arXiv subjects

Fernando D. Stefani

Publications and source records attributed to Fernando D. Stefani.

12 recordsLinked to original sources

arXiv2024

Coupling single-molecules to DNA-based optical antennas with position and orientation control

Optical antennas have been extensively employed to manipulate the photophysical properties of single photon emitters. Coupling between an emitter and a given resonant mode of an optical antenna depends mainly on three parameters: spectral overlap, relative distance, and relative orientation between the emitter's transition dipole moment and the antenna. While the first two have been already extensively demonstrated, achieving full coupling control remains unexplored due to the challenges in manipulating at the same time both the position and orientation of single molecules. Here, we use the DNA origami technique to assemble a dimer optical antenna and position a single fluorescent molecule at the antenna gap with controlled orientation, predominately parallel or perpendicular to the antenna's main axis. We study the coupling for both conditions through fluorescence measurements correlated with scanning electron microscopy images, revealing a 5-fold higher average fluorescence intensity when the emitter is aligned with the antenna's main axis and a maximum fluorescence enhancement of ~ 1400-fold. A comparison to realistic numerical simulations suggests that the observed distribution of fluorescence enhancement arises from small variations in emitter orientation and gap size. This work establishes DNA origami as a versatile platform to fully control the coupling between emitters and optical antennas, trailblazing the way for self-assembled nanophotonic devices with optimized and more homogenous performance.

physics.optics↗

arXiv2024

Towards full control of molecular exciton energy transfer via FRET in DNA origami assemblies

Controlling the flow of excitons between organic molecules holds immense promise for various applications, including energy conversion, spectroscopy, photocatalysis, sensing, and microscopy. DNA nanotechnology has shown promise in achieving this control by using synthetic DNA as a platform for positioning and, very recently, for also orienting organic dyes. In this study, the orientation of doubly-linked dyes in DNA origami structures was manipulated to control energy transfer. By controlling independently the orientation of single donor and acceptor molecules, the average energy transfer efficiency was doubled. This work demonstrates the potential of DNA nanotechnology for precise control of the excitonic energy transfer with implications for artificial light-harvesting antennas.

cond-mat.soft↗

arXiv2022

Super-resolved FRET imaging by confocal fluorescence-lifetime single-molecule localization microscopy

FRET-based approaches are a unique tool for sensing the immediate surroundings and interactions of (bio)molecules. FRET imaging and FLIM (Fluorescence Lifetime Imaging Microscopy) enable the visualization of the spatial distribution of molecular interactions and functional states. However, conventional FLIM and FRET imaging provide average information over an ensemble of molecules within a diffraction-limited volume, which limits the spatial information, accuracy, and dynamic range of the observed signals. Here, we demonstrate an approach to obtain super-resolved FRET imaging based on single-molecule localization microscopy using an early prototype of a commercial time-resolved confocal microscope. DNA Points Accumulation for Imaging in Nanoscale Topography (DNA-PAINT) with fluorogenic probes provides a suitable combination of background reduction and blinking kinetics compatible with the scanning speed of usual confocal microscopes. A single laser is used to excite the donor, a broad detection band is employed to retrieve both donor and acceptor emission, and FRET events are detected from lifetime information.

physics.optics↗

arXiv2022

DNA self-assembly of single molecules with deterministic position and orientation

An ideal nanofabrication method should allow the organization of nanoparticles and molecules with nanometric positional precision, stoichiometric control and well-defined orientation. The DNA origami technique has evolved into a highly versatile bottom-up nanofabrication methodology that fulfils almost all of these features. It enables the nanometric positioning of molecules and nanoparticles with stoichiometric control, and even the orientation of asymmetrical nanoparticles along predefined directions. However, orienting individual molecules has been a standing challenge, mainly due to unspecific electrostatic interactions. Here, we show how single molecules, namely Cy5 and Cy3 fluorophores, can be incorporated in a DNA origami with controlled orientation by doubly linking them to oligonucleotide strands that are hybridized while leaving enough unpaired bases to induce a stretching force. Particularly, we explore the effects of leaving 0, 2, 4, 6, and 8 unpaired bases and find extreme orientations for 0 and 8 unpaired bases, corresponding to the molecules being perpendicular and parallel to the DNA double helix, respectively. We foresee that these results will expand the application field of DNA origami towards the fabrication of nanodevices involving a wide range of orientation-dependent molecular interactions, such as energy transfer, intermolecular electron transport, catalysis, exciton delocalization, or the electromagnetic coupling of a molecule to specific resonant nano-antennas modes.

cond-mat.soft↗

arXiv2022

Unidirectional ultracompact DNA-templated optical antennas

Optical nanoantennas are structures designed to manipulate light-matter interactions at the nanoscale by interfacing propagating light with localized optical fields. In recent years, a plethora of devices have been realized that are able to efficiently tailor the absorption and/or emission rates of fluorophores. By contrast, modifying the spatial characteristics of their radiation fields remains a challenge. Up to date, the designs providing directionality to fluorescence emission have required compound, complex geometries with overall dimensions comparable to the operating wavelength. Here, we present the fabrication and characterization of DNA-templated ultracompact optical antennas, with sub-wavelength sizes and capable of directing single-molecule fluorescence into predefined directions. Using the DNA origami methodology, two gold nanorods are assembled side-to-side with a separation gap of 5 nm. We show that a single fluorescent molecule placed at the tip of one of the nanorods drives the dimer antenna in anti-phase, leading to unidirectional emission.

physics.optics↗

arXiv2021

Challenges on Optical Printing of Colloidal Nanoparticles

While colloidal chemistry provides ways to obtain a great variety of nanoparticles, with different shapes, sizes, material composition, and surface functions, their controlled deposition and combination on arbitrary positions of substrates remains a considerable challenge. Over the last ten years, optical printing arose as a versatile method to achieve this purpose for different kinds of nanoparticles. In this article we review the state of the art of optical printing of single nanoparticles, and discuss its strengths, limitations, and future perspectives, by focusing on four main challenges: printing accuracy, resolution, selectivity, and nanoparticles photostability.

cond-mat.mes-hall↗

arXiv2021

PyFocus a Python package for vectorial calculations of focused optical fields under realistic conditions. Application to toroidal foci

Focused optical fields are key to a multitude of applications involving light-matter interactions, such as optical microscopy, single-molecule spectroscopy, optical tweezers, lithography, or quantum coherent control. A detailed vectorial characterization of the focused optical fields that includes a description beyond the paraxial approximation is key to optimize technological performance as well as for the design of meaningful experiments and interpret properly their results. Here, we present PyFocus, an open-source Python software package to perform fully vectorial calculations of focused electromagnetic fields after modulation by an arbitrary phase mask and in the presence of a multilayer system. We provide a graphical user interface and high-level functions to easily integrate PyFocus into custom scripts. Furthermore, to demonstrate the potential of PyFocus, we apply it to extensively characterize the generation of toroidal foci with a high numerical aperture objective, as it is commonly done in super-resolution fluorescence microscopy methods such as STED or MINFLUX. We provide examples of the effects of different experimental factors such as polarization, aberrations, and misalignments of key optical elements. Finally, we present calculations of toroidal foci through an interface of different mediums, and, to our knowledge, the first calculations of toroidal foci generated in total internal reflection conditions.

physics.optics↗

arXiv2021

A common framework for single-molecule localization using sequential structured illumination

Localization of single fluorescent molecules is key for physicochemical and biophysical measurements such as single-molecule tracking and super-resolution imaging by single-molecule localization microscopy (SMLM). Recently a series of methods have been developed in which the localization precision is enhanced by interrogating the molecular position with a sequence of spatially modulated patterns of light. Among them, the MINFLUX technique outstands for achieving a ~10-fold improvement compared to wide-field camera-based single-molecule localization, reaching ~1-2 nm localization precision at moderate photon counts. Here, we present a common mathematical framework for this type of measurement that allows a fair comparison between reported methods and facilitates the design and evaluation of new methods. With it, we benchmark all reported methods for single-molecule localization using sequential structured illumination, including long-established methods such as orbital tracking, along with two new proposed methods: orbital tracking and raster scanning with a minimum of intensity.

physics.optics↗

arXiv2021

In Situ Photothermal Response of Single Gold Nanoparticles Through Hyperspectral Imaging AntiStokes Thermometry

Several fields of applications require a reliable characterization of the photothermal response and heat dissipation of nanoscopic systems, which remains a challenging task both for modeling and experimental measurements. Here, we present a new implementation of anti-Stokes thermometry that enables the in situ photothermal characterization of individual nanoparticles (NPs) from a single hyperspectral photoluminescence confocal image. The method is label-free, applicable to any NP with detectable anti-Stokes emission, and does not require any prior information about the NP itself or the surrounding media. With it, we first studied the photothermal response of spherical gold NPs of different sizes on glass substrates, immersed in water, and found that heat dissipation is mainly dominated by the water for NPs larger than 50 nm. Then, the role of the substrate was studied by comparing the photothermal response of 80 nm gold NPs on glass with sapphire and graphene, two materials with high thermal conductivity. For a given irradiance level, the NPs reach temperatures 18% lower on sapphire and 24% higher on graphene than on bare glass. The fact that the presence of a highly conductive material such as graphene leads to a poorer thermal dissipation demonstrates that interfacial thermal resistances play a very significant role in nanoscopic systems, and emphasize the need for in situ experimental thermometry techniques. The developed method will allow addressing several open questions about the role of temperature in plasmon-assisted applications, especially ones where NPs of arbitrary shapes are present in complex matrixes and environments.

physics.optics↗

arXiv2020

Size-Selective Optical Printing of Silicon Nanoparticles through Their Dipolar Magnetic Resonance

Silicon nanoparticles possess unique size-dependent optical properties due to their strong electric and magnetic resonances in the visible range. However, their widespread application has been limited, in comparison to other (e.g. metallic) nanoparticles, because their preparation on monodisperse colloids remains challenging. Exploiting the unique properties of Si nanoparticles in nano- and micro-devices calls for methods able to sort and organize them from a colloidal suspension onto specific positions of solid substrates with nanometric precision. Here, we demonstrate that surfactant-free Silicon nanoparticles of a predefined and narrow ($σ$ < 10 nm) size range can be selectively immobilized on a substrate by optical printing from a polydisperse colloidal suspension. The size selectivity is based on differential optical forces that can be applied on nanoparticles of different sizes by tuning the light wavelength to the size-dependent magnetic dipolar resonance of the nanoparticles.

physics.optics↗

arXiv2016

Nanometer resolution imaging and tracking of fluorescent molecules with minimal photon fluxes

We introduce MINFLUX, a concept for localizing photon emitters in space. By probing the emitter with a local intensity minimum of excitation light, MINFLUX minimizes the fluorescence photons needed for high localization precision. A 22-fold reduction of photon detections over that required in popular centroid-localization is demonstrated. In superresolution microscopy, MINFLUX attained ~1 nm precision, resolving molecules only 6 nm apart. Tracking single fluorescent proteins by MINFLUX increased the temporal resolution and the localizations per trace by 100-fold, as demonstrated with diffusing 30S ribosomal subunits in living E. coli. Since conceptual limits have not been reached, we expect this localization modality to break new ground for observing the dynamics, distribution, and structure of macromolecules in living cells and beyond.

physics.optics↗

arXiv2009

Nanorod optical antennas for dipolar transitions

Optical antennas link objects to light. Here, we analyze metal nanorod antennas as cavities with variable reflection coefficients to derive the interaction of dipolar transitions with radiation through the antenna modes. The presented analytical model accurately describes the complete emission process, and is summarized in a phase-matching equation. We show how antenna modes evolve as they become increasingly more bound, i.e. plasmonic. The results illustrate why efficient antennas should not be too plasmonic, and how subradiant even modes can evolve into weakly-interacting dark modes. Our description is valid for the interaction of nanorods with light in general, and is thus widely applicable.

physics.optics↗