Stress-induced changes in the Schizosaccharomyces pombe proteome using two-dimensional difference gel electrophoresis, mass spectrometry and a novel integrated robotics platform

Robotic and manual methods have been used to obtain identification of significantly changing proteins regulated when Schizosaccharomyces pombe is exposed to oxidative stress. Differently treated S. pombe cells were lysed, labelled with CyDye (TM) and analysed by two-dimensional difference gel. electrophoresis. Gel images analysed off-line, using the DeCyder (TM) image analysis software [GE Healthcare, Amersham, UK] allowed selection of significantly regulated proteins. Proteins displaying differential expression were excised robotically for manual digestion and identified by matrix-assisted laser desorption/ionisation - mass spectrometry (MALDI-MS). Additionally the same set of proteins displaying differential expression were automatically cut and digested using a prototype robotic platform. Automated MALDI-MS, peak label assignment and database searching were utilised to identify as many proteins as possible. The results achieved by the robotic system were compared to manual methods. The identification of all significantly altered proteins provides an annotated peroxide stress-related proteome that can be used as a base resource against which other stress-induced proteomic changes can be compared.

Two-dimensional similarity between forms I and II of cytenamide, a carbamazepine analogue

Cytenamide form I (R (3) over bar) undergoes a solid-state transformation upon heating to form II (P (1) over bar), with the structures exhibiting the same two-dimensional similarity that exists between the R (3) over bar and P (1) over bar forms of carbamazepine.

Approximate Riemann solutions of the two-dimensional shallow-water equations

A finite-difference scheme based on flux difference splitting is presented for the solution of the two-dimensional shallow-water equations of ideal fluid flow. A linearised problem, analogous to that of Riemann for gasdynamics, is defined and a scheme, based on numerical characteristic decomposition, is presented for obtaining approximate solutions to the linearised problem. The method of upwind differencing is used for the resulting scalar problems, together with a flux limiter for obtaining a second-order scheme which avoids non-physical, spurious oscillations. An extension to the two-dimensional equations with source terms, is included. The scheme is applied to a dam-break problem with cylindrical symmetry.

Solutions of a two-dimensional dam-break problem

Solutions of a two-dimensional dam break problem are presented for two tailwater/reservoir height ratios. The numerical scheme used is an extension of one previously given by the author [J. Hyd. Res. 26(3), 293–306 (1988)], and is based on numerical characteristic decomposition. Thus approximate solutions are obtained via linearised problems, and the method of upwind differencing is used for the resulting scalar problems, together with a flux limiter for obtaining a second order scheme which avoids non-physical, spurious oscillations.

A finite difference scheme for steady, supersonic, two-dimensional, compressible flow of real gases

A finite difference scheme is presented for the solution of the two-dimensional equations of steady, supersonic, compressible flow of real gases. The scheme incorparates numerical characteristic decomposition, is shock-capturing by design and incorporates space-marching as a result of the assumption that the flow is wholly supersonic in at least one space dimension. Results are shown for problems involving oblique hydraulic jumps and reflection from a wall.

A numerical scheme for two-dimensional, open channel flows with non-rectangular geometries

An algorithm based on flux difference splitting is presented for the solution of two-dimensional, open channel flows. A transformation maps a non-rectangular, physical domain into a rectangular one. The governing equations are then the shallow water equations, including terms of slope and friction, in a generalized coordinate system. A regular mesh on a rectangular computational domain can then be employed. The resulting scheme has good jump capturing properties and the advantage of using boundary/body-fitted meshes. The scheme is applied to a problem of flow in a river whose geometry induces a region of supercritical flow.

Riemann solvers with primitive parameter vectors for two-dimensional compressible flows of a real gas

An analysis of averaging procedures is presented for an approximate Riemann solver for the equations governing the compressible flow of a real gas. This study extends earlier work for the Euler equations with ideal gases.

Switching on a two-dimensional time-harmonic scalar wave in the presence of a diffracting edge

This paper concerns the switching on of two-dimensional time-harmonic scalar waves. We first review the switch-on problem for a point source in free space, then proceed to analyse the analogous problem for the diffraction of a plane wave by a half-line (the ‘Sommerfeld problem’), determining in both cases the conditions under which the field is well-approximated by the solution of the corresponding frequency domain problem. In both cases the rate of convergence to the frequency domain solution is found to be dependent on the strength of the singularity on the leading wavefront. In the case of plane wave diffraction at grazing incidence the frequency domain solution is immediately attained along the shadow boundary after the arrival of the leading wavefront. The case of non-grazing incidence is also considered.

Wave trapping in a two-dimensional sound-soft or sound-hard acoustic waveguide of slowly-varying width

In this paper we derive novel approximations to trapped waves in a two-dimensional acoustic waveguide whose walls vary slowly along the guide, and at which either Dirichlet (sound-soft) or Neumann (sound-hard) conditions are imposed. The guide contains a single smoothly bulging region of arbitrary amplitude, but is otherwise straight, and the modes are trapped within this localised increase in width. Using a similar approach to that in Rienstra (2003), a WKBJ-type expansion yields an approximate expression for the modes which can be present, which display either propagating or evanescent behaviour; matched asymptotic expansions are then used to derive connection formulae which bridge the gap across the cut-off between propagating and evanescent solutions in a tapering waveguide. A uniform expansion is then determined, and it is shown that appropriate zeros of this expansion correspond to trapped mode wavenumbers; the trapped modes themselves are then approximated by the uniform expansion. Numerical results determined via a standard iterative method are then compared to results of the full linear problem calculated using a spectral method, and the two are shown to be in excellent agreement, even when $\epsilon$, the parameter characterising the slow variations of the guide’s walls, is relatively large.