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Correctly capturing the symmetry transformations of data can lead to efficient models with strong generalization capabilities, though methods incorporating symmetries often require prior knowledge. While recent advancements have been made…
A recent burst of dynamic single-cell growth-division data makes it possible to characterize the stochastic dynamics of cell division control in bacteria. Different modeling frameworks were used to infer specific mechanisms from such data,…
Replication through cell division is one of the most fundamental processes of life and a major driver of dynamics in systems ranging from bacterial colonies to embryogenesis, tissues and tumors. While regulation often plays a role in…
Hybrid modeling provides an effective solution to cope with multiple time scales dynamics in systems biology. Among the applications of this method, one of the most important is the cell cycle regulation. The machinery of the cell cycle,…
Cell colonies of bacteria, tumour cells and fungi, under nutrient limited growth conditions, exhibit complex branched growth patterns. In order to investigate this phenomenon we present a simple hybrid cellular automaton model of cell…
This work presents a data-driven framework for multi-scale parametrization of velocity-dependent dispersive transport in porous media. Pore-scale flow and transport simulations are conducted on periodic pore geometries, and volume-averaging…
Understanding individual cortical development is essential for identifying deviations linked to neurodevelopmental disorders. However, current normative modelling frameworks struggle to capture fine-scale anatomical details due to their…
We study reduced-order models of three-dimensional perturbations in linearized channel flow using balanced proper orthogonal decomposition (BPOD). The models are obtained from three-dimensional simulations in physical space as opposed to…
Cell spreading is investigated at various scales in order to understand motility of living cells which is essential for a range of physiological activities in higher organisms as well as in microbes. At a microscopic scale, it has been seen…
Cell migration is an indispensable physiological and pathological process for normal tissue development and cancer metastasis, which is greatly regulated by intracellular signal pathways and extracellular microenvironment (ECM). However,…
While existing mathematical descriptions can accurately account for phenomena at microscopic scales (e.g. molecular dynamics), these are often high-dimensional, stochastic and their applicability over macroscopic time scales of physical…
Cell migration is a fundamental process underlying the survival and function of both unicellular and multicellular organisms. Crawling motility in eukaryotic cells arises from cyclic protrusion and retraction driven by the cytoskeleton,…
Morphological development into evolutionary patterns under structural instability is ubiquitous in living systems and often of vital importance for engineering structures. Here we propose a data-driven approach to understand and predict…
Cell-cell adhesion is one the most fundamental mechanisms regulating collective cell migration during tissue development, homeostasis and repair, allowing cell populations to self-organize and eventually form and maintain complex tissue…
Cell segmentation is a critical step for quantitative single-cell analysis in microscopy images. Existing cell segmentation methods are often tailored to specific modalities or require manual interventions to specify hyper-parameters in…
The emergence of complex patterns of organization close to the Cambrian boundary is known to have happened over a (geologically) short period of time. It involved the rapid diversification of body plans and stands as one of the major…
The morphogenesis of cells and tissues involves an interplay between chemical signals and active forces on their surrounding surface layers. The complex interaction of hydrodynamics and material flows on such active surfaces leads to…
We study the mechanical unfolding of a simple model protein. The Langevin dynamics results are analyzed using Markov-model methods which allow to describe completely the configurational space of the system. Using transition path theory we…
The growth, form, and division of prebiotic vesicles, membraneous bags of fluid of varying components and shapes is hypothesized to have served as the substrate for the origin of life. The dynamics of these out-of-equilibrium structures is…
During the development of an organism, cells must coordinate and organize to generate the correct shape, structure, and spatial patterns of tissues and organs, a process known as morphogenesis. The morphogenesis of embryonic tissues is…