RIBFIND: a web server for identifying rigid bodies in protein structures and to aid flexible fitting into cryo EM maps

Motivation: To better analyze low-resolution cryo electron microscopy maps of macromolecular assemblies, component atomic structures frequently have to be flexibly fitted into them. Reaching an optimal fit and preventing the fitting process from getting trapped in local minima can be significantly improved by identifying appropriate rigid bodies in the fitted component. Results: Here we present the RIBFIND server, a tool for identifying rigid bodies in protein structures. The server identifies rigid bodies in proteins by calculating spatial proximity between their secondary structural elements. Availability: The RIBFIND web server and its standalone program are available at http://ribfind.ismb.lon.ac.uk

Advances in chiral lasers and transformation theory

The first part of the presented thesis begins by developing the lasing mode theory of a structurally chiral laser and highlighting the possibilities for a structurally chiral laser to lase both left and right circularly polarised light, as well as within the photonic bandgap. The discoveries are utilised in order to develop the lasing mode theory of a chiral distributed Bragg reflector laser, which consists of structurally chiral mirrors and a uniform lasing cavity, as well as of a hybrid chiral laser, which consists of structurally chiral mirrors with a contrahanded structurally chiral lasing cavity. Applications towards more efficient 3D projectors as well as 3D displays are discussed. The second part of the thesis develops the theory of transformation optics from first principles using differential geometry. The rigorously constructed structure is manipulated in order to examine the effects of a transformation on the refractive index. The analysis reveals the existence of a refractive index ellipsoid, which encodes the complete transformation and can be used to intuitively grasp the effects of any given transformation on light rays travelling inside the transformation optics device. The refractive index ellipse is calculated for the well known cylindrical cloak as well as for a new type of twist deformation, providing insights into the inner workings of these devices.Open Acces

Examining Success at the Domestic Box-Office in the Motion Picture Industry

The movie business is a multi-billion dollar industry involving production crews, marketing crews, actors, directors, distribution companies, movie theaters, and movie rental companies, but while each movie created follows the same routine, why do some perform so much better than others at the box-office? Why did Juno become a smash hit, while Poseidon is regarded as a major box-office bomb? This study investigates the impact of production cost, star power, professional reviews, release date, sequels, genre, age-rating, and distribution company on total domestic box-office revenue of the widely released films from January 2006 to December 2008

Examining Success in the Motion Picture Industry

This paper focuses on the effects of several variables on the domestic box-office demand for the 189 widely-released movies of 2007. I will examine if there are factors that ultimately lead to movie success at the box-office or if there are factors that are believed to be important, but in all actuality have very little impact on revenues. Box-office receipts, however, are not the ultimate determinant of success in the industry. Some companies may use theaters as extended advertising medias and capitalize on the relatively cheap cost of producing DVDs and digital copies of films, but success typically has to occur in the theaters in order for other forms of the film to sell. Nevertheless, examining box-office revenue is the best way to determine the success of a film at this time because the information is readily available and movie theaters are still accepted as the major source of revenue for a particular movie

Augustin Daly; Certain Writings on His Life and Livelihood

The American theatre of the early nineteenth century was strongly dependent upon the European theatre. American theatre goers looked across the ocean to import talent, playwrights, plays, and actors. Not until mid-century did America begin to develop its wold-wide theatre influence. Specifically, the latter half of the nineteenth century yielded one of the most influential director/playwrights of the American theatre until that time. Modern American drama begins with Augustin Daly (Quinn 1). John Augustin Daly, the son of an American sea captain and a British Lieutenant\u27s daughter, was born on the seventh of July, 1838 in Plymouth, North Carolina (Johnson 8). His father died soon after his birth, so his mother moved to New York City where Daly developed his strict Catholic faith, a loyalty he maintained until his death in 1899 (Winter, Vagrant Memories 246). From the outset, the young Daly had a passion for the theatre; but not as an actor but as a new creative force, the director. Judge Joseph Daly, Augustin\u27s older brother, attributes (at least partially) his desire for directing to Daly\u27s disheartening first acting experience

Mitochondrial DNA diversity and origin of human communities from 4th- 11th century Britain.

Neither the archaeological nor the historical data have yet allowed a full understanding of the nature of the Germanic settlement in England. Analysis of the genetic structure of past history has mostly been carried out by inference from extant populations. However, genetic flow through migration over time is likely to have altered the genetic composition of modem samples. Analysis of the genetic composition of ancient populations (provided the authenticity of their DNA is obtained) gives a direct sight into the past. Thus, mitochondrial DNA from pre-Saxon (4th century), early Saxon (5th -7th century) and late Saxon (9th – 11th century) settlements has been analysed to obtain a better understanding of the population history of Britain. A methodology has been optimised, by which, ancient DNA from 1,000-1,800 year old archaeological material was extracted and ~200-bp fragments of the HVS-1, amplified and sequenced. Rigorous controls for work in human ancient DNA were undertaken to prevent and recognise contamination. Established authenticity criteria were followed, including expected ancient DNA behaviour, internal replication of sequences and confirmation by independent labs. The sample size obtained has enabled a population-level study of communities of ancient Britain. In addition, an extensive database of >6500 mitochondrial DNA sequences was compiled for comparisons. Several estimates of haplotype and nucleotide genetic diversity were computed for modem and ancient populations. Counter-intuitively, the modem population of England, encompassing all successive waves of migration to the island, has a lower diversity than the ancient population, suggesting that diversity has been lost over the last millennium. In addition, mtDNA genetic continuity between ancient and modem England seems to have been intermpted. Founder analyses of early (5th -7th century) and late (9th -11th century) periods indicate that, whereas the late period seems to have had Viking genetic influences, the early period has no close relationship with Germanic populations. Instead, the females of the early Anglo-Saxon period seem to represent the native British population. The female contribution of the Anglo-Saxon invasion would have therefore been minor, at least at that time and at these sites. The close genetic affinity between the ancient British population and the northern most populations of Europe suggests they might have shared a common past during pre-history. It is proposed that, after post-glacial times, inhabitants of areas now submerged expanded to northern territories. The early settlements analysed reflect that very early expansion. Some time since then, reduction in diversity seem to have occurred (possibly due to variation in family size after repeated epidemics) leading to the present day mtDNA composition of England

Foundation and Revolution: Hannah Arendt and the Problem of Legitimacy and Stability in Constitutional Consolidation

This chapter investigates the relations of revolutionary consolidation to the American constitutional founding. The concepts of consolidation and augmenta- tion have received little attention in relation to the central question of constitutional legitimacy. Hannah Arendt’s theory of revolution is paradigmatic in this respect. Notwithstanding her influential discussion of foundation, Arendt gives relatively little attention to the pragmatic role of consolidation in acts of constitutional founding. Further, scholarly analyses of Arendt on revolution rarely offer critiques of her concept of foundation in this respect. I focus on Arendt partly owing to her influential theories regarding founding of bodies politic and partly because I believe that within her political thought on what for her was the uniquely success- ful consolidation of the American Revolution lies an explanation for that success that she herself does not expressly offer. Further, Arendt’s thinking may be a useful launchpad in considering the dynamics of founding moments