Ionic current blockade in a nanopore due to an ellipsoidal particle

Nanopores in solid-state membranes have been used to detect, identify, filter, and characterize nanoparticles and biological molecules. In this work, we simulate an ionic flow through a nanopore while an ellipsoidal nanoparticle translocates through a pore. We numerically solve the Poisson-Nernst-Planck equations to obtain the ionic current values for different aspect ratios, sizes, and orientations of a translocating particle. By extending the existing theoretical model for the ionic current in the nanopore to the particles of ellipsoidal shape, we propose semiempirical fitting formulas which describe our computed data within 5% accuracy. We also demonstrate how the derived formulas can be used to identify the dimensions of nanoparticles from the available experimental data which may have useful applications in bionanotechnology.

Catalytic ability characterization of in situ synthesized Pt NP coated SBA-15 within a sub-micropipette

An individual catalytic entity of an n-Pt/SBA-15 composite was synthesized in situ within a sub-micropipette nanoreactor, and its size-dependent catalytic ability was evaluated using the resistance pulse signals of O2 nanobubbles, originating from H2O2 decomposition catalyzed by decorated Pt NPs in the composite.

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.

A reversibly gated protein-transporting membrane channel made of DNA

Controlled transport of biomolecules across lipid bilayer membranes is of profound significance in biological processes. In cells, cargo exchange is mediated by dedicated channels that respond to triggers, undergo a nanomechanical change to reversibly open, and thus regulate cargo flux. Replicating these processes with simple yet programmable chemical means is of fundamental scientific interest. Artificial systems that go beyond nature's remit in transport control and cargo are also of considerable interest for biotechnological applications but challenging to build. Here, we describe a synthetic channel that allows precisely timed, stimulus-controlled transport of folded and functional proteins across bilayer membranes. The channel is made via DNA nanotechnology design principles and features a 416 nm2 opening cross-section and a nanomechanical lid which can be controllably closed and re-opened via a lock-and-key mechanism. We envision that the functional DNA device may be used in highly sensitive biosensing, drug delivery of proteins, and the creation of artificial cell networks.

Effects of off-axis translocation through nanopores on the determination of shape and volume estimates for individual particles

Resistive pulses generated by nanoparticles that translocate through a nanopore contain multi-parametric information about the physical properties of those particles. For example, non-spherical particles sample several different orientations during translocation, producing fluctuations in blockade current that relate to their shape. Due to the heterogenous distribution of electric field from the center to the wall of a nanopore while a particle travels through the pore, its radial position influences the blockade current, thereby affecting the quantification of parameters related to the particle's characteristics. Here, we investigate the influence of these off-axis effects on parameters estimated by performing finite element simulations of dielectric particles transiting a cylindrical nanopore. We varied the size, ellipsoidal shape, and radial position of individual particles, as well as the size of the nanopore. As expected, nanoparticles translocating near the nanopore wall produce increase current blockades, resulting in overestimates of particle volume. We demonstrated that off-axis effects also influence estimates of shape determined from resistive pulse analyses, sometimes producing a multiple-fold deviation in ellipsoidal length-to-diameter ratio between estimates and reference values. By using a nanopore with the minimum possible diameter that still allows the particle to rotate while translocating, off-axis effects on the determination of both volume and shape can be minimized. In addition, tethering the nanoparticles to a fluid coating on the nanopore wall makes it possible to determine an accurate particle shape with an overestimated volume. This work provides a framework to select optimal ratios of nanopore to nanoparticle size for experiments targeting free translocations.

Studies on the Morphology Effect on Catalytic Ability of a Single MnO2 Catalyst Particle with a Solid Nanopipette

Investigating the catalytic ability of an individual catalyst particle helps to understand heterogeneity and can provide new insights into the synthesis of high-efficiency catalysts. Solid-state nanopores have become a promising tool for detecting single molecules/particles due to their high temporal and spatial resolution. Here, we report a nanopore-based strategy for the evaluation and comparison of a single MnO₂ catalyst particle with different morphologies by monitoring the generated O₂ bubbles from the catalytic decomposition of H₂O₂. The finite element simulation was introduced to account for the flow velocity and bubble-induced current variation in the nanopore. In particular, the differences in catalytic ability of spherical and cubic MnO₂ have been studied by calculating the production rate and volume of O₂. It demonstrates that the shape of a single MnO₂ catalyst particle has a significant effect on its catalytic activity indeed.

Application of Micropore Device for Accurate, Easy, and Rapid Discrimination of Saccharomyces pastorianus from Dekkera spp

Traceability analysis, such as identification and discrimination of yeasts used for fermentation, is important for ensuring manufacturing efficiency and product safety during brewing. However, conventional methods based on morphological and physiological properties have disadvantages such as time consumption and low sensitivity. In this study, the resistive pulse method (RPM) was employed to discriminate between Saccharomyces pastorianus and Dekkera anomala and S. pastorianus and D. bruxellensis by measuring the ionic current response of cells flowing through a microsized pore. The height and shape of the pulse signal were used for the simultaneous measurement of the size, shape, and surface charge of individual cells. Accurate discrimination of S. pastorianus from Dekkera spp. was observed with a recall rate of 96.3 ± 0.8%. Furthermore, budding S. pastorianus was quantitatively detected by evaluating the shape of the waveform of the current ionic blockade. We showed a proof-of-concept demonstration of RPM for the detection of contamination of Dekkera spp. in S. pastorianus and for monitoring the fermentation of S. pastorianus through the quantitative detection of budding cells.

Understanding the Giant Gap between Single-Pore- and Membrane-Based Nanofluidic Osmotic Power Generators

Nanofluidic blue energy harvesting attracts great interest due to its high power density and easy-to-implement nature. Proof-of-concept studies on single-pore platforms show that the power density approaches up to 10³ to 10⁶ W m^-2 . However, to translate the estimated high power density into real high power becomes a challenge in membrane-scale applications. The actual power density from existing membrane materials is merely several watts per square meter. Understanding the origin and thereby bridging the giant gap between the single-pore demonstration and the membrane-scale application is therefore highly demanded. In this work, an intuitive resistance paradigm is adopted to show that this giant gap originates from the different ion transport property in porous membrane, which is dominated by both the constant reservoir resistance and the reservoir/nanopore interfacial resistance. In this case, the generated electric power becomes saturated despite the increasing pore number. The theoretical predictions are further compared with existing experimental results in literature. For both single nanopore and multipore membrane, the simulation results excellently cover the range of the experimental results. Importantly, by suppressing the reservoir and interfacial resistances, kW m^-2 to MW m^-2 power density can be achieved with multipore membranes, approaching the level of a single-pore system.

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.

Large Scale Parallel DNA Detection by Two-Dimensional Solid-State Multipore Systems

We describe a scalable device design of a dense array of multiple nanopores made from nanoscale semiconductor materials to detect and identify translocations of many biomolecules in a massively parallel detection scheme. We use molecular dynamics coupled to nanoscale device simulations to illustrate the ability of this device setup to uniquely identify DNA parallel translocations. We show that the transverse sheet currents along membranes are immune to the crosstalk effects arising from simultaneous translocations of biomolecules through multiple pores, due to their ability to sense only the local potential changes. We also show that electronic sensing across the nanopore membrane offers a higher detection resolution compared to ionic current blocking technique in a multipore setup, irrespective of the irregularities that occur while fabricating the nanopores in a two-dimensional membrane.

Signal and Noise in FET-Nanopore Devices

The combination of a nanopore with a local field-effect transistor (FET-nanopore), like a nanoribbon, nanotube, or nanowire, in order to sense single molecules translocating through the pore is promising for DNA sequencing at megahertz bandwidths. Previously, it was experimentally determined that the detection mechanism was due to local potential fluctuations that arise when an analyte enters a nanopore and constricts ion flow through it, rather than the theoretically proposed mechanism of direct charge coupling between the DNA and nanowire. However, there has been little discussion on the experimentally observed detection mechanism and its relation to the operation of real devices. We model the intrinsic signal and noise in such an FET-nanopore device and compare the results to the ionic current signal. The physical dimensions of DNA molecules limit the change in gate voltage on the FET to below 40 mV. We discuss the low-frequency flicker noise (<10 kHz), medium-frequency thermal noise (<100 kHz), and high-frequency capacitive noise (>100 kHz) in FET-nanopore devices. At bandwidths dominated by thermal noise, the signal-to-noise ratio in FET-nanopore devices is lower than in the ionic current signal. At high frequencies, where noise due to parasitic capacitances in the amplifier and chip is the dominant source of noise in ionic current measurements, high-transconductance FET-nanopore devices can outperform ionic current measurements.

Entrance Effects Induced Rectified Ionic Transport in a Nanopore/Channel

The nanofluidic diode, as one of the emerging nanofluidic logic devices, has been used in many fields such as biosensors, energy harvesting, and so on. However, the entrance effects of the nanofluidic ionic conductance were less discussed, which can be a crucial factor for the ionic conduction. Here we calculate the ionic conductance as a function of the length-to-pore ratio (L/r), which has a clear boundary between nanopore (surface dominated) and nanochannel (geometry dominated) electrically in diluted salt solution. These entrance effects are even more obvious in the rectified ionic conduction with oppositely charged exterior surfaces of a nanopore. We build three models-Exterior Charged Surface model (ECS), Inner Charged Surface model (ICS), and All Charged Surface model (ACS)-to discuss the entrance effects on the ionic conduction. Our results demonstrate, for a thin nanopore, that the ECS model has a larger ionic rectification factor (Q) than that of ICS model, with a totally reversed tendency of Q compared to the ICS and ACS models as L/r increases. Our models predict an alternative option of building nanofluidic biosensors that only need to modify the exterior surface of a nanopore, avoiding the slow diffusion of molecules in the nanochannel.

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.

Physical Model for Rapid and Accurate Determination of Nanopore Size via Conductance Measurement

Nanopores have been explored for various biochemical and nanoparticle analyses, primarily via characterizing the ionic current through the pores. At present, however, size determination for solid-state nanopores is experimentally tedious and theoretically unaccountable. Here, we establish a physical model by introducing an effective transport length, L_eff, that measures, for a symmetric nanopore, twice the distance from the center of the nanopore where the electric field is the highest to the point along the nanopore axis where the electric field falls to e^-1 of this maximum. By [Formula: see text], a simple expression S₀ = f (G, σ, h, β) is derived to algebraically correlate minimum nanopore cross-section area S₀ to nanopore conductance G, electrolyte conductivity σ, and membrane thickness h with β to denote pore shape that is determined by the pore fabrication technique. The model agrees excellently with experimental results for nanopores in graphene, single-layer MoS₂, and ultrathin SiN_x films. The generality of the model is verified by applying it to micrometer-size pores.

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.

Nanopore-CMOS Interfaces for DNA Sequencing

DNA sequencers based on nanopore sensors present an opportunity for a significant break from the template-based incumbents of the last forty years. Key advantages ushered by nanopore technology include a simplified chemistry and the ability to interface to CMOS technology. The latter opportunity offers substantial promise for improvement in sequencing speed, size and cost. This paper reviews existing and emerging means of interfacing nanopores to CMOS technology with an emphasis on massively-arrayed structures. It presents this in the context of incumbent DNA sequencing techniques, reviews and quantifies nanopore characteristics and models and presents CMOS circuit methods for the amplification of low-current nanopore signals in such interfaces.

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

Resistive pulse sensing with nanopores having a low thickness-to-diameter aspect-ratio structure is expected to enable high-spatial-resolution analysis of nanoscale objects in a liquid. Here we investigated the sensing capability of low-aspect-ratio pore sensors by monitoring the ionic current blockades during translocation of polymeric nanobeads. We detected numerous small current spikes due to partial occlusion of the pore orifice by particles diffusing therein reflecting the expansive electrical sensing zone of the low-aspect-ratio pores. We also found wide variations in the ion current line-shapes in the particle capture stage suggesting random incident angle of the particles drawn into the pore. In sharp contrast, the ionic profiles were highly reproducible in the post-translocation regime by virtue of the spatial confinement in the pore that effectively constricts the stochastic capture dynamics into a well-defined ballistic motion. These results, together with multiphysics simulations, indicate that the resistive pulse height is highly dependent on the nanoscopic single-particle trajectories involved in ultrathin pore sensors. The present finding indicates the importance of regulating the translocation pathways of analytes in low-aspect-ratio pores for improving the discriminability toward single-bioparticle tomography in liquid.

A capacitive-pulse model for nanoparticle sensing by single conical nanochannels

Nanochannel based devices have been widely used for single-molecule detection. The detection usually relies on the resistive-pulse model, where the change of the monitored current depends on the physical volumetric blocking of the nanochannel by the analyte. However, this mechanism requires that the nanochannel diameter should not be much larger than the analyte size, because, otherwise, the resultant current change would be too small to detect, and therefore poses particular challenges for the fabrication of nanochannels. To circumvent this issue, in this report, we propose a different mechanism of capacitive-pulse model, where the transport signals can be significantly magnified by the capacitive effect of the nanochannel. We experimentally demonstrate that current pulses with an averaged peak height of 0.87 nA can be achieved for transporting 60 nm nanoparticles through a conical nanochannel device, whereas the traditional resistive-pulse model only predicts one-order-of-magnitude lowered value. With further comprehensive simulation, the dependence of this effect on the nanochannel geometry as well as the surface charge density for both the nanochannel and the analyte is predicted, which would provide important guidance for better designing of the nanochannel-based sensors.

Ultra-sensitive flow measurement in individual nanopores through pressure – driven particle translocation

A challenge for the development of nanofluidics is to develop new instrumentation tools, able to probe the extremely small mass transport across individual nanochannels.

Interpreting the conductance blockades of DNA translocations through solid-state nanopores

Solid-state nanopore electrical signatures can be convoluted and are thus challenging to interpret. In order to better understand the origin of these conductance changes, we investigate the translocation of DNA through small, thin pores over a range of voltage. We observe multiple, discrete populations of conductance blockades that vary with applied voltage. To describe our observations, we develop a simple model that is applicable to solid-state nanopores generally. These results represent an important step toward understanding the dynamics of the electrokinetic translocation process.

Ion diffusion coefficient measurements in nanochannels at various concentrations

Diffusion is one of the most fundamental properties of ionic transport in solutions. Here, we present experimental studies and theoretical analysis on the ion diffusion in nanochannels. Based on Fick's second law, we develop a current monitoring method to measure ion diffusion coefficient of high solution concentrations in nanochannels. This method is further extended to the cases at medium and low concentrations. Through monitoring ionic current during diffusion, we obtain diffusion coefficients of potassium chloride solution at different concentrations in nanochannels. These diffusion coefficients within the confined space are close to theirs bulk values. It is also found that the apparent ion diffusion equilibrium in the present experiments is very slow at low concentration, which we attribute to the slow equilibrium of the nanochannel surface charge. Finally, we get a primary acknowledge of the equilibrium rate between the nanochannel surface charge and electrolyte solution. The results in this work have improved the understanding of nanoscale diffusion and nanochannel surface charge and may be useful in nanofluidic applications such as ion-selective transport, energy conversion, and nanopore biosensors.