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NASA NTRS2007

Miniature L-Band Radar Transceiver

A miniature L-band transceiver that operates at a carrier frequency of 1.25 GHz has been developed as part of a generic radar electronics module (REM) that would constitute one unit in an array of many identical units in a very-large-aperture phased-array antenna. NASA and the Department of Defense are considering the deployment of such antennas in outer space; the underlying principles of operation, and some of those of design, also are applicable on Earth. The large dimensions of the antennas make it advantageous to distribute radio-frequency electronic circuitry into elements of the arrays. The design of the REM is intended to implement the distribution. The design also reflects a requirement to minimize the size and weight of the circuitry in order to minimize the weight of any such antenna. Other requirements include making the transceiver robust and radiation-hard and minimizing power demand. Figure 1 depicts the functional blocks of the REM, including the L-band transceiver. The key functions of the REM include signal generation, frequency translation, amplification, detection, handling of data, and radar control and timing. An arbitrary-waveform generator that includes logic circuitry and a digital-to-analog converter (DAC) generates a linear-frequency-modulation chirp waveform. A frequency synthesizer produces local-oscillator signals used for frequency conversion and clock signals for the arbitrary-waveform generator, for a digitizer [that is, an analog-to-digital converter (ADC)], and for a control and timing unit. Digital functions include command, timing, telemetry, filtering, and high-rate framing and serialization of data for a high-speed scientific-data interface. The aforementioned digital implementation of filtering is a key feature of the REM architecture. Digital filters, in contradistinction to analog ones, provide consistent and temperature-independent performance, which is particularly important when REMs are distributed throughout a large array. Digital filtering also enables selection among multiple filter parameters as required for different radar operating modes. After digital filtering, data are decimated appropriately in order to minimize the data rate out of an antenna panel. The L-band transceiver (see Figure 2) includes a radio-frequency (RF)-to-baseband down-converter chain and an intermediate- frequency (IF)-to-RF up-converter chain. Transmit/receive (T/R) switches enable the use of a single feed to the antenna for both transmission and reception. The T/R switches also afford a built-in test capability by enabling injection of a calibration signal into the receiver chain. In order of decreasing priority, components of the transceiver were selected according to requirements of radiation hardness, then compactness, then low power. All of the RF components are radiation-hard. The noise figure (NF) was optimized to the extent that (1) a low-noise amplifier (LNA) (characterized by NF < 2 dB) was selected but (2) the receiver front-end T/R switches were selected for a high degree of isolation and acceptably low loss, regardless of the requirement to minimize noise.

McWatters, Dalia↗

DOE OSTI2024

Identifying Interaction Location in SuperCDMS Detectors

The Super Cryogenic Dark Matter Search (SuperCDMS) experiment uses silicon and germanium particle detectors operated at temperatures of ∼ 30 mK to search for Weakly Interacting Massive Particles (WIMPs), which are candidate dark matter particles that interact weakly with nuclei in the detectors. In operating these detectors, it is required not only to measure the energy of the interaction between the WIMP and the nuclei, but also to reconstruct where the interaction occurred, as the location can be used to separate background interactions from signal and to correct for variations with the location of the energy response. In this project, we, as a team from the University of Minnesota, aim to address the problem of accurately reconstructing the locations of interactions in the SuperCDMS detectors using machine learning methods. The dataset we provided here includes interactions at thirteen different locations from test data taken at the University of Minnesota. For each interaction, a set of parameters was extracted from the signals from each of the five sensors. These parameters represent information known to be sensitive to interaction location, including the relative timing between pulses in different channels, and features like the pulse shape. The relative amplitudes of the pulses are also relevant but due to instabilities in amplification during the test, this data is not included. The parameters included for each interaction are described in our project document. For more details, feel free to check our Github page: https://fair-umn.github.io/FAIR-UMN-CDMS/

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2018

Optimizing de novo genome assembly from PCR-amplified metagenomes

Background. Metagenomics has transformed our understanding of microbial diversity across ecosystems, with recent advances enabling de novo assembly of genomes from metagenomes. These metagenome-assembled genomes are critical to provide ecological, evolutionary, and metabolic context for all the microbes and viruses yet to be cultivated. Metagenomes can now be generated from nanogram to subnanogram amounts of DNA. However, these libraries require several rounds of PCR amplification before sequencing, and recent data suggest these typically yield smaller and more fragmented assemblies than regular metagenomes. Methods. Here we evaluate de novo assembly methods of 169 PCR-amplified metagenomes, including 25 for which an unamplified counterpart is available, to optimize specific assembly approaches for PCR-amplified libraries. We first evaluated coverage bias by mapping reads from PCR-amplified metagenomes onto reference contigs obtained from unamplified metagenomes of the same samples. Then, we compared different assembly pipelines in terms of assembly size (number of bp in contigs ≥ 10kb) and error rates to evaluate which are the best suited for PCR-amplified metagenomes. Results. Read mapping analyses revealed that the depth of coverage within individual genomes is significantly more uneven in PCR-amplified datasets versus unamplified metagenomes, with regions of high depth of coverage enriched in short inserts. This enrichment scales with the number of PCR cycles performed, and is presumably due to preferential amplification of short inserts. Standard assembly pipelines are confounded by this type of coverage unevenness, so we evaluated other assembly options to mitigate these issues. We found that a pipeline combining read deduplication and an assembly algorithm originally designed to recover genomes from libraries generated after whole genome amplification (single-cell SPAdes) frequently improved assembly of contigs ≥ 10kb by 10 to 100-fold for low input metagenomes. Conclusions. PCR-amplified metagenomes have enabled scientists to explore communities traditionally challenging to describe, including some with extremely low biomass or from which DNA is particularly difficult to extract. Here we show that a modified assembly pipeline can lead to an improved de novo genome assembly from PCR-amplified datasets, and enables a better genome recovery from low input metagenomes.

Roux, Simon↗

DOE OSTI2018

Optimizing de novo genome assembly from PCR-amplified metagenomes

Background: Metagenomics has transformed our understanding of microbial diversity across ecosystems, with recent advances enabling de novo assembly of genomes from metagenomes. These metagenome-assembled genomes are critical to provide ecological, evolutionary, and metabolic context for all the microbes and viruses yet to be cultivated. Metagenomes can now be generated from nanogram to subnanogram amounts of DNA. However, these libraries require several rounds of PCR amplification before sequencing, and recent data suggest these typically yield smaller and more fragmented assemblies than regular metagenomes. Methods: Here we evaluate de novo assembly methods of 169 PCR-amplified metagenomes, including 25 for which an unamplified counterpart is available, to optimize specific assembly approaches for PCR-amplified libraries. We first evaluated coverage bias by mapping reads from PCR-amplified metagenomes onto reference contigs obtained from unamplified metagenomes of the same samples. Then, we compared different assembly pipelines in terms of assembly size (number of bp in contigs ≥ 10kb) and error rates to evaluate which are the best suited for PCR-amplified metagenomes. Results: . Read mapping analyses revealed that the depth of coverage within individual genomes is significantly more uneven in PCR-amplified datasets versus unamplified metagenomes, with regions of high depth of coverage enriched in short inserts. This enrichment scales with the number of PCR cycles performed, and is presumably due to preferential amplification of short inserts. Standard assembly pipelines are confounded by this type of coverage unevenness, so we evaluated other assembly options to mitigate these issues. We found that a pipeline combining read deduplication and an assembly algorithm originally designed to recover genomes from libraries generated after whole genome amplification (single-cell SPAdes) frequently improved assembly of contigs ≥ 10kb by 10 to 100-fold for low input metagenomes. Conclusions: PCR-amplified metagenomes have enabled scientists to explore communities traditionally challenging to describe, including some with extremely low biomass or from which DNA is particularly difficult to extract. Here we show that a modified assembly pipeline can lead to an improved de novo genome assembly from PCR-amplified datasets, and enables a better genome recovery from low input metagenomes.

Roux, Simon↗

DOE OSTI2019

Optimizing de novo genome assembly from PCR-amplified metagenomes

Background. Metagenomics has transformed our understanding of microbial diversity across ecosystems, with recent advances enabling de novo assembly of genomes from metagenomes. These metagenome-assembled genomes are critical to provide ecological, evolutionary, and metabolic context for all the microbes and viruses yet to be cultivated. Metagenomes can now be generated from nanogram to subnanogram amounts of DNA. However, these libraries require several rounds of PCR amplification before sequencing, and recent data suggest these typically yield smaller and more fragmented assemblies than regular metagenomes. Methods. Here we evaluate de novo assembly methods of 169 PCR-amplified metagenomes, including 25 for which an unamplified counterpart is available, to optimize specific assembly approaches for PCR-amplified libraries. We first evaluated coverage bias by mapping reads from PCR-amplified metagenomes onto reference contigs obtained from unamplified metagenomes of the same samples. Then, we compared different assembly pipelines in terms of assembly size (number of bp in contigs ≥ 10 kb) and error rates to evaluate which are the best suited for PCR-amplified metagenomes. Results. Read mapping analyses revealed that the depth of coverage within individual genomes is significantly more uneven in PCR-amplified datasets versus unamplified metagenomes, with regions of high depth of coverage enriched in short inserts. This enrichment scales with the number of PCR cycles performed, and is presumably due to preferential amplification of short inserts. Standard assembly pipelines are confounded by this type of coverage unevenness, so we evaluated other assembly options to mitigate these issues. We found that a pipeline combining read deduplication and an assembly algorithm originally designed to recover genomes from libraries generated after whole genome amplification (single-cell SPAdes) frequently improved assembly of contigs ≥10 kb by 10 to 100-fold for low input metagenomes. Conclusions. PCR-amplified metagenomes have enabled scientists to explore communities traditionally challenging to describe, including some with extremely low biomass or from which DNA is particularly difficult to extract. Here we show that a modified assembly pipeline can lead to an improved de novo genome assembly from PCR-amplified datasets, and enables a better genome recovery from low input metagenomes.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS1975

Installation and airspeed effects on jet shock-associated noise

Experimental acoustic data are presented to illustrate, at model scale, the effect of varying the nozzle-wing installation on shock-associated noise, statically and with airspeed. The variation in installations included nozzle only, nozzle under-the-wing (with and without flaps deflected), and nozzle over-the-wing (unattached flow). The nozzles used were a conical and a 6-tube mixer nozzle with a cold-flow nozzle pressure ratio of 2.1. A 33-cm diameter free jet was used to simulate airspeed. With the nozzle only, shock wave noise dominated the spectra in the forward quadrant, while jet mixing noise dominated in the rearward quadrant. Similar trends were observed when a wing (flaps retracted) was included. Shock noise was attenuated with an over-the-wing configuration and increased with an under-the-wing configuration (due to reflection from the wing surface). With increasing flap deflection (under-the-wing configuration), the jet-flap interaction noise exceeded the shock noise and became dominant in both quadrants. The free jet results showed that airspeed had no effect on shock noise. The free jet noise data were corrected for convective amplification to approximate flight and comparisons between the various configurations are made.

Vonglahn, U.↗

DOE OSTI2020

TRT Compton Scattering Data: Comparisons between LLNL and LANL: Pointwise

This memo is one of a pair of reports comparing Compton scattering data in the context of thermal radiation transport (TRT). This document focuses on Pointwise (PW) data while the other report focuses on Multigroup (MG) data. These complementary analyses, via PW comparisons, show if the same physics are used and if fundamental bugs are present, and, via MG comparisons, quantify macroscopic Compton effects such as mean amplification factors. No averaging of Compton data over photon energy is done for the PW comparisons, while lab-dependent numerical resolution choices become relevant for the MG comparisons. This document plots and quantifies differences in PW Compton scattering data between LANL and LLNL for four disparate temperatures on a logarithmically-spaced energy grid. PW comparisons means we use the received LLNL data as-is, without any averaging or integration over energy. In addition to LANL-to-LLNL comparisons, we investigate the impact of numerical choices on LANL PW data. For the purposes of this comparison, we neglect induced scattering.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2020

TRT Compton Scattering Data: Comparisons between LLNL and LANL: Multigroup

This memo is one of a pair of reports comparing Compton scattering data in the context of thermal radiation transport (TRT). This document focuses on Multigroup (MG) data while the other report focuses on Pointwise (PW) data. These complementary analyses, via PW comparisons, show if the same physics are used and if fundamental bugs are present, and, via MG comparisons, quantify macroscopic Compton effects such as mean amplification factors. No averaging of Compton data over photon energy is done for the PW comparisons, while lab-dependent numerical resolution choices become relevant for the MG comparisons. For this MG-comparison report, we make and document the numerical assumptions we use to convert LLNL PW data into MG data. This document plots and quantifies differences in Compton scattering data between MG LANL and LLNL for four disparate temperatures on a logarithmically-spaced photon-energy grid. In addition to LANL and LLNL data, we add a third and fourth independent vote from data generated by Brooks Kinch (LANL postdoc). For the purposes of these comparisons, we neglect induced scattering.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2020

Fluorescent amplification for next generation sequencing (FA-NGS) library preparation

BACKGROUND: Next generation sequencing (NGS) has become a universal practice in modern molecular biology. As the throughput of sequencing experiments increases, the preparation of conventional multiplexed libraries becomes more labor intensive. Conventional library preparation typically requires quality control (QC) testing for individual libraries such as amplification success evaluation and quantification, none of which occur until the end of the library preparation process. RESULTS: In this study, we address the need for a more streamlined high-throughput NGS workflow by tethering real-time quantitative PCR (qPCR) to conventional workflows to save time and implement single tube and single reagent QC. We modified two distinct library preparation workflows by replacing PCR and quantification with qPCR using SYBR Green I. qPCR enabled individual library quantification for pooling in a single tube without the need for additional reagents. Additionally, a melting curve analysis was implemented as an intermediate QC test to confirm successful amplification. Sequencing analysis showed comparable percent reads for each indexed library, demonstrating that pooling calculations based on qPCR allow for an even representation of sequencing reads. To aid the modified workflow, a software toolkit was developed and used to generate pooling instructions and analyze qPCR and melting curve data. CONCLUSIONS: We successfully applied fluorescent amplification for next generation sequencing (FA-NGS) library preparation to both plasmids and bacterial genomes. As a result of using qPCR for quantification and proceeding directly to library pooling, the modified library preparation workflow has fewer overall steps. Therefore, we speculate that the FA-NGS workflow has less risk of user error. The melting curve analysis provides the necessary QC test to identify and troubleshoot library failures prior to sequencing. While this study demonstrates the value of FA-NGS for plasmid or gDNA libraries, we speculate that its versatility could lead to successful application across other library types.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Regularized Differentiation for Bioburden Density Estimation in Planetary Protection

In this paper, we propose and investigate the performance of two novel shrinkage estimators for bioburden density estimation in planetary protection. The estimators are based on the regularized differentiation of a cumulative count of colony forming units collected throughout the data collecting session or the life cycle of the entire mission. The regularized differentiation recasts the problem of bioburden density estimation as a linear least squares problem. The least squares problem is then solved through regularization techniques, such as truncated singular value decomposition and penalized least squares. The regularization is necessary to avoid noise amplification during the differentiation of noisy data. The two regularization estimators are compared with four other commonly used estimators to simultaneously evaluate the means of multivariable independent Poisson distributions: the maximum likelihood, noninformative Bayes estimator with Jeffreys prior, Empirical Bayes using conjugate gamma-Poisson model with gamma parameters selected by method of moments, and the Clevenson-Zidek estimator. It is shown through computer-simulated data that the regularized differentiation based on ridge regression has the smallest mean-squared error among all estimators. The analysis of shrinkage mechanism implemented by regularized differentiation is performed, and it is shown that the regularized differentiation amounts to performing a weighted averaging of all the samples. The weights are determined by the regularization parameter automatically selected by the L-curve technique. Since the method of least squares makes no distributional assumptions about the data, it presents an attractive technique for bioburden density estimation when there are concerns about the misspecification of the distributional model. The paper concludes with the analysis of the bioburden data collected during InSight mission and directions for future work.

97 - MATHEMATICS AND COMPUTING↗

DOE OSTI2023

Characterizing and mitigating coherent errors in a trapped ion quantum processor using hidden inverses

Quantum computing testbeds exhibit high-fidelity quantum control over small collections of qubits, enabling performance of precise, repeatable operations followed by measurements. Currently, these noisy intermediate-scale devices can support a sufficient number of sequential operations prior to decoherence such that near term algorithms can be performed with proximate accuracy (like chemical accuracy for quantum chemistry problems). While the results of these algorithms are imperfect, these imperfections can help bootstrap quantum computer testbed development. Demonstrations of these algorithms over the past few years, coupled with the idea that imperfect algorithm performance can be caused by several dominant noise sources in the quantum processor, which can be measured and calibrated during algorithm execution or in post-processing, has led to the use of noise mitigation to improve typical computational results. Conversely, benchmark algorithms coupled with noise mitigation can help diagnose the nature of the noise, whether systematic or purely random. Here, we outline the use of coherent noise mitigation techniques as a characterization tool in trapped-ion testbeds. We perform model-fitting of the noisy data to determine the noise source based on realistic physics focused noise models and demonstrate that systematic noise amplification coupled with error mitigation schemes provides useful data for noise model deduction. Further, in order to connect lower level noise model details with application specific performance of near term algorithms, we experimentally construct the loss landscape of a variational algorithm under various injected noise sources coupled with error mitigation techniques. This type of connection enables application-aware hardware codesign, in which the most important noise sources in specific applications, like quantum chemistry, become foci of improvement in subsequent hardware generations.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

NASA NTRS2013

Large-Scale Features of Pliocene Climate: Results from the Pliocene Model Intercomparison Project

Climate and environments of the mid-Pliocene warm period (3.264 to 3.025 Ma) have been extensively studied.Whilst numerical models have shed light on the nature of climate at the time, uncertainties in their predictions have not been systematically examined. The Pliocene Model Intercomparison Project quantifies uncertainties in model outputs through a coordinated multi-model and multi-mode data intercomparison. Whilst commonalities in model outputs for the Pliocene are clearly evident, we show substantial variation in the sensitivity of models to the implementation of Pliocene boundary conditions. Models appear able to reproduce many regional changes in temperature reconstructed from geological proxies. However, data model comparison highlights that models potentially underestimate polar amplification. To assert this conclusion with greater confidence, limitations in the time-averaged proxy data currently available must be addressed. Furthermore, sensitivity tests exploring the known unknowns in modelling Pliocene climate specifically relevant to the high latitudes are essential (e.g. palaeogeography, gateways, orbital forcing and trace gasses). Estimates of longer-term sensitivity to CO2 (also known as Earth System Sensitivity; ESS), support previous work suggesting that ESS is greater than Climate Sensitivity (CS), and suggest that the ratio of ESS to CS is between 1 and 2, with a "best" estimate of 1.5.

mathematical models↗

NASA NTRS2014

In-Service Monitoring of Steam Pipe Systems at High Temperatures

A system and method for monitoring the properties of a fluid, such as water, in a steam pipe without mechanically penetrating the wall of the pipe. The system uses a piezoelectric transducer to launch an ultrasonic probe signal into the pipe. Reflected ultrasonic signals are captured in a transducer, which can be the same transducer that launched the probe signal. The reflected signals are subjected to data processing, which can include filtering, amplification, analog-to-digital conversion and autocorrelation analysis. A result is extracted which is indicative of a property of the fluid, such as a height of the condensed fluid, a cavitation of the condensed fluid, and a surface perturbation of the condensed fluid. The result can be recorded, displayed, and/or transmitted to another location. One embodiment of the system has been constructed and tested based on a general purpose programmable computer using instructions recorded in machine-readable non-volatile memory.

Bar-Cohen, Yoseph↗

NASA NTRS2016

Apparatus for and Method of Monitoring Condensed Water in Steam Pipes at High Temperature

Lih, Shyh-Shiuh↗

DOE OSTI2020

More chemical detection through less sampling: amplifying chemical signals in hyperspectral data cubes through compressive sensing

Compressive sensing (CS) is a method of sampling which permits some classes of signals to be reconstructed with high accuracy even when they were sampled at sub-Nyquist rates. In this paper we explore a phenomenon in which bandwise CS sampling of a hyperspectral data cube followed by reconstruction can actually result in amplification of chemical signals contained in the cube. Perhaps most surprisingly, chemical signal amplification generally seems to increase as the level of sampling decreases. In some examples, the chemical signal is significantly stronger in a data cube reconstructed from 10% CS sampling than it is in the raw, 100% sampled data cube. We explore this phenomenon in two real-world datasets including the Physical Sciences Inc. Fabry-Perot interferometer sensor multispectral dataset and the Johns Hopkins Applied Physics Lab FTIR-based longwave infrared sensor hyperspectral dataset. Each of these datasets contains the release of a chemical simulant, such as glacial acetic acid, triethyl phospate, and sulfur hexafluoride, and in all cases we use the adaptive coherence estimator (ACE) to detect a target signal in the hyperspectral data cube. We end the paper by suggesting some theoretical justifications for why chemical signals would be amplified in CS sampled and reconstructed hyperspectral data cubes and discuss some practical implications.

Hyperspectral imagery, Compressive Sensing, single↗

NASA NTRS1973

Effect of reaction control system jet-flow field interactions on a 0.015 scale model space shuttle orbiter aerodynamic characteristics

The effects of the reaction control system (RCS) jet-flow field interactions on the space shuttle orbiter system during entry are discussed. The primary objective of the test program was to obtain data for the shuttle orbiter configuration to determine control amplification factors resulting from jet interaction between the RCS plumes and the external flow over the vehicle. A secondary objective was to provide data for comparison and improvement of analytic jet interaction prediction techniques. The test program was divided into two phases; (1) force and moment measurements were made with and without RCS blowing, investigating environment parameters (R sub e, Alpha, Beta), RCS plume parameters (Jet pressure ratio, momentum ratio and thrust level), and geometry parameters (RCS pod locations) on the orbiter model, (2) oil flow visualization tests were conducted on a dummy balance at the end of the test.

Monta, W. J.↗

NASA NTRS1979

Nuclear pumped laser research at the Jet Propulsion Laboratory

Using a partially nuclear excited xenon flashlamp to pump an iodine laser, laser pulse shapes were analyzed with and without nuclear flashlamp augmentation. The pulse shapes indicate that the deposition of nuclear energy is equally as effective as electrical energy deposition in producing laser pulse energy output. The amplification of the E-beam pumped CF3I was measured at pressures of several atmospheres. Preliminary data shows that, for a part of the iodine laser pulse, amplification of almost a factor of two is measured. This measurement indicates that the gain in an E-beam pumped CF3I is an order of magnitude greater than in the coaxial laser tube.

Russell, G. R.↗

NASA NTRS2013

Simulations of the Mid-Pliocene Warm Period Using Two Versions of the NASA-GISS ModelE2-R Coupled Model

The mid-Pliocene Warm Period (mPWP) bears many similarities to aspects of future global warming as projected by the Intergovernmental Panel on Climate Change (IPCC, 2007). Both marine and terrestrial data point to high-latitude temperature amplification, including large decreases in sea ice and land ice, as well as expansion of warmer climate biomes into higher latitudes. Here we present our most recent simulations of the mid-Pliocene climate using the CMIP5 version of the NASAGISS Earth System Model (ModelE2-R). We describe the substantial impact associated with a recent correction made in the implementation of the Gent-McWilliams ocean mixing scheme (GM), which has a large effect on the simulation of ocean surface temperatures, particularly in the North Atlantic Ocean. The effect of this correction on the Pliocene climate results would not have been easily determined from examining its impact on the preindustrial runs alone, a useful demonstration of how the consequences of code improvements as seen in modern climate control runs do not necessarily portend the impacts in extreme climates.Both the GM-corrected and GM-uncorrected simulations were contributed to the Pliocene Model Intercomparison Project (PlioMIP) Experiment 2. Many findings presented here corroborate results from other PlioMIP multi-model ensemble papers, but we also emphasize features in the ModelE2-R simulations that are unlike the ensemble means. The corrected version yields results that more closely resemble the ocean core data as well as the PRISM3D reconstructions of the mid-Pliocene, especially the dramatic warming in the North Atlantic and Greenland-Iceland-Norwegian Sea, which in the new simulation appears to be far more realistic than previously found with older versions of the GISS model. Our belief is that continued development of key physical routines in the atmospheric model, along with higher resolution and recent corrections to mixing parameterisations in the ocean model, have led to an Earth System Model that will produce more accurate projections of future climate.

climate change↗