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This paper presents a real-time simulation involving ''protozoan-like'' cells that evolve by natural selection in a physical 2D ecosystem. Selection pressure is exerted via the requirements to collect mass and energy from the surroundings…
When our immune system encounters foreign antigens (i.e., from pathogens), the B cells that produce our antibodies undergo a cyclic process of proliferation, mutation, and selection, improving their ability to bind to the specific antigen.…
Conventional phase segregation is controlled by a positive interfacial tension, which implies that the system relaxes towards a state in which the interfacial area (or length) is minimized, typically manifesting as a single droplet that…
We introduce and analyze a class of neural network models motivated by the Drosophila central complex nervous system, designed to capture the emergence and dynamics of orientation-selective activity bumps. Starting from a biologically…
The transport of bio-particles in viscous flows exhibits a rich variety of dynamical behaviour, such as morphological transitions, complex orientation dynamics or deformations. Characterising such complex behaviour under well controlled…
We measure the reliability of signals at three levels within the blowfly visual system, and present a theoretical framework for analyzing the experimental results, starting from the Poisson process. We find that blowfly photoreceptors, up…
The diffusive arrival of transcription factors at the promoter sites on the DNA sets a lower bound on how accurately a cell can regulate its protein levels. Using results from the literature on diffusion-influenced reactions, we derive an…
A central problem in biology is to understand how organisms evolve and adapt to their environment by acquiring variations in the observable characteristics or traits of species across the tree of life. With the growing availability of…
Embryonic development is driven by spatial patterns of gene expression that determine the fate of each cell in the embryo. While gene expression is often highly erratic, embryonic development is usually exceedingly precise. In particular,…
We consider an extension of model-based clustering to the semi-supervised case, where some of the data are pre-labeled. We provide a derivation of the Bayesian Information Criterion (BIC) approximation to the Bayes factor in this setting.…
Cytoplasmic streaming, the coherent flow of cytoplasm, plays a critical role in transport and mixing over large scales in eukaryotic cells. In many large cells, this process is driven by active forces at the cell boundary, such as cortical…
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.,…
Continuous-time birth-death-shift (BDS) processes are frequently used in stochastic modeling, with many applications in ecology and epidemiology. In particular, such processes can model evolutionary dynamics of transposable elements -…
Recent advancements in the ability to construct three-dimensional (3D) tissues and organoids from stem cells and biomaterials have not only opened abundant new research avenues in disease modeling and regenerative medicine but also have…
The concept of internal anatomical asymmetry is familiar; usually in humans the heart is on the left and the liver is on the right, however how does the developing embryo know to produce this consistent laterality? Symmetry breaking…
While most processes in biology are highly deterministic, stochastic mechanisms are sometimes used to increase cellular diversity, such as in the specification of sensory receptors. In the human and Drosophila eye, photoreceptors sensitive…
Gene expression is a central process to any form of life. It involves multiple temporal and functional scales that extend from specific protein-DNA interactions to the coordinated regulation of multiple genes in response to intracellular…
Atomic level defects such as dislocations play key roles in determining the macroscopic properties of crystalline materials. Their effects are important and wide-reaching, and range from increased chemical reactivity to enhanced mechanical…
How does growth encode form in developing organisms? Many different spatiotemporal growth profiles may sculpt tissues into the same target 3D shapes, but only specific growth patterns are observed in animal and plant development. In…
Morphological traits are physical characteristics of biological organisms that provide vital clues on how organisms interact with their environment. Yet extracting these traits remains a slow, expert-driven process, limiting their use in…