Coupled Two-Way Clustering Analysis of Gene Microarray Data

We present a novel coupled two-way clustering approach to gene microarray data analysis. The main idea is to identify subsets of the genes and samples, such that when one of these is used to cluster the other, stable and significant partitions emerge. The search for such subsets is a computationally complex task: we present an algorithm, based on iterative clustering, which performs such a search. This analysis is especially suitable for gene microarray data, where the contributions of a variety of biological mechanisms to the gene expression levels are entangled in a large body of experimental data. The method was applied to two gene microarray data sets, on colon cancer and leukemia. By identifying relevant subsets of the data and focusing on them we were able to discover partitions and correlations that were masked and hidden when the full dataset was used in the analysis. Some of these partitions have clear biological interpretation; others can serve to identify possible directions for future research

A Single Atom as a Mirror of an Optical Cavity

By tightly focussing a laser field onto a single cold ion trapped in front of a far-distant dielectric mirror, we could observe a quantum electrodynamic effect whereby the ion behaves as the optical mirror of a Fabry-P\'erot cavity. We show that the amplitude of the laser field is significantly altered due to a modification of the electromagnetic mode structure around the atom in a novel regime in which the laser intensity is already changed by the atom alone. e propose a direct application of this system as a quantum memory for single photons.Comment: 7 pages, 3 figures, to appear in Physical Review Letter

Effective-range approach and scaling laws for electromagnetic strength in neutron-halo nuclei

We study low-lying multipole strength in neutron-halo nuclei. The strength depends only on a few low-energy constants: the neutron separation energy, the asymptotic normalization coefficient of the bound state wave function, and the scattering length that contains the information on the interaction in the continuum. The shape of the transition probability shows a characteristic dependence on few scaling parameters and the angular momenta. The total E1 strength is related to the root-mean-square radius of the neutron wave function in the ground state and shows corresponding scaling properties. We apply our approach to the E1 strength distribution of 11Be.Comment: 4 pages, 1 figure (modified), additional table, extended discussion of example, accepted for publication in Phys. Rev. Let

Turbofan forced mixer lobe flow modeling. Part 3: Application to augment engines

Military engines frequently need large quantities of thrust for short periods of time. The addition of an augmentor can provide such thrust increases but with a penalty of increased duct length and engine weight. The addition of a forced mixer to the augmentor improves performance and reduces the penalty, as well as providing a method for siting the required flame holders. In this report two augmentor concepts are investigated: a swirl-mixer augmentor and a mixer-flameholder augmentor. Several designs for each concept are included and an experimental assessment of one of the swirl-mixer augmentors is presented

QED with a spherical mirror

We investigate the Quantum-Electro-Dynamic properties of an atomic electron close to the focus of a spherical mirror. We first show that the spontaneous emission and excited state level shift of the atom can be fully suppressed with mirror-atom distances of many wavelengths. A three-dimensional theory predicts that the spectral density of vacuum fluctuations can indeed vanish within a volume $\lambda^3$ around the atom, with the use of a far distant mirror covering only half of the atomic emission solid angle. The modification of these QED atomic properties is also computed as a function of the mirror size and large effects are found for only moderate numerical apertures. We also evaluate the long distance ground state energy shift (Casimir-Polder shift) and find that it scales as $(\lambda/R)^2$ at the focus of a hemi-spherical mirror of radius $R$, as opposed to the well known $(\lambda/R)^4$ scaling law for an atom at a distance $R$ from an infinite plane mirror. Our results are relevant for investigations of QED effects, and also free space coupling to single atoms using high-numerical aperture lenses.Comment: 12 pages, 4 figure

Effective generation of cat and kitten states

We present an effective method of coherent state superposition (cat state) generation using single trapped ion in a Paul trap. The method is experimentally feasible for coherent states with amplitude $\alpha \le 2$ using available technology. It works both in and beyond the Lamb-Dicke regime.Comment: 11 pages, 8 figure

Experimental quantum information processing with 43Ca+ ions

For quantum information processing (QIP) with trapped ions, the isotope 43Ca+ offers the combined advantages of a quantum memory with long coherence time, a high fidelity read out and the possibility of performing two qubit gates on a quadrupole transition with a narrow-band laser. Compared to other ions used for quantum computing, 43Ca+ has a relatively complicated level structure. In this paper we discuss how to meet the basic requirements for QIP and demonstrate ground state cooling, robust state initialization and efficient read out for the hyperfine qubit with a single 43Ca+ ion. A microwave field and a Raman light field are used to drive qubit transitions, and the coherence times for both fields are compared. Phase errors due to interferometric instabilities in the Raman field generation do not limit the experiments on a time scale of 100 ms. We find a quantum information storage time of many seconds for the hyperfine qubit.Comment: 9 pages, 10 figure

Electromagnetically Induced Transparency from a Single Atom in Free Space

We report an absorption spectroscopy experiment and the observation of electromagnetically induced transparency from a single trapped atom. We focus a weak and narrowband Gaussian light beam onto an optically cooled Barium ion using a high numerical aperture lens. Extinction of this beam is observed with measured values of up to 1.3 %. We demonstrate electromagnetically induced transparency of the ion by tuning a strong control beam over a two-photon resonance in a three-level lambda-type system. The probe beam extinction is inhibited by more than 75 % due to population trapping.Comment: 4 pages, 3 figure

Super-paramagnetic clustering of yeast gene expression profiles

High-density DNA arrays, used to monitor gene expression at a genomic scale, have produced vast amounts of information which require the development of efficient computational methods to analyze them. The important first step is to extract the fundamental patterns of gene expression inherent in the data. This paper describes the application of a novel clustering algorithm, Super-Paramagnetic Clustering (SPC) to analysis of gene expression profiles that were generated recently during a study of the yeast cell cycle. SPC was used to organize genes into biologically relevant clusters that are suggestive for their co-regulation. Some of the advantages of SPC are its robustness against noise and initialization, a clear signature of cluster formation and splitting, and an unsupervised self-organized determination of the number of clusters at each resolution. Our analysis revealed interesting correlated behavior of several groups of genes which has not been previously identified

Quasirelativistic quasilocal finite wave-function collapse model

A Markovian wave function collapse model is presented where the collapse-inducing operator, constructed from quantum fields, is a manifestly covariant generalization of the mass density operator utilized in the nonrelativistic Continuous Spontaneous Localization (CSL) wave function collapse model. However, the model is not Lorentz invariant because two such operators do not commute at spacelike separation, i.e., the time-ordering operation in one Lorentz frame, the "preferred" frame, is not the time-ordering operation in another frame. However, the characteristic spacelike distance over which the commutator decays is the particle's Compton wavelength so, since the commutator rapidly gets quite small, the model is "almost" relativistic. This "QRCSL" model is completely finite: unlike previous, relativistic, models, it has no (infinite) energy production from the vacuum state. QRCSL calculations are given of the collapse rate for a single free particle in a superposition of spatially separated packets, and of the energy production rate for any number of free particles: these reduce to the CSL rates if the particle's Compton wavelength is small compared to the model's distance parameter. One motivation for QRCSL is the realization that previous relativistic models entail excitation of nuclear states which exceeds that of experiment, whereas QRCSL does not: an example is given involving quadrupole excitation of the $^{74}$Ge nucleus.Comment: 10 pages, to be published in Phys. Rev.