Amino acid metabolism conflicts with protein diversity

The twenty protein coding amino acids are found in proteomes with different relative abundances. The most abundant amino acid, leucine, is nearly an order of magnitude more prevalent than the least abundant amino acid, cysteine. Amino acid metabolic costs differ similarly, constraining their incorporation into proteins. On the other hand, sequence diversity is necessary for protein folding, function and evolution. Here we present a simple model for a cost-diversity trade-off postulating that natural proteomes minimize amino acid metabolic flux while maximizing sequence entropy. The model explains the relative abundances of amino acids across a diverse set of proteomes. We found that the data is remarkably well explained when the cost function accounts for amino acid chemical decay. More than one hundred proteomes reach comparable solutions to the trade-off by different combinations of cost and diversity. Quantifying the interplay between proteome size and entropy shows that proteomes can get optimally large and diverse

The Transiting Exoplanet Community Early Release Science Program for JWST

The James Webb Space Telescope (JWST) presents the opportunity to transform our understanding of planets and the origins of life by revealing the atmospheric compositions, structures, and dynamics of transiting exoplanets in unprecedented detail. However, the high-precision, timeseries observations required for such investigations have unique technical challenges, and prior experience with Hubble, Spitzer, and other facilities indicates that there will be a steep learning curve when JWST becomes operational. In this paper, we describe the science objectives and detailed plans of the Transiting Exoplanet Community Early Release Science (ERS) Program, which is a recently approved program for JWST observations early in Cycle 1. We also describe the simulations used to establish the program. The goal of this project, for which the obtained data will have no exclusive access period, is to accelerate the acquisition and diffusion of technical expertise for transiting exoplanet observations with JWST, while also providing a compelling set of representative data sets that will enable immediate scientific breakthroughs. The Transiting Exoplanet Community ERS Program will exercise the timeseries modes of all four JWST instruments that have been identified as the consensus highest priorities, observe the full suite of transiting planet characterization geometries (transits, eclipses, and phase curves), and target planets with host stars that span an illustrative range of brightnesses. The observations in this program were defined through an inclusive and transparent process that had participation from JWST instrument experts and international leaders in transiting exoplanet studies. The targets have been vetted with previous measurements, will be observable early in the mission, and have exceptional scientific merit. Community engagement in the project will be centered on a two-phase Data Challenge that culminates with the delivery of planetary spectra, timeseries instrument performance reports, and open-source data analysis toolkits in time to inform the agenda for Cycle 2 of the JWST mission

Introducing a level-set based shape and topology optimization method for the wear of composite materials with geometric constraints

International audienceThe wear of materials continues to be a limiting factor in the lifetime and performance of mechanical systems with sliding surfaces. As the demand for low wear materials grows so does the need for models and methods to systematically optimize tribological systems. Elastic foundation models offer a simplified framework to study the wear of multimaterial composites subject to abrasive sliding. Previously, the evolving wear profile has been shown to converge to a steady-state that is characterized by a time-independent elliptic equation. In this article, the steady-state formulation is generalized and integrated with shape optimization to improve the wear performance of bi-material composites. Both macroscopic structures and periodic material microstructures are considered. Several common tribological objectives for systems undergoing wear are identified and mathematically formalized with shape derivatives. These include (i) achieving a planar wear surface from multimaterial composites and (ii) minimizing the run-in volume of material lost before steady-state wear is achieved. A level-set based topology optimization algorithm that incorporates a novel constraint on the level-set function is presented. In particular, a new scheme is developed to update material interfaces ; the scheme (i) conveniently enforces volume constraints at each iteration, (ii) controls the complexity of design features using perimeter penalization, and (iii) nucleates holes or inclusions with the topological gradient. The broad applicability of the proposed formulation for problems beyond wear is discussed, especially for problems where convenient control of the complexity of geometric features is desired

Pyrochemical multiplicity counter development

Impure plutonium-bearing materials from pyrochemical processes often display both significant self-multiplication and variable ({alpha},n) reaction rates. Standard neutron coincidence counting techniques usually fail to accurately measure these materials. Neutron multiplicity counters measure the third moment of the neutron multiplicity distribution and thus make it possible to deduce the fertile plutonium mass of a sample even when both the self-multiplication and the ({alpha},n) reaction rate are unknown. A multiplicity counter suitable for measuring pyrochemical materials has been designed and built. This paper describes the results of characterization studies for the new counter. The counter consists of 126 helium-3 tubes arranged in 4 concentric rings in a polyethylene moderator; the average spacing between the tubes is 1.59 cm. The end plugs for the counter are made of graphite, and the 24.1- by 37.5-cm sample cavity is cadmium lined. The counter consists of two distinct halves from which the neutron counts are summed. The counter is capable of operation in either a freestanding mode with the two halves coupled together by an external cabinet or in a glove-box mode with the two halves placed around a glovebox well and then mated. For a {sup 252}Cf source centered in the sample cavity, the measured efficiency of the new multiplicity counter is 57.7% and its die-away time is 47.2{mu}s. 8 refs., 9 figs

Dynamical difference between the cD galaxy and the stellar diffuse component in simulated galaxy clusters

Member galaxies within galaxy clusters nowadays can be routinely identified in cosmological, hydrodynamical simulations using methods based on identifying self bound, locally over dense substructures. However, distinguishing the central galaxy from the stellar diffuse component within clusters is notoriously difficult, and in the center it is not even clear if two distinct stellar populations exist. Here, after subtracting all member galaxies, we use the velocity distribution of the remaining stars and detect two dynamically, well-distinct stellar components within simulated galaxy clusters. These differences in the dynamics can be used to apply an un-binding procedure which leads to a spatial separation of the two components into a cD and a diffuse stellar component (DSC). Applying our new algorithm to a cosmological, hydrodynamical simulation we find that -- in line with previous studies -- these two components have clearly distinguished spatial and velocity distributions as well as different star formation histories. We show that the DSC fraction -- which can broadly be associated with the observed intra cluster light -- does not depend on the virial mass of the galaxy cluster and is much more sensitive to the formation history of the cluster. We conclude that the separation of the cD and the DSC in simulations, based on our dynamical criteria, is more physically motivated than current methods which depend on implicit assumptions on a length scale associated with the cD galaxy and therefore represent a step forward in understanding the different stellar components within galaxy clusters. Our results also show the importance of analyzing the dynamics of the DSC to characterize its properties and understand its origin.Comment: 15 pages, 18 figures, MNRAS in pres

The faint stellar halos of massive red galaxies from stacks of more than 42000 SDSS LRG images

We study the properties of massive galaxies at an average redshift of z~0.34 through stacking more than 42000 images of Luminous Red Galaxies from the Sloan Digital Sky Survey. This is the largest dataset ever used for such an analysis and it allows us to explore the outskirts of massive red galaxies at unprecedented physical scales. Our image stacks extend farther than 400 kpc, where the r-band profile surface brightness reaches 30 mag arcsec-2. This analysis confirms that the stellar bodies of luminous red galaxies follow a simple Sersic profile out to 100 kpc. At larger radii the profiles deviate from the best-fit Sersic models and exhibit extra light in the g, r, i and z-band stacks. This excess light can probably be attributed to unresolved intragroup or intracluster light or a change in the light profile itself. We further show that standard analyses of SDSS-depth images typically miss 20% of the total stellar light and underestimate the size of LRGs by 10% compared to our best fit r-band Sersic model of n=5.5 and r_e=13.1 kpc. If the excess light at r>100 kpc is considered to be part of the galaxy, the best fit r-band Sersic parameters are n=5.8 and r_e=13.6 kpc. In addition we study the radially dependent stack ellipticity and find an increase with radius from e=0.25 at r=10 kpc to e=0.3 at r=100 kpc. This provides support that the stellar light that we trace out to at least 100 kpc is physically associated with the galaxies themselves and may confirm that the halos of individual LRGs have higher ellipticities than their central parts. Lastly we show that the broadband color gradients of the stacked images are flat beyond roughly 40 kpc, suggesting that the stellar populations do not vary significantly with radius in the outer parts of massive ellipticals.Comment: Accepted for publication in Ap

Calibration and data quality of warm IRAC

We present an overview of the calibration and properties of data from the IRAC instrument aboard the Spitzer Space Telescope taken after the depletion of cryogen. The cryogen depleted on 15 May 2009, and shortly afterward a two-month- long calibration and characterization campaign was conducted. The array temperature and bias setpoints were revised on 19 September 2009 to take advantage of lower than expected power dissipation by the instrument and to improve sensitivity. The final operating temperature of the arrays is 28.7 K, the applied bias across each detector is 500 mV and the equilibrium temperature of the instrument chamber is 27.55 K. The final sensitivities are essentially the same as the cryogenic mission with the 3.6 μm array being slightly less sensitive (10%) and the 4.5 μm array within 5% of the cryogenic sensitivity. The current absolute photometric uncertainties are 4% at 3.6 and 4.5 μm, and better than milli-mag photometry is achievable for long-stare photometric observations. With continued analysis, we expect the absolute calibration to improve to the cryogenic value of 3%. Warm IRAC operations fully support all science that was conducted in the cryogenic mission and all currently planned warm science projects (including Exploration Science programs). We expect that IRAC will continue to make ground-breaking discoveries in star formation, the nature of the early universe, and in our understanding of the properties of exoplanets