Nanopores: synergy from DNA sequencing to industrial filtration - small holes with big impact

Nanopores in thin membranes play important roles in science and industry. Single nanopores have provided a step-change in portable DNA sequencing and understanding nanoscale transport while multipore membranes facilitate food processing and purification of water and medicine. Despite the unifying use of nanopores, the fields of single nanopores and multipore membranes differ - to varying degrees - in terms of materials, fabrication, analysis, and applications. Such a partial disconnect hinders scientific progress as important challenges are best resolved together. This Viewpoint suggests how synergistic crosstalk between the two fields can provide considerable mutual benefits in fundamental understanding and the development of advanced membranes. We first describe the main differences including the atomistic definition of single pores compared to the less defined conduits in multipore membranes. We then outline steps to improve communication between the two fields such as harmonizing measurements and modelling of transport and selectivity. The resulting insight is expected to improve the rational design of porous membranes. The Viewpoint concludes with an outlook of other developments that can be best achieved by collaboration across the two fields to advance the understanding of transport in nanopores and create next-generation porous membranes tailored for sensing, filtration, and other applications

Searching for self-similarity in switching time and turbulent cascades in ion transport through a biochannel. A time delay asymmetry

The process of ion transport through a locust potassium channel is described by means of the Fokker-Planck equation (FPE). The deterministic and stochastic components of the process of switching between various conducting states of the channel are expressed by two coefficients, $D^{(1)}$ and $D^{(2)}$, a drift and a diffusion coefficient, respectively. The FPE leads to a Langevin equation. This analysis reveals beside the well known deterministic aspects a turbulent, cascade type of action. The (noisy-like) switching between different conducting states prevents the channel from staying in one, closed or open state. The similarity between the hydrodynamic flow in the turbulent regime and hierarchical switching between conducting states of this biochannel is discussed. A non-trivial character of $D^{(1)}$ and $D^{(2)}$ coefficients is shown, which points to different processes governing the channel's action, asymetrically depending on the history of the previously conducting states. Moreover, the Fokker-Planck and Langevin equations provide information on whether and how the statistics of the channel action change over various time scales.Comment: submitted to physica A text : 12 pages + 8 figure

Rectification properties of conically shaped nanopores: consequences of miniaturization

Nanopores attracted a great deal of scientific interest as templates for biological sensors as well as model systems to understand transport phenomena at the nanoscale. The experimental and theoretical analysis of nanopores has been so far focused on understanding the effect of the pore opening diameter on ionic transport. In this article we present systematic studies on the dependence of ion transport properties on the pore length. Particular attention was given to the effect of ion current rectification exhibited for conically shaped nanopores with homogeneous surface charges. We found that reducing the length of conically shaped nanopores significantly lowered their ability to rectify ion current. However, rectification properties of short pores can be enhanced by tailoring the surface charge and the shape of the narrow opening. Furthermore we analyze the relationship of the rectification behavior and ion selectivity for different pore lengths. All simulations were performed using MsSimPore, a software package for solving the Poisson-Nernst-Planck (PNP) equations. It is based on a novel finite element solver and allows for simulations up to surface charge densities of -2 e/nm^2. MsSimPore is based on 1D reduction of the PNP model, but allows for a direct treatment of the pore with bulk electrolyte reservoirs, a feature which was previously used in higher dimensional models only. MsSimPore includes these reservoirs in the calculations; a property especially important for short pores, where the ionic concentrations and the electric potential vary strongly inside the pore as well as in the regions next to pore entrance

The design and characterization of multifunctional aptamer nanopore sensors

Aptamer-modified nanomaterials provide a simple, yet powerful sensing platform when combined with resistive pulse sensing technologies. Aptamers adopt a more stable tertiary structure in the presence of a target analyte, which results in a change in charge density and velocity of the carrier particle. In practice the tertiary structure is specific for each aptamer and target, and the strength of the signal varies with different applications and experimental conditions. Resistive pulse sensors (RPS) have single particle resolution, allowing for the detailed characterization of the sample. Measuring the velocity of aptamer-modified nanomaterials as they traverse the RPS provides information on their charge state and densities. To help understand how the aptamer structure and charge density effects the sensitivity of aptamer-RPS assays, here we study two metal binding aptamers. This creates a sensor for mercury and lead ions that is capable of being run in a range of electrolyte concentrations, equivalent to river to seawater conditions. The observed results are in excellent agreement with our proposed model. Building on this we combine two aptamers together in an attempt to form a dual sensing strand of DNA for the simultaneous detection of two metal ions. We show experimental and theoretical responses for the aptamer which creates layers of differing charge densities around the nanomaterial. The density and diameter of these zones effects both the viability and sensitivity of the assay. While this approach allows the interrogation of the DNA structure, the data also highlight the limitations and considerations for future assays

Correlation studies of open and closed states fluctuations in an ion channel: Analysis of ion current through a large conductance locust potassium channel

Ion current fluctuations occurring within open and closed states of large conductance locust potassium channel (BK channel) were investigated for the existence of correlation. Both time series, extracted from the ion current signal, were studied by the autocorrelation function (AFA) and the detrended fluctuation analysis (DFA) methods. The persistent character of the short- and middle-range correlations of time series is shown by the slow decay of the autocorrelation function. The DFA exponent $\alpha$ is significantly larger than 0.5. The existence of strongly-persistent long-range correlations was detected only for closed-states fluctuations, with $\alpha=0.98\pm0.02$. The long-range correlation of the BK channel action is therefore determined by the character of closed states. The main outcome of this study is that the memory effect is present not only between successive conducting states of the channel but also independently within the open and closed states themselves. As the ion current fluctuations give information about the dynamics of the channel protein, our results point to the correlated character of the protein movement regardless whether the channel is in its open or closed state.Comment: 12 pages, 5 figures; to be published in Phys. Rev.