On the continuous spectral component of the Floquet operator for a periodically kicked quantum system

By a straightforward generalisation, we extend the work of Combescure from rank-1 to rank-N perturbations. The requirement for the Floquet operator to be pure point is established and compared to that in Combescure. The result matches that in McCaw. The method here is an alternative to that work. We show that if the condition for the Floquet operator to be pure point is relaxed, then in the case of the delta-kicked Harmonic oscillator, a singularly continuous component of the Floquet operator spectrum exists. We also provide an in depth discussion of the conjecture presented in Combescure of the case where the unperturbed Hamiltonian is more general. We link the physics conjecture directly to a number-theoretic conjecture of Vinogradov and show that a solution of Vinogradov's conjecture solves the physics conjecture. The result is extended to the rank-N case. The relationship between our work and the work of Bourget on the physics conjecture is discussed.Comment: 25 pages, published in Journal of Mathematical Physic

The Discrete Frenet Frame, Inflection Point Solitons And Curve Visualization with Applications to Folded Proteins

We develop a transfer matrix formalism to visualize the framing of discrete piecewise linear curves in three dimensional space. Our approach is based on the concept of an intrinsically discrete curve, which enables us to more effectively describe curves that in the limit where the length of line segments vanishes approach fractal structures in lieu of continuous curves. We verify that in the case of differentiable curves the continuum limit of our discrete equation does reproduce the generalized Frenet equation. As an application we consider folded proteins, their Hausdorff dimension is known to be fractal. We explain how to employ the orientation of $C_\beta$ carbons of amino acids along a protein backbone to introduce a preferred framing along the backbone. By analyzing the experimentally resolved fold geometries in the Protein Data Bank we observe that this $C_\beta$ framing relates intimately to the discrete Frenet framing. We also explain how inflection points can be located in the loops, and clarify their distinctive r\^ole in determining the loop structure of foldel proteins.Comment: 14 pages 12 figure

MOTIFATOR: detection and characterization of regulatory motifs using prokaryote transcriptome data

Summary: Unraveling regulatory mechanisms (e.g. identification of motifs in cis-regulatory regions) remains a major challenge in the analysis of transcriptome experiments. Existing applications identify putative motifs from gene lists obtained at rather arbitrary cutoff and require additional manual processing steps. Our standalone application MOTIFATOR identifies the most optimal parameters for motif discovery and creates an interactive visualization of the results. Discovered putative motifs are functionally characterized, thereby providing valuable insight in the biological processes that could be controlled by the motif.

Biochemical characterization of mutants in the active site residues of the beta-galactosidase enzyme of Bacillus circulans ATCC 31382

The Bacillus circulans ATCC 31382 beta-galactosidase (BgaD) is a retaining-type glycosidase of glycoside hydrolase family 2 (GH2). Its commercial enzyme preparation, Biolacta N5, is used for commercial-scale production of galacto-oligosaccharides (GOS). The BgaD active site and catalytic amino acid residues have not been studied. Using bioinformatic routines we identified two putative catalytic glutamates and two highly conserved active site histidines. The site-directed mutants E447N, E532Q, and H345F, H379F had lost (almost) all catalytic activity. This confirmed their essential role in catalysis, as general acid/base catalyst (E447) and nucleophile (E532), and as transition state stabilizers (H345, H379), respectively. (C) 2014 The Authors. Published by Elsevier B.V. on behalf of the Federation of European Biochemical Societies.</p

The Atomic Slide Puzzle: Self-Diffusion of an Impure Atom

In a series of recent papers van Gastel et al have presented first experimental evidence that impure, Indium atoms, embedded into the first layer of a Cu(001) surface, are not localized within the close-packed surface layers but make concerted, long excursions visualized in a series of STM images. Such excursions occur due to continuous reshuffling of the surface following the position exchanges of both impure and host atoms with the naturally occuring surface vacancies. Van Gastel et al have also formulated an original lattice-gas type model with asymmetric exchange probabilities, whose numerical solution is in a good agreement with the experimental data. In this paper we propose an exact lattice solution of several versions of this model.Comment: Latex, 4 pages, 2 figures, to appear in Phys. Rev. E (RC

Twenty-Four Hour Tonometry in Patients Suspected of Chronic Gastrointestinal Ischemia

Background and aims: Gastrointestinal tonometry is currently the only clinical diagnostic test that enables identification of symptomatic chronic gastrointestinal ischemia. Gastric exercise tonometry has proven its value for detection of ischemia in this patients group, but has its disadvantages. Earlier studies with postprandial tonometry gave unreliable results. In this study we challenged (again) the use of postprandial tonometry in patients suspected of gastrointestinal ischemia. Methods: Patients suspected for chronic gastrointestinal ischemia had standard diagnostic work up, including gastric exercise tonometry and 24-h tonometry using standard meals. Results: Thirty-three patients were enrolled in the study. Chronic gastrointestinal ischemia was diagnosed in 17 (52%) patients. The 24-h tonometry correctly predicted the presence of ischemia in 13/17 patients, and absence of ischemia in 15/16 patients. Conclusions: The use of 24-h tonometry after meals in patients suspected of gastrointestinal ischemia seems feasible, with promising accuracy for the detection of ischemia

FISH mapping and molecular organization of the major repetitive sequences of tomato

This paper presents a bird's-eye view of the major repeats and chromatin types of tomato. Using fluorescence in-situ hybridization (FISH) with Cot-1, Cot-10 and Cot-100 DNA as probes we mapped repetitive sequences of different complexity on pachytene complements. Cot-100 was found to cover all heterochromatin regions, and could be used to identify repeat-rich clones in BAC filter hybridization. Next we established the chromosomal locations of the tandem and dispersed repeats with respect to euchromatin, nucleolar organizer regions (NORs), heterochromatin, and centromeres. The tomato genomic repeats TGRII and TGRIII appeared to be major components of the pericentromeres, whereas the newly discovered TGRIV repeat was found mainly in the structural centromeres. The highly methylated NOR of chromosome 2 is rich in [GACA](4), a microsatellite that also forms part of the pericentromeres, together with [GA](8), [GATA](4) and Ty1-copia. Based on the morphology of pachytene chromosomes and the distribution of repeats studied so far, we now propose six different chromatin classes for tomato: (1) euchromatin, (2) chromomeres, (3) distal heterochromatin and interstitial heterochromatic knobs, (4) pericentromere heterochromatin, (5) functional centromere heterochromatin and (6) nucleolar organizer regio

The Counterpart Principle of Analogical Support by Structural Similarity

We propose and investigate an Analogy Principle in the context of Unary Inductive Logic based on a notion of support by structural similarity which is often employed to motivate scientific conjectures