The operation of a BEC based atom interferometer, where the atoms are held in a weaklyconfining magnetic trap and manipulated with counter-propagating laser beams, is analyzed. A simple analytic model is developed to describe the dynamics of the interferometer. It is used to find the regions of parameter space with high and low contrast of the interference fringes for both single and double reflection interferometers. We demonstrate that for a double reflection interferometer the coherence time can be increased by shifting the recombination time. The theory is compared with recent experimental realizations of these interferometers.

We analyze a Bose-Einstein condensate (BEC) -based free oscillation atom Michelson interferometer in a weakly confining harmonic magnetic trap. A BEC at the center of the trap is split into two harmonics by a laser standing wave. The harmonics move in opposite directions with equal speeds and turn back under the influence of the trapping potential at their classical turning points.The harmonics are allowed to pass through each other and a recombination pulse is applied when they overlap at the end of a cycle after they return for the second time. We derive an expression for the contrast of the interferometric fringes and obtain the fundamental limit of performance of the interferometer in the parameter space.

Fluorescence correlation spectroscopy (FCS) is a powerful tool to quantitatively study the diffusion of fluorescently labeled molecules. It allows in principle important questions of macromolecular transport and supramolecular aggregation in living cells to be addressed. However, the crowded environment inside the cells slows diffusion and limits the reservoir of labeled molecules, causing artifacts that arise especially from photobleaching and limit the utility of FCS in these applications. We present a method to compute the time correlation function from weighted photon arrival times, which compensates computationally during the data analysis for the effect of photobleaching. We demonstrate the performance of this method using numerical simulations and experimental data from model solutions. Using this technique, we obtain correlation functions in which the effect of photobleaching has been removed and in turn recover quantitatively accurate mean-square displacements of the fluorophores, especially when deviations from an ideal Gaussian excitation volume are accounted for by using a reference calibration correlation function. This allows quantitative FCS studies of transport processes in challenging environments with substantial photobleaching like in living cells in the future.

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