Related papers: Quaternionic representation of the genetic code
Modern biomedicine is challenged to predict the effects of genetic variation. Systematic functional assays of point mutants of proteins have provided valuable empirical information, but vast regions of sequence space remain unexplored.…
Motivated by the geometric advantages of quaternions in representing rotations and postures, we propose a quaternion-valued supervised learning Hopfield-structured neural network (QSHNN) with a fully connected structure inspired by the…
One of the important ways development takes place in mathematics is via a process of generalization. On the basis of a recent characterization of this process we propose a principle that generalizations of mathematical structures that are…
There is an intrinsic relationship between the molecular evolution in primordial period and the properties of genomes and proteomes of contemporary species. The genomic data may help us understand the driving force of evolution of life at…
Quaternionic Clifford analysis is a recent new branch of Clifford analysis, a higher dimensional function theory which refines harmonic analysis and generalizes to higher dimension the theory of holomorphic functions in the complex plane.…
In this paper, we use four-dimensional quaternionic algebra to describing space-time field equations in curvature form. The transformation relations of a quaternionic variable are established with the help of basis transformations of…
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…
Degeneracy is a salient feature of genetic codes, because there are more codons than amino acids. The conventional table for genetic codes suffers from an inability of illustrating a symmetrical nature among genetic base codes. In fact,…
Important aspects of the process of information storage and retrieval in DNA and RNA, and its evolution, are the role of the anticodons and associated $t$RNA's, and correlations between anticodons and amino acids; the degeneracy of the…
Ultrametric approach to the genetic code and the genome is considered and developed. $p$-Adic degeneracy of the genetic code is pointed out. Ultrametric tree of the codon space is presented. It is shown that codons and amino acids can be…
Replication of DNA and synthesis of proteins are studied from the view-point of quantum database search. Identification of a base-pairing with a quantum query gives a natural (and first ever) explanation of why living organisms have 4…
In this work it is shown that 20 canonical amino acids (AAs) within genetic code appear to be a whole system with strict AAs positions; more exactly, with AAs ordinal number in three variants; first variant 00-19, second 00-21 and third…
A comparative classification scheme provides a good basis for several approaches to understand proteins, including prediction of relations between their structure and biological function. But it remains a challenge to combine a…
Rotations on the 3-dimensional Euclidean vector-space can be represented by real quaternions, as was shown by Hamilton. Introducing complex quaternions allows us to extend the result to elliptic and hyperbolic rotations on the Minkowski…
The attitude space has been parameterized in various ways for practical purposes. Different representations gain preferences over others based on their intuitive understanding, ease of implementation, formulaic simplicity, and physical as…
Quaternion, an extension of complex number, is the first discovered non-commutative division algebra by William Rowan Hamilton in 1843. In this article, we review the recent progress on building up the connection between the mathematical…
Protein design is a technique to engineer proteins by modifying their sequence to obtain novel functionalities. In this method, amino acids in the sequence are permutated to find the low energy states satisfying the configuration. However,…
Quark-hadron duality is an interesting and potentially very useful phenomenon, as it relates the properly averaged hadronic data to a perturbative QCD result in some kinematic regions. While duality is well established experimentally, our…
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…
The matrix form of the presentation of the genetic code is described as the cognitive form to analyze structures of the genetic code. A similar matrix form is utilized in the theory of signal processing. The Kronecker family of the genetic…