Fast, Label-Free Tracking of Single Viruses and Weakly Scattering Nanoparticles in a Nanofluidic Optical Fiber

Label-Free Optical Imaging of Nanoscale Single Entities

The advancement of optical microscopy technologies has achieved imaging of nanoscale objects, including nanomaterials, virions, organelles, and biological molecules, at the single entity level. Recently developed plasmonic and scattering based optical microscopy technologies have enabled label-free imaging of single entities with high spatial and temporal resolutions. These label-free methods eliminate the complexity of sample labeling and minimize the perturbation of the analyte native state. Additionally, these imaging-based methods can noninvasively probe the dynamics and functions of single entities with sufficient throughput for heterogeneity analysis. This perspective will review label-free single entity imaging technologies and discuss their principles, applications, and key challenges.

Nanomechanical Sensing for Mass Flow Control in Nanowire-Based Open Nanofluidic Systems

Open nanofluidic systems, where liquids flow along the outer surface of nanoscale structures, provide otherwise unfeasible capabilities for extremely miniaturized liquid handling applications. A critical step toward fully functional applications is to obtain quantitative mass flow control. We demonstrate the application of nanomechanical sensing for this purpose by integrating voltage-driven liquid flow along nanowire open channels with mass detection based on flexural resonators. This approach is validated by assembling the nanowires with microcantilever resonators, enabling high-precision control of larger flows, and by using the nanowires as resonators themselves, allowing extremely small liquid volume handling. Both implementations are demonstrated by characterizing voltage-driven flow of ionic liquids along the surface of the nanowires. We find a voltage range where mass flow rate follows a nonlinear monotonic increase, establishing a steady flow regime for which we show mass flow control at rates from below 1 ag/s to above 100 fg/s and precise liquid handling down to the zeptoliter scale. The observed behavior of mass flow rate is consistent with a voltage-induced transition from static wetting to dynamic spreading as the mechanism underlying liquid transport along the nanowires.

An optical nanofibre-enabled on-chip single-nanoparticle sensor

Single-nanoparticle detection has received tremendous interest due to its significance in fundamental physics and biological applications. Here, we demonstrate an optical nanofibre-enabled microfluidic sensor for the detection and sizing of nanoparticles. Benefitting from the strong evanescent field outside the nanofibre, a nanoparticle close to the nanofibre can scatter a portion of the field energy to the environment, resulting in a decrease in the transmitted intensity of the nanofibre. On the other hand, the narrow and shallow microfluidic channel provides a femtoliter-scale detection region, making nanoparticles flow through the detection region one by one. By real-time monitoring of the transmitted intensity of the nanofibre, the detection of a single polystyrene (PS) nanoparticle as small as 100 nm in diameter and exosomes in solution is realised. Based on a statistical analysis, the mean scattering signal is related to the size of the nanoparticle. Experimentally, a mixture of nanoparticles of different diameters (200, 500, and 1000 nm) in solution is identified. To demonstrate its potential in biological applications, high-throughput counting of yeasts using a pair of microchannels and dual-wavelength detection of fluorescently labelled nanoparticles are realised. We believe that the developed nanoparticle sensor holds great potential for the multiplexed and rapid sensing of diverse viruses.

Single virus fingerprinting by widefield interferometric defocus-enhanced mid-infrared photothermal microscopy

Clinical identification and fundamental study of viruses rely on the detection of viral proteins or viral nucleic acids. Yet, amplification-based and antigen-based methods are not able to provide precise compositional information of individual virions due to small particle size and low-abundance chemical contents (e.g., ~ 5000 proteins in a vesicular stomatitis virus). Here, we report a widefield interferometric defocus-enhanced mid-infrared photothermal (WIDE-MIP) microscope for high-throughput fingerprinting of single viruses. With the identification of feature absorption peaks, WIDE-MIP reveals the contents of viral proteins and nucleic acids in single DNA vaccinia viruses and RNA vesicular stomatitis viruses. Different nucleic acid signatures of thymine and uracil residue vibrations are obtained to differentiate DNA and RNA viruses. WIDE-MIP imaging further reveals an enriched β sheet components in DNA varicella-zoster virus proteins. Together, these advances open a new avenue for compositional analysis of viral vectors and elucidating protein function in an assembled virion.

Digital Detection of Single Virus Particles by Multi-Spot, Label-Free Imaging Biosensor on Anti-Reflective Glass

Rapid detection of whole virus particles in biological or environmental samples represents an unmet need for the containment of infectious diseases. Here, an optical device enabling the enumeration of single virion particles binding on antibody or aptamers immobilized on a surface with anti-reflective coating is described. In this regime, nanoparticles adhering to the sensor surface provide localized contributions to the reflected field that become detectable because of their mixing with the interfering waves in the reflection direction. Thus, these settings are exploited to realize a scan-free, label-free, micro-array-type digital assay on a disposable cartridge, in which the virion counting takes place in wide field-of-view imaging. With this approach we could quantify, by enumeration, different variants of SARS-CoV-2 virions interacting with antibodies and aptamers immobilized on different spots. For all tested variants, the aptamers showed larger affinity but lower specificity relative to the antibodies. It is found that the combination of different probes on the same surface enables increasing specificity of detection and dynamic range.

Characterization of diffusing sub-10 nm nano-objects using single anti-resonant element optical fibers

Accurate characterization of diffusing nanoscale species is increasingly important for revealing processes at the nanoscale, with fiber-assisted nanoparticle-tracking-analysis representing a new and promising approach in this field. In this work, we uncover the potential of this approach for the characterization of very small nanoparticles (<20 nm) through experimental studies, statistical analysis and the employment of a sophisticated fiber and chip design. The central results is the characterization of diffusing nanoparticles as small as 9 nm with record-high precision, corresponding to the smallest diameter yet determined for an individual nanoparticle with nanoparticle-tracking-analysis using elastic light scattering alone. Here, the detectable scattering cross-section is limited only by the background scattering of the ultrapure water, thus reaching the fundamental limit of Nanoparticle-Tracking-Analysis in general. The obtained results outperform other realizations and allow access to previously difficult to address application fields such as understanding nanoparticle growth or control of pharmaceuticals.

Fiber Bragg gratings inscribed in nanobore fibers

The nanobore fiber (NBF) is a promising nanoscale optofluidic platform due to its long nanochannel and unique optical properties. However, so far, the applications of NBF have been based only on its original fiber geometry without any extra functionalities, in contrast with various telecom fiber devices, which may limit its wide applications. Here, we provide the first, to the best of our knowledge, demonstration of NBF-based fiber Bragg gratings (FBGs) introduced by either the femtosecond (fs) laser direct writing technique or the ultraviolet (UV) laser phase mask technique. Moreover, the FBG fabricated via the UV laser was optimized, achieving a high reflectivity of 96.89% and simultaneously preserving the open nanochannel. The NBF-based FBGs were characterized in terms of temperature variation and the infiltration of different liquids, and they showed high potential for nanofluidic applications.

Stokes-Mueller polarization-based analysis of model SARS-CoV-2 virions

Understanding the virology of the coronavirus at the structural level has gained utmost importance to overcome the constant and long-term health complications induced by them. In this work, the light scattering properties of SARS-CoV-2 of size 140 nm were simulated by using discrete dipole approximation (DDA) for two incident wavelengths 200 nm and 350 nm, respectively. Three different 3-dimensional (3D) models of SARS-CoV-2 corresponding to 15, 20, and 40 numbers of spike proteins on the viral capsid surface were constructed as target geometries for the DDA calculations. These models were assessed by employing Stokes-Mueller polarimetry to obtain individual polarization properties such as degree of polarization (DOP), degree of linear polarization (DOLP), and degree of circular polarization (DOCP). Irrespective of its spike numbers, all the coronavirus models were found to display higher DOP and DOCP values and negligibly small DOLP values for circularly polarized incident light, indicating the presence of chiral structures. On the other hand, the lack of understanding about the dependence of the Mueller matrix on its microstructural properties was overcome by transforming 16 Mueller elements into sub-matrices with specific structural and physical properties using Lu-Chipman-based Mueller matrix polar decomposition method. The obtained properties such as retardance, diattenuation, and depolarization were used for investigating the composition and microstructural information. The approach presented in this work has the potential to understand the virology of the coronavirus at the structural level and, therefore, will be beneficial in developing effective detection strategies by exploiting their characteristic electromagnetic scattering signatures.

Locally Structured On-Chip Optofluidic Hollow-Core Light Cages for Single Nanoparticle Tracking

Nanoparticle tracking analysis (NTA) is a widely used methodology to investigate nanoscale systems at the single species level. Here, we introduce the locally structured on-chip optofluidic hollow-core light cage, as a novel platform for waveguide-assisted NTA. This hollow waveguide guides light by the antiresonant effect in a sparse array of dielectric strands and includes a local modification to realize aberration-free tracking of individual nano-objects, defining a novel on-chip solution with properties specifically tailored for NTA. The key features of our system are (i) well-controlled nano-object illumination through the waveguide mode, (ii) diffraction-limited and aberration-free imaging at the observation site, and (iii) a high level of integration, achieved by on-chip interfacing to fibers. The present study covers all aspects relevant for NTA including design, simulation, implementation via 3D nanoprinting, and optical characterization. The capabilities of the approach to precisely characterize practically relevant nanosystems have been demonstrated by measuring the solvency-induced collapse of a nanoparticle system which includes polymer brush-based shells that react to changes in the liquid environment. Our study unlocks the advantages of the light cage approach in the context of NTA, suggesting its application in various areas such as bioanalytics, life science, environmental science, or nanoscale material science in general.

Apoptotic bodies for advanced drug delivery and therapy

Extracellular vesicles (EVs) have emerged as promising candidates for multiple biomedical applications. Major types of EVs include exosomes, microvesicles, and apoptotic bodies (ABs). ABs are conferred most properties from parent cells in the final stages of apoptosis. A wide variety of sources and stable morphological features are endowed to ABs by the rigorous apoptotic program. ABs accommodate more functional biomolecules by relying on the larger volume and maintaining their naturalness in circulation. The predominant body surface ratio of ABs facilitates their recognition by recipient cells and is advantageous for interactions with microenvironments. ABs can modulate and alleviate symptoms of numerous diseases for their origins, circulation, and high biocompatibility. In addition, ABs have been emerging in disease diagnosis, immunotherapy, regenerative therapy, and drug delivery. Here, we aim to present a thorough discussion on current knowledge about ABs. Of particular interest, we will summarize the application of AB-based strategies for diagnosis and disease therapy. Perspectives for the development of ABs in biomedical applications are highlighted.

Nanoparticle Tracking in Single-Antiresonant-Element Fiber for High-Precision Size Distribution Analysis of Mono- and Polydisperse Samples

Accurate determination of the size distribution of nanoparticle ensembles remains a challenge in nanotechnology-related applications due to the limitations of established methods. Here, a microstructured fiber-assisted nanoparticle tracking analysis (FaNTA) realization is introduced that breaks existing limitations through the recording of exceptionally long trajectories of rapidly diffusing polydisperse nanoparticles, resulting in excellent sizing precision and unprecedented separation capabilities of bimodal nanoparticle mixtures. An effective-single-mode antiresonant-element fiber allows to efficiently confine nanoparticles in a light-guiding microchannel and individually track them over more than 1000 frames, while aberration-free imaging is experimentally confirmed by cross-correlation analysis. Unique features of the approach are (i) the highly precise determination of the size distribution of monodisperse nanoparticle ensembles (only 7% coefficient of variation) and (ii) the accurate characterization of individual components in a bimodal mixture with very close mean diameters, both experimentally demonstrated for polymer nanospheres. The outstanding performance of the FaNTA realization can be quantified by introducing a new model for the bimodal separation index. Since FaNTA is applicable to all types of nano-objects down to sub-20 nm diameters, the method will improve the precision standard of mono- and polydisperse nanoparticle samples such as nano-plastics or extracellular vesicles.

Microfluidic flow cytometry for blood-based biomarker analysis

Flow cytometry has proven its capability for rapid and quantitative analysis of individual cells and the separation of targeted biological samples from others. The emerging microfluidics technology makes it possible to develop portable microfluidic diagnostic devices for point-of-care testing (POCT) applications. Microfluidic flow cytometry (MFCM), where flow cytometry and microfluidics are combined to achieve similar or even superior functionalities on microfluidic chips, provides a powerful single-cell characterisation and sorting tool for various biological samples. In recent years, researchers have made great progress in the development of the MFCM including focusing, detecting, and sorting subsystems, and its unique capabilities have been demonstrated in various biological applications. Moreover, liquid biopsy using blood can provide various physiological and pathological information. Thus, biomarkers from blood are regarded as meaningful circulating transporters of signal molecules or particles and have great potential to be used as non (or minimally)-invasive diagnostic tools. In this review, we summarise the recent progress of the key subsystems for MFCM and its achievements in blood-based biomarker analysis. Finally, foresight is offered to highlight the research challenges faced by MFCM in expanding into blood-based POCT applications, potentially yielding commercialisation opportunities.

Nanogap Electrode-Enabled Versatile Electrokinetic Manipulation of Nanometric Species in Fluids

Noninvasive manipulation of nanoscopic species in liquids has attracted considerable attention due to its potential applications in diverse fields. Many sophisticated methodologies have been developed to control and study nanoscopic entities, but the low-power, cost-effective, and versatile manipulation of nanometer-sized objects in liquids remains challenging. Here, we present a dielectrophoretic (DEP) manipulation technique based on nanogap electrodes, with which the on-demand capturing, enriching, and sorting of nano-objects in microfluidic systems can be achieved. The dielectrophoretic control unit consists of a pair of swelling-induced nanogap electrodes crossing a microchannel, generating a steep electric field gradient and thus strong DEP force for the effective manipulation of nano-objects microfluidics. The trapping, enriching, and sorting of nanoparticles and DNAs were performed with this device to demonstrate its potential applications in micro/nanofluidics, which opens an alternative avenue for the non-invasive manipulation and characterization of nanoparticles such as DNA, proteins, and viruses.

The competing influence of surface roughness, hydrophobicity, and electrostatics on protein dynamics on a self-assembled monolayer

Surface morphology, in addition to hydrophobic and electrostatic effects, can alter how proteins interact with solid surfaces. Understanding the heterogeneous dynamics of protein adsorption on surfaces with varying roughness is experimentally challenging. In this work, we use single-molecule fluorescence microscopy to study the adsorption of α-lactalbumin protein on the glass substrate covered with a self-assembled monolayer (SAM) with varying surface concentrations. Two distinct interaction mechanisms are observed: localized adsorption/desorption and continuous-time random walk (CTRW). We investigate the origin of these two populations by simultaneous single-molecule imaging of substrates with both bare glass and SAM-covered regions. SAM-covered areas of substrates are found to promote CTRW, whereas glass surfaces promote localized motion. Contact angle measurements and atomic force microscopy imaging show that increasing SAM concentration results in both increasing hydrophobicity and surface roughness. These properties lead to two opposing effects: increasing hydrophobicity promotes longer protein flights, but increasing surface roughness suppresses protein dynamics resulting in shorter residence times. Our studies suggest that controlling hydrophobicity and roughness, in addition to electrostatics, as independent parameters could provide a means to tune desirable or undesirable protein interactions with surfaces.

Three-dimensional tracking of nanoparticles by dual-color position retrieval in a double-core microstructured optical fiber

Elastic light scattering-based three-dimensional (3D) tracking of objects at the nanoscale level is essential for unlocking the dynamics of individual species or interactions in fields such as biology or surface chemistry. In this work, we introduce the concept of dual-color 3D tracking in a double-core microstructured optical fiber that for the first time allows for full 3D reconstruction of the trajectory of a diffusing nanoparticle in a water-filled fiber-integrated microchannel. The use of two single-mode cores provides two opposite decaying evanescent fields of different wavelengths within the microchannel, bypassing spatial domains of ambiguous correlation between the scattered intensity and position. The novelty of the fiber design is the use of two slightly different single-mode cores, preventing modal crosstalk and thus allowing for longitudinally invariant dual-color illumination across the entire field of view. To demonstrate the capabilities of the scheme, a single gold nanosphere (80 nm) diffusing in the water-filled microchannel was tracked for a large number of images (about 32 000) at a high frame rate (1.389 kHz) over a long time (23 s), with the determined hydrodynamic diameters matching expectations. The presented 3D tracking approach yields unique opportunities to unlock processes at the nanoscale level and is highly relevant for a multitude of fields, particularly within the context of understanding sophisticated interaction of diffusing species with functionalized surfaces within the context of bioanalytics, nanoscale materials science, surface chemistry or life science.

Scattering-based Light Microscopy: From Metal Nanoparticles to Single Proteins

Our ability to detect, image, and quantify nanoscopic objects and molecules with visible light has undergone dramatic improvements over the past few decades. While fluorescence has historically been the go-to contrast mechanism for ultrasensitive light microscopy due to its superior background suppression and specificity, recent developments based on light scattering have reached single-molecule sensitivity. They also have the advantages of universal applicability and the ability to obtain information about the species of interest beyond its presence and location. Many of the recent advances are driven by novel approaches to illumination, detection, and background suppression, all aimed at isolating and maximizing the signal of interest. Here, we review these developments grouped according to the basic principles used, namely darkfield imaging, interferometric detection, and surface plasmon resonance microscopy.

Label-free detection of virus-like particles employing rotationally symmetric nanowire array based whispering gallery and quasi-whispering gallery resonant modes onto a silicon platform

In spite of tremendous advancements in modern diagnostics, there is a dire need for reliable, label-free detection of highly contagious pathogens like viruses. In view of the limitations of existing diagnostic techniques, the present theoretical study proposes a novel scheme of detecting virus-like particles employing whispering gallery and quasi-whispering gallery resonant modes of a composite optical system. Whereas whispering gallery mode (WGM) resonators are conventionally realized using micro-disk, -ring, -toroid or spherical structures, the present study utilizes a rotationally symmetric array of silicon nanowires which offers higher sensitivity compared to the conventional WGM resonator while detecting virus-like particles. Notwithstanding the relatively low quality factor of the system, the underlying multiple-scattering mediated photon entrapment, coupled with peripheral total-internal reflection, results in high fidelity of the system against low signal-to-noise ratio. Finite difference time domain based numerical analysis has been performed to correlate resonant modes of the array with spatial location of the virus. The correlation has been subsequently utilized for statistical analysis of simulated test cases. Assuming detection to be limited by resolution of the measurement system, results of the analysis suggest that for only about 5% of the simulate test cases the resonant wavelength shift lies within the minimum detection range of 0.001-0.01 nm. For a single virus of 160 nm diameter, more than 8 nm shift of the resonant mode and nearly 100% change of quality factor are attained with the proposed nanowire array based photonic structure.

On-Chip Optical Detection of Viruses: A Review

The current outbreak of the coronavirus disease-19 (COVID-19) pandemic worldwide has caused millions of fatalities and imposed a severe impact on our daily lives. Thus, the global healthcare system urgently calls for rapid, affordable, and reliable detection toolkits. Although the gold-standard nucleic acid amplification tests have been widely accepted and utilized, they are time-consuming and labor-intensive, which exceedingly hinder the mass detection in low-income populations, especially in developing countries. Recently, due to the blooming development of photonics, various optical chips have been developed to detect single viruses with the advantages of fast, label-free, affordable, and point of care deployment. Herein, optical approaches especially in three perspectives, e.g., flow-free optical methods, optofluidics, and surface-modification-assisted approaches, are summarized. The future development of on-chip optical-detection methods in the wave of emerging new ideas in nanophotonics is also briefly discussed.

1/f-noise-free optical sensing with an integrated heterodyne interferometer

Optical evanescent sensors can non-invasively detect unlabeled nanoscale objects in real time with unprecedented sensitivity, enabling a variety of advances in fundamental physics and biological applications. However, the intrinsic low-frequency noise therein with an approximately 1/f-shaped spectral density imposes an ultimate detection limit for monitoring many paramount processes, such as antigen-antibody reactions, cell motions and DNA hybridizations. Here, we propose and demonstrate a 1/f-noise-free optical sensor through an up-converted detection system. Experimentally, in a CMOS-compatible heterodyne interferometer, the sampling noise amplitude is suppressed by two orders of magnitude. It pushes the label-free single-nanoparticle detection limit down to the attogram level without exploiting cavity resonances, plasmonic effects, or surface charges on the analytes. Single polystyrene nanobeads and HIV-1 virus-like particles are detected as a proof-of-concept demonstration for airborne biosensing. Based on integrated waveguide arrays, our devices hold great potentials for multiplexed and rapid sensing of diverse viruses or molecules.

Suppressing 1/f-shaped low-frequency noise is critical but fundamentally challenging to both electrical and optical transducers. Here, the authors demonstrate a 1/f-noise-free optical sensor with integrated CMOS-compatible heterodyne interferometer and an upconversion amplifying technique, which suppresses the noise by two orders of magnitude.

Precise Nanosizing with High Dynamic Range Holography

Optical sensing is one of the key enablers of modern diagnostics. Especially label-free imaging modalities hold great promise as they eliminate labeling procedures prior to analysis. However, scattering signals of nanometric particles scale with their volume square. This unfavorable scaling makes it extremely difficult to quantitatively characterize intrinsically heterogeneous clinical samples, such as extracellular vesicles, as their signal variation easily exceeds the dynamic range of currently available cameras. Here, we introduce off-axis k-space holography that circumvents this limitation. By imaging the back-focal plane of our microscope, we project the scattering signal of all particles onto all camera pixels, thus dramatically boosting the achievable dynamic range to up to 110 dB. We validate our platform by detecting and quantitatively sizing metallic and dielectric particles over a 200 × 200 μm field of view and demonstrate that independently performed signal calibrations allow correctly sizing particles made from different materials. Finally, we present quantitative size distributions of extracellular vesicle samples.

Label-Free Plasmonic Detection of Untethered Nanometer-Sized Brownian Particles

Optical detection of individual nanometer-sized analytes, virus particles, and protein molecules holds great promise for understanding and control of biological samples and healthcare applications. As fluorescent labels impose restrictions on detection bandwidth and require lengthy and invasive processes, label-free optical techniques are highly desirable. Here, we introduce an optical technique capable of transforming gold nanorods commonly used as photostable labels into highly localized high-speed probes. Our method detects single untethered 5 nm diameter gold particles as they traverse subattoliter volumes in Brownian motion with a time resolution below microseconds.

Light and corona: guided-wave readout for coronavirus spike protein-host-receptor binding

We show that waveguide sensors can enable a quantitative characterization of coronavirus spike glycoprotein-host-receptor binding-the process whereby coronaviruses enter human cells, causing disease. We demonstrate that such sensors can help quantify and eventually understand kinetic and thermodynamic properties of viruses that control their affinity to targeted cells, which is known to significantly vary in the course of virus evolution, e.g., from SARS-CoV to SARS-CoV-2, making the development of virus-specific drugs and vaccine difficult. With the binding rate constants and thermodynamic parameters as suggested by the latest SARS-CoV-2 research, optical sensors of SARS-CoV-2 spike protein-receptor binding may be within sight.

Advances in Label-Free Detections for Nanofluidic Analytical Devices

Nanofluidics, a discipline of science and engineering of fluids confined to structures at the 1-1000 nm scale, has experienced significant growth over the past decade. Nanofluidics have offered fascinating platforms for chemical and biological analyses by exploiting the unique characteristics of liquids and molecules confined in nanospaces; however, the difficulty to detect molecules in extremely small spaces hampers the practical applications of nanofluidic devices. Laser-induced fluorescence microscopy with single-molecule sensitivity has been so far a major detection method in nanofluidics, but issues arising from labeling and photobleaching limit its application. Recently, numerous label-free detection methods have been developed to identify and determine the number of molecules, as well as provide chemical, conformational, and kinetic information of molecules. This review focuses on label-free detection techniques designed for nanofluidics; these techniques are divided into two groups: optical and electrical/electrochemical detection methods. In this review, we discuss on the developed nanofluidic device architectures, elucidate the mechanisms by which the utilization of nanofluidics in manipulating molecules and controlling light-matter interactions enhances the capabilities of biological and chemical analyses, and highlight new research directions in the field of detections in nanofluidics.

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.

Independent Size and Fluorescence Emission Determination of Individual Biological Nanoparticles Reveals that Lipophilic Dye Incorporation Does Not Scale with Particle Size

Advancements in nanoparticle characterization techniques are critical for improving the understanding of how biological nanoparticles (BNPs) contribute to different cellular processes, such as cellular communication, viral infection, as well as various drug-delivery applications. Since BNPs are intrinsically heterogeneous, there is a need for characterization methods that are capable of providing information about multiple parameters simultaneously, preferably at the single-nanoparticle level. In this work, fluorescence microscopy was combined with surface-based two-dimensional flow nanometry, allowing for simultaneous and independent determination of size and fluorescence emission of individual BNPs. In this way, the dependence of the fluorescence emission of the commonly used self-inserting lipophilic dye 3,3'-dioctadecyl-5,5'-di(4-sulfophenyl)oxacarbocyanine (SP-DiO) could successfully be correlated with nanoparticle size for different types of BNPs, including synthetic lipid vesicles, lipid vesicles derived from cellular membrane extracts, and extracellular vesicles derived from human SH-SY5Y cell cultures; all vesicles had a radius, r, of ∼50 nm and similar size distributions. The results demonstrate that the dependence of fluorescence emission of SP-DiO on nanoparticle size varies significantly between the different types of BNPs, with the expected dependence on membrane area, r², being observed for synthetic lipid vesicles, while a significant weaker dependence on size was observed for BNPs with more complex composition. The latter observation is attributed to a size-dependent difference in membrane composition, which may influence either the optical properties of the dye and/or the insertion efficiency, indicating that the fluorescence emission of this type of self-inserting dye may not be reliable for determining size or size distribution of BNPs with complex lipid compositions.

Quantitative Particle Uptake by Cells as Analyzed by Different Methods

There is a large number of two-dimensional static in vitro studies about the uptake of colloidal nano- and microparticles, which has been published in the last decade. In this Minireview, different methods used for such studies are summarized and critically discussed. Supplementary experimental data allow for a direct comparison of the different techniques. Emphasis is given on how quantitative parameters can be extracted from studies in which different experimental techniques have been used, with the goal of allowing better comparison.

Tracking and Analyzing the Brownian Motion of Nano-objects Inside Hollow Core Fibers

Tracking and analyzing the individual diffusion of nanoscale objects such as proteins and viruses is an important methodology in life science. Here, we show a sensor that combines the efficiency of light line illumination with the advantages of fluidic confinement. Tracking of freely diffusing nano-objects inside water-filled hollow core fibers with core diameters of tens of micrometers using elastically scattered light from the core mode allows retrieving information about the Brownian motion and the size of each particle of the investigated ensemble individually using standard tracking algorithms and the mean squared displacement analysis. Specifically, we successfully measure the diameter of every gold nanosphere in an ensemble that consists of several hundreds of 40 nm particles, with an individual precision below 17% (±8 nm). In addition, we confirm the relevance of our approach with respect to bioanalytics by analyzing 70 nm λ-phages. Overall these features, together with the strongly reduced demand for memory space, principally allows us to record thousands of frames and to achieve high frame rates for high precision tracking of nanoscale objects.

Analysis and refinement of 2D single-particle tracking experiments

In recent decades, single particle tracking (SPT) has been developed into a sophisticated analytical approach involving complex instruments and data analysis schemes to extract information from time-resolved particle trajectories. Very often, mobility-related properties are extracted from these particle trajectories, as they often contain information about local interactions experienced by the particles while moving through the sample. This tutorial aims to provide a comprehensive overview about the accuracies that can be achieved when extracting mobility-related properties from 2D particle trajectories and how these accuracies depend on experimental parameters. Proper interpretation of SPT data requires an assessment of whether the obtained accuracies are sufficient to resolve the effect under investigation. This is demonstrated by calculating mean square displacement curves that show an apparent super- or subdiffusive behavior due to poor measurement statistics instead of the presence of true anomalous diffusion. Furthermore, the refinement of parameters involved in the design or analysis of SPT experiments is discussed and an approach is proposed in which square displacement distributions are inspected to evaluate the quality of SPT data and to extract information about the maximum distance over which particles should be tracked during the linking process.

Three dimensional spatiotemporal nano-scale position retrieval of the confined diffusion of nano-objects inside optofluidic microstructured fibers

Understanding the dynamics of single nano-scale species at high spatiotemporal resolution is of utmost importance within fields such as bioanalytics or microrheology. Here we introduce the concept of axial position retrieval via scattered light at evanescent fields inside a corralled geometry using optofluidic microstructured optical fibers allowing to unlock information about diffusing nano-scale objects in all three spatial dimensions at kHz acquisition rate for several seconds. Our method yields the lateral positions by localizing the particle in a wide-field microscopy image. In addition, the axial position is retrieved via the scattered light intensity of the particle, as a result of the homogenized evanescent fields inside a microchannel running parallel to an optical core. This method yields spatial localization accuracies <3 nm along the transverse and <21 nm along the retrieved directions. Due to its unique properties such as three dimensional tracking, straightforward operation, mechanical flexibility, strong confinement, fast and efficient data recording, long observation times, low background scattering, and compatibility with microscopy and fiber circuitry, our concept represents a new paradigm in light-based nanoscale detection techniques, extending the capabilities of the field of nanoparticle tracking analysis and potentially allowing for the observation of so far inaccessible processes at the nanoscale level.

Nanobore fiber focus trap with enhanced tuning capabilities

Confinement in fiber traps with two optical fibers facing one another relies on balancing the optical forces originating from the interaction of a scattering micro-object with the light beams delivered through the fibers. Here we demonstrate a novel type of dual fiber trap that involves the use of nanobore fibers, having a nano-channel located in the center of their fiber cores. This nano-element leads to a profound redistribution of the optical intensity and to considerably higher field gradients, yielding a trapping potential with greatly improved tuning properties compared to standard step-index fiber types. We evaluate the trap performance as a function of the fiber separation and find substantially higher stiffness for the nanobore fiber trap, especially in the range of short inter-fiber separations, while intermediate distances exhibit axial stiffness below that of the standard fiber. The results are in agreement with theoretical predictions and reveal that the exploitation of nanobore fibers allows for combinations of transverse and axial stiffness that cannot be accessed with common step-index fibers.

Quantum noise limited nanoparticle detection with exposed-core fiber

Label-free biosensors are important tools for clinical diagnostics and for studying biology at the single molecule level. The development of optical label-free sensors has allowed extreme sensitivity but can expose the biological sample to photodamage. Moreover, the fragility and complexity of these sensors can be prohibitive to applications. To overcome these problems, we develop a quantum noise limited exposed-core fiber sensor providing robust platform for label-free biosensing with a natural path toward microfluidic integration. We demonstrate the detection of single nanoparticles down to 25 nm in radius with optical intensities beneath known biophysical damage thresholds.

Artificial Microbial Arenas: Materials for Observing and Manipulating Microbial Consortia

From the smallest ecological niche to global scale, communities of microbial life present a major factor in system regulation and stability. As long as laboratory studies remain restricted to single or few species assemblies, however, very little is known about the interaction patterns and exogenous factors controlling the dynamics of natural microbial communities. In combination with microfluidic technologies, progress in the manufacture of functional and stimuli-responsive materials makes artificial microbial arenas accessible. As habitats for natural or multispecies synthetic consortia, they are expected to not only enable detailed investigations, but also the training and the directed evolution of microbial communities in states of balance and disturbance, or under the effects of modulated stimuli and spontaneous response triggers. Here, a perspective on how materials research will play an essential role in generating answers to the most pertinent questions of microbial engineering is presented, and the concept of adaptive microbial arenas and possibilities for their construction from particulate microniches to 3D habitats is introduced. Materials as active and tunable components at the interface of living and nonliving matter offer exciting opportunities in this field. Beyond forming the physical horizon for microbial cultivates, they will enable dedicated intervention, training, and observation of microbial consortia.

Photonic candle - focusing light using nano-bore optical fibers

Focusing light represents one of the fundamental optical functionalities that is used in a countless number of situations. Here we introduce the concept of nano-bore optical fiber mediated light focusing that allows to efficiently focus light at micrometer distance from the fiber end face. Since the focusing effect is provided by the fundamental fiber mode, device implementation is extremely straightforward since no post-processing or nano-structuring is necessary. Far-field measurements on implemented fibers, simulations, and a dual-Gaussian beam toy model confirm the validity of the concept. Due to its unique properties such as strong light localization, a close to 100% implementation success rate, extremely high reproducibility, and its compatibility with current fiber circuitry, the concept will find application in numerous areas that demand to focus at remote distances.

Bending losses and modal properties of nano-bore optical fibers

The nano-bore optical fiber geometry represents a new waveguide platform that uniquely allows studying the interaction of low-index fluids and light inside the core of an optical fiber while maintaining total internal reflection as a light guidance mechanism. Here, we have analyzed several application-relevant properties of this novel geometry experimentally and from the simulation perspective, including the analysis of the power fraction inside the bore, the determination of radius-dependent cutoffs, and the identification of single-mode operation domains. The obtained results will pave the way for new application of fiber optics in fields such as optofluidics, nonlinear light generation, and bioanalytics.

Selective counting and sizing of single virus particles using fluorescent aptamer-based nanoparticle tracking analysis

Detection and counting of single virus particles in liquid samples are largely limited to narrow size distribution of viruses and purified formulations. To address these limitations, here we propose a calibration-free method that enables concurrently the selective recognition, counting and sizing of virus particles as demonstrated through the detection of human respiratory syncytial virus (RSV), an enveloped virus with a broad size distribution, in throat swab samples. RSV viruses were selectively labeled through their attachment glycoproteins (G) with fluorescent aptamers, which further enabled their identification, sizing and counting at the single particle level by fluorescent nanoparticle tracking analysis. The proposed approach seems to be generally applicable to virus detection and quantification. Moreover, it could be successfully applied to detect single RSV particles in swab samples of diagnostic relevance. Since the selective recognition is associated with the sizing of each detected particle, this method enables to discriminate viral elements linked to the virus as well as various virus forms and associations.

Programming hierarchical self-assembly of colloids: matching stability and accessibility

Encoding hierarchical self-assembly in colloidal building blocks is a promising bottom-up route to high-level structural complexity often observed in biological materials. However, harnessing this promise faces the grand challenge of bridging hierarchies of multiple length- and time-scales, associated with structure and dynamics respectively along the self-assembly pathway. Here we report on a case study, which examines the kinetic accessibility of a series of hollow spherical structures with a two-level structural hierarchy self-assembled from charge-stabilized colloidal magnetic particles. By means of a variety of computational methods, we find that for a staged assembly pathway, the structure, which derives the strongest energetic stability from the first stage of assembly and the weakest from the second stage, is most kinetically accessible. Such a striking correspondence between energetics and kinetics for optimal design principles should have general implications for programming hierarchical self-assembly pathways for nano- and micro-particles, while matching stability and accessibility.

On-Chip Spiral Waveguides for Ultrasensitive and Rapid Detection of Nanoscale Objects

Ultrasensitive and rapid detection of nano-objects is crucial in both fundamental studies and practical applications. Optical sensors using evanescent fields in microcavities, plasmonic resonators, and nanofibers allow label-free detection down to single molecules, but practical applications are severely hindered by long response time and device reproducibility. Here, an on-chip dense waveguide sensor to monitor single unlabeled nanoparticles in a strong optical evanescent field is demonstrated. The spiral nanowaveguide design enables two orders of magnitude enhancement in sensing area compared to a straight waveguide, significantly improving the particle capture ability and shortening the target analysis time. In addition, the measurement noise is suppressed to a level of 10^-4 in the transmitted power, pushing the detection limit of single particles down to the size of 100 nm. The waveguide sensor on the silicon-on-isolator platform can be fabricated reproducibly by the conventional semiconductor processing and compatible with surface functionalization chemistries and microfluidics, which could lead to widespread use for sensing in environmental monitoring and human health.

Excitation of epsilon-near-zero resonance in ultra-thin indium tin oxide shell embedded nanostructured optical fiber

We report a novel optical waveguide design of a hollow step index fiber modified with a thin layer of indium tin oxide (ITO). We show an excitation of highly confined waveguide mode in the proposed fiber near the wavelength where permittivity of ITO approaches zero. Due to the high field confinement within thin ITO shell inside the fiber, the epsilon-near-zero (ENZ) mode can be characterized by a peak in modal loss of the hybrid waveguide. Our results show that such in-fiber excitation of ENZ mode is due to the coupling of the guided core mode to the thin-film ENZ mode. We also show that the phase matching wavelength, where the coupling takes place, varies depending on the refractive index of the constituents inside the central bore of the fiber. These ENZ nanostructured optical fibers have many potential applications, for example, in ENZ nonlinear and magneto-optics, as in-fiber wavelength-dependent filters, and as subwavelength fluid channel for optical and bio-photonic sensing.

Nanofluidics: A New Arena for Materials Science

A significant growth of research in nanofluidics is achieved over the past decade, but the field is still facing considerable challenges toward the transition from the current physics-centered stage to the next application-oriented stage. Many of these challenges are associated with materials science, so the field of nanofluidics offers great opportunities for materials scientists to exploit. In addition, the use of unusual effects and ultrasmall confined spaces of well-defined nanofluidic environments would offer new mechanisms and technologies to manipulate nanoscale objects as well as to synthesize novel nanomaterials in the liquid phase. Therefore, nanofluidics will be a new arena for materials science. In the past few years, burgeoning progress has been made toward this trend, as overviewed in this article, including materials and methods for fabricating nanofluidic devices, nanofluidics with functionalized surfaces and functional material components, as well as nanofluidics for manipulating nanoscale materials and fabricating new nanomaterials. Many critical challenges as well as fantastic opportunities in this arena lie ahead. Some of those, which are of particular interest, are also discussed.

A New Label-Free Technique for Analysing Evaporation Induced Self-Assembly of Viral Nanoparticles Based on Enhanced Dark-Field Optical Imaging

Nanoparticle self-assembly is a complex phenomenon, the control of which is complicated by the lack of appropriate tools and techniques for monitoring the phenomenon with adequate resolution in real-time. In this work, a label-free technique based on dark-field microscopy was developed to investigate the self-assembly of nanoparticles. A bio-nanoparticle with complex shape (T4 bacteriophage) that self-assembles on glass substrates upon drying was developed. The fluid flow regime during the drying process, as well as the final self-assembled structures, were studied using dark-field microscopy, while phage diffusion was analysed by tracking of the phage nanoparticles in the bulk solutions. The concentrations of T4 phage nanoparticles and salt ions were identified as the main parameters influencing the fluid flow, particle motion and, consequently, the resulting self-assembled structure. This work demonstrates the utility of enhanced dark-field microscopy as a label-free technique for the observation of drying-induced self-assembly of bacteriophage T4. This technique provides the ability to track the nano-sized particles in different matrices and serves as a strong tool for monitoring self-assembled structures and bottom-up assembly of nano-sized building blocks in real-time.

Noninvasive characterization of optical fibers

Capillary optical fibers with hole diameters of several micrometers are important for novel plasmonic applications and medical diagnosis. In order to ensure the optical functionality of these fibers, the diameter of the capillary hole needs to be realized with high accuracy. Here, we introduce a novel and noninvasive methodology to characterize optical fibers and discuss it for the assessment of capillaries. In this method, the fiber is side-illuminated by a coherent beam, and the resulting diffraction pattern is analyzed. This corresponds to an in-line holographic measurement in the presence of strong scattering. A numerical parameter retrieval allows us to characterize the capillary hole diameter with an accuracy of approximately 100 nm for radii between several hundreds of nanometers and several tens of micrometers.

Investigating the thermal dissociation of viral capsid by lattice model

The dissociation of icosahedral viral capsids was investigated by a homogeneous and a heterogeneous lattice model. In thermal dissociation experiments with cowpea chlorotic mottle virus and probed by small-angle neutron scattering, we observed a slight shrinkage of viral capsids, which can be related to the strengthening of the hydrophobic interaction between subunits at increasing temperature. By considering the temperature dependence of hydrophobic interaction in the homogeneous lattice model, we were able to give a better estimate of the effective charge. In the heterogeneous lattice model, two sets of lattice sites represented different capsid subunits with asymmetric interaction strengths. In that case, the dissociation of capsids was found to shift from a sharp one-step transition to a gradual two-step transition by weakening the hydrophobic interaction between AB and CC subunits. We anticipate that such lattice models will shed further light on the statistical mechanics underlying virus assembly and disassembly.

Isolation and characterization of urinary extracellular vesicles: implications for biomarker discovery

Urine is a valuable diagnostic medium and, with the discovery of urinary extracellular vesicles, is viewed as a dynamic bioactive fluid. Extracellular vesicles are lipid-enclosed structures that can be classified into three categories: exosomes, microvesicles (or ectosomes) and apoptotic bodies. This classification is based on the mechanisms by which membrane vesicles are formed: fusion of multivesicular bodies with the plasma membranes (exosomes), budding of vesicles directly from the plasma membrane (microvesicles) or those shed from dying cells (apoptotic bodies). During their formation, urinary extracellular vesicles incorporate various cell-specific components (proteins, lipids and nucleic acids) that can be transferred to target cells. The rigour needed for comparative studies has fueled the search for optimal approaches for their isolation, purification, and characterization. RNA, the newest extracellular vesicle component to be discovered, has received substantial attention as an extracellular vesicle therapeutic, and compelling evidence suggests that ex vivo manipulation of microRNA composition may have uses in the treatment of kidney disorders. The results of these studies are building the case that urinary extracellular vesicles act as mediators of renal pathophysiology. As the field of extracellular vesicle studies is burgeoning, this Review focuses on primary data obtained from studies of human urine rather than on data from studies of laboratory animals or cultured immortalized cells.