Related papers: Energy dissipation in an adaptive molecular circui…
Adaptation is used by biological sensory systems to respond to a wide range of environmental signals, by adapting their response properties to the statistics of the stimulus in order to maximize information transmission. We derive rules of…
Sensory adaptation enables organisms to adjust their perception in a changing environment. A paradigm is bacterial chemotaxis, where the output activity of chemoreceptors is adapted to different baseline concentrations via receptor…
We show that a rate of conditional Shannon entropy reduction, characterizing the learning of an internal process about an external process, is bounded by the thermodynamic entropy production. This approach allows for the definition of an…
The Escherichia coli chemotaxis signaling pathway has served as a model system for studying the adaptive sensing of environmental signals by large protein complexes. The chemoreceptors control the kinase activity of CheA in response to the…
Biological systems process information under noisy environment. Sensory adaptation model of E. coli is suitable for investigation because of its simplicity. To understand the adaptation processing quantitatively, stochastic thermodynamic…
Climate response metrics are used to quantify the Earth's climate response to anthropogenic changes of atmospheric CO2. Equilibrium Climate Sensitivity (ECS) is one such metric that measures the equilibrium response to CO2 doubling.…
Unlike many physical nonequilibrium systems, in biological systems, the coupling to external energy sources is not a fixed parameter but adaptively controlled by the system itself. We do not have theoretical frameworks that allow for such…
The linear response to temperature changes is derived for systems with overdamped stochastic dynamics. Holding both in transient and steady state conditions, the results allow to compute nonequilibrium thermal susceptibilities from…
Living systems need to be highly responsive, and also to keep fluctuations low. These goals are incompatible in equilibrium systems due to the Fluctuation Dissipation Theorem (FDT). Here, we show that biological sensory systems, driven far…
Adaptation of the chemotaxis sensory pathway of the bacterium Escherichia coli is integral for detecting chemicals over a wide range of background concentrations, ultimately allowing cells to swim towards sources of attractant and away from…
A resistor-network picture of transitions is appropriate for the study of energy absorption by weakly chaotic or weakly interacting driven systems. Such "sparse" systems reach a novel non-equilibrium steady state (NESS) once coupled to a…
Constructing a thermodynamic framework for nonequilibrium systems remains a major challenge, as quantities such as temperature and free energy often become ambiguous when inferred solely from steady-state properties. Here we take a…
We study two specific measures of quality of chemical reaction networks, Precision and Sensitivity. The two measures arise in the study of sensory adaptation, in which the reaction network is viewed as an input-output system. Given a step…
How can a microorganism adapt to a variety of environmental conditions despite there exists a limited number of signal transduction machineries? We show that for any growing cells whose gene expression is under stochastic fluctuations,…
A large number of processes in the mesoscopic world occur out of equilibrium, where the time course of a system evolution becomes immensely important since it is driven principally by dissipative effects. Non-equilibrium steady states…
Biological sensory systems react to changes in their surroundings. They are characterized by fast response and slow adaptation to varying environmental cues. Insofar as sensory adaptive systems map environmental changes to changes of their…
Energy-based models are a simple yet powerful class of probabilistic models, but their widespread adoption has been limited by the computational burden of training them. We propose a novel loss function called Energy Discrepancy (ED) which…
A simple model of charge transport is provided by a classical particle in a smooth random potential and a dissipative coupling to the environment in the form of Markovian noise and friction. The corresponding Non-Equilibrium Steady State…
We present an \emph{Effective Static Approximation} (ESA) to the local field correction (LFC) of the electron gas that enables highly accurate calculations of electronic properties like the dynamic structure factor $S(q,\omega)$, the static…
Cooperativity arising from local interactions in equilibrium receptor systems provides gain, but does not increase sensory performance, as measured by the signal-to-noise ratio (SNR) due to a fundamental tradeoff between gain and intrinsic…