Engraving of stainless-steel wires to improve optical quality of closed-loop wire-guided flow jet systems for optical and X-ray spectroscopy.

This paper describes performance enhancement developments to a closed-loop pump-driven wire-guided flow jet (WGJ) for ultrafast X-ray spectroscopy of liquid samples. Achievements include dramatically improved sample surface quality and reduced equipment footprint from 7 × 20 cm2 to 6 × 6 cm2, cost, and manufacturing time. Qualitative and quantitative measurements show that micro-scale wire surface modification yields significant improvements to the topography of the sample liquid surface. By manipulating their wettability, it is possible to better control the liquid sheet thickness and to obtain a smooth liquid sample surface, as demonstrated in this work.

Imaging Cu2O nanocube hollowing in solution by quantitative in situ X-ray ptychography.

Understanding morphological changes of nanoparticles in solution is essential to tailor the functionality of devices used in energy generation and storage. However, we lack experimental methods that can visualize these processes in solution, or in electrolyte, and provide three-dimensional information. Here, we show how X-ray ptychography enables in situ nano-imaging of the formation and hollowing of nanoparticles in solution at 155 °C. We simultaneously image the growth of about 100 nanocubes with a spatial resolution of 66 nm. The quantitative phase images give access to the third dimension, allowing to additionally study particle thickness. We reveal that the substrate hinders their out-of-plane growth, thus the nanocubes are in fact nanocuboids. Moreover, we observe that the reduction of Cu2O to Cu triggers the hollowing of the nanocuboids. We critically assess the interaction of X-rays with the liquid sample. Our method enables detailed in-solution imaging for a wide range of reaction conditions.

Pillar-structured 3D inlets fabricated by dose-modulated e-beam lithography and nanoimprinting for DNA analysis in passive, clogging-free, nanofluidic devices.

We present the fabrication of three-dimensional inlets with gradually decreasing widths and depths and with nanopillars on the slope, all defined in just one lithography step. In addition, as an application, we show how these micro- and nanostructures can be used for micro- and nanofluidics and lab-on-a-chip devices to facilitate the flow and analyze single molecules of DNA. For the fabrication of 3D inlets in a single layer process, dose-modulated electron beam lithography was used, producing depths between 750 nm and 50 nm along a 30 µm long inlet, which is additionally structured with nanometer-scale pillars randomly distributed on top, as a result of incomplete exposure and underdevelopment of the resist. The fabrication conditions affect the slope of the inlet, the nanopillar density and coverage. The key parameters are the dose used for the electron beam exposure and the development conditions, like the developer's dilution, stirring and development time. The 3D inlets with nanostructured pillars were integrated into fluidic devices, acting as a transition between micro and nanofluidic structures for pre-stretching and unfolding DNA molecules, avoiding the intrusion of folded molecules and clogging the analysis channel. After patterning these structures in silicon, they can be replicated in polymer by UV nanoimprinting. We show here how the inlets with pillars slow down the molecules before they enter the nanochannels, resulting in a 3-fold decrease in speed, which would translate to an improvement in the resolution for DNA optical mapping.

Optofluidic systems enabling detection in real samples: A review.

Optofluidics, understood as the synergistic combination between microfluidics and photonics, has been at the forefront of the scientific research due to its outmatching properties: on the one hand, microfluidics allows the handling of minute amounts of liquid samples at the microscale. On the other hand, photonics has proved to outmatch other detection methods (e.g. electrochemistry) in terms of sensitivity and selectivity. From the initial single analyte or spiked samples, currently the technology is mature enough for selective detection of a variety of analytes in raw, complex liquid samples. This will pave the way for the applicability of optofluidic devices for applications in the field or at the point of care. Here, we will revisit the current state of the art of optofluidic and photonic lab-on-a-chip systems for the analysis of real and biologically relevant samples: body fluids and water.

Development, Processing and Applications of a UV-Curable Polymer with Surface Active Thiol Groups.

We present here a novel resist formulation with active thiol groups at the surface. The material is UV curable, and can be patterned at the micro- and nanoscale by UV nanoimprint lithography. The resist formulation development, its processing, patterning and surface characterization are presented here. In addition, a possible application, including its use to modify the electrical properties of graphene devices is shown. The cured material is highly transparent, intrinsically hydrophilic and can be made more hydrophilic following a UV-ozone or an O2 plasma activation. We evaluated the hydrophilicity of the polymer for different polymer formulations and curing conditions. In addition, a protocol for patterning of the polymer in the micro and nanoscale by nanoimprinting is given and preliminary etching rates together with the polymer selectivity are measured. The main characteristic and unique advantage of the polymer is that it has thiol functional groups at the surface and in the bulk after curing. These groups allow for direct surface modifications with thiol-based chemistry e.g., thiol-ene reactions. We prove the presence of the thiol groups by Raman spectroscopy and perform a thiol-ene reaction to show the potential of the easy "click chemistry". This opens the way for very straightforward surface chemistry on nanoimprinted polymer samples. Furthermore, we show how the polymer improves the electrical properties of a graphene field effect transistor, allowing for optimal performance at ambient conditions.

High-resolution analysis of Merkel Cell Polyomavirus in Merkel Cell Carcinoma reveals distinct integration patterns and suggests NHEJ and MMBIR as underlying mechanisms.

Merkel Cell Polyomavirus (MCPyV) is the etiological agent of the majority of Merkel Cell Carcinomas (MCC). MCPyV positive MCCs harbor integrated, defective viral genomes that constitutively express viral oncogenes. Which molecular mechanisms promote viral integration, if distinct integration patterns exist, and if integration occurs preferentially at loci with specific chromatin states is unknown. We here combined short and long-read (nanopore) next-generation sequencing and present the first high-resolution analysis of integration site structure in MCC cell lines as well as primary tumor material. We find two main types of integration site structure: Linear patterns with chromosomal breakpoints that map closely together, and complex integration loci that exhibit local amplification of genomic sequences flanking the viral DNA. Sequence analysis suggests that linear patterns are produced during viral replication by integration of defective/linear genomes into host DNA double strand breaks via non-homologous end joining, NHEJ. In contrast, our data strongly suggest that complex integration patterns are mediated by microhomology-mediated break-induced replication, MMBIR. Furthermore, we show by ChIP-Seq and RNA-Seq analysis that MCPyV preferably integrates in open chromatin and provide evidence that viral oncogene expression is driven by the viral promoter region, rather than transcription from juxtaposed host promoters. Taken together, our data explain the characteristics of MCPyV integration and may also provide a model for integration of other oncogenic DNA viruses such as papillomaviruses.

Sculpturing wafer-scale nanofluidic devices for DNA single molecule analysis.

We present micro- and nanofluidic devices with 3D structures and nanochannels with multiple depths for the analysis of single molecules of DNA. Interfacing the nanochannels with graded and 3D inlets allows the improvement of the flow and controls not only the translocation speed of the DNA but also its conformation inside the nanochannels. The complex, multilevel, multiscale fluidic circuits are patterned in a simple, two-minute imprinting step. The stamp, the key of the technology, is directly milled by focused ion beam, which allows patterning nanochannels with different cross sections and depths, together with 3D transient inlets, all at once. Having such a variety of structures integrated in the same sample allows studying, optimizing and directly comparing their effect on the DNA flow. Here, DNA translocation is studied in long (160 µm) and short (5-40 µm) nanochannels. We study the homogeneity of the stretched molecules in long, meander nanochannels made with this technology. In addition, we analyze the effect of the different types of inlet structures interfacing short nanochannels. We observe pre-stretching and an optimal flow, and no hairpin formation, when the inlets have gradually decreasing widths and depths. In contrast, when the nanochannels are faced with an abrupt transition, we observe clogging and hairpin formation. In addition, 3D inlets strongly decrease the DNA molecules' speed before they enter the nanochannels, and help capturing more DNA molecules. The robustness and versatility of this technology and DNA testing results evidence the potential of imprinted devices in biomedical applications as low cost, disposable lab-on-a-chip devices.

A nanochannel through a plasmonic antenna gap: an integrated device for single particle counting.

Plasmonic nanoantennas are ideal for single molecule detection since they nano-focus the light beyond diffraction and enhance the optical fields by several orders of magnitude. But delivering the molecules into these nanometric hot-spots is a real challenge. Here, we present a dynamic sensor, with label-free real-time detection capabilities, which can detect and count molecules and particles one by one in their native environment independently of their concentration. To this end, we have integrated a 35 nm gap plasmonic bowtie antenna with a 30 nm × 30 nm nanochannel. The channel runs through the antenna gap, and delivers the analyte directly into the hot spot. We show how the antenna probes into zeptoliter volumes inside the nanochannel by observing the dark field resonance shift during the filling process of a non-fluorescent liquid. Moreover, we detect and count single quantum dots, one by one, at ultra-high concentrations of up to 25 mg mL-1. The nano-focusing of light, reduces the observation volume in five orders of magnitude compared to the diffraction limited spot, beating the diffraction limit. These results prove the unique sensitivity of the device and in the future can be extended to detection of a variety of molecules for biomedical applications.

Culturing and patch clamping of Jurkat T cells and neurons on Al2O3 coated nanowire arrays of altered morphology.

Nanowire substrates play an increasingly important role for cell cultures as an approach for hybrid bio-semiconductor junctions. We investigate Jurkat T cells and neurons from mice cultured on Al2O3 coated ordered and randomly distributed nanowires. Cell viability was examined by life/membrane staining reporting comparable viability on planar and nanowire substrates. Imaging the hybrid interface reveals a wrapping of the cell membrane around the very nanowire tip. Patch clamp recordings show similar electrophysiological responses on each type of nanowires compared to planar control substrates. We demonstrate that the morphological characteristic of the nanowire substrate plays a subordinate role which opens up the arena for a large range of nanowire substrates in a functionalized application such as stimulation or sensing.

Correction: Culturing and patch clamping of Jurkat T cells and neurons on Al2O3 coated nanowire arrays of altered morphology.

[This corrects the article DOI: 10.1039/C8RA05320K.].

Plasmonic V-groove waveguides with Bragg grating filters via nanoimprint lithography.

We demonstrate spectral filtering with state-of-the-art Bragg gratings in plasmonic V-groove waveguides fabricated by wafer scale processing based on nanoimprint lithography. Transmission spectra of the devices having 16 grating periods exhibit spectral rejection of the channel plasmon polaritons with 8.2 dB extinction ratio and -3 dB bandwidth of Δλ = 39.9 nm near telecommunications wavelengths. Near-field scanning optical microscopy measurements verify spectral reflection from the grating structures, and the oscillations of propagating modes along grating-less V-grooves correspond well with effective refractive index values calculated by finite element simulations in COMSOL. The results represent advancement towards the implementation of plasmonic V-grooves with greater functional complexity and mass-production compatibility.

Channel plasmon polariton propagation in nanoimprinted V-groove waveguides.

We present the results of optical characterization of metal V-groove waveguides using scanning near-field microscopy, showing broadband transmission with subwavelength confinement and propagation lengths exceeding 100 microm. An updated fabrication method using a combination of UV and nanoimprint lithography is presented. The developed approach is mass-production compatible, adaptable to different designs, and offers wafer-scale parallel fabrication of plasmonic components based on profiled metal surfaces.