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At least 955 records · Page 53

Anomaly Detection for the Roman Space Telescope Wide Field Instrument’s Science Data Processing Pipeline

The Roman Space Telescope (RST) Wide Field Instrument (WFI) will be utilizing a preliminary Science Data Processing (SDP) pipeline during its Integration and Test, and to some extent during Operations, to track basic statistics and identify known features such as cosmic rays, snowballs as well as possible anomalies in raw detector data. In our detectors, these anomalies appear as jumps in the ramp of a readout and are classified as cosmic rays if they appear as a streak or snowballs if they’re more circular. The WFI employs an array of 18 H4RG-10 detectors that collect image samples. Each set of raw frames within a non-destructive exposure is packaged by the SDP pipeline into image cubes for each detector. Each cube is a time series of 4096 × 4096 accumulating pixel frames. The preliminary analysis pipeline is used to locate anomalies in these time-series accumulation frames and identify the type of anomaly, either natural phenomena or detector characteristic. To compare different methods, we’ve implemented both heuristic-based and data-driven methods to identify anomalies. For the heuristic-based approach, we identify snowballs and cosmic rays by the size and shape of outlier pixel clusters between consecutive frames. For data driven methods, we evaluated a Convolutional Neural Network (CNN) model, and more traditional methods like Principal Component Analysis (PCA). CNN is a supervised learning/classification method. Thus, we used a labeled dataset of anomalies to perform segmentation of the image and identify anomalies. We used previously identified cosmic rays and snowballs to measure the accuracy and efficiency of the mentioned approaches. In evaluating these methods, we aim to pick the best fit for the SDP pipeline’s anomaly detection in terms of both performance and runtime.

Paul Horton↗

Spin-free formulation of the multireference driven similarity renormalization group: A benchmark study of first-row diatomic molecules and spin-crossover energetics

We report a spin-free formulation of the multireference (MR) driven similarity renormalization group (DSRG) based on the ensemble normal ordering of Mukherjee and Kutzelnigg (1997). This ensemble averages over all microstates of a given total spin quantum number, and therefore, it is invariant with respect to SU(2) transformations. As such, all equations may be reformulated in terms of spin-free quantities and they closely resemble those of spin-adapted closed-shell coupled cluster (CC) theory. The current implementation is used to assess the accuracy of various truncated MR-DSRG methods (perturbation theory up to third order and iterative methods with single and double excitations) in computing the constants of 33 first-row diatomic molecules. The accuracy trends for these first-row diatomics are consistent with our previous benchmark on a small subset of closed-shell diatomic molecules. We then present the first MR-DSRG application on transition-metal complexes by computing the spin splittings of the [Fe(H 2 O) 6 ] 2+ and [Fe(NH 3 ) 6 ] 2+ molecules. A focal point analysis (FPA) shows that third-order perturbative corrections are essential to achieve reasonably converged energetics. The FPA based on the linearized MR-DSRG theory with one- and two-body operators and up to a quintuple- ζ basis set predicts the spin splittings of [Fe(H 2 O) 6 ] 2+ and [Fe(NH 3 ) 6 ] 2+ to be –35.7 and –17.1 kcal mol –1 , respectively, showing good agreement with the results of local CC theory with singles, doubles, and perturbative triples.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

A Detailed Investigation into the Use of Planetary Nebulae as Standard Candles

The program's goal was to understand the physics underlying the [O III] (lambda)5007 planetary nebula luminosity function (PNLF) and evaluate its accuracy as an extragalactic distance indicator. Work under the grant concentrated in two areas. The first major goal was to extensively test the PNLF method to find its limits. We did this performing yet another internal test of the method in the core galaxies of the Fornax Cluster, performing external comparisons of PNLF distances with distances derived from Cepheids and the Surface Brightness Fluctuation method (SBF), and, in general, examining the PNLF in as many different galactic environments as possible, including the disks of late-type spirals. Because of the difficulty distinguishing planetary nebulae (PNe) from H II regions, and because spiral galaxies have uneven internal extinction, the process of identifying "statistical" samples of PNe in these objects is extremely complicated. Nevertheless, by using the ratio of [O III] (lambda)5007 to H(alpha) as a diagnostic, we were able to effectively discriminate PNe from most H II regions, and apply the method to systems such as NGC 300, M101, M51, and M96. The second goal of this research was to determine theoretically, why the PNLF is such an excellent standard candle.

Ciardullo, Robin↗

Weak-lensing Detection of Intercluster Filaments in Three Nearby Cluster Systems

Abstract Direct detection of intercluster filaments is challenging due to their low surface density, resulting in a weak deflection field. We present weak-lensing detections of intercluster filaments using wide-field Dark Energy Camera observations from the Local Volume Complete Cluster Survey. A matched-filter method was applied to identify filamentary structures in three nearby ( z < 0.1) systems centered on A401, A2029, and A3558. We discover two filaments (>3 σ ) in each system, with the strongest detections (5.2 σ –5.8 σ ) around A401 and A2029. In particular, we report the first robust weak-lensing detections (≳5 σ ) of the intercluster bridges connecting the cluster pairs A401/399, A2029/2033, A2029/SIG, and A3558/3556. Adopting a filament convergence model motivated by numerical simulations, we infer the maximum convergence ( κ 0 ) and characteristic width ( h c ) for all six filaments, yielding κ 0 ∼ 0.016–0.040 and h c ∼ 0.23–0.43 Mpc. The performance of the matched-filter technique is validated using mock shear catalogs and further tested on a null field around A2351. We explore the potential of using the B-mode lensing signal of filaments to suppress cluster-induced shear contamination. We also quantify the biasing effect of closely separated terminal clusters to the filament signal. These results demonstrate the feasibility of directly mapping dark matter filaments with current and future wide-field weak-lensing datasets.

Shinde, Rahul [Brown University] (ORCID:0000000273↗

Biophysical Characterization of Iron-Sulfur Proteins

Iron-sulfur proteins are primordial catalysts and biological electron carriers that today drive major metabolic pathways across all forms of life. They can access a diversity of oxidation states and can mediate electron transfer over an extended range of reduction potentials spanning more than 1 V. Depending on the protein micro-environment and geometry of ligand, co-ordination the iron-sulfur clusters can occur in different forms [2Fe-2S], [3Fe-4S], HiPIP [4Fe-4S], and [4Fe-4S]. There are several spectroscopic methods available to characterize the composition and electronic configuration of the iron-sulfur clusters, such as optical methods and electron paramagnetic resonance. This paper presents the protocols used to characterize the metal center of Coiled-Coil Iron-Sulfur (CCIS), an artificial metalloprotein containing one [4Fe-4S] cluster. It is expected that these protocols will be of general utility for other iron-sulfur proteins.

Iron-sulfur proteins↗

Theoretical and experimental investigation of geometry and stability of small potassium‐iodide KnI(n=2–6) clusters

Small heterogeneous potassium-iodide clusters are investigated by means of ab initio electronic structural methods together with experimental production and detection in mass spectrometry. Experiments were done by using Knudsen cell mass spectrometry (KCMS) modification method, which provided simultaneous generating of all KnI0,+1 (n = 2–6) clusters at once. Clusters with more than two potassium atoms are produced for the first time. The lowest lying isomers of those KnI0,+1 (n = 2–6) clusters were found by using a random-kick procedure. The best description of growth of these clusters is the addition of one potassium atom to a smaller-neighbor cluster. Subsequently, stability of these species was examined. In spite of general trend of decreasing of binding energies, the closed-shell species have slightly larger stability with respect to the open-shell species. Alternation of dissociation energies between closed-shell and open-shell clusters is presented. Experimental setup also allows determination of ionization energies of clusters: the obtained values are in the range of 3.46–3.98 eV, which classify these clusters as “superalkali.” For closed-shell clusters, the theoretical adiabatic ionization energies are close to experimental values, whereas in the case of open-shell clusters, the vertical ionization energies are those that are close to experimental values. © 2019 Wiley Periodicals, Inc.

60 APPLIED LIFE SCIENCES↗

ManiNetCluster: a novel manifold learning approach to reveal the functional links between gene networks

BACKGROUND:The coordination of genomic functions is a critical and complex process across biological systems such as phenotypes or states (e.g., time, disease, organism, environmental perturbation). Understanding how the complexity of genomic function relates to these states remains a challenge. To address this, we have developed a novel computational method, ManiNetCluster, which simultaneously aligns and clusters gene networks (e.g., co-expression) to systematically reveal the links of genomic function between different conditions. Specifically, ManiNetCluster employs manifold learning to uncover and match local and non-linear structures among networks, and identifies cross-network functional links. RESULTS:We demonstrated that ManiNetCluster better aligns the orthologous genes from their developmental expression profiles across model organisms than state-of-the-art methods (p-value <2.2×10-16). This indicates the potential non-linear interactions of evolutionarily conserved genes across species in development. Furthermore, we applied ManiNetCluster to time series transcriptome data measured in the green alga Chlamydomonas reinhardtii to discover the genomic functions linking various metabolic processes between the light and dark periods of a diurnally cycling culture. We identified a number of genes putatively regulating processes across each lighting regime. CONCLUSIONS:ManiNetCluster provides a novel computational tool to uncover the genes linking various functions from different networks, providing new insight on how gene functions coordinate across different conditions. ManiNetCluster is publicly available as an R package at https://github.com/daifengwanglab/ManiNetCluster.

Comparative network analysis↗

Open-Shell Tensor Hypercontraction

The extension of least-squares tensor hypercontracted second- and third-order Møller–Plesset perturbation theory (LS-THC-MP2 and LS-THC-MP3) to open-shell systems is an important development due to the scaling reduction afforded by THC and the ubiquity of molecular ions, radicals, and other open-shell reactive species. The complexity of wavefunction-based quantum-chemical methods such as Møller–Plesset and coupled cluster theory is reflected in the steep scaling of the computational costs with the molecular size. The least-squares tensor hypercontraction (LS-THC) method is an efficient, single-step factorization for the two-electron integral tensor but can also be used to factorize the double excitation amplitudes, leading to significant scaling reduction. Herein we extend this promising method to open-shell variants of LS-THC-MP2 and -MP3 by using diagrammatic techniques and explicit spin summation. The accuracy of the resulting methods for open-shell species is benchmarked on standard test systems such as regular alkanes as well as realistic systems involving bond breaking, radical stabilization, and other effects. We find that open-shell LS-THC-MPn methods exhibit errors highly comparable to those produced by closed-shell LS-THC-MPn and are highly insensitive to particular chemical interactions, geometries, or even moderate spin contamination.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

From closed shells to open shells: Coupled-cluster calculations of atomic nuclei

Coupled-cluster theory is a powerful tool for first-principles calculations of atomic nuclei, enabling accurate predictions of nuclear observables across the Segrè chart. While coupled-cluster computations are especially efficient at shell closures, extensions have been developed to tackle open-shell nuclei, by exploiting the equation-of-motion method or by expanding the coupled-cluster wave function on top of a symmetry-breaking (either deformed or superfluid) reference state. In this study, we provide a comprehensive comparison of these different formulations applied to the calcium and nickel isotopes using nuclear two-and three-body interactions from chiral effective field theory. Here, based on ground-state energies, two-neutron separation energies, and two-neutron shell gaps, different coupled-cluster computations—based on symmetry-broken reference states and equationof-motion techniques— offer consistent descriptions of bulk properties across medium-mass isotopic chains.

Marino, Francesco [Johannes Gutenberg-Universität ↗

Time-dependent equation-of-motion coupled-cluster simulations with a defective Hamiltonian

Here simulations of laser-induced electron dynamics in a molecular system are performed using time-dependent (TD) equation-of-motion (EOM) coupled-cluster (CC) theory. The target system has been chosen to highlight potential shortcomings of truncated TD-EOM-CC methods [represented in this work by TD-EOM-CC with single and double excitations (TD-EOM-CCSD)], where unphysical spectroscopic features can emerge. Specifically, we explore driven resonant electronic excitations in magnesium fluoride in the proximity of an avoided crossing. Near the avoided crossing, the CCSD similarity-transformed Hamiltonian is defective, meaning that it has complex eigenvalues, and oscillator strengths may take on negative values. When an external field is applied to drive transitions to states exhibiting these traits, unphysical dynamics are observed. For example, the stationary states that make up the time-dependent state acquire populations that can be negative, exceed one, or even complex-valued.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

A multicomponent matched filter cluster confirmation tool for eROSITA: initial application to the RASS and DES-SV data sets

We describe a multi-component matched filter cluster confirmation tool (MCMF) designed for the study of large X-ray source catalogs produced by the upcoming X-ray all-sky survey mission eROSITA. We apply the method to confirm a sample of 88 clusters with redshifts $0.05<z<0.8$ in the recently published 2RXS catalog from the ROSAT all-sky survey (RASS) over the 208 deg$^2$ region overlapped by the Dark Energy Survey (DES) science verification (DES-SV) dataset. In our pilot study, we examine all X-ray sources, regardless of their extent. Our method employs a multi-color red sequence (RS) algorithm that incorporates the X-ray count rate and peak position in determining the region of interest for followup and extracts the positionally and color weighted optical richness $\lambda_{\mathrm{MCMF}}$ as a function of redshift for each source. Peaks in the $\lambda_{\mathrm{MCMF}}$-redshift distribution are identified and used to extract photometric redshifts, richness and uncertainties. The significances of all optical counterparts are characterized using the distribution of richnesses defined along random lines of sight. These significances are used to extract cluster catalogs and to estimate the contamination by random superpositions of unassociated optical systems. The delivered photometric redshift accuracy is $\delta z / (1+z)=0.010$. We find a well defined X-ray luminosity-$\lambda_{\mathrm{MCMF}}$ relation with an intrinsic scatter of $\delta \ln(\lambda_\mathrm{MCMF}| L_\mathrm{x})=0.21$. Matching our catalog with the DES-SV redMaPPer catalog yields good agreement in redshift and richness estimates; comparing our catalog with the South Pole Telescope (SPT) selected clusters shows no inconsistencies. SPT clusters in our dataset are consistent with the high mass extension of the RASS based $\lambda_{\mathrm{MCMF}}$-mass relation

79 ASTRONOMY AND ASTROPHYSICS↗

An energy-dependent map of the X-ray emission of the Perseus cluster

Results are discussed for X-ray scans of the Perseus cluster with the SAS 3 slat detectors. Counting rates in two broadband channels (1.5 to 5.5 keV and 5.5 to 15.5 keV) are compared as a function of the instrument scan angle measured from the center of emission, and it is found that the emission in the higher energy range is broader in extent. Tests for a systematic energy-dependent error in the background demonstrate that the discovered energy dependence of the Perseus cluster emission is valid. Iron line emission is determined by two methods, various models are fitted to the data, and the total cluster emission in the two energy ranges is computed. The iron line emission is determined to be 0.003 photon/sq cm per sec. It is concluded that the diffuse emission increases in the range from 1.5 to 15.5 keV within the bounds of a model involving a point source with a radius not exceeding about 3 arcmin plus a diffuse source.

Ulmer, M. P.↗

Brome isotope selective control of CF{sub 3}Br molecule clustering by IR laser radiation in gas-dynamic expansion of CF{sub 3}Br – Ar mixture

We report the results of research on the experimental control of CF{sub 3}Br molecule clustering under gas-dynamic expansion of the CF{sub 3}Br – Ar mixture at a nozzle exit by using IR laser radiation. A cw CO{sub 2} laser is used for exciting molecules and clusters in the beam and a time-of-flight mass-spectrometer with laser UV ionisation of particles for their detection. The parameters of the gas above the nozzle are determined (compositions and pressure) at which intensive molecule clustering occurs. It is found that in the case of the CF{sub 3}Br gas without carrier when the pressure P{sub 0} above the nozzle does not exceed 4 atm, molecular clusters actually are not generated in the beam. If the gas mixture of CF{sub 3}Br with argon is used at a pressure ratio 1 : N, where N ⩾ 3, and the total pressure above the nozzle is P{sub 0} ⩾ 2 atm, then there occurs molecule clustering. We study the dependences of the efficiency of suppressing the molecule clustering on parameters of the exciting pulse, gas parameters above the nozzle, and on a distance of the molecule irradiation zone from the nozzle exit section. It is shown that in the case of resonant vibrational excitation of gas-dynamically cooled CF{sub 3}Br molecules at the nozzle exit one can realise isotope-selective suppression of molecule clustering with respect to bromine isotopes. With the CF{sub 3}Br – Ar mixtures having the pressure ratio 1 : 3 and 1 : 15, the enrichment factors obtained with respect to bromine isotopes are k{sub enr} ≈ 1.05 ± 0.005 and k{sub enr} ≈ 1.06 ± 0.007, respectively, under jet irradiation by laser emission in the 9R(30) line (1084.635 cm{sup −1}). The results obtained let us assume that this method can be used to control clustering of molecules comprising heavy element isotopes, which have a small isotopic shift in IR absorption spectra. (paper)

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Spatially Accelerated Winding Numbers for Curved Geometry

The generalized winding number (GWN) is a scalar field that supports robust containment queries on curved geometry, including non-watertight, overlapping, and nested boundary representations. While queries can be easily parallelized over samples, direct evaluation on parametric curves and surfaces remains costly for large and complex models. Fast, state-of-the-art GWN approaches leverage a spatial index to approximate the GWN, typically coupled with a Taylor expansion which approximates the GWN contribution for far clusters of geometric primitives. However, such methods operate only on discrete inputs such as triangle meshes and point clouds, and would introduce containment errors near boundaries if applied to curved input. We extend support for fast GWN evaluation over arbitrary collections of NURBS curves in 2D and trimmed NURBS patches in 3D via a Bounding Volume Hierarchy that stores efficiently precomputed moment data in the hierarchy nodes. When querying the hierarchy, approximations for far clusters are used alongside direct evaluation for nearby NURBS primitives, achieving sub-linear complexity while preserving the geometric features in the vicinity of the query point. Central to our performance improvements is an adaptive subdivision strategy for NURBS primitives during a preprocessing phase, creating better spatial partitions while retaining the same accuracy for containment decisions as a direct evaluation. We demonstrate the performance and accuracy of our approach across a large collection of 2D and 3D datasets.

Computer science↗

Structured background grids for generation of unstructured grids by advancing front method

A new method of background grid construction is introduced for generation of unstructured tetrahedral grids using the advancing-front technique. Unlike the conventional triangular/tetrahedral background grids which are difficult to construct and usually inadequate in performance, the new method exploits the simplicity of uniform Cartesian meshes and provides grids of better quality. The approach is analogous to solving a steady-state heat conduction problem with discrete heat sources. The spacing parameters of grid points are distributed over the nodes of a Cartesian background grid by interpolating from a few prescribed sources and solving a Poisson equation. To increase the control over the grid point distribution, a directional clustering approach is used. The new method is convenient to use and provides better grid quality and flexibility. Sample results are presented to demonstrate the power of the method.

Pirzadeh, Shahyar↗

BiG-SCAPE 2.0 and BiG-SLiCE 2.0: scalable, accurate and interactive sequence clustering of metabolic gene clusters

Microbial metabolic gene clusters encode the biosynthesis or catabolism of metabolites that facilitate ecological specialization, mediate microbiome interactions and constitute a major source of medicines and crop protection agents. Here, we present BiG-SCAPE and BiG-SLiCE 2.0, next-generation methods that facilitate scalable, accurate and interactive gene cluster analyses. BiG-SCAPE 2.0 updates its classification, alignment methods, and visualizations, enabling more accurate analysis, up to 8x faster runtimes and halved memory requirements. BiG-SLiCE 2.0 updates its distance metric, pHMM database, and classification logic, resulting in increased sensitivity nearing that of BiG-SCAPE. Analysis of 260,630 biosynthetic gene clusters from publicly available genomes reveals that both tools generate concurring estimates of gene cluster diversity, thus providing significantly extended methodological support for recent evidence indicating that the vast majority of natural product diversity remains unexplored. Together, these updates will facilitate global genome mining efforts for natural product discovery and microbiome analyses scalable with current data sizes.

Draisma, Arjan [Wageningen University & Research (↗

Analytic marginalization of N(z) uncertainties in tomographic galaxy surveys

In this paper, we present a new method to marginalize over uncertainties in redshift distributions, N(z), within tomographic cosmological analyses applicable to current and upcoming photometric galaxy surveys. We allow for arbitrary deviations from the best-guess N(z) governed by a general covariance matrix describing the uncertainty in our knowledge of redshift distributions. In principle, this is marginalization over hundreds or thousands of new parameters describing potential deviations as a function of redshift and tomographic bin. However, by linearly expanding the theory predictions around a fiducial model, this marginalization can be performed analytically, resulting in a modified data covariance matrix that effectively downweights the modes of the data vector that are more sensitive to redshift distribution variations. We showcase this method by applying it to the galaxy clustering measurements from the Hyper Suprime-Cam first data release. We illustrate how to marginalize over sample variance of the calibration sample and a large general systematic uncertainty in photometric estimation methods, and explore the impact of priors imposing smoothness in the redshift distributions.

79 ASTRONOMY AND ASTROPHYSICS↗

The behavior of methane–water mixtures under elevated pressures from simulations using many-body potentials

Non-polarizable empirical potentials have been proven to be incapable of capturing the mixing of methane–water mixtures at elevated pressures. Although density functional theory-based ab initio simulations may circumvent this discrepancy, they are limited in terms of the relevant time and length scales associated with mixing phenomena. Here, we show that the many-body MB-nrg potential, designed to reproduce methane–water interactions with coupled cluster accuracy, successfully captures this phenomenon up to 3 GPa and 500 K with varying methane concentrations. Two-phase simulations and long time scales that are required to fully capture the mixing, affordable due to the speed and accuracy of the MBX software, are assessed. Constructing the methane–water equation of state across the phase diagram shows that the stable mixtures are denser than the sum of their parts at a given pressure and temperature. As a result, we find that many-body polarization plays a central role, enhancing the induced dipole moments of methane by 0.20 D during mixing under pressure. Overall, the mixed system adopts a denser state, which involves a significant enthalpic driving force as elucidated by a systematic many-body energy decomposition analysis.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗