Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “Biological resources”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 55 records · Page 3

RCSB Protein Data Bank: supporting research and education worldwide through explorations of experimentally determined and computationally predicted atomic level 3D biostructures

The Protein Data Bank (PDB) was established as the first open-access digital data resource in biology and medicine in 1971 with seven X-ray crystal structures of proteins. Today, the PDB houses >210 000 experimentally determined, atomic level, 3D structures of proteins and nucleic acids as well as their complexes with one another and small molecules ( e.g. approved drugs, enzyme cofactors). These data provide insights into fundamental biology, biomedicine, bioenergy and biotechnology. They proved particularly important for understanding the SARS-CoV-2 global pandemic. The US-funded Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) and other members of the Worldwide Protein Data Bank (wwPDB) partnership jointly manage the PDB archive and support >60 000 `data depositors' (structural biologists) around the world. wwPDB ensures the quality and integrity of the data in the ever-expanding PDB archive and supports global open access without limitations on data usage. The RCSB PDB research-focused web portal at https://www.rcsb.org/ (RCSB.org) supports millions of users worldwide, representing a broad range of expertise and interests. In addition to retrieving 3D structure data, PDB `data consumers' access comparative data and external annotations, such as information about disease-causing point mutations and genetic variations. RCSB.org also provides access to >1 000 000 computed structure models (CSMs) generated using artificial intelligence/machine-learning methods. To avoid doubt, the provenance and reliability of experimentally determined PDB structures and CSMs are identified. Related training materials are available to support users in their RCSB.org explorations.

59 BASIC BIOLOGICAL SCIENCES↗

Bayesian inference of Stochastic reaction networks using Multifidelity Sequential Tempered Markov Chain Monte Carlo

Stochastic reaction network models are often used to explain and predict the dynamics of gene regulation in single cells.These models usually involve several parameters, such as the kinetic rates of chemical reactions, that are not directly measurable and must be inferred from experimental data. Bayesian inference provides a rigorous probabilistic frame-work for identifying these parameters by finding a posterior parameter distribution that captures their uncertainty.Traditional computational methods for solving inference problems such as Markov Chain Monte Carlo methods based on classical Metropolis-Hastings algorithm involve numerous serial evaluations of the likelihood function, which in turn requires expensive forward solutions of the chemical master equation (CME). We propose an alternate approach based on a multifidelity extension of the Sequential Tempered Markov Chain Monte Carlo (ST-MCMC) sampler. This algorithm is built upon Sequential Monte Carlo and solves the Bayesian inference problem by decomposing it into a sequence of efficiently solved subproblems that gradually increase both model fidelity and the influence of the observed data. We reformulate the finite state projection (FSP) algorithm, a well-known method for solving the CME, to produce a hierarchy of surrogate master equations to be used in this multifidelity scheme. To determine the appropriate fidelity, we introduce a novel information-theoretic criteria that seeks to extract the most information about the ultimate Bayesian posterior from each model in the hierarchy without inducing significant bias. This novel sampling scheme is tested with high performance computing resources using biologically relevant problems.

97 MATHEMATICS AND COMPUTING↗

2018 Annual Site Environmental Report Summary

We are committed to act as stewards of our environment to achieve our mission in accordance with all applicable environmental requirements. We set continual improvement objectives and targets, measure and document our progress, and share our results with our workforce, sponsors, and public. We reduce our environmental risk through legacy cleanup, pollution prevention, and long-term sustainability programs.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Implementing Environmental Requirements

The purpose of this document is to describe the processes for identifying, communicating, and implementing environmental requirements at the Los Alamos National Laboratory (LANL) for Triad National Security, LLC (Triad). References to LANL or the Laboratory refer to the Department of Energy, National Nuclear Security Administration (DOE/NNSA) managed portion of LANL. References to the Prime Contract refer to the contract between DOE/NNSA and Triad and does not apply to the portion of Technical Area 54 now managed and operated by DOE Environmental Management (EM-LA).

54 ENVIRONMENTAL SCIENCES↗

Annual Site Environmental Report (2019)

Los Alamos National Laboratory’s (the Laboratory’s) annual site environmental reports are prepared by the Laboratory’s environmental organizations, as required by U.S. Department of Energy Order 231.1B, Administrative Change 1, Environment, Safety, and Health Reporting, and Order 458.1, Administrative Change 3, Radiation Protection of the Public and the Environment. The following chapters in this report discuss our success in complying with environmental laws, regulations, and orders (Chapter 2, Compliance Summary); how we manage the Laboratory’s environmental performance (Chapter 3, Environmental Programs); how we monitor for air emissions of radioactive materials and climate conditions (Chapter 4, Air Quality); how we monitor for effects of Laboratory operations on groundwater quality (Chapter 5, Groundwater Protection); how we monitor the movement of chemicals and radionuclides by storm water runoff and the levels of chemicals and radionuclides in deposited sediment (Chapter 6, Watershed Quality); how we monitor for the presence, levels, and effects of chemicals and radionuclides in plants, animals, and soil (Chapter 7, Ecosystem Health); and finally, what radionuclide dose or risk from chemical exposure members of the public may experience as a result of Laboratory operations (Chapter 8, Public Dose and Risk Assessment).

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

2020 Results for Avian Monitoring at the Technical Area 36 Minie Site, Technical Area 39 Point 6, and Technical Area 16 Burn Ground at Los Alamos National Laboratory

Los Alamos National Laboratory (LANL) biologists in the Environmental Protection and Compliance Division initiated a multi-year program in 2013 to monitor avifauna (birds) at two open detonation sites and one open burn site on LANL property. In this annual report we compare monitoring results from these efforts among years to monitor trends. The objectives of this study are to 1) determine whether LANL operations impact bird species richness, diversity, or abundance and 2) examine occupancy and nest success of secondary-cavity nesting birds using nestboxes. LANL biologists completed the eighth year of this effort in 2020

54 ENVIRONMENTAL SCIENCES↗

Pacific Northwest National Laboratory Annual Site Environmental Report for Calendar Year 2020. Final Report

The U.S. Department of Energy requires that all its site facilities develop an annual site environmental report to comply with DOE Order 231.1B, Chg 1, and DOE Order 458.1, Admin Chg 4. This report provides a synopsis of calendar year 2020 information related to environmental management performance and compliance efforts at Pacific Northwest National Laboratory. It summarizes site compliance with federal, state, and local environmental laws, regulations, policies, directives, permits, and Orders, and provides environmental management performance benchmarks and their status to the public, regulatory agencies, community officials, Native American tribes, and public interest groups.

54 ENVIRONMENTAL SCIENCES↗

Los Alamos National Laboratory 2021 Annual Site Environmental Report

Los Alamos National Laboratory’s (LANL’s or the Laboratory’s) annual site environmental reports are prepared each year by the Laboratory’s environmental organizations as required by U.S. Department of Energy Order 231.1B, Administrative Change 1, Environment, Safety, and Health Reporting, and Order 458.1, Administrative Change 4, Radiation Protection of the Public and the Environment.

54 ENVIRONMENTAL SCIENCES↗

Pacific Northwest National Laboratory Annual Site Environmental Report for Calendar Year 2019 (Final Report)

The PNNL Annual Site Environmental Report is prepared to meet the requirements of DOE Order 231.1B, Environmental, Safety and Health Reporting, and DOE Order 458.1, Radiation Protection of the Public and the Environment, assuring that the public is informed of any PNNL Richland Campus or PNNL Sequim Campus event that could adversely affect the health and safety of the public, site staff, or the environment. The report provides a synopsis of ongoing environmental management performance and compliance activities for operations that occur on the PNNL Richland Campus in Richland, Washington, and at the PNNL Sequim Campus near Sequim, Washington. It describes the location of and background for each facility; addresses compliance with applicable DOE, federal, state, and local regulations and site-specific permits; documents environmental monitoring efforts and their status; presents potential radiation doses to staff and the public in the surrounding areas; and describes DOE-required data quality assurance methods used for data verification.

54 ENVIRONMENTAL SCIENCES↗

Pacific Northwest National Laboratory Annual Site Environmental Report for Calendar Year 2021 (Final Report)

The U.S. Department of Energy requires that all its site facilities develop an annual site environmental report to comply with DOE Order 231.1B Chg 1 and DOE Order 458.1 Admin Chg 4. This report provides a synopsis of calendar year 2021 information related to environmental management performance and compliance efforts at the Pacific Northwest National Laboratory. It summarizes site compliance with federal, state, and local environmental laws, regulations, policies, directives, permits, and Orders, and provides environmental management performance benchmarks and their status to the public, regulatory agencies, community officials, Native American tribes, and public interest groups.

54 ENVIRONMENTAL SCIENCES↗

Pacific Northwest National Laboratory Annual Site Environmental Report for Calendar Year 2022 (Final Report)

Pacific Northwest National Laboratory (PNNL), one of the U.S. Department of Energy (DOE) Office of Science’s 10 national laboratories, provides innovative science and technology development in the areas of energy and the environment, fundamental and computational science, and national security. There are three DOE offices within the Richland area. Two are responsible for the Hanford Site, whereas the Pacific Northwest Site Office (PNSO) oversees PNNL. PNNL prepares this Annual Site Environmental Report to meet the requirements of DOE Order 231.1B, Environmental, Safety and Health Reporting, and DOE Order 458.1, Radiation Protection of the Public and the Environment, assuring that the public is informed of any PNNL-Richland Campus or PNNL-Sequim Campus event that could adversely affect the health and safety of the public, site staff, or the environment. The report provides a synopsis of ongoing environmental management performance and compliance activities for operations that occur on the PNNL-Richland Campus in Richland, Washington, and at the PNNL-Sequim Campus near Sequim, Washington. It describes the location of and background for each facility; addresses compliance with applicable DOE, federal, state, and local regulations, and site-specific permits; documents environmental monitoring efforts and their status; presents potential radiation doses to staff and the public in the surrounding areas; and describes DOE-required data quality assurance methods used for data verification. The ASER summarizes site compliance with federal, state, and local environmental laws, regulations, policies, directives, permits, and Orders, and provides environmental management performance benchmarks and their status to the public, regulatory agencies, community officials, Native American tribes, and public interest groups.

54 ENVIRONMENTAL SCIENCES↗

Los Alamos National Laboratory 2022 Annual Site Environmental Report (Rev. 2)

Los Alamos National Laboratory (Laboratory) annual site environmental reports are prepared each year by the Laboratory’s environmental organizations as required by U.S. Department of Energy Order 231.1B, Administrative Change 1, Environment, Safety, and Health Reporting, and Order 458.1, Administrative Change 4, Radiation Protection of the Public and the Environment. The chapters in this report discuss our compliance with environmental laws, regulations, and orders (Chapter 2, Compliance Summary); how we manage the Laboratory’s environmental performance and assure the quality of data from analysis of environmental samples (Chapter 3, Environmental Programs and Analytical Data Quality); how we monitor for air emissions of radioactive materials and for weather conditions (Chapter 4, Air Quality); how we monitor for effects of Laboratory operations on groundwater quality (Chapter 5, Groundwater Protection); how we monitor the levels of chemicals and radionuclides in storm water runoff and sediment (Chapter 6, Watershed Quality); how we monitor for the levels and effects of chemicals and radionuclides in plants, animals, soil, and vegetation (Chapter 7, Ecosystem Health); and finally, what radioactive dose or risk from chemical exposure that members of the public could experience as a result of Laboratory operations (Chapter 8, Public Dose and Risk Assessment).

54 ENVIRONMENTAL SCIENCES↗

2024 Results for Avian Monitoring at the Technical Area 36 Minie Site, Technical Area 39 Point 6, Technical Area 16 Burn Ground, and DARHT at Los Alamos National Laboratory

Los Alamos National Laboratory (LANL) biological subject matter experts in the Environmental Protection and Compliance Division initiated a multi-year program in 2013 to monitor avifauna (birds) at two open detonation sites and one open burn site on LANL property. Additional monitoring began in 2017 at a third firing site, the Dual-Axis Radiographic Hydrodynamic Test (DARHT) Facility. In this annual report, we compare monitoring results from these efforts among years to identify and evaluate firing and open burn site impacts on the local bird community. The objectives of this study are • to determine whether LANL operations impact bird abundance, species richness, or diversity; • to examine occupancy and nest success of secondary-cavity nesting birds that use nest boxes; and • to examine chemical concentrations (such as radionuclides, inorganic elements, and/or organic compounds) in nonviable eggs and deceased nestlings that are collected opportunistically with the upper-level bounds of background concentrations, when available. During May through July 2024, LANL biologists completed multiple avian point count surveys at each of the following treatment sites: • Technical Area (TA) 36 Minie Site, • TA-39 Point 6, • TA-16 Burn Ground, and • DARHT. We recorded a total of 1,088 birds that represented 65 species at the four treatment sites and compared these results with data from their associated control sites. In 2024, abundance and species richness at treatment and control sites continued to trend similarly from year to year, with minor random deviations expected from bird communities. Species richness at firing sites differed little from the previous year’s values. Two new bird species were observed at the firing sites—cedar waxwing (Bombycilla cedrorum) and pinyon jay (Gymnorhinus cyanocephalus). Shannon diversity values at TA-36 Minie Site, TA-39, and DARHT were statistically higher than one or more of their associated controls. Annual species diversity at treatment sites was high in 2024 across all firing sites relative to similar habitat control sites. We also monitored avian nest boxes to compare occupancy and nest success data from nest boxes at treatment sites with the overall avian nest box monitoring network and against a subset of relevant control sites. Nest box success has decreased at both treatment and control sites since monitoring began, suggesting that overlapping climatic factors are responsible for patterns of declining nest success. In 2024, nonviable avian eggs and one nestling were opportunistically collected at Bandelier National Monument, TA-16 Burn Ground, TA-36 Minie, TA-39 Point 6, and DARHT. All egg samples and the one nestling sample were evaluated for per- and polyfluoroalkyl substances, which were detected from all locations, including the control site at Bandelier National Monument. Overall results from 2024 continue to suggest that operations at the four treatment sites are not negatively impacting bird populations. This long-term project will continue to monitor for any changes over time.

54 ENVIRONMENTAL SCIENCES↗

Multiple Cases of Bacterial Sequence Erroneously Incorporated Into Publicly Available Chloroplast Genomes

Public sequencing databases are invaluable resources to biological researchers, but assessing data veracity as well as the curation and maintenance of such large collections of data can be challenging. Genomes of eukaryotic organelles, such as chloroplasts and other plastids, are particularly susceptible to assembly errors and misrepresentations in these databases due to their close evolutionary relationships with bacteria, which may co-occur within the same environment, as can be the case when sequencing plants. Here, based on sequence similarities with bacterial genomes, we identified several suspicious chloroplast assemblies present in the National Institutes of Health (NIH) Reference Sequence (RefSeq) collection. Investigations into these chloroplast assemblies reveal examples of erroneous integration of bacterial sequences into chloroplast ribosomal RNA (rRNA) loci, often within the rRNA genes, presumably due to the high similarity between plastid and bacterial rRNAs. The bacterial lineages identified within the examined chloroplasts as the most likely source of contamination are either known associates of plants, or co-occur in the same environmental niches as the examined plants. Modifications to the methods used to process untargeted ‘raw’ shotgun sequencing data from whole genome sequencing efforts, such as the identification and removal of bacterial reads prior to plastome assembly, could eliminate similar errors in the future.

59 BASIC BIOLOGICAL SCIENCES↗

Overview of NASA ISRU Plans, Priorites, and Activities

Introduction:The National Aeronautics andSpace Administration (NASA) of the United States ofAmerica (US) has initiated the Artemis Moon to Marsprogram to send astronauts (the first woman andperson of color) back to the lunar surface, create asustainable human lunar exploration program, andlead the first human exploration mission to the Marssurface in the 2030’s [1]. A major objective of thisprogram is to characterize the resources that exist onthe Moon and Mars, and learn how to utilize them forsustained and affordable exploration. Commonlyknown as In Situ Resource Utilization (ISRU), thesearch for, acquisition, and processing of resources inspace has the potential to greatly reduce thedependency on transporting mission consumables andinfrastructure from Earth, thereby reducing missioncosts, risks, and dependency on Earth.ISRU is Enabling: Through the extraction andprocessing of resources into mission commoditiessuch as rocket propellants, life support consumables,and fuel cell reactants, ISRU enhances and evolvesthe cis-lunar, lander, and surface transportationsystems required for human exploration; expandingand enhancing HOW humans can explore and returnfrom the Moon. Through the extraction andprocessing of resources into metals, silicon, and othermanufacturing and construction feedstock, ISRUenhances and allows for the expansion of criticalinfrastructure using in situ manufacturing andconstruction capabilities that influence WHAT humanscan do on the Moon and in cis-lunar space. Becauseof this, ISRU supports and enables commercialinvolvement beyond NASA and governmentalagencies by both lowering the cost of sustainedtransportation to/from/on the Moon as well assupporting the market required for needing thesetransportation systems. Strategic Framework:To achieve this vision,NASA’s Space Technology Mission Directorate(STMD) ensures the coordinated development ofISRU and other critical space and surfaceinfrastructure elements such as propulsion, power,manufacturing, construction, and robotics through theStrategic Technology Architecture Roundtable(STAR) process. Through STAR, an integratedframework and process has been created allowing forcapabilities and technologies to be linked andassessed, gaps to be identified, specifications andmetrics to be established, and provide a means toprioritize and implement technology development andmissions. A critical part of the STAR effort has beenthe establishment of the Strategic Framework thatorganizes all work under four major Thrusts (Go,Land, Live, and Explore) and identifies the drivingOutcomes for each of these Thrusts. From the Thrustsand Outcomes, all work can be categorized and linkedbetween Capability Areas, and Technology Gaps canbe identified and addressed (Figure 1.)Figure 1. Strategic Framework and STAR FrameworkISRU Envisioned Future: To drive thedevelopment of technologies and capabilities, theSTAR process starts with establishing a ‘grand vision’of where each Outcome and Capability is aiming tobe considered complete. For ISRU, the EnvisionedFuture is “Scalable ISRU production/utilizationcapabilities including sustainable commodities on thelunar and Mars Surface”. This involves starting with10’s of metric tons of products, but evolves into 100’sto 1000’s of metric tons of water, oxygen, propellants,construction and manufacturing feedstock, andcommodities for habitat and food production andoperations. For ISRU, the ‘Prospect to Product’philosophy starts with Destination Reconnaissance &Resource Assessment, followed by ResourceAcquisition, Isolation, and Preparation, leading intoResource Processing (which is further subdivided intomission consumables and feedstocks for constructionand manufacturing). The ISRU Envisioned Futurealso considers what resources are available andattempts to address what and when these resourceswill be evaluated and harnessed, as well asconsidering which products/commodities can beobtained for early use and which ones require moretime and/or users of refined products.It Takes an Architecture: ISRU does not existon its own. By definition, it requires customers/users SHORT TITLE HERE: A. B. Author and C. D. Authorto use the products/commodities produced by ISRUsystems. Also, for an ISRU capability to exist, itmust obtain products and services from other systemsand infrastructure. An important aspect of the STARprocess and the ISRU Envisioned Futures Prioritiesstrategy is to identify and link all of these systems andcapabilities to achieve the desired end state (Figure2).Figure 2. ISRU as Part of a Larger ArchitectureISRU Capability Drivers: The guidingprinciples for NASA’s Space TechnologyDevelopment for Artemis are to develop criticaltechnologies and capabilities that enable (i) asustainable Lunar surface presence, (ii) the future goalof sending humans to Mars, and (iii) promotingcritical technologies to enable future science andcommercial missions. It is a major goal of theArtemis campaign to establish some sort of base campat the lunar South Pole by approximately the end ofthe decade. The ISRU Envisioned Futures Prioritiesstrategy is aligned with the Artemis campaign todevelop and demonstrate ISRU capabilities in thistimeframe that could lead to sustained surfaceoperations, infrastructure growth, and commercialoperations in the next decade (Figure 3).Figure 3. ISRU Dual Path to Full Implementation and CommercializationState of the Art and Gaps: To achieve theenvisioned future, an extensive effort was performedto understand the State of the Art (SOA) for ISRUgoing back decades, and to assess the SOA against thenear and long-term goals and objectives of the ISRUStrategic Outcome objectives. While the releasedISRU Envisioned Futures Priorities only includes atop-level definition of both the SOA and Gaps, furtherinformation on these for ISRU can be found in theISRU Gap Assessment Study performed for theInternational Space Exploration Coordination Group(ISECG) [2]. To provide further guidance to industryand academia, a top level assessment was performedand provide that divides critical areas of ISRUcapabilities and technologies into 3 categories:Significant Funding, Partially Covered/MoreRequired, and Limited/No Funded Activities.Envisioned Future Priorities- Next Steps forISRU: While a significant amount of work over abroad range of technology areas has been performedover the last several years for lunar ISRU, to reach theenvisioned future for ISRU, a lot more work isrequired at the technology level leading to bothsystems and technology demonstrations in the nearfuture. To guide investments within NASA, industry,and academia, 5 specific areas of high priority wereidentified. These are:1.Complete development of the Water and Oxygen Mining Paths and close technology gaps, with emphasis on oxygen extraction from Highland regolith and parallel paths for polar water mining.2.Expand development of metal extraction and feedstock for manufacturing and construction, with emphasis on aluminum and initial/easy to obtain/make construction feedstocks leading to more refined metals and other regolith resources. Also, evaluate biologically inspired/derived technologies in bio-mining, bio-plastic, and other feedstock commodities.3.Ensure the resource assessment needed for future ISRU commercial operations is coordinated with both near/long-term science objectives as well as Artemis mission locations of interest.4.Initiate NASA and industry-led system-level analyses, integration, and testing activities for ISRU capabilities. While significant work has been performed at the technology and subsystemlevel, it is now important to understand how these technology investments can be leveraged and utilized in actual systems and applications5.Initiate lunar ISRU technology flight demonstrations leading to initial ‘Pilot Plant’ end-to-end production capability demonstrations, led by industry

ISRU↗

GeneLab: NASA's Open Access, Collaborative Platform for Systems Biology and Space Medicine

NASA is investing in GeneLab1 (http:genelab.nasa.gov), a multi-year effort to maximize utilization of the limited resources to conduct biological and medical research in space, principally aboard the International Space Station (ISS). High-throughput genomic, transcriptomic, proteomic or other omics analyses from experiments conducted on the ISS will be stored in the GeneLab Data Systems (GLDS), an open-science information system that will also include a biocomputation platform with collaborative science capabilities, to enable the discovery and validation of molecular networks.

Berrios, Daniel C.↗