2-D reconstruction of atmospheric concentration peaks from horizontal long path DOAS tomographic measurements: parametrisation and geometry within a discrete approach

International audienceIn this study, we theoretically investigate the reconstruction of 2-D cross sections through Gaussian concentration distributions, e.g. emission plumes, from long path DOAS measurements along a limited number of light paths. This is done systematically with respect to the extension of the up to four peaks and for six different measurement setups with 2-4 telescopes and 36 light paths each. We distinguish between cases with and without additional background concentrations. Our approach parametrises the unknown distribution by local piecewise constant or linear functions on a regular grid and solves the resulting discrete, linear system by a least squares minimum norm principle. We show that the linear parametrisation not only allows better representation of the distributions in terms of discretisation errors, but also better inversion of the system. We calculate area integrals of the concentration field (i.e. total emissions rates for non-vanishing perpendicular wind speed components) and show that reconstruction errors and reconstructed area integrals within the peaks for narrow distributions crucially depend on the resolution of the reconstruction grid. A recently suggested grid translation method for the piecewise constant basis functions, combining reconstructions from several shifted grids, is modified for the linear basis functions and proven to reduce overall reconstruction errors, but not the uncertainty of concentration integrals. We suggest a procedure to subtract additional background concentration fields before inversion. We find large differences in reconstruction quality between the geometries and conclude that, in general, for a constant number of light paths increasing the number of telescopes leads to better reconstruction results. It appears that geometries that give better results for negligible measurement errors and parts of the geometry that are better resolved are also less sensitive to increasing measurement errors

SMaSH: A Benchmarking Toolkit for Human Genome Variant Calling

Motivation: Computational methods are essential to extract actionable information from raw sequencing data, and to thus fulfill the promise of next-generation sequencing technology. Unfortunately, computational tools developed to call variants from human sequencing data disagree on many of their predictions, and current methods to evaluate accuracy and computational performance are ad-hoc and incomplete. Agreement on benchmarking variant calling methods would stimulate development of genomic processing tools and facilitate communication among researchers. Results: We propose SMaSH, a benchmarking methodology for evaluating human genome variant calling algorithms. We generate synthetic datasets, organize and interpret a wide range of existing benchmarking data for real genomes, and propose a set of accuracy and computational performance metrics for evaluating variant calling methods on this benchmarking data. Moreover, we illustrate the utility of SMaSH to evaluate the performance of some leading single nucleotide polymorphism (SNP), indel, and structural variant calling algorithms. Availability: We provide free and open access online to the SMaSH toolkit, along with detailed documentation, at smash.cs.berkeley.edu

Error threshold in the evolution of diploid organisms

The effects of error propagation in the reproduction of diploid organisms are studied within the populational genetics framework of the quasispecies model. The dependence of the error threshold on the dominance parameter is fully investigated. In particular, it is shown that dominance can protect the wild-type alleles from the error catastrophe. The analysis is restricted to a diploid analogue of the single-peaked landscape.Comment: 9 pages, 4 Postscript figures. Submitted to J. Phy. A: Mat. and Ge

Dimer, trimer and FFLO liquids in mass- and spin-imbalanced trapped binary mixtures in one dimension

We present a systematic investigation of attractive binary mixtures in presence of both spin- and mass-imbalance in one dimensional setups described by the Hubbard model. After discussing typical cold atomic experimental realizations and the relation between microscopic and effective parameters, we study several many-body features of trapped Fermi-Fermi and Bose-Bose mixtures such as density profiles, momentum distributions and correlation functions by means of numerical density-matrix-renormalization-group and Quantum Monte Carlo simulations. In particular, we focus on the stability of Fulde-Ferrell-Larkin-Ovchinnikov, dimer and trimer fluids in inhomogeneous situations, as typically realized in cold gas experiments due to the harmonic confinement. We finally consider possible experimental signatures of these phases both in the presence of a finite polarization and of a finite temperature.Comment: 19 pages, 25 figure

A Population Genetic Approach to the Quasispecies Model

A population genetics formulation of Eigen's molecular quasispecies model is proposed and several simple replication landscapes are investigated analytically. Our results show a remarcable similarity to those obtained with the original kinetics formulation of the quasispecies model. However, due to the simplicity of our approach, the space of the parameters that define the model can be explored. In particular, for the simgle-sharp-peak landscape our analysis yelds some interesting predictions such as the existence of a maximum peak height and a mini- mum molecule length for the onset of the error threshold transition.Comment: 16 pages, 4 Postscript figures. Submited to Phy. Rev.

EHL traction analysis of perfluoropolyether fluids based on bulk modulus

Using three kinds of commercial perfluoropolyether (PFPE) fluids, the authors carried out high pressure density test at the pressure up to 1.2 GPa. Tangent bulk modulus and secant bulk modulus of the PFPE fluids were calculated by using the test results. Relationships of these moduli with pressure and temperature were examined. High pressure viscosity of each PFPE fluid was measured and the pressure viscosity coefficients of the PFPE fluids were obtained. In addition, the maximum traction coefficient and the limiting shear stress of each fluid were evaluated from the traction test employing a ball-on-disk testing machine. As a result, it was found that the maximum traction coefficient and the limiting shear stress are closely related to the tangent bulk modulus and the secant bulk modulus, respectively. The significant relationship of the maximum traction coefficient with the molecular packing parameter represented by the product of the pressure viscosity coefficient and the mean Hertzian pressure was also confirmed

General-Relativistic Curvature of Pulsar Vortex Structure

The motion of a neutron superfluid condensate in a pulsar is studied. Several theorems of general-relativistic hydrodynamics are proved for a superfluid. The average density distribution of vortex lines in pulsars and their general-relativistic curvature are derived.Comment: 18 pages, 1 figure

WTC2005-63183 EXPERIMENTAL STUDY OF REAL ROUGHNESS FEATURES WITHIN EHD POINT CONTACTS

ABSTRACT A combination of thin film colorimetric interferometry and phase shifting interferometry has been used to study the effect of slide-to-roll ratio on the micro-elastohydrodynamic action and asperity-contact mechanism on the real asperity scale. The phase shifting interferometry was used to measure in-situ initial undeformed rough surface profiles and thin film colorimetric interferometry provided accurate information about micro-EHD film thickness behaviour over a wide range of operating conditions. Lubricant film thickness distribution within mixed EHD contact has been found to change significantly as a function of a slide-roll ratio. A high resolution color camera has enabled a closer look at film thickness changes in the vicinity of surface irregularities that helped to describe these processes in detail. Obtained results indicate the presence of either a boundary film less than 1 nm thick or some solid-like contact in front of roughness features for positive slide to roll ratios. No such a local film thickness reduction has been found for negative slide-to-roll ratio conditions

Full phase stabilization of a Yb:fiber femtosecond frequency comb via high-bandwidth transducers

We present full phase stabilization of an amplified Yb:fiber femtosecond frequency comb using an intra-cavity electro-optic modulator and an acousto-optic modulator. These transducers provide high servo bandwidths of 580 kHz and 250 kHz for frep and fceo, producing a robust and low phase noise fiber frequency comb. The comb was self-referenced with an f - 2f interferometer and phase locked to an ultra-stable optical reference used for the JILA Sr optical clock at 698 nm, exhibiting 0.21 rad and 0.47 rad of integrated phase errors (over 1 mHz - 1 MHz) respectively. Alternatively, the comb was locked to two optical references at 698 nm and 1064 nm, obtaining 0.43 rad and 0.14 rad of integrated phase errors respectively