Label-free nanofluidic scattering microscopy of size and mass of single diffusing molecules and nanoparticles.

Label-free characterization of single biomolecules aims to complement fluorescence microscopy in situations where labeling compromises data interpretation, is technically challenging or even impossible. However, existing methods require the investigated species to bind to a surface to be visible, thereby leaving a large fraction of analytes undetected. Here, we present nanofluidic scattering microscopy (NSM), which overcomes these limitations by enabling label-free, real-time imaging of single biomolecules diffusing inside a nanofluidic channel. NSM facilitates accurate determination of molecular weight from the measured optical contrast and of the hydrodynamic radius from the measured diffusivity, from which information about the conformational state can be inferred. Furthermore, we demonstrate its applicability to the analysis of a complex biofluid, using conditioned cell culture medium containing extracellular vesicles as an example. We foresee the application of NSM to monitor conformational changes, aggregation and interactions of single biomolecules, and to analyze single-cell secretomes.

Single Particle Nanoplasmonic Sensing in Individual Nanofluidic Channels.

Nanoplasmonics allows label-free optical sensing and spectroscopy at the single nanoparticle level by exploiting plasmonic excitations in metal nanoparticles. Nanofluidics offers exclusive possibilities for applying and controlling fluid flow and mass transport at the nanoscale and toward nanosized objects. Here, we combine these two concepts in a single device, by integrating single particle nanoplasmonic sensing with nanofluidics using advanced nanofabrication. The developed devices enable on-chip referenced parallel single particle nanoplasmonic sensing inside multiple individual nanofluidic channels with dimensions down to the 100 nm range. Beyond detailed discussion of the nanofabrication, general device characterization, and parallelized single particle plasmonic readout concepts, we demonstrate device function on two examples: (i) in situ measurements of local buffer concentrations inside a nanofluidic channel; (ii) real time binding kinetics of alkanethiol molecules to a single plasmonic nanonatenna sensor in a single nanochannel. Our concept thus provides a powerful solution for controlling mass transport to and from individual (plasmonic) nanoparticles, which in a long-term perspective offers unique opportunities for label-free detection of analyte molecules at low concentrations and for fundamental studies of fluids in extreme confinement.

Visualizing the Nonhomogeneous Structure of RAD51 Filaments Using Nanofluidic Channels.

RAD51 is the key component of the homologous recombination pathway in eukaryotic cells and performs its task by forming filaments on DNA. In this study we investigate the physical properties of RAD51 filaments formed on DNA using nanofluidic channels and fluorescence microscopy. Contrary to the bacterial ortholog RecA, RAD51 forms inhomogeneous filaments on long DNA in vitro, consisting of several protein patches. We demonstrate that a permanent "kink" in the filament is formed where two patches meet if the stretch of naked DNA between the patches is short. The kinks are readily seen in the present microscopy approach but would be hard to identify using conventional single DNA molecule techniques where the DNA is more stretched. We also demonstrate that protein patches separated by longer stretches of bare DNA roll up on each other and this is visualized as transiently overlapping filaments. RAD51 filaments can be formed at several different conditions, varying the cation (Mg(2+) or Ca(2+)), the DNA substrate (single-stranded or double-stranded), and the RAD51 concentration during filament nucleation, and we compare the properties of the different filaments formed. The results provide important information regarding the physical properties of RAD51 filaments but also demonstrate that nanofluidic channels are perfectly suited to study protein-DNA complexes.

Competitive binding-based optical DNA mapping for fast identification of bacteria--multi-ligand transfer matrix theory and experimental applications on Escherichia coli.

We demonstrate a single DNA molecule optical mapping assay able to resolve a specific Escherichia coli strain from other strains. The assay is based on competitive binding of the fluorescent dye YOYO-1 and the AT-specific antibiotic netropsin. The optical map is visualized by stretching the DNA molecules in nanofluidic channels. We optimize the experimental conditions to obtain reproducible barcodes containing as much information as possible. We implement a multi-ligand transfer matrix method for calculating theoretical barcodes from known DNA sequences. Our method extends previous theoretical approaches for competitive binding of two types of ligands to many types of ligands and introduces a recursive approach that allows long barcodes to be calculated with standard computer floating point formats. The identification of a specific E. coli strain (CCUG 10979) is based on mapping of 50-160 kilobasepair experimental DNA fragments onto the theoretical genome using the developed theory. Our identification protocol introduces two theoretical constructs: a P-value for a best experiment-theory match and an information score threshold. The developed methods provide a novel optical mapping toolbox for identification of bacterial species and strains. The protocol does not require cultivation of bacteria or DNA amplification, which allows for ultra-fast identification of bacterial pathogens.

Probing physical properties of a DNA-protein complex using nanofluidic channels.

A method to investigate physical properties of a DNA-protein complex in solution is demonstrated. By using tapered nanochannels and lipid passivation the persistence length of a RecA filament formed on double-stranded DNA is determined to 1.15 µm, in agreement with the literature, without attaching protein or DNA to any handles or surfaces.

Lipid-based passivation in nanofluidics.

Stretching DNA in nanochannels is a useful tool for direct, visual studies of genomic DNA at the single molecule level. To facilitate the study of the interaction of linear DNA with proteins in nanochannels, we have implemented a highly effective passivation scheme based on lipid bilayers. We demonstrate virtually complete long-term passivation of nanochannel surfaces to a range of relevant reagents, including streptavidin-coated quantum dots, RecA proteins, and RecA-DNA complexes. We show that the performance of the lipid bilayer is significantly better than that of standard bovine serum albumin-based passivation. Finally, we show how the passivated devices allow us to monitor single DNA cleavage events during enzymatic degradation by DNase I. We expect that our approach will open up for detailed, systematic studies of a wide range of protein-DNA interactions with high spatial and temporal resolution.

A Microshutter for the Nanofabrication of Plasmonic Metal Alloys with Single Nanoparticle Composition Control.

Alloying offers an increasingly important handle in nanomaterials design in addition to the already widely explored size and geometry of nanostructures of interest. As the key trait, the mixing of elements at the atomic level enables nanomaterials with physical or chemical properties that cannot be obtained by a single element alone, and subtle compositional variations can significantly impact these properties. Alongside the great potential of alloying, the experimental scrutiny of its impact on nanomaterial function is a challenge because the parameter space that encompasses nanostructure size, geometry, chemical composition, and structural atomic-level differences among individuals is vast and requires unrealistically large sample sets if statistically relevant and systematic data are to be obtained. To address this challenge, we have developed a microshutter device for spatially highly resolved physical vapor deposition in the lithography-based fabrication of nanostructured surfaces. As we demonstrate, it enables establishing compositional gradients across a surface with single nanostructure resolution in terms of alloy composition, which subsequently can be probed in a single experiment. As a showcase, we have nanofabricated arrays of AuAg, AuPd, and AgPd alloy nanoparticles with compositions systematically controlled at the level of single particle rows, as verified by energy dispersive X-ray and single particle plasmonic nanospectroscopy measurements, which we also compared to finite-difference time-domain simulations. Finally, motivated by their application in state-of-the-art plasmonic hydrogen sensors, we investigated PdAu alloy gradient arrays for their hydrogen sorption properties. We found distinctly composition-dependent kinetics and hysteresis and revealed a composition-dependent contribution of a single nanoparticle response to the ensemble average, which highlights the importance of alloy composition screening in single experiments with single nanoparticle resolution, as offered by the microshutter nanofabrication approach.

Label-Free Imaging of Catalytic H2O2 Decomposition on Single Colloidal Pt Nanoparticles Using Nanofluidic Scattering Microscopy.

Single-particle catalysis aims at determining factors that dictate the nanoparticle activity and selectivity. Existing methods often use fluorescent model reactions at low reactant concentrations, operate at low pressures, or rely on plasmonic enhancement effects. Hence, methods to measure single-nanoparticle activity under technically relevant conditions and without fluorescence or other enhancement mechanisms are still lacking. Here, we introduce nanofluidic scattering microscopy of catalytic reactions on single colloidal nanoparticles trapped inside nanofluidic channels to fill this gap. By detecting minuscule refractive index changes in a liquid flushed trough a nanochannel, we demonstrate that local H2O2 concentration changes in water can be accurately measured. Applying this principle, we analyze the H2O2 concentration profiles adjacent to single colloidal Pt nanoparticles during catalytic H2O2 decomposition into O2 and H2O and derive the particles' individual turnover frequencies from the growth rate of the O2 gas bubbles formed in their respective nanochannel during reaction.

The Role of Grain Boundary Sites for the Oxidation of Copper Catalysts during the CO Oxidation Reaction.

The oxidation of transition metal surfaces is a process that takes place readily at ambient conditions and that, depending on the specific catalytic reaction at hand, can either boost or hamper activity and selectivity. Cu catalysts are no exception in this respect since they exhibit different oxidation states for which contradicting activities have been reported, as, for example, in the catalytic oxidation of CO. Here, we investigate the impact of low-coordination sites on nanofabricated Cu nanoparticles with engineered grain boundaries on the oxidation of the Cu surface under CO oxidation reaction conditions. Combining multiplexed in situ single particle plasmonic nanoimaging, ex situ transmission electron microscopy imaging, and density functional theory calculations reveals a distinct dependence of particle oxidation rate on grain boundary density. Additionally, we found that the oxide predominantly nucleates at grain boundary-surface intersections, which leads to nonuniform oxide growth that suppresses Kirkendall-void formation. The oxide nucleation rate on Cu metal catalysts was revealed to be an interplay of surface coordination and CO oxidation behavior, with low coordination favoring Cu oxidation and high coordination favoring CO oxidation. These findings explain the observed single particle-specific onset of Cu oxidation as being the consequence of the individual particle grain structure and provide an explanation for widely distributed activity states of particles in catalyst bed ensembles.

Bandpass filtering of DNA elastic modes using confinement and tension.

During a variety of biological and technological processes, biopolymers are simultaneously subject to both confinement and external forces. Although significant efforts have gone into understanding the physics of polymers that are only confined, or only under tension, little work has been done to explore the effects of the interplay of force and confinement. Here, we study the combined effects of stretching and confinement on a polymer's configurational freedom. We measure the elastic response of long double-stranded DNA molecules that are partially confined to thin, nanofabricated slits. We account for the data through a model in which the DNA's short-wavelength transverse elastic modes are cut off by applied force and the DNA's bending stiffness, whereas long-wavelength modes are cut off by confinement. Thus, we show that confinement and stretching combine to permit tunable bandpass filtering of the elastic modes of long polymers.

Competing oxidation mechanisms in Cu nanoparticles and their plasmonic signatures.

Chemical reactions involving nanoparticles often follow complex processes. In this respect, real-time probing of single nanoparticles under reactive conditions is crucial for uncovering the mechanisms driving the reaction pathway. Here, we have captured in situ the oxidation of single Cu nanoparticles to unravel a sequential competitive activation of different mechanisms at temperatures 50-200 °C. Using environmental scanning transmission electron microscopy, we monitor the evolution of oxide formation with sub-nanometre spatial resolution, and show how the prevalence of oxide island nucleation, Cabrera-Mott, Valensi-Carter and Kirkendall mechanisms under different conditions determines the morphology of the particles. Moreover, using in situ electron energy-loss spectroscopy, we probe the localised surface plasmons of individual particles during oxidation, and with the aid of finite-difference time-domain electrodynamic simulations investigate the signature of each mechanism in their plasmonic response. Our results shed light on the rich and intricate processes involved in the oxidation of nanoparticles, and provide in-depth insight into how these processes govern their morphology and optical response, beneficial for applications in catalysis, sensing, nanomedicine and plasmonics.

Nanoplasmonic NO2 Sensor with a Sub-10 Parts per Billion Limit of Detection in Urban Air.

Urban air pollution is a critical health problem in cities all around the world. Therefore, spatially highly resolved real-time monitoring of airborne pollutants, in general, and of nitrogen dioxide, NO2, in particular, is of utmost importance. However, highly accurate but fixed and bulky measurement stations or satellites are used for this purpose to date. This defines a need for miniaturized NO2 sensor solutions with detection limits in the low parts per billion range to finally enable indicative air quality monitoring at low cost that facilitates detection of highly local emission peaks and enables the implementation of direct local actions like traffic control, to immediately reduce local emissions. To address this challenge, we present a nanoplasmonic NO2 sensor based on arrays of Au nanoparticles coated with a thin layer of polycrystalline WO3, which displays a spectral redshift in the localized surface plasmon resonance in response to NO2. Sensor performance is characterized under (i) idealized laboratory conditions, (ii) conditions simulating humid urban air, and (iii) an outdoor field test in a miniaturized device benchmarked against a commercial NO2 sensor approved according to European and American standards. The limit of detection of the plasmonic solution is below 10 ppb in all conditions. The observed plasmonic response is attributed to a combination of charge transfer between the WO3 layer and the plasmonic Au nanoparticles, WO3 layer volume expansion, and changes in WO3 permittivity. The obtained results highlight the viability of nanoplasmonic gas sensors, in general, and their potential for practical application in indicative urban air monitoring, in particular.

Nanofluidic Trapping of Faceted Colloidal Nanocrystals for Parallel Single-Particle Catalysis.

Catalyst activity can depend distinctly on nanoparticle size and shape. Therefore, understanding the structure sensitivity of catalytic reactions is of fundamental and technical importance. Experiments with single-particle resolution, where ensemble-averaging is eliminated, are required to study it. Here, we implement the selective trapping of individual spherical, cubic, and octahedral colloidal Au nanocrystals in 100 parallel nanofluidic channels to determine their activity for fluorescein reduction by sodium borohydride using fluorescence microscopy. As the main result, we identify distinct structure sensitivity of the rate-limiting borohydride oxidation step originating from different edge site abundance on the three particle types, as confirmed by first-principles calculations. This advertises nanofluidic reactors for the study of structure-function correlations in catalysis and identifies nanoparticle shape as a key factor in borohydride-mediated catalytic reactions.

Inverse designed plasmonic metasurface with parts per billion optical hydrogen detection.

Plasmonic sensors rely on optical resonances in metal nanoparticles and are typically limited by their broad spectral features. This constraint is particularly taxing for optical hydrogen sensors, in which hydrogen is absorbed inside optically-lossy Pd nanostructures and for which state-of-the-art detection limits are only at the low parts-per-million (ppm) range. Here, we overcome this limitation by inversely designing a plasmonic metasurface based on a periodic array of Pd nanoparticles. Guided by a particle swarm optimization algorithm, we numerically identify and experimentally demonstrate a sensor with an optimal balance between a narrow spectral linewidth and a large field enhancement inside the nanoparticles, enabling a measured hydrogen detection limit of 250 parts-per-billion (ppb). Our work significantly improves current plasmonic hydrogen sensor capabilities and, in a broader context, highlights the power of inverse design of plasmonic metasurfaces for ultrasensitive optical (gas) detection.

Nanoplasmonic-Nanofluidic Single-Molecule Biosensors for Ultrasmall Sample Volumes.

Detection of small amounts of biological compounds is of ever-increasing importance but also remains an experimental challenge. In this context, plasmonic nanoparticles have emerged as strong contenders enabling label-free optical sensing with single-molecule resolution. However, the performance of a plasmonic single-molecule biosensor is not only dependent on its ability to detect a molecule but equally importantly on its efficiency to transport it to the binding site. Here, we present a theoretical study of the impact of downscaling fluidic structures decorated with plasmonic nanoparticles from conventional microfluidics to nanofluidics. We find that for ultrasmall picolitre sample volumes, nanofluidics enables unprecedented binding characteristics inaccessible with conventional microfluidic devices, and that both detection times and number of detected binding events can be improved by several orders of magnitude. Therefore, we propose nanoplasmonic-nanofluidic biosensing platforms as an efficient tool that paves the way for label-free single-molecule detection from ultrasmall volumes, such as single cells.

Grain-growth mediated hydrogen sorption kinetics and compensation effect in single Pd nanoparticles.

Grains constitute the building blocks of polycrystalline materials and their boundaries determine bulk physical properties like electrical conductivity, diffusivity and ductility. However, the structure and evolution of grains in nanostructured materials and the role of grain boundaries in reaction or phase transformation kinetics are poorly understood, despite likely importance in catalysis, batteries and hydrogen energy technology applications. Here we report an investigation of the kinetics of (de)hydriding phase transformations in individual Pd nanoparticles. We find dramatic evolution of single particle grain morphology upon cyclic exposure to hydrogen, which we identify as the reason for the observed rapidly slowing sorption kinetics, and as the origin of the observed kinetic compensation effect. These results shed light on the impact of grain growth on kinetic processes occurring inside nanoparticles, and provide mechanistic insight in the observed kinetic compensation effect.

Shedding Light on CO Oxidation Surface Chemistry on Single Pt Catalyst Nanoparticles Inside a Nanofluidic Model Pore.

Investigating a catalyst under relevant application conditions is experimentally challenging and parameters like reaction conditions in terms of temperature, pressure, and reactant mixing ratios, as well as catalyst design, may significantly impact the obtained experimental results. For Pt catalysts widely used for the oxidation of carbon monoxide, there is keen debate on the oxidation state of the surface at high temperatures and at/above atmospheric pressure, as well as on the most active surface state under these conditions. Here, we employ a nanoreactor in combination with single-particle plasmonic nanospectroscopy to investigate individual Pt catalyst nanoparticles localized inside a nanofluidic model pore during carbon monoxide oxidation at 2 bar in the 450-550 K temperature range. As a main finding, we demonstrate that our single-particle measurements effectively resolve a kinetic phase transition during the reaction and that each individual particle has a unique response. Based on spatially resolved measurements, we furthermore observe how reactant concentration gradients formed due to conversion inside the model pore give rise to position-dependent kinetic phase transitions of the individual particles. Finally, employing extensive electrodynamics simulations, we unravel the surface chemistry of the individual Pt nanoparticles as a function of reactant composition and find strongly temperature-dependent Pt-oxide formation and oxygen spillover to the SiO2 support as the main processes. These results therefore support the existence of a Pt surface oxide in the regime of high catalyst activity and demonstrate the possibility to use plasmonic nanospectroscopy in combination with nanofluidics as a tool for in situ studies of individual catalyst particles.

Light-Off in Plasmon-Mediated Photocatalysis.

In plasmon-mediated photocatalysis it is of critical importance to differentiate light-induced catalytic reaction rate enhancement channels, which include near-field effects, direct hot carrier injection, and photothermal catalyst heating. In particular, the discrimination of photothermal and hot electron channels is experimentally challenging, and their role is under keen debate. Here we demonstrate using the example of CO oxidation over nanofabricated neat Pd and Au50Pd50 alloy catalysts, how photothermal rate enhancement differs by up to 3 orders of magnitude for the same photon flux, and how this effect is controlled solely by the position of catalyst operation along the light-off curve measured in the dark. This highlights that small fluctuations in reactor temperature or temperature gradients across a sample may dramatically impact global and local photothermal rate enhancement, respectively, and thus control both the balance between different rate enhancement mechanisms and the way strategies to efficiently distinguish between them should be devised.

Operando detection of single nanoparticle activity dynamics inside a model pore catalyst material.

Nanoconfinement in porous catalysts may induce reactant concentration gradients inside the pores due to local conversion. This leads to inefficient active material use since parts of the catalyst may be trapped in an inactive state. Experimentally, these effects remain unstudied due to material complexity and required high spatial resolution. Here, we have nanofabricated quasi-two-dimensional mimics of porous catalysts, which combine the traits of nanofluidics with single particle plasmonics and online mass spectrometry readout. Enabled by single particle resolution at operando conditions during CO oxidation over a Cu model catalyst, we directly visualize reactant concentration gradient formation due to conversion on single Cu nanoparticles inside the "model pore" and how it dynamically controls oxidation state-and, thus, activity-of particles downstream. Our results provide a general framework for single particle catalysis in the gas phase and highlight the importance of single particle approaches for the understanding of complex catalyst materials.

Resolving single Cu nanoparticle oxidation and Kirkendall void formation with in situ plasmonic nanospectroscopy and electrodynamic simulations.

Copper nanostructures are ubiquitous in microelectronics and heterogeneous catalysis and their oxidation is a topic of high current interest and broad relevance. It relates to important questions, such as catalyst active phase, activity and selectivity, as well as fatal failure of microelectronic devices. Despite the obvious importance of understanding the mechanism of Cu nanostructure oxidation, numerous open questions remain, including under what conditions homogeneous oxide layer growth occurs and when the nanoscale Kirkendall void forms. Experimentally, this is not trivial to investigate because when a large number of nanoparticles are simultaneously probed, ensemble averaging makes rigorous conclusions difficult. On the other hand, when (in situ) electron-microscopy approaches with single nanoparticle resolution are applied, concerns about beam effects that may both reduce the oxide or prevent oxidation via the deposition and cross-linking of carbonaceous species cannot be neglected. In response we present how single particle plasmonic nanospectroscopy can be used for the in situ real time characterization of multiple individual Cu nanoparticles during oxidation. Our analysis of their optical response combined with post mortem electron microscopy imaging and detailed Finite-Difference Time-Domain electrodynamics simulations enables in situ identification of the oxidation mechanism both in the initial oxide shell growth phase and during Kirkendall void formation, as well as the transition between them. In a wider perspective, this work presents the foundation for the application of single particle plasmonic nanospectroscopy in investigations of the impact of parameters like particle size, shape and grain structure with respect to defects and grain boundaries on the oxidation of metal nanoparticles.