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

Phase transition in inelastic disks

This letter investigates the molecular dynamics of inelastic disks without external forcing. By introducing a new observation frame with a rescaled time, we observe the virtual steady states converted from asymptotic energy dissipation processes. System behavior in the thermodynamic limit is carefully investigated. It is found that a phase transition with symmetry breaking occurs when the magnitude of dissipation is greater than a critical value.Comment: 9 pages, 6 figure

Uncertainty reconciles complementarity with joint measurability

The fundamental principles of complementarity and uncertainty are shown to be related to the possibility of joint unsharp measurements of pairs of noncommuting quantum observables. A new joint measurement scheme for complementary observables is proposed. The measured observables are represented as positive operator valued measures (POVMs), whose intrinsic fuzziness parameters are found to satisfy an intriguing pay-off relation reflecting the complementarity. At the same time, this relation represents an instance of a Heisenberg uncertainty relation for measurement imprecisions. A model-independent consideration show that this uncertainty relation is logically connected with the joint measurability of the POVMs in question.Comment: 4 pages, RevTeX. Title of previous version: "Complementarity and uncertainty - entangled in joint path-interference measurements". This new version focuses on the "measurement uncertainty relation" and its role, disentangling this issue from the special context of path interference duality. See also http://www.vjquantuminfo.org (October 2003

Breakdown of self-organized criticality

We introduce two sandpile models which show the same behavior of real sandpiles, that is, an almost self-organized critical behavior for small systems and the dominance of large avalanches as the system size increases. The systems become fully self-organized critical, with the critical exponents of the Bak, Tang and Wiesenfeld model, as the system parameters are changed, showing that these systems can make a bridge between the well known theoretical and numerical results and what is observed in real experiments. We find that a simple mechanism determines the boundary where self-organized can or cannot exist, which is the presence of local chaos.Comment: 3 pages, 4 figure

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.

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

Inelastic Collapse of Three Particles

A system of three particles undergoing inelastic collisions in arbitrary spatial dimensions is studied with the aim of establishing the domain of ``inelastic collapse''---an infinite number of collisions which take place in a finite time. Analytic and simulation results show that for a sufficiently small restitution coefficient, $0\leq r<7-4\sqrt{3}\approx 0.072$, collapse can occur. In one dimension, such a collapse is stable against small perturbations within this entire range. In higher dimensions, the collapse can be stable against small variations of initial conditions, within a smaller $r$ range, $0\leq r<9-4\sqrt{5}\approx 0.056$.Comment: 6 pages, figures on request, accepted by PR

Demonstration of the Complementarity of One- and Two-Photon Interference

The visibilities of second-order (single-photon) and fourth-order (two-photon) interference have been observed in a Young's double-slit experiment using light generated by spontaneous parametric down-conversion and a photon-counting intensified CCD camera. Coherence and entanglement underlie one-and two-photon interference, respectively. As the effective source size is increased, coherence is diminished while entanglement is enhanced, so that the visibility of single-photon interference decreases while that of two-photon interference increases. This is the first experimental demonstration of the complementarity between single- and two-photon interference (coherence and entanglement) in the spatial domain.Comment: 21 pages, 7 figure

Heap Formation in Granular Media

Using molecular dynamics (MD) simulations, we find the formation of heaps in a system of granular particles contained in a box with oscillating bottom and fixed sidewalls. The simulation includes the effect of static friction, which is found to be crucial in maintaining a stable heap. We also find another mechanism for heap formation in systems under constant vertical shear. In both systems, heaps are formed due to a net downward shear by the sidewalls. We discuss the origin of net downward shear for the vibration induced heap.Comment: 11 pages, 4 figures available upon request, Plain TeX, HLRZ-101/9

Size Segregation of Granular Matter in Silo Discharges

We present an experimental study of segregation of granular matter in a quasi-two dimensional silo emptying out of an orifice. Size separation is observed when multi-sized particles are used with the larger particles found in the center of the silo in the region of fastest flow. We use imaging to study the flow inside the silo and quantitatively measure the concentration profiles of bi-disperse beads as a function of position and time. The angle of the surface is given by the angle of repose of the particles, and the flow occurs in a few layers only near the top of this inclined surface. The flowing region becomes deeper near the center of the silo and is confined to a parabolic region centered at the orifice which is approximately described by the kinematic model. The experimental evidence suggests that the segregation occurs on the surface and not in the flow deep inside the silo where velocity gradients also are present. We report the time development of the concentrations of the bi-disperse particles as a function of size ratios, flow rate, and the ratio of initial mixture. The qualitative aspects of the observed phenomena may be explained by a void filling model of segregation.Comment: 6 pages, 10 figures (gif format), postscript version at http://physics.clarku.edu/~akudrolli/nls.htm