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At least 1,621 records · Page 90
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Parallel String Graph Construction and Transitive Reduction for De Novo Genome Assembly

One of the most computationally intensive tasks in computational biology is de novo genome assembly, the decoding of the sequence of an unknown genome from redundant and erroneous short sequences. A common assembly paradigm identifies overlapping sequences, simplifies their layout, and creates consensus. Despite many algorithms developed in the literature, the efficient assembly of large genomes is still an open problem. In this work, we introduce new distributed-memory parallel algorithms for overlap detection and layout simplification steps of de novo genome assembly, and implement them in the diBELLA 2D pipeline. Our distributed memory algorithms for both overlap detection and layout simplification are based on linear-algebra operations over semirings using 2D distributed sparse matrices. Our layout step consists of performing a transitive reduction from the overlap graph to a string graph. We provide a detailed communication analysis of the main stages of our new algorithms. diBELLA 2D achieves near linear scaling with over 80% parallel efficiency for the human genome, reducing the runtime for overlap detection by 1.2-1.3× for the human genome and 1.5-1.9× for C.elegans compared to the state-of-the-art. Our transitive reduction algorithm outperforms an existing distributed-memory implementation by 10.5-13.3× for the human genome and 18-29× for the C. elegans. Our work paves the way for efficient de novo assembly of large genomes using long reads in distributed memory.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Surface Modification of Silicon Pillar Arrays To Enhance Fluorescence Detection of Uranium and DNA

There is an ever-growing need for detection methods that are both sensitive and efficient, such that reagent and sample consumption is minimized. Nanopillar arrays offer an attractive option to fill this need by virtue of their small scale in conjunction with their field enhancement intensity gains. This work investigates the use of nanopillar substrates for the detection of the uranyl ion and DNA, two analytes unalike but for their low quantum efficiencies combined with the need for high-throughput analyses. Here in this paper, the adaptability of these platforms was explored, as methods for the successful surface immobilization of both analytes were developed and compared, resulting in a limit of detection for the uranyl ion of less than 1 ppm with a 0.2 μL sample volume. Moreover, differentiation between single-stranded and double-stranded DNA was possible, including qualitative identification between double-stranded DNA and DNA of the same sequence, but with a 10-base-pair mismatch.

36 MATERIALS SCIENCE↗
DOE OSTI2017

A Robust Mass Estimator for Dark Matter Subhalo Perturbations in Strong Gravitational Lenses

A few dark matter substructures have recently been detected in strong gravitational lenses through their perturbations of highly magnified images. We derive a characteristic scale for lensing perturbations and show that they are significantly larger than the perturber’s Einstein radius. We show that the perturber’s projected mass enclosed within this radius, scaled by the log-slope of the host galaxy’s density profile, can be robustly inferred even if the inferred density profile and tidal radius of the perturber are biased. We demonstrate the validity of our analytic derivation using several gravitational lens simulations where the tidal radii and the inner log-slopes of the density profile of the perturbing subhalo are allowed to vary. By modeling these simulated data, we find that our mass estimator, which we call the effective subhalo lensing mass, is accurate to within about 10% or smaller in each case, whereas the inferred total subhalo mass can potentially be biased by nearly an order of magnitude. We therefore recommend that the effective subhalo lensing mass be reported in future lensing reconstructions, as this will allow for a more accurate comparison with the results of dark matter simulations.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2023

Robust neural network-enhanced estimation of local primordial non-Gaussianity

When applied to the nonlinear matter distribution of the universe, neural networks have been shown to be very statistically sensitive probes of cosmological parameters, such as the linear perturbation amplitude σ 8 . However, when used as a “black box,” neural networks are not robust to baryonic uncertainty. We propose a robust architecture for constraining primordial non-Gaussianity f NL , by training a neural network to locally estimate σ 8 , and correlating these local estimates with the large-scale density field. We apply our method to N-body simulations, and show that σ⁡(f NL ) is 3.5 times better than the constraint obtained from a standard halo-based approach. Finally, we show that our method has the same robustness property as large-scale halo bias: baryonic physics can change the normalization of the estimated f NL , but cannot change whether f NL is detected.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2013

Unruh effect in vacua with anisotropic scaling: Applications to multilayer graphene

We extend the calculation of the Unruh effect to the universality classes of quantum vacua obeying topologically protected invariance under anisotropic scaling r→br, t→b{sup z}t. Two situations are considered. The first one is related to the accelerated detector which detects the electron–hole pairs. The second one is related to the system in external electric field, when the electron–hole pairs are created due to the Schwinger process. As distinct from the Unruh effect in relativistic systems (where z=1) the calculated radiation is not thermal, but has properties of systems in the vicinity of quantum criticality. The vacuum obeying anisotropic scaling can be realized, in particular, in multilayer graphene with the rhombohedral stacking. Opportunities of the experimental realization of the Unruh effect in this situation are discussed. -- Highlights: •Unruh effect in the system with anisotropic scaling (multilayer graphene) is investigated. •The accelerated detector is considered which detects the electron–hole pairs. •The system in external electric field is considered as the “accelerated vacuum”. •Unruh effect in the nonrelativistic case differs from that of the relativistic case.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2023

The haloes and environments of nearby galaxies ( HERON ) – III. A 45-kpc spiral structure in the GLSB galaxy UGC 4599

ABSTRACT We use a 0.7-m telescope in the framework of the Halos and Environments of Nearby Galaxies (HERON) survey to probe low surface brightness (LSB) structures in nearby galaxies. One of our targets, UGC 4599, is usually classified as an early-type galaxy surrounded by a blue ring making it a potential Hoag’s Object analogue. Prior photometric studies of UGC 4599 were focused on its bright core and the blue ring. However, the HERON survey allows us to study its faint extended regions. With an 8-h integration, we detect an extremely faint outer disc with an extrapolated central surface brightness of μ0, d(r) = 25.5 mag arcsec−2 down to 31 mag arcsec−2 and a scale length of 15 kpc. We identify two distinct spiral arms of pitch angle ∼6○ surrounding the ring. The spiral arms are detected out to ∼45 kpc in radius and the faint disc continues to ∼70 kpc. These features are also seen in the GALEX far- and near-ultraviolet bands, in a deep u-band image from the 4.3-m Lowell Discovery Telescope (which reveals inner spiral structure emerging from the core), and in H i. We compare this galaxy to ordinary spiral and elliptical galaxies, giant low surface brightness (GLSB) galaxies, and Hoag’s Object itself using several standard galaxy scaling relations. We conclude that the pseudo-bulge and disc properties of UGC 4599 significantly differ from those of Hoag’s Object and of normal galaxies, pointing toward a GLSB galaxy nature and filamentary accretion of gas to generate its outer disc.

Astronomy & Astrophysics↗
NASA NTRS2002

Evaluation of Small Mass Spectrometer Systems

This work is aimed at understanding the aspects of designing a miniature mass spectrometer (MS) system. A multitude of commercial and government sectors, such as the military, environmental agencies and industrial manufacturers of semiconductors, refrigerants, and petroleum products, would find a small, portable, rugged and reliable MS system beneficial. Several types of small MS systems are evaluated and discussed, including linear quadrupole, quadrupole ion trap, time of flight and sector. The performance of each system in terms of accuracy, precision, limits of detection, response time, recovery time, scan rate, volume and weight is assessed. A performance scale is setup to rank each systems and an overall performance score is given to each system. All experiments involved the analysis of hydrogen, helium, oxygen and argon in a nitrogen background with the concentrations of the components of interest ranging from 0-5000 part-per-million (ppm). The relative accuracies of the systems vary from < 1% to approx. 40% with an average below 10%. Relative precisions varied from 1% to 20%, with an average below 5%. The detection limits had a large distribution, ranging from 0.2 to 170 ppm. The systems had a diverse response time ranging from 4 s to 210 s as did the recovery time with a 6 s to 210 s distribution. Most instruments had scan times near, 1 s, however one instrument exceeded 13 s. System weights varied from 9 to 52 kg and sizes from 15 x 10(exp 3)cu cm to 110 x 10(exp 3) cu cm.

Arkin, C. Richard↗
NASA NTRS2000

Balloon-Borne Observations of the Anisotropy of the Cosmic Microwave'Background on Angular Scales of 0.2 to 40 Degrees'

During this final period, BOOMERANG was deployed to McMurdo Mtn., Antarctica in late 1998 and successfully flew a 10.5 day long duration flight. The experiment returned excellent data, and produced the first resolved images of the early universe. These results, as well as those produced during a test flight over North America in August, 1997, are given in the references below. Analysis of the data from the 1998 flight is continuing. In parallel, we have begun to prepare the payload for a long-duration flight from McMurdo in December 2001. For this flight, the focal plane is being outfitted with polarization sensitive detectors, with the goal of detecting the polarization of the CMB that is predicted to exist at degree angular scales.

Source record↗
DOE OSTI2021

Phase noise limited frequency shift impulsive Raman spectroscopy

We introduce a method to enable optical amplification of a coherent Raman spectroscopy signal, which we call radio frequency (RF) Doppler Raman spectroscopy. In this article, we consider the perturbation of a probe pulse in a sample due to an excited Raman vibrational coherence as a generalized Doppler shift, which connects a time-varying optical path length (the product of the propagation length and refractive index, OPL = n ℓ) with an optical frequency shift. Amplification of a Raman signal outside of the focused interaction is enabled by converting the Doppler frequency shift experienced by a laser probe pulse into a periodic timing jitter. This transit time perturbation is detected through the phase of a RF electronic signal measured at a harmonic of the probe pulse train with a method adapted from precision metrology techniques used to measure laser pulse train timing jitter. Measurement of a timing jitter allows access to much lower noise floors than other coherent Raman techniques, and by exploiting the new capability to scale the signal of a coherent Raman spectroscopic signal, this method opens the potential to detect very weak Raman signals that are currently not observable due to limits of illumination intensity imposed by laser damage to the specimen and noise.

47 OTHER INSTRUMENTATION↗
DOE OSTI2017

Chiral effective theory of dark matter direct detection

We present the effective field theory for dark matter interactions with the visible sector that is valid at scales of O(1 GeV). Starting with an effective theory describing the interactions of fermionic and scalar dark matter with quarks, gluons and photons via higher dimension operators that would arise from dimension-five and dimension-six operators above electroweak scale, we perform a nonperturbative matching onto a heavy baryon chiral perturbation theory that describes dark matter interactions with light mesons and nucleons. This is then used to obtain the coefficients of the nuclear response functions using a chiral effective theory description of nuclear forces. Our results consistently keep the leading contributions in chiral counting for each of the initial Wilson coefficients.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2014

The X-ray Zurich environmental study (X-zens). I. Chandra and XMM-Newton observations of active galactic nuclei in galaxies in nearby groups

We describe X-ray observations with Chandra and XMM-Newton of 18 M {sub group} ∼ 1-6 × 10{sup 13} M {sub ☉}, z ∼ 0.05 galaxy groups from the Zurich ENvironmental Study. The X-ray data aim at establishing the frequency and properties, unaffected by host galaxy dilution and obscuration, of active galactic nuclei (AGNs) in central and satellite galaxies, also as a function of halo-centric distance. X-ray point-source detections are reported for 22 of the 177 galaxies, down to a sensitivity level of f {sub 0.5} {sub –} {sub 8} {sub keV} ∼ 5 × 10{sup –15} erg cm{sup –2} s{sup –1}, corresponding to a limiting luminosity of L {sub 0.5} {sub –} {sub 8} {sub keV} ∼ 3 × 10{sup 40} erg s{sup –1}. With the majority of the X-ray sources attributed to AGNs of low-to-moderate levels (L/L {sub Edd} ≳ 10{sup –4}), we discuss the detection rate in the context of the occupation of AGNs to halos of this mass scale and redshift and compare the structural and morphological properties between AGN-active and non-active galaxies. At galaxy mass scales <10{sup 11} M {sub ☉}, central galaxies appear to be a factor of ∼4 more likely to host AGNs than satellite galaxies of similar mass. This effect, coupled with the tendency for AGNs to be hosted by massive galaxies, explains the (weak) trend for AGNs to be preferentially found in the inner parts of group halos, with no detectable trend with halo-centric distance in the frequency of AGNs within the satellite population. Finally, our data indicate that the rate of decline with redshift of AGN activity in galaxy groups matches that of the global AGN population, indicating that either AGN activity occurs preferentially in group halos or that the evolution rate is independent of halo mass.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2014

Comparison of galaxy clusters selected by weak-lensing, optical spectroscopy, and X-rays in the deep lens survey F2 field

We compare galaxy clusters selected in Chandra and XMM-Newton X-ray observations of the 4 deg{sup 2} Deep Lens Survey (DLS) F2 field to the cluster samples previously selected in the same field from a sensitive weak-lensing shear map derived from the DLS and from a detailed galaxy redshift survey—the Smithsonian Hectospec Lensing Survey (SHELS). Our Chandra and XMM-Newton observations cover 1.6 deg{sup 2} of the DLS F2 field, including all 12 weak-lensing peaks above a signal-to-noise ratio of 3.5, along with 16 of the 20 SHELS clusters with published velocity dispersions >500 km s{sup –1}. We detect 26 extended X-ray sources in this area and confirm 23 of them as galaxy clusters using the optical imaging. Approximately 75% of clusters detected in either X-ray or spectroscopic surveys are found in both; these follow the previously established scaling relations between velocity dispersion, L {sub X}, and T {sub X}. A lower percentage, 60%, of clusters are in common between X-ray and DLS samples. With the exception of a high false-positive rate in the DLS weak-lensing search (5 out of 12 DLS candidates appear to be false), differences between the three cluster detection methods can be attributed primarily to observational uncertainties and intrinsic scatter between different observables and cluster mass.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2023

Exclusion and Verification of Remote Nuclear Reactors with a 1-kiloton Gd -Doped Water Detector

To date, antineutrino experiments built for the purpose of demonstrating a nonproliferation capability have typically employed organic scintillators situated as close to the core as possible (typically at a distance of a few meters to tens of meters) and have not exceeded a few tons in size. One problem with this approach is that proximity to the reactor core requires accommodation by the host facility. Water Cherenkov detectors located offsite, at distances of a few kilometers or greater, may facilitate nonintrusive monitoring and verification of reactor activities over a large area. As the standoff distance increases, the detector target mass must scale accordingly. This paper quantifies the degree to which a kiloton-scale gadolinium-doped water Cherenkov detector can exclude the existence of undeclared reactors within a specified distance, and remotely detect the presence of a hidden reactor in the presence of declared reactors, by verifying the operational power and standoff distance using a Feldman-Cousins-based likelihood analysis. A 1-kton scale (fiducial) water Cherenkov detector can exclude gigawatt-scale nuclear reactors up to tens of kilometers within a year. In conclusion, when attempting to identify the specific range and power of a reactor, the detector energy resolution is not sufficient to delineate between the two.

42 ENGINEERING↗
DOE OSTI2025

Grand unification at the cosmological collider with chemical potential

We introduce a tree-level chemical potential mechanism for spin-1 particles within cosmological collider physics, allowing them to be detected in primordial non-Gaussianities for masses above the inflationary Hubble scale. We apply this mechanism to orbifold grand unification and the massive unification partners of the standard model gauge bosons. Our mechanism requires at least a pair of massive vector fields which are singlets of the standard model, a condition which is satisfied in the classic “trinification” scenario. Assuming that the gauge hierarchy problem is solved by supersymmetry, gauge coupling running points to unification partners at ~ 10$^{15}$ GeV. We show that, within high-scale inflation, chemical potential enhancement can lead to observably strong signals for trinification partners in future cosmological surveys.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2018

Association of Vampirovibrio chlorellavorus with decline and death of Chlorella sorokiniana in outdoor reactors

The outdoor ARID raceway was established for optimizing the cultivation of microalgae for biofuel production. During the summers of 2014 and 2015, discoloration was observed in cultures of Chlorella sorokiniana , which shifted from a vibrant green color to yellow, followed by cell clumping, decline in density, and rapid death, resulting in 40–60% reduced biomass production. To investigate, total DNA was purified from the raceway samples and subjected to polymerase chain reaction (PCR) amplification using degenerate primers that amplify the 16S rRNA gene of eubacteria. BLASTn analysis of the cloned amplicon sequences revealed the presence of the Gram-negative, predatory bacterium, Vampirovibrio chlorellavorus . Scanning electron microscopic examination showed an abundance of coccoid cells, 0.3–0.6 μm in diameter, some of which were attached to C. sorokiniana cells. PCR amplification indicated the presence of V. chlorellavorus in raceway vessels, water lines, connective tubing, and in early, scaled-up DOE1412 cultures used to inoculate the raceway. Based on PCR detection, the decontamination of the equipment and water line with "Wal-Clean" more effectively eliminated V. chlorellavorus and delayed the onset of attack, compared to the chlorine disinfectant, trichloromelamine (TCM). Total DNA was isolated from soil samples collected monthly from the nearby Rillito River during 2014–2015 and subjected to PCR amplification using primers designed to amplify the 16S rRNA and 18S rRNA gene of V. chlorellavorus and C. sorokiniana , respectively. Results indicated that V. chlorellavorus and Chlorella spp. were present in most of the riverbed samples nearly year round, suggesting a possible naturally occurring reservoir of the predatory bacterium.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Electromagnetic and gravitational interactions from Lagrangian mechanics

Highlights: • Background Maxwell and Einstein fields are universal features of Lagrangian systems. • The Lagrangian function is promoted to a dynamic field. • The Einstein–Maxwell theory is derived from Lagrangian mechanics. Background fields of electromagnetic and gravitational type emerge in the low kinetic energy limit of any regular Lagrangian system and, in particular, in the corresponding limit of any spacetime theory in which the free motion of test particles is described by an unspecified regular Lagrangian. Electromagnetic and gravitational type interactions are therefore a universal feature of low kinetic energy Lagrangian systems. These background interactions can be consistently turned into dynamic Einstein–Maxwell fields by promoting the Lagrangian function to a dynamic scalar field on the tangent bundle of the configuration space. Accordingly, Einstein–Maxwell theory can be deduced from the assumption that the motion of elementary test particles in spacetime is described by Lagrangian mechanics. For higher kinetic energy-type values, identified with the square of the invariant mass of the particle, the Lagrangian induces higher rank interactions that seem however too weak to have been detected in spacetime physics, but which might prove relevant at the Planck scale.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗