Related papers: On reversible and reversible-complementary DNA cod…
In this paper, we discuss DNA codes that are cyclic or quasi-cyclic over $\Z_{4}+\omega \Z_{4}$, where $\omega^{2}=2+2\omega$ along with methods to construct these with combinatorial constraints. We also generalize results obtained for the…
This paper considers cyclic DNA codes of arbitrary length over the ring $R=\F_2[u]/u^4-1$. A mapping is given between the elements of $R$ and the alphabet $\{A,C,G,T\}$ which allows the additive stem distance to be extended to this ring.…
In this paper we give constructions for infinite sequences of finite non-linear locally recoverable codes $\mathcal C\subseteq \prod\limits^N_{i=1}\mathbb F_{q_i}$ over a product of finite fields arising from basis expansions in algebraic…
DNA as a data storage medium has several advantages, including far greater data density compared to electronic media. We propose that schemes for data storage in the DNA of living organisms may benefit from studying the reconstruction…
We design a heuristic method, a genetic algorithm, for the computation of an upper bound of the minimum distance of a linear code over a finite field. By the use of the row reduced echelon form, we obtain a permutation encoding of the…
We describe a family of recursive methods for the synthesis of qubit permutations on quantum computers with limited qubit connectivity. Two objectives are of importance: circuit size and depth. In each case we combine a scalable heuristic…
Tandem duplication is the process of inserting a copy of a segment of DNA adjacent to the original position. Motivated by applications that store data in living organisms, Jain et al. (2017) proposed the study of codes that correct tandem…
In this paper, necessary and sufficient conditions for the reversibility of a cyclic code of arbitrary length over a finite commutative chain ring have been derived. MDS reversible cyclic codes having length p^s over a finite chain ring…
In this paper, necessary and sufficient conditions for a cyclic code of arbitrary length over the non-chain rings $Z_{4}+\nu Z_{4}$ for $\nu^{2} \in \{0,1,\nu,2\nu,3\nu,2+\nu,2+3\nu,3+2\nu\}$ to be a reversible cyclic code have been…
We consider recursive decoding techniques for RM codes, their subcodes, and newly designed codes. For moderate lengths up to 512, we obtain near-optimum decoding with feasible complexity.
For a prime $p$ and a positive integer $m$, let $\mathbb{F}_{p^m}$ be the finite field of characteristic $p$, and $\mathfrak{R}_l:=\mathbb{F}_{p^m}[v]/\langle v^l-v\rangle$ be a non-chain ring. In this paper, we study the…
The problem of RNA secondary structure design (also called inverse folding) is the following: given a target secondary structure, one aims to create a sequence that folds into, or is compatible with, a given structure. In several practical…
The biggest challenge when using DNA as a storage medium is maintaining its stability. The relative occurrence of Guanine (G) and Cytosine (C) is essential for the longevity of DNA. In addition to that, reverse complementary base pairs…
A quantum code is a subspace of a Hilbert space of a physical system chosen to be correctable against a given class of errors, where information can be encoded. Ideally, the quantum code lies within the ground space of the physical system.…
Designing short DNA words is a problem of constructing a set (i.e., code) of n DNA strings (i.e., words) with the minimum length such that the Hamming distance between each pair of words is at least k and the n words satisfy a set of…
Tandem duplication in DNA is the process of inserting a copy of a segment of DNA adjacent to the original position. Motivated by applications that store data in living organisms, Jain {\em et al.} (2016) proposed the study of codes that…
We derive theoretical upper and lower bounds on the maximum size of DNA codes of length n with constant GC-content w and minimum Hamming distance d, both with and without the additional constraint that the minimum Hamming distance between…
Rank modulation is a way of encoding information to correct errors in flash memory devices as well as impulse noise in transmission lines. Modeling rank modulation involves construction of packings of the space of permutations equipped with…
We present new constructions of binary quantum codes from quaternary linear Hermitian self-dual codes. Our main ingredients for these constructions are nearly self-orthogonal cyclic or duadic codes over F_4. An infinite family of…
In recent years, reversible logic has emerged as a promising computing paradigm having its applications in low power computing, quantum computing, nanotechnology, optical computing and DNA computing. The classical set of gates such as AND,…