Person:

Hoogerheide, David Paul

We describe experiments and modeling results that reveal and explain the distribution of times that identical double-stranded DNA (dsDNA) molecules take to pass through a voltage-biased solid-state nanopore. We show that the observed spread in this distribution is caused by viscous-drag-induced velocity fluctuations that are correlated with the initial conformation of nanopore-captured molecules. This contribution exceeds that due to diffusional Brownian motion during the passage. Nevertheless, and somewhat counterintuitively, the diffusional Brownian motion determines the fundamental limitations of rapid DNA strand sequencing with a nanopore. We model both diffusional and conformational fluctuations in a Langevin description. It accounts well for passage time variations for DNA molecules of different lengths, and predicts conditions required for low-error-rate nanopore-strand DNA sequencing with nanopores.

We report the closure of nanopores to single-digit nanometer dimensions by ion sculpting in a range of amorphous materials including insulators (SiO(2) and SiN), semiconductors (a-Si), and metallic glasses (Pd({80})Si(_{20})) — the building blocks of a single-digit nanometer electronic device. Ion irradiation of nanopores in crystalline materials (Pt and Ag) does not cause nanopore closure. Ion irradiation of c-Si pores below 100 °C and above 600 °C, straddling the amorphous-crystalline dynamic transition temperature, yields closure at the lower temperature but no mass transport at the higher temperature. Ion beam nanosculpting appears to be restricted to materials that either are or become amorphous during ion irradiation.

We report a material-dependent critical temperature for ion beam sculpting of nanopores in amorphous materials under keV ion irradiation. At temperatures below the critical temperature, irradiated pores open at a rate that soon saturates with decreasing temperature. At temperatures above the critical temperature, the pore closing rate rises rapidly and eventually saturates with increasing temperature. The observed behavior is well described by a model based on adatom diffusion, but is difficult to reconcile with an ion-stimulated viscous flow model.

We report experimental escape time distributions of double-stranded DNA molecules initially threaded halfway through a thin solid-state nanopore. We find a universal behavior of the escape time distributions consistent with a one-dimensional first passage formulation notwithstanding the geometry of the experiment and the potential role of complex molecule-liquid-pore interactions. Diffusion constants that depend on the molecule length and pore size are determined. Also discussed are the practical implications of long time diffusive molecule trapping in the nanopore.

We explore the ion beam-induced dynamics of the formation of large features at the edges of nanopores in freestanding silicon nitride membranes. The shape and size of these ìnanovolcanoesî, together with the rate at which the nanopores open or close, are shown to be strongly influenced by sample temperature. Volcano formation and pore closing slow and stop at low temperatures and saturate at high temperatures. Nanopore volcano size and closing rates are dependent on initial pore size. We discuss both surface diffusion and viscous flow models in the context of these observed phenomena.

We demonstrate the formation of nanoscale volcanolike structures induced by ion-beam irradiation of nanoscale pores in freestanding silicon nitride membranes. Accreted matter is delivered to the volcanoes from micrometer distances along the surface. Volcano formation accompanies nanopore shrinking and depends on geometrical factors and the presence of a conducting layer on the membrane’s back surface. We argue that surface electric fields play an important role in accounting for the experimental observations.

Voltage-biased solid-state nanopores are well established in their ability to detect and characterize single polymers, such as DNA, in electrolytes. The addition of a pressure gradient across the nanopore yields a second molecular driving force that provides new freedom for studying molecules in nanopores. In this work, we show that opposing pressure and voltage bias enables nanopores to detect and resolve very short DNA molecules, as well as to detect near-neutral polymers.

We identify a contribution to the ionic current noise spectrum in solid-state nanopores that exceeds all other noise sources in the frequency band 0.1-10 kHz. Experimental studies of the dependence of this excess noise on pH and electrolyte concentration indicate that the noise arises from surface charge fluctuations. A quantitative model based on surface functional group protonization predicts the observed behaviors and allows us to locally measure protonization reaction rates. This noise can be minimized by operating the nanopore at a deliberately chosen pH.

We report the formation of a tunable single DNA molecule trap near a solid-state nanopore in an electrolyte solution under conditions where an electric force and a pressure induced viscous flow force on the molecule are nearly balanced. Trapped molecules can enter the pore multiple times before escaping the trap by passing through the pore or by diffusing away. Statistical analysis of many individually trapped molecules yields a detailed picture of the fluctuation phenomena involved, which are successfully modeled by a one-dimensional first passage approach.