Sum rules of codon usage probabilities

In the crystal basis model of the genetic code, it is deduced that the sum of usage probabilities of the codons with C and A in the third position for the quartets and/or sextets is independent of the biological species for vertebrates. A comparison with experimental data shows that the prediction is satisfied within about 5 %.Comment: 7 page

Classification of three-state Hamiltonians solvable by Coordinate Bethe Ansatz

We classify all Hamiltonians with rank 1 symmetry, acting on a periodic three-state spin chain, and solvable through (generalisation of) the coordinate Bethe ansatz (CBA). We obtain in this way four multi-parametric extensions of the known 19-vertex Hamiltonians (such as Zamolodchikov-Fateev, Izergin-Korepin, Bariev Hamiltonians). Apart from the 19-vertex Hamiltonians, there exists 17-vertex and 14-vertex Hamiltonians that cannot be viewed as subcases of the 19-vertex ones. In the case of 17-vertex Hamiltonian, we get a generalization of the genus 5 special branch found by Martins, plus three new ones. We get also two 14-vertex Hamiltonians. We solve all these Hamiltonians using CBA, and provide their spectrum, eigenfunctions and Bethe equations. A special attention is made to provide the specifications of our multi-parametric Hamiltonians that give back known Hamiltonians.Comment: 30 pages; web page: http://www.coulomb.univ-montp2.fr/3Ha

Crystalizing the genetic code

New developments are presented in the framework of the model introduced by the authors in refs. [1,2] and in which nucleotides as well as codons are classified in crystal bases of the quantum group U_q(sl(2)+sl(2)) in the limit q -> 0. An operator which gives the correspondence between the amino-acids and the codons is now obtained for any known genetic code. The free energy released by base pairing of dinucleotides as well as the relative hydrophilicity and hydrophobicity of the dinucleosides are also computed. For the vertebrate series, a universal behaviour in the ratios of codon usage frequencies is put in evidence and is shown to fit nicely in our model. Then a first attempt to represent the mutations relative to the deletion of a pyrimidine by action of a suitable crystal spinor operator is proposed. Finally recent theoretical descriptions are reviewed and compared with our model

Many-body spin Berry phases emerging from the π\pi-flux state: antiferromagnetic/valence-bond-solid competition

We uncover new topology-related features of the $\pi$-flux saddle-point solution of the $D$=2+1 Heisenberg antiferromagnet. We note that symmetries of the spinons sustain a built-in competition between antiferromagnetic (AF) and valence-bond-solid (VBS) orders, the two tendencies central to recent developments on quantum criticality. An effective theory containing an analogue of the Wess-Zumino-Witten term is derived, which generates quantum phases related to AF monopoles with VBS cores, and reproduces Haldane's hedgehog Berry phases. The theory readily generalizes to $\pi$-flux states for all $D$.Comment: 4 pages, revise

On Casimir's Ghost

We define on the universal enveloping superalgebra of osp(1|2n) a nonstandard adjoint action, endowing it with a module structure. This allows, in particular, to construct a bosonic operator which anticommutes with all the fermionic generators and which appears to be the square root of a certain Casimir operator.Comment: LaTeX2e, 13 pages,also available at http://lapphp0.in2p3.fr/preplapp/psth/ENSLAPP587.ps.gz ; one sentence removed and a note added. Not a major revisio

A minimum principle in mRNA editing ?

mRNA editing of sequences of many species is analyzed. The nature of the inserted nucleotides and the position of the insertion sites, once fixed the edited peptide chain, are explained by introducing a minimum principle in the framework of the crystal basis model of the genetic code introduced by the authors.Comment: revised extended version - includes analysis on more dat

Dictionary on Lie Superalgebras

The main definitions and properties of Lie superalgebras are proposed a la facon de a short dictionary, the different items following the alphabetical order. The main topics deal with the structure of simple Lie superalgebras and their finite dimensional representations; rather naturally, a few pages are devoted to supersymmetry. This modest booklet has two ambitious goals: to be elementary and easy to use. The beginner is supposed to find out here the main concepts on superalgebras, while a more experimented theorist should recognize the necessary tools and informations for a specific use.Comment: 145p LaTeX Document, also available at http://lapphp0.in2p3.fr/preplapp/psth/DICTIONARY_SUPER.ps.g