Group Theory of Syntactical Freedom in DNA Transcription and Genome Decoding

Transcription factors (TFs) are proteins that recognize specific DNA fragments in order to decode the genome and ensure its optimal functioning. TFs work at the local and global scales by specifying cell type, cell growth and death, cell migration, organization and timely tasks. We investigate the structure of DNA-binding motifs with the theory of finitely generated groups. The DNA ‘word’ in the binding domain -the motif- may be seen as the generator of a finitely generated group Fdna on four letters, the bases A, T, G and C. It is shown that, most of the time, the DNA-binding motifs have subgroup structure close to free groups of rank three or less, a property that we call ‘syntactical freedom’. Such a property is associated to the aperiodicity of the motif when it is seen as a substitution sequence. Examples are provided for the major families of TFs such as leucine zipper factors, zinc finger factors, homeo-domain factors, etc. We also discuss the exceptions to the existence of such a DNA syntactical rule and their functional role. This includes the TATA box in the promoter region of some genes, the single nucleotide markers (SNP) and the motifs of some genes of ubiquitous role in transcription and regulation.

Gorensteinness and iteration of Cox rings for Fano type varieties

We show that finitely generated Cox rings are Gorenstein. This leads to a refined characterization of varieties of Fano type: they are exactly those projective varieties with Gorenstein canonical quasicone Cox ring. We then show that for varieties of Fano type and Kawamata log terminal quasicones X, iteration of Cox rings is finite with factorial master Cox ring. In particular, even if the class group has torsion, we can express such X as quotients of a factorial canonical quasicone by a solvable reductive group.

Finite generation of the cohomology rings for the extension algebras of monomial algebras

We describe the cohomology ring of a monomial algebra in the language of dimension tree or minimal resolution graph and in this context we study the finite generation of the cohomology rings of the extension algebras, showing among others that the cohomology ring [Formula: see text] is finitely generated [Formula: see text] is [Formula: see text] is, where [Formula: see text] is the dual extension of a monomial algebra [Formula: see text] and [Formula: see text] is the opposite algebra of [Formula: see text].

Cyclic Lattices, Ideal Lattices and Bounds for the Smoothing Parameter

<div>Cyclic lattices and ideal lattices were introduced by Micciancio in \cite{D2}, Lyubashevsky and Micciancio in \cite{L1} respectively, which play an efficient role in Ajtai's construction of a collision resistant Hash function (see \cite{M1} and \cite{M2}) and in Gentry's construction of fully homomorphic encryption (see \cite{G}). Let $R=Z[x]/\langle \phi(x)\rangle$ be a quotient ring of the integer coefficients polynomials ring, Lyubashevsky and Micciancio regarded an ideal lattice as the correspondence of an ideal of $R$, but they neither explain how to extend this definition to whole Euclidean space $\mathbb{R}^n$, nor exhibit the relationship of cyclic lattices and ideal lattices.</div><div>In this paper, we regard the cyclic lattices and ideal lattices as the correspondences of finitely generated $R$-modules, so that we may show that ideal lattices are actually a special subclass of cyclic lattices, namely, cyclic integer lattices. In fact, there is a one to one correspondence between cyclic lattices in $\mathbb{R}^n$ and finitely generated $R$-modules (see Theorem \ref{th4} below). On the other hand, since $R$ is a Noether ring, each ideal of $R$ is a finitely generated $R$-module, so it is natural and reasonable to regard ideal lattices as a special subclass of cyclic lattices (see corollary \ref{co3.4} below). It is worth noting that we use more general rotation matrix here, so our definition and results on cyclic lattices and ideal lattices are more general forms. As application, we provide cyclic lattice with an explicit and countable upper bound for the smoothing parameter (see Theorem \ref{th5} below). It is an open problem that is the shortest vector problem on cyclic lattice NP-hard? (see \cite{D2}). Our results may be viewed as a substantial progress in this direction.</div>

Cyclic Lattices, Ideal Lattices and Bounds for the Smoothing Parameter

<div>Cyclic lattices and ideal lattices were introduced by Micciancio in \cite{D2}, Lyubashevsky and Micciancio in \cite{L1} respectively, which play an efficient role in Ajtai's construction of a collision resistant Hash function (see \cite{M1} and \cite{M2}) and in Gentry's construction of fully homomorphic encryption (see \cite{G}). Let $R=Z[x]/\langle \phi(x)\rangle$ be a quotient ring of the integer coefficients polynomials ring, Lyubashevsky and Micciancio regarded an ideal lattice as the correspondence of an ideal of $R$, but they neither explain how to extend this definition to whole Euclidean space $\mathbb{R}^n$, nor exhibit the relationship of cyclic lattices and ideal lattices.</div><div>In this paper, we regard the cyclic lattices and ideal lattices as the correspondences of finitely generated $R$-modules, so that we may show that ideal lattices are actually a special subclass of cyclic lattices, namely, cyclic integer lattices. In fact, there is a one to one correspondence between cyclic lattices in $\mathbb{R}^n$ and finitely generated $R$-modules (see Theorem \ref{th4} below). On the other hand, since $R$ is a Noether ring, each ideal of $R$ is a finitely generated $R$-module, so it is natural and reasonable to regard ideal lattices as a special subclass of cyclic lattices (see corollary \ref{co3.4} below). It is worth noting that we use more general rotation matrix here, so our definition and results on cyclic lattices and ideal lattices are more general forms. As application, we provide cyclic lattice with an explicit and countable upper bound for the smoothing parameter (see Theorem \ref{th5} below). It is an open problem that is the shortest vector problem on cyclic lattice NP-hard? (see \cite{D2}). Our results may be viewed as a substantial progress in this direction.</div>

Group Theory of Syntactical Freedom in DNA Transcription and Genome Decoding

Transcription factors (TFs) are proteins that recognize specific DNA fragments in order to decode the genome and ensure its optimal functioning. TFs work at the local and global scales by specifying cell type, cell growth and death, cell migration, organization and timely tasks. We investigate the structure of DNA-binding motifs with the theory of finitely generated groups. The DNA &lsquo;word&rsquo; in the binding domain -the motif- may be seen as the generator of a finitely generated group Fdna on four letters, the bases A, T, G and C. It is shown that, most of the time, the DNA-binding motifs have subgroup structure close to free groups of rank three or less, a property that we call &lsquo;syntactical freedom&rsquo;. Such a property is associated to the aperiodicity of the motif when it is seen as a substitution sequence. Examples are provided for the major families of TFs such as leucine zipper factors, zinc finger factors, homeo-domain factors, etc. We also discuss the exceptions to the existence of such a DNA syntactical rule and their functional role. This includes the TATA box in the promoter region of some genes, the single nucleotide markers (SNP) and the motifs of some genes of ubiquitous role in transcription and regulation.

On the structure of some non-periodic groups whose subgroups of infinite special rank are transitively normal

A group G has a finite special rank r, if every finitely generated subgroup of G can be generated by at most r elements, and there exists a finitely generated subgroup H which has exactly r generators. This paper is devoted to genera lized radical non-Abelian groups of infinite special rank whose subgroups of infinite special rank are transitively normal.

Stability for Representations of Hecke Algebras of Type A

In this paper, we introduce the concept of the stability of a sequence of modules over Hecke algebras. We prove that a finitely generated consistent sequence of the representations of Hecke algebras is representation stable.

A FREENESS CRITERION WITHOUT PATCHING FOR MODULES OVER LOCAL RINGS

It is proved that if $\varphi \colon A\to B$ is a local homomorphism of commutative noetherian local rings, a nonzero finitely generated B-module N whose flat dimension over A is at most $\operatorname {edim} A - \operatorname {edim} B$ is free over B and $\varphi $ is a special type of complete intersection. This result is motivated by a ‘patching method’ developed by Taylor and Wiles and a conjecture of de Smit, proved by the first author, dealing with the special case when N is flat over A.