Explosive synchronization in weighted complex networks

The emergence of dynamical abrupt transitions in the macroscopic state of a system is currently a subject of the utmost interest. Given a set of phase oscillators networking with a generic wiring of connections and displaying a generic frequency distribution, we show how combining dynamical local information on frequency mismatches and global information on the graph topology suggests a judicious and yet practical weighting procedure which is able to induce and enhance explosive, irreversible, transitions to synchronization. We report extensive numerical and analytical evidence of the validity and scalability of such a procedure for different initial frequency distributions, for both homogeneous and heterogeneous networks, as well as for both linear and non linear weighting functions. We furthermore report on the possibility of parametrically controlling the width and extent of the hysteretic region of coexistence of the unsynchronized and synchronized states

The interplay of university and industry through the FP5 network

To improve the quality of life in a modern society it is essential to reduce the distance between basic research and applications, whose crucial roles in shaping today's society prompt us to seek their understanding. Existing studies on this subject, however, have neglected the network character of the interaction between university and industry. Here we use state-of-the-art network theory methods to analyze this interplay in the so-called Framework Programme--an initiative which sets out the priorities for the European Union's research and technological development. In particular we study in the 5th Framework Programme (FP5) the role played by companies and scientific institutions and how they contribute to enhance the relationship between research and industry. Our approach provides quantitative evidence that while firms are size hierarchically organized, universities and research organizations keep the network from falling into pieces, paving the way for an effective knowledge transfer.Comment: 21 pages (including Appendix), 8 figures. Published online at http://stacks.iop.org/1367-2630/9/18

Synchronization interfaces and overlapping communities in complex networks

We show that a complex network of phase oscillators may display interfaces between domains (clusters) of synchronized oscillations. The emergence and dynamics of these interfaces are studied in the general framework of interacting phase oscillators composed of either dynamical domains (influenced by different forcing processes), or structural domains (modular networks). The obtained results allow to give a functional definition of overlapping structures in modular networks, and suggest a practical method to identify them. As a result, our algorithm could detect information on both single overlapping nodes and overlapping clusters.Comment: 5 pages, 4 figure

Deterministic and stochastic cooperation transitions in evolutionary games on networks

Although the cooperative dynamics emerging from a network of interacting players has been exhaustively investigated, it is not yet fully understood when and how network reciprocity drives cooperation transitions. In this work, we investigate the critical behavior of evolutionary social dilemmas on structured populations by using the framework of master equations and Monte Carlo simulations. The developed theory describes the existence of absorbing, quasi-absorbing, and mixed strategy states and the transition nature, continuous or discontinuous, between the states as the parameters of the system change. In particular, when the decision-making process is deterministic, in the limit of zero effective temperature of the Fermi function, we find that the copying probabilities are discontinuous functions of the system's parameters and of the network degrees sequence. This may induce abrupt changes in the final state for any system size, in excellent agreement with the Monte Carlo simulation results. Our analysis also reveals the existence of continuous and discontinuous phase transitions for large systems as the temperature increases, which is explained in the mean-field approximation. Interestingly, for some game parameters, we find optimal "social temperatures" maximizing/minimizing the cooperation frequency/density.Comment: 14 pages, 5 figure

The Mammalian Cell Cycle Regulates Parvovirus Nuclear Capsid Assembly.

It is unknown whether the mammalian cell cycle could impact the assembly of viruses maturing in the nucleus. We addressed this question using MVM, a reference member of the icosahedral ssDNA nuclear parvoviruses, which requires cell proliferation to infect by mechanisms partly understood. Constitutively expressed MVM capsid subunits (VPs) accumulated in the cytoplasm of mouse and human fibroblasts synchronized at G0, G1, and G1/S transition. Upon arrest release, VPs translocated to the nucleus as cells entered S phase, at efficiencies relying on cell origin and arrest method, and immediately assembled into capsids. In synchronously infected cells, the consecutive virus life cycle steps (gene expression, proteins nuclear translocation, capsid assembly, genome replication and encapsidation) proceeded tightly coupled to cell cycle progression from G0/G1 through S into G2 phase. However, a DNA synthesis stress caused by thymidine irreversibly disrupted virus life cycle, as VPs became increasingly retained in the cytoplasm hours post-stress, forming empty capsids in mouse fibroblasts, thereby impairing encapsidation of the nuclear viral DNA replicative intermediates. Synchronously infected cells subjected to density-arrest signals while traversing early S phase also blocked VPs transport, resulting in a similar misplaced cytoplasmic capsid assembly in mouse fibroblasts. In contrast, thymidine and density arrest signals deregulating virus assembly neither perturbed nuclear translocation of the NS1 protein nor viral genome replication occurring under S/G2 cycle arrest. An underlying mechanism of cell cycle control was identified in the nuclear translocation of phosphorylated VPs trimeric assembly intermediates, which accessed a non-conserved route distinct from the importin α2/β1 and transportin pathways. The exquisite cell cycle-dependence of parvovirus nuclear capsid assembly conforms a novel paradigm of time and functional coupling between cellular and virus life cycles. This junction may determine the characteristic parvovirus tropism for proliferative and cancer cells, and its disturbance could critically contribute to persistence in host tissues

Diverse strategic identities induce dynamical states in evolutionary games

Evolutionary games provide the theoretical backbone for many aspects of our social life: from cooperation to crime, from climate inaction to imperfect vaccination and epidemic spreading, from antibiotics overuse to biodiversity preservation. An important, and so far overlooked, aspect of reality is the diverse strategic identities of individuals. While applying the same strategy to all interaction partners may be an acceptable assumption for simpler forms of life, this fails to account} for the behavior of more complex living beings. For instance, we humans act differently around different people. Here we show that allowing individuals to adopt different strategies with different partners yields a very rich evolutionary dynamics, including time-dependent coexistence of cooperation and defection, system-wide shifts in the dominant strategy, and maturation in individual choices. Our results are robust to variations in network type and size, and strategy updating rules. Accounting for diverse strategic identities thus has far-reaching implications in the mathematical modeling of social games.Comment: 9 pages, 4 figure

Rational Enzyme Engineering Through Biophysical and Biochemical Modeling

Due to its importance in the pharmaceutical industry, ligand dynamic simulations have experienced a great expansion. Using all-atom models and cutting edge hardware, one can perform non-biased ligand migration, active site search and binding studies. In this letter we demonstrate (and validate by PCR mutagenesis) how these techniques, when combined with quantum mechanics, open new possibilities in enzyme engineering. We provide a complete analysis where: 1) biophysical simulations produce ligand diffusion and, 2) biochemical modeling samples the chemical event. Using such broad analysis we engineer a highly stable peroxidase activating the enzyme for new substrate oxidation after rational mutation of two non-conserved surface residues. In particular, we create a new surface-binding site, quantitatively predicting the in vitro change in oxidation rate obtained by mutagenic PCR and achieving a comparable specificity constant to active peroxidases.This work was supported by the INDOX (KBBE-2013-7-613549 to ATM) European project, and the CTQ2013-48287 (to VG) and BIO2014-56388-R (to FJR-D) projects of the Spanish Ministry of Economy and Competitiveness (MINECO). FJR-D acknowledges a MINECO Ramón&Cajal contract.Peer ReviewedPostprint (author's final draft