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At least 865 records · Page 48
All sourcesNASA NTRSDOE OSTI
DOE OSTI2010

Blackbody radiation shift in the {sup 87}Rb frequency standard

The operation of atomic clocks is generally carried out at room temperature, whereas the definition of the second refers to the clock transition in an atom at absolute zero. This implies that the clock transition frequency should be corrected in practice for the effect of finite temperature, of which the leading contributor is the blackbody radiation (BBR) shift. Experimental measurements of the BBR shifts are difficult. In this work, we have calculated the blackbody radiation shift of the ground-state hyperfine microwave transition in {sup 87}Rb using the relativistic all-order method and carried out a detailed evaluation of the accuracy of our final value. Particular care is taken to accurately account for the contributions from highly excited states. Our predicted value for the Stark coefficient, k{sub S}=-1.240(4)x10{sup -10} Hz/(V/m){sup 2}, is three times more accurate than the previous calculation [E. J. Angstman, V. A. Dzuba, and V. V. Flambaum, Phys. Rev. A 74, 023405 (2006)].

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2011

Potential of electric quadrupole transitions in radium isotopes for single-ion optical frequency standards

We explore the potential of the electric quadrupole transitions 7s {sup 2}S{sub 1/2}-6d {sup 2}D{sub 3/2}, 6d {sup 2}D{sub 5/2} in radium isotopes as single-ion optical frequency standards. The frequency shifts of the clock transitions due to external fields and the corresponding uncertainties are calculated. Several competitive {sup A}Ra{sup +} candidates, with A= 223-229, are identified. In particular, we show that the transition 7s {sup 2}S{sub 1/2} (F=2,m{sub F}=0)-6d {sup 2}D{sub 3/2} (F=0,m{sub F}=0) at 828 nm in {sup 223}Ra{sup +}, with no linear Zeeman and electric quadrupole shifts, stands out as a relatively simple case, which could be exploited as a compact, robust, and low-cost atomic clock operating at a fractional frequency uncertainty of 10{sup -17}. With more experimental effort, the {sup 223,225,226}Ra{sup +} clocks could be pushed to a projected performance reaching the 10{sup -18} level.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2011

Evaluation of the systematic shifts of a single-{sup 40}Ca{sup +}-ion frequency standard

Progress on the evaluation of systematic frequency shifts is described in the development of the optical frequency standard based on single-trapped {sup 40}Ca{sup +} with a ''clock'' transition at 729 nm. The overall systematic uncertainty of the 4s {sup 2} S{sub 1/2}-3d {sup 2} D{sub 5/2} clock resonance has been characterized to be 7.8 x 10{sup -16}. This uncertainty is at a level similar to the Cs fountain primary standard, while the potential stability for the {sup 40}Ca{sup +} clock exceeds that of Cs.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2022

Register-Like Storage Block Used as Histograms, Cluster Buffers, and Hough Transform Accumulators for HEP Trigger Systems

In high energy physics experiment trigger systems, block memories are utilized for various purposes, especially in binned searching algorithms. In these algorithms, the storages are demanded to perform like a large set of registers. The writing and reading operation must be performed in single clock cycle and once an event is processed, the memory must be globally reset. These demands can be fulfilled with registers but the cost of using registers for large memory is unaffordable. Another common requirement is the boundary coverage feature during reading process. Additionally, when a memory bin is addressed, the stored contents in the addressed bin and its neighboring bin must be output simultaneously. In this paper, a register-like block storage design scheme is described, which allows updating memory locations in single clock cycle, reading two adjacent bins, and effectively refreshing entire memory within a single clock. The implementation and test results are presented.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2022

Development of DNA methylation‐based epigenetic age predictors in loblolly pine ( Pinus taeda )

Abstract Biological ageing is connected to life history variation across ecological scales and informs a basic understanding of age‐related declines in organismal function. Altered DNA methylation dynamics are a conserved aspect of biological ageing and have recently been modelled to predict chronological age among vertebrate species. In addition to their utility in estimating individual age, differences between chronological and predicted ages arise due to acceleration or deceleration of epigenetic ageing, and these discrepancies are linked to disease risk and multiple life history traits. Although evidence suggests that patterns of DNA methylation can describe ageing in plants, predictions with epigenetic clocks have yet to be performed. Here, we resolve the DNA methylome across CpG, CHG, and CHH‐methylation contexts in the loblolly pine tree ( Pinus taeda ) and construct epigenetic clocks capable of predicting ages in this species within 6% of its maximum lifespan. Although patterns of CHH‐methylation showed little association with age, both CpG and CHG‐methylation contexts were strongly associated with ageing, largely becoming hypomethylated with age. Among age‐associated loci were those in close proximity to malate dehydrogenase, NADH dehydrogenase, and 18S and 26S ribosomal RNA genes. This study reports one of the first epigenetic clocks in plants and demonstrates the universality of age‐associated DNA methylation dynamics which can inform conservation and management practices, as well as our ecological and evolutionary understanding of biological ageing in plants.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2018

Oxidation State of 229 Th Recoils Implanted into MgF 2 Crystals

A solid-state nuclear clock based on the low-lying isomeric state in 229 Th has attracted growing interest. One potential problem for the solid-state nuclear clock approach is the suitability of the doped environment for photon emission of the nuclear isomeric state. Specifically, Th n+ n < 4 ions could open non-radiative decay routes for deexcitation, hindering the photon emission. Here we have used time-resolved photoluminescence (TRPL) and density functional theory (DFT) calculations to characterize MgF 2 crystals that have been implanted with 229 Th recoils via a-decay from a 233 U source with the goal of determining the charge state of the implanted thorium atoms. The DFT calculations predicted Th4+ to be the lowest energy oxidation state with Th3+ the next lowest in the MgF2 crystal environment. The DFT calculations also show Th4+:MgF 2 system has a band gap large enough so that the internal electron conversion decay channel is suppressed. Experimentally, we found no evidence for thorium in oxidations state other than +4 using TRPL spectroscopy that has a detection limit for Thn+ n < 4 ions several orders of magnitude smaller than the number of implanted 229Th recoils. This work shows that the solid-state approach is a viable option for a nuclear clock.

229Th Isomeric State↗
DOE OSTI2018

Conservation and Diversification of Circadian Rhythmicity Between a Model Crassulacean Acid Metabolism Plant Kalanchoë fedtschenkoi and a Model C 3 Photosynthesis Plant Arabidopsis thaliana

Crassulacean acid metabolism (CAM) improves photosynthetic efficiency under limited water availability relative to C 3 photosynthesis. It is widely accepted that CAM plants have evolved from C 3 plants and it is hypothesized that CAM is under the control of the internal circadian clock. However, the role that the circadian clock plays in the evolution of CAM is not well understood. To identify the molecular basis of circadian control over CAM evolution, rhythmic gene sets were identified in a CAM model plant species ( Kalanchoë fedtschenkoi ) and a C 3 model plant species ( Arabidopsis thaliana ) through analysis of diel time-course gene expression data using multiple periodicity detection algorithms. Based on protein sequences, ortholog groups were constructed containing genes from each of these two species. The ortholog groups were categorized into five gene sets based on conservation and diversification of rhythmic gene expression. Interestingly, minimal functional overlap was observed when comparing the rhythmic gene sets of each species. Specifcally, metabolic processes were enriched in the gene set under circadian control in K. fedtschenkoi and numerous genes were found to have retained or gained rhythmic expression in K. fedtsechenkoi . Additonally, several rhythmic orthologs, including CAM-related orthologs, displayed phase shifts between species. Results of this analysis point to several mechanisms by which the circadian clock plays a role in the evolution of CAM. These genes provide a set of testable hypotheses for future experiments.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Rhythmic Mechanisms Governing CAM Photosynthesis in Kalanchoe fedtschenkoi : High-Resolution Temporal Transcriptomics

Crassulacean acid metabolism (CAM) is a specialized photosynthetic pathway that enhances water-use efficiency by temporally separating nocturnal CO 2 uptake from daytime decarboxylation and carbon fixation. To uncover the regulatory mechanisms coordinating these temporal dynamics, we generated high-resolution, 48 h time-course transcriptomes for the CAM model Kalanchoe fedtschenkoi under both 12 h/12 h light/dark (LD) cycles and continuous light (LL). A rhythmicity analysis revealed that diel light cues are the dominant driver of transcript oscillations: 16,810 genes (54.3% of annotated genes) exhibited rhythmic expression only under LD, whereas just 399 genes (1.3%) remained rhythmic under LL. A smaller set of 3009 genes (9.7%) oscillated in both conditions, indicating that the intrinsic circadian clock sustains rhythmicity for a limited subset of the transcriptome. A gene co-expression network analysis revealed extensive integration between circadian clock components, core CAM pathway enzymes, and stomatal regulators, defining regulatory modules that coordinate metabolic and physiological timing. Notably, key hub genes associated with post-translational and post-transcriptional regulation, including the E3 ubiquitin ligase HUB2 and several pentatricopeptide repeat (PPR) proteins, act as central nodes in CAM-associated networks. This discovery implicates epigenetic and organellar regulation as previously unrecognized critical tiers of control in CAM. Together, our results support a regulatory model in which CAM rhythmicity is governed by both external light/dark cues and the endogenous circadian clock through multi-level control spanning transcriptional and protein-level regulation. To support community exploration, we also provide an interactive eFP (electronic Fluorescent Pictograph) browser for visualizing time-resolved gene expression profiles.

09 BIOMASS FUELS↗
DOE OSTI2018

Why is the Muon g-2 Experiment Shifting Time?

Scientists on Fermilab's Muon g-2 experiment are using a finely tuned clock to precisely measure how fast the muon — a heavy cousin of the electron — precesses, or wobbles, in the presence of a magnetic field. To remove subconscious bias from the experiment's measurements, in March 2018, two Fermilab scientists outside the Muon g-2 collaboration set the clock to a certain frequency. For the period that Muon g-2 is taking data, only they will know that setting. This bias-removal technique is called clock blinding.

47 OTHER INSTRUMENTATION↗
DOE OSTI2010

PPAR{alpha} deficiency augments a ketogenic diet-induced circadian PAI-1 expression possibly through PPAR{gamma} activation in the liver

Research highlights: {yields} PPAR{alpha} deficiency augments a ketogenic diet-induced circadian PAI-1 expression. {yields} Hepatic expressions of PPAR{gamma} and PCG-1{alpha} are induced by a ketogenic diet. {yields} PPAR{gamma} antagonist attenuates a ketogenic diet-induced PAI-1 expression. {yields} Ketogenic diet advances the phase of circadian clock in a PPAR{alpha}-independent manner. -- Abstract: An increased level of plasminogen activator inhibitor-1 (PAI-1) is considered a risk factor for cardiovascular diseases, and PAI-1 gene expression is under the control of molecular circadian clocks in mammals. We recently showed that PAI-1 expression is augmented in a phase-advanced circadian manner in mice fed with a ketogenic diet (KD). To determine whether peroxisome proliferator-activated receptor {alpha} (PPAR{alpha}) is involved in hypofibrinolytic status induced by a KD, we examined the expression profiles of PAI-1 and circadian clock genes in PPAR{alpha}-null KD mice. Chronic administration of bezafibrate induced the PAI-1 gene expression in a PPAR{alpha}-dependent manner. Feeding with a KD augmented the circadian expression of PAI-1 mRNA in the hearts and livers of wild-type (WT) mice as previously described. The KD-induced mRNA expression of typical PPAR{alpha} target genes such as Cyp4A10 and FGF21 was damped in PPAR{alpha}-null mice. However, plasma PAI-1 concentrations were significantly more elevated in PPAR{alpha}-null KD mice in accordance with hepatic mRNA levels. These observations suggest that PPAR{alpha} activation is dispensable for KD-induced PAI-1 expression. We also found that hyperlipidemia, fatty liver, and the hepatic expressions of PPAR{gamma} and its coactivator PCG-1{alpha} were more effectively induced in PPAR{alpha}-null, than in WT mice on a KD. Furthermore, KD-induced hepatic PAI-1 expression was significantly suppressed by supplementation with bisphenol A diglycidyl ether, a PPAR{gamma} antagonist, in both WT and PPAR{alpha}-null mice. PPAR{gamma} activation seems to be involved in KD-induced hypofibrinolysis by augmenting PAI-1 gene expression in the fatty liver.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

Versatile function of the circadian protein CIPC as a regulator of Erk activation

The CLOCK-interacting protein, Circadian (CIPC), has been identified as an additional negative-feedback regulator of the circadian clock. However, recent study on CIPC knockout mice has shown that CIPC is not critically required for basic circadian clock function, suggesting other unknown biological roles for CIPC. In this study, we focused on the cell cycle dependent nuclear-cytoplasmic shuttling function of CIPC and on identifying its binding proteins. Lys186 and 187 were identified as the essential amino acid residues within the nuclear localization signal (NLS) of CIPC. We identified CIPC-binding proteins such as the multifunctional enzyme CAD protein (carbamoyl-phosphate synthetase 2, aspartate transcarbamoylase, and dihydroorotase), which is a key enzyme for de novo pyrimidine synthesis. Compared to control cells, HEK293 cells overexpressing wild-type CIPC showed suppressed cell proliferation and retardation of cell cycle. We also found that PMA-induced Erk activation was inhibited with expression of wild-type CIPC. In contrast, the NLS mutant of CIPC, which reduced the ability of CIPC to translocate into the nucleus, did not exhibit these biological effects. Since CAD and Erk have significant roles in cell proliferation and cell cycle, CIPC may work as a cell cycle regulator by interacting with these binding proteins. - Highlights: • CIPC is a cell cycle dependent nuclear-cytoplasmic shuttling protein. • K186 and 187are the essential amino acid residues within the NLS of CIPC. • CAD was identified as a novel CIPC-binding protein. • CIPC might regulate the activity and translocation of CAD in the cells.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

An efficient and portable SIMD algorithm for charge/current deposition in Particle-In-Cell codes

In current computer architectures, data movement (from die to network) is by far the most energy consuming part of an algorithm (≈20pJ/word on-die to ≈10,000 pJ/word on the network). To increase memory locality at the hardware level and reduce energy consumption related to data movement, future exascale computers tend to use many-core processors on each compute nodes that will have a reduced clock speed to allow for efficient cooling. To compensate for frequency decrease, machine vendors are making use of long SIMD instruction registers that are able to process multiple data with one arithmetic operator in one clock cycle. SIMD register length is expected to double every four years. As a consequence, Particle-In-Cell (PIC) codes will have to achieve good vectorization to fully take advantage of these upcoming architectures. In this paper, we present a new algorithm that allows for efficient and portable SIMD vectorization of current/charge deposition routines that are, along with the field gathering routines, among the most time consuming parts of the PIC algorithm. Our new algorithm uses a particular data structure that takes into account memory alignment constraints and avoids gather/scat;ter instructions that can significantly affect vectorization performances on current CPUs. The new algorithm was successfully implemented in the 3D skeleton PIC code PICSAR and tested on Haswell Xeon processors (AVX2-256 bits wide data registers). Results show a factor of ×2 to ×2.5 speed-up in double precision for particle shape factor of orders 1–3. The new algorithm can be applied as is on future KNL (Knights Landing) architectures that will include AVX-512 instruction sets with 512 bits register lengths (8 doubles/16 singles). Program summary Program Title: vec_deposition Program Files doi:http://dx.doi.org/10.17632/nh77fv9k8c.1 Licensing provisions: BSD 3-Clause Programming language: Fortran 90 External routines/libraries: OpenMP > 4.0 Nature of problem: Exascale architectures will have many-core processors per node with long vector data registers capable of performing one single instruction on multiple data during one clock cycle. Data register lengths are expected to double every four years and this pushes for new portable solutions for efficiently vectorizing Particle-In-Cell codes on these future many-core architectures. One of the main hotspot routines of the PIC algorithm is the current/charge deposition for which there is no efficient and portable vector algorithm. Solution method: Here we provide an efficient and portable vector algorithm of current/charge deposition routines that uses a new data structure, which significantly reduces gather/scatter operations. Vectorization is controlled using OpenMP 4.0 compiler directives for vectorization which ensures portability across different architectures. Restrictions: Here we do not provide the full PIC algorithm with an executable but only vector routines for current/charge deposition. These scalar/vector routines can be used as library routines in your 3D Particle-In-Cell code. However, to get the best performances out of vector routines you have to satisfy the two following requirements: (1) Your code should implement particle tiling (as explained in the manuscript) to allow for maximized cache reuse and reduce memory accesses that can hinder vector performances. The routines can be used directly on each particle tile. (2) You should compile your code with a Fortran 90 compiler (e.g Intel, gnu or cray) and provide proper alignment flags and compiler alignment directives (more details in README file).

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2015

Brain and muscle Arnt-like 1 promotes skeletal muscle regeneration through satellite cell expansion

Circadian clock is an evolutionarily conserved timing mechanism governing diverse biological processes and the skeletal muscle possesses intrinsic functional clocks. Interestingly, although the essential clock transcription activator, Brain and muscle Arnt-like 1 (Bmal1), participates in maintenance of muscle mass, little is known regarding its role in muscle growth and repair. In this report, we investigate the in vivo function of Bmal1 in skeletal muscle regeneration using two muscle injury models. Bmal1 is highly up-regulated by cardiotoxin injury, and its genetic ablation significantly impairs regeneration with markedly suppressed new myofiber formation and attenuated myogenic induction. A similarly defective regenerative response is observed in Bmal1-null mice as compared to wild-type controls upon freeze injury. Lack of satellite cell expansion accounts for the regeneration defect, as Bmal1{sup −/−} mice display significantly lower satellite cell number with nearly abolished induction of the satellite cell marker, Pax7. Furthermore, satellite cell-derived primary myoblasts devoid of Bmal1 display reduced growth and proliferation ex vivo. Collectively, our results demonstrate, for the first time, that Bmal1 is an integral component of the pro-myogenic response that is required for muscle repair. This mechanism may underlie its role in preserving adult muscle mass and could be targeted therapeutically to prevent muscle-wasting diseases. - Highlights: • Bmal1 is highly inducible by muscle injury and myogenic stimuli. • Genetic ablation of Bmal1 significantly impairs muscle regeneration. • Bmal1 promotes satellite cell expansion during muscle regeneration. • Bmal1-deficient primary myoblasts display attenuated growth and proliferation.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

Active laser ranging with frequency transfer using frequency comb

A comb-based active laser ranging scheme is proposed for enhanced distance resolution and a common time standard for the entire system. Three frequency combs with different repetition rates are used as light sources at the two ends where the distance is measured. Pulse positions are determined through asynchronous optical sampling and type II second harmonic generation. Results show that the system achieves a maximum residual of 379.6 nm and a standard deviation of 92.9 nm with 2000 averages over 23.6 m. Moreover, as for the frequency transfer, an atom clock and an adjustable signal generator, synchronized to the atom clock, are used as time standards for the two ends to appraise the frequency deviation introduced by the proposed system. The system achieves a residual fractional deviation of 1.3 × 10{sup −16} for 1 s, allowing precise frequency transfer between the two clocks at the two ends.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2016

DCS - A high flux beamline for time resolved dynamic compression science – Design highlights

The Dynamic Compression Sector (DCS) beamline, a national user facility for time resolved dynamic compression science supported by the National Nuclear Security Administration (NNSA) of the Department of Energy (DOE), has recently completed construction and is being commissioned at Sector 35 of the Advanced Photon Source (APS) at Argonne National Laboratory (ANL). The beamline consists of a First Optics Enclosure (FOE) and four experimental enclosures. A Kirkpatrick–Baez focusing mirror system with 2.2 mrad incident angles in the FOE delivers pink beam to the experimental stations. A refocusing Kirkpatrick–Baez mirror system is situated in each of the two most downstream enclosures. Experiments can be conducted in either white, monochromatic, pink or monochromatic-reflected beam mode in any of the experimental stations by changing the position of two interlocked components in the FOE. The beamline Radiation Safety System (RSS) components have been designed to handle the continuous beam provided by two in-line revolver undulators with periods of 27 and 30 mm, at closed gap, 150 mA beam current, and passing through a power limiting aperture of 1.5 x 1.0 mm{sup 2}. A novel pink beam end station stop [1] is used to stop the continuous and focused pink beam which can achieve a peak heat flux of 105 kW/mm{sup 2}. A new millisecond shutter design [2] is used to deliver a quick pulse of beam to the sample, synchronized with the dynamic event, the microsecond shutter, and the storage ring clock.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2019

Path-accelerated stochastic molecular dynamics: Parallel-in-time integration using path integrals

Massively parallel computer architectures create new opportunities for the performance of long-time scale molecular dynamics (MD) simulations. Here, we introduce the path-accelerated molecular dynamics method that takes advantage of distributed computing to reduce the wall-clock time of MD simulation via parallelization with respect to stochastic MD time steps. The marginal distribution for the time evolution of a system is expressed in terms of a path integral, enabling the use of path sampling techniques to numerically integrate MD trajectories. By parallelizing the evaluation of the path action with respect to time and by initializing the path configurations from a nonequilibrium distribution, the algorithm enables significant speedups in terms of the length of MD trajectories that can be integrated in a given amount of wall-clock time. The method is demonstrated for Brownian dynamics, although it is generalizable to other stochastic equations of motion including open systems. We apply the method to two simple systems, a harmonic oscillator and a Lennard-Jones liquid, and we show that in comparison to the conventional Euler integration scheme for Brownian dynamics, the new method can reduce the wall-clock time for integrating trajectories of a given length by more than three orders of magnitude in the former system and more than two in the latter. This new method for parallelizing MD in the dimension of time can be trivially combined with algorithms for parallelizing the MD force evaluation to achieve further speedup.

Rosa-Raíces, Jorge L.↗
DOE OSTI2012

Readout Chip for an L1 Tracking Trigger Using Asynchronous Logic

Adding a silicon based tracker to the level 1 trigger systems for LHC detectors can substantially increase the ability of these systems to find events with patterns of high Pt tracks. This is especially true for high luminosity running where there may be several hundred interactions per crossing. Cooling and mass constraints require that the readout chips have low power and generate little electrical noise. The LHC crossing clock and experiment trigger latency requires that a trigger be able to be made in less than 100 LHC crossings of 25 ns each. One way to minimize power and noise is to use asynchronous logic. We present a readout chip design for both level 1 trigger and event readout that is entirely asynchronous. The only clock used is the LHC crossing clock.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2010

Unimodular loop quantum cosmology

Unimodular gravity is based on a modification of the usual Einstein-Hilbert action that allows one to recover general relativity with a dynamical cosmological constant. It also has the interesting property of providing, as the momentum conjugate to the cosmological constant, an emergent clock variable. In this paper we investigate the cosmological reduction of unimodular gravity, and its quantization within the framework of flat homogeneous and isotropic loop quantum cosmology. It is shown that the unimodular clock can be used to construct the physical state space, and that the fundamental features of the previous models featuring scalar field clocks are reproduced. In particular, the classical singularity is replaced by a quantum bounce, which takes place in the same condition as obtained previously. We also find that requirement of semiclassicality demands the expectation value of the cosmological constant to be small (in Planck units). The relation to spin foam models is also studied, and we show that the use of the unimodular time variable leads to a unique vertex expansion.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗