Nonlinear shallow-water waves with vertical odd viscosity

The breaking of detailed balance in fluids through Coriolis forces or odd-viscous stresses has profound effects on the dynamics of surface waves. Here we explore both weakly and strongly non-linear waves in a three-dimensional fluid with vertical odd viscosity. Our model describes the free surface of a shallow fluid composed of nearly vertical vortex filaments, which all stand perpendicular to the surface. We find that the odd viscosity in this configuration induces previously unexplored non-linear effects in shallow-water waves, arising from both stresses on the surface and stress gradients in the bulk. By assuming weak nonlinearity, we find reduced equations including Korteweg-de Vries (KdV), Ostrovsky, and Kadomtsev-Petviashvilli (KP) equations with modified coefficients. At sufficiently large odd viscosity, the dispersion changes sign, allowing for compact two-dimensional solitary waves. We show that odd viscosity and surface tension have the same effect on the free surface, but distinct signatures in the fluid flow. Our results describe the collective dynamics of many-vortex systems, which can also occur in oceanic and atmospheric geophysics.Comment: 22 pages, 10 figure

Flow structure beneath periodic waves with constant vorticity under normal electric fields

Waves with constant vorticity and electrohydrodynamics flows are two topics in fluid dynamics that have attracted much attention from scientists for both the mathematical challenge and their industrial applications. The coupling of electric fields and vorticity is of significant research interest. In this paper, we study the flow structure of steady periodic travelling waves with constant vorticity on dielectric fluid under the effect of normal electric fields. Through the conformal mapping technique combined with pseudo-spectral numerical methods, we develop an approach that allows us to conclude that the flow can have zero, two or three stagnation points according to variations in the voltage potential. We describe in detail the recirculation zones that emerge together with the stagnation points. Besides, we show that the number of local maxima of the pressure on the bottom boundary is intrinsically connected to the saddle points

The Open Quantum Materials Database (OQMD): assessing the accuracy of DFT formation energies

The Open Quantum Materials Database (OQMD) is a high-throughput database currently consisting of nearly 300,000 density functional theory (DFT) total energy calculations of compounds from the Inorganic Crystal Structure Database (ICSD) and decorations of commonly occurring crystal structures. To maximise the impact of these data, the entire database is being made available, without restrictions, at www.oqmd.org/download. In this paper, we outline the structure and contents of the database, and then use it to evaluate the accuracy of the calculations therein by comparing DFT predictions with experimental measurements for the stability of all elemental ground-state structures and 1,670 experimental formation energies of compounds. This represents the largest comparison between DFT and experimental formation energies to date. The apparent mean absolute error between experimental measurements and our calculations is 0.096 eV/atom. In order to estimate how much error to attribute to the DFT calculations, we also examine deviation between different experimental measurements themselves where multiple sources are available, and find a surprisingly large mean absolute error of 0.082 eV/atom. Hence, we suggest that a significant fraction of the error between DFT and experimental formation energies may be attributed to experimental uncertainties. Finally, we evaluate the stability of compounds in the OQMD (including compounds obtained from the ICSD as well as hypothetical structures), which allows us to predict the existence of ~3,200 new compounds that have not been experimentally characterised and uncover trends in material discovery, based on historical data available within the ICSD

Capillary–gravity waves on a dielectric fluid of finite depth under normal electric field

In this work we consider two-dimensional capillary–gravity waves propagating under the influence of a vertical electric field on a dielectric of finite depth bounded above by a perfectly conducting and hydrodynamically passive fluid. Both linear and weakly nonlinear theories are developed, and long-wave model equations are derived based on the analyticity of the Dirichlet–Neumann operator. Fully nonlinear computations are carried out by using a time-dependent conformal mapping method. Solitary waves are found, and their stability characteristics subject to longitudinal perturbations are studied numerically. The shedding of stable solitary waves is achieved by moving a Gaussian pressure on the free surface with the speed close to a phase speed minimum and removing the pressure after a period of time. The novel result shows that a depression bright solitary wave and an elevation generalized solitary wave co-exist in the solitary-wave excitation

STAR-Fusion: Fast and Accurate Fusion Transcript Detection from RNA-Seq

Motivation Fusion genes created by genomic rearrangements can be potent drivers of tumorigenesis. However, accurate identification of functionally fusion genes from genomic sequencing requires whole genome sequencing, since exonic sequencing alone is often insufficient. Transcriptome sequencing provides a direct, highly effective alternative for capturing molecular evidence of expressed fusions in the precision medicine pipeline, but current methods tend to be inefficient or insufficiently accurate, lacking in sensitivity or predicting large numbers of false positives. Here, we describe STAR-Fusion, a method that is both fast and accurate in identifying fusion transcripts from RNA-Seq data. Results We benchmarked STAR-Fusion’s fusion detection accuracy using both simulated and genuine Illumina paired-end RNA-Seq data, and show that it has superior performance compared to popular alternative fusion detection methods. Availability and implementation STAR-Fusion is implemented in Perl, freely available as open source software at http://star-fusion.github.io, and supported on Linux

Harnessing the NEON data revolution to advance open environmental science with a diverse and data-capable community

It is a critical time to reflect on the National Ecological Observatory Network (NEON) science to date as well as envision what research can be done right now with NEON (and other) data and what training is needed to enable a diverse user community. NEON became fully operational in May 2019 and has pivoted from planning and construction to operation and maintenance. In this overview, the history of and foundational thinking around NEON are discussed. A framework of open science is described with a discussion of how NEON can be situated as part of a larger data constellation—across existing networks and different suites of ecological measurements and sensors. Next, a synthesis of early NEON science, based on >100 existing publications, funded proposal efforts, and emergent science at the very first NEON Science Summit (hosted by Earth Lab at the University of Colorado Boulder in October 2019) is provided. Key questions that the ecology community will address with NEON data in the next 10 yr are outlined, from understanding drivers of biodiversity across spatial and temporal scales to defining complex feedback mechanisms in human–environmental systems. Last, the essential elements needed to engage and support a diverse and inclusive NEON user community are highlighted: training resources and tools that are openly available, funding for broad community engagement initiatives, and a mechanism to share and advertise those opportunities. NEON users require both the skills to work with NEON data and the ecological or environmental science domain knowledge to understand and interpret them. This paper synthesizes early directions in the community’s use of NEON data, and opportunities for the next 10 yr of NEON operations in emergent science themes, open science best practices, education and training, and community building

Large mode-2 internal solitary waves in three-layer flows

In this paper, we investigate mode-2 solitary waves in a three-layer stratified flow model. Localised travelling wave solutions to both the fully nonlinear problem (Euler equations), and the three-layer Miyata-Choi-Camassa equations are found numerically and compared. Mode-2 solitary waves with speeds slower than the linear mode-1 long-wave speed are typically generalised solitary waves with infinite tails consisting of a resonant mode-one periodic wave train. Herein we evidence the existence of mode-2 embedded solitary waves, that is, we show that for specific values of the parameters, the amplitude of the oscillations in the tail are zero. For sufficiently thick middle layers, we also find branches of mode-2 solitary waves with speeds that extend beyond the mode-1 linear waves and are no longer embedded. In addition, we show how large amplitude embedded solitary waves are intimately linked to the conjugate states of the problem.Comment: 28 pages, 24 figure