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Charge transfer can take place along double helical DNA over distances as long as 30 nanometers. However, given the active role of the thermal environment surrounding charge carriers in DNA, physical mechanisms driving the transfer process…
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…
In [1], the authors proposed a new model of DNA storage system that integrates all three steps of retrieval and introduced the concept of DNA-correcting codes, which guarantees that the output of the storage system can be decoded to the…
The biochemical processes underlying DNA data storage, including synthesis, amplification, and sequencing, are inherently noisy. Consequently, base-level insertion, deletion, and substitution (IDS) errors, as well as sequence-level…
Portable genome sequencing technology is revolutionizing genomic research by providing a faster, more flexible method of sequencing DNA and RNA [1, 2]. The unprecedented shift from bulky stand-alone benchtop equipment confined in a…
DNA-coated particles are promising as building blocks for functional and finite-sized assemblies because they can be programmed with orthogonal interactions owing to the sequence-specific hybridization of DNA strands. To fully exploit this…
The potential of a double nanopore system to determine DNA barcodes has been demonstrated experimentally. By carrying out Brownian dynamics simulation on a coarse-grained model DNA with protein tag (barcodes) at known locations along the…
DNA sequencing is the process of determining the exact order of the nucleotide bases of an individual's genome in order to catalogue sequence variation and understand its biological implications. Whole-genome sequencing techniques produce…
DNA sequencing has faced a huge demand since it was first introduced as a service to the public. This service is often offloaded to the sequencing companies who will have access to full knowledge of individuals' sequences, a major violation…
The short lifespan of traditional data storage media, coupled with an exponential increase in storage demand, has made long-term archival a fundamental problem in the data storage industry and beyond. Consequently, researchers are looking…
DNA sequence encoding is fundamental to gene function prediction, protein synthesis, and diverse downstream biological tasks. Despite the substantial progress achieved by large-scale DNA sequence pretraining, existing studies have…
Deep neural networks (DNN) have been used successfully in many scientific problems for their high prediction accuracy, but their application to genetic studies remains challenging due to their poor interpretability. In this paper, we…
We report a novel simulation strategy that enables us to identify key parameters controlling the experimentally measurable characteristics of structural protein tags on dsDNA construct translocating through a double nanopore setup. First,…
Solid-state nanopores have received substantial attention in the past years owing to their simplicity and potential applications expected in genomics, sensing, archival information storage, and computing. The underlying sensing technique of…
Nanopore sequencing offers the ability for real-time analysis of long DNA sequences at a low cost, enabling new applications such as early detection of cancer. Due to the complex nature of nanopore measurements and the high cost of…
The nucleotide sequence representation of DNA can be inadequate for resolving protein-DNA binding sites and regulatory substrates, such as those involved in gene expression and horizontal gene transfer. Considering that sequence-like…
The synthesis of DNA strands remains the most costly part of the DNA storage system. Thus, to make DNA storage system more practical, the time and materials used in the synthesis process have to be optimized. We consider the most common…
Motivation: The MinION device by Oxford Nanopore is the first portable sequencing device. MinION is able to produce very long reads (reads over 100~kBp were reported), however it suffers from high sequencing error rate. In this paper, we…
Owing to its several merits over other DNA sequencing technologies, nanopore sequencers hold an immense potential to revolutionize the efficiency of DNA storage systems. However, their higher error rates necessitate further research to…
Genetic engineering of cells has a range of applications in treating incurable diseases. Plasmid DNA is a popular choice of nucleic acid for cell engineering due to its low cost and stability. However, plasmid DNA must survive the…