Two-dimensional Nanopores Research Articles

Anisotropic relaxation of nuclear spins dipolar energy of water molecules in two-dimensional nanopores - A single crystal NMR study

Energy transfer from Zeeman to dipolar order discovered by Jeener et al. is usually observed in solids with a strong dipole-dipole interaction of nuclear spins. It is not observed in liquids, where fast molecular motion completely averages this interaction. The intermediate case, when the dipole-dipole interaction of nuclear spins is only partially averaged, has been poorly studied. We report on the first measurement of an angular-dependent proton spin relaxation of a dipolar reservoir in mobile water molecules confined in the interlayer pores of a vermiculite single crystal. In this layered crystal, the intramolecular dipole-dipole interactions of nuclear spins are only partially averaged due to the restricted anisotropic molecular motion in nanopores. We show that this allows the formation of dipolar echo. We measured the spin-lattice relaxation times of the dipolar order T1D at different angles between the normal to the crystal surface and the applied magnetic field and obtained a distinct angular dependence of T1D. The minimum relaxation rate R1D was found around the magic angle of 54.74°.

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

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

Effect of surface functionalization on DNA sequencing using MXene-based nanopores.

As one of the most promising types of label-free nanopores has great potential for DNA sequencing via fast detection of different DNA bases. As one of the most promising types of label-free nanopores, two-dimensional nanopore materials have been developed over the past two decades. However, how to detect different DNA bases efficiently and accurately is still a challenging problem. In the present work, the translocation of four homogeneous DNA strands (i.e., poly(A)20, poly(C)20, poly(G)20, and poly(T)20) through two-dimensional transition-metal carbide (MXene) membrane nanopores with different surface terminal groups is investigated via all-atom molecular dynamics simulations. Interestingly, it is found that the four types of bases can be distinguished by different ion currents and dwell times when they are transported through the Ti3C2(OH)2 nanopore. This is mainly attributed to the different orientation and position distributions of the bases, the hydrogen bonding inside the MXene nanopore, and the interaction of the ssDNA with the nanopore. The present study enhances the understanding of the interaction between DNA strands and MXene nanopores with different functional groups, which may provide useful guidelines for the design of MXene-based devices for DNA sequencing in the future.

Glass Capillary-Based Nanopores for Single Molecule/Single Cell Detection.

A glass capillary-based nanopore (G-nanopore), due to its tapered tip, easy tunability in orifice size, and especially its flexible surface modifications that can be tailored to effectively capture and enhance the ionic current signal of single entities (single molecules, single cells, and single particles), offers a powerful and nanoconfined sensing platform for diverse biological measurements of single cells and single molecules. Compared with other artificial two-dimensional solid-state nanopores, its conical tip and high spatial and temporal resolution characteristics facilitate noninvasive single molecule and selected area (subcellular) single cell detections (e.g., DNA mutations, highly expressed proteins, and small molecule markers that reflect the change characteristics of the tumor), as a small G-nanopore (≤100 nm) does negligible damage to cell functions and cell membrane integrity when inserted through the cell membrane. In this brief review, we summarize the preparation of G-nanopores and discuss the advantages of them as solid-state sensing platforms for single molecule and single cell detection applications as well as for cancer diagnosis and treatment applications. We also describe the current bottlenecks that limit the widespread use of G-nanopores in clinical applications and provide an outlook on future developments. The brief review will provide the reader with a quick survey of this field and facilitate the rapid development of a G-nanopore sensing platform for future tumor diagnosis and personalized medicine based on single-molecule/single-cell bioassay.

Stretch-activated ionic currents through Ti3C2(OH)2 MXene nanopores

Ion transport through nanopores is a major biological signal transduction mechanism that converts various external stimuli into electrical signals. However, despite potential applications in fields such as sensing, versatile functions comparable to those of cell membranes have not yet been achieved in synthetic nanopores. In this study, the possibility of mechanical-to-electrical transduction was explored using two-dimensional MXene nanopores. Molecular dynamics simulations were used to measure the change in ionic currents when applying a mechanical strain. The on/off gating characteristics of current generation above the threshold mechanical strain were found to be expressed by the Boltzmann equation. The effect of mechanical strain on ion transport was analyzed from various perspectives, including the potential of the mean force profile and analysis of pore residence properties. Additionally, this study provided insight into the size exclusion of ions as minute changes in the area of nanopores and ions with marginally different sizes were considered.

Electric Field-Controlled Peptide Self-Assembly through Funnel-Shaped Two-Dimensional Nanopores.

Self-assembly of biomolecules is critical for the realization of biological functions. Thus, the precise control of self-assembly has great significance in the design of biochips and biomedical agents. In this report, we design a Y-shaped funnel on a two-dimensional (2D) heterostructure, called 2D funnel, based on monolayered polyaniline carbon nitride (C3N) and boron carbide (BC3), and study its application in the self-assembly state regulation of the peptide oligomer, using Aβ16-21 as the representative model. Structurally, the 2D funnel is composed of three regions: channel area, triangle area, and barrier area. The channel and triangle areas show higher binding affinity to the peptide than that of the barrier area, which leads to the confinement of the peptide in the 2D funnel. Our results show that when an external electric field is applied along the 2D funnel, the oligomer is driven to migrate across the funnel. Its trajectory is confined inside the narrow channel area, which effectively causes peptide dissociation into the individual peptide chains. Then, when the external electric field is turned off, the separated peptide chains spontaneously assemble in the triangle area and tend to reunite. Our present findings propose a novel heterostructure platform, which enables the manipulation of the self-assembly state of peptides by switching the electric field, which could guide the design and fabrication of nanodevices for sensing and sequencing applications.

Single-molecule DNA sequencing using two-dimensional Ti2C(OH)2 MXene nanopores: A first-principles investigation

Nanopore-based devices have provided exciting opportunities to develop affordable label-free DNA sequencing platforms. Over a decade ago, graphene has been proposed as a two-dimensional (2D) nanopore membrane in order to achieve single-base resolution. However, it was experimentally revealed that clogging of the graphene nanopore can occur due to the hydrophobic nature of graphene, thus hindering the translocation of DNA. To overcome this problem, the exploration of alternative 2D materials has gained considerable interest over the last decade. Here we show that a Ti2C-based MXene nanopore functionalized by hydroxyl groups (−OH) exhibits transverse conductance properties that allow for the distinction between all four naturally occurring DNA bases. We have used a combination of density functional theory and non-equilibrium Green’s function method to sample over multiple orientations of the nucleotides in the nanopore, as generated from molecular dynamics simulations. The conductance variation resulting from sweeping an applied gate voltage demonstrates that the Ti2C-based MXene nanopore possesses high potential to rapidly and reliably sequence DNA. Our findings open the door to further theoretical and experimental explorations of MXene nanopores as a promising 2D material for nanopore-based DNA sensing.

High Spatial Resolution of Ultrathin Covalent Organic Framework Nanopores for Single-Molecule DNA Sensing

Ultrathin nanosheets of two-dimensional covalent organic frameworks covered a quartz nanopipette and then acted as a nanopore device for single-molecule DNA sensing. Our results showed that a single DNA homopolymer as short as 6 bases could be detected. The dwell times of 30-mer DNA homopolymers were obviously longer than the times of 10- or 6-mer ones. For different bases, poly(dA)6 showed the slowest transport speed (∼595 μs/base) compared with cytosine (∼355 μs/base) in poly(dC)6 and thymine (∼220 μs/base) in poly(dT)6. Such translocation speeds are the slowest ever reported in two-dimensional material-based nanopores. Poly(dA)6 also showed the biggest current blockade (94.74 pA) compared with poly(dC)6 (79.54 pA) and poly(dT)6 (71.41 pA). However, the present difference in blockade current was not big enough to distinguish the four DNA bases. Our study exhibits the shortest single DNA molecules that can be detected by COF nanopores at the present stage and lights the way for DNA sequencing based on solid-state nanopores.

Ionic heat dissipation in solid-state pores.

Energy dissipation in solid-state nanopores is an important issue for their use as a sensor for detecting and analyzing individual objects in electrolyte solution by ionic current measurements. Here, we report on evaluations of heating via diffusive ion transport in the nanoscale conduits using thermocouple-embedded SiNx pores. We found a linear rise in the nanopore temperature with the input electrical power suggestive of steady-state ionic heat dissipation in the confined nanospace. Meanwhile, the heating efficiency was elucidated to become higher in a smaller pore due to a rapid decrease in the through-water thermal conduction for cooling the fluidic channel. The scaling law suggested nonnegligible influence of the heating to raise the temperature of single-nanometer two-dimensional nanopores by a few kelvins under the standard cross-membrane voltage and ionic strength conditions. The present findings may be useful in advancing our understanding of ion and mass transport phenomena in nanopores.

Quasi-Unidirectional Transport Bilayer Two-Dimensional Nanopores for Highly-Efficient Molecular Sieving

Two-dimensional nanopores are very promising for high-permeance molecular sieving, but the molecular backflow from permeate-side to feed-side is not beneficial for improving molecular permeance. We study the quasi-unidirectional molecular transport through a graphene-hexagonal boron nitride bilayer nanopore, aiming to realize a high-permeance molecular sieving. Molecular dynamics simulations of CO2/CH4 separations show that the bilayer pore presents 3.7 times higher selectivity comparing to the single-layer graphene nanopore with the same size. The quasi-unidirectional molecular transport is attributed to the distinctive adsorption abilities of gas molecules on the two sides of bilayer nanopores and the inhibited molecular backflow from permeate-side to feed-side. This work provides a promising way to realize the ultra-permeable porous membranes with molecular permeance even higher than the single-layer atomic-thickness membranes.

Tunable Pore Size from Sub-Nanometer to a Few Nanometers in Large-Area Graphene Nanoporous Atomically Thin Membranes.

Membranes are key components in chemical purification, biological separation, and water desalination. Traditional polymeric membranes are subjected to a ubiquitous trade-off between permeance and selectivity, which significantly hinders the separation performance. Nanoporous atomically thin membranes (NATMs), such as graphene NATMs, have the potential to break this trade-off. Owing to their uniqueness of two-dimensional structure and potential nanopore structure controllability, NATMs are expected to have outstanding selectivity through molecular sieving while achieving ultimate permeance at the same time. However, a drastic selectivity discrepancy exists between the proof-of-concept demonstrations and scalable separation applications in graphene membranes. In this paper, we offer a possible solution to narrow this discrepancy by tuning the pore density and pore size separately with two successive plasma treatments. We demonstrate that by narrowing the pore size distribution, the selectivity of graphene membranes can be greatly increased. Low-energy argon plasma is first applied to nucleate high density of defects in graphene. Controlled oxygen plasma is then utilized to selectively enlarge the defects into nanopores with desired sizes. This method is scalable, and the fabricated 1 cm2 graphene NATMs with sub-nanometer pores can separate KCl and Allura Red with a selectivity of 104 and a permeance of 1.1 × 10-6 m s-1. The pores in NATMs can be further tuned from gas-selective sub-nanometer pores to a few nanometer size. The fabricated NATMs show a selectivity of 35 between CO2 and N2. With longer enlargement time, a selectivity of 21.2 between a lysozyme and bovine serum albumin can also be achieved with roughly four times higher permeance than that of a commercial dialysis membrane. This research offers a solution to realize NATMs of tunable pore size with a narrow pore size distribution for different separation processes from sub-nanometer in gas separation or desalination to a few nanometers in dialysis.

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.

DNA Translocation through Vertically Stacked 2D Layers of Graphene and Hexagonal Boron Nitride Heterostructure Nanopore.

Cost-effective, fast, and reliable DNA sequencing can be enabled by advances in nanopore-based methods, such as the use of atomically thin graphene membranes. However, strong interaction of DNA bases with graphene leads to undesirable effects such as sticking of DNA strands to the membrane surface. While surface functionalization is one way to counter this problem, here, we present another solution based on a heterostructure nanopore system, consisting of a monolayer of graphene and hexagonal boron nitride (hBN) each. Molecular dynamics studies of DNA translocation through this heterostructure nanopore revealed a surprising and crucial influence of the heterostructure layer order in controlling the base specific signal variability. Specifically, the heterostructure with graphene on top of hBN had nearly 3-10× lower signal variability than the one with hBN on top of graphene. Simulations point to the role of differential underside sticking of DNA bases as a possible reason for the observed influence of the layer order. Our studies can guide the development of experimental systems to study and exploit DNA translocation through two-dimensional heterostructure nanopores for single molecule sequencing and sensing applications.

Electrochemical biosensor for detection of MON89788 gene fragments with spiny trisoctahedron gold nanocrystal and target DNA recycling amplification.

Theshape-controlled synthesis of gold nanocrystals via shape induction of hexadecyltrimethylammonium chloride, potassium bromide, and potassium iodide and enantioselective direction of L-cysteineis reported. The resulting gold nanocrystals (STO-Au) offer spiny trisoctahedron nanostructures with good monodispersity and enhanced exposed high-index facets and high catalytic activity. Construction of the electrochemical sensing platform for MON89788 gene involves the modification of STO-Au, thionine (Thi), and labeled bipedal DNA probe 1 or 2 (P1 or P2) for target DNA-induced recycling amplification. In the detection, two surface DNA probes were immobilized on gold electrode via the Au-S bond. Then, hairpin DNA 1 (H1), Thi-STO-Au-P1, and Thi-STO-Au-P2 self-assemble into two-dimensional DNA nanopores (DNPs) on the electrode surface. Target DNA hybridizes with hairpin DNA 2 (H2) to open hairpin structure of H2. The opened H2 binds with H1 in the DNPs to release Thi-STO-Au-P1, Thi-STO-Au-P2, and target DNA by toehold-mediated strand-displacement. The utilization of target DNA-induced recycling allows one target DNA to release 2N STO-Au-labeled DNA strands, promoting significant signal amplification. The detection signal is further enhanced by the catalyzed redox reaction of Thi with STO-Au. The differential pulse voltammetric signal, best measured at - 0.18V vs. Ag/AgCl, decreases linearly with increasing concentration of MON89788 in the range 0.02-8 × 104 fM, and the detection limit is 0.0048 fM (S/N= 3). The proposed method was successfully applied for electrochemical detection of MON89788 gene fragments in the PCR products from genetically modified soybean. Graphical Abstract We develop l-cysteine controlled synthesis of spiny trisoctahedron gold nanocrystals with good monodispersity and highly exposed high-index facets. The architecture achieves to ultrahigh catalytic activity. The electrochemical biosensor based on gold nanocrystals and target DNA recycling amplification provides advantage of sensitivity, repeatability, and regeneration-free.

The effect of temperature on water desalination through two-dimensional nanopores.

Two-dimensional (2D) materials such as graphene, molybdenum sulfide, and hexagonal boron nitride are widely studied for separation applications such as water desalination. Desalination across such 2D nanoporous membranes is largely influenced by the bulk transport properties of water, which are, in turn, sensitive to the operating temperature. However, there have been no studies on the effect of temperature on desalination through 2D nanopores. We investigated water desalination through hydrogen functionalized graphene nanopores of varying pore areas at temperatures 275.0 K, 300.0 K, 325.0 K, and 350.0 K. The water flux showed a direct relation with the diffusion coefficient and an inverse relation with the hydrogen-bond lifetime. As a direct consequence, the water flux was found to be related to the temperature as per the Arrhenius equation, similar to an activated process. The results from the present study improve the understanding on water and ion permeation across nanoporous 2D materials at different temperatures. Furthermore, the present investigation suggests a kinetic model, which can predict the water and ion permeation based on the characteristics of the nanopore.

Bifunctional porous Co-doped NiO nanoflowers electrocatalysts for rechargeable zinc-air batteries

Zinc-air batteries (ZnABs) represent one of the most promising options to power next-generation electric vehicles owing to their high theoretical energy density and reliable safety. However, their further development and application is hampered due to the lack of high-efficiency bifunctional air electrocatalysts. Herein, porous Co-doped NiO nanoflowers (Co-NiO NFs) with outstanding electrocatalytic activity and stability toward oxygen evolution reaction (ORR) and oxygen reduction reaction (OER) is reported for the first time, including a positive half-wave potential (0.79 V) for ORR and a small overpotential (1.53 V at 10 mA cm−2) for OER. Firstly, the synergistic effect between the sound two-dimensional (2D) hexagonal framework and numerous nanopores inside the nanosheets offers an available surface for O2 adsorption/diffusion, and a large effective electrochemical active surface area for exploring and utilizing more active sites. Secondly, Co dopants can effectively increase the conductivity of pristine NiO nanoflowers (NFs) and simultaneously enhances the intrinsic ORR and OER activity. Notably, the liquid ZnABs with engineered Co-NiO NFs electrode exhibits a high discharge peak power density of 93 mW cm−2, a satisfactory specific capacity of 830 mA h g-1 at the current density of 5 mA cm−2, together with excellent cycling stability of 110 h at 2 mA cm−2. Additionally, the corresponding all-solid-state ZnABs assembled with Co-NiO NFs shows a long durability with the stable charge-discharge cycles of 6 h and good flexible nature.

Theory of Transport-Induced-Charge Electroosmotic Pumping toward Alternating Current Resistive Pulse Sensing.

In this work, we study transport-induced-charge electroosmosis toward alternating current resistive pulse sensing for the next generation of biomedical applications. Transport-induced-charge electroosmosis, being a new class of electrokinetic phenomenon, occurs as a salt concentration gradient works in synergy with an electric field in ultrathin nanopores. Apart from the conventional electric double layer-governed electroosmotic flow in which the flow behavior is subject to the surface charge, it is found that the transport-induced-charge electroosmotic flow behaves independently of surface charge magnitude but can be linearly regulated by the bulk salt concentration bias. The reversal of the electric field simultaneously inverses the induced charge allowing the establishment of a unidirectional flow under the application of a periodic alternating current field. This unique phenomenon permits continuous water and nanoparticles pumping through a two-dimensional material nanopore in spite of the reversal of the electric field. Built upon this mechanism, we propose a theoretical prototype of alternating current resistive pulse sensing in a two-dimensional nanopore system.

Towards the Ultimate Membranes: Two-dimensional Nanoporous Materials and Films.

The energy-efficient separation of molecules has been a popular topic in chemistry and chemical engineering as a consequence of the large energy-footprint of separation processes in the chemical industry. The Laboratory of Advanced Separations (LAS) at EPFL, led by Prof. Kumar Varoon Agrawal, is focused to develop next-generation, high-performance membranes that can improve the energy efficiency of hydrogen purification, carbon capture, hydrocarbon and water purification. For this, LAS is seeking to develop the ultimate nanoporous membranes, those with a thickness of 1 nm and possessing an array of size-selective nanopores. In this article, the research activities at LAS, especially in the bottom-up and top-down synthesis of chemically and thermally stable, nanoporous two-dimensional materials and membranes are discussed.

Design of tunable-size 2D nanopore membranes from self-assembled amphiphilic nanosheets using dissipative particle dynamics simulations

Two-dimensional (2D) nanopore membranes play a pivotal role in the application of molecular separation, DNA sequencing, drug release and biosensing. Owing to their special properties including 2D symmetry and interfacial activity, amphiphilic nanosheets (ANs) have great potential for generating functional nanomaterials. In this work, the dissipative particle dynamics (DPD) simulations are employed to design 2D nanopore membranes with tunable size using AN molecules. We find that these two-dimensional membranes are much stable due to the double-layer assembled framework of the membrane with the thickness from 2.5 to 7.8 nm. Different sized nanopores ranging from 2.45 to 6.15 nm are also identified in the membrane architecture, which can be controlled by the concentration ratio, the length of grafting polymer and the affinity of ANs. Moreover, when at low concentration ratio (<10%), the ANs tend to form different core-shell structured micelles, including spherical, ellipsoidal and long rod-like self-assembled morphologies. From our study findings, the ANs could be extendedly used for drug delivery and release, multi-layer 2D nanomaterials by the advantage of their chemical tunability, including the affinity and stimulus-responsive properties of grafting polymer as well as the geometry of scaffold structure in the ANs.

Direct Visualization of Evaporation in a Two-Dimensional Nanoporous Model for Unconventional Natural Gas

Evaporation at the nanoscale is critical to many natural and synthetic systems including rapidly emerging unconventional oil and gas production from nanoporous shale reservoirs. During extraction processes, hydrocarbons confined to nanoscopic pores (ranging from one to a few hundred nanometers in size) can undergo phase change as pressure is reduced. Here, we directly observe evaporation in two-dimensional (2D) nanoporous media at the sub-10 nm scale. Using an experimental procedure that mimics pressure drawdown during shale oil/gas production, our results show that evaporation takes place at pressures significantly lower than predictions from the Kelvin equation (maximum deviation of 11%). We probe evaporation dynamics as a function of superheat and find that vapor transport resistance dominates evaporation rate. The transport resistance is made up of both Knudsen and viscous flow effects, with the magnitude of the Knudsen effect being approximately twice that of the viscous effects here. We also observe...