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At least 1,045 records · Page 58
All sourcesNASA NTRSDOE OSTI
DOE OSTI2019

ECHO: an application for detection and analysis of oscillators identifies metabolic regulation on genome-wide circadian output

Abstract Motivation Time courses utilizing genome scale data are a common approach to identifying the biological pathways that are controlled by the circadian clock, an important regulator of organismal fitness. However, the methods used to detect circadian oscillations in these datasets are not able to accommodate changes in the amplitude of the oscillations over time, leading to an underestimation of the impact of the clock on biological systems. Results We have created a program to efficaciously identify oscillations in large-scale datasets, called the Extended Circadian Harmonic Oscillator application, or ECHO. ECHO utilizes an extended solution of the fixed amplitude oscillator that incorporates the amplitude change coefficient. Employing synthetic datasets, we determined that ECHO outperforms existing methods in detecting rhythms with decreasing oscillation amplitudes and in recovering phase shift. Rhythms with changing amplitudes identified from published biological datasets revealed distinct functions from those oscillations that were harmonic, suggesting purposeful biologic regulation to create this subtype of circadian rhythms. Availability and implementation ECHO’s full interface is available at https://github.com/delosh653/ECHO. An R package for this functionality, echo.find, can be downloaded at https://CRAN.R-project.org/package=echo.find. Supplementary information Supplementary data are available at Bioinformatics online.

De los Santos, Hannah↗
DOE OSTI2024

A universal and constant rate of gene content change traces pangenome flux to LUCA

Abstract Prokaryotic genomes constantly undergo gene flux via lateral gene transfer, generating a pangenome structure consisting of a conserved core genome surrounded by a more variable accessory genome shell. Over time, flux generates change in genome content. Here, we measure and compare the rate of genome flux for 5655 prokaryotic genomes as a function of amino acid sequence divergence in 36 universally distributed proteins of the informational core (IC). We find a clock of gene content change. The long-term average rate of gene content flux is remarkably constant across all higher prokaryotic taxa sampled, whereby the size of the accessory genome—the proportion of the genome harboring gene content difference for genome pairs—varies across taxa. The proportion of species-level accessory genes per genome, varies from 0% (Chlamydia) to 30%–33% (Alphaproteobacteria, Gammaproteobacteria, and Clostridia). A clock-like rate of gene content change across all prokaryotic taxa sampled suggest that pangenome structure is a general feature of prokaryotic genomes and that it has been in existence since the divergence of bacteria and archaea.

Microbiology↗
DOE OSTI2014

Light quality modulates metabolic synchronization over the diel phases of crassulacean acid metabolism

Temporal compartmentation of carboxylation processes is a defining feature of crassulacean acid metabolism and involves circadian control of key metabolic and transport steps that regulate the supply and demand for carbon over a 24h cycle. Recent insights on the molecular workings of the circadian clock and its connection with environmental inputs raise new questions on the importance of light quality and, by analogy, certain photoreceptors for synchronizing the metabolic components of CAM. The present work tested the hypothesis that optimal coupling of stomatal conductance, net CO2 uptake, and the reciprocal turnover of carbohydrates and organic acids over the diel CAM cycle requires both blue and red light input signals. Contrasting monochromatic wavelengths of blue, green, and red light (i.e. 475, 530, 630nm) with low fluence rates (10 μmol m–2 s–1) were administered for 16 hours each diel cycle for a total treatment time of 48 hours to the obligate CAM bromeliad, Aechmea ‘Maya’. Of the light treatments imposed, low-fluence blue light was a key determinant in regulating stomatal responses, organic acid mobilization from the vacuole, and daytime decarboxylation. However, the reciprocal relationship between starch and organic acid turnover that is typical for CAM was uncoupled under low-fluence blue light. Under low-fluence red or green light, the diel turnover of storage carbohydrates was orchestrated in line with the requirements of CAM, but a consistent delay in acid consumption at dawn compared with plants under white or low-fluence blue light was noted. Consistent with the acknowledged influences of both red and blue light as input signals for the circadian clock, the data stress the importance of both red and blue-light signalling pathways for synchronizing the metabolic and physiological components of CAM over the day/night cycle.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2026

Floquet operator dynamics and orthogonal polynomials on the unit circle

Operator spreading under stroboscopic time evolution under a unitary is studied. An operator Krylov space is constructed and mapped to orthogonal polynomials on a unit circle (OPUC), as well as to the Krylov space of the edge operator of the Floquet transverse field Ising model with inhomogeneous couplings (ITFIM). The Verblunsky coefficients in the OPUC representation are related to the Krylov angles parametrizing the ITFIM. The relations between the OPUC and spectral functions are summarized and several applications are presented. These include derivation of analytic expressions for the OPUC under persistent m-periodic dynamics, and the numerical construction of the OPUC for autocorrelations of the homogeneous Floquet-Ising model as well as the Z 3 clock model. The numerically obtained Krylov angles of the Z 3 clock model with long-lived period tripled autocorrelations show a spatial periodicity of six, and this observation is used to develop an analytically solvable model for the ITFIM that mimics this behavior.

Floquet systems↗
DOE OSTI2020

YbH + formation in an ytterbium ion trap

The trapped 171 Yb + ion is a promising candidate for portable atomic clock applications. However, with buffer-gas cooled ytterbium ions, the ions can be pumped into a low-lying 2 F 7 / 2 state or form YbH + molecules. These dark states reduce the fluorescence signal from the ions and can degrade the clock stability. In this work, we study the dynamics of the populations of the 2 F 7 / 2 state and YbH + molecules under different operating conditions of our 171 Yb + ion system. Our study indicates that 2 F 7 / 2 -state ions can form YbH + molecules through interactions with hydrogen gas. As observed previously, dissociation of YbH + is observed at wavelengths around 369 nm. We also demonstrate YbH+ dissociation using 405 nm light. Moreover, we show that the population in the dark states can be limited by using a single repump laser at 935 nm. Our study provides insights into the molecular formation in a trapped ion system.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2011

Search for variation of fundamental constants and violations of fundamental symmetries using isotope comparisons

Atomic microwave clocks based on hyperfine transitions, such as the caesium standard, tick with a frequency that is proportional to the magnetic moment of the nucleus. This magnetic moment varies strongly between isotopes of the same atom, while all atomic electron parameters remain the same. Therefore the comparison of two microwave clocks based on different isotopes of the same atom can be used to constrain variation of fundamental constants. In this paper, we calculate the neutron and proton contributions to the nuclear magnetic moments, as well as their sensitivity to any potential quark-mass variation, in a number of isotopes of experimental interest including {sup 201,199}Hg and {sup 87,85}Rb, where experiments are underway. We also include a brief treatment of the dependence of the hyperfine transitions to variation in nuclear radius, which in turn is proportional to any change in quark mass. Our calculations of expectation values of proton and neutron spin in nuclei are also needed to interpret measurements of violations of fundamental symmetries.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2024

Classification of electronic nematicity in three-dimensional crystals and quasicrystals

Electronic nematic order has been reported in a rich landscape of materials, encompassing not only a range of intertwined correlated and topological phenomena but also different underlying lattice symmetries. Motivated by these findings, we investigate the behavior of electronic nematicity as the spherical symmetry of three-dimensional (3D) space is systematically lowered by the lattice environment. Here, we consider all 32 crystallographic point groups as well as four major classes of quasicrystalline point groups, given the recent observations of electronic phases of interest in quasicrystalline materials and artificial twisted quasicrystals. Valuable insights are gained by establishing a mapping between the five-component charge-quadrupolar nematic order parameter of the electronic fluid and the 3D tensorial order parameter of nematic liquid crystals. We find that a uniaxial nematic state is only generically realized in polyhedral point groups (icosahedral and cubic), with the nematic director pointing along different sets of rotational symmetry axes. Interestingly, icosahedral point groups are the only ones in which the five nematic order parameter components transform as the same irreducible representation, making them the closest analog of 3D isotropic nematics. In axial point groups, one of the nematic components is always condensed, whereas the other four components decompose into an in-plane and an out-of-plane nematic doublet, resulting in biaxial nematic ground states. Because these two nematic doublets behave as Z q clock order parameters, this allows us to identify the types of crystals and quasicrystals that can host interesting electronic nematic phenomena enabled by the critical properties of the q ≥ 4 clock model, such as emergent continuous nematic fluctuations in 3D, critical phases with quasi-long-range nematic order in two dimensions (2D), and Ashkin-Teller nematicity in 2D.

3-dimensional systems↗
DOE OSTI2010

Single-crystal sapphire resonator at millikelvin temperatures: Observation of thermal bistability in high-Q factor whispering gallery modes

Resonance modes in single crystal sapphire ({alpha}-Al{sub 2}O{sub 3}) exhibit extremely high electrical and mechanical Q factors ({approx_equal}10{sup 9} at 4 K), which are important characteristics for electromechanical experiments at the quantum limit. We report the cool down of a bulk sapphire sample below superfluid liquid-helium temperature (1.6 K) to as low as 25 mK. The electromagnetic properties were characterized at microwave frequencies, and we report the observation of electromagnetically induced thermal bistability in whispering gallery modes due to the material T{sup 3} dependence on thermal conductivity and the ultralow dielectric loss tangent. We identify ''magic temperatures'' between 80 and 2100 mK, the lowest ever measured, at which the onset of bistability is suppressed and the frequency-temperature dependence is annulled. These phenomena at low temperatures make sapphire suitable for quantum metrology and ultrastable clock applications, including the possible realization of the quantum-limited sapphire clock.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2011

Equivalence Principle and Gravitational Redshift

We investigate leading order deviations from general relativity that violate the Einstein equivalence principle in the gravitational standard model extension. We show that redshift experiments based on matter waves and clock comparisons are equivalent to one another. Consideration of torsion balance tests, along with matter-wave, microwave, optical, and Moessbauer clock tests, yields comprehensive limits on spin-independent Einstein equivalence principle-violating standard model extension terms at the 10{sup -6} level.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2019

Entropic Energy-Time Uncertainty Relation

We report that energy-time uncertainty plays an important role in quantum foundations and technologies, and it was even discussed by the founders of quantum mechanics. However, standard approaches (e.g., Robertson’s uncertainty relation) do not apply to energy-time uncertainty because, in general, there is no Hermitian operator associated with time. Following previous approaches, we quantify time uncertainty by how well one can read off the time from a quantum clock. We then use entropy to quantify the information-theoretic distinguishability of the various time states of the clock. Our main result is an entropic energy-time uncertainty relation for general time-independent Hamiltonians, stated for both the discrete-time and continuous-time cases. Additionally, our uncertainty relation is strong, in the sense that it allows for a quantum memory to help reduce the uncertainty, and this formulation leads us to reinterpret it as a bound on the relative entropy of asymmetry. Because of the operational relevance of entropy, we anticipate that our uncertainty relation will have information-processing applications.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2019

Systematic Construction of Scarred Many-Body Dynamics in 1D Lattice Models

In this paper, we introduce a family of nonintegrable 1D lattice models that feature robust periodic revivals under a global quench from certain initial product states, thus generalizing the phenomenon of many-body scarring recently observed in Rydberg atom quantum simulators. Our construction is based on a systematic embedding of the single-site unitary dynamics into a kinetically constrained many-body system. We numerically demonstrate that this construction yields new families of models with robust wave-function revivals, and it includes kinetically constrained quantum clock models as a special case. We show that scarring dynamics in these models can be decomposed into a period of nearly free clock precession and an interacting bottleneck, shedding light on their anomalously slow thermalization when quenched from special initial states.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2021

Dipole-Dipole Frequency Shifts in Multilevel Atoms

Dipole-dipole interactions lead to frequency shifts that are expected to limit the performance of next-generation atomic clocks. In this work, we compute dipolar frequency shifts accounting for the intrinsic atomic multilevel structure in standard Ramsey spectroscopy. When interrogating the transitions featuring the smallest Clebsch-Gordan coefficients, we find that a simplified two-level treatment becomes inappropriate, even in the presence of large Zeeman shifts. Further, for these cases, we show a net suppression of dipolar frequency shifts and the emergence of dominant nonclassical effects for experimentally relevant parameters. Our findings are pertinent to current generations of optical lattice and optical tweezer clocks, opening a way to further increase their current accuracy, and thus their potential to probe fundamental and many-body physics.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2025

An Open-Access Repository of Synchrophasor Data Quality Examples: Curation and Example Applications

Synchrophasor measurements are critical in providing wide-area situational awareness to power system operators. However, data artifacts may be introduced due to various issues such as loss of communication, loss of GPS signal, internal clock error, and vendor-specific implementation of phasor estimation algorithms. Tools designed to provide actionable insights from synchrophasor data, hence, must be designed to be robust to these data quality issues. In this work, two years of synchrophasor data sourced from multiple electric utilities in the United States were analyzed to identify examples of data quality problems. These examples were then labeled and published in the Grid Event Signature Library, a publicly available repository of power system measurements hosted by the Oak Ridge National Laboratory. This paper describes the data curation process, and illustrates two application use cases where the dataset can be valuable to the research community. In the first use case, a random forest classifier is trained to distinguish power system disturbance signatures from data anomalies introduced in synchrophasor measurements due to clock errors. The second use case studies the impact of data quality issues on an example synchrophasor application (specifically, event start time determination). The choice of data quality problems investigated is informed by the examples in the repository curated in this work.

24 POWER TRANSMISSION AND DISTRIBUTION↗
DOE OSTI2011

An on-line acoustic fluorocarbon coolant mixture analyzer for the ATLAS silicon tracker

The ATLAS silicon tracker community foresees an upgrade from the present octafluoro-propane (C{sub 3}F{sub 8}) evaporative cooling fluid - to a composite fluid with a probable 10-20% admixture of hexafluoro-ethane (C{sub 2}F{sub 6}). Such a fluid will allow a lower evaporation temperature and will afford the tracker silicon substrates a better safety margin against leakage current-induced thermal runaway caused by cumulative radiation damage as the luminosity profile at the CERN Large Hadron Collider increases. Central to the use of this new fluid is a new custom-developed speed-of-sound instrument for continuous real-time measurement of the C{sub 3}F{sub 8}/C{sub 2}F{sub 6} mixture ratio and flow. An acoustic vapour mixture analyzer/flow meter with new custom electronics allowing ultrasonic frequency transmission through gas mixtures has been developed for this application. Synchronous with the emission of an ultrasound 'chirp' from an acoustic transmitter, a fast readout clock (40 MHz) is started. The clock is stopped on receipt of an above threshold sound pulse at the receiver. Sound is alternately transmitted parallel and anti-parallel with the vapour flow for volume flow measurement from transducers that can serve as acoustic transmitters or receivers. In the development version, continuous real-time measurement of C{sub 3}F{sub 8}/C{sub 2}F{sub 6} flow and calculation of the mixture ratio is performed within a graphical user interface developed in PVSS-II, the Supervisory, Control and Data Acquisition standard chosen for LHC and its experiments at CERN. The described instrument has numerous potential applications - including refrigerant leak detection, the analysis of hydrocarbons, vapour mixtures for semiconductor manufacture and anesthetic gas mixtures. (authors)

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2015

Adaptive linear predictor FIR filter based on the Cyclone V FPGA with HPS to reduce narrow band RFI in AERA radio detection of cosmic rays

We present the new approach to a filtering of radio frequency interferences (RFI) in the Auger Engineering Radio Array (AERA) which study the electromagnetic part of the Extensive Air Showers. The radio stations can observe radio signals caused by coherent emissions due to geomagnetic radiation and charge excess processes. AERA observes frequency band from 30 to 80 MHz. This range is highly contaminated by human-made RFI. In order to improve the signal to noise ratio RFI filters are used in AERA to suppress this contamination. The first kind of filter used by AERA was the Median one, based on the Fast Fourier Transform (FFT) technique. The second one, which is currently in use, is the infinite impulse response (IIR) notch filter. The proposed new filter is a finite impulse response (FIR) filter based on a linear prediction (LP). A periodic contamination hidden in a registered signal (digitized in the ADC) can be extracted and next subtracted to make signal cleaner. The FIR filter requires a calculation of n=32, 64 or even 128 coefficients (dependent on a required speed or accuracy) by solving of n linear equations with coefficients built from the covariance Toeplitz matrix. This matrix can be solved by the Levinson recursion, which is much faster than the Gauss procedure. The filter has been already tested in the real AERA radio stations on Argentinean pampas with a very successful results. The linear equations were solved either in the virtual soft-core NIOSR processor (implemented in the FPGA chip as a net of logic elements) or in the external Voipac PXA270M ARM processor. The NIOS processor is relatively slow (50 MHz internal clock), calculations performed in an external processor consume a significant amount of time for data exchange between the FPGA and the processor. Test showed a very good efficiency of the RFI suppression for stationary (long-term) contaminations. However, we observed a short-time contaminations, which could not be suppressed either by the IIR-notch filter or by the FIR filter based on the linear predictions. For the LP FIR filter the refreshment time of the filter coefficients was to long and filter did not keep up with the changes of a contamination structure, mainly due to a long calculation time in a slow processors. We propose to use the Cyclone V SE chip with embedded micro-controller operating with 925 MHz internal clock to significantly reduce a refreshment time of the FIR coefficients. The lab results are promising. (authors)

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2015

First results of the silicon telescope using an 'artificial retina' for fast track finding

We present the first results of the prototype of a silicon tracker with trigger capabilities based on a novel approach for fast track finding. The working principle of the 'artificial retina' is inspired by the processing of visual images by the brain and it is based on extensive parallelization of data distribution and pattern recognition. The algorithm has been implemented in commercial FPGAs in three main logic modules: a switch for the routing of the detector hits, a pool of engines for the digital processing of the hits, and a block for the calculation of the track parameters. The architecture is fully pipelined and allows the reconstruction of real-time tracks with a latency less then 100 clock cycles, corresponding to 0.25 microsecond at 400 MHz clock. The silicon telescope consists of 8 layers of single-sided silicon strip detectors with 512 strips each. The detector size is about 10 cm x 10 cm and the strip pitch is 183 μm. The detectors are read out by the Beetle chip, a custom ASICs developed for LHCb, which provides the measurement of the hit position and pulse height of 128 channels. The 'artificial retina' algorithm has been implemented on custom data acquisition boards based on FPGAs Xilinx Kintex 7 lx160. The parameters of the tracks detected are finally transferred to host PC via USB 3.0. The boards manage the read-out ASICs and the sampling of the analog channels. The read-out is performed at 40 MHz on 4 channels for each ASIC that corresponds to a decoding of the telescope information at 1.1 MHz. We report on the first results of the fast tracking device and compare with simulations. (authors)

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2019

A Novel TDC Scheme: Combinatorial Gray Code Oscillator Based TDC for Low Power and Low Resource Usage Applications

In common digital electronics design practice, combinatorial loop is less preferable, especially in the multi-bit cases. An exception of multi-bit feedback system that is allowed to be implemented in combinatorial loop is the Gray code sequence generator. The Gray code sequence generator runs by itself without being driven by an external clock. It steps through Gray code sequence significantly faster than the Gray code counter under the same silicon technology. In high energy physics experiments, it is necessary to find a low resource usage and low power TDC (Time-to-Digital-Converter) scheme for high channel count detectors. A Gray code oscillator based TDC is a good candidate for such a scheme. In this paper, we describe our work of design and implementation of a TDC based on combinatorial Gray code oscillator in a Xilinx Kintex-7 FPGA (Field-Programmable Gate Array). The implementation and test results are presented. The test result shows that the TDC using only 8 logic elements is able to reach a RMS precision of 160 ps for time difference measurements of a single pulse. The single pulse measurement precision can be further improved to 51 ps with the weighted average scheme using data from the same TDC channels captured by 4 consecutive system clock edges.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2022

An Alternative Timing and Synchronization Approach for Situational Awareness and Predictive Analytics

Accurate and synchronized timing information is required by power system operators for controlling the grid infrastructure (relays, Phasor Measurement Units (PMUs), etc.) and determining asset positions. Satellite-based global positioning system (GPS) is the primary source of timing information. However, GPS disruptions today (both intentional and unintentional) can significantly compromise the reliability and security of our electric grids. A robust alternate source for accurate timing is critical to serve both as a deterrent against malicious attacks and as a redundant system in enhancing the resilience against extreme events that could disrupt the GPS network. To achieve this, we rely on the highly accurate, terrestrial atomic clock-based network for alternative timing and synchronization. In this paper, we discuss an experimental setup for an alternative timing approach. The data obtained from this experimental setup is continuously monitored and analyzed using various time deviation metrics. We also use these metrics to compute deviations of our clock with respect to the National Institute of Standards and Technologys (NIST) GPS data. The results obtained from these metric computations are elaborately discussed. Finally, we discuss the integration of the procedures involved, like real-time data ingestion, metric computation, and result visualization, in a novel microservices-based architecture for situational awareness.

Chinthavali, Supriya↗