A nonequilibrium allosteric model for receptor-kinase complexes: The role of energy dissipation in chemotaxis signaling

D Hathcock, Q Yu, BA Mello, DN Amin… - Proceedings of the …, 2023 - National Acad Sciences
The Escherichia coli chemotaxis signaling pathway has served as a model system for the
adaptive sensing of environmental signals by large protein complexes. The chemoreceptors …

The renormalization group for non-equilibrium systems

Y Tu - Nature Physics, 2023 - nature.com
The renormalization group for non-equilibrium systems | Nature Physics Skip to main content
Thank you for visiting nature.com. You are using a browser version with limited support for …

Milestoning estimators of dissipation in systems observed at a coarse resolution

K Blom, K Song, E Vouga, A Godec… - Proceedings of the …, 2024 - National Acad Sciences
Many nonequilibrium, active processes are observed at a coarse-grained level, where
different microscopic configurations are projected onto the same observable state. Such …

Dissipation and energy propagation across scales in an active cytoskeletal material

PJ Foster, J Bae, B Lemma, J Zheng… - Proceedings of the …, 2023 - National Acad Sciences
Living systems are intrinsically nonequilibrium: They use metabolically derived chemical
energy to power their emergent dynamics and self-organization. A crucial driver of these …

Unraveling active baths through their hidden degrees of freedom

DM Busiello, M Ciarchi, I Di Terlizzi - Physical Review Research, 2024 - APS
The dynamics of a probe particle is highly influenced by the nature of the bath in which it is
immersed. In particular, baths composed by active (eg, self-propelled) particles induce …

Optimal power extraction from active particles with hidden states

L Cocconi, J Knight, C Roberts - Physical Review Letters, 2023 - APS
We identify generic protocols achieving optimal power extraction from a single active particle
subject to continuous feedback control under the assumption that its spatial trajectory, but …

Energy cost for flocking of active spins: the cusped dissipation maximum at the flocking transition

Q Yu, Y Tu - Physical review letters, 2022 - APS
We study the energy cost of flocking in the active Ising model (AIM) and show that, besides
the energy cost for self-propelled motion, an additional energy dissipation is required to …

[HTML][HTML] Eukaryotic gene regulation at equilibrium, or non?

B Zoller, T Gregor, G Tkačik - Current opinion in systems biology, 2022 - Elsevier
Abstract Models of transcriptional regulation that assume equilibrium binding of transcription
factors have been less successful at predicting gene expression from sequence in …

Flexibility and sensitivity in gene regulation out of equilibrium

S Mahdavi, GL Salmon, P Daghlian, HG Garcia… - bioRxiv, 2023 - biorxiv.org
Cells adapt to environments and tune gene expression by controlling the concentrations of
proteins and their kinetics in regulatory networks. In both eukaryotes and prokaryotes …

Thermodynamics for reduced models of chemical reactions by PEA and QSSA

L Peng, L Hong - Physical Review Research, 2024 - APS
The partial equilibrium approximation (PEA) and the quasi-steady-state approximation
(QSSA) are two classical methods for reducing complex macroscopic chemical reactions …