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,

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

Destabilization of dark states and optical spectroscopy in Zeeman-degenerate atomic systems

We present a general discussion of the techniques of destabilizing dark states in laser-driven atoms with either a magnetic field or modulated laser polarization. We show that the photon scattering rate is maximized at a particular evolution rate of the dark state. We also find that the atomic resonance curve is significantly broadened when the evolution rate is far from this optimum value. These results are illustrated with detailed examples of destabilizing dark states in some commonly-trapped ions and supported by insights derived from numerical calculations and simple theoretical models.Comment: 14 pages, 10 figure