Design Principles of DNA-Barcodes for Nanopore-FET Readout, Based on Molecular Dynamics and TCAD Simulations.

Nanopore field-effect transistor (NP-FET) devices hold great promise as sensitive single-molecule sensors, which provide CMOS-based on-chip readout and are also highly amenable to parallelization. A plethora of applications will therefore benefit from NP-FET technology, such as large-scale molecular analysis (e.g., proteomics). Due to its potential for parallelization, the NP-FET looks particularly well-suited for the high-throughput readout of DNA-based barcodes. However, to date, no study exists that unravels the bit-rate capabilities of NP-FET devices. In this paper, we design DNA-based barcodes by labeling a piece of double-stranded DNA with dumbbell-like DNA structures. We explore the impact of both the size of the dumbbells and their spacing on achievable bit-rates. The conformational fluctuations of this DNA-origami, as observed by molecular dynamics (MD) simulation, are accounted for when selecting label sizes. An experimentally informed 3D continuum nanofluidic-nanoelectronic device model subsequently predicts both the ionic current and FET signals. We present a barcode design for a conceptually generic NP-FET, with a 14 nm diameter pore, operating in conditions corresponding to experiments. By adjusting the spacing between the labels to half the length of the pore, we show that a bit-rate of 78 kbit·s-1 is achievable. This lies well beyond the state-of-the-art of ≈40 kbit·s-1, with significant headroom for further optimizations. We also highlight the advantages of NP-FET readout based on the larger signal size and sinusoidal signal shape.

Inverse design assisted coherent optical lattices.

We explore the use of inverse design methods for the generation of periodic optical patterns in photonic integrated circuits. A carefully selected objective function based on the integer lattice method, which is an algebraic technique for optical lattice generation, is shown to be key for successful device design. Furthermore, we present a polychromatic pattern generating device that switches between optical lattices with different symmetry and periodicity depending on the operating wavelength. Important links are drawn between optical coherent lattices and optical potentials, pointing towards practical applications in the fields of quantum simulations and computing, optical trapping, and bio-sensing.

Performance and limitation estimation of a three-tap gated imaging sensor in wide field time-gated fluorescence lifetime imaging systems.

In this paper, a computational performance analysis is presented of a wide-field time-gated fluorescence lifetime imaging microscope (FLIM) using practically realizable properties of the laser, sample, and a three-tap time-gated CMOS image sensor. The impact of these component-level properties on the accuracy and the precision of the measurement results are estimated and discussed based on Monte Carlo simulations. The correlation between the detector speed and the accuracy of the extracted fluorescence lifetime is studied, and the minimum required incident photoelectron number of each pixel is estimated for different detector speeds and different fluorescence lifetime measurements. In addition, the detection limits due to the dark current and the parasitic light sensitivity of the detector are also investigated. This work gives an overview of the required fluorescence emission condition as well as the required detector properties for a three-tap time-gated image sensor to achieve good FLIM data in biological applications.

Electro-Osmotic Vortices Promote the Capture of Folded Proteins by PlyAB Nanopores.

Biological nanopores are emerging as powerful tools for single-molecule analysis and sequencing. Here, we engineered the two-component pleurotolysin (PlyAB) toxin to assemble into 7.2 × 10.5 nm cylindrical nanopores with a low level of electrical noise in lipid bilayers, and we addressed the nanofluidic properties of the nanopore by continuum simulations. Surprisingly, proteins such as human albumin (66.5 kDa) and human transferrin (76-81 kDa) did not enter the nanopore. We found that the precise engineering of the inner surface charge of the PlyAB induced electro-osmotic vortices that allowed the electrophoretic capture of the proteins. Once inside the nanopore, two human plasma proteins could be distinguished by the characteristics of their current blockades. This fundamental understanding of the nanofluidic properties of nanopores provides a practical method to promote the capture and analysis of folded proteins by nanopores.

Revival and Expansion of the Theory of Coherent Lattices.

An effective way to design structured coherent wave interference patterns that builds on the theory of coherent lattices, is presented. The technique combines prime number factorization in the complex plane with moiré theory to provide a robust way to design structured patterns with variable spacing of intensity maxima. In addition, the proposed theoretical framework facilitates an elegant computation of previously unexplored high-order superlattices both for the periodic and quasiperiodic case. A number of beam configurations highlighting prime examples of patterns for lattices with three-, four-, and fivefold symmetry are verified in a multibeam interference experiment.

Two-Photon Microscopy with a Double-Wavelength Metasurface Objective Lens.

Two-photon microscopy is a key imaging technique in life sciences due to its superior deep-tissue imaging capabilities. Light-weight and compact two-photon microscopes are of great interest because of their applications for in vivo deep brain imaging. Recently, dielectric metasurfaces have enabled a new category of small and lightweight optical elements, including objective lenses. Here we experimentally demonstrate two-photon microscopy using a double-wavelength metasurface lens. It is specifically designed to focus 820 and 605 nm light, corresponding to the excitation and emission wavelengths of the measured fluorophors, to the same focal distance. The captured two-photon images are qualitatively comparable to the ones taken by a conventional objective lens. Our metasurface lens can enable ultracompact two-photon microscopes with similar performance compared to current systems that are usually based on graded-index-lenses. In addition, further development of tunable metasurface lenses will enable fast axial scanning for volumetric imaging.

Supercritical Angle Fluorescence Characterization Using Spatially Resolved Fourier Plane Spectroscopy.

Most fluorescent immunoassays require a wash step prior to read-out due to the otherwise overwhelming signal of the large number of unbound (bulk) fluorescent molecules that dominate over the signal from the molecules of interest, usually bound to a substrate. Supercritical angle fluorescence (SAF) sensing is one of the most promising alternatives to total internal reflection fluorescence for fluorescence imaging and sensing. However, detailed experimental investigation of the influence of collection angle on the SAF surface sensitivity, i.e., signal to background ratio (SBR), is still lacking. In this Letter, we present a novel technique that allows to discriminate the emission patterns of free and bound fluorophores simultaneously by collecting both angular and spectral information. The spectrum was probed at multiple positions in the back focal plane using a multimode fiber connected to a spectrometer and the difference in intensity between two fluorophores was used to calculate the SBR. Our study clearly reveals that increasing the angle of SAF collection enhances the surface sensitivity, albeit at the cost of decreased signal intensity. Furthermore, our findings are fully supported by full-field 3D simulations.

Electrically Driven Unidirectional Optical Nanoantennas.

Directional antennas revolutionized modern day telecommunication by enabling precise beaming of radio and microwave signals with minimal loss of energy. Similarly, directional optical nanoantennas are expected to pave the way toward on-chip wireless communication and information processing. Currently, on-chip integration of such antennas is hampered by their multielement design or the requirement of complicated excitation schemes. Here, we experimentally demonstrate electrical driving of in-plane tunneling nanoantennas to achieve broadband unidirectional emission of light. Far-field interference, as a result of the spectral overlap between the dipolar emission of the tunnel junction and the fundamental quadrupole-like resonance of the nanoantenna, gives rise to a directional radiation pattern. By tuning this overlap using the applied voltage, we record directivities as high as 5 dB. In addition to electrical tunability, we also demonstrate passive tunability of the directivity using the antenna geometry. These fully configurable electrically driven nanoantennas provide a simple way to direct optical energy on-chip using an extremely small device footprint.

Near-Field Mapping of Optical Fabry-Perot Modes in All-Dielectric Nanoantennas.

Subwavelength optical resonators and scatterers are dramatically expanding the toolset of the optical sciences and photonics engineering. By offering the opportunity to control and shape light waves in nanoscale volumes, recent developments using high-refractive-index dielectric scatterers gave rise to efficient flat-optical components such as lenses, polarizers, phase plates, color routers, and nonlinear elements with a subwavelength thickness. In this work, we take a deeper look into the unique interaction of light with rod-shaped amorphous silicon scatterers by tapping into their resonant modes with a localized subwavelength light source-an aperture scanning near-field probe. Our experimental configuration essentially constitutes a dielectric antenna that is locally driven by the aperture probe. We show how leaky transverse electric and magnetic modes can selectively be excited and form specific near-field distribution depending on wavelength and antenna dimensions. The probe's transmittance is furthermore enhanced upon coupling to the Fabry-Perot cavity modes, revealing all-dielectric nanorods as efficient transmitter antennas for the radiation of subwavelength emitters, in addition to constituting an elementary building block for all-dielectric metasurfaces and flat optics.

All-Dielectric Antenna Wavelength Router with Bidirectional Scattering of Visible Light.

An optical antenna forms the subwavelength bridge between free space optical radiation and localized electromagnetic energy. Its localized electromagnetic modes strongly depend on its geometry and material composition. Here, we present the design and experimental realization of a novel V-shaped all-dielectric antenna based on high-index amorphous silicon with a strong magnetic dipole resonance in the visible range. As a result, it exhibits extraordinary bidirectional scattering into diametrically opposite directions. The scattering direction is effectively controlled by the incident wavelength, rendering the antenna a passive bidirectional wavelength router. A detailed multipole decomposition analysis reveals that the excitation and abrupt phase change of an out-of-plane polarized magnetic dipole and an in-plane electric quadrupole are essential for the directivity switching. Previously, noble metals have been extensively exploited for plasmonic directional nanoantenna design. However, these inevitably suffer from high intrinsic ohmic losses and a relatively weak magnetic response to the incident light. Compared to a similar gold plasmonic nanoantenna design, we show that the silicon-based antennas demonstrate stronger magnetic scattering with minimal absorption losses. Our results indicate that all-dielectric antennas will open exciting possibilities for efficient manipulation of light-matter interactions.

Photoresistance switching of plasmonic nanopores.

Fast and reversible modulation of ion flow through nanosized apertures is important for many nanofluidic applications, including sensing and separation systems. Here, we present the first demonstration of a reversible plasmon-controlled nanofluidic valve. We show that plasmonic nanopores (solid-state nanopores integrated with metal nanocavities) can be used as a fluidic switch upon optical excitation. We systematically investigate the effects of laser illumination of single plasmonic nanopores and experimentally demonstrate photoresistance switching where fluidic transport and ion flow are switched on or off. This is manifested as a large (∼ 1-2 orders of magnitude) increase in the ionic nanopore resistance and an accompanying current rectification upon illumination at high laser powers (tens of milliwatts). At lower laser powers, the resistance decreases monotonically with increasing power, followed by an abrupt transition to high resistances at a certain threshold power. A similar rapid transition, although at a lower threshold power, is observed when the power is instead swept from high to low power. This hysteretic behavior is found to be dependent on the rate of the power sweep. The photoresistance switching effect is attributed to plasmon-induced formation and growth of nanobubbles that reversibly block the ionic current through the nanopore from one side of the membrane. This explanation is corroborated by finite-element simulations of a nanobubble in the nanopore that show the switching and the rectification.

Bright and dark plasmon resonances of nanoplasmonic antennas evanescently coupled with a silicon nitride waveguide.

In this work we investigate numerically and experimentally the resonance wavelength tuning of different nanoplasmonic antennas excited through the evanescent field of a single mode silicon nitride waveguide and study their interaction with this excitation field. Experimental interaction efficiencies up to 19% are reported and it is shown that the waveguide geometry can be tuned in order to optimize this interaction. Apart from the excitation of bright plasmon modes, an efficient coupling between the evanescent field and a dark plasmonic resonance is experimentally demonstrated and theoretically explained as a result of the propagation induced phase delay.

Mode parity-controlled Fano- and Lorentz-like line shapes arising in plasmonic nanorods.

We present the experimental observation of spectral lines of distinctly different shapes in the optical extinction cross-section of metallic nanorod antennas under near-normal plane wave illumination. Surface plasmon resonances of odd mode parity present Fano interference in the scattering cross-section, resulting in asymmetric spectral lines. Contrarily, modes with even parity appear as symmetric Lorentzian lines. Finite element simulations are used to verify the experimental results. The emergence of either constructive or destructive mode interference is explained with a semianalytical 1D line current model. This simple model directly explains the mode-parity dependence of the Fano-like interference. Plasmonic nanorods are widely used as half-wave optical dipole antennas. Our findings offer a perspective and theoretical framework for operating these antennas at higher-order modes.

Lateral magnetic near-field imaging of plasmonic nanoantennas with increasing complexity.

The design of many promising, newly emerging classes of photonic metamaterials and subwavelength confinement structures requires detailed knowledge and understanding of the electromagnetic near-field interactions between their building blocks. While the electric field distributions and, respectively, the electric interactions of different nanostructures can be routinely measured, for example, by scattering near-field microscopy, only recently experimental methods for imaging the magnetic field distributions became available. In this paper, we provide direct experimental maps of the lateral magnetic near-field distributions of variously shaped plasmonic nanoantennas by using hollow-pyramid aperture scanning near-field optical microscopy (SNOM). We study both simple plasmonic nanoresonators, such as bars, disks, rings and more complex antennas. For the studied structures, the magnetic near-field distributions of the complex resonators have been found to be a superposition of the magnetic near-fields of the individual constituting elements. These experimental results, explained and validated by numerical simulations, open new possibilities for engineering and characterization of complex plasmonic antennas with increased functionality.

Harnessing plasmon-induced ionic noise in metallic nanopores.

The ionic properties of a metal-coated silicon nanopore were examined in a nanofluidic system. We observed a strong increase of the ionic noise upon laser light illumination. The effect appeared to be strongly mediated by the resonant excitation of surface plasmons in the nanopore as was demonstrated by means of ionic mapping of the plasmonic electromagnetic field. Evidence from both simulations and experiments ruled out plasmonic heating as the main source of the noise, and point toward photoinduced electrochemical catalysis at the semiconductor-electrolyte interface. This ionic mapping technique described is opening up new opportunities on noninvasive applications ranging from biosensing to energy conversion.

Unidirectional side scattering of light by a single-element nanoantenna.

Unidirectional side scattering of light by a single-element plasmonic nanoantenna is demonstrated using full-field simulations and back focal plane measurements. We show that the phase and amplitude matching that occurs at the Fano interference between two localized surface plasmon modes in a V-shaped nanoparticle lies at the origin of this effect. A detailed analysis of the V-antenna modeled as a system of two coherent point-dipole sources elucidates the mechanisms that give rise to a tunable experimental directivity as large as 15 dB. The understanding of Fano-based directional scattering opens a way to develop new directional optical antennas for subwavelength color routing and self-referenced directional sensing. In addition, the directionality of these nanoantennas can increase the detection efficiency of fluorescence and surface enhanced Raman scattering.

On-chip flow cytometer using integrated photonics for the detection of human leukocytes.

Differentiation between leukocyte subtypes like monocytes and lymphocytes is essential for cell therapy and research applications. To guarantee the cost-effective delivery of functional cells in cell therapies, billions of cells must be processed in a limited time. Yet, the sorting rates of commercial cell sorters are not high enough to reach the required yield. Process parallelization by using multiple instruments increases variability and production cost. A compact solution with higher throughput can be provided by multichannel flow cytometers combining fluidics and optics on-chip. In this work, we present a micro-flow cytometer with monolithically integrated photonics and fluidics and demonstrate that both the illumination of cells, as well as the collection of scattered light, can be realized using photonic integrated circuits. Our device is the first with sufficient resolution for the discrimination of lymphocytes and monocytes. Innovations in microfabrication have enabled complete integration of miniaturized photonic components and fluidics in a CMOS-compatible wafer stack. In combination with external optics, the device is ready for the collection of fluorescence using the on-chip excitation.

Boosting the figure-of-merit of LSPR-based refractive index sensing by phase-sensitive measurements.

Localized surface plasmon resonances possess very interesting properties for a wide variety of sensing applications. In many of the existing applications, only the intensity of the reflected or transmitted signals is taken into account, while the phase information is ignored. At the center frequency of a (localized) surface plasmon resonance, the electron cloud makes the transition between in- and out-of-phase oscillation with respect to the incident wave. Here we show that this information can experimentally be extracted by performing phase-sensitive measurements, which result in linewidths that are almost 1 order of magnitude smaller than those for intensity based measurements. As this phase change is an intrinsic property of a plasmon resonance, this opens up many possibilities for boosting the figure-of-merit (FOM) of refractive index sensing by taking into account the phase of the plasmon resonance. We experimentally investigated this for two model systems: randomly distributed gold nanodisks and gold nanorings on top of a continuous gold layer and a dielectric spacer and observed FOM values up to 8.3 and 16.5 for the respective nanoparticles.

Plasmon transmutation: inducing new modes in nanoclusters by adding dielectric nanoparticles.

Planar clusters of coupled plasmonic nanoparticles support nanoscale electromagnetic "hot spots" and coherent effects, such as Fano resonances, with unique near and far field signatures, currently of prime interest for sensing applications. Here we show that plasmonic cluster properties can be substantially modified by the addition of individual, discrete dielectric nanoparticles at specific locations on the cluster, introducing new plasmon modes, or transmuting existing plasmon modes to new ones, in the resulting metallodielectric nanocomplex. Depositing a single carbon nanoparticle in the junction between a pair of adjacent nanodisks induces a metal-dielectric-metal quadrupolar plasmon mode. In a ten-membered cluster, placement of several carbon nanoparticles in junctions between multiple adjacent nanoparticles introduces a collective magnetic plasmon mode into the Fano dip, giving rise to an additional subradiant mode in the metallodielectric nanocluster response. These examples illustrate that adding dielectric nanoparticles to metallic nanoclusters expands the number and types of plasmon modes supported by these new mixed-media nanoscale assemblies.

Enhanced optical trapping and arrangement of nano-objects in a plasmonic nanocavity.

Gentle manipulation of micrometer-sized dielectric objects with optical forces has found many applications in both life and physical sciences. To further extend optical trapping toward the true nanometer scale, we present an original approach combining self-induced back action (SIBA) trapping with the latest advances in nanoscale plasmon engineering. The designed resonant trap, formed by a rectangular plasmonic nanopore, is successfully tested on 22 nm polystyrene beads, showing both single- and double-bead trapping events. The mechanism responsible for the higher stability of the double-bead trapping is discussed, in light of the statistical analysis of the experimental data and numerical calculations. Furthermore, we propose a figure of merit that we use to quantify the achieved trapping efficiency and compare it to prior optical nanotweezers. Our approach may open new routes toward ultra-accurate immobilization and arrangement of nanoscale objects, such as biomolecules.