Related papers: On the optimality of the standard genetic code: th…
Random coding arguments are the backbone of most channel capacity achievability proofs. In this paper, we show that in their standard form, such arguments are insufficient for proving some network capacity theorems: structured coding…
In this work it is shown that 20 canonical amino acids (AAs) within genetic code appear to be a whole system with strict distinction in Genetic Code Table (GCT) into some different quantums: 20, 23, 61 amino acid molecules. These molecules…
We study the amount of reliable information that can be stored in a DNA-based storage system composed of short DNA molecules. In this regime, Shomorony and Heckel (2022) put forward a conjecture on the scaling of the number of information…
In this paper, we prove that with high probability, random Reed-Solomon codes approach the half-Singleton bound - the optimal rate versus error tradeoff for linear insdel codes - with linear-sized alphabets. More precisely, we prove that,…
Optimal zero-delay coding (quantization) of $\mathbb{R}^d$-valued linearly generated Markov sources is studied under quadratic distortion. The structure and existence of deterministic and stationary coding policies that are optimal for the…
The tendencies described in this work were revealed in the course of examination of adenine and uracil distribution in the mRNA encoding sequence. The study also discusses the usage of codons occupied by the amino acid arginine in the table…
We revisit the source coding problem for a Markov chain under the assumption that the transmission times and how fast the Markov chain transitions its state happen at the same time-scale. Specifically, we assume that the transmission of…
The paper represents three supplements to the source paper, q-bio/0610044 [q-bio.OT], with three new series of harmonic structures of the genetic code, determined by Gauss arithmetical algorithm; by Table of Minimal Adding, as in…
It is shown that there is a sense in splitting Genetic Code Table (GCT) into three parts using the harmonic mean, calculated by the formula H (a, b) = 2ab / (a + b), where a = 63 and b = 31.5. Within these three parts, the amino acids (AAs)…
The number of atoms in the four ribonucleotides uridine monophosphate, cytidine monophosphate, adenine monophosphate and guanine monophosphate is taken as a key parameter. A mathematical relation describing the condensation of the three…
A hypothesis of the evolution of the genetic code is proposed, the leading mechanism of which is the nucleotide spontaneous damage leading to AT-enrichment of the genome. The hypothesis accounts for stability of the genetic code towards…
Let C be a linear code with length n and minimum distance d. The stopping redundancy of C is defined as the minimum number of rows in a parity-check matrix for C such that the smallest stopping sets in the corresponding Tanner graph have…
MDS convolutional codes have the property that their free distance is maximal among all codes of the same rate and the same degree. In this paper we introduce a class of MDS convolutional codes whose column distances reach the generalized…
Shaping codes are used to generate code sequences in which the symbols obey a prescribed probability distribution. They arise naturally in the context of source coding for noiseless channels with unequal symbol costs. Recently, shaping…
The global dynamics of gene regulatory networks are known to show robustness to perturbations in the form of intrinsic and extrinsic noise, as well as mutations of individual genes. One molecular mechanism underlying this robustness has…
Composite DNA is a recent method to increase the base alphabet size in DNA-based data storage.This paper models synthesizing and sequencing of composite DNA and introduces coding techniques to correct substitutions, losses of entire…
The evolution of gene regulatory networks in variable environments poses Multi-objective Optimization Problem (MOP), where the expression levels of genes must be tuned to meet the demands of each environment. When formalized in the context…
Place cells are neurons that act as biological position sensors, associated with and firing in response to regions of an environment to situate an organism in space. These associations are recorded in (combinatorial) neural codes,…
Fracton models provide examples of novel gapped quantum phases of matter that host intrinsically immobile excitations and therefore lie beyond the conventional notion of topological order. Here, we calculate optimal error thresholds for…
We re-investigate a fundamental question: how effective is crossover in Genetic Algorithms in combining building blocks of good solutions? Although this has been discussed controversially for decades, we are still lacking a rigorous and…