Rigidity and flexibility of biological networks

The network approach became a widely used tool to understand the behaviour of complex systems in the last decade. We start from a short description of structural rigidity theory. A detailed account on the combinatorial rigidity analysis of protein structures, as well as local flexibility measures of proteins and their applications in explaining allostery and thermostability is given. We also briefly discuss the network aspects of cytoskeletal tensegrity. Finally, we show the importance of the balance between functional flexibility and rigidity in protein-protein interaction, metabolic, gene regulatory and neuronal networks. Our summary raises the possibility that the concepts of flexibility and rigidity can be generalized to all networks.Comment: 21 pages, 4 figures, 1 tabl

Combinatorial Gradient Fields for 2D Images with Empirically Convergent Separatrices

This paper proposes an efficient probabilistic method that computes combinatorial gradient fields for two dimensional image data. In contrast to existing algorithms, this approach yields a geometric Morse-Smale complex that converges almost surely to its continuous counterpart when the image resolution is increased. This approach is motivated using basic ideas from probability theory and builds upon an algorithm from discrete Morse theory with a strong mathematical foundation. While a formal proof is only hinted at, we do provide a thorough numerical evaluation of our method and compare it to established algorithms.Comment: 17 pages, 7 figure

Hierarchical models of rigidity percolation

We introduce models of generic rigidity percolation in two dimensions on hierarchical networks, and solve them exactly by means of a renormalization transformation. We then study how the possibility for the network to self organize in order to avoid stressed bonds may change the phase diagram. In contrast to what happens on random graphs and in some recent numerical studies at zero temperature, we do not find a true intermediate phase separating the usual rigid and floppy ones.Comment: 20 pages, 8 figures. Figures improved, references added, small modifications. Accepted in Phys. Rev.

Dense packing on uniform lattices

We study the Hard Core Model on the graphs ${\rm {\bf \scriptstyle G}}$ obtained from Archimedean tilings i.e. configurations in $\scriptstyle \{0,1\}^{{\rm {\bf G}}}$ with the nearest neighbor 1's forbidden. Our particular aim in choosing these graphs is to obtain insight to the geometry of the densest packings in a uniform discrete set-up. We establish density bounds, optimal configurations reaching them in all cases, and introduce a probabilistic cellular automaton that generates the legal configurations. Its rule involves a parameter which can be naturally characterized as packing pressure. It can have a critical value but from packing point of view just as interesting are the noncritical cases. These phenomena are related to the exponential size of the set of densest packings and more specifically whether these packings are maximally symmetric, simple laminated or essentially random packings.Comment: 18 page