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A common feature of biological networks is the geometric property of self-similarity. Molecular regulatory networks through to circulatory systems, nervous systems, social systems and ecological trophic networks, show self-similar…

Molecular Networks · Quantitative Biology 2012-03-09 Simon DeDeo , David C. Krakauer

Recent genomic and bioinformatic advances have motivated the development of numerous random network models purporting to describe graphs of biological, technological, and sociological origin. The success of a model has been evaluated by how…

Molecular Networks · Quantitative Biology 2007-05-23 Manuel Middendorf , Etay Ziv , Carter Adams , Jen Hom , Robin Koytcheff , Chaya Levovitz , Gregory Woods , Linda Chen , Chris Wiggins

Changes in environmental or system parameters often drive major biological transitions, including ecosystem collapse, disease outbreaks, and tumor development. Analyzing the stability of steady states in dynamical systems provides critical…

Populations and Evolution · Quantitative Biology 2025-05-02 Joseph Cummings , Kyle J. -M. Dahlin , Elizabeth Gross , Jonathan D. Hauenstein

We describe a new type of discrete symmetry that relates heterotic-string models. It is based on the spectral flow operator which normally acts within a general N=(2,2) model and we use this operator to construct a map between N=(2,0)…

High Energy Physics - Theory · Physics 2015-08-03 Panos Athanasopoulos

This work proposes to model the space environment as a stochastic dynamic network where each node is a group of objects of a given class, or species, and their relationship is represented by stochastic links. A set of stochastic dynamic…

Dynamical Systems · Mathematics 2025-05-23 Yirui Wang , Pietro De Marchi , Massimiliano Vasile

The concept of typed topological space is introduced, for which open sets in a topology on a finite set will be assigned types (from lattice). The neighborhood system of a point, the closure and the connectedness can be defined according to…

General Topology · Mathematics 2018-04-13 Wanjun Hu

When three species compete cyclically in a well-mixed, stochastic system of $N$ individuals, extinction is known to typically occur at times scaling as the system size $N$. This happens, for example, in rock-paper-scissors games or…

Physics and Society · Physics 2019-02-20 Kevin E. Bassler , Erwin Frey , R. K. P. Zia

Ecosystems display a complex spatial organization. Ecologists have long tried to characterize them by looking at how different measures of biodiversity change across spatial scales. Ecological neutral theory has provided simple predictions…

Populations and Evolution · Quantitative Biology 2017-12-13 Simone Pigolotti , Massimo Cencini , Daniel Molina , Miguel A. Muñoz

A broad set of empirical phenomenon in the study of social, economic and machine behaviour can be modelled as complex systems with averaging dynamics. However many of these models naturally result in consensus or consensus-like outcomes. In…

Multiagent Systems · Computer Science 2020-07-03 Orowa Sikder

We present a general theoretical model for the spatio-temporal dynamics of animal contests. Inspired by interactions between physical particles, the model is formulated in terms of effective interaction potentials, which map typical…

Biological Physics · Physics 2022-12-01 Amir Haluts , Alex Jordan , Nir S. Gov

In boundary conformal field theories, global symmetries can be broken by boundary conditions, generating a homogeneous conformal manifold. We investigate these geometries, showing they have a coset structure, and give fully worked out…

High Energy Physics - Theory · Physics 2023-01-27 Christopher P. Herzog , Vladimir Schaub

The construction of a network of cell-to-cell contacts makes it possible to characterize the patterns and spatial organisation of tissues. Such networks are highly dynamic, depending on the changes of the tissue architecture caused by cell…

Tissues and Organs · Quantitative Biology 2013-06-25 Attila Csikász-Nagy , Luis M. Escudero , Martial Guillaud , Sean Sedwards , Buzz Baum , Matteo Cavaliere

We give a constructive method for realizing an arbitrary directed graph (with no one-cycles) as a heteroclinic or an excitable dynamic network in the phase space of a system of coupled cells of two types. In each case, the system is…

Adaptation and Self-Organizing Systems · Physics 2015-12-17 Peter Ashwin , Claire Postlethwaite

Coexistence of competing species is, due to unavoidable fluctuations, always transient. In this Letter, we investigate the ultimate survival probabilities characterizing different species in cyclic competition. We show that they often obey…

Populations and Evolution · Quantitative Biology 2009-01-30 Maximilian Berr , Tobias Reichenbach , Martin Schottenloher , Erwin Frey

We perform an analytical investigation of the cell interface dynamics in the framework of a minimal phase field model of cell motility suggested in [1], which consists of two coupled evolution equations for the order parameter and a…

Biological Physics · Physics 2019-10-04 Mohammad Abu Hamed , Alexander A. Nepomnyashchy

The persistence of biodiversity of species is a challenging proposition in ecological communities in the face of Darwinian selection. The present article investigates beyond the pairwise competitive interactions and provides a novel…

Populations and Evolution · Quantitative Biology 2022-11-09 Sourin Chatterjee , Sayantan Nag Chowdhury , Dibakar Ghosh , Chittaranjan Hens

The authors investigate the ideal, nondriven multifluid equations of motion to identify consistent (i.e., truly stationary), mechanically static models for composition profiles within the thermosphere. These physically faithful functions…

Space Physics · Physics 2016-07-13 J. M. Picone , J. T. Emmert , D. P. Drob

In a recent paper [Phys. Rev. Lett. 129, 120601] we have shown that the dynamics of interfaces, in the symmetry-broken phase of the two-dimensional ferromagnetic quantum Ising model, displays a robust form of ergodicity breaking. In this…

Statistical Mechanics · Physics 2023-01-24 Federico Balducci , Andrea Gambassi , Alessio Lerose , Antonello Scardicchio , Carlo Vanoni

Predicting competitive outcomes typically requires fitting dynamical models to data, from which interaction strengths and coexistence indicators such as invasion criteria can be produced. Methods that allow to propagate parameter…

Populations and Evolution · Quantitative Biology 2025-04-10 Matthieu Paquet , Frédéric Barraquand

Discrete models have a long tradition in engineering, including finite state machines, Boolean networks, Petri nets, and agent-based models. Of particular importance is the question of how the model structure constrains its dynamics. This…

Molecular Networks · Quantitative Biology 2011-08-02 Reinhard Laubenbacher , David Murrugarra , Alan Veliz-Cuba