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1.
  • Janssen, Xander J. A., et al. (författare)
  • Rapid manufacturing of low-noise membranes for nanopore sensors by trans-chip illumination lithography
  • 2012
  • Ingår i: Nanotechnology. - IOP Publishing: Hybrid Open Access. - 0957-4484. ; 23:47
  • Tidskriftsartikel (refereegranskat)abstract
    • In recent years, the concept of nanopore sensing has matured from a proof-of-principle method to a widespread, versatile technique for the study of biomolecular properties and interactions. While traditional nanopore devices based on a nanopore in a single layer membrane supported on a silicon chip can be rapidly fabricated using standard microfabrication methods, chips with additional insulating layers beyond the membrane region can provide significantly lower noise levels, but at the expense of requiring more costly and time-consuming fabrication steps. Here we present a novel fabrication protocol that overcomes this issue by enabling rapid and reproducible manufacturing of low-noise membranes for nanopore experiments. The fabrication protocol, termed trans-chip illumination lithography, is based on illuminating a membrane-containing wafer from its backside such that a photoresist (applied on the wafers top side) is exposed exclusively in the membrane regions. Trans-chip illumination lithography permits the local modification of membrane regions and hence the fabrication of nanopore chips containing locally patterned insulating layers. This is achieved while maintaining a well-defined area containing a single thin membrane for nanopore drilling. The trans-chip illumination lithography method achieves this without relying on separate masks, thereby eliminating time-consuming alignment steps as well as the need for a mask aligner. Using the presented approach, we demonstrate rapid and reproducible fabrication of nanopore chips that contain small (12 mu m x 12 mu m) free-standing silicon nitride membranes surrounded by insulating layers. The electrical noise characteristics of these nanopore chips are shown to be superior to those of simpler designs without insulating layers and comparable in quality to more complex designs that are more challenging to fabricate.
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2.
  • Belkin, Maxim, et al. (författare)
  • Plasmonic Nanopores for Trapping, Controlling Displacement, and Sequencing of DNA
  • 2015
  • Ingår i: ACS Nano. - AMER CHEMICAL SOC. - 1936-0851. ; 9:11, s. 10598-10611
  • Tidskriftsartikel (refereegranskat)abstract
    • With the aim of developing a DNA sequencing methodology, we theoretically examine the feasibility of using nanoplasmonics to control the translocation of a DNA molecule through a solid-state nanopore and to read off sequence information using surface-enhanced Raman spectroscopy. Using molecular dynamics simulations, we show that high-intensity optical hot spots produced by a metallic nanostructure can arrest DNA translocation through a solid-state nanopore, thus providing a physical knob for controlling the DNA speed. Switching the plasmonic field on and off can displace the DNA molecule in discrete steps, sequentially exposing neighboring fragments of a DNA molecule to the pore as well as to the plasmonic hot spot. Surface-enhanced Raman scattering from the exposed DNA fragments contains information about their nucleotide composition, possibly allowing the identification of the nucleotide sequence of a DNA molecule transported through the hot spot. The principles of plasmonic nanopore sequencing can be extended to detection of DNA modifications and RNA characterization.
3.
  • Jonsson, Magnus P., et al. (författare)
  • Plasmonic Nanopore for Electrical Profiling of Optical Intensity Landscapes
  • 2013
  • Ingår i: Nano letters (Print). - American Chemical Society. - 1530-6984. ; 13:3, s. 1029-1033
  • Tidskriftsartikel (refereegranskat)abstract
    • We present a novel method for sensitive mapping of optical intensity distributions at subdiffraction-limited resolution. This is achieved with a novel device, a plasmonic nanopore, which combines a plasmonic bowtie nanoantenna with a 10 nm-in-diameter solid-state nanopore. Variations in the local optical intensity modulate the plasmonic heating, which we measure electrically through changes in the ionic conductance of the nanopore. We demonstrate the method by profiling the focal volume of a 10 mW laser beam that is tightly focused by a high-numerical-aperture microscope objective. The results show a complex three-dimensional intensity distribution that closely matches predictions obtained by theoretical calculations of the optical system. In addition to laser profiling, the ionic conductance of a nanopore is also shown to provide quantitative estimates of the temperature in the proximity of single plasmonic nanostructures.
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4.
  • Li, Yi, et al. (författare)
  • Photoresistance Switching of Plasmonic Nanopores
  • 2015
  • Ingår i: Nano letters (Print). - American Chemical Society. - 1530-6984. ; 15:1, s. 776-782
  • Tidskriftsartikel (refereegranskat)abstract
    • 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 (similar to 12 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.
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5.
  • McGinn, Steven, et al. (författare)
  • New technologies for DNA analysis : a review of the READNA Project
  • 2016
  • Ingår i: New Biotechnology. - 1871-6784 .- 1876-4347. ; 33:3, s. 311-330
  • Forskningsöversikt (övrigt vetenskapligt)abstract
    • The REvolutionary Approaches and Devices for Nucleic Acid analysis (READNA) project received funding from the European Commission for 4 1/2 years. The objectives of the project revolved around technological developments in nucleic acid analysis. The project partners have discovered, created and developed a huge body of insights into nucleic acid analysis, ranging from improvements and implementation of current technologies to the most promising sequencing technologies that constitute a 3rd and 4th generation of sequencing methods with nanopores and in situ sequencing, respectively.
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6.
  • McGinn, Steven, et al. (författare)
  • New Technologies for DNA analysis-A review of the READNA Project.
  • 2015
  • Ingår i: New Biotechnology. - Elsevier. - 1876-4347.
  • Forskningsöversikt (refereegranskat)abstract
    • The REvolutionary Approaches and Devices for Nucleic Acid analysis (READNA) project received funding from the European Commission for 4 1/2 years. The objectives of the project revolved around technological developments in nucleic acid analysis. The project partners have discovered, created and developed a huge body of insights into nucleic acid analysis, ranging from improvements and implementation of current technologies to the most promising sequencing technologies that constitute a 3(rd) and 4(th) generation of sequencing methods with nanopores and in situ sequencing, respectively.
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7.
  • Nicoli, Francesca, et al. (författare)
  • DNA Translocations through Solid-State Plasmonic Nanopores
  • 2014
  • Ingår i: Nano letters (Print). - American Chemical Society. - 1530-6984. ; 14:12, s. 6917-6925
  • Tidskriftsartikel (refereegranskat)abstract
    • Nanopores enable label-free detection and analysis of single biomolecules. Here, we investigate DNA translocations through a novel type of plasmonic nanopore based on a gold bowtie nanoantenna with a solid-state nanopore at the plasmonic hot spot. Plasmonic excitation of the nanopore is found to influence both the sensor signal (nanopore ionic conductance blockade during DNA translocation) and the process that captures DNA into the nanopore, without affecting the duration time of the translocations. Most striking is a strong plasmon-induced enhancement of the rate of DNA translocation events in lithium chloride (LiCl, already 10-fold enhancement at a few mW of laser power). This provides a means to utilize the excellent spatiotemporal resolution of DNA interrogations with nanopores in LiCl buffers, which is known to suffer from low event rates. We propose a mechanism based on plasmon-induced local heating and thermophoresis as explanation of our observations.
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8.
  • Plesa, Calin, et al. (författare)
  • Direct observation of DNA knots using a solid-state nanopore
  • 2016
  • Ingår i: Nature Nanotechnology. - NATURE PUBLISHING GROUP. - 1748-3387. ; 11:12, s. 1093-1097
  • Tidskriftsartikel (refereegranskat)abstract
    • Long DNA molecules can self-entangle into knots. Experimental techniques for observing such DNA knots (primarily gel electrophoresis) are limited to bulk methods and circular molecules below 10 kilobase pairs in length. Here, we show that solid-state nanopores can be used to directly observe individual knots in both linear and circular single DNA molecules of arbitrary length. The DNA knots are observed as short spikes in the nanopore current traces of the traversing DNA molecules and their detection is dependent on a sufficiently high measurement resolution, which can be achieved using high-concentration LiCI buffers. We study the percentage of molecules with knots for DNA molecules of up to 166 kilobase pairs in length and find that the knotting occurrence rises with the length of the DNA molecule, consistent with a constant knotting probability per unit length. Our experimental data compare favourably with previous simulation based predictions for long polymers. From the translocation time of the knot through the nanopore, we estimate that the majority of the DNA knots are tight, with remarkably small sizes below 100 nm. In the case of linear molecules, we also observe that knots are able to slide out on application of high driving forces (voltage).
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9.
  • Pud, Sergii, et al. (författare)
  • Self-Aligned Plasmonic Nanopores by Optically Controlled Dielectric Breakdown
  • 2015
  • Ingår i: Nano letters (Print). - 1530-6984. ; 15:10, s. 7112-7117
  • Tidskriftsartikel (refereegranskat)abstract
    • We present a novel cost-efficient method for the fabrication of high-quality self-aligned plasmonic nanopores by means of an optically controlled dielectric breakdown. Excitation of a plasmonic bowtie nanoantenna on a dielectric membrane localizes the high-voltage-driven breakdown of the membrane to the hotspot of the enhanced optical field, creating a nanopore that is automatically self-aligned to the plasmonic hotspot of the bowtie. We show that the approach provides precise control over the nanopore size and that these plasmonic nanopores can be used as single molecule DNA sensors with a performance matching that of TEM-drilled nanopores. The principle of optically controlled breakdown can also be used to fabricate nonplasmonic nanopores at a controlled position. Our novel fabrication process guarantees alignment of the nanopore with the optical hotspot of the nanoantenna, thus ensuring that pore-translocating biomolecules interact with the concentrated optical field that can be used for detection and manipulation of analytes.
10.
  • Soni, Gautam V., et al. (författare)
  • Periodic Modulations of Optical Tweezers Near Solid-State Membranes
  • 2013
  • Ingår i: Small. - Wiley-VCH Verlag. - 1613-6810. ; 9:5, s. 679-684
  • Tidskriftsartikel (refereegranskat)abstract
    • Optical tweezers operated near solid-state membranes show unexplained periodic modulations in the optical trap position. An experimental study of the oscillations is presented, as well as optical simulations based on the finite-difference time-domain method, providing insight into the underlying interference phenomenon. This work provides a complete description as well as a solution to the enduring problem of modulations in optical traps near solid-state membranes.
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