Allosteric regulation at the crossroads of new technologies: multiscale modeling, networks, and machine learning

GM Verkhivker, S Agajanian, G Hu… - Frontiers in molecular …, 2020 - frontiersin.org
Allosteric regulation is a common mechanism employed by complex biomolecular systems
for regulation of activity and adaptability in the cellular environment, serving as an effective …

Geometrical aspects of entropy production in stochastic thermodynamics based on Wasserstein distance

M Nakazato, S Ito - Physical Review Research, 2021 - APS
We study a relationship between optimal transport theory and stochastic thermodynamics for
the Fokker-Planck equation. We show that the lower bound on the entropy production is the …

Stochastic thermodynamic interpretation of information geometry

S Ito - Physical review letters, 2018 - APS
In recent years, the unified theory of information and thermodynamics has been intensively
discussed in the context of stochastic thermodynamics. The unified theory reveals that …

Optimal information networks: Application for data-driven integrated health in populations

JL Servadio, M Convertino - Science Advances, 2018 - science.org
Development of composite indicators for integrated health in populations typically relies on a
priori assumptions rather than model-free, data-driven evidence. Traditional variable …

An Introduction to Stochastic Thermodynamics

N Shiraishi - Fundamental Theories of Physics. Springer, Singapore, 2023 - Springer
In the past three decades, the field of stochastic thermodynamics has been formulated and
highly developed. Stochastic thermodynamics extends the framework of thermodynamics …

Geometric thermodynamics for the Fokker–Planck equation: stochastic thermodynamic links between information geometry and optimal transport

S Ito - Information Geometry, 2024 - Springer
We propose a geometric theory of non-equilibrium thermodynamics, namely geometric
thermodynamics, using our recent developments of differential-geometric aspects of entropy …

Thermodynamics of gambling demons

G Manzano, D Subero, O Maillet, R Fazio, JP Pekola… - Physical Review Letters, 2021 - APS
We introduce and realize demons that follow a customary gambling strategy to stop a
nonequilibrium process at stochastic times. We derive second-law-like inequalities for the …

Unified framework for the entropy production and the stochastic interaction based on information geometry

S Ito, M Oizumi, S Amari - Physical Review Research, 2020 - APS
We show a relation between the entropy production in stochastic thermodynamics and the
stochastic interaction in the integrated information theory. To clarify this relation, we …

Quantum fluctuation theorem under quantum jumps with continuous measurement and feedback

T Yada, N Yoshioka, T Sagawa - Physical Review Letters, 2022 - APS
While the fluctuation theorem in classical systems has been thoroughly generalized under
various feedback control setups, an intriguing situation in quantum systems, namely under …

Information thermodynamics for interacting stochastic systems without bipartite structure

R Chetrite, ML Rosinberg, T Sagawa… - Journal of Statistical …, 2019 - iopscience.iop.org
Fluctuations in biochemical networks, eg in a living cell, have a complex origin that
precludes a description of such systems in terms of bipartite or multipartite processes, as is …