Molecular dynamics simulations of complex systems including HIV-1 protease

Advances in supercomputer architectures have resulted in a situation where many scienti�fic codes are used on systems whose performance characteristics di�ffer considerably from the platform they were developed and optimised for. This is particularly apparent in the realm of Grid computing, where new technologies such as MPIg allow researchers to connect geographically disparate resources together into virtual parallel machines. Finding ways to exploit these new resources efficiently is necessary both to extract the maximum bene�fit from them, and to provide the enticing possibility of enabling new science. In this thesis, an existing general purpose molecular dynamics code (LAMMPS) is extended to allow it to perform more efficiently in a geographically distributed Grid environment showing considerable performance gains as a result. The technique of replica exchange molecular dynamics is discussed along with its applicability to the Grid model and its bene�fits with respect to increasing sampling of configurational space. The dynamics of two sub-structures of the HIV-1 protease (known as the flaps) are investigated using replica exchange molecular dynamics in LAMMPS showing considerable movement that would have been difficult to investigate by traditional methods. To complement this, a study was carried out investigating the use of computational tools to calculate binding affinity between HIV-1 protease mutants and the drug lopinavir in comparison with results derived experimentally by other research groups. The results demonstrate some promise for computational methods in helping to determine the most eff�ective course of treatment for patients in the future

Progress in building an International Lattice Data Grid

We report on progress in setting up the International Lattice Data Grid. We describe the aims and objectives of the ILDG, what has been achieved during its first year of activity and invite feedback from the community.Comment: Lattice2003(activity), 5 pages 2 figures. Edinburgh address correcte

Art and The Ordinary: Literary and Visual Constructs of the Mundane

My research has shown that it is typical of the mundane to be overlooked. The mundane spools out continuously before us unheeded in the form of tasks accomplished almost without our notice. In moment of pause, we look and are overwhelmed with a level of detail and experience which, relieved of the typical haze of inattention, is practically foreign to us. As a student of literature, I’ve discovered the rich exchange between the depiction and the description of mundane objects even though the two are more often treated separately. My observations and arguments below seek to bridge that division by taking an interdisciplinary approach to the aesthetics of the mundane and looking for interconnections, that is by, using each discipline to pry open the other. Inherent within the mundane is the presumption of an object or action free from pretense or affectation – in a word, something genuine. In taking up the subject of the mundane, both writer and visual artist seek to peel back the sociological coating and reveal an instance of raw unmediated human experience - the glistening kernel of the genuine. Pulling on the thread of the genuine woven into the mundane, my thesis describes key points in three literary case studies in which the mundane is used to access the genuine: the use of domestic tasks by Jane Austen to both comment on and locate genuine sensibility; the search for the genuine in poetry located within commonplace objects by Marianne Moore; and lastly Karl Ove Knausgaard’s determined autobiographical record sifting for intrinsic substance seeks the genuine within mundane acts of life

Quenched Light Hadron Spectrum and Decay Constants using Improved Wilson Fermion Actions

We compare results obtained using the Sheikholeslami-Wohlert (SW) fermion action with tree-level and tadpole-improved coefficients for $5.7\le\beta\le 6.2$.Comment: Talk presented at LATTICE96(spectrum), 3 LaTeX pages plus 5 ps figures, espcrc2.sty (included

Spacelike Geodesics and Other Puzzles in the Mixmaster Universe

In this thesis we are going to investigate the behaviour of geodesics in a metric with a singularity known as the ``Mixmaster Universe''. This was motivated from previous work done, where the now well-known AdS/CFT correspondence was used to extract information about an AdS Schwarzschild black hole singularity beyond the horizon by studying correlators on the boundary that correspond to spacelike geodesics which bounce off the singularity. It was then shown that when the singularity was a cosmological one (in this case a Friedmann Robertson Walker cosmology with a Big Crunch), this was no longer possible as it is impossible for spacelike geodesics to bounce off this kind of singularity. This raises the question of whether, when an example of a more general singularity (the ``Mixmaster Universe'') is considered, it is possible for the spacelike geodesics to bounce away from this kind of singularity. This would enable us to potentially extract information about the singularity from the boundary correlators. Unfortunately, it will be shown that bouncing of such geodesics is extremely unlikely (if not impossible) and thus we would be unable to extract information about the singularity in the mixmaster universe using such a technique. We also discuss another aspect of the evolution of the mixmaster universe which shows that it does indeed have a very complicated evolution