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Fluctuating environments pose tremendous challenges to bacterial populations. It is observed in numerous bacterial species that individual cells can stochastically switch among multiple phenotypes for the population to survive in rapidly…
What makes living things special is how they manage matter, energy, and entropy. A general theory of organismal metabolism should therefore be quantified in these three currencies while capturing the unique way they flow between individuals…
Systems biology and whole-cell modelling are demanding increasingly comprehensive mathematical models of cellular biochemistry. These models require the development of simplified models of specific processes which capture essential…
Measurement in biological systems became a subject of concern as a consequence of numerous reports on limited reproducibility of experimental results. To reveal origins of this inconsistency, we have examined general features of biological…
Polynomial dynamical systems are widely used to model and study real phenomena. In biochemistry, they are the preferred choice for modelling the concentration of chemical species in reaction networks with mass-action kinetics. These systems…
One of the major challenges in biology concerns the integration of data across length and time scales into a consistent framework: how do macroscopic properties and functionalities arise from the molecular regulatory networks - and how can…
Mathematical and statistical models underlie many of the world's most important fisheries management decisions. Since the 19th century, difficulty calibrating and fitting such models has been used to justify the selection of simple,…
Microbial populations exhibit a broad spectrum of nutrient utilization strategies, ranging from strategies utilizing diverse nutrients, called "generalists," to those being highly adapted to specific nutrients, called "specialists." The…
Nutrient gradients and limitations play a pivotal role in the life of all microbes, both in their natural habitat as well as in artificial, microfluidic systems. Spatial concentration gradients of nutrients in densely packed cell…
High-throughput experimental techniques and bioinformatics tools make it possible to obtain reconstructions of the metabolism of microbial species. Combined with mathematical frameworks such as flux balance analysis, which assumes that…
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…
Coherence evolution of two food web models can be obtained under the stirring effect of chaotic advection. Each food web model sustains a three--level trophic system composed of interacting predators, consumers and vegetation. These…
This paper presents a conceptual model describing the medium and long-term co-evolution of natural and socio-economic subsystems of Earth. An economy is viewed as an out-of-equilibrium dissipative structure that can only be maintained with…
Growth rates and biomass yields are key descriptors used in microbiology studies to understand how microbial species respond to changes in the environment. Of these, biomass yield estimates are typically obtained using cell counts and…
We investigate the stability properties of two different classes of metabolic cycles using a combination of analytical and computational methods. Using principles from structural kinetic modeling (SKM), we show that the stability of…
Evolutionary transitions among ecological interactions are widely known, although their detailed dynamics remain absent for most population models. Adaptive dynamics has been used to illustrate how the parameters of population models might…
This paper deals with a general system of equations and conditions arising from a mathematical model of prostate cancer growth with chemotherapy and antiangiogenic therapy that has been recently introduced and analyzed (see [P. Colli et…
Generalizing the cyclically competing three-species model (often referred to as the rock-paper-scissors game), we consider a simple system of population dynamics without spatial structures that involves four species. Unlike the previous…
In this paper we study the dynamics of stochastic microorganism flocculation models. Given the strong influence of environmental and seasonal fluctuations that are present in these models, we propose a stochastic model that includes…
State machine formalisms equipped with hierarchy and parallelism allow to compactly model complex system behaviours. Such models can then be transformed into executable code or inputs for model-based testing and verification techniques.…