Related papers: Thermodynamically Stable DNA Code Design using a S…
Composite DNA is a recent novel method to increase the information capacity of DNA-based data storage above the theoretical limit of 2 bits/symbol. In this method, every composite symbol does not store a single DNA nucleotide but a mixture…
By exploiting the exquisite selectivity of DNA hybridization, DNA-Coated Colloids (DNACCs) can be made to self-assemble in a wide variety of structures. The beauty of this system stems largely from its exceptional versatility and from the…
Storing digital data in synthetic DNA faces challenges in ensuring data reliability in the presence of edit errors--deletions, insertions, and substitutions--that occur randomly during various stages of the storage process. Current…
The yearly global production of data is growing exponentially, outpacing the capacity of existing storage media, such as tape and disk, and surpassing our ability to store it. DNA storage - the representation of arbitrary information as…
We present a generic model for DNA at the base-pair level. We use a variant of the Gay-Berne potential to represent the stacking energy between neighboring base-pairs. The sugar-phosphate backbones are taken into account by semi-rigid…
Our understanding of radiation induced cellular damage has greatly improved over the past decades. Despite this progress, there are still many obstacles to fully understanding how radiation interacts with biologically relevant cellular…
The detection of similarities between long DNA and protein sequences is studied using concepts of statistical physics. It is shown that mutual similarities can be detected by sequence alignment methods only if their amount exceeds a…
An example of a nonspecific molecular bond is the affinity of any positive charge for any negative charge (like-unlike), or of nonpolar material for itself when in aqueous solution (like-like). This contrasts specific bonds such as the…
Understanding the functional (dis)-similarity of source code is significant for code modeling tasks such as software vulnerability and code clone detection. We present DISCO(DIS-similarity of COde), a novel self-supervised model focusing on…
Sequencing by tunneling is a next-generation approach to read single-base information using electronic tunneling transverse to the single-stranded DNA (ssDNA) backbone while the latter is translocated through a narrow channel. The original…
This work presents a novel spiking neural network (SNN) decoding method, combining SNNs with Hyperdimensional computing (HDC). The goal is to create a decoding method with high accuracy, high noise robustness, low latency and low energy…
We consider a novel approach of measuring the homology of DNA sequences based of the variety of optimal alignments in the longest common subsequence sense. The proposed approach is compared with BLAST in measuring the homology of four…
Social network alignment, aligning different social networks on their common users, is receiving dramatic attention from both academic and industry. All existing studies consider the social network to be static and neglect its inherent…
This study explores the self-synchronization problem in DNA coding, specifically addressing single-deletion errors without using delimiters between codewords. We aim to identify the beginning of each codeword without using delimiters,…
At present, there have been suggested two types of physical mechanism that may facilitate preferential pairing between DNA molecules, with identical or similar base pair texts, without separation of base pairs. One solely relies on base…
DNA is emerging as an increasingly attractive medium for data storage due to a number of important and unique advantages it offers, most notably the unprecedented durability and density. While the technology is evolving rapidly, the…
The combination of self-assembly and electronic properties as well as its true nanoscale dimensions make DNA a promising candidate for a building block of single molecule electronics. We argue that the intrinsic double helix conformation of…
By exploiting discrete signal processing and simulating brain neuron communication, Spiking Neural Networks (SNNs) offer a low-energy alternative to Artificial Neural Networks (ANNs). However, existing SNN models, still face high…
Special functions, coding theory and $t$-designs have close connections and interesting interplay. A standard approach to constructing $t$-designs is the use of linear codes with certain regularity. The Assmus-Mattson Theorem and the…
Secure communication is the cornerstone of modern infrastructures, yet achieving unconditional security -resistant to any computational attack- remains a fundamental challenge. The One-Time Pad (OTP), proven by Shannon to offer perfect…