Plasmonic antennas and zero mode waveguides to enhance single molecule fluorescence detection and fluorescence correlation spectroscopy towards physiological concentrations

Single-molecule approaches to biology offer a powerful new vision to elucidate the mechanisms that underpin the functioning of living cells. However, conventional optical single molecule spectroscopy techniques such as F\"orster fluorescence resonance energy transfer (FRET) or fluorescence correlation spectroscopy (FCS) are limited by diffraction to the nanomolar concentration range, far below the physiological micromolar concentration range where most biological reaction occur. To breach the diffraction limit, zero mode waveguides and plasmonic antennas exploit the surface plasmon resonances to confine and enhance light down to the nanometre scale. The ability of plasmonics to achieve extreme light concentration unlocks an enormous potential to enhance fluorescence detection, FRET and FCS. Single molecule spectroscopy techniques greatly benefit from zero mode waveguides and plasmonic antennas to enter a new dimension of molecular concentration reaching physiological conditions. The application of nano-optics to biological problems with FRET and FCS is an emerging and exciting field, and is promising to reveal new insights on biological functions and dynamics.Comment: WIREs Nanomed Nanobiotechnol 201

Single-molecule study for a graphene-based nano-position sensor

In this study we lay the groundwork for a graphene-based fundamental ruler at the nanoscale. It relies on the efficient energy-transfer mechanism between single quantum emitters and low-doped graphene monolayers. Our experiments, conducted with dibenzoterrylene (DBT) molecules, allow going beyond ensemble analysis due to the emitter photo-stability and brightness. A quantitative characterization of the fluorescence decay-rate modification is presented and compared to a simple model, showing agreement with the $d^{-4}$ dependence, a genuine manifestation of a dipole interacting with a 2D material. With DBT molecules, we can estimate a potential uncertainty in position measurements as low as 5nm in the range below 30nm

Fluorescent nanoparticles for sensing

Nanoparticle-based fluorescent sensors have emerged as a competitive alternative to small molecule sensors, due to their excellent fluorescence-based sensing capabilities. The tailorability of design, architecture, and photophysical properties has attracted the attention of many research groups, resulting in numerous reports related to novel nanosensors applied in sensing a vast variety of biological analytes. Although semiconducting quantum dots have been the best-known representative of fluorescent nanoparticles for a long time, the increasing popularity of new classes of organic nanoparticle-based sensors, such as carbon dots and polymeric nanoparticles, is due to their biocompatibility, ease of synthesis, and biofunctionalization capabilities. For instance, fluorescent gold and silver nanoclusters have emerged as a less cytotoxic replacement for semiconducting quantum dot sensors. This chapter provides an overview of recent developments in nanoparticle-based sensors for chemical and biological sensing and includes a discussion on unique properties of nanoparticles of different composition, along with their basic mechanism of fluorescence, route of synthesis, and their advantages and limitations

Electrons, Photons, and Force: Quantitative Single-Molecule Measurements from Physics to Biology

Single-molecule measurement techniques have illuminated unprecedented details of chemical behavior, including observations of the motion of a single molecule on a surface, and even the vibration of a single bond within a molecule. Such measurements are critical to our understanding of entities ranging from single atoms to the most complex protein assemblies. We provide an overview of the strikingly diverse classes of measurements that can be used to quantify single-molecule properties, including those of single macromolecules and single molecular assemblies, and discuss the quantitative insights they provide. Examples are drawn from across the single-molecule literature, ranging from ultrahigh vacuum scanning tunneling microscopy studies of adsorbate diffusion on surfaces to fluorescence studies of protein conformational changes in solution

Optothermal Energy Conversion and Transport in Plasmonic Structures

Plasmonic structures can efficiently interact with electromagnetic waves at their interfaces, leading to strong light confinement and field enhancement, which has been crucial for many nanotechnology applications in manufacturing, lithography, data storage, biosensing, spectroscopy, molecular trapping and other molecular level studies. Due to the intrinsic losses of metallic structures, the strong light-matter interaction also generates significant energy dissipation, making the thermal management of the devices very challenging. The purpose of this dissertation is to study the optothermal energy conversion and transport in plasmonic structures, especially in structures at the nanoscale. We first investigate the general optothermal responses of plasmonic structures by developing a theoretical framework where the coupled optical and thermal responses can be numerically simulated. Nonlocal electromagnetic responses are considered since the nonlocal effect plays a very important role in small structures with a characteristic length of ∼10 nm or even smaller. Meanwhile, non-diffusive (ballistic) thermal transport is included since the characteristic length is comparable to or even smaller than the mean free paths of thermal carriers. Using a newly developed integrated diffusion model (IDM), the ballistic property can be calculated with a accuracy of the linear Boltzmann transport equation by solving commercial software compatible diffusion equations. Besides, when the structures are at the nanoscale, energy conversion and energy transfer can be strongly affected by the interfaces and the outside environment. Our theoretical and numerical results suggest wave amplification may happen near interfaces where nonlocal responses of electrons are strong. The strong electron interactions may drive current opposite to local electric field, resulting in negative optical energy absorption, which is unexpected from the perspective of local electromagnetic responses. The effect of interfaces is also measured experimentally. We simultaneously measure the responses both inside and outside small gold nanoparticles (AuNPs) using ultrafast pump-probe methods on a newly proposed platform. The platform consists of AuNPs in solution mixed with fluorescent molecules. These molecules serve as sensitive probes the measure the energy transfer from the plasmon-induced hot electrons in photoexcited AuNPs based on stimulated-emission depletion (STED). Together with the traditional transient absorption spectroscopy measurement, STED signal gives a comprehensive description of the inside and outside responses of AuNPs after photoexcitation with a sub-picosecond temporal resolution. The measured data suggest that direct energy transfer from hot electrons to the outside environment may occur before electrons thermalize with inside phonons. To our knowledge, this is the first time to probe ultrafast optothermal energy conversion at both sides of the nanoscale metallic interfaces. Besides, fluorescence thermometry is also studied since it may be integrated into STED spectroscopy and offer an opportunity to directly measure temperature on a picosecond time scale. For that purpose, two new thermometries based on molecular rotation are proposed and developed. These fluorescence thermometries potentially can provide more detailed information than the current transient absorption measurement and help understand energy conversion and energy transfer processes in nanoscale plasmonic structures. As stand-alone thermometries, they have the advantages of compatibility with polarizing materials since the measured ratiometric parameters essentially characterize the inequality in fluorescence intensity along different directions, as well as the stability against intensity variation, suitability of two-dimensional mapping and rapidity in readout rate