Related papers: Biocompatible Writing of Data into DNA
All known life forms are based upon a hierarchy of interwoven feedback loops, operating over a cascade of space, time and energy scales. Among the most basic loops are those connecting DNA and proteins. For example, in genetic networks, DNA…
Over the past years, the ever-growing trend on data storage demand, more specifically for "cold" data (i.e. rarely accessed), has motivated research for alternative systems of data storage. Because of its biochemical characteristics,…
A fundamental design rule that nature has developed for biological machines is the intimate correlation between motion and function. One class of biological machines is molecular motors in living cells, which directly convert chemical…
We live in a period where bio-informatics is rapidly expanding, a significant quantity of genomic data has been produced as a result of the advancement of high-throughput genome sequencing technology, raising concerns about the costs…
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…
Double-stranded DNA translocates through sufficiently large nanopores either in a linear, single-file fashion or in a folded hairpin conformation when captured somewhere along its length. We show that the folding state of DNA can be…
The main obstacles for the practical deployment of DNA-based data storage platforms are the prohibitively high cost of synthetic DNA and the large number of errors introduced during synthesis. In particular, synthetic DNA products contain…
The DNA molecule, apart from carrying the genetic information, plays a crucial role in a variety of biological processes and find applications in drug design, nanotechnology and nanoelectronics. The molecule undergoes significant structural…
From a nanoscience perspective, cellular processes and their reduced in vitro imitations provide extraordinary examples for highly robust few or single molecule reaction pathways. A prime example are biochemical reactions involving DNA…
Emerging DNA storage technologies use composite DNA letters, where information is represented by a probability vector, leading to higher information density and lower synthesis costs. However, it faces the problem of information leakage in…
DNA codes have many applications, such as in data storage, DNA computing, etc. Good DNA codes have large sizes and satisfy some certain constraints. In this paper, we present a new construction method for reversible DNA codes. We show that…
Recent genomic foundation models largely adopt large language model architectures that treat DNA as a one-dimensional token sequence. However, exhaustive sequential reading is structurally misaligned with sparse and discontinuous genomic…
Nucleic acids, like DNA and RNA, are molecules that are present in any life form. Their most notable function is to encode biological information. Why then would a physicist be interested in these molecules? As we will see, DNA is an…
We describe properties and constructions of constraint-based codes for DNA-based data storage which account for the maximum repetition length and AT/GC balance. We present algorithms for computing the number of sequences with maximum…
Due to the redundant nature of DNA synthesis and sequencing technologies, a basic model for a DNA storage system is a multi-draw "shuffling-sampling" channel. In this model, a random number of noisy copies of each sequence is observed at…
Owing to its immense storage density and durability, DNA has emerged as a promising storage medium. However, due to technological constraints, data can only be written onto many short DNA molecules called data blocks that are stored in an…
Motivated by average-case trace reconstruction and coding for portable DNA-based storage systems, we initiate the study of \emph{coded trace reconstruction}, the design and analysis of high-rate efficiently encodable codes that can be…
Molecular biology is a nanotechnology that works--it has worked for billions of years and in an amazing variety of circumstances. At its core is a system for acquiring, processing and communicating information that is universal, from…
DNA storage is now being considered as a new archival storage method for its durability and high information density, but still facing some challenges like high costs and low throughput. By reducing sequencing sample size for decoding…
Most DNA sequencing technologies are based on the shotgun paradigm: many short reads are obtained from random unknown locations in the DNA sequence. A fundamental question, studied in arXiv:1203.6233, is what read length and coverage depth…