arXiv subjects

Charo I. del Genio

Publications and source records attributed to Charo I. del Genio.

14 recordsLinked to original sources

arXiv2026

Inertial synchronization of networked oscillators in arbitrary dimensions

The Kuramoto model provides a paradigmatic framework for studying synchronization of interacting oscillators, and has been generalized to arbitrary dimensions to describe swarms, flocks and multi-dimensional opinion dynamics. Yet, existing formulations neglect inertia, a key mechanism known to enhance information propagation and collective responsiveness. Here, we introduce and analyze an inertial Kuramoto model in arbitrary dimensions. We show that inertia fundamentally alters the nature of the synchronization transition, inducing a crossover from continuous to discontinuous behavior, with the onset of hysteresis depending explicitly on both inertia and dimensionality parity. Our analytical theory is supported by extensive numerical simulations. These results establish inertia as a crucial ingredient of high-dimensional collective dynamics and reveal a novel universal structure in synchronization phenomena.

nlin.AO↗

arXiv2026

Offer of a reward does not always promote trust in spatial games

Trust is one of the cornerstones of human society. One of the evolutionary pressure mechanisms that may have led to its emergence is the presence of incentives for trustworthy behavior. However, this type of reward has received relatively little attention in the context of spatial trust games, which are often used to build models in evolutionary game theory. To fill this gap, we introduce an inter-role reward mechanism in the spatial trust game, so that an investing trustor can choose to pay an extra cost to reward a trustworthy trustee. With extensive numerical simulations, we find that this type of reward does not always promote trust. Rather, while moderate rewards break the dominance of mistrust, thereby favoring investment, excessive rewards eventually stimulate a nonreturn strategy, ultimately suppressing the evolution of trust. Additionally, lower reward costs do not necessarily promote trust. Instead, more costly, but not excessive, rewards enhance the advantage of the original investment, consolidating the clusters of rewarders and improving trust. Our model thus provides evidence about the counterintuitive nature of the relationship between trust and rewards in a complex society.

cond-mat.stat-mech↗

arXiv2025

Equitability and explosive synchronisation in multiplex and higher-order networks

Cluster synchronisation is a key phenomenon observed in networks of coupled dynamical units. Its presence has been linked to symmetry and, more generally, to equability of the underlying pattern of interactions between dynamical units. However, it is not known under which conditions equitability-induced synchronisation is the only cluster synchronisation that can occur on a particular system. Here, we reveal a natural linear independent condition such that equitability becomes necessary, and sufficient, for the existence of cluster synchronised solutions on a very general dynamical system which allows multiplex or higher-order, arbitrarily weighted interactions. Our results explain the ubiquity of explosive synchronisation, as opposed to cluster synchronisation, in multiplex and higher-order networks: equitability imposes additional constraints that must be simultaneously satisfied on the same set of nodes. Our results have significant implications for the design of complex dynamical systems of coupled dynamical units with arbitrary cluster synchronisation patterns and coupling functions.

nlin.AO↗

arXiv2025

Solitary states in spiking oscillators with higher-order interactions

We study a system of globally coupled FitzHugh-Nagumo oscillators, showing that the presence of higher-order interactions affects the character of the transition between synchronous and asynchronous states. In particular, we demonstrate that, around the synchronization transition, solitary states emerge due to the presence of second-order interactions. In difference to the phenomenology observed in systems of phase oscillators, we show that, at low coupling strengths, solitary states appear for both transition directions, whereas for higher couplings they only occur in the forward direction, with the backwards one characterized by explosive desynchronization.

nlin.AO↗

arXiv2025

Hypermodularity and community detection in hypergraphs

Numerous networked systems feature a structure of nontrivial communities, which often correspond to their functional modules. Such communities have been detected in real-world biological, social and technological systems, as well as in synthetic models thereof. While much effort has been devoted to developing methods for community detection in traditional networks, the study of community structure in networks with higher-order interactions is still not as extensively explored. In this article, we introduce a formalism for the hypermodularity of higher-order networks that allows us to use spectral methods to detect community structures in hypergraphs. We apply this approach to synthetic random networks as well as to real-world data, showing that it produces results that reflect the nature and the dynamics of the interactions modelled, thereby constituting a valuable tool for the extraction of hidden information from complex higher-order data sets.

physics.soc-ph↗

arXiv2025

Reconstructing simplicial complexes from evolutionary games

In distributed systems, knowledge of the network structure of the connections among the unitary components is often a requirement for an accurate prediction of the emerging collective dynamics. However, in many real-world situations, one has, at best, access to partial connectivity data, and therefore the entire graph structure needs to be reconstructed from a limited number of observations of the dynamical processes that take place on it. While existing studies predominantly focused on reconstructing traditional pairwise networks, higher-order interactions remain largely unexplored. Here, we introduce three methods to reconstruct a simplicial complex structure of connection from observations of evolutionary games that take place on it, and demonstrate their high accuracy and excellent overall performance in synthetic and empirical complexes. The methods have different requirements and different complexity, thereby constituting a series of approaches from which one can pick the most appropriate one given the specific circumstances of the application under study.

physics.soc-ph↗

arXiv2024

Periodic systems have new classes of synchronization stability

The Master Stability Function is a robust and useful tool for determining the conditions of synchronization stability in a network of coupled systems. While a comprehensive classification exists in the case in which the nodes are chaotic dynamical systems, its application to periodic systems has been less explored. By studying several well-known periodic systems, we establish a comprehensive framework to understand and classify their properties of synchronizability. This allows us to define five distinct classes of synchronization stability, including some that are unique to periodic systems. Specifically, in periodic systems, the Master Stability Function vanishes at the origin, and it can therefore display behavioral classes that are not achievable in chaotic systems, where it starts, instead, at a strictly positive value. Moreover, our results challenge the widely-held belief that periodic systems are easily put in a stable synchronous state, showing, instead, the common occurrence of a lower threshold for synchronization stability.

cond-mat.stat-mech↗

arXiv2022

Mean-field nature of synchronization stability in networks with multiple interaction layers

The interactions between the components of many real-world systems are best modelled by networks with multiple layers. Different theories have been proposed to explain how multilayered connections affect the linear stability of synchronization in dynamical systems. However, the resulting equations are computationally expensive, and therefore difficult, if not impossible, to solve for large systems. To bridge this gap, we develop a mean-field theory of synchronization for networks with multiple interaction layers. By assuming quasi-identical layers, we obtain accurate assessments of synchronization stability that are comparable with the exact results. In fact, the accuracy of our theory remains high even for networks with very dissimilar layers, thus posing a general question about the mean-field nature of synchronization stability in multilayer networks. Moreover, the computational complexity of our approach is only quadratic in the number of nodes, thereby allowing the study of systems whose investigation was thus far precluded.

physics.soc-ph↗

arXiv2018

The tetrazole analogue of the auxin indole-3-acetic acid binds preferentially to TIR1 and not AFB5

Auxin is considered one of the cardinal hormones in plant growth and development. It regulates a wide range of processes throughout the plant. Synthetic auxins exploit the auxin-signalling pathway and are valuable as herbicidal agrochemicals. Currently, despite a diversity of chemical scaffolds all synthetic auxins have a carboxylic acid as the active core group. By applying bio-isosteric replacement we discovered that indole-3-tetrazole was active by surface plasmon resonance (SPR) spectrometry, showing that the tetrazole could initiate assembly of the TIR1 auxin co-receptor complex. We then tested the tetrazole's efficacy in a range of whole plant physiological assays and in protoplast reporter assays which all confirmed auxin activity, albeit rather weak. We then tested indole-3-tetrazole against the AFB5 homologue of TIR1, finding that binding was selective against TIR1, absent with AFB5. The kinetics of binding to TIR1 are contrasted to those for the herbicide picloram, which shows the opposite receptor preference as it binds to AFB5 with far greater affinity than to TIR1. The basis of the preference of indole-3-tetrazole for TIR1 was revealed to be a single residue substitution using molecular docking, and assays using tir1 and afb5 mutant lines confirmed selectivity in vivo. Given the potential that a TIR1-selective auxin might have for unmasking receptor-specific actions, we followed a rational design, lead optimisation campaign and a set of chlorinated indole-3-tetrazoles was synthesised. Improved affinity for TIR1 and the preference for binding to TIR1 was maintained for 4- and 6-chloroindole-3-tetrazoles, coupled with improved efficacy in vivo. This work expands the range of auxin chemistry for the design of receptor-selective synthetic auxins.

q-bio.BM↗

arXiv2018

Datamining a medieval medical text reveals patterns in ingredient choice that reflect biological activity against the causative agents of specified infections

The pharmacopeia used by physicians and lay people in medieval Europe has largely been dismissed as placebo or superstition. While we now recognise that some of the materia medica used by medieval physicians could have had useful biological properties, research in this area is limited by the labour-intensive process of searching and interpreting historical medical texts. Here, we demonstrate the potential power of turning medieval medical texts into contextualised electronic databases amenable to exploration by algorithm. We use established methodologies from network science to reveal statistically significant patterns in ingredient selection and usage in a key text, the fifteenth-century Lylye of Medicynes, focusing on remedies to treat symptoms of microbial infection. We discuss the potential that these patterns reflect rational medical decisions. In providing a worked example of data-driven textual analysis, we demonstrate the potential of this approach to encourage interdisciplinary collaboration and to shine a new light on the ethnopharmacology of historical medical texts.

q-bio.QM↗

arXiv2016

Finding network communities using modularity density

Many real-world complex networks exhibit a community structure, in which the modules correspond to actual functional units. Identifying these communities is a key challenge for scientists. A common approach is to search for the network partition that maximizes a quality function. Here, we present a detailed analysis of a recently proposed function, namely modularity density. We show that it does not incur in the drawbacks suffered by traditional modularity, and that it can identify networks without ground-truth community structure, deriving its analytical dependence on link density in generic random graphs. In addition, we show that modularity density allows an easy comparison between networks of different sizes, and we also present some limitations that methods based on modularity density may suffer from. Finally, we introduce an efficient, quadratic community detection algorithm based on modularity density maximization, validating its accuracy against theoretical predictions and on a set of benchmark networks.

physics.soc-ph↗

arXiv2016

Synchronization in networks with multiple interaction layers

The structure of many real-world systems is best captured by networks consisting of several interaction layers. Understanding how a multi-layered structure of connections affects the synchronization properties of dynamical systems evolving on top of it is a highly relevant endeavour in mathematics and physics, and has potential applications to several societally relevant topics, such as power grids engineering and neural dynamics. We propose a general framework to assess stability of the synchronized state in networks with multiple interaction layers, deriving a necessary condition that generalizes the Master Stability Function approach. We validate our method applying it to a network of Rössler oscillators with a double layer of interactions, and show that highly rich phenomenology emerges. This includes cases where the stability of synchronization can be induced even if both layers would have individually induced unstable synchrony, an effect genuinely due to the true multi-layer structure of the interactions amongst the units in the network.

physics.soc-ph↗

arXiv2016

Tomographic docking suggests the mechanism of auxin receptor TIR1 selectivity

We study the binding of plant hormone IAA on its receptor TIR1 introducing a novel computational method that we call tomographic docking and that accounts for interactions occurring along the depth of the binding pocket. Our results suggest that selectivity is related to constraints that potential ligands encounter on their way from the surface of the protein to their final position at the pocket bottom. Tomographic docking helps develop specific hypotheses about ligand binding, distinguishing binders from non-binders, and suggests that binding is a three-step mechanism, consisting of engagement with a niche in the back wall of the pocket, interaction with a molecular filter which allows or precludes further descent of ligands, and binding on the pocket base. Only molecules that are able to descend the pocket and bind at its base allow the co-receptor IAA7 to bind on the complex, thus behaving as active auxins. Analyzing the interactions at different depths, our new method helps in identifying critical residues that constitute preferred future study targets and in the quest for safe and effective herbicides. Also, it has the potential to extend the utility of docking from ligand searches to the study of processes contributing to selectivity.

q-bio.BM↗

arXiv2015

Synchronization in dynamical networks with unconstrained structure switching

We provide a rigorous solution to the problem of constructing a structural evolution for a network of coupled identical dynamical units that switches between specified topologies without constraints on their structure. The evolution of the structure is determined indirectly, from a carefully built transformation of the eigenvector matrices of the coupling Laplacians, which are guaranteed to change smoothly in time. In turn, this allows to extend the Master Stability Function formalism, which can be used to assess the stability of a synchronized state. This approach is independent from the particular topologies that the network visits, and is not restricted to commuting structures. Also, it does not depend on the time scale of the evolution, which can be faster than, comparable to, or even secular with respect to the the dynamics of the units.

physics.soc-ph↗