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At least 127 records · Page 7

Full structural ensembles of intrinsically disordered proteins from unbiased molecular dynamics simulations

Abstract Molecular dynamics (MD) simulation is widely used to complement ensemble-averaged experiments of intrinsically disordered proteins (IDPs). However, MD often suffers from limitations of inaccuracy. Here, we show that enhancing the sampling using Hamiltonian replica-exchange MD (HREMD) led to unbiased and accurate ensembles, reproducing small-angle scattering and NMR chemical shift experiments, for three IDPs of varying sequence properties using two recently optimized force fields, indicating the general applicability of HREMD for IDPs. We further demonstrate that, unlike HREMD, standard MD can reproduce experimental NMR chemical shifts, but not small-angle scattering data, suggesting chemical shifts are insufficient for testing the validity of IDP ensembles. Surprisingly, we reveal that despite differences in their sequence, the inter-chain statistics of all three IDPs are similar for short contour lengths (< 10 residues). The results suggest that the major hurdle of generating an accurate unbiased ensemble for IDPs has now been largely overcome.

59 BASIC BIOLOGICAL SCIENCES↗

Connecting ground-state properties of 6 Li to each other and to scattering data

We examine the relationship between the asymptotic normalization coefficient (ANC) of 6 Li and other low-energy observables in the α–deuteron system. Our analysis uses a set of calculations carried out within the ab initio no core shell model with continuum (NCSMC) using a variety of inter-nucleon interactions and basis sizes, and yielding 6 Li deuteron separation energies between 1.3 and 1.8 MeV (Hebborn et al 2022 Phys. Rev. Lett. 129 042503). These NCSMC calculations show that the square of the ANC is strongly correlated with the separation energy over this range. In this work, we investigate the origin of this correlation using the phenomenological R-matrix, a single-channel potential and a perturbative approach. We show that this correlation occurs because the depth of the α–deuteron central potential changes by only a small relative amount as the separation energy varies. We then investigate if the ANC can be accurately extracted from α–deuteron phase shifts in an ideal case in which low-energy data are available and there are no experimental errors. We find that both R-matrix and Coulomb-modified effective-range theory (CM-ERE) yield extracted ANCs close to, although not exactly equal to, the NCSMC value, provided the extrapolation is constrained by the known position of the bound-state pole and at least three terms are included in the fit function. The R-matrix approach converges faster than the CM-ERE as the number of parameters increases and is also more robust against the inclusion of low-energy and high-energy phase shift data. Finally, our study also shows that a naive quantification of uncertainties by comparing different truncations used in both theories is not accurate, and suggests the accuracy of ANCs extracted from phase shift data needs further investigation.

R-matrix↗

A National Infrastructure for Artificial Intelligence on the Grid (NI4AI) (Final Scientific/Technical Report)

Electric utilities have traditionally taken a very pragmatic yet myopic approach with grid sensors and the resulting collected data. Sensors are purchased and deployed to solve a specific, known problem that has risen to sufficient awareness as to justify the effort of deploying sensors and the needed capital investment. This sensor data flows into proprietary software packages with limited functionality intended only to address the initial problem. This approach aligns with the financial incentives of the utility to deploy capital into fixed hardware assets for which the corporations earn a rate of return. This mentality stands in stark contrast to the big data revolution that started nearly 25 years ago with the rise of Google. In this worldview, data is a fundamental business asset; successful organizations collect, store, explore, merge, and exploit as much data as possible to not only solve problems well understood today but also to tackle new problems that will inevitably rise tomorrow. The ARPA-E Open Innovation 2018 project entitled A National Infrastructure for Artificial Intelligence on the Grid or NI4AI for short was designed to demonstrate this alternative paradigm for using data. To do this, the project was composed of three key thrust areas. The first major component deployed a variety of high-frequency grid sensors and captured terabytes of both wide-scale and localized grid measurements, generating high-value datasets for grid research and algorithm development. The second aspect made available PingThings’ PredictiveGridTM, a horizontally scalable, cloud-based data management and AI platform built for time series data to explore and exploit the collected data. Finally, the project fostered a diverse and open research community composed of experts from numerous fields through focused educational content, code sharing, and data science competitions. Shifting away from “single use” sensors and closed data silos within electric utilities is a major benefit to the public at large. This legacy approach to data is incredibly (1) capital intensive (new sensors must be deployed for each new problem and problems tend to arise continuously) and (2) painfully slow (new problems must be identified first and then new sensors must be deployed to collect data to begin to address the issue). The transition to a carbon neutral grid requires a massive transformation of the existing grid infrastructure and will continue to challenge the legacy grid in unforeseen ways. The only way to make the energy transition cost effective is for utilities to abandon this dated data paradigm and adopt more contemporary approaches. NI4AI has shown that it is technically possible and economically feasible to ingest, explore, and exploit grid data collected from even very high frequency sensing, such as continuous point on wave sensors collecting measurements 10,000 times a second. In fact, the PredictiveGrid platform used is commercially available and deployed at several utilities in the United States. Project accomplishments were numerous and included (1) making available a state of the art time series platform to the community, (2) collecting over 520 streams of time series data from grid sensors totaling over 1 trillion grid measurements, and (3) developing and nurturing a community within the industry focused on the use of data to create value for utilities and, ultimately, end consumers.

97 MATHEMATICS AND COMPUTING↗

Numerical interactive controller

Device allows interaction of operator with data in computer central processor in order to shift frame of data in Cartesian coordinates and slew desired data into view. ''Cursor generator program,'' in conjunction with device, provides light pen with sufficient resolving power to identify any particular set of coordinates with single-cell accuracy.

Brokl, S. S.↗

Prediction of space sickness in astronauts from preflight fluid, electrolyte, and cardiovascular variables and Weightless Environmental Training Facility (WETF) training

Nine preflight variables related to fluid, electrolyte, and cardiovascular status from 64 first-time Shuttle crewmembers were differentially weighted by discrimination analysis to predict the incidence and severity of each crewmember's space sickness as rated by NASA flight surgeons. The nine variables are serum uric acid, red cell count, environmental temperature at the launch site, serum phosphate, urine osmolality, serum thyroxine, sitting systolic blood pressure, calculated blood volume, and serum chloride. Using two methods of cross-validation on the original samples (jackknife and a stratefied random subsample), these variables enable the prediction of space sickness incidence (NONE or SICK) with 80 percent sickness and space severity (NONE, MILD, MODERATE, of SEVERE) with 59 percent success by one method of cross-validation and 67 percent by another method. Addition of a tenth variable, hours spent in the Weightlessness Environment Training Facility (WETF) did not improve the prediction of space sickness incidences but did improve the prediction of space sickness severity to 66 percent success by the first method of cross-validation of original samples and to 71 percent by the second method. Results to date suggest the presence of predisposing physiologic factors to space sickness that implicate fluid shift etiology. The data also suggest that prior exposure to fluid shift during WETF training may produce some circulatory pre-adaption to fluid shifts in weightlessness that results in a reduction of space sickness severity.

Simanonok, K.↗

Modeling Surface Structure Derived from Laser Altimeter Return Waveforms Using High-Resolution Elevation Data

The upcoming generation of operational spaceborne laser altimeters (i.e VCL and GLAS) record the interaction of emitted laser radiation with terrestrial surfaces in the form of a digitized waveform. We show that we can accurately model return laser altimeter waveforms as the sum of the reflections from individual surfaces within laser footprints. In one case, we predict return waveforms using high resolution elevation data generated by a small-footprint laser altimeter in a dense tropical forest. We compare over 3000 modeled and recorded waveform pairs using the Pearson correlation. The modeled and recorded waveforms are highly correlated, with a mean correlation of 0.90 and a median of 0.95. The mean correlation is highly dependent on the relative positions of the data sets. By shifting the relative locations of the two compared data sets, we infer that the data are colocated to within 0.4$\sim$m horizontally and 0.12$\sim$m vertically. The high degree of correlation shows that we can reliably synthesize the vertical structure information measured by medium-large footprint laser altimeters for complex, dense vegetation.

Blair, J. Bryan↗

Decadal Seasonal Shifts of Precipitation and Temperature in TRMM and AIRS Data

We present results from an analysis of seasonal phase shifts in the global precipitation and surface temperatures. We use data from the TRMM (Tropical Rainfall Measuring Mission) Multi-satellite Precipitation Algorithm (TMPA), and the Atmospheric Infrared Sounder (AIRS) on Aqua satellite, all hosted at NASA Goddard Earth Science Data and Information Services Center (GES DISC). We explore the information content and data usability by first aggregating daily grids from the entire records of both missions to pentad (5-day) series which are then processed using Singular Value Decomposition approach. A strength of this approach is the normalized principal components that can then be easily converted from real to complex time series. Thus, we can separate the most informative, the seasonal, components and analyze unambiguously for potential seasonal phase drifts. TMPA and AIRS records represent correspondingly 20 and 15 years of data, which allows us to run simple “phase learning†from the first 5 years of records and use it as reference. The most recent 5 years are then phase-compared with the reference. We demonstrate that the seasonal phase of global precipitation and surface temperatures has been stable in the past two decades. However, a small global trend of delayed precipitation, and earlier arrival of surface temperatures seasons, are detectable at 95% confidence level. Larger phase shifts are detectable at regional level, in regions recognizable from the Eigen vectors to having strong seasonal patterns. For instance, in Central North America, including the North American Monsoon region, confident phase shifts of 1-2 days per decade are detected at 95% confidence level. While seemingly symbolic, these shifts are indicative of larger changes in the Earth Climate System. We thus also demonstrate a potential usability scenario of Earth Science Data Records curated at the NASA GES DISC in partnership with Earth Science Missions.

surface temperatures↗

Experimental and Semiclassical Stark Widths and Shifts for Spectral Lines of Neutral and Ionized Atoms (A Critical Review of Experimental and Semiclassical Data for the Period 2008 through 2020)

This Review Article compares new experimental and corresponding semiclassical Stark broadened data for non-hydrogenic spectral lines of neutral atoms and positive ions. This Review covers the period 2008 until the end of 2020 and presents the continuation of previous critical reviews from 1976 (two), 1984 (two), 1990, 2002, and one from 2009. This Review reports the Stark broadening parameters of 1665 spectral lines belonging to 35 elements with 61 different atomic and ion species. The data are taken from 60 papers. Experimental data are arranged by elements and spectra, and these are reported in tables in alphabetical and numerical order, respectively. Each experimental Stark broadening parameter is followed with estimated accuracy. The experimental Stark broadening and shift data presented in the tables are compared with the corresponding semiclassical results available in the literature. In addition, for comparison experiments versus semiclassical theoretical Stark broadening parameters, a numerically improved theoretical approach developed based on Griem and co-workers’ theory is used to evaluate Stark widths and shifts of all studied lines whenever required atomic energy levels data and transition probabilities are available. At the end of the text report, for each analyzed neutral or ion species, the information about the location of the same species data in preceding reviews is given.

Plasma line broadening↗

Achieving precise multiparameter measurements with distributed optical fiber sensor using wavelength diversity and deep neural networks

The development of advanced distributed optical fiber sensing systems that are capable of performing accurate and spatially resolved multiparameter measurements is of great interest to a wide range of scientific and industrial applications. Here, in this paper, we propose and experimentally demonstrate a wavelength diversity based advanced distributed optical fiber sensor system to accomplish multiparameter sensing while greatly enhancing measurement accuracy. A suite of deep neural network (DNN) algorithms are developed and verified for data denoising, rapid Brillouin frequency shift estimation, and vibration data event classification. As a proof-of-concept, we demonstrate the effectiveness of the proposed advanced wavelength diversity distributed fiber sensor system assisted by DNN for simultaneous, independent measurements of static strain, temperature, and acoustic vibrations over a 25 km long sensing fiber at 3 m spatial resolution. These results suggest the potential for an intelligent multiparameter monitoring system with enhanced performance in advanced structural health monitoring applications.

47 OTHER INSTRUMENTATION↗

Gimbal Bearing Friction in the SLS Core Stage Thrust Vector Control System

The Space Launch System (SLS) Core Stage Thrust Vector Control (TVC) system is comprised of eight mechanical feedback Shuttle heritage Type III TVC actuators that vector the four Shuttle heritage RS-25 engines about a Shuttle heritage gimbal block/bearing. The MSFC Controls community has long regarded gimbal friction to be a negligible effect on the overall control of gimbaled RS-25 engines. This is corroborated by Space Shuttle test and flight data that does not appear to show degraded effects, nor limit cycling at the end of the shuttle flight. For this reason, friction was not expected to be a driving factor of performance and control of the reused RS-25 engines aboard the SLS. However, after test data showed a large shift in frequency behavior and a highly damped step-response in the time series, there was further investigation into what could have caused this behavior. Heritage friction models used in previous gimbal and ball bearings were evaluated such as Coulomb, Dahl and LuGre, but the single degree of freedom friction models alone were not enough to explain the behavior and shifts seen in the test data. This paper presents the additional findings and modeling efforts regarding friction on the RS-25 engines. Using the Two Actuator Operational Simulation (TAOS), the difference from modeling separate friction degrees of freedom to coupled degrees of freedom was investigated to deduce the effects of one axis’s movement on the other. Next, due to the vibration environment, a modified LuGre model has been proposed that adds an additional term to decrease the friction coefficient at low engine velocity amplitudes. Lastly, the addition of the stiffness in each half of the gimbal bearing has increased modeling fidelity by also adding the effect on the gimbal bearing bending in compliance to both the friction torque on the surface of the gimbal bearing and the actuator force that is forcing the engine in a specified direction. Through these effects, the time and frequency domain behavior seen in test can be characterized accurately.

Friction↗

Gimbal Bearing Friction in the SLS Core Stage Thrust Vector Control System

The Space Launch System (SLS) Core Stage Thrust Vector Control (TVC) system is comprised of eight mechanical feedback Shuttle heritage Type III TVC actuators that vector the four Shuttle heritage RS-25 engines about a Shuttle heritage gimbal block/bearing. The MSFC Controls community has long regarded gimbal friction to be a negligible effect on the overall control of gimbaled RS-25 engines. This is corroborated by Space Shuttle test and flight data that does not appear to show degraded effects, nor limit cycling at the end of the shuttle flight. For this reason, friction was not expected to be a driving factor of performance and control of the reused RS-25 engines aboard the SLS. However, after test data showed a large shift in frequency behavior and a highly damped step-response in the time series, there was further investigation into what could have caused this behavior. Heritage friction models used in previous gimbal and ball bearings were evaluated such as Coulomb, Dahl and LuGre, but the single degree of freedom friction models alone were not enough to explain the behavior and shifts seen in the test data. This paper presents the additional findings and modeling efforts regarding friction on the RS-25 engines. Using the Two Actuator Operational Simulation (TAOS), the difference from modeling separate friction degrees of freedom to coupled degrees of freedom was investigated to deduce the effects of one axis’s movement on the other. Next, due to the vibration environment, a modified LuGre model has been proposed that adds an additional term to decrease the friction coefficient at low engine velocity amplitudes. Lastly, the addition of the stiffness in each half of the gimbal bearing has increased modeling fidelity by also adding the effect on the gimbal bearing bending in compliance to both the friction torque on the surface of the gimbal bearing and the actuator force that is forcing the engine in a specified direction. Through these effects, the time and frequency domain behavior seen in test can be characterized accurately.

Friction↗

Data from: "Warming of alpine tundra enhances belowground production and shifts community towards resource acquisition traits"

This archive contains data used to draw conclusions in “Warming of alpine tundra enhances belowground production and shifts community towards resource acquisition traits”, by Yang et al. 2020. Data were collected on Niwot Ridge, in an alpine meadow within the Alpine Treeline Warming Experiment (ATWE) field sites in Colorado, USA. Samples were also processed in the U.S. Geological Survey Forest and Rangeland Ecosystem Science Center, in Boise, Idaho. File formats in this archive include comma-separated values (.csv), portable document format (.pdf), Microsoft Excel (.xlsx), and two types of geospatial files: keyhole markup language (.kml), and ESRI shapefiles (.shp). Leaf scans are .jpg images, and root scans are .tiff/.tif images.The .csv files can be opened using R, Microsoft Excel, or any simple text-editing software such as TextEdit and Notepad. Microsoft Excel files can be opened using Microsoft Excel, and .pdf files can be opened with Adobe Acrobat Reader, Preview, or other compatible programs. Scanned images can be opened using any photo and/or picture viewing software.The .kml file can be opened using Google Earth and Google Maps, and the shapefiles can be opened by any programs compatible with shapefiles, such as the ArcGIS Desktop suite, and QGIS.------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Measures of belowground net primary productivity (BNPP) are required to understand whether aboveground net primary production (ANPP) changes reflect changes in allocation or are indicative of a whole plant NPP response. Plant functional traits provide a key way to scale from the individual plant to the community level, and provide insight into drivers of NPP responses to environmental change. We used infrared heaters to warm an alpine plant community at Niwot Ridge, Colorado, and applied supplemental water to compensate for soil water loss induced by warming. We measured ANPP, BNPP, and leaf and root functional traits across treatments after 5 years of continuous warming. Community-level ANPP and total NPP (ANPP + BNPP) did not respond to heating or watering, but BNPP increased in response to heating. Heating decreased community-level leaf dry matter content and increased total root length, indicating a shift in strategy from resource conservation to acquisition in response to warming.

13C/12C isotope ratio↗

Tunneling magnetoresistance in MgO tunnel junctions with Fe-based leads in empirically corrected density functional theory

The minority-spin Fe/MgO interface states are at the Fermi level in density functional theory (DFT), but experimental evidence and GW calculations place them slightly higher in energy. This small shift can strongly influence tunneling magnetoresistance (TMR) in junctions with a thin MgO barrier and its dependence on the concentration of Co in the electrodes. Here, in this study, an empirical potential correction to DFT is introduced to shift the interface states up to match the tunnel spectroscopy data. With this shift, TMR in Fe/MgO/Fe junctions exceeds 800% and 3000% at 3 and 4 monolayers (ML) of MgO, respectively. We further consider the effect of alloying of the Fe electrodes with up to 30% Co or 10% V, treating them in the coherent potential approximation (CPA). Alloying with Co broadens the interface states and brings a large incoherent minority-spin spectral weight to the Fermi level. Alloying with V brings the minority-spin resonant states close to the Fermi level. However, in both cases the minority-spin spectral weight at the Fermi level resides primarily at the periphery of the Brillouin zone, which is favorable for spin filtering. Using convolutions of k II -resolved barrier densities of states calculated in CPA, it is found that TMR is strongly reduced by alloying with Co or V but still remains above 500% at 4 ML of MgO up to 30% of Co or 5% V. At 5 ML, the TMR increases above 1000% in all systems considered. However, while TMR declines sharply with increasing bias up to 0.2 eV in the tunnel junctions with pure Fe leads, it remains almost constant up to 0.5 eV if leads are alloyed with Co.

74 ATOMIC AND MOLECULAR PHYSICS↗

Nitrogen-Pressure Shifts in the v3 Band of Methane Measured at Several Temperatures between 300 and 90 K

Remote sensing of the Earth's atmosphere requires accurate knowledge of spectroscopic line parameters for the molecules investigated. Knowledge of the temperature dependence of these parameters is also essential if agreement, at the noise level, between calculated and experimental data is to be achieved. The authors recently published results of nitrogen broadening measurements in the v3 band of 12CH4 using the 5.37 m long absorption path length all-copper Herriott cell. The temperature dependent line parameters determined in the laboratory were applied to fit a portion of the atmospheric spectrum recorded with a balloon-borne remote sensing FTIR instrument, called the Limb Profile Monitor of the Atmosphere, and operating in absorption against the sun. Since the authors had a relatively complete series of data for the P(9) transition in the v3 band of 12CH4, the A2 1 as well as the F2 1, F1 1 and A1 1 lines recorded at different pressures and at four temperatures between 300 and 90 K, we reanalyzed the data to derive pressure shift information at different temperatures. The temperatures for which data were collected and analyzed are 298, 140 and 90K. The high precision pressure shift data obtained here over a large range of temperature demonstrate the ability of our experimental arrangement to address specific questions on a given spectral window like in the balloon experiment or in a satellite project, for example.

Tumuhimbise, Anthony T.↗

Data Curation for Machine Learning Applied to Geothermal Power Plant Operational Data for GOOML: Geothermal Operational Optimization with Machine Learning: Preprint

Geothermal Operational Optimization with Machine Learning (GOOML) is a transferable and extensible component-based geothermal asset modeling framework that considers complex steamfield relationships and identifies optimization prospects using a data-driven approach to physics-guided, data-centric machine learning. This framework has been used to develop digital twins that provide steamfield operators with operational environments to analyze and understand historical and forecasted power production, explore new steamfield configuration possibilities, and seek optimal asset management in real world applications. To create, test, and apply the GOOML framework, diverse time-series datasets spanning multiple years were sourced from various geothermal power plant components within several complex real-world geothermal operations. These operations are based in the United States and New Zealand and include a variety of technologies, end-uses and configurations, collectively covering nearly all relevant operating conditions for modern geothermal fields. Datasets were acquired from multiple sources to ensure that machine learning experiments generalized properly to various operating conditions. It was found that the data varied in quality, format, and completeness. To ensure consistency between the various datasets, a standardized data curation process was developed to reliably streamline data preparation. This paper will discuss best practices as learned from the GOOML data curation process which takes the following steps: 1) acquisition of large quantities of data from power plant operators, 2) digestion of data to gain an initial understanding of what is included, 3) data transformation, which includes converting the data into a standardized machine-readable format so that they can be visualized, quality checked, and cleaned, 4) quality assurance and quality control, involving identification of significant data gaps and apparent anomalies through mapping of data features to real world componentry via the GOOML historical model, followed by discussion with modelers and power plant operators to identify additional data needs and to resolve issues, 5) use in machine learning algorithms, and 6) repetition of steps one through five until all data needs are met and data are deemed suitable for producing trustworthy modeling results which may be disseminated, ideally along with the curated dataset. This iterative process is focused on improving the quality of the data rather than tuning machine learning model parameters and supports a shift towards data-centric AI as a means to improving real-world applicability of geothermal machine learning projects.

access↗

Testing hadronic-model predictions of depth of maximum of air-shower profiles and ground-particle signals using hybrid data of the Pierre Auger Observatory

We test the predictions of hadronic interaction models regarding the depth of maximum of air-shower profiles, X max , and ground-particle signals in water-Cherenkov detectors at 1000 m from the shower core, S ( 1000 ) , using the data from the fluorescence and surface detectors of the Pierre Auger Observatory. The test consists of fitting the measured two-dimensional ( S ( 1000 ) , X max ) distributions using templates for simulated air showers produced with hadronic interaction models pos-, et--04, 2.3d and leaving the scales of predicted X max and the signals from hadronic component at ground as free-fit parameters. The method relies on the assumption that the mass composition remains the same at all zenith angles, while the longitudinal shower development and attenuation of ground signal depend on the mass composition in a correlated way. The analysis was applied to 2239 events detected by both the fluorescence and surface detectors of the Pierre Auger Observatory with energies between 10 18.5 eV to 10 19.0 eV and zenith angles below 60°. We found, that within the assumptions of the method, the best description of the data is achieved if the predictions of the hadronic interaction models are shifted to deeper X max values and larger hadronic signals at all zenith angles. Given the magnitude of the shifts and the data sample size, the statistical significance of the improvement of data description using the modifications considered in the paper is larger than 5 σ even for any linear combination of experimental systematic uncertainties. Published by the American Physical Society 2024

79 ASTRONOMY AND ASTROPHYSICS↗

Digital demodulator

A digital demodulator for converting pulse code modulated data from phase shift key (PSK) to non return to zero (NRZ) and to biphase data is described. The demodulator is composed of standard integrated logic circuits. The key to the demodulation function is a pair of cross coupled one shot multivibrators and which with a flip-flop produce the NRZ-L is all that is required, the circuitry is greatly simplified and the 2(v) times bit rate contraint can be removed from the carrier. A flip-flop, an OR gate, and AND gate and a binary counter generate the bit rate clock (BTCK) for the NRZ-L. The remainder of the circuitry is for converting the NRZ-L and BTCK into biphase data. The device was designed for use in the space shuttle bay environment measurements.

Shull, T. A.↗