Network characterization of packing architecture for condensed matter systems

Official URL: http://192.168.1.20/record=b1306370 (Table of Contents)

Networks have currently been used to model real life complex systems and they have provided additional understanding for characterizing structure-functiondynamics relationships of these complex architectures. Here we investigate statistical and spectral properties and the connections between local motifs and global behavior of networks that are formed from condensed matter systems, particularly proteins, as well as micelles, polymeric melts and Lennard-Jones clusters. Proteins are considered as interacting residue networks. Pathways for information transfer manifested in the average path lengths are analyzed, where the energy of residue-residue interactions are imposed as edge weights in networks. Systematic removal of ''low energy'' interactions reveals that the network contains significant number of redundancies that provide high local clustering. The information transfer is achieved by a small number of highly clustered groups of residues, which makes the hub architecture different from that of scale-free networks. This result is then extended to protein complexes, where two proteins (ligand and receptor) interact, in order to identify essential pair-wise interactions between two proteins. In the presence of local clustering, establishing a relationship between local structure and global properties is far from trivial. But for certain cases, applying a bottom-up approach, a relation between nearest neighbors and next-to-nearest neighbors is obtained and this relation is observed in different networks formed from condensed matter systems, as well as perfect lattice models. To further investigate the association between local order and global structure, residue networks are considered in further detail. To outline local order, we compared residue networks to perfect lattice systems by creating self-avoiding chains on chains via Metropolis Monte Carlo method that capture three dimensional structure of protein chains as much as possible. Results show that, proteins conform to close packed ordered structures with significant voids irrespective of the underlying lattice bases. Finally, we analyzed the spectral properties of networks used throughout the thesis. Spectral changes while breaking and rewiring the edges revealed the importance and roles of short and long-ranged contacts in determining the network structure. Comparison of spectra distributions of different networks constructed from condensed matter systems supported the result from statistical parameters that these systems have structural similarities.