UBC Theses and Dissertations
Transport and structure in nanoscale channels Lakatos, Gregory William
Driven by the rapidly advancing fields of nano- and biotechnology, there has been an explosion of interest in molecular transport and structure formation on small length scales. A canonical model for the transport of particles along one dimensional pathways in nanoscale channels is the Totally Asymmetric Simple Exclusion Process (TASEP). After introducing the standard TASEP, modifications of the TASEP designed to increase its utility in modeling biological transport processes are described. One variant of the TASEP is particularly suitable for modeling protein translation, and the results of using this variant to investigate the effects of slow-codons on the translation process are discussed. A related topic is the voltage-driven translocation of DNA hairpins through membrane-embedded nanopores. Motivated by recent experiments, a stochastic model is developed that couples the translocation and dehybridization of the DNA hairpin. This model is used to explore the behaviour of the mean translocation time of hairpins as a function of driving voltage, and two translocation mechanisms are identified and discussed. Finally, the adsorption and equilibrium structures of water in the interior of ion-bearing nanoscale pores are considered. The behaviour of water and ions under confinement is critical to the functioning of biological ion channels and nanoporous filters. Here, the adsorption isotherms of water are examined, and the layered structures formed by the confined water are described.
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