RNA-RNA interaction prediction based on multiple sequence alignments

Many computerized methods for RNA-RNA interaction structure prediction have been developed. Recently, $O(N^6)$ time and $O(N^4)$ space dynamic programming algorithms have become available that compute the partition function of RNA-RNA interaction complexes. However, few of these methods incorporate the knowledge concerning related sequences, thus relevant evolutionary information is often neglected from the structure determination. Therefore, it is of considerable practical interest to introduce a method taking into consideration both thermodynamic stability and sequence covariation. We present the \emph{a priori} folding algorithm \texttt{ripalign}, whose input consists of two (given) multiple sequence alignments (MSA). \texttt{ripalign} outputs (1) the partition function, (2) base-pairing probabilities, (3) hybrid probabilities and (4) a set of Boltzmann-sampled suboptimal structures consisting of canonical joint structures that are compatible to the alignments. Compared to the single sequence-pair folding algorithm \texttt{rip}, \texttt{ripalign} requires negligible additional memory resource. Furthermore, we incorporate possible structure constraints as input parameters into our algorithm. The algorithm described here is implemented in C as part of the \texttt{rip} package. The supplemental material, source code and input/output files can freely be downloaded from \url{http://www.combinatorics.cn/cbpc/ripalign.html}. \section{Contact} Christian Reidys \texttt{[email protected]}Comment: 8 pages, 9 figure

Kondo correlation and spin-flip scattering in spin-dependent transport through a quantum dot coupled to ferromagnetic leads

We investigate the linear and nonlinear dc transport through an interacting quantum dot connected to two ferromagnetic electrodes around Kondo regime with spin-flip scattering in the dot. Using a slave-boson mean field approach for the Anderson Hamiltonian having finite on-site Coulomb repulsion, we find that a spin-flip scattering always depresses the Kondo correlation at arbitrary polarization strength in both parallel and antiparallel alignment of the lead magnetization and that it effectively reinforces the tunneling related conductance in the antiparallel configuration. For systems deep in the Kondo regime, the zero-bias single Kondo peak in the differential conductance is split into two peaks by the intradot spin-flip scattering; while for systems somewhat further from the Kondo center, the spin-flip process in the dot may turn the zero-bias anomaly into a three-peak structure.Comment: 4 pages, 2 figure

Electromagnetic manipulation for anti-Zeno effect in an engineered quantum tunneling process

We investigate the quantum Zeno and anti-Zeno effects for the irreversible quantum tunneling from a quantum dot to a ring array of quantum dots. By modeling the total system with the Anderson-Fano-Lee model, it is found that the transition from the quantum Zeno effect to quantum anti-Zeno effect can happen as the magnetic flux and the gate voltage were adjusted.Comment: 6 pages, 5 figure

Is the Number of Giant Arcs in LCDM Consistent With Observations?

We use high-resolution N-body simulations to study the galaxy-cluster cross-sections and the abundance of giant arcs in the $\Lambda$CDM model. Clusters are selected from the simulations using the friends-of-friends method, and their cross-sections for forming giant arcs are analyzed. The background sources are assumed to follow a uniform ellipticity distribution from 0 to 0.5 and to have an area identical to a circular source with diameter 1\arcsec. We find that the optical depth scales as the source redshift approximately as \tau_{1''} = 2.25 \times 10^{-6}/[1+(\zs/3.14)^{-3.42}] (0.6<\zs<7). The amplitude is about 50% higher for an effective source diameter of 0.5\arcsec. The optimal lens redshift for giant arcs with the length-to-width ratio ($L/W$) larger than 10 increases from 0.3 for \zs=1, to 0.5 for \zs=2, and to 0.7-0.8 for \zs>3. The optical depth is sensitive to the source redshift, in qualitative agreement with Wambsganss et al. (2004). However, our overall optical depth appears to be only $\sim$ 10% to 70% of those from previous studies. The differences can be mostly explained by different power spectrum normalizations ($\sigma_8$) used and different ways of determining the $L/W$ ratio. Finite source size and ellipticity have modest effects on the optical depth. We also found that the number of highly magnified (with magnification $|\mu|>10$) and ``undistorted'' images (with $L/W<3$) is comparable to the number of giant arcs with $|\mu|>10$ and $L/W>10$. We conclude that our predicted rate of giant arcs may be lower than the observed rate, although the precise `discrepancy' is still unclear due to uncertainties both in theory and observations.Comment: Revised version after the referee's reports (32 pages,13figures). The paper has been significantly revised with many additions. The new version includes more detailed comparisons with previous studies, including the effects of source size and ellipticity. New discussions about the redshift distribution of lensing clusters and the width of giant arcs have been adde

Tunnelling Effect and Hawking Radiation from a Vaidya Black Hole

In this paper, we extend Parikh' work to the non-stationary black hole. As an example of the non-stationary black hole, we study the tunnelling effect and Hawking radiation from a Vaidya black hole whose Bondi mass is identical to its mass parameter. We view Hawking radiation as a tunnelling process across the event horizon and calculate the tunnelling probability. We find that the result is different from Parikh's work because $\frac{dr_{H}}{dv}$ is the function of Bondi mass m(v)

Enhancement of quantum correlations for the system of cavity QED by applying bang-bang pulses

We propose a scheme of increasing quantum correlations for the cavity quantum electrodynamics system consisting of two noninteracting two-level atoms each locally interacting with its own quantized field mode by bang-bang pulses. We investigate the influence of the bang-bang pulses on the dynamics of quantum discord, entanglement, quantum mutual information and classical correlation between the two atoms. It is shown that the amount of quantum discord and entanglement of the two atoms can be improved by applying the bang-bang pulses.Comment: 6 pages, 5 figure

Coherent population trapping in a dressed two-level atom via a bichromatic field

We show theoretically that by applying a bichromatic electromagnetic field, the dressed states of a monochromatically driven two-level atom can be pumped into a coherent superposition termed as dressed-state coherent population trapping. Such effect can be viewed as a new doorknob to manipulate a two-level system via its control over dressed-state populations. Application of this effect in the precision measurement of Rabi frequency, the unexpected population inversion and lasing without inversion are discussed to demonstrate such controllability.Comment: 14 pages, 6 figure

Control the entanglement of two atoms in an optical cavity via white noise

Two two-level atoms within a leaky optical cavity is driven by two independent external optical white noise fields. We investigate how entanglement between two atoms arises in such a situation. The steady state entanglement of two atoms is also investigated. A stochastic-resonance-like behavior of entanglement is revealed. Finally, the Bell violation between atoms is discussed.Comment: 10 pages, 9 figure

An extended view of the Pisces Overdensity from the SCUSS survey

SCUSS is a u-band photometric survey covering about 4000 square degree of the South Galactic Cap, reaching depths of up to 23 mag. By extending around 1.5 mag deeper than SDSS single-epoch u data, SCUSS is able to probe much a larger volume of the outer halo, i.e. with SCUSS data blue horizontal branch (BHB) stars can trace the outer halo of the Milky Way as far as 100-150 kpc. Utilizing this advantage we combine SCUSS u band with SDSS DR9 gri photometric bands to identify BHB stars and explore halo substructures. We confirm the existence of the Pisces overdensity, which is a structure in the outer halo (at around 80 kpc) that was discovered using RR Lyrae stars. For the first time we are able to determine its spatial extent, finding that it appears to be part of a stream with a clear distance gradient. The stream, which is ~5 degrees wide and stretches along ~25 degrees, consists of 20-30 BHBs with a total significance of around 6sigma over the background. Assuming we have detected the entire stream and that the progenitor has fully disrupted, then the number of BHBs suggests the original system was similar to smaller classical or a larger ultra-faint dwarf galaxy. On the other hand, if the progenitor still exists, it can be hunted for by reconstructing its orbit from the distance gradient of the stream. This new picture of the Pisces overdensity sheds new light on the origin of this intriguing system.Comment: 8 pages, 4 figures, accepted by Ap