Thermodynamics aspects of noise-induced phase synchronization

NASA Astrophysics Data System (ADS)

Pinto, Pedro D.; Oliveira, Fernando A.; Penna, André L. A.

2016-05-01

In this article, we present an approach for the thermodynamics of phase oscillators induced by an internal multiplicative noise. We analytically derive the free energy, entropy, internal energy, and specific heat. In this framework, the formulation of the first law of thermodynamics requires the definition of a synchronization field acting on the phase oscillators. By introducing the synchronization field, we have consistently obtained the susceptibility and analyzed its behavior. This allows us to characterize distinct phases in the system, which we have denoted as synchronized and parasynchronized phases, in analogy with magnetism. The system also shows a rich complex behavior, exhibiting ideal gas characteristics for low temperatures and susceptibility anomalies that are similar to those present in complex fluids such as water.

Thermodynamics aspects of noise-induced phase synchronization.

PubMed

Pinto, Pedro D; Oliveira, Fernando A; Penna, André L A

2016-05-01

In this article, we present an approach for the thermodynamics of phase oscillators induced by an internal multiplicative noise. We analytically derive the free energy, entropy, internal energy, and specific heat. In this framework, the formulation of the first law of thermodynamics requires the definition of a synchronization field acting on the phase oscillators. By introducing the synchronization field, we have consistently obtained the susceptibility and analyzed its behavior. This allows us to characterize distinct phases in the system, which we have denoted as synchronized and parasynchronized phases, in analogy with magnetism. The system also shows a rich complex behavior, exhibiting ideal gas characteristics for low temperatures and susceptibility anomalies that are similar to those present in complex fluids such as water.

Thermodynamic framework for compact q-Gaussian distributions

NASA Astrophysics Data System (ADS)

Souza, Andre M. C.; Andrade, Roberto F. S.; Nobre, Fernando D.; Curado, Evaldo M. F.

2018-02-01

Recent works have associated systems of particles, characterized by short-range repulsive interactions and evolving under overdamped motion, to a nonlinear Fokker-Planck equation within the class of nonextensive statistical mechanics, with a nonlinear diffusion contribution whose exponent is given by ν = 2 - q. The particular case ν = 2 applies to interacting vortices in type-II superconductors, whereas ν > 2 covers systems of particles characterized by short-range power-law interactions, where correlations among particles are taken into account. In the former case, several studies presented a consistent thermodynamic framework based on the definition of an effective temperature θ (presenting experimental values much higher than typical room temperatures T, so that thermal noise could be neglected), conjugated to a generalized entropy sν (with ν = 2). Herein, the whole thermodynamic scheme is revisited and extended to systems of particles interacting repulsively, through short-ranged potentials, described by an entropy sν, with ν > 1, covering the ν = 2 (vortices in type-II superconductors) and ν > 2 (short-range power-law interactions) physical examples. One basic requirement concerns a cutoff in the equilibrium distribution Peq(x) , approached due to a confining external harmonic potential, ϕ(x) = αx2 / 2 (α > 0). The main results achieved are: (a) The definition of an effective temperature θ conjugated to the entropy sν; (b) The construction of a Carnot cycle, whose efficiency is shown to be η = 1 -(θ2 /θ1) , where θ1 and θ2 are the effective temperatures associated with two isothermal transformations, with θ1 >θ2; (c) Thermodynamic potentials, Maxwell relations, and response functions. The present thermodynamic framework, for a system of interacting particles under the above-mentioned conditions, and associated to an entropy sν, with ν > 1, certainly enlarges the possibility of experimental verifications.

A thermo-chemo-mechanically coupled constitutive model for curing of glassy polymers

NASA Astrophysics Data System (ADS)

Sain, Trisha; Loeffel, Kaspar; Chester, Shawn

2018-07-01

Curing of a polymer is the process through which a polymer liquid transitions into a solid polymer, capable of bearing mechanical loads. The curing process is a coupled thermo-chemo-mechanical conversion process which requires a thorough understanding of the system behavior to predict the cure dependent mechanical behavior of the solid polymer. In this paper, a thermodynamically consistent, frame indifferent, thermo-chemo-mechanically coupled continuum level constitutive framework is proposed for thermally cured glassy polymers. The constitutive framework considers the thermodynamics of chemical reactions, as well as the material behavior for a glassy polymer. A stress-free intermediate configuration is introduced within a finite deformation setting to capture the formation of the network in a stress-free configuration. This work considers a definition for the degree of cure based on the chemistry of the curing reactions. A simplified version of the proposed model has been numerically implemented, and simulations are used to understand the capabilities of the model and framework.

Scale covariance and G-varying cosmology. II - Thermodynamics, radiation, and the 3 K background

NASA Technical Reports Server (NTRS)

Canuto, V. M.; Hsieh, S.-H.

1979-01-01

Within the framework of a scale-covariant theory of gravitation, a semiclassical description of particles and photons is given. Thermodynamic relations consistent with the modified conservation equations are derived. Application to a system of radiation shows that the observed 3-K background radiation can be interpreted, within the present framework, as a remnant of equilibrium radiation in the past. As the theory postulates a nonstandard coupling between gravitation and electrodynamics, the assumption that Einstein's theory of gravitation is unchanged forces modifications at the atomic level. The use of Minkowskian spacetime in atomic physics is found to be adequate only over small, but not large, time scales compared with the age of the universe. As a result, a relation between energy and the frequency of a free photon is demonstrated. Possible observational consequences of this relation are discussed.

Putative regulatory sites unraveled by network-embedded thermodynamic analysis of metabolome data

PubMed Central

Kümmel, Anne; Panke, Sven; Heinemann, Matthias

2006-01-01

As one of the most recent members of the omics family, large-scale quantitative metabolomics data are currently complementing our systems biology data pool and offer the chance to integrate the metabolite level into the functional analysis of cellular networks. Network-embedded thermodynamic analysis (NET analysis) is presented as a framework for mechanistic and model-based analysis of these data. By coupling the data to an operating metabolic network via the second law of thermodynamics and the metabolites' Gibbs energies of formation, NET analysis allows inferring functional principles from quantitative metabolite data; for example it identifies reactions that are subject to active allosteric or genetic regulation as exemplified with quantitative metabolite data from Escherichia coli and Saccharomyces cerevisiae. Moreover, the optimization framework of NET analysis was demonstrated to be a valuable tool to systematically investigate data sets for consistency, for the extension of sub-omic metabolome data sets and for resolving intracompartmental concentrations from cell-averaged metabolome data. Without requiring any kind of kinetic modeling, NET analysis represents a perfectly scalable and unbiased approach to uncover insights from quantitative metabolome data. PMID:16788595

Unified framework to evaluate panmixia and migration direction among multiple sampling locations.

PubMed

Beerli, Peter; Palczewski, Michal

2010-05-01

For many biological investigations, groups of individuals are genetically sampled from several geographic locations. These sampling locations often do not reflect the genetic population structure. We describe a framework using marginal likelihoods to compare and order structured population models, such as testing whether the sampling locations belong to the same randomly mating population or comparing unidirectional and multidirectional gene flow models. In the context of inferences employing Markov chain Monte Carlo methods, the accuracy of the marginal likelihoods depends heavily on the approximation method used to calculate the marginal likelihood. Two methods, modified thermodynamic integration and a stabilized harmonic mean estimator, are compared. With finite Markov chain Monte Carlo run lengths, the harmonic mean estimator may not be consistent. Thermodynamic integration, in contrast, delivers considerably better estimates of the marginal likelihood. The choice of prior distributions does not influence the order and choice of the better models when the marginal likelihood is estimated using thermodynamic integration, whereas with the harmonic mean estimator the influence of the prior is pronounced and the order of the models changes. The approximation of marginal likelihood using thermodynamic integration in MIGRATE allows the evaluation of complex population genetic models, not only of whether sampling locations belong to a single panmictic population, but also of competing complex structured population models.

Assessing exchange-correlation functionals for elasticity and thermodynamics of α -ZrW2O8 : A density functional perturbation theory study

NASA Astrophysics Data System (ADS)

Weck, Philippe F.; Kim, Eunja; Greathouse, Jeffery A.; Gordon, Margaret E.; Bryan, Charles R.

2018-04-01

Elastic and thermodynamic properties of negative thermal expansion (NTE) α -ZrW2O8 have been calculated using PBEsol and PBE exchange-correlation functionals within the framework of density functional perturbation theory (DFPT). Measured elastic constants are reproduced within ∼ 2 % with PBEsol and ∼ 6 % with PBE. The thermal evolution of the Grüneisen parameter computed within the quasi-harmonic approximation exhibits negative values below the Debye temperature, consistent with observation. The standard molar heat capacity is predicted to be CP0 = 192.2 and 193.8 J mol-1K-1 with PBEsol and PBE, respectively. These results suggest superior accuracy of DFPT/PBEsol for studying the lattice dynamics, elasticity and thermodynamics of NTE materials.

Framework for non-coherent interface models at finite displacement jumps and finite strains

NASA Astrophysics Data System (ADS)

Ottosen, Niels Saabye; Ristinmaa, Matti; Mosler, Jörn

2016-05-01

This paper deals with a novel constitutive framework suitable for non-coherent interfaces, such as cracks, undergoing large deformations in a geometrically exact setting. For this type of interface, the displacement field shows a jump across the interface. Within the engineering community, so-called cohesive zone models are frequently applied in order to describe non-coherent interfaces. However, for existing models to comply with the restrictions imposed by (a) thermodynamical consistency (e.g., the second law of thermodynamics), (b) balance equations (in particular, balance of angular momentum) and (c) material frame indifference, these models are essentially fiber models, i.e. models where the traction vector is collinear with the displacement jump. This constraints the ability to model shear and, in addition, anisotropic effects are excluded. A novel, extended constitutive framework which is consistent with the above mentioned fundamental physical principles is elaborated in this paper. In addition to the classical tractions associated with a cohesive zone model, the main idea is to consider additional tractions related to membrane-like forces and out-of-plane shear forces acting within the interface. For zero displacement jump, i.e. coherent interfaces, this framework degenerates to existing formulations presented in the literature. For hyperelasticity, the Helmholtz energy of the proposed novel framework depends on the displacement jump as well as on the tangent vectors of the interface with respect to the current configuration - or equivalently - the Helmholtz energy depends on the displacement jump and the surface deformation gradient. It turns out that by defining the Helmholtz energy in terms of the invariants of these variables, all above-mentioned fundamental physical principles are automatically fulfilled. Extensions of the novel framework necessary for material degradation (damage) and plasticity are also covered.

Consistent thermodynamic framework for interacting particles by neglecting thermal noise.

PubMed

Nobre, Fernando D; Curado, Evaldo M F; Souza, Andre M C; Andrade, Roberto F S

2015-02-01

An effective temperature θ, conjugated to a generalized entropy s(q), was introduced recently for a system of interacting particles. Since θ presents values much higher than those of typical room temperatures T≪θ, the thermal noise can be neglected (T/θ≃0) in these systems. Moreover, the consistency of this definition, as well as of a form analogous to the first law of thermodynamics, du=θds(q)+δW, were verified lately by means of a Carnot cycle, whose efficiency was shown to present the usual form, η=1-(θ(2)/θ(1)). Herein we explore further the heat contribution δQ=θds(q) by proposing a way for a heat exchange between two such systems, as well as its associated thermal equilibrium. As a consequence, the zeroth principle is also established. Moreover, we consolidate the first-law proposal by following the usual procedure for obtaining different potentials, i.e., applying Legendre transformations for distinct pairs of independent variables. From these potentials we derive the equation of state, Maxwell relations, and define response functions. All results presented are shown to be consistent with those of standard thermodynamics for T>0.

On nonlinear thermo-electro-elasticity.

PubMed

Mehnert, Markus; Hossain, Mokarram; Steinmann, Paul

2016-06-01

Electro-active polymers (EAPs) for large actuations are nowadays well-known and promising candidates for producing sensors, actuators and generators. In general, polymeric materials are sensitive to differential temperature histories. During experimental characterizations of EAPs under electro-mechanically coupled loads, it is difficult to maintain constant temperature not only because of an external differential temperature history but also because of the changes in internal temperature caused by the application of high electric loads. In this contribution, a thermo-electro-mechanically coupled constitutive framework is proposed based on the total energy approach. Departing from relevant laws of thermodynamics, thermodynamically consistent constitutive equations are formulated. To demonstrate the performance of the proposed thermo-electro-mechanically coupled framework, a frequently used non-homogeneous boundary-value problem, i.e. the extension and inflation of a cylindrical tube, is solved analytically. The results illustrate the influence of various thermo-electro-mechanical couplings.

On nonlinear thermo-electro-elasticity

PubMed Central

Mehnert, Markus; Hossain, Mokarram

2016-01-01

Electro-active polymers (EAPs) for large actuations are nowadays well-known and promising candidates for producing sensors, actuators and generators. In general, polymeric materials are sensitive to differential temperature histories. During experimental characterizations of EAPs under electro-mechanically coupled loads, it is difficult to maintain constant temperature not only because of an external differential temperature history but also because of the changes in internal temperature caused by the application of high electric loads. In this contribution, a thermo-electro-mechanically coupled constitutive framework is proposed based on the total energy approach. Departing from relevant laws of thermodynamics, thermodynamically consistent constitutive equations are formulated. To demonstrate the performance of the proposed thermo-electro-mechanically coupled framework, a frequently used non-homogeneous boundary-value problem, i.e. the extension and inflation of a cylindrical tube, is solved analytically. The results illustrate the influence of various thermo-electro-mechanical couplings. PMID:27436985

MMA-EoS: A Computational Framework for Mineralogical Thermodynamics

NASA Astrophysics Data System (ADS)

Chust, T. C.; Steinle-Neumann, G.; Dolejš, D.; Schuberth, B. S. A.; Bunge, H.-P.

2017-12-01

We present a newly developed software framework, MMA-EoS, that evaluates phase equilibria and thermodynamic properties of multicomponent systems by Gibbs energy minimization, with application to mantle petrology. The code is versatile in terms of the equation-of-state and mixing properties and allows for the computation of properties of single phases, solution phases, and multiphase aggregates. Currently, the open program distribution contains equation-of-state formulations widely used, that is, Caloric-Murnaghan, Caloric-Modified-Tait, and Birch-Murnaghan-Mie-Grüneisen-Debye models, with published databases included. Through its modular design and easily scripted database, MMA-EoS can readily be extended with new formulations of equations-of-state and changes or extensions to thermodynamic data sets. We demonstrate the application of the program by reproducing and comparing physical properties of mantle phases and assemblages with previously published work and experimental data, successively increasing complexity, up to computing phase equilibria of six-component compositions. Chemically complex systems allow us to trace the budget of minor chemical components in order to explore whether they lead to the formation of new phases or extend stability fields of existing ones. Self-consistently computed thermophysical properties for a homogeneous mantle and a mechanical mixture of slab lithologies show no discernible differences that require a heterogeneous mantle structure as has been suggested previously. Such examples illustrate how thermodynamics of mantle mineralogy can advance the study of Earth's interior.

Assessing exchange-correlation functionals for elasticity and thermodynamics of α - ZrW 2 O 8 : A density functional perturbation theory study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Weck, Philippe F.; Kim, Eunja; Greathouse, Jeffery A.

Elastic and thermodynamic properties of negative thermal expansion (NTE) αα-ZrW2O8 have been calculated using PBEsol and PBE exchange-correlation functionals within the framework of density functional perturbation theory (DFPT). Measured elastic constants are reproduced within ~2% with PBEsol and 6% with PBE. The thermal evolution of the Grüneisen parameter computed within the quasi-harmonic approximation exhibits negative values below the Debye temperature, consistent with observation. The standard molar heat capacity is predicted to be Cmore » $$O\\atop{P}$$=192.2 and 193.8 J mol -1K -1 with PBEsol and PBE, respectively. These results suggest superior accuracy of DFPT/PBEsol for studying the lattice dynamics, elasticity and thermodynamics of NTE materials.« less

Assessing exchange-correlation functionals for elasticity and thermodynamics of α - ZrW 2 O 8 : A density functional perturbation theory study

DOE PAGES

Weck, Philippe F.; Kim, Eunja; Greathouse, Jeffery A.; ...

2018-03-15

Elastic and thermodynamic properties of negative thermal expansion (NTE) αα-ZrW2O8 have been calculated using PBEsol and PBE exchange-correlation functionals within the framework of density functional perturbation theory (DFPT). Measured elastic constants are reproduced within ~2% with PBEsol and 6% with PBE. The thermal evolution of the Grüneisen parameter computed within the quasi-harmonic approximation exhibits negative values below the Debye temperature, consistent with observation. The standard molar heat capacity is predicted to be Cmore » $$O\\atop{P}$$=192.2 and 193.8 J mol -1K -1 with PBEsol and PBE, respectively. These results suggest superior accuracy of DFPT/PBEsol for studying the lattice dynamics, elasticity and thermodynamics of NTE materials.« less

Asymptotically free theory with scale invariant thermodynamics

NASA Astrophysics Data System (ADS)

Ferrari, Gabriel N.; Kneur, Jean-Loïc; Pinto, Marcus Benghi; Ramos, Rudnei O.

2017-12-01

A recently developed variational resummation technique, incorporating renormalization group properties consistently, has been shown to solve the scale dependence problem that plagues the evaluation of thermodynamical quantities, e.g., within the framework of approximations such as in the hard-thermal-loop resummed perturbation theory. This method is used in the present work to evaluate thermodynamical quantities within the two-dimensional nonlinear sigma model, which, apart from providing a technically simpler testing ground, shares some common features with Yang-Mills theories, like asymptotic freedom, trace anomaly and the nonperturbative generation of a mass gap. The present application confirms that nonperturbative results can be readily generated solely by considering the lowest-order (quasiparticle) contribution to the thermodynamic effective potential, when this quantity is required to be renormalization group invariant. We also show that when the next-to-leading correction from the method is accounted for, the results indicate convergence, apart from optimally preserving, within the approximations here considered, the sought-after scale invariance.

Consistent data-driven computational mechanics

NASA Astrophysics Data System (ADS)

González, D.; Chinesta, F.; Cueto, E.

2018-05-01

We present a novel method, within the realm of data-driven computational mechanics, to obtain reliable and thermodynamically sound simulation from experimental data. We thus avoid the need to fit any phenomenological model in the construction of the simulation model. This kind of techniques opens unprecedented possibilities in the framework of data-driven application systems and, particularly, in the paradigm of industry 4.0.

The Differential Gibbs Free Energy of Activation and its Implications in the Transition-State of Enzymatic Reactions

NASA Astrophysics Data System (ADS)

Maggi, F.; Riley, W. J.

2016-12-01

We propose a mathematical framework to introduce the concept of differential free energy of activation in enzymatically catalyzed reactions, and apply it to N uptake by microalgae and bacteria. This framework extends the thermodynamic capabilities of the classical transition-state theory in and harmonizes the consolidated definitions of kinetic parameters with their thermodynamic and physical meaning. Here, the activation energy is assumed to be a necessary energetic level for equilibrium complexation between reactants and activated complex; however, an additional energy contribution is required for the equilibrium activated complex to release reaction products. We call this "differential free energy of activation"; it can be described by a Boltzmann distribution, and corresponds to a free energy level different from that of complexation. Whether this level is above or below the free energy of activation depends on the reaction, and defines energy domains that correspond to "superactivated", "activated", and "subactivated" complexes. The activated complex reaching one of those states will eventually release the products from an energy level different than that of activation. The concept of differential free energy of activation was tested on 57 independent experiments of NH­4+ and NO3- uptake by various microalgae and bacteria at temperatures ranging between 1 and 45oC. Results showed that the complexation equilibrium always favored the activated complex, but the differential energy of activation led to an apparent energy barrier consistent with observations. Temperature affected all energy levels within this framework but did not alter substantially these thermodynamic features. Overall the approach: (1) provides a thermodynamic and mathematical link between Michaelis-Menten and rate constants; (2) shows that both kinetic parameters can be described or approximated by Arrhenius' like equations; (3) describes the likelihood of formation of sub-, super-, and activated complexes; and (4) shows direction and thermodynamic likelihood of each reaction branch within the transition state. The approach suites particularly well for calibration of kinetic parameters against experimentally acquired reaction dynamics measurements of nutrient biogeochemical cycles.

Thermodynamic properties and equations of state for Ag, Al, Au, Cu and MgO using a lattice vibrational method

NASA Astrophysics Data System (ADS)

Jacobs, M.; Schmid-Fetzer, R.

2012-04-01

A prerequisite for the determination of pressure in static high pressure measurements, such as in diamond anvil cells is the availability of accurate equations of state for reference materials. These materials serve as luminescence gauges or as X-ray gauges and equations of state for these materials serve as secondary pressure scales. Recently, successful progress has been made in the development of consistency between static, dynamic shock-wave and ultrasonic measurements of equations of state (e.g. Dewaele et al. Phys. Rev. B70, 094112, 2004, Dorogokupets and Oganov, Doklady Earth Sciences, 410, 1091-1095, 2006, Holzapfel, High Pressure Research 30, 372-394, 2010) allowing testing models to arrive at consistent thermodynamic descriptions for X-ray gauges. Apart from applications of metallic elements in high-pressure work, thermodynamic properties of metallic elements are also of mandatory interest in the field of metallurgy for studying phase equilibria of alloys, kinetics of phase transformation and diffusion related problems, requiring accurate thermodynamic properties in the low pressure regime. Our aim is to develop a thermodynamic data base for metallic alloy systems containing Ag, Al, Au, Cu, Fe, Ni, Pt, from which volume properties in P-T space can be predicted when it is coupled to vibrational models. This mandates the description of metallic elements as a first step aiming not only at consistency in the pressure scales for the elements, but also at accurate representations of thermodynamic properties in the low pressure regime commonly addressed in metallurgical applications. In previous works (e.g. Jacobs and de Jong, Geochim. Cosmochim. Acta, 71, 3630-3655, 2007, Jacobs and van den Berg, Phys. Earth Planet. Inter., 186, 36-48, 2011) it was demonstrated that a lattice vibrational framework based on Kieffer's model for the vibrational density of states, is suitable to construct a thermodynamic database for Earth mantle materials. Such a database aims at, when coupled to a thermodynamic computation program, the calculation and prediction of phase equilibria and thermo-physical properties of phase equilibrium assemblages in pressure-temperature-composition space. In Jacobs and van den Berg (2011) the vibrational method, together with a thermodynamic data base, was successfully applied to mantle convection of materials in the Earth. These works demonstrate that the vibrational method has the advantages of (1) computational speed, (2) coupling or making comparisons with ab initio methods and (3) making reliable extrapolations to extreme conditions. We present results of thermodynamic analyses, using lattice vibrational methods, of Ag, Al, Au, Cu and MgO covering the pressure and temperature regime of the Earth's interior. We show results on consistency of the pressure scales for these materials using different equations of state, under the constraint that thermodynamic properties in the low-pressure regime are accurately represented.

Stochastic thermodynamics

NASA Astrophysics Data System (ADS)

Eichhorn, Ralf; Aurell, Erik

2014-04-01

'Stochastic thermodynamics as a conceptual framework combines the stochastic energetics approach introduced a decade ago by Sekimoto [1] with the idea that entropy can consistently be assigned to a single fluctuating trajectory [2]'. This quote, taken from Udo Seifert's [3] 2008 review, nicely summarizes the basic ideas behind stochastic thermodynamics: for small systems, driven by external forces and in contact with a heat bath at a well-defined temperature, stochastic energetics [4] defines the exchanged work and heat along a single fluctuating trajectory and connects them to changes in the internal (system) energy by an energy balance analogous to the first law of thermodynamics. Additionally, providing a consistent definition of trajectory-wise entropy production gives rise to second-law-like relations and forms the basis for a 'stochastic thermodynamics' along individual fluctuating trajectories. In order to construct meaningful concepts of work, heat and entropy production for single trajectories, their definitions are based on the stochastic equations of motion modeling the physical system of interest. Because of this, they are valid even for systems that are prevented from equilibrating with the thermal environment by external driving forces (or other sources of non-equilibrium). In that way, the central notions of equilibrium thermodynamics, such as heat, work and entropy, are consistently extended to the non-equilibrium realm. In the (non-equilibrium) ensemble, the trajectory-wise quantities acquire distributions. General statements derived within stochastic thermodynamics typically refer to properties of these distributions, and are valid in the non-equilibrium regime even beyond the linear response. The extension of statistical mechanics and of exact thermodynamic statements to the non-equilibrium realm has been discussed from the early days of statistical mechanics more than 100 years ago. This debate culminated in the development of linear response theory for small deviations from equilibrium, in which a general framework is constructed from the analysis of non-equilibrium states close to equilibrium. In a next step, Prigogine and others developed linear irreversible thermodynamics, which establishes relations between transport coefficients and entropy production on a phenomenological level in terms of thermodynamic forces and fluxes. However, beyond the realm of linear response no general theoretical results were available for quite a long time. This situation has changed drastically over the last 20 years with the development of stochastic thermodynamics, revealing that the range of validity of thermodynamic statements can indeed be extended deep into the non-equilibrium regime. Early developments in that direction trace back to the observations of symmetry relations between the probabilities for entropy production and entropy annihilation in non-equilibrium steady states [5-8] (nowadays categorized in the class of so-called detailed fluctuation theorems), and the derivations of the Bochkov-Kuzovlev [9, 10] and Jarzynski relations [11] (which are now classified as so-called integral fluctuation theorems). Apart from its fundamental theoretical interest, the developments in stochastic thermodynamics have experienced an additional boost from the recent experimental progress in fabricating, manipulating, controlling and observing systems on the micro- and nano-scale. These advances are not only of formidable use for probing and monitoring biological processes on the cellular, sub-cellular and molecular level, but even include the realization of a microscopic thermodynamic heat engine [12] or the experimental verification of Landauer's principle in a colloidal system [13]. The scientific program Stochastic Thermodynamics held between 4 and 15 March 2013, and hosted by The Nordic Institute for Theoretical Physics (Nordita), was attended by more than 50 scientists from the Nordic countries and elsewhere, amongst them many leading experts in the field. During the program, the most recent developments, open questions and new ideas in stochastic thermodynamics were presented and discussed. From the talks and debates, the notion of information in stochastic thermodynamics, the fundamental properties of entropy production (rate) in non-equilibrium, the efficiency of small thermodynamic machines and the characteristics of optimal protocols for the applied (cyclic) forces were crystallizing as main themes. Surprisingly, the long-studied adiabatic piston, its peculiarities and its relation to stochastic thermodynamics were also the subject of intense discussions. The comment on the Nordita program Stochastic Thermodynamics published in this issue of Physica Scripta exploits the Jarzynski relation for determining free energy differences in the adiabatic piston. This scientific program and the contribution presented here were made possible by the financial and administrative support of The Nordic Institute for Theoretical Physics.

Nonextensive kinetic theory and H-theorem in general relativity

NASA Astrophysics Data System (ADS)

Santos, A. P.; Silva, R.; Alcaniz, J. S.; Lima, J. A. S.

2017-11-01

The nonextensive kinetic theory for degenerate quantum gases is discussed in the general relativistic framework. By incorporating nonadditive modifications in the collisional term of the relativistic Boltzmann equation and entropy current, it is shown that Tsallis entropic framework satisfies a H-theorem in the presence of gravitational fields. Consistency with the 2nd law of thermodynamics is obtained only whether the entropic q-parameter lies in the interval q ∈ [ 0 , 2 ] . As occurs in the absence of gravitational fields, it is also proved that the local collisional equilibrium is described by the extended Bose-Einstein (Fermi-Dirac) q-distributions.

The thermodynamics of dense granular flow and jamming

NASA Astrophysics Data System (ADS)

Lu, Shih Yu

The scope of the thesis is to propose, based on experimental evidence and theoretical validation, a quantifiable connection between systems that exhibit the jamming phenomenon. When jammed, some materials that flow are able to resist deformation so that they appear solid-like on the laboratory scale. But unlike ordinary fusion, which has a critically defined criterion in pressure and temperature, jamming occurs under a wide range of conditions. These condition have been rigorously investigated but at the moment, no self-consistent framework can apply to grains, foam and colloids that may have suddenly ceased to flow. To quantify the jamming behavior, a constitutive model of dense granular flows is deduced from shear-flow experiments. The empirical equations are then generalized, via a thermodynamic approach, into an equation-of-state for jamming. Notably, the unifying theory also predicts the experimental data on the behavior of molecular glassy liquids. This analogy paves a crucial road map for a unifying theoretical framework in condensed matter, for example, ranging from sand to fire retardants to toothpaste.

Modelling electro-active polymers with a dispersion-type anisotropy

NASA Astrophysics Data System (ADS)

Hossain, Mokarram; Steinmann, Paul

2018-02-01

We propose a novel constitutive framework for electro-active polymers (EAPs) that can take into account anisotropy with a chain dispersion. To enhance actuation behaviour, particle-filled EAPs become promising candidates nowadays. Recent studies suggest that particle-filled EAPs, which can be cured under an electric field during the manufacturing time, do not necessarily form perfect anisotropic composites, rather they create composites with dispersed chains. Hence in this contribution, an electro-mechanically coupled constitutive model is devised that considers the chain dispersion with a probability distribution function in an integral form. To obtain relevant quantities in discrete form, numerical integration over the unit sphere is utilized. Necessary constitutive equations are derived exploiting the basic laws of thermodynamics that result in a thermodynamically consistent formulation. To demonstrate the performance of the proposed electro-mechanically coupled framework, we analytically solve a non-homogeneous boundary value problem, the extension and inflation of an axisymmetric cylindrical tube under electro-mechanically coupled load. The results capture various electro-mechanical couplings with the formulation proposed for EAP composites.

Quantum and Information Thermodynamics: A Unifying Framework Based on Repeated Interactions

NASA Astrophysics Data System (ADS)

Strasberg, Philipp; Schaller, Gernot; Brandes, Tobias; Esposito, Massimiliano

2017-04-01

We expand the standard thermodynamic framework of a system coupled to a thermal reservoir by considering a stream of independently prepared units repeatedly put into contact with the system. These units can be in any nonequilibrium state and interact with the system with an arbitrary strength and duration. We show that this stream constitutes an effective resource of nonequilibrium free energy, and we identify the conditions under which it behaves as a heat, work, or information reservoir. We also show that this setup provides a natural framework to analyze information erasure ("Landauer's principle") and feedback-controlled systems ("Maxwell's demon"). In the limit of a short system-unit interaction time, we further demonstrate that this setup can be used to provide a thermodynamically sound interpretation to many effective master equations. We discuss how nonautonomously driven systems, micromasers, lasing without inversion and the electronic Maxwell demon can be thermodynamically analyzed within our framework. While the present framework accounts for quantum features (e.g., squeezing, entanglement, coherence), we also show that quantum resources do not offer any advantage compared to classical ones in terms of the maximum extractable work.

Statistical Irreversible Thermodynamics in the Framework of Zubarev's Nonequilibrium Statistical Operator Method

NASA Astrophysics Data System (ADS)

Luzzi, R.; Vasconcellos, A. R.; Ramos, J. G.; Rodrigues, C. G.

2018-01-01

We describe the formalism of statistical irreversible thermodynamics constructed based on Zubarev's nonequilibrium statistical operator (NSO) method, which is a powerful and universal tool for investigating the most varied physical phenomena. We present brief overviews of the statistical ensemble formalism and statistical irreversible thermodynamics. The first can be constructed either based on a heuristic approach or in the framework of information theory in the Jeffreys-Jaynes scheme of scientific inference; Zubarev and his school used both approaches in formulating the NSO method. We describe the main characteristics of statistical irreversible thermodynamics and discuss some particular considerations of several authors. We briefly describe how Rosenfeld, Bohr, and Prigogine proposed to derive a thermodynamic uncertainty principle.

Thermodynamic framework for the ground state of a simple quantum system

NASA Astrophysics Data System (ADS)

Souza, Andre M. C.; Nobre, Fernando D.

2017-01-01

The ground state of a two-level system (associated with probabilities p and 1 -p , respectively) defined by a general Hamiltonian H ̂=Ĥ0+λ V ̂ is studied. The simple case characterized by λ =0 , whose Hamiltonian Ĥ0 is represented by a diagonal matrix, is well established and solvable within Boltzmann-Gibbs statistical mechanics; in particular, it follows the third law of thermodynamics, presenting zero entropy (SBG=0 ) at zero temperature (T =0 ). Herein it is shown that the introduction of a perturbation λ V ̂ (λ >0 ) in the Hamiltonian may lead to a nontrivial ground state, characterized by an entropy S [p ] (with S [p ] ≠SBG[p ] ), if the Hermitian operator V ̂ is represented by a 2 ×2 matrix, defined by nonzero off-diagonal elements V12=V21=-z , where z is a real positive number. Hence, this new term in the Hamiltonian, presenting V12≠0 , may produce physically significant changes in the ground state, and especially, it allows for the introduction of an effective temperature θ (θ ∝λ z ), which is shown to be a parameter conjugated to the entropy S . Based on this, one introduces an infinitesimal heatlike quantity, δ Q =θ d S , leading to a consistent thermodynamic framework, and by proposing an infinitesimal form for the first law, a Carnot cycle and thermodynamic potentials are obtained. All results found are very similar to those of usual thermodynamics, through the identification T ↔θ , and particularly the form for the efficiency of the proposed Carnot Cycle. Moreover, S also follows a behavior typical of a third law, i.e., S →0 , when θ →0 .

Thermodynamic framework for the ground state of a simple quantum system.

PubMed

Souza, Andre M C; Nobre, Fernando D

2017-01-01

The ground state of a two-level system (associated with probabilities p and 1-p, respectively) defined by a general Hamiltonian H[over ̂]=H[over ̂]_{0}+λV[over ̂] is studied. The simple case characterized by λ=0, whose Hamiltonian H[over ̂]_{0} is represented by a diagonal matrix, is well established and solvable within Boltzmann-Gibbs statistical mechanics; in particular, it follows the third law of thermodynamics, presenting zero entropy (S_{BG}=0) at zero temperature (T=0). Herein it is shown that the introduction of a perturbation λV[over ̂] (λ>0) in the Hamiltonian may lead to a nontrivial ground state, characterized by an entropy S[p] (with S[p]≠S_{BG}[p]), if the Hermitian operator V[over ̂] is represented by a 2×2 matrix, defined by nonzero off-diagonal elements V_{12}=V_{21}=-z, where z is a real positive number. Hence, this new term in the Hamiltonian, presenting V_{12}≠0, may produce physically significant changes in the ground state, and especially, it allows for the introduction of an effective temperature θ (θ∝λz), which is shown to be a parameter conjugated to the entropy S. Based on this, one introduces an infinitesimal heatlike quantity, δQ=θdS, leading to a consistent thermodynamic framework, and by proposing an infinitesimal form for the first law, a Carnot cycle and thermodynamic potentials are obtained. All results found are very similar to those of usual thermodynamics, through the identification T↔θ, and particularly the form for the efficiency of the proposed Carnot Cycle. Moreover, S also follows a behavior typical of a third law, i.e., S→0, when θ→0.

Density Functional Methods for Shock Physics and High Energy Density Science

NASA Astrophysics Data System (ADS)

Desjarlais, Michael

2017-06-01

Molecular dynamics with density functional theory has emerged over the last two decades as a powerful and accurate framework for calculating thermodynamic and transport properties with broad application to dynamic compression, high energy density science, and warm dense matter. These calculations have been extensively validated against shock and ramp wave experiments, are a principal component of high-fidelity equation of state generation, and are having wide-ranging impacts on inertial confinement fusion, planetary science, and shock physics research. In addition to thermodynamic properties, phase boundaries, and the equation of state, one also has access to electrical conductivity, thermal conductivity, and lower energy optical properties. Importantly, all these properties are obtained within the same theoretical framework and are manifestly consistent. In this talk I will give a brief history and overview of molecular dynamics with density functional theory and its use in calculating a wide variety of thermodynamic and transport properties for materials ranging from ambient to extreme conditions and with comparisons to experimental data. I will also discuss some of the limitations and difficulties, as well as active research areas. Sandia is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000.

Thermodynamics and the structure of quantum theory

NASA Astrophysics Data System (ADS)

Krumm, Marius; Barnum, Howard; Barrett, Jonathan; Müller, Markus P.

2017-04-01

Despite its enormous empirical success, the formalism of quantum theory still raises fundamental questions: why is nature described in terms of complex Hilbert spaces, and what modifications of it could we reasonably expect to find in some regimes of physics? Here we address these questions by studying how compatibility with thermodynamics constrains the structure of quantum theory. We employ two postulates that any probabilistic theory with reasonable thermodynamic behaviour should arguably satisfy. In the framework of generalised probabilistic theories, we show that these postulates already imply important aspects of quantum theory, like self-duality and analogues of projective measurements, subspaces and eigenvalues. However, they may still admit a class of theories beyond quantum mechanics. Using a thought experiment by von Neumann, we show that these theories admit a consistent thermodynamic notion of entropy, and prove that the second law holds for projective measurements and mixing procedures. Furthermore, we study additional entropy-like quantities based on measurement probabilities and convex decomposition probabilities, and uncover a relation between one of these quantities and Sorkin’s notion of higher-order interference.

Thermodynamic accounting of ecosystem contribution to economic sectors with application to 1992 U.S. economy.

PubMed

Ukidwe, Nandan U; Bakshi, Bhavik R

2004-09-15

Incorporation of ecological considerations in decision-making is essential for sustainable development, but is hindered by inadequate appreciation of the role of ecosystems, and lack of scientifically rigorous techniques for including their contribution. This paper develops a novel thermodynamic accounting framework for including the contribution of natural capital via thermodynamic input-output analysis. This framework is applied to the 1992 US economy comprising 91 industry sectors, resulting in delineation of the myriad ways in which sectors of the US economy rely on ecosystem products and services. The contribution of ecosystems is represented via the concept of ecological cumulative exergy consumption (ECEC), which is related to emergy analysis but avoids any of its controversial assumptions and claims. The use of thermodynamics permits representation of all kinds of inputs and outputs in consistent units, facilitating the definition of aggregate metrics. Total ECEC requirement indicates the extent to which each economic sector relies directly and indirectly on ecological inputs. The ECEC/money ratio indicates the relative monetary versus ecological throughputs in each sector, and indicates the relationship between the thermodynamic work needed to produce a product or service and the corresponding economic activity. This ratio is found to decrease along economic supply chains, indicating industries that are higher up in the economic food chain price ecosystem contribution more than the basic infrastructure industries such as mining and manufacturing. The ratio of CEC with and without inclusion of ecosystems indicates the extent to which conventional thermoeconomic analysis underestimates the contribution of ecosystems. Such ratios, made available for the first time, provide unique insight into the importance of natural capital, and are especially useful in hybrid thermodynamic life cycle analysis of industrial systems. The approach, data compiled in this work, and the resulting insight provide a more ecologically conscious tool for environmental decision-making, and has potential applications at micro as well as macro scales.

Nanothermodynamics in the strong coupling regime

NASA Astrophysics Data System (ADS)

Jarzynski, Christopher

In macroscopic thermodynamics, energy gained by a system is lost by its surroundings (or vice-versa), in accordance with the first law of thermodynamics. However, if the system-environment interaction energy cannot be neglected - as in the case of a microscopic system such as a single molecule in solution - then it is not immediately clear where to draw the line between the energy of the system and that of the environment. To which subsystem does the interaction energy belong? I will describe a microscopic formulation of both the first and second laws of thermodynamics that applies to this situation. In this framework, seven key thermodynamic quantities - internal energy, entropy, volume, enthalpy, Gibbs free energy, heat and work - are given precise microscopic definitions, and the first and second laws are preserved without requiring corrections due to finite system-environment coupling. Furthermore, these definitions reduce to the usual ones in the limit of macroscopic systems of interest. This condition establishes that a unifying framework can be developed, encompassing stochastic thermodynamics at one end and macroscopic thermodynamics at the other. A central element of this framework is a thermodynamic definition of the volume of the system of interest, which converges to the usual geometric definition when the system is large. This research was supported by the U.S. National Science Foundation through Grant No. DMR-1506969.

A universal surface complexation framework for modeling proton binding onto bacterial surfaces in geologic settings

USGS Publications Warehouse

Borrok, D.; Turner, B.F.; Fein, J.B.

2005-01-01

Adsorption onto bacterial cell walls can significantly affect the speciation and mobility of aqueous metal cations in many geologic settings. However, a unified thermodynamic framework for describing bacterial adsorption reactions does not exist. This problem originates from the numerous approaches that have been chosen for modeling bacterial surface protonation reactions. In this study, we compile all currently available potentiometric titration datasets for individual bacterial species, bacterial consortia, and bacterial cell wall components. Using a consistent, four discrete site, non-electrostatic surface complexation model, we determine total functional group site densities for all suitable datasets, and present an averaged set of 'universal' thermodynamic proton binding and site density parameters for modeling bacterial adsorption reactions in geologic systems. Modeling results demonstrate that the total concentrations of proton-active functional group sites for the 36 bacterial species and consortia tested are remarkably similar, averaging 3.2 ?? 1.0 (1??) ?? 10-4 moles/wet gram. Examination of the uncertainties involved in the development of proton-binding modeling parameters suggests that ignoring factors such as bacterial species, ionic strength, temperature, and growth conditions introduces relatively small error compared to the unavoidable uncertainty associated with the determination of cell abundances in realistic geologic systems. Hence, we propose that reasonable estimates of the extent of bacterial cell wall deprotonation can be made using averaged thermodynamic modeling parameters from all of the experiments that are considered in this study, regardless of bacterial species used, ionic strength, temperature, or growth condition of the experiment. The average site densities for the four discrete sites are 1.1 ?? 0.7 ?? 10-4, 9.1 ?? 3.8 ?? 10-5, 5.3 ?? 2.1 ?? 10-5, and 6.6 ?? 3.0 ?? 10-5 moles/wet gram bacteria for the sites with pKa values of 3.1, 4.7, 6.6, and 9.0, respectively. It is our hope that this thermodynamic framework for modeling bacteria-proton binding reactions will also provide the basis for the development of an internally consistent set of bacteria-metal binding constants. 'Universal' constants for bacteria-metal binding reactions can then be used in conjunction with equilibrium constants for other important metal adsorption and complexation reactions to calculate the overall distribution of metals in realistic geologic systems.

Calibration and Propagation of Uncertainty for Independence

DOE Office of Scientific and Technical Information (OSTI.GOV)

Holland, Troy Michael; Kress, Joel David; Bhat, Kabekode Ghanasham

This document reports on progress and methods for the calibration and uncertainty quantification of the Independence model developed at UT Austin. The Independence model is an advanced thermodynamic and process model framework for piperazine solutions as a high-performance CO 2 capture solvent. Progress is presented in the framework of the CCSI standard basic data model inference framework. Recent work has largely focused on the thermodynamic submodels of Independence.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Venkatesan, R.C., E-mail: ravi@systemsresearchcorp.com; Plastino, A., E-mail: plastino@fisica.unlp.edu.ar

The (i) reciprocity relations for the relative Fisher information (RFI, hereafter) and (ii) a generalized RFI–Euler theorem are self-consistently derived from the Hellmann–Feynman theorem. These new reciprocity relations generalize the RFI–Euler theorem and constitute the basis for building up a mathematical Legendre transform structure (LTS, hereafter), akin to that of thermodynamics, that underlies the RFI scenario. This demonstrates the possibility of translating the entire mathematical structure of thermodynamics into a RFI-based theoretical framework. Virial theorems play a prominent role in this endeavor, as a Schrödinger-like equation can be associated to the RFI. Lagrange multipliers are determined invoking the RFI–LTS linkmore » and the quantum mechanical virial theorem. An appropriate ansatz allows for the inference of probability density functions (pdf’s, hereafter) and energy-eigenvalues of the above mentioned Schrödinger-like equation. The energy-eigenvalues obtained here via inference are benchmarked against established theoretical and numerical results. A principled theoretical basis to reconstruct the RFI-framework from the FIM framework is established. Numerical examples for exemplary cases are provided. - Highlights: • Legendre transform structure for the RFI is obtained with the Hellmann–Feynman theorem. • Inference of the energy-eigenvalues of the SWE-like equation for the RFI is accomplished. • Basis for reconstruction of the RFI framework from the FIM-case is established. • Substantial qualitative and quantitative distinctions with prior studies are discussed.« less

Unified phonon-based approach to the thermodynamics of solid, liquid and gas states

NASA Astrophysics Data System (ADS)

Bolmatov, Dima; Zav'yalov, Dmitry; Zhernenkov, Mikhail; Musaev, Edvard T.; Cai, Yong Q.

2015-12-01

We introduce a unified approach to states of matter (solid, liquid and gas) and describe the thermodynamics of the pressure-temperature phase diagram in terms of phonon excitations. We derive the effective Hamiltonian with low-energy cutoff in two transverse phonon polarizations (phononic band gaps) by breaking the symmetry in phonon interactions. Further, we construct the statistical mechanics of states of aggregation employing the Debye approximation. The introduced formalism covers the Debye theory of solids, the phonon theory of liquids, and thermodynamic limits such as the Dulong-Petit thermodynamic limit (cV = 3kB), the ideal gas limit (cV =3/2 kB) and the new thermodynamic limit (cV = 2kB), dubbed here the Frenkel line thermodynamic limit. We discuss the phonon propagation and localization effects in liquids above and below the Frenkel line, and explain the "fast sound" phenomenon. As a test for our theory we calculate velocity-velocity autocorrelation and pair distribution functions within the Green-Kubo formalism. We show the consistency between dynamics of phonons and pair correlations in the framework of the unified approach. New directions towards advancements in phononic band gaps engineering, hypersound manipulation technologies and exploration of exotic behaviour of fluids relevant to geo- and planetary sciences are discussed. The presented results are equally important both for practical implications and for fundamental research.

Thermodynamics of rare events and impulsive relaxation events in the magnetospheric substorm dynamics

NASA Astrophysics Data System (ADS)

Consolini, Giuseppe; Kretzschmar, Matthieu

2007-12-01

The magnetosphere dynamics shows fast relaxation events following power-law distribution for many observable quantities during magnetic substorms. The emergence of such power-law distributions has been widely discussed in the framework of self-organized criticality and/or turbulence. Here, a different approach to the statistical features of these impulsive dynamical events is proposed in the framework of the thermodynamics of rare events [Lavenda, B.H., Florio, A., 1992. Thermodynamics of rare events, Int. J. Theor. Phys. 31, 1455-1475; Lavenda, B.H., 1995. Thermodynamics of Extremes. Albion]. In detail, an application of such a novel approach to the magnetospheric substorm avalanching dynamics as monitored by the auroral electroject index is discussed.

Self-assembly of a binodal metal-organic framework exhibiting a demi-regular lattice.

PubMed

Yan, Linghao; Kuang, Guowen; Zhang, Qiushi; Shang, Xuesong; Liu, Pei Nian; Lin, Nian

2017-10-26

Designing metal-organic frameworks with new topologies is a long-standing quest because new topologies often accompany new properties and functions. Here we report that 1,3,5-tris[4-(pyridin-4-yl)phenyl]benzene molecules coordinate with Cu atoms to form a two-dimensional framework in which Cu adatoms form a nanometer-scale demi-regular lattice. The lattice is articulated by perfectly arranged twofold and threefold pyridyl-Cu coordination motifs in a ratio of 1 : 6 and features local dodecagonal symmetry. This structure is thermodynamically robust and emerges solely when the molecular density is at a critical value. In comparison, we present three framework structures that consist of semi-regular and regular lattices of Cu atoms self-assembled out of 1,3,5-tris[4-(pyridin-4-yl)phenyl]benzene and trispyridylbenzene molecules. Thus a family of regular, semi-regular and demi-regular lattices can be achieved by Cu-pyridyl coordination.

Consistent Estimation of Gibbs Energy Using Component Contributions

PubMed Central

Milo, Ron; Fleming, Ronan M. T.

2013-01-01

Standard Gibbs energies of reactions are increasingly being used in metabolic modeling for applying thermodynamic constraints on reaction rates, metabolite concentrations and kinetic parameters. The increasing scope and diversity of metabolic models has led scientists to look for genome-scale solutions that can estimate the standard Gibbs energy of all the reactions in metabolism. Group contribution methods greatly increase coverage, albeit at the price of decreased precision. We present here a way to combine the estimations of group contribution with the more accurate reactant contributions by decomposing each reaction into two parts and applying one of the methods on each of them. This method gives priority to the reactant contributions over group contributions while guaranteeing that all estimations will be consistent, i.e. will not violate the first law of thermodynamics. We show that there is a significant increase in the accuracy of our estimations compared to standard group contribution. Specifically, our cross-validation results show an 80% reduction in the median absolute residual for reactions that can be derived by reactant contributions only. We provide the full framework and source code for deriving estimates of standard reaction Gibbs energy, as well as confidence intervals, and believe this will facilitate the wide use of thermodynamic data for a better understanding of metabolism. PMID:23874165

Quantum statistical relation for black holes in nonlinear electrodynamics coupled to Einstein-Gauss-Bonnet AdS gravity

DOE Office of Scientific and Technical Information (OSTI.GOV)

Miskovic, Olivera; Olea, Rodrigo

2011-03-15

We consider curvature-squared corrections to Einstein-Hilbert gravity action in the form of a Gauss-Bonnet term in D>4 dimensions. In this theory, we study the thermodynamics of charged static black holes with anti-de Sitter (AdS) asymptotics, and whose electric field is described by nonlinear electrodynamics. These objects have received considerable attention in recent literature on gravity/gauge dualities. It is well-known that, within the framework of anti-de Sitter/conformal field theory (AdS/CFT) correspondence, there exists a nonvanishing Casimir contribution to the internal energy of the system, manifested as the vacuum energy for global AdS spacetime in odd dimensions. Because of this reason, wemore » derive a quantum statistical relation directly from the Euclidean action and not from the integration of the first law of thermodynamics. To this end, we employ a background-independent regularization scheme which consists, in addition to the bulk action, of counterterms that depend on both extrinsic and intrinsic curvatures of the boundary (Kounterterm series). This procedure results in a consistent inclusion of the vacuum energy and chemical potential in the thermodynamic description for Einstein-Gauss-Bonnet AdS gravity regardless of the explicit form of the nonlinear electrodynamics Lagrangian.« less

On the thermodynamics of smooth muscle contraction

NASA Astrophysics Data System (ADS)

Stålhand, Jonas; McMeeking, Robert M.; Holzapfel, Gerhard A.

2016-09-01

Cell function is based on many dynamically complex networks of interacting biochemical reactions. Enzymes may increase the rate of only those reactions that are thermodynamically consistent. In this paper we specifically treat the contraction of smooth muscle cells from the continuum thermodynamics point of view by considering them as an open system where matter passes through the cell membrane. We systematically set up a well-known four-state kinetic model for the cross-bridge interaction of actin and myosin in smooth muscle, where the transition between each state is driven by forward and reverse reactions. Chemical, mechanical and energy balance laws are provided in local forms, while energy balance is also formulated in the more convenient temperature form. We derive the local (non-negative) production of entropy from which we deduce the reduced entropy inequality and the constitutive equations for the first Piola-Kirchhoff stress tensor, the heat flux, the ion and molecular flux and the entropy. One example for smooth muscle contraction is analyzed in more detail in order to provide orientation within the established general thermodynamic framework. In particular the stress evolution, heat generation, muscle shorting rate and a condition for muscle cooling are derived.

Weighted reciprocal of temperature, weighted thermal flux, and their applications in finite-time thermodynamics.

PubMed

Sheng, Shiqi; Tu, Z C

2014-01-01

The concepts of weighted reciprocal of temperature and weighted thermal flux are proposed for a heat engine operating between two heat baths and outputting mechanical work. With the aid of these two concepts, the generalized thermodynamic fluxes and forces can be expressed in a consistent way within the framework of irreversible thermodynamics. Then the efficiency at maximum power output for a heat engine, one of key topics in finite-time thermodynamics, is investigated on the basis of a generic model under the tight-coupling condition. The corresponding results have the same forms as those of low-dissipation heat engines [ M. Esposito, R. Kawai, K. Lindenberg and C. Van den Broeck Phys. Rev. Lett. 105 150603 (2010)]. The mappings from two kinds of typical heat engines, such as the low-dissipation heat engine and the Feynman ratchet, into the present generic model are constructed. The universal efficiency at maximum power output up to the quadratic order is found to be valid for a heat engine coupled symmetrically and tightly with two baths. The concepts of weighted reciprocal of temperature and weighted thermal flux are also transplanted to the optimization of refrigerators.

Radiative, two-temperature simulations of low-luminosity black hole accretion flows in general relativity

NASA Astrophysics Data System (ADS)

Sądowski, Aleksander; Wielgus, Maciek; Narayan, Ramesh; Abarca, David; McKinney, Jonathan C.; Chael, Andrew

2017-04-01

We present a numerical method that evolves a two-temperature, magnetized, radiative, accretion flow around a black hole, within the framework of general relativistic radiation magnetohydrodynamics. As implemented in the code KORAL, the gas consists of two sub-components - ions and electrons - which share the same dynamics but experience independent, relativistically consistent, thermodynamical evolution. The electrons and ions are heated independently according to a prescription from the literature for magnetohydrodynamical turbulent dissipation. Energy exchange between the particle species via Coulomb collisions is included. In addition, electrons gain and lose energy and momentum by absorbing and emitting synchrotron and bremsstrahlung radiation and through Compton scattering. All evolution equations are handled within a fully covariant framework in the relativistic fixed-metric space-time of the black hole. Numerical results are presented for five models of low-luminosity black hole accretion. In the case of a model with a mass accretion rate dot{M}˜ 4× 10^{-8} dot{M}_Edd, we find that radiation has a negligible effect on either the dynamics or the thermodynamics of the accreting gas. In contrast, a model with a larger dot{M}˜ 4× 10^{-4} dot{M}_Edd behaves very differently. The accreting gas is much cooler and the flow is geometrically less thick, though it is not quite a thin accretion disc.

Knowledge Extraction from Atomically Resolved Images.

PubMed

Vlcek, Lukas; Maksov, Artem; Pan, Minghu; Vasudevan, Rama K; Kalinin, Sergei V

2017-10-24

Tremendous strides in experimental capabilities of scanning transmission electron microscopy and scanning tunneling microscopy (STM) over the past 30 years made atomically resolved imaging routine. However, consistent integration and use of atomically resolved data with generative models is unavailable, so information on local thermodynamics and other microscopic driving forces encoded in the observed atomic configurations remains hidden. Here, we present a framework based on statistical distance minimization to consistently utilize the information available from atomic configurations obtained from an atomically resolved image and extract meaningful physical interaction parameters. We illustrate the applicability of the framework on an STM image of a FeSe x Te 1-x superconductor, with the segregation of the chalcogen atoms investigated using a nonideal interacting solid solution model. This universal method makes full use of the microscopic degrees of freedom sampled in an atomically resolved image and can be extended via Bayesian inference toward unbiased model selection with uncertainty quantification.

Equivalent formulations of “the equation of life”

NASA Astrophysics Data System (ADS)

Ao, Ping

2014-07-01

Motivated by progress in theoretical biology a recent proposal on a general and quantitative dynamical framework for nonequilibrium processes and dynamics of complex systems is briefly reviewed. It is nothing but the evolutionary process discovered by Charles Darwin and Alfred Wallace. Such general and structured dynamics may be tentatively named “the equation of life”. Three equivalent formulations are discussed, and it is also pointed out that such a quantitative dynamical framework leads naturally to the powerful Boltzmann-Gibbs distribution and the second law in physics. In this way, the equation of life provides a logically consistent foundation for thermodynamics. This view clarifies a particular outstanding problem and further suggests a unifying principle for physics and biology.

Work extraction and thermodynamics for individual quantum systems

NASA Astrophysics Data System (ADS)

Skrzypczyk, Paul; Short, Anthony J.; Popescu, Sandu

2014-06-01

Thermodynamics is traditionally concerned with systems comprised of a large number of particles. Here we present a framework for extending thermodynamics to individual quantum systems, including explicitly a thermal bath and work-storage device (essentially a ‘weight’ that can be raised or lowered). We prove that the second law of thermodynamics holds in our framework, and gives a simple protocol to extract the optimal amount of work from the system, equal to its change in free energy. Our results apply to any quantum system in an arbitrary initial state, in particular including non-equilibrium situations. The optimal protocol is essentially reversible, similar to classical Carnot cycles, and indeed, we show that it can be used to construct a quantum Carnot engine.

Work extraction and thermodynamics for individual quantum systems.

PubMed

Skrzypczyk, Paul; Short, Anthony J; Popescu, Sandu

2014-06-27

Thermodynamics is traditionally concerned with systems comprised of a large number of particles. Here we present a framework for extending thermodynamics to individual quantum systems, including explicitly a thermal bath and work-storage device (essentially a 'weight' that can be raised or lowered). We prove that the second law of thermodynamics holds in our framework, and gives a simple protocol to extract the optimal amount of work from the system, equal to its change in free energy. Our results apply to any quantum system in an arbitrary initial state, in particular including non-equilibrium situations. The optimal protocol is essentially reversible, similar to classical Carnot cycles, and indeed, we show that it can be used to construct a quantum Carnot engine.

Stochastic thermodynamics, fluctuation theorems and molecular machines.

PubMed

Seifert, Udo

2012-12-01

Stochastic thermodynamics as reviewed here systematically provides a framework for extending the notions of classical thermodynamics such as work, heat and entropy production to the level of individual trajectories of well-defined non-equilibrium ensembles. It applies whenever a non-equilibrium process is still coupled to one (or several) heat bath(s) of constant temperature. Paradigmatic systems are single colloidal particles in time-dependent laser traps, polymers in external flow, enzymes and molecular motors in single molecule assays, small biochemical networks and thermoelectric devices involving single electron transport. For such systems, a first-law like energy balance can be identified along fluctuating trajectories. For a basic Markovian dynamics implemented either on the continuum level with Langevin equations or on a discrete set of states as a master equation, thermodynamic consistency imposes a local-detailed balance constraint on noise and rates, respectively. Various integral and detailed fluctuation theorems, which are derived here in a unifying approach from one master theorem, constrain the probability distributions for work, heat and entropy production depending on the nature of the system and the choice of non-equilibrium conditions. For non-equilibrium steady states, particularly strong results hold like a generalized fluctuation-dissipation theorem involving entropy production. Ramifications and applications of these concepts include optimal driving between specified states in finite time, the role of measurement-based feedback processes and the relation between dissipation and irreversibility. Efficiency and, in particular, efficiency at maximum power can be discussed systematically beyond the linear response regime for two classes of molecular machines, isothermal ones such as molecular motors, and heat engines such as thermoelectric devices, using a common framework based on a cycle decomposition of entropy production.

Brain activity and cognition: a connection from thermodynamics and information theory.

PubMed

Collell, Guillem; Fauquet, Jordi

2015-01-01

The connection between brain and mind is an important scientific and philosophical question that we are still far from completely understanding. A crucial point to our work is noticing that thermodynamics provides a convenient framework to model brain activity, whereas cognition can be modeled in information-theoretical terms. In fact, several models have been proposed so far from both approaches. A second critical remark is the existence of deep theoretical connections between thermodynamics and information theory. In fact, some well-known authors claim that the laws of thermodynamics are nothing but principles in information theory. Unlike in physics or chemistry, a formalization of the relationship between information and energy is currently lacking in neuroscience. In this paper we propose a framework to connect physical brain and cognitive models by means of the theoretical connections between information theory and thermodynamics. Ultimately, this article aims at providing further insight on the formal relationship between cognition and neural activity.

A Cosserat crystal plasticity and phase field theory for grain boundary migration

NASA Astrophysics Data System (ADS)

Ask, Anna; Forest, Samuel; Appolaire, Benoit; Ammar, Kais; Salman, Oguz Umut

2018-06-01

The microstructure evolution due to thermomechanical treatment of metals can largely be described by viscoplastic deformation, nucleation and grain growth. These processes take place over different length and time scales which present significant challenges when formulating simulation models. In particular, no overall unified field framework exists to model concurrent viscoplastic deformation and recrystallization and grain growth in metal polycrystals. In this work a thermodynamically consistent diffuse interface framework incorporating crystal viscoplasticity and grain boundary migration is elaborated. The Kobayashi-Warren-Carter (KWC) phase field model is extended to incorporate the full mechanical coupling with material and lattice rotations and evolution of dislocation densities. The Cosserat crystal plasticity theory is shown to be the appropriate framework to formulate the coupling between phase field and mechanics with proper distinction between bulk and grain boundary behaviour.

Grand Canonical adaptive resolution simulation for molecules with electrons: A theoretical framework based on physical consistency

NASA Astrophysics Data System (ADS)

Delle Site, Luigi

2018-01-01

A theoretical scheme for the treatment of an open molecular system with electrons and nuclei is proposed. The idea is based on the Grand Canonical description of a quantum region embedded in a classical reservoir of molecules. Electronic properties of the quantum region are calculated at constant electronic chemical potential equal to that of the corresponding (large) bulk system treated at full quantum level. Instead, the exchange of molecules between the quantum region and the classical environment occurs at the chemical potential of the macroscopic thermodynamic conditions. The Grand Canonical Adaptive Resolution Scheme is proposed for the treatment of the classical environment; such an approach can treat the exchange of molecules according to first principles of statistical mechanics and thermodynamic. The overall scheme is build on the basis of physical consistency, with the corresponding definition of numerical criteria of control of the approximations implied by the coupling. Given the wide range of expertise required, this work has the intention of providing guiding principles for the construction of a well founded computational protocol for actual multiscale simulations from the electronic to the mesoscopic scale.

Thermodynamics of urban population flows.

PubMed

Hernando, A; Plastino, A

2012-12-01

Orderliness, reflected via mathematical laws, is encountered in different frameworks involving social groups. Here we show that a thermodynamics can be constructed that macroscopically describes urban population flows. Microscopic dynamic equations and simulations with random walkers underlie the macroscopic approach. Our results might be regarded, via suitable analogies, as a step towards building an explicit social thermodynamics.

Some comments on thermodynamic consistency for equilibrium mixture equations of state

DOE PAGES

Grove, John W.

2018-03-28

We investigate sufficient conditions for thermodynamic consistency for equilibrium mixtures. Such models assume that the mass fraction average of the material component equations of state, when closed by a suitable equilibrium condition, provide a composite equation of state for the mixture. Here, we show that the two common equilibrium models of component pressure/temperature equilibrium and volume/temperature equilibrium (Dalton, 1808) define thermodynamically consistent mixture equations of state and that other equilibrium conditions can be thermodynamically consistent provided appropriate values are used for the mixture specific entropy and pressure.

Brain activity and cognition: a connection from thermodynamics and information theory

PubMed Central

Collell, Guillem; Fauquet, Jordi

2015-01-01

The connection between brain and mind is an important scientific and philosophical question that we are still far from completely understanding. A crucial point to our work is noticing that thermodynamics provides a convenient framework to model brain activity, whereas cognition can be modeled in information-theoretical terms. In fact, several models have been proposed so far from both approaches. A second critical remark is the existence of deep theoretical connections between thermodynamics and information theory. In fact, some well-known authors claim that the laws of thermodynamics are nothing but principles in information theory. Unlike in physics or chemistry, a formalization of the relationship between information and energy is currently lacking in neuroscience. In this paper we propose a framework to connect physical brain and cognitive models by means of the theoretical connections between information theory and thermodynamics. Ultimately, this article aims at providing further insight on the formal relationship between cognition and neural activity. PMID:26136709

Steepest entropy ascent quantum thermodynamic model of electron and phonon transport

NASA Astrophysics Data System (ADS)

Li, Guanchen; von Spakovsky, Michael R.; Hin, Celine

2018-01-01

An advanced nonequilibrium thermodynamic model for electron and phonon transport is formulated based on the steepest-entropy-ascent quantum thermodynamics framework. This framework, based on the principle of steepest entropy ascent (or the equivalent maximum entropy production principle), inherently satisfies the laws of thermodynamics and mechanics and is applicable at all temporal and spatial scales even in the far-from-equilibrium realm. Specifically, the model is proven to recover the Boltzmann transport equations in the near-equilibrium limit and the two-temperature model of electron-phonon coupling when no dispersion is assumed. The heat and mass transport at a temperature discontinuity across a homogeneous interface where the dispersion and coupling of electron and phonon transport are both considered are then modeled. Local nonequilibrium system evolution and nonquasiequilibrium interactions are predicted and the results discussed.

On the thermodynamic framework of generalized coupled thermoelastic-viscoplastic-damage modeling

NASA Technical Reports Server (NTRS)

Arnold, S. M.; Saleeb, A. F.

1991-01-01

A complete potential based framework using internal state variables is put forth for the derivation of reversible and irreversible constitutive equations. In this framework, the existence of the total (integrated) form of either the (Helmholtz) free energy or the (Gibbs) complementary free energy are assumed a priori. Two options for describing the flow and evolutionary equations are described, wherein option one (the fully coupled form) is shown to be over restrictive while the second option (the decoupled form) provides significant flexibility. As a consequence of the decoupled form, a new operator, i.e., the Compliance operator, is defined which provides a link between the assumed Gibb's and complementary dissipation potential and ensures a number of desirable numerical features, for example the symmetry of the resulting consistent tangent stiffness matrix. An important conclusion reached, is that although many theories in the literature do not conform to the general potential framework outlined, it is still possible in some cases, by slight modifications of the used forms, to restore the complete potential structure.

Mimicking Nonequilibrium Steady States with Time-Periodic Driving

DTIC Science & Technology

2016-08-29

nonequilibrium steady states, and vice versa, within the theoretical framework of discrete-state stochastic thermodynamics . Nonequilibrium steady states...equilibrium [2], spontaneous relaxation towards equilibrium [3], nonequilibrium steady states generated by fixed thermodynamic forces [4], and stochastic pumps...paradigm, a system driven by fixed thermodynamic forces—such as temperature gradients or chemical potential differences— reaches a steady state in

Hawking radiation and entropy of a black hole in Lovelock-Born-Infeld gravity from the quantum tunneling approach

NASA Astrophysics Data System (ADS)

Li, Gu-Qiang

2017-04-01

The tunneling radiation of particles from black holes in Lovelock-Born-Infeld (LBI) gravity is studied by using the Parikh-Wilczek (PW) method, and the emission rate of a particle is calculated. It is shown that the emission spectrum deviates from the purely thermal spectrum but is consistent with an underlying unitary theory. Compared to the conventional tunneling rate related to the increment of black hole entropy, the entropy of the black hole in LBI gravity is obtained. The entropy does not obey the area law unless all the Lovelock coefficients equal zero, but it satisfies the first law of thermodynamics and is in accordance with earlier results. It is distinctly shown that the PW tunneling framework is related to the thermodynamic laws of the black hole. Supported by Guangdong Natural Science Foundation (2016A030307051, 2015A030313789)

A flamelet model for transcritical LOx/GCH4 flames

NASA Astrophysics Data System (ADS)

Müller, Hagen; Pfitzner, Michael

2017-03-01

This work presents a numerical framework to efficiently simulate methane combustion at supercritical pressures. A LES flamelet approach is adapted to account for real-gas thermodynamics effects which are a prominent feature of flames at near-critical injection conditions. The thermodynamics model is based on the Peng-Robinson equation of state (PR-EoS) in conjunction with a novel volume-translation method to correct deficiencies in the transcritical regime. The resulting formulation is more accurate than standard cubic EoSs without deteriorating their good computational performance. To consistently account for pressure and strain fluctuations in the flamelet model, an additional enthalpy equation is solved along with the transport equations for mixture fraction and mixture fraction variance. The method is validated against available experimental data for a laboratory scale LOx/GCH4 flame at conditions that resemble those in liquid-propellant rocket engines. The LES result is in good agreement with the measured OH* radiation.

Communication: Role of explicit water models in the helix folding/unfolding processes

NASA Astrophysics Data System (ADS)

Palazzesi, Ferruccio; Salvalaglio, Matteo; Barducci, Alessandro; Parrinello, Michele

2016-09-01

In the last years, it has become evident that computer simulations can assume a relevant role in modelling protein dynamical motions for their ability to provide a full atomistic image of the processes under investigation. The ability of the current protein force-fields in reproducing the correct thermodynamics and kinetics systems behaviour is thus an essential ingredient to improve our understanding of many relevant biological functionalities. In this work, employing the last developments of the metadynamics framework, we compare the ability of state-of-the-art all-atom empirical functions and water models to consistently reproduce the folding and unfolding of a helix turn motif in a model peptide. This theoretical study puts in evidence that the choice of the water models can influence the thermodynamic and the kinetics of the system under investigation, and for this reason cannot be considered trivial.

Quantum thermodynamics: a nonequilibrium Green's function approach.

PubMed

Esposito, Massimiliano; Ochoa, Maicol A; Galperin, Michael

2015-02-27

We establish the foundations of a nonequilibrium theory of quantum thermodynamics for noninteracting open quantum systems strongly coupled to their reservoirs within the framework of the nonequilibrium Green's functions. The energy of the system and its coupling to the reservoirs are controlled by a slow external time-dependent force treated to first order beyond the quasistatic limit. We derive the four basic laws of thermodynamics and characterize reversible transformations. Stochastic thermodynamics is recovered in the weak coupling limit.

Phase transition and thermodynamic stability of topological black holes in Hořava-Lifshitz gravity

NASA Astrophysics Data System (ADS)

Ma, Meng-Sen; Zhao, Ren; Liu, Yan-Song

2017-08-01

On the basis of horizon thermodynamics, we study the thermodynamic stability and P-V criticality of topological black holes constructed in Hořava-Lifshitz (HL) gravity without the detailed-balance condition (with general ɛ). In the framework of horizon thermodynamics, we do not need the concrete black hole solution (the metric function) and the concrete matter fields. It is shown that the HL black hole for k=0 is always thermodynamically stable. For k=1 , the thermodynamic behaviors and P-V criticality of the HL black hole are similar to those of RN-AdS black hole for some \

Multiphase flows of N immiscible incompressible fluids: A reduction-consistent and thermodynamically-consistent formulation and associated algorithm

NASA Astrophysics Data System (ADS)

Dong, S.

2018-05-01

We present a reduction-consistent and thermodynamically consistent formulation and an associated numerical algorithm for simulating the dynamics of an isothermal mixture consisting of N (N ⩾ 2) immiscible incompressible fluids with different physical properties (densities, viscosities, and pair-wise surface tensions). By reduction consistency we refer to the property that if only a set of M (1 ⩽ M ⩽ N - 1) fluids are present in the system then the N-phase governing equations and boundary conditions will exactly reduce to those for the corresponding M-phase system. By thermodynamic consistency we refer to the property that the formulation honors the thermodynamic principles. Our N-phase formulation is developed based on a more general method that allows for the systematic construction of reduction-consistent formulations, and the method suggests the existence of many possible forms of reduction-consistent and thermodynamically consistent N-phase formulations. Extensive numerical experiments have been presented for flow problems involving multiple fluid components and large density ratios and large viscosity ratios, and the simulation results are compared with the physical theories or the available physical solutions. The comparisons demonstrate that our method produces physically accurate results for this class of problems.

Computational Thermodynamics and Kinetics-Based ICME Framework for High-Temperature Shape Memory Alloys

NASA Astrophysics Data System (ADS)

Arróyave, Raymundo; Talapatra, Anjana; Johnson, Luke; Singh, Navdeep; Ma, Ji; Karaman, Ibrahim

2015-11-01

Over the last decade, considerable interest in the development of High-Temperature Shape Memory Alloys (HTSMAs) for solid-state actuation has increased dramatically as key applications in the aerospace and automotive industry demand actuation temperatures well above those of conventional SMAs. Most of the research to date has focused on establishing the (forward) connections between chemistry, processing, (micro)structure, properties, and performance. Much less work has been dedicated to the development of frameworks capable of addressing the inverse problem of establishing necessary chemistry and processing schedules to achieve specific performance goals. Integrated Computational Materials Engineering (ICME) has emerged as a powerful framework to address this problem, although it has yet to be applied to the development of HTSMAs. In this paper, the contributions of computational thermodynamics and kinetics to ICME of HTSMAs are described. Some representative examples of the use of computational thermodynamics and kinetics to understand the phase stability and microstructural evolution in HTSMAs are discussed. Some very recent efforts at combining both to assist in the design of HTSMAs and limitations to the full implementation of ICME frameworks for HTSMA development are presented.

Mimicking Nonequilibrium Steady States with Time-Periodic Driving (Open Source)

DTIC Science & Technology

2016-05-18

nonequilibrium steady states, and vice versa, within the theoretical framework of discrete-state stochastic thermodynamics . Nonequilibrium steady states...equilibrium [2], spontaneous relaxation towards equilibrium [3], nonequilibrium steady states generated by fixed thermodynamic forces [4], and stochastic pumps...paradigm, a system driven by fixed thermodynamic forces—such as temperature gradients or chemical potential differences— reaches a steady state in

Implications of causality for quantum biology - I: topology change

NASA Astrophysics Data System (ADS)

Scofield, D. F.; Collins, T. C.

2018-06-01

A framework for describing the causal, topology changing, evolution of interacting biomolecules is developed. The quantum dynamical manifold equations (QDMEs) derived from this framework can be related to the causality restrictions implied by a finite speed of light and to Planck's constant to set a transition frequency scale. The QDMEs imply conserved stress-energy, angular-momentum and Noether currents. The functional whose extremisation leads to this result provides a causal, time-dependent, non-equilibrium generalisation of the Hohenberg-Kohn theorem. The system of dynamical equations derived from this functional and the currents J derived from the QDMEs are shown to be causal and consistent with the first and second laws of thermodynamics. This has the potential of allowing living systems to be quantum mechanically distinguished from non-living ones.

A generalized framework for nucleosynthesis calculations

NASA Astrophysics Data System (ADS)

Sprouse, Trevor; Mumpower, Matthew; Aprahamian, Ani

2014-09-01

Simulating astrophysical events is a difficult process, requiring a detailed pairing of knowledge from both astrophysics and nuclear physics. Astrophysics guides the thermodynamic evolution of an astrophysical event. We present a nucleosynthesis framework written in Fortran that combines as inputs a thermodynamic evolution and nuclear data to time evolve the abundances of nuclear species. Through our coding practices, we have emphasized the applicability of our framework to any astrophysical event, including those involving nuclear fission. Because these calculations are often very complicated, our framework dynamically optimizes itself based on the conditions at each time step in order to greatly minimize total computation time. To highlight the power of this new approach, we demonstrate the use of our framework to simulate both Big Bang nucleosynthesis and r-process nucleosynthesis with speeds competitive with current solutions dedicated to either process alone.

Propulsion System Simulation Using the Toolbox for the Modeling and Analysis of Thermodynamic System (T-MATS)

NASA Technical Reports Server (NTRS)

Chapman, Jeffryes W.; Lavelle, Thomas M.; May, Ryan D.; Litt, Jonathan S.; Guo, Ten-Huei (OA)

2014-01-01

A simulation toolbox has been developed for the creation of both steady-state and dynamic thermodynamic software models. This presentation describes the Toolbox for the Modeling and Analysis of Thermodynamic Systems (T-MATS), which combines generic thermodynamic and controls modeling libraries with a numerical iterative solver to create a framework for the development of thermodynamic system simulations, such as gas turbine engines. The objective of this presentation is to present an overview of T-MATS, the theory used in the creation of the module sets, and a possible propulsion simulation architecture.

Development of a representational conceptual evaluation in the first law of thermodynamics

NASA Astrophysics Data System (ADS)

Sriyansyah, S. P.; Suhandi, A.

2016-08-01

As part of an ongoing research to investigate student consistency in understanding the first law of thermodynamics, a representational conceptual evaluation (RCET) has been developed to assess student conceptual understanding, representational consistency, and scientific consistency in the introductory physics course. Previous physics education research findings were used to develop the test. RCET items were 30 items which designed as an isomorphic multiple-choice test with three different representations concerning the concept of work, heat, first law of thermodynamics, and its application in the thermodynamic processes. Here, we present preliminary measures of the validity and reliability of the instrument, including the classical test statistics. This instrument can be used to measure the intended concept in the first law of thermodynamics and it will give the consistent results with the ability to differentiate well between high-achieving students and low-achieving students and also students at different level. As well as measuring the effectiveness of the learning process in the concept of the first law of thermodynamics.

Thermodynamic framework for identifying free energy inventories of enzyme catalytic cycles

PubMed Central

Fried, Stephen D.; Boxer, Steven G.

2013-01-01

Pauling’s suggestion that enzymes are complementary in structure to the activated complexes of the reactions they catalyze has provided the conceptual basis to explain how enzymes obtain their fantastic catalytic prowess, and has served as a guiding principle in drug design for over 50 y. However, this model by itself fails to predict the magnitude of enzymes’ rate accelerations. We construct a thermodynamic framework that begins with the classic concept of differential binding but invokes additional terms that are needed to account for subtle effects in the catalytic cycle’s proton inventory. Although the model presented can be applied generally, this analysis focuses on ketosteroid isomerase (KSI) as an example, where recent experiments along with a large body of kinetic and thermodynamic data have provided strong support for the noncanonical thermodynamic contribution described. The resulting analysis precisely predicts the free energy barrier of KSI’s reaction as determined from transition-state theory using only empirical thermodynamic data. This agreement is suggestive that a complete free energy inventory of the KSI catalytic cycle has been identified. PMID:23840058

A Hamiltonian approach to Thermodynamics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Baldiotti, M.C., E-mail: baldiotti@uel.br; Fresneda, R., E-mail: rodrigo.fresneda@ufabc.edu.br; Molina, C., E-mail: cmolina@usp.br

In the present work we develop a strictly Hamiltonian approach to Thermodynamics. A thermodynamic description based on symplectic geometry is introduced, where all thermodynamic processes can be described within the framework of Analytic Mechanics. Our proposal is constructed on top of a usual symplectic manifold, where phase space is even dimensional and one has well-defined Poisson brackets. The main idea is the introduction of an extended phase space where thermodynamic equations of state are realized as constraints. We are then able to apply the canonical transformation toolkit to thermodynamic problems. Throughout this development, Dirac’s theory of constrained systems is extensivelymore » used. To illustrate the formalism, we consider paradigmatic examples, namely, the ideal, van der Waals and Clausius gases. - Highlights: • A strictly Hamiltonian approach to Thermodynamics is proposed. • Dirac’s theory of constrained systems is extensively used. • Thermodynamic equations of state are realized as constraints. • Thermodynamic potentials are related by canonical transformations.« less

Quantitative Connection Between Ensemble Thermodynamics and Single-Molecule Kinetics: A Case Study Using Cryo-EM and smFRET Investigations of the Ribosome

PubMed Central

Frank, Joachim; Gonzalez, Ruben L.

2015-01-01

At equilibrium, thermodynamic and kinetic information can be extracted from biomolecular energy landscapes by many techniques. However, while static, ensemble techniques yield thermodynamic data, often only dynamic, single-molecule techniques can yield the kinetic data that describes transition-state energy barriers. Here we present a generalized framework based upon dwell-time distributions that can be used to connect such static, ensemble techniques with dynamic, single-molecule techniques, and thus characterize energy landscapes to greater resolutions. We demonstrate the utility of this framework by applying it to cryogenic electron microscopy and single-molecule fluorescence resonance energy transfer studies of the bacterial ribosomal pretranslocation complex. Among other benefits, application of this framework to these data explains why two transient, intermediate conformations of the pretranslocation complex, which are observed in a cryogenic electron microscopy study, may not be observed in several single-molecule fluorescence resonance energy transfer studies. PMID:25785884

A thermodynamic approach to nonlinear ultrasonics for material state awareness and prognosis

NASA Astrophysics Data System (ADS)

Chillara, Vamshi Krishna

2017-11-01

We develop a thermodynamic framework for modeling nonlinear ultrasonic damage sensing and prognosis in materials undergoing progressive damage. The framework is based on the internal variable approach and relies on the construction of a pseudo-elastic strain energy function that captures the energetics associated with the damage progression. The pseudo-elastic strain energy function is composed of two energy functions—one that describes how a material stores energy in an elastic fashion and the other describes how material dissipates energy or stores it in an inelastic fashion. Experimental motivation for the choice of the above two functionals is discussed and some specific choices pertaining to damage progression during fatigue and creep are presented. The thermodynamic framework is employed to model the nonlinear response of material undergoing stress relaxation and creep-like degradation. For each of the above cases, evolution of the nonlinearity parameter with damage as well as with macroscopic measurables like accumulated plastic strain is obtained.

Quantitative Connection between Ensemble Thermodynamics and Single-Molecule Kinetics: A Case Study Using Cryogenic Electron Microscopy and Single-Molecule Fluorescence Resonance Energy Transfer Investigations of the Ribosome.

PubMed

Thompson, Colin D Kinz; Sharma, Ajeet K; Frank, Joachim; Gonzalez, Ruben L; Chowdhury, Debashish

2015-08-27

At equilibrium, thermodynamic and kinetic information can be extracted from biomolecular energy landscapes by many techniques. However, while static, ensemble techniques yield thermodynamic data, often only dynamic, single-molecule techniques can yield the kinetic data that describe transition-state energy barriers. Here we present a generalized framework based upon dwell-time distributions that can be used to connect such static, ensemble techniques with dynamic, single-molecule techniques, and thus characterize energy landscapes to greater resolutions. We demonstrate the utility of this framework by applying it to cryogenic electron microscopy (cryo-EM) and single-molecule fluorescence resonance energy transfer (smFRET) studies of the bacterial ribosomal pre-translocation complex. Among other benefits, application of this framework to these data explains why two transient, intermediate conformations of the pre-translocation complex, which are observed in a cryo-EM study, may not be observed in several smFRET studies.

Bell scenarios in which nonlocality and entanglement are inversely related

NASA Astrophysics Data System (ADS)

Vallone, Giuseppe; Lima, Gustavo; Gómez, Esteban S.; Cañas, Gustavo; Larsson, Jan-Åke; Mataloni, Paolo; Cabello, Adán

2014-06-01

Several studies in recent years have demonstrated that upper-division students struggle with the mathematics of thermodynamics. This paper presents a task analysis based on several expert attempts to solve a challenging mathematics problem in thermodynamics. The purpose of this paper is twofold. First, we highlight the importance of cognitive task analysis for understanding expert performance and show how the epistemic games framework can be used as a tool for this type of analysis, with thermodynamics as an example. Second, through this analysis, we identify several issues related to thermodynamics that are relevant to future research into student understanding and learning of the mathematics of thermodynamics.

Sequential-Optimization-Based Framework for Robust Modeling and Design of Heterogeneous Catalytic Systems

DOE PAGES

Rangarajan, Srinivas; Maravelias, Christos T.; Mavrikakis, Manos

2017-11-09

Here, we present a general optimization-based framework for (i) ab initio and experimental data driven mechanistic modeling and (ii) optimal catalyst design of heterogeneous catalytic systems. Both cases are formulated as a nonlinear optimization problem that is subject to a mean-field microkinetic model and thermodynamic consistency requirements as constraints, for which we seek sparse solutions through a ridge (L 2 regularization) penalty. The solution procedure involves an iterative sequence of forward simulation of the differential algebraic equations pertaining to the microkinetic model using a numerical tool capable of handling stiff systems, sensitivity calculations using linear algebra, and gradient-based nonlinear optimization.more » A multistart approach is used to explore the solution space, and a hierarchical clustering procedure is implemented for statistically classifying potentially competing solutions. An example of methanol synthesis through hydrogenation of CO and CO 2 on a Cu-based catalyst is used to illustrate the framework. The framework is fast, is robust, and can be used to comprehensively explore the model solution and design space of any heterogeneous catalytic system.« less

A continuum mechanics constitutive framework for transverse isotropic soft tissues

NASA Astrophysics Data System (ADS)

Garcia-Gonzalez, D.; Jérusalem, A.; Garzon-Hernandez, S.; Zaera, R.; Arias, A.

2018-03-01

In this work, a continuum constitutive framework for the mechanical modelling of soft tissues that incorporates strain rate and temperature dependencies as well as the transverse isotropy arising from fibres embedded into a soft matrix is developed. The constitutive formulation is based on a Helmholtz free energy function decoupled into the contribution of a viscous-hyperelastic matrix and the contribution of fibres introducing dispersion dependent transverse isotropy. The proposed framework considers finite deformation kinematics, is thermodynamically consistent and allows for the particularisation of the energy potentials and flow equations of each constitutive branch. In this regard, the approach developed herein provides the basis on which specific constitutive models can be potentially formulated for a wide variety of soft tissues. To illustrate this versatility, the constitutive framework is particularised here for animal and human white matter and skin, for which constitutive models are provided. In both cases, different energy functions are considered: Neo-Hookean, Gent and Ogden. Finally, the ability of the approach at capturing the experimental behaviour of the two soft tissues is confirmed.

Sequential-Optimization-Based Framework for Robust Modeling and Design of Heterogeneous Catalytic Systems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rangarajan, Srinivas; Maravelias, Christos T.; Mavrikakis, Manos

Here, we present a general optimization-based framework for (i) ab initio and experimental data driven mechanistic modeling and (ii) optimal catalyst design of heterogeneous catalytic systems. Both cases are formulated as a nonlinear optimization problem that is subject to a mean-field microkinetic model and thermodynamic consistency requirements as constraints, for which we seek sparse solutions through a ridge (L 2 regularization) penalty. The solution procedure involves an iterative sequence of forward simulation of the differential algebraic equations pertaining to the microkinetic model using a numerical tool capable of handling stiff systems, sensitivity calculations using linear algebra, and gradient-based nonlinear optimization.more » A multistart approach is used to explore the solution space, and a hierarchical clustering procedure is implemented for statistically classifying potentially competing solutions. An example of methanol synthesis through hydrogenation of CO and CO 2 on a Cu-based catalyst is used to illustrate the framework. The framework is fast, is robust, and can be used to comprehensively explore the model solution and design space of any heterogeneous catalytic system.« less

Developpement de techniques numeriques pour l'estimation, la modelisation et la prediction de proprietes thermodynamiques et structurales de systems metalliques a fort ordonnancement chimique

NASA Astrophysics Data System (ADS)

Harvey, Jean-Philippe

In this work, the possibility to calculate and evaluate with a high degree of precision the Gibbs energy of complex multiphase equilibria for which chemical ordering is explicitly and simultaneously considered in the thermodynamic description of solid (short range order and long range order) and liquid (short range order) metallic phases is studied. The cluster site approximation (CSA) and the cluster variation method (CVM) are implemented in a new minimization technique of the Gibbs energy of multicomponent and multiphase systems to describe the thermodynamic behaviour of metallic solid solutions showing strong chemical ordering. The modified quasichemical model in the pair approximation (MQMPA) is also implemented in the new minimization algorithm presented in this work to describe the thermodynamic behaviour of metallic liquid solutions. The constrained minimization technique implemented in this work consists of a sequential quadratic programming technique based on an exact Newton’s method (i.e. the use of exact second derivatives in the determination of the Hessian of the objective function) combined to a line search method to identify a direction of sufficient decrease of the merit function. The implementation of a new algorithm to perform the constrained minimization of the Gibbs energy is justified by the difficulty to identify, in specific cases, the correct multiphase assemblage of a system where the thermodynamic behaviour of the equilibrium phases is described by one of the previously quoted models using the FactSage software (ex.: solid_CSA+liquid_MQMPA; solid1_CSA+solid2_CSA). After a rigorous validation of the constrained Gibbs energy minimization algorithm using several assessed binary and ternary systems found in the literature, the CVM and the CSA models used to describe the energetic behaviour of metallic solid solutions present in systems with key industrial applications such as the Cu-Zr and the Al-Zr systems are parameterized using fully consistent thermodynamic an structural data generated from a Monte Carlo (MC) simulator also implemented in the framework of this project. In this MC simulator, the modified embedded atom model in the second nearest neighbour formalism (MEAM-2NN) is used to describe the cohesive energy of each studied structure. A new Al-Zr MEAM-2NN interatomic potential needed to evaluate the cohesive energy of the condensed phases of this system is presented in this work. The thermodynamic integration (TI) method implemented in the MC simulator allows the evaluation of the absolute Gibbs energy of the considered solid or liquid structures. The original implementation of the TI method allowed us to evaluate theoretically for the first time all the thermodynamic mixing contributions (i.e., mixing enthalpy and mixing entropy contributions) of a metallic liquid (Cu-Zr and Al-Zr) and of a solid solution (face-centered cubic (FCC) Al-Zr solid solution) described by the MEAM-2NN. Thermodynamic and structural data obtained from MC and molecular dynamic simulations are then used to parameterize the CVM for the Al-Zr FCC solid solution and the MQMPA for the Al-Zr and the Cu-Zr liquid phase respectively. The extended thermodynamic study of these systems allow the introduction of a new type of configuration-dependent excess parameters in the definition of the thermodynamic function of solid solutions described by the CVM or the CSA. These parameters greatly improve the precision of these thermodynamic models based on experimental evidences found in the literature. A new parameterization approach of the MQMPA model of metallic liquid solutions is presented throughout this work. In this new approach, calculated pair fractions obtained from MC/MD simulations are taken into account as well as configuration-independent volumetric relaxation effects (regular like excess parameters) in order to parameterize precisely the Gibbs energy function of metallic melts. The generation of a complete set of fully consistent thermodynamic, physical and structural data for solid, liquid, and stoichiometric compounds and the subsequent parameterization of their respective thermodynamic model lead to the first description of the complete Al-Zr phase diagram in the range of composition [0 ≤ XZr ≤ 5 / 9] based on theoretical and fully consistent thermodynamic properties. MC and MD simulations are performed for the Al-Zr system to define for the first time the precise thermodynamic behaviour of the amorphous phase for its entire range of composition. Finally, all the thermodynamic models for the liquid phase, the FCC solid solution and the amorphous phase are used to define conditions based on thermodynamic and volumetric considerations that favor the amorphization of Al-Zr alloys.

Protein solubility modeling

NASA Technical Reports Server (NTRS)

Agena, S. M.; Pusey, M. L.; Bogle, I. D.

1999-01-01

A thermodynamic framework (UNIQUAC model with temperature dependent parameters) is applied to model the salt-induced protein crystallization equilibrium, i.e., protein solubility. The framework introduces a term for the solubility product describing protein transfer between the liquid and solid phase and a term for the solution behavior describing deviation from ideal solution. Protein solubility is modeled as a function of salt concentration and temperature for a four-component system consisting of a protein, pseudo solvent (water and buffer), cation, and anion (salt). Two different systems, lysozyme with sodium chloride and concanavalin A with ammonium sulfate, are investigated. Comparison of the modeled and experimental protein solubility data results in an average root mean square deviation of 5.8%, demonstrating that the model closely follows the experimental behavior. Model calculations and model parameters are reviewed to examine the model and protein crystallization process. Copyright 1999 John Wiley & Sons, Inc.

Contact symmetries and Hamiltonian thermodynamics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bravetti, A., E-mail: bravetti@correo.nucleares.unam.mx; Lopez-Monsalvo, C.S., E-mail: cesar.slm@correo.nucleares.unam.mx; Nettel, F., E-mail: Francisco.Nettel@roma1.infn.it

It has been shown that contact geometry is the proper framework underlying classical thermodynamics and that thermodynamic fluctuations are captured by an additional metric structure related to Fisher’s Information Matrix. In this work we analyse several unaddressed aspects about the application of contact and metric geometry to thermodynamics. We consider here the Thermodynamic Phase Space and start by investigating the role of gauge transformations and Legendre symmetries for metric contact manifolds and their significance in thermodynamics. Then we present a novel mathematical characterization of first order phase transitions as equilibrium processes on the Thermodynamic Phase Space for which the Legendremore » symmetry is broken. Moreover, we use contact Hamiltonian dynamics to represent thermodynamic processes in a way that resembles the classical Hamiltonian formulation of conservative mechanics and we show that the relevant Hamiltonian coincides with the irreversible entropy production along thermodynamic processes. Therefore, we use such property to give a geometric definition of thermodynamically admissible fluctuations according to the Second Law of thermodynamics. Finally, we show that the length of a curve describing a thermodynamic process measures its entropy production.« less

Thermodynamic power of non-Markovianity

PubMed Central

Bylicka, Bogna; Tukiainen, Mikko; Chruściński, Dariusz; Piilo, Jyrki; Maniscalco, Sabrina

2016-01-01

The natural framework to discuss thermodynamics at the quantum level is the theory of open quantum systems. Memory effects arising from strong system-environment correlations may lead to information back-flow, that is non-Markovian behaviour. The relation between non-Markovianity and quantum thermodynamics has been until now largely unexplored. Here we show by means of Landauer’s principle that memory effects control the amount of work extraction by erasure in presence of realistic environments. PMID:27323947

Thermodynamic forces in coarse-grained simulations

NASA Astrophysics Data System (ADS)

Noid, William

Atomically detailed molecular dynamics simulations have profoundly advanced our understanding of the structure and interactions in soft condensed phases. Nevertheless, despite dramatic advances in the methodology and resources for simulating atomically detailed models, low-resolution coarse-grained (CG) models play a central and rapidly growing role in science. CG models not only empower researchers to investigate phenomena beyond the scope of atomically detailed simulations, but also to precisely tailor models for specific phenomena. However, in contrast to atomically detailed simulations, which evolve on a potential energy surface, CG simulations should evolve on a free energy surface. Therefore, the forces in CG models should reflect the thermodynamic information that has been eliminated from the CG configuration space. As a consequence of these thermodynamic forces, CG models often demonstrate limited transferability and, moreover, rarely provide an accurate description of both structural and thermodynamic properties. In this talk, I will present a framework that clarifies the origin and impact of these thermodynamic forces. Additionally, I will present computational methods for quantifying these forces and incorporating their effects into CG MD simulations. As time allows, I will demonstrate applications of this framework for liquids, polymers, and interfaces. We gratefully acknowledge the support of the National Science Foundation via CHE 1565631.

Thermodynamic Analysis of Chemically Reacting Mixtures-Comparison of First and Second Order Models.

PubMed

Pekař, Miloslav

2018-01-01

Recently, a method based on non-equilibrium continuum thermodynamics which derives thermodynamically consistent reaction rate models together with thermodynamic constraints on their parameters was analyzed using a triangular reaction scheme. The scheme was kinetically of the first order. Here, the analysis is further developed for several first and second order schemes to gain a deeper insight into the thermodynamic consistency of rate equations and relationships between chemical thermodynamic and kinetics. It is shown that the thermodynamic constraints on the so-called proper rate coefficient are usually simple sign restrictions consistent with the supposed reaction directions. Constraints on the so-called coupling rate coefficients are more complex and weaker. This means more freedom in kinetic coupling between reaction steps in a scheme, i.e., in the kinetic effects of other reactions on the rate of some reaction in a reacting system. When compared with traditional mass-action rate equations, the method allows a reduction in the number of traditional rate constants to be evaluated from data, i.e., a reduction in the dimensionality of the parameter estimation problem. This is due to identifying relationships between mass-action rate constants (relationships which also include thermodynamic equilibrium constants) which have so far been unknown.

Memory behaviors of entropy production rates in heat conduction

NASA Astrophysics Data System (ADS)

Li, Shu-Nan; Cao, Bing-Yang

2018-02-01

Based on the relaxation time approximation and first-order expansion, memory behaviors in heat conduction are found between the macroscopic and Boltzmann-Gibbs-Shannon (BGS) entropy production rates with exponentially decaying memory kernels. In the frameworks of classical irreversible thermodynamics (CIT) and BGS statistical mechanics, the memory dependency on the integrated history is unidirectional, while for the extended irreversible thermodynamics (EIT) and BGS entropy production rates, the memory dependences are bidirectional and coexist with the linear terms. When macroscopic and microscopic relaxation times satisfy a specific relationship, the entropic memory dependences will be eliminated. There also exist initial effects in entropic memory behaviors, which decay exponentially. The second-order term are also discussed, which can be understood as the global non-equilibrium degree. The effects of the second-order term are consisted of three parts: memory dependency, initial value and linear term. The corresponding memory kernels are still exponential and the initial effects of the global non-equilibrium degree also decay exponentially.

Thermodynamically consistent relations involving plasticity, internal energy and thermal effects.

PubMed

Schreyer, H L; Maudlin, P J

2005-11-15

Experimental data associated with plastic deformations indicate that the temperature is less than that predicted from dissipation based on plastic work. To obtain reasonable correlation between theoretical and experimental results, the plastic work is often multiplied by a constant beta. This paper provides an alternative thermodynamic framework in which it is proposed that there is an additional internal energy associated with dislocation pile-up or increase in dislocation density. The form of this internal energy follows from experimental data that relates flow stress to dislocation density and to equivalent plastic strain. The result is that beta is not a constant but a derived function. Representative results for beta and temperature as functions of effective plastic strain are provided for both an uncoupled and a coupled thermoplastic theory. In addition to providing features that are believed to be representative of many metals, the formulation can be used as a basis for more advanced theories such as those needed for large deformations and general forms of internal energy.

Oxygen nonstoichiometry and thermodynamic quantities in solid solution SrFe1-xSnxO3-δ

NASA Astrophysics Data System (ADS)

Merkulov, O. V.; Markov, A. A.; Leonidov, I. A.; Patrakeev, M. V.; Kozhevnikov, V. L.

2018-06-01

The oxygen content (3-δ) variations in tin substituted derivatives SrFe1-xSnxO3-δ, where x = 0.05, 0.1, 0.17 and 0.25, of perovskite-like strontium ferrite, have been studied by coulometric titration measurements within oxygen partial pressure (pO2) range 10-19-10-2 atm at 800-950 °С. The obtained dependencies of (3-δ) from pO2 and temperature are used for calculations of partial molar thermodynamic functions of oxygen in the oxide structure. It is found that a satisfactory explanation of the experimental results can be attained within frameworks of the ideal solution model with ion and electron defects appearing in the result of oxidation and disproportionation of iron cations. The increase of the oxidation reaction enthalpy with tin content is consistent with the increase of the unit cell parameter, i.e., the stretch and relaxation of Fe-O chemical bonds.

On Thermodynamic Constraints upon Turbulence Modeling

NASA Astrophysics Data System (ADS)

Huang, Yu-Ning; Durst, Franz

2000-11-01

Turbulence is a continuum phenomenon which can be described within the framework of continuum mechanics. Such foundation has the potential for improving turbulence modeling, making it less heuristic and more rational. In the present research, we consider the compatibility of turbulence modeling with the second law of thermodynamics. We show that the Clausius-Planck inequality, as an expression of the principle of entropy growth, places a thermodynamic restriction upon the turbulence modeling of an incompressible Navier-Stokes fluid in an isothermal temperature field. This thermodynamic restriction is given in the form of an inequality, which ensures non-negativeness of the mean internal dissipation. As an illustration, we show the thermodynamic constraints on the modeling of a few typical homogeneous turbulent flows.

Thermodynamic equilibrium with acceleration and the Unruh effect

NASA Astrophysics Data System (ADS)

Becattini, F.

2018-04-01

We address the problem of thermodynamic equilibrium with constant acceleration along the velocity field lines in a quantum relativistic statistical mechanics framework. We show that for a free scalar quantum field, after vacuum subtraction, all mean values vanish when the local temperature T is as low as the Unruh temperature TU=A /2 π where A is the magnitude of the acceleration four-vector. We argue that the Unruh temperature is an absolute lower bound for the temperature of any accelerated fluid at global thermodynamic equilibrium. We discuss the conditions of this bound to be applicable in a local thermodynamic equilibrium situation.

Analyzing Data for Systems Biology: Working at the Intersection of Thermodynamics and Data Analytics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cannon, William R.; Baxter, Douglas J.

2012-08-15

Many challenges in systems biology have to do with analyzing data within the framework of molecular phenomena and cellular pathways. How does this relate to thermodynamics that we know govern the behavior of molecules? Making progress in relating data analysis to thermodynamics is essential in systems biology if we are to build predictive models that enable the field of synthetic biology. This report discusses work at the crossroads of thermodynamics and data analysis, and demonstrates that statistical mechanical free energy is a multinomial log likelihood. Applications to systems biology are presented.

Thermodynamically consistent model calibration in chemical kinetics

PubMed Central

2011-01-01

Background The dynamics of biochemical reaction systems are constrained by the fundamental laws of thermodynamics, which impose well-defined relationships among the reaction rate constants characterizing these systems. Constructing biochemical reaction systems from experimental observations often leads to parameter values that do not satisfy the necessary thermodynamic constraints. This can result in models that are not physically realizable and may lead to inaccurate, or even erroneous, descriptions of cellular function. Results We introduce a thermodynamically consistent model calibration (TCMC) method that can be effectively used to provide thermodynamically feasible values for the parameters of an open biochemical reaction system. The proposed method formulates the model calibration problem as a constrained optimization problem that takes thermodynamic constraints (and, if desired, additional non-thermodynamic constraints) into account. By calculating thermodynamically feasible values for the kinetic parameters of a well-known model of the EGF/ERK signaling cascade, we demonstrate the qualitative and quantitative significance of imposing thermodynamic constraints on these parameters and the effectiveness of our method for accomplishing this important task. MATLAB software, using the Systems Biology Toolbox 2.1, can be accessed from http://www.cis.jhu.edu/~goutsias/CSS lab/software.html. An SBML file containing the thermodynamically feasible EGF/ERK signaling cascade model can be found in the BioModels database. Conclusions TCMC is a simple and flexible method for obtaining physically plausible values for the kinetic parameters of open biochemical reaction systems. It can be effectively used to recalculate a thermodynamically consistent set of parameter values for existing thermodynamically infeasible biochemical reaction models of cellular function as well as to estimate thermodynamically feasible values for the parameters of new models. Furthermore, TCMC can provide dimensionality reduction, better estimation performance, and lower computational complexity, and can help to alleviate the problem of data overfitting. PMID:21548948

An integrated open framework for thermodynamics of reactions that combines accuracy and coverage.

PubMed

Noor, Elad; Bar-Even, Arren; Flamholz, Avi; Lubling, Yaniv; Davidi, Dan; Milo, Ron

2012-08-01

The laws of thermodynamics describe a direct, quantitative relationship between metabolite concentrations and reaction directionality. Despite great efforts, thermodynamic data suffer from limited coverage, scattered accessibility and non-standard annotations. We present a framework for unifying thermodynamic data from multiple sources and demonstrate two new techniques for extrapolating the Gibbs energies of unmeasured reactions and conditions. Both methods account for changes in cellular conditions (pH, ionic strength, etc.) by using linear regression over the ΔG(○) of pseudoisomers and reactions. The Pseudoisomeric Reactant Contribution method systematically infers compound formation energies using measured K' and pK(a) data. The Pseudoisomeric Group Contribution method extends the group contribution method and achieves a high coverage of unmeasured reactions. We define a continuous index that predicts the reversibility of a reaction under a given physiological concentration range. In the characteristic physiological range 3μM-3mM, we find that roughly half of the reactions in Escherichia coli's metabolism are reversible. These new tools can increase the accuracy of thermodynamic-based models, especially in non-standard pH and ionic strengths. The reversibility index can help modelers decide which reactions are reversible in physiological conditions. Freely available on the web at: http://equilibrator.weizmann.ac.il. Website implemented in Python, MySQL, Apache and Django, with all major browsers supported. The framework is open-source (code.google.com/p/milo-lab), implemented in pure Python and tested mainly on Linux. ron.milo@weizmann.ac.il Supplementary data are available at Bioinformatics online.

An integrated open framework for thermodynamics of reactions that combines accuracy and coverage

PubMed Central

Noor, Elad; Bar-Even, Arren; Flamholz, Avi; Lubling, Yaniv; Davidi, Dan; Milo, Ron

2012-01-01

Motivation: The laws of thermodynamics describe a direct, quantitative relationship between metabolite concentrations and reaction directionality. Despite great efforts, thermodynamic data suffer from limited coverage, scattered accessibility and non-standard annotations. We present a framework for unifying thermodynamic data from multiple sources and demonstrate two new techniques for extrapolating the Gibbs energies of unmeasured reactions and conditions. Results: Both methods account for changes in cellular conditions (pH, ionic strength, etc.) by using linear regression over the ΔG○ of pseudoisomers and reactions. The Pseudoisomeric Reactant Contribution method systematically infers compound formation energies using measured K′ and pKa data. The Pseudoisomeric Group Contribution method extends the group contribution method and achieves a high coverage of unmeasured reactions. We define a continuous index that predicts the reversibility of a reaction under a given physiological concentration range. In the characteristic physiological range 3μM–3mM, we find that roughly half of the reactions in Escherichia coli's metabolism are reversible. These new tools can increase the accuracy of thermodynamic-based models, especially in non-standard pH and ionic strengths. The reversibility index can help modelers decide which reactions are reversible in physiological conditions. Availability: Freely available on the web at: http://equilibrator.weizmann.ac.il. Website implemented in Python, MySQL, Apache and Django, with all major browsers supported. The framework is open-source (code.google.com/p/milo-lab), implemented in pure Python and tested mainly on Linux. Contact: ron.milo@weizmann.ac.il Supplementary Information: Supplementary data are available at Bioinformatics online. PMID:22645166

DOE Office of Scientific and Technical Information (OSTI.GOV)

Grove, John W.

We investigate sufficient conditions for thermodynamic consistency for equilibrium mixtures. Such models assume that the mass fraction average of the material component equations of state, when closed by a suitable equilibrium condition, provide a composite equation of state for the mixture. Here, we show that the two common equilibrium models of component pressure/temperature equilibrium and volume/temperature equilibrium (Dalton, 1808) define thermodynamically consistent mixture equations of state and that other equilibrium conditions can be thermodynamically consistent provided appropriate values are used for the mixture specific entropy and pressure.

Volumetrically Derived Thermodynamic Profile of Interactions of Urea with a Native Protein.

PubMed

Son, Ikbae; Chalikian, Tigran V

2016-11-29

We report the first experimental characterization of the full thermodynamic profile for binding of urea to a native protein. We measured the volumetric parameters of lysozyme at pH 7.0 as a function of urea within a temperature range of 18-45 °C. At neutral pH, lysozyme retains its native conformation between 0 and 8 M urea over the entire range of temperatures studied. Consequently, our measured volumetric properties reflect solely the interactions of urea with the native protein and do not involve contributions from urea-induced conformational transitions. We analyzed our data within the framework of a statistical thermodynamic analytical model in which urea-protein interactions are viewed as solvent exchange in the vicinity of the protein. The analysis produced the equilibrium constant, k, for an elementary reaction of urea-protein binding with a change in standard state free energy (ΔG° = -RT ln k) at each experimental temperature. We used the van't Hoff equation to compute from the temperature dependence of the equilibrium constant, k, changes in enthalpy, ΔH°, and entropy, ΔS°, accompanying binding. The thermodynamic profile of urea-protein interactions, in conjunction with published molecular dynamics simulation results, is consistent with the picture in which urea molecules, being underhydrated in the bulk, form strong, enthalpically favorable interactions with the surface protein groups while paying a high entropic price. We discuss ramifications of our results for providing insights into the combined effects of urea, temperature, and pressure on the conformational preferences of proteins.

GENERIC Integrators: Structure Preserving Time Integration for Thermodynamic Systems

NASA Astrophysics Data System (ADS)

Öttinger, Hans Christian

2018-04-01

Thermodynamically admissible evolution equations for non-equilibrium systems are known to possess a distinct mathematical structure. Within the GENERIC (general equation for the non-equilibrium reversible-irreversible coupling) framework of non-equilibrium thermodynamics, which is based on continuous time evolution, we investigate the possibility of preserving all the structural elements in time-discretized equations. Our approach, which follows Moser's [1] construction of symplectic integrators for Hamiltonian systems, is illustrated for the damped harmonic oscillator. Alternative approaches are sketched.

Ab initio thermodynamic model for magnesium carbonates and hydrates.

PubMed

Chaka, Anne M; Felmy, Andrew R

2014-09-04

An ab initio thermodynamic framework for predicting properties of hydrated magnesium carbonate minerals has been developed using density-functional theory linked to macroscopic thermodynamics through the experimental chemical potentials for MgO, water, and CO2. Including semiempirical dispersion via the Grimme method and small corrections to the generalized gradient approximation of Perdew, Burke, and Ernzerhof for the heat of formation yields a model with quantitative agreement for the benchmark minerals brucite, magnesite, nesquehonite, and hydromagnesite. The model shows how small differences in experimental conditions determine whether nesquehonite, hydromagnesite, or magnesite is the result of laboratory synthesis from carbonation of brucite, and what transformations are expected to occur on geological time scales. Because of the reliance on parameter-free first-principles methods, the model is reliably extensible to experimental conditions not readily accessible to experiment and to any mineral composition for which the structure is known or can be hypothesized, including structures containing defects, substitutions, or transitional structures during solid state transformations induced by temperature changes or processes such as water, CO2, or O2 diffusion. Demonstrated applications of the ab initio thermodynamic framework include an independent means to evaluate differences in thermodynamic data for lansfordite, predicting the properties of Mg analogues of Ca-based hydrated carbonates monohydrocalcite and ikaite, which have not been observed in nature, and an estimation of the thermodynamics of barringtonite from the stoichiometry and a single experimental observation.

Microbial diversity arising from thermodynamic constraints

PubMed Central

Großkopf, Tobias; Soyer, Orkun S

2016-01-01

The microbial world displays an immense taxonomic diversity. This diversity is manifested also in a multitude of metabolic pathways that can utilise different substrates and produce different products. Here, we propose that these observations directly link to thermodynamic constraints that inherently arise from the metabolic basis of microbial growth. We show that thermodynamic constraints can enable coexistence of microbes that utilise the same substrate but produce different end products. We find that this thermodynamics-driven emergence of diversity is most relevant for metabolic conversions with low free energy as seen for example under anaerobic conditions, where population dynamics is governed by thermodynamic effects rather than kinetic factors such as substrate uptake rates. These findings provide a general understanding of the microbial diversity based on the first principles of thermodynamics. As such they provide a thermodynamics-based framework for explaining the observed microbial diversity in different natural and synthetic environments. PMID:27035705

Thermodynamic criteria for estimating the kinetic parameters of catalytic reactions

NASA Astrophysics Data System (ADS)

Mitrichev, I. I.; Zhensa, A. V.; Kol'tsova, E. M.

2017-01-01

Kinetic parameters are estimated using two criteria in addition to the traditional criterion that considers the consistency between experimental and modeled conversion data: thermodynamic consistency and the consistency with entropy production (i.e., the absolute rate of the change in entropy due to exchange with the environment is consistent with the rate of entropy production in the steady state). A special procedure is developed and executed on a computer to achieve the thermodynamic consistency of a set of kinetic parameters with respect to both the standard entropy of a reaction and the standard enthalpy of a reaction. A problem of multi-criterion optimization, reduced to a single-criterion problem by summing weighted values of the three criteria listed above, is solved. Using the reaction of NO reduction with CO on a platinum catalyst as an example, it is shown that the set of parameters proposed by D.B. Mantri and P. Aghalayam gives much worse agreement with experimental values than the set obtained on the basis of three criteria: the sum of the squares of deviations for conversion, the thermodynamic consistency, and the consistency with entropy production.

Self-consistent description of a system of interacting phonons

NASA Astrophysics Data System (ADS)

Poluektov, Yu. M.

2015-11-01

A proposal for a method of self-consistent description of phonon systems. This method generalizes the Debye model to account for phonon-phonon interaction. The idea of "self-consistent" phonons is introduced; their speed depends on the temperature and is determined by solving a non-linear equation. The Debye energy is also a function of the temperature within the framework of the proposed approach. The thermodynamics of "self-consistent" phonon gas are built. It is shown that at low temperatures the cubic law temperature dependence of specific heat acquires an additional term that is proportional to the seventh power of the temperature. This seems to explain the reason why the cubic law for specific heat is observed only at relatively low temperatures. At high temperatures, the theory predicts a linear deviation with respect to temperature from the Dulong-Petit law, which is observed experimentally. A modification to the melting criteria is considered, to account for the phonon-phonon interaction.

Diffusion approximations to the chemical master equation only have a consistent stochastic thermodynamics at chemical equilibrium

NASA Astrophysics Data System (ADS)

Horowitz, Jordan M.

2015-07-01

The stochastic thermodynamics of a dilute, well-stirred mixture of chemically reacting species is built on the stochastic trajectories of reaction events obtained from the chemical master equation. However, when the molecular populations are large, the discrete chemical master equation can be approximated with a continuous diffusion process, like the chemical Langevin equation or low noise approximation. In this paper, we investigate to what extent these diffusion approximations inherit the stochastic thermodynamics of the chemical master equation. We find that a stochastic-thermodynamic description is only valid at a detailed-balanced, equilibrium steady state. Away from equilibrium, where there is no consistent stochastic thermodynamics, we show that one can still use the diffusive solutions to approximate the underlying thermodynamics of the chemical master equation.

Diffusion approximations to the chemical master equation only have a consistent stochastic thermodynamics at chemical equilibrium.

PubMed

Horowitz, Jordan M

2015-07-28

The stochastic thermodynamics of a dilute, well-stirred mixture of chemically reacting species is built on the stochastic trajectories of reaction events obtained from the chemical master equation. However, when the molecular populations are large, the discrete chemical master equation can be approximated with a continuous diffusion process, like the chemical Langevin equation or low noise approximation. In this paper, we investigate to what extent these diffusion approximations inherit the stochastic thermodynamics of the chemical master equation. We find that a stochastic-thermodynamic description is only valid at a detailed-balanced, equilibrium steady state. Away from equilibrium, where there is no consistent stochastic thermodynamics, we show that one can still use the diffusive solutions to approximate the underlying thermodynamics of the chemical master equation.

Bottom-up coarse-grained models with predictive accuracy and transferability for both structural and thermodynamic properties of heptane-toluene mixtures

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dunn, Nicholas J. H.; Noid, W. G., E-mail: wnoid@chem.psu.edu

This work investigates the promise of a “bottom-up” extended ensemble framework for developing coarse-grained (CG) models that provide predictive accuracy and transferability for describing both structural and thermodynamic properties. We employ a force-matching variational principle to determine system-independent, i.e., transferable, interaction potentials that optimally model the interactions in five distinct heptane-toluene mixtures. Similarly, we employ a self-consistent pressure-matching approach to determine a system-specific pressure correction for each mixture. The resulting CG potentials accurately reproduce the site-site rdfs, the volume fluctuations, and the pressure equations of state that are determined by all-atom (AA) models for the five mixtures. Furthermore, we demonstratemore » that these CG potentials provide similar accuracy for additional heptane-toluene mixtures that were not included their parameterization. Surprisingly, the extended ensemble approach improves not only the transferability but also the accuracy of the calculated potentials. Additionally, we observe that the required pressure corrections strongly correlate with the intermolecular cohesion of the system-specific CG potentials. Moreover, this cohesion correlates with the relative “structure” within the corresponding mapped AA ensemble. Finally, the appendix demonstrates that the self-consistent pressure-matching approach corresponds to minimizing an appropriate relative entropy.« less

Bottom-up coarse-grained models with predictive accuracy and transferability for both structural and thermodynamic properties of heptane-toluene mixtures.

PubMed

Dunn, Nicholas J H; Noid, W G

2016-05-28

This work investigates the promise of a "bottom-up" extended ensemble framework for developing coarse-grained (CG) models that provide predictive accuracy and transferability for describing both structural and thermodynamic properties. We employ a force-matching variational principle to determine system-independent, i.e., transferable, interaction potentials that optimally model the interactions in five distinct heptane-toluene mixtures. Similarly, we employ a self-consistent pressure-matching approach to determine a system-specific pressure correction for each mixture. The resulting CG potentials accurately reproduce the site-site rdfs, the volume fluctuations, and the pressure equations of state that are determined by all-atom (AA) models for the five mixtures. Furthermore, we demonstrate that these CG potentials provide similar accuracy for additional heptane-toluene mixtures that were not included their parameterization. Surprisingly, the extended ensemble approach improves not only the transferability but also the accuracy of the calculated potentials. Additionally, we observe that the required pressure corrections strongly correlate with the intermolecular cohesion of the system-specific CG potentials. Moreover, this cohesion correlates with the relative "structure" within the corresponding mapped AA ensemble. Finally, the appendix demonstrates that the self-consistent pressure-matching approach corresponds to minimizing an appropriate relative entropy.

Radioactivity and Environmental Security in the Oceans: New Research and Policy Priorities in the Arctic and North Atlantic

DTIC Science & Technology

1993-06-09

within the framework of an update for the computer database "DiaNIK" which has been developed at the Vernadsky Institute of Geochemistry and Analytical...chemical thermodynamic data for minerals and mineral-forming substances. The structure of thermodynamic database "DiaNIK" is based on the principles...in the database . A substantial portion of the thermodynamic values recommended by "DiaNIK" experts for the substances in User Version 3.1 resulted from

Global Passivity in Microscopic Thermodynamics

NASA Astrophysics Data System (ADS)

Uzdin, Raam; Rahav, Saar

2018-04-01

The main thread that links classical thermodynamics and the thermodynamics of small quantum systems is the celebrated Clausius inequality form of the second law. However, its application to small quantum systems suffers from two cardinal problems. (i) The Clausius inequality does not hold when the system and environment are initially correlated—a commonly encountered scenario in microscopic setups. (ii) In some other cases, the Clausius inequality does not provide any useful information (e.g., in dephasing scenarios). We address these deficiencies by developing the notion of global passivity and employing it as a tool for deriving thermodynamic inequalities on observables. For initially uncorrelated thermal environments the global passivity framework recovers the Clausius inequality. More generally, global passivity provides an extension of the Clausius inequality that holds even in the presences of strong initial system-environment correlations. Crucially, the present framework provides additional thermodynamic bounds on expectation values. To illustrate the role of the additional bounds, we use them to detect unaccounted heat leaks and weak feedback operations ("Maxwell demons") that the Clausius inequality cannot detect. In addition, it is shown that global passivity can put practical upper and lower bounds on the buildup of system-environment correlations for dephasing interactions. Our findings are highly relevant for experiments in various systems such as ion traps, superconducting circuits, atoms in optical cavities, and more.

Maxwell's demon and the management of ignorance in stochastic thermodynamics

NASA Astrophysics Data System (ADS)

Ford, Ian J.

2016-07-01

It is nearly 150 years since Maxwell challenged the validity of the second law of thermodynamics by imagining a tiny creature who could sort the molecules of a gas in such a way that would decrease entropy without exerting any work. The demon has been discussed largely using thought experiments, but it has recently become possible to exert control over nanoscale systems, just as Maxwell imagined, and the status of the second law has become a more practical matter, raising the issue of how measurements manage our ignorance in a way that can be exploited. The framework of stochastic thermodynamics extends macroscopic concepts such as heat, work, entropy and irreversibility to small systems and allows us explore the matter. Some arguments against a successful demon imply a second law that can be suspended indefinitely until we dissipate energy in order to remove the records of his operations. In contrast, under stochastic thermodynamics, the demon fails because on average, more work is performed upfront in making a measurement than can be extracted by exploiting the outcome. This requires us to exclude systems and a demon that evolve under what might be termed self-sorting dynamics, and we reflect on the constraints on control that this implies while still working within a thermodynamic framework.

Anharmonicity and self-similarity of the free energy landscape of protein G.

PubMed

Pontiggia, F; Colombo, G; Micheletti, C; Orland, H

2007-01-26

The near-native free-energy landscape of protein G is investigated through 0.4-micros-long atomistic molecular dynamics simulations in an explicit solvent. A theoretical and computational framework is used to assess the time dependence of salient thermodynamical features. While the quasiharmonic character of the free energy is found to degrade in a few ns, the slow modes display a very mild dependence on the trajectory duration. This property originates from a striking self-similarity of the free-energy landscape embodied by the consistency of the principal directions of the local minima, where the system dwells for several ns, and of the virtual jumps connecting them.

Non-equilibrium thermodynamics in cells.

PubMed

Jülicher, Frank; Grill, Stephan W; Salbreux, Guillaume

2018-03-15

We review the general hydrodynamic theory of active soft materials that is motivated in partic- ular by biological matter. We present basic concepts of irreversible thermodynamics of spatially extended multicomponent active systems. Starting from the rate of entropy production, we iden- tify conjugate thermodynamic fluxes and forces and present generic constitutive equations of polar active fluids and active gels. We also discuss angular momentum conservation which plays a role in the the physics of active chiral gels. The irreversible thermodynamics of active gels provides a general framework to discuss the physics that underlies a wide variety of biological processes in cells and in multicellular tissues. © 2018 IOP Publishing Ltd.

Flow line asymmetric nonimaging concentrating optics

NASA Astrophysics Data System (ADS)

Jiang, Lun; Winston, Roland

2016-09-01

Nonimaging Optics has shown that it achieves the theoretical limits by utilizing thermodynamic principles rather than conventional optics. Hence in this paper the condition of the "best" design are both defined and fulfilled in the framework of thermodynamic arguments, which we believe has profound consequences for the designs of thermal and even photovoltaic systems, even illumination and optical communication tasks. This new way of looking at the problem of efficient concentration depends on probabilities, geometric flux field and radiative heat transfer while "optics" in the conventional sense recedes into the background. Some of the new development of flow line designs will be introduced and the connection between the thermodynamics and flow line design will be officially formulated in the framework of geometric flux field. A new way of using geometric flux to design nonimaging optics will be introduced. And finally, we discuss the possibility of 3D ideal nonimaing optics.

Diffusion approximations to the chemical master equation only have a consistent stochastic thermodynamics at chemical equilibrium

DOE Office of Scientific and Technical Information (OSTI.GOV)

Horowitz, Jordan M., E-mail: jordan.horowitz@umb.edu

The stochastic thermodynamics of a dilute, well-stirred mixture of chemically reacting species is built on the stochastic trajectories of reaction events obtained from the chemical master equation. However, when the molecular populations are large, the discrete chemical master equation can be approximated with a continuous diffusion process, like the chemical Langevin equation or low noise approximation. In this paper, we investigate to what extent these diffusion approximations inherit the stochastic thermodynamics of the chemical master equation. We find that a stochastic-thermodynamic description is only valid at a detailed-balanced, equilibrium steady state. Away from equilibrium, where there is no consistent stochasticmore » thermodynamics, we show that one can still use the diffusive solutions to approximate the underlying thermodynamics of the chemical master equation.« less

Pathway Thermodynamics Highlights Kinetic Obstacles in Central Metabolism

PubMed Central

Flamholz, Avi; Reznik, Ed; Liebermeister, Wolfram; Milo, Ron

2014-01-01

In metabolism research, thermodynamics is usually used to determine the directionality of a reaction or the feasibility of a pathway. However, the relationship between thermodynamic potentials and fluxes is not limited to questions of directionality: thermodynamics also affects the kinetics of reactions through the flux-force relationship, which states that the logarithm of the ratio between the forward and reverse fluxes is directly proportional to the change in Gibbs energy due to a reaction (ΔrG′). Accordingly, if an enzyme catalyzes a reaction with a ΔrG′ of -5.7 kJ/mol then the forward flux will be roughly ten times the reverse flux. As ΔrG′ approaches equilibrium (ΔrG′ = 0 kJ/mol), exponentially more enzyme counterproductively catalyzes the reverse reaction, reducing the net rate at which the reaction proceeds. Thus, the enzyme level required to achieve a given flux increases dramatically near equilibrium. Here, we develop a framework for quantifying the degree to which pathways suffer these thermodynamic limitations on flux. For each pathway, we calculate a single thermodynamically-derived metric (the Max-min Driving Force, MDF), which enables objective ranking of pathways by the degree to which their flux is constrained by low thermodynamic driving force. Our framework accounts for the effect of pH, ionic strength and metabolite concentration ranges and allows us to quantify how alterations to the pathway structure affect the pathway's thermodynamics. Applying this methodology to pathways of central metabolism sheds light on some of their features, including metabolic bypasses (e.g., fermentation pathways bypassing substrate-level phosphorylation), substrate channeling (e.g., of oxaloacetate from malate dehydrogenase to citrate synthase), and use of alternative cofactors (e.g., quinone as an electron acceptor instead of NAD). The methods presented here place another arrow in metabolic engineers' quiver, providing a simple means of evaluating the thermodynamic and kinetic quality of different pathway chemistries that produce the same molecules. PMID:24586134

Development of a Thermodynamic Model for the Hanford Tank Waste Operations Simulator - 12193

DOE Office of Scientific and Technical Information (OSTI.GOV)

Carter, Robert; Seniow, Kendra

The Hanford Tank Waste Operations Simulator (HTWOS) is the current tool used by the Hanford Tank Operations Contractor for system planning and assessment of different operational strategies. Activities such as waste retrievals in the Hanford tank farms and washing and leaching of waste in the Waste Treatment and Immobilization Plant (WTP) are currently modeled in HTWOS. To predict phase compositions during these activities, HTWOS currently uses simple wash and leach factors that were developed many years ago. To improve these predictions, a rigorous thermodynamic framework has been developed based on the multi-component Pitzer ion interaction model for use with severalmore » important chemical species in Hanford tank waste. These chemical species are those with the greatest impact on high-level waste glass production in the WTP and whose solubility depends on the processing conditions. Starting with Pitzer parameter coefficients and species chemical potential coefficients collated from open literature sources, reconciliation with published experimental data led to a self-consistent set of coefficients known as the HTWOS Pitzer database. Using Gibbs energy minimization with the Pitzer ion interaction equations in Microsoft Excel,1 a number of successful predictions were made for the solubility of simple mixtures of the chosen species. Currently, this thermodynamic framework is being programmed into HTWOS as the mechanism for determining the solid-liquid phase distributions for the chosen species, replacing their simple wash and leach factors. Starting from a variety of open literature sources, a collection of Pitzer parameters and species chemical potentials, as functions of temperature, was tested for consistency and accuracy by comparison with available experimental thermodynamic data (e.g., osmotic coefficients and solubility). Reconciliation of the initial set of parameter coefficients with the experimental data led to the development of the self-consistent set known as the HTWOS Pitzer database. Using Microsoft Excel to formulate the Gibbs energy minimization method and the multi-component Pitzer ion interaction equations, several predictions of the solubility of solute mixtures at various temperatures were made using the HTWOS Pitzer database coefficients. Examples of these predictions are shown in Figure 3 and Figure 4. A listing of the entire HTWOS Pitzer database can be found in RPP-RPT-50703. Currently, work is underway to install the Pitzer ion interaction model in HTWOS as the mechanism for determining the solid-liquid phase distributions of select waste constituents during tank retrievals and subsequent washing and leaching of the waste. Validation of the Pitzer ion interaction model in HTWOS will be performed with analytical laboratory data of actual tank waste. This change in HTWOS is expected to elicit shifts in mission criteria, such as mission end date and quantity of high-level waste glass produced by WTP, as predicted by HTWOS. These improvements to the speciation calculations in HTWOS, however, will establish a better planning basis and facilitate more effective and efficient future operations of the WTP. (authors)« less

Nonequilibrium thermodynamics of restricted Boltzmann machines.

PubMed

Salazar, Domingos S P

2017-08-01

In this work, we analyze the nonequilibrium thermodynamics of a class of neural networks known as restricted Boltzmann machines (RBMs) in the context of unsupervised learning. We show how the network is described as a discrete Markov process and how the detailed balance condition and the Maxwell-Boltzmann equilibrium distribution are sufficient conditions for a complete thermodynamics description, including nonequilibrium fluctuation theorems. Numerical simulations in a fully trained RBM are performed and the heat exchange fluctuation theorem is verified with excellent agreement to the theory. We observe how the contrastive divergence functional, mostly used in unsupervised learning of RBMs, is closely related to nonequilibrium thermodynamic quantities. We also use the framework to interpret the estimation of the partition function of RBMs with the annealed importance sampling method from a thermodynamics standpoint. Finally, we argue that unsupervised learning of RBMs is equivalent to a work protocol in a system driven by the laws of thermodynamics in the absence of labeled data.

Coherence and measurement in quantum thermodynamics

PubMed Central

Kammerlander, P.; Anders, J.

2016-01-01

Thermodynamics is a highly successful macroscopic theory widely used across the natural sciences and for the construction of everyday devices, from car engines to solar cells. With thermodynamics predating quantum theory, research now aims to uncover the thermodynamic laws that govern finite size systems which may in addition host quantum effects. Recent theoretical breakthroughs include the characterisation of the efficiency of quantum thermal engines, the extension of classical non-equilibrium fluctuation theorems to the quantum regime and a new thermodynamic resource theory has led to the discovery of a set of second laws for finite size systems. These results have substantially advanced our understanding of nanoscale thermodynamics, however putting a finger on what is genuinely quantum in quantum thermodynamics has remained a challenge. Here we identify information processing tasks, the so-called projections, that can only be formulated within the framework of quantum mechanics. We show that the physical realisation of such projections can come with a non-trivial thermodynamic work only for quantum states with coherences. This contrasts with information erasure, first investigated by Landauer, for which a thermodynamic work cost applies for classical and quantum erasure alike. Repercussions on quantum work fluctuation relations and thermodynamic single-shot approaches are also discussed. PMID:26916503

Coherence and measurement in quantum thermodynamics.

PubMed

Kammerlander, P; Anders, J

2016-02-26

Thermodynamics is a highly successful macroscopic theory widely used across the natural sciences and for the construction of everyday devices, from car engines to solar cells. With thermodynamics predating quantum theory, research now aims to uncover the thermodynamic laws that govern finite size systems which may in addition host quantum effects. Recent theoretical breakthroughs include the characterisation of the efficiency of quantum thermal engines, the extension of classical non-equilibrium fluctuation theorems to the quantum regime and a new thermodynamic resource theory has led to the discovery of a set of second laws for finite size systems. These results have substantially advanced our understanding of nanoscale thermodynamics, however putting a finger on what is genuinely quantum in quantum thermodynamics has remained a challenge. Here we identify information processing tasks, the so-called projections, that can only be formulated within the framework of quantum mechanics. We show that the physical realisation of such projections can come with a non-trivial thermodynamic work only for quantum states with coherences. This contrasts with information erasure, first investigated by Landauer, for which a thermodynamic work cost applies for classical and quantum erasure alike. Repercussions on quantum work fluctuation relations and thermodynamic single-shot approaches are also discussed.

Coherence and measurement in quantum thermodynamics

NASA Astrophysics Data System (ADS)

Kammerlander, P.; Anders, J.

2016-02-01

Thermodynamics is a highly successful macroscopic theory widely used across the natural sciences and for the construction of everyday devices, from car engines to solar cells. With thermodynamics predating quantum theory, research now aims to uncover the thermodynamic laws that govern finite size systems which may in addition host quantum effects. Recent theoretical breakthroughs include the characterisation of the efficiency of quantum thermal engines, the extension of classical non-equilibrium fluctuation theorems to the quantum regime and a new thermodynamic resource theory has led to the discovery of a set of second laws for finite size systems. These results have substantially advanced our understanding of nanoscale thermodynamics, however putting a finger on what is genuinely quantum in quantum thermodynamics has remained a challenge. Here we identify information processing tasks, the so-called projections, that can only be formulated within the framework of quantum mechanics. We show that the physical realisation of such projections can come with a non-trivial thermodynamic work only for quantum states with coherences. This contrasts with information erasure, first investigated by Landauer, for which a thermodynamic work cost applies for classical and quantum erasure alike. Repercussions on quantum work fluctuation relations and thermodynamic single-shot approaches are also discussed.

Final Report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Issen, Kathleen

2017-06-05

This project employed a continuum approach to formulate an elastic constitutive model for Castlegate sandstone. The resulting constitutive framework for high porosity sandstone is thermodynamically sound, (i.e., does not violate the 1st and 2nd law of thermodynamics), represents known material constitutive response, and is able to be calibrated using available mechanical response data. To authenticate the accuracy of this model, a series of validation criteria were employed, using an existing mechanical response data set for Castlegate sandstone. The resulting constitutive framework is applicable to high porosity sandstones in general, and is tractable for scientists and researchers endeavoring to solve problemsmore » of practical interest.« less

Thermodynamic framework to assess low abundance DNA mutation detection by hybridization.

PubMed

Willems, Hanny; Jacobs, An; Hadiwikarta, Wahyu Wijaya; Venken, Tom; Valkenborg, Dirk; Van Roy, Nadine; Vandesompele, Jo; Hooyberghs, Jef

2017-01-01

The knowledge of genomic DNA variations in patient samples has a high and increasing value for human diagnostics in its broadest sense. Although many methods and sensors to detect or quantify these variations are available or under development, the number of underlying physico-chemical detection principles is limited. One of these principles is the hybridization of sample target DNA versus nucleic acid probes. We introduce a novel thermodynamics approach and develop a framework to exploit the specific detection capabilities of nucleic acid hybridization, using generic principles applicable to any platform. As a case study, we detect point mutations in the KRAS oncogene on a microarray platform. For the given platform and hybridization conditions, we demonstrate the multiplex detection capability of hybridization and assess the detection limit using thermodynamic considerations; DNA containing point mutations in a background of wild type sequences can be identified down to at least 1% relative concentration. In order to show the clinical relevance, the detection capabilities are confirmed on challenging formalin-fixed paraffin-embedded clinical tumor samples. This enzyme-free detection framework contains the accuracy and efficiency to screen for hundreds of mutations in a single run with many potential applications in molecular diagnostics and the field of personalised medicine.

A Thermodynamic Approach to Soil-Plant-Atmosphere Modeling: From Metabolic Biochemical Processes to Water-Carbon-Nitrogen Balance

NASA Astrophysics Data System (ADS)

Clavijo, H. W.

2016-12-01

Modeling the soil-plant-atmosphere continuum has been central part of understanding interrelationships among biogeochemical and hydrological processes. Theory behind of couplings Land Surface Models (LSM) and Dynamical Global Vegetation Models (DGVM) are based on physical and physiological processes connected by input-output interactions mainly. This modeling framework could be improved by the application of non-equilibrium thermodynamic basis that could encompass the majority of biophysical processes in a standard fashion. This study presents an alternative model for plant-water-atmosphere based on energy-mass thermodynamics. The system of dynamic equations derived is based on the total entropy, the total energy balance for the plant, the biomass dynamics at metabolic level and the water-carbon-nitrogen fluxes and balances. One advantage of this formulation is the capability to describe adaptation and evolution of dynamics of plant as a bio-system coupled to the environment. Second, it opens a window for applications on specific conditions from individual plant scale, to watershed scale, to global scale. Third, it enhances the possibility of analyzing anthropogenic impacts on the system, benefiting from the mathematical formulation and its non-linearity. This non-linear model formulation is analyzed under the concepts of qualitative system dynamics theory, for different state-space phase portraits. The attractors and sources are pointed out with its stability analysis. Possibility of bifurcations are explored and reported. Simulations for the system dynamics under different conditions are presented. These results show strong consistency and applicability that validates the use of the non-equilibrium thermodynamic theory.

A two-dimensional statistical framework connecting thermodynamic profiles with filaments in the scrape off layer and application to experiments

NASA Astrophysics Data System (ADS)

Militello, F.; Farley, T.; Mukhi, K.; Walkden, N.; Omotani, J. T.

2018-05-01

A statistical framework was introduced in Militello and Omotani [Nucl. Fusion 56, 104004 (2016)] to correlate the dynamics and statistics of L-mode and inter-ELM plasma filaments with the radial profiles of thermodynamic quantities they generate in the Scrape Off Layer. This paper extends the framework to cases in which the filaments are emitted from the separatrix at different toroidal positions and with a finite toroidal velocity. It is found that the toroidal velocity does not affect the profiles, while the toroidal distribution of filament emission renormalises the waiting time between two events. Experimental data collected by visual camera imaging are used to evaluate the statistics of the fluctuations, to inform the choice of the probability distribution functions used in the application of the framework. It is found that the toroidal separation of the filaments is exponentially distributed, thus suggesting the lack of a toroidal modal structure. Finally, using these measurements, the framework is applied to an experimental case and good agreement is found.

Revisiting thermodynamics and kinetic diffusivities of uranium–niobium with Bayesian uncertainty analysis

DOE PAGES

Duong, Thien C.; Hackenberg, Robert E.; Landa, Alex; ...

2016-09-20

In this paper, thermodynamic and kinetic diffusivities of uranium–niobium (U–Nb) are re-assessed by means of the CALPHAD (CALculation of PHAse Diagram) methodology. In order to improve the consistency and reliability of the assessments, first-principles calculations are coupled with CALPHAD. In particular, heats of formation of γ -U–Nb are estimated and verified using various density-functional theory (DFT) approaches. These thermochemistry data are then used as constraints to guide the thermodynamic optimization process in such a way that the mutual-consistency between first-principles calculations and CALPHAD assessment is satisfactory. In addition, long-term aging experiments are conducted in order to generate new phase equilibriamore » data at the γ 2/α+γ 2 boundary. These data are meant to verify the thermodynamic model. Assessment results are generally in good agreement with experiments and previous calculations, without showing the artifacts that were observed in previous modeling. The mutual-consistent thermodynamic description is then used to evaluate atomic mobility and diffusivity of γ-U–Nb. Finally, Bayesian analysis is conducted to evaluate the uncertainty of the thermodynamic model and its impact on the system's phase stability.« less

Landau's statistical mechanics for quasi-particle models

NASA Astrophysics Data System (ADS)

Bannur, Vishnu M.

2014-04-01

Landau's formalism of statistical mechanics [following L. D. Landau and E. M. Lifshitz, Statistical Physics (Pergamon Press, Oxford, 1980)] is applied to the quasi-particle model of quark-gluon plasma. Here, one starts from the expression for pressure and develop all thermodynamics. It is a general formalism and consistent with our earlier studies [V. M. Bannur, Phys. Lett. B647, 271 (2007)] based on Pathria's formalism [following R. K. Pathria, Statistical Mechanics (Butterworth-Heinemann, Oxford, 1977)]. In Pathria's formalism, one starts from the expression for energy density and develop thermodynamics. Both the formalisms are consistent with thermodynamics and statistical mechanics. Under certain conditions, which are wrongly called thermodynamic consistent relation, we recover other formalism of quasi-particle system, like in M. I. Gorenstein and S. N. Yang, Phys. Rev. D52, 5206 (1995), widely studied in quark-gluon plasma.

Prediction and Experimental Evidence for Thermodynamically Stable Charged Orbital Domain Walls

DOE PAGES

Li, Qing’an; Gray, K. E.; Wilkins, S. B.; ...

2014-08-18

On theoretical grounds, we show that orbital domain walls (ODWs), which are known to exist in the charge and orbital ordered layered manganite LaSr 2Mn 2O 7, should be partially charged as a result of competition between orbital-induced strain and Coulomb repulsion. Furthermore, this unexpected result provides the necessary condition for the known thermodynamic stability of these ODWs, which are unlike the more typical domain walls that arise only from an external field. We offer experimental data consistent with this theoretical framework through a combined transport and x-ray-diffraction study. In particular, our transport data on this charge and orbital orderedmore » manganite exhibit abrupt transformations to higher conductance at a threshold electric field. As transport phenomena closely resemble effects found for sliding charge-density waves (SCDWs) in pseudo-one-dimensional (1D) materials, a SCDW along such pseudo-1D ODWs provides a natural explanation of our data. Importantly, x-ray-diffraction data eliminate heating and melting of charge order as tenable alternative explanations of our data.« less

Stochastic many-particle model for LFP electrodes

NASA Astrophysics Data System (ADS)

Guhlke, Clemens; Gajewski, Paul; Maurelli, Mario; Friz, Peter K.; Dreyer, Wolfgang

2018-02-01

In the framework of non-equilibrium thermodynamics, we derive a new model for many-particle electrodes. The model is applied to LiFePO4 (LFP) electrodes consisting of many LFP particles of nanometer size. The phase transition from a lithium-poor to a lithium-rich phase within LFP electrodes is controlled by both different particle sizes and surface fluctuations leading to a system of stochastic differential equations. An explicit relation between battery voltage and current controlled by the thermodynamic state variables is derived. This voltage-current relation reveals that in thin LFP electrodes lithium intercalation from the particle surfaces into the LFP particles is the principal rate-limiting process. There are only two constant kinetic parameters in the model describing the intercalation rate and the fluctuation strength, respectively. The model correctly predicts several features of LFP electrodes, viz. the phase transition, the observed voltage plateaus, hysteresis and the rate-limiting capacity. Moreover we study the impact of both the particle size distribution and the active surface area on the voltage-charge characteristics of the electrode. Finally we carefully discuss the phase transition for varying charging/discharging rates.

Carnot's cycle for small systems: Irreversibility and cost of operations

NASA Astrophysics Data System (ADS)

Sekimoto, Ken; Takagi, Fumiko; Hondou, Tsuyoshi

2000-12-01

In the thermodynamic limit, the existence of a maximal efficiency of energy conversion attainable by a Carnot cycle consisting of quasistatic isothermal and adiabatic processes precludes the existence of a perpetual machine of the second kind, whose cycles yield positive work in an isothermal environment. We employ the recently developed framework of the energetics of stochastic processes (called ``stochastic energetics'') to reanalyze the Carnot cycle in detail, taking account of fluctuations, without taking the thermodynamic limit. We find that in this nonmacroscopic situation both processes of connection to and disconnection from heat baths and adiabatic processes that cause distortion of the energy distribution are sources of inevitable irreversibility within the cycle. Also, the so-called null-recurrence property of the cumulative efficiency of energy conversion over many cycles and the irreversible property of isolated, purely mechanical processes under external ``macroscopic'' operations are discussed in relation to the impossibility of a perpetual machine, or Maxwell's demon. This analysis may serve as the basis for the design and analysis of mesoscopic energy converters in the near future.

Autonomous Quantum Clocks: Does Thermodynamics Limit Our Ability to Measure Time?

NASA Astrophysics Data System (ADS)

Erker, Paul; Mitchison, Mark T.; Silva, Ralph; Woods, Mischa P.; Brunner, Nicolas; Huber, Marcus

2017-07-01

Time remains one of the least well-understood concepts in physics, most notably in quantum mechanics. A central goal is to find the fundamental limits of measuring time. One of the main obstacles is the fact that time is not an observable and thus has to be measured indirectly. Here, we explore these questions by introducing a model of time measurements that is complete and autonomous. Specifically, our autonomous quantum clock consists of a system out of thermal equilibrium—a prerequisite for any system to function as a clock—powered by minimal resources, namely, two thermal baths at different temperatures. Through a detailed analysis of this specific clock model, we find that the laws of thermodynamics dictate a trade-off between the amount of dissipated heat and the clock's performance in terms of its accuracy and resolution. Our results furthermore imply that a fundamental entropy production is associated with the operation of any autonomous quantum clock, assuming that quantum machines cannot achieve perfect efficiency at finite power. More generally, autonomous clocks provide a natural framework for the exploration of fundamental questions about time in quantum theory and beyond.

Propulsion System Simulation Using the Toolbox for the Modeling and Analysis of Thermodynamic System T-MATS

NASA Technical Reports Server (NTRS)

Chapman, Jeffryes W.; Lavelle, Thomas M.; May, Ryan D.; Litt, Jonathan S.; Guo, Ten-Huei

2014-01-01

A simulation toolbox has been developed for the creation of both steady-state and dynamic thermodynamic software models. This paper describes the Toolbox for the Modeling and Analysis of Thermodynamic Systems (T-MATS), which combines generic thermodynamic and controls modeling libraries with a numerical iterative solver to create a framework for the development of thermodynamic system simulations, such as gas turbine engines. The objective of this paper is to present an overview of T-MATS, the theory used in the creation of the module sets, and a possible propulsion simulation architecture. A model comparison was conducted by matching steady-state performance results from a T-MATS developed gas turbine simulation to a well-documented steady-state simulation. Transient modeling capabilities are then demonstrated when the steady-state T-MATS model is updated to run dynamically.

Propulsion System Simulation Using the Toolbox for the Modeling and Analysis of Thermodynamic Systems (T-MATS)

NASA Technical Reports Server (NTRS)

Chapman, Jeffryes W.; Lavelle, Thomas M.; May, Ryan D.; Litt, Jonathan S.; Guo, Ten-Huei

2014-01-01

A simulation toolbox has been developed for the creation of both steady-state and dynamic thermodynamic software models. This paper describes the Toolbox for the Modeling and Analysis of Thermodynamic Systems (T-MATS), which combines generic thermodynamic and controls modeling libraries with a numerical iterative solver to create a framework for the development of thermodynamic system simulations, such as gas turbine engines. The objective of this paper is to present an overview of T-MATS, the theory used in the creation of the module sets, and a possible propulsion simulation architecture. A model comparison was conducted by matching steady-state performance results from a T-MATS developed gas turbine simulation to a well-documented steady-state simulation. Transient modeling capabilities are then demonstrated when the steady-state T-MATS model is updated to run dynamically.

Entropy corrected holographic dark energy models in modified gravity

NASA Astrophysics Data System (ADS)

Jawad, Abdul; Azhar, Nadeem; Rani, Shamaila

We consider the power law and the entropy corrected holographic dark energy (HDE) models with Hubble horizon in the dynamical Chern-Simons modified gravity. We explore various cosmological parameters and planes in this framework. The Hubble parameter lies within the consistent range at the present and later epoch for both entropy corrected models. The deceleration parameter explains the accelerated expansion of the universe. The equation of state (EoS) parameter corresponds to quintessence and cold dark matter (ΛCDM) limit. The ωΛ-ωΛ‧ approaches to ΛCDM limit and freezing region in both entropy corrected models. The statefinder parameters are consistent with ΛCDM limit and dark energy (DE) models. The generalized second law of thermodynamics remain valid in all cases of interacting parameter. It is interesting to mention here that our results of Hubble, EoS parameter and ωΛ-ωΛ‧ plane show consistency with the present observations like Planck, WP, BAO, H0, SNLS and nine-year WMAP.

Statistical foundations of liquid-crystal theory

PubMed Central

Seguin, Brian; Fried, Eliot

2013-01-01

We develop a mechanical theory for systems of rod-like particles. Central to our approach is the assumption that the external power expenditure for any subsystem of rods is independent of the underlying frame of reference. This assumption is used to derive the basic balance laws for forces and torques. By considering inertial forces on par with other forces, these laws hold relative to any frame of reference, inertial or noninertial. Finally, we introduce a simple set of constitutive relations to govern the interactions between rods and find restrictions necessary and sufficient for these laws to be consistent with thermodynamics. Our framework provides a foundation for a statistical mechanical derivation of the macroscopic balance laws governing liquid crystals. PMID:23772091

The effect of meteorological and chemical factors on the agreement between observations and predictions of fine aerosol composition in southwestern Ontario during BAQS-Met

NASA Astrophysics Data System (ADS)

Markovic, M. Z.; Hayden, K. L.; Murphy, J. G.; Makar, P. A.; Ellis, R. A.; Chang, R. Y.-W.; Slowik, J. G.; Mihele, C.; Brook, J.

2011-04-01

The Border Air Quality and Meteorology Study (BAQS-Met) was an intensive, collaborative field campaign during the summer of 2007 that investigated the effects of transboundary pollution, local pollution, and local meteorology on air quality in southwestern Ontario. This analysis focuses on the measurements of the inorganic constituents of particulate matter with diameter of less than 1 μm (PM1), with a specific emphasis on nitrate. We evaluate the ability of AURAMS, Environment Canada's chemical transport model, to represent regional air pollution in SW Ontario by comparing modelled aerosol inorganic chemical composition with measurements from Aerosol Mass Spectrometers (AMS) onboard the National Research Council (NRC) of Canada Twin Otter aircraft and at a ground site in Harrow, ON. The agreement between modelled and measured pNO3- at the ground site (observed mean (Mobs) = 0.50 μg m-3; modelled mean (Mmod) = 0.58 μg m-3; root mean square error (RSME) = 1.27 μg m-3) was better than aloft (Mobs = 0.32 μg m-3; Mmod = 0.09 μg m-3; RSME = 0.48 μg m-3). Possible reasons for discrepancies include errors in (i) emission inventories, (ii) atmospheric chemistry, (iii) predicted meteorological parameters, or (iv) gas/particle thermodynamics in the model framework. Using the inorganic thermodynamics model, ISORROPIA, in an offline mode, we find that the assumption of thermodynamic equilibrium is consistent with observations of gas and particle composition at Harrow. We develop a framework to assess the sensitivity of PM1 nitrate to meteorological and chemical parameters and find that errors in both the predictions of relative humidity and free ammonia (FA ≡ NH3(g) + pNH4+ - 2 · pSO42-) are responsible for the poor agreement between modelled and measured values.

The effect of meteorological and chemical factors on the agreement between observations and predictions of fine aerosol composition in Southwestern Ontario during BAQS-Met

NASA Astrophysics Data System (ADS)

Markovic, M. Z.; Hayden, K. L.; Murphy, J. G.; Makar, P. A.; Ellis, R. A.; Chang, R. Y.-W.; Slowik, J. G.; Mihele, C.; Brook, J.

2010-10-01

The Border Air Quality and Meteorology Study (BAQS-Met) was an intensive, collaborative field campaign during the summer of 2007 that investigated the effects of transboundary pollution, local pollution, and local meteorology on regional air quality in Southwestern Ontario. This analysis focuses on the measurements of the inorganic constituents of particulate matter with diameter of less than 1 μm (PM1), with a specific emphasis on nitrate. We evaluate the ability of AURAMS, the Environment Canada's chemical transport model, to represent regional air pollution in SW Ontario by comparing modelled aerosol inorganic chemical composition with measurements from Aerosol Mass Spectrometers (AMS) onboard the National Research Council (NRC) of Canada Twin Otter aircraft and at a ground site in Harrow, ON. The agreement between modelled and measured pNO3- at the ground site (observed mean (M_obs) = 0.50 μg m-3; modelled mean (M_mod) = 0.58 μg m-3; root mean square error (RSME) = 1.27 μg m-3) was better than aloft (M_obs = 0.32 μg m-3; M_mod = 0.09 μg m-3; RSME = 0.48 μg m-3). Possible reasons for discrepancies include errors in (i) emission inventories, (ii) atmospheric chemistry, (iii) predicted meteorological parameters, or (iv) gas/particle thermodynamics in the model framework. Using the inorganic thermodynamics model, ISORROPIA, in an offline mode, we find that the assumption of thermodynamic equilibrium is consistent with observations of gas and particle composition at Harrow. We develop a framework to assess the sensitivity of PM1 nitrate to meteorological and chemical parameters and find that errors in both the predictions of relative humidity and free ammonia (FA ≡ NH3(g) + NH4+ - SO42-) are responsible for the poor agreement between modelled and measured values.

The Markov process admits a consistent steady-state thermodynamic formalism

NASA Astrophysics Data System (ADS)

Peng, Liangrong; Zhu, Yi; Hong, Liu

2018-01-01

The search for a unified formulation for describing various non-equilibrium processes is a central task of modern non-equilibrium thermodynamics. In this paper, a novel steady-state thermodynamic formalism was established for general Markov processes described by the Chapman-Kolmogorov equation. Furthermore, corresponding formalisms of steady-state thermodynamics for the master equation and Fokker-Planck equation could be rigorously derived in mathematics. To be concrete, we proved that (1) in the limit of continuous time, the steady-state thermodynamic formalism for the Chapman-Kolmogorov equation fully agrees with that for the master equation; (2) a similar one-to-one correspondence could be established rigorously between the master equation and Fokker-Planck equation in the limit of large system size; (3) when a Markov process is restrained to one-step jump, the steady-state thermodynamic formalism for the Fokker-Planck equation with discrete state variables also goes to that for master equations, as the discretization step gets smaller and smaller. Our analysis indicated that general Markov processes admit a unified and self-consistent non-equilibrium steady-state thermodynamic formalism, regardless of underlying detailed models.

Improving the Kinetics and Thermodynamics of Mg(BH 4) 2 for Hydrogen Storage

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wood, Brandon; Klebanoff, Lennie; Stavila, Vitalie

The objective of this project is to (1) combine theory, synthesis, and characterization across multiple scales to understand the intrinsic kinetic and thermodynamic limitations in MgB 2/Mg(BH 4) 2; (2) construct and apply a flexible, validated, multiscale theoretical framework for modeling (de)hydrogenation kinetics of the Mg-B-H system and related metal hydrides; and (3) devise strategies for improving kinetics and thermodynamics, particularly through nanostructuring and doping. The project has an emphasis on understanding and improving rehydrogenation of MgB 2, which has generally been less explored and is key to enabling practical use.

Fluctuation theorem: A critical review

NASA Astrophysics Data System (ADS)

Malek Mansour, M.; Baras, F.

2017-10-01

Fluctuation theorem for entropy production is revisited in the framework of stochastic processes. The applicability of the fluctuation theorem to physico-chemical systems and the resulting stochastic thermodynamics were analyzed. Some unexpected limitations are highlighted in the context of jump Markov processes. We have shown that these limitations handicap the ability of the resulting stochastic thermodynamics to correctly describe the state of non-equilibrium systems in terms of the thermodynamic properties of individual processes therein. Finally, we considered the case of diffusion processes and proved that the fluctuation theorem for entropy production becomes irrelevant at the stationary state in the case of one variable systems.

Multi-band description of the specific heat and thermodynamic critical field in MgB2 superconductor

NASA Astrophysics Data System (ADS)

Szcześniak, R.; Jarosik, M. W.; Tarasewicz, P.; Durajski, A. P.

2018-05-01

The thermodynamic properties of MgB2 superconductor can be explained using the multi-band models. In the present paper we have examined the experimental data available in literature and we have found out that it is possible to reproduce the measured values of the superconducting energy gaps, the thermodynamic critical magnetic field and specific heat jump within the framework of two-band Eliashberg formalism and appropriate defined free energy difference between superconducting and normal state. Moreover, we found that the obtained results differ significantly from the predictions of the conventional Bardeen-Cooper-Schrieffer theory.

Hydrodynamic theory of active matter

NASA Astrophysics Data System (ADS)

Jülicher, Frank; Grill, Stephan W.; Salbreux, Guillaume

2018-07-01

We review the general hydrodynamic theory of active soft materials that is motivated in particular by biological matter. We present basic concepts of irreversible thermodynamics of spatially extended multicomponent active systems. Starting from the rate of entropy production, we identify conjugate thermodynamic fluxes and forces and present generic constitutive equations of polar active fluids and active gels. We also discuss angular momentum conservation which plays a role in the the physics of active chiral gels. The irreversible thermodynamics of active gels provides a general framework to discuss the physics that underlies a wide variety of biological processes in cells and in multicellular tissues.

Thermodynamic Model Formulations for Inhomogeneous Solids with Application to Non-isothermal Phase Field Modelling

NASA Astrophysics Data System (ADS)

Gladkov, Svyatoslav; Kochmann, Julian; Reese, Stefanie; Hütter, Markus; Svendsen, Bob

2016-04-01

The purpose of the current work is the comparison of thermodynamic model formulations for chemically and structurally inhomogeneous solids at finite deformation based on "standard" non-equilibrium thermodynamics [SNET: e. g. S. de Groot and P. Mazur, Non-equilibrium Thermodynamics, North Holland, 1962] and the general equation for non-equilibrium reversible-irreversible coupling (GENERIC) [H. C. Öttinger, Beyond Equilibrium Thermodynamics, Wiley Interscience, 2005]. In the process, non-isothermal generalizations of standard isothermal conservative [e. g. J. W. Cahn and J. E. Hilliard, Free energy of a non-uniform system. I. Interfacial energy. J. Chem. Phys. 28 (1958), 258-267] and non-conservative [e. g. S. M. Allen and J. W. Cahn, A macroscopic theory for antiphase boundary motion and its application to antiphase domain coarsening. Acta Metall. 27 (1979), 1085-1095; A. G. Khachaturyan, Theory of Structural Transformations in Solids, Wiley, New York, 1983] diffuse interface or "phase-field" models [e. g. P. C. Hohenberg and B. I. Halperin, Theory of dynamic critical phenomena, Rev. Modern Phys. 49 (1977), 435-479; N. Provatas and K. Elder, Phase Field Methods in Material Science and Engineering, Wiley-VCH, 2010.] for solids are obtained. The current treatment is consistent with, and includes, previous works [e. g. O. Penrose and P. C. Fife, Thermodynamically consistent models of phase-field type for the kinetics of phase transitions, Phys. D 43 (1990), 44-62; O. Penrose and P. C. Fife, On the relation between the standard phase-field model and a "thermodynamically consistent" phase-field model. Phys. D 69 (1993), 107-113] on non-isothermal systems as a special case. In the context of no-flux boundary conditions, the SNET- and GENERIC-based approaches are shown to be completely consistent with each other and result in equivalent temperature evolution relations.

Thermodynamic framework to assess low abundance DNA mutation detection by hybridization

PubMed Central

Willems, Hanny; Jacobs, An; Hadiwikarta, Wahyu Wijaya; Venken, Tom; Valkenborg, Dirk; Van Roy, Nadine; Vandesompele, Jo; Hooyberghs, Jef

2017-01-01

The knowledge of genomic DNA variations in patient samples has a high and increasing value for human diagnostics in its broadest sense. Although many methods and sensors to detect or quantify these variations are available or under development, the number of underlying physico-chemical detection principles is limited. One of these principles is the hybridization of sample target DNA versus nucleic acid probes. We introduce a novel thermodynamics approach and develop a framework to exploit the specific detection capabilities of nucleic acid hybridization, using generic principles applicable to any platform. As a case study, we detect point mutations in the KRAS oncogene on a microarray platform. For the given platform and hybridization conditions, we demonstrate the multiplex detection capability of hybridization and assess the detection limit using thermodynamic considerations; DNA containing point mutations in a background of wild type sequences can be identified down to at least 1% relative concentration. In order to show the clinical relevance, the detection capabilities are confirmed on challenging formalin-fixed paraffin-embedded clinical tumor samples. This enzyme-free detection framework contains the accuracy and efficiency to screen for hundreds of mutations in a single run with many potential applications in molecular diagnostics and the field of personalised medicine. PMID:28542229

Impact of metal and anion substitutions on the hydrogen storage properties of M-BTT metal-organic frameworks.

PubMed

Sumida, Kenji; Stück, David; Mino, Lorenzo; Chai, Jeng-Da; Bloch, Eric D; Zavorotynska, Olena; Murray, Leslie J; Dincă, Mircea; Chavan, Sachin; Bordiga, Silvia; Head-Gordon, Martin; Long, Jeffrey R

2013-01-23

Microporous metal-organic frameworks are a class of materials being vigorously investigated for mobile hydrogen storage applications. For high-pressure storage at ambient temperatures, the M(3)[(M(4)Cl)(3)(BTT)(8)](2) (M-BTT; BTT(3-) = 1,3,5-benzenetristetrazolate) series of frameworks are of particular interest due to the high density of exposed metal cation sites on the pore surface. These sites give enhanced zero-coverage isosteric heats of adsorption (Q(st)) approaching the optimal value for ambient storage applications. However, the Q(st) parameter provides only a limited insight into the thermodynamics of the individual adsorption sites, the tuning of which is paramount for optimizing the storage performance. Here, we begin by performing variable-temperature infrared spectroscopy studies of Mn-, Fe-, and Cu-BTT, allowing the thermodynamics of H(2) adsorption to be probed experimentally. This is complemented by a detailed DFT study, in which molecular fragments representing the metal clusters within the extended solid are simulated to obtain a more thorough description of the structural and thermodynamic aspects of H(2) adsorption at the strongest binding sites. Then, the effect of substitutions at the metal cluster (metal ion and anion within the tetranuclear cluster) is discussed, showing that the configuration of this unit indeed plays an important role in determining the affinity of the framework toward H(2). Interestingly, the theoretical study has identified that the Zn-based analogs would be expected to facilitate enhanced adsorption profiles over the compounds synthesized experimentally, highlighting the importance of a combined experimental and theoretical approach to the design and synthesis of new frameworks for H(2) storage applications.

Network Thermodynamic Curation of Human and Yeast Genome-Scale Metabolic Models

PubMed Central

Martínez, Verónica S.; Quek, Lake-Ee; Nielsen, Lars K.

2014-01-01

Genome-scale models are used for an ever-widening range of applications. Although there has been much focus on specifying the stoichiometric matrix, the predictive power of genome-scale models equally depends on reaction directions. Two-thirds of reactions in the two eukaryotic reconstructions Homo sapiens Recon 1 and Yeast 5 are specified as irreversible. However, these specifications are mainly based on biochemical textbooks or on their similarity to other organisms and are rarely underpinned by detailed thermodynamic analysis. In this study, a to our knowledge new workflow combining network-embedded thermodynamic and flux variability analysis was used to evaluate existing irreversibility constraints in Recon 1 and Yeast 5 and to identify new ones. A total of 27 and 16 new irreversible reactions were identified in Recon 1 and Yeast 5, respectively, whereas only four reactions were found with directions incorrectly specified against thermodynamics (three in Yeast 5 and one in Recon 1). The workflow further identified for both models several isolated internal loops that require further curation. The framework also highlighted the need for substrate channeling (in human) and ATP hydrolysis (in yeast) for the essential reaction catalyzed by phosphoribosylaminoimidazole carboxylase in purine metabolism. Finally, the framework highlighted differences in proline metabolism between yeast (cytosolic anabolism and mitochondrial catabolism) and humans (exclusively mitochondrial metabolism). We conclude that network-embedded thermodynamics facilitates the specification and validation of irreversibility constraints in compartmentalized metabolic models, at the same time providing further insight into network properties. PMID:25028891

Thermodynamic modelling of the C-U and B-U binary systems

NASA Astrophysics Data System (ADS)

Chevalier, P. Y.; Fischer, E.

2001-02-01

The thermodynamic modelling of the carbon-uranium (C-U) and boron-uranium (B-U) binary systems is being performed in the framework of the development of a thermodynamic database for nuclear materials, for increasing the basic knowledge of key phenomena which may occur in the event of a severe accident in a nuclear power plant. Applications are foreseen in the nuclear safety field to the physico-chemical interaction modelling, on the one hand the in-vessel core degradation producing the corium (fuel, zircaloy, steel, control rods) and on the other hand the ex-vessel molten corium-concrete interaction (MCCI). The key O-U-Zr ternary system, previously modelled, allows us to describe the first interaction of the fuel with zircaloy cladding. Then, the three binary systems Fe-U, Cr-U and Ni-U were modelled as a preliminary work for modelling the O-U-Zr-Fe-Cr-Ni multicomponent system, allowing us to introduce the steel components in the corium. In the existing database (TDBCR, thermodynamic data base for corium), Ag and In were introduced for modelling AIC (silver-indium-cadmium) control rods which are used in French pressurized water reactors (PWR). Elsewhere, B 4C is also used for control rods. That is why it was agreed to extend in the next years the database with two new components, B and C. Such a work needs the thermodynamic modelling of all the binary and pseudo-binary sub-systems resulting from the combination of B, B 2O 3 and C with the major components of TDBCR, O-U-Zr-Fe-Cr-Ni-Ag-In-Ba-La-Ru-Sr-Al-Ca-Mg-Si + Ar-H. The critical assessment of the very numerous experimental information available for the C-U and B-U binary systems was performed by using a classical optimization procedure and the Scientific Group Thermodata Europe (SGTE). New optimized Gibbs energy parameters are given, and comparisons between calculated and experimental equilibrium phase diagrams or thermodynamic properties are presented. The self-consistency obtained is quite satisfactory.

Steepest-entropy-ascent quantum thermodynamic modeling of the relaxation process of isolated chemically reactive systems using density of states and the concept of hypoequilibrium state

NASA Astrophysics Data System (ADS)

Li, Guanchen; von Spakovsky, Michael R.

2016-01-01

This paper presents a study of the nonequilibrium relaxation process of chemically reactive systems using steepest-entropy-ascent quantum thermodynamics (SEAQT). The trajectory of the chemical reaction, i.e., the accessible intermediate states, is predicted and discussed. The prediction is made using a thermodynamic-ensemble approach, which does not require detailed information about the particle mechanics involved (e.g., the collision of particles). Instead, modeling the kinetics and dynamics of the relaxation process is based on the principle of steepest-entropy ascent (SEA) or maximum-entropy production, which suggests a constrained gradient dynamics in state space. The SEAQT framework is based on general definitions for energy and entropy and at least theoretically enables the prediction of the nonequilibrium relaxation of system state at all temporal and spatial scales. However, to make this not just theoretically but computationally possible, the concept of density of states is introduced to simplify the application of the relaxation model, which in effect extends the application of the SEAQT framework even to infinite energy eigenlevel systems. The energy eigenstructure of the reactive system considered here consists of an extremely large number of such levels (on the order of 10130) and yields to the quasicontinuous assumption. The principle of SEA results in a unique trajectory of system thermodynamic state evolution in Hilbert space in the nonequilibrium realm, even far from equilibrium. To describe this trajectory, the concepts of subsystem hypoequilibrium state and temperature are introduced and used to characterize each system-level, nonequilibrium state. This definition of temperature is fundamental rather than phenomenological and is a generalization of the temperature defined at stable equilibrium. In addition, to deal with the large number of energy eigenlevels, the equation of motion is formulated on the basis of the density of states and a set of associated degeneracies. Their significance for the nonequilibrium evolution of system state is discussed. For the application presented, the numerical method used is described and is based on the density of states, which is specifically developed to solve the SEAQT equation of motion. Results for different kinds of initial nonequilibrium conditions, i.e., those for gamma and Maxwellian distributions, are studied. The advantage of the concept of hypoequilibrium state in studying nonequilibrium trajectories is discussed.

Viscoplasticity: A thermodynamic formulation

NASA Technical Reports Server (NTRS)

Freed, A. D.; Chaboche, J. L.

1989-01-01

A thermodynamic foundation using the concept of internal state variables is given for a general theory of viscoplasticity, as it applies to initially isotropic materials. Three fundamental internal state variables are admitted. They are: a tensor valued back stress for kinematic effects, and the scalar valued drag and yield strengths for isotropic effects. All three are considered to phenomenologically evolve according to competitive processes between strain hardening, strain induced dynamic recovery, and time induced static recovery. Within this phenomenological framework, a thermodynamically admissible set of evolution equations is put forth. This theory allows each of the three fundamental internal variables to be composed as a sum of independently evolving constituents.

Mixed phase clouds: observations and theoretical advances (overview)

NASA Astrophysics Data System (ADS)

Korolev, Alexei

2013-04-01

Mixed phase clouds play important role in precipitation formation and radiation budget of the Earth. The microphysical measurements in mixed phase clouds are notoriously difficult due to many technical challenges. The airborne instrumentation for characterization of the microstructure of mixed phase clouds is discussed. The results multiyear airborne observations and measurements of frequency of occurrence of mixed phase, characteristic spatial scales, humidity in mixed phase and ice clouds are presented. A theoretical framework describing the thermodynamics and phase transformation of a three phase component system consisting of ice particles, liquid droplets and water vapor is discussed. It is shown that the Wegener-Bergeron-Findeisen process plays different role in clouds with different dynamics. The problem of maintenance and longevity of mixed phase clouds is discussed.

A non-conventional discontinuous Lagrangian for viscous flow

PubMed Central

Marner, F.

2017-01-01

Drawing an analogy with quantum mechanics, a new Lagrangian is proposed for a variational formulation of the Navier–Stokes equations which to-date has remained elusive. A key feature is that the resulting Lagrangian is discontinuous in nature, posing additional challenges apropos the mathematical treatment of the related variational problem, all of which are resolvable. In addition to extending Lagrange's formalism to problems involving discontinuous behaviour, it is demonstrated that the associated equations of motion can self-consistently be interpreted within the framework of thermodynamics beyond local equilibrium, with the limiting case recovering the classical Navier–Stokes equations. Perspectives for applying the new formalism to discontinuous physical phenomena such as phase and grain boundaries, shock waves and flame fronts are provided. PMID:28386415

Statistical foundations of liquid-crystal theory: I. Discrete systems of rod-like molecules.

PubMed

Seguin, Brian; Fried, Eliot

2012-12-01

We develop a mechanical theory for systems of rod-like particles. Central to our approach is the assumption that the external power expenditure for any subsystem of rods is independent of the underlying frame of reference. This assumption is used to derive the basic balance laws for forces and torques. By considering inertial forces on par with other forces, these laws hold relative to any frame of reference, inertial or noninertial. Finally, we introduce a simple set of constitutive relations to govern the interactions between rods and find restrictions necessary and sufficient for these laws to be consistent with thermodynamics. Our framework provides a foundation for a statistical mechanical derivation of the macroscopic balance laws governing liquid crystals.

Higher-order correlations for fluctuations in the presence of fields.

PubMed

Boer, A; Dumitru, S

2002-10-01

The higher-order moments of the fluctuations for thermodynamic systems in the presence of fields are investigated in the framework of a theoretical method. The method uses a generalized statistical ensemble consistent with an adequate expression for the internal energy. The applications refer to the case of a system in a magnetoquasistatic field. In the case of linear magnetic media, one finds that, for the description of the magnetic induction fluctuations, the Gaussian approximation is satisfactory. For nonlinear media, the corresponding fluctuations are non-Gaussian, having a non-null asymmetry. Furthermore, the respective fluctuations have characteristics of leptokurtic, mesokurtic and platykurtic type, depending on the value of the magnetic field strength as compared with a scaling factor of the magnetization curve.

A non-conventional discontinuous Lagrangian for viscous flow.

PubMed

Scholle, M; Marner, F

2017-02-01

Drawing an analogy with quantum mechanics, a new Lagrangian is proposed for a variational formulation of the Navier-Stokes equations which to-date has remained elusive. A key feature is that the resulting Lagrangian is discontinuous in nature, posing additional challenges apropos the mathematical treatment of the related variational problem, all of which are resolvable. In addition to extending Lagrange's formalism to problems involving discontinuous behaviour, it is demonstrated that the associated equations of motion can self-consistently be interpreted within the framework of thermodynamics beyond local equilibrium, with the limiting case recovering the classical Navier-Stokes equations. Perspectives for applying the new formalism to discontinuous physical phenomena such as phase and grain boundaries, shock waves and flame fronts are provided.

Quantum Behavior of an Autonomous Maxwell Demon

NASA Astrophysics Data System (ADS)

Chapman, Adrian; Miyake, Akimasa

2015-03-01

A Maxwell Demon is an agent that can exploit knowledge of a system's microstate to perform useful work. The second law of thermodynamics is only recovered upon taking into account the work required to irreversibly update the demon's memory, bringing information theoretic concepts into a thermodynamic framework. Recently, there has been interest in modeling a classical Maxwell demon as an autonomous physical system to study this information-work tradeoff explicitly. Motivated by the idea that states with non-local entanglement structure can be used as a computational resource, we ask whether these states have thermodynamic resource quality as well by generalizing a particular classical autonomous Maxwell demon to the quantum regime. We treat the full quantum description using a matrix product operator formalism, which allows us to handle quantum and classical correlations in a unified framework. Applying this, together with techniques from statistical mechanics, we are able to approximate nonlocal quantities such as the erasure performed on the demon's memory register when correlations are present. Finally, we examine how the demon may use these correlations as a resource to outperform its classical counterpart.

ThermoFit: A Set of Software Tools, Protocols and Schema for the Organization of Thermodynamic Data and for the Development, Maintenance, and Distribution of Internally Consistent Thermodynamic Data/Model Collections

NASA Astrophysics Data System (ADS)

Ghiorso, M. S.

2013-12-01

Internally consistent thermodynamic databases are critical resources that facilitate the calculation of heterogeneous phase equilibria and thereby support geochemical, petrological, and geodynamical modeling. These 'databases' are actually derived data/model systems that depend on a diverse suite of physical property measurements, calorimetric data, and experimental phase equilibrium brackets. In addition, such databases are calibrated with the adoption of various models for extrapolation of heat capacities and volumetric equations of state to elevated temperature and pressure conditions. Finally, these databases require specification of thermochemical models for the mixing properties of solid, liquid, and fluid solutions, which are often rooted in physical theory and, in turn, depend on additional experimental observations. The process of 'calibrating' a thermochemical database involves considerable effort and an extensive computational infrastructure. Because of these complexities, the community tends to rely on a small number of thermochemical databases, generated by a few researchers; these databases often have limited longevity and are universally difficult to maintain. ThermoFit is a software framework and user interface whose aim is to provide a modeling environment that facilitates creation, maintenance and distribution of thermodynamic data/model collections. Underlying ThermoFit are data archives of fundamental physical property, calorimetric, crystallographic, and phase equilibrium constraints that provide the essential experimental information from which thermodynamic databases are traditionally calibrated. ThermoFit standardizes schema for accessing these data archives and provides web services for data mining these collections. Beyond simple data management and interoperability, ThermoFit provides a collection of visualization and software modeling tools that streamline the model/database generation process. Most notably, ThermoFit facilitates the rapid visualization of predicted model outcomes and permits the user to modify these outcomes using tactile- or mouse-based GUI interaction, permitting real-time updates that reflect users choices, preferences, and priorities involving derived model results. This ability permits some resolution of the problem of correlated model parameters in the common situation where thermodynamic models must be calibrated from inadequate data resources. The ability also allows modeling constraints to be imposed using natural data and observations (i.e. petrologic or geochemical intuition). Once formulated, ThermoFit facilitates deployment of data/model collections by automated creation of web services. Users consume these services via web-, excel-, or desktop-clients. ThermoFit is currently under active development and not yet generally available; a limited capability prototype system has been coded for Macintosh computers and utilized to construct thermochemical models for H2O-CO2 mixed fluid saturation in silicate liquids. The longer term goal is to release ThermoFit as a web portal application client with server-based cloud computations supporting the modeling environment.

Finite size effects in the thermodynamics of a free neutral scalar field

NASA Astrophysics Data System (ADS)

Parvan, A. S.

2018-04-01

The exact analytical lattice results for the partition function of the free neutral scalar field in one spatial dimension in both the configuration and the momentum space were obtained in the framework of the path integral method. The symmetric square matrices of the bilinear forms on the vector space of fields in both configuration space and momentum space were found explicitly. The exact lattice results for the partition function were generalized to the three-dimensional spatial momentum space and the main thermodynamic quantities were derived both on the lattice and in the continuum limit. The thermodynamic properties and the finite volume corrections to the thermodynamic quantities of the free real scalar field were studied. We found that on the finite lattice the exact lattice results for the free massive neutral scalar field agree with the continuum limit only in the region of small values of temperature and volume. However, at these temperatures and volumes the continuum physical quantities for both massive and massless scalar field deviate essentially from their thermodynamic limit values and recover them only at high temperatures or/and large volumes in the thermodynamic limit.

High-order accurate finite-volume formulations for the pressure gradient force in layered ocean models

NASA Astrophysics Data System (ADS)

Engwirda, Darren; Kelley, Maxwell; Marshall, John

2017-08-01

Discretisation of the horizontal pressure gradient force in layered ocean models is a challenging task, with non-trivial interactions between the thermodynamics of the fluid and the geometry of the layers often leading to numerical difficulties. We present two new finite-volume schemes for the pressure gradient operator designed to address these issues. In each case, the horizontal acceleration is computed as an integration of the contact pressure force that acts along the perimeter of an associated momentum control-volume. A pair of new schemes are developed by exploring different control-volume geometries. Non-linearities in the underlying equation-of-state definitions and thermodynamic profiles are treated using a high-order accurate numerical integration framework, designed to preserve hydrostatic balance in a non-linear manner. Numerical experiments show that the new methods achieve high levels of consistency, maintaining hydrostatic and thermobaric equilibrium in the presence of strongly-sloping layer geometries, non-linear equations-of-state and non-uniform vertical stratification profiles. These results suggest that the new pressure gradient formulations may be appropriate for general circulation models that employ hybrid vertical coordinates and/or terrain-following representations.

Problems of low-parameter equations of state

NASA Astrophysics Data System (ADS)

Petrik, G. G.

2017-11-01

The paper focuses on the system approach to problems of low-parametric equations of state (EOS). It is a continuation of the investigations in the field of substantiated prognosis of properties on two levels, molecular and thermodynamic. Two sets of low-parameter EOS have been considered based on two very simple molecular-level models. The first one consists of EOS of van der Waals type (a modification of van der Waals EOS proposed for spheres). The main problem of these EOS is a weak connection with the micro-level, which raise many uncertainties. The second group of EOS has been derived by the author independently of the ideas of van der Waals based on the model of interacting point centers (IPC). All the parameters of the EOS have a meaning and are associated with the manifestation of attractive and repulsive forces. The relationship between them is found to be the control parameter of the thermodynamic level. In this case, EOS IPC passes into a one-parameter family. It is shown that many EOS of vdW-type can be included in the framework of the PC model. Simultaneously, all their parameters acquire a physical meaning.

Network thermodynamic curation of human and yeast genome-scale metabolic models.

PubMed

Martínez, Verónica S; Quek, Lake-Ee; Nielsen, Lars K

2014-07-15

Genome-scale models are used for an ever-widening range of applications. Although there has been much focus on specifying the stoichiometric matrix, the predictive power of genome-scale models equally depends on reaction directions. Two-thirds of reactions in the two eukaryotic reconstructions Homo sapiens Recon 1 and Yeast 5 are specified as irreversible. However, these specifications are mainly based on biochemical textbooks or on their similarity to other organisms and are rarely underpinned by detailed thermodynamic analysis. In this study, a to our knowledge new workflow combining network-embedded thermodynamic and flux variability analysis was used to evaluate existing irreversibility constraints in Recon 1 and Yeast 5 and to identify new ones. A total of 27 and 16 new irreversible reactions were identified in Recon 1 and Yeast 5, respectively, whereas only four reactions were found with directions incorrectly specified against thermodynamics (three in Yeast 5 and one in Recon 1). The workflow further identified for both models several isolated internal loops that require further curation. The framework also highlighted the need for substrate channeling (in human) and ATP hydrolysis (in yeast) for the essential reaction catalyzed by phosphoribosylaminoimidazole carboxylase in purine metabolism. Finally, the framework highlighted differences in proline metabolism between yeast (cytosolic anabolism and mitochondrial catabolism) and humans (exclusively mitochondrial metabolism). We conclude that network-embedded thermodynamics facilitates the specification and validation of irreversibility constraints in compartmentalized metabolic models, at the same time providing further insight into network properties. Copyright © 2014 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Grasping the Second Law of Thermodynamics at University: The Consistency of Macroscopic and Microscopic Explanations

ERIC Educational Resources Information Center

Leinonen, Risto; Asikainen, Mervi A.; Hirvonen, Pekka E.

2015-01-01

This study concentrates on evaluating the consistency of upper-division students' use of the second law of thermodynamics at macroscopic and microscopic levels. Data were collected by means of a paper and pencil test (N = 48) focusing on the macroscopic and microscopic features of the second law concerned with heat transfer processes. The data…

Thermodynamic phase transition of a black hole in rainbow gravity

NASA Astrophysics Data System (ADS)

Feng, Zhong-Wen; Yang, Shu-Zheng

2017-09-01

In this letter, using the rainbow functions that were proposed by Magueijo and Smolin, we investigate the thermodynamics and the phase transition of rainbow Schwarzschild black hole. First, we calculate the rainbow gravity corrected Hawking temperature. From this modification, we then derive the local temperature, free energy, and other thermodynamic quantities in an isothermal cavity. Finally, we analyze the critical behavior, thermodynamic stability, and phase transition of the rainbow Schwarzschild black hole. The results show that the rainbow gravity can stop the Hawking radiation in the final stages of black holes' evolution and lead to the remnants of black holes. Furthermore, one can observe that the rainbow Schwarzschild black hole has one first-order phase transition, two second-order phase transitions, and three Hawking-Page-type phase transitions in the framework of rainbow gravity theory.

Towards a thermodynamics of active matter.

PubMed

Takatori, S C; Brady, J F

2015-03-01

Self-propulsion allows living systems to display self-organization and unusual phase behavior. Unlike passive systems in thermal equilibrium, active matter systems are not constrained by conventional thermodynamic laws. A question arises, however, as to what extent, if any, can concepts from classical thermodynamics be applied to nonequilibrium systems like active matter. Here we use the new swim pressure perspective to develop a simple theory for predicting phase separation in active matter. Using purely mechanical arguments we generate a phase diagram with a spinodal and critical point, and define a nonequilibrium chemical potential to interpret the "binodal." We provide a generalization of thermodynamic concepts like the free energy and temperature for nonequilibrium active systems. Our theory agrees with existing simulation data both qualitatively and quantitatively and may provide a framework for understanding and predicting the behavior of nonequilibrium active systems.

Demystifying Introductory Chemistry. Part 4: An Approach to Reaction Thermodynamics through Enthalpies, Entropies, and Free Energies of Atomization.

ERIC Educational Resources Information Center

Spencer, James N.; And Others

1996-01-01

Presents an alternative approach to teaching reaction thermodynamics in introductory chemistry courses using calculations of enthalpies, entropies, and free energies of atomization. Uses a consistent concept, that of decomposition of a compound to its gaseous atoms, to discuss not only thermodynamic parameters but also equilibrium and…

Comparison of Coarse-Grained Approaches in Predicting Polymer Nanocomposite Phase Behavior

DOE PAGES

Koski, Jason P.; Ferrier, Robert C.; Krook, Nadia M.; ...

2017-11-02

Because of the considerable parameter space, efficient theoretical and simulation methods are required to predict the morphology and guide experiments in polymer nanocomposites (PNCs). Unfortunately, theoretical and simulation methods are restricted in their ability to accurately map to experiments based on necessary approximations and numerical limitations. In this study, we provide direct comparisons of two recently developed coarse-grained approaches for modeling polymer nanocomposites (PNCs): polymer nanocomposite field theory (PNC-FT) and dynamic mean-field theory (DMFT). These methods are uniquely suited to efficiently capture mesoscale phase behavior of PNCs in comparison to other theoretical and simulation frameworks. We demonstrate the ability ofmore » both methods to capture macrophase separation and describe the thermodynamics of PNCs. We systematically test how the nanoparticle morphology in PNCs is affected by a uniform probability distribution of grafting sites, common in field-based methods, versus random discrete grafting sites on the nanoparticle surface. We also analyze the accuracy of the mean-field approximation in capturing the phase behavior of PNCs. Moreover, the DMFT method introduces the ability to describe nonequilibrium phase behavior while the PNC-FT method is strictly an equilibrium method. With the DMFT method we are able to show the evolution of nonequilibrium states toward their equilibrium state and a qualitative assessment of the dynamics in these systems. These simulations are compared to experiments consisting of polystyrene grafted gold nanorods in a poly(methyl methacrylate) matrix to ensure the model gives results that qualitatively agree with the experiments. This study reveals that nanoparticles in a relatively high matrix molecular weight are trapped in a nonequilibrium state and demonstrates the utility of the DMFT framework in capturing nonequilibrium phase behavior of PNCs. In conclusion, both the PNC-FT and DMFT framework are promising methods to describe the thermodynamic and nonequilibrium phase behavior of PNCs.« less

Comparison of Coarse-Grained Approaches in Predicting Polymer Nanocomposite Phase Behavior

DOE Office of Scientific and Technical Information (OSTI.GOV)

Koski, Jason P.; Ferrier, Robert C.; Krook, Nadia M.

Because of the considerable parameter space, efficient theoretical and simulation methods are required to predict the morphology and guide experiments in polymer nanocomposites (PNCs). Unfortunately, theoretical and simulation methods are restricted in their ability to accurately map to experiments based on necessary approximations and numerical limitations. In this study, we provide direct comparisons of two recently developed coarse-grained approaches for modeling polymer nanocomposites (PNCs): polymer nanocomposite field theory (PNC-FT) and dynamic mean-field theory (DMFT). These methods are uniquely suited to efficiently capture mesoscale phase behavior of PNCs in comparison to other theoretical and simulation frameworks. We demonstrate the ability ofmore » both methods to capture macrophase separation and describe the thermodynamics of PNCs. We systematically test how the nanoparticle morphology in PNCs is affected by a uniform probability distribution of grafting sites, common in field-based methods, versus random discrete grafting sites on the nanoparticle surface. We also analyze the accuracy of the mean-field approximation in capturing the phase behavior of PNCs. Moreover, the DMFT method introduces the ability to describe nonequilibrium phase behavior while the PNC-FT method is strictly an equilibrium method. With the DMFT method we are able to show the evolution of nonequilibrium states toward their equilibrium state and a qualitative assessment of the dynamics in these systems. These simulations are compared to experiments consisting of polystyrene grafted gold nanorods in a poly(methyl methacrylate) matrix to ensure the model gives results that qualitatively agree with the experiments. This study reveals that nanoparticles in a relatively high matrix molecular weight are trapped in a nonequilibrium state and demonstrates the utility of the DMFT framework in capturing nonequilibrium phase behavior of PNCs. In conclusion, both the PNC-FT and DMFT framework are promising methods to describe the thermodynamic and nonequilibrium phase behavior of PNCs.« less

Beyond heat baths II: framework for generalized thermodynamic resource theories

NASA Astrophysics Data System (ADS)

Yunger Halpern, Nicole

2018-03-01

Thermodynamics, which describes vast systems, has been reconciled with small scales, relevant to single-molecule experiments, in resource theories. Resource theories have been used to model exchanges of energy and information. Recently, particle exchanges were modeled; and an umbrella family of thermodynamic resource theories was proposed to model diverse baths, interactions, and free energies. This paper motivates and details the family’s structure and prospective applications. How to model electrochemical, gravitational, magnetic, and other thermodynamic systems is explained. Szilárd’s engine and Landauer’s Principle are generalized, as resourcefulness is shown to be convertible not only between information and gravitational energy, but also among diverse degrees of freedom. Extensive variables are associated with quantum operators that might fail to commute, introducing extra nonclassicality into thermodynamic resource theories. An early version of this paper partially motivated the later development of noncommutative thermalization. This generalization expands the theories’ potential for modeling realistic systems with which small-scale statistical mechanics might be tested experimentally.

Nonperturbative quark-gluon thermodynamics at finite density

NASA Astrophysics Data System (ADS)

Andreichikov, M. A.; Lukashov, M. S.; Simonov, Yu. A.

2018-03-01

Thermodynamics of the quark-gluon plasma at finite density is studied in the framework of the Field Correlator Method, where thermodynamical effects of Polyakov loops and color magnetic confinement are taken into account. Having found good agreement with numerical lattice data for zero density, we calculate pressure P(T,μ), for 0 < μ < 400 MeV and 150 < T < 1000 MeV. For the first time, the explicit integral form is found in this region, demonstrating analytic structure in the complex μ plane. The resulting multiple complex branch points are found at the Roberge-Weiss values of Imμ, with Reμ defined by the values of Polyakov lines and color magnetic confinement.

Thermodynamic properties of a hard/soft-magnetic bilayer model

DOE Office of Scientific and Technical Information (OSTI.GOV)

Taaev, T. A., E-mail: taaev89@mail.ru; Khizriev, K. Sh.; Murtazaev, A. K.

2016-05-15

A model for describing the thermodynamic properties of a hard/soft-magnetic bilayer is proposed and thoroughly studied using the Monte Carlo method. Temperature dependences of the heat capacity, total magnetization, magnetizations of the hard- and soft-magnetic layers, total magnetic susceptibility, and susceptibilities of the hard- and soft-magnetic layers have been calculated by this method in the framework of the proposed model. The obtained temperature dependences of the heat capacity and magnetic susceptibility display double maxima that result from the two phase transitions that take place in the system. The influence of system dimensions on the thermodynamic properties of the model hasmore » been considered.« less

Corridor of existence of thermodynamically consistent solution of the Ornstein-Zernike equation.

PubMed

Vorob'ev, V S; Martynov, G A

2007-07-14

We obtain the exact equation for a correction to the Ornstein-Zernike (OZ) equation based on the assumption of the uniqueness of thermodynamical functions. We show that this equation is reduced to a differential equation with one arbitrary parameter for the hard sphere model. The compressibility factor within narrow limits of this parameter variation can either coincide with one of the formulas obtained on the basis of analytical solutions of the OZ equation or assume all intermediate values lying in a corridor between these solutions. In particular, we find the value of this parameter when the thermodynamically consistent compressibility factor corresponds to the Carnahan-Stirling formula.

The influence of precipitation kinetics on trace element partitioning between solid and liquid solutions: A coupled fluid dynamics/thermodynamics framework to predict distribution coefficients

NASA Astrophysics Data System (ADS)

Kavner, A.

2017-12-01

In a multicomponent multiphase geochemical system undergoing a chemical reaction such as precipitation and/or dissolution, the partitioning of species between phases is determined by a combination of thermodynamic properties and transport processes. The interpretation of the observed distribution of trace elements requires models integrating coupled chemistry and mechanical transport. Here, a framework is presented that predicts the kinetic effects on the distribution of species between two reacting phases. Based on a perturbation theory combining Navier-Stokes fluid flow and chemical reactivity, the framework predicts rate-dependent partition coefficients in a variety of different systems. We present the theoretical framework, with applications to two systems: 1. species- and isotope-dependent Soret diffusion of species in a multicomponent silicate melt subjected to a temperature gradient, and 2. Elemental partitioning and isotope fractionation during precipitation of a multicomponent solid from a multicomponent liquid phase. Predictions will be compared with results from experimental studies. The approach has applications for understanding chemical exchange in at boundary layers such as the Earth's surface magmatic systems and at the core/mantle boundary.

A thermodynamic framework for thermo-chemo-elastic interactions in chemically active materials

NASA Astrophysics Data System (ADS)

Zhang, XiaoLong; Zhong, Zheng

2017-08-01

In this paper, a general thermodynamic framework is developed to describe the thermo-chemo-mechanical interactions in elastic solids undergoing mechanical deformation, imbibition of diffusive chemical species, chemical reactions and heat exchanges. Fully coupled constitutive relations and evolving laws for irreversible fluxes are provided based on entropy imbalance and stoichiometry that governs reactions. The framework manifests itself with a special feature that the change of Helmholtz free energy is attributed to separate contributions of the diffusion-swelling process and chemical reaction-dilation process. Both the extent of reaction and the concentrations of diffusive species are taken as independent state variables, which describe the reaction-activated responses with underlying variation of microstructures and properties of a material in an explicit way. A specialized isothermal formulation for isotropic materials is proposed that can properly account for volumetric constraints from material incompressibility under chemo-mechanical loadings, in which inhomogeneous deformation is associated with reaction and diffusion under various kinetic time scales. This framework can be easily applied to model the transient volumetric swelling of a solid caused by imbibition of external chemical species and simultaneous chemical dilation arising from reactions between the diffusing species and the solid.

Structure of the thermodynamic arrow of time in classical and quantum theories

NASA Astrophysics Data System (ADS)

Korzekwa, Kamil

2017-05-01

In this work we analyze the structure of the thermodynamic arrow of time, defined by transformations that leave the thermal equilibrium state unchanged, in classical (incoherent) and quantum (coherent) regimes. We note that in the infinite-temperature limit, the thermodynamic ordering of states in both regimes exhibits a lattice structure. This means that when energy does not matter and the only thermodynamic resource is given by information, the thermodynamic arrow of time has a very specific structure. Namely, for any two states at present there exists a unique state in the past consistent with them and with all possible joint pasts. Similarly, there also exists a unique state in the future consistent with those states and with all possible joint futures. We also show that the lattice structure in the classical regime is broken at finite temperatures, i.e., when energy is a relevant thermodynamic resource. Surprisingly, however, we prove that in the simplest quantum scenario of a two-dimensional system, this structure is preserved at finite temperatures. We provide the physical interpretation of these results by introducing and analyzing the history erasure process, and point out that quantum coherence may be a necessary resource for the existence of an optimal erasure process.

The Finite Strain Johnson Cook Plasticity and Damage Constitutive Model in ALEGRA.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sanchez, Jason James

A finite strain formulation of the Johnson Cook plasticity and damage model and it's numerical implementation into the ALEGRA code is presented. The goal of this work is to improve the predictive material failure capability of the Johnson Cook model. The new implementation consists of a coupling of damage and the stored elastic energy as well as the minimum failure strain criteria for spall included in the original model development. This effort establishes the necessary foundation for a thermodynamically consistent and complete continuum solid material model, for which all intensive properties derive from a common energy. The motivation for developingmore » such a model is to improve upon ALEGRA's present combined model framework. Several applications of the new Johnson Cook implementation are presented. Deformation driven loading paths demonstrate the basic features of the new model formulation. Use of the model produces good comparisons with experimental Taylor impact data. Localized deformation leading to fragmentation is produced for expanding ring and exploding cylinder applications.« less

The OpenCalphad thermodynamic software interface.

PubMed

Sundman, Bo; Kattner, Ursula R; Sigli, Christophe; Stratmann, Matthias; Le Tellier, Romain; Palumbo, Mauro; Fries, Suzana G

2016-12-01

Thermodynamic data are needed for all kinds of simulations of materials processes. Thermodynamics determines the set of stable phases and also provides chemical potentials, compositions and driving forces for nucleation of new phases and phase transformations. Software to simulate materials properties needs accurate and consistent thermodynamic data to predict metastable states that occur during phase transformations. Due to long calculation times thermodynamic data are frequently pre-calculated into "lookup tables" to speed up calculations. This creates additional uncertainties as data must be interpolated or extrapolated and conditions may differ from those assumed for creating the lookup table. Speed and accuracy requires that thermodynamic software is fully parallelized and the Open-Calphad (OC) software is the first thermodynamic software supporting this feature. This paper gives a brief introduction to computational thermodynamics and introduces the basic features of the OC software and presents four different application examples to demonstrate its versatility.

The OpenCalphad thermodynamic software interface

PubMed Central

Sundman, Bo; Kattner, Ursula R; Sigli, Christophe; Stratmann, Matthias; Le Tellier, Romain; Palumbo, Mauro; Fries, Suzana G

2017-01-01

Thermodynamic data are needed for all kinds of simulations of materials processes. Thermodynamics determines the set of stable phases and also provides chemical potentials, compositions and driving forces for nucleation of new phases and phase transformations. Software to simulate materials properties needs accurate and consistent thermodynamic data to predict metastable states that occur during phase transformations. Due to long calculation times thermodynamic data are frequently pre-calculated into “lookup tables” to speed up calculations. This creates additional uncertainties as data must be interpolated or extrapolated and conditions may differ from those assumed for creating the lookup table. Speed and accuracy requires that thermodynamic software is fully parallelized and the Open-Calphad (OC) software is the first thermodynamic software supporting this feature. This paper gives a brief introduction to computational thermodynamics and introduces the basic features of the OC software and presents four different application examples to demonstrate its versatility. PMID:28260838

Mathematical and information-geometrical entropy for phenomenological Fourier and non-Fourier heat conduction

NASA Astrophysics Data System (ADS)

Li, Shu-Nan; Cao, Bing-Yang

2017-09-01

The second law of thermodynamics governs the direction of heat transport, which provides the foundational definition of thermodynamic Clausius entropy. The definitions of entropy are further generalized for the phenomenological heat transport models in the frameworks of classical irreversible thermodynamics and extended irreversible thermodynamics (EIT). In this work, entropic functions from mathematics are combined with phenomenological heat conduction models and connected to several information-geometrical conceptions. The long-time behaviors of these mathematical entropies exhibit a wide diversity and physical pictures in phenomenological heat conductions, including the tendency to thermal equilibrium, and exponential decay of nonequilibrium and asymptotics, which build a bridge between the macroscopic and microscopic modelings. In contrast with the EIT entropies, the mathematical entropies expressed in terms of the internal energy function can avoid singularity paired with nonpositive local absolute temperature caused by non-Fourier heat conduction models.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Holland, Troy Michael; Kress, Joel David; Bhat, Kabekode Ghanasham

Year 1 Objectives (August 2016 – December 2016) – The original Independence model is a sequentially regressed set of parameters from numerous data sets in the Aspen Plus modeling framework. The immediate goal with the basic data model is to collect and evaluate those data sets relevant to the thermodynamic submodels (pure substance heat capacity, solvent mixture heat capacity, loaded solvent heat capacities, and volatility data). These data are informative for the thermodynamic parameters involved in both vapor-liquid equilibrium, and in the chemical equilibrium of the liquid phase.

Entropy in statistical energy analysis.

PubMed

Le Bot, Alain

2009-03-01

In this paper, the second principle of thermodynamics is discussed in the framework of statistical energy analysis (SEA). It is shown that the "vibrational entropy" and the "vibrational temperature" of sub-systems only depend on the vibrational energy and the number of resonant modes. A SEA system can be described as a thermodynamic system slightly out of equilibrium. In steady-state condition, the entropy exchanged with exterior by sources and dissipation exactly balances the production of entropy by irreversible processes at interface between SEA sub-systems.

A Hamiltonian approach for the Thermodynamics of AdS black holes

NASA Astrophysics Data System (ADS)

Baldiotti, M. C.; Fresneda, R.; Molina, C.

2017-07-01

In this work we study the Thermodynamics of D-dimensional Schwarzschild-anti de Sitter (SAdS) black holes. The minimal Thermodynamics of the SAdS spacetime is briefly discussed, highlighting some of its strong points and shortcomings. The minimal SAdS Thermodynamics is extended within a Hamiltonian approach, by means of the introduction of an additional degree of freedom. We demonstrate that the cosmological constant can be introduced in the thermodynamic description of the SAdS black hole with a canonical transformation of the Schwarzschild problem, closely related to the introduction of an anti-de Sitter thermodynamic volume. The treatment presented is consistent, in the sense that it is compatible with the introduction of new thermodynamic potentials, and respects the laws of black hole Thermodynamics. By demanding homogeneity of the thermodynamic variables, we are able to construct a new equation of state that completely characterizes the Thermodynamics of SAdS black holes. The treatment naturally generates phenomenological constants that can be associated with different boundary conditions in underlying microscopic theories. A whole new set of phenomena can be expected from the proposed generalization of SAdS Thermodynamics.

Non-hard sphere thermodynamic perturbation theory.

PubMed

Zhou, Shiqi

2011-08-21

A non-hard sphere (HS) perturbation scheme, recently advanced by the present author, is elaborated for several technical matters, which are key mathematical details for implementation of the non-HS perturbation scheme in a coupling parameter expansion (CPE) thermodynamic perturbation framework. NVT-Monte Carlo simulation is carried out for a generalized Lennard-Jones (LJ) 2n-n potential to obtain routine thermodynamic quantities such as excess internal energy, pressure, excess chemical potential, excess Helmholtz free energy, and excess constant volume heat capacity. Then, these new simulation data, and available simulation data in literatures about a hard core attractive Yukawa fluid and a Sutherland fluid, are used to test the non-HS CPE 3rd-order thermodynamic perturbation theory (TPT) and give a comparison between the non-HS CPE 3rd-order TPT and other theoretical approaches. It is indicated that the non-HS CPE 3rd-order TPT is superior to other traditional TPT such as van der Waals/HS (vdW/HS), perturbation theory 2 (PT2)/HS, and vdW/Yukawa (vdW/Y) theory or analytical equation of state such as mean spherical approximation (MSA)-equation of state and is at least comparable to several currently the most accurate Ornstein-Zernike integral equation theories. It is discovered that three technical issues, i.e., opening up new bridge function approximation for the reference potential, choosing proper reference potential, and/or using proper thermodynamic route for calculation of f(ex-ref), chiefly decide the quality of the non-HS CPE TPT. Considering that the non-HS perturbation scheme applies for a wide variety of model fluids, and its implementation in the CPE thermodynamic perturbation framework is amenable to high-order truncation, the non-HS CPE 3rd-order or higher order TPT will be more promising once the above-mentioned three technological advances are established. © 2011 American Institute of Physics

Classical nucleation theory of homogeneous freezing of water: thermodynamic and kinetic parameters.

PubMed

Ickes, Luisa; Welti, André; Hoose, Corinna; Lohmann, Ulrike

2015-02-28

The probability of homogeneous ice nucleation under a set of ambient conditions can be described by nucleation rates using the theoretical framework of Classical Nucleation Theory (CNT). This framework consists of kinetic and thermodynamic parameters, of which three are not well-defined (namely the interfacial tension between ice and water, the activation energy and the prefactor), so that any CNT-based parameterization of homogeneous ice formation is less well-constrained than desired for modeling applications. Different approaches to estimate the thermodynamic and kinetic parameters of CNT are reviewed in this paper and the sensitivity of the calculated nucleation rate to the choice of parameters is investigated. We show that nucleation rates are very sensitive to this choice. The sensitivity is governed by one parameter - the interfacial tension between ice and water, which determines the energetic barrier of the nucleation process. The calculated nucleation rate can differ by more than 25 orders of magnitude depending on the choice of parameterization for this parameter. The second most important parameter is the activation energy of the nucleation process. It can lead to a variation of 16 orders of magnitude. By estimating the nucleation rate from a collection of droplet freezing experiments from the literature, the dependence of these two parameters on temperature is narrowed down. It can be seen that the temperature behavior of these two parameters assumed in the literature does not match with the predicted nucleation rates from the fit in most cases. Moreover a comparison of all possible combinations of theoretical parameterizations of the dominant two free parameters shows that one combination fits the fitted nucleation rates best, which is a description of the interfacial tension coming from a molecular model [Reinhardt and Doye, J. Chem. Phys., 2013, 139, 096102] in combination with the activation energy derived from self-diffusion measurements [Zobrist et al., J. Phys. Chem. C, 2007, 111, 2149]. However, some fundamental understanding of the processes is still missing. Further research in future might help to tackle this problem. The most important questions, which need to be answered to constrain CNT, are raised in this study.

The thermodynamical foundation of electronic conduction in solids

NASA Astrophysics Data System (ADS)

Bringuier, E.

2018-03-01

In elementary textbooks, the microscopic justification of Ohm’s local law in a solid medium starts with Drude’s classical model of electron transport and next discusses the quantum-dynamical and statistical amendments. In this paper, emphasis is laid instead upon the thermodynamical background motivated by the Joule-Lenz heating effect accompanying conduction and the fact that the conduction electrons are thermalized at the lattice temperature. Both metals and n-type semiconductors are considered; but conduction under a magnetic field is not. Proficiency in second-year thermodynamics and vector analysis is required from an undergraduate university student in physics so that the content of the paper can be taught to third-year students. The necessary elements of quantum mechanics are posited in this paper without detailed justification. We start with the equilibrium-thermodynamic notion of the chemical potential of the electron gas, the value of which distinguishes metals from semiconductors. Then we turn to the usage of the electrochemical potential in the description of near-equilibrium electron transport. The response of charge carriers to the electrochemical gradient involves the mobility, which is the reciprocal of the coefficient of the effective friction force opposing the carrier drift. Drude’s calculation of mobility is restated with the dynamical requirements of quantum physics. Where the carrier density is inhomogeneous, there appears diffusion, the coefficient of which is thermodynamically related to the mobility. Next, it is remarked that the release of heat was ignored in Drude’s original model. In this paper, the flow of Joule heat is handled thermodynamically within an energy balance where the voltage generator, the conduction electrons and the host lattice are involved in an explicit way. The notion of dissipation is introduced as the rate of entropy creation in a steady state. The body of the paper is restricted to the case of one homogeneous temperature. The generalisation of the thermodynamical framework to an inhomogeneous temperature field is sketched in an appendix. A fluid-mechanical picture of electronic conduction is obtained as a by-product of that framework.

Nonequilibrium thermodynamics and information theory: basic concepts and relaxing dynamics

NASA Astrophysics Data System (ADS)

Altaner, Bernhard

2017-11-01

Thermodynamics is based on the notions of energy and entropy. While energy is the elementary quantity governing physical dynamics, entropy is the fundamental concept in information theory. In this work, starting from first principles, we give a detailed didactic account on the relations between energy and entropy and thus physics and information theory. We show that thermodynamic process inequalities, like the second law, are equivalent to the requirement that an effective description for physical dynamics is strongly relaxing. From the perspective of information theory, strongly relaxing dynamics govern the irreversible convergence of a statistical ensemble towards the maximally non-commital probability distribution that is compatible with thermodynamic equilibrium parameters. In particular, Markov processes that converge to a thermodynamic equilibrium state are strongly relaxing. Our framework generalizes previous results to arbitrary open and driven systems, yielding novel thermodynamic bounds for idealized and real processes. , which features invited work from the best early-career researchers working within the scope of J. Phys. A. This project is part of the Journal of Physics series’ 50th anniversary celebrations in 2017. Bernhard Altaner was selected by the Editorial Board of J. Phys. A as an Emerging Talent.

Gassmann Theory Applies to Nanoporous Media

NASA Astrophysics Data System (ADS)

Gor, Gennady Y.; Gurevich, Boris

2018-01-01

Recent progress in extraction of unconventional hydrocarbon resources has ignited the interest in the studies of nanoporous media. Since many thermodynamic and mechanical properties of nanoscale solids and fluids differ from the analogous bulk materials, it is not obvious whether wave propagation in nanoporous media can be described using the same framework as in macroporous media. Here we test the validity of Gassmann equation using two published sets of ultrasonic measurements for a model nanoporous medium, Vycor glass, saturated with two different fluids, argon, and n-hexane. Predictions of the Gassmann theory depend on the bulk and shear moduli of the dry samples, which are known from ultrasonic measurements and the bulk moduli of the solid and fluid constituents. The solid bulk modulus can be estimated from adsorption-induced deformation or from elastic effective medium theory. The fluid modulus can be calculated according to the Tait-Murnaghan equation at the solvation pressure in the pore. Substitution of these parameters into the Gassmann equation provides predictions consistent with measured data. Our findings set up a theoretical framework for investigation of fluid-saturated nanoporous media using ultrasonic elastic wave propagation.

Experimental study of phase equilibria and thermodynamic optimization of the Fe-Zn-O system

NASA Astrophysics Data System (ADS)

Degterov, Sergei A.; Pelton, Arthur D.; Jak, Evgueni; Hayes, Peter C.

2001-08-01

The Fe-Zn-O phase diagram in air was studied over the temperature range from 900 °C to 1500 °C. The compositions of the phases in quenched samples were obtained by electron probe X-ray microanalysis (EPMA). This experimental technique is not affected by zinc losses resulting from vaporization of zinc at high temperatures. The model for the spinel solid solution was developed within the framework of the compound-energy formalism (CEF). The choice of parameters of the CEF and the sequence of their optimization can have a major influence on the predictions in multicomponent phases. These choices can only be made rationally by reference to the specific model being represented in the CEF. This is discussed for the case of the two-sublattice spinel model. In the limiting case, the proposed model reduces to the model by O’Neill and Navrotsky for spinels. When the CEF is used in combination with the equation of Hillert and Jarl to describe the magnetic contribution to thermodynamic functions of a solution, it is necessary to assign certain values of magnetic properties to all pseudocomponents and to magnetic interaction parameters to obtain the most reasonable approximation of the magnetic properties of a solution. It was shown how this can be done based on very limited experimental data. The same equations can be used when the Murnaghan or the Birch-Murnaghan equation is combined with the CEF to describe the pressure dependence of thermodynamic functions. The polynomial model was used to describe the properties of wustite and zincite, and the modified quasichemical model was used for the liquid slag. All thermodynamic and phase-equilibria data on the Fe-O and Fe-Zn-O systems were critically evaluated, and parameters of the models were optimized to give a self-consistent set of thermodynamic functions of the phases in these systems. All experimental data are reproduced within experimental error limits. These include the thermodynamic properties of phases (such as specific heat, heat content, entropy, enthalpy, and Gibbs energy); the cation distribution between octahedral and tetrahedral sites in spinel; the oxygen partial pressure over single-phase, two-phase, and three-phase regions; the phase boundaries (liquidus, solidus, and subsolidus); and the tie-lines.

Ideal GLM-MHD: About the entropy consistent nine-wave magnetic field divergence diminishing ideal magnetohydrodynamics equations

NASA Astrophysics Data System (ADS)

Derigs, Dominik; Winters, Andrew R.; Gassner, Gregor J.; Walch, Stefanie; Bohm, Marvin

2018-07-01

The paper presents two contributions in the context of the numerical simulation of magnetized fluid dynamics. First, we show how to extend the ideal magnetohydrodynamics (MHD) equations with an inbuilt magnetic field divergence cleaning mechanism in such a way that the resulting model is consistent with the second law of thermodynamics. As a byproduct of these derivations, we show that not all of the commonly used divergence cleaning extensions of the ideal MHD equations are thermodynamically consistent. Secondly, we present a numerical scheme obtained by constructing a specific finite volume discretization that is consistent with the discrete thermodynamic entropy. It includes a mechanism to control the discrete divergence error of the magnetic field by construction and is Galilean invariant. We implement the new high-order MHD solver in the adaptive mesh refinement code FLASH where we compare the divergence cleaning efficiency to the constrained transport solver available in FLASH (unsplit staggered mesh scheme).

Thermodynamic Parameterization of Subduction-Zone Devolatilization and Application to Quantify Carbon Fluxes from Slab

NASA Astrophysics Data System (ADS)

Tian, M.; Katz, R. F.; Rees Jones, D. W.; May, D.

2017-12-01

Compared with other plate-tectonic boundaries, subduction zones (SZ) host the most drastic mechanical, thermal, and chemical changes. The transport of carbon through this complex environment is crucial to mantle carbon budget but remains the subject of active debate. Synthesis of field studies suggests that carbon subducted with the incoming slab is almost completely returned to the surface environment [Kelemen and Manning, 2015], whereas thermodynamic modelling indicates that a significant portion of carbon is retained in the slab and descends into the deep mantle [Gorman et al., 2006]. To address this controversy and quantify the carbon fluxes within SZs, it is necessary to treat the chemistry of fluid/volatile-rock interaction and the mechanics of porous fluid/volatile migration in a consistent modelling framework. This requirement is met by coupling a thermodynamic parameterization of de/re-volatilization with a two-phase flow model of subduction zones. The two-phase system is assumed to comprise three chemical components: rock containing only non-volatile oxides, H2O and CO2; the fluid phase includes only the latter two. Perple_X is used to map out the binary subsystems rock+H2O and rock+CO2; the results are parameterised in terms of volatile partition coefficients as a function of pressure and temperature. In synthesising the binary subsystems to describe phase equilibria that incorporate all three components, a Margules coefficient is introduced to account for non-ideal mixing of CO2/H2O in the fluid, such that the partition coefficients depend further on bulk composition. This procedure is applied to representative compositions of sediment, MORB, and gabbro for the slab, and peridotite for the mantle. The derived parameterization of each rock type serves as a lightweight thermodynamic module interfaceable with two-phase flow models of SZs. We demonstrate the application of this thermodynamic module through a simple model of carbon flux with a prescribed flow direction through (and out of) the slab. This model allows us to evaluate the effects of flow path and lithology on carbon storage within the slab.

The response to selection in Glycoside Hydrolase Family 13 structures: A comparative quantitative genetics approach.

PubMed

Hleap, Jose Sergio; Blouin, Christian

2018-01-01

The Glycoside Hydrolase Family 13 (GH13) is both evolutionarily diverse and relevant to many industrial applications. Its members hydrolyze starch into smaller carbohydrates and members of the family have been bioengineered to improve catalytic function under industrial environments. We introduce a framework to analyze the response to selection of GH13 protein structures given some phylogenetic and simulated dynamic information. We find that the TIM-barrel (a conserved protein fold consisting of eight α-helices and eight parallel β-strands that alternate along the peptide backbone, common to all amylases) is not selectable since it is under purifying selection. We also show a method to rank important residues with higher inferred response to selection. These residues can be altered to effect change in properties. In this work, we define fitness as inferred thermodynamic stability. We show that under the developed framework, residues 112Y, 122K, 124D, 125W, and 126P are good candidates to increase the stability of the truncated α-amylase protein from Geobacillus thermoleovorans (PDB code: 4E2O; α-1,4-glucan-4-glucanohydrolase; EC 3.2.1.1). Overall, this paper demonstrates the feasibility of a framework for the analysis of protein structures for any other fitness landscape.

The response to selection in Glycoside Hydrolase Family 13 structures: A comparative quantitative genetics approach

PubMed Central

2018-01-01

The Glycoside Hydrolase Family 13 (GH13) is both evolutionarily diverse and relevant to many industrial applications. Its members hydrolyze starch into smaller carbohydrates and members of the family have been bioengineered to improve catalytic function under industrial environments. We introduce a framework to analyze the response to selection of GH13 protein structures given some phylogenetic and simulated dynamic information. We find that the TIM-barrel (a conserved protein fold consisting of eight α-helices and eight parallel β-strands that alternate along the peptide backbone, common to all amylases) is not selectable since it is under purifying selection. We also show a method to rank important residues with higher inferred response to selection. These residues can be altered to effect change in properties. In this work, we define fitness as inferred thermodynamic stability. We show that under the developed framework, residues 112Y, 122K, 124D, 125W, and 126P are good candidates to increase the stability of the truncated α-amylase protein from Geobacillus thermoleovorans (PDB code: 4E2O; α-1,4-glucan-4-glucanohydrolase; EC 3.2.1.1). Overall, this paper demonstrates the feasibility of a framework for the analysis of protein structures for any other fitness landscape. PMID:29698417

A multiscale coupled finite-element and phase-field framework to modeling stressed grain growth in polycrystalline thin films

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jamshidian, M., E-mail: jamshidian@cc.iut.ac.ir; Institute of Structural Mechanics, Bauhaus-University Weimar, Marienstrasse 15, 99423 Weimar; Thamburaja, P., E-mail: prakash.thamburaja@gmail.com

A previously-developed finite-deformation- and crystal-elasticity-based constitutive theory for stressed grain growth in cubic polycrystalline bodies has been augmented to include a description of excess surface energy and grain-growth stagnation mechanisms through the use of surface effect state variables in a thermodynamically-consistent manner. The constitutive theory was also implemented into a multiscale coupled finite-element and phase-field computational framework. With the material parameters in the constitutive theory suitably calibrated, our three-dimensional numerical simulations show that the constitutive model is able to accurately predict the experimentally-determined evolution of crystallographic texture and grain size statistics in polycrystalline copper thin films deposited on polyimide substratemore » and annealed at high-homologous temperatures. In particular, our numerical analyses show that the broad texture transition observed in the annealing experiments of polycrystalline thin films is caused by grain growth stagnation mechanisms. - Graphical abstract: - Highlights: • Developing a theory for stressed grain growth in polycrystalline thin films. • Implementation into a multiscale coupled finite-element and phase-field framework. • Quantitative reproduction of the experimental grain growth data by simulations. • Revealing the cause of texture transition to be due to the stagnation mechanisms.« less

Linking Thermodynamics to Pollutant Reduction Kinetics by Fe2+ Bound to Iron Oxides.

PubMed

Stewart, Sydney M; Hofstetter, Thomas B; Joshi, Prachi; Gorski, Christopher A

2018-05-15

Numerous studies have reported that pollutant reduction rates by ferrous iron (Fe 2+ ) are substantially enhanced in the presence of an iron (oxyhydr)oxide mineral. Developing a thermodynamic framework to explain this phenomenon has been historically difficult due to challenges in quantifying reduction potential ( E H ) values for oxide-bound Fe 2+ species. Recently, our group demonstrated that E H values for hematite- and goethite-bound Fe 2+ can be accurately calculated using Gibbs free energy of formation values. Here, we tested if calculated E H values for oxide-bound Fe 2+ could be used to develop a free energy relationship capable of describing variations in reduction rate constants of substituted nitrobenzenes, a class of model pollutants that contain reducible aromatic nitro groups, using data collected here and compiled from the literature. All the data could be described by a single linear relationship between the logarithms of the surface-area-normalized rate constant ( k SA ) values and E H and pH values [log( k SA ) = - E H /0.059 V - pH + 3.42]. This framework provides mechanistic insights into how the thermodynamic favorability of electron transfer from oxide-bound Fe 2+ relates to redox reaction kinetics.

Thermodynamics of axial substitution and kinetics of reactions with amino acids for the paddlewheel complex tetrakis(acetato)chloridodiruthenium(II,III).

PubMed

Santos, Rodrigo L S R; van Eldik, Rudi; de Oliveira Silva, Denise

2012-06-18

The known paddlewheel, tetrakis(acetato)chloridodiruthenium(II,III), offers a versatile synthetic route to a novel class of antitumor diruthenium(II,III) metallo drugs, where the equatorial ligands are nonsteroidal anti-inflammatory carboxylates. This complex was studied here as a soluble starting prototype model for antitumor analogues to elucidate the reactivity of the [Ru(2)(CH(3)COO)(4)](+) framework. Thermodynamic studies on equilibration reactions for axial substitution of water by chloride and kinetic studies on reactions of the diaqua complexes with the amino acids glycine, cysteine, histidine, and tryptophan were performed. The standard thermodynamic reaction parameters ΔH°, ΔS°, and ΔV° were determined and showed that both of the sequential axial substitution reactions are enthalpy driven. Kinetic rate laws and rate constants were determined for the axial substitution reactions of coordinated water by the amino acids that gave the corresponding aqua(amino acid)-Ru(2) substituted species. The results revealed that the [Ru(2)(CH(3)COO)(4)](+) paddlewheel framework remained stable during the axial ligand substitution reactions and was also mostly preserved in the presence of the amino acids.

Calculation of kinetic rate constants from thermodynamic data

NASA Technical Reports Server (NTRS)

Marek, C. John

1995-01-01

A new scheme for relating the absolute value for the kinetic rate constant k to the thermodynamic constant Kp is developed for gases. In this report the forward and reverse rate constants are individually related to the thermodynamic data. The kinetic rate constants computed from thermodynamics compare well with the current kinetic rate constants. This method is self consistent and does not have extensive rules. It is first demonstrated and calibrated by computing the HBr reaction from H2 and Br2. This method then is used on other reactions.

Total individual ion activity coefficients of calcium and carbonate in seawater at 25°C and 35%. salinity, and implications to the agreement between apparent and thermodynamic constants of calcite and aragonite

USGS Publications Warehouse

Plummer, Niel; Sundquist, Eric T.

1982-01-01

We have calculated the total individual ion activity coefficients of carbonate and calcium,  and , in seawater. Using the ratios of stoichiometric and thermodynamic constants of carbonic acid dissociation and total mean activity coefficient data measured in seawater, we have obtained values which differ significantly from those widely accepted in the literature. In seawater at 25°C and 35%. salinity the (molal) values of  and  are 0.038 ± 0.002 and 0.173 ± 0.010, respectively. These values of  and  are independent of liquid junction errors and internally consistent with the value . By defining  and  on a common scale (), the product  is independent of the assigned value of  and may be determined directly from thermodynamic measurements in seawater. Using the value  and new thermodynamic equilibrium constants for calcite and aragonite, we show that the apparent constants of calcite and aragonite are consistent with the thermodynamic equilibrium constants at 25°C and 35%. salinity. The demonstrated consistency between thermodynamic and apparent constants of calcite and aragonite does not support a hypothesis of stable Mg-calcite coatings on calcite or aragonite surfaces in seawater, and suggests that the calcite critical carbonate ion curve of Broecker and Takahashi (1978,Deep-Sea Research25, 65–95) defines the calcite equilibrium boundary in the oceans, within the uncertainty of the data.

Thermodynamic behavior and enhanced magnetocaloric effect in a frustrated spin-1/2 Ising-Heisenberg triangular tube

NASA Astrophysics Data System (ADS)

Alécio, Raphael Cavalcante; Strečka, Jozef; Lyra, Marcelo L.

2018-04-01

The thermodynamic behavior of an Ising-Heisenberg triangular tube with Heisenberg intra-rung and Ising inter-rung interactions is exactly obtained in an external magnetic field within the framework of the transfer-matrix method. We report rigorous results for the temperature dependence of the magnetization, entropy, pair correlations and specific heat, as well as typical iso-entropic curves. The discontinuous field-driven ground-state phase transitions are reflected in some anomalous thermodynamic behavior as for instance a striking low-temperature peak of the specific heat and an enhanced magnetocaloric effect. It is demonstrated that the intermediate magnetization plateaus shrink in and the relevant sharp edges associated with the magnetization jump round off upon increasing temperature.

An integrated computational tool for precipitation simulation

NASA Astrophysics Data System (ADS)

Cao, W.; Zhang, F.; Chen, S.-L.; Zhang, C.; Chang, Y. A.

2011-07-01

Computer aided materials design is of increasing interest because the conventional approach solely relying on experimentation is no longer viable within the constraint of available resources. Modeling of microstructure and mechanical properties during precipitation plays a critical role in understanding the behavior of materials and thus accelerating the development of materials. Nevertheless, an integrated computational tool coupling reliable thermodynamic calculation, kinetic simulation, and property prediction of multi-component systems for industrial applications is rarely available. In this regard, we are developing a software package, PanPrecipitation, under the framework of integrated computational materials engineering to simulate precipitation kinetics. It is seamlessly integrated with the thermodynamic calculation engine, PanEngine, to obtain accurate thermodynamic properties and atomic mobility data necessary for precipitation simulation.

Thermodynamic Model of Spatial Memory

NASA Astrophysics Data System (ADS)

Kaufman, Miron; Allen, P.

1998-03-01

We develop and test a thermodynamic model of spatial memory. Our model is an application of statistical thermodynamics to cognitive science. It is related to applications of the statistical mechanics framework in parallel distributed processes research. Our macroscopic model allows us to evaluate an entropy associated with spatial memory tasks. We find that older adults exhibit higher levels of entropy than younger adults. Thurstone's Law of Categorical Judgment, according to which the discriminal processes along the psychological continuum produced by presentations of a single stimulus are normally distributed, is explained by using a Hooke spring model of spatial memory. We have also analyzed a nonlinear modification of the ideal spring model of spatial memory. This work is supported by NIH/NIA grant AG09282-06.

A Comparative Study of the Coupling of Flow with Non-Fickean Thermodiffusion. Part I: Extended Irreversible Thermodynamics

NASA Astrophysics Data System (ADS)

Lebon, G.; Grmela, M.; Lhuillier, D.

2003-03-01

Our main objective is to describe non-Fickean thermodiffusion in binary fluids within the framework of three recent theories of non-equilibrium thermodynamics, namely Extended Irreversible Thermodynamics (EIT), GENERIC (General Equation for the Non-Equilibrium Reversible Irreversible Coupling) and Thermodynamics with Internal Variables (IVT). In the first part presented in this paper, we develop the EIT description. For pedagogical reasons, we start from the simplest situation to end with the most intricate one. Therefore, we first examine the simple problem of mass diffusion at uniform temperature. Then we study heat transport in a one-component fluid before considering the more complex coupled heat and mass transfer. In Part II developed in the accompanying paper, we follow the same hierarchy of situations from the point of view of GENERIC. Finally, in Part III, we present the point of view of the thermodynamic theory of internal variables. Similarities and differences between EIT, GENERIC and IVT are stressed. In the present work, we have taken advantage of the problem of heat conduction to revisit the notion of caloric.

The Physics of Popping Corn.

ERIC Educational Resources Information Center

Hunt, Robert G.

1991-01-01

Presents a framework for teachers to use the thermodynamic system of popping corn to generate student interest. Examines the popping mechanism and the role of steam in, the heat required during, and the energy efficiency of the popping process. (MDH)

Generalized Stefan-Boltzmann Law

NASA Astrophysics Data System (ADS)

Montambaux, Gilles

2018-03-01

We reconsider the thermodynamic derivation by L. Boltzmann of the Stefan law and we generalize it for various different physical systems whose chemical potential vanishes. Being only based on classical arguments, therefore independent of the quantum statistics, this derivation applies as well to the saturated Bose gas in various geometries as to "compensated" Fermi gas near a neutrality point, such as a gas of Weyl Fermions. It unifies in the same framework the thermodynamics of many different bosonic or fermionic non-interacting gases which were until now described in completely different contexts.

The Operational Equations of State. 5: The APA - Equation of State

DTIC Science & Technology

2013-09-01

Arlington, VA 22202-4302. Respondents should be aware that notwithstanding any other provision of law , no person shall be subject to any penalty for...physical measurements. Thermodynamic consistency means that theEOS is totally consistent with the first and second laws of thermodynamics. Remember...form equation 1. From that standpoint, the EOS reminds the classical Boyle- Mariotte-Gay- Lussac model (when the heat capacity must be function of

The Operational Equations of State, 3: Recovery of the EOS for Hydrocode From the Measured Heat Capacity, Isentrope, and Hugoniot Adiabat

DTIC Science & Technology

2012-07-01

hydrocode from experimental data. It is assumed that the substance in question possesses only two thermodynamic degrees of freedom – the specific volume V...excludes the possibility of phase transformations). 15. SUBJECT TERMS thermodynamics , EOS, hydrocode 16. SECURITY CLASSIFICATION OF: 17. LIMITATION...we gave several examples of generating complete thermodynamically consistent equations of state (EOS). The methodology used there was based on

Correlations in quantum thermodynamics: Heat, work, and entropy production

PubMed Central

Alipour, S.; Benatti, F.; Bakhshinezhad, F.; Afsary, M.; Marcantoni, S.; Rezakhani, A. T.

2016-01-01

We provide a characterization of energy in the form of exchanged heat and work between two interacting constituents of a closed, bipartite, correlated quantum system. By defining a binding energy we derive a consistent quantum formulation of the first law of thermodynamics, in which the role of correlations becomes evident, and this formulation reduces to the standard classical picture in relevant systems. We next discuss the emergence of the second law of thermodynamics under certain—but fairly general—conditions such as the Markovian assumption. We illustrate the role of correlations and interactions in thermodynamics through two examples. PMID:27767124

Thermodynamic Modeling of the YO(l.5)-ZrO2 System

NASA Technical Reports Server (NTRS)

Jacobson, Nathan S.; Liu, Zi-Kui; Kaufman, Larry; Zhang, Fan

2003-01-01

The YO1.5-ZrO2 system consists of five solid solutions, one liquid solution, and one intermediate compound. A thermodynamic description of this system is developed, which allows calculation of the phase diagram and thermodynamic properties. Two different solution models are used-a neutral species model with YO1.5 and ZrO2 as the components and a charged species model with Y(+3), Zr(+4), O(-2), and vacancies as components. For each model, regular and sub-regular solution parameters are derived fiom selected equilibrium phase and thermodynamic data.

Thermodynamics of Einstein-Born-Infeld black holes with negative cosmological constant

DOE Office of Scientific and Technical Information (OSTI.GOV)

Miskovic, Olivera; Olea, Rodrigo; INFN, Sezione di Milano, Via Celoria 16, I-20133, Milano

2008-06-15

We study the thermodynamics associated to topological black hole solutions of AdS gravity coupled to nonlinear electrodynamics (Born-Infeld) in any dimension, using a background-independent regularization prescription for the Euclidean action given by boundary terms, which explicitly depend on the extrinsic curvature (Kounterterms series). A finite action principle leads to the correct definition of thermodynamic variables as Noether charges, which satisfy a Smarr-like relation. In particular, for the odd-dimensional case, a consistent thermodynamic description is achieved if the internal energy of the system includes the vacuum energy for AdS spacetime.

Thermodynamic Optimization of the Ag-Bi-Cu-Ni Quaternary System: Part I, Binary Subsystems

NASA Astrophysics Data System (ADS)

Wang, Jian; Cui, Senlin; Rao, Weifeng

2018-07-01

A comprehensive literature review and thermodynamic optimization of the phase diagrams and thermodynamic properties of the Ag-Bi, Ag-Cu, Ag-Ni, Bi-Cu, and Bi-Ni binary systems are presented. CALculation of PHAse Diagrams (CALPHAD)-type thermodynamic optimization was carried out to reproduce all available and reliable experimental phase equilibrium and thermodynamic data. The modified quasichemical model was used to model the liquid solution. The compound energy formalism was utilized to describe the Gibbs energies of all terminal solid solutions and intermetallic compounds. A self-consistent thermodynamic database for the Ag-Bi, Ag-Cu, Ag-Ni, Bi-Cu, and Bi-Ni binary subsystems of the Ag-Bi-Cu-Ni quaternary system was developed. This database can be used as a guide for research and development of lead-free solders.

Thermodynamic Optimization of the Ag-Bi-Cu-Ni Quaternary System: Part I, Binary Subsystems

NASA Astrophysics Data System (ADS)

Wang, Jian; Cui, Senlin; Rao, Weifeng

2018-05-01

A comprehensive literature review and thermodynamic optimization of the phase diagrams and thermodynamic properties of the Ag-Bi, Ag-Cu, Ag-Ni, Bi-Cu, and Bi-Ni binary systems are presented. CALculation of PHAse Diagrams (CALPHAD)-type thermodynamic optimization was carried out to reproduce all available and reliable experimental phase equilibrium and thermodynamic data. The modified quasichemical model was used to model the liquid solution. The compound energy formalism was utilized to describe the Gibbs energies of all terminal solid solutions and intermetallic compounds. A self-consistent thermodynamic database for the Ag-Bi, Ag-Cu, Ag-Ni, Bi-Cu, and Bi-Ni binary subsystems of the Ag-Bi-Cu-Ni quaternary system was developed. This database can be used as a guide for research and development of lead-free solders.

Thermodynamics of Gas Turbine Cycles with Analytic Derivatives in OpenMDAO

NASA Technical Reports Server (NTRS)

Gray, Justin; Chin, Jeffrey; Hearn, Tristan; Hendricks, Eric; Lavelle, Thomas; Martins, Joaquim R. R. A.

2016-01-01

A new equilibrium thermodynamics analysis tool was built based on the CEA method using the OpenMDAO framework. The new tool provides forward and adjoint analytic derivatives for use with gradient based optimization algorithms. The new tool was validated against the original CEA code to ensure an accurate analysis and the analytic derivatives were validated against finite-difference approximations. Performance comparisons between analytic and finite difference methods showed a significant speed advantage for the analytic methods. To further test the new analysis tool, a sample optimization was performed to find the optimal air-fuel equivalence ratio, , maximizing combustion temperature for a range of different pressures. Collectively, the results demonstrate the viability of the new tool to serve as the thermodynamic backbone for future work on a full propulsion modeling tool.

Thermodynamic Laws of Neutrino and Photon Emission.

ERIC Educational Resources Information Center

Walsh, P. J.; Gallo, C. F.

1980-01-01

Compares neutrino and photon emissions, develops the thermodynamic blackbody laws of neutrino emission analogous to laws governing photon emission, points out that combined radiation from a "true blackbody" consists of both photon and neutrino emissions of comparable magnitude, and speculates upon the existence of blackbody neutrino…

Gas solubility in dilute solutions: A novel molecular thermodynamic perspective

NASA Astrophysics Data System (ADS)

Chialvo, Ariel A.

2018-05-01

We present an explicit molecular-based interpretation of the thermodynamic phase equilibrium underlying gas solubility in liquids, through rigorous links between the microstructure of the dilute systems and the relevant macroscopic quantities that characterize their solution thermodynamics. We apply the formal analysis to unravel and highlight the molecular-level nature of the approximations behind the widely used Krichevsky-Kasarnovsky [J. Am. Chem. Soc. 57, 2168 (1935)] and Krichevsky-Ilinskaya [Acta Physicochim. 20, 327 (1945)] equations for the modeling of gas solubility. Then, we implement a general molecular-based approach to gas solubility and illustrate it by studying Lennard-Jones binary systems whose microstructure and thermodynamic properties were consistently generated via integral equation calculations. Furthermore, guided by the molecular-based analysis, we propose a novel macroscopic modeling approach to gas solubility, emphasize some usually overlook modeling subtleties, and identify novel interdependences among relevant solubility quantities that can be used as either handy modeling constraints or tools for consistency tests.

A general approach to the testing of binary solubility systems for thermodynamic consistency. Consolidated Fuel Reprocessing Program

NASA Astrophysics Data System (ADS)

Hamm, L. L.; Vanbrunt, V.

1982-08-01

The numerical solution to the ordinary differential equation which describes the high-pressure vapor-liquid equilibria of a binary system where one of the components is supercritical and exists as a noncondensable gas in the pure state is considered with emphasis on the implicit Runge-Kuta and orthogonal collocation methods. Some preliminary results indicate that the implicit Runge-Kutta method is superior. Due to the extreme nonlinearity of thermodynamic properties in the region near the critical locus, and extended cubic spline fitting technique is devised for correlating the P-x data. The least-squares criterion is employed in smoothing the experimental data. The technique could easily be applied to any thermodynamic data by changing the endpoint requirements. The volumetric behavior of the systems must be given or predicted in order to perform thermodynamic consistency tests. A general procedure is developed for predicting the volumetric behavior required and some indication as to the expected limit of accuracy is given.

Thermodynamic assessments and inter-relationships between systems involving Al, Am, Ga, Pu, and U

NASA Astrophysics Data System (ADS)

Perron, A.; Turchi, P. E. A.; Landa, A.; Oudot, B.; Ravat, B.; Delaunay, F.

2016-12-01

A newly developed self-consistent CALPHAD thermodynamic database involving Al, Am, Ga, Pu, and U is presented. A first optimization of the slightly characterized Am-Al and completely unknown Am-Ga phase diagrams is proposed. To this end, phase diagram features as crystal structures, stoichiometric compounds, solubility limits, and melting temperatures have been studied along the U-Al → Pu-Al → Am-Al, and U-Ga → Pu-Ga → Am-Ga series, and the thermodynamic assessments involving Al and Ga alloying are compared. In addition, two distinct optimizations of the Pu-Al phase diagram are proposed to account for the low temperature and Pu-rich region controversy. The previously assessed thermodynamics of the other binary systems (Am-Pu, Am-U, Pu-U, and Al-Ga) is also included in the database and is briefly described in the present work. Finally, predictions on phase stability of ternary and quaternary systems of interest are reported to check the consistency of the database.

Thermodynamic assessments and inter-relationships between systems involving Al, Am, Ga, Pu, and U

DOE PAGES

Perron, A.; Turchi, P. E. A.; Landa, A.; ...

2016-12-01

We present a newly developed self-consistent CALPHAD thermodynamic database involving Al, Am, Ga, Pu, and U. A first optimization of the slightly characterized Am-Al and completely unknown Am-Ga phase diagrams is proposed. To this end, phase diagram features as crystal structures, stoichiometric compounds, solubility limits, and melting temperatures have been studied along the U-Al → Pu-Al → Am-Al, and U-Ga → Pu-Ga → Am-Ga series, and the thermodynamic assessments involving Al and Ga alloying are compared. In addition, two distinct optimizations of the Pu-Al phase diagram are proposed to account for the low temperature and Pu-rich region controversy. We includedmore » the previously assessed thermodynamics of the other binary systems (Am-Pu, Am-U, Pu-U, and Al-Ga) in the database and is briefly described in the present work. In conclusion, predictions on phase stability of ternary and quaternary systems of interest are reported to check the consistency of the database.« less

Gas solubility in dilute solutions: A novel molecular thermodynamic perspective.

PubMed

Chialvo, Ariel A

2018-05-07

We present an explicit molecular-based interpretation of the thermodynamic phase equilibrium underlying gas solubility in liquids, through rigorous links between the microstructure of the dilute systems and the relevant macroscopic quantities that characterize their solution thermodynamics. We apply the formal analysis to unravel and highlight the molecular-level nature of the approximations behind the widely used Krichevsky-Kasarnovsky [J. Am. Chem. Soc. 57, 2168 (1935)] and Krichevsky-Ilinskaya [Acta Physicochim. 20, 327 (1945)] equations for the modeling of gas solubility. Then, we implement a general molecular-based approach to gas solubility and illustrate it by studying Lennard-Jones binary systems whose microstructure and thermodynamic properties were consistently generated via integral equation calculations. Furthermore, guided by the molecular-based analysis, we propose a novel macroscopic modeling approach to gas solubility, emphasize some usually overlook modeling subtleties, and identify novel interdependences among relevant solubility quantities that can be used as either handy modeling constraints or tools for consistency tests.

Thermodynamically consistent coarse graining of biocatalysts beyond Michaelis–Menten

NASA Astrophysics Data System (ADS)

Wachtel, Artur; Rao, Riccardo; Esposito, Massimiliano

2018-04-01

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 reaction forces (Gibbs energies of reaction) for the coarse-grained level. It can treat active transporters and molecular machines, and thus extends the applicability of ideas that originated in enzyme kinetics. Our results lay the foundations for systematic studies of the thermodynamics of large-scale biochemical reaction networks. Moreover, we identify the conditions under which a relation between one-way fluxes and forces holds at the coarse-grained level as it holds at the detailed level. In doing so, we clarify the speculations and broad claims made in the literature about such a general flux–force relation. As a further consequence we show that, in contrast to common belief, the second law of thermodynamics does not require the currents and the forces of biochemical reaction networks to be always aligned.

An internally consistent set of thermodynamic data for twentyone CaO-Al2O3-SiO2- H2O phases by linear parametric programming

NASA Astrophysics Data System (ADS)

Halbach, Heiner; Chatterjee, Niranjan D.

1984-11-01

The technique of linear parametric programming has been applied to derive sets of internally consistent thermodynamic data for 21 condensed phases of the quaternary system CaO-Al2O3-SiO2-H2O (CASH) (Table 4). This was achieved by simultaneously processing: a) calorimetric data for 16 of these phases (Table 1), and b) experimental phase equilibria reversal brackets for 27 reactions (Table 3) involving these phases. Calculation of equilibrium P-T curves of several arbitrarily picked reactions employing the preferred set of internally consistent thermodynamic data from Table 4 shows that the input brackets are invariably satisfied by the calculations (Fig. 2a). By contrast, the same equilibria calculated on the basis of a set of thermodynamic data derived by applying statistical methods to a large body of comparable input data (Haas et al. 1981; Hemingway et al. 1982) do not necessarily agree with the experimental reversal brackets. Prediction of some experimentally investigated phase relations not included into the linear programming input database also appears to be remarkably successful. Indications are, therefore, that the thermodynamic data listed in Table 4 may be used with confidence to predict geologic phase relations in the CASH system with considerable accuracy. For such calculated phase diagrams and their petrological implications, the reader's attention is drawn to the paper by Chatterjee et al. (1984).

Multiple Ion Binding Equilibria, Reaction Kinetics, and Thermodynamics in Dynamic Models of Biochemical Pathways

PubMed Central

Vinnakota, Kalyan C.; Wu, Fan; Kushmerick, Martin J.; Beard, Daniel A.

2009-01-01

The operation of biochemical systems in vivo and in vitro is strongly influenced by complex interactions between biochemical reactants and ions such as H+, Mg2+, K+, and Ca2+. These are important second messengers in metabolic and signaling pathways that directly influence the kinetics and thermodynamics of biochemical systems. Herein we describe the biophysical theory and computational methods to account for multiple ion binding to biochemical reactants and demonstrate the crucial effects of ion binding on biochemical reaction kinetics and thermodynamics. In simulations of realistic systems, the concentrations of these ions change with time due to dynamic buffering and competitive binding. In turn, the effective thermodynamic properties vary as functions of cation concentrations and important environmental variables such as temperature and overall ionic strength. Physically realistic simulations of biochemical systems require incorporating all of these phenomena into a coherent mathematical description. Several applications to physiological systems are demonstrated based on this coherent simulation framework. PMID:19216922

Effects of physical properties on thermo-fluids cavitating flows

NASA Astrophysics Data System (ADS)

Chen, T. R.; Wang, G. Y.; Huang, B.; Li, D. Q.; Ma, X. J.; Li, X. L.

2015-12-01

The aims of this paper are to study the thermo-fluid cavitating flows and to evaluate the effects of physical properties on cavitation behaviours. The Favre-averaged Navier-Stokes equations with the energy equation are applied to numerically investigate the liquid nitrogen cavitating flows around a NASA hydrofoil. Meanwhile, the thermodynamic parameter Σ is used to assess the thermodynamic effects on cavitating flows. The results indicate that the thermodynamic effects on the thermo-fluid cavitating flows significantly affect the cavitation behaviours, including pressure and temperature distribution, the variation of physical properties, and cavity structures. The thermodynamic effects can be evaluated by physical properties under the same free-stream conditions. The global sensitivity analysis of liquid nitrogen suggests that ρv, Cl and L significantly influence temperature drop and cavity structure in the existing numerical framework, while pv plays the dominant role when these properties vary with temperature. The liquid viscosity μl slightly affects the flow structure via changing the Reynolds number Re equivalently, however, it hardly affects the temperature distribution.

New Density Functional Approach for Solid-Liquid-Vapor Transitions in Pure Materials

NASA Astrophysics Data System (ADS)

Kocher, Gabriel; Provatas, Nikolas

2015-04-01

A new phase field crystal (PFC) type theory is presented, which accounts for the full spectrum of solid-liquid-vapor phase transitions within the framework of a single density order parameter. Its equilibrium properties show the most quantitative features to date in PFC modeling of pure substances, and full consistency with thermodynamics in pressure-volume-temperature space is demonstrated. A method to control either the volume or the pressure of the system is also introduced. Nonequilibrium simulations show that 2- and 3-phase growth of solid, vapor, and liquid can be achieved, while our formalism also allows for a full range of pressure-induced transformations. This model opens up a new window for the study of pressure driven interactions of condensed phases with vapor, an experimentally relevant paradigm previously missing from phase field crystal theories.

Open Thermodynamic System Concept for Fluviokarst Underground Temperature and Discharge Flow Assessments

NASA Astrophysics Data System (ADS)

Machetel, P.; Yuen, D. A.

2012-12-01

In this work, we propose to use Open Thermodynamic System (OTS) frameworks to assess temperatures and discharges of underground flows in fluviokarstic systems. The theoretical formulation is built on the first and second laws of thermodynamics. However, such assumptions would require steady states in the Control Volume to cancel the heat exchanges between underground water and embedding rocks. This situation is obviously never perfectly reached in Nature where flow discharges and temperatures vary with rainfalls, recessions and seasonal or diurnal fluctuations. First, we will shortly show that the results of a pumping test campaign on the Cent-Font (Hérault, France) fluviokarst during summer 2005 are consistent with this theoretical approach. Second, we will present the theoretical formalism of the OTS framework that leads to equation systems involving the temperatures and/or the discharges of the underground and surface flows.Third, this approach will be applied to the white (2003) conceptual model of fluviokarst, and we will present the numerical model built to assess the applicability of these assumptions. The first order of the field hydrologic properties observed at the Cent-Fonts resurgence are well described by the calculations based on this OTS framework. If this agreement is necessary, it is not sufficient to validate the method. In order to test its applicability, the mixing process has been modelized as a cooling reaction in a Continuous Stirred Tank Reactor (CSTR) for which matrix and intrusive flows are introduced continuously while effluent water is recovered at the output. The enthalpy of the various flows is conserved except for the part that exchanges heat with the embedding rocks. However the numerical model shows that in the water saturated part of the CS, the matrix flow swepts heat by convective-advective processes while temporal heat fluctuations from intrusive flows cross the CV walls. The numerical model shows that the convective flow from matrix damps the diurnal fluctuations on very short space and time scales. The case of the seasonal temperature fluctuations depends on the relative global space and time scales between the global transport properties of the fluviokarst and the fluctuations. This works shows that, under these circumstances and framework, temperature can be considered as a conservative tracer because most of the heat exchanged with the embedding rocks during non-steady periods is brought back by the convergence of matrix flows toward the CV. This mechanism cancels the effects of the heat exchanges for the diurnal fluctuations and also reduces those that are due to seasonal variations of temperature. The OTS approach may therefore bring new tools for underground fluid temperatures and discharges assessment and may also probably offer potential applications for geothermal studies. The mixing process in the fluviokarst Conduit System is analogous to a chemical reaction in a Continuous Stirred Tank Reactor (CSTR).

Thermodynamic consistency test procedure using orthogonal collocation and the Peng-Robinson equation of state

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hamm, L.L.; Van Brunt, V.

The Christiansen and Fredenslund programs for calculating vapor-liquid equilibria have been modified by replacing the Soave-Redlich-Kwong equation of state with the newly developed Peng-Robinson equation of state. This modification was shown to be a decided improvement for high pressure systems, especially in the critical and upper retrograde regions. Thermodynamic consistency tests were developed and used to evaluate and compare calculated values from both the modified and unmodified programs with reported experimental data for several vapor-liquid systems.

Efficient Construction of Free Energy Profiles of Breathing Metal–Organic Frameworks Using Advanced Molecular Dynamics Simulations

PubMed Central

2017-01-01

In order to reliably predict and understand the breathing behavior of highly flexible metal–organic frameworks from thermodynamic considerations, an accurate estimation of the free energy difference between their different metastable states is a prerequisite. Herein, a variety of free energy estimation methods are thoroughly tested for their ability to construct the free energy profile as a function of the unit cell volume of MIL-53(Al). The methods comprise free energy perturbation, thermodynamic integration, umbrella sampling, metadynamics, and variationally enhanced sampling. A series of molecular dynamics simulations have been performed in the frame of each of the five methods to describe structural transformations in flexible materials with the volume as the collective variable, which offers a unique opportunity to assess their computational efficiency. Subsequently, the most efficient method, umbrella sampling, is used to construct an accurate free energy profile at different temperatures for MIL-53(Al) from first principles at the PBE+D3(BJ) level of theory. This study yields insight into the importance of the different aspects such as entropy contributions and anharmonic contributions on the resulting free energy profile. As such, this thorough study provides unparalleled insight in the thermodynamics of the large structural deformations of flexible materials. PMID:29131647

Efficient Construction of Free Energy Profiles of Breathing Metal-Organic Frameworks Using Advanced Molecular Dynamics Simulations.

PubMed

Demuynck, Ruben; Rogge, Sven M J; Vanduyfhuys, Louis; Wieme, Jelle; Waroquier, Michel; Van Speybroeck, Veronique

2017-12-12

In order to reliably predict and understand the breathing behavior of highly flexible metal-organic frameworks from thermodynamic considerations, an accurate estimation of the free energy difference between their different metastable states is a prerequisite. Herein, a variety of free energy estimation methods are thoroughly tested for their ability to construct the free energy profile as a function of the unit cell volume of MIL-53(Al). The methods comprise free energy perturbation, thermodynamic integration, umbrella sampling, metadynamics, and variationally enhanced sampling. A series of molecular dynamics simulations have been performed in the frame of each of the five methods to describe structural transformations in flexible materials with the volume as the collective variable, which offers a unique opportunity to assess their computational efficiency. Subsequently, the most efficient method, umbrella sampling, is used to construct an accurate free energy profile at different temperatures for MIL-53(Al) from first principles at the PBE+D3(BJ) level of theory. This study yields insight into the importance of the different aspects such as entropy contributions and anharmonic contributions on the resulting free energy profile. As such, this thorough study provides unparalleled insight in the thermodynamics of the large structural deformations of flexible materials.

Using Spreadsheets and Internally Consistent Databases to Explore Thermodynamics

NASA Astrophysics Data System (ADS)

Dasgupta, S.; Chakraborty, S.

2003-12-01

Much common wisdom has been handed down to generations of petrology students in words - a non-exhaustive list may include (a) do not mix data from two different thermodynamic databases, (b) use of different heat capacity functions or extrapolation beyond the P-T range of fit can have disastrous results, (c) consideration of errors in thermodynamic calculations is crucial, (d) consideration of non-ideality, interaction parameters etc. are important in some cases, but not in others. Actual calculations to demonstrate these effects were either too laborious, tedious, time consuming or involved elaborate computer programming beyond the reaches of the average undergraduate. We have produced "Live" thermodynamic tables in the form of ExcelTM spreadsheets based on standard internally consistent thermodynamic databases (e.g. Berman, Holland and Powell) that allow quick, easy and most importantly, transparent manipulation of thermodynamic data to calculate mineral stabilities and to explore the role of different parameters. We have intentionally avoided the use of advanced tools such as macros, and have set up columns of data that are easy to relate to thermodynamic relationships to enhance transparency. The approach consists of the following basic steps: (i) use a simple supporting spreadsheet to enter mineral compositions (in formula units) to obtain a balanced reaction by matrix inversion. (ii) enter the stoichiometry of this reaction in a designated space and a P and T to get the delta G of the reaction (iii) vary P and or T to locate equilibrium through a change of sign of delta G. These results can be collected to explore practically any problem of chemical equilibrium and mineral stability. Some of our favorites include (a) hierarchical addition of complexity to equilibrium calculations - start with a simple end member reaction ignoring heat capacity and volume derivatives, add the effects of these, followed by addition of compositional effects in the form of ideal solutions, add non-ideality next and finally, explore the role of varying parameters in simple models of non-ideality. (b) Arbitrarily change (i.e. simulate error) or mix data from different sources to see the consequences directly. More traditional exercises such as exploration of slopes of reaction in P-T space are trivial, and other thermodynamic tidbits such as "bigger the mineral formula, greater its thermodynamic weight" become apparent to undergraduates early on through such direct handling of data. The overall outcome is a far more quantitative appreciation of mineral stabilities and thermodynamic variables without actually doing any Math!

Ab initio atomistic thermodynamics study on the oxidation mechanism of binary and ternary alloy surfaces

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liu, Shi-Yu, E-mail: buaasyliu@gmail.com; Department of Mechanical and Biomedical Engineering, City University of Hong Kong, Kowloon, Hong Kong; Liu, Shiyang

Utilizing a combination of ab initio density-functional theory and thermodynamics formalism, we have established the microscopic mechanisms for oxidation of the binary and ternary alloy surfaces and provided a clear explanation for the experimental results of the oxidation. We construct three-dimensional surface phase diagrams (SPDs) for oxygen adsorption on three different Nb-X(110) (X = Ti, Al or Si) binary alloy surfaces. On the basis of the obtained SPDs, we conclude a general microscopic mechanism for the thermodynamic oxidation, that is, under O-rich conditions, a uniform single-phase SPD (type I) and a nonuniform double-phase SPD (type II) correspond to the sustainedmore » complete selective oxidation and the non-sustained partial selective oxidation by adding the X element, respectively. Furthermore, by revealing the framework of thermodynamics for the oxidation mechanism of ternary alloys through the comparison of the surface energies of two separated binary alloys, we provide an understanding for the selective oxidation behavior of the Nb ternary alloy surfaces. Using these general microscopic mechanisms, one could predict the oxidation behavior of any binary and multi-component alloy surfaces based on thermodynamics considerations.« less

The Use of the ’BLAKE’ Computer Program to Calculate Thermodynamic Properties of Australian-Made Gun Propellants.

DTIC Science & Technology

1982-04-01

data for gun propellants manufactured in Australia, and several which are candidates for local production, are tabulated for reference. A summary of the theoretical framework of the program is included. (Author)

A thermodynamically consistent model for granular-fluid mixtures considering pore pressure evolution and hypoplastic behavior

NASA Astrophysics Data System (ADS)

Hess, Julian; Wang, Yongqi

2016-11-01

A new mixture model for granular-fluid flows, which is thermodynamically consistent with the entropy principle, is presented. The extra pore pressure described by a pressure diffusion equation and the hypoplastic material behavior obeying a transport equation are taken into account. The model is applied to granular-fluid flows, using a closing assumption in conjunction with the dynamic fluid pressure to describe the pressure-like residual unknowns, hereby overcoming previous uncertainties in the modeling process. Besides the thermodynamically consistent modeling, numerical simulations are carried out and demonstrate physically reasonable results, including simple shear flow in order to investigate the vertical distribution of the physical quantities, and a mixture flow down an inclined plane by means of the depth-integrated model. Results presented give insight in the ability of the deduced model to capture the key characteristics of granular-fluid flows. We acknowledge the support of the Deutsche Forschungsgemeinschaft (DFG) for this work within the Project Number WA 2610/3-1.

Thermodynamic model of a solid with RKKY interaction and magnetoelastic coupling

NASA Astrophysics Data System (ADS)

Balcerzak, T.; Szałowski, K.; Jaščur, M.

2018-04-01

Thermodynamic description of a model system with magnetoelastic coupling is presented. The elastic, vibrational, electronic and magnetic energy contributions are taken into account. The long-range RKKY interaction is considered together with the nearest-neighbour direct exchange. The generalized Gibbs potential and the set of equations of state are derived, from which all thermodynamic functions are self-consistently obtained. Thermodynamic properties are calculated numerically for FCC structure for arbitrary external pressure, magnetic field and temperature, and widely discussed. In particular, for some parameters of interaction potential and electron concentration corresponding to antiferromagnetic phase, the existence of negative thermal expansion coefficient is predicted.

Optimization of binary thermodynamic and phase diagram data

NASA Astrophysics Data System (ADS)

Bale, Christopher W.; Pelton, A. D.

1983-03-01

An optimization technique based upon least squares regression is presented to permit the simultaneous analysis of diverse experimental binary thermodynamic and phase diagram data. Coefficients of polynomial expansions for the enthalpy and excess entropy of binary solutions are obtained which can subsequently be used to calculate the thermodynamic properties or the phase diagram. In an interactive computer-assisted analysis employing this technique, one can critically analyze a large number of diverse data in a binary system rapidly, in a manner which is fully self-consistent thermodynamically. Examples of applications to the Bi-Zn, Cd-Pb, PbCl2-KCl, LiCl-FeCl2, and Au-Ni binary systems are given.

Numerical Mantle Convection Models With a Flexible Thermodynamic Interface

NASA Astrophysics Data System (ADS)

van den Berg, A. P.; Jacobs, M. H.; de Jong, B. H.

2001-12-01

Accurate material properties are needed for deep mantle (P,T) conditions in order to predict the longterm behavior of convection planetary mantles. Also the interpretation of seismological observations concerning the deep mantle in terms of mantle flow models calls for a consistent thermodynamical description of the basic physical parameters. We have interfaced a compressible convection code using the anelastic liquid approach based on finite element methods, to a database containing a full thermodynamic description of mantle silicates (Ita and King, J. Geophys. Res., 99, 15,939-15,940, 1994). The model is based on high resolution (P,T) tables of the relevant thermodynamic properties containing typically 50 million (P,T) table gridpoints to obtain resolution in (P,T) space of 1 K and an equivalent of 1 km. The resulting model is completely flexible such that numerical mantle convection experiments can be performed for any mantle composition for which the thermodynamic database is available. We present results of experiments for 2D cartesian models using a data base for magnesium-iron silicate in a pyrolitic composition (Stixrude and Bukowinski, Geoph.Monogr.Ser., 74, 131-142, 1993) and a recent thermodynamical model for magnesium silicate for the complete mantle (P,T) range, (Jacobs and Oonk, Phys. Chem. Mineral, 269, inpress 2001). Preliminary results of bulksound velocity distribution derived in a consistent way from the convection results and the thermodynamic database show a `realistic' mantle profile with bulkvelocity variations decreasing from several percent in the upper mantle to less than a percent in the deep lower mantle.

A multiscale quasi-continuum theory to determine thermodynamic properties of fluid mixtures in nanochannels

NASA Astrophysics Data System (ADS)

Motevaselian, Mohammad Hossein; Mashayak, Sikandar Y.; Aluru, Narayana R.

2015-11-01

We present an empirical potential-based quasi-continuum theory (EQT) that seamlessly integrates the interatomic potentials into a continuum framework such as the Nernst-Planck equation. EQT is a simple and fast approach, which provides accurate predictions of potential of mean force (PMF) and density distribution of confined fluids at multiple length-scales, ranging from few Angstroms to macro meters. The EQT potentials can be used to construct the excess free energy functional in the classical density functional theory (cDFT). The combination of EQT and cDFT (EQT-cDFT), allows one to predict the thermodynamic properties of confined fluids. Recently, the EQT-cDFT framework was developed for single component LJ fluids confined in slit-like graphene channels. In this work, we extend the framework to confined LJ fluid mixtures and demonstrate it by simulating a mixture of methane and hydrogen molecules inside slit-like graphene channels. We show that the EQT-cDFT predictions for the structure of the confined fluid mixture compare well with the MD simulations. In addition, our results show that graphene nanochannels exhibit a selective adsorption of methane over hydrogen.

On the representability problem and the physical meaning of coarse-grained models

NASA Astrophysics Data System (ADS)

Wagner, Jacob W.; Dama, James F.; Durumeric, Aleksander E. P.; Voth, Gregory A.

2016-07-01

In coarse-grained (CG) models where certain fine-grained (FG, i.e., atomistic resolution) observables are not directly represented, one can nonetheless identify indirect the CG observables that capture the FG observable's dependence on CG coordinates. Often, in these cases it appears that a CG observable can be defined by analogy to an all-atom or FG observable, but the similarity is misleading and significantly undermines the interpretation of both bottom-up and top-down CG models. Such problems emerge especially clearly in the framework of the systematic bottom-up CG modeling, where a direct and transparent correspondence between FG and CG variables establishes precise conditions for consistency between CG observables and underlying FG models. Here we present and investigate these representability challenges and illustrate them via the bottom-up conceptual framework for several simple analytically tractable polymer models. The examples provide special focus on the observables of configurational internal energy, entropy, and pressure, which have been at the root of controversy in the CG literature, as well as discuss observables that would seem to be entirely missing in the CG representation but can nonetheless be correlated with CG behavior. Though we investigate these problems in the framework of systematic coarse-graining, the lessons apply to top-down CG modeling also, with crucial implications for simulation at constant pressure and surface tension and for the interpretations of structural and thermodynamic correlations for comparison to experiment.

Self-consistent phonon calculations of lattice dynamical properties in cubic SrTiO3 with first-principles anharmonic force constants

NASA Astrophysics Data System (ADS)

Tadano, Terumasa; Tsuneyuki, Shinji

2015-08-01

We present an ab initio framework to calculate anharmonic phonon frequency and phonon lifetime that is applicable to severely anharmonic systems. We employ self-consistent phonon (SCPH) theory with microscopic anharmonic force constants, which are extracted from density functional calculations using the least absolute shrinkage and selection operator technique. We apply the method to the high-temperature phase of SrTiO3 and obtain well-defined phonon quasiparticles that are free from imaginary frequencies. Here we show that the anharmonic phonon frequency of the antiferrodistortive mode depends significantly on the system size near the critical temperature of the cubic-to-tetragonal phase transition. By applying perturbation theory to the SCPH result, phonon lifetimes are calculated for cubic SrTiO3, which are then employed to predict lattice thermal conductivity using the Boltzmann transport equation within the relaxation-time approximation. The presented methodology is efficient and accurate, paving the way toward a reliable description of thermodynamic, dynamic, and transport properties of systems with severe anharmonicity, including thermoelectric, ferroelectric, and superconducting materials.

Quantum thermodynamics of general quantum processes.

PubMed

Binder, Felix; Vinjanampathy, Sai; Modi, Kavan; Goold, John

2015-03-01

Accurately describing work extraction from a quantum system is a central objective for the extension of thermodynamics to individual quantum systems. The concepts of work and heat are surprisingly subtle when generalizations are made to arbitrary quantum states. We formulate an operational thermodynamics suitable for application to an open quantum system undergoing quantum evolution under a general quantum process by which we mean a completely positive and trace-preserving map. We derive an operational first law of thermodynamics for such processes and show consistency with the second law. We show that heat, from the first law, is positive when the input state of the map majorizes the output state. Moreover, the change in entropy is also positive for the same majorization condition. This makes a strong connection between the two operational laws of thermodynamics.

Thermodynamics of organic compounds

NASA Astrophysics Data System (ADS)

Gammon, B. E.; Smith, N. K.

1982-11-01

This research program consisted of an integrated and interrelated effort of basic and applied research in chemical thermodynamics and thermochemistry. Knowledge of variation of physical and thermodynamic properties with molecular structure was used to select compounds for study that because of high ring strain or unusual steric effects may have good energy characteristics per unit volume or per unit mass and thus be useful in the synthesis of high energy fuels. These materials were synthesized, and their thermodynamic properties were evaluated. In cooperation with researcher at Wright-Patterson Air Force Base, ramjet fuels currently in use were subjected to careful thermodynamic evaluation by measurements of heat capacity, enthalpy of combustion and vapor pressure. During the last year of this effort, seven kerosene-type fuels produced by British Petroleum and seven jet fuels produced from shale oil were studied.

How the Hilbert integral theorem inspired flow lines

NASA Astrophysics Data System (ADS)

Winston, Roland; Jiang, Lun

2017-09-01

Nonimaging Optics has been shown to achieve the theoretical limits constrained only by thermodynamic principles. The designing principles of nonimaging optics allow a non-conventional way of thinking about and generating new optical devices. Compared to conventional imaging optics which rarely utilizes the framework of thermodynamic arguments, nonimaging optics chooses to map etendue instead of rays. This fundamental shift of design paradigm frees the optics design from ray based designs which heavily relies on error tolerance analysis. Instead, the underlying thermodynamic principles guide the nonimaging design to be naturally constructed for extended light source for illumination, non-tracking concentrators and sensors that require sharp cut-off angles. We argue in this article that such optical devices which has enabled a multitude of applications depends on probabilities, geometric flux field and radiative heat transfer while "optics" in the conventional sense recedes into the background.

Thermodynamics of inequalities: From precariousness to economic stratification

NASA Astrophysics Data System (ADS)

Smerlak, Matteo

2016-01-01

Growing economic inequalities are observed in several countries throughout the world. Following Pareto, the power-law structure of these inequalities has been the subject of much theoretical and empirical work. But their nonequilibrium dynamics, e.g. after a policy change, remains incompletely understood. Here we introduce a thermodynamical theory of inequalities based on the analogy between economic stratification and statistical entropy. Within this framework we identify the combination of upward mobility with precariousness as a fundamental driver of inequality. We formalize this statement by a "second-law" inequality displaying upward mobility and precariousness as thermodynamic conjugate variables. We estimate the time scale for the "relaxation" of the wealth distribution after a sudden change of the after-tax return on capital. Our method can be generalized to gain insight into the dynamics of inequalities in any Markovian model of socioeconomic interactions.

Causal Mathematical Logic as a guiding framework for the prediction of "Intelligence Signals" in brain simulations

NASA Astrophysics Data System (ADS)

Lanzalaco, Felix; Pissanetzky, Sergio

2013-12-01

A recent theory of physical information based on the fundamental principles of causality and thermodynamics has proposed that a large number of observable life and intelligence signals can be described in terms of the Causal Mathematical Logic (CML), which is proposed to encode the natural principles of intelligence across any physical domain and substrate. We attempt to expound the current definition of CML, the "Action functional" as a theory in terms of its ability to possess a superior explanatory power for the current neuroscientific data we use to measure the mammalian brains "intelligence" processes at its most general biophysical level. Brain simulation projects define their success partly in terms of the emergence of "non-explicitly programmed" complex biophysical signals such as self-oscillation and spreading cortical waves. Here we propose to extend the causal theory to predict and guide the understanding of these more complex emergent "intelligence Signals". To achieve this we review whether causal logic is consistent with, can explain and predict the function of complete perceptual processes associated with intelligence. Primarily those are defined as the range of Event Related Potentials (ERP) which include their primary subcomponents; Event Related Desynchronization (ERD) and Event Related Synchronization (ERS). This approach is aiming for a universal and predictive logic for neurosimulation and AGi. The result of this investigation has produced a general "Information Engine" model from translation of the ERD and ERS. The CML algorithm run in terms of action cost predicts ERP signal contents and is consistent with the fundamental laws of thermodynamics. A working substrate independent natural information logic would be a major asset. An information theory consistent with fundamental physics can be an AGi. It can also operate within genetic information space and provides a roadmap to understand the live biophysical operation of the phenotype

Thermodynamics of technetium: Reconciling theory and experiment using density functional perturbation analysis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Weck, Philippe F.; Kim, Eunja

The structure, lattice dynamics and thermodynamic properties of bulk technetium were investigated within the framework of density functional theory. The phonon density of states spectrum computed with density functional perturbation theory closely matches inelastic coherent neutron scattering measurements. The thermal properties of technetium were derived from phonon frequencies calculated within the quasi-harmonic approximation (QHA), which introduces a volume dependence of phonon frequencies as a part of the anharmonic effect. As a result, the predicted thermal expansion and isobaric heat capacity of technetium are in excellent agreement with available experimental data for temperatures up to ~1600 K.

Thermodynamics of technetium: Reconciling theory and experiment using density functional perturbation analysis

DOE PAGES

Weck, Philippe F.; Kim, Eunja

2015-06-11

The structure, lattice dynamics and thermodynamic properties of bulk technetium were investigated within the framework of density functional theory. The phonon density of states spectrum computed with density functional perturbation theory closely matches inelastic coherent neutron scattering measurements. The thermal properties of technetium were derived from phonon frequencies calculated within the quasi-harmonic approximation (QHA), which introduces a volume dependence of phonon frequencies as a part of the anharmonic effect. As a result, the predicted thermal expansion and isobaric heat capacity of technetium are in excellent agreement with available experimental data for temperatures up to ~1600 K.

Work cost of thermal operations in quantum thermodynamics

NASA Astrophysics Data System (ADS)

Renes, Joseph M.

2014-07-01

Adopting a resource theory framework of thermodynamics for quantum and nano systems pioneered by Janzing et al. (Int. J. Th. Phys. 39, 2717 (2000)), we formulate the cost in the useful work of transforming one resource state into another as a linear program of convex optimization. This approach is based on the characterization of thermal quasiorder given by Janzing et al. and later by Horodecki and Oppenheim (Nat. Comm. 4, 2059 (2013)). Both characterizations are related to an extended version of majorization studied by Ruch, Schranner and Seligman under the name mixing distance (J. Chem. Phys. 69, 386 (1978)).

Bayesian energy landscape tilting: towards concordant models of molecular ensembles.

PubMed

Beauchamp, Kyle A; Pande, Vijay S; Das, Rhiju

2014-03-18

Predicting biological structure has remained challenging for systems such as disordered proteins that take on myriad conformations. Hybrid simulation/experiment strategies have been undermined by difficulties in evaluating errors from computational model inaccuracies and data uncertainties. Building on recent proposals from maximum entropy theory and nonequilibrium thermodynamics, we address these issues through a Bayesian energy landscape tilting (BELT) scheme for computing Bayesian hyperensembles over conformational ensembles. BELT uses Markov chain Monte Carlo to directly sample maximum-entropy conformational ensembles consistent with a set of input experimental observables. To test this framework, we apply BELT to model trialanine, starting from disagreeing simulations with the force fields ff96, ff99, ff99sbnmr-ildn, CHARMM27, and OPLS-AA. BELT incorporation of limited chemical shift and (3)J measurements gives convergent values of the peptide's α, β, and PPII conformational populations in all cases. As a test of predictive power, all five BELT hyperensembles recover set-aside measurements not used in the fitting and report accurate errors, even when starting from highly inaccurate simulations. BELT's principled framework thus enables practical predictions for complex biomolecular systems from discordant simulations and sparse data. Copyright © 2014 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Mapping Chemical Selection Pathways for Designing Multicomponent Alloys: an informatics framework for materials design.

PubMed

Srinivasan, Srikant; Broderick, Scott R; Zhang, Ruifeng; Mishra, Amrita; Sinnott, Susan B; Saxena, Surendra K; LeBeau, James M; Rajan, Krishna

2015-12-18

A data driven methodology is developed for tracking the collective influence of the multiple attributes of alloying elements on both thermodynamic and mechanical properties of metal alloys. Cobalt-based superalloys are used as a template to demonstrate the approach. By mapping the high dimensional nature of the systematics of elemental data embedded in the periodic table into the form of a network graph, one can guide targeted first principles calculations that identify the influence of specific elements on phase stability, crystal structure and elastic properties. This provides a fundamentally new means to rapidly identify new stable alloy chemistries with enhanced high temperature properties. The resulting visualization scheme exhibits the grouping and proximity of elements based on their impact on the properties of intermetallic alloys. Unlike the periodic table however, the distance between neighboring elements uncovers relationships in a complex high dimensional information space that would not have been easily seen otherwise. The predictions of the methodology are found to be consistent with reported experimental and theoretical studies. The informatics based methodology presented in this study can be generalized to a framework for data analysis and knowledge discovery that can be applied to many material systems and recreated for different design objectives.

Modeling the glass transition of amorphous networks for shape-memory behavior

NASA Astrophysics Data System (ADS)

Xiao, Rui; Choi, Jinwoo; Lakhera, Nishant; Yakacki, Christopher M.; Frick, Carl P.; Nguyen, Thao D.

2013-07-01

In this paper, a thermomechanical constitutive model was developed for the time-dependent behaviors of the glass transition of amorphous networks. The model used multiple discrete relaxation processes to describe the distribution of relaxation times for stress relaxation, structural relaxation, and stress-activated viscous flow. A non-equilibrium thermodynamic framework based on the fictive temperature was introduced to demonstrate the thermodynamic consistency of the constitutive theory. Experimental and theoretical methods were developed to determine the parameters describing the distribution of stress and structural relaxation times and the dependence of the relaxation times on temperature, structure, and driving stress. The model was applied to study the effects of deformation temperatures and physical aging on the shape-memory behavior of amorphous networks. The model was able to reproduce important features of the partially constrained recovery response observed in experiments. Specifically, the model demonstrated a strain-recovery overshoot for cases programmed below Tg and subjected to a constant mechanical load. This phenomenon was not observed for materials programmed above Tg. Physical aging, in which the material was annealed for an extended period of time below Tg, shifted the activation of strain recovery to higher temperatures and increased significantly the initial recovery rate. For fixed-strain recovery, the model showed a larger overshoot in the stress response for cases programmed below Tg, which was consistent with previous experimental observations. Altogether, this work demonstrates how an understanding of the time-dependent behaviors of the glass transition can be used to tailor the temperature and deformation history of the shape-memory programming process to achieve more complex shape recovery pathways, faster recovery responses, and larger activation stresses.

Phonon thermodynamics of iron and cementite

NASA Astrophysics Data System (ADS)

Mauger, Lisa Mary

The vibrational properties of materials are essential to understanding material stability and thermodynamics. In this thesis I outline vibrational thermodynamic models and the experimental tools that provide evidence on phonon behavior. The introductory section discusses the history of metallurgy and thermodynamic theory, with an emphasis on the role of iron and cementite, two important components of steels. The thermodynamic framework for understanding vibrational material behavior is provided alongside the growing body of experimental and computational tools that provide physical insight on vibrational properties. The high temperature vibrational behavior of iron and cementite are explored within this context in the final chapters. Body-centered-cubic iron exhibits decreasing phonon energies at elevated temperatures. The observed energy change in not uniform across phonon modes in iron, and specific phonon modes show significant decreases in energy that are not explained by simple vibrational models. This anomalously energy decrease is linked to the second-nearest-neighbor interactions in the bcc structure, through examination of fitted interatomic force constants. The large changes in phonon energy result in a significant increase in the vibrational entropy, called the nonharmonic vibrational entropy, which emulates the temperature behavior of the magnetic entropy across the Curie temperature. The nonharmonic vibrational entropy is attributed to interactions between the vibrations and state of magnetic disorder in the material, which persists above the magnetic transitions and extends the stability region of the bcc phase. Orthorombic cementite, Fe3C, exhibits anisotropic magneto-volume behavior in the ferromagnetic phase including regions very low thermal expansion. The phonon modes of cementite show anomalous temperature dependence, with low energy phonon modes increasing their energy at elevated temperatures in the ferromagnetic phase. This behavior is reversed after the magnetic transition and these same phonon modes lower their energies with temperature, consistent with observed thermal expansion. This atypical phonon behavior lowers the vibrational entropy of cementite up to the Curie temperature. The experimentally observed increase in low energy acoustic phonons affects the elastic behavior of Fe3C, increasing the isotropy of elastic response. First principles calculations link the observed phonon energy increases to specific vibrational modes that are polarized along the b-axis, which aligns with the closest Fe-Fe bonding direction. The nonharmonic behavior of the vibrational modes are discussed in the context of other observations of anomalous anisotropic magneto-volume behavior in Fe3C.

Functional Entropy Variables: A New Methodology for Deriving Thermodynamically Consistent Algorithms for Complex Fluids, with Particular Reference to the Isothermal Navier-Stokes-Korteweg Equations

DTIC Science & Technology

2012-11-01

multicorrector algorithm . Predictor stage: Set Cρn+1,(0) = C ρ n, (157) Cun+1,(0) = C u n, (158) Cvn+1,(0) = C v n. (159) Multicorrector stage: Repeat the... corrector algorithm given by (157)-(178). Remark 20. We adopt the preconditioned GMRES algorithm [53] from PETSc [2] to solve the linear system given by (175...ICES REPORT 12-43 November 2012 Functional Entropy Variables: A New Methodology for Deriving Thermodynamically Consistent Algorithms for Complex

Thermodynamic and Kinetic Effects in the Crystallization of Metal-Organic Frameworks.

PubMed

Cheetham, Anthony K; Kieslich, G; Yeung, H H-M

2018-03-20

The evolution of metal-organic frameworks (MOFs) has been one of the most exciting aspects of materials chemistry over the last 20 years. In this Account, we discuss the development during this period in our understanding of the factors that control the crystallization of MOFs from solution. Both classical porous MOFs and dense MOF phases are considered. This is an opportune time at which to examine this complex area because the experimental tools now available to interrogate crystallization processes have matured significantly in the last 5 years, particularly with the use of in situ synchrotron X-ray diffraction. There have also been impressive developments in the use of density functional theory (DFT) to treat not only the energies of very complex structures but also their entropies. This is particularly important in MOF frameworks because of their much greater flexibility compared with inorganic structures such as zeolites. The first section of the Account describes how early empirical observations on the crystallization of dense MOFs pointed to a strong degree of thermodynamic control, with both enthalpic and entropic factors playing important roles. For example, reactions at higher temperatures tend to lead to denser structures with higher degrees of framework connectivity and lower levels of solvation, and polymorphs tend to form according to their thermodynamic stabilities. In the case of metal tartrates, these trends have been validated by calorimetric studies. It has been clear for more than a decade, however, that certain phases crystallize under kinetic control, especially when a change in conformation of the ligand or coordination around a metal center might be necessary to form the thermodynamically preferred product. We describe how this can lead to time-dependent crystallization processes that evolve according to the Ostwald rule of stages and can be observed by in situ methods. We then consider the crystallization of porous MOFs, which presents additional challenges because of solvation effects. In spite of these problems, much has been learned about the energetics of the underlying frameworks, where the relationship between porosity and stability initially seemed to mirror the behavior of zeolites, with more porous structures being less stable. Recently, however, this simple relationship has had to be reconsidered with the emergence of some very flexible structures wherein the open structures are more stable than their denser analogues at finite temperatures because of their large vibrational entropies. In the final section we describe how the concepts developed in the MOF work have been extended into the closely related area of hybrid organic-inorganic perovskites. We describe recent studies on polymorphism in hybrid perovskites, which is amenable to total free energy calculations using a combination of DFT and lattice dynamics methods.

The second law of thermodynamics under unitary evolution and external operations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ikeda, Tatsuhiko N., E-mail: ikeda@cat.phys.s.u-tokyo.ac.jp; Physics Department, Boston University, Boston, MA 02215; Sakumichi, Naoyuki

The von Neumann entropy cannot represent the thermodynamic entropy of equilibrium pure states in isolated quantum systems. The diagonal entropy, which is the Shannon entropy in the energy eigenbasis at each instant of time, is a natural generalization of the von Neumann entropy and applicable to equilibrium pure states. We show that the diagonal entropy is consistent with the second law of thermodynamics upon arbitrary external unitary operations. In terms of the diagonal entropy, thermodynamic irreversibility follows from the facts that quantum trajectories under unitary evolution are restricted by the Hamiltonian dynamics and that the external operation is performed withoutmore » reference to the microscopic state of the system.« less

Quantum thermodynamics of the resonant-level model with driven system-bath coupling

NASA Astrophysics Data System (ADS)

Haughian, Patrick; Esposito, Massimiliano; Schmidt, Thomas L.

2018-02-01

We study nonequilibrium thermodynamics in a fermionic resonant-level model with arbitrary coupling strength to a fermionic bath, taking the wide-band limit. In contrast to previous theories, we consider a system where both the level energy and the coupling strength depend explicitly on time. We find that, even in this generalized model, consistent thermodynamic laws can be obtained, up to the second order in the drive speed, by splitting the coupling energy symmetrically between system and bath. We define observables for the system energy, work, heat, and entropy, and calculate them using nonequilibrium Green's functions. We find that the observables fulfill the laws of thermodynamics, and connect smoothly to the known equilibrium results.

Characteristics of Subcooled Liquid Methane During Passage Through a Spray-Bar Joule-Thompson Thermodynamic Vent System

NASA Technical Reports Server (NTRS)

Hastings, L. J.; Bolshinskiy, L. G.; Hedayat, A.; Schnell, A.

2011-01-01

NASA s Marshall Space Flight Center (MSFC) conducted liquid methane (LCH4) testing in November 2006 using the multipurpose hydrogen test bed (MHTB) outfitted with a spray-bar thermodynamic vent system (TVS). The basic objective was to identify any unusual or unique thermodynamic characteristics associated with subcooled LCH4 that should be considered in the design of space-based TVSs. Thirteen days of testing were performed with total tank heat loads ranging from 720 W to 420 W at a fill level of approximately 90%. During an updated evaluation of the data, it was noted that as the fluid passed through the Joule Thompson expansion, thermodynamic conditions consistent with the pervasive presence of metastability were indicated. This paper describes the observed thermodynamic conditions that correspond with metastability and effects on TVS performance.

Solid and liquid Equation of state for initially porous aluminum where specific heat is constant

NASA Astrophysics Data System (ADS)

Forbes, Jerry W.; Lemar, E. R.; Brown, Mary

2011-06-01

A porous solid's initial state is off the thermodynamic surface of the non-porous solid to start with but when pressure is high enough to cause total pore collapse or crush up, then the final states are on the condensed matter thermodynamic surfaces. The Hugoniot for the fully compacted solid is above the Principle Hugoniot with pressure, temperature and internal energy increased at a given v. There are a number of ways to define this hotter Hugoniot, which can be referenced to other thermodynamic paths on this thermodynamic surface. The choice here was to use the Vinet isotherm to define a consistent thermodynamic surface for the solid and melt phase of 6061 aluminum where specific heat is constant for the P-v-T space of interest. Analytical equations are developed for PH and TH.

Understanding the tropical cloud feedback from an analysis of the circulation and stability regimes simulated from an upgraded multiscale modeling framework

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xu, Kuan-Man; Cheng, Anning

As revealed from studies using conventional general circulation models (GCMs), the thermodynamic contribution to the tropical cloud feedback dominates the dynamic contribution, but these models have difficulty in simulating the subsidence regimes in the tropics. In this study, we analyze the tropical cloud feedback from a 2 K sea surface temperature (SST) perturbation experiment performed with a multiscale modeling framework (MMF). The MMF explicitly represents cloud processes using 2-D cloud-resolving models with an advanced higher-order turbulence closure in each atmospheric column of the host GCM. We sort the monthly mean cloud properties and cloud radiative effects according to circulation andmore » stability regimes. Here, we find that the regime-sorted dynamic changes dominate the thermodynamic changes in terms of the absolute magnitude. The dynamic changes in the weak subsidence regimes exhibit strong negative cloud feedback due to increases in shallow cumulus and deep clouds while those in strongly convective and moderate-to-strong subsidence regimes have opposite signs, resulting in a small contribution to cloud feedback. On the other hand, the thermodynamic changes are large due to decreases in stratocumulus clouds in the moderate-to-strong subsidence regimes with small opposite changes in the weak subsidence and strongly convective regimes, resulting in a relatively large contribution to positive cloud feedback. The dynamic and thermodynamic changes contribute equally to positive cloud feedback and are relatively insensitive to stability in the moderate-to-strong subsidence regimes. But they are sensitive to stability changes from the SST increase in convective and weak subsidence regimes. Lastly, these results have implications for interpreting cloud feedback mechanisms.« less

Understanding the tropical cloud feedback from an analysis of the circulation and stability regimes simulated from an upgraded multiscale modeling framework

DOE PAGES

Xu, Kuan-Man; Cheng, Anning

2016-11-15

As revealed from studies using conventional general circulation models (GCMs), the thermodynamic contribution to the tropical cloud feedback dominates the dynamic contribution, but these models have difficulty in simulating the subsidence regimes in the tropics. In this study, we analyze the tropical cloud feedback from a 2 K sea surface temperature (SST) perturbation experiment performed with a multiscale modeling framework (MMF). The MMF explicitly represents cloud processes using 2-D cloud-resolving models with an advanced higher-order turbulence closure in each atmospheric column of the host GCM. We sort the monthly mean cloud properties and cloud radiative effects according to circulation andmore » stability regimes. Here, we find that the regime-sorted dynamic changes dominate the thermodynamic changes in terms of the absolute magnitude. The dynamic changes in the weak subsidence regimes exhibit strong negative cloud feedback due to increases in shallow cumulus and deep clouds while those in strongly convective and moderate-to-strong subsidence regimes have opposite signs, resulting in a small contribution to cloud feedback. On the other hand, the thermodynamic changes are large due to decreases in stratocumulus clouds in the moderate-to-strong subsidence regimes with small opposite changes in the weak subsidence and strongly convective regimes, resulting in a relatively large contribution to positive cloud feedback. The dynamic and thermodynamic changes contribute equally to positive cloud feedback and are relatively insensitive to stability in the moderate-to-strong subsidence regimes. But they are sensitive to stability changes from the SST increase in convective and weak subsidence regimes. Lastly, these results have implications for interpreting cloud feedback mechanisms.« less

Hyper-elastoplastic/damage modeling of rock with application to porous limestone

DOE PAGES

Bennett, Kane C.; Borja, Ronaldo I.

2018-03-13

Relations between porosity, damage, and bulk plasticity are examined in the context of continuum damage and hyper-elastoplasticity of porous rocks. Attention is given to a thermodynamically consistent derivation of the damage evolution equations and their role in the constitutive equations, for which the Eshelby stress is found to be important. The provided phenomenological framework allows for volumetric damage associated with pore growth to be distinguished from the isochoric damage associated with distributed microcracks, and a novel Drucker-Prager/cap type material model that includes damage evolution is presented. The model is shown to capture well the hardening/softening behavior and pressure dependence ofmore » the so-called brittle-ductile transition by comparison with confined triaxial compression measurements from the literature. Non-linear finite element simulations are also provided of the prediction of damage within porous limestone around a horizontal borehole wall.« less

Numerical homogenization of elastic and thermal material properties for metal matrix composites (MMC)

NASA Astrophysics Data System (ADS)

Schindler, Stefan; Mergheim, Julia; Zimmermann, Marco; Aurich, Jan C.; Steinmann, Paul

2017-01-01

A two-scale material modeling approach is adopted in order to determine macroscopic thermal and elastic constitutive laws and the respective parameters for metal matrix composite (MMC). Since the common homogenization framework violates the thermodynamical consistency for non-constant temperature fields, i.e., the dissipation is not conserved through the scale transition, the respective error is calculated numerically in order to prove the applicability of the homogenization method. The thermomechanical homogenization is applied to compute the macroscopic mass density, thermal expansion, elasticity, heat capacity and thermal conductivity for two specific MMCs, i.e., aluminum alloy Al2024 reinforced with 17 or 30 % silicon carbide particles. The temperature dependency of the material properties has been considered in the range from 0 to 500°C, the melting temperature of the alloy. The numerically determined material properties are validated with experimental data from the literature as far as possible.

Energy landscapes for a machine-learning prediction of patient discharge

NASA Astrophysics Data System (ADS)

Das, Ritankar; Wales, David J.

2016-06-01

The energy landscapes framework is applied to a configuration space generated by training the parameters of a neural network. In this study the input data consists of time series for a collection of vital signs monitored for hospital patients, and the outcomes are patient discharge or continued hospitalisation. Using machine learning as a predictive diagnostic tool to identify patterns in large quantities of electronic health record data in real time is a very attractive approach for supporting clinical decisions, which have the potential to improve patient outcomes and reduce waiting times for discharge. Here we report some preliminary analysis to show how machine learning might be applied. In particular, we visualize the fitting landscape in terms of locally optimal neural networks and the connections between them in parameter space. We anticipate that these results, and analogues of thermodynamic properties for molecular systems, may help in the future design of improved predictive tools.

Binary nanoparticle superlattices of soft-particle systems

DOE PAGES

Travesset, Alex

2015-08-04

The solid-phase diagram of binary systems consisting of particles of diameter σ A=σ and σ B=γσ (γ≤1) interacting with an inverse p = 12 power law is investigated as a paradigm of a soft potential. In addition to the diameter ratio γ that characterizes hard-sphere models, the phase diagram is a function of an additional parameter that controls the relative interaction strength between the different particle types. Phase diagrams are determined from extremes of thermodynamic functions by considering 15 candidate lattices. In general, it is shown that the phase diagram of a soft repulsive potential leads to the morphological diversitymore » observed in experiments with binary nanoparticles, thus providing a general framework to understand their phase diagrams. In addition, particular emphasis is shown to the two most successful crystallization strategies so far: evaporation of solvent from nanoparticles with grafted hydrocarbon ligands and DNA programmable self-assembly.« less

Hyper-elastoplastic/damage modeling of rock with application to porous limestone

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bennett, Kane C.; Borja, Ronaldo I.

Relations between porosity, damage, and bulk plasticity are examined in the context of continuum damage and hyper-elastoplasticity of porous rocks. Attention is given to a thermodynamically consistent derivation of the damage evolution equations and their role in the constitutive equations, for which the Eshelby stress is found to be important. The provided phenomenological framework allows for volumetric damage associated with pore growth to be distinguished from the isochoric damage associated with distributed microcracks, and a novel Drucker-Prager/cap type material model that includes damage evolution is presented. The model is shown to capture well the hardening/softening behavior and pressure dependence ofmore » the so-called brittle-ductile transition by comparison with confined triaxial compression measurements from the literature. Non-linear finite element simulations are also provided of the prediction of damage within porous limestone around a horizontal borehole wall.« less

High-throughput computational design of cathode coatings for Li-ion batteries

PubMed Central

Aykol, Muratahan; Kim, Soo; Hegde, Vinay I.; Snydacker, David; Lu, Zhi; Hao, Shiqiang; Kirklin, Scott; Morgan, Dane; Wolverton, C.

2016-01-01

Cathode degradation is a key factor that limits the lifetime of Li-ion batteries. To identify functional coatings that can suppress this degradation, we present a high-throughput density functional theory based framework which consists of reaction models that describe thermodynamic and electrochemical stabilities, and acid-scavenging capabilities of materials. Screening more than 130,000 oxygen-bearing materials, we suggest physical and hydrofluoric-acid barrier coatings such as WO3, LiAl5O8 and ZrP2O7 and hydrofluoric-acid scavengers such as Sc2O3, Li2CaGeO4, LiBO2, Li3NbO4, Mg3(BO3)2 and Li2MgSiO4. Using a design strategy to find the thermodynamically optimal coatings for a cathode, we further present optimal hydrofluoric-acid scavengers such as Li2SrSiO4, Li2CaSiO4 and CaIn2O4 for the layered LiCoO2, and Li2GeO3, Li4NiTeO6 and Li2MnO3 for the spinel LiMn2O4 cathodes. These coating materials have the potential to prolong the cycle-life of Li-ion batteries and surpass the performance of common coatings based on conventional materials such as Al2O3, ZnO, MgO or ZrO2. PMID:27966537

The stability analysis of magnetohydrodynamic equilibria - Comparing the thermodynamic approach with the energy principle

NASA Technical Reports Server (NTRS)

Brinkmann, R. P.

1989-01-01

This paper is a contribution to the stability analysis of current-carrying plasmas, i.e., plasma systems that are forced by external mchanisms to carry a nonrelaxing electrical current. Under restriction to translationally invariant configurations, the thermodynamic stability criterion for a multicomponent plasma is rederived within the framework of nonideal MHD. The chosen dynamics neglects scalar resistivity, but allows for other types of dissipation effects both in Ohm's law and in the equation of motion. In the second section of the paper, the thermodynamic stability criterion is compared with the ideal MHD based energy principle of Bernstein et al. With the help of Schwarz's inequality, it is shown that the former criterion is always more 'pessimistic' than the latter, i.e., that thermodynamic stability implies stability according to the MHD principle, but not vice versa. This reuslt confirms the physical plausible idea that dissipational effects tend to weaken the stability properties of current-carrying plasma equilibria by breaking the constraints of ideal MHD and allowing for possibly destabilizing effects such as magnetic field line reconfiguration.

Association effects in the {methanol + inert solvent} system via Monte Carlo simulations. II. Thermodynamics

NASA Astrophysics Data System (ADS)

Gómez-Álvarez, Paula; Romaní, Luis; González-Salgado, Diego

2013-05-01

Mixtures containing associated substances show a singular thermodynamic behaviour that has attracted to scientific community during the last century. Particularly, binary systems composed of an associating fluid and an inert solvent, where association occurs only between molecules of the same kind, have been extensively studied. A number of theoretical approaches were used in order to gain insights into the effect of the association on the macroscopic behaviour, especially on the second-order thermodynamic derivatives (or response functions). Curiously, to our knowledge, molecular simulations have not been used to that end despite describing the molecules and their interactions in a more complete and realistic way than theoretical models. With this in mind, a simple methodology developed in the framework of Monte Carlo molecular simulation is used in this work to quantify the association contribution to a wide set of thermodynamic properties for the {methanol + Lennard Jones} specific system under room conditions and throughout the composition range. Special attention was paid to the response functions and their respective excess properties, for which a detailed comparison with selected previous works in the field has been established.

Iron(III) solubility and speciation in aqueous solutions. experimental study and modelling: part 1. hematite solubility from 60 to 300°C in NaOH-NaCl solutions and thermodynamic properties of Fe(OH) 4 -(aq)

NASA Astrophysics Data System (ADS)

Diakonov, Igor I.; Schott, Jacques; Martin, Francois; Harrichourry, Jean-Claude; Escalier, Jocelyne

1999-08-01

The solubility of natural and synthetic hematite (α-Fe 2O 3) was measured in NaOH-NaCl solutions (0.007 ≤ m(NaOH) ≤ 2.0) between 60 and 300°C at saturated water vapour pressure and under excess oxygen. Solubility constants determined in the present study and by Yishan et al. (1986) at 300°C were combined with the thermodynamic properties of hematite (Hemingway, 1990) and water (SUPCRT92, Johnson et al., 1992) to generate within the framework of the revised Helgeson-Kirkham-Flowers (HKF) model the standard partial molal thermodynamic properties at 25°C and 1 bar, and the revised HKF equations of state parameters of Fe(OH) 4 -. The extrapolated value for the Gibbs energy of formation for Fe(OH) 4 - at 25°C is -201.97 kcal/mol. Thermodynamic calculations show that Fe(OH) 4 - exhibits a chemical behaviour different from that of Ga(OH) 4 - and Al(OH) 4 -.

Characterization of the superconducting state in hafnium hydride under high pressure

NASA Astrophysics Data System (ADS)

Duda, A. M.; Szewczyk, K. A.; Jarosik, M. W.; Szcześniak, K. M.; Sowińska, M. A.; Szcześniak, D.

2018-05-01

The hydrogen-rich compounds at high pressure may exhibit notably high superconducting transition temperatures. In the paper, we have calculated the basic thermodynamic parameters of the superconducting state in two selected phases of HfH2 hydride under high-pressure respectively at 180 GPa for Cmma and 260 GPa for P21 / m . Calculations has been conducted in the framework of the Eliashberg formalism. In particular, we have determined the values of the critical temperature (TC) to be equal to 8 K and 13 K for the Cmma and P21 / m phases, respectively. Moreover, we have estimated other thermodynamic properties such as the order parameter (Δ (T)) , the thermodynamic critical field (HC (T)) , and the specific heat for the normal (CN) and superconducting (CS) state. Finally, we have shown that the characteristic ratios: RΔ = 2 Δ (0) /kBTC and RC = ΔC (TC) /CN (TC) , which are related to the above thermodynamic functions, slightly differ from the predictions of the Bardeen-Cooper-Schrieffer theory due to the strong-coupling and retardation effects.

Thermodynamic precursors, liquid-liquid transitions, dynamic and topological anomalies in densified liquid germania

NASA Astrophysics Data System (ADS)

Pacaud, F.; Micoulaut, M.

2015-08-01

The thermodynamic, dynamic, structural, and rigidity properties of densified liquid germania (GeO2) have been investigated using classical molecular dynamics simulation. We construct from a thermodynamic framework an analytical equation of state for the liquid allowing the possible detection of thermodynamic precursors (extrema of the derivatives of the free energy), which usually indicate the possibility of a liquid-liquid transition. It is found that for the present germania system, such precursors and the possible underlying liquid-liquid transition are hidden by the slowing down of the dynamics with decreasing temperature. In this respect, germania behaves quite differently when compared to parent tetrahedral systems such as silica or water. We then detect a diffusivity anomaly (a maximum of diffusion with changing density/volume) that is strongly correlated with changes in coordinated species, and the softening of bond-bending (BB) topological constraints that decrease the liquid rigidity and enhance transport. The diffusivity anomaly is finally substantiated from a Rosenfeld-type scaling law linked to the pair correlation entropy, and to structural relaxation.

Quantum stochastic thermodynamic on harmonic networks

DOE PAGES

Deffner, Sebastian

2016-01-04

Fluctuation theorems are symmetry relations for the probability to observe an amount of entropy production in a finite-time process. In a recent paper Pigeon et al (2016 New. J. Phys. 18 013009) derived fluctuation theorems for harmonic networks by means of the large deviation theory. Furthermore, their novel approach is illustrated with various examples of experimentally relevant systems. As a main result, however, Pigeon et al provide new insight how to consistently formulate quantum stochastic thermodynamics, and provide new and robust tools for the study of the thermodynamics of quantum harmonic networks.

Quantum stochastic thermodynamic on harmonic networks

DOE Office of Scientific and Technical Information (OSTI.GOV)

Deffner, Sebastian

Fluctuation theorems are symmetry relations for the probability to observe an amount of entropy production in a finite-time process. In a recent paper Pigeon et al (2016 New. J. Phys. 18 013009) derived fluctuation theorems for harmonic networks by means of the large deviation theory. Furthermore, their novel approach is illustrated with various examples of experimentally relevant systems. As a main result, however, Pigeon et al provide new insight how to consistently formulate quantum stochastic thermodynamics, and provide new and robust tools for the study of the thermodynamics of quantum harmonic networks.

Consistency of the structure of Legendre transform in thermodynamics with the Kolmogorov-Nagumo average

NASA Astrophysics Data System (ADS)

Scarfone, A. M.; Matsuzoe, H.; Wada, T.

2016-09-01

We show the robustness of the structure of Legendre transform in thermodynamics against the replacement of the standard linear average with the Kolmogorov-Nagumo nonlinear average to evaluate the expectation values of the macroscopic physical observables. The consequence of this statement is twofold: 1) the relationships between the expectation values and the corresponding Lagrange multipliers still hold in the present formalism; 2) the universality of the Gibbs equation as well as other thermodynamic relations are unaffected by the structure of the average used in the theory.

Carnot cycle for interacting particles in the absence of thermal noise.

PubMed

Curado, Evaldo M F; Souza, Andre M C; Nobre, Fernando D; Andrade, Roberto F S

2014-02-01

A thermodynamic formalism is developed for a system of interacting particles under overdamped motion, which has been recently analyzed within the framework of nonextensive statistical mechanics. It amounts to expressing the interaction energy of the system in terms of a temperature θ, conjugated to a generalized entropy s(q), with q = 2. Since θ assumes much higher values than those of typical room temperatures T ≪ θ, the thermal noise can be neglected for this system (T/θ ≃ 0). This framework is now extended by the introduction of a work term δW which, together with the formerly defined heat contribution (δ Q = θ ds(q)), allows for the statement of a proper energy conservation law that is analogous to the first law of thermodynamics. These definitions lead to the derivation of an equation of state and to the characterization of s(q) adiabatic and θ isothermic transformations. On this basis, a Carnot cycle is constructed, whose efficiency is shown to be η = 1-(θ(2)/θ(1)), where θ(1) and θ(2) are the effective temperatures of the two isothermic transformations, with θ(1)>θ(2). The results for a generalized thermodynamic description of this system open the possibility for further physical consequences, like the realization of a thermal engine based on energy exchanges gauged by the temperature θ.

A thermodynamic framework for understanding temperature sensing by transient receptor potential (TRP) channels

PubMed Central

Clapham, David E.; Miller, Christopher

2011-01-01

The exceptionally high temperature sensitivity of certain transient receptor potential (TRP) family ion channels is the molecular basis of hot and cold sensation in sensory neurons. The laws of thermodynamics dictate that opening of these specialized TRP channels must involve an unusually large conformational standard-state enthalpy, ΔHo: positive ΔHo for heat-activated and negative ΔHo for cold-activated TRPs. However, the molecular source of such high-enthalpy changes has eluded neurobiologists and biophysicists. Here we offer a general, unifying mechanism for both hot and cold activation that recalls long-appreciated principles of protein folding. We suggest that TRP channel gating is accompanied by large changes in molar heat capacity, ΔCP. This postulate, along with the laws of thermodynamics and independent of mechanistic detail, leads to the conclusion that hot- and cold-sensing TRPs operate by identical conformational changes. PMID:22109551

A thermodynamic framework for understanding temperature sensing by transient receptor potential (TRP) channels.

PubMed

Clapham, David E; Miller, Christopher

2011-12-06

The exceptionally high temperature sensitivity of certain transient receptor potential (TRP) family ion channels is the molecular basis of hot and cold sensation in sensory neurons. The laws of thermodynamics dictate that opening of these specialized TRP channels must involve an unusually large conformational standard-state enthalpy, ΔH(o): positive ΔH(o) for heat-activated and negative ΔH(o) for cold-activated TRPs. However, the molecular source of such high-enthalpy changes has eluded neurobiologists and biophysicists. Here we offer a general, unifying mechanism for both hot and cold activation that recalls long-appreciated principles of protein folding. We suggest that TRP channel gating is accompanied by large changes in molar heat capacity, ΔC(P). This postulate, along with the laws of thermodynamics and independent of mechanistic detail, leads to the conclusion that hot- and cold-sensing TRPs operate by identical conformational changes.

Thermodynamics of complexity and pattern manipulation.

PubMed

Garner, Andrew J P; Thompson, Jayne; Vedral, Vlatko; Gu, Mile

2017-04-01

Many organisms capitalize on their ability to predict the environment to maximize available free energy and reinvest this energy to create new complex structures. This functionality relies on the manipulation of patterns-temporally ordered sequences of data. Here, we propose a framework to describe pattern manipulators-devices that convert thermodynamic work to patterns or vice versa-and use them to build a "pattern engine" that facilitates a thermodynamic cycle of pattern creation and consumption. We show that the least heat dissipation is achieved by the provably simplest devices, the ones that exhibit desired operational behavior while maintaining the least internal memory. We derive the ultimate limits of this heat dissipation and show that it is generally nonzero and connected with the pattern's intrinsic crypticity-a complexity theoretic quantity that captures the puzzling difference between the amount of information the pattern's past behavior reveals about its future and the amount one needs to communicate about this past to optimally predict the future.

Signal Transduction in Histidine Kinases: Insights from New Structures

PubMed Central

Bhate, Manasi P.; Molnar, Kathleen S.; Goulian, Mark; DeGrado, William F.

2015-01-01

Histidine kinases (HKs) are major players in bacterial signaling. There has been an explosion of new HK crystal structures in the last five years. We globally analyze the structures of HKs to yield insights into the mechanisms by which signals are transmitted to and across protein structures in this family. We interpret known enzymological data in the context of new structural data to show how asymmetry across the dimer interface is a key feature of signal transduction in HKs, and discuss how different HK domains undergo asymmetric-to-symmetric transitions during signal transduction and catalysis. A thermodynamic framework for signaling that encompasses these various properties is presented and the consequences of weak thermodynamic coupling are discussed. The synthesis of observations from enzymology, structural biology, protein engineering and thermodynamics paves the way for a deeper molecular understanding of histidine kinase signal transduction. PMID:25982528

Thermodynamics of Surface Nanobubbles.

PubMed

Zargarzadeh, Leila; Elliott, Janet A W

2016-11-01

In this paper, we examine the thermodynamic stability of surface nanobubbles. The appropriate free energy is defined for the system of nanobubbles on a solid surface submerged in a supersaturated liquid solution at constant pressure and temperature, under conditions where an individual nanobubble is not in diffusive contact with a gas phase outside of the system or with other nanobubbles on the time scale of the experiment. The conditions under which plots of free energy versus the radius of curvature of the nanobubbles show a global minimum, which denotes the stable equilibrium state, are explored. Our investigation shows that supersaturation and an anomalously high contact angle (measured through the liquid) are required to have stable surface nanobubbles. In addition, the anomalously high contact angle of surface nanobubbles is discussed from the standpoint of a framework recently proposed by Koch, Amirfazli, and Elliott that relates advancing and receding contact angles to thermodynamic equilibrium contact angles, combined with the existence of a gas enrichment layer.

Thermodynamics of complexity and pattern manipulation

NASA Astrophysics Data System (ADS)

Garner, Andrew J. P.; Thompson, Jayne; Vedral, Vlatko; Gu, Mile

2017-04-01

Many organisms capitalize on their ability to predict the environment to maximize available free energy and reinvest this energy to create new complex structures. This functionality relies on the manipulation of patterns—temporally ordered sequences of data. Here, we propose a framework to describe pattern manipulators—devices that convert thermodynamic work to patterns or vice versa—and use them to build a "pattern engine" that facilitates a thermodynamic cycle of pattern creation and consumption. We show that the least heat dissipation is achieved by the provably simplest devices, the ones that exhibit desired operational behavior while maintaining the least internal memory. We derive the ultimate limits of this heat dissipation and show that it is generally nonzero and connected with the pattern's intrinsic crypticity—a complexity theoretic quantity that captures the puzzling difference between the amount of information the pattern's past behavior reveals about its future and the amount one needs to communicate about this past to optimally predict the future.

Stochastic Thermodynamics of a Particle in a Box.

PubMed

Gong, Zongping; Lan, Yueheng; Quan, H T

2016-10-28

The piston system (particles in a box) is the simplest paradigmatic model in traditional thermodynamics. However, the recently established framework of stochastic thermodynamics (ST) fails to apply to this model system due to the embedded singularity in the potential. In this Letter, we study the ST of a particle in a box by adopting a novel coordinate transformation technique. Through comparing with the exact solution of a breathing harmonic oscillator, we obtain analytical results of work distribution for an arbitrary protocol in the linear response regime and verify various predictions of the fluctuation-dissipation relation. When applying to the Brownian Szilard engine model, we obtain the optimal protocol λ_{t}=λ_{0}2^{t/τ} for a given sufficiently long total time τ. Our study not only establishes a paradigm for studying ST of a particle in a box but also bridges the long-standing gap in the development of ST.

Condensate statistics and thermodynamics of weakly interacting Bose gas: Recursion relation approach

NASA Astrophysics Data System (ADS)

Dorfman, K. E.; Kim, M.; Svidzinsky, A. A.

2011-03-01

We study condensate statistics and thermodynamics of weakly interacting Bose gas with a fixed total number N of particles in a cubic box. We find the exact recursion relation for the canonical ensemble partition function. Using this relation, we calculate the distribution function of condensate particles for N=200. We also calculate the distribution function based on multinomial expansion of the characteristic function. Similar to the ideal gas, both approaches give exact statistical moments for all temperatures in the framework of Bogoliubov model. We compare them with the results of unconstraint canonical ensemble quasiparticle formalism and the hybrid master equation approach. The present recursion relation can be used for any external potential and boundary conditions. We investigate the temperature dependence of the first few statistical moments of condensate fluctuations as well as thermodynamic potentials and heat capacity analytically and numerically in the whole temperature range.

Influence of phonon-phonon coupling on superconducting state in honeycomb-type crystal lattice

NASA Astrophysics Data System (ADS)

Drzazga, E. A.; Szczȩśniak, R.; Domagalska, I. A.

2018-01-01

We have taken into account the superconducting state inducing in the crystal lattice of the honeycomb-type. In the framework of the Eliashberg theory, we have determined the thermodynamic properties of the system. The phonon spectral function, which is the input parameter in the Eliashberg equations, has been calculated by using the thermodynamic Green functions. We have considered the model of the coupled Einstein oscillators with frequency ω0 = 100 meV. We have shown that the increasing inter-phonon coupling constant (f) causes the rapid growth of the critical temperature ([TC]max = 36.2 K) just below the maximum value of f equal to 0.25ω0. Simultaneously, the order parameter and the thermodynamic critical field take the values increasingly distant from the predictions of the BCS theory, which results from the strong-coupling and the retardation effects.

Fluctuation relation based continuum model for thermoviscoplasticity in metals

NASA Astrophysics Data System (ADS)

Roy Chowdhury, Shubhankar; Roy, Debasish; Reddy, J. N.; Srinivasa, Arun

2016-11-01

A continuum plasticity model for metals is presented from considerations of non-equilibrium thermodynamics. Of specific interest is the application of a fluctuation relation that subsumes the second law of thermodynamics en route to deriving the evolution equations for the internal state variables. The modelling itself is accomplished in a two-temperature framework that appears naturally by considering the thermodynamic system to be composed of two weakly interacting subsystems, viz. a kinetic vibrational subsystem corresponding to the atomic lattice vibrations and a configurational subsystem of the slower degrees of freedom describing the motion of defects in a plastically deforming metal. An apparently physical nature of the present model derives upon considering the dislocation density, which characterizes the configurational subsystem, as a state variable. Unlike the usual constitutive modelling aided by the second law of thermodynamics that merely provides a guideline to select the admissible (though possibly non-unique) processes, the present formalism strictly determines the process or the evolution equations for the thermodynamic states while including the effect of fluctuations. The continuum model accommodates finite deformation and describes plastic deformation in a yield-free setup. The theory here is essentially limited to face-centered cubic metals modelled with a single dislocation density as the internal variable. Limited numerical simulations are presented with validation against relevant experimental data.

Discerning Thermodynamic Basis of Self-Organization in Critical Zone Structure and Function

NASA Astrophysics Data System (ADS)

Richardson, M.; Kumar, P.

2017-12-01

Self-organization characterizes the spontaneous emergence of order. Self-organization in the Critical Zone, the region of Earth's skin from below the groundwater table to the top of the vegetation canopy, involves the interaction of biotic and abiotic processes occurring through a hierarchy of temporal and spatial scales. The self-organization is sustained through input of energy and material in an open system framework, and the resulting formations are called dissipative structures. Why do these local states of organization form and how are they thermodynamically favorable? We hypothesize that structure formation is linked to energy conversion and matter throughput rates across driving gradients. Furthermore, we predict that structures in the Critical Zone evolve based on local availability of nutrients, water, and energy. By considering ecosystems as open thermodynamic systems, we model and study the throughput signatures on short times scales to determine origins and characteristics of ecosystem structure. This diagnostic approach allows us to use fluxes of matter and energy to understand the thermodynamic drivers of the system. By classifying the fluxes and dynamics in a system, we can identify patterns to determine the thermodynamic drivers for organized states. Additionally, studying the partitioning of nutrients, water, and energy throughout ecosystems through dissipative structures will help identify reasons for structure shapes and how these shapes impact major Critical Zone functions.

Quantum Mechanics of the Einstein-Hopf Model.

ERIC Educational Resources Information Center

Milonni, P. W.

1981-01-01

The Einstein-Hopf model for the thermodynamic equilibrium between the electromagnetic field and dipole oscillators is considered within the framework of quantum mechanics. Both the wave and particle aspects of the Einstein fluctuation formula are interpreted in terms of the fundamental absorption and emission processes. (Author/SK)

Coupling Fluid Dynamics and Multiphase Disequilibria: Applications to Eutectic and Peritectic Systems

NASA Astrophysics Data System (ADS)

Tweed, L. E. L.; Spiegelman, M. W.; Kelemen, P. B.

2017-12-01

Computational thermodynamics has yielded great insights into petrological processes. However, on its own it cannot capture the inherently dynamic nature of many of these processes which depend on the interaction between time-dependent processes including advection, diffusion and chemical reaction. To understand this interplay, and to move away from a purely equilibrium view, requires the integration of computational thermodynamics and fluid mechanics. A key aspect of doing this is the treatment of chemical reactions as time-dependent, irreversible processes. Such a development is integral to understanding a host of petrological questions from the open system evolution of magma chambers to the dynamics of melt migration beneath mid-ocean ridges and flux melting of the mantle wedge in subduction zones. A simple thermodynamically consistent reactive model is developed that can be integrated with conservation equations for mass, momentum and energy. The model rests on the thermodynamic characterization of an independent set of reactions and has the advantage of being completely general and easily extensible to systems comprising multiple solid and liquid phases. The underlying theory is described in detail in another contribution in this session. Here we apply the framework to experimentally constrained simple systems of petrological interest including the fo-qz binary and the fo-qz-k2o ternary. These systems contain a variety of phase topologies including eutectic and peritectic reactions. As the model allows for the seamless exhaustion and stabilization of phases, we can explore the effect that these discontinuous changes have on the compositional and dynamic evolution of the system. To do this we track how the systems respond to sudden changes in intensive variables that perturb them from equilibrium. Such changes are rife in crustal magmatic systems. Simulations for decompression melting are also run to explore the interplay between reactive and advective fluxes. Buffering between the multiple reactions can result in surprising reaction paths highlighting that micro-mechanics could play a significant role in magmatic evolution. By building up the complexity of the problems gradually, we develop an intuition for the effect of model choices including the kinetic law and the set of reactions used.

Modelling of the reactive transport for rock salt-brine in geological repository systems based on improved thermodynamic database (Invited)

NASA Astrophysics Data System (ADS)

Müller, W.; Alkan, H.; Xie, M.; Moog, H.; Sonnenthal, E. L.

2009-12-01

The release and migration of toxic contaminants from the disposed wastes is one of the main issues in long-term safety assessment of geological repositories. In the engineered and geological barriers around the nuclear waste emplacements chemical interactions between the components of the system may affect the isolation properties considerably. As the chemical issues change the transport properties in the near and far field of a nuclear repository, modelling of the transport should also take the chemistry into account. The reactive transport modelling consists of two main components: a code that combines the possible chemical reactions with thermo-hydrogeological processes interactively and a thermodynamic databank supporting the required parameters for the calculation of the chemical reactions. In the last decade many thermo-hydrogeological codes were upgraded to include the modelling of the chemical processes. TOUGHREACT is one of these codes. This is an extension of the well known simulator TOUGH2 for modelling geoprocesses. The code is developed by LBNL (Lawrence Berkeley National Laboratory, Univ. of California) for the simulation of the multi-phase transport of gas and liquid in porous media including heat transfer. After the release of its first version in 1998, this code has been applied and improved many times in conjunction with considerations for nuclear waste emplacement. A recent version has been extended to calculate ion activities in concentrated salt solutions applying the Pitzer model. In TOUGHREACT, the incorporated equation of state module ECO2N is applied as the EOS module for non-isothermal multiphase flow in a fluid system of H2O-NaCl-CO2. The partitioning of H2O and CO2 between liquid and gas phases is modelled as a function of temperature, pressure, and salinity. This module is applicable for waste repositories being expected to generate or having originally CO2 in the fluid system. The enhanced TOUGHREACT uses an EQ3/6-formatted database for both Pitzer ion-interaction parameters and thermodynamic equilibrium constants. The reliability of the parameters is as important as the accuracy of the modelling tool. For this purpose the project THEREDA (www.thereda.de)was set up. The project aims at a comprehensive and internally consistent thermodynamic reference database for geochemical modelling of near and far-field processes occurring in repositories for radioactive wastes in various host rock formations. In the framework of the project all data necessary to perform thermodynamic equilibrium calculations for elevated temperature in the system of oceanic salts are under revision, and it is expected that related data will be available for download by 2010-03. In this paper the geochemical issues that can play an essential role for the transport of radioactive contaminants within and around waste repositories are discussed. Some generic calculations are given to illustrate the geochemical interactions and their probable effects on the transport properties around HLW emplacements and on CO2 generating and/or containing repository systems.

Enhancing the Effectiveness of Carbon Dioxide Flooding by Managing Asphaltene Precipitation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Deo, Milind D.

2002-02-21

This project was undertaken to understand fundamental aspects of carbon dioxide (CO2) induced asphaltene precipitation. Oil and asphaltene samples from the Rangely field in Colorado were used for most of the project. The project consisted of pure component and high-pressure, thermodynamic experiments, thermodynamic modeling, kinetic experiments and modeling, targeted corefloods and compositional modeling.

Liquid state isomorphism, Rosenfeld-Tarazona temperature scaling, and Riemannian thermodynamic geometry.

PubMed

Mausbach, Peter; Köster, Andreas; Vrabec, Jadran

2018-05-01

Aspects of isomorph theory, Rosenfeld-Tarazona temperature scaling, and thermodynamic geometry are comparatively discussed on the basis of the Lennard-Jones potential. The first two approaches approximate the high-density fluid state well when the repulsive interparticle interactions become dominant, which is typically the case close to the freezing line. However, previous studies of Rosenfeld-Tarazona scaling for the isochoric heat capacity and its relation to isomorph theory reveal deviations for the temperature dependence. It turns out that a definition of a state region in which repulsive interactions dominate is required for achieving consistent results. The Riemannian thermodynamic scalar curvature R allows for such a classification, indicating predominantly repulsive interactions by R>0. An analysis of the isomorphic character of the freezing line and the validity of Rosenfeld-Tarazona temperature scaling show that these approaches are consistent only in a small state region.

Numerical Predictions of Damage and Failure in Carbon Fiber Reinforced Laminates Using a Thermodynamically-Based Work Potential Theory

NASA Technical Reports Server (NTRS)

Pineda, Evan Jorge; Waas, Anthony M.

2013-01-01

A thermodynamically-based work potential theory for modeling progressive damage and failure in fiber-reinforced laminates is presented. The current, multiple-internal state variable (ISV) formulation, referred to as enhanced Schapery theory (EST), utilizes separate ISVs for modeling the effects of damage and failure. Consistent characteristic lengths are introduced into the formulation to govern the evolution of the failure ISVs. Using the stationarity of the total work potential with respect to each ISV, a set of thermodynamically consistent evolution equations for the ISVs are derived. The theory is implemented into a commercial finite element code. The model is verified against experimental results from two laminated, T800/3900-2 panels containing a central notch and different fiber-orientation stacking sequences. Global load versus displacement, global load versus local strain gage data, and macroscopic failure paths obtained from the models are compared against the experimental results.

Generalized Dynamic Equations Related to Condensation and Freezing Processes

NASA Astrophysics Data System (ADS)

Wang, Xingrong; Huang, Yong

2018-01-01

The generalized thermodynamic equation related to condensation and freezing processes was derived by introducing the condensation and freezing probability function into the dynamic framework based on the statistical thermodynamic fluctuation theory. As a result, the physical mechanism of some weather phenomena covered by using δ(0,1) can in turn be studied and uncovered. From the generalized dynamic equations, the tendency equation of the generalized potential vorticity (GPV) is derived. From the discussion of tendency equation of GPV, in some very thin transitional areas, GPV is found nonconserved because of the introduction of the condensation and freezing probability function, even in frictionless and moist adiabatic air motion.

Kinetics and thermodynamics of exonuclease-deficient DNA polymerases

NASA Astrophysics Data System (ADS)

Gaspard, Pierre

2016-04-01

A kinetic theory is developed for exonuclease-deficient DNA polymerases, based on the experimental observation that the rates depend not only on the newly incorporated nucleotide, but also on the previous one, leading to the growth of Markovian DNA sequences from a Bernoullian template. The dependencies on nucleotide concentrations and template sequence are explicitly taken into account. In this framework, the kinetic and thermodynamic properties of DNA replication, in particular, the mean growth velocity, the error probability, and the entropy production are calculated analytically in terms of the rate constants and the concentrations. Theory is compared with numerical simulations for the DNA polymerases of T7 viruses and human mitochondria.

Thermodynamic properties of fullerite C70

NASA Astrophysics Data System (ADS)

Rekhviashvili, S. Sh.

2017-08-01

A new expression for the isochoric heat capacity and the equation of state of fullerite C70 are obtained in the framework of a quantum-statistical method. Analogs of the Debye law and Dulong-Petit law for this fullerite are formulated. Fullerene C70 molecules are modeled by isotropic quantum oscillators under the assumption that their nonsphericity weakly influences the thermodynamic properties of the condensed phase. The intramolecular oscillations of carbon atoms are described using the Debye theory and the cold contribution to the free energy of fullerite is calculated using the Lennard-Jones pair potential for fullerene molecules. A comparison of the proposed theory to experiment shows good agreement.

The first principles study of elastic and thermodynamic properties of ZnSe

NASA Astrophysics Data System (ADS)

Khatta, Swati; Kaur, Veerpal; Tripathi, S. K.; Prakash, Satya

2018-05-01

The elastic and thermodynamic properties of ZnSe are investigated using thermo_pw package implemented in Quantum espresso code within the framework of density functional theory. The pseudopotential method within the local density approximation is used for the exchange-correlation potential. The physical parameters of ZnSe bulk modulus and shear modulus, anisotropy factor, Young's modulus, Poisson's ratio, Pugh's ratio and Frantsevich's ratio are calculated. The sound velocity and Debye temperature are obtained from elastic constant calculations. The Helmholtz free energy and internal energy of ZnSe are also calculated. The results are compared with available theoretical calculations and experimental data.

Quantum work and the thermodynamic cost of quantum measurements

DOE PAGES

Deffner, Sebastian; Paz, Juan Pablo; Zurek, Wojciech H.

2016-07-07

Quantum work is usually determined from two projective measurements of the energy at the beginning and at the end of a thermodynamic process. However, this paradigm cannot be considered thermodynamically consistent as it does not account for the thermodynamic cost of these measurements. To remedy this conceptual inconsistency we introduce a paradigm that relies only on the expected change of the average energy given the initial energy eigenbasis. In particular, we completely omit quantum measurements in the definition of quantum work, and hence quantum work is identified as a thermodynamic quantity of only the system. As main results we derivemore » a modified quantum Jarzynski equality and a sharpened maximum work theorem in terms of the information free energy. Lastly, a comparison of our results with the standard approach allows one to quantify the informational cost of projective measurements.« less

Liquid Methane Testing With a Large-Scale Spray Bar Thermodynamic Vent System

NASA Technical Reports Server (NTRS)

Hastings, L. J.; Bolshinskiy, L. G.; Hedayat, A.; Flachbart, R. H.; Sisco, J. D.; Schnell. A. R.

2014-01-01

NASA's Marshall Space Flight Center conducted liquid methane testing in November 2006 using the multipurpose hydrogen test bed outfitted with a spray bar thermodynamic vent system (TVS). The basic objective was to identify any unusual or unique thermodynamic characteristics associated with densified methane that should be considered in the design of space-based TVSs. Thirteen days of testing were performed with total tank heat loads ranging from 720 to 420 W at a fill level of approximately 90%. It was noted that as the fluid passed through the Joule-Thompson expansion, thermodynamic conditions consistent with the pervasive presence of metastability were indicated. This Technical Publication describes conditions that correspond with metastability and its detrimental effects on TVS performance. The observed conditions were primarily functions of methane densification and helium pressurization; therefore, assurance must be provided that metastable conditions have been circumvented in future applications of thermodynamic venting to in-space methane storage.

Analysis of the Glass-Forming Ability of Fe-Er Alloys, Based on Thermodynamic Modeling

NASA Astrophysics Data System (ADS)

Arutyunyan, N. A.; Zaitsev, A. I.; Dunaev, S. F.; Kalmykov, K. B.; El'nyakov, D. D.; Shaposhnikov, N. G.

2018-05-01

The Fe-Er phase diagram and thermodynamic properties of all its phases are assessed by means of self-consistent analysis. To refine the data on phase equilibria in the Fe-Er system, an investigation is performed in the 10-40 at % range of Er concentrations. The temperature-concentration dependences of the thermodynamic properties of a melt are presented using the model of ideal associated solutions. Thermodynamic parameters of each phase are obtained, and the calculated results are in agreement with available experimental data. The correlation between the thermodynamic properties of liquid Fe-Er alloys and their tendency toward amorphization are studied. It is shown that compositions of amorphous alloys prepared by melt quenching coincide with the ranges of concentration with the predominance of Fe3Er and FeEr2 associative groups that have large negative entropies of formation.

Thermodynamic properties for arsenic minerals and aqueous species

USGS Publications Warehouse

Nordstrom, D. Kirk; Majzlan, Juraj; Königsberger, Erich; Bowell, Robert J.; Alpers, Charles N.; Jamieson, Heather E.; Nordstrom, D. Kirk; Majzlan, Juraj

2014-01-01

Quantitative geochemical calculations are not possible without thermodynamic databases and considerable advances in the quantity and quality of these databases have been made since the early days of Lewis and Randall (1923), Latimer (1952), and Rossini et al. (1952). Oelkers et al. (2009) wrote, “The creation of thermodynamic databases may be one of the greatest advances in the field of geochemistry of the last century.” Thermodynamic data have been used for basic research needs and for a countless variety of applications in hazardous waste management and policy making (Zhu and Anderson 2002; Nordstrom and Archer 2003; Bethke 2008; Oelkers and Schott 2009). The challenge today is to evaluate thermodynamic data for internal consistency, to reach a better consensus of the most reliable properties, to determine the degree of certainty needed for geochemical modeling, and to agree on priorities for further measurements and evaluations.

Statistical thermodynamics of clustered populations.

PubMed

Matsoukas, Themis

2014-08-01

We present a thermodynamic theory for a generic population of M individuals distributed into N groups (clusters). We construct the ensemble of all distributions with fixed M and N, introduce a selection functional that embodies the physics that governs the population, and obtain the distribution that emerges in the scaling limit as the most probable among all distributions consistent with the given physics. We develop the thermodynamics of the ensemble and establish a rigorous mapping to regular thermodynamics. We treat the emergence of a so-called giant component as a formal phase transition and show that the criteria for its emergence are entirely analogous to the equilibrium conditions in molecular systems. We demonstrate the theory by an analytic model and confirm the predictions by Monte Carlo simulation.

The second laws of quantum thermodynamics.

PubMed

Brandão, Fernando; Horodecki, Michał; Ng, Nelly; Oppenheim, Jonathan; Wehner, Stephanie

2015-03-17

The second law of thermodynamics places constraints on state transformations. It applies to systems composed of many particles, however, we are seeing that one can formulate laws of thermodynamics when only a small number of particles are interacting with a heat bath. Is there a second law of thermodynamics in this regime? Here, we find that for processes which are approximately cyclic, the second law for microscopic systems takes on a different form compared to the macroscopic scale, imposing not just one constraint on state transformations, but an entire family of constraints. We find a family of free energies which generalize the traditional one, and show that they can never increase. The ordinary second law relates to one of these, with the remainder imposing additional constraints on thermodynamic transitions. We find three regimes which determine which family of second laws govern state transitions, depending on how cyclic the process is. In one regime one can cause an apparent violation of the usual second law, through a process of embezzling work from a large system which remains arbitrarily close to its original state. These second laws are relevant for small systems, and also apply to individual macroscopic systems interacting via long-range interactions. By making precise the definition of thermal operations, the laws of thermodynamics are unified in this framework, with the first law defining the class of operations, the zeroth law emerging as an equivalence relation between thermal states, and the remaining laws being monotonicity of our generalized free energies.

The second laws of quantum thermodynamics

PubMed Central

Brandão, Fernando; Horodecki, Michał; Ng, Nelly; Oppenheim, Jonathan; Wehner, Stephanie

2015-01-01

The second law of thermodynamics places constraints on state transformations. It applies to systems composed of many particles, however, we are seeing that one can formulate laws of thermodynamics when only a small number of particles are interacting with a heat bath. Is there a second law of thermodynamics in this regime? Here, we find that for processes which are approximately cyclic, the second law for microscopic systems takes on a different form compared to the macroscopic scale, imposing not just one constraint on state transformations, but an entire family of constraints. We find a family of free energies which generalize the traditional one, and show that they can never increase. The ordinary second law relates to one of these, with the remainder imposing additional constraints on thermodynamic transitions. We find three regimes which determine which family of second laws govern state transitions, depending on how cyclic the process is. In one regime one can cause an apparent violation of the usual second law, through a process of embezzling work from a large system which remains arbitrarily close to its original state. These second laws are relevant for small systems, and also apply to individual macroscopic systems interacting via long-range interactions. By making precise the definition of thermal operations, the laws of thermodynamics are unified in this framework, with the first law defining the class of operations, the zeroth law emerging as an equivalence relation between thermal states, and the remaining laws being monotonicity of our generalized free energies. PMID:25675476

Acid Gas Stability of Zeolitic Imidazolate Frameworks: Generalized Kinetic and Thermodynamic Characteristics

DOE PAGES

Bhattacharyya, Souryadeep; Han, Rebecca; Kim, Wun -Gwi; ...

2018-05-29

Here, acid gases such as SO 2 and CO 2 are present in many environments in which the use of nanoporous metal-organic frameworks (MOFs) is envisaged. Among metal-organic frameworks, zeolitic imidazolate frameworks (ZIFs) have been extensively explored as membranes or adsorbents. However, there is little systematic knowledge of the effects of acid gas exposure on the structure of ZIFs, in particular the mechanistic aspects of ZIF degradation by acid gases as well as the effects of ZIF crystal topology and linker composition on their stability. Here we present a generalized and quantitative investigation of the kinetic and thermodynamic acid gasmore » stability of a diverse range of ZIF materials. The stability of 16 ZIFs (of SOD, RHO, ANA, and GME topologies) under different environments – humid air, liquid water, and acid gases CO 2 and SO 2 (dry, humid, and aqueous) – are investigated by a suite of experimental and computational methods. The kinetics of ZIF degradation under exposure to humid SO 2 is studied in detail, and effective rate constants for acid gas degradation of ZIFs are reported for the first time. Remarkably, the kinetics of degradation of the diverse ZIFs correlate strongly with the linker pKa and ZIF water adsorption in a manner contrary to that expected from previous predictions in the literature. Furthermore, we find that the material ZIF-71 (RHO topology) shows much higher stability relative to the other ZIFs in humid SO 2 and CO 2 environments.« less

Acid Gas Stability of Zeolitic Imidazolate Frameworks: Generalized Kinetic and Thermodynamic Characteristics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bhattacharyya, Souryadeep; Han, Rebecca; Kim, Wun -Gwi

Here, acid gases such as SO 2 and CO 2 are present in many environments in which the use of nanoporous metal-organic frameworks (MOFs) is envisaged. Among metal-organic frameworks, zeolitic imidazolate frameworks (ZIFs) have been extensively explored as membranes or adsorbents. However, there is little systematic knowledge of the effects of acid gas exposure on the structure of ZIFs, in particular the mechanistic aspects of ZIF degradation by acid gases as well as the effects of ZIF crystal topology and linker composition on their stability. Here we present a generalized and quantitative investigation of the kinetic and thermodynamic acid gasmore » stability of a diverse range of ZIF materials. The stability of 16 ZIFs (of SOD, RHO, ANA, and GME topologies) under different environments – humid air, liquid water, and acid gases CO 2 and SO 2 (dry, humid, and aqueous) – are investigated by a suite of experimental and computational methods. The kinetics of ZIF degradation under exposure to humid SO 2 is studied in detail, and effective rate constants for acid gas degradation of ZIFs are reported for the first time. Remarkably, the kinetics of degradation of the diverse ZIFs correlate strongly with the linker pKa and ZIF water adsorption in a manner contrary to that expected from previous predictions in the literature. Furthermore, we find that the material ZIF-71 (RHO topology) shows much higher stability relative to the other ZIFs in humid SO 2 and CO 2 environments.« less

Stochastic thermodynamics across scales: Emergent inter-attractoral discrete Markov jump process and its underlying continuous diffusion

NASA Astrophysics Data System (ADS)

Santillán, Moisés; Qian, Hong

2013-01-01

We investigate the internal consistency of a recently developed mathematical thermodynamic structure across scales, between a continuous stochastic nonlinear dynamical system, i.e., a diffusion process with Langevin and Fokker-Planck equations, and its emergent discrete, inter-attractoral Markov jump process. We analyze how the system’s thermodynamic state functions, e.g. free energy F, entropy S, entropy production ep, free energy dissipation Ḟ, etc., are related when the continuous system is described with coarse-grained discrete variables. It is shown that the thermodynamics derived from the underlying, detailed continuous dynamics gives rise to exactly the free-energy representation of Gibbs and Helmholtz. That is, the system’s thermodynamic structure is the same as if one only takes a middle road and starts with the natural discrete description, with the corresponding transition rates empirically determined. By natural we mean in the thermodynamic limit of a large system, with an inherent separation of time scales between inter- and intra-attractoral dynamics. This result generalizes a fundamental idea from chemistry, and the theory of Kramers, by incorporating thermodynamics: while a mechanical description of a molecule is in terms of continuous bond lengths and angles, chemical reactions are phenomenologically described by a discrete representation, in terms of exponential rate laws and a stochastic thermodynamics.

On the representability problem and the physical meaning of coarse-grained models

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wagner, Jacob W.; Dama, James F.; Durumeric, Aleksander E. P.

2016-07-28

In coarse-grained (CG) models where certain fine-grained (FG, i.e., atomistic resolution) observables are not directly represented, one can nonetheless identify indirect the CG observables that capture the FG observable’s dependence on CG coordinates. Often, in these cases it appears that a CG observable can be defined by analogy to an all-atom or FG observable, but the similarity is misleading and significantly undermines the interpretation of both bottom-up and top-down CG models. Such problems emerge especially clearly in the framework of the systematic bottom-up CG modeling, where a direct and transparent correspondence between FG and CG variables establishes precise conditions formore » consistency between CG observables and underlying FG models. Here we present and investigate these representability challenges and illustrate them via the bottom-up conceptual framework for several simple analytically tractable polymer models. The examples provide special focus on the observables of configurational internal energy, entropy, and pressure, which have been at the root of controversy in the CG literature, as well as discuss observables that would seem to be entirely missing in the CG representation but can nonetheless be correlated with CG behavior. Though we investigate these problems in the framework of systematic coarse-graining, the lessons apply to top-down CG modeling also, with crucial implications for simulation at constant pressure and surface tension and for the interpretations of structural and thermodynamic correlations for comparison to experiment.« less

Quantum thermodynamic cycles and quantum heat engines. II.

PubMed

Quan, H T

2009-04-01

We study the quantum-mechanical generalization of force or pressure, and then we extend the classical thermodynamic isobaric process to quantum-mechanical systems. Based on these efforts, we are able to study the quantum version of thermodynamic cycles that consist of quantum isobaric processes, such as the quantum Brayton cycle and quantum Diesel cycle. We also consider the implementation of the quantum Brayton cycle and quantum Diesel cycle with some model systems, such as single particle in a one-dimensional box and single-mode radiation field in a cavity. These studies lay the microscopic (quantum-mechanical) foundation for Szilard-Zurek single-molecule engine.

Vapor-liquid equilibrium thermodynamics of N2 + CH4 - Model and Titan applications

NASA Technical Reports Server (NTRS)

Thompson, W. R.; Zollweg, John A.; Gabis, David H.

1992-01-01

A thermodynamic model is presented for vapor-liquid equilibrium in the N2 + CH4 system, which is implicated in calculations of the Titan tropospheric clouds' vapor-liquid equilibrium thermodynamics. This model imposes constraints on the consistency of experimental equilibrium data, and embodies temperature effects by encompassing enthalpy data; it readily calculates the saturation criteria, condensate composition, and latent heat for a given pressure-temperature profile of the Titan atmosphere. The N2 content of condensate is about half of that computed from Raoult's law, and about 30 percent greater than that computed from Henry's law.

Towards the rational design of the Py5-ligand framework for ruthenium-based water oxidation catalysts.

PubMed

Schilling, Mauro; Böhler, Michael; Luber, Sandra

2018-05-21

In order to rationally design water oxidation catalysts (WOCs), an in-depth understanding of the reaction mechanism is essential. In this study we showcase the complexity of catalytic water oxidation, by elucidating how modifications of the pentapyridyl (Py5) ligand-framework influence the thermodynamics and kinetics of the process. In the reaction mechanism the pyridine-water exchange was identified as a key reaction which appears to determine the reactivity of the Py5-WOCs. Exploring the capabilities of in silico design we show which modifications of the ligand framework appear promising when attempting to improve the catalytic performance of WOCs derived from Py5.

Noether charge, black hole volume, and complexity

NASA Astrophysics Data System (ADS)

Couch, Josiah; Fischler, Willy; Nguyen, Phuc H.

2017-03-01

In this paper, we study the physical significance of the thermodynamic volumes of AdS black holes using the Noether charge formalism of Iyer and Wald. After applying this formalism to study the extended thermodynamics of a few examples, we discuss how the extended thermodynamics interacts with the recent complexity = action proposal of Brown et al. (CA-duality). We, in particular, discover that their proposal for the late time rate of change of complexity has a nice decomposition in terms of thermodynamic quantities reminiscent of the Smarr relation. This decomposition strongly suggests a geometric, and via CA-duality holographic, interpretation for the thermodynamic volume of an AdS black hole. We go on to discuss the role of thermodynamics in complexity = action for a number of black hole solutions, and then point out the possibility of an alternate proposal, which we dub "complexity = volume 2.0". In this alternate proposal the complexity would be thought of as the spacetime volume of the Wheeler-DeWitt patch. Finally, we provide evidence that, in certain cases, our proposal for complexity is consistent with the Lloyd bound whereas CA-duality is not.

A mathematical model of sentimental dynamics accounting for marital dissolution.

PubMed

Rey, José-Manuel

2010-03-31

Marital dissolution is ubiquitous in western societies. It poses major scientific and sociological problems both in theoretical and therapeutic terms. Scholars and therapists agree on the existence of a sort of second law of thermodynamics for sentimental relationships. Effort is required to sustain them. Love is not enough. Building on a simple version of the second law we use optimal control theory as a novel approach to model sentimental dynamics. Our analysis is consistent with sociological data. We show that, when both partners have similar emotional attributes, there is an optimal effort policy yielding a durable happy union. This policy is prey to structural destabilization resulting from a combination of two factors: there is an effort gap because the optimal policy always entails discomfort and there is a tendency to lower effort to non-sustaining levels due to the instability of the dynamics. These mathematical facts implied by the model unveil an underlying mechanism that may explain couple disruption in real scenarios. Within this framework the apparent paradox that a union consistently planned to last forever will probably break up is explained as a mechanistic consequence of the second law.

Modelling DNA origami self-assembly at the domain level.

PubMed

Dannenberg, Frits; Dunn, Katherine E; Bath, Jonathan; Kwiatkowska, Marta; Turberfield, Andrew J; Ouldridge, Thomas E

2015-10-28

We present a modelling framework, and basic model parameterization, for the study of DNA origami folding at the level of DNA domains. Our approach is explicitly kinetic and does not assume a specific folding pathway. The binding of each staple is associated with a free-energy change that depends on staple sequence, the possibility of coaxial stacking with neighbouring domains, and the entropic cost of constraining the scaffold by inserting staple crossovers. A rigorous thermodynamic model is difficult to implement as a result of the complex, multiply connected geometry of the scaffold: we present a solution to this problem for planar origami. Coaxial stacking of helices and entropic terms, particularly when loop closure exponents are taken to be larger than those for ideal chains, introduce interactions between staples. These cooperative interactions lead to the prediction of sharp assembly transitions with notable hysteresis that are consistent with experimental observations. We show that the model reproduces the experimentally observed consequences of reducing staple concentration, accelerated cooling, and absent staples. We also present a simpler methodology that gives consistent results and can be used to study a wider range of systems including non-planar origami.

Modelling DNA origami self-assembly at the domain level

NASA Astrophysics Data System (ADS)

Dannenberg, Frits; Dunn, Katherine E.; Bath, Jonathan; Kwiatkowska, Marta; Turberfield, Andrew J.; Ouldridge, Thomas E.

2015-10-01

We present a modelling framework, and basic model parameterization, for the study of DNA origami folding at the level of DNA domains. Our approach is explicitly kinetic and does not assume a specific folding pathway. The binding of each staple is associated with a free-energy change that depends on staple sequence, the possibility of coaxial stacking with neighbouring domains, and the entropic cost of constraining the scaffold by inserting staple crossovers. A rigorous thermodynamic model is difficult to implement as a result of the complex, multiply connected geometry of the scaffold: we present a solution to this problem for planar origami. Coaxial stacking of helices and entropic terms, particularly when loop closure exponents are taken to be larger than those for ideal chains, introduce interactions between staples. These cooperative interactions lead to the prediction of sharp assembly transitions with notable hysteresis that are consistent with experimental observations. We show that the model reproduces the experimentally observed consequences of reducing staple concentration, accelerated cooling, and absent staples. We also present a simpler methodology that gives consistent results and can be used to study a wider range of systems including non-planar origami.

A Mathematical Model of Sentimental Dynamics Accounting for Marital Dissolution

PubMed Central

Rey, José-Manuel

2010-01-01

Background Marital dissolution is ubiquitous in western societies. It poses major scientific and sociological problems both in theoretical and therapeutic terms. Scholars and therapists agree on the existence of a sort of second law of thermodynamics for sentimental relationships. Effort is required to sustain them. Love is not enough. Methodology/Principal Findings Building on a simple version of the second law we use optimal control theory as a novel approach to model sentimental dynamics. Our analysis is consistent with sociological data. We show that, when both partners have similar emotional attributes, there is an optimal effort policy yielding a durable happy union. This policy is prey to structural destabilization resulting from a combination of two factors: there is an effort gap because the optimal policy always entails discomfort and there is a tendency to lower effort to non-sustaining levels due to the instability of the dynamics. Conclusions/Significance These mathematical facts implied by the model unveil an underlying mechanism that may explain couple disruption in real scenarios. Within this framework the apparent paradox that a union consistently planned to last forever will probably break up is explained as a mechanistic consequence of the second law. PMID:20360987

A thermodynamically consistent model of the post-translational Kai circadian clock

PubMed Central

Lubensky, David K.; ten Wolde, Pieter Rein

2017-01-01

The principal pacemaker of the circadian clock of the cyanobacterium S. elongatus is a protein phosphorylation cycle consisting of three proteins, KaiA, KaiB and KaiC. KaiC forms a homohexamer, with each monomer consisting of two domains, CI and CII. Both domains can bind and hydrolyze ATP, but only the CII domain can be phosphorylated, at two residues, in a well-defined sequence. While this system has been studied extensively, how the clock is driven thermodynamically has remained elusive. Inspired by recent experimental observations and building on ideas from previous mathematical models, we present a new, thermodynamically consistent, statistical-mechanical model of the clock. At its heart are two main ideas: i) ATP hydrolysis in the CI domain provides the thermodynamic driving force for the clock, switching KaiC between an active conformational state in which its phosphorylation level tends to rise and an inactive one in which it tends to fall; ii) phosphorylation of the CII domain provides the timer for the hydrolysis in the CI domain. The model also naturally explains how KaiA, by acting as a nucleotide exchange factor, can stimulate phosphorylation of KaiC, and how the differential affinity of KaiA for the different KaiC phosphoforms generates the characteristic temporal order of KaiC phosphorylation. As the phosphorylation level in the CII domain rises, the release of ADP from CI slows down, making the inactive conformational state of KaiC more stable. In the inactive state, KaiC binds KaiB, which not only stabilizes this state further, but also leads to the sequestration of KaiA, and hence to KaiC dephosphorylation. Using a dedicated kinetic Monte Carlo algorithm, which makes it possible to efficiently simulate this system consisting of more than a billion reactions, we show that the model can describe a wealth of experimental data. PMID:28296888

Nature of self-diffusion in two-dimensional fluids

NASA Astrophysics Data System (ADS)

Choi, Bongsik; Han, Kyeong Hwan; Kim, Changho; Talkner, Peter; Kidera, Akinori; Lee, Eok Kyun

2017-12-01

Self-diffusion in a two-dimensional simple fluid is investigated by both analytical and numerical means. We investigate the anomalous aspects of self-diffusion in two-dimensional fluids with regards to the mean square displacement, the time-dependent diffusion coefficient, and the velocity autocorrelation function (VACF) using a consistency equation relating these quantities. We numerically confirm the consistency equation by extensive molecular dynamics simulations for finite systems, corroborate earlier results indicating that the kinematic viscosity approaches a finite, non-vanishing value in the thermodynamic limit, and establish the finite size behavior of the diffusion coefficient. We obtain the exact solution of the consistency equation in the thermodynamic limit and use this solution to determine the large time asymptotics of the mean square displacement, the diffusion coefficient, and the VACF. An asymptotic decay law of the VACF resembles the previously known self-consistent form, 1/(t\\sqrt{{ln}t}), however with a rescaled time.

General formalism of local thermodynamics with an example: Quantum Otto engine with a spin-1/2 coupled to an arbitrary spin.

PubMed

Altintas, Ferdi; Müstecaplıoğlu, Özgür E

2015-08-01

We investigate a quantum heat engine with a working substance of two particles, one with a spin-1/2 and the other with an arbitrary spin (spin s), coupled by Heisenberg exchange interaction, and subject to an external magnetic field. The engine operates in a quantum Otto cycle. Work harvested in the cycle and its efficiency are calculated using quantum thermodynamical definitions. It is found that the engine has higher efficiencies at higher spins and can harvest work at higher exchange interaction strengths. The role of exchange coupling and spin s on the work output and the thermal efficiency is studied in detail. In addition, the engine operation is analyzed from the perspective of local work and efficiency. We develop a general formalism to explore local thermodynamics applicable to any coupled bipartite system. Our general framework allows for examination of local thermodynamics even when global parameters of the system are varied in thermodynamic cycles. The generalized definitions of local and cooperative work are introduced by using mean field Hamiltonians. The general conditions for which the global work is not equal to the sum of the local works are given in terms of the covariance of the subsystems. Our coupled spin quantum Otto engine is used as an example of the general formalism.

General formalism of local thermodynamics with an example: Quantum Otto engine with a spin-1 /2 coupled to an arbitrary spin

NASA Astrophysics Data System (ADS)

Altintas, Ferdi; Müstecaplıoǧlu, Ã.-zgür E.

2015-08-01

We investigate a quantum heat engine with a working substance of two particles, one with a spin-1 /2 and the other with an arbitrary spin (spin s ), coupled by Heisenberg exchange interaction, and subject to an external magnetic field. The engine operates in a quantum Otto cycle. Work harvested in the cycle and its efficiency are calculated using quantum thermodynamical definitions. It is found that the engine has higher efficiencies at higher spins and can harvest work at higher exchange interaction strengths. The role of exchange coupling and spin s on the work output and the thermal efficiency is studied in detail. In addition, the engine operation is analyzed from the perspective of local work and efficiency. We develop a general formalism to explore local thermodynamics applicable to any coupled bipartite system. Our general framework allows for examination of local thermodynamics even when global parameters of the system are varied in thermodynamic cycles. The generalized definitions of local and cooperative work are introduced by using mean field Hamiltonians. The general conditions for which the global work is not equal to the sum of the local works are given in terms of the covariance of the subsystems. Our coupled spin quantum Otto engine is used as an example of the general formalism.

Gradient plasticity for thermo-mechanical processes in metals with length and time scales

NASA Astrophysics Data System (ADS)

Voyiadjis, George Z.; Faghihi, Danial

2013-03-01

A thermodynamically consistent framework is developed in order to characterize the mechanical and thermal behavior of metals in small volume and on the fast transient time. In this regard, an enhanced gradient plasticity theory is coupled with the application of a micromorphic approach to the temperature variable. A physically based yield function based on the concept of thermal activation energy and the dislocation interaction mechanisms including nonlinear hardening is taken into consideration in the derivation. The effect of the material microstructural interface between two materials is also incorporated in the formulation with both temperature and rate effects. In order to accurately address the strengthening and hardening mechanisms, the theory is developed based on the decomposition of the mechanical state variables into energetic and dissipative counterparts which endowed the constitutive equations to have both energetic and dissipative gradient length scales for the bulk material and the interface. Moreover, the microstructural interaction effect in the fast transient process is addressed by incorporating two time scales into the microscopic heat equation. The numerical example of thin film on elastic substrate or a single phase bicrystal under uniform tension is addressed here. The effects of individual counterparts of the framework on the thermal and mechanical responses are investigated. The model is also compared with experimental results.

The Hydrothermal Chemistry of Gold, Arsenic, Antimony, Mercury and Silver

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bessinger, Brad; Apps, John A.

2003-03-23

A comprehensive thermodynamic database based on the Helgeson-Kirkham-Flowers (HKF) equation of state was developed for metal complexes in hydrothermal systems. Because this equation of state has been shown to accurately predict standard partial molal thermodynamic properties of aqueous species at elevated temperatures and pressures, this study provides the necessary foundation for future exploration into transport and depositional processes in polymetallic ore deposits. The HKF equation of state parameters for gold, arsenic, antimony, mercury, and silver sulfide and hydroxide complexes were derived from experimental equilibrium constants using nonlinear regression calculations. In order to ensure that the resulting parameters were internally consistent,more » those experiments utilizing incompatible thermodynamic data were re-speciated prior to regression. Because new experimental studies were used to revise the HKF parameters for H2S0 and HS-1, those metal complexes for which HKF parameters had been previously derived were also updated. It was found that predicted thermodynamic properties of metal complexes are consistent with linear correlations between standard partial molal thermodynamic properties. This result allowed assessment of several complexes for which experimental data necessary to perform regression calculations was limited. Oxygen fugacity-temperature diagrams were calculated to illustrate how thermodynamic data improves our understanding of depositional processes. Predicted thermodynamic properties were used to investigate metal transport in Carlin-type gold deposits. Assuming a linear relationship between temperature and pressure, metals are predicted to predominantly be transported as sulfide complexes at a total aqueous sulfur concentration of 0.05 m. Also, the presence of arsenic and antimony mineral phases in the deposits are shown to restrict mineralization within a limited range of chemical conditions. Finally, at a lesser aqueous sulfur concentration of 0.01 m, host rock sulfidation can explain the origin of arsenic and antimony minerals within the paragenetic sequence.« less

Technical Work Plan for: Thermodynamic Database for Chemical Modeling

DOE Office of Scientific and Technical Information (OSTI.GOV)

C.F. Jovecolon

The objective of the work scope covered by this Technical Work Plan (TWP) is to correct and improve the Yucca Mountain Project (YMP) thermodynamic databases, to update their documentation, and to ensure reasonable consistency among them. In addition, the work scope will continue to generate database revisions, which are organized and named so as to be transparent to internal and external users and reviewers. Regarding consistency among databases, it is noted that aqueous speciation and mineral solubility data for a given system may differ according to how solubility was determined, and the method used for subsequent retrieval of thermodynamic parametermore » values from measured data. Of particular concern are the details of the determination of ''infinite dilution'' constants, which involve the use of specific methods for activity coefficient corrections. That is, equilibrium constants developed for a given system for one set of conditions may not be consistent with constants developed for other conditions, depending on the species considered in the chemical reactions and the methods used in the reported studies. Hence, there will be some differences (for example in log K values) between the Pitzer and ''B-dot'' database parameters for the same reactions or species.« less

Phase Equilibrium, Chemical Equilibrium, and a Test of the Third Law: Experiments for Physical Chemistry.

ERIC Educational Resources Information Center

Dannhauser, Walter

1980-01-01

Described is an experiment designed to provide an experimental basis for a unifying point of view (utilizing theoretical framework and chemistry laboratory experiments) for physical chemistry students. Three experiments are described: phase equilibrium, chemical equilibrium, and a test of the third law of thermodynamics. (Author/DS)

Psychological Entropy: A Framework for Understanding Uncertainty-Related Anxiety

ERIC Educational Resources Information Center

Hirsh, Jacob B.; Mar, Raymond A.; Peterson, Jordan B.

2012-01-01

Entropy, a concept derived from thermodynamics and information theory, describes the amount of uncertainty and disorder within a system. Self-organizing systems engage in a continual dialogue with the environment and must adapt themselves to changing circumstances to keep internal entropy at a manageable level. We propose the entropy model of…

The Determination of Heat Capacity Ratios in a Simple Open System

ERIC Educational Resources Information Center

Holden, Glen L.

2007-01-01

A virtually closed system is treated as open and compared to known results. The classic experiment of Clement and Desormes provides the conceptual framework for this open system approach in determining the molar heat capacity ratios, lambda. This alternate view, extends the theoretical treatment beyond the first law of thermodynamics for closed…

Vapor-Liquid Equilibria Using the Gibbs Energy and the Common Tangent Plane Criterion

ERIC Educational Resources Information Center

Olaya, Maria del Mar; Reyes-Labarta, Juan A.; Serrano, Maria Dolores; Marcilla, Antonio

2010-01-01

Phase thermodynamics is often perceived as a difficult subject with which many students never become fully comfortable. The Gibbsian geometrical framework can help students to gain a better understanding of phase equilibria. An exercise to interpret the vapor-liquid equilibrium of a binary azeotropic mixture, using the equilibrium condition based…

Arrow of Time: Metaphorical Construals of Entropy and the Second Law of Thermodynamics

ERIC Educational Resources Information Center

Amin, Tamer G.; Jeppsson, Fredrik; Haglund, Jesper; Stromdahl, Helge

2012-01-01

Various features of scientific discourse have been characterized in the science education literature, and challenges students face in appropriating these features have been explored. Using the framework of conceptual metaphor, this paper sought to identify explicit and implicit metaphors in pedagogical texts dealing with the concept of entropy and…

Ab-initio thermodynamic and elastic properties of AlNi and AlNi3 intermetallic compounds

NASA Astrophysics Data System (ADS)

Yalameha, Shahram; Vaez, Aminollah

2018-04-01

In this paper, thermodynamic and elastic properties of the AlNi and AlNi3 were investigated using density functional theory (DFT). The full-potential linearized augmented plane-wave (APW) in the framework of the generalized gradient approximation as used as implemented in the Wien2k package. The temperature dependence of thermal expansion coefficient, bulk modulus and heat capacity in a wide range of temperature (0-1600 K) were investigated. The calculated elastic properties of the compounds show that both intermetallic compounds of AlNi and AlNi3 have surprisingly negative Poisson’s ratio (NPR). The results were compared with other experimental and computational data.

Influence of electric field on the hydrogen bond network of methanol.

PubMed

Suresh, S J; Prabhu, Arun Laxman; Arora, Abhinav

2007-04-07

The understanding of the structure of hydrogen (H) bonding liquids in electric (E) fields is important in the context of several areas of research, such as electrochemistry, surface science, and thermodynamics of electrolyte solutions. We had earlier presented a general thermodynamic framework for this purpose, and had shown that the application of E field enhances H-bond interactions among water molecules. The present investigation with methanol suggests a different result-the H-bond structure, as indicated by the average number of H bonds per molecule, goes through a maxima with increasing field strength. This result is explained based on the symmetry in the location of the H-bonding sites in the two types of molecules.

Aspects of noncommutative (1+1)-dimensional black holes

NASA Astrophysics Data System (ADS)

Mureika, Jonas R.; Nicolini, Piero

2011-08-01

We present a comprehensive analysis of the spacetime structure and thermodynamics of (1+1)-dimensional black holes in a noncommutative framework. It is shown that a wider variety of solutions are possible than the commutative case considered previously in the literature. As expected, the introduction of a minimal length θ cures singularity pathologies that plague the standard two-dimensional general relativistic case, where the latter solution is recovered at large length scales. Depending on the choice of input parameters (black hole mass M, cosmological constant Λ, etc.), black hole solutions with zero, up to six, horizons are possible. The associated thermodynamics allows for the either complete evaporation, or the production of black hole remnants.

An analysis of science content and representations in introductory college physics textbooks and multimodal learning resources

NASA Astrophysics Data System (ADS)

Donnelly, Suzanne M.

This study features a comparative descriptive analysis of the physics content and representations surrounding the first law of thermodynamics as presented in four widely used introductory college physics textbooks representing each of four physics textbook categories (calculus-based, algebra/trigonometry-based, conceptual, and technical/applied). Introducing and employing a newly developed theoretical framework, multimodal generative learning theory (MGLT), an analysis of the multimodal characteristics of textbook and multimedia representations of physics principles was conducted. The modal affordances of textbook representations were identified, characterized, and compared across the four physics textbook categories in the context of their support of problem-solving. Keywords: college science, science textbooks, multimodal learning theory, thermodynamics, representations

Do the Modified Uncertainty Principle and Polymer Quantization predict same physics?

NASA Astrophysics Data System (ADS)

Majumder, Barun; Sen, Sourav

2012-10-01

In this Letter we study the effects of the Modified Uncertainty Principle as proposed in Ali et al. (2009) [5] in simple quantum mechanical systems and study its thermodynamic properties. We have assumed that the quantum particles follow Maxwell-Boltzmann statistics with no spin. We compare our results with the results found in the GUP and polymer quantum mechanical frameworks. Interestingly we find that the corrected thermodynamic entities are exactly the same compared to the polymer results but the length scale considered has a theoretically different origin. Hence we express the need of further study for an investigation whether these two approaches are conceptually connected in the fundamental level.

Thermodynamic framework for information in nanoscale systems with memory

NASA Astrophysics Data System (ADS)

Arias-Gonzalez, J. Ricardo

2017-11-01

Information is represented by linear strings of symbols with memory that carry errors as a result of their stochastic nature. Proofreading and edition are assumed to improve certainty although such processes may not be effective. Here, we develop a thermodynamic theory for material chains made up of nanoscopic subunits with symbolic meaning in the presence of memory. This framework is based on the characterization of single sequences of symbols constructed under a protocol and is used to derive the behavior of ensembles of sequences similarly constructed. We then analyze the role of proofreading and edition in the presence of memory finding conditions to make revision an effective process, namely, to decrease the entropy of the chain. Finally, we apply our formalism to DNA replication and RNA transcription finding that Watson and Crick hybridization energies with which nucleotides are branched to the template strand during the copying process are optimal to regulate the fidelity in proofreading. These results are important in applications of information theory to a variety of solid-state physical systems and other biomolecular processes.

Digital Alchemy for Materials Design: Colloids and Beyond

NASA Astrophysics Data System (ADS)

van Anders, Greg; Klotsa, Daphne; Karas, Andrew; Dodd, Paul; Glotzer, Sharon

Starting with the early alchemists, a holy grail of science has been to make desired materials by manipulating basic building blocks. Building blocks that show promise for assembling new complex materials can be synthesized at the nanoscale with attributes that would astonish the ancient alchemists in their versatility. However, this versatility means that connecting building-block attributes to bulk structure is both necessary for rationally engineering materials and difficult because building block attributes can be altered in many ways. We show how to exploit the malleability of colloidal nanoparticle ``elements'' to quantitatively link building-block attributes to bulk structure through a statistical thermodynamic framework we term ``digital alchemy''. We use this framework to optimize building blocks for a given target structure and to determine which building-block attributes are most important to control for self-assembly, through a set of novel thermodynamic response functions. We thereby establish direct links between the attributes of colloidal building blocks and the bulk structures they form. Moreover, our results give concrete solutions to the more general conceptual challenge of optimizing emergent behaviors in nature and can be applied to other types of matter.

Phase Transitions in Finite Systems

NASA Astrophysics Data System (ADS)

Chomaz, Philippe; Gulminelli, Francesca

In this series of lectures we will first review the general theory of phase transition in the framework of information theory and briefly address some of the well known mean field solutions of three dimensional problems. The theory of phase transitions in finite systems will then be discussed, with a special emphasis to the conceptual problems linked to a thermodynamical description for small, short-lived, open systems as metal clusters and data samples coming from nuclear collisions. The concept of negative heat capacity developed in the early seventies in the context of self-gravitating systems will be reinterpreted in the general framework of convexity anomalies of thermostatistical potentials. The connection with the distribution of the order parameter will lead us to a definition of first order phase transitions in finite systems based on topology anomalies of the event distribution in the space of observations. Finally a careful study of the thermodynamical limit will provide a bridge with the standard theory of phase transitions and show that in a wide class of physical situations the different statistical ensembles are irreducibly inequivalent.

Regulation of star formation in giant galaxies by precipitation, feedback and conduction.

PubMed

Voit, G M; Donahue, M; Bryan, G L; McDonald, M

2015-03-12

The Universe's largest galaxies reside at the centres of galaxy clusters and are embedded in hot gas that, if left undisturbed, would cool quickly and create many more new stars than are actually observed. Cooling can be regulated by feedback from accretion of cooling gas onto the central black hole, but requires an accretion rate finely tuned to the thermodynamic state of the hot gas. Theoretical models in which cold clouds precipitate out of the hot gas via thermal instability and accrete onto the black hole exhibit the necessary tuning. Recent observational evidence shows that the abundance of cold gas in the centres of clusters increases rapidly near the predicted threshold for instability. Here we report observations showing that this precipitation threshold extends over a large range in cluster radius, cluster mass and cosmic time. We incorporate the precipitation threshold into a framework of theoretical models for the thermodynamic state of hot gas in galaxy clusters. According to that framework, precipitation regulates star formation in some giant galaxies, while thermal conduction prevents star formation in others if it can compensate for radiative cooling and shut off precipitation.

Thermodynamic framework for information in nanoscale systems with memory.

PubMed

Arias-Gonzalez, J Ricardo

2017-11-28

Information is represented by linear strings of symbols with memory that carry errors as a result of their stochastic nature. Proofreading and edition are assumed to improve certainty although such processes may not be effective. Here, we develop a thermodynamic theory for material chains made up of nanoscopic subunits with symbolic meaning in the presence of memory. This framework is based on the characterization of single sequences of symbols constructed under a protocol and is used to derive the behavior of ensembles of sequences similarly constructed. We then analyze the role of proofreading and edition in the presence of memory finding conditions to make revision an effective process, namely, to decrease the entropy of the chain. Finally, we apply our formalism to DNA replication and RNA transcription finding that Watson and Crick hybridization energies with which nucleotides are branched to the template strand during the copying process are optimal to regulate the fidelity in proofreading. These results are important in applications of information theory to a variety of solid-state physical systems and other biomolecular processes.

Thermodynamic properties of sea air

NASA Astrophysics Data System (ADS)

Feistel, R.; Wright, D. G.; Kretzschmar, H.-J.; Hagen, E.; Herrmann, S.; Span, R.

2010-02-01

Very accurate thermodynamic potential functions are available for fluid water, ice, seawater and humid air covering wide ranges of temperature and pressure conditions. They permit the consistent computation of all equilibrium properties as, for example, required for coupled atmosphere-ocean models or the analysis of observational or experimental data. With the exception of humid air, these potential functions are already formulated as international standards released by the International Association for the Properties of Water and Steam (IAPWS), and have been adopted in 2009 for oceanography by IOC/UNESCO. In this paper, we derive a collection of formulas for important quantities expressed in terms of the thermodynamic potentials, valid for typical phase transitions and composite systems of humid air and water/ice/seawater. Particular attention is given to equilibria between seawater and humid air, referred to as "sea air" here. In a related initiative, these formulas will soon be implemented in a source-code library for easy practical use. The library is primarily aimed at oceanographic applications but will be relevant to air-sea interaction and meteorology as well. The formulas provided are valid for any consistent set of suitable thermodynamic potential functions. Here we adopt potential functions from previous publications in which they are constructed from theoretical laws and empirical data; they are briefly summarized in the appendix. The formulas make use of the full accuracy of these thermodynamic potentials, without additional approximations or empirical coefficients. They are expressed in the temperature scale ITS-90 and the 2008 Reference-Composition Salinity Scale.

Thermodynamic properties of sea air

NASA Astrophysics Data System (ADS)

Feistel, R.; Kretzschmar, H.-J.; Span, R.; Hagen, E.; Wright, D. G.; Herrmann, S.

2009-10-01

Very accurate thermodynamic potential functions are available for fluid water, ice, seawater and humid air covering wide ranges of temperature and pressure conditions. They permit the consistent computation of all equilibrium properties as, for example, required for coupled atmosphere-ocean models or the analysis of observational or experimental data. With the exception of humid air, these potential functions are already formulated as international standards released by the International Association for the Properties of Water and Steam (IAPWS), and have been adopted in 2009 for oceanography by IOC/UNESCO. In this paper, we derive a collection of formulas for important quantities expressed in terms of the thermodynamic potentials, valid for typical phase transitions and composite systems of humid air and water/ice/seawater. Particular attention is given to equilibria between seawater and humid air, referred to as ''sea air'' here. In a related initiative, these formulas will soon be implemented in a source-code library for easy practical use. The library is primarily aimed at oceanographic applications but will be relevant to air-sea interaction and meteorology as well. The formulas provided are valid for any consistent set of suitable thermodynamic potential functions. Here we adopt potential functions from previous publications in which they are constructed from theoretical laws and empirical data; they are briefly summarized in the appendix. The formulas make use of the full accuracy of these thermodynamic potentials, without additional approximations or empirical coefficients. They are expressed in the temperature scale ITS-90 and the 2008 Reference-Composition Salinity Scale.

Quasi-linear versus potential-based formulations of force-flux relations and the GENERIC for irreversible processes: comparisons and examples

NASA Astrophysics Data System (ADS)

Hütter, Markus; Svendsen, Bob

2013-11-01

An essential part in modeling out-of-equilibrium dynamics is the formulation of irreversible dynamics. In the latter, the major task consists in specifying the relations between thermodynamic forces and fluxes. In the literature, mainly two distinct approaches are used for the specification of force-flux relations. On the one hand, quasi-linear relations are employed, which are based on the physics of transport processes and fluctuation-dissipation theorems (de Groot and Mazur in Non-equilibrium thermodynamics, North Holland, Amsterdam, 1962, Lifshitz and Pitaevskii in Physical kinetics. Volume 10, Landau and Lifshitz series on theoretical physics, Pergamon Press, Oxford, 1981). On the other hand, force-flux relations are also often represented in potential form with the help of a dissipation potential (Šilhavý in The mechanics and thermodynamics of continuous media, Springer, Berlin, 1997). We address the question of how these two approaches are related. The main result of this presentation states that the class of models formulated by quasi-linear relations is larger than what can be described in a potential-based formulation. While the relation between the two methods is shown in general terms, it is demonstrated also with the help of three examples. The finding that quasi-linear force-flux relations are more general than dissipation-based ones also has ramifications for the general equation for non-equilibrium reversible-irreversible coupling (GENERIC: e.g., Grmela and Öttinger in Phys Rev E 56:6620-6632, 6633-6655, 1997, Öttinger in Beyond equilibrium thermodynamics, Wiley Interscience Publishers, Hoboken, 2005). This framework has been formulated and used in two different forms, namely a quasi-linear (Öttinger and Grmela in Phys Rev E 56:6633-6655, 1997, Öttinger in Beyond equilibrium thermodynamics, Wiley Interscience Publishers, Hoboken, 2005) and a dissipation potential-based (Grmela in Adv Chem Eng 39:75-129, 2010, Grmela in J Non-Newton Fluid Mech 165:980-986, 2010, Mielke in Continuum Mech Therm 23:233-256, 2011) form, respectively, relating the irreversible evolution to the entropy gradient. It is found that also in the case of GENERIC, the quasi-linear representation encompasses a wider class of phenomena as compared to the dissipation-based formulation. Furthermore, it is found that a potential exists for the irreversible part of the GENERIC if and only if one does for the underlying force-flux relations.

Some general remarks on hyperplasticity modelling and its extension to partially saturated soils

NASA Astrophysics Data System (ADS)

Lei, Xiaoqin; Wong, Henry; Fabbri, Antonin; Bui, Tuan Anh; Limam, Ali

2016-06-01

The essential ideas and equations of classic plasticity and hyperplasticity are successively recalled and compared, in order to highlight their differences and complementarities. The former is based on the mathematical framework proposed by Hill (The mathematical theory of plasticity. Oxford University Press, Oxford, 1950), whereas the latter is founded on the orthogonality hypothesis of Ziegler (An introduction to thermomechanics. Elsevier, North-Holland, 1983). The main drawback of classic plasticity is the possibility of violating the second principle of thermodynamics, while the relative ease to conjecture the yield function in order to approach experimental results is its main advantage. By opposition, the a priori satisfaction of thermodynamic principles constitutes the chief advantage of hyperplasticity theory. Noteworthy is also the fact that this latter approach allows a finer energy partition; in particular, the existence of frozen energy emerges as a natural consequence from its theoretical formulation. On the other hand, the relative difficulty to conjecture an efficient dissipation function to produce accurate predictions is its main drawback. The two theories are thus better viewed as two complementary approaches. Following this comparative study, a methodology to extend the hyperplasticity approach initially developed for dry or saturated materials to the case of partially saturated materials, accounting for interface energies and suction effects, is developed. A particular example based on the yield function of modified Cam-Clay model is then presented. It is shown that the approach developed leads to a model consistent with other existing works.

Early history of extended irreversible thermodynamics (1953-1983): An exploration beyond local equilibrium and classical transport theory

NASA Astrophysics Data System (ADS)

Lebon, G.; Jou, D.

2015-06-01

This paper gives a historical account of the early years (1953-1983) of extended irreversible thermodynamics (EIT). The salient features of this formalism are to upgrade the thermodynamic fluxes of mass, momentum, energy, and others, to the status of independent variables, and to explore the consistency between generalized transport equations and a generalized version of the second law of thermodynamics. This requires going beyond classical irreversible thermodynamics by redefining entropy and entropy flux. EIT provides deeper foundations, closer relations with microscopic formalisms, a wider spectrum of applications, and a more exciting conceptual appeal to non-equilibrium thermodynamics. We first recall the historical contributions by Maxwell, Cattaneo, and Grad on generalized transport equations. A thermodynamic theory wide enough to cope with such transport equations was independently proposed between 1953 and 1983 by several authors, each emphasizing different kinds of problems. In 1983, the first international meeting on this theory took place in Bellaterra (Barcelona). It provided the opportunity for the various authors to meet together for the first time and to discuss the common points and the specific differences of their previous formulations. From then on, a large amount of applications and theoretical confirmations have emerged. From the historical point of view, the emergence of EIT has been an opportunity to revisit the foundations and to open new avenues in thermodynamics, one of the most classical and well consolidated physical theories.

Unlocking Ft: Modeling thermodynamic controls and isotope fractionation factors in nutrient limited environments

NASA Astrophysics Data System (ADS)

Druhan, J. L.; Giannetta, M.; Sanford, R. A.

2017-12-01

In recent years, reactive transport principles have expanded from early applications, largely based in contaminant hydrology, to a wide range of biologically mediated redox environments including marine sedimentary diagenesis, terrestrial metal ore deposits, soils, and critical zone weathering profiles. A common observation across this diversity of systems is that they often function under energetically limited conditions in comparison to those typical of contaminated aquifers subject to engineered remediation techniques. As a result, the kinetic rate expressions traditionally employed within reactive transport frameworks to simulate microbially mediated redox transformations have required modification. This was recognized in a series of seminal papers by Jin and Bethke (2005, 2007) in which the authors expanded upon a Monod rate law to include a thermodynamic potential factor `Ft' which exerts a limitation on the overall rate based on the thermodynamic driving force of the electron transfer reaction. This new rate expression is now commonly implemented within many of the major reactive transport software packages, though appropriate application has yet to be thoroughly demonstrated. Notably, the characteristically large partitioning of stable isotopes during microbially mediated reactions, which is extensively utilized to identify and quantify these redox transformations, has yet to be simulated under conditions in which the Ft term may be expected to exert a significant mass dependent influence. Here, we develop a series of simplified simulations for the microbially mediated reduction of sulfate based on the datasets reported by Jin and Bethke, and apply appropriate mass-bias within the Ft term to consider the extent to which the resulting isotopic fractionation is consistent with that observed in energetically limited systems. We show that the Ft term can exert a significant influence on the observed fractionation factor under common environmental conditions, resulting in model behavior which is, in effect, a microbial redox analog to the variable observed fractionation factor resulting from a transition state theory rate law as derived by DePaolo (2011).

Theoretical Prediction of Melting Relations in the Deep Mantle: the Phase Diagram Approach

NASA Astrophysics Data System (ADS)

Belmonte, D.; Ottonello, G. A.; Vetuschi Zuccolini, M.; Attene, M.

2016-12-01

Despite the outstanding progress in computer technology and experimental facilities, understanding melting phase relations in the deep mantle is still an open challenge. In this work a novel computational scheme to predict melting relations at HP-HT by a combination of first principles DFT calculations, polymer chemistry and equilibrium thermodynamics is presented and discussed. The adopted theoretical framework is physically-consistent and allows to compute multi-component phase diagrams relevant to Earth's deep interior in a broad range of P-T conditions by a convex-hull algorithm for Gibbs free energy minimisation purposely developed for high-rank simplexes. The calculated phase diagrams are in turn used as a source of information to gain new insights on the P-T-X evolution of magmas in the deep mantle, providing some thermodynamic constraints to both present-day and early Earth melting processes. High-pressure melting curves of mantle silicates are also obtained as by-product of phase diagram calculation. Application of the above method to the MgO-Al2O3-SiO2 (MAS) ternary system highlights as pressure effects are not only able to change the nature of melting of some minerals (like olivine and pyroxene) from eutectic to peritectic (and vice versa), but also simplify melting relations by drastically reducing the number of phases with a primary phase field at HP-HT conditions. It turns out that mineral phases like Majorite-Pyrope garnet and Anhydrous Phase B (Mg14Si5O24), which are often disregarded in modelling melting processes of mantle assemblages, are stable phases at solidus or liquidus conditions in a P-T range compatible with the mantle transition zone (i.e. P = 16 - 23 GPa and T = 2200 - 2700 °C) when their thermodynamic and thermophysical properties are properly assessed. Financial support to the Senior Author (D.B.) during his stay as Invited Scientist at the Institut de Physique du Globe de Paris (IPGP, Paris) is warmly acknowledged.

Thermodynamics and kinetics of RNA tertiary structure formation in the junctionless hairpin ribozyme.

PubMed

White, Neil A; Hoogstraten, Charles G

2017-09-01

The hairpin ribozyme consists of two RNA internal loops that interact to form the catalytically active structure. This docking transition is a rare example of intermolecular formation of RNA tertiary structure without coupling to helix annealing. We have used temperature-dependent surface plasmon resonance (SPR) to characterize the thermodynamics and kinetics of RNA tertiary structure formation for the junctionless form of the ribozyme, in which loops A and B reside on separate molecules. We find docking to be strongly enthalpy-driven and to be accompanied by substantial activation barriers for association and dissociation, consistent with the structural reorganization of both internal loops upon complex formation. Comparisons with the parallel analysis of a ribozyme variant carrying a 2'-O-methyl modification at the self-cleavage site and with published data in other systems reveal a surprising diversity of thermodynamic signatures, emphasizing the delicate balance of contributions to the free energy of formation of RNA tertiary structure. Copyright © 2017 Elsevier B.V. All rights reserved.

Thermodynamics of multicaloric effects in multiferroic materials: application to metamagnetic shape-memory alloys and ferrotoroidics

DOE PAGES

Planes, Antoni; Castán, Teresa; Saxena, Avadh

2016-07-11

In this paper, we develop a general thermodynamic framework to investigate multicaloric effects in multiferroic materials. This is applied to the study of both magnetostructural and magnetoelectric multiferroics. Landau models with appropriate interplay between the corresponding ferroic properties (order parameters) are proposed for metamagnetic shape-memory and ferrotoroidic materials, which, respectively, belong to the two classes of multiferroics. For each ferroic property, caloric effects are quantified by the isothermal entropy change induced by the application of the corresponding thermodynamically conjugated field. The multicaloric effect is obtained as a function of the two relevant applied fields in each class of multiferroics. Itmore » is further shown that multicaloric effects comprise the corresponding contributions from caloric effects associated with each ferroic property and the cross-contribution arising from the interplay between these ferroic properties. Finally, this article is part of the themed issue ‘Taking the temperature of phase transitions in cool materials’.« less

Jarzynski equality: connections to thermodynamics and the second law.

PubMed

Palmieri, Benoit; Ronis, David

2007-01-01

The one-dimensional expanding ideal gas model is used to compute the exact nonequilibrium distribution function. The state of the system during the expansion is defined in terms of local thermodynamics quantities. The final equilibrium free energy, obtained a long time after the expansion, is compared against the free energy that appears in the Jarzynski equality. Within this model, where the Jarzynski equality holds rigorously, the free energy change that appears in the equality does not equal the actual free energy change of the system at any time of the process. More generally, the work bound that is obtained from the Jarzynski equality is an upper bound to the upper bound that is obtained from the first and second laws of thermodynamics. The cancellation of the dissipative (nonequilibrium) terms that result in the Jarzynski equality is shown in the framework of response theory. This is used to show that the intuitive assumption that the Jarzynski work bound becomes equal to the average work done when the system evolves quasistatically is incorrect under some conditions.

Combined Molecular Dynamics Simulation-Molecular-Thermodynamic Theory Framework for Predicting Surface Tensions.

PubMed

Sresht, Vishnu; Lewandowski, Eric P; Blankschtein, Daniel; Jusufi, Arben

2017-08-22

A molecular modeling approach is presented with a focus on quantitative predictions of the surface tension of aqueous surfactant solutions. The approach combines classical Molecular Dynamics (MD) simulations with a molecular-thermodynamic theory (MTT) [ Y. J. Nikas, S. Puvvada, D. Blankschtein, Langmuir 1992 , 8 , 2680 ]. The MD component is used to calculate thermodynamic and molecular parameters that are needed in the MTT model to determine the surface tension isotherm. The MD/MTT approach provides the important link between the surfactant bulk concentration, the experimental control parameter, and the surfactant surface concentration, the MD control parameter. We demonstrate the capability of the MD/MTT modeling approach on nonionic alkyl polyethylene glycol surfactants at the air-water interface and observe reasonable agreement of the predicted surface tensions and the experimental surface tension data over a wide range of surfactant concentrations below the critical micelle concentration. Our modeling approach can be extended to ionic surfactants and their mixtures with both ionic and nonionic surfactants at liquid-liquid interfaces.

Thermodynamic theory of dislocation-enabled plasticity

NASA Astrophysics Data System (ADS)

Langer, J. S.

2017-11-01

The thermodynamic theory of dislocation-enabled plasticity is based on two unconventional hypotheses. The first of these is that a system of dislocations, driven by external forces and irreversibly exchanging heat with its environment, must be characterized by a thermodynamically defined effective temperature that is not the same as the ordinary temperature. The second hypothesis is that the overwhelmingly dominant mechanism controlling plastic deformation is thermally activated depinning of entangled pairs of dislocations. This paper consists of a systematic reformulation of this theory followed by examples of its use in analyses of experimentally observed phenomena including strain hardening, grain-size (Hall-Petch) effects, yielding transitions, and adiabatic shear banding.

Indirect determination of the thermodynamic temperature of the copper point by a multi-fixed-point technique

NASA Astrophysics Data System (ADS)

Battuello, M.; Florio, M.; Girard, F.

2010-06-01

An indirect determination of the thermodynamic temperature of the fixed point of copper was made at INRIM by measuring four cells with a Si-based and an InGaAs-based precision radiation thermometer carrying approximated thermodynamic scales realized up to the Ag point. An average value TCu = 1357.840 K was found with a standard uncertainty of 0.047 K. A consequent (T - T90)Cu value of 70 mK can be derived which is 18 mK higher than, but consistent with, the presently available (T - T90)Cu as elaborated by the CCT-WG4.

Extended forms of the second law for general time-dependent stochastic processes.

PubMed

Ge, Hao

2009-08-01

The second law of thermodynamics represents a universal principle applicable to all natural processes, physical systems, and engineering devices. Hatano and Sasa have recently put forward an extended form of the second law for transitions between nonequilibrium stationary states [Phys. Rev. Lett. 86, 3463 (2001)]. In this paper we further extend this form to an instantaneous interpretation, which is satisfied by quite general time-dependent stochastic processes including master-equation models and Langevin dynamics without the requirements of the stationarity for the initial and final states. The theory is applied to several thermodynamic processes, and its consistence with the classical thermodynamics is shown.

Liquid metal-organic frameworks

NASA Astrophysics Data System (ADS)

Gaillac, Romain; Pullumbi, Pluton; Beyer, Kevin A.; Chapman, Karena W.; Keen, David A.; Bennett, Thomas D.; Coudert, François-Xavier

2017-11-01

Metal-organic frameworks (MOFs) are a family of chemically diverse materials, with applications in a wide range of fields, covering engineering, physics, chemistry, biology and medicine. Until recently, research has focused almost entirely on crystalline structures, yet now a clear trend is emerging, shifting the emphasis onto disordered states, including `defective by design’ crystals, as well as amorphous phases such as glasses and gels. Here we introduce a strongly associated MOF liquid, obtained by melting a zeolitic imidazolate framework. We combine in situ variable temperature X-ray, ex situ neutron pair distribution function experiments, and first-principles molecular dynamics simulations to study the melting phenomenon and the nature of the liquid obtained. We demonstrate from structural, dynamical, and thermodynamical information that the chemical configuration, coordinative bonding, and porosity of the parent crystalline framework survive upon formation of the MOF liquid.

Liquid metal-organic frameworks.

PubMed

Gaillac, Romain; Pullumbi, Pluton; Beyer, Kevin A; Chapman, Karena W; Keen, David A; Bennett, Thomas D; Coudert, François-Xavier

2017-11-01

Metal-organic frameworks (MOFs) are a family of chemically diverse materials, with applications in a wide range of fields, covering engineering, physics, chemistry, biology and medicine. Until recently, research has focused almost entirely on crystalline structures, yet now a clear trend is emerging, shifting the emphasis onto disordered states, including 'defective by design' crystals, as well as amorphous phases such as glasses and gels. Here we introduce a strongly associated MOF liquid, obtained by melting a zeolitic imidazolate framework. We combine in situ variable temperature X-ray, ex situ neutron pair distribution function experiments, and first-principles molecular dynamics simulations to study the melting phenomenon and the nature of the liquid obtained. We demonstrate from structural, dynamical, and thermodynamical information that the chemical configuration, coordinative bonding, and porosity of the parent crystalline framework survive upon formation of the MOF liquid.

Liquid metal–organic frameworks

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gaillac, Romain; Pullumbi, Pluton; Beyer, Kevin A.

Metal–organic frameworks (MOFs) are a family of chemically diverse materials, with applications in a wide range of fields, covering engineering, physics, chemistry, biology and medicine. Until recently, research has focused almost entirely on crystalline structures, yet now a clear trend is emerging, shifting the emphasis onto disordered states, including ‘defective by design’ crystals, as well as amorphous phases such as glasses and gels. Here we introduce a strongly associated MOF liquid, obtained by melting a zeolitic imidazolate framework. We combine in situ variable temperature X-ray, ex situ neutron pair distribution function experiments, and first-principles molecular dynamics simulations to study themore » melting phenomenon and the nature of the liquid obtained. We demonstrate from structural, dynamical, and thermodynamical information that the chemical configuration, coordinative bonding, and porosity of the parent crystalline framework survive upon formation of the MOF liquid.« less

Quantum Feynman Ratchet

NASA Astrophysics Data System (ADS)

Goyal, Ketan; Kawai, Ryoichi

As nanotechnology advances, understanding of the thermodynamic properties of small systems becomes increasingly important. Such systems are found throughout physics, biology, and chemistry manifesting striking properties that are a direct result of their small dimensions where fluctuations become predominant. The standard theory of thermodynamics for macroscopic systems is powerless for such ever fluctuating systems. Furthermore, as small systems are inherently quantum mechanical, influence of quantum effects such as discreteness and quantum entanglement on their thermodynamic properties is of great interest. In particular, the quantum fluctuations due to quantum uncertainty principles may play a significant role. In this talk, we investigate thermodynamic properties of an autonomous quantum heat engine, resembling a quantum version of the Feynman Ratchet, in non-equilibrium condition based on the theory of open quantum systems. The heat engine consists of multiple subsystems individually contacted to different thermal environments.

Polynomial approximations of thermodynamic properties of arbitrary gas mixtures over wide pressure and density ranges

NASA Technical Reports Server (NTRS)

Allison, D. O.

1972-01-01

Computer programs for flow fields around planetary entry vehicles require real-gas equilibrium thermodynamic properties in a simple form which can be evaluated quickly. To fill this need, polynomial approximations were found for thermodynamic properties of air and model planetary atmospheres. A coefficient-averaging technique was used for curve fitting in lieu of the usual least-squares method. The polynomials consist of terms up to the ninth degree in each of two variables (essentially pressure and density) including all cross terms. Four of these polynomials can be joined to cover, for example, a range of about 1000 to 11000 K and 0.00001 to 1 atmosphere (1 atm = 1.0133 x 100,000 N/m sq) for a given thermodynamic property. Relative errors of less than 1 percent are found over most of the applicable range.

Systematic assignment of thermodynamic constraints in metabolic network models

PubMed Central

Kümmel, Anne; Panke, Sven; Heinemann, Matthias

2006-01-01

Background The availability of genome sequences for many organisms enabled the reconstruction of several genome-scale metabolic network models. Currently, significant efforts are put into the automated reconstruction of such models. For this, several computational tools have been developed that particularly assist in identifying and compiling the organism-specific lists of metabolic reactions. In contrast, the last step of the model reconstruction process, which is the definition of the thermodynamic constraints in terms of reaction directionalities, still needs to be done manually. No computational method exists that allows for an automated and systematic assignment of reaction directions in genome-scale models. Results We present an algorithm that – based on thermodynamics, network topology and heuristic rules – automatically assigns reaction directions in metabolic models such that the reaction network is thermodynamically feasible with respect to the production of energy equivalents. It first exploits all available experimentally derived Gibbs energies of formation to identify irreversible reactions. As these thermodynamic data are not available for all metabolites, in a next step, further reaction directions are assigned on the basis of network topology considerations and thermodynamics-based heuristic rules. Briefly, the algorithm identifies reaction subsets from the metabolic network that are able to convert low-energy co-substrates into their high-energy counterparts and thus net produce energy. Our algorithm aims at disabling such thermodynamically infeasible cyclic operation of reaction subnetworks by assigning reaction directions based on a set of thermodynamics-derived heuristic rules. We demonstrate our algorithm on a genome-scale metabolic model of E. coli. The introduced systematic direction assignment yielded 130 irreversible reactions (out of 920 total reactions), which corresponds to about 70% of all irreversible reactions that are required to disable thermodynamically infeasible energy production. Conclusion Although not being fully comprehensive, our algorithm for systematic reaction direction assignment could define a significant number of irreversible reactions automatically with low computational effort. We envision that the presented algorithm is a valuable part of a computational framework that assists the automated reconstruction of genome-scale metabolic models. PMID:17123434

Constitutive relations of ferroelectric ceramics

NASA Astrophysics Data System (ADS)

Su, Yu

The objective of this thesis is to obtain a better understanding on the fundamental constitutive behavior of ferroelectric ceramics based on the physics of phase transition, micromechanics of heterogeneous materials, and principles of irreversible thermodynamics. Within this framework, a self-consistent model is developed to investigate the electromechanical responses of ferroelectric polycrystals under temperature change and electromechanical loading. Cooling of a paraelectric crystal below its curie temperature Tc would result in spontaneous polarization, whereas electromechanical loading on a poled crystal could lead to domain switch. Domain growth and reorientation inside ferroelectric crystals are studied in light of these phase transition and domain switch. In this process, the change of the effective elastic, dielectric and piezoelectric constants during the evolution of microstructures are examined. In addition, hysteresis loops for the electric displacement and other related phenomena are computed under cyclic electric load. On top of all methods implemented in this work, the kinetic equation derived from the irreversible thermodynamics is the key to study the domain evolution in ferroelectric crystals. The kinetic relation not only governs the growth of new domain in a ferroelectric crystal, but it also determines the onset of phase transition. This characteristic is used to study the effect of hydrostatic pressure on the shift of Curie temperature of a ferroelectric crystal. Based on the derived expressions, it is observed that the deriving force can increase or decrease upon applied hydrostatic mechanical loading, depending on the change of electromechanical moduli, eigenstrain and electro-polarization. Several typical cases are computed and it is found that the change of the electromechanical moduli during phase transformation plays the key role in the shift of Curie temperature. Since ferroelectric ceramics are in a polycrystal form, a self-consistent model is used to examine the issues involved. In this model, each grain is represented by a spherical inclusion embedded in an infinitely extended piezoelectric matrix, and the inclusion further possesses an eigenstrain and eigen polarization. Secant relations between the polycrystal-matrix and the embedded inclusion are established by extending Hill's [1] incremental relations. An iterative computational program is developed for this self-consistent model.

EOSlib, Version 3

DOE Office of Scientific and Technical Information (OSTI.GOV)

Woods, Nathan; Menikoff, Ralph

2017-02-03

Equilibrium thermodynamics underpins many of the technologies used throughout theoretical physics, yet verification of the various theoretical models in the open literature remains challenging. EOSlib provides a single, consistent, verifiable implementation of these models, in a single, easy-to-use software package. It consists of three parts: a software library implementing various published equation-of-state (EOS) models; a database of fitting parameters for various materials for these models; and a number of useful utility functions for simplifying thermodynamic calculations such as computing Hugoniot curves or Riemann problem solutions. Ready availability of this library will enable reliable code-to- code testing of equation-of-state implementations, asmore » well as a starting point for more rigorous verification work. EOSlib also provides a single, consistent API for its analytic and tabular EOS models, which simplifies the process of comparing models for a particular application.« less

Chemical thermodynamic data. 1. The concept of links to the chemical elements and the historical development of key thermodynamic data [plus Supplementary Electronic Annex 2

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wolery, Thomas J.; Jove Colon, Carlos F.

Chemical thermodynamic data remain a keystone for geochemical modeling and reactive transport simulation as applied to an increasing number of applications in the earth sciences, as well as applications in other areas including metallurgy, material science, and industrial process design. The last century has seen the development of a large body of thermodynamic data and a number of major compilations. The past several decades have seen the development of thermodynamic databases in digital form designed to support computer calculations. However, problems with thermodynamic data appear to be persistent. One problem pertains to the use of inconsistent primary key reference data.more » Such data pertain to elemental reference forms and key, stoichiometrically simple chemical species including metal oxides, CO 2, water, and aqueous species such as Na + and Cl -. A consistent set of primary key data (standard Gibbs energies, standard enthalpies, and standard entropies for key chemical species) for 298.15K and 1 bar pressure is essential. Thermochemical convention is to define the standard Gibbs energy and the standard enthalpy of an individual chemical species in terms of formation from reference forms of the constituent chemical elements. We propose a formal concept of “links” to the elemental reference forms. This concept involves a documented understanding of all reactions and calculations leading to values for a formation property (standard Gibbs energy or enthalpy). A valid link consists of two parts: (a) the path of reactions and corrections and (b) the associated data, which are key data. Such a link differs from a bare “key” or “reference” datum in that it requires additional information. Some or all of its associated data may also be key data. In evaluating a reported thermodynamic datum, one should identify the links to the chemical elements, a process which can be time-consuming and which may lead to a dead end (an incomplete link). The use of two or more inconsistent links to the same elemental reference form in a thermodynamic database will result in an inconsistency in the database. Thus, in constructing a database, it is important to establish a set of reliable links (generally resulting in a set of primary reference data) and then correct all data adopted subsequently for consistency with that set. Recommended values of key data have not been constant through history. We review some of this history through the lens of major compilations and other influential reports, and note a number of problem areas. Finally, we illustrate the concepts developed in this paper by applying them to some key species of geochemical interest, including liquid water; quartz and aqueous silica; and gibbsite, corundum, and the aqueous aluminum ion.« less

Chemical thermodynamic data. 1. The concept of links to the chemical elements and the historical development of key thermodynamic data

NASA Astrophysics Data System (ADS)

Wolery, Thomas J.; Jové Colón, Carlos F.

2017-09-01

Chemical thermodynamic data remain a keystone for geochemical modeling and reactive transport simulation as applied to an increasing number of applications in the earth sciences, as well as applications in other areas including metallurgy, material science, and industrial process design. The last century has seen the development of a large body of thermodynamic data and a number of major compilations. The past several decades have seen the development of thermodynamic databases in digital form designed to support computer calculations. However, problems with thermodynamic data appear to be persistent. One problem pertains to the use of inconsistent primary key reference data. Such data pertain to elemental reference forms and key, stoichiometrically simple chemical species including metal oxides, CO2, water, and aqueous species such as Na+ and Cl-. A consistent set of primary key data (standard Gibbs energies, standard enthalpies, and standard entropies for key chemical species) for 298.15 K and 1 bar pressure is essential. Thermochemical convention is to define the standard Gibbs energy and the standard enthalpy of an individual chemical species in terms of formation from reference forms of the constituent chemical elements. We propose a formal concept of "links" to the elemental reference forms. This concept involves a documented understanding of all reactions and calculations leading to values for a formation property (standard Gibbs energy or enthalpy). A valid link consists of two parts: (a) the path of reactions and corrections and (b) the associated data, which are key data. Such a link differs from a bare "key" or "reference" datum in that it requires additional information. Some or all of its associated data may also be key data. In evaluating a reported thermodynamic datum, one should identify the links to the chemical elements, a process which can be time-consuming and which may lead to a dead end (an incomplete link). The use of two or more inconsistent links to the same elemental reference form in a thermodynamic database will result in an inconsistency in the database. Thus, in constructing a database, it is important to establish a set of reliable links (generally resulting in a set of primary reference data) and then correct all data adopted subsequently for consistency with that set. Recommended values of key data have not been constant through history. We review some of this history through the lens of major compilations and other influential reports, and note a number of problem areas. Finally, we illustrate the concepts developed in this paper by applying them to some key species of geochemical interest, including liquid water; quartz and aqueous silica; and gibbsite, corundum, and the aqueous aluminum ion.

Chemical thermodynamic data. 1. The concept of links to the chemical elements and the historical development of key thermodynamic data [plus Supplementary Electronic Annex 2

DOE PAGES

Wolery, Thomas J.; Jove Colon, Carlos F.

2016-09-26

Chemical thermodynamic data remain a keystone for geochemical modeling and reactive transport simulation as applied to an increasing number of applications in the earth sciences, as well as applications in other areas including metallurgy, material science, and industrial process design. The last century has seen the development of a large body of thermodynamic data and a number of major compilations. The past several decades have seen the development of thermodynamic databases in digital form designed to support computer calculations. However, problems with thermodynamic data appear to be persistent. One problem pertains to the use of inconsistent primary key reference data.more » Such data pertain to elemental reference forms and key, stoichiometrically simple chemical species including metal oxides, CO 2, water, and aqueous species such as Na + and Cl -. A consistent set of primary key data (standard Gibbs energies, standard enthalpies, and standard entropies for key chemical species) for 298.15K and 1 bar pressure is essential. Thermochemical convention is to define the standard Gibbs energy and the standard enthalpy of an individual chemical species in terms of formation from reference forms of the constituent chemical elements. We propose a formal concept of “links” to the elemental reference forms. This concept involves a documented understanding of all reactions and calculations leading to values for a formation property (standard Gibbs energy or enthalpy). A valid link consists of two parts: (a) the path of reactions and corrections and (b) the associated data, which are key data. Such a link differs from a bare “key” or “reference” datum in that it requires additional information. Some or all of its associated data may also be key data. In evaluating a reported thermodynamic datum, one should identify the links to the chemical elements, a process which can be time-consuming and which may lead to a dead end (an incomplete link). The use of two or more inconsistent links to the same elemental reference form in a thermodynamic database will result in an inconsistency in the database. Thus, in constructing a database, it is important to establish a set of reliable links (generally resulting in a set of primary reference data) and then correct all data adopted subsequently for consistency with that set. Recommended values of key data have not been constant through history. We review some of this history through the lens of major compilations and other influential reports, and note a number of problem areas. Finally, we illustrate the concepts developed in this paper by applying them to some key species of geochemical interest, including liquid water; quartz and aqueous silica; and gibbsite, corundum, and the aqueous aluminum ion.« less

Thermodynamics of finite systems: a key issues review

NASA Astrophysics Data System (ADS)

Swendsen, Robert H.

2018-07-01

A little over ten years ago, Campisi, and Dunkel and Hilbert, published papers claiming that the Gibbs (volume) entropy of a classical system was correct, and that the Boltzmann (surface) entropy was not. They claimed further that the quantum version of the Gibbs entropy was also correct, and that the phenomenon of negative temperatures was thermodynamically inconsistent. Their work began a vigorous debate of exactly how the entropy, both classical and quantum, should be defined. The debate has called into question the basis of thermodynamics, along with fundamental ideas such as whether heat always flows from hot to cold. The purpose of this paper is to sum up the present status—admittedly from my point of view. I will show that standard thermodynamics, with some minor generalizations, is correct, and the alternative thermodynamics suggested by Hilbert, Hänggi, and Dunkel is not. Heat does not flow from cold to hot. Negative temperatures are thermodynamically consistent. The small ‘errors’ in the Boltzmann entropy that started the whole debate are shown to be a consequence of the micro-canonical assumption of an energy distribution of zero width. Improved expressions for the entropy are found when this assumption is abandoned.

Thermodynamically self-consistent theory for the Blume-Capel model.

PubMed

Grollau, S; Kierlik, E; Rosinberg, M L; Tarjus, G

2001-04-01

We use a self-consistent Ornstein-Zernike approximation to study the Blume-Capel ferromagnet on three-dimensional lattices. The correlation functions and the thermodynamics are obtained from the solution of two coupled partial differential equations. The theory provides a comprehensive and accurate description of the phase diagram in all regions, including the wing boundaries in a nonzero magnetic field. In particular, the coordinates of the tricritical point are in very good agreement with the best estimates from simulation or series expansion. Numerical and analytical analysis strongly suggest that the theory predicts a universal Ising-like critical behavior along the lambda line and the wing critical lines, and a tricritical behavior governed by mean-field exponents.

Replica-exchange Wang Landau sampling: pushing the limits of Monte Carlo simulations in materials sciences

DOE Office of Scientific and Technical Information (OSTI.GOV)

Perera, Meewanage Dilina N; Li, Ying Wai; Eisenbach, Markus

We describe the study of thermodynamics of materials using replica-exchange Wang Landau (REWL) sampling, a generic framework for massively parallel implementations of the Wang Landau Monte Carlo method. To evaluate the performance and scalability of the method, we investigate the magnetic phase transition in body-centered cubic (bcc) iron using the classical Heisenberg model parameterized with first principles calculations. We demonstrate that our framework leads to a significant speedup without compromising the accuracy and precision and facilitates the study of much larger systems than is possible with its serial counterpart.

Numerical simulation of a helical shape electric arc in the external axial magnetic field

NASA Astrophysics Data System (ADS)

Urusov, R. M.; Urusova, I. R.

2016-10-01

Within the frameworks of non-stationary three-dimensional mathematical model, in approximation of a partial local thermodynamic equilibrium, a numerical calculation was made of characteristics of DC electric arc burning in a cylindrical channel in the uniform external axial magnetic field. The method of numerical simulation of the arc of helical shape in a uniform external axial magnetic field was proposed. This method consists in that that in the computational algorithm, a "scheme" analog of fluctuations for electrons temperature is supplemented. The "scheme" analogue of fluctuations increases a weak numerical asymmetry of electrons temperature distribution, which occurs randomly in the course of computing. This asymmetry can be "picked up" by the external magnetic field that continues to increase up to a certain value, which is sufficient for the formation of helical structure of the arc column. In the absence of fluctuations in the computational algorithm, the arc column in the external axial magnetic field maintains cylindrical axial symmetry, and a helical form of the arc is not observed.

Bipotential continuum models for granular mechanics

NASA Astrophysics Data System (ADS)

Goddard, Joe

2014-03-01

Most currently popular continuum models for granular media are special cases of a generalized Maxwell fluid model, which describes the evolution of stress and internal variables such as granular particle fraction and fabric,in terms of imposed strain rate. It is shown how such models can be obtained from two scalar potentials, a standard elastic free energy and a ``dissipation potential'' given rigorously by the mathematical theory of Edelen. This allows for a relatively easy derivation of properly invariant continuum models for granular media and fluid-particle suspensions within a thermodynamically consistent framework. The resulting continuum models encompass all the prominent regimes of granular flow, ranging from the quasi-static to rapidly sheared, and are readily extended to include higher-gradient or Cosserat effects. Models involving stress diffusion, such as that proposed recently by Kamrin and Koval (PRL 108 178301), provide an alternative approach that is mentioned in passing. This paper provides a brief overview of a forthcoming review articles by the speaker (The Princeton Companion to Applied Mathematics, and Appl. Mech. Rev.,in the press, 2013).

Geometrically nonlinear continuum thermomechanics with surface energies coupled to diffusion

NASA Astrophysics Data System (ADS)

McBride, A. T.; Javili, A.; Steinmann, P.; Bargmann, S.

2011-10-01

Surfaces can have a significant influence on the overall response of a continuum body but are often neglected or accounted for in an ad hoc manner. This work is concerned with a nonlinear continuum thermomechanics formulation which accounts for surface structures and includes the effects of diffusion and viscoelasticity. The formulation is presented within a thermodynamically consistent framework and elucidates the nature of the coupling between the various fields, and the surface and the bulk. Conservation principles are used to determine the form of the constitutive relations and the evolution equations. Restrictions on the jump in the temperature and the chemical potential between the surface and the bulk are not a priori assumptions, rather they arise from the reduced dissipation inequality on the surface and are shown to be satisfiable without imposing the standard assumptions of thermal and chemical slavery. The nature of the constitutive relations is made clear via an example wherein the form of the Helmholtz energy is explicitly given.

A Generalized Multi-Phase Framework for Modeling Cavitation in Cryogenic Fluids

NASA Technical Reports Server (NTRS)

Dorney, Dan (Technical Monitor); Hosangadi, Ashvin; Ahuja, Vineet

2003-01-01

A generalized multi-phase formulation for cavitation in fluids operating at temperatures elevated relative to their critical temperatures is presented. The thermal effects and the accompanying property variations due to phase change are modeled rigorously. Thermal equilibrium is assumed and fluid thermodynamic properties are specified along the saturation line using the NIST-12 databank. Fundamental changes in the physical characteristics of the cavity when thermal effects become pronounced are identified; the cavity becomes more porous, the interface less distinct, and has increased entrainment when temperature variations are present. Quantitative estimates of temperature and pressure depressions in both liquid nitrogen and liquid hydrogen were computed and compared with experimental data of Hord for hydrofoils. Excellent estimates of the leading edge temperature and pressure depression were obtained while the comparisons in the cavity closure region were reasonable. Liquid nitrogen cavities were consistently found to be in thermal equilibrium while liquid hydrogen cavities exhibited small, but distinct, non-equilibrium effects.

A continuum theory for two-phase flows of particulate solids: application to Poiseuille flows

NASA Astrophysics Data System (ADS)

Monsorno, Davide; Varsakelis, Christos; Papalexandris, Miltiadis V.

2015-11-01

In the first part of this talk, we present a novel two-phase continuum model for incompressible fluid-saturated granular flows. The model accounts for both compaction and shear-induced dilatancy and accommodates correlations for the granular rheology in a thermodynamically consistent way. In the second part of this talk, we exercise this two-phase model in the numerical simulation of a fully-developed Poiseuille flow of a dense suspension. The numerical predictions are shown to compare favorably against experimental measurements and confirm that the model can capture the important characteristics of the flow field, such as segregation and formation of plug zones. Finally, results from parametric studies with respect to the initial concentration, the magnitude of the external forcing and the width of the channel are presented and the role of these physical parameters is quantified. Financial Support has been provided by SEDITRANS, an Initial Training Network of the European Commission's 7th Framework Programme

Quantum mechanical force field for hydrogen fluoride with explicit electronic polarization.

PubMed

Mazack, Michael J M; Gao, Jiali

2014-05-28

The explicit polarization (X-Pol) theory is a fragment-based quantum chemical method that explicitly models the internal electronic polarization and intermolecular interactions of a chemical system. X-Pol theory provides a framework to construct a quantum mechanical force field, which we have extended to liquid hydrogen fluoride (HF) in this work. The parameterization, called XPHF, is built upon the same formalism introduced for the XP3P model of liquid water, which is based on the polarized molecular orbital (PMO) semiempirical quantum chemistry method and the dipole-preserving polarization consistent point charge model. We introduce a fluorine parameter set for PMO, and find good agreement for various gas-phase results of small HF clusters compared to experiments and ab initio calculations at the M06-2X/MG3S level of theory. In addition, the XPHF model shows reasonable agreement with experiments for a variety of structural and thermodynamic properties in the liquid state, including radial distribution functions, interaction energies, diffusion coefficients, and densities at various state points.

Viscoelastic Waves Simulation in a Blocky Medium with Fluid-Saturated Interlayers Using High-Performance Computing

NASA Astrophysics Data System (ADS)

Sadovskii, Vladimir; Sadovskaya, Oxana

2017-04-01

A thermodynamically consistent approach to the description of linear and nonlinear wave processes in a blocky medium, which consists of a large number of elastic blocks interacting with each other via pliant interlayers, is proposed. The mechanical properties of interlayers are defined by means of the rheological schemes of different levels of complexity. Elastic interaction between the blocks is considered in the framework of the linear elasticity theory [1]. The effects of viscoelastic shear in the interblock interlayers are taken into consideration using the Pointing-Thomson rheological scheme. The model of an elastic porous material is used in the interlayers, where the pores collapse if an abrupt compressive stress is applied. On the basis of the Biot equations for a fluid-saturated porous medium, a new mathematical model of a blocky medium is worked out, in which the interlayers provide a convective fluid motion due to the external perturbations. The collapse of pores is modeled within the generalized rheological approach, wherein the mechanical properties of a material are simulated using four rheological elements. Three of them are the traditional elastic, viscous and plastic elements, the fourth element is the so-called rigid contact [2], which is used to describe the behavior of materials with different resistance to tension and compression. Thermodynamic consistency of the equations in interlayers with the equations in blocks guarantees fulfillment of the energy conservation law for a blocky medium in a whole, i.e. kinetic and potential energy of the system is the sum of kinetic and potential energies of the blocks and interlayers. As a result of discretization of the equations of the model, robust computational algorithm is constructed, that is stable because of the thermodynamic consistency of the finite difference equations at a discrete level. The splitting method by the spatial variables and the Godunov gap decay scheme are used in the blocks, the dissipationless finite difference Ivanov scheme is applied in the interlayers. The parallel program is designed, using the MPI technology. By means of this software, nonlinear wave processes in the case of initial rotation of the central block in a rock mass as well as in the case of concentrated couple stress load, applied at the boundary of a rock mass, are analyzed. Results of computations on the multiprocessor computer systems demonstrate the strong anisotropy of a blocky medium. This work was supported by the Complex Fundamental Research Program no. II.2P "Integration and Development" of Siberian Branch of the Russian Academy of Sciences. References 1. Sadovskii V.M., Sadovskaya O.V. Modeling of Elastic Waves in a Blocky Medium Based on Equations of the Cosserat Continuum // Wave Motion. 2015. V. 52. P. 138-150. 2. Sadovskaya O., Sadovskii V. Mathematical Modeling in Mechanics of Granular Materials. Ser.: Advanced Structured Materials, V. 21. Heidelberg - New York - Dordrecht - London, Springer, 2012. 390 p.

The role of language in learning physics

NASA Astrophysics Data System (ADS)

Brookes, David T.

Many studies in PER suggest that language poses a serious difficulty for students learning physics. These difficulties are mostly attributed to misunderstanding of specialized terminology. This terminology often assigns new meanings to everyday terms used to describe physical models and phenomena. In this dissertation I present a novel approach to analyzing of the role of language in learning physics. This approach is based on the analysis of the historical development of physics ideas, the language of modern physicists, and students' difficulties in the areas of quantum mechanics, classical mechanics, and thermodynamics. These data are analyzed using linguistic tools borrowed from cognitive linguistics and systemic functional grammar. Specifically, I combine the idea of conceptual metaphor and grammar to build a theoretical framework that accounts for: (1) the role and function that language serves for physicists when they speak and reason about physical ideas and phenomena, (2) specific features of students' reasoning and difficulties that may be related to or derived from language that students read or hear. The theoretical framework is developed using the methodology of a grounded theoretical approach. The theoretical framework allows us to make predictions about the relationship between student discourse and their conceptual and problem solving difficulties. Tests of the theoretical framework are presented in the context of "heat" in thermodynamics and "force" in dynamics. In each case the language that students use to reason about the concepts of "heat" and "force" is analyzed using the theoretical framework. The results of this analysis show that language is very important in students' learning. In particular, students are (1) using features of physicists' conceptual metaphors to reason about physical phenomena, often overextending and misapplying these features, (2) drawing cues from the grammar of physicists' speech and writing to categorize physics concepts; this categorization of physics concepts plays a key role in students' ability to solve physics problems. In summary, I present a theoretical framework that provides a possible explanation of the role that language plays in learning physics. The framework also attempts to account for how and why physicists' language influences students in the way that it does.

Irreversible thermodynamics of open chemical networks. I. Emergent cycles and broken conservation laws

DOE Office of Scientific and Technical Information (OSTI.GOV)

Polettini, Matteo, E-mail: matteo.polettini@uni.lu; Esposito, Massimiliano

In this paper and Paper II, we outline a general framework for the thermodynamic description of open chemical reaction networks, with special regard to metabolic networks regulating cellular physiology and biochemical functions. We first introduce closed networks “in a box”, whose thermodynamics is subjected to strict physical constraints: the mass-action law, elementarity of processes, and detailed balance. We further digress on the role of solvents and on the seemingly unacknowledged property of network independence of free energy landscapes. We then open the system by assuming that the concentrations of certain substrate species (the chemostats) are fixed, whether because promptly regulatedmore » by the environment via contact with reservoirs, or because nearly constant in a time window. As a result, the system is driven out of equilibrium. A rich algebraic and topological structure ensues in the network of internal species: Emergent irreversible cycles are associated with nonvanishing affinities, whose symmetries are dictated by the breakage of conservation laws. These central results are resumed in the relation a + b = s{sup Y} between the number of fundamental affinities a, that of broken conservation laws b and the number of chemostats s{sup Y}. We decompose the steady state entropy production rate in terms of fundamental fluxes and affinities in the spirit of Schnakenberg's theory of network thermodynamics, paving the way for the forthcoming treatment of the linear regime, of efficiency and tight coupling, of free energy transduction, and of thermodynamic constraints for network reconstruction.« less

Irreversible thermodynamics of open chemical networks. I. Emergent cycles and broken conservation laws.

PubMed

Polettini, Matteo; Esposito, Massimiliano

2014-07-14

In this paper and Paper II, we outline a general framework for the thermodynamic description of open chemical reaction networks, with special regard to metabolic networks regulating cellular physiology and biochemical functions. We first introduce closed networks "in a box", whose thermodynamics is subjected to strict physical constraints: the mass-action law, elementarity of processes, and detailed balance. We further digress on the role of solvents and on the seemingly unacknowledged property of network independence of free energy landscapes. We then open the system by assuming that the concentrations of certain substrate species (the chemostats) are fixed, whether because promptly regulated by the environment via contact with reservoirs, or because nearly constant in a time window. As a result, the system is driven out of equilibrium. A rich algebraic and topological structure ensues in the network of internal species: Emergent irreversible cycles are associated with nonvanishing affinities, whose symmetries are dictated by the breakage of conservation laws. These central results are resumed in the relation a + b = s(Y) between the number of fundamental affinities a, that of broken conservation laws b and the number of chemostats s(Y). We decompose the steady state entropy production rate in terms of fundamental fluxes and affinities in the spirit of Schnakenberg's theory of network thermodynamics, paving the way for the forthcoming treatment of the linear regime, of efficiency and tight coupling, of free energy transduction, and of thermodynamic constraints for network reconstruction.

Irreversible thermodynamics of open chemical networks. I. Emergent cycles and broken conservation laws

NASA Astrophysics Data System (ADS)

Polettini, Matteo; Esposito, Massimiliano

2014-07-01

In this paper and Paper II, we outline a general framework for the thermodynamic description of open chemical reaction networks, with special regard to metabolic networks regulating cellular physiology and biochemical functions. We first introduce closed networks "in a box", whose thermodynamics is subjected to strict physical constraints: the mass-action law, elementarity of processes, and detailed balance. We further digress on the role of solvents and on the seemingly unacknowledged property of network independence of free energy landscapes. We then open the system by assuming that the concentrations of certain substrate species (the chemostats) are fixed, whether because promptly regulated by the environment via contact with reservoirs, or because nearly constant in a time window. As a result, the system is driven out of equilibrium. A rich algebraic and topological structure ensues in the network of internal species: Emergent irreversible cycles are associated with nonvanishing affinities, whose symmetries are dictated by the breakage of conservation laws. These central results are resumed in the relation a + b = sY between the number of fundamental affinities a, that of broken conservation laws b and the number of chemostats sY. We decompose the steady state entropy production rate in terms of fundamental fluxes and affinities in the spirit of Schnakenberg's theory of network thermodynamics, paving the way for the forthcoming treatment of the linear regime, of efficiency and tight coupling, of free energy transduction, and of thermodynamic constraints for network reconstruction.

Nonequilibrium steady state of biochemical cycle kinetics under non-isothermal conditions

NASA Astrophysics Data System (ADS)

Jin, Xiao; Ge, Hao

2018-04-01

The nonequilibrium steady state of isothermal biochemical cycle kinetics has been extensively studied, but that under non-isothermal conditions has been much less extensively investigated. When the heat exchange between subsystems is slow, the isothermal assumption of the whole system breaks down, as is true for many types of living organisms. Here, starting with a four-state model of molecular transporter across the cell membrane, we generalize the nonequilibrium steady-state theory of isothermal biochemical cycle kinetics to the circumstances with non-uniform temperatures of subsystems in terms of general master equation models. We obtain a new thermodynamic relationship between the chemical reaction rates and thermodynamic potentials in non-isothermal circumstances, based on the overdamped dynamics along the continuous reaction coordinate. We show that the entropy production can vary up to 3% in real cells, even when the temperature difference across the cell membrane is only approximately 1 K. We then decompose the total thermodynamic driving force into its thermal and chemical components and predict that the net flux of molecules transported by the molecular transporter can potentially go against the temperature gradient in the absence of a chemical driving force. Furthermore, we demonstrate that the simple application of the isothermal transition-state rate formula for each chemical reaction in terms of only the reactant’ temperature is not thermodynamically consistent. Therefore, we mathematically derive several revised reaction rate formulas that are not only consistent with the new thermodynamic relationship but also approximate the exact reaction rate better than Kramers’ rate formula under isothermal conditions.

Quantum approach to classical statistical mechanics.

PubMed

Somma, R D; Batista, C D; Ortiz, G

2007-07-20

We present a new approach to study the thermodynamic properties of d-dimensional classical systems by reducing the problem to the computation of ground state properties of a d-dimensional quantum model. This classical-to-quantum mapping allows us to extend the scope of standard optimization methods by unifying them under a general framework. The quantum annealing method is naturally extended to simulate classical systems at finite temperatures. We derive the rates to assure convergence to the optimal thermodynamic state using the adiabatic theorem of quantum mechanics. For simulated and quantum annealing, we obtain the asymptotic rates of T(t) approximately (pN)/(k(B)logt) and gamma(t) approximately (Nt)(-c/N), for the temperature and magnetic field, respectively. Other annealing strategies are also discussed.

Anomalous behaviour of thermodynamic properties at successive phase transitions in (NH4)3GeF7

NASA Astrophysics Data System (ADS)

Bogdanov, Evgeniy V.; Kartashev, Andrey V.; Pogoreltsev, Evgeniy I.; Gorev, Mikhail V.; Laptash, Natalia M.; Flerov, Igor N.

2017-12-01

Heat capacity, thermal dilatation, susceptibility to hydrostatic pressure and dielectric properties associated with succession of three phase transitions below room temperature in double fluoride salt (NH4)3GeF7 were studied. A possible transformation into the parent Pm-3m cubic phase was not observed up to the decomposition of compound. Nonferroelectric nature of structural distortions was confirmed. The DTA under pressure studies revealed a high temperature stability of two phases: P4/mbm and Pbam. The entropies of the phase transitions agree well with the model of structural distortions. Analysis of the thermal properties associated with the individual phase transitions in the framework of thermodynamic equations has shown a high reliability of the data obtained.

Nonrelativistic fluids on scale covariant Newton-Cartan backgrounds

NASA Astrophysics Data System (ADS)

Mitra, Arpita

2017-12-01

The nonrelativistic covariant framework for fields is extended to investigate fields and fluids on scale covariant curved backgrounds. The scale covariant Newton-Cartan background is constructed using the localization of space-time symmetries of nonrelativistic fields in flat space. Following this, we provide a Weyl covariant formalism which can be used to study scale invariant fluids. By considering ideal fluids as an example, we describe its thermodynamic and hydrodynamic properties and explicitly demonstrate that it satisfies the local second law of thermodynamics. As a further application, we consider the low energy description of Hall fluids. Specifically, we find that the gauge fields for scale transformations lead to corrections of the Wen-Zee and Berry phase terms contained in the effective action.

A thermodynamically-consistent large deformation theory coupling photochemical reaction and electrochemistry for light-responsive gels

NASA Astrophysics Data System (ADS)

Dehghany, Mohammad; Zhang, Haohui; Naghdabadi, Reza; Hu, Yuhang

2018-07-01

Gels are composed of crosslinked polymer network and solvent molecules. When the main chain network is incorporated with functional groups that can undergo photo-chemical reaction upon light irradiation, the gel becomes light-responsive. Under irradiation, the photosensitive groups may undergo photo-ionization process and generate charges that are attached to the main chain or diffuse into the solvent. The newly generated ions disturb the osmotic balance of the gel medium. As a result, water molecules and mobile ions are driven into or out of the network to compensate the osmotic imbalance, which eventually leads to macroscopic swelling or shrinking of the gel. In this work, we develop a rigorous nonequilibrium thermodynamic framework to study the coupled photo-chemo-electro-mechanical responses of the photo-ionizable gels. We first discuss the mathematical descriptions of the light propagation and photo-induced chemical reactions inside the gel, as well as the equations governing the kinetics of the photo-chemical reactions. We then explore the consequences of the fundamental laws of thermodynamics in deriving the governing equations of the photo-ionizable gels. The continuous light irradiation drives the gel system towards a new thermodynamic stationary state that is away from equilibrium and is accompanied by energy dissipation. Next, we focus on the photo stationary state of the gel and explore the consequences of the continuous irradiation on the mechanical response of the gel in both optically thin and optically thick configurations. In the optically thin cases, we quantitatively compare the theoretical prediction with experimental data available in the literature. In one example, we show that the model can quantitatively capture the photo-tunable volume-phase transition of the Poly(N-isopropylacrylamide) (PNIPAM) gel grafted with photo-responsive triphenylmethane leucocyanide groups. In another example, we show that the model can quantitatively study the effect of salt concentration and pH value of the external solution on the photo-induced swelling of the polyacrylamide gels incorporated with triphenylmethane leucohydroxide groups. Finally, for the optically thick gels, we develop a finite element code to study their inhomogeneous deformations due to the light attenuation. This work will be of great importance for precise control and optimal design of photo-ionizable gels in future applications.

Thermodynamic free energy methods to investigate shape transitions in bilayer membranes.

PubMed

Ramakrishnan, N; Tourdot, Richard W; Radhakrishnan, Ravi

2016-06-01

The conformational free energy landscape of a system is a fundamental thermodynamic quantity of importance particularly in the study of soft matter and biological systems, in which the entropic contributions play a dominant role. While computational methods to delineate the free energy landscape are routinely used to analyze the relative stability of conformational states, to determine phase boundaries, and to compute ligand-receptor binding energies its use in problems involving the cell membrane is limited. Here, we present an overview of four different free energy methods to study morphological transitions in bilayer membranes, induced either by the action of curvature remodeling proteins or due to the application of external forces. Using a triangulated surface as a model for the cell membrane and using the framework of dynamical triangulation Monte Carlo, we have focused on the methods of Widom insertion, thermodynamic integration, Bennett acceptance scheme, and umbrella sampling and weighted histogram analysis. We have demonstrated how these methods can be employed in a variety of problems involving the cell membrane. Specifically, we have shown that the chemical potential, computed using Widom insertion, and the relative free energies, computed using thermodynamic integration and Bennett acceptance method, are excellent measures to study the transition from curvature sensing to curvature inducing behavior of membrane associated proteins. The umbrella sampling and WHAM analysis has been used to study the thermodynamics of tether formation in cell membranes and the quantitative predictions of the computational model are in excellent agreement with experimental measurements. Furthermore, we also present a method based on WHAM and thermodynamic integration to handle problems related to end-point-catastrophe that are common in most free energy methods.

Dirac structures in nonequilibrium thermodynamics

NASA Astrophysics Data System (ADS)

Gay-Balmaz, François; Yoshimura, Hiroaki

2018-01-01

Dirac structures are geometric objects that generalize both Poisson structures and presymplectic structures on manifolds. They naturally appear in the formulation of constrained mechanical systems. In this paper, we show that the evolution equations for nonequilibrium thermodynamics admit an intrinsic formulation in terms of Dirac structures, both on the Lagrangian and the Hamiltonian settings. In the absence of irreversible processes, these Dirac structures reduce to canonical Dirac structures associated with canonical symplectic forms on phase spaces. Our geometric formulation of nonequilibrium thermodynamic thus consistently extends the geometric formulation of mechanics, to which it reduces in the absence of irreversible processes. The Dirac structures are associated with the variational formulation of nonequilibrium thermodynamics developed in the work of Gay-Balmaz and Yoshimura, J. Geom. Phys. 111, 169-193 (2017a) and are induced from a nonlinear nonholonomic constraint given by the expression of the entropy production of the system.

Direct measurement of weakly nonequilibrium system entropy is consistent with Gibbs–Shannon form

PubMed Central

2017-01-01

Stochastic thermodynamics extends classical thermodynamics to small systems in contact with one or more heat baths. It can account for the effects of thermal fluctuations and describe systems far from thermodynamic equilibrium. A basic assumption is that the expression for Shannon entropy is the appropriate description for the entropy of a nonequilibrium system in such a setting. Here we measure experimentally this function in a system that is in local but not global equilibrium. Our system is a micron-scale colloidal particle in water, in a virtual double-well potential created by a feedback trap. We measure the work to erase a fraction of a bit of information and show that it is bounded by the Shannon entropy for a two-state system. Further, by measuring directly the reversibility of slow protocols, we can distinguish unambiguously between protocols that can and cannot reach the expected thermodynamic bounds. PMID:29073017

Generalized laws of thermodynamics in the presence of correlations.

PubMed

Bera, Manabendra N; Riera, Arnau; Lewenstein, Maciej; Winter, Andreas

2017-12-19

The laws of thermodynamics, despite their wide range of applicability, are known to break down when systems are correlated with their environments. Here we generalize thermodynamics to physical scenarios which allow presence of correlations, including those where strong correlations are present. We exploit the connection between information and physics, and introduce a consistent redefinition of heat dissipation by systematically accounting for the information flow from system to bath in terms of the conditional entropy. As a consequence, the formula for the Helmholtz free energy is accordingly modified. Such a remedy not only fixes the apparent violations of Landauer's erasure principle and the second law due to anomalous heat flows, but also leads to a generally valid reformulation of the laws of thermodynamics. In this information-theoretic approach, correlations between system and environment store work potential. Thus, in this view, the apparent anomalous heat flows are the refrigeration processes driven by such potentials.

Non-Equilibrium Thermodynamics of Transcriptional Bursts

NASA Astrophysics Data System (ADS)

Hernández-Lemus, Enrique

Gene transcription or Gene Expression (GE) is the process which transforms the information encoded in DNA into a functional RNA message. It is known that GE can occur in bursts or pulses. Transcription is irregular, with strong periods of activity, interspersed by long periods of inactivity. If we consider the average behavior over millions of cells, this process appears to be continuous. But at the individual cell level, there is considerable variability, and for most genes, very little activity at any one time. Some have claimed that GE bursting can account for the high variability in gene expression occurring between cells in isogenic populations. This variability has a big impact on cell behavior and thus on phenotypic conditions and disease. In view of these facts, the development of a thermodynamic framework to study gene expression and transcriptional regulation to integrate the vast amount of molecular biophysical GE data is appealing. Application of such thermodynamic formalism is useful to observe various dissipative phenomena in GE regulatory dynamics. In this chapter we will examine at some detail the complex phenomena of transcriptional bursts (specially of a certain class of anomalous bursts) in the context of a non-equilibrium thermodynamics formalism and will make some initial comments on the relevance of some irreversible processes that may be connected to anomalous transcriptional bursts.

Soft matter: rubber and networks

NASA Astrophysics Data System (ADS)

McKenna, Gregory B.

2018-06-01

Rubber networks are important and form the basis for materials with properties ranging from rubber tires to super absorbents and contact lenses. The development of the entropy ideas of rubber deformation thermodynamics provides a powerful framework from which to understand and to use these materials. In addition, swelling of the rubber in the presence of small molecule liquids or solvents leads to materials that are very soft and ‘gel’ like in nature. The review covers the thermodynamics of polymer networks and gels from the perspective of the thermodynamics and mechanics of the strain energy density function. Important relationships are presented and experimental results show that the continuum ideas contained in the phenomenological thermodynamics are valid, but that the molecular bases for some of them remain to be fully elucidated. This is particularly so in the case of the entropic gels or swollen networks. The review is concluded with some perspectives on other networks, ranging from entropic polymer networks such as thermoplastic elastomers to physical gels in which cross-link points are formed by glassy or crystalline domains. A discussion is provided for other physical gels in which the network forms a spinodal-like decomposition, both in thermoplastic polymers that form a glassy network upon phase separation and for colloidal gels that seem to have a similar behavior.

Thermodynamically consistent Langevin dynamics with spatially correlated noise predicting frictionless regime and transient attraction effect

NASA Astrophysics Data System (ADS)

Majka, M.; Góra, P. F.

2016-10-01

While the origins of temporal correlations in Langevin dynamics have been thoroughly researched, the understanding of spatially correlated noise (SCN) is rather incomplete. In particular, very little is known about the relation between friction and SCN. In this article, starting from the microscopic, deterministic model, we derive the analytical formula for the spatial correlation function in the particle-bath interactions. This expression shows that SCN is the inherent component of binary mixtures, originating from the effective (entropic) interactions. Further, employing this spatial correlation function, we postulate the thermodynamically consistent Langevin equation driven by the Gaussian SCN and calculate the adequate fluctuation-dissipation relation. The thermodynamical consistency is achieved by introducing the spatially variant friction coefficient, which can be also derived analytically. This coefficient exhibits a number of intriguing properties, e.g., the singular behavior for certain types of interactions. Eventually, we apply this new theory to the system of two charged particles in the presence of counter-ions. Such particles interact via the screened-charge Yukawa potential and the inclusion of SCN leads to the emergence of the anomalous frictionless regime. In this regime the particles can experience active propulsion leading to the transient attraction effect. This effect suggests a nonequilibrium mechanism facilitating the molecular binding of the like-charged particles.

Thermodynamic assessment of the Pr-O system

DOE PAGES

McMurray, Jake W.

2015-12-24

We found that the Calphad method was used to perform a thermodynamic assessment of the Pr–O system. Compound energy formalism representations were developed for the fluorite α-PrO 2–x and bixbyite σ-Pr 3 O 5 ± x solid solutions while the two-sublattice liquid model was used to describe the binary melt. The series of phases between Pr 2 O 3 and PrO 2 were taken to be stoichiometric. Moreover, the equilibrium oxygen pressure, phase equilibria, and enthalpy data were used to optimize the adjustable parameters of the models for a self-consistent representation of the thermodynamic behavior of the Pr–O system frommore » 298 K to melting.« less

Thermodynamic theory of dislocation-enabled plasticity

DOE PAGES

Langer, J. S.

2017-11-30

The thermodynamic theory of dislocation-enabled plasticity is based on two unconventional hypotheses. The first of these is that a system of dislocations, driven by external forces and irreversibly exchanging heat with its environment, must be characterized by a thermodynamically defined effective temperature that is not the same as the ordinary temperature. The second hypothesis is that the overwhelmingly dominant mechanism controlling plastic deformation is thermally activated depinning of entangled pairs of dislocations. This paper consists of a systematic reformulation of this theory followed by examples of its use in analyses of experimentally observed phenomena including strain hardening, grain-size (Hall-Petch) effects,more » yielding transitions, and adiabatic shear banding.« less

Finite-size polyelectrolyte bundles at thermodynamic equilibrium

NASA Astrophysics Data System (ADS)

Sayar, M.; Holm, C.

2007-01-01

We present the results of extensive computer simulations performed on solutions of monodisperse charged rod-like polyelectrolytes in the presence of trivalent counterions. To overcome energy barriers we used a combination of parallel tempering and hybrid Monte Carlo techniques. Our results show that for small values of the electrostatic interaction the solution mostly consists of dispersed single rods. The potential of mean force between the polyelectrolyte monomers yields an attractive interaction at short distances. For a range of larger values of the Bjerrum length, we find finite-size polyelectrolyte bundles at thermodynamic equilibrium. Further increase of the Bjerrum length eventually leads to phase separation and precipitation. We discuss the origin of the observed thermodynamic stability of the finite-size aggregates.

Nature of self-diffusion in two-dimensional fluids

DOE Office of Scientific and Technical Information (OSTI.GOV)

Choi, Bongsik; Han, Kyeong Hwan; Kim, Changho

Self-diffusion in a two-dimensional simple fluid is investigated by both analytical and numerical means. We investigate the anomalous aspects of self-diffusion in two-dimensional fluids with regards to the mean square displacement, the time-dependent diffusion coefficient, and the velocity autocorrelation function (VACF) using a consistency equation relating these quantities. Here, we numerically confirm the consistency equation by extensive molecular dynamics simulations for finite systems, corroborate earlier results indicating that the kinematic viscosity approaches a finite, non-vanishing value in the thermodynamic limit, and establish the finite size behavior of the diffusion coefficient. We obtain the exact solution of the consistency equation in the thermodynamic limit and use this solution to determine the large time asymptotics of the mean square displacement, the diffusion coefficient, and the VACF. An asymptotic decay law of the VACF resembles the previously known self-consistent form, 1/(more » $$t\\sqrt{In t)}$$ however with a rescaled time.« less

Nature of self-diffusion in two-dimensional fluids

DOE PAGES

Choi, Bongsik; Han, Kyeong Hwan; Kim, Changho; ...

2017-12-18

Self-diffusion in a two-dimensional simple fluid is investigated by both analytical and numerical means. We investigate the anomalous aspects of self-diffusion in two-dimensional fluids with regards to the mean square displacement, the time-dependent diffusion coefficient, and the velocity autocorrelation function (VACF) using a consistency equation relating these quantities. Here, we numerically confirm the consistency equation by extensive molecular dynamics simulations for finite systems, corroborate earlier results indicating that the kinematic viscosity approaches a finite, non-vanishing value in the thermodynamic limit, and establish the finite size behavior of the diffusion coefficient. We obtain the exact solution of the consistency equation in the thermodynamic limit and use this solution to determine the large time asymptotics of the mean square displacement, the diffusion coefficient, and the VACF. An asymptotic decay law of the VACF resembles the previously known self-consistent form, 1/(more » $$t\\sqrt{In t)}$$ however with a rescaled time.« less

Critical Evaluations and Thermodynamic Optimizations of the MnO-Mn2O3-SiO2 and FeO-Fe2O3-MnO-Mn2O3-SiO2 Systems

NASA Astrophysics Data System (ADS)

Kang, Youn-Bae; Jung, In-Ho

2017-06-01

A critical evaluation and thermodynamic modeling for thermodynamic properties of all oxide phases and phase diagrams in the Fe-Mn-Si-O system (MnO-Mn2O3-SiO2 and FeO-Fe2O3-MnO-Mn2O3-SiO2 systems) are presented. Optimized Gibbs energy parameters for the thermodynamic models of the oxide phases were obtained which reproduce all available and reliable experimental data within error limits from 298 K (25°C) to above the liquidus temperatures at all compositions covering from known oxide phases, and oxygen partial pressure from metal saturation to 0.21 bar. The optimized thermodynamic properties and phase diagrams are believed to be the best estimates presently available. Slag (molten oxide) was modeled using the modified quasichemical model in the pair approximation. Olivine (Fe2SiO4-Mn2SiO4) was modeled using two-sublattice model in the framework of the compound energy formalism (CEF), while rhodonite (MnSiO3-FeSiO3) and braunite (Mn7SiO_{12} with excess Mn2O3) were modeled as simple Henrian solutions. It is shown that the already developed models and databases of two spinel phases (cubic- and tetragonal-(Fe, Mn)3O4) using CEF [Kang and Jung, J. Phys. Chem. Solids (2016), vol. 98, pp. 237-246] can successfully be integrated into a larger thermodynamic database to be used in practically important higher order system such as silicate. The database of the model parameters can be used along with a software for Gibbs energy minimization in order to calculate any type of phase diagram section and thermodynamic properties.

Integrating Thermodynamic Models in Geodynamic Simulations: The Example of the Community Software ASPECT

NASA Astrophysics Data System (ADS)

Dannberg, J.; Heister, T.; Grove, R. R.; Gassmoeller, R.; Spiegelman, M. W.; Bangerth, W.

2017-12-01

Earth's surface shows many features whose genesis can only be understood through the interplay of geodynamic and thermodynamic models. This is particularly important in the context of melt generation and transport: Mantle convection determines the distribution of temperature and chemical composition, the melting process itself is then controlled by the thermodynamic relations and in turn influences the properties and the transport of melt. Here, we present our extension of the community geodynamics code ASPECT, which solves the equations of coupled magma/mantle dynamics, and allows to integrate different parametrizations of reactions and phase transitions: They may alternatively be implemented as simple analytical expressions, look-up tables, or computed by a thermodynamics software. As ASPECT uses a variety of numerical methods and solvers, this also gives us the opportunity to compare different approaches of modelling the melting process. In particular, we will elaborate on the spatial and temporal resolution that is required to accurately model phase transitions, and show the potential of adaptive mesh refinement when applied to melt generation and transport. We will assess the advantages and disadvantages of iterating between fluid dynamics and chemical reactions derived from thermodynamic models within each time step, or decoupling them, allowing for different time step sizes. Beyond that, we will expand on the functionality required for an interface between computational thermodynamics and fluid dynamics models from the geodynamics side. Finally, using a simple example of melting of a two-phase, two-component system, we compare different time-stepping and solver schemes in terms of accuracy and efficiency, in dependence of the time scales of fluid flow and chemical reactions relative to each other. Our software provides a framework to integrate thermodynamic models in high resolution, 3d simulations of coupled magma/mantle dynamics, and can be used as a tool to study links between physical processes and geochemical signals in the Earth.

Resource theory for work and heat

NASA Astrophysics Data System (ADS)

Sparaciari, Carlo; Oppenheim, Jonathan; Fritz, Tobias

2017-11-01

Several recent results on thermodynamics have been obtained using the tools of quantum information theory and resource theories. So far, the resource theories utilized to describe thermodynamics have assumed the existence of an infinite thermal reservoir, by declaring that thermal states at some background temperature come for free. Here, we propose a resource theory of quantum thermodynamics without a background temperature, so that no states at all come for free. We apply this resource theory to the case of many noninteracting systems and show that all quantum states are classified by their entropy and average energy, even arbitrarily far away from equilibrium. This implies that thermodynamics takes place in a two-dimensional convex set that we call the energy-entropy diagram. The answers to many resource-theoretic questions about thermodynamics can be read off from this diagram, such as the efficiency of a heat engine consisting of finite reservoirs, or the rate of conversion between two states. This allows us to consider a resource theory which puts work and heat on an equal footing, and serves as a model for other resource theories.

Dissipation, generalized free energy, and a self-consistent nonequilibrium thermodynamics of chemically driven open subsystems.

PubMed

Ge, Hao; Qian, Hong

2013-06-01

Nonequilibrium thermodynamics of a system situated in a sustained environment with influx and efflux is usually treated as a subsystem in a larger, closed "universe." A question remains with regard to what the minimally required description for the surrounding of such an open driven system is so that its nonequilibrium thermodynamics can be established solely based on the internal stochastic kinetics. We provide a solution to this problem using insights from studies of molecular motors in a chemical nonequilibrium steady state (NESS) with sustained external drive through a regenerating system or in a quasisteady state (QSS) with an excess amount of adenosine triphosphate (ATP), adenosine diphosphate (ADP), and inorganic phosphate (Pi). We introduce the key notion of minimal work that is needed, W(min), for the external regenerating system to sustain a NESS (e.g., maintaining constant concentrations of ATP, ADP and Pi for a molecular motor). Using a Markov (master-equation) description of a motor protein, we illustrate that the NESS and QSS have identical kinetics as well as the second law in terms of the same positive entropy production rate. The heat dissipation of a NESS without mechanical output is exactly the W(min). This provides a justification for introducing an ideal external regenerating system and yields a free-energy balance equation between the net free-energy input F(in) and total dissipation F(dis) in an NESS: F(in) consists of chemical input minus mechanical output; F(dis) consists of dissipative heat, i.e. the amount of useful energy becoming heat, which also equals the NESS entropy production. Furthermore, we show that for nonstationary systems, the F(dis) and F(in) correspond to the entropy production rate and housekeeping heat in stochastic thermodynamics and identify a relative entropy H as a generalized free energy. We reach a new formulation of Markovian nonequilibrium thermodynamics based on only the internal kinetic equation without further reference to the intrinsic degree of freedom within each Markov state. It includes an extended free-energy balance and a second law which are valid for driven stochastic dynamics with an ideal external regenerating system. Our result suggests new ingredients for a generalized thermodynamics of self-organization in driven systems.

Putting proteins back into water

NASA Astrophysics Data System (ADS)

de Los Rios, Paolo; Caldarelli, Guido

2000-12-01

We introduce a simplified protein model where the solvent (water) degrees of freedom appear explicitly (although in an extremely simplified fashion). Using this model we are able to recover the thermodynamic phenomenology of proteins over a wide range of temperatures. In particular we describe both the warm and the cold protein denaturation within a single framework, while addressing important issues about the structure of model proteins.

Thermomechanical Modeling of Shape Memory Alloys and Applications

NASA Astrophysics Data System (ADS)

Lexcellent, C.; Leclercq, S.

The aim of the present paper is a general macroscopic description of the thermomechanical behavior of shape memory alloys (SMA). We use for framework the thermodynamics of irreversible processes. This model is efficient for describing the behavior of "smart" structures as a bronchial, a tentacle element and an prosthesis hybrid structure made of Ti Ni SMA wires embedded in a resin epoxy matrix.

On the thermodynamic origin of metabolic scaling.

PubMed

Ballesteros, Fernando J; Martinez, Vicent J; Luque, Bartolo; Lacasa, Lucas; Valor, Enric; Moya, Andrés

2018-01-23

The origin and shape of metabolic scaling has been controversial since Kleiber found that basal metabolic rate of animals seemed to vary as a power law of their body mass with exponent 3/4, instead of 2/3, as a surface-to-volume argument predicts. The universality of exponent 3/4 -claimed in terms of the fractal properties of the nutrient network- has recently been challenged according to empirical evidence that observed a wealth of robust exponents deviating from 3/4. Here we present a conceptually simple thermodynamic framework, where the dependence of metabolic rate with body mass emerges from a trade-off between the energy dissipated as heat and the energy efficiently used by the organism to maintain its metabolism. This balance tunes the shape of an additive model from which different effective scalings can be recovered as particular cases, thereby reconciling previously inconsistent empirical evidence in mammals, birds, insects and even plants under a unified framework. This model is biologically motivated, fits remarkably well the data, and also explains additional features such as the relation between energy lost as heat and mass, the role and influence of different climatic environments or the difference found between endotherms and ectotherms.

Dynamical diagnostics of the SST annual cycle in the eastern equatorial Pacific: part I a linear coupled framework

NASA Astrophysics Data System (ADS)

Chen, Ying-Ying; Jin, Fei-Fei

2018-03-01

The eastern equatorial Pacific has a pronounced westward propagating SST annual cycle resulting from ocean-atmosphere interactions with equatorial semiannual solar forcing and off-equatorial annual solar forcing conveyed to the equator. In this two-part paper, a simple linear coupled framework is proposed to quantify the internal dynamics and external forcing for a better understanding of the linear part of the dynamics annual cycle. It is shown that an essential internal dynamical factor is the SST damping rate which measures the coupled stability in a similar way as the Bjerknes instability index for the El Niño-Southern Oscillation. It comprises three major negative terms (dynamic damping due to the Ekman pumping feedback, mean circulation advection, and thermodynamic feedback) and two positive terms (thermocline feedback and zonal advection). Another dynamical factor is the westward-propagation speed that is mainly determined by the thermodynamic feedback, the Ekman pumping feedback, and the mean circulation. The external forcing is measured by the annual and semiannual forcing factors. These linear internal and external factors, which can be estimated from data, determine the amplitude of the annual cycle.

Self and transport diffusivity of CO2 in the metal-organic framework MIL-47(V) explored by quasi-elastic neutron scattering experiments and molecular dynamics simulations.

PubMed

Salles, Fabrice; Jobic, Hervé; Devic, Thomas; Llewellyn, Philip L; Serre, Christian; Férey, Gérard; Maurin, Guillaume

2010-01-26

Quasi-elastic neutron scattering measurements are combined with molecular dynamics simulations to determine the self-diffusivity, corrected diffusivity, and transport diffusivity of CO(2) in the metal-organic framework MIL-47(V) (MIL = Materials Institut Lavoisier) over a wide range of loading. The force field used for describing the host/guest interactions is first validated on the thermodynamics of the MIL-47(V)/CO(2) system, prior to being transferred to the investigations of the dynamics. A decreasing profile is then deduced for D(s) and D(o) whereas D(t) presents a non monotonous evolution with a slight decrease at low loading followed by a sharp increase at higher loading. Such decrease of D(t) which has never been evidenced in any microporous systems comes from the atypical evolution of the thermodynamic correction factor that reaches values below 1 at low loading. This implies that, due to intermolecular interactions, the CO(2) molecules in MIL-47(V) do not behave like an ideal gas. Further, molecular simulations enabled us to elucidate unambiguously a 3D diffusion mechanism within the pores of MIL-47(V).

A Damage Model for the Simulation of Delamination in Advanced Composites under Variable-Mode Loading

NASA Technical Reports Server (NTRS)

Turon, A.; Camanho, P. P.; Costa, J.; Davila, C. G.

2006-01-01

A thermodynamically consistent damage model is proposed for the simulation of progressive delamination in composite materials under variable-mode ratio. The model is formulated in the context of Damage Mechanics. A novel constitutive equation is developed to model the initiation and propagation of delamination. A delamination initiation criterion is proposed to assure that the formulation can account for changes in the loading mode in a thermodynamically consistent way. The formulation accounts for crack closure effects to avoid interfacial penetration of two adjacent layers after complete decohesion. The model is implemented in a finite element formulation, and the numerical predictions are compared with experimental results obtained in both composite test specimens and structural components.

Atmospheric environment for Space Shuttle (STS-41D) launch

NASA Technical Reports Server (NTRS)

Johnson, D. L.; Hill, C. K.; Jasper, G.; Batts, G. W.

1984-01-01

Selected atmospheric conditions observed near Space Shuttle STS-41D launch time on August 30, 1984, at Kennedy Space Center, Florida are summarized. Values of ambient pressure, temperature, moisture, ground winds, visual observations (cloud), and winds aloft are included. The sequence of prelaunch Jimsphere measured vertical wind profiles is given as well as wind and thermodynamic parameters representative of surface and aloft conditions in the SRB descent/impact ocean area. Final atmospheric tapes, which consist of wind and thermodynamic parameters versus altitude, for STS-41D vehicle ascent and SRB descent/impact were constructed. The STS-41D ascent meteorological data tape was constructed by Marshall Space Flight Center's Atmospheric Science Division to provide an internally consistent data set for use in post flight performance assessments.

Thermodynamic stability of boron: the role of defects and zero point motion.

PubMed

van Setten, Michiel J; Uijttewaal, Matthé A; de Wijs, Gilles A; de Groot, Robert A

2007-03-07

Its low weight, high melting point, and large degree of hardness make elemental boron a technologically interesting material. The large number of allotropes, mostly containing over a hundred atoms in the unit cell, and their difficult characterization challenge both experimentalists and theoreticians. Even the ground state of this element is still under discussion. For over 30 years, scientists have attempted to determine the relative stability of alpha- and beta-rhombohedral boron. We use density functional calculations in the generalized gradient approximation to study a broad range of possible beta-rhombohedral structures containing interstitial atoms and partially occupied sites within a 105 atoms framework. The two most stable structures are practically degenerate in energy and semiconducting. One contains the experimental 320 atoms in the hexagonal unit cell, and the other contains 106 atoms in the triclinic unit cell. When populated with the experimental 320 electrons, the 106 atom structure exhibits a band gap of 1.4 eV and an in-gap hole trap at 0.35 eV above the valence band, consistent with known experiments. The total energy of these two structures is 23 meV/B lower than the original 105 atom framework, but it is still 1 meV/B above the alpha phase. Adding zero point energies finally makes the beta phase the ground state of elemental boron by 3 meV/B. At finite temperatures, the difference becomes even larger.

Matching time and spatial scales of rapid solidification: dynamic TEM experiments coupled to CALPHAD-informed phase-field simulations

NASA Astrophysics Data System (ADS)

Perron, Aurelien; Roehling, John D.; Turchi, Patrice E. A.; Fattebert, Jean-Luc; McKeown, Joseph T.

2018-01-01

A combination of dynamic transmission electron microscopy (DTEM) experiments and CALPHAD-informed phase-field simulations was used to study rapid solidification in Cu-Ni thin-film alloys. Experiments—conducted in the DTEM—consisted of in situ laser melting and determination of the solidification kinetics by monitoring the solid-liquid interface and the overall microstructure evolution (time-resolved measurements) during the solidification process. Modelling of the Cu-Ni alloy microstructure evolution was based on a phase-field model that included realistic Gibbs energies and diffusion coefficients from the CALPHAD framework (thermodynamic and mobility databases). DTEM and post mortem experiments highlighted the formation of microsegregation-free columnar grains with interface velocities varying from ˜0.1 to ˜0.6 m s-1. After an ‘incubation’ time, the velocity of the planar solid-liquid interface accelerated until solidification was complete. In addition, a decrease of the temperature gradient induced a decrease in the interface velocity. The modelling strategy permitted the simulation (in 1D and 2D) of the solidification process from the initially diffusion-controlled to the nearly partitionless regimes. Finally, results of DTEM experiments and phase-field simulations (grain morphology, solute distribution, and solid-liquid interface velocity) were consistent at similar time (μs) and spatial scales (μm).

Matching time and spatial scales of rapid solidification: Dynamic TEM experiments coupled to CALPHAD-informed phase-field simulations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Perron, Aurelien; Roehling, John D.; Turchi, Patrice E. A.

A combination of dynamic transmission electron microscopy (DTEM) experiments and CALPHAD-informed phase-field simulations was used to study rapid solidification in Cu–Ni thin-film alloys. Experiments—conducted in the DTEM—consisted of in situ laser melting and determination of the solidification kinetics by monitoring the solid–liquid interface and the overall microstructure evolution (time-resolved measurements) during the solidification process. Modelling of the Cu–Ni alloy microstructure evolution was based on a phase-field model that included realistic Gibbs energies and diffusion coefficients from the CALPHAD framework (thermodynamic and mobility databases). DTEM and post mortem experiments highlighted the formation of microsegregation-free columnar grains with interface velocities varying frommore » ~0.1 to ~0.6 m s –1. After an 'incubation' time, the velocity of the planar solid–liquid interface accelerated until solidification was complete. In addition, a decrease of the temperature gradient induced a decrease in the interface velocity. The modelling strategy permitted the simulation (in 1D and 2D) of the solidification process from the initially diffusion-controlled to the nearly partitionless regimes. Lastly, results of DTEM experiments and phase-field simulations (grain morphology, solute distribution, and solid–liquid interface velocity) were consistent at similar time (μs) and spatial scales (μm).« less

Modeling elasto-viscoplasticity in a consistent phase field framework

DOE PAGES

Cheng, Tian -Le; Wen, You -Hai; Hawk, Jeffrey A.

2017-05-19

Existing continuum level phase field plasticity theories seek to solve plastic strain by minimizing the shear strain energy. However, rigorously speaking, for thermodynamic consistency it is required to minimize the total strain energy unless there is proof that hydrostatic strain energy is independent of plastic strain which is unfortunately absent. In this work, we extend the phase-field microelasticity theory of Khachaturyan et al. by minimizing the total elastic energy with constraint of incompressibility of plastic strain. We show that the flow rules derived from the Ginzburg-Landau type kinetic equation can be in line with Odqvist's law for viscoplasticity and Prandtl-Reussmore » theory. Free surfaces (external surfaces or internal cracks/voids) are treated in the model. Deformation caused by a misfitting spherical precipitate in an elasto-plastic matrix is studied by large-scale three-dimensional simulations in four different regimes in terms of the matrix: (a) elasto-perfectly-plastic, (b) elastoplastic with linear hardening, (c) elastoplastic with power-law hardening, and (d) elasto-perfectly-plastic with a free surface. The results are compared with analytical/numerical solutions of Lee et al. for (a-c) and analytical solution derived in this work for (d). Additionally, the J integral of a fixed crack is calculated in the phase-field model and discussed in the context of fracture mechanics.« less

Modeling elasto-viscoplasticity in a consistent phase field framework

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cheng, Tian -Le; Wen, You -Hai; Hawk, Jeffrey A.

Existing continuum level phase field plasticity theories seek to solve plastic strain by minimizing the shear strain energy. However, rigorously speaking, for thermodynamic consistency it is required to minimize the total strain energy unless there is proof that hydrostatic strain energy is independent of plastic strain which is unfortunately absent. In this work, we extend the phase-field microelasticity theory of Khachaturyan et al. by minimizing the total elastic energy with constraint of incompressibility of plastic strain. We show that the flow rules derived from the Ginzburg-Landau type kinetic equation can be in line with Odqvist's law for viscoplasticity and Prandtl-Reussmore » theory. Free surfaces (external surfaces or internal cracks/voids) are treated in the model. Deformation caused by a misfitting spherical precipitate in an elasto-plastic matrix is studied by large-scale three-dimensional simulations in four different regimes in terms of the matrix: (a) elasto-perfectly-plastic, (b) elastoplastic with linear hardening, (c) elastoplastic with power-law hardening, and (d) elasto-perfectly-plastic with a free surface. The results are compared with analytical/numerical solutions of Lee et al. for (a-c) and analytical solution derived in this work for (d). Additionally, the J integral of a fixed crack is calculated in the phase-field model and discussed in the context of fracture mechanics.« less

Consistent integration of experimental and ab initio data into molecular and coarse-grained models

NASA Astrophysics Data System (ADS)

Vlcek, Lukas

As computer simulations are increasingly used to complement or replace experiments, highly accurate descriptions of physical systems at different time and length scales are required to achieve realistic predictions. The questions of how to objectively measure model quality in relation to reference experimental or ab initio data, and how to transition seamlessly between different levels of resolution are therefore of prime interest. To address these issues, we use the concept of statistical distance to define a measure of similarity between statistical mechanical systems, i.e., a model and its target, and show that its minimization leads to general convergence of the systems' measurable properties. Through systematic coarse-graining, we arrive at appropriate expressions for optimization loss functions consistently incorporating microscopic ab initio data as well as macroscopic experimental data. The design of coarse-grained and multiscale models is then based on factoring the model system partition function into terms describing the system at different resolution levels. The optimization algorithm takes advantage of thermodynamic perturbation expressions for fast exploration of the model parameter space, enabling us to scan millions of parameter combinations per hour on a single CPU. The robustness and generality of the new model optimization framework and its efficient implementation are illustrated on selected examples including aqueous solutions, magnetic systems, and metal alloys.

Matching time and spatial scales of rapid solidification: Dynamic TEM experiments coupled to CALPHAD-informed phase-field simulations

DOE PAGES

Perron, Aurelien; Roehling, John D.; Turchi, Patrice E. A.; ...

2017-12-05

A combination of dynamic transmission electron microscopy (DTEM) experiments and CALPHAD-informed phase-field simulations was used to study rapid solidification in Cu–Ni thin-film alloys. Experiments—conducted in the DTEM—consisted of in situ laser melting and determination of the solidification kinetics by monitoring the solid–liquid interface and the overall microstructure evolution (time-resolved measurements) during the solidification process. Modelling of the Cu–Ni alloy microstructure evolution was based on a phase-field model that included realistic Gibbs energies and diffusion coefficients from the CALPHAD framework (thermodynamic and mobility databases). DTEM and post mortem experiments highlighted the formation of microsegregation-free columnar grains with interface velocities varying frommore » ~0.1 to ~0.6 m s –1. After an 'incubation' time, the velocity of the planar solid–liquid interface accelerated until solidification was complete. In addition, a decrease of the temperature gradient induced a decrease in the interface velocity. The modelling strategy permitted the simulation (in 1D and 2D) of the solidification process from the initially diffusion-controlled to the nearly partitionless regimes. Lastly, results of DTEM experiments and phase-field simulations (grain morphology, solute distribution, and solid–liquid interface velocity) were consistent at similar time (μs) and spatial scales (μm).« less

Insights into Atlantic multidecadal variability using the Last Millennium Reanalysis framework

NASA Astrophysics Data System (ADS)

Singh, Hansi K. A.; Hakim, Gregory J.; Tardif, Robert; Emile-Geay, Julien; Noone, David C.

2018-02-01

The Last Millennium Reanalysis (LMR) employs a data assimilation approach to reconstruct climate fields from annually resolved proxy data over years 0-2000 CE. We use the LMR to examine Atlantic multidecadal variability (AMV) over the last 2 millennia and find several robust thermodynamic features associated with a positive Atlantic Multidecadal Oscillation (AMO) index that reveal a dynamically consistent pattern of variability: the Atlantic and most continents warm; sea ice thins over the Arctic and retreats over the Greenland, Iceland, and Norwegian seas; and equatorial precipitation shifts northward. The latter is consistent with anomalous southward energy transport mediated by the atmosphere. Net downward shortwave radiation increases at both the top of the atmosphere and the surface, indicating a decrease in planetary albedo, likely due to a decrease in low clouds. Heat is absorbed by the climate system and the oceans warm. Wavelet analysis of the AMO time series shows a reddening of the frequency spectrum on the 50- to 100-year timescale, but no evidence of a distinct multidecadal or centennial spectral peak. This latter result is insensitive to both the choice of prior model and the calibration dataset used in the data assimilation algorithm, suggesting that the lack of a distinct multidecadal spectral peak is a robust result.

Coupling continuum dislocation transport with crystal plasticity for application to shock loading conditions

DOE PAGES

Luscher, Darby Jon; Mayeur, Jason Rhea; Mourad, Hashem Mohamed; ...

2015-08-05

Here, we have developed a multi-physics modeling approach that couples continuum dislocation transport, nonlinear thermoelasticity, crystal plasticity, and consistent internal stress and deformation fields to simulate the single-crystal response of materials under extreme dynamic conditions. Dislocation transport is modeled by enforcing dislocation conservation at a slip-system level through the solution of advection-diffusion equations. Nonlinear thermoelasticity provides a thermodynamically consistent equation of state to relate stress (including pressure), temperature, energy densities, and dissipation. Crystal plasticity is coupled to dislocation transport via Orowan's expression where the constitutive description makes use of recent advances in dislocation velocity theories applicable under extreme loading conditions.more » The configuration of geometrically necessary dislocation density gives rise to an internal stress field that can either inhibit or accentuate the flow of dislocations. An internal strain field associated with the internal stress field contributes to the kinematic decomposition of the overall deformation. The paper describes each theoretical component of the framework, key aspects of the constitutive theory, and some details of a one-dimensional implementation. Results from single-crystal copper plate impact simulations are discussed in order to highlight the role of dislocation transport and pile-up in shock loading regimes. The main conclusions of the paper reinforce the utility of the modeling approach to shock problems.« less

Controls of Polysaccharide Chemistry on the Kinetics and Thermodynamics of Heterogeneous Calcium Carbonate Nucleation

NASA Astrophysics Data System (ADS)

Giuffre, A. J.; Han, N.; Dove, P. M.

2011-12-01

Polysaccharide fibrils control the orientation of calcium carbonate (CaCO3) biominerals. Good examples are found in the multilayered extracellular mucilaginous sheath of green algae and cyanobacteria and in specialized vesicles inside coccolithophorids. More complex organisms such as arthropods and mollusks form biomineralized exoskeletons and shells that consist of insoluble polysaccharides and soluble acid-rich proteins. In these structures, CaCO3 mineral orientation occurs along fibers of the polysaccharide chitin. This raises the question of whether polysaccharide chemistry has specific roles in directing biomineralization. The last three decades of research show that acidic proteins influence CaCO3 polymorph selection, crystallographic orientation, and nucleation and growth rates but little is known about the function of polysaccharides. In fact, polysaccharides are long considered an inert component of organic frameworks. In this experimental investigation, we test the hypothesis that polysaccharides have chemistry-specific influences on calcification by measuring the kinetics of calcite nucleation onto three types of polysaccharide films under controlled solution compositions. Characterized polysaccharides of simple repeating monomer sequences were chosen as model compounds to represent the major carbohydrates seen in microbial and calcifying environments: 1) alginic acid with carboxyl groups, 2) hyaluronic acid with alternating carboxyl and acetylamine groups, and 3) chitosan with amine and acetylamine groups. Biosubstrates were prepared by electrodeposition of these compounds as thin gel-like films onto gold-coated silicon wafers. Using a flow-through cell, heterogeneous nucleation rates of calcite were measured for a suite of supersaturation conditions. These rate data were compared to similar measurements for carboxyl- and hydroxyl-terminated self-assembled monolayers. Calcite nucleation rates onto the three polysaccharides vary by a factor of 400x. Preliminary analyses of the data attribute these differences to changes in both kinetic and thermodynamic barriers to nucleation. These initial findings indicate that polysaccharide chemistry can have active roles in regulating the kinetics of calcite formation. It may be time to reconsider their presumed function as inert framework molecules for mineralized structures. Future work will investigate CaCO3 nucleation on substrates of polysaccharides with more complex functionalization and monomer sequences to decipher the origins of these effects in promoting or inhibiting mineralization.

Long-ranged contributions to solvation free energies from theory and short-ranged models

PubMed Central

Remsing, Richard C.; Liu, Shule; Weeks, John D.

2016-01-01

Long-standing problems associated with long-ranged electrostatic interactions have plagued theory and simulation alike. Traditional lattice sum (Ewald-like) treatments of Coulomb interactions add significant overhead to computer simulations and can produce artifacts from spurious interactions between simulation cell images. These subtle issues become particularly apparent when estimating thermodynamic quantities, such as free energies of solvation in charged and polar systems, to which long-ranged Coulomb interactions typically make a large contribution. In this paper, we develop a framework for determining very accurate solvation free energies of systems with long-ranged interactions from models that interact with purely short-ranged potentials. Our approach is generally applicable and can be combined with existing computational and theoretical techniques for estimating solvation thermodynamics. We demonstrate the utility of our approach by examining the hydration thermodynamics of hydrophobic and ionic solutes and the solvation of a large, highly charged colloid that exhibits overcharging, a complex nonlinear electrostatic phenomenon whereby counterions from the solvent effectively overscreen and locally invert the integrated charge of the solvated object. PMID:26929375

Thermodynamics-based Metabolite Sensitivity Analysis in metabolic networks.

PubMed

Kiparissides, A; Hatzimanikatis, V

2017-01-01

The increasing availability of large metabolomics datasets enhances the need for computational methodologies that can organize the data in a way that can lead to the inference of meaningful relationships. Knowledge of the metabolic state of a cell and how it responds to various stimuli and extracellular conditions can offer significant insight in the regulatory functions and how to manipulate them. Constraint based methods, such as Flux Balance Analysis (FBA) and Thermodynamics-based flux analysis (TFA), are commonly used to estimate the flow of metabolites through genome-wide metabolic networks, making it possible to identify the ranges of flux values that are consistent with the studied physiological and thermodynamic conditions. However, unless key intracellular fluxes and metabolite concentrations are known, constraint-based models lead to underdetermined problem formulations. This lack of information propagates as uncertainty in the estimation of fluxes and basic reaction properties such as the determination of reaction directionalities. Therefore, knowledge of which metabolites, if measured, would contribute the most to reducing this uncertainty can significantly improve our ability to define the internal state of the cell. In the present work we combine constraint based modeling, Design of Experiments (DoE) and Global Sensitivity Analysis (GSA) into the Thermodynamics-based Metabolite Sensitivity Analysis (TMSA) method. TMSA ranks metabolites comprising a metabolic network based on their ability to constrain the gamut of possible solutions to a limited, thermodynamically consistent set of internal states. TMSA is modular and can be applied to a single reaction, a metabolic pathway or an entire metabolic network. This is, to our knowledge, the first attempt to use metabolic modeling in order to provide a significance ranking of metabolites to guide experimental measurements. Copyright © 2016 International Metabolic Engineering Society. Published by Elsevier Inc. All rights reserved.

An analytical coarse-graining method which preserves the free energy, structural correlations, and thermodynamic state of polymer melts from the atomistic to the mesoscale.

PubMed

McCarty, J; Clark, A J; Copperman, J; Guenza, M G

2014-05-28

Structural and thermodynamic consistency of coarse-graining models across multiple length scales is essential for the predictive role of multi-scale modeling and molecular dynamic simulations that use mesoscale descriptions. Our approach is a coarse-grained model based on integral equation theory, which can represent polymer chains at variable levels of chemical details. The model is analytical and depends on molecular and thermodynamic parameters of the system under study, as well as on the direct correlation function in the k → 0 limit, c0. A numerical solution to the PRISM integral equations is used to determine c0, by adjusting the value of the effective hard sphere diameter, dHS, to agree with the predicted equation of state. This single quantity parameterizes the coarse-grained potential, which is used to perform mesoscale simulations that are directly compared with atomistic-level simulations of the same system. We test our coarse-graining formalism by comparing structural correlations, isothermal compressibility, equation of state, Helmholtz and Gibbs free energies, and potential energy and entropy using both united atom and coarse-grained descriptions. We find quantitative agreement between the analytical formalism for the thermodynamic properties, and the results of Molecular Dynamics simulations, independent of the chosen level of representation. In the mesoscale description, the potential energy of the soft-particle interaction becomes a free energy in the coarse-grained coordinates which preserves the excess free energy from an ideal gas across all levels of description. The structural consistency between the united-atom and mesoscale descriptions means the relative entropy between descriptions has been minimized without any variational optimization parameters. The approach is general and applicable to any polymeric system in different thermodynamic conditions.

Heat capacities and thermodynamic functions for beryl, Be3Al2Si6O18, phenakite, Be2SiO4, euclase, BeAlSiO4(OH), bertrandite, Be4Si2O7(OH)2, and chrysoberyl, BeAl2O4.

USGS Publications Warehouse

Hemingway, B.S.; Barton, M.D.; Robie, R.A.; Haselton, H.T.

1986-01-01

The heat capacities of beryl, phenakite, euclase and bertrandite have been measured between approx 5 and 800 K by combined quasi-adiabatic cryogenic calorimetry and differential scanning calorimetry. The heat capacities of chrysoberyl have been measured from 340 to 800 K. The resulting data have been combined with solution and phase-equilibrium experimental data and simultaneously adjusted using the programme PHAS20 to provide an internally consistent set of thermodynamic properties for several important beryllium phases. The experimental heat capacities and tables of derived thermodynamic properties are presented.-J.A.Z.

An improved thermodynamic perturbation theory for Mercedes-Benz water

NASA Astrophysics Data System (ADS)

Urbic, T.; Vlachy, V.; Kalyuzhnyi, Yu. V.; Dill, K. A.

2007-11-01

We previously applied Wertheim's thermodynamic perturbation theory for associative fluids to the simple Mercedes-Benz model of water. We found that the theory reproduced well the physical properties of hot water, but was less successful in capturing the more structured hydrogen bonding that occurs in cold water. Here, we propose an improved version of the thermodynamic perturbation theory in which the effective density of the reference system is calculated self-consistently. The new theory is a significant improvement, giving good agreement with Monte Carlo simulations of the model, and predicting key anomalies of cold water, such as minima in the molar volume and large heat capacity, in addition to giving good agreement with the isothermal compressibility and thermal expansion coefficient.

Thermodynamic constraints on fluctuation phenomena

NASA Astrophysics Data System (ADS)

Maroney, O. J. E.

2009-12-01

The relationships among reversible Carnot cycles, the absence of perpetual motion machines, and the existence of a nondecreasing globally unique entropy function form the starting point of many textbook presentations of the foundations of thermodynamics. However, the thermal fluctuation phenomena associated with statistical mechanics has been argued to restrict the domain of validity of this basis of the second law of thermodynamics. Here we demonstrate that fluctuation phenomena can be incorporated into the traditional presentation, extending rather than restricting the domain of validity of the phenomenologically motivated second law. Consistency conditions lead to constraints upon the possible spectrum of thermal fluctuations. In a special case this uniquely selects the Gibbs canonical distribution and more generally incorporates the Tsallis distributions. No particular model of microscopic dynamics need be assumed.

Thermodynamic constraints on fluctuation phenomena.

PubMed

Maroney, O J E

2009-12-01

The relationships among reversible Carnot cycles, the absence of perpetual motion machines, and the existence of a nondecreasing globally unique entropy function form the starting point of many textbook presentations of the foundations of thermodynamics. However, the thermal fluctuation phenomena associated with statistical mechanics has been argued to restrict the domain of validity of this basis of the second law of thermodynamics. Here we demonstrate that fluctuation phenomena can be incorporated into the traditional presentation, extending rather than restricting the domain of validity of the phenomenologically motivated second law. Consistency conditions lead to constraints upon the possible spectrum of thermal fluctuations. In a special case this uniquely selects the Gibbs canonical distribution and more generally incorporates the Tsallis distributions. No particular model of microscopic dynamics need be assumed.

An improved thermodynamic perturbation theory for Mercedes-Benz water.

PubMed

Urbic, T; Vlachy, V; Kalyuzhnyi, Yu V; Dill, K A

2007-11-07

We previously applied Wertheim's thermodynamic perturbation theory for associative fluids to the simple Mercedes-Benz model of water. We found that the theory reproduced well the physical properties of hot water, but was less successful in capturing the more structured hydrogen bonding that occurs in cold water. Here, we propose an improved version of the thermodynamic perturbation theory in which the effective density of the reference system is calculated self-consistently. The new theory is a significant improvement, giving good agreement with Monte Carlo simulations of the model, and predicting key anomalies of cold water, such as minima in the molar volume and large heat capacity, in addition to giving good agreement with the isothermal compressibility and thermal expansion coefficient.

Kinetics versus thermodynamics in materials modeling: The case of the di-vacancy in iron

NASA Astrophysics Data System (ADS)

Djurabekova, F.; Malerba, L.; Pasianot, R. C.; Olsson, P.; Nordlund, K.

2010-07-01

Monte Carlo models are widely used for the study of microstructural and microchemical evolution of materials under irradiation. However, they often link explicitly the relevant activation energies to the energy difference between local equilibrium states. We provide a simple example (di-vacancy migration in iron) in which a rigorous activation energy calculation, by means of both empirical interatomic potentials and density functional theory methods, clearly shows that such a link is not granted, revealing a migration mechanism that a thermodynamics-linked activation energy model cannot predict. Such a mechanism is, however, fully consistent with thermodynamics. This example emphasizes the importance of basing Monte Carlo methods on models where the activation energies are rigorously calculated, rather than deduced from widespread heuristic equations.

Second generation biofuels: Thermochemistry of glucose and fructose

DOE Office of Scientific and Technical Information (OSTI.GOV)

Osmont, A.; Catoire, L.; C.N.R.S. - I.N.S.I.S., I.C.A.R.E., 1C, Avenue de la Recherche Scientifique, 45071 Orleans Cedex 2

2010-06-15

The energetic conversion of biomass into syngas or biogas is a more and more important topic. In the framework of these studies, improved understanding of glucose and fructose thermal decomposition and oxidation appears crucial. For this task, thermodynamic data are needed to make possible, for instance, the building of a detailed chemical kinetic model of glucose and fructose reactivity at high temperature. A semitheoretical protocol, presented elsewhere, is used for the estimation of the thermodynamic data of glucose and fructose in the gas phase. Five isomers of glucose and five isomers of fructose are considered and the lowest-energy conformers aremore » found to be {beta}-D-glucopyranose for glucose and {beta}-D-fructopyranose for fructose. The data for all 10 isomers are provided in the CHEMKIN-NASA format. (author)« less

Thermodynamics of freezing and melting

PubMed Central

Pedersen, Ulf R.; Costigliola, Lorenzo; Bailey, Nicholas P.; Schrøder, Thomas B.; Dyre, Jeppe C.

2016-01-01

Although the freezing of liquids and melting of crystals are fundamental for many areas of the sciences, even simple properties like the temperature–pressure relation along the melting line cannot be predicted today. Here we present a theory in which properties of the coexisting crystal and liquid phases at a single thermodynamic state point provide the basis for calculating the pressure, density and entropy of fusion as functions of temperature along the melting line, as well as the variation along this line of the reduced crystalline vibrational mean-square displacement (the Lindemann ratio), and the liquid's diffusion constant and viscosity. The framework developed, which applies for the sizable class of systems characterized by hidden scale invariance, is validated by computer simulations of the standard 12-6 Lennard-Jones system. PMID:27530064

Modeling the dynamics of shape generation and sensing by proteins on lipid membranes

NASA Astrophysics Data System (ADS)

Walani, Nikhil; Arroyo, Marino

Lipid membranes are fluid surfaces with flexural resistance that interact with proteins to perform their function in a biological context. A set of these proteins are responsible for shaping the lipid membranes, or of sensing curvature. A large body of work has examined the curvature sensing and generation properties of these proteins. Even though such processes are fundamentally dynamical in cells and in in vitro reconstituted systems, theoretical and computational studies have largely focussed on equilibrium thermodynamics. In this work, we propose a theoretical framework based on Onsager's variational principle of irreversible thermodynamics that captures the dynamics of adsorption, diffusion, and shape generation or sensing of proteins on lipid surfaces. We acknowledge the funds from European Research Council CoG- 681434 to support this research.

Phase structure of the Polyakov-quark-meson model

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schaefer, B.-J.; Pawlowski, J. M.; Wambach, J.

2007-10-01

The relation between the deconfinement and chiral phase transition is explored in the framework of a Polyakov-loop-extended two-flavor quark-meson (PQM) model. In this model the Polyakov loop dynamics is represented by a background temporal gauge field which also couples to the quarks. As a novelty an explicit quark chemical potential and N{sub f}-dependence in the Polyakov loop potential is proposed by using renormalization group arguments. The behavior of the Polyakov loop as well as the chiral condensate as function of temperature and quark chemical potential is obtained by minimizing the grand canonical thermodynamic potential of the system. The effect ofmore » the Polyakov loop dynamics on the chiral phase diagram and on several thermodynamic bulk quantities is presented.« less

Shaping Crystal-Crystal Phase Transitions

NASA Astrophysics Data System (ADS)

Du, Xiyu; van Anders, Greg; Dshemuchadse, Julia; Glotzer, Sharon

Previous computational and experimental studies have shown self-assembled structure depends strongly on building block shape. New synthesis techniques have led to building blocks with reconfigurable shape and it has been demonstrated that building block reconfiguration can induce bulk structural reconfiguration. However, we do not understand systematically how this transition happens as a function of building block shape. Using a recently developed ``digital alchemy'' framework, we study the thermodynamics of shape-driven crystal-crystal transitions. We find examples of shape-driven bulk reconfiguration that are accompanied by first-order phase transitions, and bulk reconfiguration that occurs without any thermodynamic phase transition. Our results suggest that for well-chosen shapes and structures, there exist facile means of bulk reconfiguration, and that shape-driven bulk reconfiguration provides a viable mechanism for developing functional materials.

Nonequilibrium thermodynamic potentials for continuous-time Markov chains.

PubMed

Verley, Gatien

2016-01-01

We connect the rare fluctuations of an equilibrium (EQ) process and the typical fluctuations of a nonequilibrium (NE) stationary process. In the framework of large deviation theory, this observation allows us to introduce NE thermodynamic potentials. For continuous-time Markov chains, we identify the relevant pairs of conjugated variables and propose two NE ensembles: one with fixed dynamics and fluctuating time-averaged variables, and another with fixed time-averaged variables, but a fluctuating dynamics. Accordingly, we show that NE processes are equivalent to conditioned EQ processes ensuring that NE potentials are Legendre dual. We find a variational principle satisfied by the NE potentials that reach their maximum in the NE stationary state and whose first derivatives produce the NE equations of state and second derivatives produce the NE Maxwell relations generalizing the Onsager reciprocity relations.

Large deviation analysis of a simple information engine

NASA Astrophysics Data System (ADS)

Maitland, Michael; Grosskinsky, Stefan; Harris, Rosemary J.

2015-11-01

Information thermodynamics provides a framework for studying the effect of feedback loops on entropy production. It has enabled the understanding of novel thermodynamic systems such as the information engine, which can be seen as a modern version of "Maxwell's Dæmon," whereby a feedback controller processes information gained by measurements in order to extract work. Here, we analyze a simple model of such an engine that uses feedback control based on measurements to obtain negative entropy production. We focus on the distribution and fluctuations of the information obtained by the feedback controller. Significantly, our model allows an analytic treatment for a two-state system with exact calculation of the large deviation rate function. These results suggest an approximate technique for larger systems, which is corroborated by simulation data.

Thermodynamic evidence for the Bose glass transition in twinned YBa 2 Cu 3 O 7 - δ crystals

DOE PAGES

Pérez-Morelo, D. J.; Osquiguil, E.; Kolton, A. B.; ...

2015-07-21

We used a micromechanical torsional o scillator to measure the magnetic response of a twinned YBaBa2Cu3O7-δ single crystal disk near the Bose glass transition. We observe an anomaly in the temperature dependence of the magnetization consistent with the appearance of a magnetic shielding perpendicular to the correlated pinning of the twin boundaries. This effect is related to the thermodynamic transition from the vortex liquid phase to a Bose glass state.

Hot string soup: Thermodynamics of strings near the Hagedorn transition

NASA Astrophysics Data System (ADS)

Lowe, David A.; Thorlacius, Lárus

1995-01-01

Above the Hagedorn energy density closed fundamental strings form a long string phase. The dynamics of weakly interacting long strings is described by a simple Boltzmann equation which can be solved explicitly for equilibrium distributions. The averge total number of long strings grows logarithmically with total energy in the microcanonical ensemble. This is consistent with calculations of the free single string density of states provided the thermodynamic limit is carefully defined. If the theory contains open strings the long string phase is suppressed.

Development of a critically evaluated thermodynamic database for the systems containing alkaline-earth oxides

NASA Astrophysics Data System (ADS)

Shukla, Adarsh

In a thermodynamic system which contains several elements, the phase relationships among the components are usually very complex. Especially, systems containing oxides are generally very difficult to investigate owing to the very high experimental temperatures and corrosive action of slags. Due to such difficulties, large inconsistencies are often observed among the available experimental data. In order to investigate and understand the complex phase relationships effectively, it is very useful to develop thermodynamic databases containing optimized model parameters giving the thermodynamic properties of all phases as functions of temperature and composition. In a thermodynamic optimization, adjustable model parameters are calculated using, simultaneously, all available thermodynamic and phase-equilibrium data in order to obtain one set of model equations as functions of temperature and composition. Thermodynamic data, such as activities, can aid in the evaluation of the phase diagrams, and information on phase equilibria can be used to deduce thermodynamic properties. Thus, it is frequently possible to resolve discrepancies in the available data. From the model equations, all the thermodynamic properties and phase diagrams can be back-calculated, and interpolations and extrapolations can be made in a thermodynamically correct manner. The data are thereby rendered self-consistent and consistent with thermodynamic principles, and the available data are distilled into a small set of model parameters, ideal for computer storage. As part of a broader research project at the Centre de Recherche en Calcul Thermochimique (CRCT), Ecole Polytechnique to develop a thermodynamic database for multicomponent oxide systems, this thesis deals with the addition of components SrO and BaO to the existing multicomponent database of the SiO2-B2O3-Al2O 3-CaO-MgO system. Over the years, in collaboration with many industrial companies, a thermodynamic database for the SiO2-B2O 3-Al2O3-CaO-MgO system has been built quite satisfactorily. The aim of the present work was to improve the applicability of this five component database by adding SrO and BaO to it. The databases prepared in this work will be of special importance to the glass and steel industries. In the SiO2-B2O3-Al2O 3-CaO-MgO-BaO-SrO system there are 11 binary systems and 25 ternary systems which contain either BaO or SrO or both. For most of these binary systems, and for none of these ternary systems, is there a previous thermodynamic optimization available in the literature. In this thesis, thermodynamic evaluation and optimization for the 11 binary, 17 ternary and 5 quaternary BaO- and SrO- containing systems in the SiO2-B2O3-Al 2O3-CaO-MgO-BaO-SrO system is presented. All these thermodynamic optimizations were performed based on the experimental data available in the literature, except for the SrO-B2O3-SiO2 system. This latter system was optimized on the basis of a few experimental data points generated in the present work together with the data from the literature. In the present work, all the calculations were performed using the FactSage™ thermochemical software. The Modified Quasichemical Model (MQM), which is capable of taking short-range ordering into account, was used for the liquid phase. All the binary systems were critically evaluated and optimized using available phase equilibrium and thermodynamic data. The model parameters obtained as a result of this simultaneous optimization were used to represent the Gibbs energies of all phases as functions of temperature and composition. Optimized binary model parameters were used to estimate the thermodynamic properties of phases in the ternary systems. Proper “geometric” models were used for these estimations. Ternary phase diagram were calculated and compared with available experimental data. Wherever required, ternary interaction parameters were also added. The first part of this thesis comprises a general literature review on the subject of thermodynamic modeling and experimental techniques for phase diagram determination. The next chapters include the literature review and the thermodynamic optimizations of the various systems. The last part of the thesis is the presentation of experiments performed in the present work, by quenching and EPMA, in the SrO-B2O3-SiO2 system. The experiments were designed to generate the maximum amount of information with the minimum number of experiments using the thermodynamic optimization, based only on the data available in the literature, as a guide. These newly-obtained data improved the (preceding) thermodynamic optimization, based on the experimental data in the literature, of this ternary system.

A Network Thermodynamic Framework for the Analysis and Control Design of Large-Scale Dynamical Systems

DTIC Science & Technology

2006-03-31

Nonnegative Dynamical Sys- tems................................................. 18 2.10. Adaptive Control for General Anesthesia and Intensive Care...Unit Sedation 20 2.11. Neural Network Adaptive Control for Intensive Care Unit Sedation and In- traoperative Anesthesia ...control for operating room hypnosis and intefisive care unit sedation. 1.3. Goals of this Report The main goal of this report is to summarize the

Light fragments from (C + Be) interactions at 0.6 GeV/nucleon

DOE PAGES

Abramov, B. M.; Alekseev, P. N.; Borodin, Yu. A.; ...

2016-05-01

We measured nuclear fragments emitted at 3.5° in 12C fragmentation at 0.6 GeV/nucleon. We also used the spectra obtained to test the predictions of four ion-ion interaction models: INCL++, BC, LAQGSM03.03 and QMD as well as for the comparison with the analytical parametrization in the framework of thermodynamical picture of fragmentation.

Modeling of Water-Breathing Propulsion Systems Utilizing the Aluminum-Seawater Reaction and Solid-Oxide Fuel Cells

DTIC Science & Technology

2011-01-01

ABSTRACT Title of Document: MODELING OF WATER-BREATHING PROPULSION SYSTEMS UTILIZING THE ALUMINUM-SEAWATER REACTION AND SOLID...Hybrid Aluminum Combustor (HAC): a novel underwater power system based on the exothermic reaction of aluminum with seawater. The system is modeled ...using a NASA-developed framework called Numerical Propulsion System Simulation (NPSS) by assembling thermodynamic models developed for each component

Phase transition in tumor growth: I avascular development

NASA Astrophysics Data System (ADS)

Izquierdo-Kulich, E.; Rebelo, I.; Tejera, E.; Nieto-Villar, J. M.

2013-12-01

We propose a mechanism for avascular tumor growth based on a simple chemical network. This model presents a logistic behavior and shows a “second order” phase transition. We prove the fractal origin of the empirical logistics and Gompertz constant and its relation to mitosis and apoptosis rate. Finally, the thermodynamics framework developed demonstrates the entropy production rate as a Lyapunov function during avascular tumor growth.

The Use of History and Philosophy of Science as a Core for a Socioconstructivist Teaching Approach of the Concept of Energy in Primary Education

ERIC Educational Resources Information Center

Rizaki, Aikaterini; Kokkotas, Panagiotis

2013-01-01

The present study should be thought as a socioconstructivist teaching approach (a teaching model) for the concept of energy in primary education. It contains important and crucial aspects of the History and Philosophy of Natural Sciences, introduces the concept of energy using the macroscopic framework of thermodynamics, takes into consideration…

Spin caloritronics, origin and outlook

NASA Astrophysics Data System (ADS)

Yu, Haiming; Brechet, Sylvain D.; Ansermet, Jean-Philippe

2017-03-01

Spin caloritronics refers to research efforts in spintronics when a heat current plays a role. In this review, we start out by reviewing the predictions that can be drawn from the thermodynamics of irreversible processes. This serves as a conceptual framework in which to analyze the interplay of charge, spin and heat transport. This formalism predicts tensorial relations between vectorial quantities such as currents and gradients of chemical potentials or of temperature. Transverse effects such as the Nernst or Hall effects are predicted on the basis that these tensors can include an anti-symmetric contribution, which can be written with a vectorial cross-product. The local symmetry of the system may determine the direction of the vector defining such transverse effects, such as the surface of an isotropic medium. By including magnetization as state field in the thermodynamic description, spin currents appear naturally from the continuity equation for the magnetization, and dissipative spin torques are derived, which are charge-driven or heat-driven. Thermodynamics does not give the strength of these effects, but may provide relationships between them. Based on this framework, the review proceeds by showing how these effects have been observed in various systems. Spintronics has become a vast field of research, and the experiments highlighted in this review pertain only to heat effects on transport and magnetization dynamics, such as magneto-thermoelectric power, or the spin-dependence of the Seebeck effect, the spin-dependence of the Peltier effect, the spin Seebeck effect, the magnetic Seebeck effect, or the Nernst effect. The review concludes by pointing out predicted effects that are yet to be verified experimentally, and in what novel materials the standard thermal spin effects could be investigated.

Metal-organic frameworks as selectivity regulators for hydrogenation reactions

NASA Astrophysics Data System (ADS)

Zhao, Meiting; Yuan, Kuo; Wang, Yun; Li, Guodong; Guo, Jun; Gu, Lin; Hu, Wenping; Zhao, Huijun; Tang, Zhiyong

2016-11-01

Owing to the limited availability of natural sources, the widespread demand of the flavouring, perfume and pharmaceutical industries for unsaturated alcohols is met by producing them from α,β-unsaturated aldehydes, through the selective hydrogenation of the carbon-oxygen group (in preference to the carbon-carbon group). However, developing effective catalysts for this transformation is challenging, because hydrogenation of the carbon-carbon group is thermodynamically favoured. This difficulty is particularly relevant for one major category of heterogeneous catalyst: metal nanoparticles supported on metal oxides. These systems are generally incapable of significantly enhancing the selectivity towards thermodynamically unfavoured reactions, because only the edges of nanoparticles that are in direct contact with the metal-oxide support possess selective catalytic properties; most of the exposed nanoparticle surfaces do not. This has inspired the use of metal-organic frameworks (MOFs) to encapsulate metal nanoparticles within their layers or inside their channels, to influence the activity of the entire nanoparticle surface while maintaining efficient reactant and product transport owing to the porous nature of the material. Here we show that MOFs can also serve as effective selectivity regulators for the hydrogenation of α,β-unsaturated aldehydes. Sandwiching platinum nanoparticles between an inner core and an outer shell composed of an MOF with metal nodes of Fe3+, Cr3+ or both (known as MIL-101; refs 19, 20, 21) results in stable catalysts that convert a range of α,β-unsaturated aldehydes with high efficiency and with significantly enhanced selectivity towards unsaturated alcohols. Calculations reveal that preferential interaction of MOF metal sites with the carbon-oxygen rather than the carbon-carbon group renders hydrogenation of the former by the embedded platinum nanoparticles a thermodynamically favoured reaction. We anticipate that our basic design strategy will allow the development of other selective heterogeneous catalysts for important yet challenging transformations.

Metal-organic frameworks as selectivity regulators for hydrogenation reactions.

PubMed

Zhao, Meiting; Yuan, Kuo; Wang, Yun; Li, Guodong; Guo, Jun; Gu, Lin; Hu, Wenping; Zhao, Huijun; Tang, Zhiyong

2016-11-03

Owing to the limited availability of natural sources, the widespread demand of the flavouring, perfume and pharmaceutical industries for unsaturated alcohols is met by producing them from α,β-unsaturated aldehydes, through the selective hydrogenation of the carbon-oxygen group (in preference to the carbon-carbon group). However, developing effective catalysts for this transformation is challenging, because hydrogenation of the carbon-carbon group is thermodynamically favoured. This difficulty is particularly relevant for one major category of heterogeneous catalyst: metal nanoparticles supported on metal oxides. These systems are generally incapable of significantly enhancing the selectivity towards thermodynamically unfavoured reactions, because only the edges of nanoparticles that are in direct contact with the metal-oxide support possess selective catalytic properties; most of the exposed nanoparticle surfaces do not. This has inspired the use of metal-organic frameworks (MOFs) to encapsulate metal nanoparticles within their layers or inside their channels, to influence the activity of the entire nanoparticle surface while maintaining efficient reactant and product transport owing to the porous nature of the material. Here we show that MOFs can also serve as effective selectivity regulators for the hydrogenation of α,β-unsaturated aldehydes. Sandwiching platinum nanoparticles between an inner core and an outer shell composed of an MOF with metal nodes of Fe 3+ , Cr 3+ or both (known as MIL-101; refs 19, 20, 21) results in stable catalysts that convert a range of α,β-unsaturated aldehydes with high efficiency and with significantly enhanced selectivity towards unsaturated alcohols. Calculations reveal that preferential interaction of MOF metal sites with the carbon-oxygen rather than the carbon-carbon group renders hydrogenation of the former by the embedded platinum nanoparticles a thermodynamically favoured reaction. We anticipate that our basic design strategy will allow the development of other selective heterogeneous catalysts for important yet challenging transformations.

Thermodynamics of cosmological matter creation.

PubMed

Prigogine, I; Geheniau, J; Gunzig, E; Nardone, P

1988-10-01

A type of cosmological history that includes large-scale entropy production is proposed. These cosmologies are based on reinterpretation of the matter-energy stress tensor in Einstein's equations. This modifies the usual adiabatic energy conservation laws, thereby including irreversible matter creation. This creation corresponds to an irreversible energy flow from the gravitational field to the created matter constituents. This point of view results from consideration of the thermodynamics of open systems in the framework of cosmology. It is shown that the second law of thermodynamics requires that space-time transforms into matter, while the inverse transformation is forbidden. It appears that the usual initial singularity associated with the big bang is structurally unstable with respect to irreversible matter creation. The corresponding cosmological history therefore starts from an instability of the vacuum rather than from a singularity. This is exemplified in the framework of a simple phenomenological model that leads to a three-stage cosmology: the first drives the cosmological system from the initial instability to a de Sitter regime, and the last connects with the usual matter-radiation Robertson-Walker universe. Matter as well as entropy creation occurs during the first two stages, while the third involves the traditional cosmological evolution. A remarkable fact is that the de Sitter stage appears to be an attractor independent of the initial fluctuation. This is also the case for all the physical predictions involving the present Robertson-Walker universe. Most results obtained previously, in the framework of quantum field theory, can now be obtained on a macroscopic basis. It is shown that this description leads quite naturally to the introduction of primeval black holes as the intermediate stage between the Minkowski vacuum and the present matter-radiation universe. The instability at the origin of the universe is the result of fluctuations of the vacuum in which black holes act as membranes that stabilize these fluctuations. In short, black holes will be produced by and "inverse" Hawking radiation process and, once formed, will decompose into "real" matter through the usual Hawking radiation. In this way, the irreversible transformation of space-time into matter can be described as a phase separation between matter and gravitation in which black holes play the role of "critical nuclei."

Thermodynamics and mechanics of stretch-induced crystallization in rubbers

NASA Astrophysics Data System (ADS)

Guo, Qiang; Zaïri, Fahmi; Guo, Xinglin

2018-05-01

The aim of the present paper is to provide a quantitative prediction of the stretch-induced crystallization in natural rubber, the exclusive reason for its history-dependent thermomechanical features. A constitutive model based on a micromechanism inspired molecular chain approach is formulated within the context of the thermodynamic framework. The molecular configuration of the partially crystallized single chain is analyzed and calculated by means of some statistical mechanical methods. The random thermal oscillation of the crystal orientation, considered as a continuous random variable, is treated by means of a representative angle. The physical expression of the chain free energy is derived according to a two-step strategy by separating crystallization and stretching. This strategy ensures that the stretch-induced part of the thermodynamic crystallization force is null at the initial instant and allows, without any additional constraint, the formulation of a simple linear relationship for the crystallinity evolution law. The model contains very few physically interpretable material constants to simulate the complex mechanism: two chain-scale constants, one crystallinity kinetics constant, three thermodynamic constants related to the newly formed crystallites, and a function controlling the crystal orientation with respect to the chain. The model is used to discuss some important aspects of the micromechanism and the macroresponse under the equilibrium state and the nonequilibrium state involved during stretching and recovery, and continuous relaxation.

Thermostatistical description of gas mixtures from space partitions

NASA Astrophysics Data System (ADS)

Rohrmann, R. D.; Zorec, J.

2006-10-01

The new mathematical framework based on the free energy of pure classical fluids presented by Rohrmann [Physica A 347, 221 (2005)] is extended to multicomponent systems to determine thermodynamic and structural properties of chemically complex fluids. Presently, the theory focuses on D -dimensional mixtures in the low-density limit (packing factor η<0.01 ). The formalism combines the free-energy minimization technique with space partitions that assign an available volume v to each particle. v is related to the closeness of the nearest neighbor and provides a useful tool to evaluate the perturbations experimented by particles in a fluid. The theory shows a close relationship between statistical geometry and statistical mechanics. New, unconventional thermodynamic variables and mathematical identities are derived as a result of the space division. Thermodynamic potentials μil , conjugate variable of the populations Nil of particles class i with the nearest neighbors of class l are defined and their relationships with the usual chemical potentials μi are established. Systems of hard spheres are treated as illustrative examples and their thermodynamics functions are derived analytically. The low-density expressions obtained agree nicely with those of scaled-particle theory and Percus-Yevick approximation. Several pair distribution functions are introduced and evaluated. Analytical expressions are also presented for hard spheres with attractive forces due to Kac-tails and square-well potentials. Finally, we derive general chemical equilibrium conditions.

The real limits to marine life: a further critique of the Respiration Index

NASA Astrophysics Data System (ADS)

Seibel, B. A.; Childress, J. J.

2013-05-01

The recently proposed "Respiration Index" (RI = log PO2/PCO2) suggests that aerobic metabolism is limited by the ratio of reactants (oxygen) to products (carbon dioxide) according to the thermodynamics of cellular respiration. Here, we demonstrate further that, because of the large standard free energy change for organic carbon oxidation (ΔG° = -686 kcal mol-1), carbon dioxide can never reach concentrations that would limit the thermodynamics of this reaction. A PCO2 to PO2 ratio of 10503 would be required to reach equilibrium (equilibrium constant, Keq = 10503), where ΔG = 0. Thus, a Respiration Index of -503 would be the real thermodynamic limit to aerobic life. Such a Respiration Index is never reached, either in the cell or in the environment. Moreover, cellular respiration and oxygen provision are kinetically controlled such that, within limits, environmental oxygen and CO2 concentrations have little to do with intracellular concentrations. The RI is fundamentally different from the aragonite saturation state, a thermodynamic index used to quantify the potential effect of CO2 on calcification rates, because of its failure to incorporate the equilibrium constant of the reaction. Not only is the RI invalid, but its use leads to incorrect and misleading predictions of the threat of changing oxygen and carbon dioxide to marine life. We provide a physiological framework that identifies oxygen thresholds and allows for synergistic effects of ocean acidification and global warming.

Econophysics and bio-chemical engineering thermodynamics: The exergetic analysis of a municipality

NASA Astrophysics Data System (ADS)

Lucia, Umberto

2016-11-01

Exergy is a fundamental quantity because it allows us to obtain information on the useful work obtainable in a process. The analyses of irreversibility are important not only in the design and development of the industrial devices, but also in fundamental thermodynamics and in the socio-economic analysis of municipality. Consequently, the link between entropy and exergy is discussed in order to link econophysics to the bio-chemical engineering thermodynamics. Last, this link holds to the fundamental role of fluxes and to the exergy exchanged in the interaction between the system and its environment. The result consists in a thermodynamic approach to the analysis of the unavailability of the economic, productive or social systems. The unavailability is what the system cannot use in relation to its internal processes. This quantity result is interesting also as a support to public manager for economic decisions. Here, the Alessandria Municipality is analyzed in order to highlight the application of the theoretical results.

Heat of supersaturation-limited amyloid burst directly monitored by isothermal titration calorimetry.

PubMed

Ikenoue, Tatsuya; Lee, Young-Ho; Kardos, József; Yagi, Hisashi; Ikegami, Takahisa; Naiki, Hironobu; Goto, Yuji

2014-05-06

Amyloid fibrils form in supersaturated solutions via a nucleation and growth mechanism. Although the structural features of amyloid fibrils have become increasingly clearer, knowledge on the thermodynamics of fibrillation is limited. Furthermore, protein aggregation is not a target of calorimetry, one of the most powerful approaches used to study proteins. Here, with β2-microglobulin, a protein responsible for dialysis-related amyloidosis, we show direct heat measurements of the formation of amyloid fibrils using isothermal titration calorimetry (ITC). The spontaneous fibrillation after a lag phase was accompanied by exothermic heat. The thermodynamic parameters of fibrillation obtained under various protein concentrations and temperatures were consistent with the main-chain dominated structural model of fibrils, in which overall packing was less than that of the native structures. We also characterized the thermodynamics of amorphous aggregation, enabling the comparison of protein folding, amyloid fibrillation, and amorphous aggregation. These results indicate that ITC will become a promising approach for clarifying comprehensively the thermodynamics of protein folding and misfolding.

A sharp interface model for void growth in irradiated materials

NASA Astrophysics Data System (ADS)

Hochrainer, Thomas; El-Azab, Anter

2015-03-01

A thermodynamic formalism for the interaction of point defects with free surfaces in single-component solids has been developed and applied to the problem of void growth by absorption of point defects in irradiated metals. This formalism consists of two parts, a detailed description of the dynamics of defects within the non-equilibrium thermodynamic frame, and the application of the second law of thermodynamics to provide closure relations for all kinetic equations. Enforcing the principle of non-negative entropy production showed that the description of the problem of void evolution under irradiation must include a relationship between the normal fluxes of defects into the void surface and the driving thermodynamic forces for the void surface motion; these thermodynamic forces are identified for both vacancies and interstitials and the relationships between these forces and the normal point defect fluxes are established using the concepts of transition state theory. The latter theory implies that the defect accommodation into the surface is a thermally activated process. Numerical examples are given to illustrate void growth dynamics in this new formalism and to investigate the effect of the surface energy barriers on void growth. Consequences for phase field models of void growth are discussed.

Implementation of a High Explosive Equation of State into an Eulerian Hydrocode

NASA Astrophysics Data System (ADS)

Littlefield, David L.; Baker, Ernest L.

2004-07-01

The implementation of a high explosive equation of state into the Eulerian hydrocode CTH is described. The equation of state is an extension to JWL referred to as JWLB, and is intended to model the thermodynamic state of detonation products from a high explosive reaction. The EOS was originally cast in a form p = p(ρ, e), where p is the pressure, ρ is the density and e is the internal energy. However, the target application code requires an EOS of the form p = p(ρ, T), where T is the temperature, so it was necessary to reformulate the EOS in a thermodynamically consistent manner. A Helmholtz potential, developed from the original EOS, insures this consistency. Example calculations are shown that illustrate the veracity of this implementation.

Tables of thermodynamic properties of helium magnet coolant, revision A

NASA Astrophysics Data System (ADS)

McAshan, M.

1992-07-01

The most complete treatment of the thermodynamic properties of helium at the present time is the monograph by McCarty: 'Thermodynamic Properties of Helium 4 from 2 to 1500 K at Pressures to 10(exp 8) Pa', Robert D. McCarty, Journal of Physical and Chemical Reference Data, Vol. 2, page 923-1040 (1973). In this work the complete range of data on helium is examined and the P-V-T surface is described by an equation of state consisting of three functions P(r,T) covering different regions together with rules for making the transition from one region to another. From this thermodynamic compilation together with correlations of the transport properties of helium was published the well-known NBS Technical Note: 'Thermophysical Properties of Helium 4 from 2 to 1500 K with pressures to 1000 Atmospheres', Robert D. McCarty, US Department of Commerce, National Bureau of Standards Technical Note 631 (1972). This is the standard reference for helium cryogenics. The NBS 631 tables cover a wide range of temperature and pressure, and as a consequence, the number of points tabulated in the region of the single phase coolant for the SSC magnets are relatively few. The present work sets out to cover the range of interest in more detail in a way that is consistent with NBS 631. This new table is essentially identical to the older one and can be used as an auxiliary to it.

Thermodynamics and evolution.

PubMed

Demetrius, L

2000-09-07

The science of thermodynamics is concerned with understanding the properties of inanimate matter in so far as they are determined by changes in temperature. The Second Law asserts that in irreversible processes there is a uni-directional increase in thermodynamic entropy, a measure of the degree of uncertainty in the thermal energy state of a randomly chosen particle in the aggregate. The science of evolution is concerned with understanding the properties of populations of living matter in so far as they are regulated by changes in generation time. Directionality theory, a mathematical model of the evolutionary process, establishes that in populations subject to bounded growth constraints, there is a uni-directional increase in evolutionary entropy, a measure of the degree of uncertainty in the age of the immediate ancestor of a randomly chosen newborn. This article reviews the mathematical basis of directionality theory and analyses the relation between directionality theory and statistical thermodynamics. We exploit an analytic relation between temperature, and generation time, to show that the directionality principle for evolutionary entropy is a non-equilibrium extension of the principle of a uni-directional increase of thermodynamic entropy. The analytic relation between these directionality principles is consistent with the hypothesis of the equivalence of fundamental laws as one moves up the hierarchy, from a molecular ensemble where the thermodynamic laws apply, to a population of replicating entities (molecules, cells, higher organisms), where evolutionary principles prevail. Copyright 2000 Academic Press.

Thermodynamically equilibrium roton states of nanoparticles in molten and vapour phases

NASA Astrophysics Data System (ADS)

Karasevskii, A. I.

2015-05-01

We show a possibility for a thermodynamically equilibrium nanocrystalline structure consisting of nanosized solid inclusions to appear in a melt just beyond the melting curve. Thermodynamic stability of the nanocrystalline structure in the melt results from the free energy lowering due to rotational motion of nanoparticles. The main contribution to the reduction of the free energy of the system is due to an increase in the rotational entropy and change in formation energy of nanocrystals, i.e. the nanocrystalline structure in the melt, like vacancies in a crystal, is an equilibrium defect structure of the melt. It is demonstrated that similar nanocrystalline structures can also appear in the vapour phase in the form of liquid nanodrops and in liquid solutions, e.g. in He II.

Thermodynamics of viscoelastic rate-type fluids with stress diffusion

NASA Astrophysics Data System (ADS)

Málek, Josef; Průša, Vít; Skřivan, Tomáš; Süli, Endre

2018-02-01

We propose thermodynamically consistent models for viscoelastic fluids with a stress diffusion term. In particular, we derive variants of compressible/incompressible Maxwell/Oldroyd-B models with a stress diffusion term in the evolution equation for the extra stress tensor. It is shown that the stress diffusion term can be interpreted either as a consequence of a nonlocal energy storage mechanism or as a consequence of a nonlocal entropy production mechanism, while different interpretations of the stress diffusion mechanism lead to different evolution equations for the temperature. The benefits of the knowledge of the thermodynamical background of the derived models are documented in the study of nonlinear stability of equilibrium rest states. The derived models open up the possibility to study fully coupled thermomechanical problems involving viscoelastic rate-type fluids with stress diffusion.

A thermodynamic recipe for baking the Earth's lower mantle and core as a whole

NASA Astrophysics Data System (ADS)

Tirone, Max; Faak, Kathi

2016-04-01

A rigorous understanding of the thermal and dynamic evolution of the core and the interaction with the silicate mantle cannot preclude a non-empirical petrological description of the problem which takes the form of a thermodynamic model. Because the Earth's core is predominantly made of iron such model may seem relatively straightforward, simply delivering a representation of the phase transformations in the P,T space. However due to well known geophysical considerations, a certain amount of light elements should be added. With the Occam's razor principle in mind, potential candidates could be the most abundant and easily accessible elements in the mantle, O, Si and Mg. Given these premises, the challenging problems on developing this type of model are: - a thermodynamic formulation should not simply describe phase equilibrium relations at least in the Fe-Si-O system (a formidable task itself) but should be also consistently applicable to evaluate thermophysical properties of liquid components and solids phases at extreme conditions (P=500-2000 kbar, T=1000-5000 K). Presently these properties are unknown for certain mineral and liquid components or partially available from scattered sources. - experimental data on the phase relations for iron rich liquid are extremely difficult to obtain and could not cover the entire P,T,X spectrum. - interaction of the outer core with the silicate mantle requires a melt model that is capable of describing a vast range of compositions ranging from metal-rich liquids to silicate liquids. The compound energy formalism for liquids with variable tendency to ionization developed by Hillert and coworkers is a sublattice model with varying stoichiometry that includes vacancies and neutral species in one site. It represents the ideal candidate for the task in hand. The thermodynamic model unfortunately is rather complex and a detailed description of the formulation for practical applications like chemical equilibrium calculations is nowhere to be found, while the model is only accessible on few commercial thermodynamic programs. The latest developments regarding all these related issues will be discussed in this contribution. In particular some self-consistent but preliminary results will be presented addressing the following topics: - some details regarding the implementation of the liquid model for Gibbs free energy minimizations, - the physically consistent behavior of thermodynamic properties of certain solid phases like (Fe,O,Si) BCC, FCC, HCP and liquid components, - selected phase diagrams at core conditions in the system Fe-Si-O, - derived geotherms linking the inner-outer core with the core-mantle boundary. - brief outline of the future geodynamic applications.

Heat, temperature and Clausius inequality in a model for active Brownian particles

PubMed Central

Marconi, Umberto Marini Bettolo; Puglisi, Andrea; Maggi, Claudio

2017-01-01

Methods of stochastic thermodynamics and hydrodynamics are applied to a recently introduced model of active particles. The model consists of an overdamped particle subject to Gaussian coloured noise. Inspired by stochastic thermodynamics, we derive from the system’s Fokker-Planck equation the average exchanges of heat and work with the active bath and the associated entropy production. We show that a Clausius inequality holds, with the local (non-uniform) temperature of the active bath replacing the uniform temperature usually encountered in equilibrium systems. Furthermore, by restricting the dynamical space to the first velocity moments of the local distribution function we derive a hydrodynamic description where local pressure, kinetic temperature and internal heat fluxes appear and are consistent with the previous thermodynamic analysis. The procedure also shows under which conditions one obtains the unified coloured noise approximation (UCNA): such an approximation neglects the fast relaxation to the active bath and therefore yields detailed balance and zero entropy production. In the last part, by using multiple time-scale analysis, we provide a constructive method (alternative to UCNA) to determine the solution of the Kramers equation and go beyond the detailed balance condition determining negative entropy production. PMID:28429787

Heat, temperature and Clausius inequality in a model for active Brownian particles.

PubMed

Marconi, Umberto Marini Bettolo; Puglisi, Andrea; Maggi, Claudio

2017-04-21

Methods of stochastic thermodynamics and hydrodynamics are applied to a recently introduced model of active particles. The model consists of an overdamped particle subject to Gaussian coloured noise. Inspired by stochastic thermodynamics, we derive from the system's Fokker-Planck equation the average exchanges of heat and work with the active bath and the associated entropy production. We show that a Clausius inequality holds, with the local (non-uniform) temperature of the active bath replacing the uniform temperature usually encountered in equilibrium systems. Furthermore, by restricting the dynamical space to the first velocity moments of the local distribution function we derive a hydrodynamic description where local pressure, kinetic temperature and internal heat fluxes appear and are consistent with the previous thermodynamic analysis. The procedure also shows under which conditions one obtains the unified coloured noise approximation (UCNA): such an approximation neglects the fast relaxation to the active bath and therefore yields detailed balance and zero entropy production. In the last part, by using multiple time-scale analysis, we provide a constructive method (alternative to UCNA) to determine the solution of the Kramers equation and go beyond the detailed balance condition determining negative entropy production.

A robust and accurate numerical method for transcritical turbulent flows at supercritical pressure with an arbitrary equation of state

NASA Astrophysics Data System (ADS)

Kawai, Soshi; Terashima, Hiroshi; Negishi, Hideyo

2015-11-01

This paper addresses issues in high-fidelity numerical simulations of transcritical turbulent flows at supercritical pressure. The proposed strategy builds on a tabulated look-up table method based on REFPROP database for an accurate estimation of non-linear behaviors of thermodynamic and fluid transport properties at the transcritical conditions. Based on the look-up table method we propose a numerical method that satisfies high-order spatial accuracy, spurious-oscillation-free property, and capability of capturing the abrupt variation in thermodynamic properties across the transcritical contact surface. The method introduces artificial mass diffusivity to the continuity and momentum equations in a physically-consistent manner in order to capture the steep transcritical thermodynamic variations robustly while maintaining spurious-oscillation-free property in the velocity field. The pressure evolution equation is derived from the full compressible Navier-Stokes equations and solved instead of solving the total energy equation to achieve the spurious pressure oscillation free property with an arbitrary equation of state including the present look-up table method. Flow problems with and without physical diffusion are employed for the numerical tests to validate the robustness, accuracy, and consistency of the proposed approach.

A robust and accurate numerical method for transcritical turbulent flows at supercritical pressure with an arbitrary equation of state

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kawai, Soshi, E-mail: kawai@cfd.mech.tohoku.ac.jp; Terashima, Hiroshi; Negishi, Hideyo

2015-11-01

This paper addresses issues in high-fidelity numerical simulations of transcritical turbulent flows at supercritical pressure. The proposed strategy builds on a tabulated look-up table method based on REFPROP database for an accurate estimation of non-linear behaviors of thermodynamic and fluid transport properties at the transcritical conditions. Based on the look-up table method we propose a numerical method that satisfies high-order spatial accuracy, spurious-oscillation-free property, and capability of capturing the abrupt variation in thermodynamic properties across the transcritical contact surface. The method introduces artificial mass diffusivity to the continuity and momentum equations in a physically-consistent manner in order to capture themore » steep transcritical thermodynamic variations robustly while maintaining spurious-oscillation-free property in the velocity field. The pressure evolution equation is derived from the full compressible Navier–Stokes equations and solved instead of solving the total energy equation to achieve the spurious pressure oscillation free property with an arbitrary equation of state including the present look-up table method. Flow problems with and without physical diffusion are employed for the numerical tests to validate the robustness, accuracy, and consistency of the proposed approach.« less

Thermodynamic, geophysical and rheological modeling of the lithosphere underneath the North Atlantic Porcupine Basin (Ireland).

NASA Astrophysics Data System (ADS)

Botter, C. D.; Prada, M.; Fullea, J.

2017-12-01

The Porcupine is a North-South oriented basin located southwest of Ireland, along the North Atlantic continental margin, formed by several rifting episodes during Late Carboniferous to Early Cretaceous. The sedimentary cover is underlined by a very thin continental crust in the center of the basin (<5 km) that has been generally associated with hyperextension and mantle serpentinization. From North to South lithospheric stretching factors increase drastically from 2 in the North to >10 in the South. In spite of the abundant literature, most of the oil and gas exploration in the Porcupine Basin has been targeting its northern part and is mostly restricted to relatively shallow depths, giving a restrained overview of the basin structure. Therefore, studying the thermodynamic and composition of the deep and broader structures is needed to understand the processes linked to the formation and the symmetry signature of the basin. Here, we model the present-day thermal and compositional structure of the continental crust and lithospheric mantle underneath the Porcupine basin using gravity, seismic, heat flow and elevation data. We use an integrated geophysical-petrological framework where most relevant rock properties (density, seismic velocities) are determined as a function of temperature, pressure and composition. Our modelling approach solves simultaneously the heat transfer, thermodynamic, geopotential, seismic and isostasy equations, and fit the results to all available geophysical and petrological observables (LitMod software). In this work we have implemented a module to compute self-consistently a laterally variable lithospheric elastic thickness based on mineral physics rheological laws (yield strength envelopes over the 3D volume). An appropriate understanding of local and flexural isostatic behavior of the basin is essential to unravel its tectonic history (i.e. stretching factors, subsidence etc.). Our Porcupine basin 3D model is defined by four lithological layers, representing properties from post- and syn-rift sequences to the lithospheric mantle. The computed yield strength envelopes are representative of hyperextended lithosphere and reveal the sensitivity of the lithospheric strength to the geotherm, as well as to the thickness and composition of the crust.

Processes driving sea ice variability in the Bering Sea in an eddying ocean/sea ice model: Mean seasonal cycle

NASA Astrophysics Data System (ADS)

Li, Linghan; McClean, Julie L.; Miller, Arthur J.; Eisenman, Ian; Hendershott, Myrl C.; Papadopoulos, Caroline A.

2014-12-01

The seasonal cycle of sea ice variability in the Bering Sea, together with the thermodynamic and dynamic processes that control it, are examined in a fine resolution (1/10°) global coupled ocean/sea-ice model configured in the Community Earth System Model (CESM) framework. The ocean/sea-ice model consists of the Los Alamos National Laboratory Parallel Ocean Program (POP) and the Los Alamos Sea Ice Model (CICE). The model was forced with time-varying reanalysis atmospheric forcing for the time period 1970-1989. This study focuses on the time period 1980-1989. The simulated seasonal-mean fields of sea ice concentration strongly resemble satellite-derived observations, as quantified by root-mean-square errors and pattern correlation coefficients. The sea ice energy budget reveals that the seasonal thermodynamic ice volume changes are dominated by the surface energy flux between the atmosphere and the ice in the northern region and by heat flux from the ocean to the ice along the southern ice edge, especially on the western side. The sea ice force balance analysis shows that sea ice motion is largely associated with wind stress. The force due to divergence of the internal ice stress tensor is large near the land boundaries in the north, and it is small in the central and southern ice-covered region. During winter, which dominates the annual mean, it is found that the simulated sea ice was mainly formed in the northern Bering Sea, with the maximum ice growth rate occurring along the coast due to cold air from northerly winds and ice motion away from the coast. South of St Lawrence Island, winds drive the model sea ice southwestward from the north to the southwestern part of the ice-covered region. Along the ice edge in the western Bering Sea, model sea ice is melted by warm ocean water, which is carried by the simulated Bering Slope Current flowing to the northwest, resulting in the S-shaped asymmetric ice edge. In spring and fall, similar thermodynamic and dynamic patterns occur in the model, but with typically smaller magnitudes and with season-specific geographical and directional differences.

Thermodynamics of Hydrophobic Amino Acids in Solution: A Combined Experimental–Computational Study

DOE PAGES

Song, Lingshuang; Yang, Lin; Meng, Jie; ...

2016-12-29

Here, we present a joint experimental-computational study to quantitatively describe the thermodynamics of hydrophobic leucine amino acids in aqueous solution. X-ray scattering data were acquired at a series of solute and salt concentrations to effectively measure inter-leucine interactions, indicating that a major scattering peak is observed consistently at q = 0.83 Å -1. Atomistic molecular dynamics simulations were then performed and compared with the scattering data, achieving high consistency at both small and wider scattering angles (q = 0$-$1.5 Å -1). This experimental-computational consistence enables a first glimpse of the leucineleucine interacting landscape, where two leucine molecules are aligned mostlymore » in a parallel fashion, as opposed to anti-parallel, but also allows us to derive effective leucine-leucine interactions in solution. Collectively, this combined approach of employing experimental scattering and molecular simulation enables a quantitative characterization on effective inter-molecular interactions of hydrophobic amino acids, critical for protein function and dynamics such as protein folding.« less

Thermodynamics of Hydrophobic Amino Acids in Solution: A Combined Experimental–Computational Study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Song, Lingshuang; Yang, Lin; Meng, Jie

Here, we present a joint experimental-computational study to quantitatively describe the thermodynamics of hydrophobic leucine amino acids in aqueous solution. X-ray scattering data were acquired at a series of solute and salt concentrations to effectively measure inter-leucine interactions, indicating that a major scattering peak is observed consistently at q = 0.83 Å -1. Atomistic molecular dynamics simulations were then performed and compared with the scattering data, achieving high consistency at both small and wider scattering angles (q = 0$-$1.5 Å -1). This experimental-computational consistence enables a first glimpse of the leucineleucine interacting landscape, where two leucine molecules are aligned mostlymore » in a parallel fashion, as opposed to anti-parallel, but also allows us to derive effective leucine-leucine interactions in solution. Collectively, this combined approach of employing experimental scattering and molecular simulation enables a quantitative characterization on effective inter-molecular interactions of hydrophobic amino acids, critical for protein function and dynamics such as protein folding.« less

A kinetic and thermodynamic framework for the Azoarcus group I ribozyme reaction

PubMed Central

Gleitsman, Kristin R.

2014-01-01

Determination of quantitative thermodynamic and kinetic frameworks for ribozymes derived from the Azoarcus group I intron and comparisons to their well-studied analogs from the Tetrahymena group I intron reveal similarities and differences between these RNAs. The guanosine (G) substrate binds to the Azoarcus and Tetrahymena ribozymes with similar equilibrium binding constants and similar very slow association rate constants. These and additional literature observations support a model in which the free ribozyme is not conformationally competent to bind G and in which the probability of assuming the binding-competent state is determined by tertiary interactions of peripheral elements. As proposed previously, the slow binding of guanosine may play a role in the specificity of group I intron self-splicing, and slow binding may be used analogously in other biological processes. The internal equilibrium between ribozyme-bound substrates and products is similar for these ribozymes, but the Azoarcus ribozyme does not display the coupling in the binding of substrates that is observed with the Tetrahymena ribozyme, suggesting that local preorganization of the active site and rearrangements within the active site upon substrate binding are different for these ribozymes. Our results also confirm the much greater tertiary binding energy of the 5′-splice site analog with the Azoarcus ribozyme, binding energy that presumably compensates for the fewer base-pairing interactions to allow the 5′-exon intermediate in self splicing to remain bound subsequent to 5′-exon cleavage and prior to exon ligation. Most generally, these frameworks provide a foundation for design and interpretation of experiments investigating fundamental properties of these and other structured RNAs. PMID:25246656

Stability of bound species during alkene reactions on solid acids

NASA Astrophysics Data System (ADS)

Sarazen, Michele L.; Iglesia, Enrique

2017-05-01

This study reports the thermodynamics of bound species derived from ethene, propene, n-butene, and isobutene on solid acids with diverse strength and confining voids. Density functional theory (DFT) and kinetic data indicate that covalently bound alkoxides form C-C bonds in the kinetically relevant step for dimerization turnovers on protons within TON (0.57 nm) and MOR (0.67 nm) zeolitic channels and on stronger acids HPW (polyoxometalate clusters on silica). Turnover rates for mixed alkenes give relative alkoxide stabilities; the respective adsorption constants are obtained from in situ infrared spectra. Tertiary alkoxides (from isobutene) within larger voids (MOR, HPW) are more stable than less substituted isomers but are destabilized within smaller concave environments (TON) because framework distortions are required to avoid steric repulsion. Adsorption constants are similar on MOR and HPW for each alkoxide, indicating that binding is insensitive to acid strength for covalently bound species. DFT-derived formation free energies for alkoxides with different framework attachments and backbone length/structure agree with measurements when dispersion forces, which mediate stabilization by confinement in host-guest systems, are considered. Theory reveals previously unrecognized framework distortions that balance the C-O bond lengths required for covalency with host-guest distances that maximize van der Waals contacts. These distortions, reported here as changes in O-atom locations and dihedral angles, become stronger for larger, more substituted alkoxides. The thermodynamic properties reported here for alkoxides and acid hosts differing in size and conjugate-anion stability are benchmarked against DFT-derived free energies; their details are essential to design host-guest pairs that direct alkoxide species toward specific products.

Degree of coupling and efficiency of energy converters far-from-equilibrium

NASA Astrophysics Data System (ADS)

Vroylandt, Hadrien; Lacoste, David; Verley, Gatien

2018-02-01

In this paper, we introduce a real symmetric and positive semi-definite matrix, which we call the non-equilibrium conductance matrix, and which generalizes the Onsager response matrix for a system in a non-equilibrium stationary state. We then express the thermodynamic efficiency in terms of the coefficients of this matrix using a parametrization similar to the one used near equilibrium. This framework, then valid arbitrarily far from equilibrium allows to set bounds on the thermodynamic efficiency by a universal function depending only on the degree of coupling between input and output currents. It also leads to new general power-efficiency trade-offs valid for macroscopic machines that are compared to trade-offs previously obtained from uncertainty relations. We illustrate our results on an unicycle heat to heat converter and on a discrete model of a molecular motor.

Anharmonic effects in the quantum cluster equilibrium method

NASA Astrophysics Data System (ADS)

von Domaros, Michael; Perlt, Eva

2017-03-01

The well-established quantum cluster equilibrium (QCE) model provides a statistical thermodynamic framework to apply high-level ab initio calculations of finite cluster structures to macroscopic liquid phases using the partition function. So far, the harmonic approximation has been applied throughout the calculations. In this article, we apply an important correction in the evaluation of the one-particle partition function and account for anharmonicity. Therefore, we implemented an analytical approximation to the Morse partition function and the derivatives of its logarithm with respect to temperature, which are required for the evaluation of thermodynamic quantities. This anharmonic QCE approach has been applied to liquid hydrogen chloride and cluster distributions, and the molar volume, the volumetric thermal expansion coefficient, and the isobaric heat capacity have been calculated. An improved description for all properties is observed if anharmonic effects are considered.

Exploring N-Rich Phases in Li(x)N(y) Clusters for Hydrogen Storage at Nanoscale.

PubMed

Bhattacharya, Amrita; Bhattacharya, Saswata

2015-09-17

We have performed cascade genetic algorithm and ab initio atomistic thermodynamics under the framework of first-principles-based hybrid density functional theory to study the (meta-)stability of a wide range of Li(x)N(y) clusters. We found that hybrid xc-functional is essential to address this problem as a local/semilocal functional simply fails even to predict a qualitative prediction. Most importantly, we find that though in bulk lithium nitride, the Li-rich phase, that is, Li3N, is the stable stoichiometry; in small Li(x)N(y) clusters, N-rich phases are more stable at thermodynamic equilibrium. We further show that these N-rich clusters are promising hydrogen storage material because of their easy adsorption and desorption ability at respectively low (≤300 K) and moderately high temperature (≥600 K).

Jarzynski equality in the context of maximum path entropy

NASA Astrophysics Data System (ADS)

González, Diego; Davis, Sergio

2017-06-01

In the global framework of finding an axiomatic derivation of nonequilibrium Statistical Mechanics from fundamental principles, such as the maximum path entropy - also known as Maximum Caliber principle -, this work proposes an alternative derivation of the well-known Jarzynski equality, a nonequilibrium identity of great importance today due to its applications to irreversible processes: biological systems (protein folding), mechanical systems, among others. This equality relates the free energy differences between two equilibrium thermodynamic states with the work performed when going between those states, through an average over a path ensemble. In this work the analysis of Jarzynski's equality will be performed using the formalism of inference over path space. This derivation highlights the wide generality of Jarzynski's original result, which could even be used in non-thermodynamical settings such as social systems, financial and ecological systems.

Critical evaluation and thermodynamic optimization of the Iron-Rare-Earth systems

NASA Astrophysics Data System (ADS)

Konar, Bikram

Rare-Earth elements by virtue of its typical magnetic, electronic and chemical properties are gaining importance in power, electronics, telecommunications and sustainable green technology related industries. The Magnets from RE-alloys are more powerful than conventional magnets which have more longevity and high temperature workability. The dis-equilibrium in the Rare-Earth element supply and demand has increased the importance of recycling and extraction of REE's from used permanent Magnets. However, lack of the thermodynamic data on RE alloys has made it difficult to design an effective extraction and recycling process. In this regard, Computational Thermodynamic calculations can serve as a cost effective and less time consuming tool to design a waste magnet recycling process. The most common RE permanent magnet is Nd magnet (Nd 2Fe14B). Various elements such as Dy, Tb, Pr, Cu, Co, Ni, etc. are also added to increase its magnetic and mechanical properties. In order to perform reliable thermodynamic calculations for the RE recycling process, accurate thermodynamic database for RE and related alloys are required. The thermodynamic database can be developed using the so-called CALPHAD method. The database development based on the CALPHAD method is essentially the critical evaluation and optimization of all available thermodynamic and phase diagram data. As a results, one set of self-consistent thermodynamic functions for all phases in the given system can be obtained, which can reproduce all reliable thermodynamic and phase diagram data. The database containing the optimized Gibbs energy functions can be used to calculate complex chemical reactions for any high temperature processes. Typically a Gibbs energy minimization routine, such as in FactSage software, can be used to obtain the accurate thermodynamic equilibrium in multicomponent systems. As part of a large thermodynamic database development for permanent magnet recycling and Mg alloy design, all thermodynamic and phase diagram data in the literature for the fourteen Fe-RE binary systems: Fe-La, Fe-Ce, Fe-Pr, Fe-Nd, Fe-Sm, Fe-Gd, Fe-Tb, Fe-Dy, Fe-Ho, Fe-Er, Fe-Tm, Fe-Lu, Fe-Sc and Fe-Y are critically evaluated and optimized to obtain thermodynamic model parameters. The model parameters can be used to calculate phase diagrams and Gibbs energies of all phases as functions of temperature and composition. This database can be incorporated with the present thermodynamic database in FactSage software to perform complex chemical reactions and phase diagram calculations for RE magnet recycling process.

Product control by halide ions of ionic liquids in the ionothermal syntheses of Ni-(H)BTC metal-organic frameworks.

PubMed

Xu, Ling; Yan, Shihai; Choi, Eun-Young; Lee, Jin Yong; Kwon, Young-Uk

2009-06-21

Ni(OAc)(2)-H(3)BTC system in various ionic liquids, [RMI]X (R = ethyl, n-propyl, n-butyl; X = Cl, Br, I), produced five MOFs in two structure types; their relative thermodynamic stability varies with the size of RMI(+), and the X(-) ions govern the kinetic factors so that their combination effects determine the final product.

Thermal Remote Sensing: A Powerful Tool in the Characterization of Landscapes on a Functional Basis

NASA Technical Reports Server (NTRS)

Jeffrey, Luvall C.; Kay, James; Fraser, Roydon

1999-01-01

Thermal remote sensing instruments can function as environmental measuring tools, with capabilities leading toward new directions in functional landscape ecology. Theoretical deduction and phenomenological observation leads us to believe that the second law of thermodynamics requires that all dynamically systems develop in a manner which dissipates gradients as rapidly as possible within the constraints of the system at hand. The ramification of this requirement is that dynamical systems will evolve dissipative structures which grow and complexify over time. This perspective has allowed us to develop a framework for discussing ecosystem development and integrity. In the context of this framework we have developed measures of development and integrity for ecosystems. One set of these measures is based on destruction of the exergy content of incoming solar energy. More developed ecosystems will be more effective at dissipating the solar gradient (destroying its exergy content). This can be measured by the effective surface temperature of the ecosystem on a landscape scale. These surface temperatures are measured using airborne thermal scanners such as the Thermal Infrared Multispectral Scanner (TIMS) and the Airborne Thermal/Visible Land Application Sensor(ATLAS) sensors. An analysis of agriculture and forest ecosystems will be used to illustrate the concept of ecological thermodynamics and the development of ecosystems.

Density functional study on the structural and thermodynamic properties of aqueous DNA-electrolyte solution in the framework of cell model.

PubMed

Wang, Ke; Yu, Yang-Xin; Gao, Guang-Hua

2008-05-14

A density functional theory (DFT) in the framework of cell model is proposed to calculate the structural and thermodynamic properties of aqueous DNA-electrolyte solution with finite DNA concentrations. The hard-sphere contribution to the excess Helmholtz energy functional is derived from the modified fundamental measure theory, and the electrostatic interaction is evaluated through a quadratic functional Taylor expansion around a uniform fluid. The electroneutrality in the cell leads to a variational equation with a constraint. Since the reference fluid is selected to be a bulk phase, the Lagrange multiplier proves to be the potential drop across the cell boundary (Donnan potential). The ion profiles and electrostatic potential profiles in the cell are calculated from the present DFT-cell model. Our DFT-cell model gives better prediction of ion profiles than the Poisson-Boltzmann (PB)- or modified PB-cell models when compared to the molecular simulation data. The effects of polyelectrolyte concentration, ion size, and added-salt concentration on the electrostatic potential difference between the DNA surface and the cell boundary are investigated. The expression of osmotic coefficient is derived from the general formula of grand potential. The osmotic coefficients predicted by the DFT are lower than the PB results and are closer to the simulation results and experimental data.

Evaluating marginal likelihood with thermodynamic integration method and comparison with several other numerical methods

DOE PAGES

Liu, Peigui; Elshall, Ahmed S.; Ye, Ming; ...

2016-02-05

Evaluating marginal likelihood is the most critical and computationally expensive task, when conducting Bayesian model averaging to quantify parametric and model uncertainties. The evaluation is commonly done by using Laplace approximations to evaluate semianalytical expressions of the marginal likelihood or by using Monte Carlo (MC) methods to evaluate arithmetic or harmonic mean of a joint likelihood function. This study introduces a new MC method, i.e., thermodynamic integration, which has not been attempted in environmental modeling. Instead of using samples only from prior parameter space (as in arithmetic mean evaluation) or posterior parameter space (as in harmonic mean evaluation), the thermodynamicmore » integration method uses samples generated gradually from the prior to posterior parameter space. This is done through a path sampling that conducts Markov chain Monte Carlo simulation with different power coefficient values applied to the joint likelihood function. The thermodynamic integration method is evaluated using three analytical functions by comparing the method with two variants of the Laplace approximation method and three MC methods, including the nested sampling method that is recently introduced into environmental modeling. The thermodynamic integration method outperforms the other methods in terms of their accuracy, convergence, and consistency. The thermodynamic integration method is also applied to a synthetic case of groundwater modeling with four alternative models. The application shows that model probabilities obtained using the thermodynamic integration method improves predictive performance of Bayesian model averaging. As a result, the thermodynamic integration method is mathematically rigorous, and its MC implementation is computationally general for a wide range of environmental problems.« less

Electron Bifurcation: Thermodynamics and Kinetics of Two-Electron Brokering in Biological Redox Chemistry.

PubMed

Zhang, Peng; Yuly, Jonathon L; Lubner, Carolyn E; Mulder, David W; King, Paul W; Peters, John W; Beratan, David N

2017-09-19

How can proteins drive two electrons from a redox active donor onto two acceptors at very different potentials and distances? And how can this transaction be conducted without dissipating very much energy or violating the laws of thermodynamics? Nature appears to have addressed these challenges by coupling thermodynamically uphill and downhill electron transfer reactions, using two-electron donor cofactors that have very different potentials for the removal of the first and second electron. Although electron bifurcation is carried out with near perfection from the standpoint of energy conservation and electron delivery yields, it is a biological energy transduction paradigm that has only come into focus recently. This Account provides an exegesis of the biophysical principles that underpin electron bifurcation. Remarkably, bifurcating electron transfer (ET) proteins typically send one electron uphill and one electron downhill by similar energies, such that the overall reaction is spontaneous, but not profligate. Electron bifurcation in the NADH-dependent reduced ferredoxin: NADP + oxidoreductase I (Nfn) is explored in detail here. Recent experimental progress in understanding the structure and function of Nfn allows us to dissect its workings in the framework of modern ET theory. The first electron that leaves the two-electron donor flavin (L-FAD) executes a positive free energy "uphill" reaction, and the departure of this electron switches on a second thermodynamically spontaneous ET reaction from the flavin along a second pathway that moves electrons in the opposite direction and at a very different potential. The singly reduced ET products formed from the bifurcating flavin are more than two nanometers distant from each other. In Nfn, the second electron to leave the flavin is much more reducing than the first: the potentials are said to be "crossed." The eventually reduced cofactors, NADH and ferredoxin in the case of Nfn, perform crucial downstream redox processes of their own. We dissect the thermodynamics and kinetics of electron bifurcation in Nfn and find that the key features of electron bifurcation are (1) spatially separated transfer pathways that diverge from a two-electron donor, (2) one thermodynamically uphill and one downhill redox pathway, with a large negative shift in the donor's reduction potential after departure of the first electron, and (3) electron tunneling and activation factors that enable bifurcation, producing a 1:1 partitioning of electrons onto the two pathways. Electron bifurcation is found in the CO 2 reducing pathways of methanogenic archaea, in the hydrogen pathways of hydrogenases, in the nitrogen fixing pathway of Fix, and in the mitochondrial charge transfer chain of complex III, cytochrome bc 1 . While crossed potentials may offer the biological advantage of producing tightly regulated high energy reactive species, neither kinetic nor thermodynamic considerations mandate crossed potentials to generate successful electron bifurcation. Taken together, the theoretical framework established here, focusing on the underpinning electron tunneling barriers and activation free energies, explains the logic of electron bifurcation that enables energy conversion and conservation in Nfn, points toward bioinspired schemes to execute multielectron redox chemistry, and establishes a roadmap for examining novel electron bifurcation networks in nature.

Role of intensive and extensive variables in a soup of firms in economy to address long run prices and aggregate data

NASA Astrophysics Data System (ADS)

Hosseiny, Ali; Gallegati, Mauro

2017-03-01

We review the production function and the hypothesis of equilibrium in the neoclassical framework. We notify that in a soup of sectors in economy, while capital and labor resemble extensive variables, wage and rate of return on capital act as intensive variables. As a result, Baumol and Bowen's statement of equal wages is inevitable from the thermodynamics point of view. We try to see how aggregation can be performed concerning the extensive variables in a soup of firms. We provide a toy model to perform aggregation for production and the labor income as extensive quantities in a neoclassical framework.

Thermodynamic assessment of the rhodium-ruthenium-oxygen (Rh-Ru-O) system

NASA Astrophysics Data System (ADS)

Gossé, S.; Bordier, S.; Guéneau, C.; Brackx, E.; Domenger, R.; Rogez, J.

2018-03-01

Ruthenium (Ru) and rhodium (Rh) are abundant platinum-group metals formed during burn-up of nuclear fuels. Under normal operating conditions, Rh and Ru accumulate and predominantly form metallic precipitates with other fission products like Mo, Pd and Tc. In the framework of vitrification of high-level nuclear waste, these fission products are poorly soluble in molten glasses. They precipitate as metallic particles and oxide phases. Moreover, these Ru and Rh rich phases strongly depend on temperature and the oxygen fugacity of the glass melt. In case of severe accidental conditions with air ingress, oxidation of the Ru and Rh is possible. At low temperatures (T < 1422 K for rhodium sesquioxide and T < 1815 K for ruthenium dioxide), the formed oxides are relatively stable. On the other hand, at high temperatures (T > 1422 K for rhodium sesquioxide and T > 1815 K for ruthenium dioxide), they may decompose into (Rh)-FCC or (Ru)-HCP metallic phases and radiotoxic volatile gaseous species. A thermodynamic assessment of the Rh-Ru-O system will enable the prediction of: (1) the metallic and oxide phases that form during the vitrification of high-level nuclear wastes and (2) the release of volatile gaseous species during a severe accident. The Calphad method developed herein employs a thermodynamic approach in the investigation of the thermochemistry of rhodium and ruthenium at high temperatures. Current literature on the thermodynamic properties and phase diagram data enables preliminary thermodynamic assessments of the Rh-O and Ru-O systems. Additionally, select compositions in the ternary Rh-Ru-O system underwent experimental tests to complement data found in literature and to establish the phase equilibria in the ternary system.

Stochastic thermodynamics of quantum maps with and without equilibrium.

PubMed

Barra, Felipe; Lledó, Cristóbal

2017-11-01

We study stochastic thermodynamics for a quantum system of interest whose dynamics is described by a completely positive trace-preserving (CPTP) map as a result of its interaction with a thermal bath. We define CPTP maps with equilibrium as CPTP maps with an invariant state such that the entropy production due to the action of the map on the invariant state vanishes. Thermal maps are a subgroup of CPTP maps with equilibrium. In general, for CPTP maps, the thermodynamic quantities, such as the entropy production or work performed on the system, depend on the combined state of the system plus its environment. We show that these quantities can be written in terms of system properties for maps with equilibrium. The relations that we obtain are valid for arbitrary coupling strengths between the system and the thermal bath. The fluctuations of thermodynamic quantities are considered in the framework of a two-point measurement scheme. We derive the entropy production fluctuation theorem for general maps and a fluctuation relation for the stochastic work on a system that starts in the Gibbs state. Some simplifications for the probability distributions in the case of maps with equilibrium are presented. We illustrate our results by considering spin 1/2 systems under thermal maps, nonthermal maps with equilibrium, maps with nonequilibrium steady states, and concatenations of them. Finally, and as an important application, we consider a particular limit in which the concatenation of maps generates a continuous time evolution in Lindblad form for the system of interest, and we show that the concept of maps with and without equilibrium translates into Lindblad equations with and without quantum detailed balance, respectively. The consequences for the thermodynamic quantities in this limit are discussed.

Implications of Modern Non-Equilibrium Thermodynamics for Georgescu-Roegen's Macro-Economics: lessons from a comprehensive historical review

NASA Astrophysics Data System (ADS)

Poisson, Alexandre

2011-12-01

In the early 1970s, mathematician and economist Nicolas Georgescu-Roegen developed an alternative framework to macro-economics (his hourglass model) based on two principles of classical thermodynamics applied to the earth-system as a whole. The new model led him to the radical conclusion that "not only growth, but also a zero-growth state, nay, even a declining state which does not converge toward annihilation, cannot exist forever in a finite environment" (Georgescu-Roegen 1976, p.23). Georgescu-Roegen's novel approach long served as a devastating critique of standard neoclassical growth theories. It also helped establish the foundations for the new trans-disciplinary field of ecological economics. In recent decades however, it has remained unclear whether revolutionary developments in "modern non-equilibrium thermodynamics" (Kondepudi and Prigogine 1998) refute some of Georgescu-Roegen's initial conclusions and provide fundamentally new lessons for very long-term macro-economic analysis. Based on a broad historical review of literature from many fields (thermodynamics, cosmology, ecosystems ecology and economics), I argue that Georgescu-Roegen's hourglass model is largely based on old misconceptions and assumptions from 19th century thermodynamics (including an out-dated cosmology) which make it very misleading. Ironically, these assumptions (path independence and linearity of the entropy function in particular) replicate the non-evolutionary thinking he seemed to despise in his colleagues. In light of modern NET, I propose a different model. Contrary to Georgescu-Roegen's hourglass, I do not assume the path independence of the entropy function. In the new model, achieving critical free energy rate density thresholds can abruptly increase the level of complexity and maximum remaining lifespan of stock-based civilizations.

Stochastic thermodynamics of quantum maps with and without equilibrium

NASA Astrophysics Data System (ADS)

Barra, Felipe; Lledó, Cristóbal

2017-11-01

We study stochastic thermodynamics for a quantum system of interest whose dynamics is described by a completely positive trace-preserving (CPTP) map as a result of its interaction with a thermal bath. We define CPTP maps with equilibrium as CPTP maps with an invariant state such that the entropy production due to the action of the map on the invariant state vanishes. Thermal maps are a subgroup of CPTP maps with equilibrium. In general, for CPTP maps, the thermodynamic quantities, such as the entropy production or work performed on the system, depend on the combined state of the system plus its environment. We show that these quantities can be written in terms of system properties for maps with equilibrium. The relations that we obtain are valid for arbitrary coupling strengths between the system and the thermal bath. The fluctuations of thermodynamic quantities are considered in the framework of a two-point measurement scheme. We derive the entropy production fluctuation theorem for general maps and a fluctuation relation for the stochastic work on a system that starts in the Gibbs state. Some simplifications for the probability distributions in the case of maps with equilibrium are presented. We illustrate our results by considering spin 1/2 systems under thermal maps, nonthermal maps with equilibrium, maps with nonequilibrium steady states, and concatenations of them. Finally, and as an important application, we consider a particular limit in which the concatenation of maps generates a continuous time evolution in Lindblad form for the system of interest, and we show that the concept of maps with and without equilibrium translates into Lindblad equations with and without quantum detailed balance, respectively. The consequences for the thermodynamic quantities in this limit are discussed.

Application of computational thermodynamics in the study of magnsium alloys and bulk metallic glasses

NASA Astrophysics Data System (ADS)

Cao, Hongbo

In this thesis, the application of the computational thermodynamics has been explored on two subjects, the study of magnesium alloys (Chapter 1-5) and bulk metallic glasses (BMGs) (Chapter 6-9). For the former case, a strategy of experiments coupled with the CALPHAD approach was employed to establish a thermodynamic description of the quaternary system Mg-Al-Ca-Sr focusing on the Mg-rich phase equilibria. Multicomponent Mg-rich alloys based on the MgAl-Ca-Sr system are one of the most promising candidates for the high temperature applications in the transportation industry. The Mg-Al-Ca-Sr quaternary consists of four ternaries and six binaries. Thermodynamic descriptions of all constituent binaries are available in the literature. Thermodynamic descriptions of the two key ternaries, Mg-Al-Sr and Mg-Al-Ca, were obtained by an efficient and reliable methodology, combining computational thermodynamics with key experiments. The obtained thermodynamic descriptions were validated by performing extensive comparisons between the calculations and experimental information. Thermodynamic descriptions of the other two ternaries, MgCa-Sr and Al-Ca-Sr, were obtained by extrapolation. For the later case, a computational thermodynamic strategy was formulated to obtain a minor but optimum amount of additional element into a base alloy to improve its glass forming ability (GFA). This was done through thermodynamically calculating the maximum liquidus depressions caused by various alloying addition (or replacement) schemes. The success of this approach has been examined in two multicomponent systems, Zr-based Zr-Cu-Ni-Al-Ti and Cu-rich Cu-Zr-Ti-Y. For both cases, experimental results showed conclusively that the GFA increases more than 100% from the base alloy to the one with minor but optimal elemental addition. Furthermore, a thermodynamic computational approach was employed to identify the compositions of Zr-Ti-Ni-Cu-Al alloys exhibiting low-lying liquidus surfaces, which tend to favor the BMG formation. Guided by these calculations, several series of new Zr-based alloys with excellent GFA were synthesized. The approach using the thermodynamically calculated liquidus temperatures was proved to be robust in locating BMGs and can be considered as a universal method to predict novel BMGs not only of scientific interest but also potential technological applications.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jaques, A.

The entire report consists of tables of thermodynamic properties (including sound velocity, thermal conductivity and diffusivity, Prandtl number, density) of argon at 86 to 400/degree/K, in the form of isobars over 0.9 to 100 bars. (DLC)

Atmospheric environment for Space Shuttle (STS-11) launch

NASA Technical Reports Server (NTRS)

Johnson, D. L.; Hill, C. K.; Batts, G. W.

1984-01-01

Atmospheric conditions observed near Space Shuttle STS-11 launch time on February 3, 1984, at Kennedy Space Center, Florida are summarized. Values of ambient pressure, temperature, moisture, ground winds, visual observations (cloud), and winds aloft are included. The sequence of prelaunch Jimsphere measured vertical wind profiles are reported. Wind and thermodynamic parameters representative of surface and aloft conditions in the SRB descent/impact ocean area are presented. Meteorological tapes, which consist of wind and thermodynamic parameters vesus altitude, for STS-11 vehicle ascent and SRB descent/impact were constructed.

Thermodynamic measurement of the sound velocity of a Bose gas across the transition to Bose–Einstein condensation

NASA Astrophysics Data System (ADS)

Fritsch, A. R.; Tavares, P. E. S.; Vivanco, F. A. J.; Telles, G. D.; Bagnato, V. S.; Henn, E. A. L.

2018-05-01

We present an alternative method for determining the sound velocity in atomic Bose–Einstein condensates, based on thermodynamic global variables. The total number of trapped atoms was as a function of temperature carefully studied across the phase transition, at constant volume. It allowed us to evaluate the sound velocity resulting in consistent values from the quantum to classical regime, in good agreement with previous results found in literature. We also provide some insight about the dominant sound mode (thermal or superfluid) across a wide temperature range.

Thermodynamic analysis on the role of hydrogen in anodic stress corrosion cracking

DOE Office of Scientific and Technical Information (OSTI.GOV)

Qiao, L.; Mao, X.

1995-11-01

A synergistic effect of hydrogen and stress on a corrosion rate was analyzed with thermodynamics. The results showed that an interaction of stress and hydrogen could increase the corrosion rate remarkably. Stress corrosion cracking (SCC) of austenitic stainless steel (ASS) was investigated in boiling chloride solution to confirm the analysis. Hydrogen could be introduced into the specimen concentrated at the crack tip during SCC in boiling LiCl solution (143 C). The concentrating factor is about 3 which is consistent with calculated results according to stress induced diffusion.

Constitutive modelling of composite biopolymer networks.

PubMed

Fallqvist, B; Kroon, M

2016-04-21

The mechanical behaviour of biopolymer networks is to a large extent determined at a microstructural level where the characteristics of individual filaments and the interactions between them determine the response at a macroscopic level. Phenomena such as viscoelasticity and strain-hardening followed by strain-softening are observed experimentally in these networks, often due to microstructural changes (such as filament sliding, rupture and cross-link debonding). Further, composite structures can also be formed with vastly different mechanical properties as compared to the individual networks. In this present paper, we present a constitutive model presented in a continuum framework aimed at capturing these effects. Special care is taken to formulate thermodynamically consistent evolution laws for dissipative effects. This model, incorporating possible anisotropic network properties, is based on a strain energy function, split into an isochoric and a volumetric part. Generalisation to three dimensions is performed by numerical integration over the unit sphere. Model predictions indicate that the constitutive model is well able to predict the elastic and viscoelastic response of biological networks, and to an extent also composite structures. Copyright © 2016 Elsevier Ltd. All rights reserved.

Hypervelocity impact and dynamic fragmentation of brittle materials

NASA Astrophysics Data System (ADS)

Agrawal, Vinamra; Ortega, Alejandro; Meiron, Daniel

2017-06-01

The process of hypervelocity impact and dynamic fragmentation finds application in planetary formation, satellite design for micrometeorite impact damage mitigation, armor design and crater formations. In this work, we study high velocity impact induced dynamic fragmentation processes of brittle materials. We implement ideas of Continuum Damage Mechanics (CDM) to perform fragmentation simulations on brittle materials in various geometries. The damage formulation was implemented on an existing computational framework capable of adaptive mesh refinement that operates on an Eulerian grid, thereby avoiding problems associated with grid entanglement in large deformation processes. A damage sensitive equation of state is developed for hyperelastic materials that depends on a damage variable D, the volume fraction of micro-cracks in the brittle material. The evolution of D is governed by a modified, thermodynamically consistent Grady-Kipp model that evolves damage at points of tensile eigenvalue stresses. We simulate sphere-on-sphere and sphere-on-plate impact events with ductile and brittle materials and study the resulting damage propagation. We validate our calculations with existing literature and comment on energy dissipation and optimal design. Caltech - JPL President's and Director's Fund.

How Enzymes Work: A Look through the Perspective of Molecular Viscoelastic Properties

NASA Astrophysics Data System (ADS)

Qu, Hao; Zocchi, Giovanni

2013-01-01

We present nanorheology measurements on the folded state of an enzyme that show directly that the (ensemble-averaged) stress-strain relations are nonlinear and frequency dependent beyond 1-Å deformation. We argue that this frequency dependence allows for opening a nonequilibrium cycle in the force-deformation plane if the forward and backward conformational changes of the enzyme during catalysis happen at different speeds. Using a heuristic model for the experimentally established viscoelastic properties of the enzyme, we examine a number of general features of enzymatic action. We find that the proposed viscoelastic cycle is consistent with the linear decrease of the speed of motor proteins with load. We find a relation between the stall force and the maximum rate for enzymes (in general) and motors (in particular). We estimate the stall force of the motor protein kinesin from thermodynamic quantities and estimate the maximum rate of enzymes from purely mechanical quantities. We propose that the viscoelastic cycle provides a framework for considering mechanochemical coupling in enzymes on the basis of possibly universal materials properties of the folded state of proteins.

On the Origin of Protein Superfamilies and Superfolds

NASA Astrophysics Data System (ADS)

Magner, Abram; Szpankowski, Wojciech; Kihara, Daisuke

2015-02-01

Distributions of protein families and folds in genomes are highly skewed, having a small number of prevalent superfamiles/superfolds and a large number of families/folds of a small size. Why are the distributions of protein families and folds skewed? Why are there only a limited number of protein families? Here, we employ an information theoretic approach to investigate the protein sequence-structure relationship that leads to the skewed distributions. We consider that protein sequences and folds constitute an information theoretic channel and computed the most efficient distribution of sequences that code all protein folds. The identified distributions of sequences and folds are found to follow a power law, consistent with those observed for proteins in nature. Importantly, the skewed distributions of sequences and folds are suggested to have different origins: the skewed distribution of sequences is due to evolutionary pressure to achieve efficient coding of necessary folds, whereas that of folds is based on the thermodynamic stability of folds. The current study provides a new information theoretic framework for proteins that could be widely applied for understanding protein sequences, structures, functions, and interactions.

Structural, electronic and spectral properties of carborane-containing boron dipyrromethenes (BODIPYs): A first-principles study

NASA Astrophysics Data System (ADS)

Li, Xiaojun

2017-10-01

In this work, we reported the geometrical structures, electronic and spectral properties of the carborane-containing BODIPYs complexes using the density functional theory calculations. In two structures, the calculated main bond lengths and bond angels of structural framework are consistent with X-ray experiment, and the two BODIPYs complexes are thermodynamically and kinetically stable. The strongest DOS band is mainly dominated by the Bsbnd B and Bsbnd H σ-bonds of carborane fragment, whereas the π-type MOs on the pyrromethene fragment contribute to the high-energy DOS bands. Analysis of the AdNDP chemical bonding indicates that the carborane cage can be stabilized by eleven delocalized 3csbnd 2e and two delocalized 4csbnd 2e σ-bonds, while the pyrromethene fragment corresponds to five delocalized 3csbnd 2e π-bonds. In addition, the main characteristic peaks of the two simulated IR spectra for the BODIPYs complexes are properly assigned. Hopefully, all these results will be helpful for understanding the electronic structures, and further stimulate the study on the biological and medical applications.

Absorbing a Little Water: The Structural, Thermodynamic, and Kinetic Relationship between Pyrogallol and Its Tetarto-Hydrate

PubMed Central

2013-01-01

The anhydrate and the stoichiometric tetarto-hydrate of pyrogallol (0.25 mol water per mol pyrogallol) are both storage stable at ambient conditions, provided that they are phase pure, with the system being at equilibrium at aw (water activity) = 0.15 at 25 °C. Structures have been derived from single crystal and powder X-ray diffraction data for the anhydrate and hydrate, respectively. It is notable that the tetarto-hydrate forms a tetragonal structure with water in channels, a framework that although stabilized by water, is found as a higher energy structure on a computationally generated crystal energy landscape, which has the anhydrate crystal structure as the most stable form. Thus, a combination of slurry experiments, X-ray diffraction, spectroscopy, moisture (de)sorption, and thermo-analytical methods with the computationally generated crystal energy landscape and lattice energy calculations provides a consistent picture of the finely balanced hydration behavior of pyrogallol. In addition, two monotropically related dimethyl sulfoxide monosolvates were found in the accompanying solid form screen. PMID:24027438

GVIPS Models and Software

NASA Technical Reports Server (NTRS)

Arnold, Steven M.; Gendy, Atef; Saleeb, Atef F.; Mark, John; Wilt, Thomas E.

2007-01-01

Two reports discuss, respectively, (1) the generalized viscoplasticity with potential structure (GVIPS) class of mathematical models and (2) the Constitutive Material Parameter Estimator (COMPARE) computer program. GVIPS models are constructed within a thermodynamics- and potential-based theoretical framework, wherein one uses internal state variables and derives constitutive equations for both the reversible (elastic) and the irreversible (viscoplastic) behaviors of materials. Because of the underlying potential structure, GVIPS models not only capture a variety of material behaviors but also are very computationally efficient. COMPARE comprises (1) an analysis core and (2) a C++-language subprogram that implements a Windows-based graphical user interface (GUI) for controlling the core. The GUI relieves the user of the sometimes tedious task of preparing data for the analysis core, freeing the user to concentrate on the task of fitting experimental data and ultimately obtaining a set of material parameters. The analysis core consists of three modules: one for GVIPS material models, an analysis module containing a specialized finite-element solution algorithm, and an optimization module. COMPARE solves the problem of finding GVIPS material parameters in the manner of a design-optimization problem in which the parameters are the design variables.