Related papers: Exceptional error minimization in putative primord…
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 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…
A plausible architecture of an ancient genetic code is derived from an extended base triplet vector space over the Galois field of the extended base alphabet {D, G, A, U, C}, where the letter D represents one or more hypothetical bases with…
Background: A partially random target selection method was developed to design and produce affinity reagents (target) to any protein query. It is based on the recent concept of Proteomic Code (for review see Biro, 2007 [1]) which suggests…
Quantum error correction is essential for bridging the gap between the error rates of physical devices and the extremely low logical error rates required for quantum algorithms. Recent error-correction demonstrations on superconducting…
We present a two-step decoder for the parity code and evaluate its performance in code-capacity and faulty-measurement settings. For noiseless measurements, we find that the decoding problem can be reduced to a series of repetition codes…
Optimizing the mRNA codon has an essential impact on gene expression for a specific target protein. It is an NP-hard problem; thus, exact solutions to such optimization problems become computationally intractable for realistic problem sizes…
First-principles calculations in crystalline structures are often performed with a planewave basis set. To make the number of basis functions tractable two approximations are usually introduced: core electrons are frozen and the diverging…
This article introduces a novel binary representation of the canonical genetic code based on both the structural similarities of the nucleotides, as well as the physicochemical properties of the encoded amino acids. Each of the four mRNA…
Co-optimizing mRNA sequences for both codon optimality and secondary structure is crucial for producing stable and efficacious mRNA therapeutics. Codon optimization, which adjusts nucleotide sequences to enhance translational efficiency,…
It has been an open question in deep learning if fault-tolerant computation is possible: can arbitrarily reliable computation be achieved using only unreliable neurons? In the grid cells of the mammalian cortex, analog error correction…
A representation of the genetic code as a six-dimensional Boolean hypercube is described. This structure is the result of the hierarchical order of the interaction energies of the bases in codon-anticodon recognition. In this paper it is…
The genesis of the stand genetic code is considered as a result of a fusion of two AU- and GC-codes distributed in two dominant and two recessive domains. The fusion of these codes is described with simple empirical rules. This formal…
Message-passing iterative decoders for low-density parity-check (LDPC) block codes are known to be subject to decoding failures due to so-called pseudo-codewords. These failures can cause the large signal-to-noise ratio performance of…
Quantum error correction codes are usually designed to correct errors regardless of their physical origins. In large-scale devices, this is an essential feature. In smaller-scale devices, however, the main error sources are often…
Predictive coding is an influential theory of cortical function which posits that the principal computation the brain performs, which underlies both perception and learning, is the minimization of prediction errors. While motivated by…
The idea of the evolution of the genetic code from the CG to the CGUA alphabet has been developed further. The assumption of the originally triplet structure of the genetic code has been substantiated. The hypothesis of the emergence of…
Quantum error correction codes play a central role in the realisation of fault-tolerant quantum computing. Chamon model is a 3D generalization of the toric code. The error correction computation on this model has not been explored so far.…
In this paper upper and lower bounds on the probability of decoding failure under maximum likelihood decoding are derived for different (nonbinary) Raptor code constructions. In particular four different constructions are considered; (i)…
Empirical substitution matrices represent the average tendencies of substitutions over various protein families by sacrificing gene-level resolution. We develop a codon-based model, in which mutational tendencies of codon, a genetic code,…