Programmed synthesis of freestanding graphene nanomembrane arrays

Scaled-Up Synthesis of Freestanding Molybdenum Disulfide Membranes for Nanopore Sensing

2D materials are ideal for nanopores with optimal detection sensitivity and resolution. Among these, molybdenum disulfide (MoS₂ ) has gained traction as a less hydrophobic material than graphene. However, experiments using 2D nanopores remain challenging due to the lack of scalable methods for high-quality freestanding membranes. Herein, a site-directed, scaled-up synthesis of MoS₂ membranes on predrilled nanoapertures on 4-inch wafer substrates with 75% yields is reported. Chemical vapor deposition (CVD), which introduces sulfur and molybdenum dioxide vapors across the sub-100 nm nanoapertures results in exclusive formation of freestanding membranes that seal the apertures. Nucleation and growth near the nanoaperture edges is followed by nanoaperture decoration with MoS₂ , which proceeds until a critical flake curvature is achieved, after which fully spanning freestanding membranes form. Intentional blocking of reagent flow through the apertures inhibits MoS₂ nucleation around the nanoapertures, promoting the formation of large-crystal monolayer MoS₂ membranes. The in situ grown membranes along with facile membrane wetting and nanopore formation using dielectric breakdown enables the recording of dsDNA translocation events at an unprecedentedly high 1 MHz bandwidth. The methods presented here are important steps toward the development of scalable single-layer membrane manufacture for 2D nanofluidics and nanopore applications.

Fabrication of solid-state nanopores

Nanopores are valuable single-molecule sensing tools that have been widely applied to the detection of DNA, RNA, proteins, viruses, glycans, etc. The prominent sensing platform is helping to improve our health-related quality of life and accelerate the rapid realization of precision medicine. Solid-state nanopores have made rapid progress in the past decades due to their flexible size, structure and compatibility with semiconductor fabrication processes. With the development of semiconductor fabrication techniques, materials science and surface chemistry, nanopore preparation and modification technologies have made great breakthroughs. To date, various solid-state nanopore materials, processing technologies, and modification methods are available to us. In the review, we outline the recent advances in nanopores fabrication and analyze the virtues and limitations of various membrane materials and nanopores drilling techniques.

DNA Coil Dynamics and Hydrodynamic Gating of Pressure-Biased Nanopores

Nanopores are ideally suited for the analysis of long DNA fragments including chromosomal DNA and synthetic DNA with applications in genome sequencing and DNA data storage, respectively. Hydrodynamic fluid flow has been shown to slow down DNA transit time within the pore, however other influences of hydrodynamic forces have yet to be explored. In this report, a broad analysis of pressure-biased nanopores and the impact of hydrodynamics on DNA transit time, capture rate, current blockade depth, and DNA folding are conducted. Using a 10 nm pore, it is shown that hydrodynamic flow inhibits the early stages of linearization of DNA and produces predominately folded events which are initiated by folded DNA (2-strands) entering the pore. Furthermore, utilizing larger pores (30 nm) leads to unique DNA gating behavior in which DNA events can be switched on and off with the application of pressure. A computational model, based on combining electrophoretic drift velocities with fluid velocities, accurately predicts the pore size required to observe DNA gating. Hydrodynamic fluid flow generated by a pressure bias, or potentially more generally by other mechanisms like electroosmotic flow, is shown to have significant effects on DNA sensing and can be useful for DNA sensing technologies.

Nanopores in Graphene and Other 2D Materials: A Decade's Journey toward Sequencing

Nanopore techniques offer a low-cost, label-free, and high-throughput platform that could be used in single-molecule biosensing and in particular DNA sequencing. Since 2010, graphene and other two-dimensional (2D) materials have attracted considerable attention as membranes for producing nanopore devices, owing to their subnanometer thickness that can in theory provide the highest possible spatial resolution of detection. Moreover, 2D materials can be electrically conductive, which potentially enables alternative measurement schemes relying on the transverse current across the membrane material itself and thereby extends the technical capability of traditional ionic current-based nanopore devices. In this review, we discuss key advances in experimental and computational research into DNA sensing with nanopores built from 2D materials, focusing on both the ionic current and transverse current measurement schemes. Challenges associated with the development of 2D material nanopores toward DNA sequencing are further analyzed, concentrating on lowering the noise levels, slowing down DNA translocation, and inhibiting DNA fluctuations inside the pores. Finally, we overview future directions of research that may expedite the emergence of proof-of-concept DNA sequencing with 2D material nanopores.

Sub-10-nm-thick SiN nanopore membranes fabricated using the SiO2sacrificial layer process

In our previous studies, ultrathin SiN membranes down to 3 nm in thickness were fabricated using the poly-Si sacrificial layer process, and nanopores were formed in those membranes. The region of the SiN membrane fabricated using this process was small, and the poly-Si sacrificial layer remained throughout the other region. On the other hand, to reduce the noise of the current through the nanopore, it is preferable to reduce the capacitance of the nanopore chip by replacing the poly-Si layer with an insulator with low permittivity, such as SiO₂. Thus, in this study, the fabrication of SiN membranes with thicknesses of 3-7 nm using the SiO₂sacrificial layer process was examined. SiN membranes with thicknesses of less than 5 nm could not be formed when the thickness of the top SiN layer deposited onto the sacrificial layer was 100 nm. In contrast, SiN membranes down to 3.07 nm in thickness could be formed when the top SiN layer was 40 nm in thickness. This is thought to be due to the difference in membrane stress. Nanopores were then fabricated in the membranes via dielectric breakdown. The current noise of the nanopore membranes was approximately 3/5 that of membranes fabricated using the poly-Si sacrificial layer process. Last, ionic current blockades were measured when poly(dT)₆₀passed through the nanopores, and the effective thickness of the nanopores was estimated based on those current-blockade values. The effective thickness was approximately 4.8 nm when the deposited thickness of the SiN membrane was 6.03 nm. On the other hand, the effective thickness and the deposited thickness were almost the same when the deposited thickness was 3.07 nm. This suggests it became difficult to form a shape in which the thickness of the nanopore edge was thinner than the deposited membrane thickness as the deposited thickness decreased.

In situ solid-state nanopore fabrication

Nanopores in solid-state membranes are promising for a wide range of applications including DNA sequencing, ultra-dilute analyte detection, protein analysis, and polymer data storage. Techniques to fabricate solid-state nanopores have typically been time consuming or lacked the resolution to create pores with diameters down to a few nanometres, as required for the above applications. In recent years, several methods to fabricate nanopores in electrolyte environments have been demonstrated. These in situ methods include controlled breakdown (CBD), electrochemical reactions (ECR), laser etching and laser-assisted controlled breakdown (la-CBD). These techniques are democratising solid-state nanopores by providing the ability to fabricate pores with diameters down to a few nanometres (i.e. comparable to the size of many analytes) in a matter of minutes using relatively simple equipment. Here we review these in situ solid-state nanopore fabrication techniques and highlight the challenges and advantages of each method. Furthermore we compare these techniques by their desired application and provide insights into future research directions for in situ nanopore fabrication methods.

Biomimetic Nanomembranes: An Overview

Nanomembranes are the principal building block of basically all living organisms, and without them life as we know it would not be possible. Yet in spite of their ubiquity, for a long time their artificial counterparts have mostly been overlooked in mainstream microsystem and nanosystem technologies, being a niche topic at best, instead of holding their rightful position as one of the basic structures in such systems. Synthetic biomimetic nanomembranes are essential in a vast number of seemingly disparate fields, including separation science and technology, sensing technology, environmental protection, renewable energy, process industry, life sciences and biomedicine. In this study, we review the possibilities for the synthesis of inorganic, organic and hybrid nanomembranes mimicking and in some way surpassing living structures, consider their main properties of interest, give a short overview of possible pathways for their enhancement through multifunctionalization, and summarize some of their numerous applications reported to date, with a focus on recent findings. It is our aim to stress the role of functionalized synthetic biomimetic nanomembranes within the context of modern nanoscience and nanotechnologies. We hope to highlight the importance of the topic, as well as to stress its great applicability potentials in many facets of human life.

Comparing Current Noise in Biological and Solid-State Nanopores

Nanopores bear great potential as single-molecule tools for bioanalytical sensing and sequencing, due to their exceptional sensing capabilities, high-throughput, and low cost. The detection principle relies on detecting small differences in the ionic current as biomolecules traverse the nanopore. A major bottleneck for the further progress of this technology is the noise that is present in the ionic current recordings, because it limits the signal-to-noise ratio (SNR) and thereby the effective time resolution of the experiment. Here, we review the main types of noise at low and high frequencies and discuss the underlying physics. Moreover, we compare biological and solid-state nanopores in terms of the SNR, the important figure of merit, by measuring translocations of a short ssDNA through a selected set of nanopores under typical experimental conditions. We find that SiN_x solid-state nanopores provide the highest SNR, due to the large currents at which they can be operated and the relatively low noise at high frequencies. However, the real game-changer for many applications is a controlled slowdown of the translocation speed, which for MspA was shown to increase the SNR > 160-fold. Finally, we discuss practical approaches for lowering the noise for optimal experimental performance and further development of the nanopore technology.

Single-Molecule Sensing Using Nanopores in Two-Dimensional Transition Metal Carbide (MXene) Membranes

Label-free nanopore technology for sequencing biopolymers such as DNA and RNA could potentially replace existing methods if improvements in cost, speed, and accuracy are achieved. Solid-state nanopores have been developed over the past two decades as physically and chemically versatile sensors that mimic biological channels, through which transport and sequencing of biomolecules have already been demonstrated. Of particular interest is the use of two-dimensional (2D) materials as nanopore substrates, since these can in theory provide the highest resolution readout (<1 nm of a biopolymer segment) and opportunities for electronic multiplexed readout through their interesting electronic properties. In this work, we report on nanopores comprising atomically thin flakes of 2D transition metal carbides called MXenes. We demonstrate a high-yield (60%), contamination-free, and alignment-free transfer method that involves their self-assembly at a liquid-liquid interface to large-scale (mm-sized) films composed of sheets, followed by nanopore fabrication using focused electron beams. Our work demonstrates the feasibility of MXenes, a class of hydrophilic 2D materials with over 20 compositions known to date, as nanopore membranes for DNA translocation and single-molecule sensing applications.

Graphene Foam: Hole-Flake Network for Uniaxial Supercompression and Recovery Behavior

We employed the coarse-grained molecular dynamics simulation method to systematically study the uniaxial supercompression and recovery behavior of multiporous graphene foam, in which a mesoscopic three-dimensional network with hole-graphene flakes was proposed. The network model not only considers the physical cross-links and interlayer van der Waals interactions, but also introduces a hole in the flake to approach the imperfection of pristine graphene and the hierarchical porous configuration of real foam material. We first recreated a typical two-stage supercompression stress-strain relationship and the corresponding time-dependent recovery as well as a U-type nominal Poisson ratio. Then the recovery unloading at different strains and multicycle compression-uncompression were both conducted; the initial elastic moduli in the multicycles were found to be the same, and a multilevel residual strain was disclosed. Importantly, the residual strain is not exactly the plastic one, part of which can resurrect in the subsequent loading-unloading-holding. The mesoscopic mechanism of viscoelastic and residual deformation for the recovery can be attributed to the van der Waals repulsion and mechanical interlocking among the hole-flakes; interestingly, the local tensile stress was observed in the virial stress distribution. Particularly, an abnormal turning point in the length-time curve for the mean bead-bond length was captured during the supercompression. After the point, the length abnormally increases for different size ratios of the hole to the flake, which is in line with the mesostructure evolution. The finding may provide a mesoscopic criterion for the supercompression of graphene foam related materials.

Recent Progress in Solid-State Nanopores

The solid-state nanopore has attracted much attention as a next-generation DNA sequencing tool or a single-molecule biosensor platform with its high sensitivity of biomolecule detection. The platform has advantages of processability, robustness of the device, and flexibility in the nanopore dimensions as compared with the protein nanopore, but with the limitation of insufficient spatial and temporal resolution to be utilized in DNA sequencing. Here, the fundamental principles of the solid-state nanopore are summarized to illustrate the novelty of the device, and improvements in the performance of the platform in terms of device fabrication are explained. The efforts to reduce the electrical noise of solid-state nanopore devices, and thus to enhance the sensitivity of detection, are presented along with detailed descriptions of the noise properties of the solid-state nanopore. Applications of 2D materials including graphene, h-BN, and MoS₂ as a nanopore membrane to enhance the spatial resolution of nanopore detection, and organic coatings on the nanopore membranes for the addition of chemical functionality to the nanopore are summarized. Finally, the recently reported applications of the solid-state nanopore are categorized and described according to the target biomolecules: DNA-bound proteins, modified DNA structures, proteins, and protein oligomers.

Assembly and Self-Assembly of Nanomembrane Materials-From 2D to 3D

Nanoscience and nanotechnology offer great opportunities and challenges in both fundamental research and practical applications, which require precise control of building blocks with micro/nanoscale resolution in both individual and mass-production ways. The recent and intensive nanotechnology development gives birth to a new focus on nanomembrane materials, which are defined as structures with thickness limited to about one to several hundred nanometers and with much larger (typically at least two orders of magnitude larger, or even macroscopic scale) lateral dimensions. Nanomembranes can be readily processed in an accurate manner and integrated into functional devices and systems. In this Review, a nanotechnology perspective of nanomembranes is provided, with examples of science and applications in semiconductor, metal, insulator, polymer, and composite materials. Assisted assembly of nanomembranes leads to wrinkled/buckled geometries for flexible electronics and stacked structures for applications in photonics and thermoelectrics. Inspired by kirigami/origami, self-assembled 3D structures are constructed via strain engineering. Many advanced materials have begun to be explored in the format of nanomembranes and extend to biomimetic and 2D materials for various applications. Nanomembranes, as a new type of nanomaterials, allow nanotechnology in a controllable and precise way for practical applications and promise great potential for future nanorelated products.

Side-gated ultrathin-channel nanopore FET sensors

A side-gated, ultrathin-channel nanopore FET (SGNAFET) is proposed for fast and label-free DNA sequencing. The concept of the SGNAFET comprises the detection of changes in the channel current during DNA translocation through a nanopore and identifying the four types of nucleotides as a result of these changes. To achieve this goal, both p- and n-type SGNAFETs with a channel thicknesses of 2 or 4 nm were fabricated, and the stable transistor operation of both SGNAFETs in air, water, and a KCl buffer solution were confirmed. In addition, synchronized current changes were observed between the ionic current through the nanopore and the SGNAFET's drain current during DNA translocation through the nanopore.

Prevention of Dielectric Breakdown of Nanopore Membranes by Charge Neutralization

To achieve DNA sequencing using a solid-state nanopore, it is necessary to reduce the electric noise current. The noise current can be decreased by reducing the capacitance (C) of the nanopore device. However, we found that an electric-charge difference (ΔQ) between the electrolyte in one chamber and the electrolyte in another chamber occurred. For low capacitance devices, this electric-charge imbalance can lead to unexpectedly high voltage (ΔV = ΔQ/C) which disrupted the membrane when the two electrolytes were independently poured into the chambers. We elucidated the mechanism for the generation of initial defects and established new procedures for preventing the generation of defects by connecting an electric bypass between the chambers.

Fabrication of 3-nm-thick Si3N4 membranes for solid-state nanopores using the poly-Si sacrificial layer process

To improve the spatial resolution of solid-state nanopores, thinning the membrane is a very important issue. The most commonly used membrane material for solid-state nanopores is silicon nitride (Si3N4). However, until now, stable wafer-scale fabrication of Si3N4 membranes with a thickness of less than 5 nm has not been reported, although a further reduction in thickness is desired to improve spatial resolution. In the present study, to fabricate thinner Si3N4 membranes with a thickness of less than 5 nm in a wafer, a new fabrication process that employs a polycrystalline-Si (poly-Si) sacrificial layer was developed. This process enables the stable fabrication of Si3N4 membranes with thicknesses of 3 nm. Nanopores were fabricated in the membrane using a transmission electron microscope (TEM) beam. Based on the relationship between the ionic current through the nanopores and their diameter, the effective thickness of the nanopores was estimated to range from 0.6 to 2.2 nm. Moreover, DNA translocation through the nanopores was observed.

Direct and Scalable Deposition of Atomically Thin Low-Noise MoS2 Membranes on Apertures

Molybdenum disulfide (MoS2) flakes can grow beyond the edge of an underlying substrate into a planar freestanding crystal. When the substrate edge is in the form of an aperture, reagent-limited nucleation followed by edge growth facilitate direct and selective growth of freestanding MoS2 membranes. We have found conditions under which MoS2 grows preferentially across micrometer-scale prefabricated solid-state apertures in silicon nitride membranes, resulting in sealed membranes that are one to a few atomic layers thick. We have investigated the structure and purity of our membranes by a combination of atomic-resolution transmission electron microscopy, elemental analysis, Raman spectroscopy, photoluminescence spectroscopy, and low-noise ion-current recordings through nanopores fabricated in such membranes. Finally, we demonstrate the utility of fabricated ultrathin nanopores in such membranes for single-stranded DNA translocation detection.