Guiding of Rydberg atoms in a high-gradient magnetic guide

We study the guiding of $^{87}$Rb 59D$_{5/2}$ Rydberg atoms in a linear, high-gradient, two-wire magnetic guide. Time delayed microwave ionization and ion detection are used to probe the Rydberg atom motion. We observe guiding of Rydberg atoms over a period of 5 ms following excitation. The decay time of the guided atom signal is about five times that of the initial state. We attribute the lifetime increase to an initial phase of $l$-changing collisions and thermally induced Rydberg-Rydberg transitions. Detailed simulations of Rydberg atom guiding reproduce most experimental observations and offer insight into the internal-state evolution

Wave Packet Echoes in the Motion of Trapped Atoms

We experimentally demonstrate and systematically study the stimulated revival (echo) of motional wave packet oscillations. For this purpose, we prepare wave packets in an optical lattice by non-adiabatically shifting the potential and stimulate their reoccurence by a second shift after a variable time delay. This technique, analogous to spin echoes, enables one even in the presence of strong dephasing to determine the coherence time of the wave packets. We find that for strongly bound atoms it is comparable to the cooling time and much longer than the inverse of the photon scattering rate

The Hydrogen Atom in Combined Electric and Magnetic Fields with Arbitrary Mutual Orientations

For the hydrogen atom in combined magnetic and electric fields we investigate the dependence of the quantum spectra, classical dynamics, and statistical distributions of energy levels on the mutual orientation of the two external fields. Resonance energies and oscillator strengths are obtained by exact diagonalization of the Hamiltonian in a complete basis set, even far above the ionization threshold. At high excitation energies around the Stark saddle point the eigenenergies exhibit strong level repulsions when the angle between the fields is varied. The large avoided crossings occur between states with the same approximately conserved principal quantum number, n, and this intramanifold mixing of states cannot be explained, not even qualitatively, by conventional perturbation theory. However, it is well reproduced by an extended perturbation theory which takes into account all couplings between the angular momentum and Runge-Lenz vector. The large avoided crossings are interpreted as a quantum manifestation of classical intramanifold chaos. This interpretation is supported by both classical Poincar\'e surfaces of section, which reveal a mixed regular-chaotic intramanifold dynamics, and the statistical analysis of nearest-neighbor-spacingComment: two-column version, 10 pages, REVTeX, 10 figures, uuencoded, submitted to Rhys. Rev.

Inferential considerations for low-count RNA-seq transcripts: a case study on the dominant prairie grass Andropogon gerardii

Citation: Raithel, S., Johnson, L., Galliart, M., Brown, S., Shelton, J., Herndon, N., & Bello, N. M. (2016). Inferential considerations for low-count RNA-seq transcripts: a case study on the dominant prairie grass Andropogon gerardii. Bmc Genomics, 17, 16. doi:10.1186/s12864-016-2442-7Background: Differential expression (DE) analysis of RNA-seq data still poses inferential challenges, such as handling of transcripts characterized by low expression levels. In this study, we use a plasmode-based approach to assess the relative performance of alternative inferential strategies on RNA-seq transcripts, with special emphasis on transcripts characterized by a small number of read counts, so-called low-count transcripts, as motivated by an ecological application in prairie grasses. Big bluestem (Andropogon gerardii) is a wide-ranging dominant prairie grass of ecological and agricultural importance to the US Midwest while edaphic subspecies sand bluestem (A. gerardii ssp. Hallii) grows exclusively on sand dunes. Relative to big bluestem, sand bluestem exhibits qualitative phenotypic divergence consistent with enhanced drought tolerance, plausibly associated with transcripts of low expression levels. Our dataset consists of RNA-seq read counts for 25,582 transcripts (60 % of which are classified as low-count) collected from leaf tissue of individual plants of big bluestem (n = 4) and sand bluestem (n = 4). Focused on low-count transcripts, we compare alternative ad-hoc data filtering techniques commonly used in RNA-seq pipelines and assess the inferential performance of recently developed statistical methods for DE analysis, namely DESeq2 and edgeR robust. These methods attempt to overcome the inherently noisy behavior of low-count transcripts by either shrinkage or differential weighting of observations, respectively. Results: Both DE methods seemed to properly control family-wise type 1 error on low-count transcripts, whereas edgeR robust showed greater power and DESeq2 showed greater precision and accuracy. However, specification of the degree of freedom parameter under edgeR robust had a non-trivial impact on inference and should be handled carefully. When properly specified, both DE methods showed overall promising inferential performance on low-count transcripts, suggesting that ad-hoc data filtering steps at arbitrary expression thresholds may be unnecessary. A note of caution is in order regarding the approximate nature of DE tests under both methods. Conclusions: Practical recommendations for DE inference are provided when low-count RNA-seq transcripts are of interest, as is the case in the comparison of subspecies of bluestem grasses. Insights from this study may also be relevant to other applications focused on transcripts of low expression levels

A magneto-optical trap with millimeter ball lenses

We present a magneto-optical trap (MOT) design based on millimeter ball lenses, contained within a metal cube of 0.75$^{\prime \prime}$ side length. We present evidence of trapping approximately $4.2\times 10^5$ of $^{85}$Rb atoms with a number density of $3.2\times 10^9$ atoms/cm$^{3}$ and a loading time of 1.3 s. Measurement and a kinetic laser-cooling model are used to characterize the atom trap design. The design provides several advantages over other types of MOTs: the laser power requirement is low, the small lens and cube sizes allow for miniaturization of MOT applications, and the lack of large-diameter optical beam pathways prevents external blackbody radiation from entering the trapping region.Comment: 8 pages, 4 figure

Squeezing of Atoms in a Pulsed Optical Lattice

We study the process of squeezing of an ensemble of cold atoms in a pulsed optical lattice. The problem is treated both classically and quantum-mechanically under various thermal conditions. We show that a dramatic compression of the atomic density near the minima of the optical potential can be achieved with a proper pulsing of the lattice. Several strategies leading to the enhanced atomic squeezing are suggested, compared and optimized.Comment: Latex, 9 pages, 10 figures, submitted to PR

Symmetry breaking in crossed magnetic and electric fields

We present the first observations of cylindrical symmetry breaking in highly excited diamagnetic hydrogen with a small crossed electric field, and we give a semiclassical interpretation of this effect. As the small perpendicular electric field is added, the recurrence strengths of closed orbits decrease smoothly to a minimum, and revive again. This phenomenon, caused by interference among the electron waves that return to the nucleus, can be computed from the azimuthal dependence of the classical closed orbits.Comment: 4 page REVTeX file including 5 postscript files (using psfig) Accepted for publication in Physical Review Letters. Difference from earlier preprint: we have discovered the cause of the earlier apparent discrepancy between experiment and theory and now achieve excellent agreemen

Cold atoms in a high-Q ring-cavity

We report the confinement of large clouds of ultra-cold 85-Rb atoms in a standing-wave dipole trap formed by the two counter-propagating modes of a high-Q ring-cavity. Studying the properties of this trap we demonstrate loading of higher-order transverse cavity modes and excite recoil-induced resonances.Comment: 4 pages, 4 figure

Trapping States in the Micromaser

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