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Artificial Intelligence Virtual Cells (AIVCs) aim to learn executable, decision-relevant models of cell state from multimodal, multiscale measurements. Recent studies have introduced single-cell and spatial foundation models, improved…
Eukaryotic cells adhere to extracellular matrix during the normal development of the organism, forming static adhesion as well as during cell motility. We study this process by considering a simplified coarse-grained model of a vesicle that…
Modeling membrane interactions with arbitrarily shaped colloidal particles, such as environmental micro- and nanoplastics, at the cell scale remains particularly challenging, owing to the complexity of particle geometries and the need to…
Active nematics is an emerging paradigm for characterising biological systems. One aspect of particularly intense focus is the role active nematic defects play in these systems, as they have been found to mediate a growing number of…
Mathematical models come in many forms across biological applications. In the case of complex, spatial dynamics and pattern formation, stochastic models also face two main challenges: pattern data is largely qualitative, and model…
Vertex models are a popular approach to modeling the mechanical and dynamical properties of dense biological tissues, describing the tissue as a network of connected polygons representing the cells. Recently a class of two-dimensional…
In this paper homogenization of a mathematical model for plant tissue biomechanics is presented. The microscopic model constitutes a strongly coupled system of reaction-diffusion-convection equations for chemical processes in plant cells,…
A contemporary procedure to grow artificial tissue is to seed cells onto a porous biomaterial scaffold and culture it within a perfusion bioreactor to facilitate the transport of nutrients to growing cells. Typical models of cell growth for…
Although tissues are usually studied in isolation, this situation rarely occurs in biology, as cells, tissues, and organs, coexist and interact across scales to determine both shape and function. Here, we take a quantitative approach…
In this paper we address some modelling issues related to biological growth. Our treatment is based on a recently-proposed, general formulation for growth within the context of Mixture Theory (Journal of the Mechanics and Physics of Solids,…
Collective cell migration is a highly regulated process involved in wound healing, cancer metastasis and morphogenesis. Mechanical interactions among cells provide an important regulatory mechanism to coordinate such collective motion.…
We present SoftSMPL, a learning-based method to model realistic soft-tissue dynamics as a function of body shape and motion. Datasets to learn such task are scarce and expensive to generate, which makes training models prone to overfitting.…
Morphogenesis, tissue regeneration and cancer invasion involve transitions in tissue morphology. These transitions, caused by collective cell migration (CCM), have been interpreted as active wetting/de-wetting transitions. This phenomenon…
Understanding the behaviour of biological systems requires a complex setting of in vitro and in vivo experiments, which attracts high costs in terms of time and resources. The use of mathematical models allows researchers to perform…
Collective cell migration governs a range of physiological and pathological processes, from tissue morphogenesis to cancer invasion, in which topological defects arise as an inevitable consequence of frequent cellular rearrangement and…
Cell rearrangements are fundamental mechanisms driving large-scale deformations of living tissues. In three-dimensional (3D) space-filling cell aggregates, cells rearrange through local topological transitions of the network of cell-cell…
Virtual cell modeling aims to predict cellular responses to perturbations. Existing virtual cell models rely heavily on large-scale single-cell datasets, learning explicit mappings between gene expression and perturbations. Although recent…
We theoretically explore fluidization of epithelial tissues by active T1 neighbor exchanges. We show that the geometry of cell-cell junctions encodes important information about the local features of the energy landscape, which we support…
Most conspicuous organisms are multicellular and most multicellular organisms develop somatic cells to perform specific, non-reproductive tasks. The ubiquity of this division of labor suggests that it is highly advantageous. In this paper,…
The Dynamic Template model of biological cell membranes and the cytoplasm as spatially organised fluid layers is extended to plant cells, and is shown to offer a feasible shear driven mechanism for the co-alignment of internal and external…