Automated DNA Motif Discovery

Ensembl's human non-coding and protein coding genes are used to automatically find DNA pattern motifs. The Backus-Naur form (BNF) grammar for regular expressions (RE) is used by genetic programming to ensure the generated strings are legal. The evolved motif suggests the presence of Thymine followed by one or more Adenines etc. early in transcripts indicate a non-protein coding gene. Keywords: pseudogene, short and microRNAs, non-coding transcripts, systems biology, machine learning, Bioinformatics, motif, regular expression, strongly typed genetic programming, context-free grammar.Comment: 12 pages, 2 figure

Influence of quenched dilution on the quasi-long-range ordered phase of the 2d XY model

The influence of non magnetic impurities in the 2d XY model is investigated through Monte Carlo (MC) simulations. The general picture of the transition is fully understood from the Harris criterion which predicts that the universality class is unchanged, and the Berezinskii-Kosterlitz-Thouless description of the topological transition remains valid. We nevertheless address here the question about the influence of dilution on the quasi-long-range order at low temperatures. In particular, we study the asymptotic of the pair correlation function and report the MC estimates for the critical exponent $\eta$ at different dilutions. In the weak dilution region, our MC calculations are further supported by simple spin-wave-like calculations.Comment: 8 pages, 7 eps figure

Simple quantum model for light depolarization

Depolarization of quantum fields is handled through a master equation of the Lindblad type. The specific feature of the proposed model is that it couples dispersively the field modes to a randomly distributed atomic reservoir, much in the classical spirit of dealing with this problem. The depolarizing dynamics resulting from this model is analyzed for relevant states.Comment: Improved version. Accepted for publication in the Journal of the Optical Society of America

Virtual Hand Illusion Induced by Visuomotor Correlations

Background: Our body schema gives the subjective impression of being highly stable. However, a number of easily-evoked illusions illustrate its remarkable malleability. In the rubber-hand illusion, illusory ownership of a rubber-hand is evoked by synchronous visual and tactile stimulation on a visible rubber arm and on the hidden real arm. Ownership is concurrent with a proprioceptive illusion of displacement of the arm position towards the fake arm. We have previously shown that this illusion of ownership plus the proprioceptive displacement also occurs towards a virtual 3D projection of an arm when the appropriate synchronous visuotactile stimulation is provided. Our objective here was to explore whether these illusions (ownership and proprioceptive displacement) can be induced by only synchronous visuomotor stimulation, in the absence of tactile stimulation.Methodology/Principal Findings: To achieve this we used a data-glove that uses sensors transmitting the positions of fingers to a virtually projected hand in the synchronous but not in the asynchronous condition. The illusion of ownership was measured by means of questionnaires. Questions related to ownership gave significantly larger values for the synchronous than for the asynchronous condition. Proprioceptive displacement provided an objective measure of the illusion and had a median value of 3.5 cm difference between the synchronous and asynchronous conditions. In addition, the correlation between the feeling of ownership of the virtual arm and the size of the drift was significant.Conclusions/Significance: We conclude that synchrony between visual and proprioceptive information along with motor activity is able to induce an illusion of ownership over a virtual arm. This has implications regarding the brain mechanisms underlying body ownership as well as the use of virtual bodies in therapies and rehabilitation

Nonlinear cross-Kerr quasiclassical dynamics

We study the quasiclassical dynamics of the cross-Kerr effect. In this approximation, the typical periodical revivals of the decorrelation between the two polarization modes disappear and they remain entangled. By mapping the dynamics onto the Poincare space, we find simple conditions for polarization squeezing. When dissipation is taken into account, the shape of the states in such a space is not considerably modified, but their size is reduced.Comment: 16 pages, 5 figure

Comprehensive theory of the relative phase in atom-field interactions

We explore the role played by the quantum relative phase in a well-known model of atom-field interaction, namely, the Dicke model. We introduce an appropriate polar decomposition of the atom-field relative amplitudes that leads to a truly Hermitian relative-phase operator, whose eigenstates correctly describe the phase properties, as we demonstrate by studying the positive operator-valued measure derived from it. We find the probability distribution for this relative phase and, by resorting to a numerical procedure, we study its time evolution.Comment: 20 pages, 4 figures, submitted to Phys. Rev.

Discrete phase-space structure of nn-qubit mutually unbiased bases

We work out the phase-space structure for a system of $n$ qubits. We replace the field of real numbers that label the axes of the continuous phase space by the finite field \Gal{2^n} and investigate the geometrical structures compatible with the notion of unbiasedness. These consist of bundles of discrete curves intersecting only at the origin and satisfying certain additional properties. We provide a simple classification of such curves and study in detail the four- and eight-dimensional cases, analyzing also the effect of local transformations. In this way, we provide a comprehensive phase-space approach to the construction of mutually unbiased bases for $n$ qubits.Comment: Title changed. Improved version. Accepted for publication in Annals of Physic