Use of a novel Hill-climbing genetic algorithm in protein folding simulations

We have developed a novel Hill-climbing genetic algorithm (GA) for simulation of protein folding. The program (written in C) builds a set of Cartesian points to represent an unfolded polypeptide's backbone. The dihedral angles determining the chain's configuration are stored in an array of chromosome structures that is copied and then mutated. The fitness of the mutated chain's configuration is determined by its radius of gyration. A four-helix bundle was used to optimise simulation conditions, and the program was compared with other, larger, genetic algorithms on a variety of structures. The program ran 50% faster than other GA programs. Overall, tests on 100 non-redundant structures gave comparable results to other genetic algorithms, with the Hill-climbing program running from between 20 and 50% faster. Examples including crambin, cytochrome c, cytochrome B and hemerythrin gave good secondary structure fits with overall alpha carbon atom rms deviations of between 5 and 5.6 Angstrom with an optimised hydrophobic term in the fitness function. (C) 2003 Elsevier Ltd. All rights reserved.

A demonstration of 'broken' visual space

It has long been assumed that there is a distorted mapping between real and ‘perceived’ space, based on demonstrations of systematic errors in judgements of slant, curvature, direction and separation. Here, we have applied a direct test to the notion of a coherent visual space. In an immersive virtual environment, participants judged the relative distance of two squares displayed in separate intervals. On some trials, the virtual scene expanded by a factor of four between intervals although, in line with recent results, participants did not report any noticeable change in the scene. We found that there was no consistent depth ordering of objects that can explain the distance matches participants made in this environment (e.g. A > B > D yet also A < C < D) and hence no single one-to-one mapping between participants’ perceived space and any real 3D environment. Instead, factors that affect pairwise comparisons of distances dictate participants’ performance. These data contradict, more directly than previous experiments, the idea that the visual system builds and uses a coherent 3D internal representation of a scene.

10,000 years in the life of the river Wandle: excavations at the former Vinamul site, Butter Hill, Wallington

Archaeological excavations alongside the river Wandle in Wallington produced evidence of the environmental history and human exploitation of the area. The recovery of a large assemblage of struck flint provided information on the nature of the prehistoric activities represented, while a detailed environmental archaeological programme permitted an examination of both the local sediment successions and thus an opportunity to reconstruct the environmental history of the site. The site revealed a complex sedimentary sequence deposited in riverine conditions, commencing during the early Holocene (from c 10,000 years before present) and continuing through the late Holocene (c last 3000 years). Large flint nodules were washed by the river onto the site where they were procured and worked by Mesolithic and Bronze Age communities. Potentially usable nodules had been tested, and suitable pieces completely reduced, while the majority of useful flakes and blades had been removed for use elsewhere. Small numbers of retouched pieces, such as scrapers and piercers, indicate that domestic activities took place nearby. By the Saxon period the site had begun to stabilise, although it remained marshy and probably peripheral to habitation. Two pits from this period were excavated, one of which contained an antler pick. A small quantity of cereal grain also suggests that cultivated land lay in the vicinity of the site. During the 19th century a mill race was dug across the site, redirecting water from the river Wandle, which resulted in episodic flooding.