A Fast and Accurate Algorithm for Spherical Harmonic Analysis on HEALPix Grids with Applications to the Cosmic Microwave Background Radiation

The Hierarchical Equal Area isoLatitude Pixelation (HEALPix) scheme is used extensively in astrophysics for data collection and analysis on the sphere. The scheme was originally designed for studying the Cosmic Microwave Background (CMB) radiation, which represents the first light to travel during the early stages of the universe's development and gives the strongest evidence for the Big Bang theory to date. Refined analysis of the CMB angular power spectrum can lead to revolutionary developments in understanding the nature of dark matter and dark energy. In this paper, we present a new method for performing spherical harmonic analysis for HEALPix data, which is a central component to computing and analyzing the angular power spectrum of the massive CMB data sets. The method uses a novel combination of a non-uniform fast Fourier transform, the double Fourier sphere method, and Slevinsky's fast spherical harmonic transform (Slevinsky, 2019). For a HEALPix grid with $N$ pixels (points), the computational complexity of the method is $\mathcal{O}(N\log^2 N)$, with an initial set-up cost of $\mathcal{O}(N^{3/2}\log N)$. This compares favorably with $\mathcal{O}(N^{3/2})$ runtime complexity of the current methods available in the HEALPix software when multiple maps need to be analyzed at the same time. Using numerical experiments, we demonstrate that the new method also appears to provide better accuracy over the entire angular power spectrum of synthetic data when compared to the current methods, with a convergence rate at least two times higher

Development of a minigenome cassette for Lettuce necrotic yellows virus: A first step in rescuing a plant cytorhabdovirus

Rhabdoviruses are enveloped negative-sense RNA viruses that have numerous biotechnological applications. However, recovering plant rhabdoviruses from cDNA remains difficult due to technical difficulties such as the need for concurrent in planta expression of the viral genome together with the viral nucleoprotein (N), phosphoprotein (P) and RNA-dependent RNA polymerase (L) and viral genome instability in E. coli. Here, we developed a negative-sense minigenome cassette for Lettuce necrotic yellows virus (LNYV). We introduced introns into the unstable viral ORF and employed Agrobacterium tumefaciens to co-infiltrate Nicotiana with the genes for the N, P, and L proteins together with the minigenome cassette. The minigenome cassette included the Discosoma sp. red fluorescent protein gene (DsRed) cloned in the negative-sense between the viral trailer and leader sequences which were placed between hammerhead and hepatitis delta ribozymes. In planta DsRed expression was demonstrated by western blotting while the appropriate splicing of introduced introns was confirmed by sequencing of RT-PCR product

Proton radii of 4,6,8He isotopes from high-precision nucleon-nucleon interactions

Recently, precision laser spectroscopy on 6He atoms determined accurately the isotope shift between 4He and 6He and, consequently, the charge radius of 6He. A similar experiment for 8He is under way. We have performed large-scale ab initio calculations for 4,6,8He isotopes using high-precision nucleon-nucleon (NN) interactions within the no-core shell model (NCSM) approach. With the CD-Bonn 2000 NN potential we found point-proton root-mean-square (rms) radii of 4He and 6He 1.45(1) fm and 1.89(4), respectively, in agreement with experiment and predict the 8He point proton rms radius to be 1.88(6) fm. At the same time, our calculations show that the recently developed nonlocal INOY NN potential gives binding energies closer to experiment, but underestimates the charge radii.Comment: 5 pages, 9 figure

An investigation of Fe XVI emission lines in solar and stellar EUV and soft X-ray spectra

New fully relativistic calculations of radiative rates and electron impact excitation cross sections for Fe XVI are used to determine theoretical emission-line ratios applicable to the 251 - 361 A and 32 - 77 A portions of the extreme-ultraviolet (EUV) and soft X-ray spectral regions, respectively. A comparison of the EUV results with observations from the Solar Extreme-Ultraviolet Research Telescope and Spectrograph (SERTS) reveals excellent agreement between theory and experiment. However, for emission lines in the 32 - 49 A portion of the soft X-ray spectral region, there are large discrepancies between theory and measurement for both a solar flare spectrum obtained with the X-Ray Spectrometer/Spectrograph Telescope (XSST) and observations of Capella from the Low Energy Transmission Grating Spectrometer (LETGS) on the Chandra X-ray Observatory. These are probably due to blending in the solar flare and Capella data from both first order lines and from shorter wavelength transitions detected in second and third order. By contrast, there is very good agreement between our theoretical results and the XSST and LETGS observations in the 50 - 77 A wavelength range, contrary to previous results. In particular, there is no evidence that the Fe XVI emission from the XSST flare arises from plasma at a much higher temperature than that expected for Fe XVI in ionization equilibrium, as suggested by earlier work.Comment: 6 pages, 4 tables, 1 figure, MNRAS in pres

Three-dimensional simulations of the orientation and structure of reconnection X-lines

This work employs Hall magnetohydrodynamic (MHD) simulations to study the X-lines formed during the reconnection of magnetic fields with differing strengths and orientations embedded in plasmas of differing densities. Although random initial perturbations trigger the growth of X-lines with many orientations, at late time a few robust X-lines sharing an orientation reasonably consistent with the direction that maximizes the outflow speed, as predicted by Swisdak and Drake [Geophys. Res. Lett., 34, L11106, (2007)], dominate the system. The existence of reconnection in the geometry examined here contradicts the suggestion of Sonnerup [J. Geophys. Res., 79, 1546 (1974)] that reconnection occurs in a plane normal to the equilibrium current. At late time the growth of the X-lines stagnates, leaving them shorter than the simulation domain.Comment: Accepted by Physics of Plasma

Host-Parasite Co-evolution and Optimal Mutation Rates for Semi-conservative Quasispecies

In this paper, we extend a model of host-parasite co-evolution to incorporate the semi-conservative nature of DNA replication for both the host and the parasite. We find that the optimal mutation rate for the semi-conservative and conservative hosts converge for realistic genome lengths, thus maintaining the admirable agreement between theory and experiment found previously for the conservative model and justifying the conservative approximation in some cases. We demonstrate that, while the optimal mutation rate for a conservative and semi-conservative parasite interacting with a given immune system is similar to that of a conservative parasite, the properties away from this optimum differ significantly. We suspect that this difference, coupled with the requirement that a parasite optimize survival in a range of viable hosts, may help explain why semi-conservative viruses are known to have significantly lower mutation rates than their conservative counterparts

On the 3-D structure and dissipation of reconnection-driven flow-bursts

The structure of magnetic reconnection-driven outflows and their dissipation are explored with large-scale, 3-D particle-in-cell (PIC) simulations. Outflow jets resulting from 3-D reconnection with a finite length x-line form fronts as they propagate into the downstream medium. A large pressure increase ahead of this ``reconnection jet front'' (RJF), due to reflected and transmitted ions, slows the front so that its velocity is well below the velocity of the ambient ions in the core of the jet. As a result, the RJF slows and diverts the high-speed flow into the direction perpendicular to the reconnection plane. The consequence is that the RJF acts as a thermalization site for the ion bulk flow and contributes significantly to the dissipation of magnetic energy during reconnection even though the outflow jet is subsonic. This behavior has no counterpart in 2-D reconnection. A simple analytic model predicts the front velocity and the fraction of the ion bulk flow energy that is dissipated