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Non-equilibrium processes which convert chemical energy into mechanical motion enable the motility of organisms. Bundles of inextensible filaments driven by energy transduction of molecular motors form essential components of micron-scale…

Soft Condensed Matter · Physics 2013-06-13 Abhrajit Laskar , Rajeev Singh , Somdeb Ghose , Gayathri Jayaraman , P. B. Sunil Kumar , R. Adhikari

Cells sense external concentrations and, via biochemical signaling, respond by regulating the expression of target proteins. Both in signaling networks and gene regulation there are two main mechanisms by which the concentration can be…

Subcellular Processes · Quantitative Biology 2017-04-12 Gabriele Micali , Gerardo Aquino , David M. Richards , Robert G. Endres

Living systems implement and execute an extraordinary plethora of computational tasks. The inherent degree of large scale coordination emerges as a global property, from the intricate sea of microscopic interactions. The brain, with its…

Disordered Systems and Neural Networks · Physics 2018-01-03 Duccio Fanelli , Francesco Ginelli , Roberto Livi , Niccolò Zagli , Clement Zankoc

The cochlea's capacity to process a broad range of sound intensities has been linked to nonlinear amplification by critical oscillators. However, while the increasing sensitivity of a critical oscillator upon decreasing the stimulus…

Biological Physics · Physics 2025-12-16 Henri Ver Hulst , Carles Blanch Mercader , Frank Jülicher , Pascal Martin

Neural systems can be modeled as networks of functionally connected neural elements. The resulting network can be analyzed using mathematical tools from network science and graph theory to quantify the system's topological organization and…

Neurons and Cognition · Quantitative Biology 2020-07-01 Richard F. Betzel , Katherine C. Wood , Christopher Angeloni , Maria Neimark Geffen , Danielle S. Bassett

Neural oscillations are universal phenomena and can be observed at different levels of neural systems, from single neuron to macroscopic brain. The frequency of those oscillations are related to the brain functions. However, little is know…

Neurons and Cognition · Quantitative Biology 2015-07-30 Lianchun Yu , Longfei Wang , Fei Jia , Duojie Jia

Sensory neuroscience seeks to understand how the brain encodes natural environments. However, neural coding has largely been studied using simplified stimuli. In order to assess whether the brain's coding strategy depend on the stimulus…

Neurons and Cognition · Quantitative Biology 2007-05-23 Tatyana O. Sharpee , Hiroki Sugihara , Andrei V. Kurgansky , Sergei P. Rebrik , Michael P. Stryker , Kenneth D. Miller

The development of new techniques to quantitatively measure gene expression in cells has shed light on a number of systems that display oscillations in protein concentration. Here we review the different mechanisms which can produce…

Molecular Networks · Quantitative Biology 2009-11-13 G. Tiana , S. Krishna , S. Pigolotti , M. H. Jensen , K. Sneppen

In various biological systems information from many noisy molecular receptors must be integrated into a collective response. A striking example is the thermal imaging organ of pit vipers. Single nerve fibers in the organ reliably respond to…

Biological Physics · Physics 2024-05-31 Isabella R. Graf , Benjamin B. Machta

Sensory systems across all modalities and species exhibit adaptation to continuously changing input statistics. Individual neurons have been shown to modulate their response gains so as to maximize information transmission in different…

Neurons and Cognition · Quantitative Biology 2023-06-01 Lyndon R. Duong , Colin Bredenberg , David J. Heeger , Eero P. Simoncelli

Adaptation to environmental change is a common property of biological systems. Cells initially respond to external changes in the environment, but after some time, they regain their original state. By considering an element consisting of…

Biological Physics · Physics 2015-05-13 Masayo Inoue , Kunihiko Kaneko

During slow-wave sleep, the brain produces traveling waves of slow oscillations (SOs; $\leq 2$ Hz), characterized by the propagation of alternating high- and low-activity states. The question of internal mechanisms that modulate traveling…

Adaptation and Self-Organizing Systems · Physics 2025-10-16 Ronja Strömsdörfer , Klaus Obermayer

An optomechanical oscillator undergoes a Hopf bifurcation that connects two dynamical regimes with different information-processing capabilities: thermal Brownian motion and coherent self-sustained oscillation. Below threshold, the…

Persistent activity is postulated to drive neural network plasticity and learning. To investigate its underlying cellular mechanisms, we developed a biophysically tractable model that explains the emergence, sustenance, and eventual…

Neurons and Cognition · Quantitative Biology 2009-11-13 Vladislav Volman , Richard Gerkin , Pak-Ming Lau , Eshel Ben-Jacob , Guo-Qiang Bi

The consensus, according to which the transmission of sound from the tympanum to the Outer Hair Cells is solely mechanical, is problematic, especially with respect to high pitched sounds. We demonstrate that the collagenous fibers of the…

Biological and artificial learning systems alike confront the plasticity-stability dilemma. In the brain, neuromodulators such as acetylcholine and noradrenaline relieve this tension by tuning neuronal gain and inhibitory gating, balancing…

Neurons and Cognition · Quantitative Biology 2025-07-14 Alejandro Rodriguez-Garcia , Christopher J. Whyte , Brandon R. Munn , Jie Mei , James M. Shine , Srikanth Ramaswamy

Living cells move thanks to assemblies of actin filaments and myosin motors that range from very organized striated muscle tissue to disordered intracellular bundles. The mechanisms powering these disordered structures are debated, and all…

Biological Physics · Physics 2017-09-26 Martin Lenz

We investigate here various properties of the responses of excitable systems subject to periodic forcing and noise. While the properties of intrinsic oscillators, subject to added periodic signals, are well understood, much less is known…

Neurons and Cognition · Quantitative Biology 2025-10-22 Jonathan E. Rubin , Justyna Signerska-Rynkowska , Jonathan Touboul

Most neurons in peripheral sensory pathways initially respond vigorously when a preferred stimulus is presented, but adapt as stimulation continues. It is unclear how this phenomenon affects stimulus representation in the later stages of…

Neurons and Cognition · Quantitative Biology 2012-10-29 Farzad Farkhooi , Anja Froese , Eilif Muller , Randolf Menzel , Martin P. Nawrot

It has been shown that self-assembled chains of active colloidal particles can present sustained oscillations. These oscillations are possible because of the effective diffusiophoretic forces that mediate the interactions of colloids do not…

Soft Condensed Matter · Physics 2018-03-23 S. Gonzalez , R. Soto