UC San Diego

In this dissertation, I discuss various aspects of the dynamics of charged particles in nanopore systems. In recent years, there have been numerous studies of organic and inorganic nanopores. Nonetheless, there is still much to be understood about these systems. I begin by summarizing some of the important literature on nanopore systems as well as the dynamics of ions in aqueous solutions. An important tool for studying these systems at the nanoscopic level has been molecular dynamics. Some of the techniques and methods of molecular dynamics will be discussed. Additionally, theoretical calculations of electronic transport have been demonstrated to be potentially useful for predicting the conductivity of a DNA base between two electrodes in a nanopore. These electronic current calculations will be discussed. I continue by discussing the effect of noise on DNA sequencing via transverse electronic transport. Although previous theoretical studies have shown that measuring the transverse current across DNA strands while they translocate through a nanopore or channel may provide a statistically distinguishable signature of the DNA bases, and may thus allow for rapid DNA sequencing, fluctuations of the environment, such as ionic and DNA motion, introduce important scattering processes that may affect the viability of this approach. Theoretical calculations and modeling are used to address this issue. Next, I will present a study of the dynamics of ions in a nanopore system under an alternating electric field. In this case, a nanopore in ionic solution acts as a capacitor with memory (memcapacitor) at various frequencies and strengths of the electric field. Most importantly, the hysteresis loop of this memcapacitor shows both negative and diverging capacitance as a function of the voltage. Molecular dynamics simulations and a simple, physically motivated model is presented to explore this phenomenon. Finally, I will discuss an aspect of ionic conduction in nanopores. Making an analogy to classical Coulomb blockade, where the electrostatic interactions of electrons causes an increased resistance of a device with a tunnel junction, I discuss the buildup of ions at the neck of a nanopore and the effect of this on ionic conduction. Molecular dynamics simulations and a rate model will be employed to study this effect