Related papers: On reversible and reversible-complementary DNA cod…
We give the structure of $\lambda$-constacyclic codes of length $p^sm$ over $R=\mathbb{F}_{p^r}+u \mathbb{F}_{p^r}+...+ u^{e-1}\mathbb{F}_{p^r}$ with $\lambda \in \F_{p^r}^*$. We also give the structure of $\lambda$-constacyclic codes of…
In this paper, we consider the problem of designing DNA sequences (codewords) for DNA storage systems and DNA computing that are unlikely to fold back onto themselves to form undesirable secondary structures. The paper addresses both the…
Reversible computing is motivated by both pragmatic and foundational considerations arising from a variety of disciplines. We take a particular path through the development of reversible computation, emphasizing compositional reversible…
Encoding data as a set of unordered strings is receiving great attention as it captures one of the basic features of DNA storage systems. However, the challenge of constructing optimal redundancy codes for this channel remained elusive. In…
In this present work, we generalize the study of construction of DNA codes over the rings $\mathcal{R}_\theta=\mathbb{Z}_4+w\mathbb{Z}_4$, $w^2 = \theta $ for $\theta \in \mathbb{Z}_4+w\mathbb{Z}_4$. Rigorous study along with…
We study permutations over the set of $\ell$-grams, that are feasible in the sense that there is a sequence whose $\ell$-gram frequency has the same ranking as the permutation. Codes, which are sets of feasible permutations, protect…
Motivated by applications in polymer-based data storage, we study the problem of reconstructing a string from part of its composition multiset. We give a full description of the structure of the strings that cannot be uniquely reconstructed…
Recursive decoding techniques are considered for Reed-Muller (RM) codes of growing length $n$ and fixed order $r.$ An algorithm is designed that has complexity of order $n\log n$ and corrects most error patterns of weight up to…
Fractional repetition (FR) codes are a class of regenerating codes for distributed storage systems with an exact (table-based) repair process that is also uncoded, i.e., upon failure, a node is regenerated by simply downloading packets from…
This paper is dealing with DNA cyclic codes which play an important role in DNA computing and have attracted a particular attention in the literature. Firstly, we introduce a new family of DNA cyclic codes over the ring…
Polycyclic codes offer a natural generalization of cyclic codes and provide a broader algebraic framework for constructing linear codes with good parameters. In this paper, we study binary polycyclic codes associated with powers of…
In this work, we investigate a challenging problem, which has been considered to be an important criterion in designing codewords for DNA computing purposes, namely secondary structure avoidance in single-stranded DNA molecules. In short,…
To increase the information capacity of DNA storage, composite DNA letters were introduced. We propose a novel channel model for composite DNA in which composite sequences are decomposed into ordered standard non-composite sequences. The…
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…
Let $\mathcal{R}_{e,m}$ be a finite commutative chain ring of even characteristic with maximal ideal $\langle u \rangle$ of nilpotency index $e \geq 2,$ Teichm$\ddot{u}$ller set $\mathcal{T}_{m},$ and residue field…
Synthesis of DNA molecules offers unprecedented advances in storage technology. Yet, the microscopic world in which these molecules reside induces error patterns that are fundamentally different from their digital counterparts. Hence, to…
Motivated by applications to DNA storage, we study reconstruction and list-reconstruction schemes for integer vectors that suffer from limited-magnitude errors. We characterize the asymptotic size of the intersection of error balls in…
We propose a unified method to construct multicyclic codes of arbitrary dimension $r$ over $\mathbb{F}_q$. The approach relies on $r$-dimensional primitive idempotents defined as tensor products of univariate ones, combined with…
In this paper, we solve the reversibility problem for DNA codes over the non-chain ring $R_{k,s}=\mathbb{F}_{4^{2k}}[u_1,...,u_{s}]/< u_1^2-u_1,..., u_s^2-u_s>$. We define an automorphism $\theta$ over $R_{k,s}$ which help us both find the…
We study the complexity of identifying the integer feasibility of reverse convex sets. We present various settings where the complexity can be either NP-Hard or efficiently solvable when the dimension is fixed. Of particular interest is the…