Controllability of protein-protein interaction phosphorylation-based networks: Participation of the hub 14-3-3 protein family

Posttranslational regulation of protein function is an ubiquitous mechanism in eukaryotic cells. Here, we analyzed biological properties of nodes and edges of a human protein-protein interaction phosphorylation-based network, especially of those nodes critical for the network controllability. We found that the minimal number of critical nodes needed to control the whole network is 29%, which is considerably lower compared to other real networks. These critical nodes are more regulated by posttranslational modifications and contain more binding domains to these modifications than other kinds of nodes in the network, suggesting an intra-group fast regulation. Also, when we analyzed the edges characteristics that connect critical and non-critical nodes, we found that the former are enriched in domain-to-eukaryotic linear motif interactions, whereas the later are enriched in domain-domain interactions. Our findings suggest a possible structure for protein-protein interaction networks with a densely interconnected and self-regulated central core, composed of critical nodes with a high participation in the controllability of the full network, and less regulated peripheral nodes. Our study offers a deeper understanding of complex network control and bridges the controllability theorems for complex networks and biological protein-protein interaction phosphorylation-based networked systems.Fil: Uhart, Marina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto de Histología y Embriología de Mendoza Dr. Mario H. Burgos. Universidad Nacional de Cuyo. Facultad de Cienicas Médicas. Instituto de Histología y Embriología de Mendoza Dr. Mario H. Burgos; ArgentinaFil: Flores, Gabriel. Eventioz/eventbrite Company; ArgentinaFil: Bustos, Diego Martin. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto de Histología y Embriología de Mendoza Dr. Mario H. Burgos. Universidad Nacional de Cuyo. Facultad de Cienicas Médicas. Instituto de Histología y Embriología de Mendoza Dr. Mario H. Burgos; Argentin

Control efficacy of complex networks

Acknowledgements W.-X.W. was supported by CNNSF under Grant No. 61573064, and No. 61074116 the Fundamental Research Funds for the Central Universities and Beijing Nova Programme, China. Y.-C.L. was supported by ARO under Grant W911NF-14-1-0504.Peer reviewedPublisher PD

The web of federal crimes in Brazil: topology, weaknesses, and control

Law enforcement and intelligence agencies worldwide struggle to find effective ways to fight and control organized crime. However, illegal networks operate outside the law and much of the data collected is classified. Therefore, little is known about criminal networks structure, topological weaknesses, and control. In this contribution we present a unique criminal network of federal crimes in Brazil. We study its structure, its response to different attack strategies, and its controllability. Surprisingly, the network composed of multiple crimes of federal jurisdiction has a giant component, enclosing more than a half of all its edges. This component shows some typical social network characteristics, such as small-worldness and high clustering coefficient, however it is much "darker" than common social networks, having low levels of edge density and network efficiency. On the other side, it has a very high modularity value, $Q=0.96$. Comparing multiple attack strategies, we show that it is possible to disrupt the giant component of the network by removing only $2\%$ of its edges or nodes, according to a module-based prescription, precisely due to its high modularity. Finally, we show that the component is controllable, in the sense of the exact network control theory, by getting access to $20\%$ of the driver nodes.Comment: 9 pages, 5 figure

Efficiently Controllable Graphs

We investigate graphs that can be disconnected into small components by removing a vanishingly small fraction of their vertices. We show that when a quantum network is described by such a graph, the network is efficiently controllable, in the sense that universal quantum computation can be performed using a control sequence polynomial in the size of the network while controlling a vanishingly small fraction of subsystems. We show that networks corresponding to finite-dimensional lattices are efficently controllable, and explore generalizations to percolation clusters and random graphs. We show that the classical computational complexity of estimating the ground state of Hamiltonians described by controllable graphs is polynomial in the number of subsystems/qubits

Optimization of synchronizability in multiplex networks by rewiring one layer

Peer reviewedPublisher PD

Controlling edge dynamics in complex networks

The interaction of distinct units in physical, social, biological and technological systems naturally gives rise to complex network structures. Networks have constantly been in the focus of research for the last decade, with considerable advances in the description of their structural and dynamical properties. However, much less effort has been devoted to studying the controllability of the dynamics taking place on them. Here we introduce and evaluate a dynamical process defined on the edges of a network, and demonstrate that the controllability properties of this process significantly differ from simple nodal dynamics. Evaluation of real-world networks indicates that most of them are more controllable than their randomized counterparts. We also find that transcriptional regulatory networks are particularly easy to control. Analytic calculations show that networks with scale-free degree distributions have better controllability properties than uncorrelated networks, and positively correlated in- and out-degrees enhance the controllability of the proposed dynamics.Comment: Preprint. 24 pages, 4 figures, 2 tables. Source code available at http://github.com/ntamas/netctr