Particle Trajectory-Dependent Ionic Current Blockade in Low-Aspect-Ratio Pores

Immunological assay using a solid-state pore with a low limit of detection

Emerging infectious diseases, cancer, and other diseases are quickly tested mainly via immune reactions based on specific molecular recognition between antigens and antibodies. By changing the diameter of solid-state pores, biomolecules of various sizes can be rapidly detected at the single-molecule level. The combination of immunoreactions and solid-state pores paves the way for an efficient testing method with high specificity and sensitivity. The challenge in developing this method is achieving quantitative analysis using solid-state pores. Here, we demonstrate a method with a low limit of detection for testing tumor markers using a combination of immunoreactions and solid-state pore technology. Quantitative analysis of the mixing ratio of two and three beads with different diameters was achieved with an error rate of up to 4.7%. The hybrid solid-state pore and immunoreaction methods with prostate-specific antigen (PSA) and anti-PSA antibody-modified beads achieved a detection limit of 24.9 fM PSA in 30 min. The hybrid solid-state pore and immunoreaction enabled the rapid development of easy-to-use tests with lower limit of detection and greater throughput than commercially available immunoassay for point-of-care testing.

Precision Basecalling of Single DNA Nucleotide from Overlapped Transmission Readouts with Machine Learning Aided Solid-State Nanogap

DNA sequencing with the quantum tunneling technique heralds a paradigm shift in genetic analysis, promising rapid and accurate identification for diverging applications ranging from personalized medicine to security issues. However, the widespread distribution of molecular conductance, conduction orbital alignment for resonant transport, and decoding crisscrossing conductance signals of isomorphic nucleotides have been persistent experimental hurdles for swift and precise identification. Herein, we have reported a machine learning (ML)-driven quantum tunneling study with solid-state model nanogap to determine nucleotides at single-base resolution. The optimized ML basecaller has demonstrated a high predictive basecalling accuracy of all four nucleotides from seven distinct data pools, each containing complex transmission readouts of their different dynamic conformations. ML classification of quaternary, ternary, and binary nucleotide combinations is also performed with high precision, sensitivity, and F1 score. ML explainability unravels the evidence of how extracted normalized features within overlapped nucleotide signals contribute to classification improvement. Moreover, electronic fingerprints, conductance sensitivity, and current readout analysis of nucleotides have promised practical applicability with significant sensitivity and distinguishability. Through this ML approach, our study pushes the boundaries of quantum sequencing by highlighting the effectiveness of single nucleotide basecalling with promising implications for advancing genomics and molecular diagnostics.

Exploring single-molecule interactions: heparin and FGF-1 proteins through solid-state nanopores

Detection and characterization of protein-protein interactions are essential for many cellular processes, such as cell growth, tissue repair, drug delivery, and other physiological functions. In our research, we have utilized emerging solid-state nanopore sensing technology, which is highly sensitive to better understand heparin and fibroblast growth factor 1 (FGF-1) protein interactions at a single-molecule level without any modifications. Understanding the structure and behavior of heparin-FGF-1 complexes at the single-molecule level is very important. An abnormality in their formation can lead to life-threatening conditions like tumor growth, fibrosis, and neurological disorders. Using a controlled dielectric breakdown pore fabrication approach, we have characterized individual heparin and FGF-1 (one of the 22 known FGFs in humans) proteins through the fabrication of 17 ± 1 nm nanopores. Compared to heparin, the positively charged heparin-binding domains of some FGF-1 proteins translocationally react with the pore walls, giving rise to a distinguishable second peak with higher current blockade. Additionally, we have confirmed that the dynamic FGF-1 is stabilized upon binding with heparin-FGF-1 at the single-molecule level. The larger current blockades from the complexes relative to individual heparin and the FGF-1 recorded during the translocation ensure the binding of heparin-FGF-1 proteins, forming binding complexes with higher excluded volumes. Taken together, we demonstrate that solid-state nanopores can be employed to investigate the properties of individual proteins and their complex interactions, potentially paving the way for innovative medical therapies and advancements.

Multivariate analysis of nanoparticle translocation through a nanopore to improve the accuracy of resistive pulse sensing

The advent of nanopore-based sensors based on resistive pulse sensing gave rise to a remarkable breakthrough in the detection and characterization of nanoscale species. Some strong correlations have been reported between the resistive pulse characteristics and the particle's geometrical and physical properties. These correlations are commonly used to obtain information about the particles in commercial devices and research setups. The correlations, however, do not consider the simultaneous effect of influential factors such as particle shape and off-axis translocation, which complicates the extraction of accurate information from the resistive pulses. In this paper, we numerically studied the impact of the shape and position of particles on pulse characteristics in order to estimate the errors that arise from neglecting the influence of multiple factors on resistive pulses. We considered the sphere, oblate, and prolate particles to investigate the nanoparticle shape effect. Moreover, the trajectory dependency was examined by considering the translocation of nanoparticles away from the nanopore axis. Meanwhile, the shape effect was studied for different trajectories. We observed that the simultaneous effects of influential parameters could lead to significant errors in estimating particle properties if the coupled effects are neglected. Based on the results, we introduce the "pulse waveshape" as a novel characteristic of the resistive pulse that can be utilized as a decoupling parameter in the analysis of resistive pulses.

Study on the controllability of the fabrication of single-crystal silicon nanopores/nanoslits with a fast-stop ionic current-monitored TSWE method

The application of single-crystal silicon (SCS) nanopore structures in single-molecule-based analytical devices is an emerging approach for the separation and analysis of nanoparticles. The key challenge is to fabricate individual SCS nanopores with precise sizes in a controllable and reproducible way. This paper introduces a fast-stop ionic current-monitored three-step wet etching (TSWE) method for the controllable fabrication of SCS nanopores. Since the nanopore size has a quantitative relationship with the corresponding ionic current, it can be regulated by controlling the ionic current. Thanks to the precise current-monitored and self-stop system, an array of nanoslits with a feature size of only 3 nm was obtained, which is the smallest size ever reported using the TSWE method. Furthermore, by selecting different current jump ratios, individual nanopores of specific sizes were controllably prepared, and the smallest deviation from the theoretical value was 1.4 nm. DNA translocation measurement results revealed that the prepared SCS nanopores possessed the excellent potential to be applied in DNA sequencing.

A molecular dynamics investigation of Taq DNA polymerase and its complex with a DNA substrate using a solid-state nanopore biosensor

Proteins have a small volume difference by the diversity of amino acids, which make protein detection and identification a great challenge. Solid-state nanopore as label-free biosensors has attracted attention with high sensitivity. In this work, we investigated the Taq DNA polymerase before and after combining it with a DNA substrate on a solid-state nanopore through molecular dynamics. In simulation, we analyzed the contribution source of nanopore current blockage. In addition to considering the traditional physical exclusion volume model, the non-covalent interaction between the protein molecules and the pore wall also showed to affect the current blockage in the nanopore. When choosing pores of comparable size to protein molecules, the two states of Taq DNA polymerase produce differentiated non-covalent interactions with the pore wall, which enhanced the amplitude difference in current blockage. As a result, the two DNA polymerases can be distinguished through the distinct current blockage. However, when applying additional pulling force or increasing the pore size of the nanopore, the differences between the current blockages are not significant enough to distinguish. The introduction of the non-covalent interaction makes it clear to understand the current blockage differences, which guide the mechanism between molecules with similar structures or volumes.

Combining dynamic Monte Carlo with machine learning to study nanoparticle translocation

Resistive pulse sensing (RPS) measurements of nanoparticle translocation have the ability to provide information on single-particle level characteristics, such as diameter or mobility, as well as ensemble averages. However, interpreting these measurements is complex and requires an understanding of nanoparticle dynamics in confined spaces as well as the ways in which nanoparticles disrupt ion transport while inside a nanopore. Here, we combine Dynamic Monte Carlo (DMC) simulations with Machine Learning (ML) and Poisson-Nernst-Planck calculations to simultaneously simulate nanoparticle dynamics and ion transport during hundreds of independent particle translocations as a function of nanoparticle size, electrophoretic mobility, and nanopore length. The use of DMC simulations allowed us to explicitly investigate the effects of Brownian motion and nanoparticle/nanopore characteristics on the amplitude and duration of translocation signals. Simulation results were verified with experimental RPS measurements and found to be in quantitative agreement.

Understanding and modelling the magnitude of the change in current of nanopore sensors

Nanopores are promising sensing devices that can be used for the detection of analytes at the single molecule level. It is of importance to understand and model the current response of a nanopore sensor for improving the sensitivity of the sensor, a better interpretation of the behaviours of different analytes in confined nanoscale spaces, and quantitative analysis of the properties of the targets. The current response of a nanopore sensor, usually called a resistive pulse, results from the change in nanopore resistance when an analyte translocates through the nanopore. This article reviews the theoretical models used for the calculation of the resistance of the nanopore, and the corresponding change in nanopore resistance due to a translocation event. Models focus on the resistance of the pore cavity region and the access region of the nanopore. The influence of the sizes, shapes and surface charges of the translocating species and the nanopore, as well as the trajectory that the analyte follows are also discussed. This review aims to give a general guidance to the audience for understanding the current response of a nanopore sensor and the application of this class of sensor to a broad range of species with the theoretical models.

Biomimetic Nanochannels: From Fabrication Principles to Theoretical Insights

Biological nanochannels which can regulate ionic transport across cell membranes intelligently play a significant role in physiological functions. Inspired by these nanochannels, numerous artificial nanochannels have been developed during recent years. The exploration of smart solid-state nanochannels can lay a solid foundation, not only for fundamental studies of biological systems but also practical applications in various fields. The basic fabrication principles, functional materials, and diverse applications based on artificial nanochannels are summarized in this review. In addition, theoretical insights into transport mechanisms and structure-function relationships are discussed. Meanwhile, it is believed that improvements will be made via computer-guided strategy in designing more efficient devices with upgrading accuracy. Finally, some remaining challenges and perspectives for developments in both novel conceptions and technology of this inspiring research field are stated.

Ionic Current Fluctuation and Orientation of Tetrahedral DNA Nanostructures in a Solid-State Nanopore

Understanding the dynamic behavior of a nanostructure translocating through a nanopore is important for various applications. In this paper, the characteristics in ion current traces of tetrahedral DNA nanostructures (TDN) translocating through a solid-state nanopore are examined, by combined experimental and theoretical simulations. The results of finite element analysis reveal the correlation between orientation of TDN and the conductance blockade. The experimentally measured fluctuations in the conductance blockade, expressed as voltage-dependent histogram profiles, are consistent with the simulation, revealing the nature of a random distribution in orientation and weak influence of electrostatic and viscous torques. The step changes in orientation of a TDN during translocation are further explained by the collision with the nanopore, while the gradual changes in orientation illustrate the impact of a weak torque field in the nano-fluidic channel. The results demonstrate a general method and basic understanding in the dynamic behavior of nanostructures translocating through solid-state nanopores.

Rational ion transport management mediated through membrane structures

Unique membrane structures endow membranes with controlled ion transport properties in both biological and artificial systems, and they have shown broad application prospects from industrial production to biological interfaces. Herein, current advances in nanochannel-structured membranes for manipulating ion transport are reviewed from the perspective of membrane structures. First, the controllability of ion transport through ion selectivity, ion gating, ion rectification, and ion storage is introduced. Second, nanochannel-structured membranes are highlighted according to the nanochannel dimensions, including single-dimensional nanochannels (i.e., 1D, 2D, and 3D) functioning by the controllable geometrical parameters of 1D nanochannels, the adjustable interlayer spacing of 2D nanochannels, and the interconnected ion diffusion pathways of 3D nanochannels, and mixed-dimensional nanochannels (i.e., 1D/1D, 1D/2D, 1D/3D, 2D/2D, 2D/3D, and 3D/3D) tuned through asymmetric factors (e.g., components, geometric parameters, and interface properties). Then, ultrathin membranes with short ion transport distances and sandwich-like membranes with more delicate nanochannels and combination structures are reviewed, and stimulus-responsive nanochannels are discussed. Construction methods for nanochannel-structured membranes are briefly introduced, and a variety of applications of these membranes are summarized. Finally, future perspectives to developing nanochannel-structured membranes with unique structures (e.g., combinations of external macro/micro/nanostructures and the internal nanochannel arrangement) for mediating ion transport are presented.

Detecting Single Molecule Deoxyribonucleic Acid in a Cell Using a Three-Dimensionally Integrated Nanopore

Amplification-free genome analysis can revolutionize biology and medicine by uncovering genetic variations among individuals. Here, the authors report on a 3D-integrated nanopore for electrolysis to in situ detection of single-molecule DNA in a cell by ionic current measurements. It consists of a SiO₂ multipore sheet and a SiN_x nanopore membrane stacked vertically on a Si wafer. Single cell lysis is demonstrated by 10⁶  V m^-1 -level electrostatic field focused at the multinanopore. The intracellular molecules are then directly detected as they move through a sensing zone, wherein the authors find telegraphic current signatures reflecting folding degrees of freedom of the millimeter-long polynucleotides threaded through the SiN_x nanopore. The present device concept may enable on-chip single-molecule sequencing to multi-omics analyses at a single-cell level.

Inertial focusing and zeta potential measurements of single-nanoparticles using octet-nanochannels

Capture-to-translocation dynamics control is an important issue for single-particle and -molecule analyses by resistive pulse waveforms. Here, we report on regulated motions for accurate zeta-potential assessments of single nanoscale objects passing through an octet-nanochannel. We observed ionic spike signals consisting of eight consecutive sub-pulses signifying the ion blockage at the eight sensing zones in series upon electrophoretic translocation of individual nanoparticles. We find an exponential decrease to saturation of the channel-to-channel translocation duration as a nanobead moves forward, reflecting the more restricted radial motion degrees of freedom via inertial effects at the downstream side of the octet channel. This finding enabled a protocol for single-nanoparticle zeta potential estimation impervious to the uncertainty stemming from the stochastic nature of the translocation dynamics. The multi-channel approach presented in this study may be used as a useful tool for analyzing particles and molecules of variable sizes.

Dielectric Coatings for Resistive Pulse Sensing Using Solid-State Pores

The present study reports on the systematic characterization of the effectiveness of dielectric coating to tailor capture-to-translocation dynamics of single particles in solid-state pores. We covered the surface of SiN_x membranes with SiO₂, HfO₂, Al₂O₃, TiO₂, or ZnO, which allowed us to change the ζ-potential at the pore wall, reflecting the isoelectric points of these coating materials. Resistive pulse measurements of negatively charged polystyrene beads elucidated more facile electrophoretic capture of the particles and slower translocation motions in the channel under more negative electric potential at the oxide surface. These findings provide a guide to engineer pore wall surface for optimizing the translocation dynamics for efficient sensing of particles and molecules.

Quasi-Stable Salt Gradient and Resistive Switching in Solid-State Nanopores

Understanding and control of ion transport in a fluidic channel is of crucial importance for iontronics. The present study reports on quasi-stable ionic current characteristics in a SiN_x nanopore under a salinity gradient. An intriguing interplay between electro-osmotic flow and local ion density distributions in a solid-state pore is found to induce highly asymmetric ion transport to negative differential resistance behavior under a 100-fold difference in the cross-membrane salt concentrations. Meanwhile, a subtle change in the salinity gradient profile led to observations of resistive switching. This peculiar characteristic was suggested to stem from quasi-stable local ion density around the channel that can be switched between two distinct states via the electro-osmotic flow under voltage control. The present findings may be useful for neuromorphic devices based on micro- and nanofluidic channels.

Effects of cone angle and length of nanopores on the resistive pulse quality

Resistive pulse sensing (RPS) has proved to be a viable method for the detection and characterization of micro and nano particles. Modern fabrication methods have introduced different nanopore geometries for resistive pulse sensors. In this paper, we have numerically studied the effects of membrane thickness and the pore's cone angle, as the main geometrical parameters, on the sensing performance of the nanopores used for nanoparticle detection in the resistive pulse sensing method. To compare the sensing performance, three resistive pulse quality parameters were investigated - sensitivity, pulse duration and pulse amplitude. The thorough investigation on the relations between the geometrical parameters and the pulse quality parameters produced several interesting results, which were categorized and summarized for different nanopore structures (as different nanopore platforms) enabling the readers to more effectively compare them with one another. The results revealed that large cone angle and low aspect ratio nanopores have higher pulse amplitude and sensitivity, but their low duration could be a challenge in the process of detecting the resistive pulse. In addition, our results show small variation in sensitivity and duration of large cone angle nanopores with respect to pore length change, which is explained using the effective length concept and the definition of electric field strength and length. The findings of the present work can be used in practical applications where choosing the optimal pore geometry is of crucial significance. Furthermore, the results provide several possible ways to improve the resistive pulse quality for better sensing performance.

Machine learning-driven electronic identifications of single pathogenic bacteria

A rapid method for screening pathogens can revolutionize health care by enabling infection control through medication before symptom. Here we report on label-free single-cell identifications of clinically-important pathogenic bacteria by using a polymer-integrated low thickness-to-diameter aspect ratio pore and machine learning-driven resistive pulse analyses. A high-spatiotemporal resolution of this electrical sensor enabled to observe galvanotactic response intrinsic to the microbes during their translocation. We demonstrated discrimination of the cellular motility via signal pattern classifications in a high-dimensional feature space. As the detection-to-decision can be completed within milliseconds, the present technique may be used for real-time screening of pathogenic bacteria for environmental and medical applications.

Nano-corrugated Nanochannels for In Situ Tracking of Single-Nanoparticle Translocation Dynamics

Dynamic motions of materials in liquid present a wealth of information concerning their physical properties. While fluorescence microscopy has been widely utilized for single-particle observations, the method cannot be used for characterizing fast motions of nanoscale objects due to the limited spatiotemporal resolution. Here, we report on a nanostructure strategy for nanoscale tracking of single nanoparticles. We fabricated a straight conduit in a SiO₂ layer on a Si wafer with lithographically defined 30 nm-sized protrusions formed on the side walls. We performed resistive pulse measurements at a 1 MHz sampling rate wherein we found n-stepped current traces signifying n number of nanoparticles moving concurrently inside the nanochannel. Ensemble average of the ionic current signals revealed a peculiar feature reflecting the slightly stronger ion blockage at the nanoconstrictions between the protrusions, thereby proving the ability of nano-corrugation as physical gates to signify the precise positions of objects inside the nanofluidic channel. This in situ tracking approach elucidated steady-state motions of the nanoparticles moving at a constant speed under the counter-balanced electrophoretic and viscous drag forces, which also allowed estimations of their surface charge densities. The present method can be utilized as a speedometer for nanoscale objects of virtually any size as long as they are able to be put through the sensing zones with potential applications for single-molecule time-of-flight mass spectrometry.

Tailoring Dielectric Surface Charge via Atomic Layer Thickness

Channel surface property is a crucial factor that affects capture-to-translocation dynamics of single-particles in solid-state pores. Here, we show that atomically-thin dielectrics can be used to finely tune the pore wall surface potential. We isotopically coated alumina of atomically controlled thickness on a Si₃N₄ micropore. The surface zeta-potential in a buffer was found to decrease sharply by 1 nm thick deposition that served as a water-permeable ultra-thin sheet to modulate the effective charge density of the Al₂O₃/Si₃N₄ multilayer structure. Further thickening of the atomic layer enabled to control the zeta potential with a thickness at 3.4 mV/nm resolution. Accordingly, we observed concomitant enhancement in the capture rate and the translocation speed of negatively charged polymeric particles by virtue of the mitigated electroosmotic back flow in the functionalized pore channel. This simple method is widely applicable for tailoring the surface charge properties of essentially any sensors and devices working in aqueous media.

Shape characterization and discrimination of single nanoparticles using solid-state nanopores

Resistive pulse sensing with nanopores is expected to enable identification and analysis of nanoscale objects in ionic solutions. However, there is currently no remarkable method to characterize the three-dimensional shape of charged biomolecules or nanoparticles with low-cost and high-throughput. Here we demonstrate the sensing capability of solid-state nanopores for shape characterization of single nanoparticles by monitoring the ionic current blockades during their electrophoretic translocation through nanopores. By using nanopores that are a bit larger than the particles, shape characterization of both spherical and cubic silver nanoparticles is successfully realized due to their rapid rotation with respect to the pore axis, which is further validated by our all-atom molecular dynamics simulations. The single-molecule approach based on nanopores will allow people to measure the dimension and to characterize the shape of single nanoparticles or proteins simultaneously in real time, which is significant for its potential application in investigation of structural biology and proteomics in the near future.

Solid-State Nanopore Time-of-Flight Mass Spectrometer

Analysis of field-controlled dynamics of ionized substances in a vacuum enables mass spectroscopy of particles and molecules. Analogously, here we report that nanoscale tracking of electrophoretically driven fast motions of single nanoparticles allows label-free and nondestructive detection of their mass in liquid. We fine-traced the time-dependent positions of space-filtered regular motions of particles passed through a thin solid-state nanopore by dissecting the associated ionic blockade phenomena under a scope of multiphysics simulations. Characterizing the viscous-drag-mediated exponential decay in the electrophoretic speed of particles ejected into an electrolyte solution from the nanochannel, we demonstrated the discrimination of nanoparticles by the femtogram mass difference. The present method is viable for mass measurement of virtually any object that can be put through the sensing zone, the sensor capability of which may find many applications such as pathogen screening and proteomics.

High-throughput single nanoparticle detection using a feed-through channel-integrated nanopore

The outstanding sensitivity of solid-state nanopore sensors comes at a price of low detection efficiency due to the lack of active means to transfer objects into the nanoscale sensing zone. Here we report on a key technology for high-throughput single-nanoparticle detection which exploits mutual effects of microfluidics control and multipore electrophoresis in nanopore-in-channel units integrated on a thin Si₃N₄ membrane. Using this novel nanostructure, we demonstrated a proof-of-concept for influenza viruses via hydropressure regulation of mass transport in the fluidic channel for continuous feeding of biosamples into the effective electric field extending out from the nanopores, wherein the feed-through mechanism allowed us to selectively detect charged objects in physiological media such as human saliva. With the versatility of nanopore sensing technologies applicable to analytes of virtually any size from cells to polynucleotides, the present integration strategy may open new avenues for practical ultrasensitive bioanalytical tools.

Back-Side Polymer-Coated Solid-State Nanopore Sensors

We systematically investigated the influence of polymer coating on temporal resolution of solid-state nanopores. We fabricated a Si₃N₄ nanopore integrated with a polyimide sheet partially covering the substrate surface. Upon detecting the nanoparticles dispersed in an electrolyte buffer by ionic current measurements, we observed a larger resistive pulse height along with a faster current decay at the tails under larger coverage of the polymeric layer, thereby suggesting a prominent role of the water-touching Si₃N₄ thin film as a significant capacitor serving to retard the ionic current response to the ion blockade by fast translocation of particles through the nanopores. From this, we came up with back-side polymer-coated chip designs and demonstrated improved pore sensor temporal resolution by developing a nanopore with a thick polymethyl-methacrylate layer laminated on the bottom surface. The present findings may be useful in developing integrated solid-state nanopore sensors with embedded nanochannels and nanoelectrodes.

Electric field interference and bimodal particle translocation in nano-integrated multipores

Parallel integration of multiple channels is a fundamental strategy for high-throughput particle detection in solid-state nanopores wherein understanding and control of crosstalk is an important issue for the post resistive pulse analysis. Here we report on a prominent effect of cross-channel electric field interference on the ionic current blockade by nanoparticles in nano-spaced pore arrays in a thin Si3N4 membrane. We systematically investigated the variations in resistive pulse profiles in multipore systems of various inter-channel distances. Although each pore acted independently when they were formed at excessively far distances, we observed significant cross-pore electrostatic interactions under close-integration that led the multipores to virtually act as a single-pore of equivalent area. As a result of the interference, the resistive pulse height demonstrated bimodal distributions due to the pronounced particle trajectory-dependence of the ionic blockade effects. Most importantly, the overcrowded multi-channel structure was found to deliver significant crosstalk with serious degradation of the sensor sensitivity to particle sizes. The present results provide a guide to design multipore structures regarding the trade-off between the detection throughput and sensor sensitivity.

High-throughput single-particle detections using a dual-height-channel-integrated pore

We report a proof-of-principle demonstration of particle concentration to achieve high-throughput resistive pulse detections of bacteria using a microfluidic-channel-integrated micropore. We fabricated polymeric nanochannels to trap micrometer-sized bioparticles via a simple water pumping mechanism that allowed aggregation-free size-selective particle concentration with negligible loss. Single-bioparticle detections by ionic current measurements were then implemented through releasing and transporting the thus-collected analytes to the micropore. As a result, we attained two orders of magnitude enhancement in the detection throughput by virtue of an accumulation effect via hydrodynamic control. The device concept presented may be useful in developing nanopores and nanochannels for high-throughput single-particle and -molecule analyses.

Electrokinetic ion transport in an asymmetric double-gated nanochannel with a pH-tunable zwitterionic surface

Bioinspired, artificial functional nanochannels for intelligent molecular and ionic transport control have versatile potential applications in nanofluidics, energy conversion, and controlled drug release. To simulate the gating and rectification functions of biological ion channels, we model the electrokinetic ion transport phenomenon in an asymmetric double-gated nanochannel having a pH-regulated, zwitterionic surface. Taking account of the effect of electroosmotic flow (EOF), the conductance of the nanochannel and its ion current rectification (ICR) behavior are investigated and the associated mechanisms interpreted. In particular, the influences of the solution pH, the bulk salt concentration, and the base opening radius and the surface curvature of the nanochannel on these behaviors are examined. We show that through adjusting the base opening radius and the surface curvature of a nanochannel, its ICR behavior can be tuned effectively. In addition to proposing underlying mechanisms for the phenomena observed, the results gathered in this study also provide necessary information for designing relevant devices.

Identifying Single Particles in Air Using a 3D-Integrated Solid-State Pore

Solid-state micro- and nanopores are a versatile sensor platform capable of detecting single particles in electrolyte solution by cross-pore ionic current. Here we report on a use of this technology to identify airborne particulate matter. The detection concept lies in an electrophoretic control of air-floating particles captured in liquid to deliver them into a pore detector via microfluidic channels. We demonstrate resistive pulse measurements to machine-learning-based discriminations of intragranular contents of cypress and cedar pollens at a single-particle level. This all-electrical-sensor technique would pave a new venue toward real-time monitoring of single particles and molecules in air.

Silicon substrate effects on ionic current blockade in solid-state nanopores

We investigated the roles of silicon substrate material compositions in ionic current blockade in solid-state nanopores. When detecting single nanoparticles using an ionic current in a Si3N4 nanopore supported on a doped silicon wafer, resistive pulses were found to be blunted significantly via signal retardation due to predominant contributions of large capacitance at the ultrathin membrane. Unexpectedly, in contrast, changing the substrate material to non-doped silicon led to the sharpening of the spike-like signal feature, suggesting a better temporal resolution of the cross-channel ionic current measurements by virtue of the thick intrinsic semiconductor layer that served to diminish the net chip capacitance. The present results suggest the importance of the choice of Si compositions regarding the capacitance effects to attain better spatiotemporal resolution in solid-state nanopore sensors.

Particle Capture in Solid-State Multipores

Utilization of multiple-channel structure is a promising way of accomplishing high-throughput detections of analytes in solid-state pore sensors. Here we report on systematic investigation of particle capture efficiency in Si₃N₄ multipore systems of various array configurations. We demonstrated enhanced detection throughput with increasing numbers of pore channels in a membrane. Meanwhile, we also observed significant contributions of the interchannel crosstalk in closely integrated multipores that tended to deteriorate throughput performance by causing shrinkage of the absorption zone via the interference-derived weakening of the electric field around the pore orifice. At the same time, the interference-derived electric field distributions were also found to diminish the electroosmotic contributions to the particle capture efficiency. The present findings can be useful in designing pore arrays with optimal throughput performance.

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.

Temporal Response of Ionic Current Blockade in Solid-State Nanopores

Signal delay is a crucial factor in resistive pulse analyses using low-thickness-to-diameter aspect-ratio pores that aim to detect fine features in the ionic current blockade during the fast translocation of individual analytes to attain single-molecule tomography. Here we report on evaluations of the ionic current response to dynamic motions of nanoparticles in ultrathin solid-state nanopores. We systematically investigated the effects of pore resistance and membrane capacitance on resistive pulse waveforms under different salt concentration conditions and device configurations. The results revealed substantial modifications in the resistive pulse waveforms due to a slow charging/discharging processes at the water-touching thin dielectrics in the solid-state nanopore chips. We also provide a device design to improve the temporal resolution without compromising the spatial sensitivity. The present findings offer a breakthrough toward nanoporescopy to measure the nanoscopic shape of single-bioparticles and -molecules in electrolyte solution.

Particle detection on microfluidic chips by differential resistive pulse sensing (RPS) method

The resistive pulse sensing (RPS) method has been widely used for characterization of particles, cells, and biomolecules due to its merits of high sensitivity and resolution. This paper investigates working parameters involved in detecting submicron and micron-sized particles by the differential RPS method on microfluidic chips. Effects of particle-to-sensor size ratio, ionic concentration and pH of the electrolyte solution, and applied electric field are studied systematically by using polystyrene particles with a size range from 140 nm to 5 µm. The results show that both the amplitude and the signal-to-noise ratio (SNR) of the RPS signals increase with the particle-to-sensor size ratio as well as the ionic concentration of the electrolyte media. The amplitude of the RPS signals also increases with increasing applied voltage, while the SNR experiences an upslope at low voltages and a decline under the condition of high voltages. pH has little effect on the background noise of the differential RPS signals but reduces the amplitude of the RPS signals at high pH. Grouping of RPS signals is considered to be caused by interactions between the sensor walls and the particles. Nanoparticle detection by the differential RPS method can be enhanced by optimizing these working parameters.

Identification of Individual Bacterial Cells through the Intermolecular Interactions with Peptide-Functionalized Solid-State Pores

Bioinspired pore sensing for selective detection of flagellated bacteria was investigated. The Au micropore wall surface was modified with a synthetic peptide designed from toll-like receptor 5 (TLR5) to mimic the pathogen-recognition capability. We found that intermolecular interactions between the TLR5-derived recognition peptides and flagella induce ligand-specific perturbations in the translocation dynamics of Escherichia coli, which facilitated the discrimination between the wild-type and flagellin-deletion mutant (ΔfliC) by the resistive pulse patterns thereby demonstrating the sensing of bacteria at a single-cell level. These results provide a novel concept of utilizing weak intermolecular interactions as a recognition probes for single-cell microbial identification.

Optimal voltage for nanoparticle detection with thin nanopores

Optimal voltages were found for particle detections, at which the current blockade ratio did not depend on surface charge density.

Discriminating single-bacterial shape using low-aspect-ratio pores

Conventional concepts of resistive pulse analysis is to discriminate particles in liquid by the difference in their size through comparing the amount of ionic current blockage. In sharp contrast, we herein report a proof-of-concept demonstration of the shape sensing capability of solid-state pore sensors by leveraging the synergy between nanopore technology and machine learning. We found ionic current spikes of similar patterns for two bacteria reflecting the closely resembled morphology and size in an ultra-low thickness-to-diameter aspect-ratio pore. We examined the feasibility of a machine learning strategy to pattern-analyse the sub-nanoampere corrugations in each ionic current waveform and identify characteristic electrical signatures signifying nanoscopic differences in the microbial shape, thereby demonstrating discrimination of single-bacterial cells with accuracy up to 90%. This data-analytics-driven microporescopy capability opens new applications of resistive pulse analyses for screening viruses and bacteria by their unique morphologies at a single-particle level.

Probing charges on solid-liquid interfaces with the resistive-pulse technique

Our manuscript addresses the issue of probing an effective surface charge that any surface can acquire at the solid/liquid interface. Even if a particle is predicted to be neutral based on its chemical structure, the particle can carry finite surface charges when placed in a solution. We present tools to probe the presence of surface charge densities of meso-particles, characterized with zeta potentials below 10 mV. The tools are based on the resistive-pulse technique, which uses single pores to probe properties of individual objects including molecules, particles, and cells. The presented experiments were performed with particles 280 and 400 nm in diameter and single pores with opening diameter tuned between ∼ 200 nm and one micron. Surface charge properties were probed in two modes: (i) the passage of the particles through pores of diameters larger than the particles, as well as (ii) an approach curve of a particle to a pore that is smaller than the particle diameter. The curve in the latter mode has a biphasic character starting with a low-amplitude current decrease, followed by a current enhancement reaching an amplitude of ∼10% of the baseline current. The current increase was long-lasting and stable, and shown to strongly depend on the particle surface charge density. The results are explained via voltage-modulation of ionic concentrations in the pore.

Scanning ion conductance microscopy mapping of tunable nanopore membranes

We report on the use of scanning ion conductance microscopy (SICM) for in-situ topographical mapping of single tunable nanopores, which are used for tunable resistive pulse sensing. A customised SICM system was used to map the elastomeric pore membranes repeatedly, using pipettes with tip opening diameters of approximately 50 nm and 1000 nm. The effect of variations on current threshold, scanning step size, and stretching has been studied. Lowering the current threshold increased the sensitivity of the pipette while scanning, up to the point where the tip contacted the surface. An increase in the pore area was observed as the step size was decreased, and with increased stretching. SICM reveals details of the electric field near the pore entrance, which is important for understanding measurements of submicron particles using resistive pulse sensing.

A hybrid resistive pulse-optical detection platform for microfluidic experiments

Resistive-pulse sensing is a label-free method for characterizing individual particles as they pass through ion-conducting channels or pores. During a resistive pulse experiment, the ionic current through a conducting channel is monitored as particles suspended in the solution translocate through the channel. The amplitude of the current decrease during a translocation, or ‘pulse’, depends not only on the ratio of the particle and channel sizes, but also on the particle position, which is difficult to resolve with the resistive pulse signal alone. We present experiments of simultaneous electrical and optical detection of particles passing through microfluidic channels to resolve the positional dependencies of the resistive pulses. Particles were tracked simultaneously in the two signals to create a mapping of the particle position to resistive pulse amplitude at the same instant in time. The hybrid approach will improve the accuracy of object characterization and will pave the way for observing dynamic changes of the objects such as deformation or change in orientation. This combined approach of optical detection and resistive pulse sensing will join with other attempts at hybridizing high-throughput detection techniques such as imaging flow cytometry.

Direction- and Salt-Dependent Ionic Current Signatures for DNA Sensing with Asymmetric Nanopores

Solid-state nanopores are promising tools for single-molecule detection of both DNA and proteins. In this study, we investigated the patterns of ionic current blockades as DNA translocates into or out of the geometric confinement of conically shaped pores across a wide range of salt conditions. We studied how the geometry of a nanopore affects the detected ionic current signal of a translocating DNA molecule over a wide range of salt concentration. The blockade level in the ionic current depends on the translocation direction at a high salt concentration, and at lower salt concentrations we find a nonintuitive ionic current decrease and increase within each single event for the DNA translocations exiting from confinement. We use a recently developed method for synthesizing DNA molecules with multiple position markers, which provides further experimental characterization by matching the position of the DNA in the pore with the observed ionic current signal. Finally, we employ finite element calculations to explain the shapes of the signals observed at all salt concentrations and show that the unexpected current decrease and increase are due to the competing effects of ion concentration polarization and geometric exclusion of ions. Our analysis shows that over a wide range of geometries, voltages, and salt concentrations, we are able to understand the ionic current signals of DNA in asymmetric nanopores, enabling signal optimization in molecular sensing applications.

Electro-osmotic flow through nanopores in thin and ultrathin membranes

We theoretically study how the electro-osmotic fluid velocity in a charged cylindrical nanopore in a thin solid state membrane depends on the pore's geometry, membrane charge, and electrolyte concentration. We find that when the pore's length is comparable to its diameter, the velocity profile develops a concave shape with a minimum along the pore axis unlike the situation in very long nanopores with a maximum velocity along the central pore axis. This effect is attributed to the induced pressure along the nanopore axis due to the fluid flow expansion and contraction near the exit or entrance to the pore and to the reduction of electric field inside the nanopore. The induced pressure is maximal when the pore's length is about equal to its diameter while decreasing for both longer and shorter nanopores. A model for the fluid velocity incorporating these effects is developed and shown to be in a good agreement with numerically computed results.

Rapid structural analysis of nanomaterials in aqueous solutions

Rapid structural analysis of nanoscale matter in a liquid environment represents innovative technologies that reveal the identities and functions of biologically important molecules. However, there is currently no method with high spatio-temporal resolution that can scan individual particles in solutions to gain structural information. Here we report the development of a nanopore platform realizing quantitative structural analysis for suspended nanomaterials in solutions with a high z-axis and xy-plane spatial resolution of 35.8 ± 1.1 and 12 nm, respectively. We used a low thickness-to-diameter aspect ratio pore architecture for achieving cross sectional areas of analyte (i.e. tomograms). Combining this with multiphysics simulation methods to translate ionic current data into tomograms, we demonstrated rapid structural analysis of single polystyrene (Pst) beads and single dumbbell-like Pst beads in aqueous solutions.

Selective Trapping of DNA Using Glass Microcapillaries

We show experimentally that an inexpensive glass microcapillary can accumulate λ-phage DNA at its tip and deliver the DNA into the capillary using a combination of electro-osmotic flow, pressure-driven flow, and electrophoresis. We develop an efficient simulation model based on the electrokinetic equations and the finite-element method to explain this phenomenon. As a proof of concept for the generality of this trapping mechanism we use our numerical model to explore the effect of the salt concentration, the capillary surface charge, the applied voltage, the pressure difference, and the mobility of the analyte molecules. Our results indicate that the simple microcapillary system has the potential to capture a wide range of analyte molecules based on their electrophoretic mobility that extends well beyond our experimental example of λ-phage DNA. Our method for separation and preconcentration of analytes therefore has implications for the development of low-cost lab-on-a-chip devices.

Tailoring particle translocation via dielectrophoresis in pore channels

Understanding and controlling electrophoretic motions of nanoscopic objects in fluidic channels are a central challenge in developing nanopore technology for molecular analyses. Although progress has been made in slowing the translocation velocity to meet the requirement for electrical detections of analytes via picoampere current measurements, there exists no method useful for regulating particle flows in the transverse directions. Here, we report the use of dielectrophoresis to manipulate the single-particle passage through a solid-state pore. We created a trap field by applying AC voltage between electrodes embedded in a low-aspect-ratio micropore. We demonstrated a traffic control of particles to go through center or near side surface via the voltage frequency. We also found enhanced capture efficiency along with faster escaping speed of particles by virtue of the AC-mediated electroosmosis. This method is compatible with nanopore sensing and would be widely applied for reducing off-axis effects to achieve single-molecule identification.