16 research outputs found
New Insights into White-Light Flare Emission from Radiative-Hydrodynamic Modeling of a Chromospheric Condensation
(abridged) The heating mechanism at high densities during M dwarf flares is
poorly understood. Spectra of M dwarf flares in the optical and
near-ultraviolet wavelength regimes have revealed three continuum components
during the impulsive phase: 1) an energetically dominant blackbody component
with a color temperature of T 10,000 K in the blue-optical, 2) a smaller
amount of Balmer continuum emission in the near-ultraviolet at lambda 3646
Angstroms and 3) an apparent pseudo-continuum of blended high-order Balmer
lines. These properties are not reproduced by models that employ a typical
"solar-type" flare heating level in nonthermal electrons, and therefore our
understanding of these spectra is limited to a phenomenological interpretation.
We present a new 1D radiative-hydrodynamic model of an M dwarf flare from
precipitating nonthermal electrons with a large energy flux of erg
cm s. The simulation produces bright continuum emission from a
dense, hot chromospheric condensation. For the first time, the observed color
temperature and Balmer jump ratio are produced self-consistently in a
radiative-hydrodynamic flare model. We find that a T 10,000 K
blackbody-like continuum component and a small Balmer jump ratio result from
optically thick Balmer and Paschen recombination radiation, and thus the
properties of the flux spectrum are caused by blue light escaping over a larger
physical depth range compared to red and near-ultraviolet light. To model the
near-ultraviolet pseudo-continuum previously attributed to overlapping Balmer
lines, we include the extra Balmer continuum opacity from Landau-Zener
transitions that result from merged, high order energy levels of hydrogen in a
dense, partially ionized atmosphere. This reveals a new diagnostic of ambient
charge density in the densest regions of the atmosphere that are heated during
dMe and solar flares.Comment: 50 pages, 2 tables, 13 figures. Accepted for publication in the Solar
Physics Topical Issue, "Solar and Stellar Flares". Version 2 (June 22, 2015):
updated to include comments by Guest Editor. The final publication is
available at Springer via http://dx.doi.org/10.1007/s11207-015-0708-
Best practices for comparing optimization algorithms
Comparing, or benchmarking, of optimization algorithms is a complicated task
that involves many subtle considerations to yield a fair and unbiased
evaluation. In this paper, we systematically review the benchmarking process of
optimization algorithms, and discuss the challenges of fair comparison. We
provide suggestions for each step of the comparison process and highlight the
pitfalls to avoid when evaluating the performance of optimization algorithms.
We also discuss various methods of reporting the benchmarking results. Finally,
some suggestions for future research are presented to improve the current
benchmarking process.Comment: Optim Eng (2017
Oceanic core complex development at the ultraslow spreading Mid-Cayman Spreading Center
International audienceRoughly a third of the global mid-ocean ridge system spreads at 6 km) spreading centers, and thought to accrete some of the thinnest (∼3 km) crust. The MCSC generates end-member mid-ocean ridge basalt compositions and hosts recently discovered hydrothermal vents. Multibeam bathymetric data reveal that axial depth varies along the MCSC with intraridge rift walls defined by kilometer-scale escarpments and massifs. Dredging and near-bottom work has imaged and sampled predominantly basaltic lavas from the greatest axial depths and ∼15% peridotite surrounded by gabbroic rocks from the prominent massifs. The gabbroic rocks exhibit wide compositional variation (troctolites to ferrogabbros) and in many places contain high-temperature (amphibolite to granulite facies) shear zones. Gabbroic compositions primarily reflect the accumulation of near-liquidus phases that crystallized from a range of basaltic melts, as well as from interactions with interstitial melts in a subaxial mush zone. Magnetization variations inverted from aeromagnetic data are consistent with a discontinuous distribution of basaltic lavas and structurally asymmetric spreading. These observations support an oceanic core complex model for MCSC seafloor spreading, potentially making it a type example of ultraslow seafloor spreading through mush zone and detachment fault crustal processes
Towards complete and error-free genome assemblies of all vertebrate species
High-quality and complete reference genome assemblies are fundamental for the application of genomics to biology, disease, and biodiversity conservation. However, such assemblies are available for only a few non-microbial species1–4. To address this issue, the international Genome 10K (G10K) consortium5,6 has worked over a five-year period to evaluate and develop cost-effective methods for assembling highly accurate and nearly complete reference genomes. Here we present lessons learned from generating assemblies for 16 species that represent six major vertebrate lineages. We confirm that long-read sequencing technologies are essential for maximizing genome quality, and that unresolved complex repeats and haplotype heterozygosity are major sources of assembly error when not handled correctly. Our assemblies correct substantial errors, add missing sequence in some of the best historical reference genomes, and reveal biological discoveries. These include the identification of many false gene duplications, increases in gene sizes, chromosome rearrangements that are specific to lineages, a repeated independent chromosome breakpoint in bat genomes, and a canonical GC-rich pattern in protein-coding genes and their regulatory regions. Adopting these lessons, we have embarked on the Vertebrate Genomes Project (VGP), an international effort to generate high-quality, complete reference genomes for all of the roughly 70,000 extant vertebrate species and to help to enable a new era of discovery across the life sciences
Towards complete and error-free genome assemblies of all vertebrate species
The Vertebrate Genome Project has used an optimized pipeline to generate high-quality genome assemblies for sixteen species (representing all major vertebrate classes), which have led to new biological insights. High-quality and complete reference genome assemblies are fundamental for the application of genomics to biology, disease, and biodiversity conservation. However, such assemblies are available for only a few non-microbial species(1-4). To address this issue, the international Genome 10K (G10K) consortium(5,6) has worked over a five-year period to evaluate and develop cost-effective methods for assembling highly accurate and nearly complete reference genomes. Here we present lessons learned from generating assemblies for 16 species that represent six major vertebrate lineages. We confirm that long-read sequencing technologies are essential for maximizing genome quality, and that unresolved complex repeats and haplotype heterozygosity are major sources of assembly error when not handled correctly. Our assemblies correct substantial errors, add missing sequence in some of the best historical reference genomes, and reveal biological discoveries. These include the identification of many false gene duplications, increases in gene sizes, chromosome rearrangements that are specific to lineages, a repeated independent chromosome breakpoint in bat genomes, and a canonical GC-rich pattern in protein-coding genes and their regulatory regions. Adopting these lessons, we have embarked on the Vertebrate Genomes Project (VGP), an international effort to generate high-quality, complete reference genomes for all of the roughly 70,000 extant vertebrate species and to help to enable a new era of discovery across the life sciences
Towards complete and error-free genome assemblies of all vertebrate species.
High-quality and complete reference genome assemblies are fundamental for the application of genomics to biology, disease, and biodiversity conservation. However, such assemblies are available for only a few non-microbial species1-4. To address this issue, the international Genome 10K (G10K) consortium5,6 has worked over a five-year period to evaluate and develop cost-effective methods for assembling highly accurate and nearly complete reference genomes. Here we present lessons learned from generating assemblies for 16 species that represent six major vertebrate lineages. We confirm that long-read sequencing technologies are essential for maximizing genome quality, and that unresolved complex repeats and haplotype heterozygosity are major sources of assembly error when not handled correctly. Our assemblies correct substantial errors, add missing sequence in some of the best historical reference genomes, and reveal biological discoveries. These include the identification of many false gene duplications, increases in gene sizes, chromosome rearrangements that are specific to lineages, a repeated independent chromosome breakpoint in bat genomes, and a canonical GC-rich pattern in protein-coding genes and their regulatory regions. Adopting these lessons, we have embarked on the Vertebrate Genomes Project (VGP), an international effort to generate high-quality, complete reference genomes for all of the roughly 70,000 extant vertebrate species and to help to enable a new era of discovery across the life sciences