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The evolution of species habitat range is an important topic over a wide range of research fields. In higher organisms, habitat range evolution is generally associated with genetic events such as gene duplication. However, the specific…
Several networks occurring in real life have modular structures that are arranged in an hierarchical fashion. In this paper, we have proposed a model for such networks, using a stochastic generation method. Using this model we show that,…
In complex ecological communities, species may self-organize into clusters or clumps where highly similar species can coexist. The emergence of such species clusters can be captured by the interplay between neutral and niche theories. Based…
We study the evolution of networks when the creation and decay of links are based on the position of nodes in the network measured by their centrality. We show that the same network dynamics arises under various centrality measures, and…
This paper addresses the decomposition of biochemical networks into functional modules that preserve their dynamic properties upon interconnection with other modules, which permits the inference of network behavior from the properties of…
Signal transduction networks can form highly interconnected systems within cells due to network crosstalk, the sharing of input signals between multiple downstream responses. To better understand the evolutionary design principles…
Empirical observations show that ecological communities can have a huge number of coexisting species, also with few or limited number of resources. These ecosystems are characterized by multiple type of interactions, in particular…
Empirical observations show that ecological communities can have a huge number of coexisting species, also with few or limited number of resources. These ecosystems are characterized by multiple type of interactions, in particular…
Patterns of nestedness and specialization asymmetry, where specialist species interact mainly with generalists while generalists interact with both generalists and specialists, are often observed in mutualistic and antagonistic bi-partite…
Individual species may experience diverse outcomes, from prosperity to extinction, in an ecological community subject to external and internal variations. Despite the wealth of theoretical results derived from random matrix ensembles, a…
We propose an automatable data-driven methodology for robust nonlinear reduced-order modelling from time-resolved snapshot data. In the kinematical coarse-graining, the snapshots are clustered into few centroids representable for the whole…
Evolution produces complex and structured networks of interacting components in chemical, biological, and social systems. We describe a simple mathematical model for the evolution of an idealized chemical system to study how a network of…
Uncovering structural properties of ecological networks is a crucial starting point of studying the system's stability in response to various types of perturbations. We analyze pollination and seed disposal networks, which are…
Metapopulation models have been instrumental in demonstrating the ecological impact of landscape structure on the survival of a focal species in complex environments. However, extensions to multiple species with arbitrary dispersal networks…
Oscillatory behavior is ubiquitous in many natural and engineered systems, often emerging through self-regulating mechanisms. In this paper, we address the challenge of stabilizing a desired oscillatory pattern in a networked system where…
Constraints placed upon the phenotypes of organisms result from their interactions with the environment. Over evolutionary timescales, these constraints feed back onto smaller molecular subnetworks comprising the organism. The evolution of…
In an increasingly interconnected world, a key scientific challenge is to examine mechanisms that lead to the widespread propagation of contagions, such as misinformation and pathogens, and identify risk factors that can trigger large-scale…
Many of the chemical reactions that take place within a living cell are irreversible. Due to evolutionary pressures, the number of allowable reactions within these systems are highly constrained and thus the resulting metabolic networks…
Models of strategy evolution on static networks help us understand how population structure can promote the spread of traits like cooperation. One key mechanism is the formation of altruistic spatial clusters, where neighbors of a…
Mutualistic networks are formed when the interactions between two classes of species are mutually beneficial. They are important examples of cooperation shaped by evolution. Mutualism between animals and plants plays a key role in the…