XMDS2: Fast, scalable simulation of coupled stochastic partial differential equations

XMDS2 is a cross-platform, GPL-licensed, open source package for numerically integrating initial value problems that range from a single ordinary differential equation up to systems of coupled stochastic partial differential equations. The equations are described in a high-level XML-based script, and the package generates low-level optionally parallelised C++ code for the efficient solution of those equations. It combines the advantages of high-level simulations, namely fast and low-error development, with the speed, portability and scalability of hand-written code. XMDS2 is a complete redesign of the XMDS package, and features support for a much wider problem space while also producing faster code.Comment: 9 pages, 5 figure

Multi-region relaxed magnetohydrodynamics with anisotropy and flow

We present an extension of the multi-region relaxed magnetohydrodynamics (MRxMHD) equilibrium model that includes pressure anisotropy and general plasma flows. This anisotropic extension to our previous isotropic model is motivated by Sun and Finn's model of relaxed anisotropic magnetohydrodynamic equilibria. We prove that as the number of plasma regions becomes infinite, our anisotropic extension of MRxMHD reduces to anisotropic ideal MHD with flow. The continuously nested flux surface limit of our MRxMHD model is the first variational principle for anisotropic plasma equilibria with general flow fields.Comment: 11 pages, 2 figures. arXiv admin note: text overlap with arXiv:1401.307

Minimally Constrained Model of Self-Organized Helical States in Reversed-Field Pinches

We show that the self-organized single-helical-axis (SHAx) and double-axis (DAx) states in reversed field pinches can be reproduced in a minimally constrained equilibrium model using only five parameters. This is a significant reduction on previous repre

Generation of directional, coherent matter beams through dynamical instabilities in Bose-Einstein condensates

We present a theoretical analysis of a coupled, two-state Bose-Einstein condensate with non-equal scattering lengths, and show that dynamical instabilities can be excited. We demonstrate that these instabilities are exponentially amplified resulting in highly-directional, oppositely-propagating, coherent matter beams at specific momenta. To accomplish this we prove that the mean field of our system is periodic, and extend the standard Bogoliubov approach to consider a time-dependent, but cyclic, background. This allows us to use Floquet's theorem to gain analytic insight into such systems, rather than employing the usual Bogoliubov-de Gennes approach, which is usually limited to numerical solutions. We apply our theory to the metastable Helium atom laser experiment of Dall et al. [Phys. Rev. A 79, 011601(R) (2009)] and show it explains the anomalous beam profiles they observed. Finally we demonstrate the paired particle beams will be EPR-entangled on formation.Comment: Corrected reference

The Radiated Energy Budget of Chromospheric Plasma in a Major Solar Flare Deduced From Multi-Wavelength Observations

This paper presents measurements of the energy radiated by the lower solar atmosphere, at optical, UV, and EUV wavelengths, during an X-class solar flare (SOL2011-02-15T01:56) in response to an injection of energy assumed to be in the form of nonthermal electrons. Hard X-ray observations from RHESSI were used to track the evolution of the parameters of the nonthermal electron distribution to reveal the total power contained in flare accelerated electrons. By integrating over the duration of the impulsive phase, the total energy contained in the nonthermal electrons was found to be $>2\times10^{31}$ erg. The response of the lower solar atmosphere was measured in the free-bound EUV continua of H I (Lyman), He I, and He II, plus the emission lines of He II at 304\AA\ and H I (Ly$\alpha$) at 1216\AA\ by SDO/EVE, the UV continua at 1600\AA\ and 1700\AA\ by SDO/AIA, and the WL continuum at 4504\AA, 5550\AA, and 6684\AA, along with the Ca II H line at 3968\AA\ using Hinode/SOT. The summed energy detected by these instruments amounted to $\sim3\times10^{30}$ erg; about 15% of the total nonthermal energy. The Ly$\alpha$ line was found to dominate the measured radiative losses. Parameters of both the driving electron distribution and the resulting chromospheric response are presented in detail to encourage the numerical modelling of flare heating for this event, to determine the depth of the solar atmosphere at which these line and continuum processes originate, and the mechanism(s) responsible for their generation.Comment: 14 pages, 18 figures. Accepted for publication in Astrophysics Journa

The characterization and role of zinc binding in yeast Cox4.

Yeast Cox4 is a zinc binding subunit of cytochrome c oxidase. Cox4 is the only cofactor-containing subunit that is not directly part of the catalytic core of the enzyme located in the mitochondrial inner membrane. The Zn(II) site is shown to be distinct from the bovine ortholog, as it results from the x-ray structure of the entire cytochrome c oxidase in having a single histidyl residue and three conserved cysteines residues in the coordination sphere. Substitutions at the Cys ligand positions result in non-functional Cox4 proteins that fail to lead to cytochrome oxidase assembly. Limited function exists in His-119 mutants when overexpressed. Zn(II) binding in Cox4 is, therefore, important for the stability of the complex. The solution structure of yeast Cox4 elucidated by multidimensional NMR reveals a C-terminal globular domain consisting of two beta sheets analogous to the bovine ortholog except the loop containing the coordinating His in the yeast protein and the fourth Cys in the bovine protein are in different positions in the two structures. The conformation of this loop is dictated by the different sequence position of the fourth coordinating zinc ligand. The Zn(II) ion is buried within the domain, consistent with its role in structural stability. Potential functions of this matrix-facing subunit are discussed

The effects of inspiratory muscle training in older adults

Purpose: Declining inspiratory muscle function and structure and systemic low-level inflammation and oxidative stress may contribute to morbidity and mortality during normal ageing. Therefore, we examined the effects of inspiratory muscle training (IMT) in older adults on inspiratory muscle function and structure and systemic inflammation and oxidative stress, and re-examined the reported positive effects of IMT on respiratory muscle strength, inspiratory muscle endurance, spirometry, exercise performance, physical activity levels (PAL) and quality of life (QoL). Methods: Thirty-four healthy older adults (68 ± 3 years) with normal spirometry, respiratory muscle strength and physical fitness were divided equally into a pressure-threshold IMT or sham-hypoxic placebo group. Before and after an 8 week intervention, measurements were taken for dynamic inspiratory muscle function and inspiratory muscle endurance using a weighted plunger pressure-threshold loading device, diaphragm thickness using B-mode ultrasonography, plasma cytokine concentrations using immunoassays, DNA damage levels in peripheral blood mononuclear cells (PBMC) using Comet Assays, spirometry, maximal mouth pressures, exercise performance using a six minute walk test, PAL using a questionnaire and accelerometry, and QoL using a questionnaire

Effect of controlled hemorrhage on tissue and serum cefazolin clearance

Effects of blood loss on tissue and serum antibiotic levels were investigated in 30 New Zealand white rabbits. Studies were conducted over a 3.5-hr period after intravenous administration of cefazolin, 30 mg/kg, in control animals (Groups I and IV, n = 5 each) and animals having 50% (Groups II and V, n = 5 each) or 100% (Groups III and VI, n = 5 each) of their blood volume removed and replaced with either Ringer's solution (Groups I, II, and III) or rabbit whole blood (Groups IV, V, and VI) sufficient to maintain central venous pressures at baseline levels. Periodic samples of retroperitoneal fat, iliac artery, and serum were assayed for cefazolin concentration by disc diffusion. Decreased tissue antibiotic levels were observed in animals undergoing 100% blood replacement (Groups III and VI) compared to controls (Groups I and IV) in both fat (P [les] 0.01) and artery (P [les] 0.01) at 90 min. Decreased antibiotic serum half-life accompanying hemorrhage existed when comparing Group II to I (P [les] 0.05), Group III to I (P [les] 0.01), and Group IV to V (P [les] 0.01). The increased antibiotic clearance related to blood loss in this study justifies reassessment of intraoperative dosing intervals. More frequent dosing may be required to maintain stable tissue and serum antibiotic levels during substantial operative hemorrhage.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/29146/1/0000188.pd

Pre-discovery Activity of New Interstellar Comet 2I/Borisov Beyond 5 AU

Comet 2I/Borisov, the first unambiguous interstellar comet ever found, was discovered in August 2019 at $\sim3$ au from the Sun on its inbound leg. No pre-discovery detection beyond 3 au has yet been reported, mostly due to the comet's proximity to the Sun as seen from the Earth. Here we present a search for pre-discovery detections of comet Borisov using images taken by the Catalina Sky Survey (CSS), Pan-STARRS and Zwicky Transient Facility (ZTF), with a further comprehensive follow-up campaign being presented in \citet{Bolin2019}. We identified comet Borisov in ZTF images taken in May 2019 and use these data to update its orbit. This allowed us to identify the comet in images acquired as far back as December 2018, when it was 7.8 au from the Sun. The comet was not detected in November 2018 when it was 8.6 au from the Sun, possibly implying an onset of activity around this time. This suggests that the activity of the comet is either driven by a more volatile species other than H$_2$O, such as CO or CO$_2$, or by exothermic crystallization of amorphous ice. We derive the radius of the nucleus to be $<7$ km using the non-detection in November 2018, and estimate an area of $\sim0.5$---$10 \mathrm{km^2}$ has been active between December 2018 and September 2019, though this number is model-dependent and is highly uncertain. The behavior of comet Borisov during its inbound leg is observationally consistent with dynamically new comets observed in our solar system, suggesting some similarities between the two.Comment: AJ in pres