arXiv subjects

C. J. Burden

Publications and source records attributed to C. J. Burden.

15 recordsLinked to original sources

arXiv2008

Understanding the physics of oligonucleotide microarrays: the Affymetrix spike-in data reanalysed

The Affymetrix U95 and U133 Latin Square spike-in datasets are reanalysed, together with a dataset from a version of the U95 spike-in experiment without a complex non-specific background. The approach uses a physico-chemical model which includes the effects the specific and non-specific hybridisation and probe folding at the microarray surface, target folding and hybridisation in the bulk RNA target solution, and duplex dissociation during the post-hybridisatoin washing phase. The model predicts a three parameter hyperbolic response function that fits well with fluorescence intensity data from all three datasets. The importance of the various hybridisation and washing effects in determining each of the three parameters is examined, and some guidance is given as to how a practical algorithm for determining specific target concentrations might be developed.

q-bio.QM↗

arXiv2006

Adsorption models of hybridization and post-hybridisation behaviour on oligonucleotide microarrays

Analysis of data from an Affymetrix Latin Square spike-in experiment indicates that measured fluorescence intensities of features on an oligonucleotide microarray are related to spike-in RNA target concentrations via a hyperbolic response function, generally identified as a Langmuir adsorption isotherm. Furthermore the asymptotic signal at high spike-in concentrations is almost invariably lower for a mismatch feature than for its partner perfect match feature. We survey a number of theoretical adsorption models of hybridization at the microarray surface and find that in general they are unable to explain the differing saturation responses of perfect and mismatch features. On the other hand, we find that a simple and consistent explanation can be found in a model in which equilibrium hybridization followed by partial dissociation of duplexes during the post-hybridization washing phase.

q-bio.BM↗

arXiv2002

J^PC Exotic Mesons from the Bethe-Salpeter Equation

Masses for vector 1--, axialvector 1+-, 1++, and exotic-vector 1-+ mesons are calculated within a quantum field theoretic framework based on the Dyson-Schwinger equations using a model form of the quark-antiquark interaction that is separable. The model provides an excellent description of pion and K-meson observables and the flavor-octet ground-state meson spectrum. With no adjustments to model parameters, a numerical solution of the Bethe-Salpeter equation yields two exotic 1-+ mesons with masses of 1439 and 1498 MeV.

hep-ph↗

arXiv1999

Nonperturbative Vertices in Supersymmetric Quantum Electrodynamics

We derive the complete set of supersymmetric Ward identities involving only two- and three- point proper vertices in supersymmetric QED. We also present the most general form of the proper vertices consistent with both the supersymmetric and U(1) gauge Ward identities. These vertices are the supersymmetric equivalent of the non supersymmetric Ball-Chiu vertices.

hep-th↗

arXiv1999

Chiral Symmetry in Supersymmetric Three Dimensional Quantum Electrodynamics

We describe the investigation of spontaneous mass-generation and chiral symmetry breaking in supersymmetric QED3 using numerical solutions of the Dyson-Schwinger equation together with the CJT effective action and supersymmetric Ward identities. We find that, within the quenched bare approximation, the chirally symmetric solution is favoured.

hep-th↗

arXiv1998

The effect of the ultraviolet part of the gluon propagator on the heavy quark propagator

We revisit our recently proposed formalism for dealing with the heavy quark limit of the quark Dyson-Schwinger equation. An ambiguity inherent in the original version of method is identified and resolved. Our reanalysis illustrates the importance of correctly accounting for the effect of hard gluon momenta on the heavy quark self energy in the vicinity of the bare fermion mass pole.

hep-ph↗

arXiv1998

Heavy quark confinement from Dyson Schwinger equations

A formalism for studying the confinement of heavy quarks by considering the renormalised quark Dyson-Schwinger equation in the limit m --> infinity is described. We are particularly interested in studying the analytic structure of heavy quark propagators in the region of the complex momentum plane close to the bare fermion mass pole.

hep-ph↗

arXiv1998

Deconstructing the vertex Ansatz in three dimensional quantum electrodynamics

We consider the problem of designing an Ansatz for the fermion-photon vertex function, using three-dimensional quantum electrodynamics as a test case. In many existing studies, restrictions have been placed on the form of the vertex Ansatz by making the unsubstantiated assumption that in the quenched, massless limit the Landau gauge Dyson-Schwinger equations admit a trivial solution. We demonstrate, without recourse to this assumption, the existence of a non-local gauge in which the fermion propagator is the bare propagator. This result is used to provide a viable Ansatz for part of the vertex function.

hep-th↗

arXiv1997

The analytic structure of heavy quark propagators

The renormalised quark Dyson-Schwinger equation is studied in the limit of the renormalised current heavy quark mass m_R --> infinity. We are particularly interested in the analytic pole structure of the heavy quark propagator in the complex momentum plane. Approximations in which the quark-gluon vertex is modelled by either the bare vertex or the Ball-Chiu Ansatz, and the Landau gauge gluon propagator takes either a gaussian form or a gaussian form with an ultraviolet asymptotic tail are used.

hep-ph↗

arXiv1997

U(2)-chiral symmetries of supersymmetric QED3

Supersymmetry is studied in 2+1 dimensions. In addition to the multiplets corresponding to those in 3+1 dimensions the Clifford algebra allows an extra set. When the extra chiral multiplet is included, formulating supersymmetric QED3 in the manner of Wess and Zumino yields a lagrangian with a richer 'chiral' symmetry than that derived from supersymmetric QED by dimensional reduction.

hep-th↗

arXiv1997

Vector Positronium States in QED3

The homogeneous Bethe-Salpeter equation is solved in the quenched ladder approximation for the vector positronium states of 4-component quantum electrodynamics in 2 space and 1 time dimensions. Fermion propagator input is from a Rainbow approximation Dyson-Schwinger solution, with a broad range of fermion masses considered. This work is an extension of earlier work on the scalar spectrum of the same model. The non-relativistic limit is also considered via the large fermion mass limit. Classification of states via their transformation properties under discrete parity transformations allows analogies to be drawn with the meson spectrum of QCD.

hep-th↗

arXiv1996

A Non-perturbative Treatment of Heavy Quarks and Mesons

A formalism for studying heavy quarks in terms of model Dyson-Schwinger equations is developed. The formalism is the natural extension of a technique which has proved successful in a number of studies of light hadron physics. The dressed heavy quark propagator, calculated to leading order in the inverse quark mass, is incorporated in a treatment of mesons consisting of a heavy quark and light antiquark via the ladder approximation Bethe-Salpeter equation. In the limit of infinite heavy quark mass the model is found to respect the spectrum degeneracies present in Heavy Quark Effective Theory. An exploratory numerical analysis of a simple form of the model is carried out to assess its viability for studying $D$ and $B$ mesons.

hep-ph↗

arXiv1996

Ground-state Spectrum of Light-quark Mesons

A confining, Goldstone theorem preserving, separable Ansatz for the ladder kernel of the two-body Bethe-Salpeter equation is constructed from phenomenologically efficacious $u$, $d$ and $s$ dressed-quark propagators. The simplicity of the approach is its merit. It provides a good description of the ground-state isovector-pseudoscalar, vector and axial-vector meson spectrum; facilitates an exploration of the relative importance of various components of the two-body Bethe-Salpeter amplitudes, showing that sub-leading Dirac components are quantitatively important in the isovector-pseudoscalar meson channels; and allows a scrutiny of the domain of applicability of ladder truncation studies. A colour-antitriplet diquark spectrum is obtained. Shortcomings of separable Ansätze and the ladder kernel are highlighted.

nucl-th↗

arXiv1995

Positronium States in QED3

The $e^-$-$e^+$ bound state spectrum of QED3 is investigated in the quenched ladder approximation to the homogeneous Bethe-Salpeter equation with fermion propagators from a rainbow approximation Schwinger-Dyson equation. A detailed analysis of the analytic structure of the fermion propagator is performed so as to test the appropriateness of the methods employed. The large fermion mass limit of the Bethe-Salpeter equation is also considered, including a derivation of the Schrödinger equation, and comparisons made with existing non-relativistic calculations.

hep-th↗

arXiv1995

Electromagnetic Form Factors of Charged and Neutral Kaons

The charged and neutral kaon form factors are calculated as a phenomenological application of the QCD Dyson-Schwinger equations. The results are compared with the pion form factor calculated in the same framework and yield \mbox{$F_{K^\pm}(Q^2) > F_{π^\pm}(Q^2)$} on \mbox{$Q^2\in[0,3]$~GeV$^2$}; and a neutral kaon form factor that is similar in form and magnitude to the neutron charge form factor. These results are sensitive to the difference between the kaon and pion Bethe-Salpeter amplitude and the $u$- and $s$-quark propagation characteristics.

nucl-th↗