Bond percolation in coloured and multiplex networks

The dynamic nature of percolation on networks with triadic interactions

Percolation establishes the connectivity of complex networks and is one of the most fundamental critical phenomena for the study of complex systems. On simple networks, percolation displays a second-order phase transition; on multiplex networks, the percolation transition can become discontinuous. However, little is known about percolation in networks with higher-order interactions. Here, we show that percolation can be turned into a fully fledged dynamical process when higher-order interactions are taken into account. By introducing signed triadic interactions, in which a node can regulate the interactions between two other nodes, we define triadic percolation. We uncover that in this paradigmatic model the connectivity of the network changes in time and that the order parameter undergoes a period doubling and a route to chaos. We provide a general theory for triadic percolation which accurately predicts the full phase diagram on random graphs as confirmed by extensive numerical simulations. We find that triadic percolation on real network topologies reveals a similar phenomenology. These results radically change our understanding of percolation and may be used to study complex systems in which the functional connectivity is changing in time dynamically and in a non-trivial way, such as in neural and climate networks.

Computational prediction of the molecular configuration of three-dimensional network polymers

The three-dimensional arrangement of natural and synthetic network materials determines their application range. Control over the real-time incorporation of each building block and functional group is desired to regulate the macroscopic properties of the material from the molecular level onwards. Here we report an approach combining kinetic Monte Carlo and molecular dynamics simulations that chemically and physically predicts the interactions between building blocks in time and in space for the entire formation process of three-dimensional networks. This framework takes into account variations in inter- and intramolecular chemical reactivity, diffusivity, segmental compositions, branch/network point locations and defects. From the kinetic and three-dimensional structural information gathered, we construct structure-property relationships based on molecular descriptors such as pore size or dangling chain distribution and differentiate ideal from non-ideal structural elements. We validate such relationships by synthesizing organosilica, epoxy-amine and Diels-Alder networks with tailored properties and functions, further demonstrating the broad applicability of the platform.

The Radically Embodied Conscious Cybernetic Bayesian Brain: From Free Energy to Free Will and Back Again

Drawing from both enactivist and cognitivist perspectives on mind, I propose that explaining teleological phenomena may require reappraising both "Cartesian theaters" and mental homunculi in terms of embodied self-models (ESMs), understood as body maps with agentic properties, functioning as predictive-memory systems and cybernetic controllers. Quasi-homuncular ESMs are suggested to constitute a major organizing principle for neural architectures due to their initial and ongoing significance for solutions to inference problems in cognitive (and affective) development. Embodied experiences provide foundational lessons in learning curriculums in which agents explore increasingly challenging problem spaces, so answering an unresolved question in Bayesian cognitive science: what are biologically plausible mechanisms for equipping learners with sufficiently powerful inductive biases to adequately constrain inference spaces? Drawing on models from neurophysiology, psychology, and developmental robotics, I describe how embodiment provides fundamental sources of empirical priors (as reliably learnable posterior expectations). If ESMs play this kind of foundational role in cognitive development, then bidirectional linkages will be found between all sensory modalities and frontal-parietal control hierarchies, so infusing all senses with somatic-motoric properties, thereby structuring all perception by relevant affordances, so solving frame problems for embodied agents. Drawing upon the Free Energy Principle and Active Inference framework, I describe a particular mechanism for intentional action selection via consciously imagined (and explicitly represented) goal realization, where contrasts between desired and present states influence ongoing policy selection via predictive coding mechanisms and backward-chained imaginings (as self-realizing predictions). This embodied developmental legacy suggests a mechanism by which imaginings can be intentionally shaped by (internalized) partially-expressed motor acts, so providing means of agentic control for attention, working memory, imagination, and behavior. I further describe the nature(s) of mental causation and self-control, and also provide an account of readiness potentials in Libet paradigms wherein conscious intentions shape causal streams leading to enaction. Finally, I provide neurophenomenological handlings of prototypical qualia including pleasure, pain, and desire in terms of self-annihilating free energy gradients via quasi-synesthetic interoceptive active inference. In brief, this manuscript is intended to illustrate how radically embodied minds may create foundations for intelligence (as capacity for learning and inference), consciousness (as somatically-grounded self-world modeling), and will (as deployment of predictive models for enacting valued goals).

Learning heterogenous reaction rates from stochastic simulations

Reaction rate equations are ordinary differential equations that are frequently used to describe deterministic chemical kinetics at the macroscopic scale. At the microscopic scale, the chemical kinetics is stochastic and can be captured by complex dynamical systems reproducing spatial movements of molecules and their collisions. Such molecular dynamics systems may implicitly capture intricate phenomena that affect reaction rates but are not accounted for in the macroscopic models. In this work we present a data assimilation procedure for learning nonhomogeneous kinetic parameters from molecular simulations with many simultaneously reacting species. The learned parameters can then be plugged into the deterministic reaction rate equations to predict long time evolution of the macroscopic system. In this way, our procedure discovers an effective differential equation for reaction kinetics. To demonstrate the procedure, we upscale the kinetics of a molecular system that forms a complex covalently bonded network severely interfering with the reaction rates. Incidentally, we report that the kinetic parameters of this system feature peculiar time and temperature dependences, whereas the probability of a network strand to close a cycle follows a universal distribution.

Generative Algorithm for Molecular Graphs Uncovers Products of Oil Oxidation

The autoxidation of triglyceride (or triacylglycerol, TAG) is a poorly understood complex system. It is known from mass spectrometry measurements that, although initiated by a single molecule, this system involves an abundance of intermediate species and a complex network of reactions. For this reason, the attribution of the mass peaks to exact molecular structures is difficult without additional information about the system. We provide such information using a graph theory-based algorithm. Our algorithm performs an automatic discovery of the chemical reaction network that is responsible for the complexity of the mass spectra in drying oils. This knowledge is then applied to match experimentally measured mass spectra with computationally predicted molecular graphs. We demonstrate this methodology on the autoxidation of triolein as measured by electrospray ionization-mass spectrometry (ESI-MS). Our protocol can be readily applied to investigate other oils and their mixtures.

Robustness and lethality in multilayer biological molecular networks

Robustness is a prominent feature of most biological systems. Most previous related studies have been focused on homogeneous molecular networks. Here we propose a comprehensive framework for understanding how the interactions between genes, proteins and metabolites contribute to the determinants of robustness in a heterogeneous biological network. We integrate heterogeneous sources of data to construct a multilayer interaction network composed of a gene regulatory layer, a protein-protein interaction layer, and a metabolic layer. We design a simulated perturbation process to characterize the contribution of each gene to the overall system's robustness, and find that influential genes are enriched in essential and cancer genes. We show that the proposed mechanism predicts a higher vulnerability of the metabolic layer to perturbations applied to genes associated with metabolic diseases. Furthermore, we find that the real network is comparably or more robust than expected in multiple random realizations. Finally, we analytically derive the expected robustness of multilayer biological networks starting from the degree distributions within and between layers. These results provide insights into the non-trivial dynamics occurring in the cell after a genetic perturbation is applied, confirming the importance of including the coupling between different layers of interaction in models of complex biological systems.

Coloured random graphs explain the structure and dynamics of cross-linked polymer networks

Step-growth and chain-growth are two major families of chemical reactions that result in polymer networks with drastically different physical properties, often referred to as hyper-branched and cross-linked networks. In contrast to step-growth polymerisation, chain-growth forms networks that are history-dependent. Such networks are defined not just by the degree distribution, but also by their entire formation history, which entails a modelling and conceptual challenges. We show that the structure of chain-growth polymer networks corresponds to an edge-coloured random graph with a defined multivariate degree distribution, where the colour labels represent the formation times of chemical bonds. The theory quantifies and explains the gelation in free-radical polymerisation of cross-linked polymers and predicts conditions when history dependance has the most significant effect on the global properties of a polymer network. As such, the edge colouring is identified as the key driver behind the difference in the physical properties of step-growth and chain-growth networks. We expect that this findings will stimulate usage of network science tools for discovery and design of cross-linked polymers.

Role of bridge nodes in epidemic spreading: Different regimes and crossovers

Power-law behaviors are common in many disciplines, especially in network science. Real-world networks, like disease spreading among people, are more likely to be interconnected communities, and show richer power-law behaviors than isolated networks. In this paper, we look at the system of two communities which are connected by bridge links between a fraction r of bridge nodes, and study the effect of bridge nodes to the final state of the Susceptible-Infected-Recovered model by mapping it to link percolation. By keeping a fixed average connectivity, but allowing different transmissibilities along internal and bridge links, we theoretically derive different power-law asymptotic behaviors of the total fraction of the recovered R in the final state as r goes to zero, for different combinations of internal and bridge link transmissibilities. We also find crossover points where R follows different power-law behaviors with r on both sides when the internal transmissibility is below but close to its critical value for different bridge link transmissibilities. All of these power-law behaviors can be explained through different mechanisms of how finite clusters in each community are connected into the giant component of the whole system, and enable us to pick effective epidemic strategies and to better predict their impacts.

Modelling electrical conduction in nanostructure assemblies through complex networks

Carrier transport processes in assemblies of nanostructures rely on morphology-dependent and hierarchical conduction mechanisms, whose complexity cannot be captured by current modelling approaches. Here we apply the concept of complex networks to modelling carrier conduction in such systems. The approach permits assignment of arbitrary connectivity and connection strength between assembly constituents and is thus ideal for nanostructured films, composites and other geometries. Modelling of simplified rod-like nanostructures is consistent with analytical solutions, whereas results for more realistic nanostructure assemblies agree with experimental data and reveal conduction behaviour not captured by previous models. Fitting of ensemble measurements also allows the conduction properties of individual constituents to be extracted, which are subsequently used to guide the realization of transparent electrodes with improved performance. A global optimization process was employed to identify geometries and properties with high potential for transparent conductors. Our intuitive discretization approach, combined with a simple solver tool, allows researchers with little computational experience to carry out realistic simulations.

Effect of volume growth on the percolation threshold in random directed acyclic graphs with a given degree distribution

In every network, a distance between a pair of nodes can be defined as the length of the shortest path connecting these nodes, and therefore one may speak of a ball, its volume, and how it grows as a function of the radius. Spatial networks tend to feature peculiar volume scaling functions, as well as other topological features, including clustering, degree-degree correlation, clique complexes, and heterogeneity. Here we investigate a nongeometric random graph with a given degree distribution and an additional constraint on the volume scaling function. We show that such structures fall into the category of m-colored random graphs and study the percolation transition by using this theory. We prove that for a given degree distribution the percolation threshold for weakly connected components is not affected by the volume growth function. Additionally, we show that the size of the giant component and the cyclomatic number are not affected by volume scaling. These findings may explain the surprisingly good performance of network models that neglect volume scaling. Even though this paper focuses on the implications of the volume growth, the model is generic and might lead to insights in the field of random directed acyclic graphs and their applications.

Percolation on branching simplicial and cell complexes and its relation to interdependent percolation

Network geometry has strong effects on network dynamics. In particular, the underlying hyperbolic geometry of discrete manifolds has recently been shown to affect their critical percolation properties. Here we investigate the properties of link percolation in nonamenable two-dimensional branching simplicial and cell complexes, i.e., simplicial and cell complexes in which the boundary scales like the volume. We establish the relation between the equations determining the percolation probability in random branching cell complexes and the equation for interdependent percolation in multiplex networks with interlayer degree correlation equal to one. By using this relation we show that branching cell complexes can display more than two percolation phase transitions: the upper percolation transition, the lower percolation transition, and one or more intermediate phase transitions. At these additional transitions the percolation probability and the fractal exponent both feature a discontinuity. Furthermore, by using the renormalization group theory we show that the upper percolation transition can belong to various universality classes including the Berezinskii-Kosterlitz-Thouless (BKT) transition, the discontinuous percolation transition, and continuous transitions with anomalous singular behavior that generalize the BKT transition.

Renormalization group for link percolation on planar hyperbolic manifolds

Network geometry is currently a topic of growing scientific interest, as it opens the possibility to explore and interpret the interplay between structure and dynamics of complex networks using geometrical arguments. However, the field is still in its infancy. In this work we investigate the role of network geometry in determining the nature of the percolation transition in planar hyperbolic manifolds. Boettcher et al. [Nat. Comm. 3, 787 (2012)2041-172310.1038/ncomms1774] have shown that a special type of two-dimensional hyperbolic manifolds, the Farey graphs, display a discontinuous transition for ordinary link percolation. Here we investigate using the renormalization group the critical properties of link percolation on a wider class of two-dimensional hyperbolic deterministic and random manifolds constituting the skeletons of two-dimensional cell complexes. These hyperbolic manifolds are built iteratively by subsequently gluing m-polygons to single edges. We show that when the size m of the polygons is drawn from a distribution q_{m} with asymptotic power-law scaling q_{m}≃Cm^{-γ} for m≫1, different universality classes can be observed depending on the value of the power-law exponent γ. Interestingly, the percolation transition is hybrid for γ∈(3,4) and becomes continuous for γ∈(2,3].

Enhancing the robustness of a multiplex network leads to multiple discontinuous percolation transitions

Determining design principles that boost the robustness of interdependent networks is a fundamental question of engineering, economics, and biology. It is known that maximizing the degree correlation between replicas of the same node leads to optimal robustness. Here we show that increased robustness might also come at the expense of introducing multiple phase transitions. These results reveal yet another possible source of fragility of multiplex networks that has to be taken into the account during network optimization and design.