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Wavelet Denoising of High-Bandwidth Nanopore and Ion-Channel Signals
摘要： Recent work has pushed the noise-limited bandwidths of solid-state nanopore conductance recordings to more than 5 MHz and of ion channel conductance recordings to more than 500 kHz through the use of integrated complementary metal-oxide-semiconductor (CMOS) integrated circuits. Despite the spectral spread of the pulse-like signals that characterize these recordings when a sinusoidal basis is employed, Bessel filters are commonly used to denoise these signals to acceptable signal-to-noise ratios (SNRs) at the cost of losing many of the faster temporal features. Here, we report improvements to the SNR that can be achieved using wavelet denoising instead of Bessel filtering. When combined with state-of-the-art high-bandwidth CMOS recording instrumentation, we can reduce baseline noise levels by over a factor of four compared to a 2.5-MHz Bessel filter while retaining transient properties in the signal comparable to this filter bandwidth. Similarly, for ion channel recordings, we achieve a temporal response better than a 100-kHz Bessel filter with a noise level comparable to that achievable with a 25-kHz Bessel filter. Improvements in SNR can be used to achieve robust statistical analyses of these recordings, which may provide important insights into nanopore translocation dynamics and mechanisms of ion channel function.
关键词： ion channel,Nanopore,CMOS,wavelet,denoise.,SNR
更新于2025-09-23 15:23:52
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Atomic-Scale Fluidic Diodes Based on Triangular Nanopores in Bilayer Hexagonal Boron Nitride
摘要： Nano?uidic diodes based on nanochannels have been studied theoretically and experimentally for applications such as biosensors and logic gates. However, when analyzing attoliter-scale samples or enabling high-density integration of lab-on-a-chip devices, it is bene?cial to miniaturize the size of a nano?uidic channel. Using molecular dynamics simulations, we investigate conductance of nanopores in bilayer hexagonal Boron Nitride (h-BN). Remarkably, we found that triangular nanopores possess excellent recti?cations of ionic currents while hexagonal ones do not. It is worth highlighting that the pore length is only about 0.7 nm which is about the atomic limit for a bipolar diode. We determined scaling relations between ionic currents I and pore sizes L for small nanopores, that are I ～ L1 in a forward biasing voltage and I ～ L2 in a reverse biasing voltage. Simulation results qualitatively agree with analytical ones derived from the one-dimensional Poisson-Nerst-Planck equations.
关键词： 2D nanopore,?uidic diode,h-BN,bi-layer,recti?cation
更新于2025-09-23 15:23:52
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Track-etched membrane as fluorescence-based pH biosensor
摘要： Robust and cost-effective stimuli-responsive polymers show prominent advantages to be integrated into detection devices. In addition, modified track-etched membranes with chemical-sensing polymers possess additional robustness features such as including the sensing material into sub-micron pores. In this study, we report the preparation of track-etched PET membranes with fluorescent response in direct relation to changes in the pH of the environment. Immobilised Fluorescein and Green Fluorescent Protein have been used as pH-sensor elements. The former was not sensitive to pH, while the latter had a similar pH sensitivity to that of the free protein. Modifications of track-etched membranes were carried out by grafting polymerisation initiated by the remnant radicals, a straightforward technique for selective modification of the inner wall of pores. The biosensor prepared with the fluorescent protein was able to sense the pH of a buffer solution in the range 4 to 8. Furthermore, this membrane evidenced capacity to sense the pH of the cell growth by in situ fluorescence intensity detection during E.coli cell culture in microwells.
关键词： Track-etched PET membrane,Nanopore functionalisation,GFP immobilisation,Glycidyl methacrylate
更新于2025-09-23 15:22:29
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Fluorescence Imaging for Ultrafiltration of Individual Nanoparticles from a Colloidal Solution in Track Membranes
摘要： We have used ? uorescence nanoscopy for direct imaging of adsorption of individual colloidal quantum dots of diameter ~10 nm (spherical core/shell CdSeS/ZnS semiconductor nanocrystals, functionalized by organic oleic acid ligands) in nanopores of a nuclear ? lter (a polypropylene track membrane with pores of diameter ~500 nm). We have shown that when a colloidal toluene solution passes through the pores of the membrane, the nanoparticles are completely retained at a depth of 10 μm.
关键词： nanopore,single-photon source,CdSe,membrane,nanoscopy,entangled-photon source,quantum dot,colloidal solution,microscopy,nanoparticles,ultra? ltration,oleic acid,nuclear ? lter,luminescence,polymer
更新于2025-09-23 15:21:21
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Identification of spherical and non-spherical protein by solid-state nanopore
摘要： Three-dimensional structure of a protein plays an important role in protein dynamics in biological system of human. By now, it remains challenge to characterize and quantify the shape of a protein at single-molecule level. Nanopore, as a novel single-molecule sensor, has been widely applied in many fields such as DNA sequencing and human diseases diagnosis. In this paper, we investigated the translocation of sphere-like con.A and the prolate Bovine Serum Albumin (BSA) under electric field by solid-state nanopore. By analyzing the ionic current, the con.A and the BSA could be characterized and differentiated due to their intrinsic shape difference. Because the prolate BSA will have the preferred orientations for higher electric field when it is residing inside the nanopore, thus multiple ionic current blockade levels will be observed. While for the spherical con.A, there is only one ionic current blockade level. This method presented here will be potentially applied to fingerprint a single protein as a new method having features of low-cost and high-throughput in the near future.
关键词： orientation,solid-state nanopore,shape,electric field,ionic current,protein
更新于2025-09-23 15:21:21
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Simultaneous scanning ion conductance and atomic force microscopy with a nanopore: Effect of the aperture edge on the ion current images
摘要： Scanning ion conductance microscopy (SICM) is a technique for high-resolution non-contact imaging, particularly powerful for live cell studies. Despite debates on its lateral resolution, consensus is that a probe presenting a tip with small opening aperture, large opening angle, and large outer-to-inner radius ratio will offer a SICM current signal more sensitive to tip-sample separation, ultimately impacting the image resolution. We report here the design of such a probe, integrating a nano-opening (<20 nm opening diameter) with increased outer-to-inner radius ratio and a wide opening angle through microfabrication and ion milling. The probe consists of a microfluidic atomic force microscopy (AFM) cantilever offered by the Fluid Force Microscope (FluidFM) technology, able to act as an SICM and AFM probe. Such a combination allows investigating the implications of the new probe geometry on the SICM imaging process by simultaneously recording currents and forces. We demonstrate through experiments on well-defined samples as well as corresponding simulations that by integrating a nanopore onto the FluidFM, nanoscale features could be successfully imaged, but the increased sensitivity of the probe current to sample distance comes with higher sensitivity to an inherent SICM wall artefact.
关键词： nanopore,ion current images,Scanning ion conductance microscopy,FluidFM,atomic force microscopy
更新于2025-09-23 15:21:21
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A chromosome-scale assembly of the sorghum genome using nanopore sequencing and optical mapping
摘要： Long-read sequencing technologies have greatly facilitated assemblies of large eukaryotic genomes. In this paper, Oxford Nanopore sequences generated on a MinION sequencer are combined with Bionano Genomics Direct Label and Stain (DLS) optical maps to generate a chromosome-scale de novo assembly of the repeat-rich Sorghum bicolor Tx430 genome. The final assembly consists of 29 scaffolds, encompassing in most cases entire chromosome arms. It has a scaffold N50 of 33.28 Mbps and covers 90% of the expected genome length. A sequence accuracy of 99.85% is obtained after aligning the assembly against Illumina Tx430 data and 99.6% of the 34,211 public gene models align to the assembly. Comparisons of Tx430 and BTx623 DLS maps against the public BTx623 v3.0.1 genome assembly suggest substantial discrepancies whose origin remains to be determined. In summary, this study demonstrates that informative assemblies of complex plant genomes can be generated by combining nanopore sequencing with DLS optical maps.
关键词： optical mapping,chromosome-scale,nanopore sequencing,Sorghum bicolor,genome assembly
更新于2025-09-23 15:21:01
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Direct CW-Laser Writing Sub-Diffraction-Limit Nanopore Array Based on the Low One-Photon Absorption of Polymer
摘要： A large area nanopore array with controllable consistency has been fabricated by direct laser writing (DLW) technique with ultralow one-photon absorption (LOPA). In this technique, a doughnut-shape beam generated by 532 nm continuous-wave laser through a vortex phase plate was focused into the thin film of SU8 photoresist by a high numerical aperture objective. The low absorption of the photoresist at the excitation wavelength allowed controllable fabricating structures with sub-diffraction-limit feature size and high aspect ratio. With point-by-point scanning fabrication, nanopore array with the pore’s internal diameter, about ten percent of incident laser wavelength, far smaller than Abbe’s diffraction limit was achieved. The influences of the exposure intensity and exposure time on the fabricated nanopore size and shape were also investigated by scanning electron microscope (SEM).
关键词： ultralow one-photon absorption,direct laser writing,nanopore,doughnut-shaped beam
更新于2025-09-19 17:13:59
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Plasmonic nanopores for single-molecule detection and manipulation: towards sequencing applications
摘要： Solid-state nanopore-based sensors are promising platforms for next-generation sequencing technologies, featuring label-free single-molecule sensitivity, rapid detection, and low-cost manufacturing. In recent years, solid-state nanopores have been explored due to their miscellaneous fabrication methods and their use in a wide range of sensing applications. In this review, we highlight a novel family of solid-state nanopores which have recently appeared, namely plasmonic nanopores. The use of plasmonic nanopores to engineer electromagnetic fields around a nanopore sensor allows for enhanced optical spectroscopies, local control over temperature, thermophoresis of molecules and ions to/from the sensor, and trapping of entities. This Mini-Review offers a comprehensive understanding of the current state-of-the-art plasmonic nanopores for single-molecule detection and biomolecular sequencing applications, and discusses the latest advances and future perspectives on plasmonic nanopore-based technologies.
关键词： solid-state,single-molecule,sequencing,nanopore,plasmonics
更新于2025-09-16 10:30:52
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A novel shaped-controlled fabrication of nanopore and its applications in quantum electronics
摘要： High-intensity (107–108 A m?2) electron beams can be used to fabricate nanoscale pores. this approach enables real-time observation of nanopore drilling and precise control of the diameter of the nanopore. nevertheless, it is not suitable for tuning the nanopore’s sidewall shape. in this study, we demonstrate the use of low-intensity electron beams to fabricate nanopores on a silicon nitride (Sinx) membrane. this technique allows the precise adjustment of the nanopore dimension and the shaping of its three-dimensional (3D) nanostructure. The 3D structures of the nanopore were evaluated by electron tomography, and series of oblique images were used in reconstructing the 3D images of nanopores using a weighted back-projection method. the sidewall shape of the nanopore was observed at different electron-beam conditions, and the formation mechanism was elucidated based on these results. the nanopore fabricated with this technique can be used as a template to develop electronics at the nanoscale based on which a quantum-dot device can be prepared with a simple evaporation process. The measured results show that the device can resolve well-defined electronic states that are characteristic for the behaviors of the quantum-dot device.
关键词： electron beam,nanopore,3D nanostructure,quantum electronics,silicon nitride membrane
更新于2025-09-12 10:27:22