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DOE OSTI2020

Disentangling Sources of Gene Tree Discordance in Phylogenomic Data Sets: Testing Ancient Hybridizations in Amaranthaceae s.l

Gene tree discordance in large genomic data sets can be caused by evolutionary processes such as incomplete lineage sorting and hybridization, as well as model violation, and errors in data processing, orthology inference, and gene tree estimation. Species tree methods that identify and accommodate all sources of conflict are not available, but a combination of multiple approaches can help tease apart alternative sources of conflict. Here, using a phylotranscriptomic analysis in combination with reference genomes, we test a hypothesis of ancient hybridization events within the plant family Amaranthaceae s.l. that was previously supported by morphological, ecological, and Sanger-based molecular data. The data set included seven genomes and 88 transcriptomes, 17 generated for this study. We examined gene-tree discordance using coalescent-based species trees and network inference, gene tree discordance analyses, site pattern tests of introgression, topology tests, synteny analyses, and simulations. We found that a combination of processes might have generated the high levels of gene tree discordance in the backbone of Amaranthaceae s.l. Furthermore, we found evidence that three consecutive short internal branches produce anomalous trees contributing to the discordance. Overall, our results suggest that Amaranthaceae s.l. might be a product of an ancient and rapid lineage diversification, and remains, and probably will remain, unresolved. This work highlights the potential problems of identifiability associated with the sources of gene tree discordance including, in particular, phylogenetic network methods. Our results also demonstrate the importance of thoroughly testing for multiple sources of conflict in phylogenomic analyses, especially in the context of ancient, rapid radiations. We provide several recommendations for exploring conflicting signals in such situations.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS2003

Using a Portfolio of Algorithms for Planning and Scheduling

The Automated Scheduling and Planning Environment (ASPEN) software system, aspects of which have been reported in several previous NASA Tech Briefs articles, includes a subsystem that utilizes a portfolio of heuristic algorithms that work synergistically to solve problems. The nature of the synergy of the specific algorithms is that their likelihoods of success are negatively correlated: that is, when a combination of them is used to solve a problem, the probability that at least one of them will succeed is greater than the sum of probabilities of success of the individual algorithms operating independently of each other. In ASPEN, the portfolio of algorithms is used in a planning process of the iterative repair type, in which conflicts are detected and addressed one at a time until either no conflicts exist or a user-defined time limit has been exceeded. At each choice point (e.g., selection of conflict; selection of method of resolution of conflict; or choice of move, addition, or deletion) ASPEN makes a stochastic choice of a combination of algorithms from the portfolio. This approach makes it possible for the search to escape from looping and from solutions that are locally but not globally optimum.

Sherwood, Robert↗

NASA NTRS1987

Comment on the paper 'On the influx of small comets into the earth's upper atmosphere'

The possibility that comets containing up to 100 tons of ice encounter the earth's atmosphere at a rate of one every 20 min is discussed. Cometary 'hail storms' were proposed to explain observed regular transient decreases in the atmospheric UV dayglow intensity. The decreases take the form of dark 'holes' up to 50 km across. The probability that clouds of objects assumed to be as dark as the nucleus of Comet Halley between the earth and moon would be detectable by ground-based electrooptical deep space telescopes is considered. Conflicting projections of the number of objects which would be detected per hour are examined. High correlations are noted between cometary passages (Comets Encke, Tuttle, Tempel) and intervals of meteor showers (Taurids, Leonids, Geminis, etc.). The holes, however, are not correlated or coincident with the showers. It is suggested that dedicated searches for the unclassified dark objects be carried out in November, when cometary fluxes are high.

Soter, Steven↗

DOE OSTI2026

py-boomer v0.1.0

Py-BOOMER (Python Bayesian OWL Ontology MErgER in Python) is a probabilistic reasoning system for knowledge representation and ontological reasoning with uncertainty. Itnables reasoning over probabilistic facts and taxonomic relationships, finding the most likely consistent interpretation of potentially conflicting assertions. It uses a combination of graph-based reasoning and Bayesian probabilistic inference. Key features: Represent probabilistic ontological statements Reason over class subsumption hierarchies Evaluate class equivalence relationships Detect and resolve logical inconsistencies Calculate posterior probabilities for each assertion

Mungall, Chris [Lawrence Berkeley National Laborat↗

DOE OSTI2022

AIS-based characterization of navigation conflicts along the US Atlantic Coast prior to development of wind energy

This study characterizes navigation conflicts in a region with a large traffic volume along the US Atlantic Coast, utilizing Automated Identification System (AIS) data for 2010. The region includes areas proposed for wind energy development. The characterization could be useful in evaluating the effect of offshore wind areas on navigation conflicts. The study processes the AIS data to provide pairwise comparisons of vessel interactions (encounters and near-misses) as they occurred. Using the vessel encounter data, analyses are made using a ‘blind’ vessel assumption to evaluate the potential for both near-misses and collisions. Then statistical analyses are made to estimate the point values and uncertainty for each type of encounter (crossing, head-on, overtaking). Examination of the frequency/number of collisions from actual observations is made. The examination of actual near-misses, potential near-misses, and potential collisions provides comparable results in the number of near-misses and collisions. The potential near-miss analyses include an examination of the timing of responses made by vessels to prevent near-misses. This informed the statistical analysis but may also have utility in the simulation of navigation conflicts.

99 GENERAL AND MISCELLANEOUS↗

NASA NTRS1981

Adaptively pointing spaceborne radar for precipitation measurements

An auxiliary concept of adaptive pointing applicable to meteorological radar is discussed. This control technique would resolve the conflicts among speed of scan or scan width, resolution, and dwell time per resolution element. At T1(orbital position) a passive infrared radiometer imager scans a swath ahead of the spacecraft; an appropriate algorithm indicates which clouds are probably producing precipitation. These locations are then used by the on-board antenna controller to program the antenna scan so that the radar samples clouds A and B at times T2 and T3 respectively.

Atlas, D.↗

NASA NTRS2004

ADS-B within a Multi-Aircraft Simulation for Distributed Air-Ground Traffic Management

Automatic Dependent Surveillance Broadcast (ADS-B) is an enabling technology for NASA s Distributed Air-Ground Traffic Management (DAG-TM) concept. DAG-TM has the goal of significantly increasing capacity within the National Airspace System, while maintaining or improving safety. Under DAG-TM, aircraft exchange state and intent information over ADS-B with other aircraft and ground stations. This information supports various surveillance functions including conflict detection and resolution, scheduling, and conformance monitoring. To conduct more rigorous concept feasibility studies, NASA Langley Research Center s PC-based Air Traffic Operations Simulation models a 1090 MHz ADS-B communication structure, based on industry standards for message content, range, and reception probability. The current ADS-B model reflects a mature operating environment and message interference effects are limited to Mode S transponder replies and ADS-B squitters. This model was recently evaluated in a Joint DAG-TM Air/Ground Coordination Experiment with NASA Ames Research Center. Message probability of reception vs. range was lower at higher traffic levels. The highest message collision probability occurred near the meter fix serving as the confluence for two arrival streams. Even the highest traffic level encountered in the experiment was significantly less than the industry standard "LA Basin 2020" scenario. Future studies will account for Mode A and C message interference (a major effect in several industry studies) and will include Mode A and C aircraft in the simulation, thereby increasing the total traffic level. These changes will support ongoing enhancements to separation assurance functions that focus on accommodating longer ADS-B information update intervals.

Barhydt, Richard↗

NASA NTRSDate not supplied

ETM Industry: Tabletop Defining Notions for Cooperative Operating Practices

This tabletop plans to cover 3 main topics in regards to the research that NASA has conducted for High-E Traffic Management (ETM), as well as implementing it to stand up an ETM system in the Airspace Operations Lab to invite industry participants to join us in a collaborative evaluation at the end of 2023. (Or earlier for system architectural connectivity). Working to define the notions that go into Cooperative Operating Practices for a collaborative traffic management process, we will be showing and training to some of our early prototype concepts and discussing: 1. Operational Intent: We have built an OI generation tool and would like to discuss specifics to the requirements of OI size, update rates, and duration. 2. Strategic Conflict Detection: We have built a concept to detect overlapping OI’s and would like to discuss the output information; time horizon, geometry and confidence level of intersection. In addition we are looking at a service that would provide all users with additional information in regards to the probability of your actual flight intent getting within a specified separation envelope. 3. Cooperative Operating Practices (COPS): Specifically looking at COPs for strategic deconfliction, we are looking to industry to build the actual COPS based on various criteria; vehicle-to-vehicle interactions, or company to company agreements. What is the strategy when OIs intersect; wait and see, take a pre-negotiated COPS action, or ad-hoc negotiation and discuss what that looks like.

High-E Traffic Management (ETM)↗

NASA NTRSDate not supplied

Trajectory Planning for Mission Survivability of Autonomous Vehicles in Moderately to Extremely Uncertain Environments

Trajectory planning is a particularly challenging task for autonomous vehicles when the uncertainties in their operating environment cannot be characterized statistically. In this paper, we propose a receding horizon control strategy with novel trajectory planning policies that enable dynamic updating of the planned trajectories of autonomous vehicles operating in environments where potential conflicts are, from a statistical perspective, either partially known or completely unknown. The proposed policies utilize two metrics: (1) the number of feasible trajectories; and (2) the robustness of the feasible trajectories. We measure the effectiveness of the suggested policies in terms of mission survivability, which is defined as the probability that the primary mission is accomplished or, if that is not possible, the vehicle lands safely at an alternative site. We show that a linear combination of both metrics is an effective objective function when there is a mix of partially known and unknown uncertainties. When the operating environment is dominated by unknown disturbances, maximizing the number of feasible trajectories results in the highest mission survivability. These findings have significant implications for achieving safe aviation. autonomy.

Aviation autonomy↗

DOE OSTI2020

Characterization and identification of HPC applications at leadership computing facility

High Performance Computing (HPC) is an important method for scientific discovery via large-scale simulation, data analysis, or artificial intelligence. Leadership-class supercomputers are expensive, but essential to run large HPC applications. The Petascale era of supercomputers began in 2008, with the first machines achieving performance in excess of one petaflops, and with the advent of new supercomputers in 2021 (e.g., Aurora, Frontier), the Exascale era will soon begin. However, the high theoretical computing capability (i.e., peak FLOPS) of a machine is not the only meaningful target when designing a supercomputer, as the resources demand of applications varies. A deep understanding of the characterization of applications that run on a leadership supercomputer is one of the most important ways for planning its design, development and operation. In order to improve our understanding of HPC applications, user demands and resource usage characteristics, we perform correlative analysis of various logs for different subsystems of a leadership supercomputer. This analysis reveals surprising, sometimes counter-intuitive patterns, which, in some cases, conflicts with existing assumptions, and have important implications for future system designs as well as supercomputer operations. For example, our analysis shows that while the applications spend significant time on MPI, most applications spend very little time on file I/O. Combined analysis of hardware event logs and task failure logs show that the probability of a hardware FATAL event causing task failure is low. Combined analysis of control system logs and file I/O logs reveals that pure POSIX I/O is used more widely than higher level parallel I/O. Based on holistic insights of the application gained through combined and co-analysis of multiple logs from different perspectives and general intuition, we engineer features to "fingerprint" HPC applications. We use t-SNE (a machine learning technique for dimensionality reduction) to validate the explainability of our features and finally train machine learning models to identify HPC applications or group those with similar characteristic. To the best of our knowledge, this is the first work that combines logs on file I/O, computing, and inter-node communication for insightful analysis of HPC applications in production.

Liu, Zhengchun↗

NASA NTRS1993

Differences in Otolith and Abdominal Viscera Graviceptor Dynamics: Implications for Motion Sickness and Perceived Body Position

Human graviceptors, located in the trunk by Mittelstaedt probably transduce acceleration by abdominal viscera motion. As demonstrated previously in biodynamic vibration and impact tolerance research the thoraco-abdominal viscera exhibit a resonance at 4 to 6 Hz. Behavioral observations and mechanical models of otolith graviceptor response indicate a phase shift increasing with frequency between 0.01 and O.5 Hz. Consequently the potential exists for intermodality sensory conflict between vestibular and visceral graviceptor signals at least at the mechanical receptor level. The frequency range of this potential conflict corresponds with the primary frequency range for motion sickness incidence in transportation, in subjects rotated about Earth-horizontal axes (barbecue spit stimulation) and in periodic parabolic flight microgravity research and also for erroneous perception of vertical oscillations in helicopters. We discuss the implications of this hypothesis for previous self motion perception research and suggestions for various future studies.

vonGierke, Henning E.↗

DOE OSTI2023

A Comprehensive Assessment Tool for Low-TRL Current Energy Converters

Along with a market-competitive levelized cost of energy, a current energy converter technology strongly benefits from an extensive consideration of socioeconomic, environmental, and regulatory factors early in the design process. As part of a technology performance level assessment, a series of assessment questions and guidance are developed and presented to evaluate an early-stage current energy technology on holistic criteria considering the entire device lifecycle. The assessment represents an accumulation of industry and research experience to date and relies on regular updates to ensure alignment with industry best-practices, regulatory requirements, and up-to-date technical understanding. A cradle-to-grave (materials, manufacturing, installation and deployment, operations and maintenance, and end-of-life) assessment of capabilities and functional requirements (i.e., high, medium, and low) performance criteria for current energy converters deployed in tidal, ocean current, and/or river applications. Key considerations related to manufacturing and installation include supply chain robustness, manufacturability and related job creation in the end-user and/or adjacent communities, and the time-to-repayment of the embodied energy debt. During deployment and maintenance operations, the safety of the device and subsystems during disconnect or grid failure, the difficulty and frequency of offshore heavy-lift activities, the avoidance or mitigation of area-use conflicts, the sea-states and weather conditions that permit maintenance access, and the availability of contingency plans (should conditions change unexpectedly) are a portion of the considered assessment criteria. Results include the potential impact of early-stage design decisions on the socioeconomic, environmental, and regulatory performance of a technology that allows developers to increase the product value and probability of success, and minimize costly late-stage design iterations through early and broad consideration of factors affecting overall performance and acceptability.

life cycle analysis↗

DOE OSTI2023

A Comprehensive Assessment Tool for Low-TRL Current Energy Converters: Preprint

Along with a market-competitive levelized cost of energy, a current energy converter technology strongly benefits from an extensive consideration of socioeconomic, environmental, and regulatory factors early in the design process. As part of a technology performance level assessment, a series of assessment questions and guidance are developed and presented to evaluate an early-stage current energy technology on holistic criteria considering the entire device lifecycle. The assessment represents an accumulation of industry and research experience to date and relies on regular updates to ensure alignment with industry best-practices, regulatory requirements, and up-to-date technical understanding. A cradle-to-grave (materials, manufacturing, installation and deployment, operations and maintenance, and end-of-life) assessment of capabilities and functional requirements for tidal, river, and ocean current technologies has been completed. This work presents the evaluation questions and qualitative performance criteria for current energy converters deployed in tidal, ocean current, and/or river applications. Key considerations related to manufacturing and installation include supply chain robustness, manufacturability and related job creation in the end-user and/or adjacent communities, and the time-to-repayment of the embodied energy debt. During deployment and maintenance operations, the safety of the device and subsystems during disconnect or grid failure, the difficulty and frequency of offshore heavy-lift activities, the avoidance or mitigation of area use conflicts, the sea-states and weather conditions that permit maintenance access, and the availability of contingency plans (should conditions change unexpectedly) are a portion of the considered assessment criteria. Results include the potential impact of early-stage design decisions on the socioeconomic, environmental, and regulatory performance of a technology that allows developers to increase the product value and probability of success, and minimize costly late-stage design iterations through early and broad consideration of factors affecting overall performance and acceptability.

industry support↗

DOE OSTI2023

A Comprehensive Assessment Tool for Low-TRL Current Energy Converters

Along with a market-competitive levelized cost of energy, a current energy converter technology strongly benefits from an extensive consideration of socioeconomic, environmental, and regulatory factors early in the design process. As part of a technology performance level assessment, a series of assessment questions and guidance are developed and presented to evaluate an early-stage current energy technology on holistic criteria considering the entire device lifecycle. The assessment represents an accumulation of industry and research experience to date and relies on regular updates to ensure alignment with industry best-practices, regulatory requirements, and up-to-date technical understanding. A cradle-to-grave (materials, manufacturing, installation and deployment, operations and maintenance, and end-of-life) assessment of capabilities and functional requirements for tidal, river, and ocean current technologies has been completed. This work presents the evaluation questions and qualitative performance criteria for current energy converters deployed in tidal, ocean current, and/or river applications. Key considerations related to manufacturing and installation include supply chain robustness, manufacturability and related job creation in the end-user and/or adjacent communities, and the time-to-repayment of the embodied energy debt. During deployment and maintenance operations, the safety of the device and subsystems during disconnect or grid failure, the difficulty and frequency of offshore heavy-lift activities, the avoidance or mitigation of area use conflicts, the sea-states and weather conditions that permit maintenance access, and the availability of contingency plans (should conditions change unexpectedly) are a portion of the considered assessment criteria. Results include the potential impact of early-stage design decisions on the socioeconomic, environmental, and regulatory performance of a technology that allows developers to increase the product value and probability of success, and minimize costly late-stage design iterations through early and broad consideration of factors affecting overall performance and acceptability.

converter↗

NASA NTRS1988

Metamorphism of cordierite gneisses from Eastern Ghat Granulite Terrain, Andhra Pradesh, South India

Cordierite-bearing metapelites of the Eastern Ghat granulite terrain occur in close association of Khondalites, quartzites, calc-silicate rocks and charnockites. Rocks occurring between Bobbili in the north and Guntur in the south of Andhra Pradesh are studied. The association of the mineral and textural relationships suggest the following metamorphic reactions: Garnet + sillimanite + quartz = cordierite, hypersthene + sillimanite + quartz = cordierite, sillimanite + spinel = cordierite + corundum, and biotite + quartz + sillimanite = cordierite + K=feldspar. Generally the minerals are not chemically zoned except garnet-biotite showing zoning when they come in close contact with one another. The potential thermometers are provided by the Fe-Mg distribution of coexisting biotite-garnet and cordierite-garnet. Conflicting interpretation of the P/T dependence of these reactions involving cordierite are due to H2O in the cordierite. The presence of alkali feldspar-quartz assemblage which is common in these gneisses will be constrained from melting only if H2O activity is less than 0.5. The piezometric array inferred is convex towards the temperature array, indicating a rapid and isothermal crustal uplift probably aided by thrust tectonics.

Murthy, D. S. N.↗

NASA NTRS2003

Modeling, Analyzing, and Mitigating Dissonance Between Alerting Systems

Alerting systems are becoming pervasive in process operations, which may result in the potential for dissonance or conflict in information from different alerting systems that suggests different threat levels and/or actions to resolve hazards. Little is currently available to help in predicting or solving the dissonance problem. This thesis presents a methodology to model and analyze dissonance between alerting systems, providing both a theoretical foundation for understanding dissonance and a practical basis from which specific problems can be addressed. A state-space representation of multiple alerting system operation is generalized that can be tailored across a variety of applications. Based on the representation, two major causes of dissonance are identified: logic differences and sensor error. Additionally, several possible types of dissonance are identified. A mathematical analysis method is developed to identify the conditions for dissonance originating from logic differences. A probabilistic analysis methodology is developed to estimate the probability of dissonance originating from sensor error, and to compare the relative contribution to dissonance of sensor error against the contribution from logic differences. A hybrid model, which describes the dynamic behavior of the process with multiple alerting systems, is developed to identify dangerous dissonance space, from which the process can lead to disaster. Methodologies to avoid or mitigate dissonance are outlined. Two examples are used to demonstrate the application of the methodology. First, a conceptual In-Trail Spacing example is presented. The methodology is applied to identify the conditions for possible dissonance, to identify relative contribution of logic difference and sensor error, and to identify dangerous dissonance space. Several proposed mitigation methods are demonstrated in this example. In the second example, the methodology is applied to address the dissonance problem between two air traffic alert and avoidance systems: the existing Traffic Alert and Collision Avoidance System (TCAS) vs. the proposed Airborne Conflict Management system (ACM). Conditions on ACM resolution maneuvers are identified to avoid dynamic dissonance between TCAS and ACM. Also included in this report is an Appendix written by Lee Winder about recent and continuing work on alerting systems design. The application of Markov Decision Process (MDP) theory to complex alerting problems is discussed and illustrated with an abstract example system.

Song, Lixia↗

DOE OSTI2023

A ‘black hole theorem,’ and its implications

A general formulation of the basic conflict of the information problem is given, encapsulated in a 'black hole theorem.' This is framed in a more general context than the usual one of quantum field theory on a background, and is based on describing a black hole as a quantum subsystem of a larger system, including its environment. This sharpens the limited set of possible consistent options; as with the Coleman-Mandula theorem, the most important point is probably the loophole in the 'theorem,' and what this tells us about the fundamental structure of quantum gravity. This 'theorem' in particular involves the general question of how to define quantum subsystems in quantum gravity. If black holes do behave as quantum subsystems, at least to a good approximation, evolve unitarily, and do not leave remnants, the 'theorem' implies the presence of interactions between a black hole and its environment that go beyond a description based on local quantum fields. This provides further motivation for and connects to previous work giving a principled parameterization of these interactions, and investigating their possible observational signatures via electromagnetic or gravitational wave observations of black holes.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2022

Stochastic agent-based model for predicting turbine-scale raptor movements during updraft-subsidized directional flights

Rapid expansion of wind energy development across the world has highlighted the need to better understand turbine-caused avian mortality. The risk to golden eagles (Aquila chrysaetos) is of particular concern due to their small population size and conservation status. Golden eagles subsidize their flight in part by soaring in orographic updrafts, which can place them in conflict with wind turbines utilizing the same low-altitude wind resource. Understanding the behavior of soaring raptors in varying atmospheric conditions can therefore be relevant to predicting and mitigating their risk of collision. We present a predictive movement model that simulates individual paths of golden eagles during directional flight (such as migration) that is subsidized by orographic updraft. We modeled eagles in a 50 km by 50 km study area in Wyoming containing three wind power plants with documented golden eagle collisions with turbines. The movement model is applicable to any region where ground elevation is known at turbine scale (50 m) and wind conditions are known at facility scale (3 km). For a given set of atmospheric conditions, the model simulates movements of thousands of orographic soaring eagles to produce a density map quantifying the relative probability of eagle presence. We validated the simulated tracks with GPS telemetry data showing four directional tracks made by golden eagles transiting through the area in 2019 and 2020. For each eagle track, validation was performed using the ratio of the model-simulated eagle presence likelihood with uniform eagle presence and the presence computed using directed random-walk movements. We found that the predictive performance of the model was significantly better (likelihood ratio 1) for low-altitude movements than high-altitude movements that can involve thermal-soaring. We employed the model to produce seasonal presence maps for migrating golden eagles. We found significant turbine-level variations in eagle presence between northerly and southerly migration routes through the study area. Overall, the proposed model offers a generalizable, probabilistic, and predictive tool to assist wind energy developers, ecologists, wildlife managers, and industry consultants in estimating the potential for conflict between soaring birds and wind turbines, thereby reducing the need for site-specific data on golden eagle movements.

17 WIND ENERGY↗