We report the acquisition and analysis of spectrally resolved photobleaching data from a model system designed to exhibit FRET. Spectrally resolved photobleaching can be used to determine the presence of FRET in these systems and to investigate multi-step mechanisms of energy transfer. The model system was a previously described set of fluorescent beads consisting of a system of six fluorophore...

The complex organization of the transcription machinery has been revealed mainly by biochemical and crystallographic studies. X-ray structures describe RNA polymerases and transcription complexes on an atomic level, but fail to portray their dynamic nature. The use of fluorescence techniques has made it possible to add a new layer of information to our understanding of transcription by providin...

wear is a complicated phenomenon caused by the relative movement of two contacting surfaces compressed together by a normal force. prediction of the wear, in most cases, requires various experiments and microstructural characterization of the contacting surfaces. mathematical models based on physical concepts could provide considerable help in understanding the physical behavior and hence the p...

Energy development of decaying isotropic turbulence in a 3-D periodic cube with non-rotating or rotating frames of reference is studied through direct numerical simulation using GPU accelerated lattice Boltzmann method. The initial turbulence is isotropic, generated in spectral space with prescribed energy spectrum E(κ)~κm in a range between κmin and ...

We simulate the dynamics of triplet-triplet energy transfer in a donor-bridge-acceptor system [4-(2-naphthylmethyl)benzaldehyde] with surface hopping, using electronic energies, gradients, and derivative couplings that are calculated on the fly. Using Boys localization to diabatize electronic states, we calculate energy transfer rates that agree favorably with experiment. The atomistic nature o...

We report high time-resolution measurements of photon statistics from pairs of dye molecules coupled by fluorescence resonance energy transfer (FRET). In addition to quantum-optical photon antibunching, we observe photon bunching on a time scale of several nanoseconds. We show by numerical simulation that configuration fluctuations in the coupled fluorophore system could account for minor devia...

We report a new approach of 2D regional correlation analysis capable of analyzing fluctuation dynamics of complex multiple correlated and anticorrelated fluctuations under a noncorrelated noise background. Using this new method, by changing and scanning the start time and end time along a pair of fluctuation trajectories, we are able to map out any defined segments along the fluctuation traject...

can be controlled precisely. In the experiment reported, they designed this distance to be 23 nm, which they describe as “a compromise of strong fluorescence enhancement and sufficient space for accommodation of a biomolecular assay.” In the ‘hotspot’ between the two particles, Acuna and colleagues introduced a docking site for molecules of interest. At this site, they bound the dye ATTO647N fo...