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    Engineered Nanopores for Bioanalytical Applications
    Engineered Nanopores for Bioanalytical Applications
    Engineered Nanopores for Bioanalytical Applications
    Ebook368 pages3 hours

    Engineered Nanopores for Bioanalytical Applications

    By Joshua B. Edel and Tim Albrecht

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    About this ebook

    Engineered Nanopores for Bioanalytical Applications is the first book to focus primarily on practical analytical applications of nanopore development. These nanoscale analytical techniques have exciting potential because they can be used in applications such as DNA sequencing, DNA fragment sizing, DNA/protein binding, and protein/protein binding.

    This book provides a solid professional reference on nanopores for readers in academia, industry and engineering and biomedical fields. In addition, the book describes the instrumentation, fabrication, and experimental methods necessary to carry out nanopore-based experiments for developing new devices.
    • Includes application case studies for detection, identification and analysis of biomolecules and related functional nanomaterials
    • Introduces the techniques of manufacturing solid state materials with functional nanopores
    • Explains the use of nanopores in DNA sequencing and the wider range of applications from environmental monitoring to forensics
    LanguageEnglish
    PublisherElsevier Science
    Release dateMar 19, 2013
    ISBN9781437734744
    Engineered Nanopores for Bioanalytical Applications

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      Book preview

      Engineered Nanopores for Bioanalytical Applications - Joshua B. Edel

      1

      Ion Transport in Nanopores

      T. Albrecht, T. Gibb and P. Nuttall, Department of Chemistry, Imperial College London, Exhibition Road, London

      Chapter Outline

      1.1 Introduction

      1.2 Brownian motion

      1.3 Net transport of ions—the Nernst–Planck equation and its derivation

      1.4 The conductance of a pore with uncharged walls

      1.4.1 Cylindrical pores

      1.4.2 Pores with noncylindrical geometries

      1.4.3 Access resistance

      1.5 The effect of surface charge

      1.5.1 Charged surfaces in solution

      1.5.2 The conductance of nanopores with charged inner walls

      1.5.3 The ζ-potential of colloids and charged particles

      1.5.4 Electroosmosis—fluid motion close to a charged wall in response to an external electric field

      1.6 Particle translocation through nanopores—the model of deBlois and Bean

      1.6.1 Small spheres solution

      1.6.2 Broad range solution

      References

      1.1 Introduction

      The transport of ions and other charged species, as well as liquid, is at the heart of any nanopore sensor, Figure 1.1. The flux of ions determines the electric current, which is often used as the sensing signal, but it also affects the liquid, for example in electroosmosis. Ion and liquid motion may also have an impact on the translocation of biopolymers through the nanopore, such as DNA or proteins, both in terms of the duration and magnitude of the concomitant ion current modulation.

      Figure 1.1 Schematic of a nanopore sensor. The membrane separates the two liquid compartments of the cell with a single (or small number of) nanopore(s) allowing the exchange of ions and liquid. A bias voltage between two electrodes—one on each side of the membrane—allows electric field-driven transport through the nanopore. The current sensing electronics are not shown.

      The fundamental physics of ion motion has been long established and forms the basis for the theoretical understanding of charge transport in semiconductor physics, electrochemistry, membrane science, and other areas. This chapter does not attempt to cover the vast area of electrokinetic fluid and ion transport but rather give a brief introduction into the main factors governing ion transport in nanopores with a focus on mean-field, dielectric continuum theory, and the Nernst–Planck equation. References to the more advanced literature are given where appropriate.

      Simple models have the advantage that the resulting analytical expressions for the pore conductance Gpore and other parameters are transparent and potentially yield direct physical insight. Widely used work relations emerge from a relatively simple theory, which can be used to validate experimental data, for example, when assessing the pore dimensions. The lack of complexity, on the other hand, also implies certain limitations, in terms of quantitative accuracy and the validity range. For very small nanopores, in particular, where the pore size reaches molecular dimensions, the continuum model is expected to break down. Continuum theories have, however, an advantage compared to more sophisticated models and computer simulations in that they allow the entire electrochemical cell—including electrodes, electrolyte solution, and the membrane—to be treated with little extra difficulty. For example, in a conventional two-electrode system, the electric current is determined by the potential distribution in the entire cell, including potential drops at electrode/solution interfaces, the solution itself, and across the pore. If the pore is small and long, its resistance will usually dominate the total cell resistance and focusing on the pore itself is sufficient to capture all relevant features of the nanopore sensor. On the other hand, if the pore channel is very short—such as in graphene-based nanopores—the potential gradient between the electrodes and the pore openings is important and the so-called access resistance determines the overall pore resistance. This effect has been addressed already by Hille and Hall in the 1970s, who derive simple analytical expressions [1–3]. Finally, nanopore devices with multiple electrodes as potential current sources can readily be treated, as shown by Albrecht. However, careful consideration needs to be given to the limitations of the model used with regard to potential over-parameterization for example [4].

      The Nernst–Planck, the Poisson, and the Navier–Stokes equations are known as the governing equations for the ion flux, local charge distribution, and fluid dynamics (momentum transport), respectively. At a higher level of complexity and accuracy, these are solved self-consistently for a particular geometry. The results are remarkably accurate but only numerical. Molecular-level detail may be included in Brownian or Langevin dynamics simulations at increasing computational expense. Detailed reviews on these more advanced topics may be found in Refs [5–7].

      In order to understand the working principle, potential, and limitations of a nanopore sensor, we first need to look at the fundamental physical processes that underlie ionic and molecular motion in solution. Brownian motion is present at all times in a nanopore sensing experiment and offers a useful reference point to assess relevant length and timescales, depending on the species’ diffusion coefficient D. We will then move on to discuss ion transport in the presence of an external driving force, such as a concentration gradient (diffusion) or an electric field (migration). Based on the Langevin model, we derive the Nernst–Planck equation for the flux of ions and an expression for the steady-state ion current for different pore geometries, taking into account surface charge effects where appropriate. Finally, we describe a basic model for particle translocation through nanopores after deBlois and Bean [8].

      1.2 Brownian motion

      Brownian motion is the random motion of particles suspended in a fluid due to continual collisions with fast moving solvent molecules. With large numbers of molecules hitting the Brownian particle at any one time, momentum is transferred and the particle moves in a random, uncorrelated fashion. The mean square displacement in one dimension is given by:

      (1.1)

      where x is the displacement, D the diffusion coefficient, and t the time. Examining the equation reveals that it predicts substantial timescales for any macroscopic displacements but also indicates that Brownian motion can be considered a rapid process at the nanometer scale. Using D=10−10 m²/s as typical of a small protein and the one-dimensional model above, the particle would take roughly 13 μs to move along a pore channel of 50 nm length. This value would constitute a speed limit to translocation, since surface interactions and other such effects are ignored, and should only be taken as a crude approximation. More accurately, the escape time for a Brownian particle is described by the narrow escape model [9,10].

      Brownian motion is always present in a fluid, even in the presence of strong external fields, and causes some degree of spatial and electronic noise. Due to Brownian motion, one would expect translocating particles to have a velocity and thus translocation time distribution, even though other factors such as particle–wall interactions, fluid dynamics, and other effects may be more significant in magnitude. The potential for a particle to move backward or forward through a nanopore during translocation also causes complications in nanopore sensing and in particular nanopore-based DNA sequencing. To this end, Brownian motion enhances the error rate, for example, by causing particular bases to be read twice or not at all

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