Effects of direction decoupling in flux calculation in finite volume solvers

In a finite volume CFD method for unsteady flow, fluxes of mass, momentum and energy are exchanged between cells over a series of small time steps. The conventional approach, which we will refer to as direction decoupling, is to estimate fluxes across interfaces in a regular array of cells by using a one-dimensional flux expression based on the component of flow velocity normal to the interface between cells. This means that fluxes cannot be exchanged between diagonally adjacent cells since they share no cell interface, even if the local flow conditions dictate that the fluxes should flow diagonally. The direction decoupling imposed by the numerical method requires that the fluxes reach a diagonally adjacent cell in two time-steps. In order to evaluate the e®ects of this direction decoupling, we examine two numerical methods which differ only in that one uses direction decoupling while the other does not. We examine a generalized form of Pullin's Equilibrium Flux Method (EFM) [J. Comput. Physics, v34, 1980, pp 231-244] which we have called the True Direction Equilibrium Flux Method (TDEFM). The TDEFM fluxes, derived from kinetic theory, flow not only between cells sharing an interface, but ultimately to any cell in the grid. TDEFM is used here to simulate a blast wave and an imploding flow problem on a structured rectangular mesh and is compared with results from direction decoupled EFM. Since both EFM and TDEFM are identical in the low CFL number limit, differences between the results demonstrate the detrimental e®ect of direction decoupling. Differences resulting from direction decoupling are also shown in the simulation of hypersonic flow over a rectangular body. The computational cost of allowing the EFM fluxes to flow in the correct directions on the grid is minimal

Spin-Dependent Macroscopic Forces from New Particle Exchange

Long-range forces between macroscopic objects are mediated by light particles that interact with the electrons or nucleons, and include spin-dependent static components as well as spin- and velocity-dependent components. We parametrize the long-range potential between two fermions assuming rotational invariance, and find 16 different components. Applying this result to electrically neutral objects, we show that the macroscopic potential depends on 72 measurable parameters. We then derive the potential induced by the exchange of a new gauge boson or spinless particle, and compare the limits set by measurements of macroscopic forces to the astrophysical limits on the couplings of these particles.Comment: 37 page

Accretion, Outflows, and Winds of Magnetized Stars

Many types of stars have strong magnetic fields that can dynamically influence the flow of circumstellar matter. In stars with accretion disks, the stellar magnetic field can truncate the inner disk and determine the paths that matter can take to flow onto the star. These paths are different in stars with different magnetospheres and periods of rotation. External field lines of the magnetosphere may inflate and produce favorable conditions for outflows from the disk-magnetosphere boundary. Outflows can be particularly strong in the propeller regime, wherein a star rotates more rapidly than the inner disk. Outflows may also form at the disk-magnetosphere boundary of slowly rotating stars, if the magnetosphere is compressed by the accreting matter. In isolated, strongly magnetized stars, the magnetic field can influence formation and/or propagation of stellar wind outflows. Winds from low-mass, solar-type stars may be either thermally or magnetically driven, while winds from massive, luminous O and B type stars are radiatively driven. In all of these cases, the magnetic field influences matter flow from the stars and determines many observational properties. In this chapter we review recent studies of accretion, outflows, and winds of magnetized stars with a focus on three main topics: (1) accretion onto magnetized stars; (2) outflows from the disk-magnetosphere boundary; and (3) winds from isolated massive magnetized stars. We show results obtained from global magnetohydrodynamic simulations and, in a number of cases compare global simulations with observations.Comment: 60 pages, 44 figure

Accretion discs, low-mass protostars and planets: probing the impact of magnetic fields on stellar formation

Whereas the understanding of most phases of stellar evolution made considerable progress throughout the whole of the twentieth century, stellar formation remained rather enigmatic and poorly constrained by observations until about three decades ago, when major discoveries (e.g., that protostars are often associated with highly collimated jets) revolutionized the field. At this time, it became increasingly clearer that magnetic fields were playing a major role at all stages of stellar formation. We describe herein a quick overview of the main breakthroughs that observations and theoretical modelling yielded for our understanding of how stars (and their planetary systems) are formed and on how much these new worlds are shaped by the presence of magnetic fields, either those pervading the interstellar medium and threading molecular clouds or those produced through dynamo processes in the convective envelopes of protostars or in the accretion discs from which they feed.Comment: Proceedings of CNRS/PNPS astrophysical school on "stellar magnetic fields", EAS Publications Serie

Gating choreography and mechanism of the human proton-activated chloride channel ASOR

The proton-activated chloride channel ASOR (TMEM206/PAC) permeates anions across cellular membranes in response to acidification, thereby enhancing acid-induced cell death and regulating endocytosis. The molecular mechanisms of pH-dependent control are not understood, in part because structural information for an activated conformation of ASOR is lacking. Here, we reconstitute function from purified protein and present a 3.1-Å-resolution cryo-electron microscopy structure of human ASOR at acidic pH in an activated conformation. The work contextualizes a previous acidic pH structure as a desensitized conformation. Combined with electrophysiological studies and high-resolution structures of resting and desensitized states, the work reveals mechanisms of proton sensing and ion pore gating. Clusters of extracellular acidic residues function as pH sensors and coalesce when protonated. Ensuing conformational changes induce metamorphosis of transmembrane helices to fashion an ion conduction pathway unique to the activated conformation. The studies identify a new paradigm of channel gating in this ubiquitous ion channel

Investigation of physiological pulsatile flow in a model arterial stenosis using large-eddy and direct numerical simulations

Physiologicalpulsatileflow in a 3D model of arterialstenosis is investigated by using largeeddysimulation (LES) technique. The computational domain chosen is a simple channel with a biological type stenosis formed eccentrically on the top wall. The physiological pulsation is generated at the inlet using the first harmonic of the Fourier series of pressure pulse. In LES, the large scale flows are resolved fully while the unresolved subgrid scale (SGS) motions are modelled using a localized dynamic model. Due to the narrowing of artery the pulsatileflow becomes transition-to-turbulent in the downstream region of the stenosis, where a high level of turbulent fluctuations is achieved, and some detailed information about the nature of these fluctuations are revealed through the investigation of the turbulent energy spectra. Transition-to-turbulent of the pulsatileflow in the post stenosis is examined through the various numerical results such as velocity, streamlines, velocity vectors, vortices, wall pressure and shear stresses, turbulent kinetic energy, and pressure gradient. A comparison of the LES results with the coarse DNS are given for the Reynolds number of 2000 in terms of the mean pressure, wall shear stress as well as the turbulent characteristics. The results show that the shear stress at the upper wall is low just prior to the centre of the stenosis, while it is maximum in the throat of the stenosis. But, at the immediate post stenotic region, the wall shear stress takes the oscillating form which is quite harmful to the blood cells and vessels. In addition, the pressure drops at the throat of the stenosis where the re-circulated flow region is created due to the adverse pressure gradient. The maximum turbulent kinetic energy is located at the post stenosis with the presence of the inertial sub-range region of slope −5/3

Population structure and breed composition prediction in a multi-breed sheep population using genome-wide single nucleotide polymorphism genotypes

peer-reviewedKnowledge of population structure and breed composition of a population can be advantageous for a number of reasons; these include designing optimal (cross)breeding strategies in order to maximise non-additive genetic effects, maintaining flockbook integrity by authenticating animals being registered and as a quality control measure in the genotyping process. The objectives of the present study were to 1) describe the population structure of 24 sheep breeds, 2) quantify the breed composition of both flockbook-recorded and crossbred animals using single nucleotide polymorphism BLUP (SNP-BLUP), and 3) quantify the accuracy of breed composition prediction from low-density genotype panels containing between 2000 and 6000 SNPs. In total, 9334 autosomal SNPs on 11 144 flockbook-recorded animals and 1172 crossbred animals were used. The population structure of all breeds was characterised by principal component analysis (PCA) as well as the pairwise breed fixation index (Fst). The total number of animals, all of which were purebred, included in the calibration population for SNP-BLUP was 2579 with the number of animals per breed ranging from 9 to 500. The remaining 9559 flockbook-recorded animals, composite breeds and crossbred animals represented the test population; three breeds were excluded from breed composition prediction. The breed composition predicted using SNP-BLUP with 9334 SNPs was considered the gold standard prediction. The pairwise breed Fst ranged from 0.040 (between the Irish Blackface and Scottish Blackface) to 0.282 (between the Border Leicester and Suffolk). Principal component analysis revealed that the Suffolk from Ireland and the Suffolk from New Zealand formed distinct, non-overlapping clusters. In contrast, the Texel from Ireland and that from New Zealand formed integrated, overlapping clusters. Composite animals such as the Belclare clustered close to its founder breeds (i.e., Finn, Galway, Lleyn and Texel). When all 9334 SNPs were used to predict breed composition, an animal that had a majority breed proportion predicted to be ≥0.90 was defined as purebred for the present study. As the panel density decreased, the predicted breed proportion threshold, used to identify animals as purebred, also decreased (≥0.85 with 6000 SNPs to ≥0.60 with 2000 SNPs). In all, results from the study suggest that breed composition for purebred and crossbred animals can be determined with SNP-BLUP using ≥5000 SNPs

KEYNOTE-716: Phase III study of adjuvant pembrolizumab versus placebo in resected high-risk stage II melanoma.

Patients with high-risk stage II melanoma are at significant risk for recurrence after surgical resection. Adjuvant treatment options to lower the risk for distant metastases are limited. Although adjuvant IFN-α2b is associated with improved relapse-free survival in patients with high-risk melanoma, toxicity and limited overall survival benefits limit its use. Adjuvant treatment with the PD-1 inhibitor pembrolizumab significantly improved recurrence-free survival, compared with placebo, in patients with resected stage III melanoma in the Phase III KEYNOTE-054 trial; efficacy in patients with stage II disease has not been established. This article describes the design and rationale of KEYNOTE-716 (NCT03553836), a two-part, randomized, placebo-controlled, multicenter Phase III study of adjuvant pembrolizumab in patients with surgically resected high-risk stage II melanoma. Clinical trial registry & ID: ClinicalTrials.gov, NCT0355383

Scalar-vector Lagrangian without nonlinear self-interactions of bosonic fields in the relativistic mean-field theory

A new Lagrangian model without nonlinear scalar self-interactions in the relativistic mean-field (RMF) theory is proposed. Introducing terms for scalar-vector interactions (SVI), we have developed a RMF Lagrangian model for finite nuclei and nuclear matter. It is shown that by inclusion of SVI in the basic RMF Lagrangian, the nonlinear sigma^3 and sigma^4 terms can be dispensed with. The SVI Lagrangian thus obtained provides a good description of ground-state properties of nuclei along the stability line as well as far away from it. This Lagrangian model is also able to describe experimental data on the breathing-mode giant monopole resonance energies well.Comment: A few statements corrected and updated. To be published in Phys. Lett.