Translocation of DNA molecules through nanopores with salt gradients: the role of osmotic flow

Controlling the Dynamic Behavior of Microposts in Solution via Diffusion-Convection

Solutal buoyancy forces in solution arise from density gradients, which occur when the reactants and products of a chemical reaction occupy different volumes in the fluid. These forces drive fluids to spontaneously perform self-directed mechanical work such as shaping and organizing flexible objects in fluid-filled microchambers. Here, we use theory and simulation to show that chemical reactions are not necessary to generate useful solutal buoyancy forces; it is sufficient to just add reactants to aqueous solutions that have a different mass-to-volume ratio than water to drive such spontaneous mechanical action. To demonstrate this behavior, we model arrays of tethered, nonreactive posts in a fluid-filled chamber. Relatively dense chemicals released from the chamber's side walls diffuse into the solution and generate buoyancy-driven flows, which spontaneously trigger the posts to undergo collective dynamics. The posts' dynamics can be controllably programmed by staging the sequence of chemical release from the different walls. With chemically active posts within the array, turning on and off the influx of chemicals from the side walls leads to propagating waves that drive the posts to exhibit biomimetic coordinated motion. The introduction of cascade reactions dynamically shifts the direction of wave propagation. Our findings show how diffusion-convection and diffusion-reaction-convection processes can be used to regulate nonequilibrium spatiotemporal behavior in fluidic systems. This level of control is vital for creating portable microfluidic devices that operate without external power sources and thus function in remote or resource-poor locations.

Advances and Challenges in Solid-State Nanopores for DNA Sequencing

Solid-state nanopore sensing, a state-of-the-art technology for single-molecule detection, has rapidly advanced in recent years and demonstrates significant potential in DNA sequencing. This technology determines the nucleotide sequences by analyzing the electrical or optical signal variations that occur when DNA molecules pass through the nanopore. It offers notable advantages, including high-throughput, single-molecule detection, real-time monitoring, and the elimination of the need for polymerase chain reaction (PCR) amplification, thereby presenting broad application prospects in areas such as the diagnosis and treatment of genetic diseases. This paper reviews the solid-state nanopore DNA sequencing technology by discussing advancements in nanopore types, preparation techniques, and sequencing detection methods. It examines various nanopore materials, including silicon-based materials and two-dimensional (2D) materials, as well as preparation techniques such as transmission electron microscopy (TEM), focused ion beam (FIB) etching, and controlled breakdown (CBD). Additionally, it elucidates sequencing detection mechanisms, including ion-current blockade, transverse-current detection, and optical detection. However, this technology faces numerous challenges in its implementation and future commercialization. For instance, limited spatial resolution hampers single-base identification; the rapid translocation speed of DNA impacts time resolution; and various types of noise significantly disrupt detection signals. In response, researchers have proposed several solutions, including local thinning of the film, adjustment of surface charges, and optimization of detection materials and structures. With interdisciplinary integration and technological innovation, solid-state nanopore DNA sequencing technology is expected to make breakthroughs, bringing transformations to life sciences research and medical diagnosis.

Diffusioosmotic Reversal of Colloidal Focusing Direction in a Microfluidic T-Junction

Solute gradients next to an interface drive a diffusioosmotic flow, the origin of which lies in the intermolecular interactions between the solute and the interface. These flows on the surface of colloids introduce an effective slip velocity, driving their diffusiophoretic migration. In confined environments, the interplay between diffusiophoresis and diffusioosmosis governs the motion of colloids. Previous studies have indeed demonstrated the quantitative modulation of phoretic migration by the osmotic flows. Here, we show that diffusioosmotic flows can lead to qualitatively distinct outcomes, reversing the direction of colloidal focusing expected from diffusiophoresis alone. Using microfluidic experiments in a T-junction, numerical simulations, and theoretical modeling, we explain our observations to be due to an interplay between diffusiophoretic migration of colloids toward the walls and their entrainment in a diffusioosmotic vortex. We show this focusing to be persistent for a range of salt types, salt gradients, and flow rates, and establish a criterion for its emergence. Our work sheds light on how boundaries modulate the solute-mediated transport of colloids in confined environments and how the colloidal trajectories can be utilized to infer the surface properties.

On Diffusiophoresis of a Soft Particle with a Hydrophobic Inner Core: A Semianalytical Study

The current study deals with a theoretical analysis of diffusiophoresis of a soft particle, consisting of a hydrophobic charged rigid core coated with an ion- and fluid-penetrable charged polymer layer suspending in an electrolyte medium in reaction to an applied concentration gradient. The inner core's hydrophobicity is assumed to be characterized by a surface-charge-dependent slip length parameter. Based on a weak particle charge consideration, the governing equations describing the flow phenomena are solved theoretically to deduce a semianalytic general diffusiophoretic mobility expression applied to an arbitrary Debye layer thickness. A closed-form analytic solution is also obtained, which applies to a thin Debye length and low permeable porous layer. The impact of the charge-dependent wettability of the rigid core on the particle's diffusiophoretic motion is analyzed. We found that the inner core's hydrophobicity profoundly influences the particle mobility at a thicker Debye layer with a constant surface charge density when the chemiphoresis and electrophoresis components assist each other. At a fixed ζ-potential, the effect of the hydrophobic core is substantial for a thinner Debye length. In addition, with a critical selection of core and polymer layer charges, mobility reversal is demonstrated by modulating the salt concentration and slip length parameters.

Improving macromolecule crowding configurations in nanopores for protein sensing

We show that PEG-induced macromolecular crowding enhances protein detection in nanopores by increasing capture rate and translocation frequency. Experimental data indicate that a PEG concentration gradient boosts capture efficiency, while our theoretical model attributes this enhancement to osmotic flow, offering insights for improving nanopore-based biosensing.

Na+-Mg2+ ion effects on conformation and translocation dynamics of single-stranded RNA: Cooperation and competition

The nanopore-based translocation of a single-stranded RNA (ssRNA) in mixed salt solution has garnered increasing interest for its biological and technological significance. However, it is challenging to comprehensively understand the effects of the mixed ion species on the translocation dynamics due to their cooperation and competition, which can be directly reflected by the ion screening and neutralizing effects, respectively. In this study, Langevin dynamics simulation is employed to investigate the properties of ssRNA conformation and translocation in mixed Na+-Mg2+ ion environments. Simulation results reveal that the ion screening effect dominates the change in the ssRNA conformational size, the ion neutralizing effect controls the capture rate of the ssRNA by the nanopore, and both of them take charge of the different changes in translocation time of the ssRNA under various mixed ion environments. Under high Na+ ion concentration, as Mg2+ concentration increases, the ion neutralizing effect strengthens, weakening the driving force inside the nanopore, leading to longer translocation time. Conversely, at low Na+ concentration, an increase in Mg2+ concentration enhances the ion screening effect, aiding in faster translocation. Furthermore, these simulation results will be explained by quantitative analysis, advancing a deeper understanding of the complicated effects of the mixed Na+-Mg2+ ions.

Diffusiophoretic Behavior of Polyelectrolyte-Coated Particles

Diffusiophoresis, the movement of particles under a solute concentration gradient, has practical implications in a number of applications, such as particle sorting, focusing, and sensing. For diffusiophoresis in an electrolyte solution, the particle velocity is described by the electrolyte relative concentration gradient and the diffusiophoretic mobility of the particle. The electrolyte concentration, which typically varies throughout the system in space and time, can also influence the zeta potential of particles in space and time. This variation affects the diffusiophoretic behavior, especially when the zeta potential is highly dependent on the electrolyte concentration. In this work, we show that adsorbing a single bilayer (or 4 bilayers) of a polyelectrolyte pair (PDADMAC/PSS) on the surface of microparticles resulted in effectively constant zeta potential values with respect to salt concentration throughout the experimental range of salt concentrations. This allowed a constant potential model for diffusiophoretic transport to describe the experimental observations, which was not the case for uncoated particles in the same electrolyte system. This work highlights the use of simple polyelectrolyte pairs to tune the zeta potential and maintain constant values for precise control of diffusiophoretic transport.

Programmable and Pixelated Solute Concentration Fields Controlled by Three-Dimensionally Networked Microfluidic Source/Sink Arrays

Membrane-integrated microfluidic platforms have played a pivotal role in understanding natural phenomena coupled with solute concentration gradients at the micro- and nanoscale, enabling on-chip microscopy in well-defined planar concentration fields. However, the standardized two-dimensional fabrication schemes in microfluidics have impeded the realization of more complex and diverse chemical environmental conditions due to the limited possible arrangements of source/sink conditions in a fluidic domain. In this study, we present a microfluidic platform with a three-dimensional microchannel network design, where discretized membranes can be integrated and individually controlled in a two-dimensional array format at any location within the entire quasi-two-dimensional solute concentration field. We elucidate the principles of the device to implement operations of the pixel-like sources/sinks and dynamically programmable control of various long-lasting solute concentration fields. Furthermore, we demonstrate the application of the generated solute concentration fields in manipulating the transport of micrometer or submicrometer particles with a high degree of freedom, surpassing conventionally available solute concentration fields. This work provides an experimental tool for investigating complex systems under high-order chemical environmental conditions, thereby facilitating the extensive development of higher-performance micro- and nanotechnologies.

Spiers Memorial Lecture: Towards understanding of iontronic systems: electroosmotic flow of monovalent and divalent electrolyte through charged cylindrical nanopores

In many practical applications, ions are the primary charge carrier and must move through either semipermeable membranes or through pores, which mimic ion channels in biological systems. In analogy to electronic devices, the "iontronic" ones use electric fields to induce the charge motion. However, unlike the electrons that move through a conductor, motion of ions is usually associated with simultaneous solvent flow. A study of electroosmotic flow through narrow pores is an outstanding challenge that lies at the interface of non-equilibrium statistical mechanics and fluid dynamics. In this paper, we will review recent works that use dissipative particle dynamics simulations to tackle this difficult problem. We will also present a classical density functional theory (DFT) based on the hypernetted-chain approximation (HNC), which allows us to calculate the velocity of electroosmotic flows inside nanopores containing 1 : 1 or 2 : 1 electrolyte solution. The theoretical results will be compared with simulations. In simulations, the electrostatic interactions are treated using the recently introduced pseudo-1D Ewald summation method. The zeta potentials calculated from the location of the shear plane of a pure solvent are found to agree reasonably well with the Smoluchowski equation. However, the quantitative structure of the fluid velocity profiles deviates significantly from the predictions of the Smoluchowski equation in the case of charged pores with 2 : 1 electrolyte. For low to moderate surface charge densities, the DFT allows us to accurately calculate the electrostatic potential profiles and the zeta potentials inside the nanopores. For pores with 1 : 1 electrolyte, the agreement between theory and simulation is particularly good for large ions, for which steric effects dominate over the ionic electrostatic correlations. The electroosmotic flow is found to depend very strongly on the ionic radii. In the case of pores containing 2 : 1 electrolyte, we observe a reentrant transition in which the electroosmotic flow first reverses and then returns to normal as the surface change density of the pore is increased.

Moving dynamics of a nanorobot with three DNA legs on nanopore-based tracks

DNA nanorobots have garnered increasing attention in recent years due to their unique advantages of modularity and algorithm simplicity. To accomplish specific tasks in complex environments, various walking strategies are required for the DNA legs of the nanorobot. In this paper, we employ computational simulations to investigate a well-designed DNA-legged nanorobot moving along a nanopore-based track on a planar membrane. The nanorobot consists of a large nanoparticle as the robot core and three single-stranded DNAs (ssDNAs) as the robot legs. The nanopores linearly embedded in the membrane serve as the toeholds for the robot legs. A charge gradient along the pore distribution mainly powers the activation of the nanorobot. The nanorobot can move in two modes: a walking mode, where the robot legs sequentially enter the nanopores, and a jumping mode, where the robot legs may skip a nanopore to reach the next one. Moreover, we observe that the moving dynamics of the nanorobot on the nanopore-based tracks depends on pore-pore distance, pore charge gradient, external voltage, and leg length.

Slip-Coupled Electroosmosis and Electrophoresis Dictate DNA Translocation Speed in Solid-State Nanopores

Controlling the DNA translocation speed is critical in nanopore sequencing, but remains rather challenging in practice, as attributable to a complex coupling between nanoscale fluidics and electrically mediated migration of DNA in a dynamically evolving manner. One important factor influencing the translocation speed is the DNA-liquid slippage stemming from the hydrophobic nature of the oligonucleotide, an aspect that has been widely ignored in the reported literature. In an effort to circumvent this conceptual deficit, here we first develop an analytical model to bring out the slip-mediated coupling between the electroosmosis and DNA-electrophoresis in a solid-state nanopore at low surface charge limits, ignoring the end effects. Subsequently, we compare these results with the numerical simulation data on electrokinetically modulated DNA translocation in such a nanopore, albeit of finite length with due accommodation of the end effects, connecting two end reservoirs by deploying a fully coupled Poisson-Nernst-Plank-Stokes flow model. Both the numerical and analytical results indicate that the DNA translocation speed is a linearly increasing function of the slip length, with more than four-fold increase being observed for a slip length as minimal as 0.5 nm as compared to the no-slip scenario. Considering specific strategies on demand for arresting high translocation speeds for accurate DNA sequencing, the above results establish a theoretical proposition for the same, premised on an analytical expression of the DNA-hydrophobicity modulated enhancement in the translocation speed for designing a nanopore-based sequencing platform─a paradigm that remained to be underemphasized thus far.

Polymer Translocation and Nanopore Sequencing: A Review of Advances and Challenges

Various biological processes involve the translocation of macromolecules across nanopores; these pores are basically protein channels embedded in membranes. Understanding the mechanism of translocation is crucial to a range of technological applications, including DNA sequencing, single molecule detection, and controlled drug delivery. In this spirit, numerous efforts have been made to develop polymer translocation-based sequencing devices, these efforts include findings and insights from theoretical modeling, simulations, and experimental studies. As much as the past and ongoing studies have added to the knowledge, the practical realization of low-cost, high-throughput sequencing devices, however, has still not been realized. There are challenges, the foremost of which is controlling the speed of translocation at the single monomer level, which remain to be addressed in order to use polymer translocation-based methods for sensing applications. In this article, we review the recent studies aimed at developing control over the dynamics of polymer translocation through nanopores.

Clustering of self-thermophilic asymmetric dimers: the relevance of hydrodynamics

Self-thermophilic dimers are characterized by a net phoretic attraction which, in combination with hydrodynamic interactions, results in the formation of crystalline-like aggregates. To distinguish the effect of the different contributions is frequently an important challenge. We present a simulation investigation done in parallel in the presence and the absence of hydrodynamic interactions for the case of asymmetric self-thermophoretic dimers. In the absence of hydrodynamics, the clusters have the standard heads-in configurations. In contrast, in the presence of hydrodynamics, clusters with heads-in conformation are being formed, in which dimers with their propulsion velocity pointing out of the cluster are assembled and stabilized by strong hydrodynamic osmotic flows. Significant variation in the material properties is to be expected from such differences in the collective behavior, whose understanding and control is of great relevance for the development of new synthetic active materials.

Reversal of Electroosmotic Flow in Charged Nanopores with Multivalent Electrolyte

We study the reversal of electroosmotic flow in charged cylindrical nanopores containing multivalent electrolyte. Dissipative particle dynamics is used to simulate the hydrodynamics of the electroosmotic flow. The electrostatic interactions are treated using 3D Ewald summation, corrected for a pseudo-one-dimensional geometry of the pore. We observe that, for sufficiently large surface charge density, condensation of multivalent counterions leads to the reversal of the pore's surface charge. This results in the reversal of electroosmotic flow. Our simulations show that the Smoluchowski equation is able to quantitatively account for the electroosmotic flow through the nanopore, if the shear plane is shifted from the position of the Stern contact surface.

Self-phoretic Brownian dynamics simulations

A realistic and effective model to simulate phoretic Brownian dynamics swimmers based on the general form of the thermophoretic force is here presented. The collective behavior of self-phoretic dimers is investigated with this model and compared with two simpler versions, allowing the understanding of the subtle interplay of steric interactions, propulsion, and phoretic effects. The phoretic Brownian dynamics method has control parameters which can be tuned to closely map the properties of experiments or simulations with explicit solvent, in particular those performed with multiparticle collision dynamics. The combination of the phoretic Brownian method and multiparticle collision dynamics is a powerful tool to precisely identify the importance of hydrodynamic interactions in systems of self-phoretic swimmers.

Diffusiophoresis, Diffusioosmosis, and Microfluidics: Surface-Flow-Driven Phenomena in the Presence of Flow

Diffusiophoresis is the spontaneous motion of particles under a concentration gradient of solutes. Since the first recognition by Derjaguin and colleagues in 1947 in the form of capillary osmosis, the phenomenon has been broadly investigated theoretically and experimentally. Early studies were mostly theoretical and were largely interested in surface coating applications, which considered the directional transport of coating particles. In the past decade, advances in microfluidics enabled controlled demonstrations of diffusiophoresis of micro- and nanoparticles. The electrokinetic nature and the typical scales of interest of the phenomenon motivated various experimental studies using simple microfluidic configurations. In this review, I will discuss studies that report diffusiophoresis in microfluidic systems, with the focus on the fundamental aspects of the reported results. In particular, parameters and influences of diffusiophoresis and diffusioosmosis in microfluidic systems and their combinations are highlighted.

Salt Gradient Control of Translocation Dynamics in a Solid-State Nanopore

Tuning capture rates and translocation time of analytes in solid-state nanopores are one of the major challenges for their use in detecting and analyzing individual nanoscale objects via ionic current measurements. Here, we report on the use of salt gradient for the fine control of capture-to-translocation dynamics in 300 nm sized SiN_x nanopores. We demonstrated a decrease up to a factor of 3 in the electrophoretic speed of nanoparticles at the pore exit along with an over 3-fold increase in particle detection efficiency by subjecting a 5-fold ion concentration difference across the dielectric membrane. The improvement in the sensor performance was elucidated to be a result of the salt-gradient-mediated electric field and electroosmotic flow asymmetry at nanochannel orifices. The present findings can be used to enhance nanopore sensing capability for detecting biomolecules such as amyloids and proteins.

Electroosmotic Flow in Polarizable Charged Cylindrical Nanopores

We present a simulation method to study electroosmotic flow in charged nanopores with dielectric contrast between their interior and the surrounding medium. To perform simulations, we separate the electrostatic energy into the direct Coulomb and the polarization contributions. The polarization part is obtained using periodic Green functions and can be expressed as a sum of fast converging modified Bessel functions. On the other hand, the direct Coulomb part of the electrostatic energy is calculated using fast converging three-dimensional (3D) Ewald summation method, corrected for a pseudo one-dimensional (1D) geometry. The effects of polarization are found to be particularly important for systems with multivalent counterions and narrow nanopores. Depending on the surface charge density, polarization can increase the volumetric flow rate by 200%. For systems with 3:1 electrolyte, we observe that there is a saturation of the volumetric flow rate. In this case, for polarizable pores, the flow rate is 100% higher than for nonpolarizable pores.

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.

Hydrodynamic effects in the capture of rod-like molecules by a nanopore

In the approach of biomolecules to a nanopore, it is essential to capture the effects of hydrodynamic anisotropy of the molecules and the near-wall hydrodynamic interactions which hinder their diffusion. We present a detailed theoretical analysis of the behaviour of a rod-like molecule attracted electrostatically by a charged nanopore. We first estimate the time scales corresponding to Brownian and electrostatic translations and reorientation. We find that Brownian motion becomes negligible at distances within the pore capture radius, and numerically determine the trajectories of the nano-rod in this region to explore the effects of anisotropic mobility. This allows us to determine the range of directions from the pore in which hydrodynamic interactions with the boundary shape the approach dynamics and need to be accounted for in detailed modelling.

Electroosmotic Flow Grows with Electrostatic Coupling in Confining Charged Dielectric Surfaces

In this work, the effects of polarization of confining charged planar dielectric surfaces on induced electroosmotic flow are investigated. To this end, we use dissipative particle dynamics to model solvent and ionic particles together with a modified Ewald sum method to model electrostatic interactions and surfaces polarization. A relevant difference between counterions number density profiles, velocity profiles, and volumetric flow rates obtained with and without surface polarization for moderate and high electrostatic coupling parameters is observed. For low coupling parameters, the effect is negligible. An increase of almost 500% in volumetric flow rate for moderate/high electrostatic coupling and surface separation is found when polarizable surfaces are considered. The most important result is that the increase in electrostatic coupling substantially increases the electroosmotic flow in all studied range of separations when the dielectric constant of electrolytes is much higher than the dielectric constant of confining walls. For the higher separation simulated, an increase of around 340% in volumetric flow rate when the electrostatic coupling is increased by a factor of two orders of magnitude is obtained.

Diffusiophoresis of a Highly Charged Soft Particle in Electrolyte Solutions

Diffusiophoresis of a soft particle suspended in an infinite medium of symmetric binary electrolyte solution is investigated theoretically in this study, focusing on the chemiphoresis component when there is no global diffusion potential in the bulk solution. The general governing electrokinetic equations are solved with a pseudo-spectral method based on Chebyshev polynomials, and particle mobility, defined as the particle velocity per unit concentration gradient, is calculated. Parameters of electrokinetic interest are examined, in general, to explore their respective impact upon particle motion, such as the fixed charge density and permeability in the outer porous layer, the surface charge density and size of the inner rigid core, and the electrolyte strength in the solution. Nonlinear phenomena such as the motion-deterring double-layer polarization and the counterion condensation effects are scrutinized, in particular, for highly charged soft particles. Mobility reversal is observed in some range of electrolyte strength for highly charged particles. The generation of an axisymmetric counterclockwise vortex flow across the porous layer is found to be responsible for it. The onset of the mobility reversal is synchronized with the appearance or disappearance of this vortex flow. Mobility reversal may happen more than once, with particle moving toward or away from the region of higher solute concentration. The latter is undesirable in the application of drug delivery and thus should be avoided by delicate control of the electrokinetic environment. A local micro diffusion potential is discovered, which always speeds up the migration of coions and slows down that of counterions to guarantee that there is no net electric current across the double layer. Moreover, multilayer structure of the double-layer polarization is discovered when the electrolyte strength is high. The study presented here provides insight and crucial information for practical applications of soft particles, such as drug delivery.

Regulating the aggregation of colloidal particles in an electro-osmotic micropump

Unrestricted particle transport through microfluidic channels is of paramount importance to a wide range of applications, including lab-on-a-chip devices. In this article, we study via video microscopy the electro-osmotic aggregation of colloidal particles at the opening of a micrometer-sized silica channel in the presence of a salt gradient. Particle aggregation eventually leads to clogging of the channel, which may be undone by a time-adjusted reversal of the applied electric potential. We numerically model our system via the Stokes-Poisson-Nernst-Planck equations in a geometry that approximates the real sample. This allows us to identify the transport processes induced by the electric field and salt gradient and to provide evidence that a balance thereof leads to aggregation. We further demonstrate experimentally that a net flow of colloids through the channel may be achieved by applying a square-waveform electric potential with an appropriately tuned duty cycle. Our results serve to guide the design of microfluidic and nanofluidic pumps that allow for controlled particle transport and provide new insights for anti-fouling in ultra-filtration.

Diffusioosmotic and convective flows induced by a nonelectrolyte concentration gradient

Glucose is an important energy source in our bodies, and its consumption results in gradients over length scales ranging from the subcellular to entire organs. Concentration gradients can drive material transport through both diffusioosmosis and convection. Convection arises because concentration gradients are mass density gradients. Diffusioosmosis is fluid flow induced by the interaction between a solute and a solid surface. A concentration gradient parallel to a surface creates an osmotic pressure gradient near the surface, resulting in flow. Diffusioosmosis is well understood for electrolyte solutes, but is more poorly characterized for nonelectrolytes such as glucose. We measure fluid flow in glucose gradients formed in a millimeter-long thin channel and find that increasing the gradient causes a crossover from diffusioosmosis-dominated to convection-dominated flow. We cannot explain this with established theories of these phenomena which predict that both scale linearly. In our system, the convection speed is linear in the gradient, but the diffusioosmotic speed has a much weaker concentration dependence and is large even for dilute solutions. We develop existing models and show that a strong surface-solute interaction, a heterogeneous surface, and accounting for a concentration-dependent solution viscosity can explain our data. This demonstrates how sensitive nonelectrolyte diffusioosmosis is to surface and solution properties and to surface-solute interactions. A comprehensive understanding of this sensitivity is required to understand transport in biological systems on length scales from micrometers to millimeters where surfaces are invariably complex and heterogeneous.

Diffusiophoresis in Suspensions of Charged Soft Particles

The diffusiophoresis in a suspension of charged soft particles in electrolyte solution is analyzed. Each soft particle is composed of a hard core of radius r0 and surface charge density σ and an adsorbed fluid-penetrable porous shell of thickness a−r0 and fixed charge density Q. The effect of particle interactions is considered by using a unit cell model. The ionic concentration, electric potential, and fluid velocity distributions in a unit cell are solved as power expansions in σ and Q, and an explicit formula for the diffusiophoretic velocity of the soft particle is derived from a balance between the hydrodynamic and electrostatic forces exerted on it. This formula is correct to the second orders of σ and Q and valid for arbitrary values of κa, λa, r0/a, and the particle volume fraction of the suspension, where κ is the Debye screening parameter and λ is the reciprocal of a length featuring the flow penetration into the porous shell. The effects of the physical characteristics and particle interactions on the diffusiophoresis (including electrophoresis and chemiphoresis) in a suspension of charged soft particles, which become those of hard particles and porous particles in the limits r0=a and r0=0, respectively, are significant and complicated.

Coupled water, charge and salt transport in heterogeneous nano-fluidic systems

We theoretically study the electrokinetic transport properties of nano-fluidic devices under the influence of a pressure, voltage or salinity gradient. On a microscopic level the behaviour of the device is quantified by the Onsager matrix L, a generalised conductivity matrix relating the local driving forces and the induced volume, charge and salt flux. Extending L from a local to a global linear-response relation is trivial for homogeneous electrokinetic systems, but in this manuscript we derive a generalised conductivity matrix G from L that applies also to heterogeneous electrokinetic systems. This extension is especially important in the case of an imposed salinity gradient, which gives necessarily rise to heterogeneous devices. Within this formalism we can also incorporate a heterogeneous surface charge due to, for instance, a charge regulating boundary condition, which we show to have a significant impact on the resulting fluxes. The predictions of the Poisson-Nernst-Planck-Stokes theory show good agreement with exact solutions of the governing equations determined using the finite element method under a wide variety of parameters. Having established the validity of the theory, it provides an accessible method to analyse electrokinetic systems in general without the need of extensive numerical methods. As an example, we analyse a reverse electrodialysis "blue energy" system, and analyse how the many parameters that characterise such a system affect the generated electrical power and efficiency.

Quantitative Analysis of Factors Affecting the Event Rate in Glass Nanopore Sensors

While the solid-state nanopore sensors have shown exceptional promise with their single-molecule sensitivity and label-free operations, one of the most significant challenges in the nanopore sensor is the limited analyte translocation event rate that leads to prolonged sensor response time. This issue is more pronounced when the analyte concentration is below the nanomolar (nM) range, owing to the diffusion-limited mass transport. In this work, we systematically studied the experimental factors beyond the intrinsic analyte concentration and electrophoretic mobility that affect the event rate in glass nanopore sensors. We developed a quantitative model to capture the impact of nanopore surface charge density, ionic strength, nanopore geometry, and translocation direction on the event rate. The synergistic effects of these factors on the event rates were investigated with the aim to find the optimized experimental conditions for operating the glass nanopore sensor from the response time standpoint. The findings in the study would provide useful and practical insight to enhance the device response time and achieve a lower detection limit for various glass nanopore-sensing experiments.

Osmotically Driven and Detected DNA Translocations

A salinity gradient propels a DNA molecule through a solid-state nanopore and generates an ionic current whose change allows for the detection of the translocation. Measurements and theoretical analyses reveal the role of diffusio-osmosis in driving these phenomena: After accounting for known salinity-dependent electrode effects, the measured current change caused by the presence of a DNA molecule inside the nanopore and the DNA translocation speed through it both increase with the magnitude of the applied salinity gradients. The effects are consistent with the theory of diffuisio-osmosis and strong enough to enable DNA translocations to overcome an applied retarding potential of tens of millivolts. This work illustrates how salinity gradients can be used to power and operate a nanopore sensor.

Modulation of Charge Density and Charge Polarity of Nanopore Wall by Salt Gradient and Voltage

Surface charge plays a very important role in biological processes including ionic and molecular transport across a cell membrane. Placement of charges and charge patterns on walls of polymer and solid-state nanopores allowed preparation of ion-selective systems as well as ionic diodes and transistors to be applied in building biological sensors and ionic circuits. In this article, we show that the surface charge of a 10 nm diameter silicon nitride nanopore placed in contact with a salt gradient is not a constant value, but rather it depends on applied voltage and magnitude of the salt gradient. We found that even when a nanopore was in contact with solutions of pH equivalent to the isoelectric point of the pore surface, the pore walls became charged with voltage-dependent charge density. Implications of the charge gating for detection of proteins passing through a nanopore were considered, as well. Experiments performed with single 30 nm long silicon nitride nanopores were described by continuum modeling, which took into account the surface reactions on the nanopore walls and local modulation of the solution pH in the pore and at the pore entrances. The results revealed that manipulation of surface charge can occur without changing pH of the background electrolyte, which is especially important for applications where maintaining pH at a constant and physiological level is necessary. The system presented also offers a possibility to modulate polarity and magnitude of surface charges in a two-electrode setup, which previously was accomplished in more complex multielectrode systems.

Employing LiCl salt gradient in the wild-type α-hemolysin nanopore to slow down DNA translocation and detect methylated cytosine

In this research, we demonstrate a label-free detection, biological nanopore-based method to distinguish methylated cytosine (mC) from naked cytosine (C) in sample mixtures containing both C and mC at a prolonged translocation duration. Using a 15-fold increase in LiCl salt concentration going from a cis to trans chamber, we increased the translocation dwell time of ssDNA by over 5-fold and the event capture rate by 6-fold in comparison with the symmetric concentration of 1.0 M KCl (control). This is a consequence of counter-ion binding and effective lowering of the overall charge of DNA, which in turn lessens the electrophoretic drive of the system and slows the translocation velocity. Moreover, salt gradients can create a large electric field that will funnel ions and polymers towards the pore, increasing the capture rate and translocation dwell time of DNA. As a result, in 0.2 M-3.0 M LiCl solution, ssDNA achieved a prolonged dwell time of 52 μs per nucleotide and a capture rate of 60 ssDNA per second. Importantly, lowering the translocation speed of ssDNA enhances the resulting resolution, allowing 5'-mC to be distinguished from C without using methyl-specific labels. We successfully distinguished 5'-mC from C when mixed together at ratios of 1 : 1, 3 : 7 and 7 : 3. The distribution of current blockade amplitudes of all mixtures adopted bimodal shapes, with peak-to-peak ratios coarsely corresponding to the mixture composition (e.g. the density and distribution of events shifted in correspondence with changes in 18b-0mC and 18-2mC concentration ratios in the mixture).

Conformational fluctuations of a DNA electrophoretically translocating through a nanopore under the action of a motor protein

Single-file single-molecule electrophoresis through a nanopore has emerged as one of the successful methods in DNA sequencing. In gaining sufficient accuracy in the readout of the sequence, it is essential to position every nucleotide of the sequence with great accuracy and precision at the interrogation point of the nanopore. A combination of a ratcheting enzyme and a threaded DNA across a protein pore under an electric field is experimentally shown to be a viable method for DNA sequencing within the single-molecule electrophoresis technique. Using coarse-grained models of the enzyme and the protein nanopore, and Langevin dynamics simulations, we have characterized the conformational fluctuations of the DNA inside the nanopore. We show that the conformational fluctuations of DNA are significant for slowly operating enzymes such as phi29 DNA polymerase. Our results imply that there is considerable uncertainty in precisely positioning a nucleotide at the interrogation point of the nanopore. The discrepancy between the results of coarse-grained simulations and the experimentally successful accurate sequencing suggests that additional features of the experiments, such as explicit treatment of electrolyte ions and hydrodynamics, must be incorporated in the simulations to accurately model experimental constructs.

Facilitated polymer capture by charge inverted electroosmotic flow in voltage-driven polymer translocation

The optimal functioning of nanopore-based biosensing tools necessitates rapid polymer capture from the ion reservoir. We identify an ionic correlation-induced transport mechanism that provides this condition without the chemical modification of the polymer or the pore surface. In the typical experimental configuration where a negatively charged silicon-based pore confines a 1 : 1 electrolyte solution, anionic polymer capture is limited by electrostatic polymer-membrane repulsion and the electroosmotic (EO) flow. Added multivalent cations suppress the electrostatic barrier and reverse the pore charge, inverting the direction of the EO flow that drags the polymer to the trans side. This inverted EO flow can be used to speed up polymer capture from the reservoir and to transport weakly or non-uniformly charged polymers that cannot be controlled by electrophoresis.

Osmosis-Driven Motion-Type Modulation of Biological Nanopores for Parallel Optical Nucleic Acid Sensing

Recent developments in nanopore sequencing have inspired new concepts in precision medicine but limited in throughput. By optically encoding calcium flux from an array of nanopores, parallel measurements from hundreds of nanopores were reported, while lateral drifts of biological nanopores set obstacles for signal processing. In this paper, optical single-channel recording (oSCR) serves to track nanopores with high precision and a general principle of nanopore motion kinetics is quantitatively investigated. By finely adjusting the osmosis-oriented interactions between the lipid/substrate interfaces, motions of nanopores could be controllably restricted. Improved signal-to-noise ratio is observed from motion-restricted nanopores, which is experimentally demonstrated. To systematically evaluate oSCR with asymmetric salt concentrations, a finite element method simulation is established. oSCR with an array of immobilized nanopores suggests new strategies for sequencing DNA by microscopic imaging in high throughput and is widely applicable to the investigation of other transmembrane proteins.

Salt Gradient Improving Signal-to-Noise Ratio in Solid-State Nanopore

As the single molecule detection tool, solid-state nanopores are being applied in more and more fields, such as medicine controlled delivery, ion conductance microscopes, nanosensors, and DNA sequencing. The critical information obtained from nanopores is the signal collected, which is the ionic block current caused by the molecules passing through the pores. However, the information collected is, in part, impeded by the relatively low signal-to-noise ratio of the current solid-state nanopore measurements. Here, we report that using a salt gradient across the nanopore could improve the signal-to-noise ratio when molecules translocate through Si₃N₄ nanopore. Furthermore, we demonstrate that the improved signal-to-noise ratio is connected with not only the value of surface charge but also that of a salt gradient between cis and trans sides of the nanopore.

Nanoscale Dynamics versus Surface Interactions: What Dictates Osmotic Transport?

The classical paradigm for osmotic transport has long related the induced-flow direction to the solute membrane interactions, with the low-to-high concentration flow a direct consequence of the solute rejection from the semipermeable membrane. In principle, the same was thought to occur for the newly demonstrated membrane-free osmotic transport named diffusio-osmosis. Using a recently proposed nanofluidic setup, we revisit this cornerstone of osmotic transport by studying the diffusio-osmotic flows generated at silica surfaces by either poly(ethylene)glycol polymers or ethanol molecules in aqueous solutions. Strikingly, both neutral solutes yield osmotic flows in the usual low to high concentration direction, in contradiction with their propensity to adsorb on silica. Considering theoretically and numerically the intricate nature of the osmotic response that combines molecular-scale surface interaction and near-wall dynamics, these findings are rationalized within a generalized framework. These elements constitute a step forward toward a finer understanding of osmotically driven flows, at the core of rapidly growing fields ranging from energy harvesting to active matter.

Ionic current modulation from DNA translocation through nanopores under high ionic strength and concentration gradients

Ion transport through nanopores is an important process in nature and has important engineering applications. To date, most studies of nanopore ion transport have been carried out with electrolytes of relatively low concentrations. In this paper, we report on ionic current modulation from the translocation of dsDNA through a nanopore under high ionic strength and with an electrolyte concentration gradient across the nanopore. Results show that in this case, DNA translocation can induce either negative or positive ionic current modulation, even though usually only downward peaks are expected under this high ion concentration. Through a series of experiments and numerical simulations with nanopores of different diameters and concentration gradients, it is found that the positive pulse is due to extra ions outside the electric double layer of the DNA that are brought into the nanopore by the enhanced electroosmotic flow (EOF) with the negatively charged DNA inside the nanopore.

Analysis of electrolyte transport through charged nanopores

We revisit the classical problem of flow of electrolyte solutions through charged capillary nanopores or nanotubes as described by the capillary pore model (also called "space charge" theory). This theory assumes very long and thin pores and uses a one-dimensional flux-force formalism which relates fluxes (electrical current, salt flux, and fluid velocity) and driving forces (difference in electric potential, salt concentration, and pressure). We analyze the general case with overlapping electric double layers in the pore and a nonzero axial salt concentration gradient. The 3×3 matrix relating these quantities exhibits Onsager symmetry and we report a significant new simplification for the diagonal element relating axial salt flux to the gradient in chemical potential. We prove that Onsager symmetry is preserved under changes of variables, which we illustrate by transformation to a different flux-force matrix given by Gross and Osterle [J. Chem. Phys. 49, 228 (1968)JCPSA60021-960610.1063/1.1669814]. The capillary pore model is well suited to describe the nonlinear response of charged membranes or nanofluidic devices for electrokinetic energy conversion and water desalination, as long as the transverse ion profiles remain in local quasiequilibrium. As an example, we evaluate electrical power production from a salt concentration difference by reverse electrodialysis, using an efficiency versus power diagram. We show that since the capillary pore model allows for axial gradients in salt concentration, partial loops in current, salt flux, or fluid flow can develop in the pore. Predictions for macroscopic transport properties using a reduced model, where the potential and concentration are assumed to be invariant with radial coordinate ("uniform potential" or "fine capillary pore" model), are close to results of the full model.