Related papers: Thermodynamic bounds and error correction for faul…
Starting from the detailed catalytic mechanism of a biocatalyst we provide a coarse-graining procedure which, by construction, is thermodynamically consistent. This procedure provides stoichiometries, reaction fluxes (rate laws), and…
Observational entropy captures both the intrinsic uncertainty of a thermodynamic state and the lack of knowledge due to coarse-graining. We demonstrate two interpretations of observational entropy, one as the statistical deficiency…
Generative models of complex systems often require post-hoc parameter adjustments to produce useful outputs. For example, energy-based models for protein design are sampled at an artificially low ''temperature'' to generate novel,…
We consider dynamical systems evolving near an equilibrium statistical state where the interest is in modelling long term behavior that is consistent with thermodynamic constraints. We adjust the distribution using an entropy-optimizing…
Living systems maintain or increase local order by working against the Second Law of Thermodynamics. Thermodynamic consistency is restored as they dissipate heat, thereby increasing the net entropy of their environment. Recently introduced…
A general framework to describe a vast majority of biology-inspired systems is to model them as stochastic processes in which multiple couplings are in play at the same time. Molecular motors, chemical reaction networks, catalytic enzymes,…
We present general results on fluctuations and spatial correlations of the coarse-grained empirical density and current of Markovian diffusion in equilibrium or non-equilibrium steady states on all time scales. We unravel a deep connection…
The approach of nonequilibrium evolution thermodynamics earlier offered is developed. It helps to describe the processes of defect formation within the adiabatic approximation. The basic equations system depends on the initial defects…
Understanding the entropy production of systems strongly coupled to thermal baths is a core problem of both quantum thermodynamics and mesoscopic physics. While there exist many techniques to accurately study entropy production in such…
For a network of discrete states with a periodically driven Markovian dynamics, we develop an inference scheme for an external observer who has access to some transitions. Based on waiting-time distributions between these transitions, the…
The thermodynamic uncertainty relation originally proven for systems driven into a non-equilibrium steady state (NESS) allows one to infer the total entropy production rate by observing any current in the system. This kind of inference…
Living systems operate far from thermal equilibrium by converting the chemical potential of ATP into mechanical work to achieve growth, replication or locomotion. Given time series observations of intra-, inter- or multicellular processes,…
For configurational changes of soft matter systems affected or caused by external hydrodynamic flow, we identify applied work, exchanged heat, and entropy change on the level of a single trajectory. These expressions guarantee invariance of…
The theory of linear stochastic thermodynamics is developed for periodically driven systems in contact with a single reservoir. Appropriate thermodynamic forces and fluxes are identified, starting from the entropy production for a Markov…
We introduce an algorithmic model of heat conduction, the thermodynamic graph. The thermodynamic graph is analogous to meshes in the finite difference method in the sense that the calculation of temperature is carried out at the vertices of…
The information on a quantum process acquired through measurements plays a crucial role in the determination of its non-equilibrium thermodynamic properties. We report on the experimental inference of the stochastic entropy production rate…
The recursive property of entropy is well known in information theory; however, the concept is underutilized in thermodynamics, despite being the field where the concept of entropy originated. The zentropy approach is built on this idea,…
The nature of coarse graining is intuitively "obvious", but it is rather difficult to find explicit and calculable models of the coarse graining process (and the resulting entropy flow) discussed in the literature. What we would like to…
Safety-critical navigation applications require that estimation errors be reliably quantified and bounded. This can be challenging for linear dynamic systems if the process noise or measurement errors have uncertain time correlation. In…
Coarse-graining is central to reducing dimensionality in molecular dynamics, and is typically characterized by a mapping which projects the full state of the system to a smaller class of variables. While extensive literature has been…