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Metabolism and evolution are closely connected: if a mutation incurs extra energetic costs for an organism, there is a baseline selective disadvantage that may or may not be compensated for by other adaptive effects. A long-standing, but to…
The methodology named LIFE (Linear-in-Flux-Expressions) was developed with the purpose of simulating and analyzing large metabolic systems. With LIFE, the number of model parameters is reduced by accounting for correlations among the…
Feeding a larger and wealthier global population without transgressing ecological limits is increasingly challenging, as rising food demand (especially for animal products) intensifies pressure on ecosystems, accelerates deforestation, and…
Dormancy is an essential strategy for microorganisms to cope with environmental stress. However, global ecosystem models typically ignore microbial dormancy, resulting in major model uncertainties. To facilitate the consideration of…
The linear hydrodynamic stability of a model for confined quasi-two-dimensional granular gases is analyzed. The system exhibits homogeneous hydrodynamics, i.e. there are macroscopic evolution equations for homogeneous states. The stability…
The dynamics of microbial communities is incredibly complex, determined by competition for metabolic substrates and cross-feeding of byproducts. Species in the community grow by harvesting energy from chemical reactions that transform…
Finite stochastic Markov models play a major role for modelling biochemical pathways. Such models are a coarse-grained description of the underlying microscopic dynamics and can be considered mesoscopic. The level of coarse-graining is to a…
Metabolic networks consist of linked functional components, or modules. The mechanism underlying metabolic network modularity is of great interest not only to researchers of basic science but also to those in fields of engineering. Previous…
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…
Unravelling current complex food systems is relevant for their adjustment and redesign under the current changing climate conditions. Redesign may be necessitated by migration of people and changes of locations of major agri-food…
We propose and analyze a nonlinear age-structured multi-species model that serves as a unifying framework for ecological and biotechnological systems in complex environments (microbial communities, bioreactors, and others). The formulation…
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…
A mathematical model involving a syntrophic relationship between two populations of bacteria in a continuous culture is proposed. A detailed qualitative analysis is carried out. The local and global stability analysis of the equilibria are…
We adapt existing statistical modeling techniques for social networks to study consumption data observed in trophic food webs. These data describe the feeding volume (non-negative) among organisms grouped into nodes, called trophic species,…
Multistability is a phenomenon prevalent in many natural systems. In climate, for example, it allows the possibility of irreversible consequences on planetary scale as a result of climate change. Indeed, a climate ``tipping element'' is a…
Experimental studies of microbial communities routinely reveal that they have multiple stable states. While each of these states is generally resilient, certain perturbations such as antibiotics, probiotics and diet shifts, result in…
The global food system faces various endogeneous and exogeneous, biotic and abiotic risk factors, including a rising human population, higher population densities, price volatility and climate change. Quantitative models play an important…
For years, a main focus of ecological research has been to better understand the complex dynamical interactions between species which comprise food webs. Using the connectance properties of a widely explored synthetic food web called the…
The role of species interactions in controlling the interplay between the stability of an ecosystem and its biodiversity is still not well understood. The ability of ecological communities to recover after a small perturbation of the…
Ecological systems are complex dynamical systems. Modelling efforts on ecosystems' dynamical stability have revealed that population dynamics, being highly nonlinear, can be governed by complex fluctuations. Indeed, experimental and field…