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DOE OSTI2021

Integrating Applied Energy and BER Smart Data Capabilities to Develop a DOE Data Fabric for Energy-Water R&D

Focal Area(s): 1) Data acquisition and assimilation enabled by machine learning, AI, and advanced methods including experimental/network design/optimization, unsupervised learning (including deep learning), and hardware-related efforts involving AI (e.g., edge computing). Science Challenge: DOE R&D, including DOE’s Basic Energy Research (BER)’s Environmental Systems Science Division (EESSD) program and DOE’s applied energy research (AER) programs (EERE, FE, and NE) are producers and consumers of Earth systems datasets. This white paper focuses on the first topic area from the call in relation to how crosscutting resources and innovations from DOE’s EESSD and AER can be brought to bear to mutual benefit and more efficient energy-water, Earth system data resources through improved. The overarching challenge posed by this call focuses on how DOE can directly leverage artificial intelligence (AI) to engineer a substantial (paradigm-changing) improvement in Earth System Predictability? While stemming from DOE BER’s EESSD program, this is a challenge that is faced and also being addressed by DOE’s AER programs. Over the past decade plus, FE, EERE, and NE programs have made important strides towards addressing this need. These strides are in many ways highly complementary to EESSD’s MODEX efforts. Energy water systems spanning metocean to groundwater to surface water systems all are data driven whether for basic energy or applied energy. These are remote, multi-variate, complex natural, and in many cases engineered, systems. Key needs and challenges of both EESSD and AER include developing data-focused tools to enhance data search and discovery to fill in knowledge gaps (address sparse data challenge), and rapidly transform datasets, including disparate and multi-source data. Leveraging DOE on-premise computing (HPC, exascale) infrastructure supports the computing-intensive algorithms required to execute these data acquisition and transformation processes to derive enriched knowledge and data, driving AI/ML and big data analytics for these systems. The opportunity lies in combining BER and AER efforts to provide a more robust, advanced, efficient and complete computing data fabric to address energy-water data acquisition and assimilation needs which currently pose significant impediments to AI/ML predictions and research.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2019

Future High Energy Frontier Colliders

Colliders have been at the forefront of scientic discoveries in high-energy particle physics since the inception of the colliding beams method in the middle of the 20th century. The field of accelerators is very dynamic and many innovative concepts are currently being considered such future facilities as Higgs factories and energy frontier colliders beyond the LHC. Here we briefly overview leading proposals and studies towards the next generation colliders and discuss their major challenges as well as directions of corresponding accelerator R and D programs needed to address their cost and performance risks.

43 PARTICLE ACCELERATORS↗

DOE OSTI2017

Final Technical Report

Our BES supported program integrates molecular beam epitaxy growth with in situ atomic scale imaging using scanning tunneling microscopy/spectroscopy and atomic force microscopy. Aided by density functional theory calculations, we explore enhanced functionalities emerging from the interplay of strain, proximity, and spin-orbit interactions in heterostructures of wide band gap semiconductors, graphene, and Dirac materials, focusing on three thrusts: 1) doping wide bandgap semiconductors and graphene; 2) graphene nanoribbons and graphene-semiconductor heterostructures; and 3) Dirac materials. Our findings and discoveries have led to the publication of one book chapter and twenty-three refereed journal articles, including several in high impact journals such as Nature Communications, Physical Review Letters, and Nano Letters. Highlights of each thrust are provided in the report.

36 MATERIALS SCIENCE↗

DOE OSTI2013

VinaMPI: Facilitating multiple receptor high-throughput virtual docking on high-performance computers

The program VinaMPI has been developed to enable massively large virtual drug screens on leadership-class computing resources, using a large number of cores to decrease the time-to-completion of the screen. VinaMPI is a massively parallel Message Passing Interface (MPI) program based on the multithreaded virtual docking program AutodockVina, and is used to distribute tasks while multithreading is used to speed-up individual docking tasks. VinaMPI uses a distribution scheme in which tasks are evenly distributed to the workers based on the complexity of each task, as defined by the number of rotatable bonds in each chemical compound investigated. VinaMPI efficiently handles multiple proteins in a ligand screen, allowing for high-throughput inverse docking that presents new opportunities for improving the efficiency of the drug discovery pipeline. VinaMPI successfully ran on 84,672 cores with a continual decrease in job completion time with increasing core count. The ratio of the number of tasks in a screening to the number of workers should be at least around 100 in order to have a good load balance and an optimal job completion time. The code is freely available and downloadable. Lastly, the instructions for downloading and using the code are provided in the Supporting Information.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2013

CANDIDATE PLANETS IN THE HABITABLE ZONES OF KEPLER STARS

A key goal of the Kepler mission is the discovery of Earth-size transiting planets in ''habitable zones'' where stellar irradiance maintains a temperate climate on an Earth-like planet. Robust estimates of planet radius and irradiance require accurate stellar parameters, but most Kepler systems are faint, making spectroscopy difficult and prioritization of targets desirable. The parameters of 2035 host stars were estimated by Bayesian analysis and the probabilities p{sub HZ} that 2738 candidate or confirmed planets orbit in the habitable zone were calculated. Dartmouth Stellar Evolution Program models were compared to photometry from the Kepler Input Catalog, priors for stellar mass, age, metallicity and distance, and planet transit duration. The analysis yielded probability density functions for calculating confidence intervals of planet radius and stellar irradiance, as well as p{sub HZ}. Sixty-two planets have p{sub HZ} > 0.5 and a most probable stellar irradiance within habitable zone limits. Fourteen of these have radii less than twice the Earth; the objects most resembling Earth in terms of radius and irradiance are KOIs 2626.01 and 3010.01, which orbit late K/M-type dwarf stars. The fraction of Kepler dwarf stars with Earth-size planets in the habitable zone ({eta}{sub Circled-Plus }) is 0.46, with a 95% confidence interval of 0.31-0.64. Parallaxes from the Gaia mission will reduce uncertainties by more than a factor of five and permit definitive assignments of transiting planets to the habitable zones of Kepler stars.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2022

Management and Storage of Scientific Data

Scientific discoveries rely heavily on efficient access, search, and management of massive data sets. Data management technologies have, for decades, provided foundational capabilities for scientific computing. Just as storage, input/output (I/O), and data management have been fundamental to simulation-based science for many years, so too are capable data-management technologies key to the success of today’s scientific workflows utilizing data intensive and machine learning (ML) techniques. The Department of Energy, Office of Science, Advanced Scientific Computing Research (ASCR) program has invested broadly in data-management research focused on high-performance computing (HPC) systems, from parallel file systems that store data to application software that makes these systems more productive. Still, advances in technology combined with growing diversity of supported science strongly motivate continued investment in this area. In January 2022, ASCR convened a workshop to identify priority research directions in the area of data management for high-performance and scientific computing. Attendees were challenged to identify promising approaches that would support the breadth of the DOE mission, including the explosion of artificial intelligence (AI) uses and the growing needs of experimental and observational science. Technological and science drivers were identified and considered as they relate to key aspects of data management such as interfaces, architectural design, and FAIR principles (Findable, Accessible, Interoperable, and Reusable). The thoughts of the workshop participants were distilled into a set of four priority research directions with the potential for high impact on DOE science. These research directions are summarized in the following pages.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

DOE OSTI2021

The 2020 Nonlinear Mechanics and Dynamics Research Institute

The 2020 Nonlinear Mechanics and Dynamics (NOMAD) Research Institute was successfully held from June 15 to July 30, 2020. NOMAD brings together participants with diverse technical backgrounds to work in small teams to cultivate new ideas and approaches in engineering mechanics and dynamics research. NOMAD provides an opportunity for researchers – especially early career researchers - to develop lasting collaborations that go beyond what can be established from the limited interactions at their institutions or at annual conferences. A total of 11 students participated in the seven-week long program held virtually due to the COVID-19 health pandemic. The students collaborated on one of four research projects that were developed by various mentors from Sandia National Laboratories, the University of New Mexico, and other academic and research institutions. In addition to the research activities, the students attended weekly technical seminars, various virtual tours, and socialized at virtual gatherings. At the end of the summer, the students gave a final technical presentation on their research findings. Many of the research discoveries made at NOMAD 2020 are published as proceedings at technical conferences and have direct alignment with the critical mission work performed at Sandia.

42 ENGINEERING↗

DOE OSTI2020

Exploiting the Spinel Structure for Li-ion Battery Applications: A Tribute to John B. Goodenough

This review provides a personal account of career-long efforts, interwoven with the contributions of others, to exploit the [B 2 ]O 4 framework of an A[B 2 ]O 4 spinel structure for lithium-ion battery applications, where A = Li, and B is one or more metal cations. The narrative begins at the Council for Scientific and Industrial Research (CSIR) in South Africa in the mid-1970s when, in response to the Middle East oil crisis, worldwide efforts were turned to develop high-temperature sodium and lithium batteries to power electric vehicles. In 1981, results in CSIR's program on a high-temperature lithium battery led to a collaborative project on room-temperature lithium cells with Prof. John B. Goodenough at Oxford University, where studies of Fe 3 O 4 , Mn 3 O 4 , and LiMn 2 O 4 cathodes led to the recognition of the broad utility of the [B2]O4 spinel framework as an anode, cathode, or solid electrolyte for rechargeable lithium cells. This finding has had a profound and lasting impact, influencing further ideas and discoveries at the CSIR, Argonne National Laboratory, and elsewhere. The narrative emphasizes the compositional versatility of the spinel structure and the opportunities to tailor the electrochemical potential and stability of a Li-ion cell.

25 ENERGY STORAGE↗

DOE OSTI2020

Plant science decadal vision 2020–2030: Reimagining the potential of plants for a healthy and sustainable future

Abstract Plants, and the biological systems around them, are key to the future health of the planet and its inhabitants. The Plant Science Decadal Vision 2020–2030 frames our ability to perform vital and far‐reaching research in plant systems sciences, essential to how we value participants and apply emerging technologies. We outline a comprehensive vision for addressing some of our most pressing global problems through discovery, practical applications, and education. The Decadal Vision was developed by the participants at the Plant Summit 2019, a community event organized by the Plant Science Research Network. The Decadal Vision describes a holistic vision for the next decade of plant science that blends recommendations for research, people, and technology. Going beyond discoveries and applications, we, the plant science community, must implement bold, innovative changes to research cultures and training paradigms in this era of automation, virtualization, and the looming shadow of climate change. Our vision and hopes for the next decade are encapsulated in the phrase reimagining the potential of plants for a healthy and sustainable future. The Decadal Vision recognizes the vital intersection of human and scientific elements and demands an integrated implementation of strategies for research (Goals 1–4), people (Goals 5 and 6), and technology (Goals 7 and 8). This report is intended to help inspire and guide the research community, scientific societies, federal funding agencies, private philanthropies, corporations, educators, entrepreneurs, and early career researchers over the next 10 years. The research encompass experimental and computational approaches to understanding and predicting ecosystem behavior; novel production systems for food, feed, and fiber with greater crop diversity, efficiency, productivity, and resilience that improve ecosystem health; approaches to realize the potential for advances in nutrition, discovery and engineering of plant‐based medicines, and "green infrastructure." Launching the Transparent Plant will use experimental and computational approaches to break down the phytobiome into a "parts store" that supports tinkering and supports query, prediction, and rapid‐response problem solving. Equity, diversity, and inclusion are indispensable cornerstones of realizing our vision. We make recommendations around funding and systems that support customized professional development. Plant systems are frequently taken for granted therefore we make recommendations to improve plant awareness and community science programs to increase understanding of scientific research. We prioritize emerging technologies, focusing on non‐invasive imaging, sensors, and plug‐and‐play portable lab technologies, coupled with enabling computational advances. Plant systems science will benefit from data management and future advances in automation, machine learning, natural language processing, and artificial intelligence‐assisted data integration, pattern identification, and decision making. Implementation of this vision will transform plant systems science and ripple outwards through society and across the globe. Beyond deepening our biological understanding, we envision entirely new applications. We further anticipate a wave of diversification of plant systems practitioners while stimulating community engagement, underpinning increasing entrepreneurship. This surge of engagement and knowledge will help satisfy and stoke people's natural curiosity about the future, and their desire to prepare for it, as they seek fuller information about food, health, climate and ecological systems.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2014

The agile alert system for gamma-ray transients

In recent years, a new generation of space missions has offered great opportunities for discovery in high-energy astrophysics. In this article we focus on the scientific operations of the Gamma-Ray Imaging Detector (GRID) on board the AGILE space mission. AGILE-GRID, sensitive in the energy range of 30 MeV-30 GeV, has detected many γ-ray transients of both galactic and extragalactic origin. This work presents the AGILE innovative approach to fast γ-ray transient detection, which is a challenging task and a crucial part of the AGILE scientific program. The goals are to describe (1) the AGILE Gamma-Ray Alert System, (2) a new algorithm for blind search identification of transients within a short processing time, (3) the AGILE procedure for γ-ray transient alert management, and (4) the likelihood of ratio tests that are necessary to evaluate the post-trial statistical significance of the results. Special algorithms and an optimized sequence of tasks are necessary to reach our goal. Data are automatically analyzed at every orbital downlink by an alert pipeline operating on different timescales. As proper flux thresholds are exceeded, alerts are automatically generated and sent as SMS messages to cellular telephones, via e-mail, and via push notifications from an application for smartphones and tablets. These alerts are crosschecked with the results of two pipelines, and a manual analysis is performed. Being a small scientific-class mission, AGILE is characterized by optimization of both scientific analysis and ground-segment resources. The system is capable of generating alerts within two to three hours of a data downlink, an unprecedented reaction time in γ-ray astrophysics.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2022

Tevatron greatest hits

The Tevatron collider led the World energy frontier program in particle physics during the late 20th and early 21st centuries. During this exciting period the standard model of particle physics was in its final stages of development and the search for physics beyond the standard model became one of the main research topics. In this review article we summarize the design and performance of the Tevatron collider and its two detectors, CDF and D0, as well as their evolution. Here, highlights of the Tevatron scientific results are provided, including the discovery of the top quark and measurements of its properties, studies and discoveries of the particles containing heavy quarks, precision studies of the strong and electroweak forces, searches for beyond the standard model particles and interactions, as well as the hunt for the Higgs boson.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2014

FIVE DEBRIS DISKS NEWLY REVEALED IN SCATTERED LIGHT FROM THE HUBBLE SPACE TELESCOPE NICMOS ARCHIVE

We have spatially resolved five debris disks (HD 30447, HD 35841, HD 141943, HD 191089, and HD 202917) for the first time in near-infrared scattered light by reanalyzing archival Hubble Space Telescope (HST)/NICMOS coronagraphic images obtained between 1999 and 2006. One of these disks (HD 202917) was previously resolved at visible wavelengths using the HST/Advanced Camera for Surveys. To obtain these new disk images, we performed advanced point-spread function subtraction based on the Karhunen-Loève Image Projection algorithm on recently reprocessed NICMOS data with improved detector artifact removal (Legacy Archive PSF Library And Circumstellar Environments (LAPLACE) Legacy program). Three of the disks (HD 30447, HD 35841, and HD 141943) appear edge-on, while the other two (HD 191089 and HD 202917) appear inclined. The inclined disks have been sculpted into rings; in particular, the disk around HD 202917 exhibits strong asymmetries. All five host stars are young (8-40 Myr), nearby (40-100 pc) F and G stars, and one (HD 141943) is a close analog to the young Sun during the epoch of terrestrial planet formation. Our discoveries increase the number of debris disks resolved in scattered light from 19 to 23 (a 21% increase). Given their youth, proximity, and brightness (V = 7.2-8.5), these targets are excellent candidates for follow-up investigations of planet formation at visible wavelengths using the HST/Space Telescope Imaging Spectrograph coronagraph, at near-infrared wavelengths with the Gemini Planet Imager and Very Large Telescope/SPHERE, and at thermal infrared wavelengths with the James Webb Space Telescope NIRCam and MIRI coronagraphs.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2017

Performance Portability of HPC Discovery Science Software: Fusion Energy Turbulence Simulations at Extreme Scale

As HPC R&D moves forward on a variety of “path to exascale” architectures today, an associated objective is to demonstrate performance portability of discovery-science-capable software. Important application domains, such as Magnetic Fusion Energy (MFE), have improved modelling of increasingly complex physical systems -- especially with respect to reducing “time-to-solution” as well as “energy to solution.” The emergence of new insights on confinement scaling in MFE systems has been aided significantly by efficient software capable of harnessing powerful supercomputers to carry out simulations with unprecedented resolution and temporal duration to address increasing problem sizes. Specifically, highly scalable particle-in-cell (PIC) programing methodology is used in this paper to demonstrate how modern scientific applications can achieve efficient architecture-dependent optimizations of performance scaling and code portability for path-to-exascale platforms.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2014

Louisiana Immersive Technologies Enterprise (LITE): Enabling Coastal Stewardship and Reliable Energy

This project will focus on research and application development in the area of large scale data computing and visualization that are critical to the DoE BER program areas of climate change research, environmental sciences, life sciences, and medical sciences. Most commercial applications available today are unable to handle the sizes of data in these domains, usually in the order of terabytes and petabytes. This project will address this problem, by taking advantage of the advanced scientific computing infrastructure of the LITE and LONI to conduct research and develop software applications that run natively on these 64-bit supercomputing platforms. The project is consistent with the goals of Scientific Discovery through Advanced Computing (SciDAC), a DoE initiative.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2019

An Eccentric Massive Jupiter Orbiting a Subgiant on a 9.5-day Period Discovered in the Transiting Exoplanet Survey Satellite Full Frame Images

We report the discovery of TOI-172 b from the Transiting Exoplanet Survey Satellite (TESS) mission, a massive hot Jupiter transiting a slightly evolved G star with a 9.48-day orbital period. This is the first planet to be confirmed from analysis of only the TESS full frame images, because the host star was not chosen as a two-minute cadence target. From a global analysis of the TESS photometry and follow-up observations carried out by the TESS Follow-up Observing Program Working Group, TOI-172 (TIC 29857954) is a slightly evolved star with an effective temperature of T {sub eff} = 5645 ± 50 K, a mass of M {sub ⋆} = 1.128{sub −0.061}{sup +0.065} M {sub ⊙}, radius of R {sub ⋆} = 1.777{sub −0.044}{sup +0.047} R {sub ⊙}, a surface gravity of log g {sub ⋆} = 3.993{sub −0.028}{sup +0.027}, and an age of 7.4{sub −1.5}{sup +1.6} Gyr. Its planetary companion (TOI-172 b) has a radius of R {sub P} = 0.965{sub −0.029}{sup +0.032} R {sub J}, a mass of M {sub P} = 5.42{sub −0.20}{sup +0.22} M {sub J}, and is on an eccentric orbit (e=0.3806{sub −0.0090}{sup +0.0093}). TOI-172 b is one of the few known massive giant planets on a highly eccentric short-period orbit. Future study of the atmosphere of this planet and its system architecture offer opportunities to understand the formation and evolution of similar systems.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2012

Light Baryon Spectroscopy at Jefferson Lab: What have we learned about excited baryons?

Nucleons are complex systems of confined quarks and gluons and exhibit the characteristic spectra of excited states. These states serve as an excellent probe of quantum chromodynamics (QCD), the fundamental theory of strong interaction. Highly-excited states are sensitive to the details of quark confinement, which is only poorly understood within QCD. This is the regime of non-perturbative QCD and it is one of the key issues in hadronic physics to identify the corresponding relevant degrees of freedom and the effective forces between them. In recent years, lattice-QCD has made significant progress toward understanding the spectra of hadrons. On the experimental side, high-energy electrons and photons are a remarkably clean probe of hadronic matter, providing a microscope for examining atomic nuclei and the strong nuclear force. For more than a decade, laboratories worldwide have accumulated data for such investigations, resulting in a number of surprising discoveries and contributing to our understanding of the nucleon, its underlying quark structure, and the dynamics of the strong interaction. Current experimental efforts utilize highly-polarized frozen-spin (butanol) targets and deuterium targets in combination with polarized photon beams. These are important steps toward so-called complete experiments that will allow us to unambiguously determine the scattering amplitudes in the underlying reactions and to identify resonance contributions. In my talk, I will give an overview of the excited baryon program at Jefferson Lab and I will discuss recent results from (double-)polarization experiments.

Crede, Volker↗

DOE OSTI2023

BinaRena: a dedicated interactive platform for human-guided exploration and binning of metagenomes

Background: Exploring metagenomic contigs and “binning” them into metagenome-assembled genomes (MAGs) are essential for the delineation of functional and evolutionary guilds within microbial communities. Despite the advances in automated binning algorithms, their capabilities in recovering MAGs with accuracy and biological relevance are so far limited. Researchers often find that human involvement is necessary to achieve representative binning results. This manual process however is expertise demanding and labor intensive, and it deserves to be supported by software infrastructure. Results: We present BinaRena, a comprehensive and versatile graphic interface dedicated to aiding human operators to explore metagenome assemblies via customizable visualization and to associate contigs with bins. Contigs are rendered as an interactive scatter plot based on various data types, including sequence metrics, coverage profiles, taxonomic assignments, and functional annotations. Various contig-level operations are permitted, such as selection, masking, highlighting, focusing, and searching. Binning plans can be conveniently edited, inspected, and compared visually or using metrics including silhouette coefficient and adjusted Rand index. Completeness and contamination of user-selected contigs can be calculated in real time. In demonstration of BinaRena’s usability, we show that it facilitated biological pattern discovery, hypothesis generation, and bin refinement in a complex tropical peatland metagenome. It enabled isolation of pathogenic genomes within closely related populations from the gut microbiota of diarrheal human subjects. It significantly improved overall binning quality after curating results of automated binners using a simulated marine dataset. Conclusions: BinaRena is an installation-free, dependency-free, client-end web application that operates directly in any modern web browser, facilitating ease of deployment and accessibility for researchers of all skill levels. The program is hosted at https://github.com/qiyunlab/binarena, together with documentation, tutorials, example data, and a live demo. It effectively supports human researchers in intuitive interpretation and fine tuning of metagenomic data.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

TESS Delivers Five New Hot Giant Planets Orbiting Bright Stars from the Full-frame Images

We present the discovery and characterization of five hot and warm Jupiters—TOI-628 b (TIC 281408474; HD 288842), TOI-640 b (TIC 147977348), TOI-1333 b (TIC 395171208, BD+47 3521A), TOI-1478 b (TIC 409794137), and TOI-1601 b (TIC 139375960)—based on data from NASA’s Transiting Exoplanet Survey Satellite (TESS). The five planets were identified from the full-frame images and were confirmed through a series of photometric and spectroscopic follow-up observations by the TESS Follow-up Observing Program Working Group. The planets are all Jovian size (R {sub P} = 1.01–1.77 R {sub J}) and have masses that range from 0.85 to 6.33 M {sub J}. The host stars of these systems have F and G spectral types (5595 ≤ T {sub eff} ≤ 6460 K) and are all relatively bright (9.5 < V < 10.8, 8.2 < K < 9.3), making them well suited for future detailed characterization efforts. Three of the systems in our sample (TOI-640 b, TOI-1333 b, and TOI-1601 b) orbit subgiant host stars (log g < 4.1). TOI-640 b is one of only three known hot Jupiters to have a highly inflated radius (R {sub P} > 1.7 R {sub J}, possibly a result of its host star’s evolution) and resides on an orbit with a period longer than 5 days. TOI-628 b is the most massive, hot Jupiter discovered to date by TESS with a measured mass of 6.31{sub −0.30}{sup +0.28} M {sub J} and a statistically significant, nonzero orbital eccentricity of e = 0.074{sub −0.022}{sup +0.021}. This planet would not have had enough time to circularize through tidal forces from our analysis, suggesting that it might be remnant eccentricity from its migration. The longest-period planet in this sample, TOI-1478 b (P = 10.18 days), is a warm Jupiter in a circular orbit around a near-solar analog. NASA’s TESS mission is continuing to increase the sample of well-characterized hot and warm Jupiters, complementing its primary mission goals.

79 ASTRONOMY AND ASTROPHYSICS↗