MultiPriDe: automated batch development of quantitative real-time PCR primers

Quantitative reverse transcriptase polymerase chain reaction (qRT–PCR) is a commonly employed gene expression quantification technique. This requires the development of appropriately targeted oligonucleotide primers, which necessitates the identification of ideal amplicons, development of optimized oligonucleotide sequences under most favorable pre-determined reaction conditions, and management of the resultant target-oligonucleotide pair information for each gene to be studied. The Primer3 utility exists for development of oligonucleotide primers and fills that role effectively. However, the manual process of identifying target sites and individually generating primers is inefficient and prone to user-introduced error, especially when a large number of genes are to be examined. We have developed MultiPriDe (Multiple Primer Design), a Perl utility that accepts batch lists of Gene database identifiers, collects available intron and exon position data critical to qRT–PCR primer development, and supplies these sites as identified targets for the Primer3 utility. This automated ‘gene to primer’ procedure is coupled with a set of optimized hybridization conditions used by the Primer3 utility to maximize successful primer design. MultiPriDe and assembled repeat libraries are available upon request. Please direct requests to [email protected]

Colloquium: Trapped ions as quantum bits -- essential numerical tools

Trapped, laser-cooled atoms and ions are quantum systems which can be experimentally controlled with an as yet unmatched degree of precision. Due to the control of the motion and the internal degrees of freedom, these quantum systems can be adequately described by a well known Hamiltonian. In this colloquium, we present powerful numerical tools for the optimization of the external control of the motional and internal states of trapped neutral atoms, explicitly applied to the case of trapped laser-cooled ions in a segmented ion-trap. We then delve into solving inverse problems, when optimizing trapping potentials for ions. Our presentation is complemented by a quantum mechanical treatment of the wavepacket dynamics of a trapped ion. Efficient numerical solvers for both time-independent and time-dependent problems are provided. Shaping the motional wavefunctions and optimizing a quantum gate is realized by the application of quantum optimal control techniques. The numerical methods presented can also be used to gain an intuitive understanding of quantum experiments with trapped ions by performing virtual simulated experiments on a personal computer. Code and executables are supplied as supplementary online material (http://kilian-singer.de/ent).Comment: accepted for publication in Review of Modern Physics 201

A trapped-ion local field probe

We introduce a measurement scheme that utilizes a single ion as a local field probe. The ion is confined in a segmented Paul trap and shuttled around to reach different probing sites. By the use of a single atom probe, it becomes possible characterizing fields with spatial resolution of a few nm within an extensive region of millimeters. We demonstrate the scheme by accurately investigating the electric fields providing the confinement for the ion. For this we present all theoretical and practical methods necessary to generate these potentials. We find sub-percent agreement between measured and calculated electric field values

Sideband cooling and coherent dynamics in a microchip multi-segmented ion trap

Miniaturized ion trap arrays with many trap segments present a promising architecture for scalable quantum information processing. The miniaturization of segmented linear Paul traps allows partitioning the microtrap in different storage and processing zones. The individual position control of many ions - each of them carrying qubit information in its long-lived electronic levels - by the external trap control voltages is important for the implementation of next generation large-scale quantum algorithms. We present a novel scalable microchip multi-segmented ion trap with two different adjacent zones, one for the storage and another dedicated for the processing of quantum information using single ions and linear ion crystals: A pair of radio-frequency driven electrodes and 62 independently controlled DC electrodes allows shuttling of single ions or linear ion crystals with numerically designed axial potentials at axial and radial trap frequencies of a few MHz. We characterize and optimize the microtrap using sideband spectroscopy on the narrow S1/2 D5/2 qubit transition of the 40Ca+ ion, demonstrate coherent single qubit Rabi rotations and optical cooling methods. We determine the heating rate using sideband cooling measurements to the vibrational ground state which is necessary for subsequent two-qubit quantum logic operations. The applicability for scalable quantum information processing is proven.Comment: 17 pages, 11 figure

Fabrication of a planar micro Penning trap and numerical investigations of versatile ion positioning protocols

We describe a versatile planar Penning trap structure, which allows to dynamically modify the trapping conguration almost arbitrarily. The trap consists of 37 hexagonal electrodes, each with a circumcirle-diameter of 300 m, fabricated in a gold-on-sapphire lithographic technique. Every hexagon can be addressed individually, thus shaping the electric potential. The fabrication of such a device with clean room methods is demonstrated. We illustrate the variability of the device by a detailed numerical simulation of a lateral and a vertical transport and we simulate trapping in racetrack and articial crystal congurations. The trap may be used for ions or electrons, as a versatile container for quantum optics and quantum information experiments.Comment: 10 pages, 7 figures, pdflatex, to be published in New Journal of Physics (NJP) various changes according to the wishes of the NJP referees. Text added and moved around, title changed, abstract changed, references added rev3: one reference had a typo (ref 15), fixed (phys rev a 72, not 71

Coherent Manipulation of a Ca Spin Qubit in a Micro Ion Trap

We demonstrate the implementation of a spin qubit with a single Ca ion in a micro ion trap. The qubit is encoded in the Zeeman ground state levels mJ=+1/2 and mJ=-1/2 of the S1/2 state of the ion. We show sideband cooling close to the vibrational ground state and demonstrate the initialization and readout of the qubit levels with 99.5% efficiency. We employ a Raman transition close to the S1/2 - P1/2 resonance for coherent manipulation of the qubit. We observe single qubit rotations with 96% fidelity and gate times below 5mus. Rabi oscillations on the blue motional sideband are used to extract the phonon number distribution. The dynamics of this distribution is analyzed to deduce the trap-induced heating rate of 0.3(1) phonons/ms

Fabrication and heating rate study of microscopic surface electrode ion traps

We report heating rate measurements in a microfabricated gold-on-sapphire surface electrode ion trap with trapping height of approximately 240 micron. Using the Doppler recooling method, we characterize the trap heating rates over an extended region of the trap. The noise spectral density of the trap falls in the range of noise spectra reported in ion traps at room temperature. We find that during the first months of operation the heating rates increase by approximately one order of magnitude. The increase in heating rates is largest in the ion loading region of the trap, providing a strong hint that surface contamination plays a major role for excessive heating rates. We discuss data found in the literature and possible relation of anomalous heating to sources of noise and dissipation in other systems, namely impurity atoms adsorbed on metal surfaces and amorphous dielectrics.Comment: 17 pages, 5 figure

Quantum Phases of Trapped Ions in an Optical Lattice

We propose loading trapped ions into microtraps formed by an optical lattice. For harmonic microtraps, the Coulomb coupling of the spatial motions of neighboring ions can be used to construct a broad class of effective short-range Hamiltonians acting on an internal degree of freedom of the ions. For large anharmonicities, on the other hand, the spatial motion of the ions itself represents a spin-1/2 model with frustrated dipolar XY interactions. We illustrate the latter setup with three systems: the linear chain, the zig-zag ladder, and the triangular lattice. In the frustrated zig-zag ladder with dipolar interactions we find chiral ordering beyond what was predicted previously for a next-nearest-neighbor model. In the frustrated anisotropic triangular lattice with nearest-neighbor interactions we find that the transition from the one-dimensional gapless spin-liquid phase to the two-dimensional spiraling ordered phase passes through a gapped spin-liquid phase, similar to what has been predicted for the same model with Heisenberg interactions. Further, a second gapped spin-liquid phase marks the transition to the two-dimensional Neel-ordered phase.Comment: re-formatted; added discussion of feasibilit

MultiPriDe: automated batch development

of quantitative real-time PCR primer