A novel measure to analyze protein structures: Aspect ratio in protein alpha shapes.

Proteins' three-dimensional (3D) structures are analyzed traditionally using geometric descriptors such as torsional angles and inter-atomic distances. In this study a measure that is borrowed from computational geometry, aspect ratio of each tetrahedron in alpha shapes of proteins, is utilized. This geometric descriptor differentiates alpha and beta structural classes of proteins when combined with principal components analysis.

Reaction dynamics through kinetic transition states.

The transformation of a system from one state to another is often mediated by a bottleneck in the system's phase space. In chemistry, these bottlenecks are known as transition states through which the system has to pass in order to evolve from reactants to products. The chemical reactions are usually associated with configurational changes where the reactants and products states correspond, e.