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Microbes can affect processes from food production to human health. Such microbes are not isolated, but rather interact with each other and establish connections with their living environments. Understanding these interactions is essential…
Organogenesis is a tightly regulated process that has been studied experimentally for decades. Computational models can help to integrate available knowledge and to better understand the underlying regulatory logic. We are currently…
The solution space of genome-scale models of cellular metabolism provides a map between physically viable flux configurations and cellular metabolic phenotypes described, at the most basic level, by the corresponding growth rates. By…
We propose a generic model of eco-systems, with a {\it hierarchical} food web structure. In our computer simulations we let the eco-system evolve continuously for so long that that we can monitor extinctions as well as speciations over…
A major goal of modern computational biology is to simulate the collective behaviour of large cell populations starting from the intricate web of molecular interactions occurring at the microscopic level. In this paper we describe a…
Computation of biological processes creates great promise for everyday life and great challenges for physical scientists. Simulations of molecular dynamics appeal to biologists as a natural extension of structural biology. Once biologists…
Biochars have been attracting renewed attention as economical and environmentally friendly carbon sequestration materials with a diverse range of applications. However, experimental developments may be limited by the lack of molecular-level…
With the rise of computers, simulation models have emerged beside the more traditional statistical and mathematical models as a third pillar for ecological analysis. Broadly speaking, a simulation model is an algorithm, typically…
Living organisms rely on molecular networks, such as gene circuits and signaling pathways, for information processing and robust decision-making in crowded, noisy environments. Recent advances show that interacting biomolecules…
The modelling and analysis of biological systems has deep roots in Mathematics, specifically in the field of ordinary differential equations (ODEs). Alternative approaches based on formal calculi, often derived from process algebras or term…
Food-webs and other classes of ecological network motifs, are a means of describing feeding relationships between consumers and producers in an ecosystem. They have application across scales where they differ only in the underlying…
Particle-mesh simulations trade small-scale accuracy for speed compared to traditional, computationally expensive N-body codes in cosmological simulations. In this work, we show how a data-driven model could be used to learn an effective…
The biomolecules in and around a living cell -- proteins, nucleic acids, lipids, carbohydrates -- continuously sample myriad conformational states that are thermally accessible at physiological temperatures. Simultaneously, a given…
The modelling and analysis of biological systems has deep roots in Mathematics, specifically in the field of Ordinary Differential Equations. Alternative approaches based on formal calculi, often derived from process algebras or term…
Integrating microbial activity into underground hydrogen storage models is crucial for simulating long-term reservoir behavior. In this work, we present a coupled framework that incorporates bio-geochemical reactions and compositional flow…
Interest in the study of in-host microbial communities has increased in recent years due to our improved understanding of the communities' significant role in host health. As a result, the ability to model these communities using…
Bioconvection, a phenomenon arising from the collective motion of motile microorganisms, plays a crucial role in shaping microbial distributions, fluid dynamics, and bloom formation in aquatic environments. While extensive research has…
To develop and investigate detailed mathematical models of cellular metabolic processes is one of the primary challenges in systems biology. However, despite considerable advance in the topological analysis of metabolic networks, explicit…
Linear waste management systems are unsustainable and contribute to environmental degradation, economic inequity, and health disparities. Among the array of environmental challenges stemming from anthropogenic impacts, the management of…
For the study of complex synthetic and biological molecular systems by computer simulations one is still restricted to simple model systems or to by far too small time scales. To overcome this problem multiscale techniques are being…