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At least 901 records · Page 50
All sourcesNASA NTRSDOE OSTI
DOE OSTI2012

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↗
DOE OSTI2015

Stock-Specific Size and Timing at Ocean Entry of Columbia River Juvenile Chinook Salmon and Steelhead: Implications for Early Ocean Growth

Abstract Juvenile salmon transitioning from freshwater to marine environments experience high variation in growth and survival, yet the specific causes of this variation are poorly understood. Size at and timing of ocean entry may contribute to this variation because they influence both the availability of prey and vulnerability to predators. To explore this issue, we used stock assignments based on genetic stock identification and internal tags to document the stock-specific size and timing of juvenile hatchery and presumed wild Columbia River Chinook Salmon Oncorhynchus tshawytscha and steelhead O. mykiss at ocean entry during 2007–2011. We found that juvenile salmon and steelhead had consistent stock-specific capture dates, with lower-river stocks typically having earlier timing than those originating farther upstream. Mean size also varied among stocks and was related to hatchery practices. Hatchery yearling Chinook Salmon and steelhead were consistently larger than wild fish from the same stocks, although timing in the estuary was similar. In contrast, hatchery subyearling Chinook Salmon were of similar size to wild fish but entered the ocean up to a month earlier. We evaluated the potential importance of these traits on early marine growth by estimating stock-specific growth rates for Chinook Salmon caught in estuarine and ocean habitats. Growth rates were related to relative ocean entry timing, with lower growth rates for stocks that had only recently arrived in marine waters. Our results demonstrate that stocks within a single basin can differ in their size and timing of ocean entry, life history traits that contribute to early marine growth and potentially to the survival of juvenile salmon. Our results also highlight the necessity of considering stock-specific variation in life history traits to understand salmon ecology and survival across the entire life cycle. Received January 16, 2015; accepted April 28, 2015

Weitkamp, Laurie A.↗
DOE OSTI2012

COAGULATION CALCULATIONS OF ICY PLANET FORMATION AT 15-150 AU: A CORRELATION BETWEEN THE MAXIMUM RADIUS AND THE SLOPE OF THE SIZE DISTRIBUTION FOR TRANS-NEPTUNIAN OBJECTS

We investigate whether coagulation models of planet formation can explain the observed size distributions of trans-Neptunian objects (TNOs). Analyzing published and new calculations, we demonstrate robust relations between the size of the largest object and the slope of the size distribution for sizes 0.1 km and larger. These relations yield clear, testable predictions for TNOs and other icy objects throughout the solar system. Applying our results to existing observations, we show that a broad range of initial disk masses, planetesimal sizes, and fragmentation parameters can explain the data. Adding dynamical constraints on the initial semimajor axis of 'hot' Kuiper Belt objects along with probable TNO formation times of 10-700 Myr restricts the viable models to those with a massive disk composed of relatively small (1-10 km) planetesimals.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2012

THE COSMOLOGICAL SIZE AND VELOCITY DISPERSION EVOLUTION OF MASSIVE EARLY-TYPE GALAXIES

We analyze 40 cosmological re-simulations of individual massive galaxies with present-day stellar masses of M{sub *} > 6.3 Multiplication-Sign 10{sup 10} M{sub Sun} in order to investigate the physical origin of the observed strong increase in galaxy sizes and the decrease of the stellar velocity dispersions since redshift z Almost-Equal-To 2. At present 25 out of 40 galaxies are quiescent with structural parameters (sizes and velocity dispersions) in agreement with local early-type galaxies. At z = 2 all simulated galaxies with M{sub *} {approx}> 10{sup 11} M{sub Sun} (11 out of 40) at z = 2 are compact with projected half-mass radii of Almost-Equal-To 0.77 ({+-}0.24) kpc and line-of-sight velocity dispersions within the projected half-mass radius of Almost-Equal-To 262 ({+-}28) km s{sup -1} (3 out of 11 are already quiescent). Similar to observed compact early-type galaxies at high redshift, the simulated galaxies are clearly offset from the local mass-size and mass-velocity dispersion relations. Toward redshift zero the sizes increase by a factor of {approx}5-6, following R{sub 1/2}{proportional_to}(1 + z){sup {alpha}} with {alpha} = -1.44 for quiescent galaxies ({alpha} = -1.12 for all galaxies). The velocity dispersions drop by about one-third since z Almost-Equal-To 2, following {sigma}{sub 1/2}{proportional_to}(1 + z){sup {beta}} with {beta} = 0.44 for the quiescent galaxies ({beta} = 0.37 for all galaxies). The simulated size and dispersion evolution is in good agreement with observations and results from the subsequent accretion and merging of stellar systems at z {approx}< 2, which is a natural consequence of the hierarchical structure formation. A significant number of the simulated massive galaxies (7 out of 40) experience no merger more massive than 1:4 (usually considered as major mergers). On average, the dominant accretion mode is stellar minor mergers with a mass-weighted mass ratio of 1:5. We therefore conclude that the evolution of massive early-type galaxies since z Almost-Equal-To 2 and their present-day properties are predominantly determined by frequent 'minor' mergers of moderate mass ratios and not by major mergers alone.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2012

NUMERICAL SIMULATIONS OF CHROMOSPHERIC HARD X-RAY SOURCE SIZES IN SOLAR FLARES

X-ray observations are a powerful diagnostic tool for transport, acceleration, and heating of electrons in solar flares. Height and size measurements of X-ray footpoint sources can be used to determine the chromospheric density and constrain the parameters of magnetic field convergence and electron pitch-angle evolution. We investigate the influence of the chromospheric density, magnetic mirroring, and collisional pitch-angle scattering on the size of X-ray sources. The time-independent Fokker-Planck equation for electron transport is solved numerically and analytically to find the electron distribution as a function of height above the photosphere. From this distribution, the expected X-ray flux as a function of height, its peak height, and full width at half-maximum are calculated and compared with RHESSI observations. A purely instrumental explanation for the observed source size was ruled out by using simulated RHESSI images. We find that magnetic mirroring and collisional pitch-angle scattering tend to change the electron flux such that electrons are stopped higher in the atmosphere compared with the simple case with collisional energy loss only. However, the resulting X-ray flux is dominated by the density structure in the chromosphere and only marginal increases in source width are found. Very high loop densities (>10{sup 11} cm{sup -3}) could explain the observed sizes at higher energies, but are unrealistic and would result in no footpoint emission below about 40 keV, contrary to observations. We conclude that within a monolithic density model the vertical sizes are given mostly by the density scale height and are predicted smaller than the RHESSI results show.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2013

ON THE RELATIVE SIZES OF PLANETS WITHIN KEPLER MULTIPLE-CANDIDATE SYSTEMS

We present a study of the relative sizes of planets within the multiple-candidate systems discovered with the Kepler mission. We have compared the size of each planet to the size of every other planet within a given planetary system after correcting the sample for detection and geometric biases. We find that for planet pairs for which one or both objects are approximately Neptune-sized or larger, the larger planet is most often the planet with the longer period. No such size-location correlation is seen for pairs of planets when both planets are smaller than Neptune. Specifically, if at least one planet in a planet pair has a radius of {approx}> 3 R {sub Circled-Plus }, 68% {+-} 6% of the planet pairs have the inner planet smaller than the outer planet, while no preferred sequential ordering of the planets is observed if both planets in a pair are smaller than {approx}< 3 R {sub Circled-Plus }.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2013

UNIFICATION SCHEME OF RADIO GALAXIES AND QUASARS FALSIFIED BY THEIR OBSERVED SIZE DISTRIBUTIONS

In the currently popular orientation-based unified scheme, a radio galaxy appears as a quasar when its principal radio-axis happens to be oriented within a certain cone opening angle around the observer's line of sight. Due to geometrical projection, the observed sizes of quasars should therefore appear smaller than those of radio galaxies. We show that this simple, unambiguous prediction of the unified scheme is not borne out by the actually observed angular sizes of radio galaxies and quasars. Except in the original 3CR sample, based on which the unified scheme was proposed, in other much larger samples no statistically significant difference is apparent in the size distributions of radio galaxies and quasars. The population of low-excitation radio galaxies with apparently no hidden quasars inside, which might explain the observed excess number of radio galaxies at low redshifts, cannot account for the absence of any foreshortening of the sizes of quasars at large redshifts. On the other hand, from infrared and X-ray studies, there is evidence of a hidden quasar within a dusty torus in many radio galaxies, at z > 0.5. It is difficult to reconcile this with the absence of foreshortening of quasar sizes at even these redshifts, and perhaps one has to allow that the major radio axis may not have anything to do with the optical axis of the torus. Otherwise, to resolve the dichotomy of radio galaxies and quasars, a scheme quite different from the present might be required.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2014

Velocity dispersions and dynamical masses for a large sample of quiescent galaxies at z >1: Improved measures of the growth in mass and size

We present Keck LRIS spectroscopy for a sample of 103 massive (M > 10{sup 10.6} M {sub ☉}) galaxies with redshifts 0.9 < z < 1.6. Of these, 56 are quiescent with high signal-to-noise absorption line spectra, enabling us to determine robust stellar velocity dispersions for the largest sample yet available beyond a redshift of 1. Together with effective radii measured from deep Hubble Space Telescope images, we calculate dynamical masses and address key questions relating to the puzzling size growth claimed by many observers for quiescent galaxies over the redshift interval 0 < z < 2. Our large sample provides the first opportunity to carefully examine the relationship between stellar and dynamical masses at high redshift. We find this relation closely follows that determined locally. We also confirm the utility of the locally established empirical calibration which enables high-redshift velocity dispersions to be estimated photometrically, and we determine its accuracy to be 35%. To address recent suggestions that progenitor bias—the continued arrival of recently quenched larger galaxies—can largely explain the size evolution of quiescent galaxies, we examine the growth at fixed velocity dispersion assuming this quantity is largely unaffected by the merger history. Using the velocity dispersion-age relation observed in the local universe, we demonstrate that significant size and mass growth have clearly occurred in individual systems. Parameterizing the relation between mass and size growth over 0 < z < 1.6 as R∝M {sup α}, we find α = 1.6 ± 0.3, in agreement with theoretical expectations from simulations of minor mergers. Relaxing the assumption that the velocity dispersion is unchanging, we examine growth assuming a constant ranking in galaxy velocity dispersion. This approach is applicable only to the large-dispersion tail of the distribution, but yields a consistent growth rate of α = 1.4 ± 0.2. Both methods confirm that progenitor bias alone is insufficient to explain our new observations and that quiescent galaxies have grown in both size and stellar mass over 0 < z < 1.6.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2014

How robust are the size measurements of high-redshift compact galaxies?

Massive quiescent galaxies at z ≈ 2 are apparently much more compact than galaxies of comparable mass today. How robust are these size measurements? We perform comprehensive simulations to determine possible biases and uncertainties in fitting single-component light distributions to real galaxies. In particular, we examine the robustness of the measurements of the luminosity, size, and other structural parameters. We devise simulations with increasing realism to systematically disentangle effects due to the technique (specifically using GALFIT) and the intrinsic structures of the galaxies. By accurately capturing the detailed substructures of nearby elliptical galaxies and then rescaling their sizes and signal-to-noise to mimic galaxies at different redshifts, we confirm that the massive quiescent galaxies at z ≈ 2 are significantly more compact intrinsically than their local counterparts. Their observed compactness is not a result of missing faint outer light due to systematic errors in modeling. In fact, we find that fitting multi-component galaxies with a single Sérsic profile, the procedure most commonly adopted in the literature, biases the inferred sizes higher by up to 10%-20%, which accentuates the amount of size evolution required. If the sky estimation has been done robustly and the model for the point-spread function is fairly accurate, GALFIT can retrieve the properties of single-component galaxies over a wide range of signal-to-noise ratios without introducing any systematic errors.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2015

Probing the dark matter radial profile in lens galaxies and the size of X-ray emitting region in quasars with microlensing

We use X-ray and optical microlensing measurements to study the shape of the dark matter density profile in the lens galaxies and the size of the (soft) X-ray emission region. We show that single epoch X-ray microlensing is sensitive to the source size. Our results, in good agreement with previous estimates, show that the size of the X-ray emission region scales roughly linearly with the black hole mass, with a half-light radius of R{sub 1/2}≃(24±14)r{sub g} where r{sub g}=GM{sub BH}/c{sup 2}. This corresponds to a size of log(R{sub 1/2}/cm)=15.6{sub −0.3}{sup +0.3} or ∼1 lt-day for a black hole mass of M{sub BH}=10{sup 9} M{sub ⊙}. We simultaneously estimated the fraction of the local surface mass density in stars, finding that the stellar mass fraction is α = 0.20 ± 0.05 at an average radius of ∼1.9R{sub e}, where R{sub e} is the effective radius of the lens. This stellar mass fraction is insensitive to the X-ray source size and in excellent agreement with our earlier results based on optical data. By combining X-ray and optical microlensing data, we can divide this larger sample into two radial bins. We find that the surface mass density in the form of stars is α = 0.31 ± 0.15 and α = 0.13 ± 0.05 at (1.3±0.3)R{sub e} and (2.3±0.3)R{sub e}, respectively, in good agreement with expectations and some previous results.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2020

Heavy flavor dynamics across system size at the LHC

One of the fundamental signatures of the Quark Gluon Plasma has been the suppression of heavy flavor (specifically D mesons), which has been measured via the nuclear modification factor, R AA and azimuthal anisotropies, v n , in large systems. However, multiple competing models can reproduce the same data for R AA to v n . In this talk we break down the competing effects that conspire together to successfully reproduce R AA and v n in experimental data using Trento+v-USPhydro+DAB-MOD. Then using our best fit model we make predictions for R AA and v n across system size for 208 PbPb, 129 XeXe, 40 ArAr, and 16 OO collisions. We find that 0–10% centrality has a non-trivial interplay between the system size and eccentricities such that system size effects are masked in v 2 whereas in 30–50% centrality the eccentricities are approximately constant across system size and, therefore, is a better centrality class to study D meson dynamics across system size.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2022

Accretion disc sizes from continuum reverberation mapping of AGN selected from the ZTF survey

ABSTRACT We present the accretion disc-size estimates for a sample of 19 active galactic nuclei (AGNs) using the optical g-, r-, and i-band light curves obtained from the Zwicky Transient Facility survey. All the AGNs have reliable supermassive black hole (SMBH) mass estimates based on previous reverberation mapping measurements. The multiband light curves are cross-correlated, and the reverberation lag is estimated using the Interpolated Cross-Correlation Function method and the Bayesian method using the javelin code. As expected from the disc-reprocessing arguments, the g − r band lags are shorter than the g − i band lags for this sample. The interband lags for all, but five sources, are larger than the sizes predicted from the standard Shakura Sunyaev (SS) analytical model. We fit the light curves directly using a thin disc model implemented through the javelin code to get the accretion disc sizes. The disc sizes obtained using this model are on an average 3.9 times larger than the prediction based on the SS disc model. We find a weak correlation between the disc sizes and the known physical parameters, namely the luminosity and the SMBH mass. In the near future, a large sample of AGNs covering broader ranges of luminosity and SMBH mass from large photometric surveys would be helpful in a better understanding of the structure and physics of the accretion disc.

Jha, Vivek Kumar (ORCID:0000000232776335)↗
DOE OSTI2010

Equilibrium and off-equilibrium trap-size scaling in one-dimensional ultracold bosonic gases

We study some aspects of equilibrium and off-equilibrium quantum dynamics of dilute bosonic gases in the presence of a trapping potential. We consider systems with a fixed number of particles and study their scaling behavior with increasing the trap size. We focus on one-dimensional bosonic systems, such as gases described by the Lieb-Liniger model and its Tonks-Girardeau limit of impenetrable bosons, and gases constrained in optical lattices as described by the Bose-Hubbard model. We study their quantum (zero-temperature) behavior at equilibrium and off equilibrium during the unitary time evolution arising from changes of the trapping potential, which may be instantaneous or described by a power-law time dependence, starting from the equilibrium ground state for an initial trap size. Renormalization-group scaling arguments and analytical and numerical calculations show that the trap-size dependence of the equilibrium and off-equilibrium dynamics can be cast in the form of a trap-size scaling in the low-density regime, characterized by universal power laws of the trap size, in dilute gases with repulsive contact interactions and lattice systems described by the Bose-Hubbard model. The scaling functions corresponding to several physically interesting observables are computed. Our results are of experimental relevance for systems of cold atomic gases trapped by tunable confining potentials.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2011

Finite-size and particle-number effects in an ultracold Fermi gas at unitarity

We investigate an ultracold Fermi gas at unitarity confined in a periodic box V=L{sup 3} using renormalization group techniques. Within this approach we can quantitatively assess the long-range bosonic order parameter fluctuations, which dominate finite-size effects. We determine the finite-size and particle-number dependence of universal quantities, such as the Bertsch parameter and the fermion gap. Moreover, we analyze how these universal observables respond to the variation of an external pairing source. Our results indicate that the Bertsch parameter saturates rather quickly to its value in the thermodynamic limit as a function of increasing box size. On the other hand, we observe that the fermion gap shows a significantly stronger dependence on the box size, in particular for small values of the pairing source. Our results may contribute to a better understanding of finite-size and particle-number effects present in Monte Carlo simulations of ultracold Fermi gases.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2015

Grain-Size-Independent Plastic Flow at Ultrahigh Pressures and Strain Rates

A basic tenet of material science is that the flow stress of a metal increases as its grain size decreases, an effect described by the Hall-Petch relation. This relation is used extensively in material design to optimize the hardness, durability, survivability, and ductility of structural metals. This work reports experimental results in a new regime of high pressures and strain rates that challenge this basic tenet of mechanical metallurgy. We report measurements of the plastic flow of the model body-centered-cubic metal tantalum made under conditions of high pressure (> 100 GPa) and strain rate (~10 7 s –1 ) achieved by using the Omega laser. Under these unique plastic deformation (“flow”) conditions, the effect of grain size is found to be negligible for grain sizes > 0.25 μm sizes. A multiscale model of the plastic flow suggests that pressure and strain rate hardening dominate over the grain-size effects. Theoretical estimates, based on grain compatibility and geometrically necessary dislocations, corroborate this conclusion.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2022

Size-Dependent Nucleation in Crystal Phase Transition from Machine Learning Metadynamics

In this Letter, we present a framework that combines machine learning potential (MLP) and metadynamics to investigate solid-solid phase transition. Here, based on the spectral descriptors and neural networks regression, we develop a scalable MLP model to warrant an accurate interpolation of the energy surface where two phases coexist. Applying it to the simulation of B4–B1 phase transition of GaN under 50 GPa with different model sizes, we observe sequential change of the phase transition mechanism from collective modes to nucleation and growths. When the size is at or below 128 000 atoms, the nucleation and growth appear to follow a preferred direction. At larger sizes, the nuclei occur at multiple sites simultaneously and grow to microstructures by passing the critical size. The observed change of the atomistic mechanism manifests the importance of statistical sampling with large system size in phase transition modeling.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Inverse Volume Scaling of Finite-Size Error in Periodic Coupled Cluster Theory

Coupled cluster theory is one of the most popular post-Hartree-Fock methods for molecular quantum chemistry. The finite-size error of the correlation energy in periodic coupled cluster calculations for three-dimensional insulating systems has been observed to satisfy the inverse volume scaling, even in the absence of any correction schemes. This is surprising, as simpler theories that utilize only a subset of the coupled cluster diagrams exhibit much slower decay of the finite-size error, which scales inversely with the length of the system. In this study, we review the current understanding of finite-size error in quantum chemistry methods for periodic systems. We introduce new tools that elucidate the mechanisms behind this phenomenon in the context of coupled cluster doubles calculations. This reconciles some seemingly paradoxical statements related to finite-size scaling. Our findings also show that singularity subtraction can be a powerful method to effectively reduce finite-size errors in practical quantum chemistry calculations for periodic systems. Published by the American Physical Society 2024

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

Quantum Gravity in the Lab. I. Teleportation by Size and Traversable Wormholes

With the long-term goal of studying models of quantum gravity in the lab, we propose holographic teleportation protocols that can be readily executed in table-top experiments. These protocols exhibit similar behavior to that seen in the recent traversable-wormhole constructions of Gao et al. [J. High Energy Phys., 2017, 151 (2017)] and Maldacena et al. [Fortschr. Phys., 65, 1700034 (2017)]: information that is scrambled into one half of an entangled system will, following a weak coupling between the two halves, unscramble into the other half. We introduce the concept of teleportation by size to capture how the physics of operator-size growth naturally leads to information transmission. The transmission of a signal through a semiclassical holographic wormhole corresponds to a rather special property of the operator-size distribution that we call size winding. For more general systems (which may not have a clean emergent geometry), we argue that imperfect size winding is a generalization of the traversablewormhole phenomenon. In addition, a form of signaling continues to function at high temperature and at large times for generic chaotic systems, even though it does not correspond to a signal going through a geometrical wormhole but, rather, to an interference effect involving macroscopically different emergent geometries. Finally, we outline implementations that are feasible with current technology in two experimental platforms: Rydberg-atom arrays and trapped ions.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗