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In this work, we explore the formalism of the irreversible thermodynamics of open systems and the possibility of gravitationally generated particle production in modified gravity. More specifically, we consider the scalar-tensor representation of f(R,T) gravity, in which the matter energy-momentum tensor is not conserved due to a nonminimal curvature-matter coupling. In the context of the irreversible thermodynamics of open systems, this non-conservation of the energy-momentum tensor can be interpreted as an irreversible flow of energy from the gravitational sector to the matter sector, which, in general, could result in particle creation. We obtain and discuss the expressions for the particle creation rate, the creation pressure, and the entropy and temperature evolutions. Applied together with the modified field equations of scalar-tensor f(R,T) gravity, the thermodynamics of open systems lead to a generalization of the ΛCDM cosmological paradigm, in which the particle creation rate and pressure are considered effectively as components of the cosmological fluid energy-momentum tensor. Thus, generally, modified theories of gravity in which these two quantities do not vanish provide a macroscopic phenomenological description of particle production in the cosmological fluid filling the Universe and also lead to the possibility of cosmological models that start from empty conditions and gradually build up matter and entropy.

Previous research has suggested that molecular energy converters such as ATP synthases, ion pumps, and cotransporters operate via spatially separate pathways for free energy donor and acceptor reactions linked by a protein molecule. We present a chemical kinetics model based on these works, with the basic assumption that all molecular energy converters can be thought of as linked enzymatic reactions, one running downhill the chemical potential gradient and driving the other uphill. To develop the model we first look at how an enzyme process can be forced to go backwards using a basic kinetic model. We then use these findings to suggest a thermodynamically consistent method of linking two enzymatic reactions. Finally, in the context of the aforementioned energy converters, the thermodynamic performance of the resulting model is thoroughly investigated and the obtained results are contrasted with experimental data., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2022 Elsevier B.V. All rights reserved.)

A comprehensive overview of the irreversible port-Hamiltonian system's formulation for finite and infinite dimensional systems defined on 1D spatial domains is provided in a unified manner. The irreversible port-Hamiltonian system formulation shows the extension of classical port-Hamiltonian system formulations to cope with irreversible thermodynamic systems for finite and infinite dimensional systems. This is achieved by including, in an explicit manner, the coupling between irreversible mechanical and thermal phenomena with the thermal domain as an energy-preserving and entropy-increasing operator. Similarly to Hamiltonian systems, this operator is skew-symmetric, guaranteeing energy conservation. To distinguish from Hamiltonian systems, the operator depends on co-state variables and is, hence, a nonlinear-function in the gradient of the total energy. This is what allows encoding the second law as a structural property of irreversible port-Hamiltonian systems. The formalism encompasses coupled thermo-mechanical systems and purely reversible or conservative systems as a particular case. This appears clearly when splitting the state space such that the entropy coordinate is separated from other state variables. Several examples have been used to illustrate the formalism, both for finite and infinite dimensional systems, and a discussion on ongoing and future studies is provided.

The nonlinear mechanical behavior of rock significantly influences the design and construction of underground structures. Due to the complexity and diversity of the damage mechanisms of rock, the damage variable directly defined by partial-damage mechanisms is insufficient in reflecting the progressive-failure process of rock comprehensively. So, in this paper, a novel damage variable is introduced into the plastic-strain rate based on the theoretical framework of irreversible thermodynamics to overcome this defect. The general expression is derived according to the least energy dissipation rate principle. The proposed damage variable can represent the irreversible energy dissipation process and has a strictly theoretical basis in mechanics. Moreover, the granite and marble stress-strain curves are simulated and compared with the Lemaitre damage model, Mazars damage model, and statistical damage model. The results show that the form of the proposed damage variable is practical and straightforward and can better reflect the entire stress-strain relationship of rock. Furthermore, the initial value of the inelastic response strain can be given directly through the proposed damage variable. The model presented here can overcome the issue that the current models need to select the damage threshold indirectly or assume it in advance and ensures that the damage evolution characteristics follow the first principle entirely.

We propose a non-equilibrium framework for modelling the evolution of cities, which describes intra-urban migration as an irreversible diffusive process. We validate this framework using the actual migration data for the Australian capital cities. With respect to the residential relocation, the population is shown to be composed of two distinct groups, exhibiting different relocation frequencies. In the context of the developed framework, these groups can be interpreted as two components of a binary fluid mixture, each with its own diffusive relaxation time. Using this approach, we obtain long-term predictions of the cities' spatial structures, which define their equilibrium population distribution.

Optimization of structured reactors is not without some difficulties due to highly random economic issues. In this study, an entropic approach to optimization is proposed. The model of entropy production in a structured catalytic reactor is introduced and discussed. Entropy production due to flow friction, heat and mass transfer and chemical reaction is derived and referred to the process yield. The entropic optimization criterion is applied for the case of catalytic combustion of methane. Several variants of catalytic supports are considered including wire gauzes, classic (long-channel) and short-channel monoliths, packed bed and solid foam. The proposed entropic criterion may indicate technically rational solutions of a reactor process that is as close as possible to the equilibrium, taking into account all the process phenomena such as heat and mass transfer, flow friction and chemical reaction.

Reverse electrodialysis (RED) is an electro-membrane process for the conversion of mixing energy into electricity. One important problem researchers' face when modeling the RED process is the choice of the proper membrane transport equations. In this study, using experimental data that describe the membrane Nafion 120 in contact with NaCl aqueous solutions, the linear transport equation of irreversible thermodynamics was applied to calculate the power density of the RED system. Various simplifying assumptions about transport equation (i.e., four-, three-, and two-coefficients approaches) are proposed and discussed. We found that the two-coefficients approach, using the membrane conductivity and the apparent transport number of ions, describes the power density with good accuracy. In addition, the influence of the membrane thickness and the concentration polarization on the power density is also demonstrated.

With regard to thermodynamics out of equilibrium, seedlings are open systems that dissipate energy towards their environment. Accordingly, under nutritional steady-state conditions, changes in external concentrations of one single ion provokes instability and reorganization in the metabolic and structure/architecture of the seedling that is more favorable to the fluxes of energy and matter. This reorganization is called a bifurcation and is described in mathematics as a non-linear dynamic system. In this study, we investigate the non-linear dynamics of 15 N fluxes among cellular compartments of B. napus seedlings in response to a wide range of external NO 3 - 15 concentrations (from 0.05 to 20 mM): this allows to determine whether any stationary states and bifurcations could be found. The biphasic behavior of the root NO 3 - 15 uptake rate ( v in ) was explained by the combined cooperative properties between the v app (N uptake, storage and assimilation rate) and v out (N translocation rate) 15 N fluxes that revealed a unique and stable stationary state around 0.28 mM nitrate. The disappearance of this stationary state around 0.5 mM external nitrate concentrations provokes a dramatic bifurcation in 15 N flux pattern. This bifurcation in the v in and v out 15 N fluxes fits better with the increase of BnNPF6.3/NRT1.1 expression than BnNRT2.1 nitrate transporter genes, confirming the allosteric property of the BnNPF6/NRT1.1 transporter, as reported in the literature between low and high nitrate concentrations. Moreover, several statistically significant power-law equations were found between variations in the shoots tryptophan concentrations (i.e., IAA precursor) with changes in the v app and v out 15 N fluxes as well as a synthetic parameter of plant N status estimated from the root/shoot ratio of total free amino acids concentrations. These relationships designate IAA as one of the major biological parameters related to metabolic and structural-morphological reorganization coupled with the N and water fluxes induced by nitrate. The results seriously challenge the scientific grounds of the concept of high- and low-affinity of nitrate transporters and are therefore discussed in terms of the ecological significance and physiological implications on the basis of recent agronomic, physiological and molecular data of the literature., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2020 Le Deunff, Beauclair, Lecourt, Deleu and Malagoli.)

Non-equilibrium thermodynamics is a relevant framework from within which to address formidable difficulties encountered in explaining the origin of life; from molecular synthesis and complexation, enzyme-less proliferation, to evolution (including the acquisition of homochirality and information). From within this framework we have proposed that the origin of life was the origin of the dissipative structuring of organic pigments which became the fundamental molecules of life (e.g. RNA and DNA) proliferated through autocatalytic photochemical reactions under the thermodynamic imperative of dissipating the imposed UVC solar photon flux available at the Archean surface. Here we present experimental evidence demonstrating that the absorption and dissipation of UVC light by synthetic DNA of 25 base pairs (and also natural salmon sperm DNA) over a range of temperatures, including below their melting temperature, leads to denaturing. Since denaturing is a non-trivial step on route to enzyme-less replication, our data suggest the possibility of a dissipative route to DNA replication at the origin of life. Such a dissipation-replication relation provides a simple mechanism for the early accumulation of both homochirality and information. Possible mechanisms of UVC photon-induced denaturing of DNA are discussed.

Following a thermodynamic approach, we develop a new theoretical analysis of ion transfer across cell membranes. Supported also by experimental data from the literature, we highlight that ion channels determine the typical features of cancer cells, i.e. independence from growth-regulatory signals, avoidance of apoptosis, indefinite proliferative potential, and the capability of inducing angiogenesis. Specifically, we analyse how ion transport, with particular regards to Ca 2+ fluxes, modulates cancer cell proliferation, and regulates cell cycle checkpoints. Finally, our analysis also suggests that in malignant tumours aerobic glycolysis is the more efficient metabolic process when taking the required solvent capacity into account., (Copyright © 2018 Elsevier Ltd. All rights reserved.)

The development of sophisticated experimental means to control nanoscale systems has motivated efforts to design driving protocols that minimize the energy dissipated to the environment. Computational models are a crucial tool in this practical challenge. We describe a general method for sampling an ensemble of finite-time, nonequilibrium protocols biased toward a low average dissipation. We show that this scheme can be carried out very efficiently in several limiting cases. As an application, we sample the ensemble of low-dissipation protocols that invert the magnetization of a 2D Ising model and explore how the diversity of the protocols varies in response to constraints on the average dissipation. In this example, we find that there is a large set of protocols with average dissipation close to the optimal value, which we argue is a general phenomenon., Competing Interests: The authors declare no conflict of interest.

Here we give an overview of the history of sedimentation velocity analysis focusing on seminal and fundamental contributions that derived from early ultracentrifugation studies. We introduce the concepts of nonequilibrium thermodynamics and outline the derivation of the Svedberg and the Lamm equations and the requirements for including both hydrodynamic and thermodynamic nonideality. We introduce the phenomenological equations for coupled flows as developed from the principles of nonequilibrium or irreversible thermodynamics and derive a form of the Lamm equation that incorporates cross-diffusion coefficients and coupled gradient terms. We give an historical overview of solutions to the Lamm equation including Fujita-MacCosham solutions and Claverie finite-element numerical solutions and discuss the software that have implemented these solutions. We discuss the three major optical systems (absorbance, interference, and fluorescence) and recently developed multiwavelength systems. We also suggest a number of experimental practices and guidelines for optimizing the determination of s and D and discuss the appropriate centerpiece components and their utility. This chapter complements other recent reviews submitted by the authors (Correia, Lyons, Sherwood, & Stafford, 2015; Stafford, 2015) and should be considered an effort to revive the importance of irreversible thermodynamics in the understanding and analysis of sedimentation velocity ultracentrifugation data., (© 2015 Elsevier Inc. All rights reserved.)

Periprosthetic bone loss in response to total hip arthroplasty is a serious complication compromising patient's life quality as it may cause the premature failure of the implant. Stress shielding as a result of an uneven load sharing between the hip implant and the bone is a key factor leading to bone density decrease. A number of composite hip implants have been designed so far to improve load sharing characteristics. However, they have rarely been investigated from the bone remodeling point of view to predict a long-term response. This is the first study that employed a mechano-biochemical model, which considers the coupling effect between mechanical loading and bone biochemistry, to investigate bone remodeling after composite hip implantation. In this study, periprosthetic bone remodeling in the presence of Carbon fiber polyamide 12 (CF/PA12), CoCrMo and Ti alloy implants was predicted and compared. Our findings revealed that the most significant periprosthetic bone loss in response to metallic implants occurs in Gruen zone 7 (-43% with CoCrMo; -35% with Ti) and 6 (-40% with CoCrMo; -29% with Ti), while zone 4 has the lowest bone density decrease with all three implants (-9%). Also, the results showed that in terms of bone remodeling, the composite hip implant is more advantageous over the metallic ones as it provides a more uniform density change across the bone and induces less stress shielding which consequently results in a lower post-operative bone loss (-9% with CF/PA12 implant compared to -27% and -21% with CoCrMo and Ti alloy implants, respectively)., (Copyright © 2014 Elsevier Ltd. All rights reserved.)