INITIAL CHARACTERIZATION OF MAJOR HISTOCOMPATIBILITY COMPLEX (MHC) CLASS IIB EXON 2 IN AN ENDANGERED RATTLESNAKE, THE EASTERN MASSASAUGA (SISTRURUS CATENATUS)

Genes of the major histocompatibility complex (MHC) play an important role in the vertebrate immune system and exhibit remarkably high levels of polymorphism, maintained by strong balancing selection. While the conservation implications of MHC variation have been explored in a variety of vertebrates, non-avian reptiles (most notably snakes) have received less attention. To address this gap and take the first steps toward more extensive population-level analyses, we cloned and sequenced MHC IIB exon 2 in an endangered rattlesnake, the Eastern Massasauga (Sistrurus catenatus). Based on three individuals, we found evidence of at least four putatively functional loci. These sequences exhibited relatively high levels of variation and significantly higher rates of nonsynonymous to synonymous substitutions, especially within the antigen-binding sites, indicating strong positive selection. Phylogenetic analysis revealed a pattern of trans-species polymorphism, also suggesting positive selection. These results contribute to our understanding of MHC variation in non-avian reptiles and form a basis for more studies of MHC variation in snakes of conservation concern

Large phenotype jumps in biomolecular evolution

By defining the phenotype of a biopolymer by its active three-dimensional shape, and its genotype by its primary sequence, we propose a model that predicts and characterizes the statistical distribution of a population of biopolymers with a specific phenotype, that originated from a given genotypic sequence by a single mutational event. Depending on the ratio g0 that characterizes the spread of potential energies of the mutated population with respect to temperature, three different statistical regimes have been identified. We suggest that biopolymers found in nature are in a critical regime with g0 in the range 1-6, corresponding to a broad, but not too broad, phenotypic distribution resembling a truncated Levy flight. Thus the biopolymer phenotype can be considerably modified in just a few mutations. The proposed model is in good agreement with the experimental distribution of activities determined for a population of single mutants of a group I ribozyme.Comment: to appear in Phys. Rev. E; 7 pages, 6 figures; longer discussion in VII, new fig.

Metastability of a granular surface in a spinning bucket

The surface shape of a spinning bucket of granular material is studied using a continuum model of surface flow developed by Bouchaud et al. and Mehta et al. An experimentally observed central subcritical region is reproduced by the model. The subcritical region occurs when a metastable surface becomes unstable via a nonlinear instability mechanism. The nonlinear instability mechanism destabilizes the surface in large systems while a linear instability mechanism is relevant for smaller systems. The range of angles in which the granular surface is metastable vanishes with increasing system size.Comment: 8 pages with postscript figures, RevTex, to appear in Phys. Rev.

Optimal Dynamical Decoherence Control of a Qubit

A theory of dynamical control by modulation for optimal decoherence reduction is developed. It is based on the non-Markovian Euler-Lagrange equation for the energy-constrained field that minimizes the average dephasing rate of a qubit for any given dephasing spectrum.Comment: 6 pages, including 2 figures and an appendi

When politicians and governments fail, people blame the other party no matter what they are told by experts

Government failure and inaction has become an increasingly common aspect of the U.S. political system, whether it is due to political polarization as in the government’s shutdown in 2013, or through poor planning, which characterized the rollout of the Obamacare website. But how do voters apportion blame for these sorts of failures? In new research, that tests how people react to expert testimony that apportions blame to a particular political party, Jeffrey Lyons and William P. Jaeger find that even when experts say otherwise, people still blame the party that rivals their own political views for the failure. They write that their findings go against the idea that a better informed electorate would be less partisan – in actuality, people simply ignore the extra information they are given if it challenges their beliefs

A Model for Force Fluctuations in Bead Packs

We study theoretically the complex network of forces that is responsible for the static structure and properties of granular materials. We present detailed calculations for a model in which the fluctuations in the force distribution arise because of variations in the contact angles and the constraints imposed by the force balance on each bead of the pile. We compare our results for force distribution function for this model, including exact results for certain contact angle probability distributions, with numerical simulations of force distributions in random sphere packings. This model reproduces many aspects of the force distribution observed both in experiment and in numerical simulations of sphere packings

Damage-cluster distributions and size effect on strength in compressive failure

We investigate compressive failure of heterogeneous materials on the basis of a continuous progressive damage model. The model explicitely accounts for tensile and shear local damage and reproduces the main features of compressive failure of brittle materials like rocks or ice. We show that the size distribution of damage-clusters, as well as the evolution of an order parameter, the size of the largest damage-cluster, argue for a critical interpretation of fracture. The compressive failure strength follows a normal distribution with a very small size effect on the mean strength, in good agreement with experiments

Multiscale Analysis of the Stress State in a Granular Slope in Transition to Failure

By means of contact dynamics simulations, we analyze the stress state in a granular bed slowly tilted towards its angle of repose. An increasingly large number of grains are overloaded in the sense that they are found to carry a stress ratio above the Coulomb yield threshold of the whole packing. Using this property, we introduce a coarse-graining length scale at which all stress ratios are below the packing yield threshold. We show that this length increases with the slope angle and jumps to a length comparable to the depth of the granular bed at an angle below the angle of repose. This transition coincides with the onset of dilatation in the packing. We map this transition into a percolation transition of the overloaded grains, and we argue that in the presence of long-range correlations above the transition angle, the granular slope is metastable.Comment: 11 pages, 14 Fig, submitted to PR

Slowly driven sandpile formation with granular mixtures

We introduce a one-dimensional sandpile model with $N$ different particle types and an infinitesimal driving rate. The parameters for the model are the N^2 critical slopes for one type of particle on top of another. The model is trivial when N=1, but for N=2 we observe four broad classes of sandpile structure in different regions of the parameter space. We describe and explain the behaviour of each of these classes, giving quantitative analysis wherever possible. The behaviour of sandpiles with N>2 essentially consists of combinations of these four classes. We investigate the model's robustness and highlight the key areas that any experiment designed to reproduce these results should focus on

Mean Field Theory of Sandpile Avalanches: from the Intermittent to the Continuous Flow Regime

We model the dynamics of avalanches in granular assemblies in partly filled rotating cylinders using a mean-field approach. We show that, upon varying the cylinder angular velocity $\omega$, the system undergoes a hysteresis cycle between an intermittent and a continuous flow regimes. In the intermittent flow regime, and approaching the transition, the avalanche duration exhibits critical slowing down with a temporal power-law divergence. Upon adding a white noise term, and close to the transition, the distribution of avalanche durations is also a power-law. The hysteresis, as well as the statistics of avalanche durations, are in good qualitative agreement with recent experiments in partly filled rotating cylinders.Comment: 4 pages, RevTeX 3.0, postscript figures 1, 3 and 4 appended