A Photon Force and Flow for Dissipative Structuring: Application to Pigments, Plants and Ecosystems

Through a modern derivation of Planck’s formula for the entropy of an arbitrary beam of photons, we derive a general expression for entropy production due to the irreversible process of the absorption of an arbitrary incident photon spectrum in material and its dissipation into an infrared-shifted grey-body emitted spectrum, with the rest being reflected or transmitted. Employing the framework of Classical Irreversible Thermodynamic theory, we define the generalized thermodynamic flow as the flow of photons from the incident beam into the material and the generalized thermodynamic force is, then, the entropy production divided by the photon flow, which is the entropy production per unit photon at a given wavelength. We compare the entropy production of different inorganic and organic materials (water, desert, leaves and forests) under sunlight and show that organic materials are the greater entropy-producing materials. Intriguingly, plant and phytoplankton pigments (including chlorophyll) reach peak absorption exactly where entropy production through photon dissipation is maximal for our solar spectrum 430<λ<550 nm, while photosynthetic efficiency is maximal between 600 and 700 nm. These results suggest that the evolution of pigments, plants and ecosystems has been towards optimizing entropy production, rather than photosynthesis. We propose using the wavelength dependence of global entropy production as a biosignature for discovering life on planets of other stars.

A Photon Force and Flow for Dissipative Structuring: Application to Pigments, Plants and Ecosystems

Through a modern derivation of Planck's formula for the entropy of an arbitrary beam of photons we derive a general expression for the entropy production due to the irreversible process of the absorption of an arbitrary incident photon spectrum in material and its dissipation into an infrared-shifted grey-body emitted spectrum, the rest being reflected or transmitted. Employing the framework of Classical Irreversible Thermodynamic theory, we define the generalized thermodynamic flow as the flow of photons from the incident beam into the material and the generalized thermodynamic force is then just the entropy production divided by the photon flow which is the entropy production per unit photon at a given wavelength. We compare the entropy production under sunlight of different inorganic and organic materials (water, desert, leaves and forests) and show that organic materials are the greater entropy producing materials. Intriguingly, plant and phytoplankton pigments (including chlorophyll) have peak absorption exactly where entropy production through photon dissipation is maximal for our solar spectrum $430&lt;\lambda&lt;550$ nm, while photosynthetic efficiency is maximal between 600 and 700 nm. These results suggest that the evolution of pigments, plants and ecosystems has been towards optimizing entropy production rather than photosynthesis. We propose using the wavelength dependence of global entropy production as a biosignature for discovering life on planets of other stars.

Quantitative analysis of non-equilibrium systems from short-time experimental data

Estimating entropy production directly from experimental trajectories is of great current interest but often requires a large amount of data or knowledge of the underlying dynamics. In this paper, we propose a minimal strategy using the short-time Thermodynamic Uncertainty Relation (TUR) by means of which we can simultaneously and quantitatively infer the thermodynamic force field acting on the system and the (potentially exact) rate of entropy production from experimental short-time trajectory data. We benchmark this scheme first for an experimental study of a colloidal particle system where exact analytical results are known, prior to studying the case of a colloidal particle in a hydrodynamical flow field, where neither analytical nor numerical results are available. In the latter case, we build an effective model of the system based on our results. In both cases, we also demonstrate that our results match with those obtained from another recently introduced scheme.

Skewness and Kurtosis in Stochastic Thermodynamics

The thermodynamic uncertainty relation is a prominent result in stochastic thermodynamics that provides a bound on the fluctuations of any thermodynamic flux, also known as current, in terms of the average rate of entropy production. Such fluctuations are quantified by the second moment of the probability distribution of the current. The role of higher order standardized moments such as skewness and kurtosis remains largely unexplored. We analyze the skewness and kurtosis associated with the first passage time of thermodynamic currents within the framework of stochastic thermodynamics. We develop a method to evaluate higher order standardized moments associated with the first passage time of any current. For systems with a unicyclic network of states, we conjecture upper and lower bounds on skewness and kurtosis associated with entropy production. These bounds depend on the number of states and the thermodynamic force that drives the system out of equilibrium. We show that these bounds for skewness and kurtosis do not hold for multicyclic networks. We discuss the application of our results to infer an underlying network of states.

Quantitative analysis of non-equilibrium systems from short-time experimental data

We provide a minimal strategy for the quantitative analysis of a large class of non-equilibrium systems in a steady state using the short-time Thermodynamic Uncertainty Relation (TUR). From short-time trajectory data obtained from experiments, we demonstrate how we can simultaneously infer quantitatively, both the thermodynamic force field acting on the system, as well as the exact rate of entropy production. We benchmark this scheme first for an experimental study of a colloidal particle system where exact analytical results are known, before applying it to the case of a colloidal particle in a hydrodynamical flow field, where neither analytical nor numerical results are available. Our scheme hence provides a means, potentially exact for a large class of systems, to get a quantitative estimate of the entropy produced in maintaining a non-equilibrium system in a steady state, directly from experimental data.

Irreversible work and Maxwell demon in terms of quantum thermodynamic force

The second law of classical equilibrium thermodynamics, based on the positivity of entropy production, asserts that any process occurs only in a direction that some information may be lost (flow out of the system) due to the irreversibility inside the system. However, any thermodynamic system can exhibit fluctuations in which negative entropy production may be observed. In particular, in stochastic quantum processes due to quantum correlations and also memory effects we may see the reversal energy flow (heat flow from the cold system to the hot system) and the backflow of information into the system that leads to the negativity of the entropy production which is an apparent violation of the Second Law. In order to resolve this apparent violation, we will try to properly extend the Second Law to quantum processes by incorporating information explicitly into the Second Law. We will also provide a thermodynamic operational meaning for the flow and backflow of information. Finally, it is shown that negative and positive entropy production can be described by a quantum thermodynamic force.

Statistical Mechanics of Non-Muscle Myosin IIA in Human Bone Marrow-Derived Mesenchymal Stromal Cells Seeded in a Collagen Scaffold: A Thermodynamic Near-Equilibrium Linear System Modified by the Tripeptide Arg-Gly-Asp (RGD)

Mesenchymal stromal cells (MSCs) were obtained from human bone marrow and amplified in cultures supplemented with human platelet lysate. Once semi-confluent, cells were seeded in solid collagen scaffolds that were rapidly colonized by the cells generating a 3D cell scaffold. Here, they acquired a myofibroblast phenotype and when exposed to appropriate chemical stimulus, developed tension and cell shortening, similar to those of striated and smooth muscle cells. Myofibroblasts contained a molecular motor—the non-muscle myosin type IIA (NMMIIA) whose crossbridge (CB) kinetics are dramatically slow compared with striated and smooth muscle myosins. Huxley’s equations were used to determine the molecular mechanical properties of NMMIIA. Thank to the great number of NMMIIA molecules, we determined the statistical mechanics (SM) of MSCs, using the grand canonical ensemble which made it possible to calculate various thermodynamic entities such as the chemical affinity, statistical entropy, internal energy, thermodynamic flow, thermodynamic force, and entropy production rate. The linear relationship observed between the thermodynamic force and the thermodynamic flow allowed to establish that MSC-laden in collagen scaffolds were in a near-equilibrium stationary state (affinity ≪ RT), MSCs were also seeded in solid collagen scaffolds functionalized with the tripeptide Arg-Gly-Asp (RGD). This induced major changes in NMMIIA SM particularly by increasing the rate of entropy production. In conclusion, collagen scaffolds laden with MSCs can be viewed as a non-muscle contractile bioengineered tissue operating in a near-equilibrium linear regime, whose SM could be substantially modified by the RGD peptide.

Micromechanical modelling of damage induced by delayedettringite formation in concrete

A multi-scale poromechanical model of damage induced by Delayed Ettringite Formation (DEF) as a consequence of progression of micro-cracks at the fine aggregate scale is developed. The aim is to link the DEF-induced expansion at both the microscopic and macroscopic scales to the loss of stiffness of the mortar and the increase of its diffusion coefficient. At the microscopic scale, mortar is assumed to be constituted of three phases: cement paste, sand and micro-cracks. Damage is assumed to be driven by a free expansion of cement paste due to ettringite crystallization pressures in small capillary pores, at a lower scale. The corresponding homogenised poroelastic properties are estimated along with the diffusion coefficient by resorting either to a Mori-Tanaka scheme or to a self-consistent scheme, as a function of paste and aggregate properties as well as on the density of micro-cracks. The latter is assumed to be an evolving internal variable in order to model DEF-induced damage in the mortar. As the DEF-induced expansive free strain in the cement paste is restrained by the sand particles, internal stresses arise in the mortar. The corresponding free energy can be partially released by an increase in the micro-cracks density by analogy with the energy restitution rate of linear elastic fracture mechanics. The role of the damage criterion adopted on the thermodynamic force associated with micro-cracks density increase is investigated.

The thermodynamic uncertainty relation in biochemical oscillations

Living systems regulate many aspects of their behaviour through periodic oscillations of molecular concentrations, which function as ‘biochemical clocks.’ The chemical reactions that drive these clocks are intrinsically stochastic at the molecular level, so that the duration of a full oscillation cycle is subject to random fluctuations. Their success in carrying out their biological function is thought to depend on the degree to which these fluctuations in the cycle period can be suppressed. Biochemical oscillators also require a constant supply of free energy in order to break detailed balance and maintain their cyclic dynamics. For a given free energy budget, the recently discovered ‘thermodynamic uncertainty relation’ yields the magnitude of period fluctuations in the most precise conceivable free-running clock. In this paper, we show that computational models of real biochemical clocks severely underperform this optimum, with fluctuations several orders of magnitude larger than the theoretical minimum. We argue that this suboptimal performance is due to the small number of internal states per molecule in these models, combined with the high level of thermodynamic force required to maintain the system in the oscillatory phase. We introduce a new model with a tunable number of internal states per molecule and confirm that it approaches the optimal precision as this number increases.