ABSTRACT
ABSTRACT In the next-generation nanopore-based DNA sequencing technique, DNA nanoparticles are electrophoretically driven through a single nanopore by an externally imposed dc electric eld, and the DNA sequence is determined based on the change in the recorded ionic current owing through the nanopore as the DNA molecule passes through the nanopore. The DNA translocation process has been modeled by using a continuumbased model, composed of the coupled Poisson-Nernst-Planck (PNP) equations for the ionic mass transport and the modied Stokes equations for the hydrodynamic eld. The DNA is modeled as a rigid cylindrical nanoparticle. The DNA translocation process in three types of nanopores, including ungated solid-state nanopores, gated solid-state nanopores by eld effect transistor (FET), and soft nanopores comprising functionalized polyelectrolyte brushes engrafted to the solid-state nanopore wall, has been theoretically analyzed. The predictions of the developed model agree with the experimental data obtained from the literature. The developed model successfully captures the essential physics underlying the DNA translocation process and provides both necessary theoretical background and reasonable interpretations for the experimental observations on DNA translocation through a nanopore. In both solid-state and soft nanopores, current blockade occurs for thin electric double layer at high bulk salt concentration, while both current
CONTENTS
15.1 Introduction ........................................................................................................................ 378 15.2 Mathematical Model .......................................................................................................... 379
15.2.1 Mathematical Model for the Ionic Mass Transport ..........................................380 15.2.2 Mathematical Model for the Hydrodynamic Field ........................................... 381
15.3 Numerical Implementation and Code Validation .........................................................383 15.3.1 Code Validation 1 ...................................................................................................383 15.3.2 Code Validation 2 ...................................................................................................384 15.3.3 Code Validation 3 ...................................................................................................385 15.3.4 Code Validation 4 ...................................................................................................385
