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Cloud computing offers an opportunity to run compute-resource intensive climate models at scale by parallelising model runs such that datasets useful to the exoplanet community can be produced efficiently. To better understand the…

This is supplementary information for arXiv:1204.4896, which also appeared in Physical Biology 9, 026008 (2012). Main text abstract: Evolutionary experiments with microbes are a powerful tool to study mutations and natural selection. These…

The system decomposition theory has recently been developed for the dynamic analysis of nonlinear compartmental systems. The application of this theory to the ecosystem analysis has also been introduced in a separate article. Based on this…

Microbes are everywhere, including in and on our bodies, and have been shown to play key roles in a variety of prevalent human diseases. Consequently, there has been intense interest in the design of bacteriotherapies or "bugs as drugs,"…

To maintain homeostasis, living cells process information with networks of interacting molecules. Traditional models for cellular information processing have focused on networks of chemical reactions between molecules. Here, we describe how…

Topology transcends boundaries that conventionally delineate physical, biological and engineering sciences. Our ability to mathematically describe topology, combined with our access to precision tracking and manipulation approaches, has…

Stochastic agent-based models can account for millions of cells with spatiotemporal movement that can be a function of different factors. However, these simulations can be computationally expensive. In this work, we develop a novel…

State-space models (SSMs) are an important modeling framework for analyzing ecological time series. These hierarchical models are commonly used to model population dynamics, animal movement, and capture-recapture data, and are now…

Current mathematical frameworks for predicting the flux state and macromolecular composition of the cell do not rely on thermodynamic constraints to determine the spontaneous direction of reactions. These predictions may be biologically…

Biomolecular condensates constitute a newly recognized form of spatial organization in living cells. Although many condensates are believed to form as a result of phase separation, the physicochemical properties that determine the phase…

This is the first report, to our knowledge, on a systematic method for constructing a large scale kinetic metabolic model with incomplete information on kinetic parametersr, and its initial application to the modeling of central metabolism…

Metabolism plays a central role in cell physiology because it provides the molecular machinery for growth. At the genome-scale, metabolism is made up of thousands of reactions interacting with one another. Untangling this complexity is key…

We present a mathematical model based on a system of partial differential equations (PDEs) with cross-diffusion and reaction terms to describe ecological interactions between multiple bacterial species and substrates within microaggregates,…

First, we briefly describe the general growth mechanism, which governs the growth of living organisms, and its mathematical representation, the growth equation. Using the growth equation, we compute growth curve for S. cerevisiae and show…

Molecular simulations and biophysical experiments can be used to provide independent and complementary insights into the molecular origin of biological processes. A particularly useful strategy is to use molecular simulations as a modelling…

System and synthetic biology are rapidly evolving systems, but both lack tools such as those used in engineering environments to shift the their focus from the design of parts (details) to the design of systems (behaviors); to aggravate,…

Metabolic pathways describe chains of enzymatic reactions. Their modelling is a key point to understand living systems. An enzymatic reaction is an interaction between one or several metabolites (substrates) and an enzyme (simple protein or…

Experimental and empirical observations on cell metabolism cannot be understood as a whole without their integration into a consistent systematic framework. However, the characterization of metabolic flux phenotypes is typically reduced to…

Mathematical modelling has a long history in the context of collective cell migration, with applications throughout development, disease and regenerative medicine. The aim of modelling in this context is to provide a framework in which to…

Systems Biology is a fundamental field and paradigm that introduces a new era in Biology. The crux of its functionality and usefulness relies on metabolic networks that model the reactions occurring inside an organism and provide the means…