An improved Monte Carlo method for direct calculation of the density of states

We present an efficient Monte Carlo algorithm for determining the density of states which is based on the statistics of transition probabilities between states. By measuring the infinite temperature transition probabilities--that is, the probabilities associated with move proposal only--we are able to extract excellent estimates of the density of states. When this estimator is used in conjunction with a Wang-Landau sampling scheme [F. Wang and D. P. Landau, Phys. Rev. Lett. 86, 2050 (2001)], we quickly achieve uniform sampling of macrostates (e.g., energies) and systematically refine the calculated density of states. This approach requires only potential energy evaluations, continues to improve the statistical quality of its results as the simulation time is extended, and is applicable to both lattice and continuum systems. We test the algorithm on the Lennard-Jones liquid and demonstrate good statistical convergence properties.Comment: 7 pages, 4 figures. to appear in Journal of Chemical Physic

Development of Multiple Polymorphic Microsatellite Markers for Ceratina calcarata (Hymenoptera: Apidae) Using Genome-Wide Analysis

The small carpenter bee, Ceratina calcarata (Robertson), is a widespread native pollinator across eastern North America. The behavioral ecology and nesting biology of C. calcarata has been relatively well-studied and the species is emerging as a model organism for both native pollinator and social evolution research. C. calcarata is subsocial: reproductively mature females provide extended maternal care to their brood. As such, studies of C. calcarata may also reveal patterns of relatedness and demography unique to primitively social Hymenoptera. Here, we present 21 microsatellite loci, isolated from the recently completed C. calcarata genome. Screening in 39 individuals across their distribution revealed that no loci were in linkage disequilibrium, nor did any deviate significantly from Hardy-Weinberg following sequential Bonferroni correction. Allele count ranged from 2 to 14, and observed and expected heterozygosities ranged from 0.08 to 0.82 (mean 0.47) and 0.26 to 0.88 (mean 0.56), respectively. These markers will enable studies of population-wide genetic structuring across C. calcarata’s distribution. Such tools will also allow for exploration of between and within-colony relatedness in this subsocial native pollinator

Saddles in the energy landscape: extensivity and thermodynamic formalism

We formally extend the energy landscape approach for the thermodynamics of liquids to account for saddle points. By considering the extensive nature of macroscopic potential energies, we derive the scaling behavior of saddles with system size, as well as several approximations for the properties of low-order saddles (i.e., those with only a few unstable directions). We then cast the canonical partition function in a saddle-explicit form and develop, for the first time, a rigorous energy landscape approach capable of reproducing trends observed in simulations, in particular the temperature dependence of the energy and fractional order of sampled saddles.Comment: 4 pages, 1 figur

Even faster sorting of (not only) integers

In this paper we introduce RADULS2, the fastest parallel sorter based on radix algorithm. It is optimized to process huge amounts of data making use of modern multicore CPUs. The main novelties include: extremely optimized algorithm for handling tiny arrays (up to about a hundred of records) that could appear even billions times as subproblems to handle and improved processing of larger subarrays with better use of non-temporal memory stores

A culture of silence: modes of objectification and the silencing of disabled bodies

Throughout history different practices have attempted to silence the experiences of disabled people. In this paper we explore some of these practices including the medical, familial, and self-subjugating practices English-speaking Canadian polio survivors experienced throughout their lives. We analyze participant’s experiences of silence and silencing through a Foucauldian lens, drawing on the three modes of objectification to explain the institutional and cultural discourses around polio subjects that acted upon and through the polio body to silence it. Participants’ oral history accounts demonstrate how sociocultural and medical practices effectively silenced survivors from speaking about their polio experiences. However, the trope of silence is also uprooted within oral history traditions. We will demonstrate how participants broke their silence and shifted their perspectives on polio and disability, and how this process contributed to their resistance of hegemonic conceptualizations of disability as defective

A test of non-equilibrium thermodynamics in glassy systems: the soft-sphere case

The scaling properties of the soft-sphere potential allow the derivation of an exact expression for the pressure of a frozen liquid, i.e., the pressure corresponding to configurations which are local minima in its multidimensional potential energy landscape. The existence of such a relation offers the unique possibility for testing the recently proposed extension of the liquid free energy to glassy out-of-equilibrium conditions and the associated expression for the temperature of the configurational degrees of freedom. We demonstrate that the non-equilibrium free energy provides an exact description of the soft-sphere pressure in glass states