Theoretical and Simulation Study on Ogston Sieving of Biomolecules Using Continuum Transport Theory

Abstract

This thesis proposes a continuous transport model of Ogston sieving of rod-like double stranded DNA molecules through a microfabricated nanofilter array. It is demonstrated that the complex partitioning of DNA rods of different sizes over the nanofilter array is dominated by the loss of orientational entropy induced by the spatial confinement in the shallow regions of the nanofilter channel. As well as its role as an entropic barrier, the spatial confinement in the shallow channels also induces large changes in the effective electrophoretic mobility for longer DNA molecules in the presence of electro-osmotic flow. In addition, based on a simplified one-dimensional transport model, important analytical expressions of the mobility and the dispersion are obtained. A method for the assessment and optimization of the nanofilter arrays is proposed. It may act as the only theoretical tool available to experimentalists, which permits them to predict the performance of the nanofilters without expensive simulations.