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In biopharmaceutical manufacturing, fermentation processes play a critical role in productivity and profit. A fermentation process uses living cells with complex biological mechanisms, leading to high variability in the process outputs,…

Microscopic organisms, such as bacteria, have the ability of colonizing surfaces and developing biofilms that can determine diseases and infections. Most bacteria secrete a significant amount of extracellular polymer substances that are…

We are interested in modeling some two-level population dynamics, resulting from the interplay of ecological interactions and phenotypic variation of individuals (or hosts) and the evolution of cells (or parasites) of two types living in…

Mutation rate is a key determinant of the pace as well as outcome of evolution, and variability in this rate has been shown in different scenarios to play a key role in evolutionary adaptation and resistance evolution under stress caused by…

Living systems such as neuronal networks and animal groups process information about their environment via the dynamics of interacting units. These can transition between distinct macroscopic behaviors. Near such a transition (or critical…

For biological experiments aiming at calibrating models with unknown parameters, a good experimental design is crucial, especially for those subject to various constraints, such as financial limitations, time consumption and physical…

Bacterial biofilms are among the oldest and most prevalent multicellular life forms on Earth and are increasingly relevant in research areas related to industrial fouling, medicine and biotechnology. The main hurdles to obtaining definitive…

A mathematical model for emerging contaminants sorption in multispecies biofilms, based on a continuum approach and mass conservation principles is presented. Diffusion of contaminants within the biofilm is described using a…

Modern biological tools have made it possible to unequivocally demonstrate the deep relationship among species in terms of genes and basic molecular mechanisms. In addition, results from genetic, physical and physiological approaches…

Bacterial plant pathogens rely on a battalion of transcription factors to fine-tune their response to changing environmental conditions and marshal the genetic resources required for successful pathogenesis. Prediction of transcription…

The spatial organization of bacteria in dense biofilms is key to their collective behaviour, and understanding it will be important for medical and technological applications. Here we study the morphology of a compact biofilm that undergoes…

Living systems continuously sense, integrate, and act on chemical information using multiscale biochemical networks whose dynamics are inherently nonlinear, adaptive, and energy-efficient. Yet, most attempts to harness such "wetware" for…

Anisotropic collective patterns occur frequently in the morphogenesis of 2D biofilms. These patterns are often attributed to growth regulation mechanisms and differentiation based on gradients of diffusing nutrients and signalling…

Here we introduce a new design framework for synthetic biology that exploits the advantages of Bayesian model selection. We will argue that the difference between inference and design is that in the former we try to reconstruct the system…

The application of deep learning methods, particularly foundation models, in biological research has surged in recent years. These models can be text-based or trained on underlying biological data, especially omics data of various types.…

Ecosystems are governed by dynamic processes such as competition for resources, reproduction and dispersal. These shape their biodiversity and how the system responds to change. Current approaches to modelling ecosystems, especially plants,…

We explore how physical scale and population size shape the emergence of complex behaviors in open-ended ecological environments. In our setting, agents are unsupervised and have no explicit rewards or learning objectives but instead evolve…

Reliable predictions from systems biology models require knowing whether parameters can be estimated from available data, and with what certainty. Identifiability analysis reveals whether parameters are learnable in principle (structural…

We present a two-species population model in a well-mixed environment where the dynamics involves, in addition to birth and death, changes due to environmental factors and inter-species interactions. The novel dynamical components are…

There is an abundance of complex dynamic systems that are critical to our daily lives and our society but that are hardly understood, and even with today's possibilities to sense and collect large amounts of experimental data, they are so…