相关论文: The genetic code multiplet structure, in one numbe…
We introduce a geometric invariant of knots in the three-sphere, called the first-order genus, that is derived from certain 2-complexes called gropes, and we show it is computable for many examples. While computing this invariant, we draw…
A group code structure of a linear code is a description of the code as one-sided or two-sided ideal of a group algebra of a finite group. In these realizations, the group algebra is identified with the ambient space, and the group elements…
A primordial genetic code is proposed, having only four codons assigned, GGC meaning glycine, GAC meaning aspartate/glutamate, GCC meaning alanine-like and GUC meaning valine-like. Pathways of ambiguity reduction enlarged the codon…
A permutiple is a natural number that is a nontrivial multiple of a permutation of its digits in some base. Special cases of permutiples include cyclic numbers (multiples of cyclic permutations of their digits) and palintiple numbers…
We count the number of occurrences of restricted patterns of length 3 in permutations with respect to length and the number of cycles. The main tool is a bijection between permutations in standard cycle form and weighted Motzkin paths.
It is known that the majority of the human genome consists of repeated sequences. Furthermore, it is believed that a significant part of the rest of the genome also originated from repeated sequences and has mutated to its current form. In…
The problem of genealogy of permutations has been solved partially by Stefan (odd order) and Acosta-Hum\'anez & Bernhardt (power of two). It is well known that Sharkovskii's theorem shows the relationship between the cardinal of the set of…
A generic rectangulation is a partition of a rectangle into finitely many interior-disjoint rectangles, such that no four rectangles meet in a point. In this work we present a versatile algorithmic framework for exhaustively generating a…
A permutation-invariant quantum code on $N$ qudits is any subspace stabilized by the matrix representation of the symmetric group $S_N$ as permutation matrices that permute the underlying $N$ subsystems. When each subsystem is a complex…
We construct generating trees with one, two, and three labels for some classes of permutations avoiding generalized patterns of length 3 and 4. These trees are built by adding at each level an entry to the right end of the permutation,…
In a recent paper, Kim and Kopparty (Theory of Computing, 2017) gave a deterministic algorithm for the unique decoding problem for polynomials of bounded total degree over a general grid. We show that their algorithm can be adapted to solve…
The systematics of indices of physico-chemical properties of codons and amino acids across the genetic code are examined. Using a simple numerical labelling scheme for nucleic acid bases, data can be fitted as low-order polynomials of the 6…
Convolutional codes are error-correcting linear codes that utilize shift registers to encode. These codes have an arbitrary block size and they can incorporate both past and current information bits. DNA codes represent DNA sequences and…
A code of the natural numbers is a uniquely-decodable binary code of the natural numbers with non-decreasing codeword lengths, which satisfies Kraft's inequality tightly. We define a natural partial order on the set of codes, and show how…
A pattern class is a set of permutations closed under the formation of subpermutations. Such classes can be characterised as those permutations not involving a particular set of forbidden permutations. A simple collection of necessary and…
This letter reports complete sets of two-fold symmetries between partitions of the universal genetic code. By substituting bases at each position of the codons according to a fixed rule, it happens that properties of the degeneracy pattern…
Suppose $G$ is a tree. Graham's "Tree Reconstruction Conjecture" states that $G$ is uniquely determined by the integer sequence $|G|$, $|L(G)|$, $|L(L(G))|$, $|L(L(L(G)))|$, $\ldots$, where $L(H)$ denotes the line graph of the graph $H$.…
Networks of gene regulation govern morphogenesis, determine cell identity and regulate cell function. But we have little understanding, at the local level, of which logics are biologically preferred or even permitted. To solve this puzzle,…
We introduce and characterise grid classes, which are natural generalisations of other well-studied permutation classes. This characterisation allows us to give a new, short proof of the Fibonacci dichotomy: the number of permutations of…
We show that all permutations in $S_n$ can be generated by affine unicritical polynomials. We use the $\operatorname{PGL}$ group structure to compute the cycle structure of permutations with low Carlitz rank. The tree structure of the group…