Recent developments of MCViNE and its applications at SNS

MCViNE is an open source, object-oriented Monte Carlo neutron ray-tracing simulation software package. Its design allows for flexible, hierarchical representations of sophisticated instrument components such as detector systems, and samples with a variety of shapes and scattering kernels. Recently this flexible design has enabled several applications of MCViNE simulations at the Spallation Neutron Source (SNS) at Oak Ridge National Lab, including assisting design of neutron instruments at the second target station and design of novel sample environments, as well as studying effects of instrument resolution and multiple scattering. Here we provide an overview of the recent developments and new features of MCViNE since its initial introduction (Jiao et al 2016 Nucl. Instrum. Methods Phys. Res., Sect. A 810, 86–99), and some example applications

Nonequilibrium Reweighting on the Driven Diffusive Lattice Gas

The nonequilibrium reweighting technique, which was recently developed by the present authors, is used for the study of the nonequilibrium steady states. The renewed formulation of the nonequlibrium reweighting enables us to use the very efficient multi-spin coding. We apply the nonequilibrium reweighting to the driven diffusive lattice gas model. Combining with the dynamical finite-size scaling theory, we estimate the critical temperature Tc and the dynamical exponent z. We also argue that this technique has an interesting feature that enables explicit calculation of derivatives of thermodynamic quantities without resorting to numerical differences.Comment: Accepted for publication in J. Phys. A (Lett.

Plumage development and molt in long-tailed manakins (chiroxiphia linearis): variation according to sex and age

Lek-mating Long-tailed Manakins (Chiroxiphia linearis) exhibit an unusual pattern of delayed plumage maturation. Each year, males progress through a series of predefinitive plumages before attaining definitive plumage in their fifth calendar year. Females also exhibit variation in plumage coloration, with some females displaying male-like plumage characteristics. Using data from mist-net captures in northwest Costa Rica (n = 1,315) and museum specimens from throughout the range of Long-tailed Manakins (n = 585), we documented the plumage sequence progression of males, explored variation in female plumage, and described the timing of molt in this species. Males progressed through a series of age-specific predefinitive plumages, which enabled the accurate aging of predefinitive-plumaged males in the field; this predefinitive plumage sequence is the basis for age-related status-signaling in these males. Females tended to acquire red coloration in the crown as they aged. However, colorful plumage in females may be a byproduct of selection on bright male plumage. Females exhibited an early peak of molt activity from February to April, little molt from May through July, and a second, more pronounced peak of molt activity in October. By contrast, males in older predefinitive-plumage stages and males in definitive plumage exhibited comparable unimodal distributions in molt activity beginning in June and peaking between July and October. Our data are consistent with selective pressure to avoid the costs of molt-breeding overlap in females and older males. Our findings have important implications for social organization and signaling in Long- tailed Manakins, and for the evolution of delayed plumage maturation in birds. Desarrollo del Plumaje y Muda en Chiroxiphia linearis: Variación de Acuerdo al Sexo y la Eda

Multilevel ensemble transform particle filtering

This paper extends the multilevel Monte Carlo variance reduction technique to nonlinear filtering. In particular, multilevel Monte Carlo is applied to a certain variant of the particle filter, the ensemble transform particle filter (EPTF). A key aspect is the use of optimal transport methods to re-establish correlation between coarse and fine ensembles after resampling; this controls the variance of the estimator. Numerical examples present a proof of concept of the effectiveness of the proposed method, demonstrating significant computational cost reductions (relative to the single-level ETPF counterpart) in the propagation of ensembles

The structure of the protoplanetary disk surrounding three young intermediate mass stars. II. Spatially resolved dust and gas distribution

[Abridged] We present the first direct comparison of the distribution of the gas, as traced by the [OI] 6300 AA emission, and the dust, as traced by the 10 micron emission, in the protoplanetary disk around three intermediate-mass stars: HD 101412, HD 135344 B and HD 179218. N-band visibilities were obtained with VLTI/MIDI. Simple geometrical models are used to compare the dust emission to high-resolution optical spectra in the 6300 AA [OI] line of the same targets. The disks around HD 101412 and HD 135344 B appear strongly flared in the gas, but self-shadowed in the dust beyond ~ 2 AU. In both systems, the 10 micron emission is rather compact (< 2 AU) while the [OI] brightness profile shows a double peaked structure. The inner peak is strongest and is consistent with the location of the dust, the outer peak is fainter and is located at 5-10 AU. Spatially extended PAH emission is found in both disks. The disk around HD 179218 is flared in the dust. The 10 micron emission emerges from a double ring-like structure with the first ring peaking at ~ 1 AU and the second at ~ 20 AU. No dust emission is detected between ~ 3 -- 15 AU. The oxygen emission seems also to come from a flared structure, however, the bulk of this emission is produced between ~ 1 -- 10 AU. This could indicate a lack of gas in the outer disk or could be due to chemical effects which reduce the abundance of OH -- the parent molecule of the observed [OI] emission -- further away from the star. The three systems, HD 179218, HD 135344 B and HD 101412, may form an evolutionary sequence: the disk initially flared becomes flat under the combined action of gas-dust decoupling, grain growth and dust settling.Comment: Accepted for publication in A&

Assembly of a high-resolution map of the Acadian Usher syndrome region and localization of the nuclear EF-hand acidic gene

Usher syndrome type 1C (USH1C) occurs in a small population of Acadian descendants from southwestern Louisiana. Linkage and linkage disequilibrium analyses localize USH1C to chromosome 11p between markers D11S1397 and D11S1888, an interval of less than 680 kb. Here, we refine the USH1C linkage to a region less than 400 kb, between genetic markers D11S1397 and D11S1890. Using 17 genetic markers from this interval, we have isolated a contiguous set of 60 bacterial artificial chromosomes (BACs) that span the USH1C critical region. Exon trapping of BAC clones from this region resulted in the recovery of an exon of the nuclear EF-hand acidic (NEFA) gene. However, DNA sequence analysis of the NEFA cDNA from lymphocytes of affected individuals provided no evidence of mutation, making structural mutations in the NEFA protein unlikely as the cellular cause of Acadian Usher syndrome. Copyright (C) 1998 Elsevier Science B.V

A survey for near-infrared H2 emission in Herbig Ae/Be stars: emission from the outer disks of HD 97048 and HD 100546

We report on a sensitive search for H2 1-0 S(1), 1-0 S(0) and 2-1 S(1) ro-vibrational emission at 2.12, 2.22 and 2.25 micron in a sample of 15 Herbig Ae/Be stars employing CRIRES, the ESO-VLT near-infrared high-resolution spectrograph, at R~90,000. We detect the H2 1-0 S(1) line toward HD 100546 and HD 97048. In the other 13 targets, the line is not detected. The H2 1-0 S(0) and 2-1 S(1) lines are undetected in all sources. This is the first detection of near-IR H2 emission in HD 100546. The H2 1-0 S(1) lines observed in HD 100546 and HD 97048 are observed at a velocity consistent with the rest velocity of both stars, suggesting that they are produced in the circumstellar disk. In HD 97048, the emission is spatially resolved and it is observed to extend at least up to 200 AU. We report an increase of one order of magnitude in the H2 1-0 S(1) line flux with respect to previous measurements taken in 2003 for this star, which suggests line variability. In HD 100546 the emission is tentatively spatially resolved and may extend at least up to 50 AU. Modeling of the H2 1-0 S(1) line profiles and their spatial extent with flat keplerian disks shows that most of the emission is produced at a radius >5 AU. Upper limits to the H2 1-0 S(0)/ 1-0 S(1) and H2 2-1 S(1)/1-0 S(1) line ratios in HD 97048 are consistent with H2 gas at T>2000 K and suggest that the emission observed may be produced by X-ray excitation. The upper limits for the line ratios for HD 100546 are inconclusive. Because the H2 emission is located at large radii, for both sources a thermal emission scenario (i.e., gas heated by collisions with dust) is implausible. We argue that the observation of H2 emission at large radii may be indicative of an extended disk atmosphere at radii >5 AU. This may be explained by a hydrostatic disk in which gas and dust are thermally decoupled or by a disk wind caused by photoevaporation.Comment: Accepted by A&A. 16 pages, 7 figure