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During cell division paired (sister) chromosomes are observed to perform approximate saw-tooth oscillations across the cell mid-plane. Experimental data suggests that these oscillations are regulated through intersister tension. We propose…
Time series classification (TSC) of biological signals has progressed from handcrafted, modality-specific approaches to deep architectures capable of representing the diverse waveform structures of underlying physiological processes (i.e.,…
How the cells break symmetry and organize their edge activity to move directionally is a fun- damental question in cell biology. Physical models of cell motility commonly rely on gradients of regulatory factors and/or feedback from the…
Development from egg to embryo to adult is a fascinating instance of biological self-organization for which genetics has supplied us with a parts list. It remains to find the principles organizing the assembly of those parts. In the last…
Controlling growth via cell division is crucial in the development of higher organisms, and yet the mechanisms through which this is achieved, e.g., in epithelial tissue, is not yet fully understood. We show that by coupling the cell cycle…
The process of morphogenesis is an evolution of the shape of an organism together with the differentiation of its parts. This process encompasses numerous biological processes ranging from embryogenesis to regeneration following crisis such…
This paper deals with the numerical modeling of wave propagation in porous media described by Biot's theory. The viscous efforts between the fluid and the elastic skeleton are assumed to be a linear function of the relative velocity, which…
Understanding the rules underlying organismal development is a major unsolved problem in biology. Each cell in a developing organism responds to signals in its local environment by dividing, excreting, consuming, or reorganizing, yet how…
We present a model of systems of cells with intracellular oscillators (`clocks'). This is motivated by examples from developmental biology and from the behavior of organisms on the threshold to multicellularity. Cells undergo random motion…
Embedding efficient calculation instructions into biochemical system has always been a research focus in synthetic biology. One of the key problems is how to sequence the chemical reaction modules that act as units of computation and make…
Previous studies of lasers and nonlinear resonators have revealed that the polarisation degree of freedom allows for the formation of polarisation patterns and novel localized structures, such as vectorial defects. Type II optical…
Biological oscillators are very diverse but can be classified based on dynamical motifs such as the types of feedback loops present. The S. Elongatus circadian clock is a remarkable phosphorylation-based oscillator that can be reconstituted…
The Kuramoto model is a commonly used mathematical model for studying synchronized oscillations in biological systems, with its temporal synchronization properties well studied. However, the properties of spatial waves have received less…
Vertebrae localization, segmentation and identification in CT images is key to numerous clinical applications. While deep learning strategies have brought to this field significant improvements over recent years, transitional and…
Reaction-diffusion systems have been widely used to study spatio-temporal phenomena in cell biology, such as cell polarization. Coupled bulk-surface models naturally include compartmentalization of cytosolic and membrane-bound polarity…
Constraints in embryonic development are thought to bias the direction of evolution by making some changes less likely, and others more likely, depending on their consequences on ontogeny. Here, we characterize the constraints acting on…
Motile cilia are slender, hair-like cellular appendages that spontaneously oscillate under the action of internal molecular motors and are typically found in dense arrays. These active filaments coordinate their beating to generate…
We review the construction and evolution of mathematical models of the Arabidopsis circadian clock, structuring the discussion into two distinct historical phases of modeling strategies: extension and reduction. The extension phase explores…
During slow-wave sleep, the brain is in a self-organized regime in which slow oscillations (SOs) between up- and down-states travel across the cortex. While an isolated piece of cortex can produce SOs, the brain-wide propagation of these…
We present the results of numerical simulations of wave propagation and jet formation in solar atmosphere models with different magnetic field configurations. The presence in the chromosphere of waves with periods longer than the acoustic…