Related papers: Modelling Soil as a Living System: Feedback betwee…
A cellular automaton model is used to describe the dynamics of the catalytic oxidation of $CO$ on a $Pt(100)$ surface. The cellular automaton rules account for the structural phase transformations of the $Pt$ substrate, the reaction…
Biological systems exhibit large-scale self-organized dynamics and structures which enable organisms to perform the functions of life. The field of active matter strives to develop and understand microscopically-driven nonequilibrium…
This study investigates the role of spatial segregation, prompted by competition avoidance, as a key mechanism for emergent coexistence within microbial communities. Recognizing these communities as complex adaptive systems, we challenge…
The rise in the availability of bacterial genomes defines a need for synthesis: abstracting from individual taxa, to see larger patterns of bacterial lifestyles across systems. A key concept for such synthesis in ecology is the niche, the…
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.…
Spatial structure and species interactions jointly shape the dynamics and biodiversity of ecological systems, yet most theoretical models either neglect spatial heterogeneity or sacrifice analytical tractability. Here, we provide a unified…
Nowadays, multiscale modelling is recognized as the most suitable way to study biological processes. Indeed, almost every phenomenon in nature exhibits a multiscale behaviour, i.e., it is the outcome of interactions that occur at different…
Our planet is roughly closed to matter, but open to energy input from the sun. However, to harness this energy, organisms must transform matter from one chemical (redox) state to another. For example, photosynthetic organisms can capture…
Vegetation in semi-arid ecosystems frequently organizes into spatially heterogeneous mosaics that regulate ecosystem functioning, productivity, and resilience. These patterns arise from local biological interactions, including facilitation…
Adaptive control in biological systems, such as intestinal immunity, remains poorly understood despite detailed knowledge of underlying regulatory networks. We propose an alternative framework based on stochastic martingale turnover, in…
Activity and autonomous motion are fundamental aspects of many living and engineering systems. Here, the scale of biological agents covers a wide range, from nanomotors, cytoskeleton, and cells, to insects, fish, birds, and people. Inspired…
Biofilms in porous media critically influence hydraulic properties in environmental and engineered systems. However, a mechanistic understanding of how microbial life controls permeability remains elusive. By combining microfluidics,…
Cells coexist together in colonies or as tissues. Their behaviour is controlled by an interplay between intercellular forces and biochemical regulation. We develop a simple model of the cell cycle, the fundamental regulatory network…
Planktonic active matter represents an emergent system spanning different scales: individual, population and community; and complexity arising from sub-cellular and cellular to collective and ecosystem scale dynamics. This cross-scale…
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…
We propose a model for co-evolving ecosystems that takes into account two levels of description of an organism, for instance genotype and phenotype. Performance at the macroscopic level forces mutations at the microscopic level. These, in…
Cell colonies of bacteria, tumour cells and fungi, under nutrient limited growth conditions, exhibit complex branched growth patterns. In order to investigate this phenomenon we present a simple hybrid cellular automaton model of cell…
Microbes thrive in diverse porous environments -- from soil and riverbeds to human lungs and cancer tissues -- spanning multiple scales and conditions. Short- to long-term fluctuations in local factors induce spatio-temporal…
Alignment interactions in active matter are typically modeled as relaxational dynamics toward local consensus. In unbounded systems, this makes alignment effectively decoupled from local density and therefore unable to sustain self-confined…
Nature uses elongated shapes and filaments to build stable structures, generate motion, and allow complex geometric interactions. In this Review, we examine the role of biological filaments across different length scales. From the molecular…