A mandate to self archive? The role of open access institutional repositories

This paper argues that the best way to achieve major improvements in scholarly communication in the short and medium term is to make it mandatory to deposit research papers in open access institutional repositories. This is what the House of Commons Science and Technology Committee report of 2004 on scientific publishing recommended. The paper defines what open access repositories are and explains why they should be institutional. It also deals with question of what should be deposited in institutional repositories and why these improve scholarly communication. It then deals with the issue of mandating deposition: why deposition should be mandatory, who should mandate deposition and who should carry out deposition. The paper concludes with an analysis of the wider implications of mandating deposition in institutional repositories and a summary of the existing situation in the UK and elsewhere. The paper discusses the Select Committee report and the UK Government response in relation to institutional repositories.

Waves, bumps, and patterns in neural field theories

Neural field models of firing rate activity have had a major impact in helping to develop an understanding of the dynamics seen in brain slice preparations. These models typically take the form of integro-differential equations. Their non-local nature has led to the development of a set of analytical and numerical tools for the study of waves, bumps and patterns, based around natural extensions of those used for local differential equation models. In this paper we present a review of such techniques and show how recent advances have opened the way for future studies of neural fields in both one and two dimensions that can incorporate realistic forms of axo-dendritic interactions and the slow intrinsic currents that underlie bursting behaviour in single neurons.

A posteriori error estimation for discontinuous Galerkin discretizations of H(curl)-elliptic partial differential equations

We develop the a posteriori error estimation of interior penalty discontinuous Galerkin discretizations for H(curl)-elliptic problems that arise in eddy current models. Computable upper and lower bounds on the error measured in terms of a natural (mesh-dependent) energy norm are derived. The proposed a posteriori error estimator is validated by numerical experiments, illustrating its reliability and efficiency for a range of test problems.

Calculation of electric field strengths at a sharp edge

Sharp edges were first used for field ionisation mass spectrometry by Beckey. Although Cross and Robertson found that etched metal foils were more effective than razor blades for field ionisation, blades are very convenient for determination of field ionisation mass spectra, as reported by Robertson and Viney. The electric field at the vertex of a sharp edge can be calculated by the method of the conformal transformation. Here we give some equations for the field deduced with the assumption that the edge surface can be approximated by a hyperbola. We also compare two hyperbolae with radii of curvature at the vertex of 500 Angstrom and 1000 Angstrom with the profile of a commercial carbon-steel razor blade.

Electric field strengths and ion trajectories in sharp-edge field ionization sources

On the presumption that a sharp edge may be represented by a hyperbola, a conformal transformation method is used to derive electric field equations for a sharp edge suspended above a flat plate. A further transformation is then introduced to give electric field components for a sharp edge suspended above a thin slit. Expressions are deduced for the field strength at the vertex of the edge in both arrangements. The calculated electric field components are used to compute ion trajectories in the simple edge/flat-plate case. The results are considered in relation to future study of ion focusing and unimolecular decomposition of ions in field ionization mass spectrometers.

Symmetry properties of one- and two- electron molecular integrals

The maximum numbers of distinct one- and two-electron integrals that arise in calculating the electronic energy of a molecule are discussed. It is shown that these may be calculated easily using the character table of the symmetry group of the set of basis functions used to express the wave function. Complications arising from complex group representations and from a conflict of symmetry between the basis set and the nuclear configuration are considered and illustrated by examples.

Approximate ab initio calculations and the method of molecular fragments

A two stage approach to performing ab initio calculations on medium and large sized molecules is described. The first step is to perform SCF calculations on small molecules or molecular fragments using the OPIT Program. This employs a small basis set of spherical and p-type Gaussian functions. The Gaussian functions can be identified very closely with atomic cores, bond pairs, lone pairs, etc. The position and exponent of any of the Gaussian functions can be varied by OPIT to produce a small but fully optimised basis set. The second stage is the molecular fragments method. As an example of this, Gaussian exponents and distances are taken from an OPIT calculation on ethylene and used unchanged in a single SCF calculation on benzene. Approximate ab initio calculations of this type give much useful information and are often preferable to semi-empirical approaches, since the nature of the approximations involved is much better defined.

Symmetric Interior Penalty DG Methods for the Compressible Navier-Stokes Equations I: Method Formulation

In this article we consider the development of discontinuous Galerkin finite element methods for the numerical approximation of the compressible Navier-Stokes equations. For the discretization of the leading order terms, we propose employing the generalization of the symmetric version of the interior penalty method, originally developed for the numerical approximation of linear self-adjoint second-order elliptic partial differential equations. In order to solve the resulting system of nonlinear equations, we exploit a (damped) Newton-GMRES algorithm. Numerical experiments demonstrating the practical performance of the proposed discontinuous Galerkin method with higher-order polynomials are presented.

Symmetric Interior Penalty DG Methods for the Compressible Navier-Stokes Equations II: Goal--Oriented A Posteriori Error Estimation

In this article we consider the application of the generalization of the symmetric version of the interior penalty discontinuous Galerkin finite element method to the numerical approximation of the compressible Navier--Stokes equations. In particular, we consider the a posteriori error analysis and adaptive mesh design for the underlying discretization method. Indeed, by employing a duality argument (weighted) Type I a posteriori bounds are derived for the estimation of the error measured in terms of general target functionals of the solution; these error estimates involve the product of the finite element residuals with local weighting terms involving the solution of a certain dual problem that must be numerically approximated. This general approach leads to the design of economical finite element meshes specifically tailored to the computation of the target functional of interest, as well as providing efficient error estimation. Numerical experiments demonstrating the performance of the proposed approach will be presented.

Calculated ionization potentials of the linear alkanes

The equivalent orbital (EO) method is investigated and used for predicting outer and inner ionization potentials of the linear alkanes. The calculated ionization potentials are in good agreement with those observed in photoelectron spectra provided that a set of 12 parameters is used in the theory. An optimization technique is used to find the best values for thle parameters and a single transferable parameter set can be found which is applicable to all the n-alkanes. A good fit to the experimental results can only be obtained if the uppermost molecular orbital of the n-alkanes is an antisymmetrical orbital built up from CH equivalent orbitals.

3-body energy terms in a quartet state of H3

Calculations of the 3-body energy term in a quartet (4A2 ) state of H3 (equilateral triangle nuclear-configurations) show a minimum in the 3-body energy for a side length of about 1.3 bohrs.

Fast assembly of fock matrices utilising symmetry properties of the basis set

A method of assembling the elements of the Fock matrix is described which is a modification of that due to Dacre. Lists of symmetry equivalent one-electron integrals are used as pointers to abbreviate the process of collecting two-electron integrals into the Fock matrix.

Algol 68 Dialect Conversion -- a Syntactic Approach

A syntax directed package for converting Revised Algol 68 programs into Algol 68-R form, (where possible) is being developed at Nottingham. The package makes use of J.M. Foster's Syntax Improving Device (SID) [1]. The experience gained has underlined the value of a syntactic approach to problems of this sort. A far wider range of constructs can be translated than would ever be possible by using ad hoc methods. In many respects the difficulties encountered are those of conventional compiler writing, but some intriguing new problems arise when, as in this case, the source language and target language differ relatively little in philosophy and appearance.

Electronic Publishing -- a Journal and its Production

The use of the term "Electronic Publishing" transcends any notions of the paperless office and of a purely electronic transfer and dissemination of information over networks. It now encompasses all computer-assisted methods for the production of documents and includes the imaging of a document on paper as one of the options to be provided by an integrated processing scheme. Electronic publishing draws heavily on techniques from computer science and information technology but technical, legal, financial and organisational problems have to be overcome before it can replace traditional publication mechanisms. These problems are illustrated with reference to the publication arrangements for the journal `Electronic Publishing Origination, Dissemination and Design'. The authors of this paper are the co-editors of this journal, which appears in traditional form and relies on a wide variety of support from electronic technologies in the pre-publication phase.

Page Composition using PPML as a Link-editing Script

The advantages of a COG (Component Object Graphic) approach to the composition of PDF pages have been set out in a previous paper [1]. However, if pages are to be composed in this way then the individual graphic objects must have known bounding boxes and must be correctly placed on the page in a process that resembles the link editing of a multi-module computer program. Ideally the linker should be able to utilize all declared resource information attached to each COG. We have investigated the use of an XML application called Personalized Print Markup Language (PPML) to control the link editing process for PDF COGs. Our experiments, though successful, have shown up the shortcomings of PPML's resource handling capabilities which are currently active at the document and page levels but which cannot be elegantly applied to individual graphic objects at a sub-page level. Proposals are put forward for modifications to PPML that would make easier any COG-based approach to page composition.