Geometrical Effect in 2D Nanopores

High-Resolution and Low-Noise Single-Molecule Sensing with Bio-Inspired Solid-State Nanopores

Solid-state nanopores have been extensively explored as single-molecule sensors, bearing the potential for the sequencing of DNA. Although they offer advantages in terms of high mechanical robustness, tunable geometry, and compatibility with existing semiconductor fabrication techniques in comparison with their biological counterparts, efforts to sequence DNA with these nanopores have been hampered by insufficient spatial resolution and high noise in the measured ionic current signal. Here we show that these limitations can be overcome by the use of solid-state nanopores featuring a thin, narrow constriction as the sensing region, inspired by biological protein nanopores that have achieved notable success in DNA sequencing. Our extensive molecular dynamics simulations show that these bio-inspired nanopores can provide high spatial resolution equivalent to 2D material nanopores and, meanwhile, significantly inhibit noise levels. A theoretical model is also provided to assess the performance of the bio-inspired nanopore, which could guide its design and optimization.

The Role of MXene Surface Terminations on Peptide Transportation in Nanopore Sensing

Nanopores with two-dimensional materials have various advantages in sensing, but the fast translocation of molecules hinders their scale-up applications. In this work, we investigate the influence of -F, -O, and -OH surface terminations on the translocation of peptides through MXene nanopores. We find that the longest dwell time always occurs when peptides pass through the Ti3C2O2 nanopores. This elongated dwell time is induced by the strongest interaction between peptides and the Ti3C2O2 membrane, in which the van der Waals interactions dominate. Compared to the other two MXene nanopores, the braking effect is indicated during the whole translocation process, which evidence the advantage of Ti3C2O2 in nanopore sensing. Our work demonstrates that membrane surface chemistry has a great influence on the translocation of peptides, which can be introduced in the design of nanopores for a better performance.

Label-Free Imaging of DNA Interactions with 2D Materials

Two-dimensional (2D) materials offer potential as substrates for biosensing devices, as their properties can be engineered to tune interactions between the surface and biomolecules. Yet, not many methods can measure these interactions in a liquid environment without introducing labeling agents such as fluorophores. In this work, we harness interferometric scattering (iSCAT) microscopy, a label-free imaging technique, to investigate the interactions of single molecules of long dsDNA with 2D materials. The millisecond temporal resolution of iSCAT allows us to capture the transient interactions and to observe the dynamics of unlabeled DNA binding to a hexagonal boron nitride (hBN) surface in solution for extended periods (including a fraction of 10%, of trajectories lasting longer than 110 ms). Using a focused ion beam technique to engineer defects, we find that DNA binding affinity is enhanced at defects; when exposed to long lanes, DNA binds preferentially at the lane edges. Overall, we demonstrate that iSCAT imaging is a useful tool to study how biomolecules interact with 2D materials, a key component in engineering future biosensors.

Memristive Response and Capacitive Spiking in Aqueous Ion Transport through Two-Dimensional Nanopore Arrays

In living organisms, information is processed in interconnected symphonies of ionic currents spiking through protein ion channels. As a result of dynamic switching of their conductive states, ion channels exhibit a variety of current-voltage nonlinearities and memory effects. Fueled by the promise of computing architectures entirely different from von Neumann, recent attempts to identify and harness similar phenomena in artificial nanofluidic environments focused on demonstrating analogue circuit elements with memory. Here we explore aqueous ionic transport through two-dimensional (2D) membranes featuring arrays of ion-trapping crown-ether-like pores. We demonstrate that for aqueous salts featuring ions with different ion-pore binding affinities, memristive effects emerge through coupling between the time-delayed state of the system and its transport properties. We also demonstrate a nanopore array that behaves as a capacitor with a strain-tunable built-in barrier, yielding behaviors ranging from current spiking to an ohmic response. By focusing on the illustrative underlying mechanisms, we demonstrate that realistically observable memory effects may be achieved in nanofluidic systems featuring crown-porous 2D membranes.

Ion Trapping and Thermionic Emission across Sub-nm Pores

Ionic transport through a graphene biomimetic subnanometer (sub-nm) pore of arbitrary shape and realistically decorated by intrinsic negatively charged sites is investigated by all-atom molecular dynamics (MD) simulations. In the presence of external electric fields, cation trapping-assisted translocation occurs in the vicinity of the 2D subnanometer pore, while the anion current is blocked by the negative charges. The adsorbed cations in such asymmetrically charged nanopores are located on the top of the nanopore instead of blocking the pore, as suggested previously in highly symmetric pores such as crown ethers. Our analysis of the different types of energy involved in ion translocations indicates that electrostatics is the dominant factor controlling ion transfer across these sub-nm pores. A physical model based on the thermionic emission formalism to account for the free energy barriers to ion flow reproduces the I-V characteristics.

Adsorption of DNA nucleobases on single-layer Ti3C2 MXene and graphene: vdW-corrected DFT and NEGF studies

We investigated the interaction of DNA nucleobases [adenine (A), guanine (G), thymine (T), and cytosine (C)] with single-layer Ti3C2 MXene using Van der Waals (vdW)-corrected density functional theory and non-equilibrium Green's function methods. All calculations were benchmarked against graphene. We showed that depending on the initial vertical height of a nucleobase above the Ti3C2 surface, two interaction mechanisms are possible, namely, physisorption and chemisorption. For graphene, DNA nucleobases always physisorbed onto the graphene surface irrespective of the initial vertical height of the nucleobase above the graphene sheet. The PBE+vdW binding energies for graphene are high (0.55-0.74 eV) and follow the order G > A > T > C, with adsorption heights in the range of 3.16-3.22 Å, indicating strong physisorption. For Ti3C2, the PBE+vdW binding energies are relatively weaker (0.16-0.20 eV) and follow the order A > G = T > C, with adsorption heights in the range of 5.51-5.60 Å, indicating weak physisorption. The binding energies for chemisorption follow the order G > A > T > C, which is the same order for physisorption. The binding energy values (5.3-7.5 eV) indicate very strong chemisorption (∼40 times larger than the physisorption binding energies). Furthermore, our band structure and electronic transport analysis showed that for physisorption, there is neither significant variation in the band structure nor modulation in the transmission function and device density of states. The relatively weak physisorption and strong chemisorption show that Ti3C2 might not be capable of identifying DNA nucleobases using the physisorption method.

Evolution of nanopores in hexagonal boron nitride

The engineering of atomically-precise nanopores in two-dimensional materials presents exciting opportunities for both fundamental science studies as well as applications in energy, DNA sequencing, and quantum information technologies. The exceptional chemical and thermal stability of hexagonal boron nitride (h-BN) suggest that exposed h-BN nanopores will retain their atomic structure even when subjected to extended periods of time in gas or liquid environments. Here we employ transmission electron microscopy to examine the time evolution of h-BN nanopores in vacuum and in air and find, even at room temperature, dramatic geometry changes due to atom motion and edge contamination adsorption, for timescales ranging from one hour to one week. The discovery of nanopore evolution contrasts with general expectations and has profound implications for nanopore applications of two-dimensional materials.

Highly Sensitive and Selective DNA Sequencing Device Using Metal Adatom Adsorption on 2D Phosphorene

Two-dimensional (2D) material revolutionarily extends the technique capability of traditional nanopore/nanogap-based DNA sequencing devices. However, challenges associated with DNA sequencing on nanopores still remained in improving the sensitivity and specificity. Herein, by first-principles calculation, we theoretically studied the potential of transition-metal elements (Cr, Fe, Co, Ni, and Au) anchored on monolayer black phosphorene (BP) to act as all-electronic DNA sequencing devices. The spin-polarized band structures appeared in Cr-, Fe-, Co-, and Au-doped BP. Remarkably, the adsorption energy of nucleobases can be significantly enhanced on BP with Co, Fe, and Cr doping, which contribute to the enlarged current signal and lower noise levels. Furthermore, the order of nucleobases in terms of their adsorption energies onto the Cr@BP is C > A > G > T, which exhibits more distinct adsorption energies than Fe@BP or Co@BP. Therefore, Cr-doped BP is more effective to avoid ambiguity in recognizing various bases. We thus envisaged a possibility of a highly sensitive and selective DNA sequencing device based on phosphorene.

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.

Two Detection Modes of Nanoslit Sensing Based on Planar Heterostructure of Graphene/Hexagonal Boron Nitride

Solid-state nanopore sequencing is now confronted with problems of stochastic pore clogging and too fast speed during the DNA permeation through a nanopore, although this technique is revolutionary with long readability and high efficiency. These two problems are related to controlling molecular transportation during sequencing. To control the DNA motion and identify the four bases, we propose nanoslit sensing based on the planar heterostructure of two-dimensional graphene and hexagonal boron nitride. Molecular dynamics simulations are performed on investigating the motion of DNA molecules on the heterostructure with a nanoslit sensor. Results show that the DNA molecules are confined within the hexagonal boron nitride (HBN) domain of the heterostructure. And the confinement effects of the heterostructure can be optimized by tailoring the stripe length. Besides, there are two ways of DNA permeation through nanoslits: the DNA can cross or translocate the nanoslit under applied voltages along the y and z directions. The two detection modes are named cross-slit and trans-slit, respectively. In both modes, the ionic current drops can be observed when the nanoslit is occupied by the DNA. And the ionic currents and dwell times can be simultaneously detected to identify the four different DNA bases. This study can shed light on the sensing mechanism based on the nanoslit sensor of a planar heterostructure and provide theoretical guidance on designing devices controlling molecular transportation during nanopore sequencing.

High durability and stability of 2D nanofluidic devices for long-term single-molecule sensing

Nanopores in two-dimensional (2D) membranes hold immense potential in single-molecule sensing, osmotic power generation, and information storage. Recent advances in 2D nanopores, especially on single-layer MoS2, focus on the scalable growth and manufacturing of nanopore devices. However, there still remains a bottleneck in controlling the nanopore stability in atomically thin membranes. Here, we evaluate the major factors responsible for the instability of the monolayer MoS2 nanopores. We identify chemical oxidation and delamination of monolayers from their underlying substrates as the major reasons for the instability of MoS2 nanopores. Surface modification of the substrate and reducing the oxygen from the measurement solution improves nanopore stability and dramatically increases their shelf-life. Understanding nanopore growth and stability can provide insights into controlling the pore size, shape and can enable long-term measurements with a high signal-to-noise ratio and engineering durable nanopore devices.

Enumerating Stable Nanopores in Graphene and Their Geometrical Properties Using the Combinatorics of Hexagonal Lattices

Nanopores in two-dimensional (2D) materials, including graphene, can be used for a variety of applications, such as gas separations, water desalination, and DNA sequencing. So far, however, all plausible isomeric shapes of graphene nanopores have not been enumerated. Instead, a probabilistic approach has been followed to predict nanopore shapes in 2D materials, due to the exponential increase in the number of nanopores as the size of the vacancy increases. For example, there are 12 possible isomers when N = 6 atoms are removed, a number that theoretically increases to 11.7 million when N = 20 atoms are removed from the graphene lattice. In this regard, the development of a smaller, exhaustive data set of stable nanopore shapes can help future experimental and theoretical studies focused on using nanoporous 2D materials in various applications. In this work, we use the theory of 2D triangular "lattice animals" to create a library of all stable graphene nanopore shapes based on a modification of a well-known algorithm in the mathematical combinatorics of polyforms known as Redelmeier's algorithm. We show that there exists a correspondence between graphene nanopores and triangular polyforms (called polyiamonds) as well as hexagonal polyforms (called polyhexes). We develop the concept of a polyiamond ID to identify unique nanopore isomers. We also use concepts from polyiamond and polyhex geometries to eliminate unstable nanopores containing dangling atoms, bonds, and moieties. We verify using density functional theory calculations that such pores are indeed unstable. The exclusion of these unstable nanopores leads to a remarkable reduction in the possible nanopores from 11.7 million for N = 20 to only 0.184 million nanopores, thereby indicating that the number of stable nanopores is almost 2 orders of magnitude lower and is much more tractable. Not only that, by extracting the polyhex outline, our algorithm allows searching for nanopores with dimensions and shape factors in a specified range, thus aiding the design of the geometrical properties of nanopores for specific applications. We also provide the coordinate files of the stable nanopores as a library to facilitate future theoretical studies of these nanopores.

Nucleation and growth of stacking-dependent nanopores in bilayer h-BN

The nucleation and growth of well-defined nanopores are presented under electron irradiation in h-BN bilayers with various stacking angles. The pores are initiated by the formation of boron vacancies in each basal layer, and then evolve into either triangular or hexagonal pores, which is dependent on the relative rotation between BN layers. The result may shed light on the rational design and fabrication of nanopores.

Localized Nanopore Fabrication via Controlled Breakdown

Nanopore sensors provide a unique platform to detect individual nucleic acids, proteins, and other biomolecules without the need for fluorescent labeling or chemical modifications. Solid-state nanopores offer the potential to integrate nanopore sensing with other technologies such as field-effect transistors (FETs), optics, plasmonics, and microfluidics, thereby attracting attention to the development of commercial instruments for diagnostics and healthcare applications. Stable nanopores with ideal dimensions are particularly critical for nanopore sensors to be integrated into other sensing devices and provide a high signal-to-noise ratio. Nanopore fabrication, although having benefited largely from the development of sophisticated nanofabrication techniques, remains a challenge in terms of cost, time consumption and accessibility. One of the latest developed methods—controlled breakdown (CBD)—has made the nanopore technique broadly accessible, boosting the use of nanopore sensing in both fundamental research and biomedical applications. Many works have been developed to improve the efficiency and robustness of pore formation by CBD. However, nanopores formed by traditional CBD are randomly positioned in the membrane. To expand nanopore sensing to a wider biomedical application, controlling the localization of nanopores formed by CBD is essential. This article reviews the recent strategies to control the location of nanopores formed by CBD. We discuss the fundamental mechanism and the efforts of different approaches to confine the region of nanopore formation.

The application of single molecule nanopore sensing for quantitative analysis

Nanopore-based sensors typically work by monitoring transient pulses in conductance via current-time traces as molecules translocate through the nanopore. The unique property of being able to monitor single molecules gives nanopore sensors the potential as quantitative sensors based on the counting of single molecules. This review provides an overview of the concepts and fabrication of nanopore sensors as well as nanopore sensing with a view toward using nanopore sensors for quantitative analysis. We first introduce the classification of nanopores and highlight their applications in molecular identification with some pioneering studies. The review then shifts focus to recent strategies to extend nanopore sensors to devices that can rapidly and accurately quantify the amount of an analyte of interest. Finally, future prospects are provided and briefly discussed. The aim of this review is to aid in understanding recent advances, challenges, and prospects for nanopore sensors for quantitative analysis.

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.

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.

Ozark Graphene Nanopore for Efficient Water Desalination

A nanoporous graphene membrane is crucial to energy-efficient reverse osmosis water desalination given its high permeation rate and ion selectivity. However, the ion selectivity of the common circular graphene nanopore is dependent on the pore size and scales inversely with the water permeation rate. Larger, circular graphene nanopores give rise to the high water permeation rate but compromise the ability to reject ions. Therefore, the pursuit of a higher permeation rate while maintaining high ion selectivity can be challenging. In this work, we discover that the geometry of graphene nanopore can play a significant role in its water desalination performance. We demonstrate that the ozark graphene nanopore, which has an irregular slim shape, can reject over 12% more ions compared with a circular nanopore with the same water permeation rate. To reveal the physical reason behind the outstanding performance of the ozark nanopore, we compared it with circular, triangular, and rhombic pores from perspectives including interfacial water density, energy barrier, water/ion distribution in pores, the ion-water RDF in pores, and the hydraulic diameter. The ozark graphene nanopore further explores the potential of graphene for efficient water desalination.

Nanopores in Atomically Thin 2D Nanosheets Limit Aqueous Single-Stranded DNA Transport

Nanopores in 2D materials are highly desirable for DNA sequencing, yet achieving single-stranded DNA (ssDNA) transport through them is challenging. Using density functional theory calculations and molecular dynamics simulations we show that ssDNA transport through a pore in monolayer hexagonal boron nitride (h-BN) is marked by a basic nanomechanical conflict. It arises from the notably inhomogeneous flexural rigidity of ssDNA and causes high friction via transient DNA desorption costs exacerbated by solvation effects. For a similarly sized pore in bilayer h-BN, its self-passivated atomically smooth edge enables continuous ssDNA transport. Our findings shed light on the fundamental physics of biopolymer transport through pores in 2D materials.

Deep Learning-Enhanced Nanopore Sensing of Single-Nanoparticle Translocation Dynamics

Noise is ubiquitous in real space that hinders detection of minute yet important signals in electrical sensors. Here, the authors report on a deep learning approach for denoising ionic current in resistive pulse sensing. Electrophoretically-driven translocation motions of single-nanoparticles in a nano-corrugated nanopore are detected. The noise is reduced by a convolutional auto-encoding neural network, designed to iteratively compare and minimize differences between a pair of waveforms via a gradient descent optimization. This denoising in a high-dimensional feature space is demonstrated to allow detection of the corrugation-derived wavy signals that cannot be identified in the raw curves nor after digital processing in frequency domains under the given noise floor, thereby enabled in-situ tracking to electrokinetic analysis of fast-moving single- and double-nanoparticles. The ability of the unlabeled learning to remove noise without compromising temporal resolution may be useful in solid-state nanopore sensing of protein structure and polynucleotide sequence.

Nanopores in two-dimensional materials: accurate fabrication

Two-dimensional (2D) materials such as graphene and molybdenum disulfide have been demonstrated with a wide range of applications in electronic devices, chemical catalysis, single-molecule detection, and energy conversion. In the 2D materials, nanopores can be created, and the 2D nanoporous membranes possess many unique properties such as ultrathin thickness, high surface area, and excellent particle sieving capability, showing extraordinary promise in plenty of applications, such as sea water desalination, gas separation, and DNA sequencing. The performances of these membranes are mainly determined by the nanopore size, structure, and density, which, in turn, rely on the fabrication techniques of the nanopores. This review covers the important progress of nanopore fabrication in 2D materials and comprehensively compares these methods for the features of the introduced nanopores and their formation processes. Future perspectives are discussed on the opportunities and challenges in fabricating high-grade 2D nanopores.

Prospects of Observing Ionic Coulomb Blockade in Artificial Ion Confinements

Nanofluidics encompasses a wide range of advanced approaches to study charge and mass transport at the nanoscale. Modern technologies allow us to develop and improve artificial nanofluidic platforms that confine ions in a way similar to single-ion channels in living cells. Therefore, nanofluidic platforms show great potential to act as a test field for theoretical models. This review aims to highlight ionic Coulomb blockade (ICB)-an effect that is proposed to be the key player of ion channel selectivity, which is based upon electrostatic exclusion limiting ion transport. Thus, in this perspective, we focus on the most promising approaches that have been reported on the subject. We consider ion confinements of various dimensionalities and highlight the most recent advancements in the field. Furthermore, we concentrate on the most critical obstacles associated with these studies and suggest possible solutions to advance the field further.

Nanogap-based all-electronic DNA sequencing devices using MoS2 monolayers

The realization of nanopores in atom-thick materials may pave the way towards electrical detection of single biomolecules in a stable and scalable manner. In this work, we theoretically study the potential of different phases of MoS2 nanogaps to act as all-electronic DNA sequencing devices. We carry out simulations based on density functional theory and the non-equilibrium Green's function formalism to investigate the electronic transport across the device. Our results suggest that the 1T'-MoS2 nanogap structure is energetically more favorable than its 2H counterpart. At zero bias, the changes in the conductance of the 1T'-MoS2 device can be well distinguished, making possible the selectivity of the DNA nucleobases. Although the conductance fluctuates around the resonances, the overall results suggest that it is possible to distinguish the four DNA bases for energies close to the Fermi level.

Diffusion Limitations and Translocation Barriers in Atomically Thin Biomimetic Pores

Ionic transport in nano- to sub-nano-scale pores is highly dependent on translocation barriers and potential wells. These features in the free-energy landscape are primarily the result of ion dehydration and electrostatic interactions. For pores in atomically thin membranes, such as graphene, other factors come into play. Ion dynamics both inside and outside the geometric volume of the pore can be critical in determining the transport properties of the channel due to several commensurate length scales, such as the effective membrane thickness, radii of the first and the second hydration layers, pore radius, and Debye length. In particular, for biomimetic pores, such as the graphene crown ether we examine here, there are regimes where transport is highly sensitive to the pore size due to the interplay of dehydration and interaction with pore charge. Picometer changes in the size, e.g., due to a minute strain, can lead to a large change in conductance. Outside of these regimes, the small pore size itself gives a large resistance, even when electrostatic factors and dehydration compensate each other to give a relatively flat-e.g., near barrierless-free energy landscape. The permeability, though, can still be large and ions will translocate rapidly after they arrive within the capture radius of the pore. This, in turn, leads to diffusion and drift effects dominating the conductance. The current thus plateaus and becomes effectively independent of pore-free energy characteristics. Measurement of this effect will give an estimate of the magnitude of kinetically limiting features, and experimentally constrain the local electromechanical conditions.

Force-Controlled Formation of Dynamic Nanopores for Single-Biomolecule Sensing and Single-Cell Secretomics

Nanopore sensing of single nucleotides has emerged as a promising single-molecule technology for DNA sequencing and proteomics. Despite the conceptual simplicity of nanopores, adoption of this technology for practical applications has been limited by a lack of pore size adjustability and an inability to perform long-term recordings in complex solutions. Here we introduce a method for fast and precise on-demand formation of a nanopore with controllable size between 2 and 20 nm through force-controlled adjustment of the nanospace formed between the opening of a microfluidic device (made of silicon nitride) and a soft polymeric substrate. The introduced nanopore system enables stable measurements at arbitrary locations. By accurately positioning the nanopore in the proximity of single neurons and continuously recording single-molecule translations over several hours, we have demonstrated this is a powerful approach for single-cell proteomics and secretomics.

Spontaneous Translocation of Single-Stranded DNA in Graphene-MoS2 Heterostructure Nanopores: Shape Effect

The appropriate translocation speed of a single-stranded DNA (ssDNA) through a solid-state nanopore is crucial for DNA sequencing technologies. By studying the geometry effect of graphene-MoS₂ hetero-nanopores with molecular dynamics simulations, we have found that the shape of these nanopores (circular, square, or triangular, with similar size) may have a significant effect on the spontaneous translocation of ssDNA, with the triangular nanopore showing the slowest translocation and the circular one the fastest. Further analyses reveal that such differences in the spontaneous ssDNA translocation arise from different electrostatic attractions between the positively charged Mo atoms exposed in the pore and the negatively charged phosphate groups (PO₄^-) in nucleotides; the "sharpness" and the total number of the exposed Mo atoms of the nanopores are responsible for different electrostatic attractions between ssDNA and the nanopore. Our findings suggest that graphene-MoS₂ heterostructure nanopores with lower symmetries (i.e., having sharper corners) are capable of slowing down the ssDNA translocation, which might help better facilitate the nucleotide sensing and DNA sequencing. The conclusion from these findings might also extend to other solid-state nanopores in designing appropriate shapes for better controlling of the translocation speed.

High-Throughput Nanocapillary Filling Enabled by Microwave Radiation for Scanning Ion Conductance Microscopy Imaging

Solid-state nanopores provide a highly sensitive tool for single-molecule sensing and probing nanofluidic effects in solutions. Glass nanopipettes are a cheap and robust type of solid-state nanopore produced from pulling glass capillaries with opening orifice diameters down to below tens of nanometers. Sub-50 nm nanocapillaries allow an unprecedented resolution for translocating single molecules or for scanning ion conductance microscopy imaging. Due to the small opening orifice diameters, such nanocapillaries are difficult to fill with solutions, compromising their advantages of low cost, availability, and experimental simplicity. We present a simple and cheap method to reliably fill nanocapillaries down to sub-10 nm diameters by microwave radiation heating. Using a large statistic of filled nanocapillaries, we determine the filling efficiency and physical principle of the filling process using sub-50 nm quartz nanocapillaries. Finally, we have used multiple nanocapillaries filled by our method for high-resolution scanning ion conductance microscopy imaging.

Computational investigation of geometrical effects in 2D boron nitride nanopores for DNA detection

Nanopore-based DNA detection and analysis have been intensively pursued theoretically and experimentally over the past decade. Owing to their nanometer thickness, 2D nanopores, such as boron nitride nanopores, show great potential for achieving DNA detection at base resolution. Although 2D nanopore devices hold great promise for next-generation DNA detection, efficiently and reliably detecting different DNA sequences is still a challenging problem. To date, most of the investigated nanopores adopt circular shapes. Because of the successful fabrication of triangular nanopores, investigating the shape effect of nanopores for DNA detection has become more and more important. In this study, boron nitride nanopores with circular, hexagonal, quadrangular and triangular shapes were modeled at various sizes. The translocation of homogeneous dsDNA through these nanopores was investigated by all-atom molecular dynamic simulations. The ionic conductivity of these nanopores was characterized and formulas for the total resistance based on the pore and access resistance were derived. The ionic current, dwell time and conductance blockade of homogeneous dsDNA were compared for nanopores with different shapes. We demonstrate that the charge distribution at the pore mouth plays an important role in the transportation of ions and DNA molecules. Our findings may shed light on the design of 2D nanopores and can facilitate the development of fast, low-cost and reliable nanopore-based DNA detection.

Ions and Water Dancing through Atom-Scale Holes: A Perspective toward "Size Zero"

We provide an overview of atom-scale apertures in solid-state membranes, from "pores" and "tubes" to "channels", with characteristic sizes comparable to the sizes of ions and water molecules. In this regime of ∼1 nm diameter pores, water molecules and ions are strongly geometrically confined: the size of water molecules (∼0.3 nm) and the size of "hydrated" ions in water (∼0.7-1 nm) are similar to the pore diameters, physically limiting the ion flow through the hole. The pore sizes are comparable to the classical Debye screening length governing the spatial range of electrostatic interaction, ∼0.3 to 1 nm for 1 to 0.1 M KCl. In such small structures, charges can be unscreened, leading to new effects. We discuss experiments on ∼1 nm diameter nanopores, with a focus on carbon nanotube pores and ion transport studies. Finally, we present an outlook for artificial "size zero" pores in the regime of small diameters and small thicknesses. Beyond mimicking protein channels in nature, solid-state pores may offer additional possibilities where sensing and control are performed at the pore, such as in electrically and optically addressable solid-state materials.

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 SiNx 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.

Polynucleotide differentiation using hybrid solid-state nanopore functionalizing with α-hemolysin

We report results from full atomistic molecular dynamics simulations on the properties of biomimetic nanopores. This latter result was obtained through the direct insertion of an α-hemolysin protein inside a hydrophobic solid-state nanopore. Upon translocation of different DNA strands, we demonstrate here that the theoretical system presents the same discrimination properties as the experimental one obtained previously. This opens an interesting way to promote the stability of a specific protein inside a solid nanopore to develop further biomimetic applications for DNA or protein sequencing.

Transverse Detection of DNA Using a MoS2 Nanopore

Classical nanopore sensing relies on the measurement of the ion current passing through a nanopore. Whenever a molecule electrophoretically translocates through the narrow constriction, it modulates the ion current. Although this approach allows one to measure single molecules, the access resistance limits the spatial resolution. This physical limitation could potentially be overcome by an alternative sensing scheme taking advantage of the current across the membrane material itself. Such an electronic readout would also allow better temporal resolution than the ionic current. In this work, we present the fabrication of an electrically contacted molybdenum disulfide (MoS₂) nanoribbon integrated with a nanopore. DNA molecules are sensed by correlated signals from the ionic current through the nanopore and the transverse current through the nanoribbon. The resulting signal suggests a field-effect sensing scheme where the charge of the molecule is directly sensed by the nanoribbon. We discuss different sensing schemes such as local potential sensing and direct charge sensing. Furthermore, we show that the fabrication of freestanding MoS₂ ribbons with metal contacts is reliable and discuss the challenges that arise in the fabrication and usage of these devices.

Striated 2D Lattice with Sub-nm 1D Etch Channels by Controlled Thermally Induced Phase Transformations of PdSe2

2D crystals are typically uniform and periodic in-plane with stacked sheet-like structure in the out-of-plane direction. Breaking the in-plane 2D symmetry by creating unique lattice structures offers anisotropic electronic and optical responses that have potential in nanoelectronics. However, creating nanoscale-modulated anisotropic 2D lattices is challenging and is mostly done using top-down lithographic methods with ≈10 nm resolution. A phase transformation mechanism for creating 2D striated lattice systems is revealed, where controlled thermal annealing induces Se loss in few-layered PdSe₂ and leads to 1D sub-nm etched channels in Pd₂ Se₃ bilayers. These striated 2D crystals cannot be described by a typical unit cells of 1-2 Å for crystals, but rather long range nanoscale periodicity in each three directions. The 1D channels give rise to localized conduction states, which have no bulk layered counterpart or monolayer form. These results show how the known family of 2D crystals can be extended beyond those that exist as bulk layered van der Waals crystals by exploiting phase transformations by elemental depletion in binary systems.

Nanopatterns of arylene-alkynylene squares on graphite: self-sorting and intercalation

Supramolecular nanopatterns of arylene–alkynylene squares with side chains of different lengths are investigated by scanning tunneling microscopy at the solid/liquid interface of highly oriented pyrolytic graphite and 1,2,4-trichlorobenzene. Self-sorting leads to the intermolecular interdigitation of alkoxy side chains of identical length. Voids inside and between the squares are occupied by intercalated solvent molecules, which numbers depend on the sizes and shapes of the nanopores. In addition, planar and non-planar coronoid polycyclic aromatic hydrocarbons (i.e., butyloxy-substituted kekulene and octulene derivatives) are found to be able to intercalate into the intramolecular nanopores.

Fabrication and practical applications of molybdenum disulfide nanopores

Among the different developed solid-state nanopores, nanopores constructed in a monolayer of molybdenum disulfide (MoS₂) stand out as powerful devices for single-molecule analysis or osmotic power generation. Because the ionic current through a nanopore is inversely proportional to the thickness of the pore, ultrathin membranes have the advantage of providing relatively high ionic currents at very small pore sizes. This increases the signal generated during translocation of biomolecules and improves the nanopores' efficiency when used for desalination or reverse electrodialysis applications. The atomic thickness of MoS₂ nanopores approaches the inter-base distance of DNA, creating a potential candidate for DNA sequencing. In terms of geometry, MoS₂ nanopores have a well-defined vertical profile due to their atomic thickness, which eliminates any unwanted effects associated with uneven pore profiles observed in other materials. This protocol details all the necessary procedures for the fabrication of solid-state devices. We discuss different methods for transfer of monolayer MoS₂, different approaches for the creation of nanopores, their applicability in detecting DNA translocations and the analysis of translocation data through open-source programming packages. We present anticipated results through the application of our nanopores in DNA translocations and osmotic power generation. The procedure comprises four parts: fabrication of devices (2-3 d), transfer of MoS₂ and cleaning procedure (24 h), the creation of nanopores within MoS₂ (30 min) and performing DNA translocations (2-3 h). We anticipate that our protocol will enable large-scale manufacturing of single-molecule-analysis devices as well as next-generation DNA sequencing.

Aqueous proton-selective conduction across two-dimensional graphyne

The development of direct methanol fuel cells is hindered by the issue of methanol crossover across membranes, despite the remarkable features resulting from the use of liquid fuel. Here we investigate the proton-selective conduction behavior across 2D graphyne in an aqueous environment. The aqueous proton conduction mechanism transitions from bare proton penetration to a mixed vehicular and Grotthuss transportation when the side length of triangular graphyne pores increases to 0.95 nm. A further increase in the side length to 1.2 nm results in the formation of a patterned aqueous/vacuum interphase, enabling protons to be conducted through the water wires via Grotthuss mechanism with low energy barriers. More importantly, it is found that 2D graphyne with the side length of less than 1.45 nm can effectively block methanol crossover, suggesting that 2D graphyne with an appropriate pore size is an ideal material to achieve zero-crossover proton-selective membranes.

Atomic-Scale Fluidic Diodes Based on Triangular Nanopores in Bilayer Hexagonal Boron Nitride

Nanofluidic 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 beneficial to miniaturize the size of a nanofluidic 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 rectifications 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.

Growth of two-dimensional materials on hexagonal boron nitride (h-BN)

With its atomically smooth surface yet no dangling bond, chemical inertness and high temperature sustainability, the insulating hexagonal boron nitride (h-BN) can be an ideal substrate for two-dimensional (2D) material growth and device measurement. In this review, research progress on the chemical growth of 2D materials on h-BN has been summarized, such as chemical vapor deposition and molecular beam epitaxy of graphene and various transition metal dichalcogenides. Further, stacking of the as-grown 2D materials relative to h-BN, thermal expansion matching between the deposited materials and h-BN, electrical property of 2D materials on h-BN have been discussed in detail.

Detecting topological variations of DNA at single-molecule level

In addition to their use in DNA sequencing, ultrathin nanopore membranes have potential applications in detecting topological variations in deoxyribonucleic acid (DNA). This is due to the fact that when topologically edited DNA molecules, driven by electrophoretic forces, translocate through a narrow orifice, transient residings of edited segments inside the orifice modulate the ionic flow. Here we utilize two programmable barcoding methods based on base-pairing, namely forming a gap in dsDNA and creating protrusion sites in ssDNA for generating a hybrid DNA complex. We integrate a discriminative noise analysis for ds and ss DNA topologies into the threshold detection, resulting in improved multi-level signal detection and consequent extraction of reliable information about topological variations. Moreover, the positional information of the barcode along the template sequence can be determined unambiguously. All methods may be further modified to detect nicks in DNA, and thereby detect DNA damage and repair sites.

Defect Engineering in 2D Materials: Precise Manipulation and Improved Functionalities

Two-dimensional (2D) materials have attracted increasing interests in the last decade. The ultrathin feature of 2D materials makes them promising building blocks for next-generation electronic and optoelectronic devices. With reducing dimensionality from 3D to 2D, the inevitable defects will play more important roles in determining the properties of materials. In order to maximize the functionality of 2D materials, deep understanding and precise manipulation of the defects are indispensable. In the recent years, increasing research efforts have been made on the observation, understanding, manipulation, and control of defects in 2D materials. Here, we summarize the recent research progress of defect engineering on 2D materials. The defect engineering triggered by electron beam (e-beam), plasma, chemical treatment, and so forth is comprehensively reviewed. Firstly, e-beam irradiation-induced defect evolution, structural transformation, and novel structure fabrication are introduced. With the assistance of a high-resolution electron microscope, the dynamics of defect engineering can be visualized in situ. Subsequently, defect engineering employed to improve the performance of 2D devices by means of other methods of plasma, chemical, and ozone treatments is reviewed. At last, the challenges and opportunities of defect engineering on promoting the development of 2D materials are discussed. Through this review, we aim to build a correlation between defects and properties of 2D materials to support the design and optimization of high-performance electronic and optoelectronic devices.

State-of-the-Art and Future Prospects for Atomically Thin Membranes from 2D Materials

Atomically thin 2D materials, such as graphene, hexagonal boron-nitride, and others, offer new possibilities for ultrathin barrier and membrane applications. While the impermeability of pristine 2D materials to gas molecules, such as He, allows the realization of the thinnest physical barrier, nanoscale vacancy defects in the 2D material lattice manifest as nanopores in an atomically thin membrane. Such nanoporous atomically thin membranes (NATMs) present potential for enabling ultrahigh permeance and selectivity in a wide range of novel separation processes. Herein, the transport properties observed in NATMs are described and recent experimental progress achieved in their fabrication is summarized. Some of the challenges in NATM scale-up for practical applications are highlighted and several opportunities are identified, including the possibility of blending traditional membrane-processing approaches. Finally, a technological roadmap is presented with a contextual discussion for NATMs to progress from research to applications.

Atomic Structure and Dynamics of Self-Limiting Sub-Nanometer Pores in Monolayer WS2

We reveal a self-limiting mechanism during the formation of a specific type of circular nanopore in monolayer WS₂ that limits its diameter to sub-nm. A single W atom vacancy (triangular nanopore) is transformed into the self-limiting nanopore (SLNP) through the atomic restructuring of S atoms around the area, reducing the number of dangling bonds at the nanopore edge by shifting them further in-plane with W-W bonding instead. Bond rotations in WS₂ help accommodate the electron beam induced atomic loss and ensure the stability of the SLNP. The SLNP shows significant improvement in diameter stability during electron beam irradiation compared to other triangular nanopores in WS₂ that typically continue to expand in diameter during atom loss. The atomic structure of these SLNPs is studied using aberration-corrected scanning transmission electron microscopy with an in situ heating holder, revealing that the SLNPs are mostly formed at a temperature of ∼500 °C, which is a balance between thermally activated S vacancy diffusion and sufficient S vacancy density to initiate local atomic reconstruction. At higher temperatures ( i. e., 1000 °C), S vacancies quickly migrate away into long line vacancies, resulting in low S vacancy density and rapidly expanding holes generated at the edges of the line vacancies. At room temperature, S vacancy migration is low and vacancy density is very high, which limits atomic reconstruction, and instead many small holes open up. These results provide insights into the factors that lead to uniform sized nanopores in the sub-nm range in transition-metal dichalcogenides.

Selective detections of single-viruses using solid-state nanopores

Rapid diagnosis of flu before symptom onsets can revolutionize our health through diminishing a risk for serious complication as well as preventing infectious disease outbreak. Sensor sensitivity and selectivity are key to accomplish this goal as the number of virus is quite small at the early stage of infection. Here we report on label-free electrical diagnostics of influenza based on nanopore analytics that distinguishes individual virions by their distinct physical features. We accomplish selective resistive-pulse sensing of single flu virus having negative surface charges in a physiological media by exploiting electroosmotic flow to filter contaminants at the Si₃N₄ pore orifice. We demonstrate identifications of allotypes with 68% accuracy at the single-virus level via pattern classifications of the ionic current signatures. We also show that this discriminability becomes >95% under a binomial distribution theorem by ensembling the pulse data of >20 virions. This simple mechanism is versatile for point-of-care tests of a wide range of flu types.