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A vast array of transformative technologies developed over the past decade has enabled measurement and perturbation at ever increasing scale, yet our understanding of many systems remains limited by experimental capacity. Overcoming this…

Quantitative Methods · Quantitative Biology 2020-12-25 Brian Cleary , Aviv Regev

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…

Populations and Evolution · Quantitative Biology 2025-07-11 Guy Bunin , Olivier Rivoire

Understanding the assembly of ecosystems to estimate the number of species at different spatial scales is a challenging problem. Until now, maximum entropy approaches have lacked the important feature of considering space in an explicit…

Populations and Evolution · Quantitative Biology 2014-07-10 Matteo Adorisio , Jacopo Grilli , Samir Suweis , Sandro Azaele , Jayanth R. Banavar , Amos Maritan

Ecosystem approach to fisheries requires a thorough understanding of fishing impacts on ecosystem status and processes as well as predictive tools such as ecosystem models to provide useful information for management. The credibility of…

Quantitative Methods · Quantitative Biology 2024-04-30 Ricardo Oliveros-Ramos , Philippe Verley , Yunne-Jai Shin

Natural evolution gives the impression of leading to an open-ended process of increasing diversity and complexity. If our goal is to produce such open-endedness artificially, this suggests an approach driven by evolutionary metaphor. On the…

Adaptation and Self-Organizing Systems · Physics 2018-12-13 Nicholas Guttenberg , Nathaniel Virgo , Alexandra Penn

Coevolutionary arms races form between interacting populations that constitute each other's environment and respond to mutual changes. This inherently far-from-equilibrium process finds striking manifestations in the adaptive immune system,…

Biological Physics · Physics 2019-12-18 Hongda Jiang , Shenshen Wang

The inheritance of characteristics induced by the environment has often been opposed to the theory of evolution by natural selection. Yet, while evolution by natural selection requires new heritable traits to be produced and transmitted, it…

Populations and Evolution · Quantitative Biology 2015-06-18 Olivier Rivoire , Stanislas Leibler

Both community ecology and conservation biology seek further understanding of factors governing the advance of an invasive species. We model biological invasion as an individual-based, stochastic process on a two-dimensional landscape. An…

Populations and Evolution · Quantitative Biology 2010-07-12 Lauren O'Malley , G. Korniss , Thomas Caraco

Technology is increasingly shaping our social structures and is becoming a driving force in altering human biology. Besides, human activities already proved to have a significant impact on the Earth system which in turn generates complex…

Computers and Society · Computer Science 2018-02-15 Eugenio Maria Battaglia , Jie Mei , Guillaume Dumas

Biological processes involve a variety of spatial and temporal scales. A holistic understanding of many biological processes therefore requires multi-scale models which capture the relevant properties on all these scales. In this manuscript…

Molecular Networks · Quantitative Biology 2015-06-23 Jan Hasenauer , Nick Jagiella , Sabrina Hross , Fabian J. Theis

Collective cooperation drives the dynamics of many natural, social, and economic phenomena, making understanding the evolution of cooperation with evolutionary game theory a central question of modern science. Although human interactions…

Physics and Society · Physics 2024-04-12 Yao Meng , Alex McAvoy , Aming Li

Species sampling processes have long served as the fundamental framework for modeling random discrete distributions and exchangeable sequences. However, data arising from distinct but related sources require a broader notion of…

Statistics Theory · Mathematics 2026-02-03 Beatrice Franzolini , Antonio Lijoi , Igor Prünster , Giovanni Rebaudo

An organism that is newly introduced into an existing population has a survival probability that is dependent on both the population density of its environment and the competition it experiences with the members of that population.…

Populations and Evolution · Quantitative Biology 2024-12-17 Jason M. Gray , Rowan J. Barker-Clarke , Jacob G. Scott , Michael Hinczewski

One of the first successes of neutral ecology was to predict realistically-broad distributions of rare and abundant species. However, it has remained an outstanding theoretical challenge to describe how this distribution of abundances…

Populations and Evolution · Quantitative Biology 2018-07-18 James P. O'Dwyer , Stephen J. Cornell

This tutorial article puts forth a framework to analyze the noncooperative strategic interactions among the members of a large population of bounded rationality agents. Our approach hinges on, unifies and generalizes existing methods and…

Optimization and Control · Mathematics 2020-07-15 Shinkyu Park , Nuno C. Martins , Jeff S. Shamma

We integrate dual-process theories of human cognition with evolutionary game theory to study the evolution of automatic and controlled decision-making processes. We introduce a model where agents who make decisions using either automatic or…

Dynamical Systems · Mathematics 2015-07-07 Danielle F. P. Toupo , Steven H. Strogatz , Jonathan D. Cohen , David G. Rand

In Evolutionary game theory the payoffs are typically fixed or shaped by external environmental variables. Here, we introduce an endogenous-feedback model in which the game played coevolves directly with the population state: the payoff…

Until recently, much of the microbial world was hidden from view. A global research effort has changed this, unveiling and quantifying microbial diversity across enormous range of critically-important contexts, from the human microbiome, to…

Populations and Evolution · Quantitative Biology 2017-10-26 Alice Doucet-Beaupré , James P. O'Dwyer

Predator-prey relationships are one of the most studied interactions in population ecology. However, little attention has been paid to the possibility of role exchange between species once determined as predators and preys, despite firm…

Populations and Evolution · Quantitative Biology 2014-10-31 Faustino Sánchez-Garduño , Pedro Miramontes , Tatiana T. Marquez-Lago

When can complex ecological interactions drive an entire ecosystem into a persistent non-equilibrium state, where species abundances keep fluctuating without going to extinction? We show that high-diversity spatially-extended systems, in…

Populations and Evolution · Quantitative Biology 2019-08-27 Felix Roy , Matthieu Barbier , Giulio Biroli , Guy Bunin
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