Diagram calculus for a type affine CC Temperley--Lieb algebra, I

In this paper, we present an infinite dimensional associative diagram algebra that satisfies the relations of the generalized Temperley--Lieb algebra having a basis indexed by the fully commutative elements (in the sense of Stembridge) of the Coxeter group of type affine $C$. Moreover, we provide an explicit description of a basis for the diagram algebra. In the sequel to this paper, we show that this diagrammatic representation is faithful. The results of this paper and its sequel will be used to construct a Jones-type trace on the Hecke algebra of type affine $C$, allowing us to non-recursively compute leading coefficients of certain Kazhdan--Lusztig polynomials.Comment: Title and content updated to reflect published version. References and contact information updated. 28 pages, 26 figure

De novo construction of polyploid linkage maps using discrete graphical models

Linkage maps are used to identify the location of genes responsible for traits and diseases. New sequencing techniques have created opportunities to substantially increase the density of genetic markers. Such revolutionary advances in technology have given rise to new challenges, such as creating high-density linkage maps. Current multiple testing approaches based on pairwise recombination fractions are underpowered in the high-dimensional setting and do not extend easily to polyploid species. We propose to construct linkage maps using graphical models either via a sparse Gaussian copula or a nonparanormal skeptic approach. Linkage groups (LGs), typically chromosomes, and the order of markers in each LG are determined by inferring the conditional independence relationships among large numbers of markers in the genome. Through simulations, we illustrate the utility of our map construction method and compare its performance with other available methods, both when the data are clean and contain no missing observations and when data contain genotyping errors and are incomplete. We apply the proposed method to two genotype datasets: barley and potato from diploid and polypoid populations, respectively. Our comprehensive map construction method makes full use of the dosage SNP data to reconstruct linkage map for any bi-parental diploid and polyploid species. We have implemented the method in the R package netgwas.Comment: 25 pages, 7 figure

Vibrational transfer functions for base excited systems

Computer program GD203 develops transfer functions to compute governing vibration environment for complex structures subjected to a base motion

Impartial achievement and avoidance games for generating finite groups

We study two impartial games introduced by Anderson and Harary and further developed by Barnes. Both games are played by two players who alternately select previously unselected elements of a finite group. The first player who builds a generating set from the jointly selected elements wins the first game. The first player who cannot select an element without building a generating set loses the second game. After the development of some general results, we determine the nim-numbers of these games for abelian and dihedral groups. We also present some conjectures based on computer calculations. Our main computational and theoretical tool is the structure diagram of a game, which is a type of identification digraph of the game digraph that is compatible with the nim-numbers of the positions. Structure diagrams also provide simple yet intuitive visualizations of these games that capture the complexity of the positions.Comment: 28 pages, 44 figures. Revised in response to comments from refere

Chaos properties and localization in Lorentz lattice gases

The thermodynamic formalism of Ruelle, Sinai, and Bowen, in which chaotic properties of dynamical systems are expressed in terms of a free energy-type function - called the topological pressure - is applied to a Lorentz Lattice Gas, as typical for diffusive systems with static disorder. In the limit of large system sizes, the mechanism and effects of localization on large clusters of scatterers in the calculation of the topological pressure are elucidated and supported by strong numerical evidence. Moreover it clarifies and illustrates a previous theoretical analysis [Appert et al. J. Stat. Phys. 87, chao-dyn/9607019] of this localization phenomenon.Comment: 32 pages, 19 Postscript figures, submitted to PR