Background: It was shown recently that an anomaly in the elastic scattering of 16O on 12C at around 300 MeV is resolved by including within the scattering model the inelastic excitation of specific collective excitations of both nuclei, leading to a secondary rainbow. There is very little systematic knowledge concerning the contribution of collective excitations to the interaction between nucle...

The way knowledge is represented influences the effectiveness with which that knowledge can be shared and reconstructed. Of particular interest to this study is the hypertext knowledge representation. Based on the schema theory, we propose a model explaining the effect of the hypertext knowledge representation on the user’s problem solving performance. The sophistication of the knowledge struct...

Normal mode analysis (NMA) in internal (dihedral) coordinates naturally reproduces the collective functional motions of biological macromolecules. iMODS facilitates the exploration of such modes and generates feasible transition pathways between two homologous structures, even with large macromolecules. The distinctive internal coordinate formulation improves the efficiency of NMA and extends i...

The representation of protein flexibility is still a challenge for the state-of-the-art flexible ligand docking protocols. In this article, we use a large and diverse benchmark to prove that is possible to improve consistently the cross-docking performance against a single receptor conformation, using an equilibrium ensemble of binding site conformers. The benchmark contained 28 proteins, and o...

This paper presents a representation for natural language plurals in knowledge base queries, implementing collective, distributive, cumulative, and multiply distributive senses of the plural by means of higher predicates. The underlying semantics is based on Franconi’s theory of collections. The collective reading of a plural applies the predicate to the whole collection; the distributive readi...

Voters from m disjoint constituencies (regions, federal states, etc.) are indirectly represented in an assembly which applies a weighted voting rule. All agents have single-peaked preferences over an interval and each delegate’s preferences match the constituency’s median voter. The collective decision corresponds to the assembly’s Condorcet winner. Which voting weights w1, . . . ,wm ought to b...

Some types of animals exploit the external environment to support their cognitive processes, in the sense of patterns created in the environment that function as external mental states and serve as an extension to their mind. In the case of social animals the creation and exploitation of such patterns can be shared, thus obtaining a form of shared mind or collective intelligence. This paper exp...

Copyright and Moral Rights for the articles on this site are retained by the individual authors and/or other copyright owners. For more information on Open Research Online's data policy on reuse of materials please consult the policies page. Background: It was shown recently that an anomaly in the elastic scattering of 16 O on 12 C at around 300 MeV is resolved by including within the scatterin...

Normal mode analysis (NMA) is an efficient way to study collective motions in biomolecules that bypasses the computational costs and many limitations associated with full dynamics simulations. The NOMAD-Ref web server presented here provides tools for online calculation of the normal modes of large molecules (up to 100,000 atoms) maintaining a full all-atom representation of their structures, a...

The increasing amount of online information demands effective, scalable, and accurate mechanisms to manage and search this information. Distributed semantic-enabled architectures, which enforce semantic web technologies for resource discovery, could satisfy these requirements. In this paper, a semanticdriven adaptive architecture is presented, which improves existing resource discovery processe...