相关论文: Symmetry Scheme for Amino Acid Codons
The binary system 16 Cygni is key in studies of the planet-star chemical composition connection, as only one of the stars is known to host a planet. This allows us to better assess the possible influence of planet interactions on the…
Protein can be represented by amino acid interaction network. This network is a graph whose vertices are the proteins amino acids and whose edges are the interactions between them. This interaction network is the first step of proteins…
We review the theory behind abundance of experimentally observed nanoclusters produced in beams, aiming to understand their magic number behavior. It is shown how use of statistical physics, with certain assumptions, reduces the calculation…
We propose a novel method for the determination of the effective interaction potential between the amino acids of a protein. The strategy is based on the combination of a new optimization procedure and a geometrical argument, which also…
Methods for alignment of protein sequences typically measure similarity by using substitution matrix with scores for all possible exchanges of one amino acid with another. Although widely used, the matrices derived from homologous sequence…
The problem of enumerating meanders -- pairs of simple plane curves with transverse intersections -- was formulated about forty years ago and is still far from solved. Recently, it was discovered that meanders admit a factorization into…
Inside a cell, heterotypic proteins assemble in inhomogeneous, crowded systems where the abundance of these proteins vary with cell types. While some protein complexes form putative structures that can be visualized with imaging, there are…
Suppose $R\rightarrow S$ is a faithfully flat ring map. The theory of twisted forms lets one compute, given an $R$-module $M$, how many isomorphism classes of $R$-modules $M^{\prime}$ satisfy $S\otimes_R M\cong S\otimes_R M^{\prime}$. This…
Stellar members of binary systems are formed from the same material, therefore they should be chemically identical. However, recent high-precision studies have unveiled chemical differences between the two members of binary pairs composed…
Amino-acid substitutions are implicated in a wide range of human diseases, many of which are lethal. Distinguishing such mutations from polymorphisms without significant effect on human health is a necessary step in understanding the…
Cellular functions are established through biological evolution, but are constrained by the laws of physics. For instance, the physics of protein folding limits the lengths of cellular polypeptide chains. Consequently, many cellular…
A challenge of molecular self-assembly is to understand how to design particles that self-assemble into a desired structure and not any of a potentially large number of undesired structures. Here we use simulation to show that a strategy of…
We present a high-precision differential abundance analysis of 16 solar-type stars in the Hyades open cluster based on high resolution, high signal-to-noise ratio (S/N ~ 350 - 400) spectra obtained from the McDonald 2.7m telescope. We…
The present paper is devoted to foundations of p-adic modelling in genomics. Considering nucleotides, codons, DNA and RNA sequences, amino acids, and proteins as information systems, we have formulated the corresponding p-adic formalisms…
The evolution in coding DNA sequences brings new flexibility and freedom to the codon words, even as the underlying nucleotides get significantly ordered. These curious contra-rules of gene organisation are observed from the distribution of…
Modelising the translation errors by suitable mathematical operators in the crystal basis model of the genetic code and requiring that codons prone to be misread encode the same amino-acid, the main features of the organisation in…
Siphons in a chemical reaction system are subsets of the species that have the potential of being absent in a steady state. We present a characterization of minimal siphons in terms of primary decomposition of binomial ideals, we explore…
Physical systems evolve from one state to another along paths of least energy barrier. Without a priori knowledge of the energy landscape, multidimensional search methods aim to find such minimum energy pathways between the initial and…
Cyclically ordered graphs, or cogs, sit between abstract graphs and cellularly embedded graphs. They arise naturally in topological graph theory, knot theory, and mathematical biology. We develop a formal theory of cogs and establish a…
Using Verlinde formula and the symmetry of the modular matrix we describe an algorithm to find all conformal field theories with low number of primary fields. We employ the algorithm on up to eight primary fields. Four new conformal field…