Related papers: p-Adic Structure of the Genetic Code
The standard genetic code multiplet structure as well as the correct degeneracies, class by class, are all extracted from the (unique) number 23, the order of the permutation group of 23 objects.
Rich information on the prebiotic evolution is still stored in contemporary genomic data. The statistical mechanism at the sequence level may play a significant role in the prebiotic evolution. Based on statistical analysis of genome…
We propose a physical model to describe the mechanisms of two major scenarios of the genetic code evolution, the codon capture and ambiguous intermediate scenarios, in a consistent manner. We sketch the lowest dimensional version of our…
A quantitative theory on the construction and the evolution of the genetic code is proposed. Through introducing the concept of mutational deterioration (MD) and developing a theoretical formalism on MD minimization we have proved: 1, the…
Many modified genetic codes are found in specific genomes in which one or more codons have been reassigned to a different amino acid from that in the canonical code. We present a model that unifies four possible mechanisms for reassignment,…
The post-genomic era has brought opportunities to bridge traditionally separate fields of early history of life and brought new insight into origin and evolution of biodiversity. According to distributions of codons in genome sequences, I…
How robust is the natural genetic code with respect to mistranslation errors? It has long been known that the genetic code is very efficient in limiting the effect of point mutation. A misread codon will commonly code either for the same…
All known terrestrial proteins are coded as continuous strings of ~20 amino acids. The patterns formed by the repetitions of elements in groups of finite sequences describes the natural architectures of protein families. We present a method…
How proteins fold remains a central unsolved problem in biology. While the idea of a folding code embedded in the amino acid sequence was introduced more than 6 decades ago, this code remains undefined. While we now have powerful predictive…
The genetic code markup is the assignment of stop codons. The standard genetic code markup ensures the maximum possible stability of genetic information with respect to two fault classes: frameshift and nonsense mutations. There are only…
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…
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,…
The genetic code has a high level of error robustness. Using values of hydrophobicity scales as a proxy for amino acid character, and the Mean Square measure as a function quantifying error robustness, a value can be obtained for a genetic…
We present a geometrical analysis of the protrusion statistics of side chains in more than 4,000 high-resolution protein structures. We employ a coarse-grained representation of the protein backbone viewed as a linear chain of C{\alpha}…
Molecular evidence regarding the genetic code has been examined and the findings on the nature of the early events responsible for the amino acid distribution in the code are reported.
A model for the information transfer from DNA to protein using quantum information and computation techniques is presented. DNA is modeled as the sender and proteins are modeled as the receiver of this information. On the DNA side, a…
A theoretical construction of the genetic material establishes the unique and ideal character of DNA. A similar conclusion is reached for amino acids and proteins.
The paper represents three supplements to the source paper, q-bio/0610044 [q-bio.OT], with three new series of harmonic structures of the genetic code, determined by Gauss arithmetical algorithm; by Table of Minimal Adding, as in…
This paper investigates the fundamental building blocks of physical-layer network coding (PNC). Most prior work on PNC focused on its application in a simple two-way-relay channel (TWRC) consisting of three nodes only. Studies of the…
The evolutionary trajectory of a protein through sequence space is constrained by function and three-dimensional (3D) structure. Residues in spatial proximity tend to co-evolve, yet attempts to invert the evolutionary record to identify…