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

Two-atom dark states in electromagnetic cavities

The center-of-mass motion of two two-level atoms coupled to a single damped mode of an electromagnetic resonator is investigated. For the case of one atom being initially excited and the cavity mode in the vacuum state it is shown that the atomic time evolution is dominated by the appearance of dark states. These states, in which the initial excitation is stored in the internal atomic degrees of freedom and the atoms become quantum mechanically entangled, are almost immune against photon loss from the cavity. Various properties of the dark states within and beyond the Raman-Nath approximation of atom optics are worked out.Comment: 8 pages, 4 figure

Sympathetic Cooling of Trapped Cd+ Isotopes

We sympathetically cool a trapped 112Cd+ ion by directly Doppler-cooling a 114Cd+ ion in the same trap. This is the first demonstration of optically addressing a single trapped ion being sympathetically cooled by a different species ion. Notably, the experiment uses a single laser source, and does not require strong focusing. This paves the way toward reducing decoherence in an ion trap quantum computer based on Cd+ isotopes.Comment: 4 figure

Cooling the Collective Motion of Trapped Ions to Initialize a Quantum Register

We report preparation in the ground state of collective modes of motion of two trapped 9Be+ ions. This is a crucial step towards realizing quantum logic gates which can entangle the ions' internal electronic states. We find that heating of the modes of relative ion motion is substantially suppressed relative to that of the center-of-mass modes, suggesting the importance of these modes in future experiments.Comment: 5 pages, including 3 figures. RevTeX. PDF and PostScript available at http://www.bldrdoc.gov/timefreq/ion/qucomp/papers.htm . final (published) version. Eq. 1 and Table 1 slightly different from original submissio

q-Generalization of the inverse Fourier transform

A wide class of physical distributions appears to follow the q-Gaussian form, which plays the role of attractor according to a Central Limit Theorem generalized in the presence of specific correlations between the relevant random variables. In the realm of this theorem, a q-generalized Fourier transform plays an important role. We introduce here a method which univocally determines a distribution from the knowledge of its q-Fourier transform and some supplementary information. This procedure involves a recently q-generalized Dirac delta and the class of functions on which it acts. The present method conveniently extends the inverse of the standard Fourier transform, and is therefore expected to be very useful in the study of many complex systems.Comment: 6 pages, 3 figures. To appear in Physics Letters

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

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

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