45 research outputs found
Quenched complexity of the p-spin spherical spin-glass with external magnetic field
We consider the p-spin spherical spin-glass model in the presence of an
external magnetic field as a general example of a mean-field system where a one
step replica symmetry breaking (1-RSB) occurs. In this context we compute the
complexity of the Thouless-Anderson-Palmer states, performing a quenched
computation. We find what is the general connection between this method and the
standard static 1-RSB one, formulating a clear mapping between the parameters
used in the two different calculations. We also perform a dynamical analysis of
the model, by which we confirm the validity of our results.Comment: RevTeX, 11 pages, including 2 EPS figure
First radial velocity results from the MINiature Exoplanet Radial Velocity Array (MINERVA)
The MINiature Exoplanet Radial Velocity Array (MINERVA) is a dedicated
observatory of four 0.7m robotic telescopes fiber-fed to a KiwiSpec
spectrograph. The MINERVA mission is to discover super-Earths in the habitable
zones of nearby stars. This can be accomplished with MINERVA's unique
combination of high precision and high cadence over long time periods. In this
work, we detail changes to the MINERVA facility that have occurred since our
previous paper. We then describe MINERVA's robotic control software, the
process by which we perform 1D spectral extraction, and our forward modeling
Doppler pipeline. In the process of improving our forward modeling procedure,
we found that our spectrograph's intrinsic instrumental profile is stable for
at least nine months. Because of that, we characterized our instrumental
profile with a time-independent, cubic spline function based on the profile in
the cross dispersion direction, with which we achieved a radial velocity
precision similar to using a conventional "sum-of-Gaussians" instrumental
profile: 1.8 m s over 1.5 months on the RV standard star HD 122064.
Therefore, we conclude that the instrumental profile need not be perfectly
accurate as long as it is stable. In addition, we observed 51 Peg and our
results are consistent with the literature, confirming our spectrograph and
Doppler pipeline are producing accurate and precise radial velocities.Comment: 22 pages, 9 figures, submitted to PASP, Peer-Reviewed and Accepte
Dynamics of heteropolymers in dilute solution: effective equation of motion and relaxation spectrum
The dynamics of a heteropolymer chain in solution is studied in the limit of
long chain length. Using functional integral representation we derive an
effective equation of motion, in which the heterogeneity of the chain manifests
itself as a time-dependent excluded volume effect. At the mean field level, the
heteropolymer chain is therefore dynamically equivalent to a homopolymer chain
with both time-independent and time-dependent excluded volume effects. The
perturbed relaxation spectrum is also calculated. We find that heterogeneity
also renormalizes the relaxation spectrum. However, we find, to the lowest
order in heterogeneity, that the relaxation spectrum does not exhibit any
dynamic freezing, at the point when static (equilibrium) ``freezing''
transition occurs in heteropolymer. Namely, the breaking of
fluctuation-dissipation theorem (FDT) proposed for spin glass dynamics does not
have dynamic effect in heteropolymer, as far as relaxation spectrum is
concerned. The implication of this result is discussed
Violation of the fluctuation-dissipation theorem in glassy systems: basic notions and the numerical evidence
This review reports on the research done during the past years on violations
of the fluctuation-dissipation theorem (FDT) in glassy systems. It is focused
on the existence of a quasi-fluctuation-dissipation theorem (QFDT) in glassy
systems and the currently supporting knowledge gained from numerical simulation
studies. It covers a broad range of non-stationary aging and stationary driven
systems such as structural-glasses, spin-glasses, coarsening systems,
ferromagnetic models at criticality, trap models, models with entropy barriers,
kinetically constrained models, sheared systems and granular media. The review
is divided into four main parts: 1) An introductory section explaining basic
notions related to the existence of the FDT in equilibrium and its possible
extension to the glassy regime (QFDT), 2) A description of the basic analytical
tools and results derived in the framework of some exactly solvable models, 3)
A detailed report of the current evidence in favour of the QFDT and 4) A brief
digression on the experimental evidence in its favour. This review is intended
for inexpert readers who want to learn about the basic notions and concepts
related to the existence of the QFDT as well as for the more expert readers who
may be interested in more specific results.Comment: 120 pages, 37 figures. Topical review paper . Several typos and
misprints corrected, new references included and others updated. to be
published in J. Phys. A (Math. Gen.
Genome sequence of the necrotrophic plant pathogen Pythium ultimum reveals original pathogenicity mechanisms and effector repertoire
Background: Pythium ultimum (P. ultimum) is a ubiquitous oomycete plant pathogen responsible for a variety of diseases on a broad range of crop and ornamental species. Results: The P. ultimum genome (42.8 Mb) encodes 15,290 genes and has extensive sequence similarity and synteny with related Phytophthora species, including the potato blight pathogen Phytophthora infestans. Whole transcriptome sequencing revealed expression of 86% of genes, with detectable differential expression of suites of genes under abiotic stress and in the presence of a host. The predicted proteome includes a large repertoire of proteins involved in plant pathogen interactions although surprisingly, the P. ultimum genome does not encode any classical RXLR effectors and relatively few Crinkler genes in comparison to related phytopathogenic oomycetes. A lower number of enzymes involved in carbohydrate metabolism were present compared to Phytophthora species, with the notable absence of cutinases, suggesting a significant difference in virulence mechanisms between P. ultimum and more host specific oomycete species. Although we observed a high degree of orthology with Phytophthora genomes, there were novel features of the P. ultimum proteome including an expansion of genes involved in proteolysis and genes unique to Pythium. We identified a small gene family of cadherins, proteins involved in cell adhesion, the first report in a genome outside the metazoans. Conclusions: Access to the P. ultimum genome has revealed not only core pathogenic mechanisms within the oomycetes but also lineage specific genes associated with the alternative virulence and lifestyles found within the pythiaceous lineages compared to the Peronosporaceae
Melanism in Peromyscus Is Caused by Independent Mutations in Agouti
Identifying the molecular basis of phenotypes that have evolved independently can provide insight into the ways genetic and developmental constraints influence the maintenance of phenotypic diversity. Melanic (darkly pigmented) phenotypes in mammals provide a potent system in which to study the genetic basis of naturally occurring mutant phenotypes because melanism occurs in many mammals, and the mammalian pigmentation pathway is well understood. Spontaneous alleles of a few key pigmentation loci are known to cause melanism in domestic or laboratory populations of mammals, but in natural populations, mutations at one gene, the melanocortin-1 receptor (Mc1r), have been implicated in the vast majority of cases, possibly due to its minimal pleiotropic effects. To investigate whether mutations in this or other genes cause melanism in the wild, we investigated the genetic basis of melanism in the rodent genus Peromyscus, in which melanic mice have been reported in several populations. We focused on two genes known to cause melanism in other taxa, Mc1r and its antagonist, the agouti signaling protein (Agouti). While variation in the Mc1r coding region does not correlate with melanism in any population, in a New Hampshire population, we find that a 125-kb deletion, which includes the upstream regulatory region and exons 1 and 2 of Agouti, results in a loss of Agouti expression and is perfectly associated with melanic color. In a second population from Alaska, we find that a premature stop codon in exon 3 of Agouti is associated with a similar melanic phenotype. These results show that melanism has evolved independently in these populations through mutations in the same gene, and suggest that melanism produced by mutations in genes other than Mc1r may be more common than previously thought
Another Shipment of Six Short-Period Giant Planets from TESS
We present the discovery and characterization of six short-period, transiting
giant planets from NASA's Transiting Exoplanet Survey Satellite (TESS) --
TOI-1811 (TIC 376524552), TOI-2025 (TIC 394050135), TOI-2145 (TIC 88992642),
TOI-2152 (TIC 395393265), TOI-2154 (TIC 428787891), & TOI-2497 (TIC 97568467).
All six planets orbit bright host stars (8.9 <G< 11.8, 7.7 <K< 10.1). Using a
combination of time-series photometric and spectroscopic follow-up observations
from the TESS Follow-up Observing Program (TFOP) Working Group, we have
determined that the planets are Jovian-sized (R = 1.00-1.45 R),
have masses ranging from 0.92 to 5.35 M, and orbit F, G, and K stars
(4753 T 7360 K). We detect a significant orbital eccentricity
for the three longest-period systems in our sample: TOI-2025 b (P = 8.872 days,
= ), TOI-2145 b (P = 10.261 days, =
), and TOI-2497 b (P = 10.656 days, =
). TOI-2145 b and TOI-2497 b both orbit subgiant host
stars (3.8 g 4.0), but these planets show no sign of inflation
despite very high levels of irradiation. The lack of inflation may be explained
by the high mass of the planets; M (TOI-2145
b) and M (TOI-2497 b). These six new discoveries
contribute to the larger community effort to use {\it TESS} to create a
magnitude-complete, self-consistent sample of giant planets with
well-determined parameters for future detailed studies.Comment: 20 Pages, 6 Figures, 8 Tables, Accepted by MNRA
The James Webb Space Telescope Mission
Twenty-six years ago a small committee report, building on earlier studies,
expounded a compelling and poetic vision for the future of astronomy, calling
for an infrared-optimized space telescope with an aperture of at least .
With the support of their governments in the US, Europe, and Canada, 20,000
people realized that vision as the James Webb Space Telescope. A
generation of astronomers will celebrate their accomplishments for the life of
the mission, potentially as long as 20 years, and beyond. This report and the
scientific discoveries that follow are extended thank-you notes to the 20,000
team members. The telescope is working perfectly, with much better image
quality than expected. In this and accompanying papers, we give a brief
history, describe the observatory, outline its objectives and current observing
program, and discuss the inventions and people who made it possible. We cite
detailed reports on the design and the measured performance on orbit.Comment: Accepted by PASP for the special issue on The James Webb Space
Telescope Overview, 29 pages, 4 figure
Recommended from our members
Complete vertebrate mitogenomes reveal widespread repeats and gene duplications
Abstract: Background: Modern sequencing technologies should make the assembly of the relatively small mitochondrial genomes an easy undertaking. However, few tools exist that address mitochondrial assembly directly. Results: As part of the Vertebrate Genomes Project (VGP) we develop mitoVGP, a fully automated pipeline for similarity-based identification of mitochondrial reads and de novo assembly of mitochondrial genomes that incorporates both long (> 10 kbp, PacBio or Nanopore) and short (100–300 bp, Illumina) reads. Our pipeline leads to successful complete mitogenome assemblies of 100 vertebrate species of the VGP. We observe that tissue type and library size selection have considerable impact on mitogenome sequencing and assembly. Comparing our assemblies to purportedly complete reference mitogenomes based on short-read sequencing, we identify errors, missing sequences, and incomplete genes in those references, particularly in repetitive regions. Our assemblies also identify novel gene region duplications. The presence of repeats and duplications in over half of the species herein assembled indicates that their occurrence is a principle of mitochondrial structure rather than an exception, shedding new light on mitochondrial genome evolution and organization. Conclusions: Our results indicate that even in the “simple” case of vertebrate mitogenomes the completeness of many currently available reference sequences can be further improved, and caution should be exercised before claiming the complete assembly of a mitogenome, particularly from short reads alone