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Modeling and simulation are transforming all fields of biology. Tools like AlphaFold have revolutionized structural biology, while molecular dynamics simulations provide invaluable insights into the behavior of macromolecules in solution or…
The field of basal cognition seeks to understand how adaptive, context-specific behavior occurs in non-neural biological systems. Embryogenesis and regeneration require plasticity in many tissue types to achieve structural and functional…
Cardiac fluid dynamics fundamentally involves interactions between complex blood flows and the structural deformations of the muscular heart walls and the thin, flexible valve leaflets. There has been longstanding scientific, engineering,…
Cell migration is important in many biological processes, including embryonic development, cancer metastasis, and wound healing. In these tissues, a cell's motion is often strongly constrained by its neighbors, leading to glassy dynamics.…
The study of interactions between biomimetic membranes and micron-sized particles is crucial for understanding various biological processes. Here, we control microparticle spontaneous engulfment by giant lipid vesicles by tuning particle…
Three-dimensional (3D) biomedical image sets are often acquired with in-plane pixel spacings that are far less than the out-of-plane spacings between images. The resultant anisotropy, which can be detrimental in many applications, can be…
We demonstrate that a deep neural network can significantly improve optical microscopy, enhancing its spatial resolution over a large field-of-view and depth-of-field. After its training, the only input to this network is an image acquired…
Bacterial biofilms play a significant role in various fields that impact our daily lives, from detrimental public health hazards to beneficial applications in bioremediation, biodegradation, and wastewater treatment. However,…
In recent years there has been increased interest in understanding the interplay between deep generative models (DGMs) and the manifold hypothesis. Research in this area focuses on understanding the reasons why commonly-used DGMs succeed or…
We investigate the outflux of ions through the channels in a cell membrane. The channels undergo an open/close cycle according to a periodic schedule. Our study is based both on theoretical considerations relying on homogenization theory,…
We investigate a cellular automaton (CA) model of traffic on a bi-directional two-lane road. Our model is an extension of the one-lane CA model of {Nagel and Schreckenberg 1992}, modified to account for interactions mediated by passing, and…
The physics of how molecules, organelles, and foreign objects move within living cells has been extensively studied in organisms ranging from bacteria to human cells. In mammalian cells, in particular, cellular vesicles move across the cell…
The optical properties of liquid crystals serve as the basis for display, diagnostic, and sensing technologies. Such properties are generally controlled by relying on electric fields. In this work, we investigate the effects of microfluidic…
Understanding the information processing roles of cortical circuits is an outstanding problem in neuroscience and artificial intelligence. The theoretical setting of Bayesian inference has been suggested as a framework for understanding…
Using bioimaging technology, biologists have attempted to identify and document analytical interpretations that underlie biological phenomena in biological cells. Theoretical biology aims at distilling those interpretations into knowledge…
When our eyes are presented with the same image, the brain processes it to view it as a single coherent one. The lateral shift in the position of our eyes, causes the two images to possess certain differences, which our brain exploits for…
In this paper I present a first attempt for a possible description of fluids dynamics by mean of a cellular automata technique. With the use of simple and elementary rules, based on random behaviour either, the model permits to obtain the…
Our knowledge of how individual cells self-organize to form complex multicellular systems is being revolutionized by a data outburst, coming from high-throughput experimental breakthroughs such as single-cell RNA sequencing and spatially…
Multimode optical fibres are hair-thin strands of glass that efficiently transport light. They promise next-generation medical endoscopes that provide unprecedented sub-cellular image resolution deep inside the body. However, confining…
We investigate a probabilistic cellular automaton model which has been introduced recently. This model describes single-lane traffic flow on a ring and generalizes the asymmetric exclusion process models. We study the equilibrium properties…