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In a multi-level quantum system Fano coherences stand for the formation of quantum coherences due to the interaction with the continuum of modes characterizing an incoherent process. In this paper we propose a V-type three-level quantum system on which we certify the presence of genuinely quantum traits underlying the generation of Fano coherences. We do this by determining work conditions that allows for the loss of positivity of the Kirkwood-Dirac quasiprobability distribution of the stochastic energy changes within the discrete system. We also show the existence of nonequilibrium regimes where the generation of Fano coherences leads to a non-negligible excess energy given by the amount of energy that is left over with respect to the energy of the system at the beginning of the transformation. Excess energy is attained provided the initial state of the discrete system is in a superposition of the energy eigenbasis. We conclude the paper by studying the thermodynamic efficiency of the whole process.

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Episodes of chronic stress can result in psychic disorders like post-traumatic stress disorder, but also promote the development of metabolic syndrome and type 2 diabetes. We hypothesize that muscle, as main regulator of whole-body energy expenditure, is a central target of acute and adaptive molecular effects of stress in this context. Here, we investigate the immediate effect of a stress period on energy metabolism in Musculus gastrocnemius in our established C57BL/6 chronic variable stress (Cvs) mouse model. Cvs decreased lean body mass despite increased energy intake, reduced circadian energy expenditure (EE), and substrate utilization. Cvs altered the proteome of metabolic components but not of the oxidative phosphorylation system (OXPHOS), or other mitochondrial structural components. Functionally, Cvs impaired the electron transport chain (ETC) capacity of complex I and complex II, and reduces respiratory capacity of the ETC from complex I to ATP synthase. Complex I-OXPHOS correlated to diurnal EE and complex II-maximal uncoupled respiration correlated to diurnal and reduced nocturnal EE. Bioenergetics assessment revealed higher optimal thermodynamic efficiencies (ƞ-opt) of mitochondria via complex II after Cvs. Interestingly, transcriptome and methylome were unaffected by Cvs, thus excluding major contributions to supposed metabolic adaptation processes. In summary, the preclinical Cvs model shows that metabolic pressure by Cvs is initially compensated by adaptation of mitochondria function associated with high thermodynamic efficiency and decreased EE to manage the energy balance. This counter-regulation of mitochondrial complex II may be the driving force to longitudinal metabolic changes of muscle physiological adaptation as the basis of stress memory.

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The soma, dendrites and axon of neurons may display calcium-dependent release of transmitters and peptides. Such release is named extrasynaptic for occurring in absence of synaptic structures. This review describes the cooperative actions of three calcium sources on somatic exocytosis. Emphasis is given to the somatic release of serotonin by the classical leech Retzius neuron, which has allowed detailed studies on the fine steps from excitation to exocytosis. Trains of action potentials induce transmembrane calcium entry through L-type channels. For action potential frequencies above 5 Hz, summation of calcium transients on individual action potentials activates the second calcium source: ryanodine receptors produce calcium-induced calcium release. The resulting calcium tsunami activates mitochondrial ATP synthesis to fuel transport of vesicles to the plasma membrane. Serotonin that is released maintains a large-scale exocytosis by activating the third calcium source: serotonin autoreceptors coupled to phospholipase C promote IP3 production. Activated IP3 receptors in peripheral endoplasmic reticulum release calcium that promotes vesicle fusion. The Swiss-clock workings of the machinery for somatic exocytosis has a striking disadvantage. The essential calcium-releasing endoplasmic reticulum near the plasma membrane hinders the vesicle transport, drastically reducing the thermodynamic efficiency of the ATP expenses and elevating the energy cost of release.

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To efficiently convert and utilize intermittent solar energy, a novel solar-driven ethanol steam reforming (ESR) system integrated with a membrane reactor is proposed. It has the potential to convert low-grade solar thermal energy into high energy level chemical energy. Driven by chemical potential, hydrogen permeation membranes (HPM) can separate the generated hydrogen and shift the ESR equilibrium forward to increase conversion and thermodynamic efficiency. The thermodynamic and environmental performances are analyzed via numerical simulation under a reaction temperature range of 100-400 °C with permeate pressures of 0.01-0.75 bar. The highest theoretical conversion rate is 98.3% at 100 °C and 0.01 bar, while the highest first-law efficiency, solar-to-fuel efficiency, and exergy efficiency are 82.3%, 45.3%, and 70.4% at 215 °C and 0.20 bar. The standard coal saving rate (SCSR) and carbon dioxide reduction rate (CDRR) are maximums of 101 g·m-2·h-1 and 247 g·m-2·h-1 at 200 °C and 0.20 bar with a hydrogen generation rate of 22.4 mol·m-2·h-1. This study illustrates the feasibility of solar-driven ESR integrated with a membrane reactor and distinguishes a novel approach for distributed hydrogen generation and solar energy utilization and upgradation.

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Microbial growth is a clear example of organization and structure arising in nonequilibrium conditions. Due to the complexity of the microbial metabolic network, elucidating the fundamental principles governing microbial growth remains a challenge. Here, we present a systematic analysis of microbial growth thermodynamics, leveraging an extensive dataset on energy-limited monoculture growth. A consistent thermodynamic framework based on reaction stoichiometry allows us to quantify how much of the available energy microbes can efficiently convert into new biomass while dissipating the remaining energy into the environment and producing entropy. We show that dissipation mechanisms can be linked to the electron donor uptake rate, a fact leading to the central result that the thermodynamic efficiency is related to the electron donor uptake rate by the scaling law [Formula: see text] and to the growth yield by [Formula: see text] These findings allow us to rederive the Pirt equation from a thermodynamic perspective, providing a means to compute its coefficients, as well as a deeper understanding of the relationship between growth rate and yield. Our results provide rather general insights into the relation between mass and energy conversion in microbial growth with potentially wide application, especially in ecology and biotechnology.

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Dissipative accounts of structure formation show that the self-organisation of complex structures is thermodynamically favoured, whenever these structures dissipate free energy that could not be accessed otherwise. These structures therefore open transition channels for the state of the universe to move from a frustrated, metastable state to another metastable state of higher entropy. However, these accounts apply as well to relatively simple, dissipative systems, such as convection cells, hurricanes, candle flames, lightning strikes, or mechanical cracks, as they do to complex biological systems. Conversely, interesting computational properties-that characterize complex biological systems, such as efficient, predictive representations of environmental dynamics-can be linked to the thermodynamic efficiency of underlying physical processes. However, the potential mechanisms that underwrite the selection of dissipative structures with thermodynamically efficient subprocesses is not completely understood. We address these mechanisms by explaining how bifurcation-based, work-harvesting processes-required to sustain complex dissipative structures-might be driven towards thermodynamic efficiency. We first demonstrate a simple mechanism that leads to self-selection of efficient dissipative structures in a stochastic chemical reaction network, when the dissipated driving chemical potential difference is decreased. We then discuss how such a drive can emerge naturally in a hierarchy of self-similar dissipative structures, each feeding on the dissipative structures of a previous level, when moving away from the initial, driving disequilibrium.

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As monofacial, single-junction solar cells approach their fundamental limits, there has been significant interest in tandem solar cells in the presence of concentrated sunlight or tandem bifacial solar cells with back-reflected albedo. The bandgap sequence and thermodynamic efficiency limits of these complex cell configurations require sophisticated numerical calculation. Therefore, the analyses of specialized cases are scattered throughout the literature. In this paper, we show that a powerful graphical approach called the normalized "Shockley-Queisser (S-Q) triangle" (i.e., [Formula: see text]) is sufficient to calculate the bandgap sequence and efficiency limits of arbitrarily complex photovoltaic (PV) topologies. The results are validated against a wide variety of specialized cases reported in the literature and are accurate within a few percent. We anticipate that the widespread use of the S-Q triangle will illuminate the deeper physical principles and design trade-offs involved in the design of bifacial tandem solar cells under arbitrary concentration and series resistance.

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Through somatic exocytosis neurons liberate immense amounts of transmitter molecules that modulate the functioning of the nervous system. A stream of action potentials triggers an ATP-dependent transport of transmitter-containing vesicles to the plasma membrane, that ends with a large-scale exocytosis. It is commonly assumed that biological processes use metabolic energy with a high thermodynamic efficiency, meaning that most energy generates work with minor dissipation. However, the intricate ultrastructure underlying the pathway for the vesicle flow necessary for somatic exocytosis challenges this possibility. To study this problem here we first applied thermodynamic theory to quantify the efficiency of somatic exocytosis of the vital transmitter serotonin. Then we correlated the efficiency to the ultrastructure of the transport pathway of the vesicles. Exocytosis was evoked in cultured Retzius neurons of the leech by trains of 10 impulses delivered at 20 Hz. The kinetics of exocytosis was quantified from the gradual fluorescence increase of FM1-43 dye as it became incorporated into vesicles that underwent their exo-endocytosis cycle. By fitting a model of the vesicle transport carried by motor forces to the kinetics of exocytosis, we calculated the thermodynamic efficiency of the ATP expenses per vesicle, as the power of the transport divided by total energy ideally produced by the hydrolysis of ATP during the process. The efficiency was remarkably low (0.1-6.4%) and the values formed a W-shape distribution with the transport distances of the vesicles. Electron micrographs and fluorescent staining of the actin cortex indicated that the slopes of the W chart could be explained by the interaction of vesicles with the actin cortex and the calcium-releasing endoplasmic reticulum. We showed that the application of thermodynamic theory permitted to predict aspects of the intracellular structure. Our results suggest that the distribution of subcellular structures that are essential for somatic exocytosis abates the thermodynamic efficiency of the transport by hampering vesicle mobilization. It is remarkable that the modulation of the nervous system occurs at the expenses of an efficient use of metabolic energy.

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Water recovery is a measure of the amount of treated water produced relative to the total amount of water processed through the system, and is an important performance metric for any desalination method. Conventional operating methods for desalination using capacitive deionization (CDI) have so far limited water recovery to be about 50%. To improve water recovery for CDI, we here introduce a new operating scheme based on a variable (in time) flow rate wherein a low flow rate during discharge is used to produce a brine volume which is significantly less than the volume of diluent produced. We demonstrate experimentally and study systematically this novel variable flowrate operating scheme in the framework of both constant current and constant voltage charge-discharge modes. We show that the variable flowrate operation can increase water recovery for CDI to very high values of ∼90% and can improve thermodynamic efficiency by about 2- to 3-fold compared to conventional constant flowrate operation. Importantly, this is achieved with minimal performance reductions in salt removal, energy consumption, and volume throughput. Our work highlights that water recovery can be readily improved for CDI at very minimal additional cost using simple flow control schemes.

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Multiple experiments show that various submicron particles such as magnetosomes, RNA messengers, viruses, and even much smaller nanoparticles such as globular proteins diffuse anomalously slow in viscoelastic cytosol of living cells. Hence, their sufficiently fast directional transport by molecular motors such as kinesins is crucial for the cell operation. It has been shown recently that the traditional flashing Brownian ratchet models of molecular motors are capable to describe both normal and anomalous transport of such subdiffusing cargos by molecular motors with a very high efficiency. This work elucidates further an important role of mechanochemical coupling in such an anomalous transport. It shows a natural emergence of a perfect subdiffusive ratchet regime due to allosteric effects, where the random rotations of a "catalytic wheel" at the heart of the motor operation become perfectly synchronized with the random stepping of a heavily loaded motor, so that only one ATP molecule is consumed on average at each motor step along microtubule. However, the number of rotations made by the catalytic engine and the traveling distance both scale sublinearly in time. Nevertheless, this anomalous transport can be very fast in absolute terms.

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Urban transformations within large and growing metropolitan areas often generate critical dynamics affecting social interactions, transport connectivity and income flow distribution. We develop a statistical-mechanical model of urban transformations, exemplified for Greater Sydney, and derive a thermodynamic description highlighting critical regimes. We consider urban dynamics at two time scales: fast dynamics for the distribution of population and income, modelled via the maximum entropy principle, and slower dynamics evolving the urban structure under spatially distributed competition. We identify phase transitions between dispersed and polycentric phases, induced by varying the social disposition-a factor balancing the suburbs' attractiveness-in contrast with the travel impedance. Using the Fisher information, we identify critical thresholds and quantify the thermodynamic cost of urban transformation, as the minimal work required to vary the underlying parameter. Finally, we introduce the notion of thermodynamic efficiency of urban transformation, as the ratio of the order gained during a change to the amount of required work, showing that this measure is maximized at criticality.

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We present a novel approach to the study of epidemics on networks as thermodynamic phenomena, quantifying the thermodynamic efficiency of contagions, considered as distributed computational processes. Modelling SIS dynamics on a contact network statistical-mechanically, we follow the maximum entropy (MaxEnt) principle to obtain steady-state distributions and derive, under certain assumptions, relevant thermodynamic quantities both analytically and numerically. In particular, we obtain closed-form solutions for some cases, while interpreting key epidemic variables, such as the reproductive ratio of a SIS model, in a statistical mechanical setting. On the other hand, we consider configuration and free entropy, as well as the Fisher information, in the epidemiological context. This allowed us to identify criticality and distinct phases of epidemic processes. For each of the considered thermodynamic quantities, we compare the analytical solutions informed by the MaxEnt principle with the numerical estimates for SIS epidemics simulated on Watts-Strogatz random graphs.

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The main physical features and operating principles of isothermal nanomachines in the microworld, common to both classical and quantum machines, are reviewed. Special attention is paid to the dual, constructive role of dissipation and thermal fluctuations, the fluctuation-dissipation theorem, heat losses and free energy transduction, thermodynamic efficiency, and thermodynamic efficiency at maximum power. Several basic models are considered and discussed to highlight generic physical features. This work examines some common fallacies that continue to plague the literature. In particular, the erroneous beliefs that one should minimize friction and lower the temperature for high performance of Brownian machines, and that the thermodynamic efficiency at maximum power cannot exceed one-half are discussed. The emerging topic of anomalous molecular motors operating subdiffusively but very efficiently in the viscoelastic environment of living cells is also discussed.

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We use the results of recent publications as vehicles with which to discuss the thermodynamics of the proton-driven mitochondrial F o F1-ATP synthase, focusing particularly on the possibility that there may be dissociation between rotatory steps and ATP synthesis/hydrolysis. Such stoichiometric 'slippage' has been invoked in the literature to explain observed non-ideal behaviour. Numerical solution of the Rate Isotherm (the kinetic equivalent of the more fundamental Probability Isotherm) suggests that such 'slippage' is an unlikely explanation; instead, we suggest that the experimental results may be more consistent with damage to the enzyme caused by its isolation from the biomembrane and its experimental fixation, resulting in non-physiological friction within the enzyme's rotary mechanism. We emphasize the unavoidable constraint of the Second Law as instantiated by the obligatory dissipation of Gibbs Free Energy if the synthase is to operate at anything other than thermodynamic equilibrium. We use further numerical solution of the Rate Isotherm to demonstrate that there is no necessary association of low thermodynamic efficiency with high metabolic rates in a bio-world in which the dominating mechanism of metabolic control is multifactorial enzyme activation.

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The commonly quoted values of maximum photosynthetic efficiency have been those obtained by determining the oxygen yield from suspensions of resting algal cells in which growth was disregarded. The unpredictability of the metabolism of resting cells severely vitiates the reliability of measurements made on their energy metabolism. Also the validity of the measurements with resting cells is made doubtful by anomalous values for the photosynthetic quotient (-δCO2 /δO2 ). The measurements on resting cells fall into two categories: one in which the cells were suspended in acid media (pH 5) with a CO2 partial pressure (pCO2 ) of 5% atmospheric, and one in which the cells were suspended in alkaline media (about pH 9) with a pco2 of 0.25% atmospheric. In acid media with 5% CO2 , the most probable value of the minimum quantum demand is 5 to 6 hv/O2 . With pH 9 media, equilibrated with 0.25% CO2 , the minimum quantum demand found is about 10 hv/O2 . This low efficiency seems to be caused by a sub-optimal CO2 partial presure, since it has been observed that the value at alkaline pH agrees with that at acid pH provided the pCO2 is maintained at 2 % atmospheric. This pCQ2 effect has been neglected by many workers. To avoid the controversial methods using resting cells, it is essential to determine the photosynthetic efficiency of cells in a steady state of growth. The environmental conditions during growth of the cells have a strong influence on the efficiency of photosynthesis; for instance, the efficiency appears to be strongly dependent on the temperature during growth. Under light-limited conditions when the photosynthetic efficiency of growth is optimized the minimum quantum demand of algal cells is found to be 5 to 6 hv/O2 . The minimum quantum demand of CO2 fixation varies from 1.1 to 1.4 times the value for O2 depending on the nature of the nitrogen source for growth. Significant doubt must be attached to measurements of the maximum photosynthetic efficiency with isolated chloroplasts, on the grounds that in vitro conditions may impair their efficiency and that the efficiency may be affected by the growth conditions of the parent plant. Thus, a unified view of the experimental data indicates that the most probable value of the minimum quantum demand is 5 to 6 hv/O2 . The preference for the apparently sub-optimal value of about 10 hv/O2 found with alkaline media and a pco2 of 0.25 %, which is the prevailing view, is necessitated by the requirement of the Z-scheme paradigm of the mechanism of the electron transfer. Thus it appears that hypothesis rather than a unified view of the experimental data on the efficiency is dictating the view of the mechanism involved. A cell of Chlorella (strain 211/8k) fully charged with reducing equivalents and energy can continue to assimilate CO2 and grow at the maximum rate (doubling time 3 h) for 9 s. It is calculated that exposure to 20 W m-2 (daylight PAR) for 0.5 s is sufficient fully to charge such a cell with energy and reducing equivalents. This calculation predicts that, in the steady state of growth, cycles of exposure of each cell to 20 W m-2 for 0.5 s followed by 9 s in the dark will support growth at the maximum rate. The theoretical expressions used to express the maximum thermodynamic efficiency of conversion of radiation to chemical work (ηT ) are shown to be inconsistent. The correct value is taken to be given by Spanner's equation ηT = 1 -(T/Tr ), where T is the ambient temperature and Tr is the radiation temperature. Hence, the maximum value of ηT for conversion of the PAR in sunlight to chemical work varies from 0.93 for unscattered sunlight to 0.70 if it is isotropically scattered. It is deduced that under the usual ambient conditions the value of ηT for photosynthesis will decrease by 0.043 for each log decrease in the irradiance. Contents Summary 3 I. Introduction 4 II. The stoichiometry of photosynthesis 6 III. Thermodynamic limits to photosynthetic efficiency 7 IV. The theoretical quantum demands for production of NADPH and ATP 8 V. The dynamics and energetics of photosynthetic growth 10 VI. The physiology of cells at or near zero growth rate 12 VII. Manometric measurements of quantum demands of resting cells 13 VIII. Non-manometric measurements of quantum demands of resting cells 16 IX. Quantum demands of vascular plants and isolated chloroplasts 18 X. The quantum demands of growing cells 19 XI. The influence of wavelength of radiation on photosynthetic efficiency 22 XII. Conclusion 23 XIII. Appendices 24 References 34.