Capturing coevolutionary signals in repeat proteins

The analysis of correlations of amino acid occurrences in globular proteins has led to the development of statistical tools that can identify native contacts -- portions of the chains that come to close distance in folded structural ensembles. Here we introduce a statistical coupling analysis for repeat proteins -- natural systems for which the identification of domains remains challenging. We show that the inherent translational symmetry of repeat protein sequences introduces a strong bias in the pair correlations at precisely the length scale of the repeat-unit. Equalizing for this bias reveals true co-evolutionary signals from which local native-contacts can be identified. Importantly, parameter values obtained for all other interactions are not significantly affected by the equalization. We quantify the robustness of the procedure and assign confidence levels to the interactions, identifying the minimum number of sequences needed to extract evolutionary information in several repeat protein families. The overall procedure can be used to reconstruct the interactions at long distances, identifying the characteristics of the strongest couplings in each family, and can be applied to any system that appears translationally symmetric

Confinement-induced resonances for a two-component ultracold atom gas in arbitrary quasi-one-dimensional traps

We solve the two-particle s-wave scattering problem for ultracold atom gases confined in arbitrary quasi-one-dimensional trapping potentials, allowing for two different atom species. As a consequence, the center-of-mass and relative degrees of freedom do not factorize. We derive bound-state solutions and obtain the general scattering solution, which exhibits several resonances in the 1D scattering length induced by the confinement. We apply our formalism to two experimentally relevant cases: (i) interspecies scattering in a two-species mixture, and (ii) the two-body problem for a single species in a non-parabolic trap.Comment: 22 pages, 3 figure

Superconducting transport through a vibrating molecule

Nonequilibrium electronic transport through a molecular level weakly coupled to a single coherent phonon/vibration mode has been studied for superconducting leads. The Keldysh Green function formalism is used to compute the current for the entire bias voltage range. In the subgap regime, Multiple Andreev Reflection (MAR) processes accompanied by phonon emission cause rich structure near the onset of MAR channels, including an even-odd parity effect that can be interpreted in terms of an inelastic MAR ladder picture. Thereby we establish a connection between the Keldysh formalism and the Landauer scattering approach for inelastic MAR.Comment: 5 pages, 5 figures, version contains now more details, accepted by PR

Gauged WZW models for space-time groups and gravitational actions

In this paper we investigate gauged Wess-Zumino-Witten models for space-time groups as gravitational theories, following the trend of recent work by Anabalon, Willison and Zanelli. We discuss the field equations in any dimension and study in detail the simplest case of two space-time dimensions and gauge group SO(2,1). For this model we study black hole solutions and we calculate their mass and entropy which resulted in a null value for both.Comment: 26 pages, no figure

Improving Performance of Iterative Methods by Lossy Checkponting

Iterative methods are commonly used approaches to solve large, sparse linear systems, which are fundamental operations for many modern scientific simulations. When the large-scale iterative methods are running with a large number of ranks in parallel, they have to checkpoint the dynamic variables periodically in case of unavoidable fail-stop errors, requiring fast I/O systems and large storage space. To this end, significantly reducing the checkpointing overhead is critical to improving the overall performance of iterative methods. Our contribution is fourfold. (1) We propose a novel lossy checkpointing scheme that can significantly improve the checkpointing performance of iterative methods by leveraging lossy compressors. (2) We formulate a lossy checkpointing performance model and derive theoretically an upper bound for the extra number of iterations caused by the distortion of data in lossy checkpoints, in order to guarantee the performance improvement under the lossy checkpointing scheme. (3) We analyze the impact of lossy checkpointing (i.e., extra number of iterations caused by lossy checkpointing files) for multiple types of iterative methods. (4)We evaluate the lossy checkpointing scheme with optimal checkpointing intervals on a high-performance computing environment with 2,048 cores, using a well-known scientific computation package PETSc and a state-of-the-art checkpoint/restart toolkit. Experiments show that our optimized lossy checkpointing scheme can significantly reduce the fault tolerance overhead for iterative methods by 23%~70% compared with traditional checkpointing and 20%~58% compared with lossless-compressed checkpointing, in the presence of system failures.Comment: 14 pages, 10 figures, HPDC'1

Analysis of structure withdissipator spectra under design and control

Las estructuras de Quito, Ecuador, son diseñadas para el espectro de la norma ecuatoriana de 2015, o para el hallado en la microzonificación de la ciudad de 2012. Estos espectros consideran en forma macro las fallas ciegas inversas sobre las que se halla la ciudad. En este artículo se destaca la importancia de verificar el diseño para los espectros de control que fueron desarrollados mediante métodos determinísticos para Quito en el 2015, los mismos que consideran la generación de sismos en las fallas ciegas. En el artículo se presentan dos modelos de plasticidad extendida para los elementos estructurales y un modelo de plasticidad para los disipadores ADAS o TADAS. Luego se indica con cierto detalle la técnica del pushover multimodal y el método del espectro de capacidad con el cual se halla el punto de capacidad de una estructura que fue inicialmente calculada para los espectros de diseño. Dicha estructura ha sido reforzada con disipadores ADAS para que no colapse ante el espectro de control que tiene ordenadas más altas que el espectro de diseño.The structures of Quito, Ecuador, are designed for the spectrum of the Ecuadorian code of 2015, or using the study of microzoning of the city of 2012. These spectra consider in general the effect of the blind reverse faults belonging to the city area. In this article, it is pointed out the importance of checking the design for the deterministic control spectra developed for Quito in 2015 based on earthquakes simulated in the blinds faults. In this paper we considered two models of extended plasticity for the structural elements and one model of plasticity for the ADAS and TADAS devices. Then, the technique of multimodal pushover is described, as well as the method of the capacity spectrum used to calculate the performance point of the structure. This structure was initially calculated by using design spectra and it had to be reinforced with ADAS devices in order to avoid its collapse for the control spectrum which has higher ordinates than the design one.Peer Reviewe

Extremal Graph Theory for Metric Dimension and Diameter

A set of vertices $S$ \emph{resolves} a connected graph $G$ if every vertex is uniquely determined by its vector of distances to the vertices in $S$. The \emph{metric dimension} of $G$ is the minimum cardinality of a resolving set of $G$. Let $\mathcal{G}_{\beta,D}$ be the set of graphs with metric dimension $\beta$ and diameter $D$. It is well-known that the minimum order of a graph in $\mathcal{G}_{\beta,D}$ is exactly $\beta+D$. The first contribution of this paper is to characterise the graphs in $\mathcal{G}_{\beta,D}$ with order $\beta+D$ for all values of $\beta$ and $D$. Such a characterisation was previously only known for $D\leq2$ or $\beta\leq1$. The second contribution is to determine the maximum order of a graph in $\mathcal{G}_{\beta,D}$ for all values of $D$ and $\beta$. Only a weak upper bound was previously known