The adsorption of three- and four-atom Ag and Pd clusters on the alpha-Al(2)O(3) (0001) surface is explored with density functional theory. Within each adsorbed cluster, two different cluster-surface interactions are present. We find that clusters simultaneously form both ionic bonds with surface oxygen and intermetallic bonds with surface aluminum. The simultaneous formation of disparate elect...

The paper proposes an approach where structural systems can be developed according to the mathematical theory of fractals. Architecture can take advantage of the complexity sciences, by the use of present day computer technology, where algorithms of mathematical and geometric functions can produce new motifs of design. In order to demonstrate this, examples of the use of the elliptic and hyperb...

Determining the function of all proteins is a recurring theme in modern biology and medicine, but the sheer number of proteins makes experimental approaches impractical. For this reason, current efforts have considered in silico function prediction in order to guide and accelerate the function determination process. One approach to predicting protein function is to search functionally uncharact...

Motif discovery is a general and important problem in bioinformatics, as motifs often are used to infer biologically important sites in bio-molecular sequences. Many problems in bioinformatics are naturally cast in terms of sequences, and distance measures for sequences derived from edit distance is fundamental in bioinformatics. Geometric Crossover is a representation-independent definition of...

Motif discovery is a general and important problem in bioinformatics, as motifs often are used to infer biologically important sites in bio-molecular sequences. Many problems in bioinformatics are naturally cast in terms of sequences, and distance measures for sequences derived from edit distance is fundamental in bioinformatics. Geometric Crossover is a representation-independent definition of...

Thus far, conventional biophysical techniques, such as NMR spectroscopy or X-ray crystallography, allow the determination, at atomic resolution, of only structural domains of large RNA molecules such as group I introns. Determination of their overall spatial organization thus still relies on modeling. This requires that a relatively high number of tertiary interactions are defined in order to g...

Clotting blood contains fibrin-bound thrombin, which is a major source of procoagulant activity leading to clot extension and further activation of coagulation. When bound to fibrin, thrombin is protected from inhibition by antithrombin (AT) + heparin but is neutralized when AT and heparin are covalently linked (ATH). Here, we report the surprising observation that, rather than yielding an iner...

We consider mechanical stability of dimeric and monomeric proteins with the cystine knot motif. A structure based dynamical model is used to demonstrate that all dimeric and some monomeric proteins of this kind should have considerable resistance to stretching that is significantly larger than that of titin. The mechanisms of the large mechanostability are elucidated. In most cases, it originat...

There is an increasing number of proteins with known structure but unknown function. Determining their function would have a significant impact on understanding diseases and designing new therapeutics. However, experimental protein function determination is expensive and very time-consuming. Computational methods can facilitate function determination by identifying proteins that have high struc...