Water-Compression Gating of Nanopore Transport

From salt water to bioceramics: Mimic nature through pressure-controlled hydration and crystallization

Modern synthetic technology generally invokes high temperatures to control the hydration level of ceramics, but even the state-of-the-art technology can still only control the overall hydration content. Magically, natural organisms can produce bioceramics with tailorable hydration profiles and crystallization traits solely from amorphous precursors under physiological conditions. To mimic the biomineralization tactic, here, we report pressure-controlled hydration and crystallization in fabricated ceramics, solely from the amorphous precursors of purely inorganic gels (PIGs) synthesized from biocompatible aqueous solutions with most common ions in organisms (Ca2+, Mg2+, CO32-, and PO43-). Transparent ceramic tablets are directly produced by compressing the PIGs under mild pressure, while the pressure regulates the hydration characteristics and the subsequent crystallization behaviors of the synthesized ceramics. Among the various hydration species, the moderately bound and ordered water appears to be a key in regulating the crystallization rate. This nature-inspired study offers deeper insights into the magic behind biomineralization.

Exploring the non-monotonic DNA capture behavior in a charged graphene nanopore

Nanopore-based biomolecule detection has emerged as a promising and sought-after innovation, offering high throughput, rapidity, label-free analysis, and cost-effectiveness, with potential applications in personalized medicine. However, achieving efficient and tunable biomolecule capture into the nanopore remains a significant challenge. In this study, we employ all-atom molecular dynamics simulations to investigate the capture of double-stranded DNA (dsDNA) molecules into graphene nanopores with varying positive charges. We discover a non-monotonic relationship between the DNA capture rate and the charge of the graphene nanopore. Specifically, the capture rate initially decreases and then increases with an increase in nanopore charge. This behavior is primarily attributed to differences in the electrophoretic force, rather than the influence of electroosmosis or counterions. Furthermore, we also observe this non-monotonic trend in various ionic solutions, but not in ionless solutions. Our findings shed light on the design of novel DNA sequencing devices, offering valuable insights into enhancing biomolecule capture rates in nanopore-based sensing platforms.

DNA double helix, a tiny electromotor

Flowing fluid past chiral objects has been used for centuries to power rotary motion in man-made machines. By contrast, rotary motion in nanoscale biological or chemical systems is produced by biasing Brownian motion through cyclic chemical reactions. Here we show that a chiral biological molecule, a DNA or RNA duplex rotates unidirectionally at billions of revolutions per minute when an electric field is applied along the duplex, with the rotation direction being determined by the chirality of the duplex. The rotation is found to be powered by the drag force of the electro-osmotic flow, realizing the operating principle of a macroscopic turbine at the nanoscale. The resulting torques are sufficient to power rotation of nanoscale beads and rods, offering an engineering principle for constructing nanoscale systems powered by electric field.

Geometrically Induced Selectivity and Unidirectional Electroosmosis in Uncharged Nanopores

Selectivity toward positive and negative ions in nanopores is often associated with electroosmotic flow, the control of which is pivotal in several micro-nanofluidic technologies. Selectivity is traditionally understood to be a consequence of surface charges that alter the ion distribution in the pore lumen. Here we present a purely geometrical mechanism to induce ionic selectivity and electroosmotic flow in uncharged nanopores, and we tested it via molecular dynamics simulations. Our approach exploits the accumulation of charges, driven by an external electric field, in a coaxial cavity that decorates the membrane close to the pore entrance. The selectivity was shown to depend on the applied voltage and becomes completely inverted when reversing the voltage. The simultaneous inversion of ionic selectivity and electric field direction causes a unidirectional electroosmotic flow. We developed a quantitatively accurate theoretical model for designing pore geometry to achieve the desired electroosmotic velocity. Finally, we show that unidirectional electroosmosis also occurs in much more complex scenarios, such as a biological pore whose structure presents a coaxial cavity surrounding the pore constriction as well as a complex surface charge pattern. The capability to induce ion selectivity without altering the pore lumen shape or the surface charge may be useful for a more flexible design of selective membranes.

How capture affects polymer translocation in a solitary nanopore

DNA capture with high fidelity is an essential part of nanopore translocation. We report several important aspects of the capture process and subsequent translocation of a model DNA polymer through a solid-state nanopore in the presence of an extended electric field using the Brownian dynamics simulation that enables us to record statistics of the conformations at every stage of the translocation process. By releasing the equilibrated DNAs from different equipotentials, we observe that the capture time distribution depends on the initial starting point and follows a Poisson process. The field gradient elongates the DNA on its way toward the nanopore and favors a successful translocation even after multiple failed threading attempts. Even in the limit of an extremely narrow pore, a fully flexible chain has a finite probability of hairpin-loop capture, while this probability decreases for a stiffer chain and promotes single file translocation. Our in silico studies identify and differentiate characteristic distributions of the mean first passage time due to single file translocation from those due to translocation of different types of folds and provide direct evidence of the interpretation of the experimentally observed folds [M. Gershow and J. A. Golovchenko, Nat. Nanotechnol. 2, 775 (2007) and Mihovilovic et al., Phys. Rev. Lett. 110, 028102 (2013)] in a solitary nanopore. Finally, we show a new finding-that a charged tag attached at the 5' end of the DNA enhances both the multi-scan rate and the uni-directional translocation (5' → 3') probability that would benefit the genomic barcoding and sequencing experiments.

Beyond the Pore Size Limitation of a Nanoporous Graphene Monolayer Membrane for Water Desalination Assisted by an External Electric Field

One efficient strategy for addressing the global water shortage is advanced membrane separation, which depends on the precise pore size being close to the hydrated ion size and other surface properties like charge and polarity. However, it is very difficult to fabricate uniform pores with diameters of <1 nm on monolayer membranes. By applying an electric field (bias voltage) perpendicular to the direction of the pressure difference, herein we demonstrate for the first time that a monolayer nanoporous graphene membrane with pores much larger than hydrated ions exhibits high salt rejection and allows a high rate of water transport. This theoretical proposal goes beyond the pore size limitation and shows promise for the design of high-performance reverse osmosis membranes.

A numerical investigation of analyte size effects in nanopore sensing systems

We investigate the ionic current modulation in DNA nanopore translocation setups by numerically solving the electrokinetic mean-field equations for an idealized model. Specifically, we study the dependence of the ionic current on the relative length of the translocating molecule. Our simulations show a significantly smaller ionic current for DNA molecules that are shorter than the pore at low salt concentrations. These effects can be ascribed to the polarization of the ion cloud along the DNA that leads to an opposing electric dipole field. Our results for DNA shine light on the observed discrepancy between infinite pore models and experimental data on various sized DNA complexes.

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.

Protein Transport through Nanopores Illuminated by Long-Time-Scale Simulations

The transport of molecules through nanoscale confined space is relevant in biology, biosensing, and industrial filtration. Microscopically modeling transport through nanopores is required for a fundamental understanding and guiding engineering, but the short duration and low replica number of existing simulation approaches limit statistically relevant insight. Here we explore protein transport in nanopores with a high-throughput computational method that realistically simulates hundreds of up to seconds-long protein trajectories by combining Brownian dynamics and continuum simulation and integrating both driving forces of electroosmosis and electrophoresis. Ionic current traces are computed to enable experimental comparison. By examining three biological and synthetic nanopores, our study answers questions about the kinetics and mechanism of protein transport and additionally reveals insight that is inaccessible from experiments yet relevant for pore design. The discovery of extremely frequent unhindered passage can guide the improvement of biosensor pores to enhance desired biomolecular recognition by pore-tethered receptors. Similarly, experimentally invisible nontarget adsorption to pore walls highlights how to improve recently developed DNA nanopores. Our work can be expanded to pressure-driven flow to model industrial nanofiltration processes.

Extending the Classical Continuum Theory to Describe Water Flow through Two-Dimensional Nanopores

Water flow through two-dimensional nanopores has attracted significant attention owing to the promising water purification technology based on atomically thick membranes. However, the theoretical description of water flow in nanopores based on the classical continuum theory is very challenging owing to the pronounced entrance/exit effects. Here, we extend the classical Hagen-Poiseuille equation for describing the relationship between flow rate and pressure loss in laminar tube flow to two-dimensional nanopores. A totally theoretical model is established by appropriately considering the velocity slip on pore surfaces both in the friction pressure loss and entrance/exit pressure loss. Based on molecular dynamics simulations of water flow through graphene nanopores, it is shown that the model can not only well predict the overall flow rate but also give a good estimation of the velocity profiles. As the pore radius and length increase, the model can reduce to the equations applicable to the fluid flow in infinitely/finitely long nanotubes, thin orifices, and macroscale tubes, showing an accurate prediction of the existing experimental and simulation data of the water flow through nanotubes and nanopores in the literature. Namely, the presented model is a unified model that can uniformly describe the fluid flow from nanoscales to macroscales by modifying the classical continuum theory.

Simultaneous Sensing of Force and Current Signals to Recognize Proteinogenic Amino Acids at a Single-Molecule Level

The identification ability of nanopore sequencing is severely hindered by the diversity of amino acids in a protein. To tackle this problem, a graphene nanoslit sensor is adopted to collect force and current signals to distinguish 20 residues. Extensive molecular dynamics simulations are performed on sequencing peptides under pulling force and applied electric field. Results show that the signals of force and current can be simultaneously collected. Tailoring the geometry of the nanoslit sensor optimizes signal differences between tyrosine and alanine residues. Using the tailored geometry, the characteristic signals of 20 types of residues are detected, enabling excellent distinguishability so that the residues are well-grouped by their properties and signals. The signals reveal a trend in which the larger amino acids have larger pulling forces and lower ionic currents. Generally, the graphene nanoslit sensor can be employed to simultaneously sense two signals, thereby enhancing the identification ability and providing an effective mode of nanopore protein sequencing.

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

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

Modeling single-molecule stochastic transport for DNA exo-sequencing in nanopore sensors

We present a simulation framework for computing the probability that a single molecule reaches the recognition element in a nanopore sensor. The model consists of the Langevin equation for the diffusive motion of small particles driven by external forces and the Poisson-Nernst-Planck-Stokes equations to compute these forces. The model is applied to examine DNA exo-sequencing in α-hemolysin, whose practicability depends on whether isolated DNA monomers reliably migrate into the channel in their correct order. We find that, at moderate voltage, migration fails in the majority of trials if the exonuclease which releases monomers is located farther than 1 nm above the pore entry. However, by tuning the pore to have a higher surface charge, applying a high voltage of 1 V and ensuring the exonuclease stays close to the channel, success rates of over 95% can be achieved.

Reverse Translocation of Nucleotides through a Carbon Nanotube

We report molecular dynamics (MD) simulations of the reverse translocation of single nucleotides through a narrow carbon nanotube (CNT), with a diameter of 1.36 nm, immersed in a 1 M KCl electrolyte solution under an applied electric field along the tube axis. We observe ion selectivity by the narrow CNT, which leads to a high flow of K⁺ ions, in contrast to a negligible and opposing current of Cl^- ions. The K⁺ ions, driven by the electric field, force a negatively charged single nucleotide into the narrow CNT where it is trapped by the incoming K⁺ ions and water molecules, and the nucleotide is driven in the same direction as the K⁺ ions. This illustrates a novel mechanism of nucleotide reverse translocation that is controlled by ion selectivity. An increase in the CNT diameter to 2.71 nm or an increase in nucleotide chain length both lead to translocation in the normal direction of the applied field. The reverse translocation rate of single nucleotides is correlated to the ionic current of K⁺ ions in the narrow tube, unlike translocation in the normal direction in the wider tube.

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.

Comment on “Pressure enhancement in carbon nanopores: a major confinement effect” by Y. Long, J. C. Palmer, B. Coasne, M. Śliwinska-Bartkowiak and K. E. Gubbins, Phys. Chem. Chem. Phys., 2011, 13, 17163

A standard thermodynamic interpretation unambiguously explains the observed properties of fluids confined in pores, while a “pressure enhancement” effect emerges only from calculations in which particular choices are selected from an arbitrary set.

Spatially Controlled Fabrication and Mechanisms of Atomically Thin Nanowell Patterns in Bilayer WS2 Using in Situ High Temperature Electron Microscopy

We show controlled production of atomically thin nanowells in bilayer WS₂ using an in situ heating holder combined with a focused electron beam in a scanning transmission electron microscope (STEM). We systematically study the formation and evolvement mechanism involved in removing a single layer of WS₂ within a bilayer region with 2 nm accuracy in location and without punching through to the other layer to create a hole. Best results are found when using a high temperature of 800 °C, because it enables thermally activated atomic migration and eliminates the interference from surface carbon contamination. We demonstrate precise control over spatial distributions with 5 nm accuracy of patterning and the width of nanowells adjustable by dose-dependent parameters. The mechanism of removing a monolayer of WS₂ within a bilayer region is different than removing equivalent sections in a monolayer film due to the van der Waals interaction of the underlying remaining layer in the bilayer system that stabilizes the excess W atom stoichiometry within the edges of the nanowell structure and facilitates expansion. This study offers insights for the nanoengineering of nanowells in two-dimensional (2D) transitional metal dichalcogenides (TMDs), which could hold potential as selective traps to localize 2D reactions in molecules and ions, underpinning the broader utilization of 2D material membranes.

Electro-Mechanical Conductance Modulation of a Nanopore Using a Removable Gate

Ion channels form the basis of information processing in living cells by facilitating the exchange of electrical signals across and along cellular membranes. Applying the same principles to man-made systems requires the development of synthetic ion channels that can alter their conductance in response to a variety of external manipulations. By combining single-molecule electrical recordings with all-atom molecular dynamics simulations, we here demonstrate a hybrid nanopore system that allows for both a stepwise change of its conductance and a nonlinear current-voltage dependence. The conductance modulation is realized by using a short flexible peptide gate that carries opposite electric charge at its ends. We show that a constant transmembrane bias can position (and, in a later stage, remove) the peptide gate right at the most-sensitive sensing region of a biological nanopore FraC, thus partially blocking its channel and producing a stepwise change in the conductance. Increasing or decreasing the bias while having the peptide gate trapped in the pore stretches or compresses the peptide within the nanopore, thus modulating its conductance in a nonlinear but reproducible manner. We envision a range of applications of this removable-gate nanopore system, e.g. from an element of biological computing circuits to a test bed for probing the elasticity of intrinsically disordered proteins.

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

Nanofluidic diodes based on nanochannels have been studied theoretically and experimentally for applications such as biosensors and logic gates. However, when analyzing attoliter-scale samples or enabling high-density integration of lab-on-a-chip devices, it is beneficial to miniaturize the size of a nanofluidic channel. Using molecular dynamics simulations, we investigate conductance of nanopores in bilayer hexagonal boron nitride (h-BN). Remarkably, we found that triangular nanopores possess excellent rectifications of ionic currents while hexagonal ones do not. It is worth highlighting that the pore length is only about 0.7 nm, which is about the atomic limit for a bipolar diode. We determined scaling relations between ionic currents I and pore sizes L for small nanopores, that are I ∼ L¹ in a forward biasing voltage and I ∼ L² in a reverse biasing voltage. Simulation results qualitatively agree with analytical ones derived from the one-dimensional Poisson-Nerst-Planck equations.

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.