic carbon (DOC) dynamics in the Naches River Watershed, Washington, USA, following the 2021 Schneider Springs Fire. The modeling workflow couples ELM-BGC, the biogeochemistry-enabled Energy Exascale Earth System Model Land Model; ATS, the Advanced Terrestrial Simulator for integrated surface-subsurface hydrology; and PFLOTRAN, a reactive transport model for multicomponent aqueous geochemistry. Together, these models simulate how wildfire-induced changes in vegetation, litter, coarse woody debris, and soil organic matter influence DOC production, transport, and reaction from burned hillslopes to stream networks. The archive includes preprocessed meteorological, geospatial, hydrologic, and biogeochemical forcing data; ELM-BGC-derived DOC source terms; ATS mesh files; PFLOTRAN reactive-transport inputs; model configuration files; spin-up and transient restart files; watershed-scale diagnostic outputs; stream concentration time series; and figures or visualization files used to inspect and reproduce key results. File types include Hierarchical Data Format 5 (HDF5) files for gridded forcing and model-coupling data, model input and configuration files for ELM-BGC, ATS, and PFLOTRAN, restart and simulation-output files generated by the modeling workflow, tabular or time-series diagnostic outputs, scripts for post-processing and figure generation, and image or visualization products associated with the manuscript. Use of the package depends on the intended task. Re-running the simulations requires the relevant modeling software, including ELM-BGC, ATS, and PFLOTRAN as ATS's geochemical engine. Inspecting outputs and reproducing figures requires Python with scientific plotting libraries such as Matplotlib, and three-dimensional model outputs may be viewed with ParaView. Geographic information system files or maps may be inspected with ArcGIS Pro or comparable GIS software. The data package is intended to enable traceability, reuse, and partial reproduction of the coupled land-to-watershed hydro-biogeochemical modeling workflow used to test how wildfire disturbance affects terrestrial carbon pools and downstream DOC dynamics.

ATS↗
DOE OSTI2020

A Quantum-Based Approach to Predict Primary Radiation Damage in Polymeric Networks

Initial atomistic-level radiation damage in chemically reactive materials is thought to induce reaction cascades that can result in undesirable degradation of macroscale properties. Ensembles of quantum-based molecular dynamics (QMD) simulations can accurately predict these cascades, but extracting chemical insights from the many underlying trajectories is a labor-intensive process that can require substantial a priori intuition. We develop here a general and automated graph-based approach to extract all chemically distinct structures sampled in QMD simulations and apply our approach to predict primary radiation damage of polydimethylsiloxane (PDMS), the main constituent of silicones. A postprocessing protocol is developed to identify underlying polymer backbone structures as connected components in QMD trajectories. Furthermore, these backbones form a repository of radiation-damaged structures. A scheme for extracting and updating a library of isomorphically distinct structures is proposed to identify the spanning set and aid chemical interpretation of the repository. The analyses are applied to ensembles of cascade QMD simulations in which the four element types in PDMS are selectively excited in primary knock-on atom events. Our approach reveals a much higher degree of combinatorial complexity in this system than was inferred through radiolysis experiments. Probabilities are extracted for radiation-induced network changes including formation of branch points, carbon linkages, cycles, bond scissions, and carbon uptake into the Si–O siloxane backbone network. The general analysis framework presented here is readily extendable to modeling chemical degradation of other polymers and molecular materials and provides a basis for future quantum-informed multiscale modeling of radiation damage.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Classification of River Catchments in the Contiguous United States: Code, Dataset, Similarity Patterns, and Resulting Classes

This dataset serves as supplementary information for the paper by Ciulla F. and Varadharajan C. A Network Approach for Multiscale Catchment Classification using Traits (see reference 1). It contains environmental and physical catchment traits, such as temperatures, precipitation, land use and human interference, from 9067 sites across the contiguous United States (CONUS). The purpose of this dataset is to provide information for a better trait-based categorization of river catchments in the CONUS using networks as an analytical tool. The traits variables match the ones present in the GAGES-II dataset and the preprocessing steps are described in the Methods section (processed_dataset.csv). Additionally we include the topologies (nodes, edges and clusters, also referred as classes) of the catchment network and traits network generated by said dataset (csv and json files). A series of tables support the information carried by the network providing more detailed descriptions of cluster components (SI1.pdf). A summary of all the plots of clusters of catchments with at least 50 nodes is provided (SI2.pdf). The characteristic traits for each cluster of catchments is presented as z-score (traits_categories_zscores_per_catchment_class.csv). The link to the hydrological behavior of clusters of catchments is displayed by boxplots, each describing a particular river discharge index (SI3.pdf). Both csv and json files can be read by common text editors but the data contained into them can be better handled using programming languages like python and database oriented libraries like pandas. Pdf files can be read by any pdf reader software.[02-23-2024] Update: The code and datasets necessary to reproduce the results of the study are available as a zipped repository (code_datasets_catchments_similarity.zip).

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Investigation of design principles for metal-binding and conductive protein assemblies

Throughout the lifetime of this initiative, including renewals, we focused on understanding the fundamental principles of protein-protein interface design that enable predictable and modular spatial and kinetic control of multi-component protein self-assembly in 1D, 2D, and 3D, including the interface with inorganic materials, small molecules, and metal ions. We designed individual protein components that bind specific metal ions, including REEs and transport ions across lipid membranes. We created helical 1D filaments of repeating units with programmed periodicity, pitch, and multi-component environmentally responsive self-assembling protein fibers. We showed that these filaments reversibly assemble and disassemble under specific pH conditions and created end-specific caps that independently tune the balance of attachment and detachment rates at each terminus of the filament. Using similar filaments, we succeeded in binding arrays of heme and chlorophyll molecules and assembling patterned helical coatings around carbon nanotubes in efforts to create de novo conductive nanowires. By arraying REE binding sites in a large circular tandem array with a repeat protein-based cyclic oligomer, we created a molecular scaffold for superradiance and paramagnetic quantum sensing. We created a range of one-component and two-component self-assembling 2D arrays and showed that when designed to engage cell receptors, these arrays can control cell behavior from outside the cell signal to inside the cell. We designed helical repeat proteins with variable lengths displaying charged residues in a pattern matched to the cation lattice of mica. achieved a range of ordered states with an epitaxial match to the underlying crystal lattice. We further applied the learned principles of protein-induced biomineralization to design proteins with an interface lattice matching CaCO 3 and guide the formation of specific crystal forms of CaCO 3 from solution, a significant advance toward the global need to manage carbon. In all cases of mineral lattice matching and biomineralization, we followed assembly using molecularly resolved in situ AFM imaging and extracted information about assembly pathways and energetics, applying deep learning to quantify the dynamics of protein self-organization. We developed techniques for using dynamic metal-dependent interfaces on protein nanopores for discriminatively sensing dilute REEs in solution and demonstrated the use of strong metal-binding interfaces to drive nanocage disassembly for conditional nanocompartmentalization applications. This grant supported 11 people, including Asim Bera, Evans Brackenbrough, Andrew Borst, Nikita Hanikel, Timothy Huddy, Emily Joyce, Alex Young-Seug Kang, Ryan Kibler, Joshua Morris Lubner, Harley Pyles, and Shuai Zhang. The research effort culminated in the production of published papers and theses. Electronic Thesis/Dissertation are distributed by ProQuest/UMI Dissertation Publishing and made available on an open access basis through UW Libraries ResearchWorks Service.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Flux Cube Reconstruction from Slitless Spectroscopy

Slitless spectroscopy enables efficient, large-area surveys without target preselection, yet it faces challenges from source blending, higher noise, and lost spatial–spectral information. We present an advanced, nonparametric, data-driven algorithm that leverages multiple dispersion angles to reconstruct three-dimensional flux distributions, providing low-resolution integral field unit capabilities from slitless data. By treating each pixel as an independent element, our method naturally handles source confusion without requiring prior assumptions regarding redshifts, templates, or model libraries. We validate the algorithm using simulated Roman Space Telescope wide-field slitless spectroscopy images that are equivalent to what is expected from the High-Latitude Time-Domain Survey. First, we demonstrate that a host-galaxy model reconstructed from multiple dispersion angles can be used to accurately subtract host light from a transient, recovering a Type Ia supernova spectrum with minimal bias. Second, we showcase a high-fidelity flux-cube reconstruction of a complex galaxy, successfully measuring the redshift and recovering continuum, emission, and absorption features. This approach highlights the potential of multi-dispersion-angle slitless data to provide spatially resolved spectral information in a nonparametric way, which is traditionally accessible only with integral field spectroscopy, opening a new window into large, unbiased, and spatially resolved studies of galaxy evolution.

Griggio, M. [Space Telescope Science Institute, Ba↗
DOE OSTI2020

Description of the LASSO Data Bundles Product

The U. S. Department of Energy (DOE) Atmospheric Radiation Measurement (ARM) user facility began a pilot project in May 2015 to design a routine, high-resolution modeling capability to complement ARM’s extensive suite of measurements. This modeling capability has evolved into the Large-Eddy Simulation (LES) ARM Symbiotic Simulation and Observation (LASSO) datastream. The datastream, broadly termed data bundles, contains high-resolution model output, input files, observations for evaluation, and skill scores for the simulations. The initial focus of LASSO is on shallow convection at the ARM Southern Great Plains (SGP) atmospheric observatory. The availability of LES simulations with concurrent observations serves many purposes. LES helps bridge the scale gap between DOE ARM observations and models, and the use of routine LES adds value to observations. It provides a self-consistent representation of the atmosphere and a dynamical context for the observations. Further, it elucidates unobservable processes and properties. LASSO generates a simulation library for researchers that enables statistical approaches beyond a single-case mentality. It also provides tools necessary for modelers to reproduce the LES and conduct their own sensitivity experiments. The LASSO library of data bundles is designed to facilitate a wide range of research. For an observationalist, LASSO can help inform instrument remote-sensing retrievals, conduct observation system simulation experiments (OSSEs), and test implications of radar scan strategies or flight paths. For a theoretician, LASSO can help calculate estimates of fluxes and co-variability of values, and test relationships without having to run the model personally. For a modeler, LASSO can help one know ahead of time which days have good forcing, have co-registered observations at high-resolution scales, and have simulation inputs and corresponding outputs to test parameterizations. Further details on the overall LASSO project are available at https://www.arm.gov/capabilities/modeling/lasso.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Population-based heteropolymer design to mimic protein mixtures

Biological fluids, the most complex blends, have compositions that constantly vary and cannot be molecularly defined. Despite these uncertainties, proteins fluctuate, fold, function and evolve as programmed. We propose that in addition to the known monomeric sequence requirements, protein sequences encode multi-pair interactions at the segmental level to navigate random encounters; synthetic heteropolymers capable of emulating such interactions can replicate how proteins behave in biological fluids individually and collectively. Here, we extracted the chemical characteristics and sequential arrangement along a protein chain at the segmental level from natural protein libraries and used the information to design heteropolymer ensembles as mixtures of disordered, partially folded and folded proteins. For each heteropolymer ensemble, the level of segmental similarity to that of natural proteins determines its ability to replicate many functions of biological fluids including assisting protein folding during translation, preserving the viability of fetal bovine serum without refrigeration, enhancing the thermal stability of proteins and behaving like synthetic cytosol under biologically relevant conditions. Molecular studies further translated protein sequence information at the segmental level into intermolecular interactions with a defined range, degree of diversity and temporal and spatial availability. This framework provides valuable guiding principles to synthetically realize protein properties, engineer bio/abiotic hybrid materials and, ultimately, realize matter-to-life transformations.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Summer 2021 Internship Report

The Library Research and Prototyping team (Proto Team) under the research library explores aspects of scholarly communication, covering aspects of infrastructure, interoperability, and persistence. One of the key contributions of the team is the contribution in standardizing and forming the infrastructure for Mementos in web archiving. The Memento framework in web archiving enables access to digital resources in prior versions serving both persistence and the interoperability of the information. During the internship program, I worked on improving the Memento infrastructure by updating the memento validator. The Memento validator provides the functionality of testing the compliance of the web resources to the Memento specification. The application is intended to be used by the community at large such as web archives, researchers, librarians, and general users, with different levels of technical expertise.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗
DOE OSTI2024

WETO Software Stack Best Practices

Wind energy researchers typically share one key characteristic: a passion for increasing wind energy in the global energy mix. The U.S. Department of Energy (DOE) supports this mission in a number of ways including allocating funding directly to various aspects of wind energy research through the Office of Energy Efficiency and Renewable Energy (EERE) via the Wind Energy Technologies Office (WETO). While the traditional output of research is academic publication, software development efforts are increasingly a major focus. Software tools in the research environment allow researchers to describe an idea and quickly increase the scope and scale as they study it further. As a product of research, these tools represent a direct pipeline from researcher to industry practitioners since they are the implementation of ideas described in academic publications. Given this vital role in wind energy research and commercial development, the broad research software portfolio supported by WETO must maintain a minimum level of quality to support the wind energy field in the growing transition to renewable energy. This report outlines a series o f best practices to be adopted by all WETO-supported software projects, as well as expectations that the communities interacting with these projects should have of the developers and tools themselves. Wind energy research software has a unique standing in the field of scientific software. The stakeholders are varied with a subset being: (1) DOE EERE leadership, (2) DOE WETO leadership and program managers, (3) National lab leadership, (4) Associated project principle investigators, (5) Research software engineers, (6) Wind energy researchers in academia (including graduate students, post docs, and national lab staff), (7) Industry researchers and practitioners, (8) Commercial software developers, and (9) The general public interested in wind energy. These software are typically the end-user of other generic software libraries, so the funding cycles are often tied to applied research rather than the development of the software itself. Since the developers are also wind energy researchers, these tools are typically designed in a way that closely resembles the application in which they're used. Additionally, the expertise and incentives for the developers have a high variability, and often neither are aligned with software engineering or computer science. Given the unique environment in which wind energy research software is produced and consumed, it is critical for model owners to understand the context of their software. A framework for developing this understanding is to answer the following questions of a given software project: What is it's purpose? What is its role in the field of wind energy? What is the profile of the expected users? For how long will it be relevant? What is the expected impact? These questions allow model owners to identify the appropriate methods for the design, development, and long term maintenance of their software. Additionally, the answer provide context for future planners to understand why particular decisions were made and discern the consequences of changing course. The information is aggregated from experience within WETO-supported software development groups as well as external organizations and efforts to define the craft of research software engineering. These best practices aim to make the collaborative development process efficient and effective while improving the model understanding across stakeholders. Additionally, the general adoption of a common framework for software quality ensures that the end users of WETO software can trust these tools and accurately understand the risks to workflow integration.

17 WIND ENERGY↗
DOE OSTI2023

hIPPYlib-MUQ: A Bayesian Inference Software Framework for Integration of Data with Complex Predictive Models under Uncertainty

Bayesian inference provides a systematic framework for integration of data with mathematical models to quantify the uncertainty in the solution of the inverse problem. However, the solution of Bayesian inverse problems governed by complex forward models described by partial differential equations (PDEs) remains prohibitive with black-box Markov chain Monte Carlo (MCMC) methods. We present hIPPYlib-MUQ, an extensible and scalable software framework that contains implementations of state-of-the art algorithms aimed to overcome the challenges of high-dimensional, PDE-constrained Bayesian inverse problems. These algorithms accelerate MCMC sampling by exploiting the geometry and intrinsic low-dimensionality of parameter space via derivative information and low rank approximation. The software integrates two complementary open-source software packages, hIPPYlib and MUQ. hIPPYlib solves PDE-constrained inverse problems using automatically-generated adjoint-based derivatives, but it lacks full Bayesian capabilities. MUQ provides a spectrum of powerful Bayesian inversion models and algorithms, but expects forward models to come equipped with gradients and Hessians to permit large-scale solution. By combining these two complementary libraries, we created a robust, scalable, and efficient software framework that realizes the benefits of each and allows us to tackle complex large-scale Bayesian inverse problems across a broad spectrum of scientific and engineering disciplines. To illustrate the capabilities of hIPPYlib-MUQ, we present a comparison of a number of MCMC methods available in the integrated software on several high-dimensional Bayesian inverse problems. These include problems characterized by both linear and nonlinear PDEs, various noise models, and different parameter dimensions. The results demonstrate that large (~ 50×) speedups over conventional black box and gradient-based MCMC algorithms can be obtained by exploiting Hessian information (from the log-posterior), underscoring the power of the integrated hIPPYlib-MUQ framework.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Conceptual Design of Neutron Sensor Qualification Device

The Advanced Sensors and Instrumentation Program at Idaho National Laboratory has been formulating strategies to qualify sensors for use in nuclear environments, particularly in irradiation experiments and advanced reactors. When qualifying neutron sensors for use in high-temperature environments, the wide range of neutron flux levels and representative energy spectra presents significant challenges. This paper discusses the development of the Neutron Sensor Qualification Device (NQD), which is designed to test neutron sensors in high temperature controlled environments with known neutron spectra, addressing the spatial and spectral complexities of neutron fluxes in reactor cores. The proposed NQD will be situated in the exposure room at the Armed Forces Radiobiology Research Institute, thus affording a unique capability to expose sensors to high neutron and gamma fluxes. To achieve thermal control, the device will utilize a radiation-hardened tube furnace, accommodating multiple sensors and neutron activation dosimetry wires. Titanium, iron, and cobalt dosimeter wires are chosen from the American Society for Testing and Materials and International Reactor Dosimetry and Fusion File libraries as references for providing energy-dependent fluence measurements. The design ensures precise sensor positioning to minimize mutual shielding and flux perturbation, which are evaluated via Monte Carlo N particle Transport Code (MCNP) simulations. These simulations have informed the development of guidelines on sensor placement within the NQD. The NQD is essential to the qualification of neutron sensors for advanced reactor technologies. It enables controlled testing of a statistically significant number of sensors, thereby supporting assessments of sensor performance across various neutron flux levels and temperatures. This paper highlights the detailed planning for the NQD prototype, along with its inaugural irradiation (scheduled for fiscal year [FY] 2025). The results from this initial testing will be fundamental in evaluating the device’s performance and establishing measurement uncertainty for in-pile neutron sensor measurements.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2024

Parallax-corrected VISST-derived pixel-level products from satellite GOES-16

The NASA Langley group led by William Smith produced GOES-16 satellite cloud retrievals over an approximate 10 by 10 degree region over the CACTI field campaign location. These retrievals are described here: https://www.arm.gov/capabilities/vaps/visst and are available for download here . They use algorithms historically called VISST that are now referred to as SatCORPS. More information can be found in Trepte et al. (2019), Minnis et al. (2021), and Yost et al. (2021). If using this dataset, please cite these references, the CACTI VISST dataset DOI found at the download link above, and this dataset’s DOI. The CACTI VISST pixel-level retrievals are on a 2 km spatial grid and available every 15 minutes (every 10 minutes late in the campaign), producing 21,765 files for the entire field campaign between October 2018 and April 2019. They are not corrected for parallax error, which is an offset in the actual geographical location of a cloud above the surface due to the satellite viewing the cloud partly from the side off nadir. This dataset applies a correction for parallax using the location relative to the satellite and the retrieved cloud top height above the surface, which allows the dataset to be geo-located with surface-based observations. The parallax correction for each location depends on the longitude, latitude and cloud top height above ground level (AGL) for that longitude and latitude in the original VISST files. The cloud top height AGL requires first computing the surface elevation at each VISST grid point. Data from the Advanced Spaceborne Thermal Emission and Reflection (ASTER) Global Digital Elevation Map Version 3 at 30-m resolution is projected onto the VISST grid using conservative coarsening (conserving surface elevation) in the xESMF Python package. The surface elevation is then subtracted from the VISST-retrieved cloud top height above mean sea level. These cloud top heights AGL are then combined with longitude and latitude to estimate the latitude and longitude corrections. Due to variability in cloud top height, the parallax shifts produce an irregular grid of values since higher cloud tops are shifted further than lower cloud tops. A ball tree-based neighbor search with Haversine distance is performed using the Python-based scikit-learn library to find the nearest VISST grid point to each parallax correction-shifted point. The data value of the shifted point is then assigned to that VISST grid point. In this manner, the irregular geographical shifts to correct for parallax are projected back to the rectilinear VISST grid. Because relatively higher clouds should obscure lower clouds, the variable values for the highest cloud top are preferentially chosen if two or more values are assigned to a grid point. The parallax correction should be viewed as an improved but still imperfect estimation of the cloud top locations, largely because the cloud top height is an imperfect retrieval. Please see the attached README document for further information. Users are encouraged to contact the authors with any additional questions.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

SERTA Domain Containing Protein 1 (SERTAD1) Interacts with Classical Swine Fever Virus Structural Glycoprotein E2, Which Is Involved in Virus Virulence in Swine

E2 is the major structural glycoprotein of the classical swine fever virus (CSFV). E2 has been shown to be involved in important virus functions such as replication and virulence in swine. Using the yeast two-hybrid system, we previously identified several host proteins specifically interacting with CSFV E2. Here, we analyze the protein interaction of E2 with SERTA domain containing protein 1 (SERTAD1), a factor involved in the stimulation of the transcriptional activities of different host genes. We have confirmed that the interaction between these two proteins occurs in CSFV-infected swine cells by using a proximity ligation assay and confocal microscopy. Amino acid residues in the CSFV E2 protein that are responsible for mediating the interaction with SERTAD1 were mapped by a yeast two-hybrid approach using a randomly mutated E2 library. Using that information, a recombinant CSFV mutant (E2ΔSERTAD1v) that harbors substitutions in those residues mediating the protein-interaction with SERTAD1 was developed and used to study the role of the E2-SERTAD1 interaction in viral replication and virulence in swine. CSFV E2ΔSERTAD1v, when compared to the parental BICv, showed a clearly decreased ability to replicate in the SK6 swine cell line and a more severe replication defect in primary swine macrophage cultures. Importantly, 80% of animals infected with E2ΔSERTAD1v survived infection, remaining clinically normal during the 21-day observational period. This result would indicate that the ability of CSFV E2 to bind host SERTAD1 protein during infection plays a critical role in virus virulence.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Scaling from Flux Towers to Ecosystem Models: Regional Constraints on Carbon Cycle Processes from Atmospheric Carbonyl Sulfide (Final Report)

DOE supported research suggests that gross primary productivity (GPP) is largely underestimated by global earth system models [Welp et al., 2011], reflecting the persistent challenge in extrapolating from local-scale GPP observations to global-scale earth system models. This poor understanding of GPP at large spatial scales is of particular concern in tropical forests. In tropical forests, some earth systems models forecast a powerful feedback between a warming climate and a decline in GPP resulting in forest dieback. While this simulated feedback is intensely debated, we lack robust large-scale constraints on GPP that are needed to resolve this debate. In particular, carbon dioxide measurements provide valuable information on net carbon flux, but not on the gross flux associated with GPP. Here we conducted a study of regional-to-global scale GPP using atmospheric carbonyl sulfide to provide a new constraint on GPP mechanisms in earth system models. Our project activities integrated modeling, in situ measurement, and remote sensing techniques to resolve GPP for the Amazon as well as global scale trends. The results of this work included initiating airborne carbonyl sulfide monitoring in the Amazon, training for postdocs and graduate students at a Hispanic Serving Institution, fundamental advances in carbonyl sulfide budgets [e.g. Hilton et al., Nature Climate Change, 2017], and high-profile publications that focused on GPP trends for the Amazon [Stinecipher et al., GRL, 2022] and global historical GPP trends [Campbell, et al., Nature, 2017]. Based on the suggestion of our DOE program manager, we published a state-of-the-science commentary to the scientific community on GPP monitoring with COS [Campbell et al., EOS, 2017] which was selected as the cover story. DOE support was acknowledged in all reports. The importance of this research to understanding climate change was communicated to the general public through community seminars (Rotary, Public Libraries, State Parks), an op-ed (SF Chronicle), and interviews in the mass media including two stories in the New York Times (4/5/17; 7/30/18), one of which was especially widely read after it was featured in the New York Time’s Quote of the Day.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Two-dimensional materials for bio-realistic neuronal computing networks

Two-dimensional (2D) van der Waals materials have found broad utility in a diverse range of applications including electronics, optoelectronics, renewable energy, and quantum information technologies. Meanwhile, exponentially growing digital data coupled with the ubiquity of artificial intelligence algorithms have generated significant interest in edge neuromorphic computing as an alternative to centralized cloud computing. The drive to incorporate neuroscience principles into computing hardware is motivated by the low power consumption, parallel processing, and reconfigurability of the human brain. The diverse library of 2D materials with atomic-level thicknesses, exceptional electrostatic tunability, and integration versatility is particularly well-suited for realizing bio-realistic synaptic and neuronal functionality. Here, we summarize past and present work in this field and outline the frontier challenges that have not yet been overcome. Here we also delineate potential solutions and suggest that the neuroscience principles of criticality and synchrony have the potential to inspire breakthrough applications of 2D materials in neuronal computing networks.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Targeting tRNA-synthetase interactions towards novel therapeutic discovery against eukaryotic pathogens

The development of chemotherapies against eukaryotic pathogens is especially challenging because of both the evolutionary conservation of drug targets between host and parasite, and the evolution of strain-dependent drug resistance. There is a strong need for new nontoxic drugs with broad-spectrum activity against trypanosome parasites such as Leishmania and Trypanosoma. A relatively untested approach is to target macromolecular interactions in parasites rather than small molecular interactions, under the hypothesis that the features specifying macromolecular interactions diverge more rapidly through coevolution. We computed tRNA Class-Informative Features in humans and independently in eight distinct clades of trypanosomes, identifying parasite-specific informative features, including base pairs and base mis-pairs, that are broadly conserved over approximately 250 million years of trypanosome evolution. Validating these observations, we demonstrated biochemically that tRNA:aminoacyl-tRNA synthetase (aaRS) interactions are a promising target for anti-trypanosomal drug discovery. From a marine natural products extract library, we identified several fractions with inhibitory activity toward Leishmania major alanyl-tRNA synthetase (AlaRS) but no activity against the human homolog. These marine natural products extracts showed cross-reactivity towards Trypanosoma cruzi AlaRS indicating the broad-spectrum potential of our network predictions. We also identified Leishmania major threonyl-tRNA synthetase (ThrRS) inhibitors from the same library. We discuss why chemotherapies targeting multiple aaRSs should be less prone to the evolution of resistance than monotherapeutic or synergistic combination chemotherapies targeting only one aaRS.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

PDBx/mmCIF Ecosystem: Foundational Semantic Tools for Structural Biology

PDBx/mmCIF, Protein Data Bank Exchange (PDBx) macromolecular Crystallographic Information Framework (mmCIF), has become the data standard for structural biology. With its early roots in the domain of small-molecule crystallography, PDBx/mmCIF provides an extensible data representation that is used for deposition, archiving, remediation, and public dissemination of experimentally determined three-dimensional (3D) structures of biological macromolecules by the Worldwide Protein Data Bank (wwPDB, wwpdb.org). Extensions of PDBx/mmCIF are similarly used for computed structure models by ModelArchive (modelarchive.org), integrative/hybrid structures by PDB-Dev (pdb-dev.wwpdb.org), small angle scattering data by Small Angle Scattering Biological Data Bank SASBDB (sasbdb.org), and for models computed generated with the AlphaFold 2.0 deep learning software suite (alphafold.ebi.ac.uk). Community-driven development of PDBx/mmCIF spans three decades, involving contributions from researchers, software and methods developers in structural sciences, data repository providers, scientific publishers, and professional societies. Having a semantically rich and extensible data framework for representing a wide range of structural biology experimental and computational results, combined with expertly curated 3D biostructure data sets in public repositories, accelerates the pace of scientific discovery. Herein, we describe the architecture of the PDBx/mmCIF data standard, tools used to maintain representations of the data standard, governance, and processes by which data content standards are extended, plus community tools/software libraries available for processing and checking the integrity of PDBx/mmCIF data. Use cases exemplify how the members of the Worldwide Protein Data Bank have used PDBx/mmCIF as the foundation for its pipeline for delivering Findable, Accessible, Interoperable, and Reusable (FAIR) data to many millions of users worldwide.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Unrecognized Sources of Uncertainties ( USU ) in Experimental Nuclear Data

Evaluated nuclear data uncertainties reported in the literature or archived in data libraries are often perceived as unrealistic, most often because they are thought to be too small. The impact of this issue in applied nuclear science has been discussed widely in recent years. Commonly suggested causes are: poor estimates of specific error components, neglect of uncertainty correlations, and overlooked known error sources. However, instances have been reported where very careful, objective assessments of all known error sources have been made with realistic error magnitudes and correlations provided, yet the resulting evaluated uncertainties still appear to be inconsistent with observed scatter of predicted mean values. These discrepancies might be attributed to significant unrecognized sources of uncertainty ( USU ) that limit the accuracy to which these physical quantities can be determined. The objective of our work reported herein has been to develop qualitative and quantitative procedures for revealing and including USU estimates in nuclear data evaluations involving experimental input data. This paper identifies several specific clues that can be explored by evaluators in identifying the existence of USU . It then describes numerical procedures we have introduced to generate quantitative estimates of USU magnitudes. Key requirements for these procedures to be viable are that sufficient numbers of data points be available, for statistical reasons, and that additional supporting information about the measurements be provided by the experimenters. Several realistic examples are described here to illustrate these procedures and demonstrate their outcomes and limitations. Our work strongly supports the view that USU is an important issue in nuclear data evaluation, with significant consequences for applications, and that this topic warrants further investigation by the nuclear science community.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗