Related papers: Genetic Code as a Harmonic System: three Supplemen…
In this text we develop the formalism of products and powers of linear codes under componentwise multiplication. As an expanded version of the author's talk at AGCT-14, focus is put mostly on basic properties and descriptive statements that…
The primary structure of a ribonucleic acid (RNA) molecule can be represented as a sequence of nucleotides (bases) over the alphabet {A, C, G, U}. The secondary or tertiary structure of an RNA is a set of base pairs which form bonds between…
Polarization-adjusted convolutional (PAC) codes were recently proposed and arouse the interest of the channel coding community because they were shown to approach theoretical bounds for the (128,64) code size. In this letter, we propose…
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…
DNA storage has emerged as an important area of research. The reliability of DNA storage system depends on designing the DNA strings (called DNA codes) that are sufficiently dissimilar. In this work, we introduce DNA codes that satisfy a…
In this paper, we propose a compositional nonparametric method in which a model is expressed as a labeled binary tree of $2k+1$ nodes, where each node is either a summation, a multiplication, or the application of one of the $q$ basis…
We present superconducting quantum circuits which exhibit atomic energy spectrum and selection rules as ladder and lambda three-level configurations designed by means of genetic algorithms. These heuristic optimization techniques are…
Novel mathematical models of three different repressilator topologies are introduced. As designable transcription factors have been shown to bind to DNA non-cooperatively, we have chosen models containing non-cooperative elements. The…
The set of known dialects of the genetic code (GC) is analyzed from the viewpoint of the genetic octave Yin-Yang-algebra. This algebra was described in the previous author's publications. The algebra was discovered on the basis of…
In this paper, we propose to study and optimize a very general class of LDPC codes whose variable nodes belong to finite sets with different orders. We named this class of codes Hybrid LDPC codes. Although efficient optimization techniques…
We introduce the notion of quadratic hull of a linear code, and give some of its properties. We then show that any symmetric bilinear multiplication algorithm for a finite-dimensional algebra over a field can be obtained by…
We formulate code concatenation as the action of a unitary quantum circuit on an expanding tree geometry and find that for certain classes of gates, applied identically at each node, a binary tree circuit encodes a single logical qubit with…
Explicit coding schemes are proposed to achieve the rate-distortion function of the Heegard-Berger problem using polar codes. Specifically, a nested polar code construction is employed to achieve the rate-distortion function for the…
In this paper, we mainly study quaternary linear codes and their binary subfield codes. First we obtain a general explicit relationship between quaternary linear codes and their binary subfield codes in terms of generator matrices and…
Complex systems with tightly coadapted parts frequently appear in living systems and are difficult to account for through Darwinian evolution, that is random variation and natural selection, if the constituent parts are independently coded…
A heuristic diagram of the evolution of the standard genetic code is presented. It incorporates, in a way that resembles the energy levels of an atom, the physical notion of broken symmetry and it is consistent with original ideas by Crick…
Degeneracy of the genetic code is a biological way to minimize effects of the undesirable mutation changes. Degeneration has a natural description on the 5-adic space of 64 codons $\mathcal{C}_5 (64) = \{n_0 + n_1 5 + n_2 5^2 : n_i = 1, 2,…
DNA strings and their properties are widely studied since last 20 years due to its applications in DNA computing. In this area, one designs a set of DNA strings (called DNA code) which satisfies certain thermodynamic and combinatorial…
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.…
A generalization of the polar coding scheme called mixed-kernels is introduced. This generalization exploits several homogeneous kernels over alphabets of different sizes. An asymptotic analysis of the proposed scheme shows that its…