Plasmonic nano-objects have shown great potential in enhancing applications like biological/chemical sensing, light harvesting and energy transfer, and optical/quantum computing. Therefore, an extensive effort has been vested in optimizing plasmonic systems and exploiting their field enhancement properties. Super-resolution imaging with quantum dots (QDs) is a promising method to probe plasmonic near-fields but is hindered by the distortion of the QD radiation pattern. Here, we investigate the interaction between QDs and “L-shaped” gold nanoantennas and demonstrate both theoretically and experimentally that this strong interaction can induce polarization-dependent modifications to the apparent QD emission intensity, polarization, and localization. Based on FDTD simulations and polarization-modulated single-molecule microscopy, we show that the displacement of the emitter’s localization is due to the position-dependent interference between the emitter and the induced dipole, and can be up to 100 nm. Our results help pave a pathway for higher precision plasmonic near-field mapping and its underlying applications.

Absorption cross-section spectra for gold nanoparticles were calculated using fully quantum Stochastic Density Functional Theory and a classical Finite-Difference Time Domain Maxwell solver. Spectral shifts were monitored as a function of size (1.3-3.1 nm) and shape (octahedron, cubeoctahedron and truncated cube). Even though the classical approach is forced to fit the quantum time-dependent density functional theory at 3.1 nm, at smaller sizes there is a significant deviation as the classical theory is unable to account for peak splitting and spectral blueshifts even after quantum spectral corrections. We attribute the failure of classical methods at predicting these features to quantum effects and low density of states in small nanoparticles. Classically, plasmon resonances are modelled as collective conduction electron excitations, but at small nanoparticle size these excitations transition to few or even individual conductive electron excitations, as indicated by our results. [GRAPHICS] .

Unlike normal fluorescent methods that use the intensity as a direct measurement of the localized enhanced field, we use blinking statistics of quantum dots (QDs). We have already shown that blinking gives a more accurate characterization of the near-field. When an emitter is situated close to a metallic surface, non-radiative pathways are opened up, leading to quenching of the exciton. Blinking statistics, however, is only minimally affected by quenching, and therefore can be used to probe emitters in close proximity to metallic surfaces. We have expanded our method (COFIBINS) to high densities using superresolution technique SOFI. A proof of principle for SOFI-COFIBINS is demonstrated with a defocused point spread function. The method is then applied to surface plasmon polaritons. SOFI-COFIBINS shows excellent agreement with the average fluorescence intensity.

Computation has become a major component of modern science and, as a result, computational reproducibility has become as fundamental as reproducibility in the lab. In this talk, we present a set of open source tools for freely-diffusing single-molecule fluorescence analysis, which were designed with the goal of reproducibility. The common foundation is represented by Photon-HDF5 (www.photon-hdf5.org), a general-purpose file format for timestamp-based fluorescence data, which simplifies data archival and sharing between different analysis software. Using Photon-HDF5 as its primary input format, FRETBursts (http://tritemio.github.io/FRETBursts) is an open source burst analysis software for smFRET data, supporting continuous wave or pulsed excitation in one or two colors. FRETBursts includes time-dependent background estimation, burst search algorithms, burst filtering, population fitting and extensive plotting capabilities. Since a growing number of custom formats can be converted to Photon-HDF5 (through the phconvert utility), FRETBursts can be used to analyze and compare data acquired with a variety of systems. As a second example, PyBroMo (http://tritemio.github.io/FRETBursts), is a 3D Brownian motion simulator for fluorescent particles under confocal excitation. PyBroMo produces smFRET data files in Photon-HDF5 format containing one or multiple FRET populations, uses numerically-computed point spread function and can simulated effects such as out-of-focus particle contribution to background and burst data. PyBroMo data files can be seamlessly analyzed with FRETBursts and or with any other smFRET analysis program supporting Photon-HDF5. Both FRETBursts and PyBroMo, are written in Python, an increasingly popular open language for scientific computing, and use the interactive Jupyter Notebook environment for user-friendly interfacing. Leveraging the strengths on Photon-HDF5, the presented tools form a solid foundation for developing novel analysis methods and for reproducing third-party results. We aim to collaboratively expand this set of tools for single-molecule fluorescence while pursuing the same principles of openness and reproducibility.

We introduce Photon-HDF5, an open and efficient file format to simplify exchange and long-term accessibility of data from single-molecule fluorescence experiments based on photon-counting detectors such as single-photon avalanche diode, photomultiplier tube, or arrays of such detectors. The format is based on HDF5, a widely used platform- and language-independent hierarchical file format for which user-friendly viewers are available. Photon-HDF5 can store raw photon data (timestamp, channel number, etc.) from any acquisition hardware, but also setup and sample description, information on provenance, authorship and other metadata, and is flexible enough to include any kind of custom data. The format specifications are hosted on a public website, which is open to contributions by the biophysics community. As an initial resource, the website provides code examples to read Photon-HDF5 files in several programming languages and a reference Python library (phconvert), to create new Photon-HDF5 files and convert several existing file formats into Photon-HDF5. To encourage adoption by the academic and commercial communities, all software is released under the MIT open source license.

We demonstrate a far-field single molecule super-resolution method that maps plasmonic near-fields. The method is largely invariant to fluorescence quenching (arising from probe proximity to a metal), has reduced point-spread-function distortion compared to fluorescent dyes (arising from strong coupling to nanoscopic metallic features), and has a large dynamic range (of 2 orders of magnitude) allowing mapping of plasmonic field-enhancements regions. The method takes advantage of the sensitivity of quantum dot (QD) stochastic blinking to plasmonic near-fields. The modulation of the blinking characteristics thus provides an indirect measure of the local field strength. Since QD blinking can be monitored in the far-field, the method can measure localized plasmonic near-fields at high throughput using a simple far-field optical setup. Using this method, propagation lengths and penetration depths were mapped-out for silver nanowires of different diameters and for different dielectric environments, with a spatial accuracy of ∼15 nm. We initially use sparse sampling to ensure single molecule localization for accurate characterization of the plasmonic near-field with plans to increase density of emitters in further studies. The measured propagation lengths and penetration depths values agree well with Maxwell finite-difference time-domain calculations and with published literature values. This method offers advantages such as low cost, high throughput, and superresolved mapping of localized plasmonic fields at high sensitivity and fidelity.

We propose a general theme, labeled mechanical electrodynamics, where the relative three-dimensional (3-D) orientation of particles with nontrivial geometries is tracked based on the details of the absorption spectrum beyond a one-dimensional (1-D) distance dependence. Specifically, we simulate absorption spectra of a subwavelength denture-like nanostructure with freely moving parts. The nanodentures are made of two gold nanoarches that either open and dose or rotate about a single arch base (hinge rotation). We show how the absorption spectrum for the nanodentures changes depending on orientation and position. There is a similar to 0.1-0.2 eV shift in absorbance peak frequencies as the denture closes, corresponding to an increased coupling between the two gold arches, while a hinge rotation results in a depletion of one absorbance peak (1.48 eV) with the simultaneous emergence of a new absorbance peak at lower frequencies (0.88 eV). The unique spectral signature of each position and orientation of the nanodentures points to a variety of applications. One will be experimentally tracking and measuring orientation and position of plasmonic-coupled nanoparticles using simple methods such as UV-vis or IR spectral analysis. Additionally, the denture structure will tune in and out of different plasmon resonance frequencies, or turn "on and off," depending on its orientation. The simulations were performed efficiently by the recent near-field (NF) approach, which is a time-dependent Poisson algorithm that shares a lot of the machinery of full-fledged Maxwell equations but allows for much larger time steps and therefore can treat large systems.