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...

Phase diagrams of lipid mixtures can show several different regions of phase coexistence, which include liquid-disordered, liquid-ordered, and gel phases. Some phase regions are small, and some have sharp boundaries. The identity of the phases, their location in composition space, and the nature of the transitions between the phases are important for understanding the behavior of lipid mixtures...

HIV-1 genomic RNA has a noncoding 5' region containing sequential conserved structural motifs that control many parts of the life cycle. Very limited data exist on their three-dimensional (3D) conformation and, hence, how they work structurally. To assemble a working model, we experimentally reassessed secondary structure elements of a 240-nt region and used single-molecule distances, derived f...

The micelle system formed by an amphiphilic triblock copolymer in water serves as a novel scaffold for fluorescence resonance energy transfer as well as light-induced reversible fluorescence modulation for a hydrophobic fluorescent dye.

In established methods for analyzing ribozyme kinetics, radiolabeled RNA substrates are primarily used. Each data point requires the cumbersome sampling, gel electrophoretic separation, and quantitation of reaction products, apart from the continuous loss of substrate by radioactive decay. We have used stable, double fluorescent end-labeled RNA substrates. Fluorescence of one fluorophore is que...