Simultaneous Measurement of the Three-Dimensional Orientation of Excitation and Emission Dipoles

Self-Blinking Thioflavin T for Super-resolution Imaging

Thioflavin T (ThT) is a typical dye used to visualize the aggregation and formation of fibrillar structures, e.g., amyloid fibrils and peptide nanofibrils. ThT has been considered to produce stable fluorescence when interacting with aggregated proteins. For single-molecule localization microscopy (SMLM)-based optical super-resolution imaging, a photoswitching/blinking fluorescence property is required. Here we demonstrate that, in contrast to previous reports, ThT exhibits intrinsic stochastic blinking properties, without the need for blinking imaging buffer, in stable binding conditions. The blinking properties (photon number, blinking time, and on-off duty cycle) of ThT at the single-molecule level (for ultralow concentrations) were investigated under different conditions. As a proof of concept, we performed SMLM imaging of ThT-labeled α-synuclein fibrils measured in air and PBS buffer.

Resolving the Emission Transition Dipole Moments of Single Doubly Excited Seeded Nanorods via Heralded Defocused Imaging

Semiconductor nanocrystal emission polarization is a crucial probe of nanocrystal physics and an essential factor for nanocrystal-based technologies. While the transition dipole moment for the lowest excited state to ground state transition is well characterized, the dipole moment of higher multiexcitonic transitions is inaccessible via most spectroscopy techniques. Here, we realize direct characterization of the doubly excited-state relaxation transition dipole by heralded defocused imaging. Defocused imaging maps the dipole emission pattern onto a fast single-photon avalanche diode detector array, allowing the postselection of photon pairs emitted from the biexciton-exciton emission cascade and resolving the differences in transition dipole moments. Type-I¹/₂ seeded nanorods exhibit higher anisotropy of the biexciton-to-exciton transition compared to the exciton-to-ground state transition. In contrast, type-II seeded nanorods display a reduction of biexciton emission anisotropy. These findings are rationalized in terms of an interplay between the transient dynamics of the refractive index and the excitonic fine structure.

Interference of the scattered vector light fields from two optically levitated nanoparticles

We experimentally study the interference of dipole scattered light from two optically levitated nanoparticles in vacuum, which present an environment free of particle-substrate interactions. We illuminate the two trapped nanoparticles with a linearly polarized probe beam orthogonal to the propagation of the trapping laser beams. The scattered light from the nanoparticles are collected by a high numerical aperture (NA) objective lens and imaged. The interference fringes from the scattered vector light for the different dipole orientations in image and Fourier space are observed. Especially, the interference fringes of two scattered light fields with polarization vortex show the π shift of the interference fringes between inside and outside the center region of the two nanoparticles in the image space. As far as we know, this is the first experimental observation of the interference of scattered vector light fields from two dipoles in free space. This work also provides a simple and direct method to determine the spatial scales between optically levitated nanoparticles by the interference fringes.

Photon efficient orientation estimation using polarization modulation in single-molecule localization microscopy

Combining orientation estimation with localization microscopy opens up the possibility to analyze the underlying orientation of biomolecules on the nanometer scale. Inspired by the recent improvement of the localization precision by shifting excitation patterns (MINFLUX, SIMFLUX), we have adapted the idea towards the modulation of excitation polarization to enhance the orientation precision. For this modality two modes are analyzed: i) normally incident excitation with three polarization steps to retrieve the in-plane angle of emitters and ii) obliquely incident excitation with p-polarization with five different azimuthal angles of incidence to retrieve the full orientation. Firstly, we present a theoretical study of the lower precision limit with a Cramér-Rao bound for these modes. For the oblique incidence mode we find a favorable isotropic orientation precision for all molecular orientations if the polar angle of incidence is equal to arccos ⁡ 2 / 3 ≈ 35 degrees. Secondly, a simulation study is performed to assess the performance for low signal-to-background ratios and how inaccurate illumination polarization angles affect the outcome. We show that a precision, at the Cramér-Rao bound (CRB) limit, of just 2.4 and 1.6 degrees in the azimuthal and polar angles can be achieved with only 1000 detected signal photons and 10 background photons per pixel (about twice better than reported earlier). Lastly, the alignment and calibration of an optical microscope with polarization control is described in detail. With this microscope a proof-of-principle experiment is carried out, demonstrating an experimental in-plane precision close to the CRB limit for signal photon counts ranging from 400 to 10,000.

Calibration-Free Vector Magnetometry Using Nitrogen-Vacancy Center in Diamond Integrated with Optical Vortex Beam

We report a new method to determine the orientation of individual nitrogen-vacancy (NV) centers in a bulk diamond and use them to realize a calibration-free vector magnetometer with nanoscale resolution. Optical vortex beam is used for optical excitation and scanning the NV center in a [111]-oriented diamond. The scanning fluorescence patterns of NV center with different orientations are completely different. Thus, the orientation information on each NV center in the lattice can be known directly without any calibration process. Further, we use three differently oriented NV centers to form a magnetometer and reconstruct the complete vector information on the magnetic field based on the optically detected magnetic resonance(ODMR) technique. Compared with previous schemes to realize vector magnetometry using an NV center, our method is much more efficient and is easily applied in other NV-based quantum sensing applications.

Single-molecule confinement with uniform electrodynamic nanofluidics

To date, we could not engineer Nature's ability to dynamically handle diffusing single molecules in the liquid-phase as it takes place in pore-forming proteins and tunnelling nanotubes. Consistent handling of individual single molecules in a liquid is of paramount importance to fundamental molecular studies and technological benefits, like single-molecule level separation and sorting for early biomedical diagnostics, microscopic studies of molecular interactions and electron/optical microscopy of molecules and nanomaterials. We can consistently resolve the dynamics of diffusing single molecules if they are confined within a uniform dielectric environment at nanometre length-scales. A uniform dielectric environment is the key characteristic since intrinsic electronic properties of molecules were modified while interacting with any surfaces, and the effect is not the same from one dielectric surface to another. We present dynamic nanofluidic detection of optically active single molecules in a liquid. An all-silica nanofluidic environment was used to electrokinetically handle individual single-molecules where molecular shot noise was resolved. We recorded the single-molecule motion of small fragments of DNA, carbon-nanodots, and organic fluorophores in water. The electrokinetic 1D molecular mass transport under two-focus fluorescence correlation spectroscopy (2fFCS) showed confinement-induced modified molecular interactions (due to various inter-molecular repulsive and attractive forces), which have been theoretically interpreted as molecular shot noise. Our demonstration of high-throughput nanochannel fabrication, 2fFCS-based 1D confined detection of fast-moving single molecules and fundamental understanding of molecular shot noise may open an avenue for single-molecule experiments where physical manipulation of dynamics is necessary.

Three-Dimensional Two-Color Dual-Particle Tracking Microscope for Monitoring DNA Conformational Changes and Nanoparticle Landings on Live Cells

Here, we present a three-dimensional two-color dual-particle tracking (3D-2C-DPT) technique that can simultaneously localize two spectrally distinct targets in three dimensions with a time resolution down to 5 ms. The dual-targets can be tracked with separation distances from 33 to 250 nm with tracking precisions of ∼15 nm (for static targets) and ∼35 nm (for freely diffusing targets). Since each target is individually localized, a wealth of data can be extracted, such as the relative 3D position, the 2D rotation, and the separation distance between the two targets. Using this technique, we turn a double-stranded DNA (dsDNA)-linked dumbbell-like dimer into a nanoscopic optical ruler to quantify the bending dynamics of nicked or gapped dsDNA molecules in free solution by manipulating the design of dsDNA linkers (1-nick, 3-nt, 6-nt, or 9-nt single-strand gap), and the results show the increase of kon (linear to bent) from 3.2 to 10.7 s-1. The 3D-2C-DPT is then applied to observe translational and rotational motions of the landing of an antibody-conjugated nanoparticle on the plasma membrane of living cells, revealing the reduction of rotations possibly due to interactions with membrane receptors. This study demonstrates that this 3D-2C-DPT technique is a new tool to shed light on the conformational changes of biomolecules and the intermolecular interactions on plasma membrane.

Quantum limits for precisely estimating the orientation and wobble of dipole emitters

Precisely measuring molecular orientation is key to understanding how molecules organize and interact in soft matter, but the maximum theoretical limit of measurement precision has yet to be quantified. We use quantum estimation theory and Fisher information (QFI) to derive a fundamental bound on the precision of estimating the orientations of rotationally fixed molecules. While direct imaging of the microscope pupil achieves the quantum bound, it is not compatible with wide-field imaging, so we propose an interferometric imaging system that also achieves QFI-limited measurement precision. Extending our analysis to rotationally diffusing molecules, we derive conditions that enable a subset of second-order dipole orientation moments to be measured with quantum-limited precision. Interestingly, we find that no existing techniques can measure all second moments simultaneously with QFI-limited precision; there exists a fundamental trade-off between precisely measuring the mean orientation of a molecule versus its wobble. This theoretical analysis provides crucial insight for optimizing the design of orientation-sensitive imaging systems.

Ultralow-loss geometric phase and polarization shaping by ultrafast laser writing in silica glass

Polarization and geometric phase shaping via a space-variant anisotropy has attracted considerable interest for fabrication of flat optical elements and generation of vector beams with applications in various areas of science and technology. Among the methods for anisotropy patterning, imprinting of self-assembled nanograting structures in silica glass by femtosecond laser writing is promising for the fabrication of space-variant birefringent optics with high thermal and chemical durability and high optical damage threshold. However, a drawback is the optical loss due to the light scattering by nanograting structures, which has limited the application. Here, we report a new type of ultrafast laser-induced modification in silica glass, which consists of randomly distributed nanopores elongated in the direction perpendicular to the polarization, providing controllable birefringent structures with transmittance as high as 99% in the visible and near-infrared ranges and >90% in the UV range down to 330 nm. The observed anisotropic nanoporous silica structures are fundamentally different from the femtosecond laser-induced nanogratings and conventional nanoporous silica. A mechanism of nanocavitation via interstitial oxygen generation mediated by multiphoton and avanlanche defect ionization is proposed. We demonstrate ultralow-loss geometrical phase optical elements, including geometrical phase prism and lens, and a vector beam convertor in silica glass.

Spatio-angular fluorescence microscopy II. Paraxial 4f imaging

We investigate the properties of a single-view fluorescence microscope in a 4f geometry when imaging fluorescent dipoles without using the monopole or scalar approximations. We show that this imaging system has a spatio-angular band limit, and we exploit the band limit to perform efficient simulations. Notably, we show that information about the out-of-plane orientation of ensembles of in-focus fluorophores is recorded by paraxial fluorescence microscopes. Additionally, we show that the monopole approximation may cause biased estimates of fluorophore concentrations, but these biases are small when the sample contains either many randomly oriented fluorophores in each resolvable volume or unconstrained rotating fluorophores.

Weak Measurement of Elliptical Dipole Moments by C-Point Splitting

We investigate points of circular polarization in the far field of elliptically polarized dipoles and establish a relation between the angular position and helicity of these C points and the dipole moment. In the case of highly eccentric dipoles, the C points of opposite handedness exhibit only a small angular separation and occur in the low intensity region of the emission pattern. In this regard, we introduce an optical weak measurement approach that utilizes the transverse electric (azimuthal) and transverse magnetic (radial) far-field polarization basis. Projecting the far field onto a spatially varying postselected polarization state reveals the angular separation and the helicity of the C points. We demonstrate the applicability of this approach and determine the elliptical dipole moment of a particle sitting on an interface by measuring the C points in its far field.

Imaging the three-dimensional orientation and rotational mobility of fluorescent emitters using the Tri-spot point spread function

Fluorescence photons emitted by single molecules contain rich information regarding their rotational motions, but adapting single-molecule localization microscopy (SMLM) to measure their orientations and rotational mobilities with high precision remains a challenge. Inspired by dipole radiation patterns, we design and implement a Tri-spot point spread function (PSF) that simultaneously measures the three-dimensional orientation and the rotational mobility of dipole-like emitters across a large field of view. We show that the orientation measurements done using the Tri-spot PSF are sufficiently accurate to correct the anisotropy-based localization bias, from 30 nm to 7 nm, in SMLM. We further characterize the emission anisotropy of fluorescent beads, revealing that both 20-nm and 100-nm diameter beads emit light significantly differently from isotropic point sources. Exciting 100-nm beads with linearly polarized light, we observe significant depolarization of the emitted fluorescence using the Tri-spot PSF that is difficult to detect using other methods. Finally, we demonstrate that the Tri-spot PSF detects rotational dynamics of single molecules within a polymer thin film that are not observable by conventional SMLM.

Three-dimensional single-molecule localization with nanometer accuracy using Metal-Induced Energy Transfer (MIET) imaging

Our paper presents the first theoretical and experimental study using single-molecule Metal-Induced Energy Transfer (smMIET) for localizing single fluorescent molecules in three dimensions. Metal-Induced Energy Transfer describes the resonant energy transfer from the excited state of a fluorescent emitter to surface plasmons in a metal nanostructure. This energy transfer is strongly distance-dependent and can be used to localize an emitter along one dimension. We have used Metal-Induced Energy Transfer in the past for localizing fluorescent emitters with nanometer accuracy along the optical axis of a microscope. The combination of smMIET with single-molecule localization based super-resolution microscopy that provides nanometer lateral localization accuracy offers the prospect of achieving isotropic nanometer localization accuracy in all three spatial dimensions. We give a thorough theoretical explanation and analysis of smMIET, describe its experimental requirements, also in its combination with lateral single-molecule localization techniques, and present first proof-of-principle experiments using dye molecules immobilized on top of a silica spacer, and of dye molecules embedded in thin polymer films.

TrackNTrace: A simple and extendable open-source framework for developing single-molecule localization and tracking algorithms

Super-resolution localization microscopy and single particle tracking are important tools for fluorescence microscopy. Both rely on detecting, and tracking, a large number of fluorescent markers using increasingly sophisticated computer algorithms. However, this rise in complexity makes it difficult to fine-tune parameters and detect inconsistencies, improve existing routines, or develop new approaches founded on established principles. We present an open-source MATLAB framework for single molecule localization, tracking and super-resolution applications. The purpose of this software is to facilitate the development, distribution, and comparison of methods in the community by providing a unique, easily extendable plugin-based system and combining it with a novel visualization system. This graphical interface incorporates possibilities for quick inspection of localization and tracking results, giving direct feedback of the quality achieved with the chosen algorithms and parameter values, as well as possible sources for errors. This is of great importance in practical applications and even more so when developing new techniques. The plugin system greatly simplifies the development of new methods as well as adapting and tailoring routines towards any research problem’s individual requirements. We demonstrate its high speed and accuracy with plugins implementing state-of-the-art algorithms and show two biological applications.

Enhanced DNA imaging using super-resolution microscopy and simultaneous single-molecule orientation measurements

Single-molecule orientation measurements provide unparalleled insight into a multitude of biological and polymeric systems. We report a simple, high-throughput technique for measuring the azimuthal orientation and rotational dynamics of single fluorescent molecules, which is compatible with localization microscopy. Our method involves modulating the polarization of an excitation laser, and analyzing the corresponding intensities emitted by single dye molecules and their modulation amplitudes. To demonstrate our approach, we use intercalating and groove-binding dyes to obtain super-resolved images of stretched DNA strands through binding-induced turn-on of fluorescence. By combining our image data with thousands of dye molecule orientation measurements, we develop a means of probing the structure of individual DNA strands, while also characterizing dye-DNA interactions. This approach may hold promise as a method for monitoring DNA conformation changes resulting from DNA-binding proteins.