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All sources NASA NTRS DOE OSTI

DOE OSTI2022

An Automated Scanning Transmission Electron Microscope Guided by Sparse Data Analytics

Abstract Artificial intelligence (AI) promises to reshape scientific inquiry and enable breakthrough discoveries in areas such as energy storage, quantum computing, and biomedicine. Scanning transmission electron microscopy (STEM), a cornerstone of the study of chemical and materials systems, stands to benefit greatly from AI-driven automation. However, present barriers to low-level instrument control, as well as generalizable and interpretable feature detection, make truly automated microscopy impractical. Here, we discuss the design of a closed-loop instrument control platform guided by emerging sparse data analytics. We hypothesize that a centralized controller, informed by machine learning combining limited a priori knowledge and task-based discrimination, could drive on-the-fly experimental decision-making. This platform may unlock practical, automated analysis of a variety of material features, enabling new high-throughput and statistical studies.

47 OTHER INSTRUMENTATION↗

DOE OSTI2018

ScienceSearch: Enabling Search through Automatic Metadata Generation

© 2018 IEEE. Scientific facilities are increasingly generating and handling large amounts of data from experiments and simulations. Next-generation scientific discoveries rely on insights derived from data, especially across domain boundaries. Search capabilities are critical to enable scientists to discover datasets of interest. However, scientific datasets often lack the signals or metadata required for effective searches. Thus, we need formalized methods and systems to automatically annotate scientific datasets from the data and its surrounding context. Additionally, a search infrastructure needs to account for the scale and rate of application data volumes. In this paper, we present ScienceSearch, a system infrastructure that uses machine learning techniques to capture and learn the knowledge, context, and surrounding artifacts from data to generate metadata and enable search. Our current implementation is focused on a dataset from the National Center for Electron Microscopy (NCEM), an electron microscopy facility at Lawrence Berkeley National Laboratory sponsored by the Department of Energy which supports hundreds of users and stores millions of micrographs. In this paper, we describe a) our search infrastructure and model, b) methods for generating metadata using machine learning techniques, and c) optimizations to improve search latency, and deployment on an HPC system. We demonstrate that ScienceSearch is capable of producing valid metadata for NCEM's dataset and providing low-latency good quality search results over a scientific dataset.

Rodrigo, Gonzalo P.↗

NASA NTRSDate not supplied

Data Sharing in Radiobiology; Towards FAIR

The value of scientific data depends on their findability, accessibility, integrability and reusability according to the FAIR principles. Together with the sustainability of data preservation and access, these principles underpin the long term benefits of scientific research. Within the domain of radiobiology we have a huge array of data types, themes and complexities which make standardisation of metadata, data structure and data integration very challenging. Moreover, it is clear that, for example, in the area of disaster preparedness, the ready discovery and availability of multiple types of data, for example on biological effects of exposure, climatology, ecology, human behavioural and attitudinal studies, is important for an integrated scientific approach. Because these data are spread over many databases, journal supplementary information resources and even the computers of the investigators, their discovery and reuse can be challenging. Despite exhortations from funding agencies and scientific institutions over the past two decades there is still a serious deficit in the willingness and in some cases the ability of investigators to share data, and although much may not be formally „Public domain“, information about the existence of the data, their metadata, and how to obtain them should always be available. We report the progress of work on three databases, the STORE and the NASA GeneLab and LSDA repositories to leverage the Radiation Biology Ontology (RBO), a structured terminology for metadata that can be used by all radiation biology-relevant databases to unite federated and automated data searches across multiple databases, for example using web services, and through semantic web technologies supporting data discovery. The initial primary use-cases for RBO were archiving data in the STORE database (https://www.storedb.org/), the repository used for the RadoNorm and Pianoforte Projects among others, and in the NASA Open Science Data Repository (https://osdr.nasa.gov/bio). The scope of radiobiology research ranges from basic physics to radiation oncology to sociolegal studies; no existing ontology had the necessary breadth or depth to fulfill this need. In addition, a formal ontology has the advantage of being usable for machine learning and, importantly, for tasks like data integration, knowledge extraction from the scientific literature and for query extension and data classification. Standardisation of metadata is one of the primary objectives of the FAIR principles for open data; RBO is an important landmark for FAIR-compliant radiation biology data sharing. The RBO is developed using the open-source tools of GitHub and the OBO Foundry-led Ontology Development Kit, and published through GitHub and the NIH/NCBI BioPortal website. This initial phase of concept modeling has yielded an ontology that has more than 300 declared concepts, with more than 3500 additional concepts imported from other OBO Foundry ontologies with relevance to radiation biology (for example, concepts from the ISO standard Basic Formal Ontology, the Environment Ontology and the Gene Ontology). We welcome input into the development of RBO and encourage its adoption.

ontologies↗

NASA NTRS2023

Data Sharing in Radiation Biology: Towards FAIR

The value of scientific data depends on their findability, accessibility, integrability and reusability according to the FAIR principles. Together with the sustainability of data preservation and access, these principles underpin the long term benefits of scientific research. Within the domain of radiobiology we have a huge array of data types, themes and complexities which make standardisation of metadata, data structure and data integration very challenging. Moreover, it is clear that, for example, in the area of disaster preparedness, the ready discovery and availability of multiple types of data, for example on biological effects of exposure, climatology, ecology, human behavioural and attitudinal studies, is important for an integrated scientific approach. Because these data are spread over many databases, journal supplementary information resources and even the computers of the investigators, their discovery and reuse can be challenging. Despite exhortations from funding agencies and scientific institutions over the past two decades there is still a serious deficit in the willingness and in some cases the ability of investigators to share data, and although much may not be formally "Public domain“, information about the existence of the data, their metadata, and how to obtain them should always be available. We report the progress of work on three databases, the STORE and the NASA GeneLab and LSDA repositories to leverage the Radiation Biology Ontology (RBO), a structured terminology for metadata that can be used by all radiation biology-relevant databases to unite federated and automated data searches across multiple databases, for example using web services, and through semantic web technologies supporting data discovery. The initial primary use-cases for RBO were archiving data in the STORE database (https://www.storedb.org/), the repository used for the RadoNorm and Pianoforte Projects among others, and in the NASA Open Science Data Repository (https://osdr.nasa.gov/bio). The scope of radiobiology research ranges from basic physics to radiation oncology to sociolegal studies; no existing ontology had the necessary breadth or depth to fulfill this need. In addition, a formal ontology has the advantage of being usable for machine learning and, importantly, for tasks like data integration, knowledge extraction from the scientific literature and for query extension and data classification. Standardisation of metadata is one of the primary objectives of the FAIR principles for open data; RBO is an important landmark for FAIR-compliant radiation biology data sharing. The RBO is developed using the open-source tools of GitHub and the OBO Foundry-led Ontology Development Kit, and published through GitHub and the NIH/NCBI BioPortal website. This initial phase of concept modeling has yielded an ontology that has more than 300 declared concepts, with more than 3500 additional concepts imported from other OBO Foundry ontologies with relevance to radiation biology (for example, concepts from the ISO standard Basic Formal Ontology, the Environment Ontology and the Gene Ontology). We welcome input into the development of RBO and encourage its adoption.

ontologies↗

NASA NTRS2017

NASA's GeneLab Phase II: Federated Search and Data Discovery

GeneLab is currently being developed by NASA to accelerate 'open science' biomedical research in support of the human exploration of space and the improvement of life on earth. Phase I of the four-phase GeneLab Data Systems (GLDS) project emphasized capabilities for submission, curation, search, and retrieval of genomics, transcriptomics and proteomics ('omics') data from biomedical research of space environments. The focus of development of the GLDS for Phase II has been federated data search for and retrieval of these kinds of data across other open-access systems, so that users are able to conduct biological meta-investigations using data from a variety of sources. Such meta-investigations are key to corroborating findings from many kinds of assays and translating them into systems biology knowledge and, eventually, therapeutics.

exobiology↗

NASA NTRS2017

NASAs GeneLab Phase II: Federated Search and Data Discovery

GeneLab is currently being developed by NASA to accelerate open science biomedical research in support of the human exploration of space and the improvement of life on earth. Phase I of the four-phase GeneLab Data Systems (GLDS) project emphasized capabilities for submission, curation, search, and retrieval of genomics, transcriptomics and proteomics (omics) data from biomedical research of space environments. The focus of development of the GLDS for Phase II has been federated data search for and retrieval of these kinds of data across other open-access systems, so that users are able to conduct biological meta-investigations using data from a variety of sources. Such meta-investigations are key to corroborating findings from many kinds of assays and translating them into systems biology knowledge and, eventually, therapeutics.

genome↗

NASA NTRS2023

ECS Artemis II Upgrades

The National Aeronautics and Space Administration (NASA) actively works to further the expectations of space exploration and research. NASA has been able to develop innovative technology and methods that has allowed for continued discovery and innovation. NASA is in the midst of work for the Artemis mission, which is to return to the moon in an effort to prepare for future Mars exploration. After the successful launch of Artemis I last November, our sights have shifted to Artemis II, which is set to launch next year and bring humans into the lunar orbit for the first time in over fifty years. Artemis II will be the first crewed mission for the program and will represent another step forward in our mission to advance our knowledge of the universe around us. From there, the Artemis program will move onto building a permanent site on the moon that will allow us to eventually reach Mars. During my time at NASA, I was able to work with the NE-XF Branch, also known as the Environmental and Life Support Systems Branch. I specifically worked with the Environmental Control Systems (ECS) team. During my time here, construction on the system in the Vehicle Assembly Building (VAB) and at Launchpad 39B have been progressing at full force. ECS is used to provide processed and purged air at specific temperatures, pressures, and humidity’s to fulfill requirements necessary to support Orion and the SLS. While the Pad has been undergoing upgrades from the original Artemis I configuration, the VAB has a completely new ECS very similar to it. While both systems have been undergoing upgrades, we have been able to transition into testing the systems as we prepare for stacking in the VAB early next year. My role has allowed me to learn about how the systems work and function through walkdowns and visits out to both the Pad and the VAB. I’ve been able to see firsthand how the system operates and have learned how the system affects the vehicle. I’ve been able to shadow my mentor, my coworkers, and COMET operators to oversee the construction efforts of the system along with the testing of the software and the system itself. I even was able to aid in testing at the console myself at Pad 39B. Additionally, I am also revising and reviewing displays for Artemis IV that will be used to remotely control parts of the system. Eventually these displays will be used to support the future of Artemis.

Monique Toon↗

DOE OSTI2022

On-the-fly autonomous control of neutron diffraction via physics-informed Bayesian active learning

We demonstrate the first live, autonomous control over neutron diffraction experiments by developing and deploying ANDiE: the autonomous neutron diffraction explorer. Neutron scattering is a unique and versatile characterization technique for probing the magnetic structure and behavior of materials. However, instruments at neutron scattering facilities in the world is limited, and instruments at such facilities are perennially oversubscribed. We demonstrate a significant reduction in experimental time required for neutron diffraction experiments by implementation of autonomous navigation of measurement parameter space through machine learning. Prior scientific knowledge and Bayesian active learning are used to dynamically steer the sequence of measurements. We show that ANDiE can experimentally determine the magnetic ordering transition of both MnO and Fe 1.09 Te all while providing a fivefold enhancement in measurement efficiency. Furthermore, in a hypothesis testing post-processing step, ANDiE can determine transition behavior from a set of possible physical models. ANDiE's active learning approach is broadly applicable to a variety of neutron-based experiments and can open the door for neutron scattering as a tool of accelerated materials discovery.

36 MATERIALS SCIENCE↗

DOE OSTI2022

Sub-threshold ultrafast one-photon photoemission from a Cu(111) photocathode

Single-photon photoemission of electrons for incident photon energies below the surface work function is reported for a single-crystal Cu(111) photocathode. Spectral characterization of the quantum efficiency and mean transverse energy of the emitted electrons is shown to be consistent with emission from a thermalized hot electron distribution photoexcited on sub-picosecond time scales into an upper conduction band at the L-point of the Brillouin zone of copper. To our knowledge, this is the first time that such excited-state thermionic emission has been observed from a planar metal photocathode, and then from a commonly used photocathode material. The results, therefore, indicate the potential importance of such band structure dependent sub-threshold photoemission mechanisms on the performance of photocathodes employed for the generation of short electron pulses using sub-picosecond laser pulses. Consequently, the combined experimental and theoretical work presented in this paper contributes to solid-state photocathode-based research aimed at our understanding and selection (or discovery) of high brightness photo-electron sources required for many electron-based diffraction, imaging, and accelerator applications.

43 PARTICLE ACCELERATORS↗

DOE OSTI2022

Anaerobic Degradation of Alkanes by Marine Archaea

Alkanes are saturated apolar hydrocarbons that range from their simplest form, methane, to high-molecular-weight compounds. Although alkanes were once considered biologically recalcitrant under anaerobic conditions, microbiological investigations have now identified several microbial taxa that can anaerobically degrade alkanes. Here we review recent discoveries in the anaerobic oxidation of alkanes with a specific focus on archaea that use specific methyl coenzyme M reductases to activate their substrates. Our understanding of the diversity of uncultured alkane-oxidizing archaea has expanded through the use of environmental metagenomics and enrichment cultures of syntrophic methane-, ethane-, propane-, and butane-oxidizing marine archaea with sulfate-reducing bacteria. A recently cultured group of archaea directly couples long-chain alkane degradation with methane formation, expanding the range of substrates used for methanogenesis. This article summarizes the rapidly growing knowledge of the diversity, physiology, and habitat distribution of alkane-degrading archaea.

Microbiology↗

DOE OSTI2014

Handling Large and Complex Data in a Photovoltaic Research Institution Using a Custom Laboratory Information Management System

Twenty-five years ago the desktop computer started becoming ubiquitous in the scientific lab. Researchers were delighted with its ability to both control instrumentation and acquire data on a single system, but they were not completely satisfied. There were often gaps in knowledge that they thought might be gained if they just had more data and they could get the data faster. Computer technology has evolved in keeping with Moore’s Law meeting those desires; however those improvements have of late become both a boon and bane for researchers. Computers are now capable of producing high speed data streams containing terabytes of information; capabilities that evolved faster than envisioned last century. Software to handle large scientific data sets has not kept up. How much information might be lost through accidental mismanagement or how many discoveries are missed through data overload are now vital questions. An important new task in most scientific disciplines involves developing methods to address those issues and to create the software that can handle large data sets with an eye towards scalability. This software must create archived, indexed, and searchable data from heterogeneous instrumentation for the implementation of a strong data-driven materials development strategy. At the National Center for Photovoltaics in the National Renewable Energy Laboratory, we began development a few years ago on a Laboratory Information Management System (LIMS) designed to handle lab-wide scientific data acquisition, management, processing and mining needs for physics and materials science data, and with a specific focus towards future scalability for new equipment or research focuses. We will present the decisions, processes, and problems we went through while building our LIMS system for materials research, its current operational state and our steps for future development.

14 SOLAR ENERGY↗

DOE OSTI2020

Liquid helium fluid dynamics studies. Final Technical Report

Future high energy physics accelerators depend on a number of advanced technologies to open the many doors of scientific discovery. Among these advanced technologies, superconducting magnets and superconducting radio frequency (SRF) cavities are the backbone of the accelerator and detector systems. But all these low temperature systems depend critically on successful and reliable operation of their supporting technologies, among which the liquid helium cooling system is of the utmost importance. To improve the quality of these systems both in terms of efficiency and reliability, a robust helium cryogenics research and development (R&D) effort is required. The proposed research to be conducted by the FSU cryogenics group aims to produce fundamental knowledge that meets this R&D need. The projects that we have completed over the past grant period at Florida State University consist of experimental research on liquid helium fluid dynamics and heat transfer problems relevant to the development of future superconducting particle physics accelerators. Liquid helium is the coolant used in all such facilities and in many of these facilities He II (the low temperature phase of liquid helium also known as superfluid helium) is preferred due to its outstanding heat transfer characteristics. The work consists of two main experimental studies that probe both fundamental as well as practical aspects of liquid helium cooling. The first is a broad and fundamental study of the heat and mass transfer processes that can occur during a sudden catastrophic loss of vacuum (SCLV) incident in a superconducting accelerator. SCLV refers to the remote but extremely critical accident scenario where atmospheric pressure air is allowed to flood into the insulating vacuum system and impinge on the liquid helium cooled surfaces in the accelerator. Safe performance and recovery from such accidents is essential to the reliable operation of superconducting accelerators. The dynamics of this process is quite complex and so our approach is to conduct a series of well-orchestrated experiments that probe the various physical phenomena that can occur during an SCLV event. The experiments are coupled with analytic and numerical analysis in an effort to develop a general understanding of the process and to assist with future accelerator design and development. The second activity is directed toward fundamental understanding of heat and mass transfer in He II, which is essential to the design of superconducting magnets and radio frequency cavities in accelerators. The work consists of flow visualization of the dynamics of He II using laser assisted techniques. Two complementary techniques are used to study the fundamentals of the turbulent state. The first technique uses neutrally buoyant solid hydrogen particles to probe the flow fields of the superfluid and normal fluid components. The other technique uses laser excited He2* molecules as tracers of the normal fluid motion within the He II. The activities also included an effort to use visualization techniques to locate transient hot spots in radio frequency superconducting cavities. Such work provides valuable information about the heat transfer process in He II and its impact on the performance of superconducting devices. The research effort at Florida State University is not directly in support of a specific high energy physics experiment or facility. Rather, the work is general and coordinated with HEP accelerator laboratories to provide valuable insight that can assist with future accelerator development.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2021

Implications of the iron oxide phase transition on the interiors of rocky exoplanets

The discovery of an extraordinary number of extrasolar planets, characterized by an unexpected variety of sizes, masses and orbits, challenges our understanding of the formation and evolution of the planets in the Solar System and the perception of the Earth as the prototypical habitable world. Many exoplanets appear to be rocky and yet more massive than the Earth, with expected pressures and temperatures of hundreds of gigapascal and thousands of Kelvin in their deep interiors. At these conditions, the properties of bridgmanite and ferropericlase, expected to dominate their mantles, are largely unconstrained, limiting our knowledge of their interior structure. Here we used nano-second X-ray diffraction and dynamic compression to experimentally investigate the atomic structure and density of iron oxide (FeO), one of the end-members of the (Mg,Fe)O ferropericlase solid solution, up to 700 GPa, a pressure exceeding the core–mantle boundary of a 5 Earth masses planet. Our data document the stability of the high-pressure cesium-chloride B2 structure above 300 GPa, well below the pressure required for magnesium oxide (MgO) to adopt the same phase. These observations, complemented by the calculation of the binary MgO–FeO phase diagram, reveal complex stratification and rheology inside large terrestrial exoplanets.

58 GEOSCIENCES↗

DOE OSTI2013

Quantifying Carbon-Climate Processes at the Regional Scale Using Atmospheric Carbonyl Sulfide

Atmospheric carbonyl sulfide (COS) analysis has the potentially transformative capability for partitioning the regional carbon flux into respiration and photosynthesis components. This emerging approach is based on the observation that continental atmospheric CO2 gradients are dominated by net ecosystem fluxes while continental atmospheric COS gradients are dominated by photosynthesis-related plant uptake. Regional flux partitioning represents a critical knowledge gap due to a lack of robust methods for regional-scale flux partitioning and large uncertainties in forecasting carbon-climate feedbacks. Our completed project characterized the relationship between COS and CO2 surface fluxes using a novel measurement and modeling system in a winter wheat field at the U.S. Department of Energy?s Atmospheric and Radiation Measurement program Central Facility (DOE-ARM CF). The scope of this project included canopy flux measurements, soil flux measurements, regional atmospheric modeling, and analysis of COS and CO2 airborne observations at SGP. Three critical discoveries emerged from this investigation: (1) the new measurement system provided the first field evidence of a robust relationship between COS leaf fluxes and GPP; (2) a previously unknown seasonal soil source of COS was observed and characterized; (3) the regional atmospheric analysis of airborne measurements provided the first COS-based constraints on GPP parameterizations used in earth systems models. Dissemination of these results includes three publications [Billesbach et al., In Press; Campbell et al., In Preparation; Seibt et al., In Review], three presentations at the AGU Fall Meeting (2012), and four invited presentations to department seminars. We have leveraged this foundational project to continue our work on understanding carbon cycle processes at large scales through one funded project (DOE Lab Fee, 2012-2015) and one proposal that is under review (DOE/NASA/USDA/NOAA, 2014-2016).

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2016

Neutron Resonance Theory for Nuclear Reactor Applications: Modern Theory and Practices.

The neutron resonance phenomena constitute one of the most fundamental subjects in nuclear physics as well as in reactor physics. It is the area where the concepts of nuclear interaction and the treatment of the neutronic balance in reactor fuel lattices become intertwined. The latter requires the detailed knowledge of resonance structures of many nuclides of practical interest to the development of nuclear energy. The most essential element in reactor physics is to provide an accurate account of the intricate balance between the neutrons produced by the fission process and neutrons lost due to the absorption process as well as those leaking out of the reactor system. The presence of resonance structures in many major nuclides obviously plays an important role in such processes. There has been a great deal of theoretical and practical interest in resonance reactions since Fermi’s discovery of resonance absorption of neutrons as they were slowed down in water. The resonance absorption became the center of attention when the question was raised as to the feasibility of the self-sustaining chain reaction in a natural uranium-fueled system. The threshold of the nuclear era was crossed almost eighty years ago when Fermi and Szilard observed that a substantial reduction in resonance absorption is possible if the uranium was made into the form of lumps instead of a homogeneous mixture with water. In the West, the first practical method for estimating the resonance escape probability in a reactor cell was pioneered by Wigner et al in early forties.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2019

ASCR Workshop on In Situ Data Management

In January 2019, the U.S. Department of Energy, Office of Science program in Advanced Scientific Computing Research, convened a workshop to identify priority research directions for in situ data management (ISDM). The workshop defined ISDM as the practices, capabilities, and procedures to control the organization of data and enable the coordination and communication among heterogeneous tasks, executing simultaneously in a high-performance computing system, cooperating toward a common objective. The workshop revealed two primary, interdependent motivations for processing and managing data in situ. The first motivation is that the in situ methodology enables scientific discovery from a broad range of data sources over a wide scale of computing platforms: leadership-class systems, clusters, clouds, workstations, and embedded devices at the edge. The successful development of ISDM capabilities will benefit real-time decision-making, design optimization, and data-driven scientific discovery. The second motivation is the need to decrease data volumes. ISDM can make critical contributions to managing large data volumes from computations and experiments to minimize data movement, save storage space, and boost resource efficiency, often while simultaneously increasing scientific precision.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

DOE OSTI2016

Neutron Resonance Theory for Nuclear Reactor Applications: Modern Theory and Practices

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2023

MArVD2: a machine learning enhanced tool to discriminate between archaeal and bacterial viruses in viral datasets

Abstract Our knowledge of viral sequence space has exploded with advancing sequencing technologies and large-scale sampling and analytical efforts. Though archaea are important and abundant prokaryotes in many systems, our knowledge of archaeal viruses outside of extreme environments is limited. This largely stems from the lack of a robust, high-throughput, and systematic way to distinguish between bacterial and archaeal viruses in datasets of curated viruses. Here we upgrade our prior text-based tool (MArVD) via training and testing a random forest machine learning algorithm against a newly curated dataset of archaeal viruses. After optimization, MArVD2 presented a significant improvement over its predecessor in terms of scalability, usability, and flexibility, and will allow user-defined custom training datasets as archaeal virus discovery progresses. Benchmarking showed that a model trained with viral sequences from the hypersaline, marine, and hot spring environments correctly classified 85% of the archaeal viruses with a false detection rate below 2% using a random forest prediction threshold of 80% in a separate benchmarking dataset from the same habitats.

Vik, Dean (ORCID:000000027546899X)↗