Single-nucleotide polymorphisms: analysis by mass spectrometry

Matrix-assisted laser desorption-ionization (MALDI) mass spectrometry has evolved as a powerful method for analyzing nucleic acids. Here we provide protocols for genotyping single-nucleotide polymorphisms (SNPs) by MALDI based on PCR and primer extension to generate allele-specific products. Furthermore, we present three different approaches for sample preparation of primer-extension products before MALDI analysis and discuss their potential areas of application. The first approach, the 'GOOD' assay, is a purification-free procedure that uses DNA-modification chemistry, including alkylation of phosphorothioate linkages in the extension primers. The other two approaches use either solid-phase extraction or microarray purification for the purification of primer-extension products. Depending on the reaction steps of the various approaches, the protocols take about 6–8 hours

New calculation schemes for proton-deuteron scattering including the Coulomb interaction

The Coulomb interaction between the protons is included in the description of proton-deuteron scattering using the screening and renormalization approach in the framework of momentum-space integral equations. Two new calculational schemes are presented that confirm the reliability of the perturbative approach for treating the screened Coulomb interaction in high partial waves, used by us in earlier works.Comment: To be published in Phys. Rev.

Franck-Condon Factors and Radiative Lifetime of the A^{2}\Pi_{1/2} - X^{2}\Sigma^{+} Transition of Ytterbium Monoflouride, YbF

The fluorescence spectrum resulting from laser excitation of the A^{2}\Pi_{1/2} - X^{2}\Sigma^{+} (0,0) band of ytterbium monofluoride, YbF, has been recorded and analyzed to determine the Franck-Condon factors. The measured values are compared with those predicted from Rydberg-Klein-Rees (RKR) potential energy curves. From the fluorescence decay curve the radiative lifetime of the A^{2}\Pi_{1/2} state is measured to be 28\pm2 ns, and the corresponding transition dipole moment is 4.39\pm0.16 D. The implications for laser cooling YbF are discussed.Comment: 5 pages, 5 figure

Doppler-free laser spectroscopy of buffer gas cooled molecular radicals

We demonstrate Doppler-free saturated absorption spectroscopy of cold molecular radicals formed by laser ablation inside a cryogenic buffer gas cell. By lowering the temperature, congested regions of the spectrum can be simplified, and by using different temperatures for different regions of the spectrum a wide range of rotational states can be studied optimally. We use the technique to study the optical spectrum of YbF radicals with a resolution of 30 MHz, measuring the magnetic hyperfine parameters of the electronic ground state. The method is suitable for high resolution spectroscopy of a great variety of molecules at controlled temperature and pressure, and is particularly well-suited to those that are difficult to produce in the gas phase.Comment: 11 pages, 4 figure

Measuring the nuclear magnetic quadrupole moment in heavy polar molecules

Theories that extend the Standard Model of particle physics often introduce new interactions that violate charge-parity (CP) symmetry. CP-violating effects within an atomic nucleus can be probed by measuring its nuclear magnetic quadrupole moment (MQM). The sensitivity of such a measurement is enhanced when using a heavy polar molecule containing a nucleus with quadrupole deformation. We determine how the energy levels of a molecule are shifted by the MQM and how those shifts can be measured. The measurement scheme requires molecules in a superposition of magnetic sub-levels that differ by many units of angular momentum. We develop a generic scheme for preparing these states. Finally, we consider the sensitivity that can be reached, showing that this method can reduce the current uncertainties on several CP-violating parameters

Diffusion, thermalization and optical pumping of YbF molecules in a cold buffer gas cell

We produce YbF molecules with a density of 10^18 m^-3 using laser ablation inside a cryogenically-cooled cell filled with a helium buffer gas. Using absorption imaging and absorption spectroscopy we study the formation, diffusion, thermalization and optical pumping of the molecules. The absorption images show an initial rapid expansion of molecules away from the ablation target followed by a much slower diffusion to the cell walls. We study how the time constant for diffusion depends on the helium density and temperature, and obtain values for the YbF-He diffusion cross-section at two different temperatures. We measure the translational and rotational temperatures of the molecules as a function of time since formation, obtain the characteristic time constant for the molecules to thermalize with the cell walls, and elucidate the process responsible for limiting this thermalization rate. Finally, we make a detailed study of how the absorption of the probe laser saturates as its intensity increases, showing that the saturation intensity is proportional to the helium density. We use this to estimate collision rates and the density of molecules in the cell.Comment: 20 pages, 11 figures, minor revisions following referee suggestion

Cavity QED with optically transported atoms

Ultracold $^{87}$Rb atoms are delivered into a high-finesse optical micro-cavity using a translating optical lattice trap and detected via the cavity field. The atoms are loaded into an optical lattice from a magneto-optic trap (MOT) and transported 1.5 cm into the cavity. Our cavity satisfies the strong-coupling requirements for a single intracavity atom, thus permitting real-time observation of single atoms transported into the cavity. This transport scheme enables us to vary the number of intracavity atoms from 1 to $>$100 corresponding to a maximum atomic cooperativity parameter of 5400, the highest value ever achieved in an atom--cavity system. When many atoms are loaded into the cavity, optical bistability is directly measured in real-time cavity transmission.Comment: 4 figures, 4 page

Fluctuations and stability in front propagation

Propagating fronts arising from bistable reaction-diffusion equations are a purely deterministic effect. Stochastic reaction-diffusion processes also show front propagation which coincides with the deterministic effect in the limit of small fluctuations (usually, large populations). However, for larger fluctuations propagation can be affected. We give an example, based on the classic spruce-budworm model, where the direction of wave propagation, i.e., the relative stability of two phases, can be reversed by fluctuations.Comment: 5 pages, 5 figure