The Genome in a Bottle Consortium, hosted by the National Institute of Standards and Technology (NIST) is creating reference materials and data for human genome sequencing, as well as methods for genome comparison and benchmarking. Here, we describe a large, diverse set of sequencing data for seven human genomes; five are current or candidate NIST Reference Materials. The pilot genome, NA12878, has been released as NIST RM 8398. We also describe data from two Personal Genome Project trios, one of Ashkenazim Jewish ancestry and one of Chinese ancestry. The data come from 12 technologies: BioNano Genomics, Complete Genomics paired-end and LFR, Ion Proton exome, Oxford Nanopore, Pacific Biosciences, SOLiD, 10X Genomics GemCode WGS, and Illumina exome and WGS paired-end, mate-pair, and synthetic long reads. Cell lines, DNA, and data from these individuals are publicly available. Therefore, we expect these data to be useful for revealing novel information about the human genome and improving sequencing technologies, SNP, indel, and structural variant calling, and de novo assembly.

/pdf/extensive-sequencing-of-seven-human-genomes-to-characterize-4ir8fj9m5s.pdf

Extensive sequencing of seven human genomes to characterize benchmark reference materials

Series expressions for the net radiation force and torque for a spherical particle illuminated by an arbitrarily defined monochromatic beam are derived utilizing the spherical‐particle/arbitrary‐beam interaction theory developed in an earlier paper. Calculations of net force and torque are presented for a 5‐μm‐diam water droplet in air optically levitated by a tightly focused (2 μm beam waist diameter) TEM00‐mode argon‐ion (λ=0.5145 μm) laser beam for on and off propagation axis, and on and off structural resonance conditions. Several features of these theoretical results are related to corresponding experimental observations.

Theoretical determination of net radiation force and torque for a spherical particle illuminated by a focused laser beam

The complex interplay of processes that govern the size, composition, phase and morphology of aerosol particles in the atmosphere is challenging to understand and model. Measurements on single aerosol particles (2 to 100 μm in diameter) held in electrodynamic, optical and acoustic traps or deposited on a surface can allow the individual processes to be studied in isolation under controlled laboratory conditions. In particular, measurements can now be made of particle size with unprecedented accuracy (sub-nanometre) and over a wide range of timescales (spanning from milliseconds to many days). The physical state of a particle can be unambiguously identified and its composition and phase can be resolved with a high degree of spatial resolution. In this review, we describe the advances made in our understanding of aerosol properties and processes from measurements made of phase behaviour, hygroscopic growth, morphology, vapour pressure and the kinetics of water transport for single particles. We also show that studies of the oxidative aging of single particles, although limited in number, can allow the interplay of these properties to be investigated. We conclude by considering the contributions that single particle measurements can continue to make to our understanding of the properties and processes occurring in atmospheric aerosol.

Exploring the complexity of aerosol particle properties and processes using single particle techniques

Roughness determines many functional properties of surfaces, such as adhesion, friction, and (thermal and electrical) contact conductance. Recent analytical models and simulations enable quantitative prediction of these properties from knowledge of the power spectral density (PSD) of the surface topography. The utility of the PSD is that it contains statistical information that is unbiased by the particular scan size and pixel resolution chosen by the researcher. In this article, we first review the mathematical definition of the PSD, including the one- and two-dimensional cases, and common variations of each. We then discuss strategies for reconstructing an accurate PSD of a surface using topography measurements at different size scales. Finally, we discuss detecting and mitigating artifacts at the smallest scales, and computing upper/lower bounds on functional properties obtained from models. We accompany our discussion with virtual measurements on computer-generated surfaces. This discussion summarizes how to analyze topography measurements to reconstruct a reliable PSD. Analytical models demonstrate the potential for tuning functional properties by rationally tailoring surface topography - however, this potential can only be achieved through the accurate, quantitative reconstruction of the power spectral density of real-world surfaces.

/pdf/quantitative-characterization-of-surface-topography-using-1di6n32wn5.pdf

Quantitative characterization of surface topography using spectral analysis

Roughness determines many functional properties of surfaces, such as adhesion, friction, and (thermal and electrical) contact conductance. Recent analytical models and simulations enable quantitative prediction of these properties from knowledge of the power spectral density (PSD) of the surface topography. The utility of the PSD is that it contains statistical information that is unbiased by the particular scan size and pixel resolution chosen by the researcher. In this article, we first review the mathematical definition of the PSD, including the one- and two-dimensional cases, and common variations of each. We then discuss strategies for reconstructing an accurate PSD of a surface using topography measurements at different size scales. Finally, we discuss detecting and mitigating artifacts at the smallest scales, and computing upper/lower bounds on functional properties obtained from models. We accompany our discussion with virtual measurements on computer-generated surfaces. This discussion summarizes how to analyze topography measurements to reconstruct a reliable PSD. Analytical models demonstrate the potential for tuning functional properties by rationally tailoring surface topography—however, this potential can only be achieved through the accurate, quantitative reconstruction of the PSDs of real-world surfaces.

/pdf/quantitative-characterization-of-surface-topography-using-45kh8tzr33.pdf

In this paper we summarize a number of previous experiments on the measurement of the roughness of metallic surfaces by light scattering. We identify several regimes that permit measurement of different surface parameters and functions, and we establish approximate limits for each regime. Using a straightforward criterion, we calculate that the smooth-surface regime, in which the angular distribution of scattered light is closely related to the power spectral density of the roughness, ranges over 0 < σ/λ ≲ 0.05, where σ is the rms roughness and λ is the opitcal wavelength. Above that the surfaceautocorrelation function may be calculated from a Fourier transform of the angular distribution over 0 < σ/λ ≲ 0.14. Then comes the specular regime where the specular beam can still be identified andmeasured over 0 < σ/λ ≲ 0.3. For all these regimes and for rougher surfaces too, the rms width of thescatter distribution is proportional to the rms slope of the surface.

Regimes of surface roughness measurable with light scattering

Observation of sharp resonances in the spontaneous Raman spectrum of a single optically levitated microdroplet

Resonances observed in the polarization ratio of light scattered at 90 degrees from single optically levitated evaporating droplets are shown to provide a means for continuous high-resolution monitoring of droplet size. Due to the distinctive character of the individual features in the polarization ratio, each experimentally measured feature could be clearly identified with a specific calculated one. For evaporating droplets of glycerol from 6.6 to 11.5 microm in diameter, the sharp features which appeared in the calculations at ~0.03-microm intervals allowed measurement of droplet diameter to a resolution of 0.003 microm.

Sizing of individual optically levitated evaporating droplets by measurement of resonances in the polarization ratio

Angle-resolved light scattering (ARLS) is used to estimate the root-mean-square (rms) slopes of rough surfaces having a well-defined lay, and the effect on slope measurements caused by changing the angles of incidence and scattering is investigated. The ARLS patterns are taken with the Detector Array for Laser Light Angular Scattering (Dallas) research instrument, and the rms slopes are obtained from the angular widths of these patterns. In general, it was found that the angular width, and thus the estimated rms slope, is surprisingly insensitive to relatively large changes in both the incident and scattering angles of light. These results are independent of surface material and are valid for both sinusoidal and random rough surfaces with lay. The principles, experiments, analyses, and conclusions involved in using ARLS to estimate rms surface slopes are described.

Light-scattering measurement of the rms slopes of rough surfaces

Donnees sur l'utilisation de spectroscopie Raman pour la caracterisation chimique de gouttelettes isolees des aerosols. Cas des gouttelettes de phtalate de dioctyle, de 10 a 35 μm de diametre, mises en suspension par un faisceau de laser d'ions Ar

Thomas R. Lettieri

Papers

Regimes of surface roughness measurable with light scattering

Observation of sharp resonances in the spontaneous Raman spectrum of a single optically levitated microdroplet

Sizing of individual optically levitated evaporating droplets by measurement of resonances in the polarization ratio

Light-scattering measurement of the rms slopes of rough surfaces

Characterization of single levitated droplets by Raman spectroscopy