Related papers: On the combinatorics of circular codes
In order to extend the results obtained with minimal lattice models to more realistic systems, we study a model where proteins are described as a chain of 20 kinds of structureless amino acids moving in a continuum space and interacting…
Cyclic redundancy check (CRC) codes check if a codeword is correctly received. This paper presents an algorithm to design CRC codes that are optimized for the code-specific error behavior of a specified feedforward convolutional code. The…
mRNA technology has revolutionized vaccine development, protein replacement therapies, and cancer immunotherapies, offering rapid production and precise control over sequence and efficacy. However, the inherent instability of mRNA poses…
The cyclic shift graph of a monoid is the graph whose vertices are elements of the monoid and whose edges link elements that differ by a cyclic shift. For certain monoids connected with combinatorics, such as the plactic monoid (the monoid…
We investigate the problem of encoding data into an $(n, t)$-break-resilient code ($(n, t)$-BRC), i.e., a collections of sequences of length~$n$ from which the original data can be reconstructed even if they are adversarially broken at up…
An ensemble of directed macromolecules on a lattice is considered, where the constituting molecules are chosen as a random sequence of N different types. The same type of molecules experiences a hard-core (exclusion) interaction. We study…
In network coding, a flag code is a collection of flags, that is, sequences of nested subspaces of a vector space over a finite field. Due to its definition as the sum of the corresponding subspace distances, the flag distance parameter…
Complete complementary codes (CCCs) are highly valuable in the fields of information security, radar and communication. The spectrally null constrained (SNC) problem arises in radar and modern communication systems due to the reservation or…
One hallmark of human language is its combinatoriality -- reusing a relatively small inventory of building blocks to create a far larger inventory of increasingly complex structures. In this paper, we explore the idea that combinatoriality…
The coding space of protein sequences is shaped by evolutionary constraints set by requirements of function and stability. We show that the coding space of a given protein family--the total number of sequences in that family--can be…
In this paper, we present a novel design strategy of DNA codes with length $3n$ over the non-chain ring $R=\mathbb{Z}_4+u\mathbb{Z}_4+u^2\mathbb{Z}_4$ with $64$ elements and $u^3=1$, where $n$ denotes the length of a code over $R$. We first…
The purpose of this paper is to present the structure of the linear codes over a finite field with q elements that have a permutation automorphism of order m. These codes can be considered as generalized quasi-cyclic codes. Quasi-cyclic…
In this work, we propose a modified four circulant construction for self-dual codes and a bordered version of the construction using the properties of \lambda-circulant and \lambda-reverse circulant matrices. By using the constructions on…
Effective and reliable data retrieval is critical for the feasibility of DNA storage, and the development of random access efficiency plays a key role in its practicality and reliability. In this paper, we study the Random Access Problem,…
In this paper we construct families of bit sequences using combinatorial methods. Each sequence is derived by con- verting a collection of numbers encoding certain combinatorial nu- merics from objects exhibiting symmetry in various…
Recently, linear codes constructed by defining sets have attracted a lot of study, and many optimal linear codes with a few weights have been produced. The objective of this paper is to present a class of binary linear codes with three…
We study the amount of reliable information that can be stored in a DNA-based storage system with noisy sequencing, where each codeword is composed of short DNA molecules. We analyze a concatenated coding scheme, where the outer code is…
In this work, we consider the Combinatorial RNA Design problem, a minimal instance of the RNA design problem which aims at finding a sequence that admits a given target as its unique base pair maximizing structure. We provide complete…
In previous works [physics/0204035, physics/0404052, physics/0509126] a procedure was described for dividing the $3 \times N$-dimensional conformational space of a molecular system into a number of discrete cells, this partition allowed the…
We introduce a novel framework for implementing error-correction in constrained systems. The main idea of our scheme, called Quantized-Constraint Concatenation (QCC), is to employ a process of embedding the codewords of an error-correcting…