相关论文: Symmetry Scheme for Amino Acid Codons

Folding properties of a two-dimensional toy protein model containing only two amino-acid types, hydrophobic and hydrophilic, respectively, are analyzed. An efficient Monte Carlo procedure is employed to ensure that the ground states are…

New sets (typically found by computer search) with Sidon constant equal to the square root of their cardinalities are given. For each integer $N$ there are only a finite number of groups of prime order containing $N$-element extreme sets.…

Using the crystal basis model of the genetic code, a set of relations between the physical-chemical properties of the amino acids are derived and compared with the experimental data. A prevision for the not yet measured thermodynamical…

The previously formulated model for the evolution of the genetic code was shown to clarify why base triplets of some precursor amino acids differ by a single base from product amino acid codons, while others show less homology. First, the…

We seek to understand the interplay between amino acid sequence and local structure in proteins. Are some amino acids unique in their ability to fit harmoniously into certain local structures? What is the role of sequence in sculpting the…

The genetic code maps the sixty-four nucleotide triplets (codons) to twenty amino-acids. While the biochemical details of this code were unraveled long ago, its origin is still obscure. We review information-theoretic approaches to the…

Part 1 of the study intends to show that the universal trend of amino acid gain and loss discovered by Jordan et al. (2005) can be accounted for by the spontaneity of DNA typical damages. These damages lead to replacements of guanine and…

In this work it is shown that three pairs of the factors appear to be the key, i.e. main factors of a natural classification of protein (canonical) amino acids within the amino acid (genetic) code. First pair: the factors of the habit of an…

In several previous works, I presented the mirror symmetry in the set of protein amino acids, expressed through the number of atoms. Here, however, the same thing is shown but over the number of nucleons and molecules mass. Compared to the…

Imposing a minimum principle in the framework of the so called crystal basis model of the genetic code, we determine the structure of the minimum set of 22 anticodons which allows the translational-transcription for animal mitochondrial…

We perform an exhaustive analysis of genome statistics for organisms, particularly extremophiles, growing in a wide range of physicochemical conditions. Specifically, we demonstrate how the correlation between the frequency of amino acids…

The mathematical concept of q-deformations, in particular the one of qnumbers, is used to study the genetic code(s). After considering two kinds of q-numbers, for comparison, a phenomenological classification scheme of the genetic code…

In order to extend the results obtained with minimal lattice models to more realistic systems, we study a model where proteins are described as a chain of 20 kinds of structureless amino acids moving in a continuum space and interacting…

A simple lattice model for proteins that allows for distinct sizes of the amino acids is presented. The model is found to lead to a significant number of conformations that are the unique ground state of one or more sequences or encodable.…

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,…

In protein secondary structure prediction, each amino acid in sequence is typically treated as a distinct category and represented by a one-hot vector. In this study, we developed two novel chemical representations for amino acids utilizing…

Studies of coevolution of amino acids within and between proteins have revealed two types of coevolving units: coevolving contacts, which are pairs of amino acids distant along the sequence but in contact in the three-dimensional structure,…

The famous series of Fibonacci numbers is defined by a recursive equation saying that each number is the sum of its two predecessors, with the initial condition that the first two numbers are equal to unity. Here, we show that the numbers…

Abundances of 18 chemical elements have been derived for 27 A/Am and 16 F stars members of the Pleiades and Coma Berenices open clusters. We have specifically computed, with the Montr\'eal code, a series of evolutionary models for two A…

This paper is devoted to a new classification of the twenty amino acids based on the heronian (integer) tetrahedron.