Related papers: The Genetic Code Boolean Lattice
Several technological applications require the translation of a protein into a nucleic acid that codes for it (``backtranslation''). The degeneracy of the genetic code makes this translation ambiguous; moreover, not every translation is…
The specific rotational alignment of two-dimensional lattices results in a moir\'e superlattice with a larger period than the original lattices and allows one to engineer the electronic band structure of such materials. So far, transport…
An effective Hamiltonian is considered for hydrogen bonding between two molecules due to the quantum mechanical interaction between the orbitals of the H-atom and the donor and acceptor atoms in the molecules. The Hamiltonian acts on two…
Motivation: Proteins are known to undergo conformational changes in the course of their functions. The changes in conformation are often attributable to a small fraction of residues within the protein. Therefore identification of these…
We consider a topological stabilizer code on a honeycomb grid, the "XYZ$^2$" code. The code is inspired by the Kitaev honeycomb model and is a simple realization of a "matching code" discussed by Wootton [J. Phys. A: Math. Theor. 48, 215302…
It is presented that the positions of amino acids within Genetic Code Table follow from strict their physical and chemical properties as well as from a pure formal determination by the Golden mean.
Most of the DNA that composes a complex organism is non-coding and defined as junk. Even the coding part is composed of genes that affect the phenotype differently. Therefore, a random mutation has an effect on the specimen fitness that…
In condensed matter physics, simplified descriptions are obtained by coarse-graining the features of a system at a certain characteristic length, defined as the typical length beyond which some properties are no longer correlated. From a…
To understand the nature of a cell, one needs to understand the structure of its genome. For this purpose, experimental techniques such as Hi-C detecting chromosomal contacts are used to probe the three-dimensional genomic structure. These…
Non-coding RNA molecules fold into precise base pairing patterns to carry out critical roles in genetic regulation and protein synthesis. We show here that coupling systematic mutagenesis with high-throughput SHAPE chemical mapping enables…
It is known that steric blocking by peptide sidechains of hydrogen bonding, HB, between water and peptide groups, PGs, in beta sheets accords with an amino acid intrinsic beta sheet preference. The present observations with Quantum…
The nucleotide composition of human genes with a special emphasis on transcription-related strand asymmetries is analyzed. Such asymmetries may be associated with different mutational rates in two principal factors. The first one is…
Background: A partially random target selection method was developed to design and produce affinity reagents (target) to any protein query. It is based on the recent concept of Proteomic Code (for review see Biro, 2007 [1]) which suggests…
We show how to obtain concrete constructions of homological quantum codes based on tilings of 2D surfaces with constant negative curvature (hyperbolic surfaces). This construction results in two-dimensional quantum codes whose tradeoff of…
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…
It is now widely recognized that the toric code is a pure gauge-theory model governed by a projective Hamiltonian with topological orders. In this work, we extend the interplay between quantum information system and gauge-theory model from…
Protein structure is generally conceptualized as the global arrangement or of smaller, local motifs of helices, sheets, and loops. These regular, recurring secondary structural elements have well-understood and standardized definitions in…
Exploring and understanding the protein-folding problem has been a long-standing challenge in molecular biology. Here, using molecular dynamics simulation, we reveal how parallel distributed adjacent planar peptide groups of unfolded…
Most amino acids are encoded by multiple synonymous codons. For an amino acid, some of its synonymous codons are used much more rarely than others. Analyses of positions of such rare codons in protein sequences revealed that rare codons can…
The evaluation of the minimum distance of linear block codes remains an open problem in coding theory, and it is not easy to determine its true value by classical methods, for this reason the problem has been solved in the literature with…