A base pairing model of duplex formation I: Watson-Crick pairing geometries

We present a base-pairing model of oligonuleotide duplex formation and show in detail its equivalence to the Nearest-Neighbour dimer methods from fits to free energy of duplex formation data for short DNA-DNA and DNA-RNA hybrids containing only Watson Crick pairs. In this approach the connection between rank-deficient polymer and rank-determinant oligonucleotide parameter, sets for DNA duplexes is transparent. The method is generalised to include RNA/DNA hybrids where the rank-deficient model with 11 dimer parameters in fact provides marginally improved predictions relative to the standard method with 16 independent dimer parameters ($\Delta G$ mean errors of 4.5 and 5.4 % respectively).Comment: Latex file, 13 pages, no figures. Refereed draft of manuscript submitted to Biopolymer

Modified Relativity from the kappa-deformed Poincare Algebra

The theory of the $\kappa$-deformed Poincare algebra is applied to the analysis of various phenomena in special relativity, quantum mechanics and field theory. The method relies on the development of series expansions in $\kappa^{-1}$ of the generalised Lorentz transformations, about the special-relativistic limit. Emphasis is placed on the underlying assumptions needed in each part of the discussion, and on in principle limits for the deformation parameter, rather than on rigorous numerical bounds. In the case of the relativistic Doppler effect, and the Michelson-Morley experiment, comparisons with recent experiemntal tests yield the relatively weak lower bounds on $\kappa c$ of 90eV and 250 keV, respectively. Corrections to the Casimir effect and the Thomas precession are also discussed.Comment: 11 pages long, to appear in 'Class Q Grav

Quantum Field Theory and Phylogenetic Branching

A calculational framework is proposed for phylogenetics, using nonlocal quantum field theories in hypercubic geometry. Quadratic terms in the Hamiltonian give the underlying Markov dynamics, while higher degree terms represent branching events. The spatial dimension L is the number of leaves of the evolutionary tree under consideration. Momentum conservation modulo ${\mathbb Z}_{2}^{times L}$ in $L \leftarrow 1$ scattering corresponds to tree edge labelling using binary L-vectors. The bilocal quadratic term allows for momentum-dependent rate constants - only the tree(s) compatible with selected nonzero edge rates contribute to the branching probability distribution. Applications to models of evolutionary branching processes are discussed.Comment: LaTex file, 6 pages, 1 postscript figure. Typographical errors corrected, minor changes added. Submitted to J.Phys.Lett.

Systematics of the Genetic Code and Anticode: History, Supersymmetry, Degeneracy and Periodicity

Important aspects of the process of information storage and retrieval in DNA and RNA, and its evolution, are the role of the anticodons and associated $t$RNA's, and correlations between anticodons and amino acids; the degeneracy of the genetic code, and the periodicity of many amino acid physico-chemical properties. Such factors are analysed in the context of a $sl(6/1)$ supersymmetric model of the genetic code.Comment: 4 pages LaTex, uses icmp.sty, 2 figures, Contribution to proceedings of oXXII International Colloquium on Group Theoretical Methods in Physics (Group22) Hobart, 13-17 July 1998, to be published by International Pres

Using the tangle: a consistent construction of phylogenetic distance matrices for quartets

Distance based algorithms are a common technique in the construction of phylogenetic trees from taxonomic sequence data. The first step in the implementation of these algorithms is the calculation of a pairwise distance matrix to give a measure of the evolutionary change between any pair of the extant taxa. A standard technique is to use the log det formula to construct pairwise distances from aligned sequence data. We review a distance measure valid for the most general models, and show how the log det formula can be used as an estimator thereof. We then show that the foundation upon which the log det formula is constructed can be generalized to produce a previously unknown estimator which improves the consistency of the distance matrices constructed from the log det formula. This distance estimator provides a consistent technique for constructing quartets from phylogenetic sequence data under the assumption of the most general Markov model of sequence evolution.Comment: 18 Pges. Submitted to Mathematical Bioscience

Markov invariants for phylogenetic rate matrices derived from embedded submodels

We consider novel phylogenetic models with rate matrices that arise via the embedding of a progenitor model on a small number of character states, into a target model on a larger number of character states. Adapting representation-theoretic results from recent investigations of Markov invariants for the general rate matrix model, we give a prescription for identifying and counting Markov invariants for such `symmetric embedded' models, and we provide enumerations of these for low-dimensional cases. The simplest example is a target model on 3 states, constructed from a general 2 state model; the `2->3' embedding. We show that for 2 taxa, there exist two invariants of quadratic degree, that can be used to directly infer pairwise distances from observed sequences under this model. A simple simulation study verifies their theoretical expected values, and suggests that, given the appropriateness of the model class, they have greater statistical power than the standard (log) Det invariant (which is of cubic degree for this case).Comment: 16 pages, 1 figure, 1 appendi

Entanglement Invariants and Phylogenetic Branching

It is possible to consider stochastic models of sequence evolution in phylogenetics in the context of a dynamical tensor description inspired from physics. Approaching the problem in this framework allows for the well developed methods of mathematical physics to be exploited in the biological arena. We present the tensor description of the homogeneous continuous time Markov chain model of phylogenetics with branching events generated by dynamical operations. Standard results from phylogenetics are shown to be derivable from the tensor framework. We summarize a powerful approach to entanglement measures in quantum physics and present its relevance to phylogenetic analysis. Entanglement measures are found to give distance measures that are equivalent to, and expand upon, those already known in phylogenetics. In particular we make the connection between the group invariant functions of phylogenetic data and phylogenetic distance functions. We introduce a new distance measure valid for three taxa based on the group invariant function known in physics as the "tangle". All work is presented for the homogeneous continuous time Markov chain model with arbitrary rate matrices.Comment: 21 pages, 3 Figures. Accepted for publication in Journal of Mathematical Biolog

Resolution of the GL(3) - O(3) state labelling problem via O(3)-invariant Bethe subalgebra of the twisted Yangian

The labelling of states of irreducible representations of GL(3) in an O(3) basis is well known to require the addition of a single O(3)-invariant operator, to the standard diagonalisable set of Casimir operators in the subgroup chain GL(3) - O(3) - O(2). Moreover, this `missing label' operator must be a function of the two independent cubic and quartic invariants which can be constructed in terms of the angular momentum vector and the quadrupole tensor. It is pointed out that there is a unique (in a well-defined sense) combination of these which belongs to the O(3) invariant Bethe subalgebra of the twisted Yangian Y(GL(3);O(3)) in the enveloping algebra of GL(3).Comment: 7 pages, LaTe

Exactly solvable three-level quantum dissipative systems via bosonisation of fermion gas-impurity models

We study the relationship between one-dimensional fermion gas-impurity models and quantum dissipative systems, via the method of constructive bosonisation and unitary transformation. Starting from an anisotropic Coqblin-Schrieffer model, a new, exactly solvable, three-level quantum dissipative system is derived as a generalisation of the standard spin-half spin-boson model. The new system has two environmental oscillator baths with ohmic coupling, and admits arbitrary detuning between the three levels. All tunnelling matrix elements are equal, up to one complex phase which is itself a function of the longitudinal and transverse couplings in the integrable limit. Our work underlines the importance of re-examining the detailed structure of fermion-gas impurity models and spin chains, in the light of connections to models for quantum dissipative systems.Comment: 12 pages, accepted for publication in Journal of Physics A: Mathematical and Theoretical. (Extended discussion section, some references added and some typos corrected

Polar decomposition of a Dirac spinor

Local decompositions of a Dirac spinor into `charged' and `real' pieces psi(x) = M(x) chi(x) are considered. chi(x) is a Majorana spinor, and M(x) a suitable Dirac-algebra valued field. Specific examples of the decomposition in 2+1 dimensions are developed, along with kinematical implications, and constraints on the component fields within M(x) sufficient to encompass the correct degree of freedom count. Overall local reparametrisation and electromagnetic phase invariances are identified, and a dynamical framework of nonabelian gauge theories of noncompact groups is proposed. Connections with supersymmetric composite models are noted (including, for 2+1 dimensions, infrared effective theories of spin-charge separation in models of high-Tc superconductivity).Comment: 12 pages, LaTe