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We analyze the properties of model food webs and of fifteen community food webs from a variety of environments. We first perform a theoretical analysis of the niche model of Williams and Martinez. We derive analytical expressions for the…
A general theory is developed for the evolution of the cell order (CO) distribution in planar granular systems. Dynamic equations are constructed and solved in closed form for several examples: systems under compression; dilation of very…
Food-webs and other classes of ecological network motifs, are a means of describing feeding relationships between consumers and producers in an ecosystem. They have application across scales where they differ only in the underlying…
Inference for streaming time-series is tightly coupled with the problem of Bayesian on-line state and parameter inference. In this paper we will introduce Dynamic Generalised Linear Models, the class of models often chosen to model…
Immotile microbes inhabit nearly every environment on Earth, from soils and sediments to food matrices -- yet how they disperse through these physically confining environments is poorly understood. Here, we show that immotile microbial…
This chapter explores dynamical structural equation models (DSEMs) and their nonlinear generalizations into sheaves of dynamical systems. It demonstrates these two disciplines on part of the food web in the Bering Sea. The translation from…
Discontinuous dynamical systems with grazing solutions are discussed. The group property, continuation of solutions, continuity and smoothness of motions are thoroughly analyzed. A variational system around a grazing solution which depends…
Chlorine is a widely used disinfectant and proxy for water quality (WQ) monitoring in water distribution networks (WDN). Chlorine-based WQ regulation and control aims to maintain pathogen-free water. Chlorine residual evolution within WDN…
Complex contagion models that involve contagion along higher-order structures, such as simplicial complexes and hypergraphs, yield new classes of mean-field models. Interestingly, the differential equations arising from many such models…
Simulations of dense stellar systems currently face two major hurdles, one astrophysical and one computational. The astrophysical problem lies in the fact that several major stages in binary evolution, such as common envelope evolution, are…
A novel model of biological organisms is advanced, treating an organism as a self-consistent system subject to a pathogen flux. The principal novelty of the model is that it describes not some parts, but a biological organism as a whole.…
Recent computer simulations reveal several intriguing features in the evolution of properties of amorphous solids subjected to repeated cyclic shear deformation. These include the divergence of the number of cycles to reach steady states as…
In this work, we introduce a computational model for the study of the host-bacteria interaction and the influence of the intestinal microbiota on the behavior and feeding pattern of an individual. The model is based on digital entities,…
The myriad microscopic interactions among the individual organisms that constitute an ecological system collectively give rise, at the macroscopic scale, to evolutionary trends. The ability to detect the directionality of such trends is…
This thesis is about the study of complex systems through simple models. Our work evidences the relevance of this kind of modeling in science, which provides us with a better understanding of nature at minimum cost. The fundamentals tools…
The macroscopic behavior of the solution of a coupled system of partial differential equations arising in the modeling of reaction-diffusion processes in periodic porous media is analyzed. Our mathematical model can be used for studying…
Quantifying population dynamics is a fundamental challenge in ecology and evolutionary biology, particularly for species that are cryptic, microscopic, or extinct. Traditional approaches rely on continuous representations of population…
We present a simple physical model that recapitulates several features of biological evolution, while being based only on thermally-driven attachment and detachment of elementary building blocks. Through its dynamics, this model samples a…
Species or population that proliferate faster than others become dominant in numbers. Catalysis allows catalytic sets within a molecular reaction network to dominate the non catalytic parts of the network by processing most of the available…
Few of food web theory hypotheses/predictions can be readily tested using empirical data. An exception is represented by simple probabilistic models for food web structure, for which the likelihood has been derived. Here I test the…