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P. D. Jarvis

Publications and source records attributed to P. D. Jarvis.

33 records · Page 2Linked to original sources
arXiv2005

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 ($ΔG$ mean errors of 4.5 and 5.4 % respectively).

q-bio.BM↗
arXiv2005

New branching rules induced by plethysm

We derive group branching laws for formal characters of subgroups $H_π$ of GL(n) leaving invariant an arbitrary tensor $T^π$ of Young symmetry type $π$ where $π$ is an integer partition. The branchings $GL(n)\downarrow GL(n-1)$, $GL(n)\downarrow O(n)$ and $GL(2n)\downarrow Sp(2n)$ fixing a vector $v_i$, a symmetric tensor $g_{ij}=g_{ji}$ and an antisymmetric tensor $f_{ij}=-f_{ji}$, respectively, are obtained as special cases. All new branchings are governed by Schur function series obtained from plethysms of the Schur function $s_π\equiv {\{} π{\}}$ by the basic $M$ series of complete symmetric functions and the $L =M^{-1}$ series of elementary symmetric functions. Our main technical tool is that of Hopf algebras, and our main result is the derivation of a coproduct for any Schur function series obtained by plethysm from another such series. Therefrom one easily obtains $π$-generalized Newell-Littlewood formulae, and the algebra of the formal group characters of these subgroups is established. Concrete examples and extensive tabulations are displayed for $H_{1^3}$, $H_{21}$, and $H_{3}$, showing their involved and nontrivial representation theory. The nature of the subgroups is shown to be in general affine, and in some instances non reductive. We discuss the complexity of the coproduct formula and give a graphical notation to cope with it. We also discuss the way in which the group branching laws can be reinterpreted as twisted structures deformed by highly nontrivial 2-cocycles. The algebra of subgroup characters is identified as a cliffordization of the algebra of symmetric functions for GL(n) formal characters. Modification rules are beyond the scope of the present paper, but are briefly discussed.

math-ph↗
arXiv2005

Conformal Fluid Dynamics

We present a conformal theory of a dissipationless relativistic fluid in 2 space-time dimensions. The theory carries with it a representation of the algebra of 2-$D$ area-preserving diffeomorphisms in the target space of the complex scalar potentials. A complete canonical description is given, and the central charge of the current algebra is calculated. The passage to the quantum theory is discussed in some detail; as a result of operator ordering problems, full quantization at the level of the fields is as yet an open problem.

hep-th↗
arXiv2004

On the Structure of the Observable Algebra of QCD on the Lattice

The structure of the observable algebra ${\mathfrak O}_Λ$ of lattice QCD in the Hamiltonian approach is investigated. As was shown earlier, ${\mathfrak O}_Λ$ is isomorphic to the tensor product of a gluonic $C^{*}$-subalgebra, built from gauge fields and a hadronic subalgebra constructed from gauge invariant combinations of quark fields. The gluonic component is isomorphic to a standard CCR algebra over the group manifold SU(3). The structure of the hadronic part, as presented in terms of a number of generators and relations, is studied in detail. It is shown that its irreducible representations are classified by triality. Using this, it is proved that the hadronic algebra is isomorphic to the commutant of the triality operator in the enveloping algebra of the Lie super algebra ${\rm sl(1/n)}$ (factorized by a certain ideal).

hep-th↗
arXiv2004

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.

q-bio.PE↗
arXiv2004

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).

hep-th↗
arXiv2003

U(1)xU(1)xU(1) symmetry of the Kimura 3ST model and phylogenetic branching processes

An analysis of the Kimura 3ST model of DNA sequence evolution is given on the basis of its continuous Lie symmetries. The rate matrix commutes with a U(1)xU(1)xU(1) phase subgroup of the group GL(4) of 4x4x4 invertible complex matrices acting on a linear space spanned by the 4 nucleic acid base letters. The diagonal `branching operator' representing speciation is defined, and shown to intertwine the U(1)xU(1)xU(1) action. Using the intertwining property, a general formula for the probability density on the leaves of a binary tree under the Kimura model is derived, which is shown to be equivalent to established phylogenetic spectral transform methods.

q-bio.PE↗
arXiv2003

A Hopf laboratory for symmetric functions

An analysis of symmetric function theory is given from the perspective of the underlying Hopf and bi-algebraic structures. These are presented explicitly in terms of standard symmetric function operations. Particular attention is focussed on Laplace pairing, Sweedler cohomology for 1- and 2-cochains, and twisted products (Rota cliffordizations) induced by branching operators in the symmetric function context. The latter are shown to include the algebras of symmetric functions of orthogonal and symplectic type. A commentary on related issues in the combinatorial approach to quantum field theory is given.

math-ph↗
arXiv2003

Polynomial super-gl(n) algebras

We introduce a class of finite dimensional nonlinear superalgebras $L = L_{\bar{0}} + L_{\bar{1}}$ providing gradings of $L_{\bar{0}} = gl(n) \simeq sl(n) + gl(1)$. Odd generators close by anticommutation on polynomials (of degree $>1$) in the $gl(n)$ generators. Specifically, we investigate `type I' super-$gl(n)$ algebras, having odd generators transforming in a single irreducible representation of $gl(n)$ together with its contragredient. Admissible structure constants are discussed in terms of available $gl(n)$ couplings, and various special cases and candidate superalgebras are identified and exemplified via concrete oscillator constructions. For the case of the $n$-dimensional defining representation, with odd generators $Q_{a}, \bar{Q}{}^{b}$, and even generators ${E^{a}}_{b}$, $a,b = 1,...,n$, a three parameter family of quadratic super-$gl(n)$ algebras (deformations of $sl(n/1)$) is defined. In general, additional covariant Serre-type conditions are imposed, in order that the Jacobi identities be fulfilled. For these quadratic super-$gl(n)$ algebras, the construction of Kac modules, and conditions for atypicality, are briefly considered. Applications in quantum field theory, including Hamiltonian lattice QCD and space-time supersymmetry, are discussed.

hep-th↗
arXiv2002

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).

hep-th↗
arXiv2001

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.

physics.bio-ph↗
arXiv2000

The Genetic Code as a Periodic Table: Algebraic Aspects

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 coordinates in the 64-dimensional codon weight space. The work confirms and extends recent studies by Siemion of amino acid conformational parameters. The connections between the present work, and recent studies of the genetic code structure using dynamical symmetry algebras, are pointed out.

physics.bio-ph↗
arXiv1998

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.

physics.bio-ph↗
arXiv1996

Modified Relativity from the kappa-deformed Poincare Algebra

The theory of the $κ$-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 $κ^{-1}$ 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 $κc$ of 90eV and 250 keV, respectively. Corrections to the Casimir effect and the Thomas precession are also discussed.

gr-qc↗