QCD with light Wilson quarks on fine lattices (II): DD-HMC simulations and data analysis

In this second report on our recent numerical simulations of two-flavour QCD, we provide further technical details on the simulations and describe the methods we used to extract the meson masses and decay constants from the generated ensembles of gauge fields. Among the topics covered are the choice of the DD-HMC parameters, the issue of stability, autocorrelations and the statistical error analysis. Extensive data tables are included as well as a short discussion of the quark-mass dependence in partially quenched QCD, supplementing the physics analysis that was presented in the first paper in this series.Comment: TeX source, 35 pages, figures include

Training-free Measures Based on Algorithmic Probability Identify High Nucleosome Occupancy in DNA Sequences

We introduce and study a set of training-free methods of information-theoretic and algorithmic complexity nature applied to DNA sequences to identify their potential capabilities to determine nucleosomal binding sites. We test our measures on well-studied genomic sequences of different sizes drawn from different sources. The measures reveal the known in vivo versus in vitro predictive discrepancies and uncover their potential to pinpoint (high) nucleosome occupancy. We explore different possible signals within and beyond the nucleosome length and find that complexity indices are informative of nucleosome occupancy. We compare against the gold standard (Kaplan model) and find similar and complementary results with the main difference that our sequence complexity approach. For example, for high occupancy, complexity-based scores outperform the Kaplan model for predicting binding representing a significant advancement in predicting the highest nucleosome occupancy following a training-free approach.Comment: 8 pages main text (4 figures), 12 total with Supplementary (1 figure

Laminations and groups of homeomorphisms of the circle

If M is an atoroidal 3-manifold with a taut foliation, Thurston showed that pi_1(M) acts on a circle. Here, we show that some other classes of essential laminations also give rise to actions on circles. In particular, we show this for tight essential laminations with solid torus guts. We also show that pseudo-Anosov flows induce actions on circles. In all cases, these actions can be made into faithful ones, so pi_1(M) is isomorphic to a subgroup of Homeo(S^1). In addition, we show that the fundamental group of the Weeks manifold has no faithful action on S^1. As a corollary, the Weeks manifold does not admit a tight essential lamination, a pseudo-Anosov flow, or a taut foliation. Finally, we give a proof of Thurston's universal circle theorem for taut foliations based on a new, purely topological, proof of the Leaf Pocket Theorem.Comment: 50 pages, 12 figures. Ver 2: minor improvement

Algorithmic Thomas Decomposition of Algebraic and Differential Systems

In this paper, we consider systems of algebraic and non-linear partial differential equations and inequations. We decompose these systems into so-called simple subsystems and thereby partition the set of solutions. For algebraic systems, simplicity means triangularity, square-freeness and non-vanishing initials. Differential simplicity extends algebraic simplicity with involutivity. We build upon the constructive ideas of J. M. Thomas and develop them into a new algorithm for disjoint decomposition. The given paper is a revised version of a previous paper and includes the proofs of correctness and termination of our decomposition algorithm. In addition, we illustrate the algorithm with further instructive examples and describe its Maple implementation together with an experimental comparison to some other triangular decomposition algorithms.Comment: arXiv admin note: substantial text overlap with arXiv:1008.376

Swarm-Based Spatial Sorting

Purpose: To present an algorithm for spatially sorting objects into an annular structure. Design/Methodology/Approach: A swarm-based model that requires only stochastic agent behaviour coupled with a pheromone-inspired "attraction-repulsion" mechanism. Findings: The algorithm consistently generates high-quality annular structures, and is particularly powerful in situations where the initial configuration of objects is similar to those observed in nature. Research limitations/implications: Experimental evidence supports previous theoretical arguments about the nature and mechanism of spatial sorting by insects. Practical implications: The algorithm may find applications in distributed robotics. Originality/value: The model offers a powerful minimal algorithmic framework, and also sheds further light on the nature of attraction-repulsion algorithms and underlying natural processes.Comment: Accepted by the Int. J. Intelligent Computing and Cybernetic