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NASA NTRS1994

Degassing mechanisms of noble gases from carbonado diamonds

Diamonds are unique samples for inferring ancient mantle conditions, because of their enormous stability, antiquity and also of mantle origin. However, as temperatures in the mantle where diamonds have existed are very high (greater than 1000 C) and residence time of some diamonds could be more than a few billion years, it is imperative to examine whether or not diamonds have retained their pristine characteristics, especially those of noble gases, under such extreme conditions. As discussed in a review article by Ozima, there are rather large variations in the diffusivity of helium in diamonds obtained in the early determinations. The data are also limited to temperatures higher than 1200 C. In the present study, we conducted more refined diffusion experiments for He using carbonado diamonds, which have large amounts of radiogenic (4)He approximately 10(exp -2) cu cm STP/g. On the basis of the experimentally estimated diffusion coefficients, we will discuss retentivity of He in diamonds in the mantle condition.

Zashu, S.↗

NASA NTRS1994

Landau damping of auroral hiss

Auroral hiss is observed to propagate over distances comparable to an Earth radius from its source in the auroral oval. The role of Landau damping is investigated for upward propagating auroral hiss. By using a ray tracing code and a simplified model of the distribution function, the effect of Landau damping is calculated for auroral hiss propagation through the environment around the auroral oval. Landau damping is found to be the likely mechanism for explaining some of the one-sided auroral hiss funnels observed by Dynamics Explorer 1. It is also found that Landau damping puts a lower limit on the wavelength of auroral hiss. Poleward of the auroral oval, Landau damping is found in a typical case to limit omega/k(sub parallel) to values of 3.4 x 10(exp 4) km/s or greater, corresponding to resonance energies of 3.2 keV or greater and wavelengths of 2 km or greater. For equatorward propagation, omega/k(sub parallel) is limited to values greater than 6.8 x 10(exp 4) km/s, corresponding to resonance energies greater than 13 keV and wavelengths greater than 3 km. Independent estimates based on measured ratios of the magnetic to electric field intensity also show that omega/k(sub parallel) corresponds to resonance energies greater than 1 keV and wavelengths greater than 1 km. These results lead to the difficulty that upgoing electron beams sufficiently energetic to directly generate auroral hiss of the inferred wavelength are not usually observed. A partial transmission mechanism utilizing density discontinuities oblique to the magnetic field is proposed for converting auroral hiss to wavelengths long enough to avoid damping of the wave over long distances. Numerous reflections of the wave in an upwardly flared density cavity could convert waves to significantly increased wavelengths and resonance velocities.

Morgan, D. D.↗

DOE OSTI2022

Revealing a Hidden Intermediate of Rotatory Catalysis with X-ray Crystallography and Molecular Simulations

The mechanism of rotatory catalysis in ATPhydrolyzing molecular motors remains an unresolved puzzle in biological energy transfer. Notwithstanding the wealth of available biochemical and structural information inferred from years of experiments, knowledge on how the coupling between the chemical and mechanical steps within motors enforces directional rotatory movements remains fragmentary. Even more contentious is to pinpoint the rate-limiting step of a multistep rotation process. Here, using vacuolar or V 1 -type hexameric ATPase as an exemplary rotational motor, we present a model of the complete 4-step conformational cycle involved in rotatory catalysis. First, using Xray crystallography, a new intermediate or “dwell” is identified, which enables the release of an inorganic phosphate (or P i ) after ATP hydrolysis. Using molecular dynamics simulations, this new dwell is placed in a sequence with three other crystal structures to derive a putative cyclic rotation path. Free-energy simulations are employed to estimate the rate of the hexameric protein transformations and delineate allosteric effects that allow new reactant ATP entry only after hydrolysis product exit. An analysis of transfer entropy brings to light how the side-chain-level interactions transcend into larger-scale reorganizations, highlighting the role of the ubiquitous arginine-finger residues in coupling chemical and mechanical information. An inspection of all known rates encompassing the 4-step rotation mechanism implicates the overcoming of the ADP interactions with V 1 -ATPase to be the rate-limiting step of motor action.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

Understanding asymmetries using integrated simulations of capsule implosions in low gas-fill hohlraums at the National Ignition Facility

Current capsule implosions at the National Ignition Facility (NIF) using high-density-carbon ablators and laser energies close to 2 MJ have shown neutron yields in excess of 50 kJ. Improving on this performance requires understanding of the different degradation mechanisms. For many NIF implosions, nuclear diagnostic signatures have inferred residual hot-spot velocities that correlate with fuel areal density variations consistent with a low-order mode-1 asymmetry. A current working hypothesis attributes these asymmetries to a combination of beam to beam variations in the laser delivery and possibly coupling to target features, such as the diagnostic holes needed for x-ray imaging. Recently, a new source has been identified, thickness variation in the ablator shell. To gain better understanding and eventually mitigate the causes of <ρR> asymmetries, 3D integrated simulations using the actual delivered laser powers are needed. To capture the effect of the diagnostic holes (DHs) using direct numerical simulation would require significantly large computational resources. Instead, our 3D simulations make use of a subgrid model developed using highly-resolved 2D simulations that include several details of the DH engineering complexity. Simulations of NIF shots using hohlraums without DHs, to isolate the effect of beam-to-beam variations, reproduce fairly well the observed nuclear diagnostic signatures. Similarly, reasonable agreement between data and simulations is also obtained in the presence of diagnostic holes. To account for the remaining discrepancies a sensitivity study of ablator thickness variation showed that 1% thickness asymmetries are comparable in effect to 1% peak drive mode-1 asymmetries. Furthermore, this study identified sensitivity to variations in the imbedded doped layer (needed to shield the DT ice from the high energy x-rays generated in the hohlraum) thickness even when the inner and outer surface of the ablator are perfectly spherical.

radiation hydrodynamics↗

DOE OSTI2020

The Coupled Influence of Thermal Physiology and Biotic Interactions on the Distribution and Density of Ant Species along an Elevational Gradient

A fundamental tenet of biogeography is that abiotic and biotic factors interact to shape the distributions of species and the organization of communities, with interactions being more important in benign environments, and environmental filtering more important in stressful environments. This pattern is often inferred using large databases or phylogenetic signal, but physiological mechanisms underlying such patterns are rarely examined. We focused on 18 ant species at 29 sites along an extensive elevational gradient, coupling experimental data on critical thermal limits, null model analyses, and observational data of density and abundance to elucidate factors governing species’ elevational range limits. Thermal tolerance data showed that environmental conditions were likely to be more important in colder, more stressful environments, where physiology was the most important constraint on the distribution and density of ant species. Conversely, the evidence for species interactions was strongest in warmer, more benign conditions, as indicated by our observational data and null model analyses. Our results provide a strong test that biotic interactions drive the distributions and density of species in warm climates, but that environmental filtering predominates at colder, high-elevation sites. Such a pattern suggests that the responses of species to climate change are likely to be context-dependent and more specifically, geographically-dependent.

54 ENVIRONMENTAL SCIENCES↗

NASA NTRS1978

A dependency-based modelling mechanism for problem solving

The paper develops a technique of dependency net modeling which relies on an explicit representation of justifications for beliefs held by the problem solver. Using these justifications, the modeling mechanism is able to determine the relevant lines of inference to pursue during problem solving. Three particular problem-solving difficulties which may be handled by the dependency-based technique are discussed: (1) subgoal violation detection, (2) description binding, and (3) maintaining a consistent world model.

London, P.↗

DOE OSTI2023

Mass of a weakly measured photon

Bohmian mechanics has garnered significant attention as an interpretation of quantum theory since the paradigmatic experiments which inferred the average trajectories of photons in the nonrelativistic regime. These experiments were largely motivated by Wiseman's formulation of Bohmian mechanics, which grounded these trajectories in weak measurements. Recently, Wiseman's framework was extended to the relativistic regime by expressing the velocity field of single photons in terms of weak values of the photon energy and momentum. Here, we propose an operational, weak value-based definition for the Bohmian “local mass” of relativistic single particles. For relativistic wave functions satisfying the scalar Klein-Gordon equation, this mass coincides with the effective mass defined by de Broglie in his relativistic pilot-wave theory, a quantity closely connected with the quantum potential that is responsible for Bohmian trajectory self-bending and the anomalous photoelectric effect. Here, we demonstrate the relationship between the photon trajectories and the mass in an interferometric setup.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2021

Combination of deep neural network with attention mechanism enhances the explainability of protein contact prediction

Abstract Deep learning has emerged as a revolutionary technology for protein residue‐residue contact prediction since the 2012 CASP10 competition. Considerable advancements in the predictive power of the deep learning‐based contact predictions have been achieved since then. However, little effort has been put into interpreting the black‐box deep learning methods. Algorithms that can interpret the relationship between predicted contact maps and the internal mechanism of the deep learning architectures are needed to explore the essential components of contact inference and improve their explainability. In this study, we present an attention‐based convolutional neural network for protein contact prediction, which consists of two attention mechanism‐based modules: sequence attention and regional attention. Our benchmark results on the CASP13 free‐modeling targets demonstrate that the two attention modules added on top of existing typical deep learning models exhibit a complementary effect that contributes to prediction improvements. More importantly, the inclusion of the attention mechanism provides interpretable patterns that contain useful insights into the key fold‐determining residues in proteins. We expect the attention‐based model can provide a reliable and practically interpretable technique that helps break the current bottlenecks in explaining deep neural networks for contact prediction. The source code of our method is available at https://github.com/jianlin-cheng/InterpretContactMap .

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Satellite Observations of the Tropical Terrestrial Carbon Balance and Interactions With the Water Cycle During the 21st Century

A constellation of satellites are now in orbit providing information about terrestrial carbon and water storage and fluxes. These combined observations show that the tropical biosphere has changed significantly in the last two decades from the combined effects of climate variability and land use. Large areas of forest have been cleared in both wet and dry forests, increasing the source of carbon to the atmosphere. Concomitantly, tropical fire emissions have declined, at least until 2016, from changes in land-use practices and rainfall, increasing the net carbon sink. Measurements of carbon stocks and fluxes from disturbance and recovery and of vegetation photosynthesis show significant regional variability of net biosphere exchange (NBE) and gross primary productivity (GPP) across the tropics and are tied to seasonal and interannual changes in water fluxes and storage. Comparison of satellite based estimates of evapotranspiration (ET), photosynthesis, and the deuterium content of water vapor with patterns of total water storage and rainfall demonstrate the presence of vegetation-atmosphere interactions and feedback mechanisms across tropical forests. However, these observations of stocks, fluxes and inferred interactions between them do not point unambiguously to either positive or negative feedbacks in carbon and water exchanges. These ambiguities highlight the need for assimilation of these new measurements with Earth System models for a consistent assessment of process interactions, along with focused field campaigns that integrate ground, aircraft and satellite measurements, to quantify the controlling carbon and water processes and their feedback mechanisms.

58 GEOSCIENCES↗

NASA NTRS1985

Stress rate and proof-testing of silicon wafers

Fracture mechanics test methods were applied to evaluate the proof-test characteristics of single-crystal silicon wafers. The results indicate that the strength distribution of silicon wafers is truncated by proof-testing. No subcritical crack growth occurred during proof-loading, as inferred from the lack of a stress-rate effect on strength. Mechanical proof-testing appears to be an effective method for eliminating weak samples before cell processing.

Chen, C. P.↗

NASA NTRS1987

Isotopic fractionation of Kr and Xe implanted in solids at very low energies

Results on the implantation of Kr and Xe in W under closed system conditions at very low energies (50-500 eV) are reported. Investigation of the fraction of gas trapped as a function of time reveals the existence of competing trapping and release mechanisms, and analysis of recovered trapped gas and residual gas phases shows that both elemental and isotropic fractionation result from these mechanisms. It is determined that the mass dependence for the overall implantation process is at or near m exp 1, with heavier isotopes enriched in the implanted gas. This mass dependence is inferred to result from implantation and a combination of diffusive and gas sputtering release mechanisms. These results reaffirm the conclusion of Bernatowicz and Fahey (1986) that previously observed isotopic fractionation of Kr and Xe in carbonaceous material synthesized in electrical discharges owes its origin to low-energy ion implantation, and also suggest that this process may be relevant to incorporation of noble gases in early solar system materials. The implication of these results for noble gas mass spectrometry are discussed.

Bernatowicz, Thomas J.↗

NASA NTRS1990

A knowledge base architecture for distributed knowledge agents

A tuple space based object oriented model for knowledge base representation and interpretation is presented. An architecture for managing distributed knowledge agents is then implemented within the model. The general model is based upon a database implementation of a tuple space. Objects are then defined as an additional layer upon the database. The tuple space may or may not be distributed depending upon the database implementation. A language for representing knowledge and inference strategy is defined whose implementation takes advantage of the tuple space. The general model may then be instantiated in many different forms, each of which may be a distinct knowledge agent. Knowledge agents may communicate using tuple space mechanisms as in the LINDA model as well as using more well known message passing mechanisms. An implementation of the model is presented describing strategies used to keep inference tractable without giving up expressivity. An example applied to a power management and distribution network for Space Station Freedom is given.

Riedesel, Joel↗

NASA NTRS2011

Deep Moonquake Focal Mechanisms: Recovery and Implications

A defining characteristic of deep moonquakes is their tendency to occur with tidal periodicity, prompting previous studies to infer that they are related to the buildup and release of tidal stress within the Moon. In studies of tidal forcing, a key constraint is the focal mechanism: the fault parameters describing the type of failure moonquakes represent. The quality of the lunar seismic data and the limited source/receiver geometries of the Apollo seismic network prohibit the determination of deep moonquake fault parameters using first-motion polarities, as is typically done in terrestrial seismology. Without being able to resolve tidal stress onto a known failure plane, we can examine only gross qualities of the tidal stress tensor with respect to moonquake occurrence, so we cannot fully address the role of tidal stress in moonquake generation. We will examine the extent to which shear (S) and compression (P) wave amplitude ratios can constrain moonquake fault geometry by determining whether, for a given cluster, there exists a focal mechanism that can produce a radiation pattern consistent with the amplitudes measured by the Apollo instruments. Amplitudes are read in the ray coordinate frame, directly from seismograms for which the P and S arrivals are clearly identifiable on all long-period channels of the four Apollo stations. We apply an empirical station correction to account for site effects and the differences between P- and S-wave attenuation. Instead of focusing on the best fitting solution only, we formulate the inverse problem using a falsification criterion: all source orientations that do not reproduce the observed SV/P ratios within an error margin derived from the uncertainty of amplitude readings are rejected. All others are accepted as possible solutions. The inversion is carried out using an exhaustive grid search on a regular grid with predefined step size, encompassing all possible combinations of strike, dip and slip. To assess the sensitivity of the inversion for the uncertainty of the lunar interior structure, we carry out repeated inversions with different velocity structures. Our data set consist of a total of 106 events from 25 deep moonquake clusters. The largest contribution of 37 events originates from the most active cluster, A001, while other clusters are represented by 1 to 9 events. Since the definition of a cluster implies that all events share the same source orientation, a comparison of the inversion results of all events from one cluster will reduce ambiguities of the inversion. Once we obtain a suite of fault parameters for a given source, we can attempt to further constrain the focal mechanism with refined analyses of tidal stresses and predictions based on synthetic seismograms.

Knapmeyer, Martin↗

DOE OSTI2021

Flow over an espresso cup: inferring 3-D velocity and pressure fields from tomographic background oriented Schlieren via physics-informed neural networks

Tomographic background oriented Schlieren (Tomo-BOS) imaging measures density or temperature fields in three dimensions using multiple camera BOS projections, and is particularly useful for instantaneous flow visualizations of complex fluid dynamics problems. We propose a new method based on physics-informed neural networks (PINNs) to infer the full continuous three-dimensional (3-D) velocity and pressure fields from snapshots of 3-D temperature fields obtained by Tomo-BOS imaging. The PINNs seamlessly integrate the underlying physics of the observed fluid flow and the visualization data, hence enabling the inference of latent quantities using limited experimental data. In this hidden fluid mechanics paradigm, we train the neural network by minimizing a loss function composed of a data mismatch term and residual terms associated with the coupled Navier–Stokes and heat transfer equations. We first quantify the accuracy of the proposed method based on a two-dimensional synthetic data set for buoyancy-driven flow, and subsequently apply it to the Tomo-BOS data set, where we are able to infer the instantaneous velocity and pressure fields of the flow over an espresso cup based only on the temperature field provided by the Tomo-BOS imaging. Moreover, we conduct an independent PIV experiment to validate the PINN inference for the unsteady velocity field at a centre plane. To explain the observed flow physics, we also perform systematic PINN simulations at different Reynolds and Richardson numbers and quantify the variations in velocity and pressure fields. Furthermore, the results in this paper indicate that the proposed deep learning technique can become a promising direction in experimental fluid mechanics.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2024

Topological Interpretability for Deep Learning

With the growing adoption of AI-based systems across everyday life, the need to understand their decision-making mechanisms is correspondingly increasing. The level at which we can trust the statistical inferences made from AI-based decision systems is an increasing concern, especially in high-risk systems such as criminal justice or medical diagnosis, where incorrect inferences may have tragic consequences. Despite their successes in providing solutions to problems involving real-world data, deep learning (DL) models cannot quantify the certainty of their predictions. These models are frequently quite confident, even when their solutions are incorrect. This work presents a method to infer prominent features in two DL classification models trained on clinical and non-clinical text by employing techniques from topological and geometric data analysis. We create a graph of a model's feature space and cluster the inputs into the graph's vertices by the similarity of features and prediction statistics. We then extract subgraphs demonstrating high-predictive accuracy for a given label. These subgraphs contain a wealth of information about features that the DL model has recognized as relevant to its decisions. We infer these features for a given label using a distance metric between probability measures, and demonstrate the stability of our method compared to the LIME and SHAP interpretability methods. This work establishes that we may gain insights into the decision mechanism of a DL model. This method allows us to ascertain if the model is making its decisions based on information germane to the problem or identifies extraneous patterns within the data.

Spannaus, Adam↗

NASA NTRS2012

Deep Moonquake Focal Mechanisms: Recovery and Implications

Weber, Renee C.↗

DOE OSTI2020

Characterizing Baselines and Change in Gas Hydrate Systems using EM Methods

The objective of this project was to advance our understanding of gas hydrate systems in nature by characterizing their electrical properties in the field and in the laboratory. In the laboratory measurements, methane hydrate was synthesized from pure water ice and flash frozen seawater, with varying amounts of sand or silt added. Electrical conductivity was determined by impedance spectroscopy, using equivalent circuit modeling to separate the effects of electrodes and to gain insight into conduction mechanisms. Silt and sand increase the conductivity of pure hydrate, inferred to be contaminant NaCl contributing to conduction in hydrate, to a peak conductivity in agreement with peak resistivities observed in well logs through massive hydrate (3,000--10,000 Ωm). The addition of silt and sand lowers the conductivity of hydrate synthesized from seawater, by an amount consistent with Archie's Law. All samples were characterized using cryogenic scanning electron microscopy and energy dispersive spectroscopy, which shows good connectivity of salt and brine phases. Electrical conductivity measurements of pure hydrate and hydrate mixed with silt during pressure-induced dissociation supports previous conclusions that sediment increases dissociation rate. In order to characterize gas hydrate systems in the field, we collected 360 line kilometers of controlled-source electromagnetic data on Walker Ridge 313, Orca Basin (WR100), Mad Dog (GC781), and Green Canyon 955 in the Gulf of Mexico, all areas with known or seismically inferred gas hydrate deposits and which have be drilled or targeted for future drilling. We deep-towed an EM transmitter that generates an alternating electric field which propagates through the seafloor geology. Data were recorded on 6 receivers towed behind the transmitter at distances between 550 and 1550 m. In the presence of conductive geology, the electric fields will be attenuated, and conversely, in resistive geology the fields will be preserved. Our data were inverted using a 2D inversion method that first optimizes the model-data misfit, then finds the smoothest model fitting the data. This ensures that resistivity structures present in the final model are likely necessary. At each of the proposed drilling sites we found increased resistivity, interpreted as increased hydrate concentrations. However, not only were the primary drilling sites not always more resistive than the alternate sites, at WR313 the strongest resistors were not at the locations targeted for drilling.

03 NATURAL GAS↗

DOE OSTI2021

Artificial Intelligence for Autonomous Molecular Design: A Perspective

Domain-aware artificial intelligence has been increasingly adopted in recent years to expedite molecular design in various applications, including drug design and discovery. Recent advances in areas such as physics-informed machine learning and reasoning, software engineering, high-end hardware development, and computing infrastructures are providing opportunities to build scalable and explainable AI molecular discovery systems. This could improve a design hypothesis through feedback analysis, data integration that can provide a basis for the introduction of end-to-end automation for compound discovery and optimization, and enable more intelligent searches of chemical space. Several state-of-the-art ML architectures are predominantly and independently used for predicting the properties of small molecules, their high throughput synthesis, and screening, iteratively identifying and optimizing lead therapeutic candidates. However, such deep learning and ML approaches also raise considerable conceptual, technical, scalability, and end-to-end error quantification challenges, as well as skepticism about the current AI hype to build automated tools. To this end, synergistically and intelligently using these individual components along with robust quantum physics-based molecular representation and data generation tools in a closed-loop holds enormous promise for accelerated therapeutic design to critically analyze the opportunities and challenges for their more widespread application. This article aims to identify the most recent technology and breakthrough achieved by each of the components and discusses how such autonomous AI and ML workflows can be integrated to radically accelerate the protein target or disease model-based probe design that can be iteratively validated experimentally. Taken together, this could significantly reduce the timeline for end-to-end therapeutic discovery and optimization upon the arrival of any novel zoonotic transmission event. Our article serves as a guide for medicinal, computational chemistry and biology, analytical chemistry, and the ML community to practice autonomous molecular design in precision medicine and drug discovery.

59 BASIC BIOLOGICAL SCIENCES↗