Two-qubit gates using adiabatic passage of the Stark-tuned Förster resonances in Rydberg atoms

We propose schemes of controlled-Z and controlled-not gates with ultracold neutral atoms based on deterministic phase accumulation during double adiabatic passage of the Stark-tuned Förster resonance of Rydberg states. The effect of deterministic phase accumulation during double adiabatic passage in a two-level quantum system has been analyzed in detail. Adiabatic rapid passage using nonlinearly chirped pulses with rectangle intensity profile has been discussed. Nonlinear time dependence of the energy detuning from the Förster resonance is used to achieve a high fidelity of population transfer between Rydberg states. Fidelity of two-qubit gates has been studied with an example of the 90 S +96 S -->90 P +95 P Stark-tuned Förster resonance in Cs Rydberg atoms

Förster resonance energy transfer photoacoustic microscopy

Förster resonance energy transfer (FRET) provides fluorescence signals sensitive to intra- and inter-molecular distances in the 1-10 nm range. Widely applied in the optical imaging environment, FRET enables visualization of physicochemical processes in molecular interactions and conformation changes. We reported photoacoustic imaging of FRET, based on non-radiative decay that produces heat and subsequent acoustic waves. The experimental results show that photoacoustic imaging offers better penetration into scattering biological tissue. Through its ability to three-dimensionally image tissue with scalable resolution, photoacoustic microscopy provides a beneficial biomedical tool to broaden the in vivo application of the FRET technique

Linear approaches to intramolecular Förster Resonance Energy Transfer probe measurements for quantitative modeling

Numerous unimolecular, genetically-encoded Forster Resonance Energy Transfer (FRET) probes for monitoring biochemical activities in live cells have been developed over the past decade. As these probes allow for collection of high frequency, spatially resolved data on signaling events in live cells and tissues, they are an attractive technology for obtaining data to develop quantitative, mathematical models of spatiotemporal signaling dynamics. However, to be useful for such purposes the observed FRET from such probes should be related to a biological quantity of interest through a defined mathematical relationship, which is straightforward when this relationship is linear, and can be difficult otherwise. First, we show that only in rare circumstances is the observed FRET linearly proportional to a biochemical activity. Therefore in most cases FRET measurements should only be compared either to explicitly modeled probes or to concentrations of products of the biochemical activity, but not to activities themselves. Importantly, we find that FRET measured by standard intensity-based, ratiometric methods is inherently non-linear with respect to the fraction of probes undergoing FRET. Alternatively, we find that quantifying FRET either via (1) fluorescence lifetime imaging (FLIM) or (2) ratiometric methods where the donor emission intensity is divided by the directly-excited acceptor emission intensity (denoted R<sub>alt</sub>) is linear with respect to the fraction of probes undergoing FRET. This linearity property allows one to calculate the fraction of active probes based on the FRET measurement. Thus, our results suggest that either FLIM or ratiometric methods based on R<sub>alt</sub> are the preferred techniques for obtaining quantitative data from FRET probe experiments for mathematical modeling purpose

Step size of the rotary proton motor in single FoF1-ATP synthase from a thermoalkaliphilic bacterium by DCO-ALEX FRET

Thermophilic enzymes can operate at higher temperatures but show reduced activities at room temperature. They are in general more stable during preparation and, accordingly, are considered to be more rigid in structure. Crystallization is often easier compared to proteins from bacteria growing at ambient temperatures, especially for membrane proteins. The ATP-producing enzyme FoF1-ATP synthase from thermoalkaliphilic Caldalkalibacillus thermarum strain TA2.A1 is driven by a Fo motor consisting of a ring of 13 c-subunits. We applied a single-molecule F\"orster resonance energy transfer (FRET) approach using duty cycle-optimized alternating laser excitation (DCO-ALEX) to monitor the expected 13-stepped rotary Fo motor at work. New FRET transition histograms were developed to identify the smaller step sizes compared to the 10-stepped Fo motor of the Escherichia coli enzyme. Dwell time analysis revealed the temperature and the LDAO dependence of the Fo motor activity on the single molecule level. Back-and-forth stepping of the Fo motor occurs fast indicating a high flexibility in the membrane part of this thermophilic enzyme.Comment: 14 pages, 7 figure