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A model of pattern formation in living systems is presented. The pattern is achieved by the sequential interaction of two signaling pathways. The coupling of the pattern to the (thick) epithelial sheet changes is given, when the Gauss…
Mathematical models are vital interpretive and predictive tools used to assist in the understanding of cell migration. There are typically two approaches to modelling cell migration: either micro-scale, discrete or macro-scale, continuum.…
We present a modelling framework for the dynamics of cells structured by the concentration of a micromolecule they contain. We derive general equations for the evolution of the cell population and of the extra-cellular concentration of the…
Macrophages function as sentinel, cell-regulatory hubs capable of initiating, perpetuating and contributing to the resolution of an inflammatory response, following their activation from a resting state. Highly complex and varied gene…
Modeling and simulation are recognized as important aspects of the scientific method for more than 70 years but its adoption in biology has been slow. Debates on its representativeness, usefulness, and whether the effort spent on such…
Biological cells are able to generate intricate structures and respond to external stimuli, sculpting their membrane from within. Simplified biomimetic systems can aid in understanding the principles which govern these shape changes and…
The nematode Caenorhabditis elegans (C. elegans) is used as a model organism to better understand developmental biology and neurobiology. C. elegans features an invariant cell lineage, which has been catalogued and observed using…
Cell growth and gene expression, essential elements of all living systems, have long been the focus of biophysical interrogation. Advances in single-cell methods have invigorated theoretical studies into these processes. However, until…
Evolutionary biology shares many concepts with statistical physics: both deal with populations, whether of molecules or organisms, and both seek to simplify evolution in very many dimensions. Often, methodologies have undergone parallel and…
Medical imaging diagnosis increasingly relies on Machine Learning (ML) models. This is a task that is often hampered by severely imbalanced datasets, where positive cases can be quite rare. Their use is further compromised by their limited…
Stochastic simulation can make the molecular processes of cellular control more vivid than the traditional differential-equation approach by generating typical system histories instead of just statistical measures such as the mean and…
The aim of this paper is two-fold. First, we propose a new computational method to investigate the particularities of evolution. Second, we apply this method to a model of gene regulatory networks (GRNs) and explore the evolution of…
The correspondence of single-field cosmological models based on Einstein gravity to modern observational data is considered. A method is proposed to determine possible types of dynamics based on extreme values of the scalar field. It is…
We introduce a formalism for the geometry of eukaryotic cells and organisms.Cells are taken to be star-convex with good biological reason. This allows for a convenient description of their extent in space as well as all manner of cell…
The landscape of computational modeling in cancer systems biology is diverse, offering a spectrum of models and frameworks, each with its own trade-offs and advantages. Ideally, models are meant to be useful in refining hypotheses, to…
The applicability of computational and dynamical systems models to organisms is scrutinized, using examples from developmental biology and cognition. Developmental morphogenesis is dependent on the inherent material properties of developing…
Advances in imaging technology now provide us with detailed 3D data on gene expression patterns in developing embryos. This information can be used to build predictive mathematical models of embryogenesis. Current modelling approaches are,…
Much of our mechanistic understanding of the functions of biological macromolecules is based on static structural experiments, which can be modelled either as single structures or conformational ensembles. While these provide us with…
The growth and scaling of organs is a fundamental aspect of animal development. However, how organs grow to the right size and shape required by physiological demands, remains largely unknown. Here, we provide a framework combining theory…
Motility is an essential factor for an organism's survival and diversification. With the advent of novel single-cell technologies, analytical frameworks and theoretical methods, we can begin to probe the complex lives of microscopic motile…