Studying reactive processes with classical dynamics: rebinding dynamics in MbNO

A new surface-crossing algorithm suitable for describing bond-breaking and bond-forming processes in molecular dynamics simulations is presented. The method is formulated for two intersecting potential energy manifolds which dissociate to different adiabatic states. During simulations, crossings are detected by monitoring an energy criterion. If fulfilled, the two manifolds are mixed over a finite number of time steps, after which the system is propagated on the second adiabat and the crossing is carried out with probability one. The algorithm is extensively tested (almost 0.5 mu s of total simulation time) for the rebinding of NO to myoglobin. The unbound surface ((FeNO)-N-...) is represented using a standard force field, whereas the bound surface (Fe-NO) is described by an ab initio potential energy surface. The rebinding is found to be nonexponential in time, in agreement with experimental studies, and can be described using two time constants. Depending on the asymptotic energy separation between the manifolds, the short rebinding timescale is between 1 and 9 ps, whereas the longer timescale is about an order of magnitude larger. NO molecules which do not rebind within 1 ns are typically found in the Xenon-4 pocket, indicating the high affinity of NO to this region in the protein.

Howard Barker’s ‘monstrous assaults’: eroticism, death and the antique text

Howard Barker is a writer who has made several notable excursions into what he calls ‘the charnel house…of European drama.’ David Ian Rabey has observed that a compelling property of these classical works lies in what he calls ‘the incompleteness of [their] prescriptions’, and Barker’s Women Beware Women (1986), Seven Lears (1990) and Gertrude: The Cry (2002), are in turn based around the gaps and interstices found in Thomas Middleton’s Women Beware Women (c1627), Shakespeare’s King Lear (c1604) and Hamlet (c1601) respectively. This extends from representing the missing queen from King Lear, who Barker observes, ‘is barely quoted even in the depths of rage or pity’, to his new ending for Middleton’s Jacobean tragedy and the erotic revivification of Hamlet’s mother. This paper will argue that each modern reappropriation accentuates a hidden but powerful feature in these Elizabethan and Jacobean plays – namely their clash between obsessive desire, sexual transgression and death against the imposed restitution of a prescribed morality. This contradiction acts as the basis for Barker’s own explorations of eroticism, death and tragedy. The paper will also discuss Barker’s project for these ‘antique texts’, one that goes beyond what he derisively calls ‘relevance’, but attempts instead to recover ‘smothered genius’, whereby the transgressive is ‘concealed within structures that lend an artificial elegance.’ Together with Barker’s own rediscovery of tragedy, the paper will assert that these rewritings of Elizabethan and Jacobean drama expose their hidden, yet unsettling and provocative ideologies concerning the relationship between political corruption / justice through the power of sexuality (notably through the allure and danger of the mature woman), and an erotics of death that produces tragedy for the contemporary age.

Spectacle and value in classical Hollywood cinema

This is a primarily meta-critical essay and is in direct dialogue with the argument presented in my essay on Gone with the Wind (published in 'Screen'). Here, however, the emphasis is much more on the challenge my definition of spectacle represents for important traditions of film analysis, particularly ‘mise-en-scène criticism’. I argue for the possibility of spectacle to form part of the ‘organic’ whole of a film’s texture and form, while noting the challenge the concept represents (by dint of certain ideological associations and its taint of commercialism) with ‘organicist’ traditions of interpretative film analysis.

Meteorological phenomena in Western classical orchestral music

Depictions of the weather are common throughout the arts. Unlike in the visual arts, however, there has been little study of meteorological inspiration in music. This article catalogues and analyzes the frequencies with which weather is depicted in a sample of classical orchestral music. The depictions vary from explicit mimicry using traditional and specialized orchestral instruments, through to subtle suggestions. It is found that composers are generally influenced by their own environment in the type of weather they choose to represent. As befits the national stereotype, British composers seem disproportionately keen to depict the UK's variable weather patterns and stormy coastline

A simple analysis of thermodynamic properties for classical plasmas: I. theory

By eliminating the short range negative divergence of the Debye–Hückel pair distribution function, but retaining the exponential charge screening known to operate at large interparticle separation, the thermodynamic properties of one-component plasmas of point ions or charged hard spheres can be well represented even in the strong coupling regime. Predicted electrostatic free energies agree within 5% of simulation data for typical Coulomb interactions up to a factor of 10 times the average kinetic energy. Here, this idea is extended to the general case of a uniform ionic mixture, comprising an arbitrary number of components, embedded in a rigid neutralizing background. The new theory is implemented in two ways: (i) by an unambiguous iterative algorithm that requires numerical methods and breaks the symmetry of cross correlation functions; and (ii) by invoking generalized matrix inverses that maintain symmetry and yield completely analytic solutions, but which are not uniquely determined. The extreme computational simplicity of the theory is attractive when considering applications to complex inhomogeneous fluids of charged particles.