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We consider voltage-driving DNA translocation through a nanopore in the present study. By assuming the DNA is coaxial with the cylindrical nanopore, a hydrodynamic model for determining effective force on a single DNA molecule in a nanopore…
We consider error-correcting coding for deoxyribonucleic acid (DNA)-based storage using nanopore sequencing. We model the DNA storage channel as a sampling noise channel where the input data is chunked into $M$ short DNA strands, which are…
Polymer translocation is a promising strategy for the next-generation DNA sequencing technologies. The use of biological and synthetic nano-pores, however, still suffers from serious drawbacks. In particular, the width of the membrane layer…
The translocation of a macromolecule through a nanometer-sized pore is an interesting process with important applications in the development of biosensors for single--molecule analysis and in drug delivery and gene therapy. We have carried…
Nanopore sequencing technology remains highly error-prone, making efficient error correction essential in DNA-based data storage. Prior work addressed high error rates using convolutional codes with their decoder coupled with the…
The translocation of double-stranded DNA through a solid-state nanopore may either decrease or increase the ionic current depending on the ionic concentration of the surrounding solution. Below a certain crossover ionic concentration, the…
We investigate a model nanopore sensor that is able to detect analyte ions that are present in the electrolyte solution in very small concentrations. The nanopore selectively binds the analyte ions with which the local concentrations of the…
Feature pooling layers (e.g., max pooling) in convolutional neural networks (CNNs) serve the dual purpose of providing increasingly abstract representations as well as yielding computational savings in subsequent convolutional layers. We…
Solid-state nanopore and nanopipette sensors are powerful devices for the detection, quantification and structural analysis of biopolymers such as DNA and proteins, especially in carrier-enhanced resistive-pulse sensing. However, hundreds…
Nanofabrication techniques for achieving dimensional control at the nanometer scale are generally equipment-intensive and time-consuming. The use of energetic beams of electrons or ions has placed the fabrication of nanopores in thin…
The detection of biomolecules at the single molecular level have important applications in the fields of biosensing and biomedical diagnosis. Solid state nanopore (SS-nanopore) is an effective tool to perform the single molecular detection,…
The upcoming integration of AI in the physical layer (PHY) of 6G radio access networks (RAN) will enable a higher quality of service in challenging transmission scenarios. However, deeply optimized AI-Native PHY models impose higher…
Solid-state nanopore DNA sequencers present mechanical and chemical stability, reusability, and large-scale integrability. However, their development is hindered by the absence of a protein-free mechanism for controlling DNA translocation,…
The passage of DNA through a nanopore can be effectively decomposed into two distinct phases, docking and actual translocation. In experiments each phase is characterized by a distinct current signature which allows the discrimination of…
Deep learning (DL) is revolutionizing the scientific computing community. To reduce the data gap, active learning has been identified as a promising solution for DL in the scientific computing community. However, the deep active learning…
Convolution operations dominate the overall execution time of Convolutional Neural Networks (CNNs). This paper proposes an easy yet efficient technique for both Convolutional Neural Network training and testing. The conventional convolution…
Nanopores -- nanosized holes that can transport ions and molecules -- are very promising devices for genomic screening, in particular DNA sequencing. Both solid-state and biological pores suffer from the drawback, however, that the channel…
Proteins are arguably the most important class of biomarkers for health diagnostic purposes. Label-free solid-state nanopore sensing is a versatile technique for sensing and analysing biomolecules such as proteins at single-molecule level.…
Deep convolutional neural networks (CNN) have shown their promise as a universal representation for recognition. However, global CNN activations lack geometric invariance, which limits their robustness for classification and matching of…
We propose an aqueous functionalized molybdenum disulfide nanoribbon suspended over a solid electrode as the first capacitive displacement sensor aimed at determining the DNA sequence. The detectable sequencing events arise from the…