Grasping Gap Geometry
    By News Staff | February 1st 2013 11:04 AM | Print | E-mail | Track Comments

    Mathematicians have shown how to use an algorithm for analyzing void space in sphere packing where the spheres need not all be the same size. 

    This method could be applied to analyze the geometry of liquids present between multi-sized spheres that are akin to a model for porous material. This provides a tool for studying the flow of such fluids through porous material. More importantly, it can also be used to study the packing geometry of proteins.

    There have been several previous attempts to calculate the volume and the surface area of packing of spheres. But few methods have taken into account the connectivity of empty space between spheres, which matters, for example, when detecting buried cavities in proteins.

    To remedy this issue, the authors used a program capable of performing a very detailed study of the size distribution of the free volumes of individual spheres—that is, the volume swept by the center of the sphere without overlapping with any of the other spheres—in jammed sphere packing. It also makes it possible to calculate the exact volumes and surface areas of cavities by detecting the disconnected components of cavities. 

    The team applied this method to the analysis of protein structures. This led them to compute various key quantities such as the distribution of sizes of buried cavities and pockets between spheres, the matching of areas accessible to solvent in which protein are found with the corresponding volumes and the composition of residues lining cavities.

    The authors from the Jawaharlal Nehru Centre for Advanced Scientific Research in Bangalore, India, are planning to distribute the algorithm as open source software and so they get some free publicity on Science 2.0

     Published in EPJ E