Regular Incidence Complexes, Polytopes, and C-Groups

Regular incidence complexes are combinatorial incidence structures generalizing regular convex polytopes, regular complex polytopes, various types of incidence geometries, and many other highly symmetric objects. The special case of abstract regular polytopes has been well-studied. The paper describes the combinatorial structure of a regular incidence complex in terms of a system of distinguished generating subgroups of its automorphism group or a flag-transitive subgroup. Then the groups admitting a flag-transitive action on an incidence complex are characterized as generalized string C-groups. Further, extensions of regular incidence complexes are studied, and certain incidence complexes particularly close to abstract polytopes, called abstract polytope complexes, are investigated.Comment: 24 pages; to appear in "Discrete Geometry and Symmetry", M. Conder, A. Deza, and A. Ivic Weiss (eds), Springe

Phase coexistence of cluster crystals: beyond the Gibbs phase rule

We report a study of the phase behavior of multiple-occupancy crystals through simulation. We argue that in order to reproduce the equilibrium behavior of such crystals it is essential to treat the number of lattice sites as a constraining thermodynamic variable. The resulting free-energy calculations thus differ considerably from schemes used for single-occupancy lattices. Using our approach, we obtain the phase diagram and the bulk modulus for a generalized exponential model that forms cluster crystals at high densities. We compare the simulation results with existing theoretical predictions. We also identify two types of density fluctuations that can lead to two sound modes and evaluate the corresponding elastic constants.Comment: 4 pages, 3 figure

Using sonic anemometer temperature to measure sensible heat flux in strong winds

Sonic anemometers simultaneously measure the turbulent fluctuations of vertical wind (<i>w</i>') and sonic temperature (<i>T</i><sub>s</sub>'), and are commonly used to measure sensible heat flux (<i>H</i>). Our study examines 30-min heat fluxes measured with a Campbell Scientific CSAT3 sonic anemometer above a subalpine forest. We compared <i>H</i> calculated with <i>T</i><sub>s</sub> to <i>H</i> calculated with a co-located thermocouple and found that, for horizontal wind speed (<i>U</i>) less than 8 m s<sup>−1</sup>, the agreement was around ±30 W m<sup>−2</sup>. However, for <i>U</i> ≈ 8 m s<sup>−1</sup>, the CSAT <i>H</i> had a generally positive deviation from <i>H</i> calculated with the thermocouple, reaching a maximum difference of ≈250 W m<sup>−2</sup> at <i>U</i> ≈ 18 m s<sup>−1</sup>. With version 4 of the CSAT firmware, we found significant underestimation of the speed of sound and thus <i>T</i><sub>s</sub> in high winds (due to a delayed detection of the sonic pulse), which resulted in the large CSAT heat flux errors. Although this <i>T</i><sub>s</sub> error is qualitatively similar to the well-known fundamental correction for the crosswind component, it is quantitatively different and directly related to the firmware estimation of the pulse arrival time. For a CSAT running version 3 of the firmware, there does not appear to be a significant underestimation of <i>T</i><sub>s</sub>; however, a <i>T</i><sub>s</sub> error similar to that of version 4 may occur if the CSAT is sufficiently out of calibration. An empirical correction to the CSAT heat flux that is consistent with our conceptual understanding of the <i>T</i><sub>s</sub> error is presented. Within a broader context, the surface energy balance is used to evaluate the heat flux measurements, and the usefulness of side-by-side instrument comparisons is discussed

The properties of fully flexible Lennard-Jones chains in the solid phase: Wertheim theory and simulation

NpT ensemble Monte Carlo simulations were performed for fully flexible Lennard-Jones chains in the solid phase. The bond length between monomers within the chains is fixed to $L=\sigma$ and the molecule is free to adopt any configuration. The solid structure of fully flexible chains is obtained by randomly locating the bonds of the chain within a face centered cubic close packed arrangement of atoms. For fully flexible chains it is believed that the stable solid phase is disordered. Such a solid is considered in this work. Computer simulations were performed for chains with $m=3, 4$ and 5 monomer units, and results were obtained for the equation of state and internal energy of the chains. An extension of Wertheim's TPT1 to the solid phase of Lennard-Jones chains (C.Vega, F.J.Blas and A.Galindo, J.Chem.Phys.,{\bf 116},7645,2002) has been proposed recently. The simulation results of this work provide a check on the performance of this theory. It is found that Wertheim's TPT1 successfully predicts the equation of state and internal energies of fully flexible LJ chains in the solid phase. Finally, a rigid LJ chain in a linear configuration has been considered. Computer simulations were also performed for the rigid chain in an ordered solid structure. It is found that fully flexible and linear rigid chains present quite different equations of state and different thermodynamic properties in the solid phase.Comment: PrEprint of the paper published in Molecular Physics volume 101, pp. 2241-2255 (2003

Soil, plant, and transport influences on methane in a subalpine forest under high ultraviolet irradiance

Recent studies have demonstrated direct methane emission from plant foliage under aerobic conditions, particularly under high ultraviolet (UV) irradiance. We examined the potential importance of this phenomenon in a high-elevation conifer forest using micrometeorological techniques. Vertical profiles of methane and carbon dioxide in forest air were monitored every 2 h for 6 weeks in summer 2007. Day to day variability in above-canopy CH<sub>4</sub> was high, with observed values in the range 1790 to 1910 nmol mol<sup>−1</sup>. High CH<sub>4</sub> was correlated with high carbon monoxide and related to wind direction, consistent with pollutant transport from an urban area by a well-studied mountain-plain wind system. Soils were moderately dry during the study. Vertical gradients of CH<sub>4</sub> were small but detectable day and night, both near the ground and within the vegetation canopy. Gradients near the ground were consistent with the forest soil being a net CH<sub>4</sub> sink. Using scalar similarity with CO<sub>2</sub>, the magnitude of the summer soil CH<sub>4</sub> sink was estimated at ~1.7 mg CH<sub>4</sub> m<sup>−2</sup> h<sup>−1</sup>, which is similar to other temperate forest upland soils. The high-elevation forest was naturally exposed to high UV irradiance under clear sky conditions, with observed peak UVB irradiance >2 W m<sup>−2</sup>. Gradients and means of CO<sub>2</sub> within the canopy under daytime conditions showed net uptake of CO<sub>2</sub> due to photosynthetic drawdown as expected. No evidence was found for a significant foliar CH<sub>4</sub> source in the vegetation canopy, even under high UV conditions. While the possibility of a weak foliar source cannot be excluded given the observed soil sink, overall this subalpine forest was a net sink for atmospheric methane during the growing season

Hydration of a B-DNA Fragment in the Method of Atom-atom Correlation Functions with the Reference Interaction Site Model Approximation

We propose an efficient numerical algorithm for solving integral equations of the theory of liquids in the Reference Interaction Site Model (RISM) approximation for infinitely dilute solution of macromolecules with a large number of atoms. The algorithm is based on applying the nonstationary iterative methods for solving systems of linear algebraic equations. We calculate the solvent-solute atom-atom correlation functions for a fragment of the B-DNA duplex d(GGGGG).d(CCCCC) in infinitely dilute aqueous solution. The obtained results are compared with available experimental data and results from computer simulations.Comment: 9 pages, RevTeX, 9 pages of ps figures, accepted for publications in JC

Revision in the first steps of the biosynthesis of the red antibiotic prodigiosin: use of a synthetic thioester to validate a new intermediate.

Funder: Frances and Augustus Newman FoundationFunder: Emmanuel College, University of CambridgeFunder: Cambridge Commonwealth TrustA biosynthetic pathway for the red-antibiotic, prodigiosin, was proposed over a decade ago but not all the suggested intermediates could be detected experimentally. Here we show that a thioester that was not originally included in the pathway is an intermediate. In addition, the enzyme PigE was originally described as a transaminase but we present evidence that it also catalyses the reduction of the thioester intermediate to its aldehyde substrate

Evidence of strong stabilizing effects on the evolution of boreoeutherian (Mammalia) dental proportions.

The dentition is an extremely important organ in mammals with variation in timing and sequence of eruption, crown morphology, and tooth size enabling a range of behavioral, dietary, and functional adaptations across the class. Within this suite of variable mammalian dental phenotypes, relative sizes of teeth reflect variation in the underlying genetic and developmental mechanisms. Two ratios of postcanine tooth lengths capture the relative size of premolars to molars (premolar-molar module, PMM), and among the three molars (molar module component, MMC), and are known to be heritable, independent of body size, and to vary significantly across primates. Here, we explore how these dental traits vary across mammals more broadly, focusing on terrestrial taxa in the clade of Boreoeutheria (Euarchontoglires and Laurasiatheria). We measured the postcanine teeth of N = 1,523 boreoeutherian mammals spanning six orders, 14 families, 36 genera, and 49 species to test hypotheses about associations between dental proportions and phylogenetic relatedness, diet, and life history in mammals. Boreoeutherian postcanine dental proportions sampled in this study carry conserved phylogenetic signal and are not associated with variation in diet. The incorporation of paleontological data provides further evidence that dental proportions may be slower to change than is dietary specialization. These results have implications for our understanding of dental variation and dietary adaptation in mammals

SGAS 143845.1+145407: A Big, Cool Starburst at Redshift 0.816

We present the discovery and a detailed multi-wavelength study of a strongly-lensed luminous infrared galaxy at z=0.816. Unlike most known lensed galaxies discovered at optical or near-infrared wavelengths this lensed source is red, r-Ks = 3.9 [AB], which the data presented here demonstrate is due to ongoing dusty star formation. The overall lensing magnification (a factor of 17) facilitates observations from the blue optical through to 500micron, fully capturing both the stellar photospheric emission as well as the re-processed thermal dust emission. We also present optical and near-IR spectroscopy. These extensive data show that this lensed galaxy is in many ways typical of IR-detected sources at z~1, with both a total luminosity and size in accordance with other (albeit much less detailed) measurements in samples of galaxies observed in deep fields with the Spitzer telescope. Its far-infrared spectral energy distribution is well-fit by local templates that are an order of magnitude less luminous than the lensed galaxy; local templates of comparable luminosity are too hot to fit. Its size (D~7kpc) is much larger than local luminous infrared galaxies, but in line with sizes observed for such galaxies at z~1. The star formation appears uniform across this spatial scale. In this source, the luminosity of which is typical of sources that dominate the cosmic infrared background, we find that star formation is spatially extended and well organised, quite unlike the compact merger-driven starbursts which are typical for sources of this luminosity at z~0.Comment: 18 pages, 10 figure

Adsorption hysteresis and capillary condensation in disordered porous solids: a density functional study

We present a theoretical study of capillary condensation of fluids adsorbed in mesoporous disordered media. Combining mean-field density functional theory with a coarse-grained description in terms of a lattice-gas model allows us to investigate both the out-of-equilibrium (hysteresis) and the equilibrium behavior. We show that the main features of capillary condensation in disordered solids result from the appearance of a complex free-energy landscape with a large number of metastable states. We detail the numerical procedures for finding these states, and the presence or absence of transitions in the thermodynamic limit is determined by careful finite-size studies.Comment: 30 pages, 18 figures. To appear in J. Phys.: Condens. Matte