AFLOW-SYM: Platform for the complete, automatic and self-consistent symmetry analysis of crystals

Determination of the symmetry profile of structures is a persistent challenge in materials science. Results often vary amongst standard packages, hindering autonomous materials development by requiring continuous user attention and educated guesses. Here, we present a robust procedure for evaluating the complete suite of symmetry properties, featuring various representations for the point-, factor-, space groups, site symmetries, and Wyckoff positions. The protocol determines a system-specific mapping tolerance that yields symmetry operations entirely commensurate with fundamental crystallographic principles. The self consistent tolerance characterizes the effective spatial resolution of the reported atomic positions. The approach is compared with the most used programs and is successfully validated against the space group information provided for over 54,000 entries in the Inorganic Crystal Structure Database. Subsequently, a complete symmetry analysis is applied to all 1.7$+$ million entries of the AFLOW data repository. The AFLOW-SYM package has been implemented in, and made available for, public use through the automated, $\textit{ab-initio}$ framework AFLOW.Comment: 24 pages, 6 figure

A multi-zone model for simulating the high energy variability of TeV blazars

We present a time-dependent multi-zone code for simulating the variability of Synchrotron-Self Compton (SSC) sources. The code adopts a multi-zone pipe geometry for the emission region, appropriate for simulating emission from a standing or propagating shock in a collimated jet. Variations in the injection of relativistic electrons in the inlet propagate along the length of the pipe cooling radiatively. Our code for the first time takes into account the non-local, time-retarded nature of synchrotron self-Compton (SSC) losses that are thought to be dominant in TeV blazars. The observed synchrotron and SSC emission is followed self-consistently taking into account light travel time delays. At any given time, the emitting portion of the pipe depends on the frequency and the nature of the variation followed. Our simulation employs only one additional physical parameter relative to one-zone models, that of the pipe length and is computationally very efficient, using simplified expressions for the SSC processes. The code will be useful for observers modeling GLAST, TeV, and X-ray observations of SSC blazars.Comment: ApJ, accepte

Model of ionic currents through microtubule nanopores and the lumen

It has been suggested that microtubules and other cytoskeletal filaments may act as electrical transmission lines. An electrical circuit model of the microtubule is constructed incorporating features of its cylindrical structure with nanopores in its walls. This model is used to study how ionic conductance along the lumen is affected by flux through the nanopores when an external potential is applied across its two ends. Based on the results of Brownian dynamics simulations, the nanopores were found to have asymmetric inner and outer conductances, manifested as nonlinear IV curves. Our simulations indicate that a combination of this asymmetry and an internal voltage source arising from the motion of the C-terminal tails causes a net current to be pumped across the microtubule wall and propagate down the microtubule through the lumen. This effect is demonstrated to enhance and add directly to the longitudinal current through the lumen resulting from an external voltage source, and could be significant in amplifying low-intensity endogenous currents within the cellular environment or as a nano-bioelectronic device.Comment: 43 pages, 6 figures, revised versio

Optical and Radio Polarimetry of the M87 Jet at 0.2" Resolution

We discuss optical (HST/WFPC2 F555W) and radio (15 GHz VLA) polarimetry observations of the M87 jet taken during 1994-1995. Many knot regions are very highly polarized ($\sim 40-50$, approaching the theoretical maximum for optically thin synchrotron radiation), suggesting highly ordered magnetic fields. High degrees of polarization are also observed in interknot regions. While the optical and radio polarization maps share many similarities, we observe significant differences between the radio and optical polarized structures, particularly for bright knots in the inner jet, giving us important insight into the jet's radial structure. Unlike in the radio, the optical magnetic field position angle becomes perpendicular to the jet at the upstream ends of knots HST-1, D, E and F. Moreover, the optical polarization decreases markedly at the position of the flux maxima in these knots. In contrast, the magnetic field position angle observed in the radio remains parallel to the jet in most of these regions, and the decreases in radio polarization are smaller. More minor differences are seen in other jet regions. Many of the differences between optical and radio polarimetry results can be explained in terms of a model whereby shocks occur in the jet interior, where higher-energy electrons are concentrated and dominate both polarized and unpolarized emissions in the optical, while the radio maps show strong contributions from lower-energy electrons in regions with {\bf B} parallel, near the jet surface.Comment: 28 pages, 7 figures; accepted for publication in AJ (May 1999

Dynamic Structural Change of Plant Epidermal Cell Walls under Strain

The molecular foundations of epidermal cell wall mechanics are critical for understanding structure-function relationships of primary cell walls in plants and facilitating the design of bioinspired materials. To uncover the molecular mechanisms regulating the high extensibility and strength of the cell wall, the onion epidermal wall is stretched uniaxially to various strains and cell wall structures from mesoscale to atomic scale are characterized. Upon longitudinal stretching to high strain, epidermal walls contract in the transverse direction, resulting in a reduced area. Atomic force microscopy shows that cellulose microfibrils exhibit orientation-dependent rearrangements at high strains: longitudinal microfibrils are straightened out and become highly ordered, while transverse microfibrils curve and kink. Small-angle X-ray scattering detects a 7.4 nm spacing aligned along the stretch direction at high strain, which is attributed to distances between individual cellulose microfibrils. Furthermore, wide-angle X-ray scattering reveals a widening of (004) lattice spacing and contraction of (200) lattice spacing in longitudinally aligned cellulose microfibrils at high strain, which implies longitudinal stretching of the cellulose crystal. These findings provide molecular insights into the ability of the wall to bear additional load after yielding: the aggregation of longitudinal microfibrils impedes sliding and enables further stretching of the cellulose to bear increased loads

Niche partitioning of feather mites within a seabird host, Calonectris borealis

According to classic niche theory, species can coexist in heterogeneous environments by reducing interspecific competition via niche partitioning, e.g. trophic or spatial partitioning. However, support for the role of competition on niche partitioning remains controversial. Here, we tested for spatial and trophic partitioning in feather mites, a diverse and abundant group of arthropods. We focused on the two dominant mite species, Microspalax brevipes and Zachvatkinia ovata, inhabiting flight feathers of the Cory's shearwater, Calonectris borealis. We performed mite counts across and within primary and tail feathers on free-living shearwaters breeding on an oceanic island (Gran Canaria, Canary Islands). We then investigated trophic relationships between the two mite species and the host using stable isotope analyses of carbon and nitrogen on mite tissues and potential host food sources. The distribution of the two mite species showed clear spatial segregation among feathers; M. brevipes showed high preference for the central wing primary feathers, whereas Z. ovata was restricted to the two outermost primaries. Morphological differences between M. brevipes and Z. ovata support an adaptive basis for the spatial segregation of the two mite species. However, the two mites overlap in some central primaries and statistical modeling showed that Z. ovata tends to outcompete M. brevipes. Isotopic analyses indicated similar isotopic values for the two mite species and a strong correlation in carbon signatures between mites inhabiting the same individual host suggesting that diet is mainly based on shared host-associated resources. Among the four candidate tissues examined (blood, feather remains, skin remains and preen gland oil), we conclude that the diet is most likely dominated by preen gland oil, while the contribution of exogenous material to mite diets is less marked. Our results indicate that ongoing competition for space and resources plays a central role in structuring feather mite communities. They also illustrate that symbiotic infracommunities are excellent model systems to study trophic ecology, and can improve our understanding of mechanisms of niche differentiation and species coexistence

Evidence Against the Sciama Model of Radiative Decay of Massive Neutrinos

We report on spectral observations of the night sky in the band around 900 angstroms where the emission line in the Sciama model of radiatively decaying massive neutrinos would be present. The data were obtained with a high resolution, high sensitivity spectrometer flown on the Spanish MINISAT satellite. The observed emission is far less intense than that expected in the Sciama model.Comment: 9 pages, accepted to Ap