Failure of the Volume Function in Granular Statistical Mechanics and an Alternative Formulation

We first show that the currently accepted statistical mechanics for granular matter is flawed. The reason is that it is based on the volume function, which depends only on a minute fraction of all the structural degrees of freedom and is unaffected by most of the configurational microstates. Consequently, the commonly used partition function underestimates the entropy severely. We then propose a new formulation, replacing the volume function with a ${\it connectivity}$ function that depends on all the structural degrees of freedom and accounts correctly for the entire entropy. We discuss the advantages of the new formalism and derive explicit results for two- and three-dimensional systems. We test the formalism by calculating the entropy of an experimental two-dimensional system, as a function of system size, and showing that it is an extensive variable.Comment: 5 pages, 3 figure

Inter-dependence of the volume and stress ensembles and equipartition in statistical mechanics of granular systems

We discuss the statistical mechanics of granular matter and derive several significant results. First, we show that, contrary to common belief, the volume and stress ensembles are inter-dependent, necessitating the use of both. We use the combined ensemble to calculate explicitly expectation values of structural and stress-related quantities for two-dimensional systems. We thence demonstrate that structural properties may depend on the angoricity tensor and that stress-based quantities may depend on the compactivity. This calls into question previous statistical mechanical analyses of static granular systems and related derivations of expectation values. Second, we establish the existence of an intriguing equipartition principle - the total volume is shared equally amongst both structural and stress-related degrees of freedom. Third, we derive an expression for the compactivity that makes it possible to quantify it from macroscopic measurements.Comment: 5 pages, including 2 figures, To appear in Phys. Rev. Let

The Baryon Oscillation Spectroscopic Survey of SDSS-III

The Baryon Oscillation Spectroscopic Survey (BOSS) is designed to measure the scale of baryon acoustic oscillations (BAO) in the clustering of matter over a larger volume than the combined efforts of all previous spectroscopic surveys of large scale structure. BOSS uses 1.5 million luminous galaxies as faint as i=19.9 over 10,000 square degrees to measure BAO to redshifts z<0.7. Observations of neutral hydrogen in the Lyman alpha forest in more than 150,000 quasar spectra (g<22) will constrain BAO over the redshift range 2.15<z<3.5. Early results from BOSS include the first detection of the large-scale three-dimensional clustering of the Lyman alpha forest and a strong detection from the Data Release 9 data set of the BAO in the clustering of massive galaxies at an effective redshift z = 0.57. We project that BOSS will yield measurements of the angular diameter distance D_A to an accuracy of 1.0% at redshifts z=0.3 and z=0.57 and measurements of H(z) to 1.8% and 1.7% at the same redshifts. Forecasts for Lyman alpha forest constraints predict a measurement of an overall dilation factor that scales the highly degenerate D_A(z) and H^{-1}(z) parameters to an accuracy of 1.9% at z~2.5 when the survey is complete. Here, we provide an overview of the selection of spectroscopic targets, planning of observations, and analysis of data and data quality of BOSS.Comment: 49 pages, 16 figures, accepted by A

Validity and limitations of simple reaction kinetics to calculate concentrations of organic compounds from ion counts in PTR-MS

In September 2017, we conducted a proton-transfer-reaction mass-spectrometry (PTR-MS) intercomparison campaign at the CESAR observatory, a rural site in the central Netherlands near the village of Cabauw. Nine research groups deployed a total of 11 instruments covering a wide range of instrument types and performance. We applied a new calibration method based on fast injection of a gas standard through a sample loop. This approach allows calibrations on timescales of seconds, and within a few minutes an automated sequence can be run allowing one to retrieve diagnostic parameters that indicate the performance status. We developed a method to retrieve the mass-dependent transmission from the fast calibrations, which is an essential characteristic of PTR-MS instruments, limiting the potential to calculate concentrations based on counting statistics and simple reaction kinetics in the reactor/drift tube. Our measurements show that PTR-MS instruments follow the simple reaction kinetics if operated in the standard range for pressures and temperature of the reaction chamber (i.e. 1-4 mbar, 30-120 degrees, respectively), as well as a reduced field strength E/N in the range of 100-160 Td. If artefacts can be ruled out, it becomes possible to quantify the signals of uncalibrated organics with accuracies better than +/- 30 %. The simple reaction kinetics approach produces less accurate results at E/N levels below 100 Td, because significant fractions of primary ions form water hydronium clusters. Deprotonation through reactive collisions of protonated organics with water molecules needs to be considered when the collision energy is a substantial fraction of the exoergicity of the proton transfer reaction and/or if protonated organics undergo many collisions with water molecules.Peer reviewe

Collaborative fisheries research reveals reserve size and age determine efficacy across a network of marine protected areas

A variety of criteria may influence the efficacy of networks of marine protected areas (MPA) designed to enhance biodiversity conservation and provide fisheries benefits. Meta-analyses have evaluated the influence of MPA attributes on abundance, biomass, and size structure of harvested species, reporting that MPA size, age, depth, and connectivity influence the strength of MPA responses. However, few empirical MPA evaluation studies have used consistent sampling methodology across multiple MPAs and years. Our collaborative fisheries research program systematically sampled 12 no-take or highly protective limited-take MPAs and paired fished reference areas across a network spanning 1100 km of coastline to evaluate the factors driving MPA efficacy across a large geographic region. We found that increased size and age consistently contributed to increased fish catch, biomass, and positive species responses inside MPAs, while accounting for factors such as latitude, primary productivity, and distance to the nearest MPA. Our study provides a model framework to collaboratively engage diverse stakeholders in fisheries research and provide high-quality data to assess the success of conservation strategies

Vulnerability to climate change of managed stocks in the California Current large marine ecosystem

Introduction: Understanding how abundance, productivity and distribution of individual species may respond to climate change is a critical first step towards anticipating alterations in marine ecosystem structure and function, as well as developing strategies to adapt to the full range of potential changes. Methods: This study applies the NOAA (National Oceanic and Atmospheric Administration) Fisheries Climate Vulnerability Assessment method to 64 federally-managed species in the California Current Large Marine Ecosystem to assess their vulnerability to climate change, where vulnerability is a function of a species’ exposure to environmental change and its biological sensitivity to a set of environmental conditions, which includes components of its resiliency and adaptive capacity to respond to these new conditions. Results: Overall, two-thirds of the species were judged to have Moderate or greater vulnerability to climate change, and only one species was anticipated to have a positive response. Species classified as Highly or Very Highly vulnerable share one or more characteristics including: 1) having complex life histories that utilize a wide range of freshwater and marine habitats; 2) having habitat specialization, particularly for areas that are likely to experience increased hypoxia; 3) having long lifespans and low population growth rates; and/or 4) being of high commercial value combined with impacts from non-climate stressors such as anthropogenic habitat degradation. Species with Low or Moderate vulnerability are either habitat generalists, occupy deep-water habitats or are highly mobile and likely to shift their ranges. Discussion: As climate-related changes intensify, this work provides key information for both scientists and managers as they address the long-term sustainability of fisheries in the region. This information can inform near-term advice for prioritizing species-level data collection and research on climate impacts, help managers to determine when and where a precautionary approach might be warranted, in harvest or other management decisions, and help identify habitats or life history stages that might be especially effective to protect or restore

A long-period transiting substellar companion in the super-Jupiters to brown dwarfs mass regime and a prototypical warm-Jupiter detected by TESS

We report on the confirmation and follow-up characterization of two long-period transiting substellar companions on low-eccentricity orbits around TIC 4672985 and TOI-2529, whose transit events were detected by the TESS space mission. Ground-based photometric and spectroscopic follow-up from different facilities, confirmed the substellar nature of TIC 4672985 b, a massive gas giant, in the transition between the super Jupiters and brown dwarfs mass regime. From the joint analysis we derived the following orbital parameters: P = 69.0480 d, Mp = 12.74 Mjup, Rp = 1.026 Rjup and e = 0.018. In addition, the RV time series revealed a significant trend at the 350 m/s/yr level, which is indicative of the presence of a massive outer companion in the system. TIC 4672985 b is a unique example of a transiting substellar companion with a mass above the deuterium-burning limit, located beyond 0.1 AU and in a nearly circular orbit. These planetary properties are difficult to reproduce from canonical planet formation and evolution models. For TOI-2529 b, we obtained the following orbital parameters: P = 64.5949 d, Mp = 2.340 Mjup, Rp = 1.030 Rjup and e = 0.021, making this object a new example of a growing population of transiting warm giant planets.Comment: Accepted in A&

The khmer software package: enabling efficient nucleotide sequence analysis [version 1; referees: 2 approved, 1 approved with reservations]

The khmer package is a freely available software library for working efficiently with fixed length DNA words, or k-mers. khmer provides implementations of a probabilistic k-mer counting data structure, a compressible De Bruijn graph representation, De Bruijn graph partitioning, and digital normalization. khmer is implemented in C++ and Python, and is freely available under the BSD license at https://github.com/dib-lab/khmer/

The Baryon Oscillation Spectroscopic Survey of SDSS-III

The Baryon Oscillation Spectroscopic Survey (BOSS) is designed to measure the scale of baryon acoustic oscillations (BAO) in the clustering of matter over a larger volume than the combined efforts of all previous spectroscopic surveys of large-scale structure. BOSS uses 1.5 million luminous galaxies as faint as i = 19.9 over 10,000 deg(2) to measure BAO to redshifts z < 0.7. Observations of neutral hydrogen in the Ly alpha forest in more than 150,000 quasar spectra (g < 22) will constrain BAO over the redshift range 2.15 < z < 3.5. Early results from BOSS include the first detection of the large-scale three-dimensional clustering of the Ly alpha forest and a strong detection from the Data Release 9 data set of the BAO in the clustering of massive galaxies at an effective redshift z = 0.57. We project that BOSS will yield measurements of the angular diameter distance d(A) to an accuracy of 1.0% at redshifts z = 0.3 and z = 0.57 and measurements of H(z) to 1.8% and 1.7% at the same redshifts. Forecasts for Ly alpha forest constraints predict a measurement of an overall dilation factor that scales the highly degenerate D-A(z) and H-1(z) parameters to an accuracy of 1.9% at z similar to 2.5 when the survey is complete. Here, we provide an overview of the selection of spectroscopic targets, planning of observations, and analysis of data and data quality of BOSS