Related papers: Positional information readout in $Ca^{2+}$ signal…
Multisite protein phosphorylation plays a pivotal role in regulating cellular signaling and decision-making processes. In this study, we focus on the mathematical underpinnings and informational aspects of sequential, distributive…
Metastatic cancer cells detect the direction of lymphatic flow by self-communication: they secrete and detect a chemical which, due to the flow, returns to the cell surface anisotropically. The secretion rate is low, meaning detection noise…
Control of the cytoskeleton and mechanical contacts with the extracellular environment are essential component of motility in eukaryotic cells. In the absence of signals, cells continuously rebuild the cytoskeleton and periodically extend…
Based on a non-equilibrium mechanism for spatial pattern formation we study how position information can be controlled by locally coupled discrete dynamical networks, similar to gene regulation networks of cells in a developing…
Cells continuously interact with their environment mediating their responses through signaling cascades. Very often, external stimuli induce pulsatile behaviors in intermediaries of the cascade of increasing frequency with the stimulus…
Positional encodings enable Transformers to incorporate sequential information, yet their theoretical understanding remains limited to two properties: distance attenuation and translation invariance. Because natural language lacks purely…
How cells reliably infer information about their environment is a fundamentally important question. While sensing and signaling generally start with cell-surface receptors, the degree of accuracy with which a cell can measure external…
We investigate single-cell directional sensing from diffusing chemoattractant signals released by a localized source. We focus on the low-concentration regime in which receptor activity is discrete and cellular decisions are made on…
Signal transduction, the information processing mechanism in biological cells, is carried out by a network of biochemical reactions. The dynamics of driven biochemical reactions can be studied in terms of nonequilibrium statistical physics.…
Guiding behavior requires the brain to make predictions about future sensory inputs. Here we show that efficient predictive computation starts at the earliest stages of the visual system. We estimate how much information groups of retinal…
Living cells presumably employ optimized information transfer methods, enabling efficient communication even in noisy environments. As expected, the efficiency of chemical communications between cells depends on the properties of the…
Neuronal calcium (Ca2+) signaling represents a molecular trigger for diverse central nervous system adaptations and maladaptions. The altered function of dorsal spinal inhibitory interneurons is strongly implicated in the mechanisms…
Cells use temporal dynamical patterns to transmit information via signaling pathways. As optimality with respect to the environment plays a fundamental role in biological systems, organisms have evolved optimal ways to transmit information.…
Molecular recognition, which is essential in processing information in biological systems, takes place in a crowded noisy biochemical environment and requires the recognition of a specific target within a background of various similar…
The precision of concentration sensing is improved when cells communicate. Here we derive the physical limits to concentration sensing for cells that communicate over short distances by directly exchanging small molecules (juxtacrine…
Inter and intra-cellular signaling are essential for individual cells to execute various physiological tasks and accurately respond to changes in their environment. Signaling is carried out via diffusible molecules, the transport of which…
Cells continuously sense their surroundings to detect modifications and generate responses. Very often changes in extracellular concentrations initiate signaling cascades that eventually result in changes in gene expression. Increasing…
To maintain homeostasis, living cells process information with networks of interacting molecules. Traditional models for cellular information processing have focused on networks of chemical reactions between molecules. Here, we describe how…
Predicting protein secondary structures such as alpha helices, beta sheets, and coils from amino acid sequences is essential for understanding protein function. This work presents a transformer-based model that applies attention mechanisms…
Push-pull networks are ubiquitous in signal transduction pathways in both prokaryotic and eukaryotic cells. They allow cells to strongly amplify signals via the mechanism of zero-order ultrasensitivity. In a push-pull network, two…