Scan-rate-dependent ion current rectification and rectification inversion in charged conical nanopores

Herein we report a theoretical study of diode-like behavior of negatively charged (e.g., glass or silica) nanopores at different potential scan rates (1-1000 V·s(-1)). Finite element simulations were used to determine current-voltage characteristics of conical nanopores at various electrolyte concentrations. This study demonstrates that significant changes in rectification behavior can be observed at high scan rates because the mass transport of ionic species appears sluggish on the time scale of the voltage scan. In particular, it explains the influence of the potential scan rate on the nanopore rectifying properties in the cases of classical rectification, rectification inversion, and the "transition" rectification domain where the rectification direction in the nanopore could be modulated according to the applied scan rate.     

BROMOC suite: Monte Carlo/Brownian dynamics suite for studies of ion permeation and DNA transport in biological and artificial pores with effective potentials

The transport of ions and solutes by biological pores is central for cellular processes and has a variety of applications in modern biotechnology. The time scale involved in the polymer transport across a nanopore is beyond the accessibility of conventional MD simulations. Moreover, experimental studies lack sufficient resolution to provide details on the molecular underpinning of the transport mechanisms. BROMOC, the code presented herein, performs Brownian dynamics simulations, both serial and parallel, up to several milliseconds long. BROMOC can be used to model large biological systems. IMC‐MACRO software allows for the development of effective potentials for solute–ion interactions based on radial distribution function from all‐atom MD. BROMOC Suite also provides a versatile set of tools to do a wide variety of preprocessing and postsimulation analysis. We illustrate a potential application with ion and ssDNA transport in MspA nanopore. © 2014 Wiley Periodicals, Inc.     

PNIPAAM-modified nanoporous colloidal films with positive and negative temperature gating

The surface of nanopores in colloidal films, assembled from 205 nm silica spheres, was modified with poly(N-isopropylacrylamide), PNIPAAM, brushes using surface-initiated ATRP. The polymer thickness inside nanopores was controlled by the polymerization time. The diffusion through PNIPAAM-modified colloidal films was measured using cyclic voltammetry and studied as a function of temperature and polymer brush thickness. Nanopores modified with a thin PNIPAAM brush exhibited a positive gating behavior, where diffusion rates increased with increasing temperature. Nanopores modified with a thick PNIPAAM layer showed a negative gating behavior where diffusion rates decreased with increasing temperature. The observed temperature response is consistent with two transport mechanisms, one in which molecules diffuse through the nanopores whose volume increases with increasing temperature as the PNIPAAM brush collapses onto the nanopore surface (positive gating) and the second one where molecules diffuse through the porous PNIPAAM that fills the entire nanopore opening and collapses onto itself, becoming hydrophobic and impermeable (negative gating).     

Boronic Acid-containing Stimuli-responsive Polymers Modified Nanopores for Label-free Dual-signal-output Detection of Glucose

Herein, a dual-signal-output glass nanopore system was developed for sensing glucose. Upon binding glucose, the boronic acid-containing stimuli-responsive polymer underwent a wettability switch and pKa shift. When the polymer was immobilized on the inner wall of nanopore, the nanopore offered a sensitive method for evaluating glucose by ion rectification. Besides, due to the electrostatic assembly of cationic pyrene onto the glucose-bound anionic polymer, the pyrene excimer emission was observed. By separating the substrate binding and fluorescence reporting process, this work avoided the fluorescence labeling of the target and nanopore, thus simplifying the design of dual-signal-output nanopore for potential point-of-care test.     

Modeling electrochemical deposition inside nanotubes to obtain metal-semiconductor multiscale nanocables or conical nanopores

Nanocables with a radial metal-semiconductor heterostructure have recently been prepared by electrochemical deposition inside metal nanotubes. First, a bare nanoporous polycarbonate track-etched membrane is coated uniformly with a metal film by electroless deposition. The film forms a working electrode for further deposition of a semiconductor layer that grows radially inside the nanopore when the deposition rate is slow. We propose a new physical model for the nanocable synthesis and study the effects of the deposited species concentration, potential-dependent reaction rate, and nanopore dimensions on the electrochemical deposition. The problem involves both axial diffusion through the nanopore and radial transport to the nanopore surface, with a surface reaction rate that depends on the axial position and the time. This is so because the radial potential drop across the deposited semiconductor layer changes with the layer thickness through the nanopore. Since axially uniform nanocables are needed for most applications, we consider the relative role of reaction and axial diffusion rates on the deposition process. However, in those cases where partial, empty-core deposition should be desirable (e.g., for producing conical nanopores to be used in single nanoparticle detection), we give conditions where asymmetric geometries can be experimentally realized.     

Ion transport and molecular organization are coupled in polyelectrolyte-modified nanopores

Chemically modified nanopores show a strong and nontrivial coupling between ion current and the structure of the immobilized species. In this work we study theoretically the conductance and structure in polymer modified nanopores and explicitly address the problem of the coupling between ion transport and molecular organization. Our approach is based on a nonequilibrium molecular theory that couples ion conductivity with the conformational degrees of freedom of the polymer and the electrostatic and nonelectrostatic interactions among polyelectrolyte chains, ions, and solvent. We apply the theory to study a cylindrical nanopore between two reservoirs as a function of pore diameter and length, the length of the polyelectrolyte chains, their grafting density, and whether they are present or not on the outer reservoir walls. In the very low applied potential regime, where the distribution of polyelectrolyte and ions is similar to that in equilibrium, we present a simple analytical model based on the combination of the different resistances in the system that describes the conductance in excellent agreement with the calculations of the full nonequilibrium molecular theory. On the other hand, for a large applied potential bias, the theory predicts a dramatic reorganization of the polyelectrolyte chains and the ions. This reorganization results from the global optimization of the different interactions in the system under nonequilibrium conditions. For nanopores modified with long chains, this reorganization leads to two interesting physical phenomena: (i) control of polyelectrolyte morphology by the direction and magnitude of ion-fluxes and (ii) an unexpected decrease in system resistance with the applied potential bias for long chains due to the coupling between polyelectrolyte segment distribution and ion currents.     

Convection, diffusion and reaction in a surface-based biosensor: modeling of cooperativity and binding site competition on the surface and in the hydrogel

We study theoretically the transport and kinetic processes underlying the operation of a biosensor (particularly the surface plasmon sensor "Biacore") used to study the surface binding kinetics of biomolecules in solution to immobilized receptors. Unlike previous studies, we concentrate mainly on the modeling of system-specific phenomena rather than on the influence of mass transport limitations on the intrinsic kinetic rate constants determined from binding data. In the first problem, the case of two-site binding where each receptor unit on the surface can accommodate two analyte molecules on two different sites is considered. One analyte molecule always binds first to a specific site. Subsequently, the second analyte molecule can bind to the adjacent unoccupied site. In the second problem, two different analytes compete for one binding site on the same surface receptor. Finally, the third problem considers the case of positive cooperativity among bound molecules in the hydrogel using a simple mean-field approach. The transport in both the flow channel and the hydrogel phases of the biosensor is taken into account in this case (with few exceptions, most previous studies assume a simpler model in which the hydrogel is treated as a planar surface with the receptors). We consider simultaneously diffusion and convection through the flow channel together with diffusion and cooperativity binding on the surface and in the hydrogel. In each case, typical results for the concentration contours of the free and bound molecules in the flow channel and hydrogel regions are presented together with the time-dependent association/dissociation curves and reaction rates. For binding site competition, the analysis predicts overshoot phenomena.     

Anomalous transport in molecularly confined spaces

We develop a novel theory to predict the density dependence of the diffusivity of simple fluids in a molecularly sized nanopore with diffusely reflecting walls, incorporating nearest neighbor intermolecular interactions within the framework of the recent oscillator model of low density transport arising from this laboratory. It is shown that when the pore width is about two molecular diameters, at sufficiently high densities these interactions lead to a repulsive inner core, as a result of which the diffusing molecules undergo more frequent reflections at the wall. This leads to a reduction in diffusivity with increase in density, which is consistent with molecular dynamics simulation results, and contrasts with the behavior in larger pores where the transport coefficient has previously been shown to increase with increase in density due to viscouslike intermolecular interactions. At low densities the behavior is opposite, with the inner core becoming more attractive with increase in density, which can lead to an increase in diffusivity. The theory consistently explains molecular dynamics simulation results when the inhomogeneous pair distribution function of moving particles in the pore is axially periodic, suggesting concerted motion of neighboring molecules. It is also shown that a potential of mean force concept is inadequate for describing the influence of intermolecular interactions on transport.     

Electrokinetic translocation of a deformable nanoparticle controlled by field effect in nanopores

Nanopores have become a popular single-molecule manipulation and detection technology. In this paper, we have constructed a continuum model of the nanopore; the arbitrary Lagrangian-Eulerian (ALE) method is used to describe the motion of particles and fluid. The mathematical model couples the stress-strain equation for the dynamics of a deformable particle, the Poisson equation for the electric field, the Navier-Stokes equations for the flow field, and the Nernst-Planck equations for ionic transport. Based on the model, the mechanism of field-effect regulation of particles passing through a nanopore is investigated. The results show that the transport of particles which is controlled by the field effect depends on the electroosmotic flow (EOF) generated by the gate electrode in the nanopore and the electrostatic interaction between the nanopore and particles. That also explains the asymmetry of particle transport velocity in the nanopore with a gate electrode. When the gate potential is negative, or the gate electrode length is small, the maximum deformation of the particles is increased. The field-effect regulation in the nanopore provides an active and compatible method for nanopore detection, and provides a convenient method for the active control of the particle deformation in the nanopore.     

Surface assembly on biofunctional magnetic nanobeads for the study of protein–ligand interactions

One of the major challenges of proteomics today is to increase the power potential for the identification of as many proteins as possible and to characterize their interactions with specific free ligands (interactomics) or present on cell walls (cell marker), in order to obtain a global, integrated view of disease processes, cellular processes and networks at the protein level. The work presented here proposes the development of biofunctionalized magnetic nanobeads that might be used for interactomic investigations. The strategy consisted in immobilizing proteins via a non covalent technique that provides greater possibilities for the advent of faster, cheaper and highly miniaturizable protein analysis systems, in particular in situations where the amount of isolated protein is scarce (trace proteins). The advantage of the immobilization technique proposed here over more conventional covalent binding techniques is that it is versatile and universal (not protein specific) thus applicable to a wide range of proteins, in “mild” conditions that are non deleterious to the native structure and bioactivity of the immobilized protein. The feasibility of the technique was investigated using a model protein (streptavidin). The nanobeads were analyzed in size by light diffusion and transmission electronic spectroscopy, and in quantity of immobilized protein using a bioassay developed in the laboratory. Results are promising in that nanobeads exhibited good colloidal stability and surface concentrations in the monolayer range.     

Metal ion affinity-based biomolecular recognition and conjugation inside synthetic polymer nanopores modified with iron-terpyridine complexes

Here we demonstrate a novel biosensing platform for the detection of lactoferrin (LFN) via metal-organic frameworks, in which the metal ions have accessible free coordination sites for binding, inside the single conical nanopores fabricated in polymeric membrane. First, monolayer of amine-terminated terpyridine (metal-chelating ligand) is covalently immobilized on the inner walls of the nanopore via carbodiimide coupling chemistry. Second, iron-terpyridine (iron-terPy) complexes are obtained by treating the terpyridine modified-nanopores with ferrous sulfate solution. The immobilized iron-terPy complexes can be used as recognition elements to fabricate biosensing nanodevice. The working principle of the proposed biosensor is based on specific noncovalent interactions between LFN and chelated metal ions in the immobilized terpyridine monolayer, leading to the selective detection of analyte protein. In addition, control experiments proved that the designed biosensor exhibits excellent biospecificity and nonfouling properties. Furthermore, complementary experiments are conducted with multipore membranes containing an array of cylindrical nanopores. We demonstrate that in the presence of LFN in the feed solution, permeation of methyl viologen (MV(2+)) and 1,5-naphthalenedisulphate (NDS(2-)) is drastically suppressed across the iron-terPy modified membranes. On the basis of these findings, we envision that apart from conventional ligand-receptor interactions, the designing and immobilization of alternative functional ligands inside the synthetic nanopores would extend this method for the construction of new metal ion affinity-based biomimetic systems for the specific binding and recognition of other biomolecules.     

Electrochemical reactivity at redox-molecule-based nanoelectrode ensembles

A model describing electrochemical reactivity at nanoelectrode ensembles consisting of redox-molecule-based active sites immobilized on otherwise passivated electrode surfaces is presented. A mathematical treatment in terms of hemispherical diffusion of redox-active solutes to a layer of independent molecule-based nanoelectrode sites is shown to be equivalent to one in terms of a bimolecular diffusion-limited reaction between a layer of immobilized redox molecules and a reservoir of redox-active solutes. This equivalence derives from the fact that in both cases the mass-transfer problem is essentially that of hemispherical diffusion. The model is further developed to consider rate limitation by both the bimolecular redox reaction between the active-site molecule and redox molecules in solution and the heterogeneous redox reaction between the electrode and the active-site molecule. Analytical expressions are derived for the current–voltage relation corresponding to catalyzed electron transfer at an ensemble of redox-molecule-based nanoelectrode sites, and the expressions are used to interpret preliminary data for ultrasensitive electrochemical detection in flow streams via an electrochemical amplification process that is thought to involve redox mediation by individual analyte molecules adsorbed onto monolayer-coated electrodes.     

Solvent-extraction and Langmuir-adsorption-based transport in chemically functionalized nanopore membranes

We have investigated the transport properties of nanopore alumina membranes that were rendered hydrophobic by functionalization with octadecyltrimethoxysilane (ODS). The pores in these ODS-modified membranes are so hydrophobic that they are not wetted by water. Nevertheless, nonionic molecules can be transported from an aqueous feed solution on one side of the membrane, through the dry nanopores, and into an aqueous receiver solution on the other side. The transport mechanism involves Langmuir-type adsorption of the permeating molecule onto the ODS layers lining the pore walls, followed by solid-state diffusion along these ODS layers; we have measured the diffusion coefficients associated with this transport process. We have also investigated the transport properties of membranes prepared by filling the ODS-modified pores with the water-immiscible (hydrophobic) liquid mineral oil. In this case the transport mechanism involves solvent extraction of the permeating molecule into the mineral oil subphase confined with the pores, followed by solution-based diffusion through this liquid subphase. Because of this different transport mechanism, the supported-liquid membranes show substantially better transport selectivity than the ODS-modified membranes that contain no liquid subphase.     

Electrokinetic particle translocation through a nanopore containing a floating electrode

Electrokinetic particle translocation through a nanopore containing a floating electrode is investigated by solving a continuum model, composed of the coupled Poisson-Nernst-Planck (PNP) equations for the ionic mass transport and the modified Stokes equations for the flow field. Two effects due to the presence of the floating electrode, the induced-charge electroosmosis (ICEO) and the particle-floating electrode electrostatic interaction, could significantly affect the electrokinetic mobility of DNA nanoparticles. When the electrical double layers (EDLs) of the DNA nanoparticle and the floating electrode are not overlapped, the particle-floating electrode electrostatic interaction becomes negligible. As a result, the DNA nanoparticle could be trapped near the floating electrode arising from the induced-charge electroosmosis when the applied electric field is relatively high. The presence of the floating electrode attracts more ions inside the nanopore resulting in an increase in the ionic current flowing through the nanopore; however, it has a limited effect on the deviation of the current from its base current when the particle is far from the pore.     

Surface-charge induced ion depletion and sample stacking near single nanopores in microfluidic devices

We report integrated nanopore/microchannel devices in which single nanopores are isolated between two microfluidic channels. The devices were formed by sandwiching track-etched conical nanopores in a poly(ethylene terephthalate) membrane between two poly(dimethylsiloxane) microchannels. Integration of the nanopores into microfluidic devices improves mass transport to the nanopore and allows easy coupling of applied potentials. Electrical and optical characterization of these individual nanopores suggests double layer overlap is not required to form an ion depletion region adjacent to the nanopore in the microchannel; rather, excess surface charge in the nanopore contributes to the formation of this ion depletion region. We used fluorescent probes to optically map the ion depletion region and the stacking of fluorescein near the nanopore/microchannel junction, and current measurements confirmed formation of the ion depletion region.     

Ion transport by viscous gas flow through capillaries

The effects of a number of experimental parameters on the efficiency of ion transport by viscous gas flow through narrow capillaries have been studied. Both electrospray and corona ion sources were used. The experimental data are consistent with ions loss to the walls of the capillary, which initially is caused mainly by space-charge expansion, but later is caused by diffusion. These processes can result in severe discrimination against low mass ions. The extent of ion loss may be calculated by using a simple model for radial diffusional loss in long cylinders, with an exponential decay of the ion density along the transport capillary. However, such a simple model underestimates ion loss by ignoring the effects of space-charge, turbulent flow, and rapid decay of higher radial diffusion modes (enhanced loss of ions that enter the capillary close to the wall). In contrast, Monte Carlo simulations showed that the effect of the parabolic velocity profile, under laminar flow conditions, is to increase the transmitted ion current, sometimes by several orders of magnitude, relative to the predictions of the simple diffusion model. After considering all these factors, the transmitted current from a corona was well reproduced by using mobility values for ions formed in such discharges. However, the measured transmitted current from an electrospray source was much too high. To explain this, it was necessary to assume that about 2% of the electrospray current is carried by aerosol particles with radii in the 10-25-Å range. Finally, it is argued that in glass capillaries wall charging may explain why the transmitted ion current is observed to be very similar to that in metal capillaries.     

Solid-state nanopores for ion and small molecule analysis

Solid-state nanopore in analytical chemistry has developed rapidly in the 1990s and it is proved to be a versatile new tool for bioanalytical chemistry. This review focuses on the analysis of ions and small molecules with nanopores including nanopipettes, polymer film nanopores, Si₃N₄ nanopores, graphene nanopores, MoS₂ nanopores and MOFs.     

Solid-state nanopores for ion and small molecule analysis

Solid-state nanopore in analytical chemistry has developed rapidly in the 1990s and it is proved to be a versatile new tool for bioanalytical chemistry. The research field of solid-state nanopore starts from mimicking the biological nanopore in living cells. Understanding the transport mechanism of biological nanopore in vivo is a big challenge because of the experimental difficulty, so it is essential to establish the basic research of artificial nanopores in vitro especially for the analysis of ions and small molecules. The performance of solid-state nanopores could be evaluated by monitoring currents when ions and molecules passed through. The comparison of the two types of nanopores based on current-derived information can reveal the principle of biological nanopores, while the solid-state nanopores are applied into practical bioanalysis. In this review, we focus on the researches of the solid-state nanopores in the fabrication process and in the analysis of ions and small molecules. Fabrication methods of nanopores, ion transport mechanism, small molecule analysis and theoretical studies are discussed in detail.     

Construction by molecular dynamics modeling and simulations of the porous structures formed by dextran polymer chains attached on the surface of the pores of a base matrix: characterization of porous structures

Significant increases in the separation of bioactive molecules by using ion-exchange chromatography are realized by utilizing porous adsorbent particles in which the affinity group/ligand is linked to the base matrix of the porous particle via a polymeric extender. To study and understand the behavior of such systems, the M3B model is modified and used in molecular dynamics (MD) simulation studies to construct porous dextran layers on the surface of a base matrix, where the dextran polymer chains and the surface are covered by water. Two different porous polymer layers having 25 and 40 monomers per main polymer chain of dextran, respectively, are constructed, and their three-dimensional (3D) porous structures are characterized with respect to porosity, pore size distribution, and number of conducting pathways along the direction of net transport. It is found that the more desirable practical implications with respect to structural properties exhibited by the porous polymer layer having 40 monomers per main polymer chain, are mainly due to the higher flexibility of the polymer chains of this system, especially in the upper region of the porous structure. The characterization and analysis of the porous structures have suggested a useful definition for the physical meaning and implications of the pore connectivity of a real porous medium that is significantly different than the artificial physical meaning associated with the pore connectivity parameter employed in pore network models and whose physical limitations are discussed; furthermore, the methodology developed for the characterization of the three-dimensional structures of real porous media could be used to analyze the experimental data obtained from high-resolution noninvasive three-dimensional methods like high-resolution optical microscopy. The MD modeling and simulations methodology presented here could be used, considering that the type and size of affinity group/ligand as well as the size of the biomolecule to be adsorbed onto the affinity group/ligand are known, to construct different porous dextran layers by varying the length of the polymeric chain of dextran, the number of attachment points to the base matrix, the degree of side branching, and the number of main polymeric chains immobilized per unit surface area of base matrix. After the characterization of the porous structures of the different porous dextran layers is performed, then only a few promising structures would be selected for studying the immobilization of adsorption sites on the pore surfaces and the subsequent adsorption of the bioactive molecules onto the immobilized affinity groups/ligands.