相关论文: Phytoplankton temporal strategies increase entropy…
Circadian clocks are oscillatory genetic networks that help organisms adapt to the 24-hour day/night cycle. The clock of the green alga Ostreococcus tauri is the simplest plant clock discovered so far. Its many advantages as an experimental…
In this paper, by using a stochastic reaction-diffusion-taxis model, we analyze the picophytoplankton dynamics in the basin of the Mediterranean Sea, characterized by poorly mixed waters. The model includes intraspecific competition of…
We develop non-equilibrium theory by using averages in time and space as a generalized way to upscale thermodynamics in non-ergodic systems. The approach offers a classical perspective on the energy dynamics in fluctuating systems. The rate…
A framework for exponential time discretization of the multilayer rotating shallow water equations is developed in combination with a mimetic discretization in space. The method is based on a combination of existing exponential time…
Entropy production in stochastic mechanical systems is examined here with strict bounds on its rate. Stochastic mechanical systems include pure diffusions in Euclidean space or on Lie groups, as well as systems evolving on phase space for…
Based on the law of mass action (and its microscopic foundation) and mass conservation, we present here a method to derive consistent dynamic models for the time evolution of systems with an arbitrary number of species. Equations are…
Historically studies of behaviour on networks have focused on the behaviour of individuals (node-based) or on the aggregate behaviour of the entire network. We propose a new method to decompose a temporal network into macroscale components…
In this paper we formulate a geometric theory of the mechanics of growing solids. Bulk growth is modeled by a material manifold with an evolving metric. Time dependence of metric represents the evolution of the stress-free (natural)…
We present a model for a biological reactor in which bacteria tend to aggregate in flocs, as encountered in wastewater treatment plants. The influence of this flocculation on the growth dynamics of the bacteria is studied. We argue that a…
Measuring entropy production of a system directly from the experimental data is highly desirable since it gives a quantifiable measure of the time-irreversibility for non-equilibrium systems and can be used as a cost function to optimize…
Biochemical signaling cascades transmit intracellular information while dissipating energy under nonequilibrium conditions. We model a cascade as a code string and apply information-entropy ideas to quantify an optimal transmission rate. A…
Yeasts exist in communities that expand over space and time to form complex structures and patterns. We developed a computational lattice-based framework to perform spatial-temporal simulations of budding yeast colonies exposed to different…
Active systems comprise a class of nonequilibrium dynamics in which individual components autonomously dissipate energy. Efforts towards understanding the role played by activity have centered on computation of the entropy production rate…
In this work we develop and analyze a mathematical model of biological control to prevent or attenuate the explosive increase of an invasive species population in a three-species food chain. We allow for finite time blow-up in the model as…
Logarithmic growth-rates are fundamental observables for describing ecological systems and the characterization of their distributions with analytical techniques can greatly improve their comprehension. Here a neutral model based on a…
Collective behaviors displayed by groups of social animals are observed frequently in nature. Understanding and predicting the behavior of complex biological systems is dependent on developing effective descriptions and models. While…
Gut microbial composition has been linked to multiple health outcomes. Yet, temporal analysis of this composition had been limited to deterministic models. In this paper, we introduce a probabilistic model for the dynamics of intestinal…
Predicting the fate of ecologies is a daunting, albeit extremely important, task. As part of this task one needs to develop an understanding of the organization, hierarchies, and correlations among the species forming the ecology. Focusing…
In the growth of bacterial colonies, a great variety of complex patterns are observed in experiments, depending on external conditions and the bacterial species. Typically, existing models employ systems of reaction-diffusion equations or…
The energy consumption, the transfer of resources through the international trade, the transition towards renewable energies and the environmental sustainability appear as key drivers in order to evaluate the resilience of the energy…