UC San Diego

In this dissertation, I examine ion transport in nanopores, which has been met with increased interest in the last two decades due to its ability to detect DNA. I start with an overview of the properties of DNA and ionic transport in nanopores. I will explain some of the methods used for measuring ionic transport in nanopores using molecular dynamics. I will also discuss microcanonical formalism of electronic transport in nanoscale systems. This method of studying electronic transport is increasing in popularity as the emphasis on nanoscale devices increases. I will also discuss an open quantum systems approach to extending this formalism. Next, I will discuss the effect that small pore size has on the ionic conductance of that pore. A previous study predicted that as the radius of a nanopore increases, the conductance of a nanopore will exhibit discrete jumps when the radius of the pore is comparable to the radius of hydration layers around the current- carrying ions. I extend this prediction to different ion species, and conclude that it will be easier to detect these features by using divalent ions. I also look at what effect membrane dielectric choice and noise has on the current using the proposed theory. I will continue by proposing a new method of DNA sequencing, consisting of measuring the ionic current in a nanochannel that is transverse to a second, intersecting, nanochannel containing a single strand of DNA. The DNA will be pulled through its channel and modulations in the ionic current will allow the identities of the DNA bases to be deduced. A molecular dynamics model was used to test the feasibility of this method of sequencing. Finally, I will discuss a method for modeling electronic current in nanoscale systems. I use an open quantum systems approach (stochastic Schrodinger equation) to model a specific bath that has properties similar to how one would expect a battery to operate. This is used to increase the amount of time a system can exist in a quasi-steady current carrying state within the microcanonical formalism