Related papers: Quaternionic representation of the genetic code
We propose a model for motor proteins based on a hierarchical Hamiltonian that we have previously introduced to describe protein folding. The proposed motor model has high efficiency and is consistent with a linear load-velocity response.…
Denoting by $\mathbb{M}$ the complexification of the quaternionic algebra $\mathbb{H}$, we characterize the family of those $\mathbb{M}$-valued functions, defined on subsets of $\H$, whose values are actually quaternions, using an intrinsic…
A generalized computational method for folding proteins with a fully transferable potential and geometrically realistic all-atom model is presented and tested on seven different helix bundle proteins. The protocol, which includes…
While real Hamiltonian mechanics and Hermitian quantum mechanics can both be cast in the framework of complex canonical equations, their complex generalisations have hitherto been remained tangential. In this paper quaternionic and…
Multidimensional quaternion arrays (often referred to as "quaternion tensors") and their decompositions have recently gained increasing attention in various fields such as color and polarimetric imaging or video processing. Despite this…
Natural selection explains how life has evolved over millions of years from more primitive forms. The speed at which this happens, however, has sometimes defied formal explanations when based on random (uniformly distributed) mutations.…
The necessary appearance of Clifford algebras in the quantum description of fermions has prompted us to re-examine the fundamental role played by the quaternion Clifford algebra, C(0,2). This algebra is essentially the geometric algebra…
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,…
We study some essential arithmetic properties of a new tree-based number representation, {\em hereditarily binary numbers}, defined by applying recursively run-length encoding of bijective base-2 digits. Our representation expresses giant…
The genetic code is the function from the set of codons to the set of amino acids by which a DNA sequence encodes proteins. Since the codons also influence the shape of the DNA molecule itself, the same sequence that encodes a protein also…
Finding the minimum distance of linear codes is an NP-hard problem. Traditionally, this computation has been addressed by means of the design of algorithms that find, by a clever exhaustive search, a linear combination of some generating…
The structure of the genetic code is discussed in formal terms. A rectangular table of the code ("the code matrix"), whose properties reveal its arithmetical content tagged with the information symbols in several notations. New parameters…
The generalized parton distributions, introduced nearly a decade ago, have emerged as a universal tool to describe hadrons in terms of quark and gluonic degrees of freedom. They combine the features of form factors, parton densities and…
We present an algorithm to compute all factorizations into linear factors of univariate polynomials over the split quaternions, provided such a factorization exists. Failure of the algorithm is equivalent to non-factorizability for which we…
Natural protein sequences somehow encode the structural forms that these molecules adopt. Recent developments in structure-prediction are agnostic to the mechanisms by which proteins fold and represent them as static objects. However, the…
We propose a novel quaternion product unit (QPU) to represent data on 3D rotation groups. The QPU leverages quaternion algebra and the law of 3D rotation group, representing 3D rotation data as quaternions and merging them via a weighted…
The performance of computational methods for many-body physics and chemistry is strongly dependent on the choice of basis used to cast the problem; hence, the search for better bases and similarity transformations is important for progress…
The quantum enveloping algebra U_q(sl(2) \oplus sl(2)) in the limit q \to 0 is proposed as a symmetry algebra for the genetic code. In this approach the triplets of nucleotids or codons in the DNA chain are classified in crystal bases,…
Using the shape space of codons and tRNAs we give a physical description of the genetic code evolution on the basis of the codon capture and ambiguous intermediate scenarios in a consistent manner. In the lowest dimensional version of our…
In this paper we introduce a new algebraic device, which enables us to treat the quaternions as though they were a commutative field. This is of interest both for its own sake, and because it can be applied to develop an "algebraic…