Infinite games with finite knowledge gaps

Infinite games where several players seek to coordinate under imperfect information are deemed to be undecidable, unless the information is hierarchically ordered among the players. We identify a class of games for which joint winning strategies can be constructed effectively without restricting the direction of information flow. Instead, our condition requires that the players attain common knowledge about the actual state of the game over and over again along every play. We show that it is decidable whether a given game satisfies the condition, and prove tight complexity bounds for the strategy synthesis problem under $\omega$-regular winning conditions given by parity automata.Comment: 39 pages; 2nd revision; submitted to Information and Computatio

Brane tilings and supersymmetric gauge theories

In the last few years, brane tilings have proven to be an efficient and convenient way of studying supersymmetric gauge theories living on D3-branes or M2-branes. In these pages we present a quick and simple introduction to the subject, hoping this could tickle the reader's curiosity to learn more on this extremely fascinating subject.Comment: 3 pages, 2 figures, based on a presentation given by G.T. at the 2010 Cargese Summer School (June 21-July 3), to appear in the proceeding

An Overview of Rendering from Volume Data --- including Surface and Volume Rendering

Volume rendering is a title often ambiguously used in science. One meaning often quoted is: `to render any three volume dimensional data set'; however, within this categorisation `surface rendering'' is contained. Surface rendering is a technique for visualising a geometric representation of a surface from a three dimensional volume data set. A more correct definition of Volume Rendering would only incorporate the direct visualisation of volumes, without the use of intermediate surface geometry representations. Hence we state: `Volume Rendering is the Direct Visualisation of any three dimensional Volume data set; without the use of an intermediate geometric representation for isosurfaces'; `Surface Rendering is the Visualisation of a surface, from a geometric approximation of an isosurface, within a Volume data set'; where an isosurface is a surface formed from a cross connection of data points, within a volume, of equal value or density. This paper is an overview of both Surface Rendering and Volume Rendering techniques. Surface Rendering mainly consists of contouring lines over data points and triangulations between contours. Volume rendering methods consist of ray casting techniques that allow the ray to be cast from the viewing plane into the object and the transparency, opacity and colour calculated for each cell; the rays are often cast until an opaque object is `hit' or the ray exits the volume

Starr: Simple Tiling Array Analysis of Affymetrix ChIP-chip data

Chromatin immunoprecipitation combined with DNA microarrays (ChIP-chip) is an assay for DNA-protein-binding or post-translational chromatin/histone modifications. As with all high-throughput technologies, it requires a thorough bioinformatic processing of the data for which there is no standard yet. The primary goal is the reliable identification and localization of genomic regions that bind a specific protein. The second step comprises comparison of binding profiles of functionally related proteins, or of binding profiles of the same protein in different genetic backgrounds or environmental conditions. Ultimately, one would like to gain a mechanistic understanding of the effects of DNA binding events on gene expression. We present a free, open-source R package Starr that, in combination with the package Ringo, facilitates the comparative analysis of ChIP-chip data across experiments and across different microarray platforms. Core features are data import, quality assessment, normalization and visualization of the data, and the detection of ChIP-enriched genomic regions. The use of common Bioconductor classes ensures the compatibility with other R packages. Most importantly, Starr provides methods for integration of complementary genomics data, e.g., it enables systematic investigation of the relation between gene expression and dna binding

Combined energy -- diffraction data refinement of decagonal AlNiCo

We incorporate realistic pair potential energies directly into a non-linear least-square fit of diffraction data to quantitatively compare structure models with experiment for the Ni-rich $d$(AlNiCo) quasicrystal. The initial structure models are derived from a few {\it a priori} assumptions (gross features of the Patterson function) and the pair potentials. In place of the common hyperspace approach to the structure refinement of quasicrystals, we use a real-space tile decoration scheme, which does not rely on strict quasiperiodicity, and makes it easy to enforce sensible local arrangements of the atoms. Inclusion of the energies provides information complementary to the diffraction data and protects the fit procedure from converging on spurious solutions. The method pinpoints sites which are likely to break the symmetry of their local environment.Comment: 7 pages, 5 figures, proceedings of the Internation Conference on Quasicrystals, Bangalore, India, August 200

How Do Quasicrystals Grow?

Using molecular simulations, we show that the aperiodic growth of quasicrystals is controlled by the ability of the growing quasicrystal `nucleus' to incorporate kinetically trapped atoms into the solid phase with minimal rearrangement. In the system under investigation, which forms a dodecagonal quasicrystal, we show that this process occurs through the assimilation of stable icosahedral clusters by the growing quasicrystal. Our results demonstrate how local atomic interactions give rise to the long-range aperiodicity of quasicrystals.Comment: 4 pages, 4 figures. Figures and text have been updated to the final version of the articl