Electrolytic transport through a synthetic nanometer-diameter pore

A network model to predict ionic transport in porous materials

Understanding the dynamics of electric-double-layer (EDL) charging in porous media is essential for advancements in next-generation energy storage devices. Due to the high computational demands of direct numerical simulations and a lack of interfacial boundary conditions for reduced-order models, the current understanding of EDL charging is limited to simple geometries. Here, we present a network model to predict EDL charging in arbitrary networks of long pores in the Debye-Hückel limit without restrictions on EDL thickness and pore radii. We demonstrate that electrolyte transport is described by Kirchhoff's laws in terms of the electrochemical potential of charge (the valence-weighted average of the ion electrochemical potentials) instead of the electric potential. By employing the equivalent circuit representation suggested by these modified Kirchhoff's laws, our methodology accurately captures the spatial and temporal dependencies of charge density and electric potential, matching results obtained from computationally intensive direct numerical simulations. Our network model provides results up to six orders of magnitude faster, enabling the efficient simulation of a triangular lattice of five thousand pores in 6 min. We employ the framework to study the impact of pore connectivity and polydispersity on electrode charging dynamics for pore networks and discuss how these factors affect the time scale, energy density, and power density of capacitive charging. The scalability and versatility of our methodology make it a rational tool for designing 3D-printed electrodes and for interpreting geometric effects on electrode impedance spectroscopy measurements.

Enhanced Selective Ion Transport in Highly Charged Bacterial Cellulose/Boron Nitride Composite Membranes for Thermo-Osmotic Energy Harvesting

Significant untapped energy exists within low-grade heat sources and salinity gradients. Traditional nanofluidic membranes exhibit inherent limitations, including low ion selectivity, high internal resistance, reliance on nonrenewable resources, and instability in aqueous solutions, invariably constraining their practical application. Here, an innovative composite membrane-based nanofluidic system is reported, involving the strategy of integrating tailor-modified bacterial nanofibers with boron nitride nanosheets, enabling high surface charge densities while maintaining a delicate balance between ion selectivity and permeability, ultimately facilitating effective thermo-osmotic energy harvesting. The device exhibits an impressive output power density of 10 W m-2 with artificial seawater and river water at a 50 K temperature gradient. Furthermore, it demonstrates robust power density stability under prolonged exposure to salinity gradients or even at elevated temperatures. This work opens new avenues for the development of nanofluidic systems utilizing composite materials and presents promising solutions for low-grade heat recovery and osmotic energy harvesting.

High-resolution discrimination of homologous and isomeric proteinogenic amino acids in nanopore sensors with ultrashort single-walled carbon nanotubes

The hollow and tubular structure of single-walled carbon nanotubes (SWCNTs) makes them ideal candidates for making nanopores. However, the heterogeneity of SWCNTs hinders the fabrication of robust and reproducible carbon-based nanopore sensors. Here we develop a modified density gradient ultracentrifugation approach to separate ultrashort (≈5-10 nm) SWCNTs with a narrow conductance range and construct high-resolution nanopore sensors with those tubes inserted in lipid bilayers. By conducting ionic current recordings and fluorescent imaging of Ca²⁺ flux through different nanopores, we prove that the ion mobilities in SWCNT nanopores are 3-5 times higher than the bulk mobility. Furthermore, we employ SWCNT nanopores to discriminate homologue or isomeric proteinogenic amino acids, which are challenging tasks for other nanopore sensors. These successes, coupled with the building of SWCNT nanopore arrays, may constitute a crucial part of the recently burgeoning protein sequencing technologies.

On the origins of conductive pulse sensing inside a nanopore

Nanopore sensing is nearly synonymous with resistive pulse sensing due to the characteristic occlusion of ions during pore occupancy, particularly at high salt concentrations. Contrarily, conductive pulses are observed under low salt conditions wherein electroosmotic flow is significant. Most literature reports counterions as the dominant mechanism of conductive events (a molecule-centric theory). However, the counterion theory does not fit well with conductive events occurring via net neutral-charged protein translocation, prompting further investigation into translocation mechanics. Herein, we demonstrate theory and experiments underpinning the translocation mechanism (i.e., electroosmosis or electrophoresis), pulse direction (i.e., conductive or resistive) and shape (e.g., monophasic or biphasic) through fine control of chemical, physical, and electronic parameters. Results from these studies predict strong electroosmosis plays a role in driving DNA events and generating conductive events due to polarization effects (i.e., a pore-centric theory).

Conductive events during nanopore sensing, are seen typically under low salt conditions and widely thought to arise from counterions brought into the pore via analyte. Here, authors show that an imbalance of ionic fluxes lead to conductive events.

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.

Ion Density-Dependent Dynamic Conductance Switching in Biomimetic Graphene Nanopores

Gating in ion transport is at the center of many vital living-substance transmission processes, and understanding how gating works at an atomic level is essential but intricate. However, our understanding and finite experimental findings of subcontinuum ion transport in subnanometer nanopores are still limited, which is out of reach of the classical continuum nanofluidics. Moreover, the influence of ion density on subcontinuum ion transport is poorly understood. Here we report the ion density-dependent dynamic conductance switching process in biomimetic graphene nanopores and explain the phenomenon by a reversible ion absorption mechanism. Our molecular dynamics simulations demonstrate that the cations near the graphene nanopore can interact with the surface charges on the nanopore, thereby realizing the switching of high- and low-conductance states. This work has deepened the understanding of gating in ion transport.

Structure and dynamics of nanoconfined water and aqueous solutions

This review is devoted to discussing recent progress on the structure, thermodynamic, reactivity, and dynamics of water and aqueous systems confined within different types of nanopores, synthetic and biological. Currently, this is a branch of water science that has attracted enormous attention of researchers from different fields interested to extend the understanding of the anomalous properties of bulk water to the nanoscopic domain. From a fundamental perspective, the interactions of water and solutes with a confining surface dramatically modify the liquid's structure and, consequently, both its thermodynamical and dynamical behaviors, breaking the validity of the classical thermodynamic and phenomenological description of the transport properties of aqueous systems. Additionally, man-made nanopores and porous materials have emerged as promising solutions to challenging problems such as water purification, biosensing, nanofluidic logic and gating, and energy storage and conversion, while aquaporin, ion channels, and nuclear pore complex nanopores regulate many biological functions such as the conduction of water, the generation of action potentials, and the storage of genetic material. In this work, the more recent experimental and molecular simulations advances in this exciting and rapidly evolving field will be reported and critically discussed.

Water molecules in CNT-Si3N4 membrane: Properties and the separation effect for water-alcohol solution

Water confined in carbon nanotubes (CNTs) has been intensively studied because of its unique properties and potential for various applications and is often embedded in silicon nitride (Si₃N₄) membranes. However, the understanding of the influence of Si₃N₄ on the properties of water in CNTs lacks clarity. In this study, we performed molecular dynamics simulations to investigate the effect of the Si₃N₄ membrane on water molecules inside CNTs. The internal electric field generated in the CNTs by the point charges of the Si₃N₄ membrane changes the structure and dynamical properties of water in the nanotubes, causing it to attain a disordered structure. The Si₃N₄ membrane decreases the diffusivity of water in the CNTs; this is because the Coulomb potential energy (i.e., electrostatic interaction) of water decreases owing to the presence of Si₃N₄, whereas the Lennard-Jones potential energy (i.e., van der Waals interaction) does not change significantly. Furthermore, electrostatic interactions make the water structure more stable in the CNTs. As a result, the Si₃N₄ membrane enhances the separation effect of the water-methanol mixture with CNTs in the presence of an external electric field. Furthermore, the threshold of the external electric field strength to induce water-methanol separation with CNTs is reduced owing to the presence of a silicon nitride membrane.

Surface Charge Density Inside a Silicon Nitride Nanopore

Surface charges inside a nanopore determine the zeta potential and ion distributions and play a significant role in affecting ion transport and the sensitivity of detecting biomolecules. It is of great importance to study the fluctuation of surface charges with the salt concentration and pH in various applications of nanopores. Herein, we proposed a theoretical model to predict the surface charge density of a Si₃N₄ nanopore, in which both silanol and amine groups were taken into account. It was demonstrated that the surface charge density in the Si₃N₄ nanopore changes not only with pH but also with the salt concentration. The theoretical model could well predict the experimental results with different salt concentrations, pH values, and pore sizes. The effect of surface functional groups on the isopotential point (pH_iep) of the Si₃N₄ nanopore was also systematically studied. The results indicated that the silanol groups are major determinants of the surface charge, but the influences of the amine groups should not be ignored because the small number of amine groups can change pH_iep dramatically. The pH_iep value of the Si₃N₄ nanopore was measured as 4.1, and the ratio of amine over silanol was ascertained as 0.013.

Investigation of entrance effects on particle electrophoretic behavior near a nanopore for resistive pulse sensing

Resistive pulse sensing using solid-state nanopores provides a unique platform for detecting the structure and concentration of molecules of different types of analytes in an electrolyte solution. The capture of an entity into a nanopore is subject not only to the electrostatic force but also the effect of electroosmotic flow originating from the charged nanopore surface. In this study, we theoretically analyze spherical particle electrophoretic behavior near the entrance of a charged nanopore. By investigating the effects of pore size, particle-pore distance, and salt concentration on particle velocity, we summarize dominant mechanisms governing particle behavior for a range of conditions. In the literature, the Helmholtz-Smoluchowski equation is often adopted to evaluate particle translocation by considering the zeta potential difference between the particle and nanopore surfaces. We point out that, due to the difference of the electric field inside and outside the nanopore and the influence from the existence of the particle itself, the zeta potential of the particle, however, needs to be at least 30% higher than that of the nanopore to allow the particle to enter into the nanopore when its velocity is close to zero. Accordingly, we summarize the effective salt concentrations that enable successful particle capture and detection for different pore sizes, offering direct guidance for nanopore applications.

Ion transport in electrolytes of dielectric nanodevices

Ion transport in electrolytes with nanoscale confinements is of great importance in many fields such as nanofluidics and electrochemical energy devices. The mobility and conductance for ions are often described by the classical Debye-Hückel-Onsager (DHO) theory but this theory fails for ions near dielectric interfaces. We propose a generalized DHO theory by using the Wentzel-Kramers-Brillouin techniques for the solution of the Onsager-Fuoss equation with variable coefficients. The theory allows to quantitatively measure physical quantities of ion transport in nanodevices and is demonstrated to well explain the abnormal increase or decrease of the ionic mobility tuned via the dielectric mismatch. By numerical calculations, our theory unravels the crucial role of the size of confinements and the ionic concentration on the ion transport, and demonstrates that the dielectric polarization can provide a giant enhancement on the conductance of electrolytes in nanodevices. This mechanism provides a practical guide for related nanoscale technologies with controllable transport properties.

Enhanced Evaporation of Ultrathin Water Films on Silicon-Terminated Si3N4 Nanopore Membranes

Water evaporation confined in nanoscale is a ubiquitous phenomenon in nature and has crucial importance in a broad range of technical applications. With the nonequilibrium molecular dynamics simulation, we elucidate nanothin water film evaporation characteristics on a silicon nitride nanopore membrane considering the effects of pore size and pore chemistry. Pore chemistry plays the main role in regulating the evaporation flux. The terminated Si atoms on the pore surface lead to a higher evaporation intensity than the N ones. We attribute this enhancement to the transition of the structural properties of fluid, where liquid molecules are packed loosely and disorderedly under the inducement of terminated silicon atoms. The findings in the present work can contribute to the fundamental understanding of the nanopore-enhanced evaporation process and provide new guidance to the design of advanced nanopore membrane materials.

Overlimiting current near a nanochannel a new insight using molecular dynamics simulations

In this paper, we report for the first time overlimiting current near a nanochannel using all-atom molecular dynamics (MD) simulations. Here, the simulated system consists of a silicon nitride nanochannel integrated with two reservoirs. The reservoirs are filled with [Formula: see text] potassium chloride (KCl) solution. A total of [Formula: see text] million atoms are simulated with a total simulation time of [Formula: see text] over [Formula: see text] 30000 CPU hours using 128 core processors (Intel(R) E5-2670 2.6 GHz Processor). The origin of overlimiting current is found to be due to an increase in chloride ([Formula: see text]) ion concentration inside the nanochannel leading to an increase in ionic conductivity. Such effects are seen due to charge redistribution and focusing of the electric field near the interface of the nanochannel and source reservoir. Also, from the MD simulations, we observe that the earlier theoretical and experimental postulations of strong convective vortices resulting in overlimiting current are not the true origin for overlimiting current. Our study may open up new theories for the mechanism of overlimiting current near the nanochannel interconnect devices.

Engineering adjustable two-pore devices for parallel ion transport and DNA translocations

We report ionic current and double-stranded DNA (dsDNA) translocation measurements through solid-state membranes with two TEM-drilled ∼3-nm diameter silicon nitride nanopores in parallel. Nanopores are fabricated with similar diameters but varying in effective thicknesses (from 2.6 to 10 nm) ranging from a thickness ratio of 1:1 to 1:3.75, producing distinct conductance levels. This was made possible by locally thinning the silicon nitride membrane to shape the desired topography with nanoscale precision using electron beam lithography (EBL). Two nanopores are engineered and subsequently drilled in either the EBL-thinned or the surrounding membrane region. By designing the interpore separation a few orders of magnitude larger than the pore diameter (e.g., ∼900 vs 3 nm), we show analytically, numerically, and experimentally that the total conductance of the two pores is the sum of the individual pore conductances. For a two-pore device with similar diameters yet thicknesses in the ratio of 1:3, a ratio of ∼1:2.2 in open-pore conductances and translocation current signals is expected, as if they were measured independently. Introducing dsDNA as analytes to both pores simultaneously, we detect more than 12 000 events within 2 min and trace them back with a high likelihood to which pore the dsDNA translocated through. Moreover, we monitor translocations through one active pore only when the other pore is clogged. This work demonstrates how two-pore devices can fundamentally open up a parallel translocation reading system for solid-state nanopores. This approach could be creatively generalized to more pores with desired parameters given a sufficient signal-to-noise ratio.

Nanoscale Ion Regulation in Wood-Based Structures and Their Device Applications

Ion transport and regulation are fundamental processes for various devices and applications related to energy storage and conversion, environmental remediation, sensing, ionotronics, and biotechnology. Wood-based materials, fabricated by top-down or bottom-up approaches, possess a unique hierarchically porous fibrous structure that offers an appealing material platform for multiscale ion regulation. The ion transport behavior in these materials can be regulated through structural and compositional engineering from the macroscale down to the nanoscale, imparting wood-based materials with multiple functions for a range of emerging applications. A fundamental understanding of ion transport behavior in wood-based structures enhances the capability to design high-performance ion-regulating devices and promotes the utilization of sustainable wood materials. Combining this unique ion regulation capability with the renewable and cost-effective raw materials available, wood and its derivatives are the natural choice of materials toward sustainability.

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.

Beyond mass spectrometry, the next step in proteomics

Proteins can be the root cause of a disease, and they can be used to cure it. The need to identify these critical actors was recognized early (1951) by Sanger; the first biopolymer sequenced was a peptide, insulin. With the advent of scalable, single-molecule DNA sequencing, genomics and transcriptomics have since propelled medicine through improved sensitivity and lower costs, but proteomics has lagged behind. Currently, proteomics relies mainly on mass spectrometry (MS), but instead of truly sequencing, it classifies a protein and typically requires about a billion copies of a protein to do it. Here, we offer a survey that illuminates a few alternatives with the brightest prospects for identifying whole proteins and displacing MS for sequencing them. These alternatives all boast sensitivity superior to MS and promise to be scalable and seem to be adaptable to bioinformatics tools for calling the sequence of amino acids that constitute a protein.

Transport Properties of Nanoporous, Chemically Forced Biological Lattices

Permselective nanochannels are ubiquitous in biological systems, controlling ion transport and maintaining a potential difference across a cell surface. Surface layers (S-layers) are proteinaceous, generally charged lattices punctuated with nanoscale pores that form the outermost cell envelope component of virtually all archaea and many bacteria. Ammonia oxidizing archaea (AOA) obtain their energy exclusively from oxidizing ammonia directly below the S-layer lattice, but how the charged surfaces and nanochannels affect availability of NH₄⁺ at the reaction site is unknown. Here, we examine the electrochemical properties of negatively charged S-layers for asymmetrically forced ion transport governed by Michaelis-Menten kinetics at ultralow concentrations. Our 3-dimensional electrodiffusion reaction simulations revealed that a negatively charged S-layer can invert the potential across the nanochannel to favor chemically forced NH₄⁺ transport, analogous to polarity switching in nanofluidic field-effect transistors. Polarity switching was not observed when only the interior of the nanochannels was charged. We found that S-layer charge, nanochannel geometry, and enzymatic turnover rate are finely tuned to elevate NH₄⁺ concentration at the active site, potentially enabling AOA to occupy nutrient-poor ecological niches. Strikingly, and in contrast to voltage-biased systems, magnitudes of the co- and counterion currents in the charged nanochannels were nearly equal and amplified disproportionally to the NH₄⁺ current. Our simulations suggest that engineered arrays of crystalline proteinaceous membranes could find unique applications in industrial energy conversion or separation processes.

Specific ion effects at graphitic interfaces

Improved understanding of aqueous solutions at graphitic interfaces is critical for energy storage and water desalination. However, many mechanistic details remain unclear, including how interfacial structure and response are dictated by intrinsic properties of solvated ions under applied voltage. In this work, we combine hybrid first-principles/continuum simulations with electrochemical measurements to investigate adsorption of several alkali-metal cations at the interface with graphene and within graphene slit-pores. We confirm that adsorption energy increases with ionic radius, while being highly dependent on the pore size. In addition, in contrast with conventional electrochemical models, we find that interfacial charge transfer contributes non-negligibly to this interaction and can be further enhanced by confinement. We conclude that the measured interfacial capacitance trends result from a complex interplay between voltage, confinement, and specific ion effects-including ion hydration and charge transfer.

Understanding aqueous solutions at graphitic interfaces is critical in a wide variety of emerging technologies. Here, the authors unravel specific ion effects at the interface with graphene and within graphene slit-pores by coupling first-principles simulations and electrochemical measurements.

Current Enhancement in Solid-State Nanopores Depends on Three-Dimensional DNA Structure

The translocation of double-stranded DNA through a solid-state nanopore may either decrease or increase the ionic current depending on the ionic concentration of the surrounding solution. Below a certain crossover ionic concentration, the current change inverts from a current blockade to current enhancement. In this paper, we show that the crossover concentration for bundled DNA nanostructures composed of multiple connected DNA double-helices is lower than that of double-stranded DNA. Our measurements suggest that counterion mobility in the vicinity of DNA is reduced depending on the three-dimensional structure of the molecule. We further demonstrate that introducing neutral polymers such as polyethylene glycol into the measurement solution reduces electroosmotic outflow from the nanopore, allowing translocation of large DNA structures at low salt concentrations. Our experiments contribute to an improved understanding of ion transport in confined DNA environments, which is critical for the development of nanopore sensing techniques as well as synthetic membrane channels. Our salt-dependent measurements of model DNA nanostructures will guide the development of computational models of DNA translocation through nanopores.

Measurements of the size and correlations between ions using an electrolytic point contact

The size of an ion affects everything from the structure of water to life itself. In this report, to gauge their size, ions dissolved in water are forced electrically through a sub-nanometer-diameter pore spanning a thin membrane and the current is measured. The measurements reveal an ion-selective conductance that vanishes in pores <0.24 nm in diameter-the size of a water molecule-indicating that permeating ions have a grossly distorted hydration shell. Analysis of the current noise power spectral density exposes a threshold, below which the noise is independent of current, and beyond which it increases quadratically. This dependence proves that the spectral density, which is uncorrelated below threshold, becomes correlated above it. The onset of correlations for Li+, Mg2+, Na+ and K+-ions extrapolates to pore diameters of 0.13 ± 0.11 nm, 0.16 ± 0.11 nm, 0.22 ± 0.11 nm and 0.25 ± 0.11 nm, respectively-consonant with diameters at which the conductance vanishes and consistent with ions moving through the sub-nanopore with distorted hydration shells in a correlated way.

Review on the Macro-Transport Processes Theory for Irregular Pores able to Perform Catalytic Reactions

We review and generalize a recent theoretical framework that provides a sound physicochemical basis to describe how volume and surface diffusion are affected by adsorption and desorption processes, as well as by catalytic conversion within the space defined by the irregular geometry of the pores in a material. The theory is based on two single-dimensional mass conservation equations for irregular domains deduced for the volumetric (bulk) and surface mass concentrations. It offers a powerful tool for analyzing and modeling mass transport across porous media like zeolites or artificially build materials, since it establishes how the microscopic quantities that refer to the internal details of the geometry, the flow and the interactions within the irregular pore can be translated into macroscopic variables that are currently measured in experiments. The use of the theory in mass uptake experiments is explained in terms of breakthrough curves and effective mass diffusion coefficients which are explicitly related to the internal geometry of the pores.

Drastically Reduced Ion Mobility in a Nanopore Due to Enhanced Pairing and Collisions between Dehydrated Ions

Ion transport through nanopores is a process of fundamental significance in nature and in engineering practice. Over the past decade, it has been found that the ion conductivity in nanopores could be drastically enhanced, and different mechanisms have been proposed to explain this observation. To date, most reported studies have been carried out with relatively dilute electrolytes, while ion transport in nanopores under high electrolyte concentrations (>1 M) has been rarely explored. Through systematic experimental and atomistic simulation studies with NaCl solutions, here we show that at high electrolyte concentrations, ion mobility in small nanopores could be significantly reduced from the corresponding bulk value. Subsequent molecular dynamics studies indicate that in addition to the low mobility of surface-bound ions in the Stern layer, enhanced pairing and collisions between partially dehydrated ions of opposite charges also make important contributions to the reduced ion mobility. Furthermore, we show that the extent of mobility reduction depends on the association constant between cations and anions in different electrolytes with a more drastic reduction for a larger association constant.

Colloquium: Ionic phenomena in nanoscale pores through 2D materials

Ion transport through nanopores permeates through many areas of science and technology, from cell behavior to sensing and separation to catalysis and batteries. Two-dimensional materials, such as graphene, molybdenum disulfide (MoS₂), and hexagonal boron nitride (hBN), are recent additions to these fields. Low-dimensional materials present new opportunities to develop filtration, sensing, and power technologies, encompassing ion exclusion membranes, DNA sequencing, single molecule detection, osmotic power generation, and beyond. Moreover, the physics of ionic transport through pores and constrictions within these materials is a distinct realm of competing many-particle interactions (e.g., solvation/dehydration, electrostatic blockade, hydrogen bond dynamics) and confinement. This opens up alternative routes to creating biomimetic pores and may even give analogues of quantum phenomena, such as quantized conductance, in the classical domain. These prospects make membranes of 2D materials - i.e., 2D membranes - fascinating. We will discuss the physics and applications of ionic transport through nanopores in 2D membranes.

Method for Dynamically Detecting Secretions from Single Cells Using a Nanopore

Secreted proteins mediate cell-to-cell communications. Thus, eavesdropping on the secretome could reveal the cellular phenotype, but it is challenging to detect the proteins because they are secreted only in minute amounts and then diluted in blood plasma or contaminated by cell culture medium or the lysate. In this pilot study, it is demonstrated that secretions from single cancer cells can be detected and dynamically analyzed through measurements of blockades in the electrolytic current due to single molecules translocating through a nanopore in a thin inorganic membrane. It is established that the distribution of blockades can be used to differentiate three different cancer cell lines (U937, MDA-MB-231, and MCF-7) in real time and quickly (<20 s). Importantly, the distinctive blockades associated with the chemokine CCL5, a prognostic factor for disease progression in breast cancer, along with other low-mass biomarkers of breast cancer (PI3, TIMP1, and MMP1) were identified in the context of the secretome of these three cell types, tracked with time, and used to provide information on the cellular phenotype.

Nutrient transport suggests an evolutionary basis for charged archaeal surface layer proteins

Surface layers (S-layers) are two-dimensional, proteinaceous, porous lattices that form the outermost cell envelope component of virtually all archaea and many bacteria. Despite exceptional sequence diversity, S-layer proteins (SLPs) share important characteristics such as their ability to form crystalline sheets punctuated with nano-scale pores, and their propensity for charged amino acids, leading to acidic or basic isoelectric points. However, the precise function of S-layers, or the role of charged SLPs and how they relate to cellular metabolism is unknown. Nano-scale lattices affect the diffusion behavior of low-concentration solutes, even if they are significantly smaller than the pore size. Here, we offer a rationale for charged S-layer proteins in the context of the structural evolution of S-layers. Using the ammonia-oxidizing archaea (AOA) as a model for S-layer geometry, and a 2D electrodiffusion reaction computational framework to simulate diffusion and consumption of the charged solute ammonium (NH₄⁺), we find that the characteristic length scales of nanoporous S-layers elevate the concentration of NH₄⁺ in the pseudo-periplasmic space. Our simulations suggest an evolutionary, mechanistic basis for S-layer charge and shed light on the unique ability of some AOA to oxidize ammonia in environments with nanomolar NH₄⁺ availability, with broad implications for comparisons of ecologically distinct populations.

Reversible Immobilization of Proteins in Sensors and Solid-State Nanopores

The controlled functionalization of surfaces with proteins is crucial for many analytical methods in life science research and biomedical applications. Here, a coating for silica-based surfaces is established which enables stable and selective immobilization of proteins with controlled orientation and tunable surface density. The coating is reusable, retains functionality upon long-term storage in air, and is applicable to surfaces of complex geometry. The protein anchoring method is validated on planar surfaces, and then a method is developed to measure the anchoring process in real time using silicon nitride solid-state nanopores. For surface attachment, polyhistidine tags that are site specifically introduced into recombinant proteins are exploited, and the yeast nucleoporin Nsp1 is used as model protein. Contrary to the commonly used covalent thiol chemistry, the anchoring of proteins via polyhistidine tag is reversible, permitting to take proteins off and replace them by other ones. Such switching in real time in experiments on individual nanopores is monitored using ion conductivity. Finally, it is demonstrated that silica and gold surfaces can be orthogonally functionalized to accommodate polyhistidine-tagged proteins on silica but prevent protein binding to gold, which extends the applicability of this surface functionalization method to even more complex sensor devices.

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.

Enhanced water transport and salt rejection through hydrophobic zeolite pores

The potential of improvements to reverse osmosis (RO) desalination by incorporating porous nanostructured materials such as zeolites into the selective layer in the membrane has spurred substantial research efforts over the past decade. However, because of the lack of methods to probe transport across these materials, it is still unclear which pore size or internal surface chemistry is optimal for maximizing permeability and salt rejection. We developed a platform to measure the transport of water and salt across a single layer of zeolite crystals, elucidating the effects of internal wettability on water and salt transport through the ≈5.5 Å pores of MFI zeolites. MFI zeolites with a more hydrophobic (i.e., less attractive) internal surface chemistry facilitated an approximately order of magnitude increase in water permeability compared to more hydrophilic MFI zeolites, while simultaneously fully rejecting both potassium and chlorine ions. However, our results also demonstrated approximately two orders of magnitude lower permeability compared to molecular simulations. This decreased performance suggests that additional transport resistances (such as surface barriers, pore collapse or blockages due to contamination) may be limiting the performance of experimental nanostructured membranes. Nevertheless, the inclusion of hydrophobic sub-nanometer pores into the active layer of RO membranes should improve both the water permeability and salt rejection of future RO membranes (Fasano et al 2016 Nat. Commun. 7 12762).

Discriminating Residue Substitutions in a Single Protein Molecule Using a Sub-nanopore

It is now possible to create, in a thin inorganic membrane, a single, sub-nanometer-diameter pore (i.e., a sub-nanopore) about the size of an amino acid residue. To explore the prospects for sequencing protein with it, measurements of the force and current were performed as two denatured histones, which differed by four amino acid residue substitutions, were impelled systematically through the sub-nanopore one at a time using an atomic force microscope. The force measurements revealed that once the denatured protein, stabilized by sodium dodecyl sulfate (SDS), translocated through the sub-nanopore, a disproportionately large force was required to pull it back. This was interpreted to mean that the SDS was cleaved from the protein during the translocation. The force measurements also exposed a dichotomy in the translocation kinetics: either the molecule slid nearly frictionlessly through the pore or it slipped-and-stuck. When it slid frictionlessly, regardless of whether the molecule was pulled N-terminus or C-terminus first through the pore, regular patterns were observed intermittently in the force and blockade current fluctuations that corresponded to the distance between stretched residues. Furthermore, the amplitude of the fluctuations in the current blockade were correlated with the occluded volume associated with the amino acid residues in the pore. Finally, a comparison of the patterns in the current fluctuations associated with the two practically identical histones supported the conclusion that a sub-nanopore was sensitive enough to discriminate amino acid substitutions in the sequence of a single protein molecule by measuring volumes of 0.1 nm³ per read.

Relation between the porosity and tortuosity of a membrane formed by disconnected irregular pores and the spatial diffusion coefficient of the Fick-Jacobs model

In this work, we provide a theoretical relationship between the spatial-dependent diffusion coefficient derived in the Fick-Jacobs (FJ) approximation and the macroscopic diffusion coefficient of a membrane that depends on the porosity, tortuosity, and the constriction factors. Based on simple mass conservation arguments under equilibrium as well as in nonequilibrium conditions, we generalize previous expressions for the effective diffusion coefficient of an irregular pore, originally obtained by Festa and d'Agliano for horizontal and periodic pores, and then extended by Bradley for tortuous periodic pores, to the case of pores with arbitrary geometry. Through a formal definition of the constrictivity factor in terms of the geometry of the pore, our results provide very clear physical interpretation of experimental measurements since they link the local properties of the flow with macroscopic quantities of experimental relevance in the design and optimization of porous materials. The macroscopic diffusion coefficient as well as the spatiotemporal evolution of the concentration profiles inside a pore have been recently measured by using pulse field gradient NMR techniques. The advantage of using the FJ approach is that the spatiotemporal concentration profile inside a pore of irregular geometry is directly related to the pore's shape and, therefore, that the macroscopic diffusion coefficient can be obtained by comparing the spatiotemporal concentration profiles from such experiments with those of the theoretical model. Hence, the present study is relevant for the understanding of the transport properties of porous materials where the shape and arrangement of pores can be controlled at will.

Single-Walled Carbon Nanotubes: Mimics of Biological Ion Channels

Here we report on the ion conductance through individual, small diameter single-walled carbon nanotubes. We find that they are mimics of ion channels found in natural systems. We explore the factors governing the ion selectivity and permeation through single-walled carbon nanotubes by considering an electrostatic mechanism built around a simplified version of the Gouy-Chapman theory. We find that the single-walled carbon nanotubes preferentially transported cations and that the cation permeability is size-dependent. The ionic conductance increases as the absolute hydration enthalpy decreases for monovalent cations with similar solid-state radii, hydrated radii, and bulk mobility. Charge screening experiments using either the addition of cationic or anionic polymers, divalent metal cations, or changes in pH reveal the enormous impact of the negatively charged carboxylates at the entrance of the single-walled carbon nanotubes. These observations were modeled in the low-to-medium concentration range (0.1-2.0 M) by an electrostatic mechanism that mimics the behavior observed in many biological ion channel-forming proteins. Moreover, multi-ion conduction in the high concentration range (>2.0 M) further reinforces the similarity between single-walled carbon nanotubes and protein ion channels.

Precise fabrication of a 5 nm graphene nanopore with a helium ion microscope for biomolecule detection

We report a scalable method to fabricate high-quality graphene nanopores for biomolecule detection using a helium ion microscope (HIM). HIM milling shows promising capabilities for precisely controlling the size and shape, and may allow for the potential production of nanopores at wafer scale. Nanopores could be fabricated at different sizes ranging from 5 to 30 nm in diameter in few minutes. Compared with the current solid-state nanopore fabrication techniques, e.g. transmission electron microscopy, HIM is fast. Furthermore, we investigated the exposure-time dependence of graphene nanopore formation: the rate of pore expansion did not follow a simple linear relationship with exposure time, but a fast expansion rate at short exposure time and a slow rate at long exposure time. In addition, we performed biomolecule detection with our patterned graphene nanopore. The ionic current signals induced by 20-base single-stranded DNA homopolymers could be used as a basis for homopolymer differentiation. However, the charge interaction of homopolymer chains with graphene nanopores, and the conformations of homopolymer chains need to be further considered to improve the accuracy of discrimination.

Silicon Nitride Thin Films for Nanofluidic Device Fabrication

Silicon nitride is a ubiquitous and well-established nanofabrication material with a host of favourable properties for creating nanofluidic devices with a range of compelling designs that offer extraordinary discovery potential. Nanochannels formed between two thin silicon nitride windows can open up vistas for exploration by freeing transmission electron microscopy to interrogate static structures and structural dynamics in liquid-based samples. Nanopores present a strikingly different architecture—nanofluidic channels through a silicon nitride membrane—and are one of the most promising tools to emerge in biophysics and bioanalysis, offering outstanding capabilities for single molecule sensing. The constrained environments in such nanofluidic devices make surface chemistry a vital design and performance consideration. Silicon nitride has a rich and complex surface chemistry that, while too often formidable, can be tamed with new, robust surface functionalization approaches. We will explore how a simple structural element—a ∼100 nm-thick silicon nitride window—can be used to fabricate devices to wrest unprecedented insights from the nanoscale world. We will detail the intricacies of native silicon nitride surface chemistry, present surface chemical modification routes that leverage the richness of available surface moieties, and examine the effect of engineered chemical surface functionality on nanofluidic device character and performance.

Reading the primary structure of a protein with 0.07 nm3 resolution using a subnanometre-diameter pore

The primary structure of a protein consists of a sequence of amino acids and is a key factor in determining how a protein folds and functions. However, conventional methods for sequencing proteins, such as mass spectrometry and Edman degradation, suffer from short reads and lack sensitivity, so alternative approaches are sought. Here, we show that a subnanometre-diameter pore, sputtered through a thin silicon nitride membrane, can be used to detect the primary structure of a denatured protein molecule. When a denatured protein immersed in electrolyte is driven through the pore by an electric field, measurements of a blockade in the current reveal nearly regular fluctuations, the number of which coincides with the number of residues in the protein. Furthermore, the amplitudes of the fluctuations are highly correlated with the volumes that are occluded by quadromers (four residues) in the primary structure. Each fluctuation, therefore, represents a read of a quadromer. Scrutiny of the fluctuations reveals that the subnanometre pore is sensitive enough to read the occluded volume that is related to post-translational modifications of a single residue, measuring volume differences of ∼0.07 nm³, but it is not sensitive enough to discriminate between the volumes of all twenty amino acids.

Electrostatic-Charge- and Electric-Field-Induced Smart Gating for Water Transportation

Regulating and controlling the transport of water across nanochannels is of great importance in both fundamental research and practical applications because it is difficult to externally control water flow through nanochannels as in biological channels. To date, only a few hydrophobic nanochannels controlling the transport of water have been reported, all of which use exotic hydrophobic molecules. However, the effect of electrostatic charges, which plays an indispensable role in membrane proteins and dominates the energetics of water permeation across aquaporins, has not gained enough attention to control water transport through a solid-state nanochannel/nanopore. Here, we report electrostatic-charge-induced water gating of a single ion track-etched sub-10 nm channel. This system can directly realize the gating transition between an open, conductive state and a closed, nonconductive state by regulating the surface charge density through a process that involves alternating capillary evaporation and capillary condensation. Compared to the introduction of exotic hydrophobic molecules, water gating controlled by electrostatic charges is simple, convenient, and effective. Such a system anticipates potential applications including desalination, controllable valves, and drug delivery systems.

Observation of ionic Coulomb blockade in nanopores

Emergent behaviour from electron-transport properties is routinely observed in systems with dimensions approaching the nanoscale. However, analogous mesoscopic behaviour resulting from ionic transport has so far not been observed, most probably because of bottlenecks in the controlled fabrication of subnanometre nanopores for use in nanofluidics. Here, we report measurements of ionic transport through a single subnanometre pore junction, and the observation of ionic Coulomb blockade: the ionic counterpart of the electronic Coulomb blockade observed for quantum dots. Our findings demonstrate that nanoscopic, atomically thin pores allow for the exploration of phenomena in ionic transport, and suggest that nanopores may also further our understanding of transport through biological ion channels.

Direct Sensing and Discrimination among Ubiquitin and Ubiquitin Chains Using Solid-State Nanopores

Nanopore sensing involves an electrophoretic transport of analytes through a nanoscale pore, permitting label-free sensing at the single-molecule level. However, to date, the detection of individual small proteins has been challenging, primarily due to the poor signal/noise ratio that these molecules produce during passage through the pore. Here, we show that fine adjustment of the buffer pH, close to the isoelectric point, can be used to slow down the translocation speed of the analytes, hence permitting sensing and characterization of small globular proteins. Ubiquitin (Ub) is a small protein of 8.5 kDa, which is well conserved in all eukaryotes. Ub conjugates to proteins as a posttranslational modification called ubiquitination. The immense diversity of Ub substrates, as well as the complexity of Ub modification types and the numerous physiological consequences of these modifications, make Ub and Ub chains an interesting and challenging subject of study. The ability to detect Ub and to identify Ub linkage type at the single-molecule level may provide a novel tool for investigation in the Ub field. This is especially adequate because, for most ubiquitinated substrates, Ub modifies only a few molecules in the cell at a given time. Applying our method to the detection of mono- and poly-Ub molecules, we show that we can analyze their characteristics using nanopores. Of particular importance is that two Ub dimers that are equal in molecular weight but differ in 3D structure due to their different linkage types can be readily discriminated. Thus, to our knowledge, our method offers a novel approach for analyzing proteins in unprecedented detail using solid-state nanopores. Specifically, it provides the basis for development of single-molecule sensing of differently ubiquitinated substrates with different biological significance. Finally, our study serves as a proof of concept for approaching nanopore detection of sub-10-kDa proteins and demonstrates the ability of this method to differentiate among native and untethered proteins of the same mass.

Nanopore-based analysis of biochemical species

Biological nanochannels or nanopores play a crucial role in basic biochemical processes in cells. Artificial nanopores possessing dimensions comparable to the size of biological molecules and mimicking the function of biological ion channels are of particular interest with respect to the design of biosensors with a sensitivity that can go down to the fM level and even to single molecule detection. Nanopore-based analysis (NPA) is currently a new research field with fascinating prospects. This review (with 118 refs.) summarizes the progress made in this field in the recent 10 years. Following an introduction into the fundamentals of NPA, we demonstrate its potential by describing selected methods for sensing (a) proteins such as streptavidin, certain antibodies, or thrombin via aptamers; (b) oligomers, larger nucleic acids, or micro-RNA; (c) small molecules, (d) ions such as K(I) which is vital to the maintenance of life, or Hg(II) which is dangerous to health. We summarize the results and discuss the merits and limitations of the various methods at last. Graphical abstractSchematic of a signal-off system and a signal-on system in nanopore analysis. The effective diameter of nanopores decreases when targets undergo certain interactions with receptors attached on the inner surface of the nanopore. Correspondingly, the current will drop on appearance of the analyte. This is referred to as a "signal-off" system. Conversely, it is called a "signal-on" system.

Gate-Modulated Graphene Quantum Point Contact Device for DNA Sensing

In this paper, we present a computational model to describe the electrical response of a constricted graphene nanoribbon (GNR) to biomolecules translocating through a nanopore. For this purpose, we use a self-consistent 3D Poisson equation solver coupled with an accurate three-orbital tight-binding model to assess the ability for a gate electrode to modulate both the carrier concentration as well as the conductance in the GNR. We also investigate the role of electrolytic screening on the sensitivity of the conductance to external charges and find that the gate electrode can either suppress or enhance the screening of biomolecular charges in the nanopore depending on the value of its potential. Translocating a double-stranded DNA molecule along the pore axis imparted a large change in the conductance at particular gate voltages, suggesting that such a device can be used to sense translocating biomolecules and can be actively tuned to maximize its sensitivity.

The influence of nanopore dimensions on the electrochemical properties of nanopore arrays studied by impedance spectroscopy

The understanding of the electrochemical properties of nanopores is the key factor for better understanding their performance and applications for nanopore-based sensing devices. In this study, the influence of pore dimensions of nanoporous alumina (NPA) membranes prepared by an anodization process and their electrochemical properties as a sensing platform using impedance spectroscopy was explored. NPA with four different pore diameters (25 nm, 45 nm and 65 nm) and lengths (5 μm to 20 μm) was used and their electrochemical properties were explored using different concentration of electrolyte solution (NaCl) ranging from 1 to 100 μM. Our results show that the impedance and resistance of nanopores are influenced by the concentration and ion species of electrolytes, while the capacitance is independent of them. It was found that nanopore diameters also have a significant influence on impedance due to changes in the thickness of the double layer inside the pores.

Fabrication of sub-20 nm nanopore arrays in membranes with embedded metal electrodes at wafer scales

We introduce a method to fabricate solid-state nanopores with sub-20 nm diameter in membranes with embedded metal electrodes across a 200 mm wafer using CMOS compatible semiconductor processes. Multi-layer (metal-dielectric) structures embedded in membranes were demonstrated to have high uniformity (± 0.5 nm) across the wafer. Arrays of nanopores were fabricated with an average size of 18 ± 2 nm in diameter using a Reactive Ion Etching (RIE) method in lieu of TEM drilling. Shorts between the membrane-embedded metals were occasionally created after pore formation, but the RIE based pores had a much better yield (99%) of unshorted electrodes compared to TEM drilled pores (<10%). A double-stranded DNA of length 1 kbp was translocated through the multi-layer structure RIE-based nanopore demonstrating that the pores were open. The ionic current through the pore can be modulated with a gain of 3 using embedded electrodes functioning as a gate in 0.1 mM KCl aqueous solution. This fabrication approach can potentially pave the way to manufacturable nanopore arrays with the ability to electrically control the movement of single or double-stranded DNA inside the pore with embedded electrodes.