Related papers: ssDNA sequencing by rectification
Based on our formulation of the DNA electrophoresis near a pore [P. Rowghanian and A. Y. Grosberg, Phys. Rev. E 87, 042723 (2013)], we address the electrophoretic DNA capture into a nanopore as a steady-state process of particle absorption…
Single-molecule based 3rd generation DNA sequencing technologies have been explored with tremendous effort, among which nanopore sequencing is considered as one of the most promising to achieve the goal of $1,000 genome project towards…
Carrying out first-principles calculations, we study N-doped capped carbon nanotube (CNT) electrodes applied to DNA sequencing. While we obtain for the face-on nucleobase junction configurations a conventional conductance ordering where the…
A theory is presented of the longitudinal dispersion of DNA under equilibrium confined in a nanochannel. Orientational fluctuations of the DNA chain build up to give rise to substantial fluctuations of the coil in the longitudinal direction…
Miniature DNA sequencing hardware has begun to succeed in mobile contexts, driving demand for efficient machine learning at the edge. This domain leverages deep learning techniques familiar from speech and time-series analysis for both…
This paper introduces a new solution to DNA storage that integrates all three steps of retrieval, namely clustering, reconstruction, and error correction. DNA-correcting codes are presented as a unique solution to the problem of ensuring…
Digital information can be encoded in the building-block sequence of macromolecules, such as RNA and single-stranded DNA. Methods of "writing" and "reading" macromolecular strands are currently available, but they are slow and expensive. In…
DNA flexibility is a key determinant of biological function, from nucleosome positioning to transcriptional regulation, motivating a direct measurement of the bend-torque response of individual DNA molecules. In this work, DNA bending is…
This paper studies achievable rates of nanopore-based DNA storage when nanopore signals are decoded using a tractable channel model that does not rely on a basecalling algorithm. Specifically, the noisy nanopore channel (NNC) with the…
Expanding genetic codes from natural standard nucleotides to artificial non-standard nucleotides marks a significant advancement in synthetic biology, with profound implications for biotechnology and medicine. Decoding the biological…
The bias-dependent transport properties of short poly(G)-poly(C) A-DNA strands attached to Au electrodes are investigated with first principles electronic transport methods. By using the non- equilibrium Green's function approach combined…
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…
Non-native conformations drive protein misfolding diseases, complicate bioengineering efforts, and fuel molecular evolution. No current experimental technique is well-suited for elucidating them and their phenotypic effects. Especially…
We provide an overview of current approaches to DNA-based storage system design and accompanying synthesis, sequencing and editing methods. We also introduce and analyze a suite of new constrained coding schemes for both archival and random…
Molecular carriers represent an increasingly common strategy in the field of nanopore sensing to use secondary molecules to selectively report on the presence of target analytes in solution, allowing for sensitive assays of otherwise…
Translocation of a single stranded DNA through genetically engineered $\alpha$-hemolysin channels with positively charged walls is studied. It is predicted that transport properties of such channels are dramatically different from neutral…
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…
DNA Data storage has recently attracted much attention due to its durable preservation and extremely high information density (bits per gram) properties. In this work, we propose a hybrid coding strategy comprising of generalized…
Detecting chemical modifications on RNA molecules remains a key challenge in epitranscriptomics. Traditional reverse transcription-based sequencing methods introduce enzyme- and sequence-dependent biases and fragment RNA molecules,…
We present a simplified model of the dynamics of translocation of RNA through a nanopore which only allows the passage of unbound nucleotides. In particular, we consider the disorder averaged translocation dynamics of random, two-component,…