Structured light enhanced machine learning for fiber bend sensing.

The intricate optical distortions that occur when light interacts with complex media, such as few- or multi-mode optical fiber, often appear random in origin and are a fundamental source of error for communication and sensing systems. We propose the use of orbital angular momentum (OAM) feature extraction to mitigate phase-noise and allow for the use of intermodal-coupling as an effective tool for fiber sensing. OAM feature extraction is achieved by passive all-optical OAM demultiplexing, and we demonstrate fiber bend tracking with 94.1% accuracy. Conversely, an accuracy of only 14% was achieved for determining the same bend positions when using a convolutional-neural-network trained with intensity measurements of the output of the fiber. Further, OAM feature extraction used 120 times less information for training compared to intensity image based measurements. This work indicates that structured light enhanced machine learning could be used in a wide range of future sensing technologies.

Size-scaling effects for microparticles and cells manipulated by optoelectronic tweezers.

In this work, we investigated the use of optoelectronic tweezers (OET) to manipulate objects that are larger than those commonly positioned with standard optical tweezers. We studied the forces that could be produced on differently sized polystyrene microbeads and MCF-7 breast cancer cells with light-induced dielectrophoresis (DEP). It was found that the DEP force imposed on the bead/cell did not increase linearly with the volume of the bead/cell, primarily because of the non-uniform distribution of the electric field above the OET bottom plate. Although this size-scaling work focuses on microparticles and cells, we propose that the physical mechanism elucidated in this research will be insightful for other micro-objects, biological samples, and micro-actuators undergoing OET manipulation.

DNA-directed spatial assembly of photosynthetic light-harvesting proteins.

This manuscript describes the surface immobilization of a light-harvesting complex to prescribed locations directed by the sequence-selective recognition of duplex DNA. An engineered light-harvesting complex (RC-LH1) derived from Rhodopseudomonas (Rps.) palustris containing the zinc finger (ZF) domain zif268 was prepared. The zif268 domain directed the binding of zfRC-LH1 to target double-stranded DNA sequences both in solution and when immobilized on lithographically defined micro-patterns. Excitation energy transfer from the carotenoids to the bacteriochlorophyll pigments within zfRC-LH1 confirmed that the functional and structural integrity of the complex is retained after surface immobilization.

2'-19F labelling of ribose in RNAs: a tool to analyse RNA/protein interactions by NMR in physiological conditions.

Protein-RNA interactions are central to numerous cellular processes. In this work, we present an easy and straightforward NMR-based approach to determine the RNA binding site of RNA binding proteins and to evaluate the binding of pairs of proteins to a single-stranded RNA (ssRNA) under physiological conditions, in this case in nuclear extracts. By incorporation of a 19F atom on the ribose of different nucleotides along the ssRNA sequence, we show that, upon addition of an RNA binding protein, the intensity of the 19F NMR signal changes when the 19F atom is located near the protein binding site. Furthermore, we show that the addition of pairs of proteins to a ssRNA containing two 19F atoms at two different locations informs on their concurrent binding or competition. We demonstrate that such studies can be done in a nuclear extract that mimics the physiological environment in which these protein-ssRNA interactions occur. Finally, we demonstrate that a trifluoromethoxy group (-OCF3) incorporated in the 2'ribose position of ssRNA sequences increases the sensitivity of the NMR signal, leading to decreased measurement times, and reduces the issue of RNA degradation in cellular extracts.

Sequence-selective detection of double-stranded DNA sequences using pyrrole-imidazole polyamide microarrays.

We describe a microarray format that can detect double-stranded DNA sequences with a high degree of sequence selectivity. Cyclooctyne-derivatized pyrrole-imidazole polyamides were immobilized on azide-modified glass substrates using microcontact printing and a strain-promoted azide-alkyne cycloaddition (SPAAC) reaction. These polyamide-immobilized substrates selectively detected a seven-base-pair binding site incorporated within a double-stranded oligodeoxyribonucleotide sequence even in the presence of an excess of a sequence with a single-base-pair mismatch.

A cross-reactive plasmonic sensing array for drinking water assessment.

The continuous monitoring of remote drinking water purification systems is a global challenge with direct consequences for human and environmental health. Here, we utilise a "nano-tastebud" sensor comprised of eight chemically-tailored plasmonic metasurfaces, for testing the composition of drinking water. Through undertaking a full chemometric analysis of the water samples and likely contaminants we were able to optimise the sensor specification to create an array of suitable tastebuds. By generating a unique set of optical responses for each water sample, we show that the array-based sensor can differentiate between untreated influent and treated effluent water with over 95% accuracy in flow and can detect compositional changes in distributed modified tap water. Once fully developed, this system could be integrated into water treatment facilities and distribution systems to monitor for changes in water composition.

Fluorous-Directed Assembly of DNA Origami Nanostructures.

An orthogonal, noncovalent approach to direct the assembly of higher-order DNA origami nanostructures is described. By incorporating perfluorinated tags into the edges of DNA origami tiles we control their hierarchical assembly via fluorous-directed recognition. When we combine this approach with Watson-Crick base-pairing we form discrete dimeric constructs in significantly higher yield (8x) than when either molecular recognition method is used in isolation. This integrated "catch-and-latch" approach, which combines the strength and mobility of the fluorous effect with the specificity of base-pairing, provides an additional toolset for DNA nanotechnology, one that enables increased assembly efficiency while requiring significantly fewer DNA sequences. As a result, our integration of fluorous-directed assembly into origami systems represents a cheap, atom-efficient means to produce discrete superstructures.

Supramolecular Click Chemistry for Surface Modification of Quantum Dots Mediated by Cucurbit[7]uril.

Cucurbiturils (CBs), barrel-shaped macrocyclic molecules, are capable of self-assembling at the surface of nanomaterials in their native state, via their carbonyl-ringed portals. However, the symmetrical two-portal structure typically leads to aggregated nanomaterials. We demonstrate that fluorescent quantum dot (QD) aggregates linked with CBs can be broken-up, retaining CBs adsorbed at their surface, via inclusion of guests in the CB cavity. Simultaneously, the QD surface is modified by a functional tail on the guest, thus the high affinity host-guest binding (logKa > 9) enables a non-covalent, click-like modification of the nanoparticles in aqueous solution. We achieved excellent modification efficiency in several functional QD conjugates as protein labels. Inclusion of weaker-binding guests (logKa = 4-6) enables subsequent displacement with stronger binders, realising modular switchable surface chemistries. Our general "hook-and-eye" approach to host-guest chemistry at nanomaterial interfaces will lead to divergent routes for nano-architectures with rich functionalities for theranostics and photonics in aqueous systems.

Surface Passivation with a Perfluoroalkane Brush Improves the Precision of Single-Molecule Measurements.

Single-molecule imaging is invaluable for investigating the heterogeneous behavior and interactions of biological molecules. However, an impediment to precise sampling of single molecules is the irreversible adsorption of components onto the surfaces of cover glasses. This causes continuous changes in the concentrations of different molecules dissolved or suspended in the aqueous phase from the moment a sample is dispensed, which will shift, over time, the position of chemical equilibria between monomeric and multimeric components. Interferometric scattering microscopy (iSCAT) is a technique in the single-molecule toolkit that has the capability to detect unlabeled proteins and protein complexes both as they adsorb onto and desorb from a glass surface. Here, we examine the reversible and irreversible interactions between a number of different proteins and glass via analysis of the adsorption and desorption of protein at the single-molecule level. Furthermore, we present a method for surface passivation that virtually eliminates irreversible adsorption while still ensuring the residence time of molecules on surfaces is sufficient for detection of adsorption by iSCAT. By grafting high-density perfluoroalkane brushes on cover-glass surfaces, we observe approximately equal numbers of adsorption and desorption events for proteins at the measurement surface (±1%). The fluorous-aqueous interface also prevents the kinetic trapping of protein complexes and assists in establishing a thermodynamic equilibrium between monomeric and multimeric components. This surface passivation approach is valuable for in vitro single-molecule experiments using iSCAT microscopy because it allows for continuous monitoring of adsorption and desorption of protein without either a decline in detection events or a change in sample composition due to the irreversible binding of protein to surfaces.

Nanogap ring antennae as plasmonically coupled SERRS substrates.

The fabrication, optical characterization, and application of a new generation of ultrasmall multiple-split nanoring antennae is reported. Using electron-beam lithography, splits of ≈6 nm are engineered into silver nanophotonic ring structures to create concentrated areas of localized field coupling, which can be exploited for enhanced plasmonic applications. The plasmonic properties of three devices, containing 3, 4, and 5 splits, which have been spectrally tuned to 532 nm, are compared. Using finite-element analysis, the distinct plasmonic characteristics of each structure are explored and a description is given of how variations in the surface charge distribution affect intersegmental coupling at different polarization angles. The impact these changes have on the sensory functionality of each device was determined by a competitive DNA-hybridization assay measured using surface-enhanced resonance Raman spectroscopy. The geometry of these novel, circular, multiple-split rings leads to unique plasmon hybridization between the numerous segments of a single structure. This phenomenon is demonstrated to be applicable to extreme Raman sensitivity and may also find use in metamaterial applications.

Plasmonic split-ring resonators as dichroic nanophotonic DNA biosensors.

Surface enhanced resonance Raman spectroscopy (SERRS) is a powerful molecular sensing tool that can be applied to a number of applications in the field of molecular diagnostics. We demonstrate that by using electron beam lithography to manipulate the nanoscale geometry of Ag split-ring resonators we can tune their optical properties such that they exhibit two independently addressable high frequency plasmon resonance modes for SERRS. This tailored multimodal, polarization dependent activity enables the split rings to act as discriminating sensors, with each resonance tuned for a particular sensing purpose. The structures are used as multiwavelength, multianalyte DNA SERRS sensors, with each resonance tuned to both the absorption wavelength of a differently colored Raman reporter molecule and its corresponding laser excitation wavelength. The ability of each resonance to independently sense small concentrations of a single DNA type from within a mixed population is demonstrated. Also shown is the effect of the split ring's dichroic response on the SERRS signal and the sensor's limit of detection of each resonance mode (switching its sensory reaction "on" and "off" depending on the orientation of the exciting light).

Whisky tasting using a bimetallic nanoplasmonic tongue.

Metallic nanostructures are ideal candidates for optical tongue devices thanks to their chemical stability, the sensitivity of their plasmonic resonance to environmental changes, and their ease of chemical-functionalization. Here, we describe a reusable optical tongue comprising multiplexed gold and aluminum nano-arrays: a bimetallic device which produces two distinct resonance peaks for each sensing region. Through specific modification of these plasmonic arrays with orthogonal surface chemistries, we demonstrate that a dual-resonance device allows us to halve sensor sizes and data-acquisition times when compared to single-resonance, monometallic devices. We applied our bimetallic tongue to differentiate off-the-shelf whiskies with >99.7% accuracy by means of linear discriminant analysis (LDA). This advance in device miniaturization, functionalization, and multiplexed readout indicates nanoplasmonic tongues will have future applications in chemical mixture identification in applications where portability, reusability, and measurement speed are key.

Multilayered Nanoplasmonic Arrays for Self-Referenced Biosensing.

Nanostructured sensors based on localized surface plasmon resonance (LSPR) offer a number of advantages over other optical sensing technologies, making them excellent candidates for miniaturized, label-free chemical and biological detection. Highly sensitive to local refractive index changes, the resonance peaks of the nanosensors shift by different amounts when subject to different biological and chemical environments. Modifications to the nanostructure surface allow for the detection of specific molecules and chemicals with shifts so sensitive that the presence of single molecules can be detected. However, this extreme sensitivity has its drawbacks. Resonance shifts also occur because of temperature shifts, light-intensity fluctuations, and other environmental factors. To distinguish detection from drift, a secondary sensor region is often required. This often doubles the size of the device, requires two light sources and detectors (or complex optics), doubles the sample volume required (which may be expensive, or may not be possible if the sample quantity is limited), and subjects the reference to potential biofouling. Here, we present a new proof-of-concept multilayered LSPR sensor design that incorporates both a sensing layer and an encapsulated reference layer within the same region. By doing so, we are able to monitor and correct for sensor drift without the need for a secondary reference channel. We demonstrate the suitability of this sensor for sucrose concentration measurements and for the detection of biotin-avidin interactions, while also showing that the sensor can self-correct for drift. We believe that this multilayer sensor design holds promise for point-of-care diagnostics.

Bridging the Gap: Rewritable Electronics Using Real-Time Light-Induced Dielectrophoresis on Lithium Niobate.

In the context of micro-electronics, the real-time manipulation and placement of components using optics alone promises a route towards increasingly dynamic systems, where the geometry and function of the device is not fixed at the point of fabrication. Here, we demonstrate physically reconfigurable circuitry through light-induced dielectrophoresis on lithium niobate. Using virtual electrodes, patterned by light, to trap, move, and chain individual micro-solder-beads in real-time via dielectrophoresis, we demonstrate rewritable electrical contacts which can make electrical connections between surface-bound components. The completed micro-solder-bead bridges were found to have relatively low resistances that were not solely dominated by the number of interfaces, or the number of discrete beads, in the connection. Significantly, these connections are formed without any melting/fusing of the beads, a key feature of this technique that enables reconfigurability. Requiring only a low-power (~3.5 mW) laser source to activate, and without the need for external power supply or signal generation, the all-optical simplicity of virtual-electrodes may prove significant for the future development of reconfigurable electronic systems.

Reversible DNA micro-patterning using the fluorous effect.

We describe a new method for the immobilisation of DNA into defined patterns with sub-micron resolution, using the fluorous effect. The method is fully reversible via a simple solvent wash, allowing the patterning, regeneration and re-patterning of surfaces with no degradation in binding efficiency following multiple removal/attachment cycles of different DNA sequences.

Dual Color Plasmonic Pixels Create a Polarization Controlled Nano Color Palette.

Color filters based upon nanostructured metals have garnered significant interest in recent years, having been positioned as alternatives to the organic dye-based filters which provide color selectivity in image sensors, as nonfading "printing" technologies for producing images with nanometer pixel resolution, and as ultra-high-resolution, small foot-print optical storage and encoding solutions. Here, we demonstrate a plasmonic filter set with polarization-switchable color properties, based upon arrays of asymmetric cross-shaped nanoapertures in an aluminum thin-film. Acting as individual color-emitting nanopixels, the plasmonic cavity-apertures have dual-color selectivity, transmitting one of two visible colors, controlled by the polarization of the white light incident on the rear of the pixel and tuned by varying the critical dimensions of the geometry and periodicity of the array. This structural approach to switchable optical filtering enables a single nanoaperture to encode two information states within the same physical nanoaperture, an attribute we use here to create micro image displays containing duality in their optical information states.

SERS enhancement of silver nanoparticles prepared by a template-directed triazole ligand strategy.

Two advances in the development of a one-pot method to prepare silver nanoparticles (AgNPs) using the Tollens' reagent are described. First, a template-directed process of AgNP synthesis using resorcinol triazole ligands bearing two pendent galactose sugars is shown. Second, the conversion of these AgNPs into SERS nanotags is demonstrated using malachite green isothiocyanate as the Raman reporter molecule.