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At least 271 records · Page 15

Increased Water Storage at Ice-stream Onsets: A Critical Mechanism?

The interdependence of rapid ice flow, surface topography and the spatial distribution of subglacial water are examined by linking existing theories. The motivation is to investigate whether the acceleration of an ice-stream tributary contains a positive feedback that encourages the retention of subglacial water that leads to faster flow. Periodically varying surface and bed topographies are related through a linear ice-flow perturbation theory for various values of mean surface slope, perturbation amplitude and basal sliding speeds. The topographic variations lead to a periodic variation in hydraulic potential that is used to infer the tendency for subglacial water to be retained in local hydraulic potential minima. If water retention leads to enhanced basal sliding, a positive feedback loop is closed that could explain the transition from slower tributary flow to faster-streaming flow and the sustained downstream acceleration along the tributary-ice-stream system. A sensitivity study illustrates that the same range of topographic wavelengths most effectively transmitted from the bed to the surface also strongly influences the behavior of subglacial water. A lubrication index is defined to qualitatively measure the heterogeneity of the subglacial hydrologic system. Application of this index to field data shows that the transition from tributary to ice stream closely agrees with the location where subglacial water may be first stored.

Bindschadler, Robert↗

EnZymClass: Substrate specificity prediction tool of plant acyl-ACP thioesterases based on ensemble learning

Characterizing the functional properties of plant acyl-ACP thioesterases (TEs), a key enzyme class used in the production of renewable oleochemicals in microbial hosts, experimentally, can be an expensive and time consuming process since it requires manual screening of thousands of candidates in a database. Using amino acid sequence to computationally predict an enzyme’s function might accelerate this process; however obtaining the necessary amount of information on previously characterized enzymes and their respective sequences required by standard Machine Learning (ML) based approaches to accurately infer sequence-function relationships can be prohibitive, especially with a low-throughput testing cycle. Experimental noise, unbalanced dataset where high sequence similarity does not always imply identical functional properties will further prevent robust prediction performance. Herein we present a ML method, Ensemble method for enZyme Classification (EnZymClass), that is specifically designed to address these issues. We used EnZymClass to classify TEs into short, long and mixed free fatty acid substrate specificity categories. While general guidelines for inferring substrate specificity have been proposed before, prediction of chain-length preference from primary sequence has remained elusive for plant acyl-ACP TEs. By applying EnZymClass to a subset of TEs in the ThYme database, we identified two medium chain TEs, ClFatB3 and CwFatB2, with previously uncharacterized activity in E. coli fatty acid production hosts.

59 BASIC BIOLOGICAL SCIENCES↗

Virtual Diagnostic Suite for Electron Beam Prediction and Control at FACET-II

We discuss the implementation of a suite of virtual diagnostics at the FACET-II facility currently under commissioning at SLAC National Accelerator Laboratory. The diagnostics will be used for the prediction of the longitudinal phase space along the linac, spectral reconstruction of the bunch profile, and non-destructive inference of transverse beam quality (emittance) while using edge radiation at the injector dogleg and bunch compressor locations. These measurements will be folded into adaptive feedbacks and Machine Learning (ML)-based reinforcement learning controls to improve the stability and optimize the performance of the machine for different experimental configurations. In this paper we describe each of these diagnostics with expected measurement results that are based on simulation data and discuss progress towards implementation in regular operations.

Emma, Claudio (ORCID:0000000247191831)↗

deeprob/ThioesteraseEnzymeSpecificity: EnZymClass-first-release

Characterizing the functional properties of plant acyl-ACP thioesterases (TEs), a key enzyme class used in the production of renewable oleochemicals in microbial hosts, experimentally, can be an expensive and time consuming process since it requires manual screening of thousands of candidates in a database. Using amino acid sequence to computationally predict an enzyme’s function might accelerate this process; however obtaining the necessary amount of information on previously characterized enzymes and their respective sequences required by standard Machine Learning (ML) based approaches to accurately infer sequence-function relationships can be prohibitive, especially with a low-throughput testing cycle. Experimental noise, unbalanced dataset where high sequence similarity does not always imply identical functional properties will further prevent robust prediction performance. Herein we present a ML method, Ensemble method for enZyme Classification (EnZymClass), that is specifically designed to address these issues. We used EnZymClass to classify TEs into short, long and mixed free fatty acid substrate specificity categories. While general guidelines for inferring substrate specificity have been proposed before, prediction of chain-length preference from primary sequence has remained elusive for plant acyl-ACP TEs. By applying EnZymClass to a subset of TEs in the ThYme database, we identified two medium chain TEs, ClFatB3 and CwFatB2, with previously uncharacterized activity in E. coli fatty acid production hosts.

Banerjee, Deepro↗

Kinematics of the ion tail of comet P/Swift-Tuttle

We have obtained long-slit high resolution spectra of the H2O(+) 6199 A complex in the near tail of comet P/Swift-Tuttle. The observations were made using the Hamilton echelle spectrometer fed by the Lick Observatory 0.6 m coude auxiliary telescope. For most of our observations, the spectral slit was aligned along the Sun-tail axis and the cometary nucleus was placed at one end of the slit, giving us spectra having the spatial and spectral resolution needed to measure the radial velocity and velocity dispersion continuously down the cometary tail out to a distance of 4X10(exp 5) km. The radial velocities confirm the earlier more restricted observations by Rauer & Jockers (1993) and by Wyckoff & Lindholm (1994) showing that the tail motions are indeed bulk flows in the antisolar direction. Out to 3X10(exp 5) km in the tail typical bulk flows are at a speed of approximately 30 km/s. The velocity dispersion, (sigma(sub r)), of the H2O(+) lines follows a pattern that is quite systematic; sigma(sub r) is smallest near the cometary nucleus, and steadily increases down the tail. The highest velocity dispersions are found ahead of the nucleus and off the tail axis. These velocity dispersions are equivalent to ion temperatures ranging from 10(exp 5) to 10(exp 6) K. We note a clear anticorrelation between the H2O(+) line intensities (related to the ion density) and the bulk flow and dispersion velocities; direct mass loading of the solar wind by the observed water ions may be responsible. We discuss several approximate equipartition methods used to infer local magnetic fields induced by the interaction of the cometary ions with the solar wind particle/field stream. Typical fields derived are near 50 nT. The measured tailward accelerations are consistent with this order of magnitude B field.

Spinrad, Hyron↗

Nonlinear Optics Measurements in IOTA

Nonlinear integrable optics is a recently proposed accelerator lattice design approach which allows to generate an amplitude dependent tune shift which is needed in high brightness accelerators to mitigate fast coherent instabilities. Whereas usually octupoles are used to achieve this task, this concept allows doing so without exciting any resonances, in turn preventing any particle loss. The concept is based around a special magnet design, together with specific constraints on the optics of the accelerator. To study such a system, the Integrable Optics Test Accelerator (IOTA) was recently constructed and commissioned at Fermilab. For the assessment of the performance of this concept, good knowledge of the optics and the (non-)linear dynamics without the special magnet is of key importance. As such, measurements were conducted in the IOTA ring, using the captured turn-by-turn data by the beam position monitors after excitation to infer quantities such as amplitude detuning and resonance driving terms. In this note, first results of these measurements are presented.

43 PARTICLE ACCELERATORS↗

Adaptive sampling for accelerating neutron diffraction-based strain mapping *

Abstract Neutron diffraction is a useful technique for mapping residual strains in dense metal objects. The technique works by placing an object in the path of a neutron beam, measuring the diffracted signals and inferring the local lattice strain values from the measurement. In order to map the strains across the entire object, the object is stepped one position at a time in the path of the neutron beam, typically in raster order, and at each position a strain value is estimated. Typical dwell times at neutron diffraction instruments result in an overall measurement that can take several hours to map an object that is several tens of centimeters in each dimension at a resolution of a few millimeters, during which the end users do not have an estimate of the global strain features and are at risk of incomplete information in case of instruments outages. In this paper, we propose an object adaptive sampling strategy to measure the significant points first. We start with a small initial uniform set of measurement points across the object to be mapped, compute the strain in those positions and use a machine learning technique to predict the next position to measure in the object. Specifically, we use a Bayesian optimization based on a Gaussian process regression method to infer the underlying strain field from a sparse set of measurements and predict the next most informative positions to measure based on estimates of the mean and variance in the strain fields estimated from the previously measured points. We demonstrate our real-time measure-infer-predict workflow on additively manufactured steel parts—demonstrating that we can get an accurate strain estimate even with 30%–40% of the typical number of measurements—leading the path to faster strain mapping with useful real-time feedback. We emphasize that the proposed method is general and can be used for fast mapping of other material properties such as phase fractions from time-consuming point-wise neutron measurements.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Mapping the Solar Wind from its Source Region into the Outer Corona

Knowledge of the radial variation of the plasma conditions in the coronal source region of the solar wind is essential to exploring coronal heating and solar wind acceleration mechanisms. The goal of the proposal was to determine as many plasma parameters in the solar wind acceleration region and beyond as possible by coordinating different observational techniques, such as Interplanetary Scintillation Observations, spectral line intensity observations, polarization brightness measurements and X-ray observations. The inferred plasma parameters were then used to constrain solar wind models.

Esser, Ruth↗

Laminar-Turbulent Transition in an Electromagnetically-Levitated Droplet

During experiments on the MSL-1 (First Microgravity Science Laboratory) mission of the Space Shuttle (STS-83 and STS-94, April and July 1997), a droplet of palladium-silicon alloy was electromagnetically levitated for viscosity measurements. For the non-deforming droplet, the resultant MHD flow inside the drop can be inferred from motion of impurity particulates on the surface. In the experiments, subsequent to melting, Joule heating produces a continuous reduction of viscosity of the fluid resulting in an acceleration of the flow with time. These observations indicate formation of a pair of co-rotating toroidal flow structures inside the spheroidal drop that undergo flow instabilities. As the fluid temperature rises, the amplitude of the secondary flow increases; and beyond a point, the tracers exhibit non-coherent chaotic motion signifying emergence of turbulence inside the drop. Assuming that the observed laminar-turbulent transition is shear-layer type, the internal structure of the toroidal loops is used to develop a semi- empirical correlation for the onset of turbulence. Our calculations indicate that the suggested correlation is in modest agreement with the experimental data, with the transition occurring at a Reynolds number of 600.

Hyers, R. W.↗

Laminar-Turbulent Transition in an Electromagnetically-Levitated Droplet

During experiments on the MSL-1 (First Microgravity Science Laboratory) mission of the Space Shuttle (STS-83 and STS-94, April and July 1997), a droplet of palladium-silicon alloy was electromagnetically levitated for viscosity measurements. For the non-deforming droplet, the resultant MHD flow inside the drop can be inferred from motion of impurity particulates on the surface. In the experiments, subsequent to melting, Joule heating produces a continuous reduction of viscosity of the fluid resulting in an acceleration of the flow with time. These observations indicate formation of a pair of corotating toroidal flow structures inside the spheroidal drop that undergo flow instabilities. As the fluid temperature rises, the amplitude of the secondary flow increases; and beyond a point, the tracers exhibit non-coherent chaotic motion signifying emergence of turbulence inside the drop. Assuming that the observed laminar-turbulent transition is shear-layer type, the internal structure of the toroidal loops is used to develop a semi-empirical correlation for the onset of turbulence. Our calculations indicate that the suggested correlation is in modest agreement with the experimental data, with the transition occurring at a Reynolds number of 600.

Hyers, Robert W.↗

External and Internal Reconnection in Two Filament-Carrying Magnetic-Cavity Solar Eruptions

We observe two near-limb solar filament eruptions, one of 2000 February 26 and the other of 2002 January 4. For both we use 195 A Fe XII images from the Extreme-Ultraviolet Imaging Telescope (EIT) and magnetograms from the Michelson Doppler Imager (MDI), both of which are on the Solar and Heliospheric Observatory (SOHO). For the earlier event we also use soft X-ray telescope (SXT), hard X-ray telescope (HXT), and Bragg Crystal Spectrometer (BCS) data from the Yohkoh satellite, and hard X-ray data from the BATSE experiment on the Compton Gamma Ra.v Observatory (CGRO). Both events occur in quadrupolar magnetic regions, and both have coronal features that we infer belong to the same magnetic cavity structures as the filaments. In both cases, the cavity and filament first rise slowly at approx.10 km/s prior to eruption and then accelerate to approx.100 km/s during the eruption, although the slow-rise movement for the higher altitude cavity elements is clearer in the later event. We estimate that both filaments and both cavities contain masses of approx.10(exp 14)-10(exp 15) and approx.10(exp 15)-10(exp 16) g, respectively. We consider whether two specific magnetic reconnection-based models for eruption onset, the "tether cutting" and the "breakout" models, are consistent with our observations. In the earlier event, soft X-rays from SXT show an intensity increase during the 12 minute interval over which fast eruption begins, which is consistent with tether- cutting-model predictions. Substantial hard X-rays, however, do not occur until after fast eruption is underway, and so this is a constraint the tether-cutting model must satisfy. During the same 12 minute interval over which fast eruption begins, there are brightenings and topological changes in the corona indicative of high-altitude reconnection early in the eruption, and this is consistent with breakout predictions. In both eruptions, the state of the overlying loops at the time of onset of the fast-rise phase of the corresponding filament can be compared with expectations from the breakout model, thereby setting constraints that the breakout model must meet. Our findings are consistent with both runaway tether-cutting-type reconnection and fast breakout-type reconnection, occurring early in the fast phase of the February eruption and with both types of reconnection being important in unleashing the explosion, but we are not able to say which, if either, type of reconnection actually triggered the fast phase. In any case, we have found specific constraints that either model, or any other model, must satisfy if correct.

Sterling, Alphonse C.↗

Analytic solutions for Asay foil trajectories with implications for ejecta source models and mass measurements

We consider the trajectory of an Asay foil ejecta diagnostic for scenarios where ejecta are produced at a singly shocked planar surface and fly ballistically through a perfect vacuum to the sensor. We do so by building upon a previously established mathematical framework derived for the analytic study of stationary sensors. First, we derive the momentum conservation equation for the problem, in a form amenable to accelerating sensors, in terms of a generic ejecta source model. The result is an integrodifferential equation of motion for the foil trajectory. This equation yields an easily calculable closed-form implicit solution for the foil trajectory in instant-production scenarios. From there, we derive a boundary condition that particle velocity distributions must satisfy if their associated foil trajectories are to exhibit a smooth initial acceleration, as occurs in some experiments. This condition is identical to one derived previously from a consideration of piezoelectric voltage data obtained in similar experiments. We also compare techniques for inferring accumulated ejecta masses from foil trajectories, first by deriving the exact solution, and then by quantifying the error imposed by a frequently used approximate solution (both subject to the assumption of instantaneous ejecta production). Finally, we examine the common practice of presenting inferred cumulative ejecta masses as a function of implied ejecta velocity, establishing the conditions under which this methodology is most meaningful.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Neutron-Resonance Transmission Analysis with a Compact Deuterium-Tritium Neutron Generator

Neutron Resonance Transmission Analysis (NRTA) is a spectroscopic technique which uses the resonant absorption of neutrons in the epithermal range to infer the isotopic composition of an object. This spectroscopic technique has relevance in many traditional fields of science and nuclear security. NRTA in the past made use of large, expensive accelerator facilities to achieve precise neutron beams, significantly limiting its applicability. Here, we describe a series of NRTA experiments where we use a compact, low-cost deuterium-tritium (DT) neutron generator to produce short neutron beams (2.6 m) along with a 6 Li-glass neutron detector. The time-of-flight spectral data from five elements – silver, cadmium, tungsten, indium, and 238 U – clearly show the corresponding absorption lines in the 1-30 eV range. The experiments show the applicability of NRTA in this simplified configuration, and prove the feasibility of this compact and low-cost approach. This could significantly broaden the applicability of NRTA, and make it practical and applicable in many fields, such as material science, nuclear engineering, and arms control.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

X-ray free electron laser studies of electron and phonon dynamics of graphene adsorbed on copper

Here, we report optical pumping and x-ray absorption spectroscopy experiments at the Pohang Accelerator Laboratory free electron laser that probes the electron dynamics of a graphene monolayer adsorbed on copper in the femtosecond regime. By analyzing the results with ab initio theory we infer that the excitation of graphene is dominated by indirect excitation from hot electron-hole pairs created in the copper by the optical laser pulse. However, once the excitation is created in graphene, its decay follows a similar path as in many previous studies of graphene adsorbed on semiconductors, i.e., rapid excitation of strongly coupled optical phonons and eventual thermalization. It is likely that the lifetime of the hot electron-hole pairs in copper governs the lifetime of the electronic excitation of the graphene.

36 MATERIALS SCIENCE↗

External and Internal Reconnection in Two Filament-Carrying Magnetic Cavity Solar Eruptions

We observe two near-limb solar filament eruptions. one of 2000 February 26 and the other of 2002 January 4. For both we use 195 A Fe XII images from the Extreme-Ultraviolet Imaging Telescope (EIT) and magnetograms from the Michelson Doppler Imager (MDI). both of which are on the Solar and Heliospheric Observatory. (SOHO). For the earlier event we also use soft X-ray telescope (SXT). hard X-ray telescope (HXT). and Bragg Crystal Spectrometer (BCS) data from the Yohkoh satellite. and hard X-ray data from the BATSE experiment on the Compton Gamma Ray Observatory. (CGRO). Both events occur in quadrupolar magnetic regions. and both have coronal features that we infer belong to the same magnetic cavity structures as the filaments. In both cases. the cavity and filament first rise slowly at approx. 10 km/s prior to eruption and then accelerate to approx. 100 km/s during the eruption. although the slow-rise movement for the higher altitude cavity elements is clearer in the later event. We estimate that both filaments and both cavities contain masses of approx. 10(exp14) - 1 0(exp 15) and approx. l0(exp 15) - l0(exp 16) g. respectively. We consider whether two specific magnetic reconnection-based models for eruption onset. the "tether cutting" and the "breakout" models. are consistent with our observations. In the earlier event, soft X-rays from SXT show an intensity increase during the 12 minute interval over which fast eruption begins. which is consistent with tether- cutting-model predictions. Substantial hard X-ray. however. do not occur until after fast eruption is underway. and so this is a constraint the tether-cutting model must satisfy. During the same 12 minute interval over which fast eruption begins, there are brightenings and topological changes in the corona indicative of high-altitude reconnection early in the eruption. and this is consistent with breakout predictions. In both eruptions. the state of the overlying loops at the time of onset of the fast-rise phase of the corresponding filament can be compared with expectations from the breakout model. thereby setting constraints that the breakout model must meet. Our findings are consistent with both runaway tether-cutting-type reconnection and fast breakout-type reconnection. occurring early in the fast phase of the February eruption and with both types of reconnection being important in unleashing the explosion, but we are not able to say which. if either, type of reconnection actually triggered the fast phase. In any case. we have found specific constraints that either model. or any other model. must satisfy if correct.

Sterling, Alphonse C.↗

Dynamical Dark Energy Imprints in the Lyman-Alpha Forest

The nature of dark energy (DE) remains elusive, even though it constitutes the dominant energy-density component of the Universe and drives the late-time acceleration of cosmic expansion. By combining measurements of the expansion history from baryon acoustic oscillations, supernova surveys, and cosmic microwave background data, the Dark Energy Spectroscopic Instrument (DESI) Collaboration has inferred that the DE equation of state may evolve over time. The profound implications of a time-variable, ``dynamical" DE (DDE) that departs from a cosmological constant motivate the need for independent observational tests. In this work, we use cosmological hydrodynamical simulations of structure formation to investigate how DDE affects the properties of the Lyman-Alpha ``forest'' of absorption features produced by neutral hydrogen in the cosmic web. We find that DDE models consistent with the DESI constraints induce a spectral tilt in the forest transmitted flux power spectrum, imprinting a scale- and redshift-dependent signature relative to standard Lambda-CDM cosmologies. These models also yield higher intergalactic medium temperatures and reduced Lyman-Alpha opacity compared to Lambda-CDM. We discuss the observational implications of these trends as potential avenues for independent confirmation of DDE.

Garza, Diego [UC, Santa Cruz, Inst. Part. Phys.] (↗

Substorm associated ion acceleration in the dynamic magnetotail

Ion acceleration and flux increase associated with substorm energetic particle injections are investigated on the basis of geosynchronous observations and test proton orbits in the dynamic fields of a three dimensional magnetohydrodynamic simulation of neutral line formation and dipolarization in the magnetotail. The energetic particle flux changes obtained from the test particle orbits agree well with observations that demonstrate rapid ion flux increases at energies of above 20 keV. The injection region inferred from the test particles has a sharp earthward boundary and a sharp ragged tailward boundary. The earthward portion of the enhanced ion flux can be traced to the enhanced cross-tail electric field associated with the near-earth x-type neutral line. Due to the rapid earthward motion of accelerated ions away from the neutral line, this boundary is displaced earthward to where the energetic ions become more adiabatic in the stronger dipolar field.

Birn, J.↗

Enhancing the Quality and Reliability of Machine Learning Interatomic Potentials through Better Reporting Practices

Recent developments in machine learning interatomic potentials (MLIPs) have empowered even nonexperts in machine learning to train MLIPs for accelerating materials simulations. However, reproducibility and independent evaluation of presented MLIP results is hindered by a lack of clear standards in current literature. In this Perspective, we aim to provide guidance on best practices for documenting MLIP use while walking the reader through the development and deployment of MLIPs including hardware and software requirements, generating training data, training models, validating predictions, and MLIP inference. We also suggest useful plotting practices and analyses to validate and boost confidence in the deployed models. Finally, we provide a step-by-step checklist for practitioners to use directly before publication to standardize the information to be reported. Altogether, we hope that our work will encourage the reliable and reproducible use of these MLIPs, which will accelerate their ability to make a positive impact in various disciplines including materials science, chemistry, and biology, among others.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗