16,315 research outputs found
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 microzonificaciĂłn de la ciudad de 2012. Estos espectros consideran en forma macro las fallas ciegas inversas sobre las que se halla la ciudad. En este artĂculo se destaca la importancia de verificar el diseño para los espectros de control que fueron desarrollados mediante mĂ©todos determinĂsticos para Quito en el 2015, los mismos que consideran la generaciĂłn de sismos en las fallas ciegas.
En el artĂculo 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 tĂ©cnica del pushover multimodal y el mĂ©todo 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 \emph{resolves} a connected graph if every vertex
is uniquely determined by its vector of distances to the vertices in . The
\emph{metric dimension} of is the minimum cardinality of a resolving set of
. Let be the set of graphs with metric dimension
and diameter . It is well-known that the minimum order of a graph in
is exactly . The first contribution of this
paper is to characterise the graphs in with order
for all values of and . Such a characterisation was
previously only known for or . The second contribution is
to determine the maximum order of a graph in for all
values of and . Only a weak upper bound was previously known
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