Control of complex networks requires both structure and dynamics

The study of network structure has uncovered signatures of the organization of complex systems. However, there is also a need to understand how to control them; for example, identifying strategies to revert a diseased cell to a healthy state, or a mature cell to a pluripotent state. Two recent methodologies suggest that the controllability of complex systems can be predicted solely from the graph of interactions between variables, without considering their dynamics: structural controllability and minimum dominating sets. We demonstrate that such structure-only methods fail to characterize controllability when dynamics are introduced. We study Boolean network ensembles of network motifs as well as three models of biochemical regulation: the segment polarity network in Drosophila melanogaster, the cell cycle of budding yeast Saccharomyces cerevisiae, and the floral organ arrangement in Arabidopsis thaliana. We demonstrate that structure-only methods both undershoot and overshoot the number and which sets of critical variables best control the dynamics of these models, highlighting the importance of the actual system dynamics in determining control. Our analysis further shows that the logic of automata transition functions, namely how canalizing they are, plays an important role in the extent to which structure predicts dynamics.Comment: 15 pages, 6 figure

Geometry and beta-functions for N=2 matter models in two dimensions

We study renormalizable nonlinear sigma-models in two dimensions with N=2 supersymmetry described in superspace in terms of chiral and complex linear superfields. The geometrical structure of the underlying manifold is investigated and the one-loop divergent contribution to the effective action is computed. The condition of vanishing beta-function allows to identify a class of models which satisfy this requirement and possess N=4 supersymmetry.Comment: latex file, 20 pages, no figure

Towards a Unified Theory of Massless Superfields of All Superspins

We describe the ``universal'' action for massless superfields of all superspins in N = 1, D = 4 anti-de Sitter superspace as a gauge theory of unconstrained superfields taking their values in the commutative algebra of analytic functions over a one-sheeted hyperboloid in $R^{3,1}$. The action is invariant under N = 2 supersymmetry transformations which form a closed algebra off the mass-shell.Comment: 12 pages, LaTe

Modularity and the spread of perturbations in complex dynamical systems

We propose a method to decompose dynamical systems based on the idea that modules constrain the spread of perturbations. We find partitions of system variables that maximize 'perturbation modularity', defined as the autocovariance of coarse-grained perturbed trajectories. The measure effectively separates the fast intramodular from the slow intermodular dynamics of perturbation spreading (in this respect, it is a generalization of the 'Markov stability' method of network community detection). Our approach captures variation of modular organization across different system states, time scales, and in response to different kinds of perturbations: aspects of modularity which are all relevant to real-world dynamical systems. It offers a principled alternative to detecting communities in networks of statistical dependencies between system variables (e.g., 'relevance networks' or 'functional networks'). Using coupled logistic maps, we demonstrate that the method uncovers hierarchical modular organization planted in a system's coupling matrix. Additionally, in homogeneously-coupled map lattices, it identifies the presence of self-organized modularity that depends on the initial state, dynamical parameters, and type of perturbations. Our approach offers a powerful tool for exploring the modular organization of complex dynamical systems

Dialing in single-site reactivity of a supported calixarene-protected tetrairidium cluster catalyst.

A closed Ir4 carbonyl cluster, 1, comprising a tetrahedral metal frame and three sterically bulky tert-butyl-calix[4]arene(OPr)3(OCH2PPh2) (Ph = phenyl; Pr = propyl) ligands at the basal plane, was characterized with variable-temperature 13C NMR spectroscopy, which show the absence of scrambling of the CO ligands at temperatures up to 313 K. This demonstration of distinct sites for the CO ligands was found to extend to the reactivity and catalytic properties, as shown by selective decarbonylation in a reaction with trimethylamine N-oxide (TMAO) as an oxidant, which, reacting in the presence of ethylene, leads to the selective bonding of an ethyl ligand at the apical Ir site. These clusters were supported intact on porous silica and found to catalyze ethylene hydrogenation, and a comparison of the kinetics of the single-hydrogenation reaction and steady-state hydrogenation catalysis demonstrates a unique single-site catalyst-with each site having the same catalytic activity. Reaction orders in the catalytic ethylene hydrogenation reaction of approximately 1/2 and 0 for H2 and C2H4, respectively, nearly match those for conventional noble-metal catalysts. In contrast to oxidative decarbonylation, thermal desorption of CO from silica-supported cluster 1 occurred exclusively at the basal plane, giving rise to sites that do not react with ethylene and are catalytically inactive for ethylene hydrogenation. The evidence of distinctive sites on the cluster catalyst leads to a model that links to hydrogen-transfer catalysis on metals-involving some surface sites that bond to both hydrocarbon and hydrogen and are catalytically engaged (so-called "*" sites) and others, at the basal plane, which bond hydrogen and CO but not hydrocarbon and are reservoir sites (so-called "S" sites)

Element-centric clustering comparison unifies overlaps and hierarchy

Clustering is one of the most universal approaches for understanding complex data. A pivotal aspect of clustering analysis is quantitatively comparing clusterings; clustering comparison is the basis for many tasks such as clustering evaluation, consensus clustering, and tracking the temporal evolution of clusters. In particular, the extrinsic evaluation of clustering methods requires comparing the uncovered clusterings to planted clusterings or known metadata. Yet, as we demonstrate, existing clustering comparison measures have critical biases which undermine their usefulness, and no measure accommodates both overlapping and hierarchical clusterings. Here we unify the comparison of disjoint, overlapping, and hierarchically structured clusterings by proposing a new element-centric framework: elements are compared based on the relationships induced by the cluster structure, as opposed to the traditional cluster-centric philosophy. We demonstrate that, in contrast to standard clustering similarity measures, our framework does not suffer from critical biases and naturally provides unique insights into how the clusterings differ. We illustrate the strengths of our framework by revealing new insights into the organization of clusters in two applications: the improved classification of schizophrenia based on the overlapping and hierarchical community structure of fMRI brain networks, and the disentanglement of various social homophily factors in Facebook social networks. The universality of clustering suggests far-reaching impact of our framework throughout all areas of science

Zero Modes of Fermions Trapped by Giant Vortices

Zero-energy solutions of the Dirac equation for the fermions bound to giant vortices of large winding number $n$ are studied in the abelian Higgs and Chern-Simons Higgs models. The case of Jackiw-Rossi theory of the Majorana states in topological superconductors is discussed in detail. By expanding in inverse powers of $n$ we find an analytic result for asymptotically all $n$ solutions required by the index theorem. In the abelian Higgs model the zero modes fill the vortex core and reveal a universal structure independent of fine details of the gauge and scalar field interactions which, in particular, determines the general properties of the large-$n$ superconducting cosmic strings. On the contrary, for the Chern-Simons Higgs vortices the zero modes are localized on the core boundary and the explicit solution is obtained for the supersymmetric couplings in a self-dual background.Comment: 15 pages, 2 figure

The tensor Goldstone multiplet for partially broken supersymmetry

We show that the tensor gauge multiplet of N=1 supersymmetry can serve as the Goldstone multiplet for partially broken rigid N=2 supersymmetry. We exploit a remarkable analogy with the Goldstone-Maxwell multiplet of hep-th/9608177 to find its nonlinear transformation law and its invariant Goldstone action. We demonstrate that the tensor multiplet has two dualities. The first transforms it into the chiral Goldstone multiplet; the other leaves it invariant.Comment: 7 pages, Latex. Expanded discussion of duality symmetrie

A note on N=(2,2) superfields in two dimensions

Motivated by the results in {\tt hep-th/0508228}, we perform a careful analysis of the allowed linear constraints on $N=(2,2)$ scalar superfields. We show that only chiral, twisted-chiral and semi-chiral superfields are possible. Various subtleties are discussed.Comment: 11 pages, LaTeX2