arXiv subjects

Antonino Sciarrino

Publications and source records attributed to Antonino Sciarrino.

7 recordsLinked to original sources

arXiv2023

Hierarchy of codon usage frequencies from codon-anticodon interaction in the crystal basis model

Analyzing the codon usage frequencies of a specimen of 20 plants, for which the codon-anticodon pattern is known, we have remarked that the hierarchy of the usage frequencies present an almost "universal" behavior. Searching to explain this behavior, we assume that the codon usage probability results from the sum of two contributions: the first dominant term is an almost "universal" one and it depends on the codon-anticodon interaction; the second term is a local one, i.e. depends on the biological species. The codon-anticodon interaction is written as a spin-spin plus a z-spin term in the formalism of the crystal basis model. From general considerations, in particular from the choice of the signs and some constraints on the parameters defining the interaction, we are able to explain most of the observed data.

q-bio.OT↗

arXiv2016

Correlations in Usage Frequencies and Shannon Entropy for Codons

The usage frequencies for codons belonging to quartets are analized, over the whole exonic region, for 92 biological species. Correlation is put into evidence, between the usage frequencies of synonymous codons with third nucleotide A and C and between the usage frequencies of non synonymous codons, belonging to suitable subsets of the quartets, with the same third nucleotide. A correlation is pointed out between amino acids belonging to subsets of the set encoded by quartets of codons. It is remarked that the computed Shannon entropy for quartets is weakly dependent on the biological species. The observed correlations well fit in the mathematical scheme of the crystal basis model of the genetic code.

q-bio.OT↗

arXiv2010

About the Non Relativistic Structure of the AdS/CFT Superalgebras

The property of the conformal algebra to contain the Schrödinger algebra in one less space dimension is extended to the supersymmetric case. More precisely, we determine the counterpart of any field theory admissible super conformal algebra. Even if each type of superalgebra provides a different solution, its basis decomposition into two copies of the super Schrödinger algebra, differing only by their super Heisenberg part, remains valid in all the cases, so generalizing a feature already observed in the non supersymmetric conformal case.

hep-th↗

arXiv2006

Conspiracy in bacterial genomes

The rank ordered distribution of the codon usage frequencies for 123 bacteriae is best fitted by a three parameters function that is the sum of a constant, an exponential and a linear term in the rank n. The parameters depend (two parabolically) from the total GC content. The rank ordered distribution of the amino acids is fitted by a straight line. The Shannon entropy computed over all the codons is well fitted by a parabola in the GC content, while the partial entropies computed over subsets of the codons show peculiar different behavior, exhibiting therefore a first conspiracy effect. Moreover the sum of the codon usage frequencies over particular sets, e.g. with C and A (respectively G and U) as i-th nucleotide, shows a clear linear dependence from the GC content, exhibiting another conspiracy effect.

q-bio.GN↗

arXiv2003

From quantum groups to genetic mutations

In the framework of the crystal basis model of the genetic code, where each codon is assigned to an irreducible representation of $U_{q \to 0}(sl(2) \oplus sl(2))$, single base mutation matrices are introduced. The strength of the mutation is assumed to depend on the "distance" between the codons. Preliminary general predictions of the model are compared with experimental data, with a satisfactory agreement.

math-ph↗

arXiv1998

Tensor operators and Wigner-Eckart theorem for U_q->0(sl(2))

Crystal tensor operators, which tranform under U_q->0(sl(2)), in analogous way as the vectors of the crystal basis, are introduced. The Wigner-Eckart theorem for the crystal tensor is defined: the selection rules depend on the initial state and on the component of the tensor operator; the transition amplitudes to the states of the same final irreducible representation are all equal.

math.QA↗

arXiv1996

From Vertex Operators to Calogero-Sutherland Models

The correlation function of the product of N generalized vertex operators satisfies an infinite set of Ward identities, related to a W_{\infty} algebra, whose extention out of the mass shell gives rise to equations which can be considered as a generalization of the compactified Calogero-Sutherland (CS) hamiltonians. In particular the wave function of the ground state of the compactified CS model is shown to be given by the value of the product of N vertex operators between the vacuum and exitated state. The role of vertex algebra as underlying unifying structure is pointed out.

hep-th↗