Large-scale Oscillation of Structure-Related DNA Sequence Features in Human Chromosome 21

Human chromosome 21 is the only chromosome in human genome that exhibits oscillation of (G+C)-content of cycle length of hundreds kilobases (500 kb near the right telomere). We aim at establishing the existence of similar periodicity in structure-related sequence features in order to relate this (G+C)% oscillation to other biological phenomena. The following quantities are shown to oscillate with the same 500kb periodicity in human chromosome 21: binding energy calculated by two sets of dinucleotide-based thermodynamic parameters, AA/TT and AAA/TTT bi-/tri-nucleotide density, 5'-TA-3' dinucleotide density, and signal for 10/11-base periodicity of AA/TT or AAA/TTT. These intrinsic quantities are related to structural features of the double helix of DNA molecules, such as base-pair binding, untwisting/unwinding, stiffness, and a putative tendency for nucleosome formation.Comment: submitted to Physical Review

A microfabricated sensor for thin dielectric layers

We describe a sensor for the measurement of thin dielectric layers capable of operation in a variety of environments. The sensor is obtained by microfabricating a capacitor with interleaved aluminum fingers, exposed to the dielectric to be measured. In particular, the device can measure thin layers of solid frozen from a liquid or gaseous medium. Sensitivity to single atomic layers is achievable in many configurations and, by utilizing fast, high sensitivity capacitance read out in a feedback system onto environmental parameters, coatings of few layers can be dynamically maintained. We discuss the design, read out and calibration of several versions of the device optimized in different ways. We specifically dwell on the case in which atomically thin solid xenon layers are grown and stabilized, in cryogenic conditions, from a liquid xenon bath

Characterization of high finesse mirrors: loss, phase shifts and mode structure in an optical cavity

An extensive characterization of high finesse optical cavities used in cavity QED experiments is described. Different techniques in the measurement of the loss and phase shifts associated with the mirror coatings are discussed and their agreement shown. Issues of cavity field mode structure supported by the dielectric coatings are related to our effort to achieve the strongest possible coupling between an atom and the cavity.Comment: 8 pages, 4 figure

Comparisons of binary black hole merger waveforms

This a particularly exciting time for gravitational wave physics. Ground-based gravitational wave detectors are now operating at a sensitivity such that gravitational radiation may soon be directly detected, and recently several groups have independently made significant breakthroughs that have finally enabled numerical relativists to solve the Einstein field equations for coalescing black-hole binaries, a key source of gravitational radiation. The numerical relativity community is now in the position to begin providing simulated merger waveforms for use by the data analysis community, and it is therefore very important that we provide ways to validate the results produced by various numerical approaches. Here, we present a simple comparison of the waveforms produced by two very different, but equally successful approaches--the generalized harmonic gauge and the moving puncture methods. We compare waveforms of equal-mass black hole mergers with minimal or vanishing spins. The results show exceptional agreement for the final burst of radiation, with some differences attributable to small spins on the black holes in one case.Comment: Revtex 4, 5 pages. Published versio

Mobility of thorium ions in liquid xenon

We present a measurement of the $^{226}$Th ion mobility in LXe at 163.0 K and 0.9 bar. The result obtained, 0.240$\pm$0.011 (stat) $\pm$0.011 (syst) cm$^{2}$/(kV-s), is compared with a popular model of ion transport.Comment: 6.5 pages,

All-optical ion generation for ion trap loading

We have investigated the all-optical generation of ions by photo-ionisation of atoms generated by pulsed laser ablation. A direct comparison between a resistively heated oven source and pulsed laser ablation is reported. Pulsed laser ablation with 10 ns Nd:YAG laser pulses is shown to produce large calcium flux, corresponding to atomic beams produced with oven temperatures greater than 650 K. For an equivalent atomic flux, pulsed laser ablation is shown to produce a thermal load more than one order of magnitude smaller than the oven source. The atomic beam distributions obey Maxwell-Boltzmann statistics with most probable speeds corresponding to temperatures greater than 2200 K. Below a threshold pulse fluence between 280 mJ/cm^2 and 330 mJ/cm^2, the atomic beam is composed exclusively of ground state atoms. For higher fluences ions and excited atoms are generated.Comment: 7 pages, 9 figure

A simple radionuclide-driven single-ion source

We describe a source capable of producing single barium ions through nuclear recoils in radioactive decay. The source is fabricated by electroplating 148Gd onto a silicon {\alpha}-particle detector and vapor depositing a layer of BaF2 over it. 144Sm recoils from the alpha decay of 148Gd are used to dislodge Ba+ ions from the BaF2 layer and emit them in the surrounding environment. The simultaneous detection of an {\alpha} particle in the substrate detector allows for tagging of the nuclear decay and of the Ba+ emission. The source is simple, durable, and can be manipulated and used in different environments. We discuss the fabrication process, which can be easily adapted to emit most other chemical species, and the performance of the source

Observation of single collisionally cooled trapped ions in a buffer gas

Individual Ba ions are trapped in a gas-filled linear ion trap and observed with a high signal-to-noise ratio by resonance fluorescence. Single-ion storage times of ~5 min (~1 min) are achieved using He (Ar) as a buffer gas at pressures in the range 8e-5 - 4e-3 torr. Trap dynamics in buffer gases are experimentally studied in the simple case of single ions. In particular, the cooling effects of light gases such as He and Ar and the destabilizing properties of heavier gases such as Xe are studied. A simple model is offered to explain the observed phenomenology.Comment: 5 pages, 4 figures, accepted for publication in Phys. Rev. A. Minor text and figure change

The theory of heating of the quantum ground state of trapped ions

Using a displacement operator formalism, I analyse the depopulation of the vibrational ground state of trapped ions. Two heating times, one characterizing short time behaviour, the other long time behaviour are found. The short time behaviour is analyzed both for single and multiple ions, and a formula for the relative heating rates of different modes is derived. The possibility of correction of heating via the quantum Zeno effect, and the exploitation of the suppression of heating of higher modes to reduce errors in quantum computation is considered.Comment: 9 pages, 2 figure