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InGaN/GaN nanostructures form the active region of III-nitride emitters (light emitting diodes, laser diodes, single photon emitters) in the visible spectral range. In order to understand the optical performance of these nanostructures it is necessary to obtain a direct correlation of alloy distribution and optical features. With this purpose in mind, laser-assisted atom probe tomography (La-APT) is a unique tool to visualize the three-dimensional distribution of chemical species at the nanometer scale. Recent advances in this technique also offer the possibility of recording simultaneously the photoluminescence spectrum of the

We directly measure the dynamics of the HIV trans-activation response (TAR)–DNA hairpin with multiple loops using single-molecule Forster resonance energy transfer (smFRET) methods. Multiple FRET states are identified that correspond to intermediate melting states of the hairpin. The stability of each intermediate state is calculated from the smFRET data. The results indicate that hairpin unfolding obeys a “fraying and peeling” mechanism, and evidence for the collapse of the ends of the hairpin during folding is observed. These results suggest a possible biological function for hairpin loops serving as additional fraying centers to increase unfolding rates in otherwise stable systems. The experimental and analytical approaches developed in this article provide useful tools for studying the mechanism of multistate DNA hairpin dynamics and of other general systems with multiple parallel pathways of chemical reactions.

We introduce a step transition and state identification (STaSI) method for piecewise constant single-molecule data with a newly derived minimum description length equation as the objective function. We detect the step transitions using the Student’s t test and group the segments into states by hierarchical clustering. The optimum number of states is determined based on the minimum description length equation. This method provides comprehensive, objective analysis of multiple traces requiring few user inputs about the underlying physical models and is faster and more precise in determining the number of states than established and cutting-edge methods for single-molecule data analysis. Perhaps most importantly, the method does not require either time-tagged photon counting or photon counting in general and thus can be applied to a broad range of experimental setups and analytes.