Raman cooling and heating of two trapped Ba+ ions

We study cooling of the collective vibrational motion of two 138Ba+ ions confined in an electrodynamic trap and irradiated with laser light close to the resonances S_1/2-P_1/2 (493 nm) and P_1/2-D_3/2 (650 nm). The motional state of the ions is monitored by a spatially resolving photo multiplier. Depending on detuning and intensity of the cooling lasers, macroscopically different motional states corresponding to different ion temperatures are observed. We also derive the ions' temperature from detailed analytical calculations of laser cooling taking into account the Zeeman structure of the energy levels involved. The observed motional states perfectly match the calculated temperatures. Significant heating is observed in the vicinity of the dark resonances of the Zeeman-split S_1/2-D_3/2 Raman transitions. Here two-photon processes dominate the interaction between lasers and ions. Parameter regimes of laser light are identified that imply most efficient laser cooling.Comment: 8 pages, 5 figure

Exactly soluble model of resonant energy transfer between molecules

F\"orster's theory of resonant energy transfer (FRET) predicts the strength and range of exciton transport between separated molecules. We introduce an exactly soluble model for FRET which reproduces F\"orster's results as well as incorporating quantum coherence effects. As an application the model is used to analyze a system composed of quantum dots and the protein bacteriorhodopsin.Comment: 10 pages, 2 figure

Highest weight Macdonald and Jack Polynomials

Fractional quantum Hall states of particles in the lowest Landau levels are described by multivariate polynomials. The incompressible liquid states when described on a sphere are fully invariant under the rotation group. Excited quasiparticle/quasihole states are member of multiplets under the rotation group and generically there is a nontrivial highest weight member of the multiplet from which all states can be constructed. Some of the trial states proposed in the literature belong to classical families of symmetric polynomials. In this paper we study Macdonald and Jack polynomials that are highest weight states. For Macdonald polynomials it is a (q,t)-deformation of the raising angular momentum operator that defines the highest weight condition. By specialization of the parameters we obtain a classification of the highest weight Jack polynomials. Our results are valid in the case of staircase and rectangular partition indexing the polynomials.Comment: 17 pages, published versio

Quantum state engineering on an optical transition and decoherence in a Paul trap

A single Ca+ ion in a Paul trap has been cooled to the ground state of vibration with up to 99.9% probability. Starting from this Fock state |n=0> we have demonstrated coherent quantum state manipulation on an optical transition. Up to 30 Rabi oscillations within 1.4 ms have been observed. We find a similar number of Rabi oscillations after preparation of the ion in the |n=1> Fock state. The coherence of optical state manipulation is only limited by laser and ambient magnetic field fluctuations. Motional heating has been measured to be as low as one vibrational quantum in 190 ms.Comment: 4 pages, 5 figure

Goldstone Bosons in Effective Theories with Spontaneously Broken Flavour Symmetry

The Flavour Symmetry of the Standard Model (SM) gauge sector is broken by the fermion Yukawa couplings. Promoting the Yukawa matrices to scalar spurion fields, one can break the flavour symmetry spontaneously by giving appropriate vacuum expectation values (VEVs) to the spurion fields, and one encounters Goldstone modes for every broken flavour symmetry generator. In this paper, we point out various aspects related to the possible dynamical interpretation of the Goldstone bosons: (i) In an effective-theory framework with local flavour symmetry, the Goldstone fields represent the longitudinal modes for massive gauge bosons. The spectrum of the latter follows the sequence of flavour-symmetry breaking related to the hierarchies in Yukawa couplings and flavour mixing angles. (ii) Gauge anomalies can be consistently treated by adding higher-dimensional operators. (iii) Leaving the U(1) factors of the flavour symmetry group as global symmetries, the respective Goldstone modes behave as axions which can be used to resolve the strong CP problem by a modified Peccei-Quinn mechanism. (iv) The dynamical picture of flavour symmetry breaking implies new sources of flavour-changing neutral currents, which arise from integrating out heavy scalar spurion fields and heavy gauge bosons. The coefficients of the effective operators follow the minimal-flavour violation principle.Comment: 27 pages, abstract and introduction extended, more detailed discussion of heavy gauge boson spectrum and auxiliary heavy fermions, outline restructured. Matches version to be published in JHE

EXACT2: the semantics of biomedical protocols

© 2014 Soldatova et al.; licensee BioMed Central. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.This article has been made available through the Brunel Open Access Publishing Fund.Background: The reliability and reproducibility of experimental procedures is a cornerstone of scientific practice. There is a pressing technological need for the better representation of biomedical protocols to enable other agents (human or machine) to better reproduce results. A framework that ensures that all information required for the replication of experimental protocols is essential to achieve reproducibility. Methods: We have developed the ontology EXACT2 (EXperimental ACTions) that is designed to capture the full semantics of biomedical protocols required for their reproducibility. To construct EXACT2 we manually inspected hundreds of published and commercial biomedical protocols from several areas of biomedicine. After establishing a clear pattern for extracting the required information we utilized text-mining tools to translate the protocols into a machine amenable format. We have verified the utility of EXACT2 through the successful processing of previously ‘unseen’ (not used for the construction of EXACT2) protocols. Results: The paper reports on a fundamentally new version EXACT2 that supports the semantically-defined representation of biomedical protocols. The ability of EXACT2 to capture the semantics of biomedical procedures was verified through a text mining use case. In this EXACT2 is used as a reference model for text mining tools to identify terms pertinent to experimental actions, and their properties, in biomedical protocols expressed in natural language. An EXACT2-based framework for the translation of biomedical protocols to a machine amenable format is proposed. Conclusions: The EXACT2 ontology is sufficient to record, in a machine processable form, the essential information about biomedical protocols. EXACT2 defines explicit semantics of experimental actions, and can be used by various computer applications. It can serve as a reference model for for the translation of biomedical protocols in natural language into a semantically-defined format.This work has been partially funded by the Brunel University BRIEF award and a grant from Occams Resources

A Precision Measurement of Nuclear Muon Capture on 3He

The muon capture rate in the reaction mu- 3He -> nu + 3H has been measured at PSI using a modular high pressure ionization chamber. The rate corresponding to statistical hyperfine population of the mu-3He atom is (1496.0 +- 4.0) s^-1. This result confirms the PCAC prediction for the pseudoscalar form factors of the 3He-3H system and the nucleon.Comment: 13 pages, 6 PostScript figure

Photonuclear Reactions of Three-Nucleon Systems

We discuss the available data for the differential and the total cross section for the photodisintegration of $^3$He and $^3$H and the corresponding inverse reactions below $E_\gamma = 100$ MeV by comparing with our calculations using realistic $NN$ interactions. The theoretical results agree within the errorbars with the data for the total cross sections. Excellent agreement is achieved for the angular distribution in case of $^3$He, whereas for $^3$H a discrepancy between theory and experiment is found.Comment: 11 pages (twocolumn), 12 postscript figures included, uses psfig, RevTe

Dynamical evolution of neutrino--cooled accretion disks: detailed microphysics, lepton-driven convection, and global energetics

We present a detailed, two dimensional numerical study of the microphysical conditions and dynamical evolution of accretion disks around black holes when neutrino emission is the main source of cooling. Such structures are likely to form after the gravitational collapse of massive rotating stellar cores, or the coalescence of two compact objects in a binary (e.g., the Hulse--Taylor system). The physical composition is determined self consistently by considering two regimes: neutrino--opaque and neutrino--transparent, with a detailed equation of state which takes into account neutronization, nuclear statistical equilibrium of a gas of free nucleons and alpha particles, blackbody radiation and a relativistic Fermi gas of arbitrary degeneracy. Various neutrino emission processes are considered, with electron/positron capture onto free nucleons providing the dominant contribution to the cooling rate. We find that important temporal and spatial scales, related to the optically thin/optically thick transition are present in the disk, and manifest themselves clearly in the energy output in neutrinos. This transition produces an inversion of the lepton gradient in the innermost regions of the flow which drives convective motions, and affects the density and disk scale height radial profiles. The electron fraction remains low in the region close to the black hole, and if preserved in an outflow, could give rise to heavy element nucleosynthesis. Our specific initial conditions arise from the binary merger context, and so we explore the implications of our results for the production of gamma ray bursts.Comment: 26 pages, 12 figures, to appear in Ap

Use of Site-Specifically Tethered Chemical Nucleases to Study Macromolecular Reactions

During a complex macromolecular reaction multiple changes in molecular conformation and interactions with ligands may occur. X-ray crystallography may provide only a limited set of snapshots of these changes. Solution methods can augment such structural information to provide a more complete picture of a macromolecular reaction. We analyzed the changes in protein conformation and protein:nucleic acid interactions which occur during transcription initiation by using a chemical nuclease tethered to cysteines introduced site-specifically into the RNA polymerase of bacteriophage T7 (T7 RNAP). Changes in cleavage patterns as the polymerase steps through transcription reveal a series of structural transitions which mediate transcription initiation. Cleavage by tethered chemical nucleases is seen to be a powerful method for revealing the conformational dynamics of macromolecular reactions, and has certain advantages over cross-linking or energy transfer approaches