Related papers: A framework for studying transients in marine meta…

Models and simulations of collective behaviours are often based on considering them as assumed by interactive particle systems. The focus is then on behavioural and interaction rules by using approaches based on artificial agents designed…

Modal linear stability analysis has proven very successful in the analysis of coherent structures of turbulent flows. Formally, it describes the evolution of a disturbance in the limit of infinite time. In this work we apply modal linear…

This study presents an initial framework for distinguishing group and single pedestrians based on real-world trajectory data, with the aim of analyzing their differences in space utilization and emergent behavioral patterns. By segmenting…

A striking feature of the marine ecosystem is the regularity in its size spectrum: the abundance of organisms as a function of their weight approximately follows a power law over almost ten orders of magnitude. We interpret this as evidence…

Automated verification of living organism models allows us to gain previously unknown knowledge about underlying biological processes. In this paper, we show the benefits to use parametric time Petri nets in order to analyze precisely the…

Non-equilibrium thermodynamics has long been an area of substantial interest to ecologists because most fundamental biological processes, such as protein synthesis and respiration, are inherently energy-consuming. Microbial communities are…

This paper concerns the modeling and numerical simulation of the process of speciation. In particular, given conditions for which one or more speciation events within an ecosystem occur, our aim is to develop the necessary modeling and…

Microbiomes, which are collections of interacting microbes in an environment, often substantially impact the environmental patches or living hosts that they occupy. In microbiome models, it is important to consider both the local dynamics…

Stabilizing the dynamics of complex, non-linear systems is a major concern across several scientific disciplines including ecology and conservation biology. Unfortunately, most methods proposed to reduce the fluctuations in chaotic systems…

We introduce a numerical method to extract the parameters of run-and-tumble dynamics from experimental measurements of the intermediate scattering function. We show that proceeding in Laplace space is unpractical and employ instead renewal…

Metapopulation models are commonly used in ecology, evolution, and epidemiology. These models usually entail homogeneity assumptions within patches and study networks of migration between patches to generate insights into conservation of…

We introduce a minimal model of multilevel selection on structured populations, considering the interplay between game theory and population dynamics. Through a bottleneck process, finite groups are formed with cooperators and defectors…

Living systems operate far from equilibrium, yet few general frameworks provide global bounds on biological transients. In high-dimensional biological networks like ecosystems, long transients arise from the separate timescales of…

We have earlier constructed a generalized entropy concept to show the direction of time in an evolution following from a Markov generator. In such a dynamical system, the entity found changes in a monotonic way starting from any initial…

High-throughput sequencing techniques such as metagenomic and metatranscriptomic technologies allow cataloging of functional characteristics of microbial community members as well as their taxonomic identity. Such studies have found that a…

With a view to connecting random mutation on the molecular level to punctuated equilibrium behavior on the phenotype level, we propose a new model for biological evolution, which incorporates random mutation and natural selection. In this…

The system decomposition theory has recently been developed for the dynamic analysis of nonlinear compartmental systems. The application of this theory to the ecosystem analysis has also been introduced in a separate article. Based on this…

$\ell_1$ optimization is a well known heuristic often employed for solving various forms of sparse linear problems. In this paper we look at its a variant that we refer to as the \emph{partial} $\ell_1$ and discuss its mathematical…

Living systems, from single cells to higher vertebrates, receive a continuous stream of non-stationary inputs that they sense, e.g., via cell surface receptors or sensory organs. Integrating these time-varying, multi-sensory, and often…

Microbial ecosystems are commonly modeled by fixed interactions between species in steady exponential growth states. However, microbes often modify their environments so strongly that they are forced out of the exponential state into…