Related papers: Computation Of Microbial Ecosystems in Time and Sp…

The processes taking place inside the living cell are now understood to the point where predictive computational models can be used to gain detailed understanding of important biological phenomena. A key challenge is to extrapolate this…

Dynamic flux balance analysis uses a quasi-steady state assumption to calculate an organism's metabolic activity at each time-step of a dynamic simulation, using the well-known technique of flux balance analysis. For microbial communities,…

Computation, if treated as a set of physical processes that act on information represented by states of matter, encompasses biological systems, digital systems, and other constructs, and may be a fundamental measure of living systems. The…

Complex organic molecules (COMs), the building blocks of life, have been extensively detected under various physical conditions, from quiescent clouds to star-forming regions. They therefore serve as excellent tracers for the local physical…

Chemical reaction networks underpin biological and physical phenomena across scales, from microbial interactions to planetary atmosphere dynamics. Bacterial communities exhibit complex competitive interactions for resources, human organs…

In Part I of this article we have developed a novel mechanobiological model of a Tissue Engineering process that accounts for the mechanisms through which an isotropic or anisotropic adherence condition regulates the active functions of the…

Surveys of microbial biodiversity such as the Earth Microbiome Project (EMP) and the Human Microbiome Project (HMP) have revealed robust ecological patterns across different environments. A major goal in ecology is to leverage these…

Dynamical systems in the life sciences are often composed of complex mixtures of overlapping behavioral regimes. Cellular subpopulations may shift from cycling to equilibrium dynamics or branch towards different developmental fates. The…

Phytoplankton is the basis of marine food webs, driving both ecological processes and global biogeochemical cycles. Despite their ecological and climatic significance, accurately simulating phytoplankton dynamics remains a major challenge…

Microbes are often discussed in terms of dichotomies such as copiotrophic/oligotrophic and fast/slow-growing microbes, defined using the characterisation of microbial growth in isolated cultures. The dichotomies are usually qualitative…

With recent advances in structural biology, including experimental techniques and deep learning-enabled high-precision structure predictions, molecular dynamics methods that scale up to large biomolecular systems are required. Current…

Growth patterns generated by filamentous organisms (e.g. actinomycetes and fungi) involve spatial and temporal dynamics at different length scales. Several mathematical models have been proposed in the last thirty years to address these…

Microorganisms employ sophisticated mechanisms for intercellular communication and environmental sensing, with quorum sensing serving as a fundamental regulatory process. Dysregulation of quorum sensing has been implicated in various…

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…

Rapid environmental change and advances in data-driven analysis highlight the need not only to use computational tools, but also to foster understanding of the natural world and inspire creativity. Photosynthesis, the process that fuels…

Metabolism displays striking and robust regularities in the forms of modularity and hierarchy, whose composition may be compactly described. This renders metabolic architecture comprehensible as a system, and suggests the order in which…

The introduction of non-native organisms into complex microbiome communities holds enormous potential to benefit society. However, microbiome engineering faces several challenges including successful establishment of the organism into the…

Climate change is profoundly affecting nearly all aspects of life on earth, including human societies, economies and health. Various human activities are responsible for significant greenhouse gas emissions, including data centres and other…

The nematode Caenorhabditis elegans is a well-known model organism used to investigate fundamental questions in biology. Motility assays of this small roundworm are designed to study the relationships between genes and behavior. Commonly,…

We view Digital Ecosystems to be the digital counterparts of biological ecosystems, exploiting the self-organising properties of biological ecosystems, which are considered to be robust, self-organising and scalable architectures that can…