Parallel Mapper

The construction of Mapper has emerged in the last decade as a powerful and effective topological data analysis tool that approximates and generalizes other topological summaries, such as the Reeb graph, the contour tree, split, and joint trees. In this paper, we study the parallel analysis of the construction of Mapper. We give a provably correct parallel algorithm to execute Mapper on multiple processors and discuss the performance results that compare our approach to a reference sequential Mapper implementation. We report the performance experiments that demonstrate the efficiency of our method

The Formation of IRIS diagnostics. IV. The Mg II triplet lines as a new diagnostic for lower chromospheric heating

A triplet of subordinate lines of Mg II exists in the region around the h&k lines. In solar spectra these lines are seen mostly in absorption, but in some cases can become emission lines. The aim of this work is to study the formation of this triplet, and investigate any diagnostic value they can bring. Using 3D radiative magnetohydrodynamic simulations of quiet Sun and flaring flux emergence, we synthesize spectra and investigate how spectral features respond to the underlying atmosphere. We find that emission in the lines is rare and is typically caused by a steep temperature increase in the lower chromosphere (above 1500 K, with electron densities above 10$^{18}$ m$^{-3}$). In both simulations the lines are sensitive to temperature increases taking place at column masses >= 5e-4 g cm$^{-2}$. Additional information can also be inferred from the peak-to-wing ratio and shape of the line profiles. Using observations from NASA's Interface Region Imaging Spectrograph we find both absorption and emission line profiles with similar shapes to the synthetic spectra, which suggests that these lines represent a useful diagnostic that complements the MgII h&k lines.Comment: 8 pages, 7 figures. Accepted for publication in Ap

The formation of IRIS diagnostics I. A quintessential model atom of Mg II and general formation properties of the Mg II h&k lines

NASA's Interface Region Imaging Spectrograph (IRIS) space mission will study how the solar atmosphere is energized. IRIS contains an imaging spectrograph that covers the Mg II h&k lines as well as a slit-jaw imager centered at Mg II k. Understanding the observations will require forward modeling of Mg II h&k line formation from 3D radiation-MHD models. This paper is the first in a series where we undertake this forward modeling. We discuss the atomic physics pertinent to h&k line formation, present a quintessential model atom that can be used in radiative transfer computations and discuss the effect of partial redistribution (PRD) and 3D radiative transfer on the emergent line profiles. We conclude that Mg II h&k can be modeled accurately with a 4-level plus continuum Mg II model atom. Ideally radiative transfer computations should be done in 3D including PRD effects. In practice this is currently not possible. A reasonable compromise is to use 1D PRD computations to model the line profile up to and including the central emission peaks, and use 3D transfer assuming complete redistribution to model the central depression.Comment: 13 pages, 13 figures, accepted for Ap

RADYN simulations of non-thermal and thermal models of Ellerman bombs

Ellerman bombs (EBs) are brightenings in the H$\alpha$ line wings that are believed to be caused by magnetic reconnection in the lower atmosphere. To study the response and evolution of the chromospheric line profiles, we perform radiative hydrodynamic simulations of EBs using both non-thermal and thermal models. Overall, these models can generate line profiles that are similar to observations. However, in non-thermal models we find dimming in the H$\alpha$ line wings and continuum when the heating begins, while for the thermal models dimming occurs only in the H$\alpha$ line core, and with a longer lifetime. This difference in line profiles can be used to determine whether an EB is dominated by non-thermal heating or thermal heating. In our simulations, if a higher heating rate is applied, the H$\alpha$ line will be unrealistically strong, while there are still no clear UV burst signatures.Comment: 20 pages, 9 figures, accepted for publication in Ap

Large-scale exact diagonalizations reveal low-momentum scales of nuclei

Ab initio methods aim to solve the nuclear many-body problem with controlled approximations. Virtually exact numerical solutions for realistic interactions can only be obtained for certain special cases such as few-nucleon systems. Here we extend the reach of exact diagonalization methods to handle model spaces with dimension exceeding $10^{10}$ on a single compute node. This allows us to perform no-core shell model (NCSM) calculations for 6Li in model spaces up to $N_\mathrm{max} = 22$ and to reveal the 4He+d halo structure of this nucleus. Still, the use of a finite harmonic-oscillator basis implies truncations in both infrared (IR) and ultraviolet (UV) length scales. These truncations impose finite-size corrections on observables computed in this basis. We perform IR extrapolations of energies and radii computed in the NCSM and with the coupled-cluster method at several fixed UV cutoffs. It is shown that this strategy enables information gain also from data that is not fully UV converged. IR extrapolations improve the accuracy of relevant bound-state observables for a range of UV cutoffs, thus making them profitable tools. We relate the momentum scale that governs the exponential IR convergence to the threshold energy for the first open decay channel. Using large-scale NCSM calculations we numerically verify this small-momentum scale of finite nuclei.Comment: Minor revisions.Accepted for publication in Physical Review

Modeling of Covalent Bonding in Solids by Inversion of Cohesive Energy Curves

We provide a systematic test of empirical theories of covalent bonding in solids using an exact procedure to invert ab initio cohesive energy curves. By considering multiple structures of the same material, it is possible for the first time to test competing angular functions, expose inconsistencies in the basic assumption of a cluster expansion, and extract general features of covalent bonding. We test our methods on silicon, and provide the direct evidence that the Tersoff-type bond order formalism correctly describes coordination dependence. For bond-bending forces, we obtain skewed angular functions that favor small angles, unlike existing models. As a proof-of-principle demonstration, we derive a Si interatomic potential which exhibits comparable accuracy to existing models.Comment: 4 pages revtex (twocolumn, psfig), 3 figures. Title and some wording (but no content) changed since original submission on 24 April 199

The Effects of Spatio-temporal Resolution on Deduced Spicule Properties

Spicules have been observed on the sun for more than a century, typically in chromospheric lines such as H-alpha and Ca II H. Recent work has shown that so-called 'type II' spicules may have a role in providing mass to the corona and the solar wind. In chromospheric filtergrams these spicules are not seen to fall back down, and they are shorter-lived and more dynamic than the spicules that have been classically reported in ground-based observations. Observations of type II spicules with Hinode show fundamentally different properties from what was previously measured. In earlier work we showed that these dynamic type II spicules are the most common type, a view that was not properly identified by early observations.The aim of this work is to investigate the effects of spatio-temporal resolution in the classical spicule measurements. Making use of Hinode data degraded to match the observing conditions of older ground-based studies, we measure the properties of spicules with a semi-automated algorithm. These results are then compared to measurements using the original Hinode data. We find that degrading the data has a significant effect on the measured properties of spicules. Most importantly, the results from the degraded data agree well with older studies (e.g. mean spicule duration more than 5 minutes, and upward apparent velocities of about 25 km/s). These results illustrate how the combination of spicule superposition, low spatial resolution and cadence affect the measured properties of spicules, and that previous measurements can be misleading.Comment: Accepted for publication in ApJ. 5 pages, 3 figures. Movies of figures 1 and 3 available via Data Conservanc