Genome comparison of bacterial pathogens.

Bacterial pathogens are being sequenced at an increasing rate. To many microbiologists, it appears that there simply is not enough time to digest all the information suddenly available. In this chapter we present several tools for comparison of sequenced pathogenic genomes, and discuss differences between pathogens and non-pathogens. The presented tools allow comparison of large numbers of genomes in a hypothesis-driven manner. Visualization of the results is very important for clear presentation of the results and various ways of graphical representation are introduced.

Optical clock with ultracold neutral atoms.

We demonstrate how to realize an optical clock with neutral atoms that is competitive to the currently best single ion optical clocks in accuracy and superior in stability. Using ultracold atoms in a Ca optical frequency standard, we show how to reduce the relative uncertainty to below 10(-15). We observed atom interferences for stabilization of the laser to the clock transition with a visibility of 0.36, which is 70% of the ultimate limit achievable with atoms at rest. A novel scheme was applied to detect these atom interferences with the prospect to reach the quantum projection noise limit at an exceptional low instability of 4 x 10(-17) in 1 s.

Doppler cooling and trapping on forbidden transitions.

Ultracold atoms at temperatures close to the recoil limit have been achieved by extending Doppler cooling to forbidden transitions. A cloud of (40)Ca atoms has been cooled and trapped to a temperature as low as 6 microK by operating a magnetooptical trap on the spin-forbidden intercombination transition. Quenching the long-lived excited state with an additional laser enhanced the scattering rate by a factor of 15, while a high selectivity in velocity was preserved. With this method, more than 10% of precooled atoms from a standard magnetooptical trap have been transferred to the ultracold trap. Monte Carlo simulations of the cooling process are in good agreement with the experiments.

Photoassociation of cold Ca atoms

We present the first measurement of a photoassociative spectrum of an alkaline earth element near the dissociation limit. The observed spectrum of Ca2 formed from cold atoms shows the regular vibrational series with the characteristic spacing of the 1/R3 asymptotic potential. The interpretation is in principle simplified compared to previous measurements on alkali metals by the nondegenerate ground state and the missing hyperfine structure of 40Ca. As an example, we derive the natural decay rate of the excited atomic 4p 1P1 state from the positions of the observed vibrational and rotational resonances with reduced uncertainty compared to previous measurements.