We study the electrochemistry of single layer graphene edges using a nanopore-based structure consisting of stacked graphene and Al(2)O(3) dielectric layers. Nanopores, with diameters ranging from 5 to 20 nm, are formed by an electron beam sculpting process on the stacked layers. This leads to a unique edge structure which, along with the atomically thin nature of the embedded graphene electrod...

In this paper we developed a Poisson–Nernst– Planck model of an ionic current flowing through a nanopore in a layered solid-state membrane made of a single highlydoped n-Si layer sandwiched between two thick oxide layers which we call the ionic transistor. We studied this layered membrane for a range of source-drain voltages while keeping the gate (the semiconductor membrane) voltage fixed at a...

We present a theoretical study of nanorod translocation events through solid-state nanopores of different sizes which result in positive or negative ion conductance changes. Using theoretical models, we show that positive conductance changes or up events happen for nanopore diameters smaller than a transition diameter dt, and negative conductance changes or down events occur for nanopore diamet...

a nematode parasite of rodents, has a parasitic Nippostrongylus brasiliensis life cycle that is an extremely useful model for the study of human hookworm infection, particularly in regards to the induced immune response. The current reference genome for this parasite is highly fragmented with minimal annotation, but new advances in long-read sequencing suggest that a more complete and annotated...

In nanopore sensing experiments, the properties of molecules are probed by the variation of ionic currents flowing through the nanopore. In this context, the electronic properties and the single-layer thickness of graphene constitute a major advantage for molecule characterization. Here we analyze the translocation pathway of the thioredoxin protein across a graphene nanopore, and the related i...

Haplotypes are often critical for the interpretation of genetic laboratory observations into medically actionable findings. Current massively parallel DNA sequencing technologies produce short sequence reads that are often unable to resolve haplotype information. Phasing short read data typically requires supplemental statistical phasing based on known haplotype structure in the population or p...

The Minimum Error Correction (MEC) approach is used as a metric for reconstruction of haplotypes from NGS reads. In this paper, we show that the MEC may encounter with imprecise reconstructed haplotypes for some NGS devices. Specifically, using mathematical derivations, we evaluate this approach for the SOLiD, Illumina, 454, Ion, Pacific BioSciences, Oxford Nanopore, and 10X Genomics devices. O...

Nanopore-based sensors have been studied extensively as potential tools for DNA sequencing, characterization of epigenetic modifications such as 5-methylcytosine, and detection of microRNA biomarkers. In the studies described here, the α-hemolysin protein nanopore embedded in a lipid bilayer was used for the detection and characterization of interstrand cross-links in duplex DNA. Interstrand cr...

We demonstrate the feasibility of a nanopore based single-molecule DNA sequencing method, which employs multicolor readout. Target DNA is converted according to a binary code, which is recognized by molecular beacons with two types of fluorophores. Solid-state nanopores are then used to sequentially strip off the beacons, leading to a series of detectable photon bursts, at high speed. We show t...

This paper proposes a high precision method for nanoparticle counting and sizing using a microring resonator-waveguide system that contains a flow-through nanopore. Theoretical analysis is carried out based on the coupled-mode theory, showing that when the nanoparticle passes the nanopore a temporal pulse signal can be detected and that the peak amplitude depends linearly on the nanoparticle vo...