Related papers: Sum rules of codon usage probabilities
Degeneracy of the genetic code is a biological way to minimize effects of the undesirable mutation changes. Degeneration has a natural description on the 5-adic space of 64 codons $\mathcal{C}_5 (64) = \{n_0 + n_1 5 + n_2 5^2 : n_i = 1, 2,…
Biased-coin designs are used in clinical trials to allocate treatments with some randomness while maintaining approximately equal allocation. More recent rules are compared with Efron's [Biometrika 58 (1971) 403-417] biased-coin rule and…
The genetic code structure into distinct multiplet-classes as well as the numeric degeneracies of the latter are revealed by a two-step process. First, an empirical inventory of the degeneracies (of the shuffled multiplets) in two specific…
We study a construction, which produces surfaces $Y \subset P_3$ with cusps. For example we obtain surfaces of degree six with 18, 24 or 27 three-divisible cusps. For sextic surfaces in a particular family of up to 30 cusps the codes of…
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…
The strange form factors of baryon octet are evaluated, in the chiral models with the general chiral SU(3) group structure, to yield the theoretical predictions comparable to the recent experimental data of SAMPLE Collaboration and to study…
The persistence of life requires populations to adapt at a rate commensurate with the dynamics of their environment. Successful populations that inhabit highly variable environments have evolved mechanisms to increase the likelihood of…
The parton distribution functions determined by CTEQ at low $Q^2$ are used as inputs to test the validity of the valon model. The valon distributions in a nucleon are first found to be nearly $Q$ independent. The parton distribution in a…
We give explicit bounds for the tail probabilities for sums of independent geometric or exponential variables, possibly with different parameters.
Global textures are interesting because they are promising candidates for seeds in the structure formation of the universe. The important configurations are those who will be able to collapse. The type of configurations that I will consider…
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…
Given a gene tree and a species tree, ancestral configurations represent the combinatorially distinct sets of gene lineages that can reach a given node of the species tree. They have been introduced as a data structure for use in the…
We introduce a model of proteins in which all of the key atoms in the protein backbone are accounted for, thus extending the Freely Rotating Chain model. We use average bond lengths and average angles from the Protein Databank as input…
We study sums of independent random variables that take values $0$, $1/2$, or $1$. We show that the probability mass function of the sum splits into two interleaved parts: one supported on the integers and the other supported on the…
In a recent article, one of the authors used $c=0$ logarithmic conformal field theory to predict crossing-probability formulas for percolation clusters inside a hexagon with free boundary conditions. In this article, we verify these…
Two new sets of QCD sum rules for the nucleon axial coupling constants are derived using the external-field technique and generalized interpolating fields. An in-depth study of the predicative ability of these sum rules is carried out using…
Using topological summaries of gene trees as a basis for species tree inference is a promising approach to obtain acceptable speed on genomic-scale datasets, and to avoid some undesirable modeling assumptions. Here we study the…
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…
We investigate the typical cycle lengths, the total number of cycles, and the number of finite cycles in random permutations whose probability involves cycle weights. Typical cycle lengths and total number of cycles depend strongly on the…