Rarefaction

About: Rarefaction is a research topic. Over the lifetime, 1852 publications have been published within this topic receiving 26943 citations.

RTK: efficient rarefaction analysis of large datasets

Abstract: Motivation The rapidly expanding microbiomics field is generating increasingly larger datasets, characterizing the microbiota in diverse environments. Although classical numerical ecology methods provide a robust statistical framework for their analysis, software currently available is inadequate for large datasets and some computationally intensive tasks, like rarefaction and associated analysis. Results Here we present a software package for rarefaction analysis of large count matrices, as well as estimation and visualization of diversity, richness and evenness. Our software is designed for ease of use, operating at least 7x faster than existing solutions, despite requiring 10x less memory. Availability and implementation C ++ and R source code (GPL v.2) as well as binaries are available from https://github.com/hildebra/Rarefaction and from CRAN (https://cran.r-project.org/). Contact bork@embl.de or falk.hildebrand@embl.de. Supplementary information Supplementary data are available at Bioinformatics online.

The behaviour of a gas cavity impacted by a weak or strong shock wave

Abstract: Two-dimensional simulations of gas cavity responses to both weak shocks (p ≤ 30 MPa) and strong shocks (p ranging from 500 to 2000 MPa) are performed using a finite volume method. An artificial viscosity to capture the shock and a simple, stable, and adaptive mesh generation technique have been developed for the computations. The details of the shock propagation, rarefaction, transmission and bubble wall motions are obtained from the numerical computations. A weak shock is defined in the present context as one that does not cause liquid jet formation upon impact with the bubble. For this case, a large pressure is created within the gas upon collapse due to rapid compression of the gas, ultimately causing the re-expansion of the bubble. The bubble collapse and re-expansion time predicted by this model agree well with spherically symmetric computations. When impacted by strong shock waves, the bubble will collapse and a liquid jet is formed that propagates through the bubble to the opposite bubble wall. Jet speeds as high as 2000 m s -1 are predicted by this model.

Fast ion production by suprathermal electrons in laser fusion plasmas

Abstract: The acceleration of ions by two isothermal species of electrons, thermal and suprathermal, in a laser‐fusion plasma is investigated. The disassembly of an initially stationary plasma slab, including charge separation effects, is described. Before the rarefaction wave has penetrated appreciably into the slab, an interior Debye sheath which separates the suprathermal and thermal electrons, as well as an exterior sheath at the ion‐vacuum interface is found. As the rarefaction approaches the center of the slab, the dynamics is modified due to the conservation of species number and total energy. The energetics of the long‐time evolution is described by a quasi‐neutral similarity solution appropriate to finite two‐electron species systems.

Dispersive Dam-Break Flow of a Photon Fluid

Abstract: We investigate the temporal photonic analogue of the dam-break phenomenon for shallow water by exploiting a fiber optics setup. We clearly observe the decay of the steplike input (photonic dam) into a pair of oppositely propagating rarefaction wave and dispersive shock wave. Our results show evidence for a critical transition of the dispersive shock into a self-cavitating state. The detailed observation of the cavitating state dynamics allows for a fully quantitative test of the Whitham modulation theory applied to the universal defocusing nonlinear Schrodinger equation.

Lattice Boltzmann simulation of surface roughness effect on gaseous flow in a microchannel

Abstract: At the microscale level, it is impossible to obtain a completely smooth wall surface, and the effect of surface roughness may be a main factor responsible for some different characteristics between fluid flow in the microchannels and that in conventional size channels. In the present work, the lattice Boltzmann method is applied to investigate the gaseous flow in a microchannel with surface roughness which is modeled by an array of rectangular modules. The effects of relative surface roughness, roughness distribution, and rarefaction on gaseous flow are studied, but the compressibility effect is neglected since the Mach number is less than 0.2. It was shown that the surface roughness had an important influence on friction factor and mass flow rate. In particular, this effect becomes more significant with the decrease of the Knudsen number. This is because the rarefaction reduces the interaction between the gas molecules and the channel walls, which results in reduction of the surface roughness effect.