Related papers: Dynamic sampling and information encoding in bioch…
Individual Neurons in the nervous systems exploit various dynamics. To capture these dynamics for single neurons, we tune the parameters of an electrophysiological model of nerve cells, to fit experimental data obtained by calcium imaging.…
The dynamics of biological systems, from proteins to cells to organisms, is complex and stochastic. To decipher their physical laws, we need to bridge between experimental observations and theoretical modeling. Thanks to progress in…
In this study, we explore the information capacity of open quantum systems, focusing on the effective channels formed by the subsystem of random quantum circuits and quantum Hamiltonian evolution. By analyzing the subsystem information…
Exchange of biochemical substances is essential way in establishing communication between bacterial cells. It is noticeable that all phases of the process are heavily influenced by perturbations of either internal or external parameters.…
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.…
Statistical properties of environments experienced by biological signaling systems in the real world change, which necessitate adaptive responses to achieve high fidelity information transmission. One form of such adaptive response is gain…
Living organisms rely on molecular networks, such as gene circuits and signaling pathways, for information processing and robust decision-making in crowded, noisy environments. Recent advances show that interacting biomolecules…
Most of the functions performed by astrocytes in brain information processing are related to calcium waves. Experimental studies involving calcium waves present discrepant results, leading to gaps in the full understanding of the functions…
Biomolecules stochastically occupy different possible configurations with probabilities given by non-equilibrium steady-state distributions. These distributions are determined by the transition rate constants between different…
Microscopic biological systems operate far from equilibrium, are subject to strong fluctuations, and are composed of many coupled components with interactions varying in nature and strength. Researchers are actively investigating the…
Stochasticity is both exploited and controlled by cells. Although the intrinsic stochasticity inherent in biochemistry is relatively well understood, cellular variation, or 'noise', is predominantly generated by interactions of the system…
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…
The molecular network in an organism consists of transcription/translation regulation, protein-protein interactions/modifications and a metabolic network, together forming a system that allows the cell to respond sensibly to the multiple…
Cells can utilize chemical communication to exchange information and coordinate their behavior in the presence of noise. Communication can reduce noise to shape a collective response, or amplify noise to generate distinct phenotypic…
We quantify the influence of the topology of a transcriptional regulatory network on its ability to process environmental signals. By posing the problem in terms of information theory, we may do this without specifying the function…
Intracellular transmission of information via chemical and transcriptional networks is thwarted by a physical limitation: the finite copy number of the constituent chemical species introduces unavoidable intrinsic noise. Here we provide a…
Many biological regulatory systems process signals out of steady state and respond with a physiological delay. A simple model of regulation which respects these features shows how the ability of a delayed output to transmit information is…
Predicting and enhancing inherent properties based on molecular structures is paramount to design tasks in medicine, materials science, and environmental management. Most of the current machine learning and deep learning approaches have…
Two elements of neural information processing have primarily been proposed: firing rate and spike timing of neurons. In the case of synaptic plasticity, although spike-timing-dependent plasticity (STDP) depending on presynaptic and…
We characterize different cell states, related to cancer and ageing phenotypes, by a measure of entropy of network ensembles, integrating gene expression values and protein interaction networks. The entropy measure estimates the parameter…