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Soil is a complex, dynamic material, with physical properties that depend on its biological content. We propose a cellular automaton model for self-organizing soil structure, where soil aggregates and serves as food for microbial species.…
In evolution theory the concept of a fitness landscape has played an important role, evolution itself being portrayed as a hill-climbing process on a rugged landscape. In this article it is shown that in general, in the presence of other…
Sustainability and resilience of urban systems are multifaceted concepts, requiring information about multiple system attributes to adequately evaluate and characterize. However, despite the scientific consensus on the multivariate nature…
Bacterial conglomerates such as biofilms and microcolonies are ubiquitous in nature and play an important role in industry and medicine. In contrast to well-mixed, diluted cultures routinely used in microbial research, bacteria in a…
Quantitative predictions about the processes that promote species coexistence are a subject of active research in ecology. In particular, competitive interactions are known to shape and maintain ecological communities, and situations where…
Microbial dormancy is an evolutionary trait that has emerged independently at various positions across the tree of life. It describes the ability of a microorganism to switch to a metabolically inactive state that can withstand unfavorable…
Social interaction between microbes can be described at many levels of details, ranging from the biochemistry of cell-cell interactions to the ecological dynamics of populations. Choosing the best level to model microbial communities…
A primary motivation for our research in Digital Ecosystems is the desire to exploit the self-organising properties of biological ecosystems. Ecosystems are thought to be robust, scalable architectures that can automatically solve complex,…
Robustness is key to engineering, automation, and science as a whole. However, the property of robustness is often underpinned by costly requirements such as over-provisioning, known uncertainty and predictive models, and known adversaries.…
Inferring microbial interaction networks from abundance patterns is an important approach to advance our understanding of microbial communities in general and the human microbiome in particular. Here we suggest discriminating two levels of…
Even when concepts similar to emergence have been used since antiquity, we lack an agreed definition. However, emergence has been identified as one of the main features of complex systems. Most would agree on the statement ``life is…
Understanding how species persist under interacting stressors is a central challenge in ecology. We develop a spatially explicit reaction-diffusion framework to investigate competing species in landscapes shaped by climate variability,…
The competition for resources is a defining feature of microbial communities. In many contexts, from soils to host-associated communities, highly diverse microbes are organized into metabolic groups or guilds with similar resource…
It is generally recognized that a distinguishing feature of life is its peculiar capability to avoid equilibration. The origin of this capability and its evolution along the timeline of abiogenesis is not yet understood. We propose to study…
A challenge in global change biology is to predict how species will respond to future environmental change and to manage these responses. To make such predictions and management actions robust to novel futures, we need to accurately…
Artificial swarm systems have been extensively studied and used in computer science, robotics, engineering and other technological fields, primarily as a platform for implementing robust distributed systems to achieve pre-defined…
Ecosystems are formed by networks of species and their interactions. Traditional models of such interactions assume a constant interaction strength between a given pair of species. However, there is often significant trait variation among…
A spacially extended model of the collective behavior of a large number of locally acting organisms is proposed in which organisms move probabilistically between local cells in space, but with weights dependent on local morphogenetic…
Fitness landscapes are central in analyzing evolution, in particular for drug resistance mutations for bacteria and virus. We show that the fitness landscapes associated with antibiotic resistance are not compatible with any of the…
We propose an approach of open-ended evolution via the simulation of swarm dynamics. In nature, swarms possess remarkable properties, which allow many organisms, from swarming bacteria to ants and flocking birds, to form higher-order…