Steady state entanglement in the mechanical vibrations of two dielectric membranes

We consider two dielectric membranes suspended inside a Fabry-Perot-cavity, which are cooled to a steady state via a drive by suitable classical lasers. We show that the vibrations of the membranes can be entangled in this steady state. They thus form two mechanical, macroscopic degrees of freedom that share steady state entanglement.Comment: example for higher environment temperatures added, further explanations added to the tex

Single photon state generation from a continuous-wave non-degenerate optical parametric oscillator

We present a theoretical treatment of conditional preparation of one-photon states from a continuous-wave non-degenerate optical parametric oscillator. We obtain an analytical expression for the output state Wigner function, and we maximize the one-photon state fidelity by varying the temporal mode function of the output state. We show that a higher production rate of high fidelity Fock states is obtained if we condition the outcome on dark intervals around trigger photo detection events.Comment: 9 pages, 9 figures, v2: published versio

Properties of the stochastic Gross-Pitaevskii equation: Projected Ehrenfest relations and the optimal plane wave basis

We investigate the properties of the stochastic Gross-Pitaevskii equation describing a condensate interacting with a stationary thermal cloud derived by Gardiner and coworkers. We find the appropriate Ehrenfest relations for the SGPE, including the effect of growth noise and projector terms arising from the energy cutoff. This is carried out in the high temperature regime appropriate for the SGPE, which simplifies the action of the projectors. The validity condition for neglecting the projector terms in the Ehrenfest relations is found to be more stringent than the usual condition of validity of the truncated Wigner method or classical field method -- which is that all modes are highly occupied. In addition it is required that the overlap of the nonlinear term with the lowest energy eigenstate of the non-condensate band is small. We show how to use the Ehrenfest relations along with the corrections generated by the projector to monitor dynamical artifacts arising from the cutoff. We also investigate the effect of using different bases to describe a harmonically trapped BEC at finite temperature by comparing the condensate fraction found using the plane wave and single particle bases. We show that the equilibrium properties are strongly dependent on the choice of basis. There is thus an optimal choice of plane wave basis for a given cut-off energy and we show that this basis gives the best reproduction of the single particle spectrum, the condensate fraction and the position and momentum densities.Comment: 23 pages, 5 figure

Parametric Inference for Biological Sequence Analysis

One of the major successes in computational biology has been the unification, using the graphical model formalism, of a multitude of algorithms for annotating and comparing biological sequences. Graphical models that have been applied towards these problems include hidden Markov models for annotation, tree models for phylogenetics, and pair hidden Markov models for alignment. A single algorithm, the sum-product algorithm, solves many of the inference problems associated with different statistical models. This paper introduces the \emph{polytope propagation algorithm} for computing the Newton polytope of an observation from a graphical model. This algorithm is a geometric version of the sum-product algorithm and is used to analyze the parametric behavior of maximum a posteriori inference calculations for graphical models.Comment: 15 pages, 4 figures. See also companion paper "Tropical Geometry of Statistical Models" (q-bio.QM/0311009

Quantum Kinetic Theory VI: The Growth of a Bose-Einstein Condensate

A detailed analysis of the growth of a BEC is given, based on quantum kinetic theory, in which we take account of the evolution of the occupations of lower trap levels, and of the full Bose-Einstein formula for the occupations of higher trap levels, as well as the Bose stimulated direct transfer of atoms to the condensate level introduced by Gardiner et al. We find good agreement with experiment at higher temperatures, but at lower temperatures the experimentally observed growth rate is somewhat more rapid. We also confirm the picture of the ``kinetic'' region of evolution, introduced by Kagan et al., for the time up to the initiation of the condensate. The behavior after initiation essentially follows our original growth equation, but with a substantially increased rate coefficient. Our modelling of growth implicitly gives a model of the spatial shape of the condensate vapor system as the condensate grows, and thus provides an alternative to the present phenomenological fitting procedure, based on the sum of a zero-chemical potential vapor and a Thomas-Fermi shaped condensate. Our method may give substantially different results for condensate numbers and temperatures obtained from phenomentological fits, and indicates the need for more systematic investigation of the growth dynamics of the condensate from a supersaturated vapor.Comment: TeX source; 29 Pages including 26 PostScript figure

Does eye examination order for standard automated perimetry matter?

PURPOSE: In spite of faster examination procedures, visual field (VF) results are potentially influenced by fatigue. We use large-scale VF data collected from clinics to test the hypothesis that perimetric fatigue effects are greater in the eye examined second. METHODS: Series of six Humphrey Swedish Interactive Testing Algorithm (SITA) VFs from 6901 patients were retrospectively extracted from a VF database from four different glaucoma clinics. Mean deviation (MD) was compared between first and second tested eyes. A surrogate measure of longitudinal MD variability over time was estimated from errors using linear regression of MD against time then compared between first and second tested eye. RESULTS: Right eye VF was tested consistently first throughout in 6320 (91.6%) patients. Median (interquartile range; IQR) MD in the first tested (right) eye and second tested (left) eye was -2.57 (-6.15, -0.58) dB and -2.70 (-6.34, -0.80) dB respectively (median reduction VF sensitivity of 0.13 dB; p < 0.001). Median (IQR) increase in our surrogate measure of longitudinal MD variability in the second eye tested was 3% (-43%, 50%); this effect was not associated with patient age or rest time between examinations. CONCLUSION: Statistically significant perimetric fatigue effects manifest on average in the second eye tested in routine clinics using Humphrey Field Analyzer SITA examinations. However, the average effects were very small and there was enormous variation among patients. We recommend starting with a right eye examination so that any perimetric fatigue effects, if they exist in an individual, will be as constant as possible from visit to visit

Coupled dynamics of RNA folding and nanopore translocation

The translocation of structured RNA or DNA molecules through narrow pores necessitates the opening of all base pairs. Here, we study the interplay between the dynamics of translocation and base-pairing theoretically, using kinetic Monte Carlo simulations and analytical methods. We find that the transient formation of basepairs that do not occur in the ground state can significantly speed up translocation.Comment: 4 pages, 3 figures, to appear in Physical Review Letter

NEW PALAEOZOIC FISH REMAINS FROM SOUTHERN AFRICA

The fossil fish record of southern Africa is both sparse and spotty and the only group with a relatively complete record is the Actinopterygii; indeed several of the major fish groups have not so far been described from the African Continent. The Palaeozoic rocks of southern Africa have yielded an even more restricted fish fauna (Gardiner 1962; 1969). However, an accumulation of new, but fragmentary, material from several localities has shown the undoubted presence of two groups, coelacanths and acanthodians, hitherto unrecorded from the Palaeozoic strata of southern Africa

Segmentation and cycles of crustal accretion at mid-ocean ridges: a study of the Reykjanes Ridge

Early studies of mid-ocean ridges suggest a fundamental difference between crustal accretionary processes at slow- and fast-spreading ridges. Accretion, and the supply of melt to the crust itself, is thought to be highly episodic at slow-spreading ridges but steady-state at fast-spreading ridges. However, recent studies are beginning to question this model, with evidence for the temporal variation in crustal accretionary processes at all spreading rates emerging. This study provides evidence from bathymetry, TOBI sidescan, gravity and magnetic data, collected during different cruises to the Reykjanes Ridge, for the temporal nature of crustal accretion and its relationship to segmentation. Interpretation of TOBI images indicates that individual adjacent axial volcanic ridges (AVRs) vary in relative age, suggesting that they are at various stages of an evolutionary lifecycle, with episodic cycles of magmatic and tectonic activity. However, prior to investigating the possible effects of tectonomagmatic cycles on the crustal structure of AVRs, the effect of the Iceland hotspot on the ridge is examined. The along-axis free-air gravity anomaly is forward modelled in 2-D, revealing an along-axis increase in crustal thickness towards Iceland from 7.5 km to 10.5 km and a decrease in mantle densities from 3.30 to 3.23 g cm"^ between 57 30'N and 62 N. Calculation of the residual mantle Bouguer Anomaly (RMBA) and inversion of magnetic anomaly data, reveal intermediate-wavelength fluctuations in RMBA amplitude and magnetization intensity respectively that are attributed to hotspot pulses, with 59 N marking the southern most extent of the most recent pulse. Removal of the hotspot effect on the gravity data reveals short-wavelength RMBA lows, associated with individual AVRs, superimposed on a broad ridge-trending low. Along-AVR-axis gravity modelling shows that a number of these RMBA lows can be explained by a 200-800 m thickening of the crust and/or by the presence of 5-20% partial melt in the mid-crust. A correlation between relative AVR age and crustal structure is established, with longer, more mature AVRs having a thicker crust and shorter, younger AVRs having more partial melt in the mid-crust. Short-wavelength magnetization intensity highs, associated with younger AVRs, corroborate the TOBI age interpretations. Local spreading rate calculations reveal that total spreading rates for younger AVRs are up to 20% faster than for older AVRs over the last 1.42 Ma. On the basis of these results a model for the cyclicity of crustal accretion is presented, whereby far-field tectonic stresses result in spreading-orthogonal brittle deformation of the crust in the neovolcanic zone, and 3-D mantle upwelling, with a wavelength of -70 km, follows the ridge trend and results in second order segments that comprise ~5 AVRs. It is proposed that along-axis migration of melt within such a segment results in the observed variations in AVR age, length, RMBA amplitude, magnetization intensity and local spreading rate. The proposed model has implications for the temporal variability of crustal accretion at all spreading rates