Related papers: A Minimum Principle in Codon-Anticodon Interaction
The genetic code is nearly universal, and the arrangement of the codons in the standard codon table is highly non-random. The three main concepts on origin and evolution of the code are the stereochemical theory; the coevolution theory; and…
We study the correlation between the codon usage bias of genetic sequences and the network features of protein-protein interaction (PPI) in bacterial species. We use PCA techniques in the space of codon bias indices to show that genes with…
A new electronic structure principle, viz. the minimum magnetizability principle (MMP) has been proposed and also has been verified through ab initio calculations, to extend the domain of applicability of the conceptual density functional…
This paper presents an approach to reducing the number of fundamental parameters in the Standard Model (SM) using genetic programming, a machine learning technique based on evolutionary algorithms. We outline the core principles of our…
We study theoretical ``design principles'' for transcription factor-DNA interaction in bacteria, focusing particularly on the statistical interaction of the transcription factors (TF's) with the genomic background (i.e., the genome without…
A codon table is a useful tool for mapping codons to amino acids as they have been assigned by nature. It has become a scientific icon because of the way it embodies our understanding of this natural process and the way it immediately…
We apply the envelope function approach to abrupt heterostructures starting with the least action principle for the microscopic wave function. The interface is treated nonperturbatively, and our approach is applicable to mismatched…
Cellular development follows a stochastic yet rule-governed trajectory, though the underlying principles remain elusive. Here, we propose that cellular development follows paths of least action, aligning with foundational physical laws that…
In this paper a measure of complexity of the system of angle-angular momentum quantum states produced in hadronic scattering is introduced in terms of the scattering entropies. We presented strong experimental evidence for the saturation of…
We argue that the phenomenon of symmetry breaking in genetics can enhance the adaptability of a species to changes in the environment. In the case of a virus, the claim is that the codon bias in the neutralization epitope improves the…
Using a non-perturbative classical approach, we study the dynamics of a mobile particle interacting with an infinite one-dimensional (1D) chain of harmonic oscillators. This minimal system is an effective model for many 1D transport…
The minimal 3-state scheme of kinetic cooperativity of monomeric enzymes is subjected to detailed analysis. The rigorous criteria of positive cooperativity and its sigmoidal version are established in terms of the system parameters (rate…
We present a framework based on conditional entropy and the Dirichlet distribution for classifying chromosomes based on the degree to which they use synonymous codons uniformly or preferentially, that is, whether or not codons that code for…
Synonymous codons, i.e., DNA nucleotide triplets coding for the same amino acid, are used differently across the variety of living organisms. The biological meaning of this phenomenon, known as codon usage bias, is still controversial. In…
In the crystal basis model of the genetic code, it is deduced that the sum of usage probabilities of the codons with C and A in the third position for the quartets and/or sextets is independent of the biological species for vertebrates. A…
Intracellular protein patterns govern essential cellular functions by dynamically redistributing proteins between membrane-bound and cytosolic states, conserving their total numbers. This review presents a theoretical framework for…
We argue that the minimal chiral background for the two-pion exchange nucleon-nucleon interaction has nowadays a rather firm conceptual basis, which entitles it to become a standard ingredient of any modern potential. In order to facilitate…
We introduce a general first-principles methodology for computing electronic structure in a finite uniform magnetic field which allows for an arbitrary rational magnetic flux and nonlocal pseudopotentials, at a comparable time complexity of…
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…
There is increasing evidence that protein binding to specific sites along DNA can activate the reading out of genetic information without coming into direct physical contact with the gene. There also is evidence that these distant but…