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Bistability is a major mechanism for cellular decision making and usually results from positive feedback in biochemical control systems. Here we show theoretically that bistability between unbound and bound states of adhesion clusters…

Allosteric regulation is central to many biochemical processes. Allosteric sites provide a target to fine-tune protein activity, yet we lack computational methods to predict them. Here, we present an efficient graph-theoretical approach for…

A quantitative understanding of how cells interact with their extracellular matrix via molecular bonds is fundamental for many important processes in cell biology and engineering. In these interactions, the deformability of cells and matrix…

Chemical laboratory automation has long been constrained by rigid workflows and poor adaptability to the long-tail distribution of experimental tasks. While most automated platforms perform well on a narrow set of standardized procedures,…

Chemotaxis is the response of a particle to a gradient in the chemical composition of the environment. While it was originally observed for biological organisms, it is of great interest in the context of synthetic active particles such as…

We propose a model of mass-conserving heterogeneous nucleation to describe the dynamics of ligand-receptor binding in closed cellular compartments. When the ligand dissociation rate is small, competition among receptors for free ligands…

We consider a theoretical model for membranes with adhesive receptors, or stickers, that are actively switched between two conformational states. In their 'on'-state, the stickers bind to ligands in an apposing membrane, whereas they do not…

We study the fundamental optimization principles of self-attention, the defining mechanism of transformers, by analyzing the implicit bias of gradient-based optimizers in training a self-attention layer with a linear decoder in binary…

Allosteric proteins transmit a mechanical signal induced by binding a ligand. However, understanding the nature of the information transmitted and the architectures optimizing such transmission remains a challenge. Here we show using an…

We develop a coarse grained (CG) approach for efficiently simulating calcium dynamics in the endoplasmic reticulum membrane based on a fine stochastic lattice gas model. By grouping neighboring microscopic sites together into CG cells and…

In this paper, we derive a new chemotaxis model with degenerate diffusion and density-dependent chemotactic sensitivity, and we provide a more realistic description of cell migration process for its early and late stages. Different from the…

We propose a general method for predicting potentially good folders from a given number of amino acid sequences. Our approach is based on the calculation of the rate of convergence of each amino acid chain towards the native structure using…

Some cells have to take decision based on the quality of surroundings ligands, almost irrespective of their quantity, a problem we name "absolute discrimination". An example of absolute discrimination is recognition of not-self by immune T…

The study of a receptor-ligand system generally relies on the analysis of its dose-response (or concentration-effect) curve, which quantifies the relation between ligand concentration and the biological effect (or cellular response) induced…

Artificially engineered biosensors are highly inefficient in accurately measuring the concentration of biomarkers, particularly, during early diagnosis of diseases. On the other hand, single cellular systems such as chemotactic bacteria can…

Cellular decision-making based on information received from the external environment is frequently initiated by transmembrane receptors. These receptors are known to propagate such information by triggering a series of irreversible,…

Weak multivalent interactions govern a large variety of biological processes like cell-cell adhesion and virus-host interactions. These systems distinguish sharply between surfaces based on receptor density, known as superselectivity.…

Chemotaxis, i.e. motion generated by chemical gradients, is a motility mode shared by many living species that has been developed by evolution to optimize certain biological processes such as foraging or immune response. In particular,…

Cell adhesion proteins are transmembrane proteins that bind cells to their environment. These proteins typically cluster into disk-shaped or linear structures. Here we show that such clustering patterns spontaneously emerge when the protein…

Chemotaxis, the directional locomotion of cells towards a source of a chemical gradient, is an integral part of many biological processes - for example, bacteria motion, single-cell or multicellular organisms development, immune response,…