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At least 973 records · Page 54

Transcriptional burst frequency and burst size are equally modulated across the human genome

Gene expression occurs either as an episodic process, characterized by pulsatile bursts or as a constitutive, Poisson-like accumulation of gene products. It is not clear which mode of gene expression (constitutive versus bursty) predominates across a genome or how transcriptional dynamics are influenced by genomic position and promoter sequence. Here, we use time-lapse fluorescence microscopy, building off of theoretical studies that exploit the time-resolved structure of stochastic fluctuations in gene expression, to develop a three-dimensional method for mapping underlying gene-regulatory mechanisms. Over 8,000 individual human genomic loci were analyzed, and at virtually all loci, episodic bursting as opposed to constitutive expression was found to be the predominant mode of expression. Quantitative analysis of the expression dynamics at these 8,000 loci indicates that both frequency and size of transcriptional bursts vary equally across the human genome independent of promoter sequence. Strikingly, weaker expression loci modulate burst frequency to increase activity, while stronger expression loci modulate burst size to increase activity. Transcriptional activators, such as TNF, generate similar patterns of change in burst frequency and burst size. In summary, transcriptional bursting dominates across the human genome, both burst frequency and burst size vary by chromosomal location, and transcriptional activators alter burst frequency and burst size, depending on the expression level of the locus.

noise biology↗

THE DOUBLE PULSAR ECLIPSES. I. PHENOMENOLOGY AND MULTI-FREQUENCY ANALYSIS

The double pulsar PSR J0737-3039A/B displays short, 30 s eclipses that arise around conjunction when the radio waves emitted by pulsar A are absorbed as they propagate through the magnetosphere of its companion pulsar B. These eclipses offer a unique opportunity to directly probe the magnetospheric structure and the plasma properties of pulsar B. We have performed a comprehensive analysis of the eclipse phenomenology using multi-frequency radio observations obtained with the Green Bank Telescope. We have characterized the periodic flux modulations previously discovered at 820 MHz by McLaughlin et al. and investigated the radio frequency dependence of the duration and depth of the eclipses. Based on their weak radio frequency evolution, we conclude that the plasma in pulsar B's magnetosphere requires a large multiplicity factor ({approx}10{sup 5}). We also found that, as expected, flux modulations are present at all radio frequencies in which eclipses can be detected. Their complex behavior is consistent with the confinement of the absorbing plasma in the dipolar magnetic field of pulsar B as suggested by Lyutikov and Thompson and such a geometric connection explains that the observed periodicity is harmonically related to pulsar B's spin frequency. We observe that the eclipses require a sharp transition region beyond which the plasma density drops off abruptly. Such a region defines a plasmasphere that would be well inside the magnetospheric boundary of an undisturbed pulsar. It is also two times smaller than the expected standoff radius calculated using the balance of the wind pressure from pulsar A and the nominally estimated magnetic pressure of pulsar B.

79 ASTRONOMY AND ASTROPHYSICS↗

GLOBAL AND LOCAL CUTOFF FREQUENCIES FOR TRANSVERSE WAVES PROPAGATING ALONG SOLAR MAGNETIC FLUX TUBES

It is a well-established result that the propagation of linear transverse waves along a thin but isothermal magnetic flux tube is affected by the existence of the global cutoff frequency, which separates the propagating and non-propagating waves. In this paper, the wave propagation along a thin and non-isothermal flux tube is considered and a local cutoff frequency is derived. The effects of different temperature profiles on this local cutoff frequency are studied by considering different power-law temperature distributions, as well as the semi-empirical VAL C model of the solar atmosphere. The obtained results show that the conditions for wave propagation strongly depend on the temperature gradients. Moreover, the local cutoff frequency calculated for the VAL C model gives constraints on the range of wave frequencies that are propagating in different parts of the solar atmosphere. These theoretically predicted constraints are compared to observational data and are used to discuss the role played by transverse tube waves in the atmospheric heating and dynamics, and in the excitation of solar atmospheric oscillations.

79 ASTRONOMY AND ASTROPHYSICS↗

The density and mass of unshocked ejecta in Cassiopeia a through low frequency radio absorption

Characterizing the ejecta in young supernova remnants is a requisite step toward a better understanding of stellar evolution. In Cassiopeia A the density and total mass remaining in the unshocked ejecta are important parameters for modeling its explosion and subsequent evolution. Low frequency (<100 MHz) radio observations of sufficient angular resolution offer a unique probe of unshocked ejecta revealed via free-free absorption against the synchrotron emitting shell. We have used the Very Large Array plus Pie Town Link extension to probe this cool, ionized absorber at 9'' and 18.''5 resolution at 74 MHz. Together with higher frequency data we estimate an electron density of 4.2 cm{sup –3} and a total mass of 0.39 M {sub ☉} with uncertainties of a factor of ∼2. This is a significant improvement over the 100 cm{sup –3} upper limit offered by infrared [S III] line ratios from the Spitzer Space Telescope. Our estimates are sensitive to a number of factors including temperature and geometry. However using reasonable values for each, our unshocked mass estimate agrees with predictions from dynamical models. We also consider the presence, or absence, of cold iron- and carbon-rich ejecta and how these affect our calculations. Finally we reconcile the intrinsic absorption from unshocked ejecta with the turnover in Cas A's integrated spectrum documented decades ago at much lower frequencies. These and other recent observations below 100 MHz confirm that spatially resolved thermal absorption, when extended to lower frequencies and higher resolution, will offer a powerful new tool for low frequency astrophysics.

79 ASTRONOMY AND ASTROPHYSICS↗

Application of simulations and theory of sub-cyclotron frequency modes to DIII-D

Theoretical and numerical study of Alfvén eigenmodes (AEs) in the sub-cyclotron frequency range explains the observed frequency scaling with beam parameters in experiments across different devices. Global Alfvén (GAEs) and compressional Alfvén eigenmodes (CAEs) are frequently excited during neutral beam injection (NBI) in the National Spherical Torus Experiment (NSTX/NSTX-U), as well as other beam-heated devices such as MAST and DIII-D. These modes are driven unstable through the Doppler shifted cyclotron resonance with the NBI ions and can be excited in ITER due to super-Alfvénic velocities and anisotropy of the fast ion distribution. Numerical models and theory for sub-cyclotron frequency modes, previously developed and used to study the excitation of GAEs/CAEs in the NSTX(-U), have been successfully applied to explain the DIII-D observations. Simulations for DIII-D demonstrate that the modes with ω/ω ci ≈ 0.6, previously mis-identified as compressional Alfvén eigenmodes, have shear polarization and should be identified as the GAEs. Simulation results match the observed frequencies and estimated toroidal mode numbers in DIII-D experiments. Good agreement is found between scaling of the experimentally observed GAE frequencies with NBI parameters for NSTX, NSTX-U and DIII-D and scaling predicted by the theory and simulations. Here, the DIII-D simulation results also demonstrate that GAEs can be excited for larger aspect-ratio devices and smaller (sub- Alfvénic) beam injection velocities, therefore they can be unstable in ITER.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Dependence of ion-cyclotron range of frequencies instabilities on species mix and fast-ion distribution: I. Stability

Ion cyclotron emission (ICE) driven by fast ions has the potential to be a reactor relevant diagnostic of confined and escaping fast ions; moreover, controlled experiments in magnetic fusion devices can shed light on similar magnetospheric instabilities below and above the ion cyclotron frequency f ci . Dedicated DIII-D experiments studied instabilities below f ci and at cyclotron harmonics l f ci by injecting thirteen different neutral beam populations into plasmas with different thermal compositions of H, D, and 3He at five different values of toroidal field. High-frequency magnetic loops diagnose mode properties. Each beam type is individually injected for an approximate slowing-down time (~100 ms), resulting in a database of 2529 conditions that are analyzed in frequency bands corresponding to ICE harmonics and < f ci global Alfvén eigenmodes. The sub-cyclotron modes are more unstable at low field and in plasmas with large H concentration. For D injection, first harmonic ICE at f cD is more unstable in hydrogen plasmas but, for H injection, the converse is true (ICE at f cH is more unstable in D), suggesting that thermal same-species ions damp fundamental ICE. ICE stability also depends upon the pitch-angle anisotropy gradient and upon the ‘bump-on-tail’ gradient ∂f/∂v. Although the frequency of unstable ICE in these plasmas always occurs near the central cyclotron frequency, the precise value also depends on the Alfvén speed and beam direction, consistent with the idea that instability occurs for modes that simultaneously satisfy ω ≃ 2πlf ci , the magnetosonic dispersion relation, and the Doppler-shifted resonance condition.

electromagnetic ion cyclotron instabilities↗

Frequency multiplication with toroidal mode number of kink/fishbone modes on a static HL-2A-like tokamak

In the presence of energetic particles (EPs), the long-lived mode (LLM) frequency multiplication with n = 1, 2, 3, or higher is often observed on HL-2A, where n is the toroidal mode number. Hybrid kinetic-MHD model simulations of the energetic particle (EP) driven kink/fishbone modes on a static HL-2A-like tokamak using NIMROD code find that when the background plasma pressure is relatively high, and the EP pressure and the beam energy are relatively low, the mode frequency increases almost linearly with EP pressure, and the frequency is proportional to n (‘frequency multiplication’), even in the absence of any equilibrium plasma rotation. In addition, the frequency multiplication persists as the safety factor at the magnetic axis q 0 varies. In the absence of EPs, the growth rate of the 1/1 mode is the largest; however, as the EP pressure increases, the growth rate of 2/2 modes or 3/3 modes becomes dominant, suggesting that higher-n modes are more vulnerable to EPs. These results may shed light on the understanding of the toroidal mode number dependence of kink/fishbone modes in the advanced scenarios of tokamaks with weak or reversed central magnetic shear.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Frequency domain analysis of errors in cross-correlations of ambient seismic noise

We analyse random errors (variances) in cross-correlations of ambient seismic noise in the frequency domain, which differ from previous time domain methods. Extending previous theoretical results on ensemble averaged cross-spectrum, we estimate confidence interval of stacked cross-spectrum of finite amount of data at each frequency using non-overlapping windows with fixed length. The extended theory also connects amplitude and phase variances with the variance of each complex spectrum value. Analysis of synthetic stationary ambient noise is used to estimate the confidence interval of stacked cross-spectrum obtained with different length of noise data corresponding to different number of evenly spaced windows of the same duration. This method allows estimating Signal/Noise Ratio (SNR) of noise cross-correlation in the frequency domain, without specifying filter bandwidth or signal/noise windows that are needed for time domain SNR estimations. Based on synthetic ambient noise data, we also compare the probability distributions, causal part amplitude and SNR of stacked cross-spectrum function using one-bit normalization or pre-whitening with those obtained without these pre-processing steps. Natural continuous noise records contain both ambient noise and small earthquakes that are inseparable from the noise with the existing pre-processing steps. Using probability distributions of random cross-spectrum values based on the theoretical results provides an effective way to exclude such small earthquakes, and additional data segments (outliers) contaminated by signals of different statistics (e.g. rain, cultural noise), from continuous noise waveforms. This technique is applied to constrain values and uncertainties of amplitude and phase velocity of stacked noise cross-spectrum at different frequencies, using data from southern California at both regional scale (~35 km) and dense linear array (~20 m) across the plate-boundary faults. A block bootstrap resampling method is used to account for temporal correlation of noise cross-spectrum at low frequencies (0.05–0.2 Hz) near the ocean microseismic peaks.

58 GEOSCIENCES↗

Discovery of multiple p-mode pulsation frequencies in the roAp star, HD 86181

ABSTRACT We report the frequency analysis of a known roAp star, HD 86181 (TIC 469246567), with new inferences from Transiting Exoplanet Survey Satellite (TESS) data. We derive the rotation frequency to be νrot = 0.48753 ± 0.00001 d−1. The pulsation frequency spectrum is rich, consisting of two doublets and one quintuplet, which we interpret to be oblique pulsation multiplets from consecutive, high-overtone dipole, quadrupole, and dipole modes. The central frequency of the quintuplet is 232.7701 d−1 (2.694 mHz). The phases of the sidelobes, the pulsation phase modulation, and a spherical harmonic decomposition all show that the quadrupole mode is distorted. Following the oblique pulsator model, we calculate the rotation inclination, i, and magnetic obliquity, β, of this star, which provide detailed information about the pulsation geometry. The i and β derived from the best fit of the pulsation amplitude and phase modulation to a theoretical model, including the magnetic field effect, slightly differ from those calculated for a pure quadrupole, indicating the contributions from ℓ = 4, 6, 8,... are small. Non-adiabatic models with different envelope convection conditions and physics configurations were considered for this star. It is shown that models with envelope convection almost fully suppressed can explain the excitation at the observed pulsation frequencies.

Shi, Fangfei (ORCID:0000000323998216)↗

Photon Frequency Conversion in High-Q Superconducting Resonators: Axion Electrodynamics, QED, and Nonlinear Meissner Radiation

High-Q superconducting resonators have been proposed and developed as detectors of light-by-light scattering mediated by the hypothesized axion or virtual electron–positron pairs in quantum electrodynamics: the Euler–Heisenberg (EH) interaction. Photon frequency and mode conversion is central to the scheme for detecting such rare events. Superconducting resonators are nonlinear devices. The Meissner screening currents that confine the electromagnetic fields to the vacuum region of a superconducting RF cavity are nonlinear functions of the EM field at the vacuum–superconducting interface, and as a result can generate source currents and frequency conversion of microwave photons in the cavity. In this report we consider photon frequency and mode conversion in superconducting resonators with high quality factors from Meissner currents in single- and dual-cavity setups proposed for axion and QED searches based on light-by-light scattering. In a single cavity with two pump modes, photon frequency conversion by the Meissner screening current dominates photon generation by the EH interaction for cavities with Q≲1012⁠. The Meissner currents also generate background photons that limit the operation of the resonator for axion detection in three-mode, single-cavity setups. We also consider the leakage of photons from pump modes into the signal mode for both axion- and EH-mediated light-by-light scattering. Photon frequency conversion by the EH interaction can compete with Meissner and leakage radiation in ultra-high-Q cavities that are beyond the current state of the art. Meissner radiation and leakage backgrounds can be suppressed in dual-cavity setups with appropriate choices for pump and spectator modes, as well as the single-cavity setup proposed for heterodyne detection of galactic axion dark matter.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Quantitative evaluation of an air-monitoring network using atmospheric transport modeling and frequency of detection methods

A methodology to quantify the performance of an air monitoring network in terms of frequency of detection has been developed. The methodology utilizes an atmospheric transport model to predict air concentrations of radionuclides at the samplers for a given release time and duration. Frequency of detection is defined as the fraction of “events” that result in a detection at either a single sampler or network of samplers. An “event” is defined as a release of finite duration that begins on a given day and hour of the year from a facility with the potential to emit airborne radionuclides. Another metric of interest is the network intensity, which is defined as the fraction of samplers in the network that have a positive detection for a given event. The frequency of detection methodology allows for evaluation of short-term releases that include effects of short-term variability in meteorological conditions. The methodology was tested using the U.S. Department of Energy Idaho National Laboratory (INL) Site ambient air monitoring network consisting of 37 low-volume air samplers in 31 different locations covering a 17,630 km 2 region. Releases from six major INL facilities distributed over an area of 1,435 km 2 were modeled and included three stack sources and eight ground-level sources. A Lagrangian Puff air dispersion model (CALPUFF) was used to model atmospheric transport. The model was validated using historical 125 Sb releases and measurements. Relevant one-week release quantities from each emission source were calculated based on a dose of 1.9 × 10 –4 mSv at a public receptor (0.01 mSv assuming release persists over a year). Important radionuclides considered include 241 Am, 137 Cs, 238 Pu, 239 Pu, 90 Sr, and tritium. Results show the detection frequency is over 97.5% for the entire network considering all sources and radionuclides. Network intensities ranged from 3.75% to 62.7%. Evaluation of individual samplers indicated some samplers were poorly situated and add little to the overall effectiveness of the network. As a result, using the frequency of detection methods, optimum sampler placements were simulated that could substantially improve the performance and efficiency of the network.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Non-Gaussian photonic state engineering with the quantum frequency processor

Non-Gaussian quantum states of light are critical resources for optical quantum information processing, but methods to generate them efficiently remain challenging to implement. Here we introduce a generic approach for non-Gaussian state production from input states populating discrete frequency bins. Based on controllable unitary operations with a quantum frequency processor, followed by photon-number-resolved detection of ancilla modes, our method combines recent developments in both frequency-based quantum information and non-Gaussian state preparation. Leveraging and refining the K-function representation of quantum states in the coherent basis, we develop a theoretical model amenable to numerical optimization and, as specific examples, design quantum frequency processor circuits for the production of Schrödinger cat states, exploring the performance tradeoffs for several combinations of ancilla modes and circuit depth. Our scheme provides a valuable framework for producing complex quantum states in frequency bins, paving the way for single-spatial-mode, fiber-optic-compatible non-Gaussian resources.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Spin waves and high-frequency response in layered superconductors with helical magnetic structure

Here, we evaluate the spin-wave spectrum and dynamic susceptibility in a layered superconductor with helical interlayer magnetic structure. We especially focus on the structure in which the moments rotate 90 degrees from layer to layer realized in the iron pnictide RbEuFe 4 As 4 . While in nonmagnetic superconductors low-frequency magnetic field decays on the distance of the order of the London penetration depth, spin waves mediate its propagation to much larger distances limited by external dissipation mechanisms. The spin-wave spectrum in superconductors is strongly renormalized due to the long-range electromagnetic interactions between the oscillating magnetic moments. This leads to strong enhancement of the frequency of the mode coupled with uniform field and this enhancement exists only within a narrow range of the c-axis wave vectors of the order of the inverse London penetration depth. The key feature of materials like RbEuFe 4 As 4 is that this uniform mode corresponds to the maximum frequency of the spin-wave spectrum with respect to the c-axis wave vector. As a consequence, the high-frequency surface resistance acquires a very distinct asymmetric feature spreading between the bare and renormalized frequencies. Finally, we also consider excitation of spin waves with the Josephson effect in a tunneling contact between helical-magnetic and conventional superconductors and study the interplay between the spin-wave features and geometrical cavity resonances in the current-voltage characteristics.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Frequency dispersion of nonlinear response of thin superconducting films in the Berezinskii-Kosterlitz-Thouless state

The effects of microwave radiation on transport properties of atomically thin La 2-x Sr x CuO₄ films were studied in the 0.1-20 GHz frequency range. Resistance changes induced by microwaves were investigated at different temperatures (8–15 K) near the superconducting transition. A strong decrease of the nonlinear response is observed within a few GHz of a cutoff frequency ν cut ≈ 2GHz. The expected frequency dependence vastly underestimates the sharpness of this drop. Numerical simulations that assume ac response to follow dc V-I characteristics of the films reproduce well the low frequency behavior, but fail above ν cut . Thus, high-frequency radiation is much less effective in inducing vortex-antivortex dissociation in the oscillating superconducting condensate.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Frequency-dependent dielectric function of semiconductors with application to physisorption

Furthermore, the dielectric function is one of the most important quantities that describes the electrical and optical properties of solids. Accurate modeling of the frequency-dependent dielectric function has great significance in the study of the long-range van der Waals (vdW) interaction for solids and adsorption. In this work we calculate the frequency-dependent dielectric functions of semiconductors and insulators using the GW method with and without exciton effects, as well as efficient semilocal density functional theory (DFT), and compare these calculations with a model frequency-dependent dielectric function. We find that for semiconductors with moderate band gaps, the model dielectric functions, GW values, and DFT calculations all agree well with each other. However, for insulators with strong exciton effects, the model dielectric functions have a better agreement with accurate GW values than the DFT calculations, particularly in high-frequency region. To understand this, we repeat the DFT calculations with scissors correction, by shifting the DFT Kohn-Sham energy levels to match the experimental band gap. We find that scissors correction only moderately improves the DFT dielectric function in the low-frequency region. Based on the dielectric functions calculated with different methods, we make a comparative study by applying these dielectric functions to calculate the vdW coefficients (C3 and C5) for adsorption of rare-gas atoms on a variety of surfaces. We find that the vdW coefficients obtained with the nearly free electron gas-based model dielectric function agree quite well with those obtained from the GW dielectric function, in particular for adsorption on semiconductors, leading to an overall error of less than 7% for C 3 and 5% for C 5 . This demonstrates the reliability of the model dielectric function for the study of physisorption.

36 MATERIALS SCIENCE↗

Searching for high-frequency gravitational waves with phonons

The gravitational wave (GW) spectrum at frequencies above a kHz is a largely unexplored frontier. We show that detectors with sensitivity to single-phonon excitations in crystal targets can search for GWs with frequencies, 1 THz ≲ f ≲ 100 THz , corresponding to the range of optical phonon energies, 1 meV ≲ ω ≲ 100 meV . Such detectors are already being built to search for light dark matter (DM), and therefore sensitivity to high-frequency GWs will be achieved as a byproduct. We begin by deriving the absorption rate of a general GW signal into single phonons. We then focus on carefully defining the detector sensitivity to monochromatic and chirp signals, and compute the detector sensitivity for many proposed light DM detection targets. The detector sensitivity is then compared to the signal strength of candidate high-frequency GW sources, e.g., superradiant annihilation and black hole inspiral, as well as other recent detector proposals in the 1 MHz ≲ f ≲ 100 THz frequency range. With a judicious choice of target materials, a collection of detectors could optimistically achieve sensitivities to monochromatic signals with h 0 ∼ 10 − 23 − 10 − 25 over 1 THz ≲ f ≲ 100 THz . Published by the American Physical Society 2024

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Electro-Optic Frequency Beam Splitters and Tritters for High-Fidelity Photonic Quantum Information Processing

In this paper, we report the experimental realization of high-fidelity photonic quantum gates for frequency-encoded qubits and qutrits based on electro-optic modulation and Fourier-transform pulse shaping. Our frequency version of the Hadamard gate offers near-unity fidelity (0.99998±0.00003), requires only a single microwave drive tone for near-ideal performance, functions across the entire C band (1530–1570 nm), and can operate concurrently on multiple qubits spaced as tightly as four frequency modes apart, with no observable degradation in the fidelity. For qutrits, we implement a 3×3 extension of the Hadamard gate: the balanced tritter. This tritter—the first ever demonstrated for frequency modes—attains fidelity 0.9989±0.0004. Finally, these gates represent important building blocks toward scalable, high-fidelity quantum information processing based on frequency encoding.

36 MATERIALS SCIENCE↗

Measurement of Zero-Frequency Fluctuations Generated by Coupling between Alfvén Modes in the JET Tokamak

We report the first experimental detection of a zero-frequency fluctuation that is pumped by an Alfvén mode in a magnetically confined plasma. Core-localized Alfvén modes of frequency inside the toroidicity-induced gap (and its harmonics) exhibit three-wave coupling interactions with a zero-frequency fluctuation. The observation of the zero-frequency fluctuation is consistent with theoretical and numerical predictions of zonal modes pumped by Alfvén modes, and is correlated with an increase in the deep core ion temperature, temperature gradient, confinement factor H 89,P , and a reduction in the main ion heat diffusivity. Despite the energetic particle transport induced by the Alfvén eigenmodes, the generation of a zero-frequency fluctuation that can suppress the turbulence leads to an overall improvement of confinement.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗