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At least 109 records · Page 6

All sources NASA NTRS DOE OSTI

DOE OSTI2023

From primordial clocks to circadian oscillators

Circadian rhythms play an essential part in many biological processes, and only three prokaryotic proteins are required to constitute a true post-translational circadian oscillator1. The evolutionary history of the three Kai proteins indicates that KaiC is the oldest member and a central component of the clock. Subsequent additions of KaiB and KaiA regulate the phosphorylation state of KaiC for time synchronization. The canonical KaiABC system in cyanobacteria is well understood but little is known about more ancient systems that only possess KaiBC. However, there are reports that they might exhibit a basic, hourglass-like timekeeping mechanism. Here we investigate the primordial circadian clock in Rhodobacter sphaeroides , which contains only KaiBC, to elucidate its inner workings despite missing KaiA. Using a combination of X-ray crystallography and cryogenic electron microscopy, we find a new dodecameric fold for KaiC, in which two hexamers are held together by a coiled-coil bundle of 12 helices. This interaction is formed by the carboxy-terminal extension of KaiC and serves as an ancient regulatory moiety that is later superseded by KaiA. A coiled-coil register shift between daytime and night-time conformations is connected to phosphorylation sites through a long-range allosteric network that spans over 140 Å. Our kinetic data identify the difference in the ATP-to-ADP ratio between day and night as the environmental cue that drives the clock. They also unravel mechanistic details that shed light on the evolution of self-sustained oscillators.

59 BASIC BIOLOGICAL SCIENCES↗

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 OSTI2014

A seamless acquisition digital storage oscilloscope with three-dimensional waveform display

In traditional digital storage oscilloscope (DSO), sampled data need to be processed after each acquisition. During data processing, the acquisition is stopped and oscilloscope is blind to the input signal. Thus, this duration is called dead time. With the rapid development of modern electronic systems, the effect of infrequent events becomes significant. To capture these occasional events in shorter time, dead time in traditional DSO that causes the loss of measured signal needs to be reduced or even eliminated. In this paper, a seamless acquisition oscilloscope without dead time is proposed. In this oscilloscope, three-dimensional waveform mapping (TWM) technique, which converts sampled data to displayed waveform, is proposed. With this technique, not only the process speed is improved, but also the probability information of waveform is displayed with different brightness. Thus, a three-dimensional waveform is shown to the user. To reduce processing time further, parallel TWM which processes several sampled points simultaneously, and dual-port random access memory based pipelining technique which can process one sampling point in one clock period are proposed. Furthermore, two DDR3 (Double-Data-Rate Three Synchronous Dynamic Random Access Memory) are used for storing sampled data alternately, thus the acquisition can continue during data processing. Therefore, the dead time of DSO is eliminated. In addition, a double-pulse test method is adopted to test the waveform capturing rate (WCR) of the oscilloscope and a combined pulse test method is employed to evaluate the oscilloscope's capture ability comprehensively. The experiment results show that the WCR of the designed oscilloscope is 6 250 000 wfms/s (waveforms per second), the highest value in all existing oscilloscopes. The testing results also prove that there is no dead time in our oscilloscope, thus realizing the seamless acquisition.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2024

Distributed Order Recording Techniques for Efficient Record-and-Replay of Multi-threaded Programs

After all these years and all these other shared memory programming frameworks, OpenMP is still the most popular one. However, its greater levels of non-deterministic execution makes debugging and testing more challenging. The ability to record and deterministically replay the program execution is key to address this challenge. However, scalably replaying OpenMP programs is still an unresolved problem. In this paper, we propose two novel techniques that use Distributed Clock (DC) and Distributed Epoch (DE) recording schemes to eliminate excessive thread synchronization for OpenMP record and replay. Our evaluation on representative HPC applications with ReOMP, which we used to realize DC and DE recording, shows that our approach is 2-5x more efficient than traditional approaches that synchronize on every shared-memory access. Furthermore, we demonstrate that our approach can be easily combined with MPI-level replay tools to replay non-trivial MPI+OpenMP applications. We achieve this by integrating ReOMP into ReMPI, an existing scalable MPI record-and-replay tool, with only a small MPI-scale-independent runtime overhead.

Fu, Xiang↗

DOE OSTI2019

Optimum Full Information, Unlimited Complexity, Invariant and Minimax Clock Skew and Offset Estimators for IEEE 1588

This paper presents the problem of clock skew and offset estimation for the IEEE 1588 precision time protocol. Built on the classical two-way message exchange scheme, IEEE 1588 is a prominent synchronization protocol for packet switched networks. Because of the presence of random queuing delays in a packet switched network, the joint recovery of clock skew and offset from the received packet timestamps can be viewed as a statistical estimation problem. Recently, assuming perfect clock skew information, minimax optimum clock offset estimators were developed for IEEE 1588. Building on this work, we first develop joint optimum invariant clock skew and offset estimators for IEEE 1588 for known queuing delay statistics and unlimited computational complexity. We then show the developed estimators are minimax optimum, i.e., these estimators minimize the maximum skew normalized mean square estimation error over all possible values of the unknown parameters. Minimax optimum estimators that utilize information from past timestamps to improve accuracy are also introduced. The developed optimum estimators provide useful fundamental limits for evaluating the performance of clock skew and offset estimation schemes. These performance limits can aid system designers to develop algorithms with the desired computational complexity that achieve performance close to the performance of the optimum estimators. If a designer finds an approach with a complexity they find acceptable and which provides performance close to the optimum performance, they can use it and know they have near optimum performance. This is precisely the approach used in communications when comparing to capacity.

Cellular networks↗

DOE OSTI2018

Quantum-authenticated clock signal

The present disclosure is directed to a system and method of distributing time information to enable synchronization in an authenticated manner via a quantum channel. A source device may transmit a timing signal, T on a communication channel from the source device to a receiver device. The timing signal T may be include a time or times stored in memory or calculated using a previously agreed upon formula. The method may include transmitting a quantum system Q from the source device to the receiver device. The quantum system may be prepared in a randomly chosen state and may be measured by the receiver device in a randomly chosen measurement basis.

47 OTHER INSTRUMENTATION↗

DOE OSTI2023

Sampling synchronization through GPS signals

A method uses a distributed data acquisition system with multiple, physically unconnected, data acquisition units, that can be in wireless communication with a remote host, to timestamp measurement data with sub-microsecond time base accuracy of sampling clock relative to an absolute timeframe. A current absolute time is derived from messages received from a satellite radio beacon positioning system (GPS). Measurement data is sampled by each unit at a specified sampling rate. Using hardware logic, batches of sampled data are associated with corresponding timestamps representing the absolute time at which the data was sampled. Data and timestamps may be transmitted to the host. A time offset bias is compensated by comparing timestamps against a nominal time based on start time and nominal sampling rate. The sampling clock rate may be disciplined using time pulses from the GPS receiver. An initial start of data sampling by all units can also be synchronized.

Zhuge, James Q.↗

DOE OSTI2016

Three-phase Four-leg Inverter LabVIEW FPGA Control Code [SWR-16-26]

In the area of power electronics control, Field Programmable Gate Arrays (FPGAs) have the capability to outperform their Digital Signal Processor (DSP) counterparts due to the FPGA’s ability to implement true parallel processing and therefore facilitate higher switching frequencies, higher control bandwidth, and/or enhanced functionality. National Instruments (NI) has developed two platforms, Compact RIO (cRIO) and Single Board RIO (sbRIO), which combine a real-time processor with an FPGA. The FPGA can be programmed with a subset of the well-known LabVIEW graphical programming language. The use of cRIO and sbRIO for power electronics control has developed over the last few years to include control of three-phase inverters. Most three-phase inverter topologies include three switching legs. The addition of a fourth-leg to natively generate the neutral connection allows the inverter to serve single-phase loads in a microgrid or stand-alone power system and to balance the three-phase voltages in the presence of significant load imbalance. However, the control of a four-leg inverter is much more complex. In particular, instead of standard two-dimensional space vector modulation (SVM), the inverter requires three-dimensional space vector modulation (3D-SVM). The candidate software implements complete control algorithms in LabVIEW FPGA for a three-phase four-leg inverter. The software includes feedback control loops, three-dimensional space vector modulation gate-drive algorithms, advanced alarm handling capabilities, contactor control, power measurements, and debugging and tuning tools. The feedback control loops allow inverter operation in AC voltage control, AC current control, or DC bus voltage control modes based on external mode selection by a user or supervisory controller. The software includes the ability to synchronize its AC output to the grid or other voltage-source before connection. The software also includes provisions to allow inverter operation in parallel with other voltage regulating devices on the AC or DC buses. This flexibility allows the Inverter to operate as a stand-alone voltage source, connected to the grid, or in parallel with other controllable voltage sources as part of a microgrid or remote power system. In addition, as the inverter is expected to operate under severe unbalanced conditions, the software includes algorithms to accurately compute real and reactive power for each phase based on definitions provided in the IEEE Standard 1459: IEEE Standard Definitions for the Measurement of Electric Power Quantities Under Sinusoidal, Nonsinusoidal, Balanced, or Unbalanced Conditions. Finally, the software includes code to output analog signals for debugging and for tuning of control loops. The software fits on the Xilinx Virtex V LX110 FPGA embedded in the NI cRIO-9118 FPGA chassis, and with a 40 MHz base clock, supports a modulation update rate of 40 MHz, user-settable switching frequencies and synchronized control loop update rates of tens of kHz, and reference waveform generation, including Phase Lock Loop (PLL), update rate of 100 kHz.

Martin, Gregory↗

DOE OSTI2025

OpenSAMPL

OpenSAMPL (Open Synchronization Analytics and Monitoring PLatform) is a Python framework for processing, loading, and managing clock probe time series data and metadata from different vendors.

Grant, Josh [Oak Ridge National Laboratory (ORNL),↗

DOE OSTI2016

Dual Active Bridge based DC Transformer LabVIEW FPGA Control Code [SWR-16-25]

Source record↗

DOE OSTI2018

Low power adaptive synchronizer

A circuit adapts to the occurrence of metastable states. The circuit inhibits passing of the metastable state to circuits that follow, by clock gating the output stage. In order to determine whether or not to gate the clock of the output stage, two detect circuits may be used. One circuit detects metastability and another circuit detects metastability resolved to a wrong logic level. The results from one or both detector circuits are used to gate the next clock cycle if needed, waiting for the metastable situation to be resolved.

42 ENGINEERING↗

DOE OSTI2014

Optical-lattice clock sets new standard for timekeeping

The clock’s strength is in numbers; instead of ticking to the rhythm of a single atom, it synchronizes with thousands of atoms at once.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2013

Analysis of a free-running synchronization artifact correction for MV-imaging with aSi:H flat panels

Purpose: Solid state flat panel electronic portal imaging devices (EPIDs) are widely used for megavolt (MV) photon imaging applications in radiotherapy. In addition to their original purpose in patient position verification, they are convenient to use in quality assurance and dosimetry to verify beam geometry and dose deposition or to perform linear accelerator (linac) calibration procedures. However, native image frames from amorphous silicon (aSi:H) detectors show a range of artifacts which have to be eliminated by proper correction algorithms. When a panel is operated in free-running frame acquisition mode, moving vertical stripes (periodic synchronization artifacts) are a disturbing feature in image frames. Especially for applications in volumetric intensity modulated arc therapy (VMAT) or motion tracking, the synchronization (sync) artifacts are the limiting factor for potential and accuracy since they become even worse at higher frame rates and at lower dose rates, i.e., linac pulse repetition frequencies (PRFs). Methods: The authors introduced a synchronization correction method which is based on a theoretical model describing the interferences of the panel's readout clocking with the linac's dose pulsing. Depending on the applied PRF, a certain number of dose pulses is captured per frame which is readout columnwise, sequentially. The interference of the PRF with the panel readout is responsible for the period and the different gray value levels of the sync stripes, which can be calculated analytically. Sync artifacts can then be eliminated multiplicatively in precorrected frames without additional information about radiation pulse timing. Results: For the analysis, three aSi:H EPIDs of various types were investigated with 6 and 15 MV photon beams at varying PRFs of 25, 50, 100, 200, and 400 pulses per second. Applying the sync correction at panels with gadolinium oxysulfide scintillators improved single frame flood field image quality drastically [improvement of the signal-to-noise ratio (SNR) up to 66.1 dB for 6 MV and 66.0 dB for 15 MV]. Also for the EPID with a caesium iodide scintillator, the noise for the lower PRFs could be reduced (SNR at 6 MV of up to 56.3 dB and at 15 MV up to 46.7 dB). However, the simplistic readout interference model fails at higher PRFs, where image lag and ghosting effects due to trapped charges in the thin film transistor and scintillator postglowing require additional corrections. Conclusions: The presented free-running sync correction method improves SNR of single frames and enables imaging applications, like low-dose rate imaging at increased image frame rates (e.g., to track moving gold fiducials in the lung). Adaptive image guided radiotherapy protocols become even feasible in VMAT plans. Also simultaneous kilovolt and MV imaging applications can benefit from new possibilities of MV scatter removal in x-ray images.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2016

Coherent population trapping with polarization modulation

Coherent population trapping (CPT) is extensively studied for future vapor cell clocks of high frequency stability. In the constructive polarization modulation CPT scheme, a bichromatic laser field with polarization and phase synchronously modulated is applied on an atomic medium. A high contrast CPT signal is observed in this so-called double-modulation configuration, due to the fact that the atomic population does not leak to the extreme Zeeman states, and that the two CPT dark states, which are produced successively by the alternate polarizations, add constructively. Here, we experimentally investigate CPT signal dynamics first in the usual configuration, a single circular polarization. The double-modulation scheme is then addressed in both cases: one pulse Rabi interaction and two pulses Ramsey interaction. The impact and the optimization of the experimental parameters involved in the time sequence are reviewed. We show that a simple seven-level model explains the experimental observations. The double-modulation scheme yields a high contrast similar to the one of other high contrast configurations like push-pull optical pumping or crossed linear polarization scheme, with a setup allowing a higher compactness. The constructive polarization modulation is attractive for atomic clock, atomic magnetometer, and high precision spectroscopy applications.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2024

Quantum Networks: A New Platform for Aerospace

The ability to distribute entanglement between quantum nodes may unlock new capabilities in the future that include teleporting information across multinode networks, higher resolution detection via entangled sensor arrays, and measurements beyond the quantum limit enabled by networked atomic clocks. These new quantum networks also hold promise for the Aerospace community in areas such as deep space exploration, improved satellite communication, and synchronizing drone swarms. Although exciting, these applications are a long way off from providing a “real-world” benefit, as they have only been theoretically explored or demonstrated in small-scale experiments. An outstanding challenge is to identify near-term use cases for quantum networks; this may be an intriguing new area of interest for the aerospace community, as the quantum networking field would benefit from more multidisciplinary collaborations. This paper introduces quantum networking, discusses the difficulties in distributing entanglement within these networks, highlights recent progress toward this endeavor, and features two current case studies on mobile quantum nodes and an entangled clock network, both of which are relevant to the aerospace community.

Engineering↗

DOE OSTI2014

1 ns time to digital converters for the KM3NeT data readout system

The KM3NeT collaboration aims at the construction of a multi-km3 high-energy neutrino telescope in the Mediterranean Sea consisting of thousands of glass spheres (nodes), each of them containing 31 photomultiplier (PMT) of small photocathode area. The readout and data acquisition system of KM3NeT has to collect, treat and send to shore, in an economic way, the enormous amount of data produced by the photomultipliers. For this purpose, 31 high-resolution time-interval measuring channels are implemented on the Field-Programmable Gate Arrays (FPGA) based on Time to Digital Converter (TDC). TDC are very common devices in particles physics experiments. Architectures with low resources occupancy are desirable allowing the implementation of other instrumentation, communication and synchronization systems on the same device. The required resolution to measure both, time of flight and timestamp must be 1 ns. A 4-Oversampling technique with two high frequency clocks is used to achieve this resolution. The proposed TDC firmware is developed using very few resources in Xilinx Kintex-7.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2016

Exploration of Circadian Rhythms in Patients with Bilateral Vestibular Loss

Background New insights have expanded the influence of the vestibular system to the regulation of circadian rhythmicity. Indeed, hypergravity or bilateral vestibular loss (BVL) in rodents causes a disruption in their daily rhythmicity for several days. The vestibular system thus influences hypothalamic regulation of circadian rhythms on Earth, which raises the question of whether daily rhythms might be altered due to vestibular pathology in humans. The aim of this study was to evaluate human circadian rhythmicity in people presenting a total bilateral vestibular loss (BVL) in comparison with control participants. Methodology and Principal Findings Nine patients presenting a total idiopathic BVL and 8 healthy participants were compared. Their rest-activity cycle was recorded by actigraphy at home over 2 weeks. The daily rhythm of temperature was continuously recorded using a telemetric device and salivary cortisol was recorded every 3 hours from 6:00AM to 9:00PM over 24 hours. BVL patients displayed a similar rest activity cycle during the day to control participants but had higher nocturnal actigraphy, mainly during weekdays. Sleep efficiency was reduced in patients compared to control participants. Patients had a marked temperature rhythm but with a significant phase advance (73 min) and a higher variability of the acrophase (from 2:24 PM to 9:25 PM) with no correlation to rest-activity cycle, contrary to healthy participants. Salivary cortisol levels were higher in patients compared to healthy people at any time of day. Conclusion We observed a marked circadian rhythmicity of temperature in patients with BVL, probably due to the influence of the light dark cycle. However, the lack of synchronization between the temperature and rest-activity cycle supports the hypothesis that the vestibular inputs are salient input to the circadian clock that enhance the stabilization and precision of both external and internal entrainment.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Advanced architectures for high-performance quantum networking

As practical quantum networks prepare to serve an ever-expanding number of nodes, there has grown a need for advanced auxiliary classical systems that support the quantum protocols and maintain compatibility with the existing fiber-optic infrastructure. We propose and demonstrate a quantum local area network design that addresses current deployment limitations in timing and security in a scalable fashion using commercial off-the-shelf components. First, we employ White Rabbit switches to synchronize three remote nodes with ultra-low timing jitter, significantly increasing the fidelities of the distributed entangled states over previous work with Global Positioning System clocks. Second, using a parallel quantum key distribution channel, we secure the classical communications needed for instrument control and data management. Therefore, the conventional network that manages our entanglement network is secured using keys generated via an underlying quantum key distribution layer, preserving the integrity of the supporting systems and the relevant data in a future-proof fashion.

97 MATHEMATICS AND COMPUTING↗