Related papers: Thermodynamics of statistical inference by cells
We extend the recently developed non-gaussian thermodynamic formalism \cite{tre98} of a (presumably strongly turbulent) non-Markovian medium to its most general form that allows for the formulation of a consistent thermodynamic theory. All…
In a first part the scope of classical thermodynamics and statistical mechanics is discussed in the broader context of formal dynamical systems, including computer programmes. In this context classical thermodynamics appears as a particular…
A thermodynamic approach to the description of economic systems and processes is developed. It is shown that there is a deep analogy between the parameters of thermodynamic and economic systems (markets); so each thermodynamic parameter can…
Equilibrating proteins and other biomacromolecules is cardinal for molecular dynamics simulation of such biological systems in which they perform free dynamics without any externally-applied mechanical constraint, until thermodynamic…
Statistical analysis is used throughout biomedical research and elsewhere to assess strength of evidence. We have previously argued that typical outcome statistics (including p-values and maximum likelihood ratios) have poor…
The analysis of non-equilibrium steady states of biochemical reaction networks relies on finding the configurations of fluxes and chemical potentials satisfying stoichiometric (mass balance) and thermodynamic (energy balance) constraints.…
We review the background, theory and general equations for the analysis of equilibrium protein unfolding experiments, focusing on denaturant and heat-induced unfolding. The primary focus is on the thermodynamics of reversible…
In this paper we present a discussion of the basic aspects of the well-known problem of prediction and inference in physics, with specific attention to the role of models, the use of data and the application of recent developments in…
Situations where a spontaneous process of energy or matter transfer is enhanced by an external device are widespread in nature (human sweating system, enzyme catalysis, facilitated diffusion across bio-membranes, industrial heat…
Building on the fundamental equation, this study revisits key thermodynamic concepts in a cohesive and innovative manner. It demonstrates the consistency of thermodynamic theory while addressing and clarifying common misconceptions and…
We numerically determine the entropy for heat-conducting states, which is connected to the so-called excess heat considered as a basic quantity for steady-state thermodynamics in nonequilibrium. We adopt an efficient method to estimate the…
Experimental data bases are typically very large and high dimensional. To learn from them requires to recognize important features (a pattern), often present at scales different to that of the recorded data. Following the experience…
The relationships between reversible Carnot cycles, the absence of perpetual motion machines and the existence of a non-decreasing, globally unique entropy function forms the starting point of many textbook presentations of the foundations…
Trying to identify the entropy production within a cell has been part of debates and studies in the last century. First the idea was to make a resemblance of a cell with a Carnot engine, which is the most thermodynamically perfect machine.…
The notion of entropy is shared between statistics and thermodynamics, and is fundamental to both disciplines. This makes statistical problems particularly suitable for reaction network implementations. In this paper we show how to perform…
The development of stochastic thermodynamics during the last decades prompted the discovery of novel nonequilibrium relations refining our understanding of the second law in small fluctuating systems and its connection with information…
Thermoelectric efficiency is defined as the ratio of power delivered to the load of a device to the rate of heat flow from the source. Till date, it has been studied in presence of thermodynamic constraints set by the Onsager reciprocal…
Non-equilibrium states of a thermodynamic statistical system are investigated using the thermodynamic parameter of the system lifetime, first-passage time, the time before degeneration of the system under influence of fluctuations.…
Current mathematical frameworks for predicting the flux state and macromolecular composition of the cell do not rely on thermodynamic constraints to determine the spontaneous direction of reactions. These predictions may be biologically…
The minimal set of thermodynamic control parameters consists of a statistical (thermal) and a mechanical one. These suffice to introduce all the pertinent thermodynamic variables; thermodynamic processes can then be defined as paths on this…