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Confirming Turing's theory of morphogens in developmental processes is challenging, and synthetic biology has opened new avenues for testing Turing's predictions. Synthetic mammalian pattern formation has been recently achieved through a…
In a cellular medium, the plasmic membrane is a place of interactions between the cell and its direct external environment. A classic model describes it as a fluid mosaic. The fluid phase of the membrane allows a lateral degree of freedom…
Proteins in complex with small molecule ligands represent the core of structure-based drug discovery. However, three-dimensional representations are absent from most deep-learning-based generative models. We here present a graph-based…
Semantic associations such as the link between "bird" and "flew" are foundational for language modeling as they enable models to go beyond memorization and instead generalize and generate coherent text. Understanding how these associations…
Budding allows virus replication and macromolecular secretion in cells. It involves the formation of a bud, i.e. an outgrowth from the cell membrane that evolves into an envelope. The largest energetic barrier to bud formation is membrane…
An understanding of the underlying mechanism of side--branching is paramount in controlling and/or therapeutically treating mammalian organs, such as lungs, kidneys, and glands. Motivated by an activator-inhibitor-substrate approach that is…
Many essential cellular processes, including cell division and the establishment of cell polarity during embryogenesis, are regulated by pattern-forming proteins. These proteins often need to bind to a substrate, such as the cell membrane,…
This work aims to develop explainable models to predict the interactions between bitter molecules and TAS2Rs via traditional machine-learning and deep-learning methods starting from experimentally validated data. Bitterness is one of the…
Evidence suggests that both the interaction of so-called Merkel cells and the epidermal stress distribution play an important role in the formation of fingerprint patterns during pregnancy. To model the formation of fingerprint patterns in…
The Turing patterning mechanism is believed to underly the formation of repetitive structures in development, such as zebrafish stripes and mammalian digits, but it has proved difficult to isolate the specific biochemical species…
Notch signaling is an evolutionary conserved cell-cell communication pathway. Besides regulating cell-fate decisions at an individual cell level, Notch signaling coordinates the emergent spatiotemporal patterning in a tissue through…
Simultaneous behavioral and electrophysiological recordings call for new methods to reveal the interactions between neural activity and behavior. A milestone would be an interpretable model of the co-variability of spiking activity and…
Neural Networks (GNNs) have revolutionized the molecular discovery to understand patterns and identify unknown features that can aid in predicting biophysical properties and protein-ligand interactions. However, current models typically…
Tissue growth underpins a wide array of biological and developmental processes, and numerical modeling of growing systems has been shown to be a useful tool for understanding these processes. However, the phenomena that can be captured are…
The phenomenon of pattern formation in nonlinear optical resonators is commonly related to an off-resonance excitation mechanism, where patterns occur due to mismatch between the excitation and resonance frequency. In this paper we show…
The Turing pattern model is one type of reaction-diffusion (RD) model. The first identification of pattern formation by the Turing pattern model in an actual animal was made in the 1990s with the observation of patterns in the sea anemone.…
Turing patterns are a central paradigm for describing spatial patterns in nature. The corresponding theory of reaction-diffusion dynamics combines ideal diffusion with nonlinear reactions, resulting in patterns when species diffuse at…
Reaction-diffusion systems with time-delay defined on complex networks have been studied in the framework of the emergence of Turing instabilities. The use of the Lambert W-function allowed us get explicit analytic conditions for the onset…
Elucidating the neurophysiological mechanisms underlying neural pattern formation remains an outstanding challenge in Computational Neuroscience. In this paper, we address the issue of understanding the emergence of neural patterns by…
The adhesion of biological membranes is mediated by the binding of membrane-anchored receptor and ligand proteins. Central questions are how the binding kinetics of these proteins is affected by the membranes and by the membrane anchoring…