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We present a synthetic nanoscale piston that uses chemical energy to perform molecular transport against an applied bias. Such a device comprises a 13 by 5 nm protein cylinder, embedded in a biological membrane enclosing a single-stranded DNA (ssDNA) rod. Hybridization with DNA cargo rigidifies the rod, allowing for transport of a selected DNA molecule across the nanopore. A strand displacement reaction from ssDNA fuel on the other side of the membrane then liberates the DNA cargo back into solution and regenerates the initial configuration. The entropic penalty of ssDNA confinement inside the nanopore drives DNA transport regardless of the applied bias. Multiple automated and reciprocating cycles are observed, in which the DNA piston moves through the 10 nm length of the nanopore. In every cycle, a single DNA molecule is transported across the nanopore against an external bias force, which is the hallmark of biological transporters. ispartof: NANO LETTERS vol:21 issue:1 pages:762-768 ispartof: location:United States status: published

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. ispartof: NANO LETTERS vol:20 issue:5 pages:3819-3827 ispartof: location:United States status: published

Despite the broad success of biological nanopores as powerful instruments for the analysis of proteins and nucleic acids at the single-molecule level, a fast simulation methodology to accurately model their nanofluidic properties is currently unavailable. This limits the rational engineering of nanopore traits and makes the unambiguous interpretation of experimental results challenging. Here, we present a continuum approach that can faithfully reproduce the experimentally measured ionic conductance of the biological nanopore Cytolysin A (ClyA) over a wide range of ionic strengths and bias potentials. Our model consists of the extended Poisson-Nernst-Planck and Navier-Stokes (ePNP-NS) equations and a computationally efficient 2D-axisymmetric representation for the geometry and charge distribution of the nanopore. Importantly, the ePNP-NS equations achieve this accuracy by self-consistently considering the finite size of the ions and the influence of both the ionic strength and the nanoscopic scale of the pore on the local properties of the electrolyte. These comprise the mobility and diffusivity of the ions, and the density, viscosity and relative permittivity of the solvent. Crucially, by applying our methodology to ClyA, a biological nanopore used for single-molecule enzymology studies, we could directly quantify several nanofluidic characteristics difficult to determine experimentally. These include the ion selectivity, the ion concentration distributions, the electrostatic potential landscape, the magnitude of the electro-osmotic flow field, and the internal pressure distribution. Hence, this work provides a means to obtain fundamental new insights into the nanofluidic properties of biological nanopores and paves the way towards their rational engineering. ispartof: NANOSCALE vol:12 issue:32 pages:16775-16795 ispartof: location:England status: published

In recent years, the protein nanopore cytolysin A (ClyA) has become a valuable tool for the detection, characterization and quantification of biomarkers, proteins and nucleic acids at the single-molecule level. Despite this extensive experimental utilization, a comprehensive computational study of ion and water transport through ClyA is currently lacking. Such a study yields a wealth of information on the electrolytic conditions inside the pore and on the scale the electrophoretic forces that drive molecular transport. To this end we have built a computationally efficient continuum model of ClyA which, together with an extended version of Poison-Nernst-Planck-Navier-Stokes (ePNP-NS) equations, faithfully reproduces its ionic conductance over a wide range of salt concentrations. These ePNP-NS equations aim to tackle the shortcomings of the traditional PNP-NS models by self-consistently taking into account the influence of both the ionic strength and the nanoscopic scale of the pore on all relevant electrolyte properties. In this study, we give both a detailed description of our ePNP-NS model and apply it to the ClyA nanopore. This enabled us to gain a deeper insight into the influence of ionic strength and applied voltage on the ionic conductance through ClyA and a plethora of quantities difficult to assess experimentally. The latter includes the cation and anion concentrations inside the pore, the shape of the electrostatic potential landscape and the magnitude of the electro-osmotic flow. Our work shows that continuum models of biological nanopores—if the appropriate corrections are applied—can make both qualitatively and quantitatively meaningful predictions that could be valuable tool to aid in both the design and interpretation of nanopore experiments.

Solid-state nanopores promise a scalable platform for single-molecule DNA analysis. Direct, real-time identification of nucleobases in DNA strands is still limited by the sensitivity and the spatial resolution of established ionic sensing strategies. Here, we study a different but promising strategy based on optical spectroscopy. We use an optically engineered elongated nanopore structure, a plasmonic nanoslit, to locally enable single-molecule surface enhanced Raman spectroscopy (SERS). Combining SERS with nanopore fluidics facilitates both the electrokinetic capture of DNA analytes and their local identification through direct Raman spectroscopic fingerprinting of four nucleobases. By studying the stochastic fluctuation process of DNA analytes that are temporarily adsorbed inside the pores, we have observed asynchronous spectroscopic behavior of different nucleobases, both individual and incorporated in DNA strands. These results provide evidences for the single-molecule sensitivity and the sub-nanometer spatial resolution of plasmonic nanoslit SERS., Direct and real-time identification of nucleobases in DNA strands is still limited by the sensitivity and spatial resolution of the established solid-state nanopore devices. Here, the authors use CMOS compatible, plasmonic nanoslits to locally enable SERS for identifying nucleobases, both individual and incorporated in DNA strands.

In the manufacturing of multi-Vt FinFET transistors, the gate material deposited in the nano-spaces left by the removed dummy gate must be etched back in mask-defined wafer areas. Etch conformality is a necessary condition for the control of under-etch at the boundary between areas defined by masking. We studied the feasibility of TiN etching by APM (ammonia peroxide mixture, also known as SC1) in nano-confined volumes representative of FinFET transistors of the 7 nm node and below, namely nanotrenches with 1-D confinement and nanoholes with 2-D confinement. TiN etching was characterized for rate and conformality using different electron microscopy techniques. Etching in closed nanotrenches was conformal, starting and progressing all along the 2-D seam, with a rate that was 38% higher compared to a planar film. Etching in closed nanoholes proved also to be conformal and faster than planar films, but with a delay to open the 1-D seam that seemed to depend strongly on small variations in the hole diameter. However, holes between the fins at the bottom of the removed dummy gate, are not circular and do present 2-D seams that should lend themselves for an easier start of conformal etching as compared to the circular nanoholes used in this study. Finally, to explain the higher etch rate observed in nano-confined features, concentrations of ions in nanoholes were calculated taking the overlap of electrostatic double layers (EDL) into account. With negatively charged TiN walls, as measured by streaming potential on planar films, ammonium was the dominant ion in nanoholes. As no chemical reaction proposed in the literature for TiN etching matched with this finding, we proposed that the formation of ammine complexes, dissolving the formed Ti oxide, was the rate-determining step.

Room temperature and pressure bonding is shown for wafer-to-wafer (W2W) bonding but never for small chips. Usually, thermo-compression bonding (TCB) is employed for die-to-die (D2D) and die-to-wafer (D2W) bonding for 3D and MEMS application. TCB process is itself limited by tool capability and requires pressure and temperature for bonding which is not only time consuming but can induce coefficient of thermal expansion mismatch and damage to back-end-of-line (BEOL) stacks. To address these issue, we propose a liquid mediated direct bonding approach of inorganic dielectric which can be realized at low temperature and atmospheric pressure using a fast pick and place tool.

Optical antennas have the prospect to redirect light rays into engineered directions at the subwavelength scale. They offer new options for photodetection, color routing, fluorescence emission and sensing applications. Previously, metallic nanoantennas based on localized surface plasmon resonance (LSPR) have commonly been exploited to fulfill this purpose, e.g. the gold Yagi-Uda array and split-ring resonator. However, the intrinsic ohmic losses of metals are large especially in the visible range, hindering further efficiency improvement for practical applications. In addition, the interaction of the metallic nanoantennas with the magnetic component of light is relatively weak, adding to their lack of highly tunable scattering directionality. In this presentation, we will demonstrate our recent experimental progress on all-dielectric nanoantennas made of amorphous silicon with tunable scattering directionality. Our nanoantennas are designed as V-shaped single element and fabricated using electron-beam lithography followed by dry reactive ion etching. It is illustrated that the scattering cross section of the silicon nanoantenna can be considerably higher than that of comparable Au antennas. In addition, the extinction coefficient of amorphous silicon is adequately low in the considered wavelength range, resulting in minimal absorption losses and an enhanced scattering efficiency. More interestingly, compared to Au nanoantennas that exhibit light scattering in a single particular direction, by carefully engineering the geometry of the silicon nano-antennas, their scattering can be effectively tuned into two opposite directions within the visible range (Supporting figure). Over a spectral range of less than 100 nm, the scattering directionality gradually shifts from the leftward to the rightward. More simulation results based on the finite difference time domain (FDTD) methods are available to perfectly match and corroborate our experimental measurement. Initial analysis of the underlying physics for the tunable scattering directionality will also be discussed. Such unique optical properties make the silicon nanoantenna promising candidates for novel low-loss optical devices that can enable unprecedented control over the scattering directionality.

We present distinct asymmetric plasmon-induced noise properties of ionic transport observed through gold coated nanopores. We thoroughly investigated the effects of bias voltage and laser illumination. We show that the potential drop across top-coated silicon nanocavity pores can give rise to a large noise asymmetry (∼2–3 orders of magnitude). Varying the bias voltage has an appreciable effect on the noise density spectra, typically in the Lorentzian components. The laser power is found to strongly affect the ionic noise level as well as the voltage threshold for light-induced noise generation. The asymmetric noise phenomenon is attributed to plasmon-induced interfacial reactions which promote light-induced charge fluctuation in the ion flow and allow voltage modulation of photo-induced carriers surmounting over such Schottky junctions. We further compare the ionic noise performances of gold nanocavities containing different material stacks, among which thermal oxide passivation of the silicon successfully mitigates the light-induced noise and is also fully CMOS-compatible. The understanding of the described noise characteristics will help to foster multiple applications using related structures including plasmonic-based sensing or plasmon-induced catalysis such as water splitting or solar energy conversion devices.