ankar Nair eorgia Institute of Technology chool of Chemical and Biomolecular Engineering 11 Ferst Drive tlanta, Georgia 30332-0100 -mail: [email protected] Abstract. Nanopore-based single-molecule analysis is a subject of strong scientific and technological interest. Recently, solid state nanopores have been demonstrated to possess advantages over biological e.g., protein pores due to...

Measurements of ionic currents through nanopores partially blocked by DNA have emerged as a powerful method for characterization of the DNA nucleotide sequence. Although the effect of the nucleotide sequence on the nanopore blockade current has been experimentally demonstrated, prediction and interpretation of such measurements remain a formidable challenge. Using atomic resolution computationa...

BACKGROUND Owing to the complexity of the assembly problem, we do not yet have complete genome sequences. The difficulty in assembling reads into finished genomes is exacerbated by sequence repeats and the inability of short reads to capture sufficient genomic information to resolve those problematic regions. In this regard, established and emerging long read technologies show great promise, bu...

Nanopore technique has been developed as a powerful approach for single-molecule detection. Current nanopore data analysis method mainly involves time-domian process including the amplitude, translocation duration and interval time of current events. However, more abundant information hidden from noise which lacks quantitative to extract them appropriately. In view advantages that there are int...

This paper presents Density Functional Theory and Non-Equilibrium Green’s Function based First Principles calculations to explore the sensing property of Adenine and Thymine based hetero-junction chins for Ammonia and Phosphine gas molecules. This modeling and simulation technique plays an important and crucial role in the fast growing semiconductor based nanotechnology field. The hetero-juncti...

The motion of polarizable particles in a nonuniform electric field (i.e., dielectrophoresis) has been extensively used for concentration, separation, sorting, and transport of biological particles from cancer cells and viruses to biomolecules such as DNAs and proteins. However, current approaches to dielectrophoretic manipulation are not sensitive enough to selectively target individual molecul...

There are over 100 enzyme-catalyzed modifications on transfer RNA (tRNA) molecules. The levels and identity of wobble uridine (U) modifications are affected by environmental conditions and diseased states, making wobble U detection a potential biomarker for exposures and pathological conditions. The current detection of RNA modifications requires working with nucleosides in bulk samples. Nanopo...

Ultra-thin nanopores have become promising biological sensors because of their outstanding signal-to-noise ratio and spatial resolution. Here, we show that boron nitride (BN), which is a new two-dimensional (2D) material similar to graphene, could be utilized for making a nanopore with an atomic thickness. Using an all-atom molecular dynamics simulation, we investigated the dynamics of DNA tran...

Following a nanopore sequencing run of PCR products of three amplicons less than 1kb, an abundance of reads failed quality control due to template/complement mismatch. A BLAST search demonstrated that some of the failed reads mapped to two different genes -- an unexpected observation, given that PCR was carried out separately for each amplicon. A further investigation was carried out specifical...

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...