Optical barcoding using polarisation sensitive plasmonic biosensors for the detection of self-assembled monolayers.

Periodic subwavelength apertures have the ability to passively detect variations in the dielectric properties of the local sample environment through modification of the plasmon resonances associated with these structures. The resulting resonance peak can effectively provide a 'fingerprint' indicative of the dielectric properties of the medium within the near-surface region. Here we report on the use of bimodal silver-based plasmonic colour filters for molecular sensing. Firstly, by exploring the optical output of these devices as a function of the incident polarisation for a range of different analytes of known refractive index, we were able to both maximise and quantify their sensitivity. We then apply this concept to the real-time monitoring of the formation of self-assembled monolayers based on detection of the optical output using a spectrometer. This highlights the potential for bimodal plasmonic devices to be able to dynamically monitor variations in the local environment down to the level of single molecules without the need for specific functionalisation or labelling. Advantages of using this technique include the ability for these devices to be miniaturised and to dynamically tailor their optical output permitting the analysis of very small sample volumes and maximise their dynamic range for a specific analyte.

Observations of phase changes in monoolein during high viscous injection.

Serial crystallography of membrane proteins often employs high-viscosity injectors (HVIs) to deliver micrometre-sized crystals to the X-ray beam. Typically, the carrier medium is a lipidic cubic phase (LCP) media, which can also be used to nucleate and grow the crystals. However, despite the fact that the LCP is widely used with HVIs, the potential impact of the injection process on the LCP structure has not been reported and hence is not yet well understood. The self-assembled structure of the LCP can be affected by pressure, dehydration and temperature changes, all of which occur during continuous flow injection. These changes to the LCP structure may in turn impact the results of X-ray diffraction measurements from membrane protein crystals. To investigate the influence of HVIs on the structure of the LCP we conducted a study of the phase changes in monoolein/water and monoolein/buffer mixtures during continuous flow injection, at both atmospheric pressure and under vacuum. The reservoir pressure in the HVI was tracked to determine if there is any correlation with the phase behaviour of the LCP. The results indicated that, even though the reservoir pressure underwent (at times) significant variation, this did not appear to correlate with observed phase changes in the sample stream or correspond to shifts in the LCP lattice parameter. During vacuum injection, there was a three-way coexistence of the gyroid cubic phase, diamond cubic phase and lamellar phase. During injection at atmospheric pressure, the coexistence of a cubic phase and lamellar phase in the monoolein/water mixtures was also observed. The degree to which the lamellar phase is formed was found to be strongly dependent on the co-flowing gas conditions used to stabilize the LCP stream. A combination of laboratory-based optical polarization microscopy and simulation studies was used to investigate these observations.

Erratum: An advanced workflow for single-particle imaging with the limited data at an X-ray free-electron laser. Corrigendum.

[This corrects the article DOI: 10.1107/S2052252520012798.].

Stability, flow alignment and a phase transition of the lipidic cubic phase during continuous flow injection.

Continuous flow injection is a key technology for serial crystallography measurements of protein crystals suspended in the lipidic cubic phase (LCP). To date, there has been little discussion in the literature regarding the impact of the injection process itself on the structure of the lipidic phase. This is despite the fact that the phase of the injection matrix is critical for the flow properties of the stream and potentially for sample stability. Here we report small-angle X-ray scattering measurements of a monoolein:water mixture during continuous delivery using a high viscosity injector. We observe both an alignment and modification of the LCP as a direct result of the injection process. The orientation of the cubic lattice with respect to the beam was estimated based on the anisotropy of the diffraction pattern and does not correspond to a single low order zone axis. The solvent fraction was also observed to impact the stability of the cubic phase during injection. In addition, depending on the distance traveled by the lipid after exiting the needle, the phase is observed to transition from a pure diamond phase (Pn3m) to a mixture containing both gyriod (Ia3d) and lamellar (Lα) phases. Finite element modelling of the observed phase behaviour during injection indicates that the pressure exerted on the lipid stream during extrusion accounts for the variations in the phase composition of the monoolein:water mixture.

Colorimetric histology using plasmonically active microscope slides.

The human eye can distinguish as many as 10,000 different colours but is far less sensitive to variations in intensity1, meaning that colour is highly desirable when interpreting images. However, most biological samples are essentially transparent, and nearly invisible when viewed using a standard optical microscope2. It is therefore highly desirable to be able to produce coloured images without needing to add any stains or dyes, which can alter the sample properties. Here we demonstrate that colorimetric histology images can be generated using full-sized plasmonically active microscope slides. These slides translate subtle changes in the dielectric constant into striking colour contrast when samples are placed upon them. We demonstrate the biomedical potential of this technique, which we term histoplasmonics, by distinguishing neoplastic cells from normal breast epithelium during the earliest stages of tumorigenesis in the mouse MMTV-PyMT mammary tumour model. We then apply this method to human diagnostic tissue and validate its utility in distinguishing normal epithelium, usual ductal hyperplasia, and early-stage breast cancer (ductal carcinoma in situ). The colorimetric output of the image pixels is compared to conventional histopathology. The results we report here support the hypothesis that histoplasmonics can be used as a novel alternative or adjunct to general staining. The widespread availability of this technique and its incorporation into standard laboratory workflows may prove transformative for applications extending well beyond tissue diagnostics. This work also highlights opportunities for improvements to digital pathology that have yet to be explored.

Recent Advances and Future Perspectives on Microfluidic Mix-and-Jet Sample Delivery Devices.

The integration of the Gas Dynamic Virtual Nozzle (GDVN) and microfluidic technologies has proven to be a promising sample delivery solution for biomolecular imaging studies and has the potential to be transformative for a range of applications in physics, biology, and chemistry. Here, we review the recent advances in the emerging field of microfluidic mix-and-jet sample delivery devices for the study of biomolecular reaction dynamics. First, we introduce the key parameters and dimensionless numbers involved in their design and characterisation. Then we critically review the techniques used to fabricate these integrated devices and discuss their advantages and disadvantages. We then summarise the most common experimental methods used for the characterisation of both the mixing and jetting components. Finally, we discuss future perspectives on the emerging field of microfluidic mix-and-jet sample delivery devices. In summary, this review aims to introduce this exciting new topic to the wider microfluidics community and to help guide future research in the field.

An advanced workflow for single-particle imaging with the limited data at an X-ray free-electron laser.

An improved analysis for single-particle imaging (SPI) experiments, using the limited data, is presented here. Results are based on a study of bacteriophage PR772 performed at the Atomic, Molecular and Optical Science instrument at the Linac Coherent Light Source as part of the SPI initiative. Existing methods were modified to cope with the shortcomings of the experimental data: inaccessibility of information from half of the detector and a small fraction of single hits. The general SPI analysis workflow was upgraded with the expectation-maximization based classification of diffraction patterns and mode decomposition on the final virus-structure determination step. The presented processing pipeline allowed us to determine the 3D structure of bacteriophage PR772 without symmetry constraints with a spatial resolution of 6.9 nm. The obtained resolution was limited by the scattering intensity during the experiment and the relatively small number of single hits.

Mixing and jetting analysis using continuous flow microfluidic sample delivery devices.

Serial femtosecond crystallography (SFX) methods used at X-ray free electron lasers (XFELs) offer a range of new opportunities for structural biology. A crucial component of SFX experiments is sample delivery. Microfluidic devices can be employed in SFX experiments to precisely deliver microcrystals to the X-ray beam and to trigger molecular dynamics via rapid mix-and-inject measurements. Here, for the first time, we have developed a process based on high-resolution photolithography using SU8 on glass to fabricate microfluidic mix-and-inject devices. In order to characterise these devices a broad range of flow rates are used and the mixing and jetting response of the devices monitored. We observe that a stable jet is formed using these devices when injecting DI-water. Three different jetting regimes, liquid column, ribbon, and cylindrical jet, were observed. Furthermore, fluorescence experiments confirm that rapid and uniform mixing of the two injected solutions is possible using these devices indicating that they could be used to probe molecular dynamics on sub-microsecond timescales.

Visualization and measurement of the local absorption coefficients of single bilayer phospholipid membranes using scanning near-field optical microscopy.

Here we report the results of shear-mode thicknesses and absorption coefficient measurements made on neat membranes using scanning near-field optical microscopy (SNOM). Biomimic neat membranes composed of two different types of phoshpholipid molecules: 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) and 1,2- dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) were found to exhibit different absorption coefficients under the SNOM. The localization of the lipids could be identified and correlated to the morphology of the membrane domains indicating that SNOM can be an effective and accurate approach for the label-free characterization of the structure-function relationships in cell membranes.

Measurements of Long-range Electronic Correlations During Femtosecond Diffraction Experiments Performed on Nanocrystals of Buckminsterfullerene.

The precise details of the interaction of intense X-ray pulses with matter are a topic of intense interest to researchers attempting to interpret the results of femtosecond X-ray free electron laser (XFEL) experiments. An increasing number of experimental observations have shown that although nuclear motion can be negligible, given a short enough incident pulse duration, electronic motion cannot be ignored. The current and widely accepted models assume that although electrons undergo dynamics driven by interaction with the pulse, their motion could largely be considered 'random'. This would then allow the supposedly incoherent contribution from the electronic motion to be treated as a continuous background signal and thus ignored. The original aim of our experiment was to precisely measure the change in intensity of individual Bragg peaks, due to X-ray induced electronic damage in a model system, crystalline C60. Contrary to this expectation, we observed that at the highest X-ray intensities, the electron dynamics in C60 were in fact highly correlated, and over sufficiently long distances that the positions of the Bragg reflections are significantly altered. This paper describes in detail the methods and protocols used for these experiments, which were conducted both at the Linac Coherent Light Source (LCLS) and the Australian Synchrotron (AS) as well as the crystallographic approaches used to analyse the data.

Plasmonic Colour Filters Based on Coaxial Holes in Aluminium.

Aluminum is an alternative plasmonic material in the visible regions of the spectrum due to its attractive properties such as low cost, high natural abundance, ease of processing, and complementary metal-oxide-semiconductor (CMOS) and liquid crystal display (LCD) compatibility. Here, we present plasmonic colour filters based on coaxial holes in aluminium that operate in the visible range. Using both computational and experimental methods, fine-tuning of resonance peaks through precise geometric control of the coaxial holes is demonstrated. These results will lay the basis for the development of filters in high-resolution liquid crystal displays, RGB-spatial light modulators, liquid crystal over silicon devices and novel displays.

X-ray laser-induced electron dynamics observed by femtosecond diffraction from nanocrystals of Buckminsterfullerene.

X-ray free-electron lasers (XFELs) deliver x-ray pulses with a coherent flux that is approximately eight orders of magnitude greater than that available from a modern third-generation synchrotron source. The power density of an XFEL pulse may be so high that it can modify the electronic properties of a sample on a femtosecond time scale. Exploration of the interaction of intense coherent x-ray pulses and matter is both of intrinsic scientific interest and of critical importance to the interpretation of experiments that probe the structures of materials using high-brightness femtosecond XFEL pulses. We report observations of the diffraction of extremely intense 32-fs nanofocused x-ray pulses by a powder sample of crystalline C60. We find that the diffraction pattern at the highest available incident power significantly differs from the one obtained using either third-generation synchrotron sources or XFEL sources operating at low output power and does not correspond to the diffraction pattern expected from any known phase of crystalline C60. We interpret these data as evidence of a long-range, coherent dynamic electronic distortion that is driven by the interaction of the periodic array of C60 molecular targets with intense x-ray pulses of femtosecond duration.

Simultaneous X-ray fluorescence and scanning X-ray diffraction microscopy at the Australian Synchrotron XFM beamline.

Owing to its extreme sensitivity, quantitative mapping of elemental distributions via X-ray fluorescence microscopy (XFM) has become a key microanalytical technique. The recent realisation of scanning X-ray diffraction microscopy (SXDM) meanwhile provides an avenue for quantitative super-resolved ultra-structural visualization. The similarity of their experimental geometries indicates excellent prospects for simultaneous acquisition. Here, in both step- and fly-scanning modes, robust, simultaneous XFM-SXDM is demonstrated.

Tunable surface plasmon wave plates.

The highest resonant transmission through an array of holes perforated in metallic screens occurs when the dielectric constant of the substrate, the superstrate, and the hole are the same. Changes in the refractive index of the homogenous environment also produce the largest shift in resonances per refractive index unit. In this Letter, we first propose and apply a technique in realization of a freestanding bi-periodic array of holes perforated in a silver film. We then show both numerically and experimentally that shifts in (1,0) and (0,1) modes in response to changes in the refractive index of the surrounding dielectric provide a mechanism for realization of a miniaturized tunable quarter-wave plate that operates in an extraordinary optical transmission mode with a high throughput and a near unity state of circularly polarized light.

Continuously Tunable, Polarization Controlled, Colour Palette Produced from Nanoscale Plasmonic Pixels.

Colour filters based on nano-apertures in thin metallic films have been widely studied due to their extraordinary optical transmission and small size. These properties make them prime candidates for use in high-resolution colour displays and high accuracy bio-sensors. The inclusion of polarization sensitive plasmonic features in such devices allow additional control over the electromagnetic field distribution, critical for investigations of polarization induced phenomena. Here we demonstrate that cross-shaped nano-apertures can be used for polarization controlled color tuning in the visible range and apply fundamental theoretical models to interpret key features of the transmitted spectrum. Full color transmission was achieved by fine-tuning the periodicity of the apertures, whilst keeping the geometry of individual apertures constant. We demonstrate this effect for both transverse electric and magnetic fields. Furthermore we have been able to demonstrate the same polarization sensitivity even for nano-size, sub-wavelength sets of arrays, which is paramount for ultra-high resolution compact colour displays.

On-chip photonic Fourier transform with surface plasmon polaritons.

The Fourier transform (FT), a cornerstone of optical processing, enables rapid evaluation of fundamental mathematical operations, such as derivatives and integrals. Conventionally, a converging lens performs an optical FT in free space when light passes through it. The speed of the transformation is limited by the thickness and the focal length of the lens. By using the wave nature of surface plasmon polaritons (SPPs), here we demonstrate that the FT can be implemented in a planar configuration with a minimal propagation distance of around 10 µm, resulting in an increase of speed by four to five orders of magnitude. The photonic FT was tested by synthesizing intricate SPP waves with their Fourier components. The reduced dimensionality in the minuscule device allows the future development of an ultrafast on-chip photonic information processing platform for large-scale optical computing.

Broadband chirality-coded meta-aperture for photon-spin resolving.

The behaviour of light transmitted through an individual subwavelength aperture becomes counterintuitive in the presence of surrounding 'decoration', a phenomenon known as the extraordinary optical transmission. Despite being polarization-sensitive, such an individual nano-aperture, however, often cannot differentiate between the two distinct spin-states of photons because of the loss of photon information on light-aperture interaction. This creates a 'blind-spot' for the aperture with respect to the helicity of chiral light. Here we report the development of a subwavelength aperture embedded with metasurfaces dubbed a 'meta-aperture', which breaks this spin degeneracy. By exploiting the phase-shaping capabilities of metasurfaces, we are able to create specific meta-apertures in which the pair of circularly polarized light spin-states produces opposite transmission spectra over a broad spectral range. The concept incorporating metasurfaces with nano-apertures provides a venue for exploring new physics on spin-aperture interaction and potentially has a broad range of applications in spin-optoelectronics and chiral sensing.

Filling schemes at submicron scale: development of submicron sized plasmonic colour filters.

The pixel size imposes a fundamental limit on the amount of information that can be displayed or recorded on a sensor. Thus, there is strong motivation to reduce the pixel size down to the nanometre scale. Nanometre colour pixels cannot be fabricated by simply downscaling current pixels due to colour cross talk and diffraction caused by dyes or pigments used as colour filters. Colour filters based on plasmonic effects can overcome these difficulties. Although different plasmonic colour filters have been demonstrated at the micron scale, there have been no attempts so far to reduce the filter size to the submicron scale. Here, we present for the first time a submicron plasmonic colour filter design together with a new challenge - pixel boundary errors at the submicron scale. We present simple but powerful filling schemes to produce submicron colour filters, which are free from pixel boundary errors and colour cross- talk, are polarization independent and angle insensitive, and based on LCD compatible aluminium technology. These results lay the basis for the development of submicron pixels in displays, RGB-spatial light modulators, liquid crystal over silicon, Google glasses and pico-projectors.

X-ray micro-beam characterization of lattice rotations and distortions due to an individual dislocation.

Understanding and controlling the behaviour of dislocations is crucial for a wide range of applications, from nano-electronics and solar cells to structural engineering alloys. Quantitative X-ray diffraction measurements of the strain fields due to individual dislocations, particularly in the bulk, however, have thus far remained elusive. Here we report the first characterization of a single dislocation in a freestanding GaAs/In0.2Ga0.8As/GaAs membrane by synchrotron X-ray micro-beam Laue diffraction. Our experimental X-ray data agrees closely with textbook anisotropic elasticity solutions for dislocations, providing one of few experimental validations of this fundamental theory. On the basis of the experimental uncertainty in our measurements, we predict the X-ray beam size required for three-dimensional measurements of lattice strains and rotations due to individual dislocations in the material bulk. These findings have important implications for the in situ study of dislocation structure formation, self-organization and evolution in the bulk.

Whole-cell phase contrast imaging at the nanoscale using Fresnel coherent diffractive imaging tomography.

X-ray tomography can provide structural information of whole cells in close to their native state. Radiation-induced damage, however, imposes a practical limit to image resolution, and as such, a choice between damage, image contrast, and image resolution must be made. New coherent diffractive imaging techniques, such Fresnel Coherent Diffractive Imaging (FCDI), allows quantitative phase information with exceptional dose efficiency, high contrast, and nano-scale resolution. Here we present three-dimensional quantitative images of a whole eukaryotic cell by FCDI at a spatial resolution below 70 nm with sufficient phase contrast to distinguish major cellular components. From our data, we estimate that the minimum dose required for a similar resolution is close to that predicted by the Rose criterion, considerably below accepted estimates of the maximum dose a frozen-hydrated cell can tolerate. Based on the dose efficiency, contrast, and resolution achieved, we expect this technique will find immediate applications in tomographic cellular characterisation.