Multiple structural transitions in interacting networks

Many real-world systems can be modeled as interconnected multilayer networks, namely a set of networks interacting with each other. Here we present a perturbative approach to study the properties of a general class of interconnected networks as inter-network interactions are established. We reveal multiple structural transitions for the algebraic connectivity of such systems, between regimes in which each network layer keeps its independent identity or drives diffusive processes over the whole system, thus generalizing previous results reporting a single transition point. Furthermore we show that, at first order in perturbation theory, the growth of the algebraic connectivity of each layer depends only on the degree configuration of the interaction network (projected on the respective Fiedler vector), and not on the actual interaction topology. Our findings can have important implications in the design of robust interconnected networked system, particularly in the presence of network layers whose integrity is more crucial for the functioning of the entire system. We finally show results of perturbation theory applied to the adjacency matrix of the interconnected network, which can be useful to characterize percolation processes on such systems

Evolutionary and molecular foundations of multiple contemporary functions of the nitroreductase superfamily.

Insight regarding how diverse enzymatic functions and reactions have evolved from ancestral scaffolds is fundamental to understanding chemical and evolutionary biology, and for the exploitation of enzymes for biotechnology. We undertook an extensive computational analysis using a unique and comprehensive combination of tools that include large-scale phylogenetic reconstruction to determine the sequence, structural, and functional relationships of the functionally diverse flavin mononucleotide-dependent nitroreductase (NTR) superfamily (>24,000 sequences from all domains of life, 54 structures, and >10 enzymatic functions). Our results suggest an evolutionary model in which contemporary subgroups of the superfamily have diverged in a radial manner from a minimal flavin-binding scaffold. We identified the structural design principle for this divergence: Insertions at key positions in the minimal scaffold that, combined with the fixation of key residues, have led to functional specialization. These results will aid future efforts to delineate the emergence of functional diversity in enzyme superfamilies, provide clues for functional inference for superfamily members of unknown function, and facilitate rational redesign of the NTR scaffold

Griffiths effects of the susceptible-infected-susceptible epidemic model on random power-law networks

We provide numerical evidence for slow dynamics of the susceptible-infected-susceptible model evolving on finite-size random networks with power-law degree distributions. Extensive simulations were done by averaging the activity density over many realizations of networks. We investigated the effects of outliers in both highly fluctuating (natural cutoff) and non-fluctuating (hard cutoff) most connected vertices. Logarithmic and power-law decays in time were found for natural and hard cutoffs, respectively. This happens in extended regions of the control parameter space $\lambda_1<\lambda<\lambda_2$, suggesting Griffiths effects, induced by the topological inhomogeneities. Optimal fluctuation theory considering sample-to-sample fluctuations of the pseudo thresholds is presented to explain the observed slow dynamics. A quasistationary analysis shows that response functions remain bounded at $\lambda_2$. We argue these to be signals of a smeared transition. However, in the thermodynamic limit the Griffiths effects loose their relevancy and have a conventional critical point at $\lambda_c=0$. Since many real networks are composed by heterogeneous and weakly connected modules, the slow dynamics found in our analysis of independent and finite networks can play an important role for the deeper understanding of such systems.Comment: 10 pages, 8 figure

The evolutionary dynamics of the Saccharomyces cerevisiae protein interaction network after duplication

Gene duplication is an important mechanism in the evolution of protein interaction networks. Duplications are followed by the gain and loss of interactions, rewiring the network at some unknown rate. Because rewiring is likely to change the distribution of network motifs within the duplicated interaction set, it should be possible to study network rewiring by tracking the evolution of these motifs. We have developed a mathematical framework that, together with duplication data from comparative genomic and proteomic studies, allows us to infer the connectivity of the preduplication network and the changes in connectivity over time. We focused on the whole-genome duplication (WGD) event in Saccharomyces cerevisiae. The model allowed us to predict the frequency of intergene interaction before WGD and the post duplication probabilities of interaction gain and loss. We find that the predicted frequency of self-interactions in the preduplication network is significantly higher than that observed in today's network. This could suggest a structural difference between the modern and ancestral networks, preferential addition or retention of interactions between ohnologs, or selective pressure to preserve duplicates of self-interacting proteins

Infrastructure transitions toward sustainability: a complex adaptive systems perspective

To ensure infrastructure assets are procured and maintained by government on behalf of citizens, appropriate policy and institutional architecture is needed, particularly if a fundamental shift to more sustainable infrastructure is the goal. The shift in recent years from competitive and resource-intensive procurement to more collaborative and sustainable approaches to infrastructure governance is considered a major transition in infrastructure procurement systems. In order to better understand this transition in infrastructure procurement arrangements, the concept of emergence from Complex Adaptive Systems (CAS) theory is offered as a key construct. Emergence holds that micro interactions can result in emergent macro order. Applying the concept of emergence to infrastructure procurement, this research examines how interaction of agents in individual projects can result in different industry structural characteristics. The paper concludes that CAS theory, and particularly the concept of ‘emergence’, provides a useful construct to understand infrastructure procurement dynamics and progress towards sustainability

Water and molecular chaperones act as weak links of protein folding networks: energy landscape and punctuated equilibrium changes point towards a game theory of proteins

Water molecules and molecular chaperones efficiently help the protein folding process. Here we describe their action in the context of the energy and topological networks of proteins. In energy terms water and chaperones were suggested to decrease the activation energy between various local energy minima smoothing the energy landscape, rescuing misfolded proteins from conformational traps and stabilizing their native structure. In kinetic terms water and chaperones may make the punctuated equilibrium of conformational changes less punctuated and help protein relaxation. Finally, water and chaperones may help the convergence of multiple energy landscapes during protein-macromolecule interactions. We also discuss the possibility of the introduction of protein games to narrow the multitude of the energy landscapes when a protein binds to another macromolecule. Both water and chaperones provide a diffuse set of rapidly fluctuating weak links (low affinity and low probability interactions), which allow the generalization of all these statements to a multitude of networks.Comment: 9 pages, 1 figur

Creativity as Cognitive design \ud The case of mesoscopic variables in Meta-Structures\ud

Creativity is an open problem which has been differently approached by several disciplines since a long time. In this contribution we consider as creative the constructivist design an observer does on the description levels of complex phenomena, such as the self-organized and emergent ones ( e.g., Bènard rollers, Belousov-Zhabotinsky reactions, flocks, swarms, and more radical cognitive and social emergences). We consider this design as related to the Gestaltian creation of a language fit for representing natural processes and the observer in an integrated way. Organised systems, both artificial and most of the natural ones are designed/ modelled according to a logical closed model which masters all the inter-relation between their constitutive elements, and which can be described by an algorithm or a single formal model. We will show there that logical openness and DYSAM (Dynamical Usage of Models) are the proper tools for those phenomena which cannot be described by algorithms or by a single formal model. The strong correlation between emergence and creativity suggests that an open model is the best way to provide a formal definition of creativity. A specific application relates to the possibility to shape the emergence of Collective Behaviours. Different modelling approaches have been introduced, based on symbolic as well as sub-symbolic rules of interaction to simulate collective phenomena by means of computational emergence. Another approach is based on modelling collective phenomena as sequences of Multiple Systems established by percentages of conceptually interchangeable agents taking on the same roles at different times and different roles at the same time. In the Meta-Structures project we propose to use mesoscopic variables as creative design, invention, good continuity and imitation of the description level. In the project we propose to define the coherence of sequences of Multiple Systems by using the values taken on by the dynamic mesoscopic clusters of its constitutive elements, such as the instantaneous number of elements having, in a flock, the same speed, distance from their nearest neighbours, direction and altitude. In Meta-Structures the collective behaviour’s coherence corresponds, for instance, to the scalar values taken by speed, distance, direction and altitude along time, through statistical strategies of interpolation, quasi-periodicity, levels of ergodicity and their reciprocal relationship. In this case the constructivist role of the observer is considered creative as it relates to neither non-linear replication nor transposition of levels of description and models used for artificial systems, like reductionism. Creativity rather lies in inventing new mesoscopic variables able to identify coherent patterns in complex systems. As it is known, mesoscopic variables represent partial macroscopic properties of a system by using some of the microscopic degrees of freedom possessed by composing elements. Such partial usage of microscopic as well as macroscopic properties allows a kind of Gestaltian continuity and imitation between levels of descriptions for mesoscopic modelling. \ud \u