The effect of solute concentration on hindered gradient diffusion in polymeric gels

NASA Astrophysics Data System (ADS)

Buck, Kristan K. S.; Dungan, Stephanie R.; Phillips, Ronald J.

1999-10-01

The effect of solute concentration on hindered diffusion of sphere-like colloidal solutes in stiff polymer hydrogels is examined theoretically and experimentally. In the theoretical development, it is shown that the presence of the gel fibres enhances the effect of concentration on the thermodynamic driving force for gradient diffusion, while simultaneously reducing the effect of concentration on the hydrodynamic drag. The result is that gradient diffusion depends more strongly on solute concentration in gels than it does in pure solution, by an amount that depends on the partition coefficient and hydraulic permeability of the gel solute system. Quantitative calculations are made to determine the concentration-dependent diffusivity correct to first order in solute concentration. In order to compare the theoretical predictions with experimental data, rates of diffusion have been measured for nonionic micelles and globular proteins in solution and agarose hydrogels at two gel concentrations. The measurements were performed by using holographic interferometry, through which one monitors changes in refractive index as gradient diffusion takes place within a transparent gel. If the solutes are modelled as spheres with short-range repulsive interactions, then the experimentally measured concentration dependence of the diffusivities of both the protein and micelles is in good agreement with the theoretical predictions.

Scale matters

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

Margolin, L. G.

The applicability of Navier–Stokes equations is limited to near-equilibrium flows in which the gradients of density, velocity and energy are small. Here I propose an extension of the Chapman–Enskog approximation in which the velocity probability distribution function (PDF) is averaged in the coordinate phase space as well as the velocity phase space. I derive a PDF that depends on the gradients and represents a first-order generalization of local thermodynamic equilibrium. I then integrate this PDF to derive a hydrodynamic model. Finally, I discuss the properties of that model and its relation to the discrete equations of computational fluid dynamics.

Scale matters

DOE PAGES

Margolin, L. G.

2018-03-19

The applicability of Navier–Stokes equations is limited to near-equilibrium flows in which the gradients of density, velocity and energy are small. Here I propose an extension of the Chapman–Enskog approximation in which the velocity probability distribution function (PDF) is averaged in the coordinate phase space as well as the velocity phase space. I derive a PDF that depends on the gradients and represents a first-order generalization of local thermodynamic equilibrium. I then integrate this PDF to derive a hydrodynamic model. Finally, I discuss the properties of that model and its relation to the discrete equations of computational fluid dynamics.

A three-dimensional phase field model for nanowire growth by the vapor-liquid-solid mechanism

NASA Astrophysics Data System (ADS)

Wang, Yanming; Ryu, Seunghwa; McIntyre, Paul C.; Cai, Wei

2014-07-01

We present a three-dimensional multi-phase field model for catalyzed nanowire (NW) growth by the vapor-liquid-solid (VLS) mechanism. The equation of motion contains both a Ginzburg-Landau term for deposition and a diffusion (Cahn-Hilliard) term for interface relaxation without deposition. Direct deposition from vapor to solid, which competes with NW crystal growth through the molten catalyst droplet, is suppressed by assigning a very small kinetic coefficient at the solid-vapor interface. The thermodynamic self-consistency of the model is demonstrated by its ability to reproduce the equilibrium contact angles at the VLS junction. The incorporation of orientation dependent gradient energy leads to faceting of the solid-liquid and solid-vapor interfaces. The model successfully captures the curved shape of the NW base and the Gibbs-Thomson effect on growth velocity.

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.

Hamiltonian and Thermodynamic Modeling of Quantum Turbulence

NASA Astrophysics Data System (ADS)

Grmela, Miroslav

2010-10-01

The state variables in the novel model introduced in this paper are the fields playing this role in the classical Landau-Tisza model and additional fields of mass, entropy (or temperature), superfluid velocity, and gradient of the superfluid velocity, all depending on the position vector and another tree dimensional vector labeling the scale, describing the small-scale structure developed in 4He superfluid experiencing turbulent motion. The fluxes of mass, momentum, energy, and entropy in the position space as well as the fluxes of energy and entropy in scales, appear in the time evolution equations as explicit functions of the state variables and of their conjugates. The fundamental thermodynamic relation relating the fields to their conjugates is left in this paper undetermined. The GENERIC structure of the equations serves two purposes: (i) it guarantees that solutions to the governing equations, independently of the choice of the fundamental thermodynamic relation, agree with the observed compatibility with thermodynamics, and (ii) it is used as a guide in the construction of the novel model.

Scale matters

NASA Astrophysics Data System (ADS)

Margolin, L. G.

2018-04-01

The applicability of Navier-Stokes equations is limited to near-equilibrium flows in which the gradients of density, velocity and energy are small. Here I propose an extension of the Chapman-Enskog approximation in which the velocity probability distribution function (PDF) is averaged in the coordinate phase space as well as the velocity phase space. I derive a PDF that depends on the gradients and represents a first-order generalization of local thermodynamic equilibrium. I then integrate this PDF to derive a hydrodynamic model. I discuss the properties of that model and its relation to the discrete equations of computational fluid dynamics. This article is part of the theme issue `Hilbert's sixth problem'.

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.

Mechanical, electronic and thermodynamic properties of full Heusler compounds Fe2VX(X = Al, Ga)

NASA Astrophysics Data System (ADS)

Khalfa, M.; Khachai, H.; Chiker, F.; Baki, N.; Bougherara, K.; Yakoubi, A.; Murtaza, G.; Harmel, M.; Abu-Jafar, M. S.; Omran, S. Bin; Khenata, R.

2015-11-01

The electronic structure, mechanical and thermodynamic properties of Fe2VX, (with X = Al and Ga), have been studied self consistently by employing state-of-the-art full-potential linearized approach of augmented plane wave plus local orbitals (FP-LAPW + lo) method. The exchange-correlation potential is treated with the local density and generalized gradient approximations (LDA and GGA). Our predicted ground state properties such as lattice constants, bulk modulus and elastic constants appear more accurate when we employed the GGA rather than the LDA, and these results are in very good agreement with the available experimental and theoretical data. Further, thermodynamic properties of Fe2VAl and Fe2VGa are predicted with pressure and temperature in the ranges of 0-40 GPa and 0-1500 K using the quasi-harmonic Debye model. We have obtained successfully the variations of the heat capacities, primitive cell volume and volume expansion coefficient.

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.

Surface plasticity: theory and computation

NASA Astrophysics Data System (ADS)

Esmaeili, A.; Steinmann, P.; Javili, A.

2017-11-01

Surfaces of solids behave differently from the bulk due to different atomic rearrangements and processes such as oxidation or aging. Such behavior can become markedly dominant at the nanoscale due to the large ratio of surface area to bulk volume. The surface elasticity theory (Gurtin and Murdoch in Arch Ration Mech Anal 57(4):291-323, 1975) has proven to be a powerful strategy to capture the size-dependent response of nano-materials. While the surface elasticity theory is well-established to date, surface plasticity still remains elusive and poorly understood. The objective of this contribution is to establish a thermodynamically consistent surface elastoplasticity theory for finite deformations. A phenomenological isotropic plasticity model for the surface is developed based on the postulated elastoplastic multiplicative decomposition of the surface superficial deformation gradient. The non-linear governing equations and the weak forms thereof are derived. The numerical implementation is carried out using the finite element method and the consistent elastoplastic tangent of the surface contribution is derived. Finally, a series of numerical examples provide further insight into the problem and elucidate the key features of the proposed theory.

Physics of spinning gases and plasmas

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

Geyko, Vasily I.

Initially motivated by the problem of compression of spinning plasma in Z-pinch devices and related applications, the thesis explores a number of interesting smaller-scale problems related to physics of gas and plasma rotation. In particular, thermodynamics of ideal spinning gas is studied. It is found that rotation modifies the heat capacity of the gas and reduces the gas compressibility. It is also proposed that, by performing a series of measurement of external parameters of a spinning gas, one can infer the distribution of masses of gas constituents. It is also proposed how to use the rotation-dependent heat capacity for improvingmore » the thermodynamic efficiency of internal combustion engines. To that end, two possible engine embodiments are proposed and explored in detail. In addition, a transient piezothermal effect is discovered numerically and is given a theoretical explanation. The effect consists of the formation of a radial temperature gradient driven by gas heating or compression along the rotation axis. By elaborating on this idea, a theoretical explanation is proposed also for the operation of so-called vortex tubes, which so far have been lacking rigorous theory. Finally, adiabatic compression of spinning plasmas and ionized gases are considered, and the effect of the electrostatic interactions on the compressibility and heat capacity is predicted.« less

Gradient Dynamics and Entropy Production Maximization

NASA Astrophysics Data System (ADS)

Janečka, Adam; Pavelka, Michal

2018-01-01

We compare two methods for modeling dissipative processes, namely gradient dynamics and entropy production maximization. Both methods require similar physical inputs-how energy (or entropy) is stored and how it is dissipated. Gradient dynamics describes irreversible evolution by means of dissipation potential and entropy, it automatically satisfies Onsager reciprocal relations as well as their nonlinear generalization (Maxwell-Onsager relations), and it has statistical interpretation. Entropy production maximization is based on knowledge of free energy (or another thermodynamic potential) and entropy production. It also leads to the linear Onsager reciprocal relations and it has proven successful in thermodynamics of complex materials. Both methods are thermodynamically sound as they ensure approach to equilibrium, and we compare them and discuss their advantages and shortcomings. In particular, conditions under which the two approaches coincide and are capable of providing the same constitutive relations are identified. Besides, a commonly used but not often mentioned step in the entropy production maximization is pinpointed and the condition of incompressibility is incorporated into gradient dynamics.

A miniaturized technique for assessing protein thermodynamics and function using fast determination of quantitative cysteine reactivity.

PubMed

Isom, Daniel G; Marguet, Philippe R; Oas, Terrence G; Hellinga, Homme W

2011-04-01

Protein thermodynamic stability is a fundamental physical characteristic that determines biological function. Furthermore, alteration of thermodynamic stability by macromolecular interactions or biochemical modifications is a powerful tool for assessing the relationship between protein structure, stability, and biological function. High-throughput approaches for quantifying protein stability are beginning to emerge that enable thermodynamic measurements on small amounts of material, in short periods of time, and using readily accessible instrumentation. Here we present such a method, fast quantitative cysteine reactivity, which exploits the linkage between protein stability, sidechain protection by protein structure, and structural dynamics to characterize the thermodynamic and kinetic properties of proteins. In this approach, the reaction of a protected cysteine and thiol-reactive fluorogenic indicator is monitored over a gradient of temperatures after a short incubation time. These labeling data can be used to determine the midpoint of thermal unfolding, measure the temperature dependence of protein stability, quantify ligand-binding affinity, and, under certain conditions, estimate folding rate constants. Here, we demonstrate the fQCR method by characterizing these thermodynamic and kinetic properties for variants of Staphylococcal nuclease and E. coli ribose-binding protein engineered to contain single, protected cysteines. These straightforward, information-rich experiments are likely to find applications in protein engineering and functional genomics. Copyright © 2010 Wiley-Liss, Inc.

Solvent effects in time-dependent self-consistent field methods. II. Variational formulations and analytical gradients

DOE PAGES

Bjorgaard, J. A.; Velizhanin, K. A.; Tretiak, S.

2015-08-06

This study describes variational energy expressions and analytical excited state energy gradients for time-dependent self-consistent field methods with polarizable solvent effects. Linear response, vertical excitation, and state-specific solventmodels are examined. Enforcing a variational ground stateenergy expression in the state-specific model is found to reduce it to the vertical excitation model. Variational excited state energy expressions are then provided for the linear response and vertical excitation models and analytical gradients are formulated. Using semiempiricalmodel chemistry, the variational expressions are verified by numerical and analytical differentiation with respect to a static external electric field. Lastly, analytical gradients are further tested by performingmore » microcanonical excited state molecular dynamics with p-nitroaniline.« less

Ortho-para-hydrogen equilibration on Jupiter

NASA Technical Reports Server (NTRS)

Carlson, Barbara E.; Lacis, Andrew A.; Rossow, William B.

1992-01-01

Voyager IRIS observations reveal that the Jovian para-hydrogen fraction is not in thermodynamic equilibrium near the NH3 cloud top, implying that a vertical gradient exists between the high-temperature equilibrium value of 0.25 at depth and the cloud top values. The height-dependent para-hydrogen profile is obtained using an anisotropic multiple-scattering radiative transfer model. A vertical correlation is found to exist between the location of the para-hydrogen gradient and the NH3 cloud, strongly suggesting that paramagnetic conversion on NH3 cloud particle surfaces is the dominant equilibration mechanism. Below the NH3 cloud layer, the para fraction is constant with depth and equal to the high-temperature equilibrium value of 0.25. The degree of cloud-top equilibration appears to depend on the optical depth of the NH3 cloud layer. Belt-zone variations in the para-hydrogen profile seem to be due to differences in the strength of the vertical mixing.

Numerical modeling of temperature and species distributions in hydrocarbon reservoirs

NASA Astrophysics Data System (ADS)

Bolton, Edward W.; Firoozabadi, Abbas

2014-01-01

We examine bulk fluid motion and diffusion of multicomponent hydrocarbon species in porous media in the context of nonequilibrium thermodynamics, with particular focus on the phenomenology induced by horizontal thermal gradients at the upper and lower horizontal boundaries. The problem is formulated with respect to the barycentric (mass-averaged) frame of reference. Thermally induced convection, with fully time-dependent temperature distributions, can lead to nearly constant hydrocarbon composition, with minor unmixing due to thermal gradients near the horizontal boundaries. Alternately, the composition can be vertically segregated due to gravitational effects. Independent and essentially steady solutions have been found to depend on how the compositions are initialized in space and may have implications for reservoir history. We also examine injection (to represent filling) and extraction (to represent leakage) of hydrocarbons at independent points and find a large distortion of the gas-oil contact for low permeability.

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.

Life, hierarchy, and the thermodynamic machinery of planet Earth.

PubMed

Kleidon, Axel

2010-12-01

Throughout Earth's history, life has increased greatly in abundance, complexity, and diversity. At the same time, it has substantially altered the Earth's environment, evolving some of its variables to states further and further away from thermodynamic equilibrium. For instance, concentrations in atmospheric oxygen have increased throughout Earth's history, resulting in an increased chemical disequilibrium in the atmosphere as well as an increased redox gradient between the atmosphere and the Earth's reducing crust. These trends seem to contradict the second law of thermodynamics, which states for isolated systems that gradients and free energy are dissipated over time, resulting in a state of thermodynamic equilibrium. This seeming contradiction is resolved by considering planet Earth as a coupled, hierarchical and evolving non-equilibrium thermodynamic system that has been substantially altered by the input of free energy generated by photosynthetic life. Here, I present this hierarchical thermodynamic theory of the Earth system. I first present simple considerations to show that thermodynamic variables are driven away from a state of thermodynamic equilibrium by the transfer of power from some other process and that the resulting state of disequilibrium reflects the past net work done on the variable. This is applied to the processes of planet Earth to characterize the generation and transfer of free energy and its dissipation, from radiative gradients to temperature and chemical potential gradients that result in chemical, kinetic, and potential free energy and associated dynamics of the climate system and geochemical cycles. The maximization of power transfer among the processes within this hierarchy yields thermodynamic efficiencies much lower than the Carnot efficiency of equilibrium thermodynamics and is closely related to the proposed principle of Maximum Entropy Production (MEP). The role of life is then discussed as a photochemical process that generates substantial amounts of chemical free energy which essentially skips the limitations and inefficiencies associated with the transfer of power within the thermodynamic hierarchy of the planet. This perspective allows us to view life as being the means to transform many aspects of planet Earth to states even further away from thermodynamic equilibrium than is possible by purely abiotic means. In this perspective pockets of low-entropy life emerge from the overall trend of the Earth system to increase the entropy of the universe at the fastest possible rate. The implications of the theory are discussed regarding fundamental deficiencies in Earth system modeling, applications of the theory to reconstructions of Earth system history, and regarding the role of human activity for the future of the planet. Copyright © 2010 Elsevier B.V. All rights reserved.

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.

Influence of chemistry, interfacial width, and non-isothermal conditions on spatially heterogeneous activated relaxation and elasticity in glass-forming free standing films

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

Mirigian, Stephen; Schweizer, Kenneth S.

Here, we employ the Elastically Collective Nonlinear Langevin Equation (ECNLE) theory of activated relaxation to study several questions in free standing thin films of glass-forming molecular and polymer liquids. The influence of non-universal chemical aspects on dynamical confinement effects is found to be relatively weak, but with the caveat that for the systems examined, the bulk ECNLE polymer theory does not predict widely varying fragilities. Allowing the film model to have a realistic vapor interfacial width significantly enhances the reduction of the film-averaged glass transition temperature, T g, in a manner that depends on whether a dynamic or pseudo-thermodynamic averagingmore » of the spatial mobility gradient is adopted. The nature of film thickness effects on the spatial profiles of the alpha relaxation time and elastic modulus is studied under non-isothermal conditions and contrasted with the corresponding isothermal behavior. Modest differences are found if a film-thickness dependent T g is defined in a dynamical manner. But, adopting a pseudo-thermodynamic measure of T g leads to a qualitatively new form of the alpha relaxation time gradient where highly mobile layers near the film surface coexist with strongly vitrified regions in the film interior. Consequently, the film-averaged shear modulus can increase with decreasing film thickness, despite the T g reduction and presence of a mobile surface layer. Such a behavior stands in qualitative contrast to the predicted mechanical softening under isothermal conditions. Spatial gradients of the elastic modulus are studied as a function of temperature, film thickness, probing frequency, and experimental protocol, and a rich behavior is found.« less

Influence of chemistry, interfacial width, and non-isothermal conditions on spatially heterogeneous activated relaxation and elasticity in glass-forming free standing films

DOE PAGES

Mirigian, Stephen; Schweizer, Kenneth S.

2017-02-02

Here, we employ the Elastically Collective Nonlinear Langevin Equation (ECNLE) theory of activated relaxation to study several questions in free standing thin films of glass-forming molecular and polymer liquids. The influence of non-universal chemical aspects on dynamical confinement effects is found to be relatively weak, but with the caveat that for the systems examined, the bulk ECNLE polymer theory does not predict widely varying fragilities. Allowing the film model to have a realistic vapor interfacial width significantly enhances the reduction of the film-averaged glass transition temperature, T g, in a manner that depends on whether a dynamic or pseudo-thermodynamic averagingmore » of the spatial mobility gradient is adopted. The nature of film thickness effects on the spatial profiles of the alpha relaxation time and elastic modulus is studied under non-isothermal conditions and contrasted with the corresponding isothermal behavior. Modest differences are found if a film-thickness dependent T g is defined in a dynamical manner. But, adopting a pseudo-thermodynamic measure of T g leads to a qualitatively new form of the alpha relaxation time gradient where highly mobile layers near the film surface coexist with strongly vitrified regions in the film interior. Consequently, the film-averaged shear modulus can increase with decreasing film thickness, despite the T g reduction and presence of a mobile surface layer. Such a behavior stands in qualitative contrast to the predicted mechanical softening under isothermal conditions. Spatial gradients of the elastic modulus are studied as a function of temperature, film thickness, probing frequency, and experimental protocol, and a rich behavior is found.« less

Energy dissipation drives the gradient signal amplification through an incoherent type-1 feed-forward loop

NASA Astrophysics Data System (ADS)

Lan, Ganhui

2015-09-01

We present here the analytical relation between the gain of eukaryotic gradient sensing network and the associated thermodynamic cost. By analyzing a general incoherent type-1 feed-forward loop, we derive the gain function (G ) through the reaction network and explicitly show that G depends on the nonequilibrium factor (0 ≤γ ≤1 with γ =0 and 1 representing irreversible and equilibrium reaction systems, respectively), the Michaelis constant (KM), and the turnover ratio (rcat) of the participating enzymes. We further find the maximum possible gain is intrinsically determined by KM/Gmax=(1 /KM+2 ) /4 . Our model also indicates that the dissipated energy (measured by -lnγ ), from the intracellular energy-bearing bioparticles (e.g., ATP), is used to generate a force field Fγ∝(1 -√{γ }) that reshapes and disables the effective potential around the zero gain region, which leads to the ultrasensitive response to external chemical gradients.

Film and membrane-model thermodynamics of free thin liquid films.

PubMed

Radke, C J

2015-07-01

In spite of over 7 decades of effort, the thermodynamics of thin free liquid films (as in emulsions and foams) lacks clarity. Following a brief review of the meaning and measurement of thin-film forces (i.e., conjoining/disjoining pressures), we offer a consistent analysis of thin-film thermodynamics. By carefully defining film reversible work, two distinct thermodynamic formalisms emerge: a film model with two zero-volume membranes each of film tension γ(f) and a membrane model with a single zero-volume membrane of membrane tension 2γ(m). In both models, detailed thermodynamic analysis gives rise to thin-film Gibbs adsorption equations that allow calculation of film and membrane tensions from measurements of disjoining-pressure isotherms. A modified Young-Laplace equation arises in the film model to calculate film-thickness profiles from the film center to the surrounding bulk meniscus. No corresponding relation exists in the membrane model. Illustrative calculations of disjoining-pressure isotherms for water are presented using square-gradient theory. We report considerable deviations from Hamaker theory for films less than about 3 nm in thickness. Such thin films are considerably more attractive than in classical Hamaker theory. Available molecular simulations reinforce this finding. Copyright © 2014 Elsevier Inc. All rights reserved.

Thermodiffusion in concentrated ferrofluids: A review and current experimental and numerical results on non-magnetic thermodiffusion

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

Sprenger, Lisa, E-mail: Lisa.Sprenger@tu-dresden.de; Lange, Adrian; Odenbach, Stefan

2013-12-15

Ferrofluids are colloidal suspensions consisting of magnetic nanoparticles dispersed in a carrier liquid. Their thermodiffusive behaviour is rather strong compared to molecular binary mixtures, leading to a Soret coefficient (S{sub T}) of 0.16 K{sup −1}. Former experiments with dilute magnetic fluids have been done with thermogravitational columns or horizontal thermodiffusion cells by different research groups. Considering the horizontal thermodiffusion cell, a former analytical approach has been used to solve the phenomenological diffusion equation in one dimension assuming a constant concentration gradient over the cell's height. The current experimental work is based on the horizontal separation cell and emphasises the comparison ofmore » the concentration development in different concentrated magnetic fluids and at different temperature gradients. The ferrofluid investigated is the kerosene-based EMG905 (Ferrotec) to be compared with the APG513A (Ferrotec), both containing magnetite nanoparticles. The experiments prove that the separation process linearly depends on the temperature gradient and that a constant concentration gradient develops in the setup due to the separation. Analytical one dimensional and numerical three dimensional approaches to solve the diffusion equation are derived to be compared with the solution used so far for dilute fluids to see if formerly made assumptions also hold for higher concentrated fluids. Both, the analytical and numerical solutions, either in a phenomenological or a thermodynamic description, are able to reproduce the separation signal gained from the experiments. The Soret coefficient can then be determined to 0.184 K{sup −1} in the analytical case and 0.29 K{sup −1} in the numerical case. Former theoretical approaches for dilute magnetic fluids underestimate the strength of the separation in the case of a concentrated ferrofluid.« less

Study of homogeneous bubble nucleation in liquid carbon dioxide by a hybrid approach combining molecular dynamics simulation and density gradient theory

NASA Astrophysics Data System (ADS)

Langenbach, K.; Heilig, M.; Horsch, M.; Hasse, H.

2018-03-01

A new method for predicting homogeneous bubble nucleation rates of pure compounds from vapor-liquid equilibrium (VLE) data is presented. It combines molecular dynamics simulation on the one side with density gradient theory using an equation of state (EOS) on the other. The new method is applied here to predict bubble nucleation rates in metastable liquid carbon dioxide (CO2). The molecular model of CO2 is taken from previous work of our group. PC-SAFT is used as an EOS. The consistency between the molecular model and the EOS is achieved by adjusting the PC-SAFT parameters to VLE data obtained from the molecular model. The influence parameter of density gradient theory is fitted to the surface tension of the molecular model. Massively parallel molecular dynamics simulations are performed close to the spinodal to compute bubble nucleation rates. From these simulations, the kinetic prefactor of the hybrid nucleation theory is estimated, whereas the nucleation barrier is calculated from density gradient theory. This enables the extrapolation of molecular simulation data to the whole metastable range including technically relevant densities. The results are tested against available experimental data and found to be in good agreement. The new method does not suffer from typical deficiencies of classical nucleation theory concerning the thermodynamic barrier at the spinodal and the bubble size dependence of surface tension, which is typically neglected in classical nucleation theory. In addition, the density in the center of critical bubbles and their surface tension is determined as a function of their radius. The usual linear Tolman correction to the capillarity approximation is found to be invalid.

Study of homogeneous bubble nucleation in liquid carbon dioxide by a hybrid approach combining molecular dynamics simulation and density gradient theory.

PubMed

Langenbach, K; Heilig, M; Horsch, M; Hasse, H

2018-03-28

A new method for predicting homogeneous bubble nucleation rates of pure compounds from vapor-liquid equilibrium (VLE) data is presented. It combines molecular dynamics simulation on the one side with density gradient theory using an equation of state (EOS) on the other. The new method is applied here to predict bubble nucleation rates in metastable liquid carbon dioxide (CO 2 ). The molecular model of CO 2 is taken from previous work of our group. PC-SAFT is used as an EOS. The consistency between the molecular model and the EOS is achieved by adjusting the PC-SAFT parameters to VLE data obtained from the molecular model. The influence parameter of density gradient theory is fitted to the surface tension of the molecular model. Massively parallel molecular dynamics simulations are performed close to the spinodal to compute bubble nucleation rates. From these simulations, the kinetic prefactor of the hybrid nucleation theory is estimated, whereas the nucleation barrier is calculated from density gradient theory. This enables the extrapolation of molecular simulation data to the whole metastable range including technically relevant densities. The results are tested against available experimental data and found to be in good agreement. The new method does not suffer from typical deficiencies of classical nucleation theory concerning the thermodynamic barrier at the spinodal and the bubble size dependence of surface tension, which is typically neglected in classical nucleation theory. In addition, the density in the center of critical bubbles and their surface tension is determined as a function of their radius. The usual linear Tolman correction to the capillarity approximation is found to be invalid.

Non local-thermodynamical-equilibrium effects in the simulation of laser-produced plasmas

NASA Astrophysics Data System (ADS)

Klapisch, M.; Bar-Shalom, A.; Oreg, J.; Colombant, D.

1998-05-01

Local thermodynamic equilibrium (LTE) breaks down in directly or indirectly driven laser plasmas because of sharp gradients, energy deposition, etc. For modeling non-LTE effects in hydrodynamical simulations, Busquet's model [Phys. Fluids B 5, 4191 (1993)] is very convenient and efficient. It uses off-line generated LTE opacities and equation of states via an effective, radiation-dependent ionization temperature Tz. An overview of the model is given. The results are compared with an elaborate collisional radiative model based on superconfigurations. The agreements for average charge Z* and opacities are surprisingly good, even more so when the plasma is immersed in a radiation field. Some remaining discrepancy at low density is attributed to dielectronic recombination. Improvement appears possible, especially for emissivities, because the concept of ionization temperature seems to be validated.

A new approach to modeling the effective thermal conductivity of ceramics porous media using a generalized self-consistent method

NASA Astrophysics Data System (ADS)

Edrisi, Siroos; Bidhendi, Norollah Kasiri; Haghighi, Maryam

2017-01-01

Effective thermal conductivity of the porous media was modeled based on a self-consistent method. This model estimates the heat transfer between insulator surface and air cavities accurately. In this method, the pore size and shape, the temperature gradient and other thermodynamic properties of the fluid was taken into consideration. The results are validated by experimental data for fire bricks used in cracking furnaces at the olefin plant of Maroon petrochemical complexes well as data published for polyurethane foam (synthetic polymers) IPTM and IPM. The model predictions present a good agreement against experimental data with thermal conductivity deviating <1 %.

The energetics of organic synthesis inside and outside the cell

PubMed Central

Amend, Jan P.; LaRowe, Douglas E.; McCollom, Thomas M.; Shock, Everett L.

2013-01-01

Thermodynamic modelling of organic synthesis has largely been focused on deep-sea hydrothermal systems. When seawater mixes with hydrothermal fluids, redox gradients are established that serve as potential energy sources for the formation of organic compounds and biomolecules from inorganic starting materials. This energetic drive, which varies substantially depending on the type of host rock, is present and available both for abiotic (outside the cell) and biotic (inside the cell) processes. Here, we review and interpret a library of theoretical studies that target organic synthesis energetics. The biogeochemical scenarios evaluated include those in present-day hydrothermal systems and in putative early Earth environments. It is consistently and repeatedly shown in these studies that the formation of relatively simple organic compounds and biomolecules can be energy-yielding (exergonic) at conditions that occur in hydrothermal systems. Expanding on our ability to calculate biomass synthesis energetics, we also present here a new approach for estimating the energetics of polymerization reactions, specifically those associated with polypeptide formation from the requisite amino acids. PMID:23754809

A unified multicomponent stress-diffusion model of drug release from non-biodegradable polymeric matrix tablets.

PubMed

Salehi, Ali; Zhao, Jin; Cabelka, Tim D; Larson, Ronald G

2016-02-28

We propose a new transport model of drug release from hydrophilic polymeric matrices, based on Stefan-Maxwell flux laws for multicomponent transport. Polymer stress is incorporated in the total mixing free energy, which contributes directly to the diffusion driving force while leading to time-dependent boundary conditions at the tablet interface. Given that hydrated matrix tablets are dense multicomponent systems, extended Stefan-Maxwell (ESM) flux laws are adopted to ensure consistency with the Onsager reciprocity principle and the Gibbs-Duhem thermodynamic constraint. The ESM flux law for any given component takes into account the friction exerted by all other species and is invariant with respect to reference velocity, thus satisfying Galilean translational invariance. Our model demonstrates that penetrant-induced plasticization of polymer chains partially or even entirely offsets the steady decline of chemical potential gradients at the tablet-medium interface that drive drug release. Utilizing a Flory-Huggins thermodynamic model, a modified form of the upper convected Maxwell constitutive equation for polymer stress and a Fujita-type dependence of mutual diffusivities on composition, depending on parameters, Fickian, anomalous or case II drug transport arises naturally from the model, which are characterized by quasi-power-law release profiles with exponents ranging from 0.5 to 1, respectively. A necessary requirement for non-Fickian release in our model is that the matrix stress relaxation time is comparable to the time scale for water diffusion. Mutual diffusivities and their composition dependence are the most decisive factors in controlling drug release characteristics in our model. Regression of the experimental polymer dissolution and drug release profiles in a system of Theophylline/cellulose (K15M) demonstrate that API-water mutual diffusivity in the presence of excipient cannot generally be taken as a constant. Copyright © 2016 Elsevier B.V. All rights reserved.

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

Evaluation of differences between dual salt-pH gradient elution and mono gradient elution using a thermodynamic model: Simultaneous separation of six monoclonal antibody charge and size variants on preparative-scale ion exchange chromatographic resin.

PubMed

Lee, Yi Feng; Jöhnck, Matthias; Frech, Christian

2018-02-21

The efficiencies of mono gradient elution and dual salt-pH gradient elution for separation of six mAb charge and size variants on a preparative-scale ion exchange chromatographic resin are compared in this study. Results showed that opposite dual salt-pH gradient elution with increasing pH gradient and simultaneously decreasing salt gradient is best suited for the separation of these mAb charge and size variants on Eshmuno ® CPX. Besides giving high binding capacity, this type of opposite dual salt-pH gradient also provides better resolved mAb variant peaks and lower conductivity in the elution pools compared to single pH or salt gradients. To have a mechanistic understanding of the differences in mAb variants retention behaviors of mono pH gradient, parallel dual salt-pH gradient, and opposite dual salt-pH gradient, a linear gradient elution model was used. After determining the model parameters using the linear gradient elution model, 2D plots were used to show the pH and salt dependencies of the reciprocals of distribution coefficient, equilibrium constant, and effective ionic capacity of the mAb variants in these gradient elution systems. Comparison of the 2D plots indicated that the advantage of opposite dual salt-pH gradient system with increasing pH gradient and simultaneously decreasing salt gradient is the noncontinuous increased acceleration of protein migration. Furthermore, the fitted model parameters can be used for the prediction and optimization of mAb variants separation in dual salt-pH gradient and step elution. © 2018 American Institute of Chemical Engineers Biotechnol. Prog., 2018. © 2018 American Institute of Chemical Engineers.

Intercellular signaling through secreted proteins induces free-energy gradient-directed cell movement.

PubMed

Kravchenko-Balasha, Nataly; Shin, Young Shik; Sutherland, Alex; Levine, R D; Heath, James R

2016-05-17

Controlling cell migration is important in tissue engineering and medicine. Cell motility depends on factors such as nutrient concentration gradients and soluble factor signaling. In particular, cell-cell signaling can depend on cell-cell separation distance and can influence cellular arrangements in bulk cultures. Here, we seek a physical-based approach, which identifies a potential governed by cell-cell signaling that induces a directed cell-cell motion. A single-cell barcode chip (SCBC) was used to experimentally interrogate secreted proteins in hundreds of isolated glioblastoma brain cancer cell pairs and to monitor their relative motions over time. We used these trajectories to identify a range of cell-cell separation distances where the signaling was most stable. We then used a thermodynamics-motivated analysis of secreted protein levels to characterize free-energy changes for different cell-cell distances. We show that glioblastoma cell-cell movement can be described as Brownian motion biased by cell-cell potential. To demonstrate that the free-energy potential as determined by the signaling is the driver of motion, we inhibited two proteins most involved in maintaining the free-energy gradient. Following inhibition, cell pairs showed an essentially random Brownian motion, similar to the case for untreated, isolated single cells.

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.

On Localized Vapor Pressure Gradients Governing Condensation and Frost Phenomena.

PubMed

Nath, Saurabh; Boreyko, Jonathan B

2016-08-23

Interdroplet vapor pressure gradients are the driving mechanism for several phase-change phenomena such as condensation dry zones, interdroplet ice bridging, dry zones around ice, and frost halos. Despite the fundamental nature of the underlying pressure gradients, the majority of studies on these emerging phenomena have been primarily empirical. Using classical nucleation theory and Becker-Döring embryo formation kinetics, here we calculate the pressure field for all possible modes of condensation and desublimation in order to gain fundamental insight into how pressure gradients govern the behavior of dry zones, condensation frosting, and frost halos. Our findings reveal that in a variety of phase-change systems the thermodynamically favorable mode of nucleation can switch between condensation and desublimation depending upon the temperature and wettability of the surface. The calculated pressure field is used to model the length of a dry zone around liquid or ice droplets over a broad parameter space. The long-standing question of whether the vapor pressure at the interface of growing frost is saturated or supersaturated is resolved by considering the kinetics of interdroplet ice bridging. Finally, on the basis of theoretical calculations, we propose that there exists a new mode of frost halo that is yet to be experimentally observed; a bimodal phase map is developed, demonstrating its dependence on the temperature and wettability of the underlying substrate. We hope that the model and predictions contained herein will assist future efforts to exploit localized vapor pressure gradients for the design of spatially controlled or antifrosting phase-change systems.

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

Relativistic distribution function for particles with spin at local thermodynamical equilibrium

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

Becattini, F., E-mail: becattini@fi.infn.it; INFN Sezione di Firenze, Florence; Universität Frankfurt, Frankfurt am Main

2013-11-15

We present an extension of relativistic single-particle distribution function for weakly interacting particles at local thermodynamical equilibrium including spin degrees of freedom, for massive spin 1/2 particles. We infer, on the basis of the global equilibrium case, that at local thermodynamical equilibrium particles acquire a net polarization proportional to the vorticity of the inverse temperature four-vector field. The obtained formula for polarization also implies that a steady gradient of temperature entails a polarization orthogonal to particle momentum. The single-particle distribution function in momentum space extends the so-called Cooper–Frye formula to particles with spin 1/2 and allows us to predict theirmore » polarization in relativistic heavy ion collisions at the freeze-out. -- Highlights: •Single-particle distribution function in local thermodynamical equilibrium with spin. •Polarization of spin 1/2 particles in a fluid at local thermodynamical equilibrium. •Prediction of a new effect: a steady gradient of temperature induces a polarization. •Application to the calculation of polarization in relativistic heavy ion collisions.« less

Real-data tests of a single-Doppler radar assimilation system

NASA Astrophysics Data System (ADS)

Nehrkorn, Thomas; Hegarty, James; Hamill, Thomas M.

1994-06-01

Real data tests of a single-Doppler radar data assimilation and forecast system have been conducted for a Florida sea breeze case. The system consists of a hydrostatic mesoscale model used for prediction of the preconvective boundary layer, an objective analysis that combines model first guess fields with radar derived horizontal winds, a thermodynamic retrieval scheme that obtains temperature information from the three-dimensional wind field and its temporal evolution, and a Newtonian nudging scheme for forcing the model forecast to closer agreement with the analysis. As was found in earlier experiments with simulated data, assimilation using Newtonian nudging benefits from temperature data in addition to wind data. The thermodynamic retrieval technique was successful in retrieving a horizontal temperature gradient from the radar-derived wind fields that, when assimilated into the model, led to a significantly improved forecast of the seabreeze strength and position.

Influence of the iron spin crossover in ferropericlase on the lower mantle geotherm

NASA Astrophysics Data System (ADS)

Valencia-Cardona, Juan J.; Shukla, Gaurav; Wu, Zhongqing; Houser, Christine; Yuen, David A.; Wentzcovitch, Renata M.

2017-05-01

The iron spin crossover in ferropericlase introduces anomalies in its thermodynamics and thermoelastic properties. Here we investigate how these anomalies can affect the lower mantle geotherm using thermodynamics properties from ab initio calculations. The anomalous effect is examined in mantle aggregates consisting of mixtures of bridgmanite, ferropericlase, and CaSiO3 perovskite, with different Mg/Si ratios varying from harzburgitic to perovskitic (Mg/Si ˜ 1.5 to 0.8). We find that the anomalies introduced by the spin crossover increase the isentropic gradient and thus the geotherm proportionally to the amount of ferropericlase. The geotherms can be as much as ˜200 K hotter than the conventional adiabatic geotherm at deep lower mantle conditions. Aggregate elastic moduli and seismic velocities are also sensitive to the spin crossover and the geotherm, which impacts analyses of lower mantle velocities and composition.

Torque-coupled thermodynamic model for FoF1 -ATPase

NASA Astrophysics Data System (ADS)

Ai, Guangkuo; Liu, Pengfei; Ge, Hao

2017-05-01

FoF1 -ATPase is a motor protein complex that utilizes transmembrane ion flow to drive the synthesis of adenosine triphosphate (ATP) from adenosine diphosphate (ADP) and phosphate (Pi). While many theoretical models have been proposed to account for its rotary activity, most of them focus on the Fo or F1 portions separately rather than the complex as a whole. Here, we propose a simple but new torque-coupled thermodynamic model of FoF1 -ATPase. Solving this model at steady state, we find that the monotonic variation of each portion's efficiency becomes much more robust over a wide range of parameters when the Fo and F1 portions are coupled together, as compared to cases when they are considered separately. Furthermore, the coupled model predicts the dependence of each portion's kinetic behavior on the parameters of the other. Specifically, the power and efficiency of the F1 portion are quite sensitive to the proton gradient across the membrane, while those of the Fo portion as well as the related Michaelis constants for proton concentrations respond insensitively to concentration changes in the reactants of ATP synthesis. The physiological proton gradient across the membrane in the Fo portion is also shown to be optimal for the Michaelis constants of ADP and phosphate in the F1 portion during ATP synthesis. Together, our coupled model is able to predict key dynamic and thermodynamic features of the FoF1 -ATPase in vivo semiquantitatively, and suggests that such coupling approach could be further applied to other biophysical systems.

Modeling nanostructural surface modifications in metal cutting by an approach of thermodynamic irreversibility: Derivation and experimental validation

NASA Astrophysics Data System (ADS)

Buchkremer, S.; Klocke, F.

2017-01-01

Performance and operational safety of many metal parts in engineering depend on their surface integrity. During metal cutting, large thermomechanical loads and high gradients of the loads concerning time and location act on the surfaces and may yield significant structural material modifications, which alter the surface integrity. In this work, the derivation and validation of a model of nanostructural surface modifications in metal cutting are presented. For the first time in process modeling, initiation and kinetics of these modifications are predicted using a thermodynamic potential, which considers the interdependent developments of plastic work, dissipation, heat conduction and interface energy as well as the associated productions and flows of entropy. The potential is expressed based on the free Helmholtz energy. The irreversible thermodynamic state changes in the workpiece surface are homogenized over the volume in order to bridge the gap between discrete phenomena involved with the initiation and kinetics of dynamic recrystallization and its macroscopic implications for surface integrity. The formulation of the thermodynamic potential is implemented into a finite element model of orthogonal cutting of steel AISI 4140. Close agreement is achieved between predicted nanostructures and those obtained in transmission electron microscopical investigations of specimen produced in cutting experiments.

Thermodynamics analysis of diffusion in spark plasma sintering welding Cr3C2 and Ni

NASA Astrophysics Data System (ADS)

Zhang, Fan; Zhang, Jinyong; Leng, Xiaoxuan; Lei, Liwen; Fu, Zhengyi

2017-03-01

Spark plasma sintering (SPS) welding of chromium carbide (Cr3C2) and nickel (Ni) was used to investigate the atomic diffusion caused by bypassing current. It was found that the diffusion coefficient with bypassing current was enhanced by almost 3.57 times over that without bypassing current. Different from the previous researches, the thermodynamics analysis conducted herein showed that the enhancement included a current direction-independent part besides the known current direction-dependent part. A local temperature gradient (LTG) model was proposed to explain the current direction-independent effect. Assuming that the LTG was mainly due to the interfacial electric resistance causing heterogeneous Joule heating, the theoretical results were in good agreement with the experimental results both in the present and previous studies. This new LTG model provides a reasonable physical meaning for the low-temperature advantage of SPS welding and should be useful in a wide range of applications.

First-Principles and Thermodynamic Simulation of Elastic Stress Effect on Energy of Hydrogen Dissolution in Alpha Iron

NASA Astrophysics Data System (ADS)

Rakitin, M. S.; Mirzoev, A. A.; Mirzaev, D. A.

2018-04-01

Mobile hydrogen, when dissolving in metals, redistributes due to the density gradients and elastic stresses, and enables destruction processes or phase transformations in local volumes of a solvent metal. It is rather important in solid state physics to investigate these interactions. The first-principle calculations performed in terms of the density functional theory, are used for thermodynamic simulation of the elastic stress effect on the energy of hydrogen dissolution in α-Fe crystal lattice. The paper presents investigations of the total energy of Fe-H system depending on the lattice parameter. As a result, the relation is obtained between the hydrogen dissolution energy and stress. A good agreement is shown between the existing data and simulation results. The extended equation is suggested for the chemical potential of hydrogen atom in iron within the local stress field. Two parameters affecting the hydrogen distribution are compared, namely local stress and phase transformations.

Semi-empirical anzatz for Helmholtz free energy calculation: Thermal properties of silver along shock Hugoniot

NASA Astrophysics Data System (ADS)

Joshi, R. H.; Thakore, B. Y.; Bhatt, N. K.; Vyas, P. R.; Jani, A. R.

2018-02-01

A density functional theory along with electronic contribution is used to compute quasiharmonic total energy for silver, whereas explicit phonon anharmonic contribution is added through perturbative term in temperature. Within the Mie-Grüneisen approach, we propose a consistent computational scheme for calculating various thermophysical properties of a substance, in which the required Grüneisen parameter γth is calculated from the knowledge of binding energy. The present study demonstrates that no separate relation for volume dependence for γth is needed, and complete thermodynamics under simultaneous high-temperature and high-pressure condition can be derived in a consistent manner. We have calculated static and dynamic equation of states and some important thermodynamic properties along the shock Hugoniot. A careful examination of temperature dependence of Grüneisen parameter reveals the importance of temperature-effect on various thermal properties.

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.

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 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.

Theory of activated glassy relaxation, mobility gradients, surface diffusion, and vitrification in free standing thin films

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

Mirigian, Stephen, E-mail: kschweiz@illinois.edu, E-mail: smirigian@gmail.com; Schweizer, Kenneth S., E-mail: kschweiz@illinois.edu, E-mail: smirigian@gmail.com

2015-12-28

We have constructed a quantitative, force level, statistical mechanical theory for how confinement in free standing thin films introduces a spatial mobility gradient of the alpha relaxation time as a function of temperature, film thickness, and location in the film. The crucial idea is that relaxation speeds up due to the reduction of both near-surface barriers associated with the loss of neighbors in the local cage and the spatial cutoff and dynamical softening near the vapor interface of the spatially longer range collective elasticity cost for large amplitude hopping. These two effects are fundamentally coupled. Quantitative predictions are made formore » how an apparent glass temperature depends on the film thickness and experimental probe technique, the emergence of a two-step decay and mobile layers in time domain measurements, signatures of confinement in frequency-domain dielectric loss experiments, the dependence of film-averaged relaxation times and dynamic fragility on temperature and film thickness, surface diffusion, and the relationship between kinetic experiments and pseudo-thermodynamic measurements such as ellipsometry.« less

Theory of activated glassy relaxation, mobility gradients, surface diffusion, and vitrification in free standing thin films.

PubMed

Mirigian, Stephen; Schweizer, Kenneth S

2015-12-28

We have constructed a quantitative, force level, statistical mechanical theory for how confinement in free standing thin films introduces a spatial mobility gradient of the alpha relaxation time as a function of temperature, film thickness, and location in the film. The crucial idea is that relaxation speeds up due to the reduction of both near-surface barriers associated with the loss of neighbors in the local cage and the spatial cutoff and dynamical softening near the vapor interface of the spatially longer range collective elasticity cost for large amplitude hopping. These two effects are fundamentally coupled. Quantitative predictions are made for how an apparent glass temperature depends on the film thickness and experimental probe technique, the emergence of a two-step decay and mobile layers in time domain measurements, signatures of confinement in frequency-domain dielectric loss experiments, the dependence of film-averaged relaxation times and dynamic fragility on temperature and film thickness, surface diffusion, and the relationship between kinetic experiments and pseudo-thermodynamic measurements such as ellipsometry.

Vibrational and Thermal Properties of Oxyanionic Crystals

NASA Astrophysics Data System (ADS)

Korabel'nikov, D. V.

2018-03-01

The vibrational and thermal properties of dolomite and alkali chlorates and perchlorates were studied in the gradient approximation of density functional theory using the method of a linear combination of atomic orbitals (LCAO). Long-wave vibration frequencies, IR and Raman spectra, and mode Gruneisen parameters were calculated. Equation-of-state parameters, thermodynamic potentials, entropy, heat capacity, and thermal expansion coefficient were also determined. The thermal expansion coefficient of dolomite was established to be much lower than for chlorates and perchlorates. The temperature dependence of the heat capacity at T > 200 K was shown to be generally governed by intramolecular vibrations.

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.

Why we need to look beyond the glass transition temperature to characterize the dynamics of thin supported polymer films.

PubMed

Zhang, Wengang; Douglas, Jack F; Starr, Francis W

2018-05-29

There is significant variation in the reported magnitude and even the sign of [Formula: see text] shifts in thin polymer films with nominally the same chemistry, film thickness, and supporting substrate. The implicit assumption is that methods used to estimate [Formula: see text] in bulk materials are relevant for inferring dynamic changes in thin films. To test the validity of this assumption, we perform molecular simulations of a coarse-grained polymer melt supported on an attractive substrate. As observed in many experiments, we find that [Formula: see text] based on thermodynamic criteria (temperature dependence of film height or enthalpy) decreases with decreasing film thickness, regardless of the polymer-substrate interaction strength ε. In contrast, we find that [Formula: see text] based on a dynamic criterion (relaxation of the dynamic structure factor) also decreases with decreasing thickness when ε is relatively weak, but [Formula: see text] increases when ε exceeds the polymer-polymer interaction strength. We show that these qualitatively different trends in [Formula: see text] reflect differing sensitivities to the mobility gradient across the film. Apparently, the slowly relaxing polymer segments in the substrate region make the largest contribution to the shift of [Formula: see text] in the dynamic measurement, but this part of the film contributes less to the thermodynamic estimate of [Formula: see text] Our results emphasize the limitations of using [Formula: see text] to infer changes in the dynamics of polymer thin films. However, we show that the thermodynamic and dynamic estimates of [Formula: see text] can be combined to predict local changes in [Formula: see text] near the substrate, providing a simple method to infer information about the mobility gradient.

Structural, electronic, elastic and thermodynamic properties of Li2ZrO3: A comprehensive study using DFT formalism

NASA Astrophysics Data System (ADS)

Chattaraj, D.

2017-12-01

Lithium zirconate is considered to be potential tritium breeder material for fusion reactors. Here I report a comprehensive study on structural, electronic, elastic, and thermodynamic properties of Li2ZrO3 using plane wave based density functional theory. While the electron-ion interaction term has been described by projected-augmented wave method, the exchange-correlation energy was taken care of through generalized gradient approximation scheme. The optimized lattice and internal parameters of Li2ZrO3 unit cell agree well within ±1-2% from the experimental values. From the electronic structure analysis it is seen that the Fermi energy has significant contribution from the 2s, 2p and 4d orbitals of Li, O and Zr atoms, respectively. Elastic property calculation of Li2ZrO3 showed mechanical stability and anisotropy at ambient pressure. The formation energy (ΔfH) of Li2ZrO3 at 0 K, after zero point energy correction, has been estimated to be -1550 kJ/mol. The temperature dependent thermodynamic functions of Li2ZrO3 have also been calculated from the Debye-Grüneisen quasi-harmonic approximation and reported here.

Thermodynamic and energy efficiency analysis of power generation from natural salinity gradients by pressure retarded osmosis.

PubMed

Yip, Ngai Yin; Elimelech, Menachem

2012-05-01

The Gibbs free energy of mixing dissipated when fresh river water flows into the sea can be harnessed for sustainable power generation. Pressure retarded osmosis (PRO) is one of the methods proposed to generate power from natural salinity gradients. In this study, we carry out a thermodynamic and energy efficiency analysis of PRO work extraction. First, we present a reversible thermodynamic model for PRO and verify that the theoretical maximum extractable work in a reversible PRO process is identical to the Gibbs free energy of mixing. Work extraction in an irreversible constant-pressure PRO process is then examined. We derive an expression for the maximum extractable work in a constant-pressure PRO process and show that it is less than the ideal work (i.e., Gibbs free energy of mixing) due to inefficiencies intrinsic to the process. These inherent inefficiencies are attributed to (i) frictional losses required to overcome hydraulic resistance and drive water permeation and (ii) unutilized energy due to the discontinuation of water permeation when the osmotic pressure difference becomes equal to the applied hydraulic pressure. The highest extractable work in constant-pressure PRO with a seawater draw solution and river water feed solution is 0.75 kWh/m(3) while the free energy of mixing is 0.81 kWh/m(3)-a thermodynamic extraction efficiency of 91.1%. Our analysis further reveals that the operational objective to achieve high power density in a practical PRO process is inconsistent with the goal of maximum energy extraction. This study demonstrates thermodynamic and energetic approaches for PRO and offers insights on actual energy accessible for utilization in PRO power generation through salinity gradients. © 2012 American Chemical Society

A finite nonlinear hyper-viscoelastic model for soft biological tissues.

PubMed

Panda, Satish Kumar; Buist, Martin Lindsay

2018-03-01

Soft tissues exhibit highly nonlinear rate and time-dependent stress-strain behaviour. Strain and strain rate dependencies are often modelled using a hyperelastic model and a discrete (standard linear solid) or continuous spectrum (quasi-linear) viscoelastic model, respectively. However, these models are unable to properly capture the materials characteristics because hyperelastic models are unsuited for time-dependent events, whereas the common viscoelastic models are insufficient for the nonlinear and finite strain viscoelastic tissue responses. The convolution integral based models can demonstrate a finite viscoelastic response; however, their derivations are not consistent with the laws of thermodynamics. The aim of this work was to develop a three-dimensional finite hyper-viscoelastic model for soft tissues using a thermodynamically consistent approach. In addition, a nonlinear function, dependent on strain and strain rate, was adopted to capture the nonlinear variation of viscosity during a loading process. To demonstrate the efficacy and versatility of this approach, the model was used to recreate the experimental results performed on different types of soft tissues. In all the cases, the simulation results were well matched (R 2 ⩾0.99) with the experimental data. Copyright © 2018 Elsevier Ltd. All rights reserved.

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.

Thermodynamic stability of nanosized multicomponent bubbles/droplets: the square gradient theory and the capillary approach.

PubMed

Wilhelmsen, Øivind; Bedeaux, Dick; Kjelstrup, Signe; Reguera, David

2014-01-14

Formation of nanosized droplets/bubbles from a metastable bulk phase is connected to many unresolved scientific questions. We analyze the properties and stability of multicomponent droplets and bubbles in the canonical ensemble, and compare with single-component systems. The bubbles/droplets are described on the mesoscopic level by square gradient theory. Furthermore, we compare the results to a capillary model which gives a macroscopic description. Remarkably, the solutions of the square gradient model, representing bubbles and droplets, are accurately reproduced by the capillary model except in the vicinity of the spinodals. The solutions of the square gradient model form closed loops, which shows the inherent symmetry and connected nature of bubbles and droplets. A thermodynamic stability analysis is carried out, where the second variation of the square gradient description is compared to the eigenvalues of the Hessian matrix in the capillary description. The analysis shows that it is impossible to stabilize arbitrarily small bubbles or droplets in closed systems and gives insight into metastable regions close to the minimum bubble/droplet radii. Despite the large difference in complexity, the square gradient and the capillary model predict the same finite threshold sizes and very similar stability limits for bubbles and droplets, both for single-component and two-component systems.

Thermodynamic stability of nanosized multicomponent bubbles/droplets: The square gradient theory and the capillary approach

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

Wilhelmsen, Øivind, E-mail: oivind.wilhelmsen@ntnu.no; Bedeaux, Dick; Kjelstrup, Signe

Formation of nanosized droplets/bubbles from a metastable bulk phase is connected to many unresolved scientific questions. We analyze the properties and stability of multicomponent droplets and bubbles in the canonical ensemble, and compare with single-component systems. The bubbles/droplets are described on the mesoscopic level by square gradient theory. Furthermore, we compare the results to a capillary model which gives a macroscopic description. Remarkably, the solutions of the square gradient model, representing bubbles and droplets, are accurately reproduced by the capillary model except in the vicinity of the spinodals. The solutions of the square gradient model form closed loops, which showsmore » the inherent symmetry and connected nature of bubbles and droplets. A thermodynamic stability analysis is carried out, where the second variation of the square gradient description is compared to the eigenvalues of the Hessian matrix in the capillary description. The analysis shows that it is impossible to stabilize arbitrarily small bubbles or droplets in closed systems and gives insight into metastable regions close to the minimum bubble/droplet radii. Despite the large difference in complexity, the square gradient and the capillary model predict the same finite threshold sizes and very similar stability limits for bubbles and droplets, both for single-component and two-component systems.« less

Self-consistent implementation of meta-GGA functionals for the ONETEP linear-scaling electronic structure package.

PubMed

Womack, James C; Mardirossian, Narbe; Head-Gordon, Martin; Skylaris, Chris-Kriton

2016-11-28

Accurate and computationally efficient exchange-correlation functionals are critical to the successful application of linear-scaling density functional theory (DFT). Local and semi-local functionals of the density are naturally compatible with linear-scaling approaches, having a general form which assumes the locality of electronic interactions and which can be efficiently evaluated by numerical quadrature. Presently, the most sophisticated and flexible semi-local functionals are members of the meta-generalized-gradient approximation (meta-GGA) family, and depend upon the kinetic energy density, τ, in addition to the charge density and its gradient. In order to extend the theoretical and computational advantages of τ-dependent meta-GGA functionals to large-scale DFT calculations on thousands of atoms, we have implemented support for τ-dependent meta-GGA functionals in the ONETEP program. In this paper we lay out the theoretical innovations necessary to implement τ-dependent meta-GGA functionals within ONETEP's linear-scaling formalism. We present expressions for the gradient of the τ-dependent exchange-correlation energy, necessary for direct energy minimization. We also derive the forms of the τ-dependent exchange-correlation potential and kinetic energy density in terms of the strictly localized, self-consistently optimized orbitals used by ONETEP. To validate the numerical accuracy of our self-consistent meta-GGA implementation, we performed calculations using the B97M-V and PKZB meta-GGAs on a variety of small molecules. Using only a minimal basis set of self-consistently optimized local orbitals, we obtain energies in excellent agreement with large basis set calculations performed using other codes. Finally, to establish the linear-scaling computational cost and applicability of our approach to large-scale calculations, we present the outcome of self-consistent meta-GGA calculations on amyloid fibrils of increasing size, up to tens of thousands of atoms.

Self-consistent implementation of meta-GGA functionals for the ONETEP linear-scaling electronic structure package

NASA Astrophysics Data System (ADS)

Womack, James C.; Mardirossian, Narbe; Head-Gordon, Martin; Skylaris, Chris-Kriton

2016-11-01

Accurate and computationally efficient exchange-correlation functionals are critical to the successful application of linear-scaling density functional theory (DFT). Local and semi-local functionals of the density are naturally compatible with linear-scaling approaches, having a general form which assumes the locality of electronic interactions and which can be efficiently evaluated by numerical quadrature. Presently, the most sophisticated and flexible semi-local functionals are members of the meta-generalized-gradient approximation (meta-GGA) family, and depend upon the kinetic energy density, τ, in addition to the charge density and its gradient. In order to extend the theoretical and computational advantages of τ-dependent meta-GGA functionals to large-scale DFT calculations on thousands of atoms, we have implemented support for τ-dependent meta-GGA functionals in the ONETEP program. In this paper we lay out the theoretical innovations necessary to implement τ-dependent meta-GGA functionals within ONETEP's linear-scaling formalism. We present expressions for the gradient of the τ-dependent exchange-correlation energy, necessary for direct energy minimization. We also derive the forms of the τ-dependent exchange-correlation potential and kinetic energy density in terms of the strictly localized, self-consistently optimized orbitals used by ONETEP. To validate the numerical accuracy of our self-consistent meta-GGA implementation, we performed calculations using the B97M-V and PKZB meta-GGAs on a variety of small molecules. Using only a minimal basis set of self-consistently optimized local orbitals, we obtain energies in excellent agreement with large basis set calculations performed using other codes. Finally, to establish the linear-scaling computational cost and applicability of our approach to large-scale calculations, we present the outcome of self-consistent meta-GGA calculations on amyloid fibrils of increasing size, up to tens of thousands of atoms.

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.

Kinematic assumptions and their consequences on the structure of field equations in continuum dislocation theory

NASA Astrophysics Data System (ADS)

Silbermann, C. B.; Ihlemann, J.

2016-03-01

Continuum Dislocation Theory (CDT) relates gradients of plastic deformation in crystals with the presence of geometrically necessary dislocations. Therefore, the dislocation tensor is introduced as an additional thermodynamic state variable which reflects tensorial properties of dislocation ensembles. Moreover, the CDT captures both the strain energy from the macroscopic deformation of the crystal and the elastic energy of the dislocation network, as well as the dissipation of energy due to dislocation motion. The present contribution deals with the geometrically linear CDT. More precise, the focus is on the role of dislocation kinematics for single and multi-slip and its consequences on the field equations. Thereby, the number of active slip systems plays a crucial role since it restricts the degrees of freedom of plastic deformation. Special attention is put on the definition of proper, well-defined invariants of the dislocation tensor in order to avoid any spurious dependence of the resulting field equations on the coordinate system. It is shown how a slip system based approach can be in accordance with the tensor nature of the involved quantities. At first, only dislocation glide in one active slip system of the crystal is allowed. Then, the special case of two orthogonal (interacting) slip systems is considered and the governing field equations are presented. In addition, the structure and symmetry of the backstress tensor is investigated from the viewpoint of thermodynamical consistency. The results will again be used in order to facilitate the set of field equations and to prepare for a robust numerical implementation.

Ontology of physics for biology: representing physical dependencies as a basis for biological processes.

PubMed

Cook, Daniel L; Neal, Maxwell L; Bookstein, Fred L; Gennari, John H

2013-12-02

In prior work, we presented the Ontology of Physics for Biology (OPB) as a computational ontology for use in the annotation and representations of biophysical knowledge encoded in repositories of physics-based biosimulation models. We introduced OPB:Physical entity and OPB:Physical property classes that extend available spatiotemporal representations of physical entities and processes to explicitly represent the thermodynamics and dynamics of physiological processes. Our utilitarian, long-term aim is to develop computational tools for creating and querying formalized physiological knowledge for use by multiscale "physiome" projects such as the EU's Virtual Physiological Human (VPH) and NIH's Virtual Physiological Rat (VPR). Here we describe the OPB:Physical dependency taxonomy of classes that represent of the laws of classical physics that are the "rules" by which physical properties of physical entities change during occurrences of physical processes. For example, the fluid analog of Ohm's law (as for electric currents) is used to describe how a blood flow rate depends on a blood pressure gradient. Hooke's law (as in elastic deformations of springs) is used to describe how an increase in vascular volume increases blood pressure. We classify such dependencies according to the flow, transformation, and storage of thermodynamic energy that occurs during processes governed by the dependencies. We have developed the OPB and annotation methods to represent the meaning-the biophysical semantics-of the mathematical statements of physiological analysis and the biophysical content of models and datasets. Here we describe and discuss our approach to an ontological representation of physical laws (as dependencies) and properties as encoded for the mathematical analysis of biophysical processes.

Evaluation and Validation of a TCAT Model to Describe Non-Dilute Flow and Species Transport in Porous Media

NASA Astrophysics Data System (ADS)

Weigand, T. M.; Harrison, E.; Miller, C. T.

2017-12-01

A thermodynamically constrained averaging theory (TCAT) model has been developed to simulate non-dilute flow and species transport in porous media. This model has the advantages of a firm connection between the microscale, or pore scale, and the macroscale; a thermodynamically consistent basis; the explicit inclusion of dissipative terms that arise from spatial gradients in pressure and chemical activity; and the ability to describe both high and low concentration displacement. The TCAT model has previously been shown to provide excellent agreement for a set of laboratory data and outperformed existing macroscale models that have been used for non-dilute flow and transport. The examined experimental dataset consisted of stable brine displacements for a large range of fluid properties. This dataset however only examined one type of porous media and had a fixed flow rate for all experiments. In this work, the TCAT model is applied to a dataset that consists of two different porous media types, constant head and flow rate conditions, varying resident fluid concentrations, and internal probes that measured the pressure and salt mass fraction. Parameter estimation is performed on a subset of the experimental data for the TCAT model as well as other existing non-dilute flow and transport models. The optimized parameters are then used for forward simulations and the accuracy of the models is compared.

Solving traveling salesman problems with DNA molecules encoding numerical values.

PubMed

Lee, Ji Youn; Shin, Soo-Yong; Park, Tai Hyun; Zhang, Byoung-Tak

2004-12-01

We introduce a DNA encoding method to represent numerical values and a biased molecular algorithm based on the thermodynamic properties of DNA. DNA strands are designed to encode real values by variation of their melting temperatures. The thermodynamic properties of DNA are used for effective local search of optimal solutions using biochemical techniques, such as denaturation temperature gradient polymerase chain reaction and temperature gradient gel electrophoresis. The proposed method was successfully applied to the traveling salesman problem, an instance of optimization problems on weighted graphs. This work extends the capability of DNA computing to solving numerical optimization problems, which is contrasted with other DNA computing methods focusing on logical problem solving.

A coupled mechanical-chemical model for reflecting the influence of stress on oxidation reactions in thermal barrier coating

NASA Astrophysics Data System (ADS)

Chen, Lin; Yueming, Li

2018-06-01

In this paper, a coupled mechanical-chemical model is established based on the thermodynamic framework, in which the contribution of chemical expansion to free energy is introduced. The stress-dependent chemical potential equilibrium at the gas-solid interface and the stress gradient-dependent diffusion equation as well as a so-called generalized force which is conjugate to the oxidation rate are derived from the proposed model, which could reflect the influence of stresses on the oxidation reaction. Based on the proposed coupled mechanical-chemical model, a user element subroutine is developed in ABAQUS. The numerical simulation of the high temperature oxidation in the thermal barrier coating is carried out to verify the accuracy of the proposed model, and then the influence of stresses on the oxidation reaction is investigated. In thermally grown oxide, the considerable stresses would be induced by permanent volumetric swelling during the oxidation. The stresses play an important role in the chemical potential equilibrium at the gas-solid interface and strongly affect the oxidation reaction. The gradient of the stresses, however, only occurs in the extremely thin oxidation front layer, which plays a very limited role in the oxidation reaction. The generalized force could be divided into the stress-dependent and the stress-independent parts. Comparing with the stress-independent part, the stress-dependent part is smaller, which has little influence on oxidation reaction.

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

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

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.

Computation of Kinetics for the Hydrogen/Oxygen System Using the Thermodynamic Method

NASA Technical Reports Server (NTRS)

Marek, C. John

1996-01-01

A new method for predicting chemical rate constants using thermodynamics has been applied to the hydrogen/oxygen system. This method is based on using the gradient of the Gibbs free energy and a single proportionality constant D to determine the kinetic rate constants. Using this method the rate constants for any gas phase reaction can be computed from thermodynamic properties. A modified reaction set for the H/O system is determined. A11 of the third body efficiencies M are taken to be unity. Good agreement was obtained between the thermodynamic method and the experimental shock tube data. In addition, the hydrogen bromide experimental data presented in previous work is recomputed with M's of unity.

On Thermodiffusion and Gauge Transformations for Thermodynamic Fluxes and Driving Forces

NASA Astrophysics Data System (ADS)

Goldobin, D. S.

2017-12-01

We discuss the molecular diffusion transport in infinitely dilute liquid solutions under nonisothermal conditions. This discussion is motivated by an occurring misinterpretation of thermodynamic transport equations written in terms of chemical potential in the presence of temperature gradient. The transport equations contain the contributions owned by a gauge transformation related to the fact that chemical potential is determined up to the summand of form ( AT + B) with arbitrary constants A and B, where constant A is owned by the entropy invariance with respect to shifts by a constant value and B is owned by the potential energy invariance with respect to shifts by a constant value. The coefficients of the cross-effect terms in thermodynamic fluxes are contributed by this gauge transformation and, generally, are not the actual cross-effect physical transport coefficients. Our treatment is based on consideration of the entropy balance and suggests a promising hint for attempts of evaluation of the thermal diffusion constant from the first principles. We also discuss the impossibility of the "barodiffusion" for dilute solutions, understood in a sense of diffusion flux driven by the pressure gradient itself. When one speaks of "barodiffusion" terms in literature, these terms typically represent the drift in external potential force field (e.g., electric or gravitational fields), where in the final equations the specific force on molecules is substituted with an expression with the hydrostatic pressure gradient this external force field produces. Obviously, the interpretation of the latter as barodiffusion is fragile and may hinder the accounting for the diffusion fluxes produced by the pressure gradient itself.

Ontology of physics for biology: representing physical dependencies as a basis for biological processes

PubMed Central

2013-01-01

Background In prior work, we presented the Ontology of Physics for Biology (OPB) as a computational ontology for use in the annotation and representations of biophysical knowledge encoded in repositories of physics-based biosimulation models. We introduced OPB:Physical entity and OPB:Physical property classes that extend available spatiotemporal representations of physical entities and processes to explicitly represent the thermodynamics and dynamics of physiological processes. Our utilitarian, long-term aim is to develop computational tools for creating and querying formalized physiological knowledge for use by multiscale “physiome” projects such as the EU’s Virtual Physiological Human (VPH) and NIH’s Virtual Physiological Rat (VPR). Results Here we describe the OPB:Physical dependency taxonomy of classes that represent of the laws of classical physics that are the “rules” by which physical properties of physical entities change during occurrences of physical processes. For example, the fluid analog of Ohm’s law (as for electric currents) is used to describe how a blood flow rate depends on a blood pressure gradient. Hooke’s law (as in elastic deformations of springs) is used to describe how an increase in vascular volume increases blood pressure. We classify such dependencies according to the flow, transformation, and storage of thermodynamic energy that occurs during processes governed by the dependencies. Conclusions We have developed the OPB and annotation methods to represent the meaning—the biophysical semantics—of the mathematical statements of physiological analysis and the biophysical content of models and datasets. Here we describe and discuss our approach to an ontological representation of physical laws (as dependencies) and properties as encoded for the mathematical analysis of biophysical processes. PMID:24295137

Electro-diffusion in a plasma with two ion species

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

Kagan, Grigory; Tang Xianzhu

2012-08-15

Electric field is a thermodynamic force that can drive collisional inter-ion-species transport in a multicomponent plasma. In an inertial confinement fusion capsule, such transport causes fuel ion separation even with a target initially prepared to have equal number densities for the two fuel ion species. Unlike the baro-diffusion driven by ion pressure gradient and the thermo-diffusion driven by ion and electron temperature gradients, electro-diffusion has a critical dependence on the charge-to-mass ratio of the ion species. Specifically, it is shown here that electro-diffusion vanishes if the ion species have the same charge-to-mass ratio. An explicit expression for the electro-diffusion ratiomore » is obtained and used to investigate the relative importance of electro- and baro-diffusion mechanisms. In particular, it is found that electro-diffusion reinforces baro-diffusion in the deuterium and tritium mix, but tends to cancel it in the deuterium and helium-3 mix.« less

Information thermodynamics of near-equilibrium computation

NASA Astrophysics Data System (ADS)

Prokopenko, Mikhail; Einav, Itai

2015-06-01

In studying fundamental physical limits and properties of computational processes, one is faced with the challenges of interpreting primitive information-processing functions through well-defined information-theoretic as well as thermodynamic quantities. In particular, transfer entropy, characterizing the function of computational transmission and its predictability, is known to peak near critical regimes. We focus on a thermodynamic interpretation of transfer entropy aiming to explain the underlying critical behavior by associating information flows intrinsic to computational transmission with particular physical fluxes. Specifically, in isothermal systems near thermodynamic equilibrium, the gradient of the average transfer entropy is shown to be dynamically related to Fisher information and the curvature of system's entropy. This relationship explicitly connects the predictability, sensitivity, and uncertainty of computational processes intrinsic to complex systems and allows us to consider thermodynamic interpretations of several important extreme cases and trade-offs.

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.

Observations of Time-Dependent Behavior in the Two-Layer Rayleigh-Benard System

NASA Technical Reports Server (NTRS)

Andereck, C. David; Colovas, Peter W.; Degen, Michael M.

1996-01-01

In this paper we present results from experiments with a system consisting of two immiscible fluid layers in rectangular and annular geometries, driven by a vertical temperature gradient. Time-dependent variations in the type of coupling observed between the two layers are described and characterized.

A Metastable Equilibrium Model for the Relative Abundances of Microbial Phyla in a Hot Spring

PubMed Central

Dick, Jeffrey M.; Shock, Everett L.

2013-01-01

Many studies link the compositions of microbial communities to their environments, but the energetics of organism-specific biomass synthesis as a function of geochemical variables have rarely been assessed. We describe a thermodynamic model that integrates geochemical and metagenomic data for biofilms sampled at five sites along a thermal and chemical gradient in the outflow channel of the hot spring known as “Bison Pool” in Yellowstone National Park. The relative abundances of major phyla in individual communities sampled along the outflow channel are modeled by computing metastable equilibrium among model proteins with amino acid compositions derived from metagenomic sequences. Geochemical conditions are represented by temperature and activities of basis species, including pH and oxidation-reduction potential quantified as the activity of dissolved hydrogen. By adjusting the activity of hydrogen, the model can be tuned to closely approximate the relative abundances of the phyla observed in the community profiles generated from BLAST assignments. The findings reveal an inverse relationship between the energy demand to form the proteins at equal thermodynamic activities and the abundance of phyla in the community. The distance from metastable equilibrium of the communities, assessed using an equation derived from energetic considerations that is also consistent with the information-theoretic entropy change, decreases along the outflow channel. Specific divergences from metastable equilibrium, such as an underprediction of the relative abundances of phototrophic organisms at lower temperatures, can be explained by considering additional sources of energy and/or differences in growth efficiency. Although the metabolisms used by many members of these communities are driven by chemical disequilibria, the results support the possibility that higher-level patterns of chemotrophic microbial ecosystems are shaped by metastable equilibrium states that depend on both the composition of biomass and the environmental conditions. PMID:24023738

Climatic impact of Amazon deforestation - a mechanistic model study

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

Ning Zeng; Dickinson, R.E.; Xubin Zeng

1996-04-01

Recent general circulation model (GCM) experiments suggest a drastic change in the regional climate, especially the hydrological cycle, after hypothesized Amazon basinwide deforestation. To facilitate the theoretical understanding os such a change, we develop an intermediate-level model for tropical climatology, including atmosphere-land-ocean interaction. The model consists of linearized steady-state primitive equations with simplified thermodynamics. A simple hydrological cycle is also included. Special attention has been paid to land-surface processes. It generally better simulates tropical climatology and the ENSO anomaly than do many of the previous simple models. The climatic impact of Amazon deforestation is studied in the context of thismore » model. Model results show a much weakened Atlantic Walker-Hadley circulation as a result of the existence of a strong positive feedback loop in the atmospheric circulation system and the hydrological cycle. The regional climate is highly sensitive to albedo change and sensitive to evapotranspiration change. The pure dynamical effect of surface roughness length on convergence is small, but the surface flow anomaly displays intriguing features. Analysis of the thermodynamic equation reveals that the balance between convective heating, adiabatic cooling, and radiation largely determines the deforestation response. Studies of the consequences of hypothetical continuous deforestation suggest that the replacement of forest by desert may be able to sustain a dry climate. Scaling analysis motivated by our modeling efforts also helps to interpret the common results of many GCM simulations. When a simple mixed-layer ocean model is coupled with the atmospheric model, the results suggest a 1{degrees}C decrease in SST gradient across the equatorial Atlantic Ocean in response to Amazon deforestation. The magnitude depends on the coupling strength. 66 refs., 16 figs., 4 tabs.« 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.

Minimal universal quantum heat machine.

PubMed

Gelbwaser-Klimovsky, D; Alicki, R; Kurizki, G

2013-01-01

In traditional thermodynamics the Carnot cycle yields the ideal performance bound of heat engines and refrigerators. We propose and analyze a minimal model of a heat machine that can play a similar role in quantum regimes. The minimal model consists of a single two-level system with periodically modulated energy splitting that is permanently, weakly, coupled to two spectrally separated heat baths at different temperatures. The equation of motion allows us to compute the stationary power and heat currents in the machine consistent with the second law of thermodynamics. This dual-purpose machine can act as either an engine or a refrigerator (heat pump) depending on the modulation rate. In both modes of operation, the maximal Carnot efficiency is reached at zero power. We study the conditions for finite-time optimal performance for several variants of the model. Possible realizations of the model are discussed.

Instability and its relation to precipitation over the Eastern Iberian Peninsula

NASA Astrophysics Data System (ADS)

Iturrioz, I.; Hernández, E.; Ribera, P.; Queralt, S.

2007-04-01

Synoptic situations producing rainfall at four rawinsonde observatories at eastern Spain are classified as stratiform or convective depending on dynamic and thermodynamic instability indices. Two daily radiosonde and daily-accumulated precipitation data from four observatories in Eastern Spain are used: Madrid-Barajas (MB), Murcia (MU), Palma de Mallorca (PA) and Zaragoza (ZA). We calculated two thermodynamic instability indices from radiosonde data: CAPE and LI. Likewise, from ERA40 reanalysis data we have calculated the Q vector divergence over the Iberian Peninsula and Balearic Islands, as a parameter describing dynamical instability. Synoptic situations producing rainfall were classified as convective or stratiform, satisfying a criterion based on the values of dynamic and thermodynamic indices at each observatory. It is observed that the number of days with stratiform precipitation related to the total number of precipitation days follows a consistent annual pattern.

On the macroscopic modeling of dilute emulsions under flow in the presence of particle inertia

NASA Astrophysics Data System (ADS)

Mwasame, Paul M.; Wagner, Norman J.; Beris, Antony N.

2018-03-01

Recently, Mwasame et al. ["On the macroscopic modeling of dilute emulsions under flow," J. Fluid Mech. 831, 433 (2017)] developed a macroscopic model for the dynamics and rheology of a dilute emulsion with droplet morphology in the limit of negligible particle inertia using the bracket formulation of non-equilibrium thermodynamics of Beris and Edwards [Thermodynamics of Flowing Systems: With Internal Microstructure (Oxford University Press on Demand, 1994)]. Here, we improve upon that work to also account for particle inertia effects. This advance is facilitated by using the bracket formalism in its inertial form that allows for the natural incorporation of particle inertia effects into macroscopic level constitutive equations, while preserving consistency to the previous inertialess approximation in the limit of zero inertia. The parameters in the resultant Particle Inertia Thermodynamically Consistent Ellipsoidal Emulsion (PITCEE) model are selected by utilizing literature-available mesoscopic theory for the rheology at small capillary and particle Reynolds numbers. At steady state, the lowest level particle inertia effects can be described by including an additional non-affine inertial term into the evolution equation for the conformation tensor, thereby generalizing the Gordon-Schowalter time derivative. This additional term couples the conformation and vorticity tensors and is a function of the Ohnesorge number. The rheological and microstructural predictions arising from the PITCEE model are compared against steady-shear simulation results from the literature. They show a change in the signs of the normal stress differences that is accompanied by a change in the orientation of the major axis of the emulsion droplet toward the velocity gradient direction with increasing Reynolds number, capturing the two main signatures of particle inertia reported in simulations.

Application of Statistical Thermodynamics To Predict the Adsorption Properties of Polypeptides in Reversed-Phase HPLC.

PubMed

Tarasova, Irina A; Goloborodko, Anton A; Perlova, Tatyana Y; Pridatchenko, Marina L; Gorshkov, Alexander V; Evreinov, Victor V; Ivanov, Alexander R; Gorshkov, Mikhail V

2015-07-07

The theory of critical chromatography for biomacromolecules (BioLCCC) describes polypeptide retention in reversed-phase HPLC using the basic principles of statistical thermodynamics. However, whether this theory correctly depicts a variety of empirical observations and laws introduced for peptide chromatography over the last decades remains to be determined. In this study, by comparing theoretical results with experimental data, we demonstrate that the BioLCCC: (1) fits the empirical dependence of the polypeptide retention on the amino acid sequence length with R(2) > 0.99 and allows in silico determination of the linear regression coefficients of the log-length correction in the additive model for arbitrary sequences and lengths and (2) predicts the distribution coefficients of polypeptides with an accuracy from 0.98 to 0.99 R(2). The latter enables direct calculation of the retention factors for given solvent compositions and modeling of the migration dynamics of polypeptides separated under isocratic or gradient conditions. The obtained results demonstrate that the suggested theory correctly relates the main aspects of polypeptide separation in reversed-phase HPLC.

Knudsen Cell Studies of Ti-Al Thermodynamics

NASA Technical Reports Server (NTRS)

Jacobson, Nathan S.; Copland, Evan H.; Mehrotra, Gopal M.; Auping, Judith; Gray, Hugh R. (Technical Monitor)

2002-01-01

In this paper we describe the Knudsen cell technique for measurement of thermodynamic activities in alloys. Numerous experimental details must be adhered to in order to obtain useful experimental data. These include introduction of an in-situ standard, precise temperature measurement, elimination of thermal gradients, and precise cell positioning. Our first design is discussed and some sample data on Ti-Al alloys is presented. The second modification and associated improvements are also discussed.

The stochastic thermodynamics of a rotating Brownian particle in a gradient flow

PubMed Central

Lan, Yueheng; Aurell, Erik

2015-01-01

We compute the entropy production engendered in the environment from a single Brownian particle which moves in a gradient flow, and show that it corresponds in expectation to classical near-equilibrium entropy production in the surrounding fluid with specific mesoscopic transport coefficients. With temperature gradient, extra terms are found which result from the nonlinear interaction between the particle and the non-equilibrated environment. The calculations are based on the fluctuation relations which relate entropy production to the probabilities of stochastic paths and carried out in a multi-time formalism. PMID:26194015

Theoretical model for thin ferroelectric films and the multilayer structures based on them

NASA Astrophysics Data System (ADS)

Starkov, A. S.; Pakhomov, O. V.; Starkov, I. A.

2013-06-01

A modified Weiss mean-field theory is used to study the dependence of the properties of a thin ferroelectric film on its thickness. The possibility of introducing gradient terms into the thermodynamic potential is analyzed using the calculus of variations. An integral equation is introduced to generalize the well-known Langevin equation to the case of the boundaries of a ferroelectric. An analysis of this equation leads to the existence of a transition layer at the interface between ferroelectrics or a ferroelectric and a dielectric. The permittivity of this layer is shown to depend on the electric field direction even if the ferroelectrics in contact are homogeneous. The results obtained in terms of the Weiss model are compared with the results of the models based on the correlation effect and the presence of a dielectric layer at the boundary of a ferroelectric and with experimental data.

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.

Roles of basolateral solute uptake via NKCC1 and of myosin II in vasopressin-induced cell swelling in inner medullary collecting duct.

PubMed

Chou, Chung-Lin; Yu, Ming-Jiun; Kassai, Eliza M; Morris, Ryan G; Hoffert, Jason D; Wall, Susan M; Knepper, Mark A

2008-07-01

Collecting duct cells swell when exposed to arginine vasopressin (AVP) in the presence of a transepithelial osmolality gradient. We investigated the mechanisms of AVP-induced cell swelling in isolated, perfused rat inner medullary collecting ducts (IMCDs) using quantitative video microscopy and fluorescence-based measurements of transepithelial water transport. We tested the roles of transepithelial water flow, basolateral solute entry, and the cytoskeleton (actomyosin). When a transepithelial osmolality gradient was imposed by addition of NaCl to the bath, AVP significantly increased both water flux and cell height. When the osmolality gradient was imposed by addition of mannitol, AVP increased water flux but not cell height, suggesting that AVP-induced cell swelling requires a NaCl gradient and is not merely dependent on the associated water flux. Bumetanide (Na-K-2Cl cotransporter inhibitor) added to the bath markedly diminished the AVP-induced cell height increase. AVP-induced cell swelling was absent in IMCDs from NKCC1-knockout mice. In rat IMCDs, replacement of Na, K, or Cl in the peritubular bath caused significant cell shrinkage, consistent with a basolateral solute transport pathway dependent on all three ions. Immunocytochemistry using an antibody to NKCC1 confirmed basolateral expression in IMCD cells. The conventional nonmuscle myosin II inhibitor blebbistatin also diminished the AVP-induced cell height increase and cell shape change, consistent with a role for the actin cytoskeleton and myosin II. We conclude that the AVP-induced cell height increase is dependent on basolateral solute uptake via NKCC1 and changes in actin organization via myosin II, but is not dependent specifically on increased apical water entry.

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.

Structural, Thermodynamic, Elastic, and Electronic Properties of α-SnS at High Pressure from First-Principles Investigations

NASA Astrophysics Data System (ADS)

Liu, Chun Mei; Xu, Chao; Duan, Man Yi

2015-10-01

SnS has potential technical applications, but many of its properties are still not well studied. In this work, the structural, thermodynamic, elastic, and electronic properties of α-SnS have been investigated by the plane wave pseudo-potential density functional theory with the framework of generalised gradient approximation. The calculated pressure-dependent lattice parameters agree well with the available experimental data. Our thermodynamic properties of α-SnS, including heat capacity CP , entropy S, and Gibbs free energy relation of -(GT -H0) curves, show similar growth trends as the experimental data. At T=298.15 K, our CP =52.31 J/mol·K, S=78.93 J/mol·K, and -(GT -H0)=12.03 J/mol all agree very well with experimental data CP =48.77 J/mol·K and 49.25 J/mol·K, S=76.78 J/mol·K, and -(GT -H0)=12.38 J/mol. The elastic constants, together with other elastic properties, are also computed. The anisotropy analyses indicate obvious elastic anisotropy for α-SnS along different symmetry planes and axes. Moreover, calculations demonstrate that α-SnS is an indirect gap semiconductor, and it transforms to semimetal with pressure increasing up to 10.2 GPa. Combined with the density of states, the characters of the band structure have been analysed in detail.

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.

Synthetic receiver function profiles through the upper mantle and the transition zone for upwelling scenarios

NASA Astrophysics Data System (ADS)

Nagel, Thorsten; Düsterhöft, Erik; Schiffer, Christian

2017-04-01

We investigate the signature relevant mantle lithologies leave in the receiver function record for different adiabatic thermal gradients down to 800 kilometers depth. The parameter space is chosen to target the visibility of upwelling mantle (a plume). Seismic velocities for depleted mantle, primitive mantle, and three pyroxenites are extracted from thermodynamically calculated phases diagrams, which also provide the adiabatic decompression paths. Results suggest that compositional variations, i.e. the presence or absence of considerable amounts of pyroxenites in primitive mantle should produce a clear footprint while horizontal differences in thermal gradients for similar compositions might be more subtle. Peridotites best record the classic discontinuities at around 410 and 650 kilometers depth, which are associated with the olivin-wadsleyite and ringwoodite-perovskite transitions, respectively. Pyroxenites, instead, show the garnet-perovskite transition below 700 kilometers depth and SiO2-supersaturated compositions like MORB display the coesite-stishovite transition between 300 and 340 kilometers depth. The latter shows the strongest temperature-depth dependency of all significant transitions potentially allowing to infer information about the thermal state if the mantle contains a sufficient fraction of MORB-like compositions. For primitive and depleted mantle compositions, the olivin-wadsleyite transition shows a certain temperature-depth dependency reflected in slightly larger delay times for higher thermal gradients. The lower-upper-mantle discontinuity, however, is predicted to display larger delay times for higher thermal gradients although the associated assemblage transition occurs at shallower depths thus requiring a very careful depth migration if a thermal anomaly should be recognized. This counterintuitive behavior results from the downward replacement of the assemblage wadsleyite+garnet with the assemblage garnet+periclase at high temperatures. This transition causes even lower seismic velocities with greater depth (following an adiabatic gradient), the highly continuous nature of the reaction, however, should produce only a smooth negative conversion. In contrast, a small positive conversion is expected at normal thermal gradients in the same depth range between 500 and 550 kilometers because of the wadsleyite-ringwoodite-transition. Hence, the polarity of the 520 discontinuity also offers a possibility to recognize the thermal state of the upper mantle.

Dense simple plasmas as high-temperature liquid simple metals

NASA Technical Reports Server (NTRS)

Perrot, F.

1990-01-01

The thermodynamic properties of dense plasmas considered as high-temperature liquid metals are studied. An attempt is made to show that the neutral pseudoatom picture of liquid simple metals may be extended for describing plasmas in ranges of densities and temperatures where their electronic structure remains 'simple'. The primary features of the model when applied to plasmas include the temperature-dependent self-consistent calculation of the electron charge density and the determination of a density and temperature-dependent ionization state.

Electrochemical measurements and thermodynamic calculations of redox equilibria in pallasite meteorites - Implications for the eucrite parent body

NASA Technical Reports Server (NTRS)

Righter, Kevin; Arculus, Richard J.; Paslick, Cassi; Delano, John W.

1990-01-01

The intrinsic oxygen fugacity (IOF) of olivine separates from the Salta, Springwater, and Eagle Station pallasites was measured between 850 and 1150 C using oxygen-specific solid zirconia electrolytes at 100,000 Pa. Thermodynamic calculations of redox equilibria involving equalibrium pallasite assemblages are in good agreement with the experimental results and provide a lower limit to pallasite redox stability; others involving disequilibrium assemblages, suggest that pallasites experienced localized, late-stage oxidation and reduction effects. Consideration of the redox buffer metal-olivine-orthopyroxene utilizing calculated Eucrite Parent Body (EPB) mantle phase compositions indicates that small redox gradients may have existed in the EPB. Such gradients may have produced strong compositional variation within the EPB. In addition, there is apparently significant redox heterogeneity in the source area of Eagle Station Trio pallasites and Bocaiuva iron meteorites.

Thermodynamic evolution far from equilibrium

NASA Astrophysics Data System (ADS)

Khantuleva, Tatiana A.

2018-05-01

The presented model of thermodynamic evolution of an open system far from equilibrium is based on the modern results of nonequilibrium statistical mechanics, the nonlocal theory of nonequilibrium transport developed by the author and the Speed Gradient principle introduced in the theory of adaptive control. Transition to a description of the system internal structure evolution at the mesoscopic level allows a new insight at the stability problem of non-equilibrium processes. The new model is used in a number of specific tasks.

Hydrophobicity within the three-dimensional Mercedes-Benz model: potential of mean force.

PubMed

Dias, Cristiano L; Hynninen, Teemu; Ala-Nissila, Tapio; Foster, Adam S; Karttunen, Mikko

2011-02-14

We use the three-dimensional Mercedes-Benz model for water and Monte Carlo simulations to study the structure and thermodynamics of the hydrophobic interaction. Radial distribution functions are used to classify different cases of the interaction, namely, contact configurations, solvent separated configurations, and desolvation configurations. The temperature dependence of these cases is shown to be in qualitative agreement with atomistic models of water. In particular, while the energy for the formation of contact configurations is favored by entropy, its strengthening with increasing temperature is accounted for by enthalpy. This is consistent with our simulated heat capacity. An important feature of the model is that it can be used to account for well-converged thermodynamics quantities, e.g., the heat capacity of transfer. Microscopic mechanisms for the temperature dependence of the hydrophobic interaction are discussed at the molecular level based on the conceptual simplicity of the model.

Hydrophobicity within the three-dimensional Mercedes-Benz model: Potential of mean force

NASA Astrophysics Data System (ADS)

Dias, Cristiano L.; Hynninen, Teemu; Ala-Nissila, Tapio; Foster, Adam S.; Karttunen, Mikko

2011-02-01

We use the three-dimensional Mercedes-Benz model for water and Monte Carlo simulations to study the structure and thermodynamics of the hydrophobic interaction. Radial distribution functions are used to classify different cases of the interaction, namely, contact configurations, solvent separated configurations, and desolvation configurations. The temperature dependence of these cases is shown to be in qualitative agreement with atomistic models of water. In particular, while the energy for the formation of contact configurations is favored by entropy, its strengthening with increasing temperature is accounted for by enthalpy. This is consistent with our simulated heat capacity. An important feature of the model is that it can be used to account for well-converged thermodynamics quantities, e.g., the heat capacity of transfer. Microscopic mechanisms for the temperature dependence of the hydrophobic interaction are discussed at the molecular level based on the conceptual simplicity of the model.

A study of microindentation hardness tests by mechanism-based strain gradient plasticity

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

Huang, Y.; Xue, Z.; Gao, H.

2000-08-01

We recently proposed a theory of mechanism-based strain gradient (MSG) plasticity to account for the size dependence of plastic deformation at micron- and submicron-length scales. The MSG plasticity theory connects micron-scale plasticity to dislocation theories via a multiscale, hierarchical framework linking Taylor's dislocation hardening model to strain gradient plasticity. Here we show that the theory of MSG plasticity, when used to study micro-indentation, indeed reproduces the linear dependence observed in experiments, thus providing an important self-consistent check of the theory. The effects of pileup, sink-in, and the radius of indenter tip have been taken into account in the indentation model.more » In accomplishing this objective, we have generalized the MSG plasticity theory to include the elastic deformation in the hierarchical framework. (c) 2000 Materials Research Society.« less

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.

SDSS-IV MaNGA: environmental dependence of stellar age and metallicity gradients in nearby galaxies

NASA Astrophysics Data System (ADS)

Zheng, Zheng; Wang, Huiyuan; Ge, Junqiang; Mao, Shude; Li, Cheng; Li, Ran; Mo, Houjun; Goddard, Daniel; Bundy, Kevin; Li, Hongyu; Nair, Preethi; Lin, Lihwai; Long, R. J.; Riffel, Rogério; Thomas, Daniel; Masters, Karen; Bizyaev, Dmitry; Brownstein, Joel R.; Zhang, Kai; Law, David R.; Drory, Niv; Roman Lopes, Alexandre; Malanushenko, Olena

2017-03-01

We present a study on the stellar age and metallicity distributions for 1105 galaxies using the STARLIGHT software on MaNGA (Mapping Nearby Galaxies at APO) integral field spectra. We derive age and metallicity gradients by fitting straight lines to the radial profiles, and explore their correlations with total stellar mass M*, NUV - r colour and environments, as identified by both the large-scale structure (LSS) type and the local density. We find that the mean age and metallicity gradients are close to zero but slightly negative, which is consistent with the inside-out formation scenario. Within our sample, we find that both the age and metallicity gradients show weak or no correlation with either the LSS type or local density environment. In addition, we also study the environmental dependence of age and metallicity values at the effective radii. The age and metallicity values are highly correlated with M* and NUV - r and are also dependent on LSS type as well as local density. Low-mass galaxies tend to be younger and have lower metallicity in low-density environments while high-mass galaxies are less affected by environment.

Revisiting the positive DC corona discharge theory: Beyond Peek's and Townsend's law

NASA Astrophysics Data System (ADS)

Monrolin, Nicolas; Praud, Olivier; Plouraboué, Franck

2018-06-01

The classical positive Corona Discharge theory in a cylindrical axisymmetric configuration is revisited in order to find analytically the influence of gas properties and thermodynamic conditions on the corona current. The matched asymptotic expansion of Durbin and Turyn [J. Phys. D: Appl. Phys. 20, 1490-1495 (1987)] of a simplified but self-consistent problem is performed and explicit analytical solutions are derived. The mathematical derivation enables us to express a new positive DC corona current-voltage characteristic, choosing either a dimensionless or dimensional formulation. In dimensional variables, the current voltage law and the corona inception voltage explicitly depend on the electrode size and physical gas properties such as ionization and photoionization parameters. The analytical predictions are successfully confronted with experiments and Peek's and Townsend's laws. An analytical expression of the corona inception voltage φ o n is proposed, which depends on the known values of physical parameters without adjustable parameters. As a proof of consistency, the classical Townsend current-voltage law I = C φ ( φ - φ o n ) is retrieved by linearizing the non-dimensional analytical solution. A brief parametric study showcases the interest in this analytical current model, especially for exploring small corona wires or considering various thermodynamic conditions.

Thermodynamically constrained correction to ab initio equations of state

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

French, Martin; Mattsson, Thomas R.

2014-07-07

We show how equations of state generated by density functional theory methods can be augmented to match experimental data without distorting the correct behavior in the high- and low-density limits. The technique is thermodynamically consistent and relies on knowledge of the density and bulk modulus at a reference state and an estimation of the critical density of the liquid phase. We apply the method to four materials representing different classes of solids: carbon, molybdenum, lithium, and lithium fluoride. It is demonstrated that the corrected equations of state for both the liquid and solid phases show a significantly reduced dependence ofmore » the exchange-correlation functional used.« less

Simulation of Oxygen Disintegration and Mixing With Hydrogen or Helium at Supercritical Pressure

NASA Technical Reports Server (NTRS)

Bellan, Josette; Taskinoglu, Ezgi

2012-01-01

The simulation of high-pressure turbulent flows, where the pressure, p, is larger than the critical value, p(sub c), for the species under consideration, is relevant to a wide array of propulsion systems, e.g. gas turbine, diesel, and liquid rocket engines. Most turbulence models, however, have been developed for atmospheric-p turbulent flows. The difference between atmospheric-p and supercritical-p turbulence is that, in the former situation, the coupling between dynamics and thermodynamics is moderate to negligible, but for the latter it is very significant, and can dominate the flow characteristics. The reason for this stems from the mathematical form of the equation of state (EOS), which is the perfect-gas EOS in the former case, and the real-gas EOS in the latter case. For flows at supercritical pressure, p, the large eddy simulation (LES) equations consist of the differential conservation equations coupled with a real-gas EOS. The equations use transport properties that depend on the thermodynamic variables. Compared to previous LES models, the differential equations contain not only the subgrid scale (SGS) fluxes, but also new SGS terms, each denoted as a correction. These additional terms, typically assumed null for atmospheric pressure flows, stem from filtering the differential governing equations, and represent differences between a filtered term and the same term computed as a function of the filtered flow field. In particular, the energy equation contains a heat-flux correction (q-correction) that is the difference between the filtered divergence of the heat flux and the divergence of the heat flux computed as a function of the filtered flow field. In a previous study, there was only partial success in modeling the q-correction term, but in this innovation, success has been achieved by using a different modeling approach. This analysis, based on a temporal mixing layer Direct Numerical Simulation database, shows that the focus in modeling the q-correction should be on reconstructing the primitive variable gradients rather than their coefficients, and proposes the approximate deconvolution model (ADM) as an effective means of flow field reconstruction for LES heat flux calculation. Further, results for a study conducted for temporal mixing layers initially containing oxygen in the lower stream, and hydrogen or helium in the upper stream, show that, for any LES, including SGS-flux models (constant-coefficient Gradient or Scale-Similarity models, dynamic-coefficient Smagorinsky/Yoshizawa or mixed Smagorinsky/Yoshizawa/Gradient models), the inclusion of the q-correction in the LES leads to the theoretical maximum reduction of the SGS heat-flux difference. The remaining error in modeling this new subgrid term is thus irreducible.

Thermodynamic Equations of State for Aqueous Solutions Applied to Deep Icy Satellite and Exoplanet Oceans

NASA Astrophysics Data System (ADS)

Vance, S.; Brown, J. M.; Bollengier, O.; Journaux, B.; Sotin, C.; Choukroun, M.; Barnes, R.

2014-12-01

Supporting life in icy world or exoplanet oceans may require global seafloor chemical reactions between water and rock. Such interactions have been regarded as limited in larger icy worlds such as Ganymede and Titan, where ocean depths approach 800 km and GPa pressures (>10katm). If the oceans are composed of pure water, such conditions are consistent with the presence of dense ice phases V and VI that cover the rocky seafloor. Exoplanets with oceans can obtain pressures sufficient to generate ices VII and VIII. We have previously demonstrated temperature gradients in such oceans on the order of 20 K or more, resulting from fluid compressibility in a deep adiabatic ocean based on our experimental work. Accounting for increases in density for highly saline oceans leads to the possibility of oceans perched under and between high pressure ices. Ammonia has the opposite effect, instead decreasing ocean density, as reported by others and confirmed by our laboratory measurements in the ammonia water system. Here we report on the completed equation of state for aqueous ammonia derived from our prior measurements and optimized global b-spline fitting methods We use recent diamond anvil cell measurements for water and ammonia to extend the equation of state to 400°C and beyond 2 GPa, temperatures and pressures applicable to icy worlds and exoplanets. Densities show much less temperature dependence but comparabe high-pressure derivatives to previously published ammonia-water properties derived for application to Titan (Croft et al. 1988). Thermal expansion is in better agreement with the more self-consistent equation of state of Tillner-Roth and Friend (1998). We also describe development of a planetary NaCl equation of state using recent measurements of phase boundaries and sound speeds. We examine implications of realistic ocean-ice thermodynamics for Titan and exoplanet interiors using the methodology recently applied to Ganymede for oceans dominated by MgSO4. High pressure ices should not be present on Titan if its ocean composition is Dead-Sea like, as recently inferred from tidal dissipation and topography, and if Titan's moment of inertia has the published value of C/MR2 = 0.3414.

Quantum optomechanical piston engines powered by heat

NASA Astrophysics Data System (ADS)

Mari, A.; Farace, A.; Giovannetti, V.

2015-09-01

We study two different models of optomechanical systems where a temperature gradient between two radiation baths is exploited for inducing self-sustained coherent oscillations of a mechanical resonator. From a thermodynamic perspective, such systems represent quantum instances of self-contained thermal machines converting heat into a periodic mechanical motion and thus they can be interpreted as nano-scale analogues of macroscopic piston engines. Our models are potentially suitable for testing fundamental aspects of quantum thermodynamics in the laboratory and for applications in energy efficient nanotechnology.

Density functional description of size-dependent effects at nucleation on neutral and charged nanoparticles

NASA Astrophysics Data System (ADS)

Shchekin, Alexander K.; Lebedeva, Tatiana S.

2017-03-01

A numerical study of size-dependent effects in the thermodynamics of a small droplet formed around a solid nanoparticle has been performed within the square-gradient density functional theory. The Lennard-Jones fluid with the Carnahan-Starling model for the hard-sphere contribution to intermolecular interaction in liquid and vapor phases and interfaces has been used for description of the condensate. The intermolecular forces between the solid core and condensate molecules have been taken into account with the help of the Lennard-Jones part of the total molecular potential of the core. The influence of the electric charge of the particle has been considered under assumption of the central Coulomb potential in the medium with dielectric permittivity depending on local condensate density. The condensate density profiles and equimolecular radii for equilibrium droplets at different values of the condensate chemical potential have been computed in the cases of an uncharged solid core with the molecular potential, a charged core without molecular potential, and a core with joint action of the Coulomb and molecular potentials. The appearance of stable equilibrium droplets even in the absence of the electric charge has been commented. As a next step, the capillary, disjoining pressure, and electrostatic contributions to the condensate chemical potential have been considered and compared with the predictions of classical thermodynamics in a wide range of values of the droplet and the particle equimolecular radii. With the help of the found dependence of the condensate chemical potential in droplet on the droplet size, the activation barrier for nucleation on uncharged and charged particles has been computed as a function of the vapor supersaturation. Finally, the work of droplet formation and the work of wetting the particle have been found as functions of the droplet size.

Is the 2nd Law of Thermodynamics Conditioned? Separating Heat and Cold by a Magnetic Body Force and the Principle for a Non-Carnot Engine

NASA Astrophysics Data System (ADS)

Luo, Weili

2017-11-01

A new type of heat engine has been proposed in 2005 that defies fundamental thermodynamic law: A specifically designed magnetic body force can reverse heat flow from high temperature to low temperature. This mechanism can drive heat to higher temperature, rendering the possibility to re-use the ``waste heat''. As the result, the efficiency is much higher than that of the Carnot Engine. In a recent paper a realization of this proposed mechanism is reported: by using a specific configuration of temperature and magnetic field gradients, we observed that magnetic body force suppresses the gravito-thermal convective heat when the gradients of temperature and field are anti-parallel to each other. This driving force stops the heat flow of approaching to thermal equilibrium in the system, causing the temperature difference across the sample to increase with applied fields. In this work, I will discuss the driving mechanism for this phenomenon and its application in the proposed engine. This remarkable result suggests that the 2nd law of thermodynamics maybe conditioned and needs to be re-examined.

Modelling non-equilibrium thermodynamic systems from the speed-gradient principle.

PubMed

Khantuleva, Tatiana A; Shalymov, Dmitry S

2017-03-06

The application of the speed-gradient (SG) principle to the non-equilibrium distribution systems far away from thermodynamic equilibrium is investigated. The options for applying the SG principle to describe the non-equilibrium transport processes in real-world environments are discussed. Investigation of a non-equilibrium system's evolution at different scale levels via the SG principle allows for a fresh look at the thermodynamics problems associated with the behaviour of the system entropy. Generalized dynamic equations for finite and infinite number of constraints are proposed. It is shown that the stationary solution to the equations, resulting from the SG principle, entirely coincides with the locally equilibrium distribution function obtained by Zubarev. A new approach to describe time evolution of systems far from equilibrium is proposed based on application of the SG principle at the intermediate scale level of the system's internal structure. The problem of the high-rate shear flow of viscous fluid near the rigid plane plate is discussed. It is shown that the SG principle allows closed mathematical models of non-equilibrium processes to be constructed.This article is part of the themed issue 'Horizons of cybernetical physics'. © 2017 The Author(s).

Modelling non-equilibrium thermodynamic systems from the speed-gradient principle

NASA Astrophysics Data System (ADS)

Khantuleva, Tatiana A.; Shalymov, Dmitry S.

2017-03-01

The application of the speed-gradient (SG) principle to the non-equilibrium distribution systems far away from thermodynamic equilibrium is investigated. The options for applying the SG principle to describe the non-equilibrium transport processes in real-world environments are discussed. Investigation of a non-equilibrium system's evolution at different scale levels via the SG principle allows for a fresh look at the thermodynamics problems associated with the behaviour of the system entropy. Generalized dynamic equations for finite and infinite number of constraints are proposed. It is shown that the stationary solution to the equations, resulting from the SG principle, entirely coincides with the locally equilibrium distribution function obtained by Zubarev. A new approach to describe time evolution of systems far from equilibrium is proposed based on application of the SG principle at the intermediate scale level of the system's internal structure. The problem of the high-rate shear flow of viscous fluid near the rigid plane plate is discussed. It is shown that the SG principle allows closed mathematical models of non-equilibrium processes to be constructed. This article is part of the themed issue 'Horizons of cybernetical physics'.

Modelling non-equilibrium thermodynamic systems from the speed-gradient principle

PubMed Central

Khantuleva, Tatiana A.

2017-01-01

The application of the speed-gradient (SG) principle to the non-equilibrium distribution systems far away from thermodynamic equilibrium is investigated. The options for applying the SG principle to describe the non-equilibrium transport processes in real-world environments are discussed. Investigation of a non-equilibrium system's evolution at different scale levels via the SG principle allows for a fresh look at the thermodynamics problems associated with the behaviour of the system entropy. Generalized dynamic equations for finite and infinite number of constraints are proposed. It is shown that the stationary solution to the equations, resulting from the SG principle, entirely coincides with the locally equilibrium distribution function obtained by Zubarev. A new approach to describe time evolution of systems far from equilibrium is proposed based on application of the SG principle at the intermediate scale level of the system's internal structure. The problem of the high-rate shear flow of viscous fluid near the rigid plane plate is discussed. It is shown that the SG principle allows closed mathematical models of non-equilibrium processes to be constructed. This article is part of the themed issue ‘Horizons of cybernetical physics’. PMID:28115617

New thermodynamical force in plasma phase space that controls turbulence and turbulent transport.

PubMed

Itoh, Sanae-I; Itoh, Kimitaka

2012-01-01

Physics of turbulence and turbulent transport has been developed on the central dogma that spatial gradients constitute the controlling parameters, such as Reynolds number and Rayleigh number. Recent experiments with the nonequilibrium plasmas in magnetic confinement devices, however, have shown that the turbulence and transport change much faster than global parameters, after an abrupt change of heating power. Here we propose a theory of turbulence in inhomogeneous magnetized plasmas, showing that the heating power directly influences the turbulence. New mechanism, that an external source couples with plasma fluctuations in phase space so as to affect turbulence, is investigated. A new thermodynamical force in phase-space, i.e., the derivative of heating power by plasma pressure, plays the role of new control parameter, in addition to spatial gradients. Following the change of turbulence, turbulent transport is modified accordingly. The condition under which this new effect can be observed is also evaluated.

New Thermodynamical Force in Plasma Phase Space that Controls Turbulence and Turbulent Transport

PubMed Central

Itoh, Sanae-I.; Itoh, Kimitaka

2012-01-01

Physics of turbulence and turbulent transport has been developed on the central dogma that spatial gradients constitute the controlling parameters, such as Reynolds number and Rayleigh number. Recent experiments with the nonequilibrium plasmas in magnetic confinement devices, however, have shown that the turbulence and transport change much faster than global parameters, after an abrupt change of heating power. Here we propose a theory of turbulence in inhomogeneous magnetized plasmas, showing that the heating power directly influences the turbulence. New mechanism, that an external source couples with plasma fluctuations in phase space so as to affect turbulence, is investigated. A new thermodynamical force in phase-space, i.e., the derivative of heating power by plasma pressure, plays the role of new control parameter, in addition to spatial gradients. Following the change of turbulence, turbulent transport is modified accordingly. The condition under which this new effect can be observed is also evaluated. PMID:23155481

New Thermodynamical Force in Plasma Phase Space that Controls Turbulence and Turbulent Transport

NASA Astrophysics Data System (ADS)

Itoh, Sanae-I.; Itoh, Kimitaka

2012-11-01

Physics of turbulence and turbulent transport has been developed on the central dogma that spatial gradients constitute the controlling parameters, such as Reynolds number and Rayleigh number. Recent experiments with the nonequilibrium plasmas in magnetic confinement devices, however, have shown that the turbulence and transport change much faster than global parameters, after an abrupt change of heating power. Here we propose a theory of turbulence in inhomogeneous magnetized plasmas, showing that the heating power directly influences the turbulence. New mechanism, that an external source couples with plasma fluctuations in phase space so as to affect turbulence, is investigated. A new thermodynamical force in phase-space, i.e., the derivative of heating power by plasma pressure, plays the role of new control parameter, in addition to spatial gradients. Following the change of turbulence, turbulent transport is modified accordingly. The condition under which this new effect can be observed is also evaluated.

HPLC retention thermodynamics of grape and wine tannins.

PubMed

Barak, Jennifer A; Kennedy, James A

2013-05-08

The effect of grape and wine tannin structure on retention thermodynamics under reversed-phase high-performance liquid chromatography conditions on a polystyrene divinylbenzene column was investigated. On the basis of retention response to temperature, an alternative retention factor was developed to approximate the combined temperature response of the complex, unresolvable tannin mixture. This alternative retention factor was based upon relative tannin peak areas separated by an abrupt change in solvent gradient. Using this alternative retention factor, retention thermodynamics were calculated. Van't Hoff relationships of the natural log of the alternative retention factor against temperature followed Kirchoff's relationship. An inverse quadratic equation was fit to the data, and from this the thermodynamic parameters for tannin retention were calculated. All tannin fractions exhibited exothermic, spontaneous interaction, with enthalpy-entropy compensation observed. Normalizing for tannin size, distinct tannin compositional effects on thermodynamic parameters were observed. The results of this study indicate that HPLC can be valuable for measuring the thermodynamics of tannin interaction with a hydrophobic surface and provides a potentially valuable alternative to calorimetry. Furthermore, the information gathered may provide insight into understanding red wine astringency quality.

Spherical gradient-index lenses as perfect imaging and maximum power transfer devices.

PubMed

Gordon, J M

2000-08-01

Gradient-index lenses can be viewed from the perspectives of both imaging and nonimaging optics, that is, in terms of both image fidelity and achievable flux concentration. The simple class of gradient-index lenses with spherical symmetry, often referred to as modified Luneburg lenses, is revisited. An alternative derivation for established solutions is offered; the method of Fermat's strings and the principle of skewness conservation are invoked. Then these nominally perfect imaging devices are examined from the additional vantage point of power transfer, and the degree to which they realize the thermodynamic limit to flux concentration is determined. Finally, the spherical gradient-index lens of the fish eye is considered as a modified Luneburg lens optimized subject to material constraints.

Modeling the zonal disintegration of rocks near deep level tunnels by gradient internal variable continuous phase transition theory

NASA Astrophysics Data System (ADS)

Haoxiang, Chen; Qi, Chengzhi; Peng, Liu; Kairui, Li; Aifantis, Elias C.

2015-12-01

The occurrence of alternating damage zones surrounding underground openings (commonly known as zonal disintegration) is treated as a "far from thermodynamic equilibrium" dynamical process or a nonlinear continuous phase transition phenomenon. The approach of internal variable gradient theory with diffusive transport, which may be viewed as a subclass of Landau's phase transition theory, is adopted. The order parameter is identified with an irreversible strain quantity, the gradient of which enters into the expression for the free energy of the rock system. The gradient term stabilizes the material behavior in the post-softening regime, where zonal disintegration occurs. The results of a simplified linearized analysis are confirmed by the numerical solution of the nonlinear problem.

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.

Repulsive particles under a general external potential: Thermodynamics by neglecting thermal noise.

PubMed

Ribeiro, Mauricio S; Nobre, Fernando D

2016-08-01

A recent proposal of an effective temperature θ, conjugated to a generalized entropy s_{q}, typical of nonextensive statistical mechanics, has led to a consistent thermodynamic framework in the case q=2. The proposal was explored for repulsively interacting vortices, currently used for modeling type-II superconductors. In these systems, the variable θ presents values much higher than those of typical room temperatures T, so that the thermal noise can be neglected (T/θ≃0). The whole procedure was developed for an equilibrium state obtained after a sufficiently long-time evolution, associated with a nonlinear Fokker-Planck equation and approached due to a confining external harmonic potential, ϕ(x)=αx^{2}/2 (α>0). Herein, the thermodynamic framework is extended to a quite general confining potential, namely ϕ(x)=α|x|^{z}/z (z>1). It is shown that the main results of the previous analyses hold for any z>1: (i) The definition of the effective temperature θ conjugated to the entropy s_{2}. (ii) The construction of a Carnot cycle, whose efficiency is shown to be η=1-(θ_{2}/θ_{1}), where θ_{1} and θ_{2} are the effective temperatures associated with two isothermal transformations, with θ_{1}>θ_{2}. The special character of the Carnot cycle is indicated by analyzing another cycle that presents an efficiency depending on z. (iii) Applying Legendre transformations for a distinct pair of variables, different thermodynamic potentials are obtained, and furthermore, Maxwell relations and response functions are derived. The present approach shows a consistent thermodynamic framework, suggesting that these results should hold for a general confining potential ϕ(x), increasing the possibility of experimental verifications.

Fourier transform infrared and Raman spectroscopic characterization of homogeneous solution concentration gradients near a container wall at different temperatures

NASA Technical Reports Server (NTRS)

Loo, B. H.; Burns, D. H.; Lee, Y. G. L.; Emerson, M. T.

1991-01-01

Fourier transform infrared (FTIR) and Raman spectroscopic techniques were used to study the solution concentration gradient in succino nitrile-rich and water-rich homogeneous solutions. The spectroscopic data shows significant concentration dependency. Although FTIR-attenuated total reflectance could not yield surface spectra since the evanescent infrared wave penetrated deep into the bulk solution, it showed that water-rich clusters were decreased at higher temperatures. This result is consistent with the calorimetric results reported earlier.

Modular rate laws for enzymatic reactions: thermodynamics, elasticities and implementation.

PubMed

Liebermeister, Wolfram; Uhlendorf, Jannis; Klipp, Edda

2010-06-15

Standard rate laws are a key requisite for systematically turning metabolic networks into kinetic models. They should provide simple, general and biochemically plausible formulae for reaction velocities and reaction elasticities. At the same time, they need to respect thermodynamic relations between the kinetic constants and the metabolic fluxes and concentrations. We present a family of reversible rate laws for reactions with arbitrary stoichiometries and various types of regulation, including mass-action, Michaelis-Menten and uni-uni reversible Hill kinetics as special cases. With a thermodynamically safe parameterization of these rate laws, parameter sets obtained by model fitting, sampling or optimization are guaranteed to lead to consistent chemical equilibrium states. A reformulation using saturation values yields simple formulae for rates and elasticities, which can be easily adjusted to the given stationary flux distributions. Furthermore, this formulation highlights the role of chemical potential differences as thermodynamic driving forces. We compare the modular rate laws to the thermodynamic-kinetic modelling formalism and discuss a simplified rate law in which the reaction rate directly depends on the reaction affinity. For automatic handling of modular rate laws, we propose a standard syntax and semantic annotations for the Systems Biology Markup Language. An online tool for inserting the rate laws into SBML models is freely available at www.semanticsbml.org. Supplementary data are available at Bioinformatics online.

Ecosystem functioning and maximum entropy production: a quantitative test of hypotheses.

PubMed

Meysman, Filip J R; Bruers, Stijn

2010-05-12

The idea that entropy production puts a constraint on ecosystem functioning is quite popular in ecological thermodynamics. Yet, until now, such claims have received little quantitative verification. Here, we examine three 'entropy production' hypotheses that have been forwarded in the past. The first states that increased entropy production serves as a fingerprint of living systems. The other two hypotheses invoke stronger constraints. The state selection hypothesis states that when a system can attain multiple steady states, the stable state will show the highest entropy production rate. The gradient response principle requires that when the thermodynamic gradient increases, the system's new stable state should always be accompanied by a higher entropy production rate. We test these three hypotheses by applying them to a set of conventional food web models. Each time, we calculate the entropy production rate associated with the stable state of the ecosystem. This analysis shows that the first hypothesis holds for all the food webs tested: the living state shows always an increased entropy production over the abiotic state. In contrast, the state selection and gradient response hypotheses break down when the food web incorporates more than one trophic level, indicating that they are not generally valid.

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.

Assessing trait-based scaling theory in tropical and temperate forests spanning a broad temperature gradients

NASA Astrophysics Data System (ADS)

Enquist, B. J.

2017-12-01

Tropical and temperate elevation gradients are natural laboratories to assess how changing climate can influence tropical forests. However, there is a need for theory and integrated data collection to scale from traits to ecosystems. We assess predictions of a novel trait-based metabolic scaling theory including whether observed shifts in forest traits across a broad tropical temperature gradient is consistent with local phenotypic optima and adaptive compensation for temperature. We tested a new anaytical theory - Trait Driver Theory - that is capable of scaling from traits to entire stands and ecosystems across several elevation gradients spanning 3300m. Each gradient consists of thousands of tropical and temperate tree trait measures taken from forest plots. In several of these plots, in particular in southern Perú, gross and net primary productivity (GPP and NPP) were measured. We measured multiple traits linked to variation in tree growth and assessed their frequency distributions within and across the elevation gradient. We paired these trait measures across individuals within forests with simultaneous measures of ecosystem net and gross primary productivity. Consistent with theory, variation in forest NPP and GPP primarily scaled with forest biomass but the secondary effect of temperature on productivity was much less than expected. This weak temperature dependency appears to reflect directional shifts in several mean community traits that underlie tree growth with decreases in site temperature. The observed shift in traits of trees that dominant more cold environments appear to reflect `adaptive/acclimatory' compensation for the kinetic effects of temperature on leaf photosynthesis and tree growth. Forest trait distributions across the gradient showed peaked and skewed distributions, consistent with the importance of local filtering of optimal growth traits and recent shifts in species composition and dominance due to warming from climate change. Trait-based metabolic scaling theory provides a basis to predict how shifts in climate have and will influence the trait composition and ecosystem functioning of temperate and tropical forests.

The potential and flux landscape theory of evolution.

PubMed

Zhang, Feng; Xu, Li; Zhang, Kun; Wang, Erkang; Wang, Jin

2012-08-14

We established the potential and flux landscape theory for evolution. We found explicitly the conventional Wright's gradient adaptive landscape based on the mean fitness is inadequate to describe the general evolutionary dynamics. We show the intrinsic potential as being Lyapunov function(monotonically decreasing in time) does exist and can define the adaptive landscape for general evolution dynamics for studying global stability. The driving force determining the dynamics can be decomposed into gradient of potential landscape and curl probability flux. Non-zero flux causes detailed balance breaking and measures how far the evolution from equilibrium state. The gradient of intrinsic potential and curl flux are perpendicular to each other in zero fluctuation limit resembling electric and magnetic forces on electrons. We quantified intrinsic energy, entropy and free energy of evolution and constructed non-equilibrium thermodynamics. The intrinsic non-equilibrium free energy is a Lyapunov function. Both intrinsic potential and free energy can be used to quantify the global stability and robustness of evolution. We investigated an example of three allele evolutionary dynamics with frequency dependent selection (detailed balance broken). We uncovered the underlying single, triple, and limit cycle attractor landscapes. We found quantitative criterions for stability through landscape topography. We also quantified evolution pathways and found paths do not follow potential gradient and are irreversible due to non-zero flux. We generalized the original Fisher's fundamental theorem to the general (i.e., frequency dependent selection) regime of evolution by linking the adaptive rate with not only genetic variance related to the potential but also the flux. We show there is an optimum potential where curl flux resulting from biotic interactions of individuals within a species or between species can sustain an endless evolution even if the physical environment is unchanged. We offer a theoretical basis for explaining the corresponding Red Queen hypothesis proposed by Van Valen. Our work provides a theoretical foundation for evolutionary dynamics.

Nonlinear magnetoacoustic wave propagation with chemical reactions

NASA Astrophysics Data System (ADS)

Margulies, Timothy Scott

2002-11-01

The magnetoacoustic problem with an application to sound wave propagation through electrically conducting fluids such as the ocean in the Earth's magnetic field, liquid metals, or plasmas has been addressed taking into account several simultaneous chemical reactions. Using continuum balance equations for the total mass, linear momentum, energy; as well as Maxwell's electrodynamic equations, a nonlinear beam equation has been developed to generalize the Khokhlov-Zabolotskaya-Kuznetsov (KZK) equation for a fluid with linear viscosity but nonlinear and diffraction effects. Thermodynamic parameters are used and not tailored to only an adiabatic fluid case. The chemical kinetic equations build on a relaxing media approach presented, for example, by K. Naugolnukh and L. Ostrovsky [Nonlinear Wave Processes in Acoustics (Cambridge Univ. Press, Cambridge, 1998)] for a linearized single reaction and thermodynamic pressure equation of state. Approximations for large and small relaxation times and for magnetohydrodynamic parameters [Korsunskii, Sov. Phys. Acoust. 36 (1990)] are examined. Additionally, Cattaneo's equation for heat conduction and its generalization for a memory process rather than a Fourier's law are taken into account. It was introduced for the heat flux depends on the temperature gradient at an earlier time to generate heat pulses of finite speed.

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

More, R.M.

A new statistical model (the quantum-statistical model (QSM)) was recently introduced by Kalitkin and Kuzmina for the calculation of thermodynamic properties of compressed matter. This paper examines the QSM and gives (i) a numerical QSM calculation of pressure and energy for aluminum and comparison to existing augmented-plane-wave data; (ii) display of separate kinetic, exchange, and quantum pressure terms; (iii) a study of electron density at the nucleus; (iv) a study of the effects of the Kirzhnitz-Weizsacker parameter controlling the gradient terms; (v) an analytic expansion for very high densities; and (vi) rigorous pressure theorems including a general version of themore » virial theorem which applies to an arbitrary microscopic volume. It is concluded that the QSM represents the most accurate and consistent theory of the Thomas-Fermi type.« less

Semi-Empirical Model to Estimate the Solubility of CO2 NaCl Brine in Conditions Representative of CO2 Sequestration

NASA Astrophysics Data System (ADS)

Mohammadian, E.; Hamidi, H.; Azdarpour, A.

2018-05-01

CO2 sequestration is considered as one of the most anticipated methods to mitigate CO2 concentration in the atmosphere. Solubility mechanism is one of the most important and sophisticated mechanisms by which CO2 is rendered immobile while it is being injected into aquifers. A semi-empirical, easy to use model was developed to calculate the solubility of CO2 in NaCl brines with thermodynamic conditions (pressure, temperature) and salinity gradients representative CO2 sequestration in the Malay basin. The model was compared to the previous more sophisticated models and a good consistency was found among the data obtained using the two models. A Sensitivity analysis was also conducted on the model to test its performance beyond its limits.

Thermodynamics of protein folding using a modified Wako-Saitô-Muñoz-Eaton model.

PubMed

Tsai, Min-Yeh; Yuan, Jian-Min; Teranishi, Yoshiaki; Lin, Sheng Hsien

2012-09-01

Herein, we propose a modified version of the Wako-Saitô-Muñoz-Eaton (WSME) model. The proposed model introduces an empirical temperature parameter for the hypothetical structural units (i.e., foldons) in proteins to include site-dependent thermodynamic behavior. The thermodynamics for both our proposed model and the original WSME model were investigated. For a system with beta-hairpin topology, a mathematical treatment (contact-pair treatment) to facilitate the calculation of its partition function was developed. The results show that the proposed model provides better insight into the site-dependent thermodynamic behavior of the system, compared with the original WSME model. From this site-dependent point of view, the relationship between probe-dependent experimental results and model's thermodynamic predictions can be explained. The model allows for suggesting a general principle to identify foldon behavior. We also find that the backbone hydrogen bonds may play a role of structural constraints in modulating the cooperative system. Thus, our study may contribute to the understanding of the fundamental principles for the thermodynamics of protein folding.

Flow induced migration in polymer melts – Theory and simulation

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

Dorgan, John Robert, E-mail: jdorgan@mines.edu; Rorrer, Nicholas Andrew, E-mail: nrorrer@mines.edu

2015-04-28

Flow induced migration, whereby polymer melts are fractionated by molecular weight across a flow field, represents a significant complication in the processing of polymer melts. Despite its long history, such phenomena remain relatively poorly understood. Here a simple analytical theory is presented which predicts the phenomena based on well-established principles of non-equilibrium thermodynamics. It is unambiguously shown that for purely viscous materials, a gradient in shear rate is needed to drive migration; for purely viscometric flows no migration is expected. Molecular scale simulations of flow migration effects in dense polymer melts are also presented. In shear flow the melts exhibitmore » similar behavior as the quiescent case; a constant shear rate across the gap does not induce chain length based migration. In comparison, parabolic flow causes profound migration for both unentangled and entangled melts. These findings are consistent with the analytical theory. The picture that emerges is consistent with flow induced migration mechanisms predominating over competing chain degradation mechanisms.« less

Direct determination of the driving forces for taurocholate uptake into rat liver plasma membrane vesicles.

PubMed

Duffy, M C; Blitzer, B L; Boyer, J L

1983-10-01

To determine directly the driving forces for bile acid entry into the hepatocyte, the uptake of [3H]taurocholic acid into rat liver plasma membrane vesicles was studied. The membrane preparation contained predominantly right-side-out vesicles, and was highly enriched in plasma membrane marker enzymes. The uptake of taurocholate at equilibrium was inversely related to medium osmolarity, indicating transport into an osmotically sensitive space. In the presence of an inwardly directed sodium gradient (NaCl or sodium gluconate), the initial rate of uptake was rapid and taurocholate was transiently accumulated at a concentration twice that at equilibrium (overshoot). Other inwardly directed cation gradients (K+, Li+, choline+) or the presence of sodium in the absence of a gradient (Na+ equilibrated) resulted in a slower initial uptake rate and did not sustain an overshoot. Bile acids inhibited sodium-dependent taurocholate uptake, whereas bromsulphthalein inhibited both sodium-dependent and sodium-independent uptake and D-glucose had no effect on uptake. Uptake was temperature dependent, with maximal overshoots occurring at 25 degrees C. Imposition of a proton gradient across the vesicle (pHo less than pHi) in the absence of a sodium gradient failed to enhance taurocholate uptake, indicating that double ion exchange (Na+-H+, OH- -anion) is unlikely. Creation of a negative intravesicular potential by altering accompanying anions or by valinomycin-induced K+-diffusion potentials did not enhance taurocholate uptake, suggesting an electroneutral transport mechanism. The kinetics of taurocholate uptake demonstrated saturability with a Michaelis constant at 52 microM and maximum velocity of 4.5 nmol X mg-1 X protein X min-1. These studies provide definitive evidence for a sodium gradient-dependent, carrier-mediated, electrically neutral transport mechanism for hepatic taurocholate uptake. These findings are consistent with a model for bile secretion in which the basolateral enzyme Na+,K+-ATPase provides the driving force for "uphill" bile acid transport by establishing a trans-membrane sodium gradient.

Master curves and radial distribution functions for shear dilatancy of liquid n-hexadecane via nonequilibrium molecular dynamics simulations.

PubMed

Tseng, Huan-Chang; Wu, Jiann-Shing; Chang, Rong-Yeu

2009-04-28

Shear dilatancy, a significant nonlinear behavior of nonequilibrium thermodynamics states, has been observed in nonequilibrium molecular dynamics (NEMD) simulations for liquid n-hexadecane fluid under extreme shear conditions. The existence of shear dilatancy is relevant to the relationship between the imposed shear rate gamma and the critical shear rate gamma(c). Consequently, as gammagamma(c), the intermolecular distance is lengthened substantially by strong shear deformation breaking the equilibrium thermodynamic state so that shear dilatancy takes place. Notably, a characteristic shear rate gamma(m), which depends on the root mean square molecular velocity and the average free molecular distance, is found in nonequilibrium thermodynamics state curves. Studies of the variations in the intermolecular radial distribution function (RDF) with respect to the shear rate provide a direct measure of the variation in the degree of intermolecular separation. Additionally, the variations of the RDF curve in the microscopic regime are consistent with those of the nonequilibrium thermodynamic state in the macroscopic world. By inspecting the overall shape of the RDF curve, it can be readily corroborated that the fluid of interest exists in the liquid state. More importantly, both primary characteristic values, the equilibrium thermodynamic state variable and a particular shear rate of gamma(p), are determined cautiously, with gamma(p) depending on the gamma(m) value and the square root of pressure. Thereby, the nonequilibrium thermodynamic state curves can be normalized as temperature-, pressure-, and density-invariant master curves, formulated by applying the Cross constitutive equation. Clearly, gamma(c) occurs at which a reduced shear rate gamma/gamma(p) approaches 0.1. Furthermore, the trends in the rates of shear dilatancy in both the constant-pressure and constant-volume NEMD systems under isothermal conditions conform to the cyclic rule of pressure, as a function of density and shear rate.

Composition gradient optimization and electrical characterization of (Pb, Ca)TiO3 thin films

NASA Astrophysics Data System (ADS)

Bao, Dinghua; Mizutani, Nobuyasu; Zhang, Liangying; Yao, Xi

2001-01-01

Compositionally graded (Pb, Ca)TiO3 thin films were prepared by a monoethanolamine-modified sol-gel technique on platinum-coated silicon substrates at the annealing temperature of 600 °C. The composition gradient of the films was greatly improved by a modified annealing method. The dielectric constants, for up-graded and down-graded films annealed at 600 °C for 60 min, were found to be 469 and 355, respectively. Both were larger than those reported for conventional (Pb, Ca)TiO3 thin films. The compositionally graded films had large polarization offsets in hysteresis loops when excited by an alternating electric field. The more smooth the composition gradient of the graded film, the larger the polarization offset. This was consistent with a theoretical model reported previously by Mantese and coworkers [Appl. Phys. Lett. 71, 2047 (1997)]. The magnitude of polarization offset displayed a power-law dependence on the electric field, and the direction of the offset depended on the direction of the composition gradient with respect to the substrate. Both up-graded and down-graded films had good leakage current characteristics.

Thermodynamically efficient solar concentrators

NASA Astrophysics Data System (ADS)

Winston, Roland

2012-10-01

Non-imaging Optics is the theory of thermodynamically efficient optics and as such depends more on thermodynamics than on optics. Hence in this paper a condition for the "best" design is proposed based on purely thermodynamic arguments, which we believe has profound consequences for design of thermal and even photovoltaic systems. This new way of looking at the problem of efficient concentration depends on probabilities, the ingredients of entropy and information theory while "optics" in the conventional sense recedes into the background.

Kinematic, dynamic, and thermodynamic impacts of hook-echo hydrometeors, including explorations into the utilization of polarimetric radar data

NASA Astrophysics Data System (ADS)

Askelson, Mark Anthony

Recent studies have revealed that the thermodynamic properties of the rear flank downdraft (RFD) may dictate whether or not a supercell becomes tornadic. Since hydrometeors are thought to be an important driving force for the RFD, it is postulated that they may be important to its thermodynamic properties and, possibly, to tornadogenesis. The role hook-echo hydrometeors play in driving RFDs is investigated by estimating hook-echo hydrometeor types and amounts from polarimetric radar data and by using that information to drive a relatively simple downdraft model. Soundings for the individual cases are used to initialize the downdraft model in order to replicate the environments of the storms as closely as possible. Since this effort and others like it require the quantitative utilization of radar data, issues pertaining to this are explored. In addition to analyses of coordinate transformation equations and an innovative objective analysis technique for weather radar data, the difficult problem of response functions for arbitrary weight functions and data distributions was considered. A novel approach to this problem revealed that the local response function for distance dependent weighted averaging schemes is the complex conjugate of the normalized Fourier transform of the effective weight function. This facilitates new research avenues, especially regarding analyses of irregularly spaced data. Simulations of hydrometeor driven RFDs show that hydrometeor fields inferred from radar data are able to drive significant downdrafts without the influence of vertical perturbation pressure gradients. Moreover, they reveal that above the boundary layer supercell environments are relatively resistant to downdrafts whereas within the boundary layer they are generally supportive of downdrafts. It appears that in many supercell environments relatively large hail (≥1 cm in diameter) or vertical perturbation pressure gradients may be needed to drive deep midlevel downdrafts that penetrate into the boundary layer. Because the boundary layer is an important downdraft generation/intensification layer, its thetae profile appears to be important to the surface RFD thetae deficit and, consequently, to tornadogenesis. To further examine these issues, analyses using idealized soundings that represent multiple possible RFD environments and analyses of the complete set of VORTEX cases are planned.

Continuum and crystal strain gradient plasticity with energetic and dissipative length scales

NASA Astrophysics Data System (ADS)

Faghihi, Danial

This work, standing as an attempt to understand and mathematically model the small scale materials thermal and mechanical responses by the aid of Materials Science fundamentals, Continuum Solid Mechanics, Misro-scale experimental observations, and Numerical methods. Since conventional continuum plasticity and heat transfer theories, based on the local thermodynamic equilibrium, do not account for the microstructural characteristics of materials, they cannot be used to adequately address the observed mechanical and thermal response of the micro-scale metallic structures. Some of these cases, which are considered in this dissertation, include the dependency of thin films strength on the width of the sample and diffusive-ballistic response of temperature in the course of heat transfer. A thermodynamic-based higher order gradient framework is developed in order to characterize the mechanical and thermal behavior of metals in small volume and on the fast transient time. The concept of the thermal activation energy, the dislocations interaction mechanisms, nonlocal energy exchange between energy carriers and phonon-electrons interactions are taken into consideration in proposing the thermodynamic potentials such as Helmholtz free energy and rate of dissipation. The same approach is also adopted to incorporate the effect of the material microstructural interface between two materials (e.g. grain boundary in crystals) into the formulation. The developed grain boundary flow rule accounts for the energy storage at the grain boundary due to the dislocation pile up as well as energy dissipation caused by the dislocation transfer through the grain boundary. Some of the abovementioned responses of small scale metallic compounds are addressed by means of the numerical implementation of the developed framework within the finite element context. In this regard, both displacement and plastic strain fields are independently discretized and the numerical implementation is performed in the finite element program ABAQUS/standard via the user element subroutine UEL. Using this numerical capability, an extensive study is conducted on the major characteristics of the proposed theories for bulk and interface such as size effect on yield and kinematic hardening, features of boundary layer formation, thermal softening and grain boundary weakening, and the effect of soft and stiff interfaces.

Microscopic theory for the time irreversibility and the entropy production

NASA Astrophysics Data System (ADS)

Chun, Hyun-Myung; Noh, Jae Dong

2018-02-01

In stochastic thermodynamics, the entropy production of a thermodynamic system is defined by the irreversibility measured by the logarithm of the ratio of the path probabilities in the forward and reverse processes. We derive the relation between the irreversibility and the entropy production starting from the deterministic equations of motion of the whole system consisting of a physical system and a surrounding thermal environment. The derivation assumes the Markov approximation that the environmental degrees of freedom equilibrate instantaneously. Our approach provides a guideline for the choice of the proper reverse process to a given forward process, especially when there exists a velocity-dependent force. We demonstrate our idea with an example of a charged particle in the presence of a time-varying magnetic field.

Computer codes for the evaluation of thermodynamic and transport properties for equilibrium air to 30000 K

NASA Technical Reports Server (NTRS)

Thompson, Richard A.; Lee, Kam-Pui; Gupta, Roop N.

1991-01-01

The computer codes developed here provide self-consistent thermodynamic and transport properties for equilibrium air for temperatures from 500 to 30000 K over a temperature range of 10 (exp -4) to 10 (exp -2) atm. These properties are computed through the use of temperature dependent curve fits for discrete values of pressure. Interpolation is employed for intermediate values of pressure. The curve fits are based on mixture values calculated from an 11-species air model. Individual species properties used in the mixture relations are obtained from a recent study by the present authors. A review and discussion of the sources and accuracy of the curve fitted data used herein are given in NASA RP 1260.

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

Modified Fourth-Order Kinetic Energy Gradient Expansion with Hartree Potential-Dependent Coefficients.

PubMed

Constantin, Lucian A; Fabiano, Eduardo; Della Sala, Fabio

2017-09-12

Using the semiclassical neutral atom theory, we developed a modified fourth-order kinetic energy (KE) gradient expansion (GE4m) that keeps unchanged all the linear-response terms of the uniform electron gas and gives a significant improvement with respect to the known semilocal functionals for both large atoms and jellium surfaces. On the other hand, GE4m is not accurate for light atoms; thus, we modified the GE4m coefficients making them dependent on a novel ingredient, the reduced Hartree potential, recently introduced in the Journal of Chemical Physics 2016, 145, 084110, in the context of exchange functionals. The resulting KE gradient expansion functional, named uGE4m, belongs to the novel class of u-meta-generalized-gradient-approximations (uMGGA) whose members depend on the conventional ingredients (i.e., the reduced gradient and Laplacian of the density) as well as on the reduced Hartree potential. To test uGE4m, we defined an appropriate benchmark (including total KE and KE differences for atoms, molecules and jellium clusters) for gradient expansion functionals, that is, including only those systems which are mainly described by a slowly varying density regime. While most of the GGA and meta-GGA KE functionals (we tested 18 of them) are accurate for some properties and inaccurate for others, uGE4m shows a consistently good performance for all the properties considered. This represents a qualitative boost in the KE functional development and highlights the importance of the reduced Hartree potential for the construction of next-generation KE functionals.

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.

Localization of planarian β-CATENIN-1 reveals multiple roles during anterior-posterior regeneration and organogenesis.

PubMed

Sureda-Gómez, Miquel; Martín-Durán, José M; Adell, Teresa

2016-11-15

The β-catenin-dependent Wnt pathway exerts multiple context-dependent roles in embryonic and adult tissues. In planarians, β-catenin-1 is thought to specify posterior identities through the generation of an anteroposterior gradient. However, the existence of such a gradient has not been directly demonstrated. Here, we use a specific polyclonal antibody to demonstrate that nuclear β-CATENIN-1 exists as an anteroposterior gradient from the pre-pharyngeal region to the tail of the planarian Schmidtea polychroa High levels in the posterior region steadily decrease towards the pre-pharyngeal region but then increase again in the head region. During regeneration, β-CATENIN-1 is nuclearized in both anterior and posterior blastemas, but the canonical WNT1 ligand only influences posterior nuclearization. Additionally, β-catenin-1 is required for proper anterior morphogenesis, consistent with the high levels of nuclear β-CATENIN-1 observed in this region. We further demonstrate that β-CATENIN-1 is abundant in developing and differentiated organs, and is particularly required for the specification of the germline. Altogether, our findings provide the first direct evidence of an anteroposterior nuclear β-CATENIN-1 gradient in adult planarians and uncover novel, context-dependent roles for β-catenin-1 during anterior regeneration and organogenesis. © 2016. Published by The Company of Biologists Ltd.

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

Stability of peptides in high-temperature aqueous solutions

NASA Astrophysics Data System (ADS)

Shock, Everett L.

1992-09-01

Estimated standard molal thermodynamic properties of aqueous dipeptides and their constituent amino acids indicate that temperature increases correspond to increased stability of peptide bonds relative to hydrolysis reactions. Pressure increases cause slight decreases in peptide bond stability, which are generally offset by greater stability caused by temperature increases along geothermal gradients. These calculations suggest that peptides, polypeptides, and proteins may survive hydrothermal alteration of organic matter depending on the rates of the hydrolysis reactions. Extremely thermophilic organisms may be able to take advantage of the decreased energy required to form peptide bonds in order to maintain structural proteins and enzymes at elevated temperatures and pressures. As the rates of hydrolysis reactions increase with increasing temperature, formation of peptide bonds may become a facile process in hydrothermal systems and deep in sedimentary basins.

Thermal Remote Sensing and the Thermodynamics of Ecosystem Development

NASA Technical Reports Server (NTRS)

Luvall, Jeffrey C.; Kay, James J.; Fraser, Roydon F.

2000-01-01

Thermal remote sensing can provide environmental measuring tools with capabilities for measuring ecosystem development and integrity. Recent advances in applying principles of nonequilibrium thermodynamics to ecology provide fundamental insights into energy partitioning in ecosystems. Ecosystems are nonequilibrium systems, open to material and energy flows, which grow and develop structures and processes to increase energy degradation. More developed terrestrial ecosystems will be more effective at dissipating the solar gradient (degrading its energy content). This can be measured by the effective surface temperature of the ecosystem on a landscape scale.

Evaluation of the Thermosensitive Release Properties of Microspheres Containing an Agrochemical Compound.

PubMed

Terada, Takatoshi; Ohtsubo, Toshiro; Iwao, Yasunori; Noguchi, Shuji; Itai, Shigeru

2017-01-01

The purpose of this study was to develop a deeper understanding of the key physicochemical parameters involved in the release profiles of microsphere-encapsulated agrochemicals at different temperatures. Microspheres consisting of different polyurethanes (PUs) were prepared using our previously reported solventless microencapsulation technique. Notably, these microspheres exhibited considerable differences in their thermodynamic characteristics, including their glass transition temperature (T g ), extrapolated onset temperature (T o ) and extrapolated end temperature (T e ). At test temperatures below the T o of the PU, only 5-10% of the agrochemical was rapidly released from the microspheres within 1 d, and none was released thereafter. However, at test temperatures above the T o of the PU, the rate of agrochemical release gradually increased with increasing temperatures, and the rate of release from the microspheres was dependent on the composition of the PU. Taken together, these results show that the release profiles of the microspheres were dependent on their thermodynamic characteristics and changes in their PU composition.

Thermodynamic properties of selected uranium compounds and aqueous species at 298.15 K and 1 bar and at higher temperatures; preliminary models for the origin of coffinite deposits

USGS Publications Warehouse

Hemingway, B.S.

1982-01-01

Thermodynamic values for 110 uranium-bearing phases and 28 aqueous uranium solution species (298.15 K and l bar) are tabulated based upon evaluated experimental data (largely from calorimetric experiments) and estimated values. Molar volume data are given for most of the solid phases. Thermodynamic values for 16 uranium-bearing phases are presented for higher temperatures in the form of and as a supplement to U.S. Geological Survey Bulletin 1452 (Robie et al., 1979). The internal consistency of the thermodynamic values reported herein is dependent upon the reliability of the experimental results for several uranium phases that have been used as secondary calorimetric reference phases. The data for the reference phases and for those phases evaluated with respect to the secondary reference phases are discussed. A preliminary model for coffinite formation has been proposed together with an estimate of the free energy of formation of coffinite. Free energy values are estimated for several other uranium-bearing silicate phases that have been reported as secondary uranium phases associated with uranium ore deposits and that could be expected to develop wherever uranium is leached by groundwaters.

Radar observations of density gradients, electric fields, and plasma irregularities near polar cap patches in the context of the gradient-drift instability

NASA Astrophysics Data System (ADS)

Lamarche, Leslie J.; Makarevich, Roman A.

2017-03-01

We present observations of plasma density gradients, electric fields, and small-scale plasma irregularities near a polar cap patch made by the Super Dual Auroral Radar Network radar at Rankin Inlet (RKN) and the northern face of Resolute Bay Incoherent Scatter Radar (RISR-N). RKN echo power and occurrence are analyzed in the context of gradient-drift instability (GDI) theory, with a particular focus on the previously uninvestigated 2-D dependencies on wave propagation, electric field, and gradient vectors, with the latter two quantities evaluated directly from RISR-N measurements. It is shown that higher gradient and electric field components along the wave vector generally lead to the higher observed echo occurrence, which is consistent with the expected higher GDI growth rate, but the relationship with echo power is far less straightforward. The RKN echo power increases monotonically as the predicted linear growth rate approaches zero from negative values but does not continue this trend into positive growth rate values, in contrast with GDI predictions. The observed greater consistency of echo occurrence with GDI predictions suggests that GDI operating in the linear regime can control basic plasma structuring, but measured echo strength may be affected by other processes and factors, such as multistep or nonlinear processes or a shear-driven instability.

Characterization of geothermal paleosystem in the Lesser Antilles volcanic arc: structural, petrographic, thermodynamic and petrophysics analysis of Terre-de-Haut (Les Saintes archipelago, Lesser Antilles)

NASA Astrophysics Data System (ADS)

Favier, Alexiane; Navelot, Vivien; Verati, Chrystèle; Lardeaux, Jean-Marc; Corsini, Michel; Diraison, Marc; Géraud, Yves; Mercier de Lépinay, Jeanne; Munschy, Marc

2017-04-01

This survey takes part in the GEOTREF project (high enthalpy geothermal energy in fractured reservoirs), supported by the French government program "Investments for the future". The program focuses on the exploration of geothermal resource in the Lesser Antilles volcanic arc. An exclusive license has been issued in the Vieux-Habitants area (Basse-Terre, Guadeloupe) to carry on the development of high-temperature geothermal energy in this active volcanic region. The deep geothermal reservoir on the Basse-Terre island could be characterized in exhumed paleosystems. The reference paleosystem in the Guadeloupe archipelago is located in Terre-de-Haut. Four major fault directions have been highlighted N000-N020, N050-N070, N090-N110 and N130-N140. Field observations emphasize three major cleavage directions overlaying the fault systems: N035-N060, N080-N110, N145-N165. Volcanic rocks affected by cleavage display several metamorphic transformation grades. The more transformed calc-alkaline rocks are located at the intersection of several cleavage directions. Mineralogical transformations due to metamorphism and surimposed fractures are also responsible for strong changes of petrophysical properties. In comparison with the reference protolith of andesitic lava flows outcropping in Vieux-Habitants, which have porosity and permeability lower than 5 % and 10-15 m2, andesites of Terre-de-Haut have better reservoir properties with connected porosity and permeability higher than 15 % and 10-14-10-15 m2 respectively. Thermodynamic modelling based on petrography and chemical composition of the most transformed rocks highlights a steady state mineral assemblage between 0.25 - 1.5 kbar and 350 - 450 ˚ C. It corresponds to a geothermal gradient higher than 120 to 150˚ C/km. This is consistent with temperatures measured in Bouillante wells. However, this geothermal gradient is notably higher to a usual volcanic arc conductive gradient estimated to 70-100˚ C/km. It can be explained by the addition of a convective processes caused by hydrothermal fluid flows.

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.

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.

Theory of chemical kinetics and charge transfer based on nonequilibrium thermodynamics.

PubMed

Bazant, Martin Z

2013-05-21

Advances in the fields of catalysis and electrochemical energy conversion often involve nanoparticles, which can have kinetics surprisingly different from the bulk material. Classical theories of chemical kinetics assume independent reactions in dilute solutions, whose rates are determined by mean concentrations. In condensed matter, strong interactions alter chemical activities and create variations that can dramatically affect the reaction rate. The extreme case is that of a reaction coupled to a phase transformation, whose kinetics must depend not only on the order parameter but also on its gradients at phase boundaries. Reaction-driven phase transformations are common in electrochemistry, when charge transfer is accompanied by ion intercalation or deposition in a solid phase. Examples abound in Li-ion, metal-air, and lead-acid batteries, as well as metal electrodeposition-dissolution. Despite complex thermodynamics, however, the standard kinetic model is the Butler-Volmer equation, based on a dilute solution approximation. The Marcus theory of charge transfer likewise considers isolated reactants and neglects elastic stress, configurational entropy, and other nonidealities in condensed phases. The limitations of existing theories recently became apparent for the Li-ion battery material LixFePO4 (LFP). It has a strong tendency to separate into Li-rich and Li-poor solid phases, which scientists believe limits its performance. Chemists first modeled phase separation in LFP as an isotropic "shrinking core" within each particle, but experiments later revealed striped phase boundaries on the active crystal facet. This raised the question: What is the reaction rate at a surface undergoing a phase transformation? Meanwhile, dramatic rate enhancement was attained with LFP nanoparticles, and classical battery models could not predict the roles of phase separation and surface modification. In this Account, I present a general theory of chemical kinetics, developed over the past 7 years, which is capable of answering these questions. The reaction rate is a nonlinear function of the thermodynamic driving force, the free energy of reaction, expressed in terms of variational chemical potentials. The theory unifies and extends the Cahn-Hilliard and Allen-Cahn equations through a master equation for nonequilibrium chemical thermodynamics. For electrochemistry, I have also generalized both Marcus and Butler-Volmer kinetics for concentrated solutions and ionic solids. This new theory provides a quantitative description of LFP phase behavior. Concentration gradients and elastic coherency strain enhance the intercalation rate. At low currents, the charge-transfer rate is focused on exposed phase boundaries, which propagate as "intercalation waves", nucleated by surface wetting. Unexpectedly, homogeneous reactions are favored above a critical current and below a critical size, which helps to explain the rate capability of LFP nanoparticles. Contrary to other mechanisms, elevated temperatures and currents may enhance battery performance and lifetime by suppressing phase separation. The theory has also been extended to porous electrodes and could be used for battery engineering with multiphase active materials. More broadly, the theory describes nonequilibrium chemical systems at mesoscopic length and time scales, beyond the reach of molecular simulations and bulk continuum models. The reaction rate is consistently defined for inhomogeneous, nonequilibrium states, for example, with phase separation, large electric fields, or mechanical stresses. This research is also potentially applicable to fluid extraction from nanoporous solids, pattern formation in electrophoretic deposition, and electrochemical dynamics in biological cells.

A High-Order, Adaptive, Discontinuous Galerkin Finite Element Method for the Reynolds-Averaged Navier-Stokes Equations

DTIC Science & Technology

2008-09-01

Element Method. Wellesley- Cambridge Press, Wellesly, MA, 1988. [97] E. F. Toro . Riemann Solvers and Numerical Methods for Fluid Dynamics: A Practical...introducing additional state variables, are generally asymptotically dual consistent. Numerical results are presented to confirm the results of the analysis...dependence on the state gradient is handled by introducing additional state variables, are generally asymptotically dual consistent. Numerical results are

On axial temperature gradients due to large pressure drops in dense fluid chromatography.

PubMed

Colgate, Sam O; Berger, Terry A

2015-03-13

The effect of energy degradation (Degradation is the creation of net entropy resulting from irreversibility.) accompanying pressure drops across chromatographic columns is examined with regard to explaining axial temperature gradients in both high performance liquid chromatography (HPLC) and supercritical fluid chromatography (SFC). The observed effects of warming and cooling can be explained equally well in the language of thermodynamics or fluid dynamics. The necessary equivalence of these treatments is reviewed here to show the legitimacy of using whichever one supports the simpler determination of features of interest. The determination of temperature profiles in columns by direct application of the laws of thermodynamics is somewhat simpler than applying them indirectly by solving the Navier-Stokes (NS) equations. Both disciplines show that the preferred strategy for minimizing the reduction in peak quality caused by temperature gradients is to operate columns as nearly adiabatically as possible (i.e. as Joule-Thomson expansions). This useful fact, however, is not widely familiar or appreciated in the chromatography community due to some misunderstanding of the meaning of certain terms and expressions used in these disciplines. In fluid dynamics, the terms "resistive heating" or "frictional heating" have been widely used as synonyms for the dissipation function, Φ, in the NS energy equation. These terms have been widely used by chromatographers as well, but often misinterpreted as due to friction between the mobile phase and the column packing, when in fact Φ describes the increase in entropy of the system (dissipation, ∫TdSuniv>0) due to the irreversible decompression of the mobile phase. Two distinctly different contributions to the irreversibility are identified; (1) ΔSext, viscous dissipation of work done by the external surroundings driving the flow (the pump) contributing to its warming, and (2) ΔSint, entropy change accompanying decompression of fluid in the column, contributing either to warming or cooling depending on local density and temperature. The molecular basis for this variation is described. Sample calculations of dissipation and temperature profiles of several model fluids including carbon dioxide-methanol mixtures are presented, based on the NIST REFPROP program including select equations of state and property calculation software. Copyright © 2015 Elsevier B.V. All rights reserved.

Improvement of determinating seafloor benchmark position with large-scale horizontal heterogeneity in the ocean area

NASA Astrophysics Data System (ADS)

Uemura, Y.; Tadokoro, K.; Matsuhiro, K.; Ikuta, R.

2015-12-01

The most critical issue in reducing the accuracy of seafloor positioning system, GPS/Acoustic technique, is large-scale thermal gradient of sound-speed structure [Muto et al., 2008] due to the ocean current. For example, Kuroshio Current, near our observation station, forms this structure. To improve the accuracy of seafloor benchmark position (SBP), we need to directly measure the structure frequently, or estimate it from travel time residual. The former, we repeatedly measure the sound-speed at Kuroshio axis using Underway CTD and try to apply analysis method of seafloor positioning [Yasuda et al., 2015 AGU meeting]. The latter, however, we cannot estimate the structure using travel time residual until now. Accordingly, in this study, we focus on azimuthal dependence of Estimated Mean Sound-Speed (EMSS). EMSS is defined as distance between vessel position and estimated SBP divided by travel time. If thermal gradient exists and SBP is true, EMSS should have azimuthal dependence with the assumption of horizontal layered sound-speed structure in our previous analysis method. We use the data at KMC located on the central part of Nankai Trough, Japan on Jan. 28, 2015, because on that day KMC was on the north edge of Kuroshio, where we expect that thermal gradient exists. In our analysis method, the hyper parameter (μ value) weights travel time residual and rate of change of sound speed structure. However, EMSS derived from μ value determined by Ikuta et al. [2008] does not have azimuthal dependence, that is, we cannot estimate thermal gradient. Thus, we expect SBP has a large bias. Therefore, in this study, we use another μ value and examine whether EMSS has azimuthal dependence or not. With the μ value of this study, which is 1 order of magnitude smaller than the previous value, EMSS has azimuthal dependence that is consistent with observation day's thermal gradient. This result shows that we can estimate the thermal gradient adequately. This SBP displaces 25.6 cm to the north and 11.8 cm to the east compared to previous SBP. This displacement reduces the bias of SBP and RMS of horizontal component in time series to 1/3. Therefore, determination of SBP is suitable when the thermal gradient exists on observation day and EMSS has azimuthal dependence for redetermination of μ value.

Consistent description of quantum Brownian motors operating at strong friction.

PubMed

Machura, L; Kostur, M; Hänggi, P; Talkner, P; Luczka, J

2004-09-01

A quantum Smoluchowski equation is put forward that consistently describes thermal quantum states. In particular, it notably does not induce a violation of the second law of thermodynamics. This so modified kinetic equation is applied to study analytically directed quantum transport at strong friction in arbitrarily shaped ratchet potentials that are driven by nonthermal two-state noise. Depending on the mutual interplay of quantum tunneling and quantum reflection these quantum corrections can induce both, a sizable enhancement or a suppression of transport. Moreover, the threshold for current reversals becomes markedly shifted due to such quantum fluctuations.

Urea-temperature phase diagrams capture the thermodynamics of denatured state expansion that accompany protein unfolding

PubMed Central

Tischer, Alexander; Auton, Matthew

2013-01-01

We have analyzed the thermodynamic properties of the von Willebrand factor (VWF) A3 domain using urea-induced unfolding at variable temperature and thermal unfolding at variable urea concentrations to generate a phase diagram that quantitatively describes the equilibrium between native and denatured states. From this analysis, we were able to determine consistent thermodynamic parameters with various spectroscopic and calorimetric methods that define the urea–temperature parameter plane from cold denaturation to heat denaturation. Urea and thermal denaturation are experimentally reversible and independent of the thermal scan rate indicating that all transitions are at equilibrium and the van't Hoff and calorimetric enthalpies obtained from analysis of individual thermal transitions are equivalent demonstrating two-state character. Global analysis of the urea–temperature phase diagram results in a significantly higher enthalpy of unfolding than obtained from analysis of individual thermal transitions and significant cross correlations describing the urea dependence of and that define a complex temperature dependence of the m-value. Circular dichroism (CD) spectroscopy illustrates a large increase in secondary structure content of the urea-denatured state as temperature increases and a loss of secondary structure in the thermally denatured state upon addition of urea. These structural changes in the denatured ensemble make up ∼40% of the total ellipticity change indicating a highly compact thermally denatured state. The difference between the thermodynamic parameters obtained from phase diagram analysis and those obtained from analysis of individual thermal transitions illustrates that phase diagrams capture both contributions to unfolding and denatured state expansion and by comparison are able to decipher these contributions. PMID:23813497

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.

Structural stability, elastic and thermodynamic properties of Au-Cu alloys from first-principles calculations

NASA Astrophysics Data System (ADS)

Kong, Ge-Xing; Ma, Xiao-Juan; Liu, Qi-Jun; Li, Yong; Liu, Zheng-Tang

2018-03-01

Using first-principles calculations method based on density functional theory (DFT) with the Perdew-Burke-Ernzerhof (PBE) implementation of the generalized gradient approximation (GGA), we investigate the structural, elastic and thermodynamic properties of gold-copper intermetallic compounds (Au-Cu ICs). The calculated lattice parameters are in excellent agreement with experimental data. The elastic constants show that all the investigated Au-Cu alloys are mechanically stable. Elastic properties, including the shear modulus, Young's modulus, Poisson's ratio and Pugh's indicator, of the intermetallic compounds are evaluated and discussed, with special attention to the remarkable anisotropy displayed by Au-Cu ICs. Thermodynamic and transport properties including the Debye temperature, thermal conductivity and melting point are predicted from the averaged sound velocity and elastic moduli, using semi-empirical formulas.

Structural, electronic, magnetic and thermodynamic properties of Ni1-xTixO alloys an ab initio calculation and Monte Carlo study

NASA Astrophysics Data System (ADS)

Klaa, K.; Labidi, S.; Masrour, R.; Jabar, A.; Labidi, M.; Amara, A.; Drici, A.; Hlil, E. K.; Ellouze, M.

2018-06-01

Structural, electronic, magnetic and thermodynamic main features for Ni1-xTixO ternary alloys in rock-salt structure with Ti content in the range ? were studied using the full potential Linearized augmented plane wave (FP-LAPW) method within density functional theory. The exchange-correlation potential was calculated by the generalized gradient approximation. The analysis of the electronic density of states curves allowed the computation of the magnetic moments which are considered to lie along (010) axes. The thermodynamic stability of this alloy was investigated by calculating the excess enthalpy of mixing ? as well as the phase diagram. In addition, the Monte Carlo simulations have been exploited to calculate the transition temperature and magnetic coercive field in the alloy.

Thermodynamic Paradigm for Solution Demixing Inspired by Nuclear Transport in Living Cells

NASA Astrophysics Data System (ADS)

Wang, Ching-Hao; Mehta, Pankaj; Elbaum, Michael

2017-04-01

Living cells display a remarkable capacity to compartmentalize their functional biochemistry. A particularly fascinating example is the cell nucleus. Exchange of macromolecules between the nucleus and the surrounding cytoplasm does not involve traversing a lipid bilayer membrane. Instead, large protein channels known as nuclear pores cross the nuclear envelope and regulate the passage of other proteins and RNA molecules. Beyond simply gating diffusion, the system of nuclear pores and associated transport receptors is able to generate substantial concentration gradients, at the energetic expense of guanosine triphosphate hydrolysis. In contrast to conventional approaches to demixing such as reverse osmosis and dialysis, the biological system operates continuously, without application of cyclic changes in pressure or solvent exchange. Abstracting the biological paradigm, we examine this transport system as a thermodynamic machine of solution demixing. Building on the construct of free energy transduction and biochemical kinetics, we find conditions for the stable operation and optimization of the concentration gradients as a function of dissipation in the form of 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

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

A thermodynamic approach to link self-organization, preferential flow and rainfall-runoff behaviour

NASA Astrophysics Data System (ADS)

Zehe, E.; Ehret, U.; Blume, T.; Kleidon, A.; Scherer, U.; Westhoff, M.

2013-11-01

This study investigates whether a thermodynamically optimal hillslope structure can, if existent, serve as a first guess for uncalibrated predictions of rainfall-runoff. To this end we propose a thermodynamic framework to link rainfall-runoff processes and dynamics of potential energy, kinetic energy and capillary binding energy in catchments and hillslopes. The starting point is that hydraulic equilibrium in soil corresponds to local thermodynamic equilibrium (LTE), characterized by a local maximum entropy/minimum of free energy of soil water. Deviations from LTE occur either due to evaporative losses, which increase absolute values of negative capillary binding energy of soil water and reduce its potential energy, or due to infiltration of rainfall, which increases potential energy of soil water and reduces the strength of capillary binding energy. The amplitude and relaxation time of these deviations depend on climate, vegetation, soil hydraulic functions, topography and density of macropores. Based on this framework we analysed the free energy balance of hillslopes within numerical experiments that perturbed model structures with respect to the surface density of macropores. These model structures have been previously shown to allow successful long-term simulations of the water balances of the Weiherbach and the Malalcahuello catchments, which are located in distinctly different pedological and climatic settings. Our findings offer a new perspective on different functions of preferential flow paths depending on the pedological setting. Free energy dynamics of soil water in the cohesive soils of the Weiherbach is dominated by dynamics of capillary binding energy. Macropores act as dissipative wetting structures by enlarging water flows against steep gradients in soil water potential after long dry spells. This implies accelerated depletion of these gradients and faster relaxation back towards LTE. We found two local optima in macropore density that maximize reduction rates of free energy of soil water during rainfall-driven conditions. These two optima exist because reduction rates of free energy are, in this case, a second-order polynomial of the wetting rate, which implicitly depends on macroporosity. An uncalibrated long-term simulation of the water balance of the Weiherbach catchment based on the first optimum macroporosity performed almost as well as the best fit when macroporosity was calibrated to match rainfall-runoff. In the Malalcahuello catchment we did not find an apparent optimum density of macropores, because free energy dynamics of soil water during rainfall-driven conditions is dominated by increases of potential energy. Macropores act as dissipative drainage structures by enhancing export of potential energy. No optimum macropore density exists in this case because potential energy change rates scale linearly with the wetting rate. We found, however, a distinguished macroporosity that assures steady-state conditions of the potential energy balance of the soil, in the sense that average storage of potential energy is compensated by average potential energy export. This distinguished macroporosity was close to the value that yielded the best fit of rainfall-runoff behaviour during a calibration exercise and allowed a robust estimate of the annual runoff coefficient. Our findings are promising for predictions in ungauged catchments (PUB) as the optimal/distinguished model structures can serve as a first guess for uncalibrated predictions of rainfall-runoff. They also offer an alternative for classifying catchments according to their similarity of the free energy balance components.

A temperature-dependent coarse-grained model for the thermoresponsive polymer poly(N-isopropylacrylamide).

PubMed

Abbott, Lauren J; Stevens, Mark J

2015-12-28

A coarse-grained (CG) model is developed for the thermoresponsive polymer poly(N-isopropylacrylamide) (PNIPAM), using a hybrid top-down and bottom-up approach. Nonbonded parameters are fit to experimental thermodynamic data following the procedures of the SDK (Shinoda, DeVane, and Klein) CG force field, with minor adjustments to provide better agreement with radial distribution functions from atomistic simulations. Bonded parameters are fit to probability distributions from atomistic simulations using multi-centered Gaussian-based potentials. The temperature-dependent potentials derived for the PNIPAM CG model in this work properly capture the coil-globule transition of PNIPAM single chains and yield a chain-length dependence consistent with atomistic simulations.

Switch between competition and facilitation within a seasonal scale at colony level in bryophytes.

PubMed

Spitale, Daniel

2009-06-01

The relative importance of positive and negative interaction in species assemblages is thought to be dependent on the harshness of the physical environment. I studied the consistency of this prediction in a field experiment using growth of the target species Warnstorfia exannulata as influenced by the presence or absence of two adjacent species, Sphagnum warnstorfii and Scapania undulata. In particular, I focused on the mechanism by which colony-colony interactions occur, elucidating how the balance of positive and negative interactions changes along a water gradient. Because the natural fluctuations of the environment modify the water gradient, it was expected that the competitive hierarchies of the species would not remain consistent over time. Results indicated that the different hydrological properties of the colonies, thought to be the necessary condition for the appearance of species interactions, were not sufficient to explain the outcome of the species interactions. The switch from competition to facilitation under more stressful conditions was not confirmed along a water stress gradient. In addition, natural climatic fluctuations, by affecting the length of the water gradient, changed the competitive hierarchies of the species on a seasonal scale.

Optimization of Turbine Engine Cycle Analysis with Analytic Derivatives

NASA Technical Reports Server (NTRS)

Hearn, Tristan; Hendricks, Eric; Chin, Jeffrey; Gray, Justin; Moore, Kenneth T.

2016-01-01

A new engine cycle analysis tool, called Pycycle, was recently built using the OpenMDAO framework. This tool uses equilibrium chemistry based thermodynamics, and provides analytic derivatives. This allows for stable and efficient use of gradient-based optimization and sensitivity analysis methods on engine cycle models, without requiring the use of finite difference derivative approximation methods. To demonstrate this, a gradient-based design optimization was performed on a multi-point turbofan engine model. Results demonstrate very favorable performance compared to an optimization of an identical model using finite-difference approximated derivatives.

Gravitational Thermodynamics for Interstellar Gas and Weakly Degenerate Quantum Gas

NASA Astrophysics Data System (ADS)

Zhu, Ding Yu; Shen, Jian Qi

2016-03-01

The temperature distribution of an ideal gas in gravitational fields has been identified as a longstanding problem in thermodynamics and statistical physics. According to the principle of entropy increase (i.e., the principle of maximum entropy), we apply a variational principle to the thermodynamical entropy functional of an ideal gas and establish a relationship between temperature gradient and gravitational field strength. As an illustrative example, the temperature and density distributions of an ideal gas in two simple but typical gravitational fields (i.e., a uniform gravitational field and an inverse-square gravitational field) are considered on the basis of entropic and hydrostatic equilibrium conditions. The effect of temperature inhomogeneity in gravitational fields is also addressed for a weakly degenerate quantum gas (e.g., Fermi and Bose gas). The present gravitational thermodynamics of a gas would have potential applications in quantum fluids, e.g., Bose-Einstein condensates in Earth’s gravitational field and the temperature fluctuation spectrum in cosmic microwave background radiation.

Opinion Formation Models on a Gradient

PubMed Central

Gastner, Michael T.; Markou, Nikolitsa; Pruessner, Gunnar; Draief, Moez

2014-01-01

Statistical physicists have become interested in models of collective social behavior such as opinion formation, where individuals change their inherently preferred opinion if their friends disagree. Real preferences often depend on regional cultural differences, which we model here as a spatial gradient g in the initial opinion. The gradient does not only add reality to the model. It can also reveal that opinion clusters in two dimensions are typically in the standard (i.e., independent) percolation universality class, thus settling a recent controversy about a non-consensus model. However, using analytical and numerical tools, we also present a model where the width of the transition between opinions scales , not as in independent percolation, and the cluster size distribution is consistent with first-order percolation. PMID:25474528

Study of coherent structures of turbulence with large wall-normal gradients in thermophysical properties using direct numerical simulation

NASA Astrophysics Data System (ADS)

Reinink, Shawn K.; Yaras, Metin I.

2015-06-01

Forced-convection heat transfer in a heated working fluid at a thermodynamic state near its pseudocritical point is poorly predicted by correlations calibrated with data at subcritical temperatures and pressures. This is suggested to be primarily due to the influence of large wall-normal thermophysical property gradients that develop in proximity of the pseudocritical point on the concentration of coherent turbulence structures near the wall. The physical mechanisms dominating this influence remain poorly understood. In the present study, direct numerical simulation is used to study the development of coherent vortical structures within a turbulent spot under the influence of large wall-normal property gradients. A turbulent spot rather than a fully turbulent boundary layer is used for the study, for the coherent structures of turbulence in a spot tend to be in a more organized state which may allow for more effective identification of cause-and-effect relationships. Large wall-normal gradients in thermophysical properties are created by heating the working fluid which is near the pseudocritical thermodynamic state. It is found that during improved heat transfer, wall-normal gradients in density accelerate the growth of the Kelvin-Helmholtz instability mechanism in the shear layer enveloping low-speed streaks, causing it to roll up into hairpin vortices at a faster rate. It is suggested that this occurs by the baroclinic vorticity generation mechanism which accelerates the streamwise grouping of vorticity during shear layer roll-up. The increased roll-up frequency leads to reduced streamwise spacing between hairpin vortices in wave packets. The density gradients also promote the sinuous instability mode in low-speed streaks. The resulting oscillations in the streaks in the streamwise-spanwise plane lead to locally reduced spanwise spacing between hairpin vortices forming over adjacent low-speed streaks. The reduction in streamwise and spanwise spacing between hairpin vortices causes them to interact more frequently by merging together and by breaking apart into smaller turbulence structures.

Study of coherent structures of turbulence with large wall-normal gradients in thermophysical properties using direct numerical simulation

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

Reinink, Shawn K.; Yaras, Metin I., E-mail: Metin.Yaras@carleton.ca

2015-06-15

Forced-convection heat transfer in a heated working fluid at a thermodynamic state near its pseudocritical point is poorly predicted by correlations calibrated with data at subcritical temperatures and pressures. This is suggested to be primarily due to the influence of large wall-normal thermophysical property gradients that develop in proximity of the pseudocritical point on the concentration of coherent turbulence structures near the wall. The physical mechanisms dominating this influence remain poorly understood. In the present study, direct numerical simulation is used to study the development of coherent vortical structures within a turbulent spot under the influence of large wall-normal propertymore » gradients. A turbulent spot rather than a fully turbulent boundary layer is used for the study, for the coherent structures of turbulence in a spot tend to be in a more organized state which may allow for more effective identification of cause-and-effect relationships. Large wall-normal gradients in thermophysical properties are created by heating the working fluid which is near the pseudocritical thermodynamic state. It is found that during improved heat transfer, wall-normal gradients in density accelerate the growth of the Kelvin-Helmholtz instability mechanism in the shear layer enveloping low-speed streaks, causing it to roll up into hairpin vortices at a faster rate. It is suggested that this occurs by the baroclinic vorticity generation mechanism which accelerates the streamwise grouping of vorticity during shear layer roll-up. The increased roll-up frequency leads to reduced streamwise spacing between hairpin vortices in wave packets. The density gradients also promote the sinuous instability mode in low-speed streaks. The resulting oscillations in the streaks in the streamwise-spanwise plane lead to locally reduced spanwise spacing between hairpin vortices forming over adjacent low-speed streaks. The reduction in streamwise and spanwise spacing between hairpin vortices causes them to interact more frequently by merging together and by breaking apart into smaller turbulence structures.« less

Reversible mechanosensitive ion pumping as a part of mechanoelectrical transduction.

PubMed Central

Markin, V. S.; Tsong, T. Y.

1991-01-01

To explain the ability of some mechanosensitive cells to reverse the process of mechanotransduction and to generate mechanical oscillations and emit sound, a piezo-conformational coupling model (PCC model) is proposed. The model includes a transport protein which changes either its volume (PV-coupling) or its area in the membrane (gamma A-coupling) when undergoing conformational transitions. Such a protein can interact with an oscillating pressure to pump ions and create a transmembrane gradient if the affinities of the protein for ions are different at the two sides of membrane. The frequency and concentration windows for mechanical energy transduction were determined. Under optimal conditions, the efficiency of energy transduction can approach the theoretical maximum of 100%. If the concentration gradient exceeds the static head value (quasi-equilibrium which can be built up and maintained by this transport system), the energy transduction reverses and the transporter becomes a generator of mechanical oscillations at the expense of a concentration gradient. Estimation of thermodynamic parameters of the pump shows that the PV-coupling model would require large pressure oscillations to work while the gamma A-coupling model could work in physiological conditions. The gamma A-coupling mechanism may be used by cells for two purposes. In the reverse mode, it can be a force generator for various applications. In the direct mode, it may serve bioenergetic purposes by harvesting the energy of mechanical oscillations and storing it in the form of a concentration gradient. This pump has an unusual thermodynamic feature: it can distinguish the two components of the electrochemical potential gradient,i.e., the concentration gradient and the electrical potential, the latter serving as a permissive switch to open, or close, the pump when the potential reaches the threshold value.Predictions of the PCC model and its probable involvement in biological mechanotransduction are dicussed. PMID:1873468

Dissolved and labile concentrations of Cd, Cu, Pb, and Zn in the South Fork Coeur d'Alene River, Idaho: Comparisons among chemical equilibrium models and implications for biotic ligand models

USGS Publications Warehouse

Balistrieri, L.S.; Blank, R.G.

2008-01-01

In order to evaluate thermodynamic speciation calculations inherent in biotic ligand models, the speciation of dissolved Cd, Cu, Pb, and Zn in aquatic systems influenced by historical mining activities is examined using equilibrium computer models and the diffusive gradients in thin films (DGT) technique. Several metal/organic-matter complexation models, including WHAM VI, NICA-Donnan, and Stockholm Humic model (SHM), are used in combination with inorganic speciation models to calculate the thermodynamic speciation of dissolved metals and concentrations of metal associated with biotic ligands (e.g., fish gills). Maximum dynamic metal concentrations, determined from total dissolved metal concentrations and thermodynamic speciation calculations, are compared with labile metal concentrations measured by DGT to assess which metal/organic-matter complexation model best describes metal speciation and, thereby, biotic ligand speciation, in the studied systems. Results indicate that the choice of model that defines metal/organic-matter interactions does not affect calculated concentrations of Cd and Zn associated with biotic ligands for geochemical conditions in the study area, whereas concentrations of Cu and Pb associated with biotic ligands depend on whether the speciation calculations use WHAM VI, NICA-Donnan, or SHM. Agreement between labile metal concentrations and dynamic metal concentrations occurs when WHAM VI is used to calculate Cu speciation and SHM is used to calculate Pb speciation. Additional work in systems that contain wide ranges in concentrations of multiple metals should incorporate analytical speciation methods, such as DGT, to constrain the speciation component of biotic ligand models. ?? 2008 Elsevier Ltd.

Development of a robust modeling tool for radiation-induced segregation in austenitic stainless steels

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

Yang, Ying; Field, Kevin G; Allen, Todd R.

2015-09-01

Irradiation-assisted stress corrosion cracking (IASCC) of austenitic stainless steels in Light Water Reactor (LWR) components has been linked to changes in grain boundary composition due to irradiation induced segregation (RIS). This work developed a robust RIS modeling tool to account for thermodynamics and kinetics of the atom and defect transportation under combined thermal and radiation conditions. The diffusion flux equations were based on the Perks model formulated through the linear theory of the thermodynamics of irreversible processes. Both cross and non-cross phenomenological diffusion coefficients in the flux equations were considered and correlated to tracer diffusion coefficients through Manning’s relation. Themore » preferential atomvacancy coupling was described by the mobility model, whereas the preferential atom-interstitial coupling was described by the interstitial binding model. The composition dependence of the thermodynamic factor was modeled using the CALPHAD approach. Detailed analysis on the diffusion fluxes near and at grain boundaries of irradiated austenitic stainless steels suggested the dominant diffusion mechanism for chromium and iron is via vacancy, while that for nickel can swing from the vacancy to the interstitial dominant mechanism. The diffusion flux in the vicinity of a grain boundary was found to be greatly influenced by the composition gradient formed from the transient state, leading to the oscillatory behavior of alloy compositions in this region. This work confirms that both vacancy and interstitial diffusion, and segregation itself, have important roles in determining the microchemistry of Fe, Cr, and Ni at irradiated grain boundaries in austenitic stainless steels.« less

Structure of neutron star crusts from new Skyrme effective interactions constrained by chiral effective field theory

NASA Astrophysics Data System (ADS)

Lim, Yeunhwan; Holt, Jeremy W.

2017-06-01

We investigate the structure of neutron star crusts, including the crust-core boundary, based on new Skyrme mean field models constrained by the bulk-matter equation of state from chiral effective field theory and the ground-state energies of doubly-magic nuclei. Nuclear pasta phases are studied using both the liquid drop model as well as the Thomas-Fermi approximation. We compare the energy per nucleon for each geometry (spherical nuclei, cylindrical nuclei, nuclear slabs, cylindrical holes, and spherical holes) to obtain the ground state phase as a function of density. We find that the size of the Wigner-Seitz cell depends strongly on the model parameters, especially the coefficients of the density gradient interaction terms. We employ also the thermodynamic instability method to check the validity of the numerical solutions based on energy comparisons.

A fourth gradient to overcome slice dependent phase effects of voxel-sized coils in planar arrays.

PubMed

Bosshard, John C; Eigenbrodt, Edwin P; McDougall, Mary P; Wright, Steven M

2010-01-01

The signals from an array of densely spaced long and narrow receive coils for MRI are complicated when the voxel size is of comparable dimension to the coil size. The RF coil causes a phase gradient across each voxel, which is dependent on the distance from the coil, resulting in a slice dependent shift of k-space. A fourth gradient coil has been implemented and used with the system's gradient set to create a gradient field which varies with slice. The gradients are pulsed together to impart a slice dependent phase gradient to compensate for the slice dependent phase due to the RF coils. However the non-linearity in the fourth gradient which creates the desired slice dependency also results in a through-slice phase ramp, which disturbs normal slice refocusing and leads to additional signal cancelation and reduced field of view. This paper discusses the benefits and limitations of using a fourth gradient coil to compensate for the phase due to RF coils.

Atmospheric Moisture Budget and Spatial Resolution Dependence of Precipitation Extremes in Aquaplanet Simulations

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

Yang, Qing; Leung, Lai-Yung R.; Rauscher, Sara

This study investigates the resolution dependency of precipitation extremes in an aqua-planet framework. Strong resolution dependency of precipitation extremes is seen over both tropics and extra-tropics, and the magnitude of this dependency also varies with dynamical cores. Moisture budget analyses based on aqua-planet simulations with the Community Atmosphere Model (CAM) using the Model for Prediction Across Scales (MPAS) and High Order Method Modeling Environment (HOMME) dynamical cores but the same physics parameterizations suggest that during precipitation extremes moisture supply for surface precipitation is mainly derived from advective moisture convergence. The resolution dependency of precipitation extremes mainly originates from advective moisturemore » transport in the vertical direction. At most vertical levels over the tropics and in the lower atmosphere over the subtropics, the vertical eddy transport of mean moisture field dominates the contribution to precipitation extremes and its resolution dependency. Over the subtropics, the source of moisture, its associated energy, and the resolution dependency during extremes are dominated by eddy transport of eddies moisture at the mid- and upper-troposphere. With both MPAS and HOMME dynamical cores, the resolution dependency of the vertical advective moisture convergence is mainly explained by dynamical changes (related to vertical velocity or omega), although the vertical gradients of moisture act like averaging kernels to determine the sensitivity of the overall resolution dependency to the changes in omega at different vertical levels. The natural reduction of variability with coarser resolution, represented by areal data averaging (aggregation) effect, largely explains the resolution dependency in omega. The thermodynamic changes, which likely result from non-linear feedback in response to the large dynamical changes, are small compared to the overall changes in dynamics (omega). However, after excluding the data aggregation effect in omega, thermodynamic changes become relatively significant in offsetting the effect of dynamics leading to reduce differences between the simulated and aggregated results. Compared to MPAS, the simulated stronger vertical motion with HOMME also results in larger resolution dependency. Compared to the simulation at fine resolution, the vertical motion during extremes is insufficiently resolved/parameterized at the coarser resolution even after accounting for the natural reduction in variability with coarser resolution, and this is more distinct in the simulation with HOMME. To reduce uncertainties in simulated precipitation extremes, future development in cloud parameterizations must address their sensitivity to spatial resolution as well as dynamical cores.« less

Altering the axial light gradient affects photomorphogenesis in emerging seedlings of Zea mays L

NASA Technical Reports Server (NTRS)

Parks, B. M.; Poff, K. L.

1986-01-01

The axial (longitudinal) red light gradient (632 nanometers) of 4 day old dark-grown maize seedlings is increased by staining the peripheral cells of the coleoptile. The magnitude of increase in the light gradient is dependent solely on the light-absorbing qualities of the stain used. Metanil yellow has no effect on the axial red-light gradient, while methylene blue causes a large increase in this light gradient. These stains did not affect growth in darkness or the sensitivity of mesocotyl elongation to red light. However, mesocotyl elongation was altered for the dark-grown seedlings stained with methylene blue when these seedlings were transplanted, covered with soil, and permitted to emerge under natural lighting conditions. These observations are consistent with the idea that there is a single perceptive site below the coleoptilar node, and suggest that this perceptive site gives the actinic light which has traveled downward through the length of the shoot from an entry point in the plant tip region.

Evaluation of temperature history of a spherical nanosystem irradiated with various short-pulse laser sources

NASA Astrophysics Data System (ADS)

Lahiri, Arnab; Mondal, Pranab K.

2018-04-01

Spatiotemporal thermal response and characteristics of net entropy production rate of a gold nanosphere (radius: 50-200 nm), subjected to a short-pulse, femtosecond laser is reported. In order to correctly illustrate the temperature history of laser-metal interaction(s) at picoseconds transient with a comprehensive single temperature definition in macroscale and to further understand how the thermophysical response of the single-phase lag (SPL) and dual-phase lag (DPL) frameworks (with various lag-ratios') differs, governing energy equations derived from these benchmark non-Fourier frameworks are numerically solved and thermodynamic assessment under both the classical irreversible thermodynamics (CIT) as well as extended irreversible thermodynamics (EIT) frameworks is subsequently carried out. Under the frameworks of SPL and DPL with small lag ratio, thermophysical anomalies such as temperature overshooting characterized by adverse temperature gradient is observed to violate the local thermodynamic equilibrium (LTE) hypothesis. The EIT framework, however, justifies the compatibility of overshooting of temperature with the second law of thermodynamics under a nonequilibrium paradigm. The DPL framework with higher lag ratio was however observed to remain free from temperature overshooting and finds suitable consistency with LTE hypothesis. In order to solve the dimensional non-Fourier governing energy equation with volumetric laser-irradiation source term(s), the lattice Boltzmann method (LBM) is extended and a three-time level, fully implicit, second order accurate finite difference method (FDM) is illustrated. For all situations under observation, the LBM scheme is featured to be computationally superior to remaining FDM schemes. With detailed prediction of maximum temperature rise and the corresponding peaking time by all the numerical schemes, effects of the change of radius of the gold nanosphere, the magnitude of fluence of laser, and laser irradiation with multiple pulses on thermal energy transport and lagging behavior (if any) are further elucidated at different radial locations of the gold nanosphere. Last, efforts are further made to address the thermophysical characteristics when effective thermal conductivity (with temporal and size effects) is considered instead of the usual bulk thermal conductivity.

Increasing vertical resolution of three-dimensional atmospheric water vapor retrievals using a network of scanning compact microwave radiometers

NASA Astrophysics Data System (ADS)

Sahoo, Swaroop

2011-12-01

The thermodynamic properties of the troposphere, in particular water vapor content and temperature, change in response to physical mechanisms, including frictional drag, evaporation, transpiration, heat transfer and flow modification due to terrain. The planetary boundary layer (PBL) is characterized by a high rate of change in its thermodynamic state on time scales of typically less than one hour. Large horizontal gradients in vertical wind speed and steep vertical gradients in water vapor and temperature in the PBL are associated with high-impact weather. Observation of these gradients in the PBL with high vertical resolution and accuracy is important for improvement of weather prediction. Satellite remote sensing in the visible, infrared and microwave provide qualitative and quantitative measurements of many atmospheric properties, including cloud cover, precipitation, liquid water content and precipitable water vapor in the upper troposphere. However, the ability to characterize the thermodynamic properties of the PBL is limited by the confounding factors of ground emission in microwave channels and of cloud cover in visible and IR channels. Ground-based microwave radiometers are routinely used to measure thermodynamic profiles. The vertical resolution of such profiles retrieved from radiometric brightness temperatures depends on the number and choice of frequency channels, the scanning strategy and the accuracy of brightness temperature measurements. In the standard technique, which uses brightness temperatures from vertically pointing radiometers, the vertical resolution of the retrieved water vapor profile is similar to or larger than the altitude at which retrievals are performed. This study focuses on the improvement of the vertical resolution of water vapor retrievals by including scanning measurements at a variety of elevation angles. Elevation angle scanning increases the path length of the atmospheric emission, thus improving the signal-to-noise ratio. This thesis also discusses Colorado State University's (CSU) participation in the European Space Agency (ESA)'s "Mitigation of Electromagnetic Transmission errors induced by Atmospheric WAter Vapor Effects" (METAWAVE) experiment conducted in the fall of 2008. CSU deployed a ground-based network of three Compact Microwave Radiometers for Humidity profiling (CMR-Hs) in Rome to measure atmospheric brightness temperatures. These measurements were used to retrieve high-resolution 3-D atmospheric water vapor and its variation with time. High-resolution information about water vapor can be crucial for the mitigation of wet tropospheric path delay variations that limit the quality of Interferometric Synthetic Aperture Radar satellite interferograms. Three-dimensional water vapor retrieval makes use of radiative transfer theory, algebraic tomographic reconstruction and Bayesian optimal estimation coupled with Kalman filtering. In addition, spatial interpolation (kriging) is used to retrieve water vapor density at unsampled locations. 3-D humidity retrievals from Rome data with vertical and horizontal resolution of 0.5 km are presented. The water vapor retrieved from CMR-H measurements is compared with MM5 Mesoscale Model output, as well as with measurements from the Medium Resolution Imaging Spectrometer (MERIS) aboard ESA's ENVISAT and the Moderate Resolution Imaging Spectroradiometer (MODIS) aboard NASA's Aqua and Terra satellites.

Bottom-up coarse-grained models that accurately describe the structure, pressure, and compressibility of molecular liquids

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

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

2015-12-28

The present work investigates the capability of bottom-up coarse-graining (CG) methods for accurately modeling both structural and thermodynamic properties of all-atom (AA) models for molecular liquids. In particular, we consider 1, 2, and 3-site CG models for heptane, as well as 1 and 3-site CG models for toluene. For each model, we employ the multiscale coarse-graining method to determine interaction potentials that optimally approximate the configuration dependence of the many-body potential of mean force (PMF). We employ a previously developed “pressure-matching” variational principle to determine a volume-dependent contribution to the potential, U{sub V}(V), that approximates the volume-dependence of the PMF.more » We demonstrate that the resulting CG models describe AA density fluctuations with qualitative, but not quantitative, accuracy. Accordingly, we develop a self-consistent approach for further optimizing U{sub V}, such that the CG models accurately reproduce the equilibrium density, compressibility, and average pressure of the AA models, although the CG models still significantly underestimate the atomic pressure fluctuations. Additionally, by comparing this array of models that accurately describe the structure and thermodynamic pressure of heptane and toluene at a range of different resolutions, we investigate the impact of bottom-up coarse-graining upon thermodynamic properties. In particular, we demonstrate that U{sub V} accounts for the reduced cohesion in the CG models. Finally, we observe that bottom-up coarse-graining introduces subtle correlations between the resolution, the cohesive energy density, and the “simplicity” of the model.« less

Analysis of edge stability for models of heat flux width

DOE PAGES

Makowski, Michael A.; Lasnier, Charles J.; Leonard, Anthony W.; ...

2017-05-12

Detailed measurements of the n e, and T e, and T i profiles in the vicinity of the separatrix of ELMing H-mode discharges have been used to examine plasma stability at the extreme edge of the plasma and assess stability dependent models of the heat flux width. The results are strongly contrary to the critical gradient model, which posits that a ballooning instability determines a gradient scale length related to the heat flux width. The results of this analysis are not sensitive to the choice of location to evaluate stability. Significantly, it is also found that the results are completelymore » consistent with the heuristic drift model for the heat flux width. Here the edge pressure gradient scales with plasma density and is proportional to the pressure gradient inferred from the equilibrium in accordance with the predictions of that theory.« less

A Posteriori Study of a DNS Database Describing Super critical Binary-Species Mixing

NASA Technical Reports Server (NTRS)

Bellan, Josette; Taskinoglu, Ezgi

2012-01-01

Currently, the modeling of supercritical-pressure flows through Large Eddy Simulation (LES) uses models derived for atmospheric-pressure flows. Those atmospheric-pressure flows do not exhibit the particularities of high densitygradient magnitude features observed both in experiments and simulations of supercritical-pressure flows in the case of two species mixing. To assess whether the current LES modeling is appropriate and if found not appropriate to propose higher-fidelity models, a LES a posteriori study has been conducted for a mixing layer that initially contains different species in the lower and upper streams, and where the initial pressure is larger than the critical pressure of either species. An initially-imposed vorticity perturbation promotes roll-up and a double pairing of four initial span-wise vortices into an ultimate vortex that reaches a transitional state. The LES equations consist of the differential conservation equations coupled with a real-gas equation of state, and the equation set uses transport properties depending on the thermodynamic variables. Unlike all LES models to date, the differential equations contain, additional to the subgrid scale (SGS) fluxes, a new SGS term that is a pressure correction in the momentum equation. This additional term results from filtering of Direct Numerical Simulation (DNS) equations, and represents the gradient of the difference between the filtered pressure and the pressure computed from the filtered flow field. A previous a priori analysis, using a DNS database for the same configuration, found this term to be of leading order in the momentum equation, a fact traced to the existence of high-densitygradient magnitude regions that populated the entire flow; in the study, models were proposed for the SGS fluxes as well as this new term. In the present study, the previously proposed constantcoefficient SGS-flux models of the a priori investigation are tested a posteriori in LES, devoid of or including, the SGS pressure correction term. The present pressure-correction model is different from, and more accurate as well as less computationally intensive than that of the a priori study. The constant-coefficient SGS-flux models encompass the Smagorinsky (SMC), in conjunction with the Yoshizawa (YO) model for the trace, the Gradient (GRC) and the Scale Similarity (SSC) models, all exercised with the a priori study constant coefficients calibrated at the transitional state. The LES comparison is performed with the filtered- and-coarsened (FC) DNS, which represents an ideal LES solution. Expectably, an LES model devoid of SGS terms is shown to be considerably inferior to models containing SGS effects. Among models containing SGS effects, those including the pressure-correction term are substantially superior to those devoid of it. The sensitivity of the predictions to the initial conditions and grid size are also investigated. Thus, it has been discovered that, additional to the atmospheric-pressure models currently used, a new model is necessary to simulate supercritical-pressure flows. This model depends on the thermodynamic characteristics of the chemical species involved.

Anatomy of particle diffusion

NASA Astrophysics Data System (ADS)

Bringuier, E.

2009-11-01

The paper analyses particle diffusion from a thermodynamic standpoint. The main goal of the paper is to highlight the conceptual connection between particle diffusion, which belongs to non-equilibrium statistical physics, and mechanics, which deals with particle motion, at the level of third-year university courses. We start out from the fact that, near equilibrium, particle transport should occur down the gradient of the chemical potential. This yields Fick's law with two additional advantages. First, splitting the chemical potential into 'mechanical' and 'chemical' contributions shows how transport and mechanics are linked through the diffusivity-mobility relationship. Second, splitting the chemical potential into entropic and energetic contributions discloses the respective roles of entropy maximization and energy minimization in driving diffusion. The paper addresses first unary diffusion, where there is only one mobile species in an immobile medium, and next turns to binary diffusion, where two species are mobile with respect to each other in a fluid medium. The interrelationship between unary and binary diffusivities is brought out and it is shown how binary diffusion reduces to unary diffusion in the limit of high dilution of one species amidst the other one. Self- and mutual diffusion are considered and contrasted within the thermodynamic framework; self-diffusion is a time-dependent manifestation of the Gibbs paradox of mixing.

Thermodynamic origin of nonimaging optics

NASA Astrophysics Data System (ADS)

Jiang, Lun; Winston, Roland

2016-10-01

Nonimaging optics is the theory of thermodynamically efficient optics and as such depends more on thermodynamics than on optics. Hence, in this paper, a condition for the "best" design is proposed based on purely thermodynamic arguments, which we believe has profound consequences for the designs of thermal and even photovoltaic systems. This way of looking at the problem of efficient concentration depends on probabilities, the ingredients of entropy and information theory, while "optics" in the conventional sense recedes into the background. Much of the paper is pedagogical and retrospective. Some of the development of flowline designs will be introduced at the end and the connection between the thermodynamics and flowline design will be graphically presented. We will conclude with some speculative directions of where the ideas might lead.

Neutrophil migration under spatially-varying chemoattractant gradient profiles.

PubMed

Halilovic, Iris; Wu, Jiandong; Alexander, Murray; Lin, Francis

2015-01-01

Chemotaxis plays an important role in biological processes such as cancer metastasis, embryogenesis, wound healing, and immune response. Neutrophils are the frontline defenders against invasion of foreign microorganisms into our bodies. To achieve this important immune function, a neutrophil can sense minute chemoattractant concentration differences across its cell body and effectively migrate toward the chemoattractant source. Furthermore, it has been demonstrated in various studies that neutrophils are highly sensitive to changes in the surrounding chemoattractant environments, suggesting the role of a chemotactic memory for processing the complex spatiotemporal chemical guiding signals. Using a microfluidic device, in the present study we characterized neutrophil migration under spatially varying profiles of interleukine-8 gradients, which consist of three spatially ordered regions of a shallow gradient, a steep gradient and a nearly saturated gradient. This design allowed us to examine how neutrophils migrate under different chemoattractant gradient profiles, and how the migratory response is affected when the cell moves from one gradient profile to another in a single experiment. Our results show robust neutrophil chemotaxis in the shallow and steep gradient, but not the saturated gradient. Furthermore, neutrophils display a transition from chemotaxis to flowtaxis when they migrate across the steep gradient interface, and the relative efficiency of this transition depends on the cell's chemotaxis history. Finally, some neutrophils were observed to adjust their morphology to different gradient profiles.

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.

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

Origins of cratonic mantle discontinuities: A view from petrology, geochemistry and thermodynamic models

NASA Astrophysics Data System (ADS)

Aulbach, Sonja; Massuyeau, Malcolm; Gaillard, Fabrice

2017-01-01

Geophysically detectible mid-lithospheric discontinuities (MLD) and lithosphere-asthenosphere boundaries (LAB) beneath cratons have received much attention over recent years, but a consensus on their origin has not yet emerged. Cratonic lithosphere composition and origin is peculiar due to its ultra-depletion during plume or accretionary tectonics, cool present-day geothermal gradients, compositional and rheological stratification and multiple metasomatic overprints. Bearing this in mind, we integrate current knowledge on the physical properties, chemical composition, mineralogy and fabric of cratonic mantle with experimental and thermodynamic constraints on the formation and migration of melts, both below and within cratonic lithosphere, in order to find petrologically viable explanations for cratonic mantle discontinuities. LABs characterised by strong seismic velocity gradients and increased conductivity require the presence of melts, which can form beneath intact cratonic roots reaching to 200-250 km depth only in exceptionally warm and/or volatile-rich mantle, thus explaining the paucity of seismical LAB observations beneath cratons. When present, pervasive interaction of these - typically carbonated - melts with the deep lithosphere leads to densification and thermochemical erosion, which generates topography at the LAB and results in intermittent seismic LAB signals or conflicting seismic, petrologic and thermal LAB depths. In rare cases (e.g. Tanzanian craton), the tops of live melt percolation fronts may appear as MLDs and, after complete lithosphere rejuvenation, may be sites of future, shallower LABs (e.g. North China craton). Since intact cratons are presently tectonomagmatically quiescent, and since MLDs produce both positive and negative velocity gradients, in some cases with anisotropy, most MLDs may be best explained by accumulations (metasomes) of seismically slow minerals (pyroxenes, phlogopite, amphibole, carbonates) deposited during past magmatic-metasomatic activity, or fabric inherited from cratonisation. They may accumulate as layers at, or as subvertical veins above, the depth at which melt flow transitions from pervasive to focussed flow at the mechanical boundary layer, causing azimuthal and radial anisotropy. Thermodynamic calculations investigating the depth range in which small-volume melts can be produced relative to the field of phlogopite stability and the presence of MLDs show that phlogopite precipitates at various pressures as a function of age-dependent thermal state of the cratonic mantle, thus explaining variable MLD depths. Even if not directly observed, such metasomes have been shown to be important ingredients in small-volume volatile-rich melts typically penetrating cratonic lithospheres. The apparent sparseness of evidence for phlogopite-rich assemblages in the mantle xenolith record at geophysically imaged MLD depths, if not due to preferential disaggregation in the kimberlite or alteration, may relate to vagaries of both kimberlite and human sampling.

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.

Thermodynamics of Host–Guest Interactions between Fullerenes and a Buckycatcher

PubMed Central

2015-01-01

1H NMR and isothermal titration calorimetry (ITC) experiments were employed to obtain reliable thermodynamic data for the formation of the 1:1 inclusion complexes of fullerenes C60 and C70 with the buckycatcher (C60H28). NMR measurements were done in toluene-d8 and chlorobenzene-d5 at 288, 298, and 308 K, while the ITC titrations were performed in toluene, chlorobenzene, o-dichlorobenzene, anisole, and 1,1,2,2-tetrachloroethane at temperatures from 278 to 323 K. The association constants, Ka, obtained with both techniques are in very good agreement. The thermodynamic data obtained by ITC indicate that generally the host–guest association is enthalpy-driven. Interestingly, the entropy contributions are, with rare exceptions, slightly stabilizing or close to zero. Neither ΔH nor ΔS is constant over the temperature range studied, and these thermodynamic functions exhibit classical enthalpy/entropy compensation. The ΔCp values calculated from the temperature dependence of the calorimetric ΔH values are negative for the association of both fullerenes with the buckycatcher in toluene. The negative ΔCp values are consistent with some desolvation of the host-cavity and the guest in the inclusion complexes, C60@C60H28 and C70@C60H28. PMID:25248285

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.

Linking boundary-layer circulations and surface processes during FIFE89. Part 1: Observational analysis

NASA Technical Reports Server (NTRS)

Smith, Eric A.; Wai, Mickey M.-K.; Cooper, Harry J.; Rubes, Michael T.; Hsu, Ann

1994-01-01

Surface, aircraft, and satellite observations are analyzed for the 21-day 1989 intensive field campaign of the First ISLSCP Field Experiment (FIFE) to determine the effect of precipitation, vegetation, and soil moisture distributions on the thermal properties of the surface including the heat and moisture fluxes, and the corresponding response in the boundary-layer circulation. Mean and variance properties of the surface variables are first documented at various time and space scales. These calculations are designed to set the stage for Part 2, a modeling study that will focus on how time-space dependent rainfall distribution influences the intensity of the feedback between a vegetated surface and the atmospheric boundary layer. Further analysis shows strongly demarked vegetation and soil moisture gradients extending across the FIFE experimental site that were developed and maintained by the antecedent and ongoing spatial distribution of rainfall over the region. These gradients are shown to have a pronounced influence on the thermodynamic properties of the surface. Furthermore, perturbation surface wind analysis suggests for both short-term steady-state conditions and long-term averaged conditions that the gradient pattern maintained a diurnally oscillating local direct circulation with perturbation vertical velocities of the same order as developing cumulus clouds. Dynamical and scaling considerations suggest that the embedded perturbation circulation is driven by surface heating/cooling gradients and terrain ef fects rather than the manifestation of an inertial oscillation. The implication is that at even relatively small scales (less than 30 km), the differential evolution in vegetation density and soil moisture distribution over a relatively homogenous ecotone can give rise to preferential boundary-layer circulations capable of modifying local-scale horizontal and vertical motions.

Observations of the scale-dependent turbulence and evaluation of the flux-gradient relationship for sensible heat for a closed Douglas-Fir canopy in very weak wind conditions

DOE PAGES

Vickers, D.; Thomas, C.

2014-05-13

Observations of the scale-dependent turbulent fluxes and variances above, within and beneath a tall closed Douglas-Fir canopy in very weak winds are examined. The daytime subcanopy vertical velocity spectra exhibit a double-peak structure with peaks at time scales of 0.8 s and 51.2 s. A double-peak structure is also observed in the daytime subcanopy heat flux cospectra. The daytime momentum flux cospectra inside the canopy and in the subcanopy are characterized by a relatively large cross-wind component, likely due to the extremely light and variable winds, such that the definition of a mean wind direction, and subsequent partitioning of themore » momentum flux into along- and cross-wind components, has little physical meaning. Positive values of both momentum flux components in the subcanopy contribute to upward transfer of momentum, consistent with the observed mean wind speed profile. In the canopy at night at the smallest resolved scales, we find relatively large momentum fluxes (compared to at larger scales), and increasing vertical velocity variance with decreasing time scale, consistent with very small eddies likely generated by wake shedding from the canopy elements that transport momentum but not heat. We find unusually large values of the velocity aspect ratio within the canopy, consistent with enhanced suppression of the horizontal wind components compared to the vertical by the canopy. The flux-gradient approach for sensible heat flux is found to be valid for the subcanopy and above-canopy layers when considered separately; however, single source approaches that ignore the canopy fail because they make the heat flux appear to be counter-gradient when in fact it is aligned with the local temperature gradient in both the subcanopy and above-canopy layers. Modeled sensible heat fluxes above dark warm closed canopies are likely underestimated using typical values of the Stanton number.« less

Observations of the scale-dependent turbulence and evaluation of the flux-gradient relationship for sensible heat for a closed Douglas-Fir canopy in very weak wind conditions

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

Vickers, D.; Thomas, C.

Observations of the scale-dependent turbulent fluxes and variances above, within and beneath a tall closed Douglas-Fir canopy in very weak winds are examined. The daytime subcanopy vertical velocity spectra exhibit a double-peak structure with peaks at time scales of 0.8 s and 51.2 s. A double-peak structure is also observed in the daytime subcanopy heat flux cospectra. The daytime momentum flux cospectra inside the canopy and in the subcanopy are characterized by a relatively large cross-wind component, likely due to the extremely light and variable winds, such that the definition of a mean wind direction, and subsequent partitioning of themore » momentum flux into along- and cross-wind components, has little physical meaning. Positive values of both momentum flux components in the subcanopy contribute to upward transfer of momentum, consistent with the observed mean wind speed profile. In the canopy at night at the smallest resolved scales, we find relatively large momentum fluxes (compared to at larger scales), and increasing vertical velocity variance with decreasing time scale, consistent with very small eddies likely generated by wake shedding from the canopy elements that transport momentum but not heat. We find unusually large values of the velocity aspect ratio within the canopy, consistent with enhanced suppression of the horizontal wind components compared to the vertical by the canopy. The flux-gradient approach for sensible heat flux is found to be valid for the subcanopy and above-canopy layers when considered separately; however, single source approaches that ignore the canopy fail because they make the heat flux appear to be counter-gradient when in fact it is aligned with the local temperature gradient in both the subcanopy and above-canopy layers. Modeled sensible heat fluxes above dark warm closed canopies are likely underestimated using typical values of the Stanton number.« less

Evidence of a two-step process and pathway dependency in the thermodynamics of poly(diallyldimethylammonium chloride)/poly(sodium acrylate) complexation.

PubMed

Vitorazi, L; Ould-Moussa, N; Sekar, S; Fresnais, J; Loh, W; Chapel, J-P; Berret, J-F

2014-12-21

Recent studies have pointed out the importance of polyelectrolyte assembly in the elaboration of innovative nanomaterials. Beyond their structures, many important questions on the thermodynamics of association remain unanswered. Here, we investigate the complexation between poly(diallyldimethylammonium chloride) (PDADMAC) and poly(sodium acrylate) (PANa) chains using a combination of three techniques: isothermal titration calorimetry (ITC), static and dynamic light scattering and electrophoresis. Upon addition of PDADMAC to PANa or vice-versa, the results obtained by the different techniques agree well with each other, and reveal a two-step process. The primary process is the formation of highly charged polyelectrolyte complexes of size 100 nm. The secondary process is the transition towards a coacervate phase made of rich and poor polymer droplets. The binding isotherms measured are accounted for using a phenomenological model that provides the thermodynamic parameters for each reaction. Small positive enthalpies and large positive entropies consistent with a counterion release scenario are found throughout this study. Furthermore, this work stresses the importance of the underestimated formulation pathway or mixing order in polyelectrolyte complexation.

Combined Yamamoto approach for simultaneous estimation of adsorption isotherm and kinetic parameters in ion-exchange chromatography.

PubMed

Rüdt, Matthias; Gillet, Florian; Heege, Stefanie; Hitzler, Julian; Kalbfuss, Bernd; Guélat, Bertrand

2015-09-25

Application of model-based design is appealing to support the development of protein chromatography in the biopharmaceutical industry. However, the required efforts for parameter estimation are frequently perceived as time-consuming and expensive. In order to speed-up this work, a new parameter estimation approach for modelling ion-exchange chromatography in linear conditions was developed. It aims at reducing the time and protein demand for the model calibration. The method combines the estimation of kinetic and thermodynamic parameters based on the simultaneous variation of the gradient slope and the residence time in a set of five linear gradient elutions. The parameters are estimated from a Yamamoto plot and a gradient-adjusted Van Deemter plot. The combined approach increases the information extracted per experiment compared to the individual methods. As a proof of concept, the combined approach was successfully applied for a monoclonal antibody on a cation-exchanger and for a Fc-fusion protein on an anion-exchange resin. The individual parameter estimations for the mAb confirmed that the new approach maintained the accuracy of the usual Yamamoto and Van Deemter plots. In the second case, offline size-exclusion chromatography was performed in order to estimate the thermodynamic parameters of an impurity (high molecular weight species) simultaneously with the main product. Finally, the parameters obtained from the combined approach were used in a lumped kinetic model to simulate the chromatography runs. The simulated chromatograms obtained for a wide range of gradient lengths and residence times showed only small deviations compared to the experimental data. Copyright © 2015 Elsevier B.V. All rights reserved.

Urea-temperature phase diagrams capture the thermodynamics of denatured state expansion that accompany protein unfolding.

PubMed

Tischer, Alexander; Auton, Matthew

2013-09-01

We have analyzed the thermodynamic properties of the von Willebrand factor (VWF) A3 domain using urea-induced unfolding at variable temperature and thermal unfolding at variable urea concentrations to generate a phase diagram that quantitatively describes the equilibrium between native and denatured states. From this analysis, we were able to determine consistent thermodynamic parameters with various spectroscopic and calorimetric methods that define the urea-temperature parameter plane from cold denaturation to heat denaturation. Urea and thermal denaturation are experimentally reversible and independent of the thermal scan rate indicating that all transitions are at equilibrium and the van't Hoff and calorimetric enthalpies obtained from analysis of individual thermal transitions are equivalent demonstrating two-state character. Global analysis of the urea-temperature phase diagram results in a significantly higher enthalpy of unfolding than obtained from analysis of individual thermal transitions and significant cross correlations describing the urea dependence of ΔH0 and ΔCP0 that define a complex temperature dependence of the m-value. Circular dichroism (CD) spectroscopy illustrates a large increase in secondary structure content of the urea-denatured state as temperature increases and a loss of secondary structure in the thermally denatured state upon addition of urea. These structural changes in the denatured ensemble make up ∼40% of the total ellipticity change indicating a highly compact thermally denatured state. The difference between the thermodynamic parameters obtained from phase diagram analysis and those obtained from analysis of individual thermal transitions illustrates that phase diagrams capture both contributions to unfolding and denatured state expansion and by comparison are able to decipher these contributions. © 2013 The Protein Society.

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.

Nodal gap structure and order parameter symmetry of the unconventional superconductor UPt₃

DOE PAGES

Gannon, W. J.; Halperin, W. P.; Rastovski, C.; ...

2015-02-01

Spanning a broad range of physical systems, complex symmetry breaking is widely recognized as a hallmark of competing interactions. This is exemplified in superfluid ³He which has multiple thermodynamic phases with spin and orbital quantum numbers S = 1 and L = 1, that emerge on cooling from a nearly ferromagnetic Fermi liquid. The heavy fermion compound UPt₃ exhibits similar behavior clearly manifest in its multiple superconducting phases. However, consensus as to its order parameter symmetry has remained elusive. Our small angle neutron scattering measurements indicate a linear temperature dependence of the London penetration depth characteristic of nodal structure ofmore » the order parameter. Our theoretical analysis is consistent with assignment of its symmetry to an L = 3 odd parity state for which one of the three thermodynamic phases in non-zero magnetic field is chiral.« less

Nodal gap structure and order parameter symmetry of the unconventional superconductor UPt₃

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

Gannon, W. J.; Halperin, W. P.; Rastovski, C.

Spanning a broad range of physical systems, complex symmetry breaking is widely recognized as a hallmark of competing interactions. This is exemplified in superfluid ³He which has multiple thermodynamic phases with spin and orbital quantum numbers S = 1 and L = 1, that emerge on cooling from a nearly ferromagnetic Fermi liquid. The heavy fermion compound UPt₃ exhibits similar behavior clearly manifest in its multiple superconducting phases. However, consensus as to its order parameter symmetry has remained elusive. Our small angle neutron scattering measurements indicate a linear temperature dependence of the London penetration depth characteristic of nodal structure ofmore » the order parameter. Our theoretical analysis is consistent with assignment of its symmetry to an L = 3 odd parity state for which one of the three thermodynamic phases in non-zero magnetic field is chiral.« less

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.

Ab initio relaxation times and time-dependent Hamiltonians within the steepest-entropy-ascent quantum thermodynamic framework

NASA Astrophysics Data System (ADS)

Kim, Ilki; von Spakovsky, Michael R.

2017-08-01

Quantum systems driven by time-dependent Hamiltonians are considered here within the framework of steepest-entropy-ascent quantum thermodynamics (SEAQT) and used to study the thermodynamic characteristics of such systems. In doing so, a generalization of the SEAQT framework valid for all such systems is provided, leading to the development of an ab initio physically relevant expression for the intrarelaxation time, an important element of this framework and one that had as of yet not been uniquely determined as an integral part of the theory. The resulting expression for the relaxation time is valid as well for time-independent Hamiltonians as a special case and makes the description provided by the SEAQT framework more robust at the fundamental level. In addition, the SEAQT framework is used to help resolve a fundamental issue of thermodynamics in the quantum domain, namely, that concerning the unique definition of process-dependent work and heat functions. The developments presented lead to the conclusion that this framework is not just an alternative approach to thermodynamics in the quantum domain but instead one that uniquely sheds new light on various fundamental but as of yet not completely resolved questions of thermodynamics.

Fe-Ti oxide geothermometry: thermodynamic formulation and the estimation of intensive variables in silicic magmas

NASA Astrophysics Data System (ADS)

Ghiorso, Mark S.; Sack, O.

1991-10-01

A new thermodynamic formulation of the Fe-Ti oxide geothermometer/oxygen barometer is developed. The method is based upon recently calibrated models for spinel solid solutions in the quinary system (Fe2+, Mg)(Al,Fe3+,Cr)2O4-(Fe2+, Mg)2TiO4 by Sack and Ghiorso, and rhombohedral oxides in the quaternary system (Fe2+,Mg,Mn)TiO3-Fe2O3 (this paper). The formulation is internally consistent with thermodynamic models for (Fe2+,Mg)-olivine and -orthopyroxene solid solutions and end-member thermodynamic properties tabulated by Berman. The constituent expressions account for compositional and temperature dependent cation ordering and reproduce miscibility gap features in all of the component binaries. The calibration does not account for the excess Gibbs energy resulting from compositional and temperature dependent magnetic ordering in either phase. This limits application of the method to assemblages that equilibrated at temperatures above 600° C. Practical implementation of the proposed geothermometer/oxygen barometer requires minimal use of projection algorthms in accommodating compositions of naturally occurring phases. The new formulation is applied to the estimation of temperature and oxygen fugacity in a wide variety of intermediate to silicic volcanic rocks. In combination with previous work on olivine and orthopyroxene thermodynamics, equilibration pressures are computed for a subset of these volcanics that contain the assemblage quartz, oxides and either ferromagnesian silicate. The calculated log10 f O 2- T relations are reflected in coexisting ferromagnesian mineral assemblages. Volcanics with the lowest relative oxygen fugacity (Δlog10 f O 2) are characterized by the assemblage olivine-quartz, those with slightly higher Δ log10 f O 2 s, by the assemblage orthopyroxene-quartz. The sequence proceeds with the necessary phases biotite-feldspar, then hornblende-quartz-clinopyroxene, and finally at the highest Δ log10 f O 2 s, sphene-quartz-clinopyroxene. Quantitative analysis of these trends, utilizing thermodynamic data for the constituent phases, establishes that, in most cases, the T-log10 f O 2value computed from the oxides is consistent with the compositions of coexisting silicate phases, indicating that phenocryst equilibrium was achieved prior to eruption. There is, however, considerable evidence of oxide-silicate disequilibrium in samples collected from more slowly cooled domes and obsidians. In addition, T-log10 f O 2trends from volcanic rocks that contain biotite and orthopyroxene are interpreted to imply a condition of Fe2+-Mg exchange disequilibrium between orthopyroxene and coexisting ferromagnesian silicates and melt. It is suspected that many biotite-feldspar-quartz-orthopyroxene bearing low temperature volcanic rocks inherit orthopyroxene xenocrysts which crystallized earlier in the cooling history of the magma body.

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.

A temperature-dependent coarse-grained model for the thermoresponsive polymer poly(N-isopropylacrylamide)

DOE PAGES

Abbott, Lauren J.; Stevens, Mark J.

2015-12-22

In this study, a coarse-grained (CG) model is developed for the thermoresponsive polymer poly(N-isopropylacrylamide) (PNIPAM), using a hybrid top-down and bottom-up approach. Nonbonded parameters are fit to experimental thermodynamic data following the procedures of the SDK (Shinoda, DeVane, and Klein) CG force field, with minor adjustments to provide better agreement with radial distribution functions from atomistic simulations. Bonded parameters are fit to probability distributions from atomistic simulations using multi-centered Gaussian-based potentials. The temperature-dependent potentials derived for the PNIPAM CG model in this work properly capture the coil–globule transition of PNIPAM single chains and yield a chain-length dependence consistent with atomisticmore » simulations.« less

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.

Turbulence in Supercritical O2/H2 and C7H16/N2 Mixing Layers

NASA Technical Reports Server (NTRS)

Bellan, Josette; Harstad, Kenneth; Okong'o, Nora

2003-01-01

This report presents a study of numerical simulations of mixing layers developing between opposing flows of paired fluids under supercritical conditions, the purpose of the study being to elucidate chemical-species-specific aspects of turbulence. The simulations were performed for two different fluid pairs O2/H2 and C7H16/N2 at similar reduced initial pressures (reduced pressure is defined as pressure divided by critical pressure). Thermodynamically, O2/H2 behaves more nearly like an ideal mixture and has greater solubility, relative to C7H16/N2, which departs strongly from ideality. Because of a specified smaller initial density stratification, the C7H16/N2 layers exhibited greater levels of growth, global molecular mixing, and turbulence. However, smaller density gradients at the transitional state for the O2/H2 system were interpreted as indicating that locally, this system exhibits enhanced mixing as a consequence of its greater solubility and closer approach to ideality. These thermodynamic features were shown to affect entropy dissipation, which was found to be larger for O2/H2 and concentrated in high-density-gradient-magnitude regions that are distortions of the initial density-stratification boundary. In C7H16/N2, the regions of largest dissipation were found to lie in high-density-gradient-magnitude regions that result from mixing of the two fluids.

An inverse model for a free-boundary problem with a contact line: Steady case

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

Volkov, Oleg; Protas, Bartosz

2009-07-20

This paper reformulates the two-phase solidification problem (i.e., the Stefan problem) as an inverse problem in which a cost functional is minimized with respect to the position of the interface and subject to PDE constraints. An advantage of this formulation is that it allows for a thermodynamically consistent treatment of the interface conditions in the presence of a contact point involving a third phase. It is argued that such an approach in fact represents a closure model for the original system and some of its key properties are investigated. We describe an efficient iterative solution method for the Stefan problemmore » formulated in this way which uses shape differentiation and adjoint equations to determine the gradient of the cost functional. Performance of the proposed approach is illustrated with sample computations concerning 2D steady solidification phenomena.« less

Gyrokinetic Studies of Turbulence Reduction with Reverse Shear ETG Transport Barriers or Lithium Walls

NASA Astrophysics Data System (ADS)

Hammett, G. W.; Peterson, J. L.; Granstedt, E. M.; Bell, R.; Guttenfelder, W.; Kaye, S.; Leblanc, B.; Mikkelsen, D. R.; Smith, D. R.; Yuh, H. Y.; Candy, J.

2012-03-01

The National Spherical Torus Experiment (NSTX) can achieve high electron confinement regimes that are super-critically unstable to the electron temperature gradient (ETG) instability. These electron internal transport barriers (e-ITBs) occur when the magnetic shear becomes strongly negative. Using the gyrokinetic code GYRO, the first nonlinear ETG simulations of NSTX e-ITB plasmas demonstrate reduced turbulence consistent with this observation. This is qualitatively consistent with a secondary instability picture of reduced ETG turbulence at negative shear (Jenko and Dorland PRL 2002). Local simulations identify a strongly upshifted nonlinear critical gradient for thermal transport that depends on magnetic shear. Global simulations show that ETG-driven turbulence outside of the barrier is large enough to be experimentally relevant, but cannot propagate very far into the barrier. We also use GYRO to study turbulence in regimes that might be expected in the Lithium Torus eXperiment (LTX). While lithium has experimentally been shown to raise the edge temperature and improve performance, there can still be some turbulence from density-gradient-driven trapped electron modes, and a temperature pinch is found in some cases. (Supported by DOE.)

A molecular dynamics approach to barrodiffusion

NASA Astrophysics Data System (ADS)

Cooley, James; Marciante, Mathieu; Murillo, Michael

2016-10-01

Unexpected phenomena in the reaction rates for Inertial Confinement Fusion (ICF) capsules have led to a renewed interest in the thermo-dynamically driven diffusion process for the past 10 years, often described collectively as barodiffusion. In the current context, barodiffusion would manifest as a process that separates ions of differing mass and charge ratios due to pressure and temperature gradients set-up through shock structures in the capsule core. Barrodiffusion includes additional mass transfer terms that account for the irreversible transport of species due to gradients in the system, both thermodynamic and electric e.g, i = - ρD [ ∇c +kp ∇ln(pi) +kT(i) ∇ln(Ti) +kt(e) ∇ln(Te) +eke/Ti ∇ϕ ] . Several groups have attacked this phenomena using continuum scale models and supplemented with kinetic theory to derive coefficients for the different diffusion terms based on assumptions about the collisional processes. In contrast, we have applied a molecular dynamics (MD) simulation to this system to gain a first-principle understanding of the rate kinetics and to assess the accuracy of the differin

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.

Consistent free energy landscapes and thermodynamic properties of small proteins based on a single all-atom force field employing an implicit solvation.

PubMed

Kim, Eunae; Jang, Soonmin; Pak, Youngshang

2007-10-14

We have attempted to improve the PARAM99 force field in conjunction with the generalized Born (GB) solvation model with a surface area correction for more consistent protein folding simulations. For this purpose, using an extended alphabeta training set of five well-studied molecules with various folds (alpha, beta, and betabetaalpha), a previously modified version of PARAM99/GBSA is further refined, such that all native states of the five training species correspond to their lowest free energy minimum states. The resulting modified force field (PARAM99MOD5/GBSA) clearly produces reasonably acceptable conformational free energy surfaces of the training set with correct identifications of their native states in the free energy minimum states. Moreover, due to its well-balanced nature, this new force field is expected to describe secondary structure propensities of diverse folds in a more consistent manner. Remarkably, temperature dependent behaviors simulated with the current force field are in good agreement with the experiment. This agreement is a significant improvement over the existing standard all-atom force fields. In addition, fundamentally important thermodynamic quantities, such as folding enthalpy (DeltaH) and entropy (DeltaS), agree reasonably well with the experimental data.

Analysis of molecular mechanisms of ATP synthesis from the standpoint of the principle of electrical neutrality.

PubMed

Nath, Sunil

2017-05-01

Theories of biological energy coupling in oxidative phosphorylation (OX PHOS) and photophosphorylation (PHOTO PHOS) are reviewed and applied to ATP synthesis by an experimental system containing purified ATP synthase reconstituted into liposomes. The theories are critically evaluated from the standpoint of the principle of electrical neutrality. It is shown that the obligatory requirement to maintain overall electroneutrality of bulk aqueous phases imposes strong constraints on possible theories of energy coupling and molecular mechanisms of ATP synthesis. Mitchell's chemiosmotic theory is found to violate the electroneutrality of bulk aqueous phases and is shown to be untenable on these grounds. Purely electroneutral mechanisms or mechanisms where the anion/countercation gradient is dissipated or simply flows through the lipid bilayer are also shown to be inadequate. A dynamically electrogenic but overall electroneutral mode of ion transport postulated by Nath's torsional mechanism of energy transduction and ATP synthesis is shown to be consistent both with the experimental findings and the principle of electrical neutrality. It is concluded that the ATP synthase functions as a proton-dicarboxylic acid anion cotransporter in OX PHOS or PHOTO PHOS. A logical chemical explanation for the selection of dicarboxylic acids as intermediates in OX PHOS and PHOTO PHOS is suggested based on the pioneering classical thermodynamic work of Christensen, Izatt, and Hansen. The nonequilibrium thermodynamic consequences for theories in which the protons originate from water vis-a-vis weak organic acids are compared and contrasted, and several new mechanistic and thermodynamic insights into biological energy transduction by ATP synthase are offered. These considerations make the new theory of energy coupling more complete, and lead to a deeper understanding of the molecular mechanism of ATP synthesis. Copyright © 2017 Elsevier B.V. All rights reserved.

Spectral measurements of the cosmic microwave background

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

Kogut, A.J.

1989-04-01

Three experiments have measured the intensity of the Cosmic Microwave Background (CMB) at wavelengths 4.0, 3.0, and 0.21 cm. The measurement at 4.0 cm used a direct-gain total-power radiometer to measure the difference in power between the zenith sky and a large cryogenic reference target. Foreground signals are measured with the same instrument and subtracted from the zenith signal, leaving the CMB as the residual. The reference target consists of a large open-mouth cryostat with a microwave absorber submerged in liquid helium; thin windows block the radiative heat load and prevent condensation atmospheric gases within the cryostat. The thermodynamic temperaturemore » of the CMB at 4.0 cm is 2.59 +- 0.07 K. The measurement at 3.0 cm used a superheterodyne Dicke-switched radiometer with a similar reference target to measure the zenith sky temperature. A rotating mirror allowed one of the antenna beams to be redirected to a series of zenith angles, permitting automated atmospheric measurements without moving the radiometer. A weighted average of 5 years of data provided the thermodynamic temperature of the CMB at 3.0 cm of 2.62 +- 0.06 K. The measurement at 0.21 cm used Very Large Array observations of interstellar ortho-formaldehyde to determine the CMB intensity in molecular clouds toward the giant HII region W51A (G49.5-0.4). Solutions of the radiative transfer problem in the context of a large velocity gradient model provided estimates of the CMB temperature within the foreground clouds. Collisional excitation from neutral hydrogen molecules within the clouds limited the precision of the result. The thermodynamic temperature of the CMB at 0.21 cm is 3.2 +- 0.9 K. 72 refs., 27 figs., 38 tabs.« less

Thermodynamics of information processing based on enzyme kinetics: An exactly solvable model of an information pump.

PubMed

Cao, Yuansheng; Gong, Zongping; Quan, H T

2015-06-01

Motivated by the recent proposed models of the information engine [Proc. Natl. Acad. Sci. USA 109, 11641 (2012)] and the information refrigerator [Phys. Rev. Lett. 111, 030602 (2013)], we propose a minimal model of the information pump and the information eraser based on enzyme kinetics. This device can either pump molecules against the chemical potential gradient by consuming the information to be encoded in the bit stream or (partially) erase the information initially encoded in the bit stream by consuming the Gibbs free energy. The dynamics of this model is solved exactly, and the "phase diagram" of the operation regimes is determined. The efficiency and the power of the information machine is analyzed. The validity of the second law of thermodynamics within our model is clarified. Our model offers a simple paradigm for the investigating of the thermodynamics of information processing involving the chemical potential in small systems.

Murine intracochlear drug delivery: reducing concentration gradients within the cochlea.

PubMed

Borkholder, David A; Zhu, Xiaoxia; Hyatt, Brad T; Archilla, Alfredo S; Livingston, William J; Frisina, Robert D

2010-09-01

Direct delivery of compounds to the mammalian inner ear is most commonly achieved by absorption or direct injection through the round window membrane (RWM), or infusion through a basal turn cochleostomy. These methods provide direct access to cochlear structures, but with a strong basal-to-apical concentration gradient consistent with a diffusion-driven distribution. This gradient limits the efficacy of therapeutic approaches for apical structures, and puts constraints on practical therapeutic dose ranges. A surgical approach involving both a basal turn cochleostomy and a posterior semicircular canal canalostomy provides opportunities for facilitated perfusion of cochlear structures to reduce concentration gradients. Infusion of fixed volumes of artificial perilymph (AP) and sodium salicylate were used to evaluate two surgical approaches in the mouse: cochleostomy-only (CO), or cochleostomy-plus-canalostomy (C+C). Cochlear function was evaluated via closed-system distortion product otoacoustic emissions (DPOAE) threshold level measurements from 8 to 49 kHz. AP infusion confirmed no surgical impact to auditory function, while shifts in DPOAE thresholds were measured during infusion of salicylate and AP (washout). Frequency dependent shifts were compared for the CO and C+C approaches. Computer simulations modeling diffusion, volume flow, interscala transport, and clearance mechanisms provided estimates of drug concentration as a function of cochlear position. Simulated concentration profiles were compared to frequency-dependent shifts in measured auditory responses using a cochlear tonotopic map. The impact of flow rate on frequency dependent DPOAE threshold shifts was also evaluated for both surgical approaches. Both the C+C approach and a flow rate increase were found to provide enhanced response for lower frequencies, with evidence suggesting the C+C approach reduces concentration gradients within the cochlea. Copyright (c) 2010 Elsevier B.V. All rights reserved.

Murine Intracochlear Drug Delivery: Reducing Concentration Gradients within the Cochlea

PubMed Central

Borkholder, David A.; Zhu, Xiaoxia; Hyatt, Brad T.; Archilla, Alfredo S.; Livingston, William J.; Frisina, Robert D.

2010-01-01

Direct delivery of compounds to the mammalian inner ear is most commonly achieved by absorption or direct injection through the round window membrane (RWM), or infusion through a basal turn cochleostomy. These methods provide direct access to cochlear structures, but with a strong basal-to-apical concentration gradient consistent with a diffusion-driven distribution. This gradient limits the efficacy of therapeutic approaches for apical structures, and puts constraints on practical therapeutic dose ranges. A surgical approach involving both a basal turn cochleostomy and a posterior semicircular canal canalostomy provides opportunities for facilitated perfusion of cochlear structures to reduce concentration gradients. Infusion of fixed volumes of artificial perilymph (AP) and sodium salicylate were used to evaluate two surgical approaches in the mouse: cochleostomy-only (CO), or cochleostomy-plus-canalostomy (C+C). Cochlear function was evaluated via closed-system distortion product otoacoustic emissions (DPOAE) threshold level measurements from 8-49 kHz. AP infusion confirmed no surgical impact to auditory function, while shifts in DPOAE thresholds were measured during infusion of salicylate and AP (washout). Frequency dependent shifts were compared for the CO and C+C approaches. Computer simulations modeling diffusion, volume flow, interscala transport, and clearance mechanisms provided estimates of drug concentration as a function of cochlear position. Simulated concentration profiles were compared to frequency-dependent shifts in measured auditory responses using a cochlear tonotopic map. The impact of flow rate on frequency dependent DPOAE threshold shifts was also evaluated for both surgical approaches. Both the C+C approach and a flow rate increase were found to provide enhanced response for lower frequencies, with evidence suggesting the C+C approach reduces concentration gradients within the cochlea. PMID:20451593

Utilizing Ocean Thermal Energy in a Submarine Robot

NASA Technical Reports Server (NTRS)

Jones, Jack; Chao, Yi

2009-01-01

A proposed system would exploit the ocean thermal gradient for recharging the batteries in a battery-powered unmanned underwater vehicle [UUV (essentially, a small exploratory submarine robot)] of a type that has been deployed in large numbers in research pertaining to global warming. A UUV of this type travels between the ocean surface and depths, measuring temperature and salinity. The proposed system is related to, but not the same as, previously reported ocean thermal energy conversion (OTEC) systems that exploit the ocean thermal gradient but consist of stationary apparatuses that span large depth ranges. The system would include a turbine driven by working fluid subjected to a thermodynamic cycle. CO2 has been provisionally chosen as the working fluid because it has the requisite physical properties for use in the range of temperatures expected to be encountered in operation, is not flammable, and is much less toxic than are many other commercially available refrigerant fluids. The system would be housed in a pressurized central compartment in a UUV equipped with a double hull (see figure). The thermodynamic cycle would begin when the UUV was at maximum depth, where some of the CO2 would condense and be stored, at relatively low temperature and pressure, in the annular volume between the inner and outer hulls. The cycle would resume once the UUV had ascended to near the surface, where the ocean temperature is typically greater than or equals 20 C. At this temperature, the CO2 previously stored at depth in the annular volume between the inner and outer hulls would be pressurized to approx. equals 57 bar (5.7 MPa). The pressurized gaseous CO2 would flow through a check valve into a bladder inside the pressurized compartment, thereby storing energy of the relatively warm, pressurized CO2 for subsequent use after the next descent to maximum depth.

A facilitated diffusion model constrained by the probability isotherm: a pedagogical exercise in intuitive non-equilibrium thermodynamics.

PubMed

Chapman, Brian

2017-06-01

This paper seeks to develop a more thermodynamically sound pedagogy for students of biological transport than is currently available from either of the competing schools of linear non-equilibrium thermodynamics (LNET) or Michaelis-Menten kinetics (MMK). To this end, a minimal model of facilitated diffusion was constructed comprising four reversible steps: cis- substrate binding, cis → trans bound enzyme shuttling, trans -substrate dissociation and trans → cis free enzyme shuttling. All model parameters were subject to the second law constraint of the probability isotherm, which determined the unidirectional and net rates for each step and for the overall reaction through the law of mass action. Rapid equilibration scenarios require sensitive 'tuning' of the thermodynamic binding parameters to the equilibrium substrate concentration. All non-equilibrium scenarios show sigmoidal force-flux relations, with only a minority of cases having their quasi -linear portions close to equilibrium. Few cases fulfil the expectations of MMK relating reaction rates to enzyme saturation. This new approach illuminates and extends the concept of rate-limiting steps by focusing on the free energy dissipation associated with each reaction step and thereby deducing its respective relative chemical impedance. The crucial importance of an enzyme's being thermodynamically 'tuned' to its particular task, dependent on the cis- and trans- substrate concentrations with which it deals, is consistent with the occurrence of numerous isoforms for enzymes that transport a given substrate in physiologically different circumstances. This approach to kinetic modelling, being aligned with neither MMK nor LNET, is best described as intuitive non-equilibrium thermodynamics, and is recommended as a useful adjunct to the design and interpretation of experiments in biotransport.

A facilitated diffusion model constrained by the probability isotherm: a pedagogical exercise in intuitive non-equilibrium thermodynamics

PubMed Central

2017-01-01

This paper seeks to develop a more thermodynamically sound pedagogy for students of biological transport than is currently available from either of the competing schools of linear non-equilibrium thermodynamics (LNET) or Michaelis–Menten kinetics (MMK). To this end, a minimal model of facilitated diffusion was constructed comprising four reversible steps: cis-substrate binding, cis→trans bound enzyme shuttling, trans-substrate dissociation and trans→cis free enzyme shuttling. All model parameters were subject to the second law constraint of the probability isotherm, which determined the unidirectional and net rates for each step and for the overall reaction through the law of mass action. Rapid equilibration scenarios require sensitive ‘tuning’ of the thermodynamic binding parameters to the equilibrium substrate concentration. All non-equilibrium scenarios show sigmoidal force–flux relations, with only a minority of cases having their quasi-linear portions close to equilibrium. Few cases fulfil the expectations of MMK relating reaction rates to enzyme saturation. This new approach illuminates and extends the concept of rate-limiting steps by focusing on the free energy dissipation associated with each reaction step and thereby deducing its respective relative chemical impedance. The crucial importance of an enzyme's being thermodynamically ‘tuned’ to its particular task, dependent on the cis- and trans-substrate concentrations with which it deals, is consistent with the occurrence of numerous isoforms for enzymes that transport a given substrate in physiologically different circumstances. This approach to kinetic modelling, being aligned with neither MMK nor LNET, is best described as intuitive non-equilibrium thermodynamics, and is recommended as a useful adjunct to the design and interpretation of experiments in biotransport. PMID:28680687

The Transport of Salt and Water across Isolated Rat Ileum

PubMed Central

Clarkson, T. W.

1967-01-01

The flows of sodium, potassium, and chloride under electrical and chemical gradients and of salt and water in the presence of osmotic pressure gradients are described by phenomenological equations based on the thermodynamics of irreversible processes. The aim was to give the simplest possible description, that is to postulate the least number of active transport processes and the least number of separate pathways across the intestine. On this basis, the results were consistent with the following picture of the intestine: Two channels exist across this tissue, one allowing only passive transport of ions and the other only active. In the passive channel, the predominant resistance to ion flow is friction with the water in the channel. The electroosmotic flow indicates that the passive channel is lined with negative fixed charged groups having a surface charge density of 3000 esu cm-2. The values of the ion-water frictional coefficients, and the relationship between ionic concentrations and flows indicate that the passive channel is extracellular. The active channel behaves as two membranes in series, the first membrane being semipermeable but allowing active transport of sodium, and the second membrane being similar to the passive channel. Friction with the ions in the second "membrane" is the predominant resistance to water flow. PMID:11526854

A model for simulating random atmospheres as a function of latitude, season, and time

NASA Technical Reports Server (NTRS)

Campbell, J. W.

1977-01-01

An empirical stochastic computer model was developed with the capability of generating random thermodynamic profiles of the atmosphere below an altitude of 99 km which are characteristic of any given season, latitude, and time of day. Samples of temperature, density, and pressure profiles generated by the model are statistically similar to measured profiles in a data base of over 6000 rocket and high-altitude atmospheric soundings; that is, means and standard deviations of modeled profiles and their vertical gradients are in close agreement with data. Model-generated samples can be used for Monte Carlo simulations of aircraft or spacecraft trajectories to predict or account for the effects on a vehicle's performance of atmospheric variability. Other potential uses for the model are in simulating pollutant dispersion patterns, variations in sound propagation, and other phenomena which are dependent on atmospheric properties, and in developing data-reduction software for satellite monitoring systems.

Effect of entropy on anomalous transport in ITG-modes of magneto-plasma

NASA Astrophysics Data System (ADS)

Yaqub Khan, M.; Qaiser Manzoor, M.; Haq, A. ul; Iqbal, J.

2017-04-01

The ideal gas equation and S={{c}v}log ≤ft(P/ρ \\right) (where S is entropy, P is pressure and ρ is the mass density) define the interconnection of entropy with the temperature and density of plasma. Therefore, different phenomena relating to plasma and entropy need to be investigated. By employing the Braginskii transport equations for a nonuniform electron-ion magnetoplasma, two new parameters—the entropy distribution function and the entropy gradient drift—are defined, a new dispersion relation is obtained, and the dependence of anomalous transport on entropy is also proved. Some results, like monotonicity, the entropy principle and the second law of thermodynamics, are proved with a new definition of entropy. This work will open new horizons in fusion processes, not only by controlling entropy in tokamak plasmas—particularly in the pedestal regions of the H-mode and space plasmas—but also in engineering sciences.

Phase-space dependent critical gradient behavior of fast-ion transport due to Alfvén eigenmodes

DOE PAGES

Collins, C. S.; Heidbrink, W. W.; Podestà, M.; ...

2017-06-09

Experiments in the DIII-D tokamak show that many overlapping small-amplitude Alfv en eigenmodes (AEs) cause fast-ion transport to sharply increase above a critical threshold, leading to fast-ion density profile resilience and reduced fusion performance. The threshold is above the AE linear stability limit and varies between diagnostics that are sensitive to different parts of fast-ion phase-space. A comparison with theoretical analysis using the nova and orbit codes shows that, for the neutral particle diagnostic, the threshold corresponds to the onset of stochastic particle orbits due to wave-particle resonances with AEs in the measured region of phase space. We manipulated themore » bulk fast-ion distribution and instability behavior through variations in beam deposition geometry, and no significant differences in the onset threshold outside of measurement uncertainties were found, in agreement with the theoretical stochastic threshold analysis. Simulations using the `kick model' produce beam ion density gradients consistent with the empirically measured radial critical gradient and highlight the importance of including the energy and pitch dependence of the fast-ion distribution function in critical gradient models. The addition of electron cyclotron heating changes the types of AEs present in the experiment, comparatively increasing the measured fast-ion density and radial gradient. Our studies provide the basis for understanding how to avoid AE transport that can undesirably redistribute current and cause fast-ion losses, and the measurements are being used to validate AE-induced transport models that use the critical gradient paradigm, giving greater confidence when applied to ITER.« less

Phase-space dependent critical gradient behavior of fast-ion transport due to Alfvén eigenmodes

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

Collins, C. S.; Heidbrink, W. W.; Podestà, M.

Experiments in the DIII-D tokamak show that many overlapping small-amplitude Alfv en eigenmodes (AEs) cause fast-ion transport to sharply increase above a critical threshold, leading to fast-ion density profile resilience and reduced fusion performance. The threshold is above the AE linear stability limit and varies between diagnostics that are sensitive to different parts of fast-ion phase-space. A comparison with theoretical analysis using the nova and orbit codes shows that, for the neutral particle diagnostic, the threshold corresponds to the onset of stochastic particle orbits due to wave-particle resonances with AEs in the measured region of phase space. We manipulated themore » bulk fast-ion distribution and instability behavior through variations in beam deposition geometry, and no significant differences in the onset threshold outside of measurement uncertainties were found, in agreement with the theoretical stochastic threshold analysis. Simulations using the `kick model' produce beam ion density gradients consistent with the empirically measured radial critical gradient and highlight the importance of including the energy and pitch dependence of the fast-ion distribution function in critical gradient models. The addition of electron cyclotron heating changes the types of AEs present in the experiment, comparatively increasing the measured fast-ion density and radial gradient. Our studies provide the basis for understanding how to avoid AE transport that can undesirably redistribute current and cause fast-ion losses, and the measurements are being used to validate AE-induced transport models that use the critical gradient paradigm, giving greater confidence when applied to ITER.« less

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.

Depth-Profiling Electronic and Structural Properties of Cu(In,Ga)(S,Se)2 Thin-Film Solar Cell.

PubMed

Chiang, Ching-Yu; Hsiao, Sheng-Wei; Wu, Pin-Jiun; Yang, Chu-Shou; Chen, Chia-Hao; Chou, Wu-Ching

2016-09-14

Utilizing a scanning photoelectron microscope (SPEM) and grazing-incidence X-ray powder diffraction (GIXRD), we studied the electronic band structure and the crystalline properties of the pentanary Cu(In,Ga)(S,Se)2 (CIGSSe) thin-film solar cell as a function of sample depth on measuring the thickness-gradient sample. A novel approach is proposed for studying the depth-dependent information on thin films, which can provide a gradient thickness and a wide cross-section of the sample by polishing process. The results exhibit that the CIGSSe absorber layer possesses four distinct stoichiometries. The growth mechanism of this distinctive compositional distribution formed by a two-stage process is described according to the thermodynamic reaction and the manufacturing process. On the basis of the depth-profiling results, the gradient profiles of the conduction and valence bands were constructed to elucidate the performance of the electrical properties (in this case, Voc = 620 mV, Jsc = 34.6 mA/cm(2), and η = 14.04%); the valence-band maxima (VBM) measured with a SPEM in the spectroscopic mode coincide with this band-structure model, except for a lowering of the VBM observed in the surface region of the absorber layer due to the ordered defect compound (ODC). In addition, the depth-dependent texturing X-ray diffraction pattern presents the crystalline quality and the residual stress for each depth of a thin-film device. We find that the randomly oriented grains in the bottom region of the absorber layer and the different residual stress between the underlying Mo and the absorber interface, which can deteriorate the electrical performance due to peeling-off effect. An anion interstitial defect can be observed on comparing the anion concentration of the elemental distribution with crystalline composition; a few excess sulfur atoms insert in interstitial sites at the front side of the absorber layer, whereas the interstitial selenium atoms insert at the back side.

Effect of pressure variation on structural, elastic, mechanical, optoelectronic and thermodynamic properties of SrNaF3 fluoroperovskite

NASA Astrophysics Data System (ADS)

Erum, Nazia; Azhar Iqbal, Muhammad

2017-12-01

The effect of pressure variation on structural, electronic, elastic, mechanical, optical and thermodynamic characteristics of cubic SrNaF3 fluoroperovskite have been investigated by employing first-principles method within the framework of gradient approximation (GGA). For the total energy calculations, we have used the full-potential linearized augmented plane wave (FP-LAPW) method. Thermodynamic properties are computed in terms of quasi-harmonic Debye model. The pressure effects are determined in the range of 0-25 GPa, in which mechanical stability of SrNaF3 fluoroperovskite remains valid. A prominent decrease in lattice constant and bonds length is observed with the increase in pressure from 0 to 25 GPa. The effect of increase in pressure on band structure calculations with GGA and GGA plus Tran-Blaha modified Becke-Johnson (TB-mBJ) potential reveals a predominant characteristic associated with widening of bandgap. The influence of pressure on set of isotropic elastic parameters and their related properties are numerically estimated for SrNaF3 polycrystalline aggregate. Apart of linear dependence of elastic coefficients, transition from brittle to ductile behavior is observed as pressure is increased from 0 to 25 GPa. We have successfully obtained variation of lattice constant, volume expansion, bulk modulus, Debye temperature and specific heat capacities with pressure and temperature in the range of 0-25 GPa and 0-600 K. All the calculated optical properties such as the complex dielectric function ɛ(ω), optical conductivity σ(ω), energy loss function L(ω), absorption coefficient α(w), refractive index n(ω), reflectivity R(ω), and effective number of electrons n eff, via sum rules shift towards the higher energies under the application of pressure.

Modeling of soil nitrification responses to temperature reveals thermodynamic differences between ammonia-oxidizing activity of archaea and bacteria.

PubMed

Taylor, Anne E; Giguere, Andrew T; Zoebelein, Conor M; Myrold, David D; Bottomley, Peter J

2017-04-01

Soil nitrification potential (NP) activities of ammonia-oxidizing archaea and bacteria (AOA and AOB, respectively) were evaluated across a temperature gradient (4-42 °C) imposed upon eight soils from four different sites in Oregon and modeled with both the macromolecular rate theory and the square root growth models to quantify the thermodynamic responses. There were significant differences in response by the dominant AOA and AOB contributing to the NPs. The optimal temperatures (T opt ) for AOA- and AOB-supported NPs were significantly different (P<0.001), with AOA having T opt >12 °C greater than AOB. The change in heat capacity associated with the temperature dependence of nitrification (ΔC P ‡ ) was correlated with T opt across the eight soils, and the ΔC P ‡ of AOB activity was significantly more negative than that of AOA activity (P<0.01). Model results predicted, and confirmatory experiments showed, a significantly lower minimum temperature (T min ) and different, albeit very similar, maximum temperature (T max ) values for AOB than for AOA activity. The results also suggested that there may be different forms of AOA AMO that are active over different temperature ranges with different T min , but no evidence of multiple T min values within the AOB. Fundamental differences in temperature-influenced properties of nitrification driven by AOA and AOB provides support for the idea that the biochemical processes associated with NH 3 oxidation in AOA and AOB differ thermodynamically from each other, and that also might account for the difficulties encountered in attempting to model the response of nitrification to temperature change in soil environments.

Impact of clocking on the aero-thermodynamics of a second stator tested in a one and a half stage HP turbine

NASA Astrophysics Data System (ADS)

Billiard, N.; Paniagua, Guillermo; Dénos, R.

2008-06-01

This paper focuses on the experimental investigation of the time-averaged and time-accurate aero-thermodynamics of a second stator tested in a 1.5 stage high-pressure turbine. The effect of clocking on aerodynamic and heat transfer are investigated. Tests are performed under engine representative conditions in the VKI compression tube CT3. The test program includes four different clocking positions, i.e. relative pitch-wise positions between the first and the second stator. Probes located upstream and downstream of the second stator provide the thermodynamic conditions of the flow field. On the second stator airfoil, measurements are taken around the blade profile at 15, 50 and 85% span with pressure sensors and thin-film gauges. Both time-averaged and time-resolved aspects of the flow field are addressed. Regarding the time-averaged results, clocking effects are mainly observed within the leading edge region of the second stator, the largest effects being observed at 15% span. The surface static pressure distribution is changed locally, hence affecting the overall airfoil performance. For one clocking position, the thermal load of the airfoil is noticeably reduced. Pressure fluctuations are attributed to the passage of the upstream transonic rotor and its associated pressure gradients. The pattern of these fluctuations changes noticeably as a function of clocking. The time-resolved variations of heat flux and static pressure are analyzed together showing that the major effect is due to a potential interaction. The time-resolved pressure distribution integrated along the second stator surface yields the unsteady forces on the vane. The magnitude of the unsteady force is very dependent on the clocking position.

Modeling of soil nitrification responses to temperature reveals thermodynamic differences between ammonia-oxidizing activity of archaea and bacteria

PubMed Central

Taylor, Anne E; Giguere, Andrew T; Zoebelein, Conor M; Myrold, David D; Bottomley, Peter J

2017-01-01

Soil nitrification potential (NP) activities of ammonia-oxidizing archaea and bacteria (AOA and AOB, respectively) were evaluated across a temperature gradient (4–42 °C) imposed upon eight soils from four different sites in Oregon and modeled with both the macromolecular rate theory and the square root growth models to quantify the thermodynamic responses. There were significant differences in response by the dominant AOA and AOB contributing to the NPs. The optimal temperatures (Topt) for AOA- and AOB-supported NPs were significantly different (P<0.001), with AOA having Topt>12 °C greater than AOB. The change in heat capacity associated with the temperature dependence of nitrification (ΔCP‡) was correlated with Topt across the eight soils, and the ΔCP‡ of AOB activity was significantly more negative than that of AOA activity (P<0.01). Model results predicted, and confirmatory experiments showed, a significantly lower minimum temperature (Tmin) and different, albeit very similar, maximum temperature (Tmax) values for AOB than for AOA activity. The results also suggested that there may be different forms of AOA AMO that are active over different temperature ranges with different Tmin, but no evidence of multiple Tmin values within the AOB. Fundamental differences in temperature-influenced properties of nitrification driven by AOA and AOB provides support for the idea that the biochemical processes associated with NH3 oxidation in AOA and AOB differ thermodynamically from each other, and that also might account for the difficulties encountered in attempting to model the response of nitrification to temperature change in soil environments. PMID:27996979

Global convergence in leaf respiration from estimates of thermal acclimation across time and space.

PubMed

Vanderwel, Mark C; Slot, Martijn; Lichstein, Jeremy W; Reich, Peter B; Kattge, Jens; Atkin, Owen K; Bloomfield, Keith J; Tjoelker, Mark G; Kitajima, Kaoru

2015-09-01

Recent compilations of experimental and observational data have documented global temperature-dependent patterns of variation in leaf dark respiration (R), but it remains unclear whether local adjustments in respiration over time (through thermal acclimation) are consistent with the patterns in R found across geographical temperature gradients. We integrated results from two global empirical syntheses into a simple temperature-dependent respiration framework to compare the measured effects of respiration acclimation-over-time and variation-across-space to one another, and to a null model in which acclimation is ignored. Using these models, we projected the influence of thermal acclimation on: seasonal variation in R; spatial variation in mean annual R across a global temperature gradient; and future increases in R under climate change. The measured strength of acclimation-over-time produces differences in annual R across spatial temperature gradients that agree well with global variation-across-space. Our models further project that acclimation effects could potentially halve increases in R (compared with the null model) as the climate warms over the 21st Century. Convergence in global temperature-dependent patterns of R indicates that physiological adjustments arising from thermal acclimation are capable of explaining observed variation in leaf respiration at ambient growth temperatures across the globe. © 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.

Evaporation, diffusion and self-assembly at drying interfaces.

PubMed

Roger, K; Sparr, E; Wennerström, H

2018-04-18

Water evaporation from complex aqueous solutions leads to the build-up of structure and composition gradients at their interface with air. We recently introduced an experimental setup for quantitatively studying such gradients and discussed how structure formation can lead to a self-regulation mechanism for controlling water evaporation through self-assembly. Here, we provide a detailed theoretical analysis using an advection/diffusion transport equation that takes into account thermodynamically non-ideal conditions and we directly relate the theoretical description to quantitative experimental data. We derive that the concentration profile develops according to a general square root of time scaling law, which fully agrees with experimental observations. The evaporation rate notably decreases with time as t-1/2, which shows that diffusion in the liquid phase is the rate limiting step for this system, in contrast to pure water evaporation. For the particular binary system that was investigated experimentally, which is composed of water and a sugar-based surfactant (α-dodecylmaltoside), the interfacial layer consists in a sequence of liquid crystalline phases of different mesostructures. We extract values for mutual diffusion coefficients of lamellar, hexagonal and micellar cubic phases, which are consistent with previously reported values and simple models. We thus provide a method to estimate the transport properties of oriented mesophases. The macroscopic humidity-independence of the evaporation rate up to 85% relative humidities is shown to result from both an extremely low mutual diffusion coefficient and the large range of water activities corresponding to relative humidities below 85%, at which the lamellar phase exists. Such a humidity self-regulation mechanism is expected for a large variety of complex system.

Thermodynamics of micellization from heat-capacity measurements.

PubMed

Šarac, Bojan; Bešter-Rogač, Marija; Lah, Jurij

2014-06-23

Differential scanning calorimetry (DSC), the most important technique for studying the thermodynamics of structural transitions of biological macromolecules, is seldom used in quantitative thermodynamic studies of surfactant micellization/demicellization. The reason for this could be ascribed to an insufficient understanding of the temperature dependence of the heat capacity of surfactant solutions (DSC data) in terms of thermodynamics, which leads to problems with the design of experiments and interpretation of the output signals. We address these issues by careful design of DSC experiments performed with solutions of ionic and nonionic surfactants at various surfactant concentrations, and individual and global mass-action model analysis of the obtained DSC data. Our approach leads to reliable thermodynamic parameters of micellization for all types of surfactants, comparable with those obtained by using isothermal titration calorimetry (ITC). In summary, we demonstrate that DSC can be successfully used as an independent method to obtain temperature-dependent thermodynamic parameters for micellization. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Drastic difference between hole and electron injection through the gradient shell of CdxSeyZn1-xS1-y quantum dots.

PubMed

Abdellah, Mohamed; Poulsen, Felipe; Zhu, Qiushi; Zhu, Nan; Žídek, Karel; Chábera, Pavel; Corti, Annamaria; Hansen, Thorsten; Chi, Qijin; Canton, Sophie E; Zheng, Kaibo; Pullerits, Tõnu

2017-08-31

Ultrafast fluorescence spectroscopy was used to investigate the hole injection in Cd x Se y Zn 1-x S 1-y gradient core-shell quantum dot (CSQD) sensitized p-type NiO photocathodes. A series of CSQDs with a wide range of shell thicknesses was studied. Complementary photoelectrochemical cell measurements were carried out to confirm that the hole injection from the active core through the gradient shell to NiO takes place. The hole injection from the valence band of the QDs to NiO depends much less on the shell thickness when compared to the corresponding electron injection to n-type semiconductor (ZnO). We simulate the charge carrier tunneling through the potential barrier due to the gradient shell by numerically solving the Schrödinger equation. The details of the band alignment determining the potential barrier are obtained from X-ray spectroscopy measurements. The observed drastic differences between the hole and electron injection are consistent with a model where the hole effective mass decreases, while the gradient shell thickness increases.

Development and kinetic analysis of cobalt gradient formation in WC-Co composites

NASA Astrophysics Data System (ADS)

Guo, Jun

2011-12-01

Functionally graded cemented tungsten carbide (FG WC-Co) is one of the main research directions in the field of WC-Co over decades. Although it has long been recognized that FG WC-Co could outperform conventional homogeneous WC-Co owing to its potentially superior combinations of mechanical properties, until recently there has been a lack of effective and economical methods to make such materials. The lack of the technology has prevented the manufacturing and industrial applications of FG WC-Co from becoming a reality. This dissertation is a comprehensive study of an innovative atmosphere heat treatment process for producing FG WC-Co with a surface cobalt compositional gradient. The process exploited a triple phase field in W-C-Co phase diagram among three phases (solid WC, solid Co, and liquid Co) and the dependence of the migration of liquid Co on temperature and carbon content. WC-Co with a graded surface cobalt composition can be achieved by controlling the diffusion of carbon transported from atmosphere during sintering or during postsintering heat treatment. The feasibility of the process was validated by the successful preparations of FG WC-Co via both carburization and decarburization process following conventional liquid phase sintering. A study of the carburization process was undertaken to further understand and quantitatively modeled this process. The effects of key processing parameters (including heat treating temperature, atmosphere, and time) and key materials variables (involving Co content, WC grain size, and addition of grain growth inhibitors) on the formation of Co gradients were examined. Moreover, a carbon-diffusion controlled kinetic model was developed for simulating the formation of the gradient during the process. The parameters involved in this model were determined by thermodynamic calculations and regression-fit of simulation results with experimental data. In summary, this research first demonstrated the principle of the approach. Second, a model was developed to predict the gradients produced by the carbon-controlled atmosphere heat treatment process, which is useful for manufacturing WC-Co with designed gradients. FG WC-Co materials produced using this method are expected to exhibit superior performance in many applications and to have a profound impact on the manufacturing industries that use tungsten carbide tools.

Investigation of anisotropic thermal transport in cross-linked polymers

NASA Astrophysics Data System (ADS)

Simavilla, David Nieto

Thermal transport in lightly cross-linked polyisoprene and polybutadine subjected to uniaxial elongation is investigated experimentally. We employ two experimental techniques to assess the effect that deformation has on this class of materials. The first technique, which is based on Forced Rayleigh Scattering (FRS), allows us to measure the two independent components of the thermal diffusivity tensor as a function of deformation. These measurements along with independent measurements of the tensile stress and birefringence are used to evaluate the stress-thermal and stress-optic rules. The stress-thermal rule is found to be valid for the entire range of elongations applied. In contrast, the stress-optic rule fails for moderate to large stretch ratios. This suggests that the degree of anisotropy in thermal conductivity depends on both orientation and tension in polymer chain segments. The second technique, which is based on infrared thermography (IRT), allows us to measure anisotropy in thermal conductivity and strain induced changes in heat capacity. We validate this method measurements of anisotropic thermal conductivity by comparing them with those obtained using FRS. We find excellent agreement between the two techniques. Uncertainty in the infrared thermography method measurements is estimated to be about 2-5 %. The accuracy of the method and its potential application to non-transparent materials makes it a good alternative to extend current research on anisotropic thermal transport in polymeric materials. A second IRT application allows us to investigate the dependence of heat capacity on deformation. We find that heat capacity increases with stretch ratio in polyisoprene specimens under uniaxial extension. The deviation from the equilibrium value of heat capacity is consistent with an independent set of experiments comparing anisotropy in thermal diffusivity and conductivity employing FRS and IRT techniques. We identify finite extensibility and strain-induced crystallization as the possible causes explaining our observations and evaluate their contribution making use of classical rubber elasticity results. Finally, we study of the role of evaporation-induced thermal effects in the well-know phenomena of the tears of wine. We develop a transport model and support its predictions by experimentally measuring the temperature gradient present in wine and cognac films using IRT. Our results demonstrate that the Marangoni flow responsible for wine tears results from both composition and temperature gradients, whose relative contribution strongly depends on the thermodynamic properties of ethanol-water mixtures. The methods developed here can be used to obtain a deeper understanding of Marangoni flows, which are ubiquitous in nature and modern technology.

Protein diffusiophoresis and salt osmotic diffusion in aqueous solutions.

PubMed

Annunziata, Onofrio; Buzatu, Daniela; Albright, John G

2012-10-25

Diffusion of a solute can be induced by the concentration gradient of another solute in solution. This transport mechanism is known as cross-diffusion. We have investigated cross-diffusion in a ternary protein-salt-water system. Specifically, we measured the two cross-diffusion coefficients for the lysozyme-NaCl-water system at 25 °C and pH 4.5 as a function of protein and salt concentrations by Rayleigh interferometry. One cross-diffusion coefficient characterizes salt osmotic diffusion induced by a protein concentration gradient, and is related to protein-salt thermodynamic interactions as described by the theories of Donnan membrane equilibrium and protein preferential hydration. The other cross-diffusion coefficient characterizes protein diffusiophoresis induced by a salt concentration gradient, and is described as the difference between a preferential-interaction coefficient and a transport parameter. We first relate our experimental results to the protein net charge and the thermodynamic excess of water near the protein surface. We then extract the Stefan-Maxwell diffusion coefficient describing protein-salt interactions in water. We find that the value of this coefficient is negative, contrary to the friction interpretation of Stefan-Maxwell equations. This result is explained by considering protein hydration. Finally, protein diffusiophoresis is quantitatively examined by considering electrophoretic and hydration effects on protein migration and utilized to accurately estimate lysozyme electrophoretic mobility. To our knowledge, this is the first time that protein diffusiophoresis has been experimentally characterized and a protein-salt Stefan-Maxwell diffusion coefficient reported. This work represents a significant contribution for understanding and modeling the effect of concentration gradients in protein-salt aqueous systems relevant to diffusion-based mass-transfer technologies and transport in living systems.

Unexpectedly acidic nanoparticles formed in dimethylamine-ammonia-sulfuric-acid nucleation experiments at CLOUD

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

Lawler, Michael J.; Winkler, Paul M.; Kim, Jaeseok

New particle formation driven by acid–base chemistry was initiated in the CLOUD chamber at CERN by introducing atmospherically relevant levels of gas-phase sulfuric acid and dimethylamine (DMA). Ammonia was also present in the chamber as a gas-phase contaminant from earlier experiments. The composition of particles with volume median diameters (VMDs) as small as 10 nm was measured by the Thermal Desorption Chemical Ionization Mass Spectrometer (TDCIMS). Particulate ammonium-to-dimethylaminium ratios were higher than the gas-phase ammonia-to-DMA ratios, suggesting preferential uptake of ammonia over DMA for the collected 10–30 nm VMD particles. This behavior is not consistent with present nanoparticle physicochemical models,more » which predict a higher dimethylaminium fraction when NH 3 and DMA are present at similar gas-phase concentrations. Despite the presence in the gas phase of at least 100 times higher base concentrations than sulfuric acid, the recently formed particles always had measured base : acid ratios lower than 1 : 1. The lowest base fractions were found in particles below 15 nm VMD, with a strong size-dependent composition gradient. The reasons for the very acidic composition remain uncertain, but a plausible explanation is that the particles did not reach thermodynamic equilibrium with respect to the bases due to rapid heterogeneous conversion of SO 2 to sulfate. Furthermore, these results indicate that sulfuric acid does not require stabilization by ammonium or dimethylaminium as acid–base pairs in particles as small as 10 nm.« less

Unexpectedly acidic nanoparticles formed in dimethylamine-ammonia-sulfuric-acid nucleation experiments at CLOUD

DOE PAGES

Lawler, Michael J.; Winkler, Paul M.; Kim, Jaeseok; ...

2016-11-03

New particle formation driven by acid–base chemistry was initiated in the CLOUD chamber at CERN by introducing atmospherically relevant levels of gas-phase sulfuric acid and dimethylamine (DMA). Ammonia was also present in the chamber as a gas-phase contaminant from earlier experiments. The composition of particles with volume median diameters (VMDs) as small as 10 nm was measured by the Thermal Desorption Chemical Ionization Mass Spectrometer (TDCIMS). Particulate ammonium-to-dimethylaminium ratios were higher than the gas-phase ammonia-to-DMA ratios, suggesting preferential uptake of ammonia over DMA for the collected 10–30 nm VMD particles. This behavior is not consistent with present nanoparticle physicochemical models,more » which predict a higher dimethylaminium fraction when NH 3 and DMA are present at similar gas-phase concentrations. Despite the presence in the gas phase of at least 100 times higher base concentrations than sulfuric acid, the recently formed particles always had measured base : acid ratios lower than 1 : 1. The lowest base fractions were found in particles below 15 nm VMD, with a strong size-dependent composition gradient. The reasons for the very acidic composition remain uncertain, but a plausible explanation is that the particles did not reach thermodynamic equilibrium with respect to the bases due to rapid heterogeneous conversion of SO 2 to sulfate. Furthermore, these results indicate that sulfuric acid does not require stabilization by ammonium or dimethylaminium as acid–base pairs in particles as small as 10 nm.« less

Thermospheric neutral density estimates from heater-induced ion up-flow at EISCAT

NASA Astrophysics Data System (ADS)

Kosch, Michael; Ogawa, Yasunobu; Yamazaki, Yosuke; Vickers, Hannah; Blagoveshchenskaya, Nataly

We exploit a recently-developed technique to estimate the upper thermospheric neutral density using measurements of ionospheric plasma parameters made by the EISCAT UHF radar during ionospheric modification experiments. Heating the electrons changes the balance between upward plasma pressure gradient and downward gravity, resulting in ion up-flow up to ~200 m/s. This field-aligned flow is retarded by collisions, which is directly related to the neutral density. Whilst the ion up-flow is consistent with the plasma pressure gradient, the estimated thermospheric neutral density depends on the assumed composition, which varies with altitude. Results in the topside ionosphere are presented.

A benchmark study of electronic excitation energies, transition moments, and excited-state energy gradients on the nicotine molecule

NASA Astrophysics Data System (ADS)

Egidi, Franco; Segado, Mireia; Koch, Henrik; Cappelli, Chiara; Barone, Vincenzo

2014-12-01

In this work, we report a comparative study of computed excitation energies, oscillator strengths, and excited-state energy gradients of (S)-nicotine, chosen as a test case, using multireference methods, coupled cluster singles and doubles, and methods based on time-dependent density functional theory. This system was chosen because its apparent simplicity hides a complex electronic structure, as several different types of valence excitations are possible, including n-π*, π-π*, and charge-transfer states, and in order to simulate its spectrum it is necessary to describe all of them consistently well by the chosen method.

A benchmark study of electronic excitation energies, transition moments, and excited-state energy gradients on the nicotine molecule

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

Egidi, Franco, E-mail: franco.egidi@sns.it; Segado, Mireia; Barone, Vincenzo, E-mail: vincenzo.barone@sns.it

In this work, we report a comparative study of computed excitation energies, oscillator strengths, and excited-state energy gradients of (S)-nicotine, chosen as a test case, using multireference methods, coupled cluster singles and doubles, and methods based on time-dependent density functional theory. This system was chosen because its apparent simplicity hides a complex electronic structure, as several different types of valence excitations are possible, including n-π{sup *}, π-π{sup *}, and charge-transfer states, and in order to simulate its spectrum it is necessary to describe all of them consistently well by the chosen method.

Temperature anomalies of shock and isentropic waves of quark-hadron phase transition

NASA Astrophysics Data System (ADS)

Konyukhov, A. V.; Iosilevskiy, I. L.; Levashov, P. R.; Likhachev, A. P.

2018-01-01

In this work, we consider a phenomenological equation of state, which combinesstatistical description for hadron gas and a bag-model-based approach for the quark-gluon plasma. The equation of state is based on the excluded volume method in its thermodynamically consistent variant from Satarov et al [2009 Phys. At. Nucl. 72 1390]. The characteristic shape of the Taub adiabats and isentropes in the phase diagram is affected by the anomalous pressure-temperature dependence along the curve of phase equilibrium. The adiabats have kink points at the boundary of the two-phase region, inside which the temperature decreases with compression. Thermodynamic properties of matter observed in the quark-hadron phase transition region lead to hydrodynamic anomalies (in particular, to the appearance of composite compression and rarefaction waves). On the basis of relativistic hydrodynamics equations we investigate and discuss the structure and anomalous temperature behavior in these waves.

Dyonic AdS black holes in maximal gauged supergravity

NASA Astrophysics Data System (ADS)

Chow, David D. K.; Compère, Geoffrey

2014-03-01

We present two new classes of dyonic anti-de Sitter black hole solutions of four-dimensional maximal N =8, SO(8) gauged supergravity. They are (1) static black holes of N=2, U(1)4 gauged supergravity with four electric and four magnetic charges, with spherical, planar or hyperbolic horizons; and (2) rotating black holes of N =2, U(1)2 gauged supergravity with two electric and two magnetic charges. We study their thermodynamics, and point out that the formulation of a consistent thermodynamics for dyonic anti-de Sitter black holes is dependent on the existence of boundary conditions for the gauge fields. We identify several distinct classes of boundary conditions for gauge fields in U(1)4 supergravity. We study a general family of metrics containing the rotating solutions, and find Killing-Yano tensors with torsion in two conformal frames, which underlie separability.

Communication: Mechanochemical fluctuation theorem and thermodynamics of self-phoretic motors

NASA Astrophysics Data System (ADS)

Gaspard, Pierre; Kapral, Raymond

2017-12-01

Microscopic dynamical aspects of the propulsion of nanomotors by self-phoretic mechanisms are considered. Propulsion by self-diffusiophoresis relies on the mechanochemical coupling between the fluid velocity field and the concentration fields induced by asymmetric catalytic reactions on the motor surface. The consistency between the thermodynamics of this coupling and the microscopic reversibility of the underlying molecular dynamics is investigated. For this purpose, a mechanochemical fluctuation theorem for the joint probability to find the motor at position r after n reactive events have occurred during the time interval t is derived, starting from coupled Langevin equations for the translational, rotational, and chemical fluctuations of self-phoretic motors. An important result that follows from this analysis is the identification of an effect that is reciprocal to self-propulsion by diffusiophoresis, which leads to a dependence of the reaction rate on the value of an externally applied force.

Evaluating the accuracy of SHAPE-directed RNA secondary structure predictions

PubMed Central

Sükösd, Zsuzsanna; Swenson, M. Shel; Kjems, Jørgen; Heitsch, Christine E.

2013-01-01

Recent advances in RNA structure determination include using data from high-throughput probing experiments to improve thermodynamic prediction accuracy. We evaluate the extent and nature of improvements in data-directed predictions for a diverse set of 16S/18S ribosomal sequences using a stochastic model of experimental SHAPE data. The average accuracy for 1000 data-directed predictions always improves over the original minimum free energy (MFE) structure. However, the amount of improvement varies with the sequence, exhibiting a correlation with MFE accuracy. Further analysis of this correlation shows that accurate MFE base pairs are typically preserved in a data-directed prediction, whereas inaccurate ones are not. Thus, the positive predictive value of common base pairs is consistently higher than the directed prediction accuracy. Finally, we confirm sequence dependencies in the directability of thermodynamic predictions and investigate the potential for greater accuracy improvements in the worst performing test sequence. PMID:23325843

Idealized modeling of convective organization with changing sea surface temperatures using multiple equilibria in weak temperature gradient simulations

NASA Astrophysics Data System (ADS)

Sentić, Stipo; Sessions, Sharon L.

2017-06-01

The weak temperature gradient (WTG) approximation is a method of parameterizing the influences of the large scale on local convection in limited domain simulations. WTG simulations exhibit multiple equilibria in precipitation; depending on the initial moisture content, simulations can precipitate or remain dry for otherwise identical boundary conditions. We use a hypothesized analogy between multiple equilibria in precipitation in WTG simulations, and dry and moist regions of organized convection to study tropical convective organization. We find that the range of wind speeds that support multiple equilibria depends on sea surface temperature (SST). Compared to the present SST, low SSTs support a narrower range of multiple equilibria at higher wind speeds. In contrast, high SSTs exhibit a narrower range of multiple equilibria at low wind speeds. This suggests that at high SSTs, organized convection might occur with lower surface forcing. To characterize convection at different SSTs, we analyze the change in relationships between precipitation rate, atmospheric stability, moisture content, and the large-scale transport of moist entropy and moisture with increasing SSTs. We find an increase in large-scale export of moisture and moist entropy from dry simulations with increasing SST, which is consistent with a strengthening of the up-gradient transport of moisture from dry regions to moist regions in organized convection. Furthermore, the changes in diagnostic relationships with SST are consistent with more intense convection in precipitating regions of organized convection for higher SSTs.

Thermodynamics and folding pathway of tetraloop receptor-mediated RNA helical packing

PubMed Central

Vander Meulen, Kirk A.; Davis, Jared H.; Foster, Trenton R.; Record, M. Thomas; Butcher, Samuel E.

2008-01-01

Summary Little is known about the thermodynamic forces that drive the folding pathways of higher order RNA structure. In this study, we employ calorimetric (ITC and DSC) and spectroscopic (NMR and UV) methods to characterize the thermodynamics of the GAAA tetraloop – receptor interaction, utilizing a previously described bivalent construct. ITC studies indicate that the bivalent interaction is enthalpy-driven and highly stable, with a binding constant (Kobs) of 5.5 × 106 M−1 and enthalpy (ΔHobs°) of −33.8 kcal/mol at 45°C in 20 mM KCl and 2 mM MgCl2. Thus we derive the ΔHobs° for a single tetraloop-receptor interaction to be −16.9 kcal/mol at these conditions. UV absorbance data indicate that an increase in base stacking quality contributes to the enthalpy of complex formation. These highly favorable thermodynamics are consistent with the known critical role for the tetraloop-receptor motif in the folding of large RNAs. Additionally, a significant heat capacity change (ΔCp,obs°) of −0.24 kcal·mol−1·K−1 was determined by ITC. DSC and UV monitored thermal denaturation experiments indicate that the bivalent tetraloop-receptor construct follows a minimally 5–state unfolding pathway, and suggest the observed ΔCp,obs° for the interaction results from a temperature-dependent unbound receptor RNA structure. PMID:18845162

A thermodynamic framework for the study of crystallization in polymers

NASA Astrophysics Data System (ADS)

Rao, I. J.; Rajagopal, K. R.

In this paper, we present a new thermodynamic framework within the context of continuum mechanics, to predict the behavior of crystallizing polymers. The constitutive models that are developed within this thermodynamic setting are able to describe the main features of the crystallization process. The model is capable of capturing the transition from a fluid like behavior to a solid like behavior in a rational manner without appealing to any adhoc transition criterion. The anisotropy of the crystalline phase is built into the model and the specific anisotropy of the crystalline phase depends on the deformation in the melt. These features are incorporated into a recent framework that associates different natural configurations and material symmetries with distinct microstructural features within the body that arise during the process under consideration. Specific models are generated by choosing particular forms for the internal energy, entropy and the rate of dissipation. Equations governing the evolution of the natural configurations and the rate of crystallization are obtained by maximizing the rate of dissipation, subject to appropriate constraints. The initiation criterion, marking the onset of crystallization, arises naturally in this setting in terms of the thermodynamic functions. The model generated within such a framework is used to simulate bi-axial extension of a polymer film that is undergoing crystallization. The predictions of the theory that has been proposed are consistent with the experimental results (see [28] and [7]).

Why do high-redshift galaxies show diverse gas-phase metallicity gradients?

NASA Astrophysics Data System (ADS)

Ma, Xiangcheng; Hopkins, Philip F.; Feldmann, Robert; Torrey, Paul; Faucher-Giguère, Claude-André; Kereš, Dušan

2017-04-01

Recent spatially resolved observations of galaxies at z ˜ 0.6-3 reveal that high-redshift galaxies show complex kinematics and a broad distribution of gas-phase metallicity gradients. To understand these results, we use a suite of high-resolution cosmological zoom-in simulations from the Feedback in Realistic Environments project, which include physically motivated models of the multiphase interstellar medium, star formation and stellar feedback. Our simulations reproduce the observed diversity of kinematic properties and metallicity gradients, broadly consistent with observations at z ˜ 0-3. Strong negative metallicity gradients only appear in galaxies with a rotating disc, but not all rotationally supported galaxies have significant gradients. Strongly perturbed galaxies with little rotation always have flat gradients. The kinematic properties and metallicity gradient of a high-redshift galaxy can vary significantly on short time-scales, associated with starburst episodes. Feedback from a starburst can destroy the gas disc, drive strong outflows and flatten a pre-existing negative metallicity gradient. The time variability of a single galaxy is statistically similar to the entire simulated sample, indicating that the observed metallicity gradients in high-redshift galaxies reflect the instantaneous state of the galaxy rather than the accretion and growth history on cosmological time-scales. We find weak dependence of metallicity gradient on stellar mass and specific star formation rate (sSFR). Low-mass galaxies and galaxies with high sSFR tend to have flat gradients, likely due to the fact that feedback is more efficient in these galaxies. We argue that it is important to resolve feedback on small scales in order to produce the diverse metallicity gradients observed.

Comparison of Optimal Thermodynamic Models of the Tricarboxylic Acid Cycle from Heterotrophs, Cyanobacteria, and Green Sulfur Bacteria.

PubMed

Thomas, Dennis G; Jaramillo-Riveri, Sebastian; Baxter, Douglas J; Cannon, William R

2014-12-26

We have applied a new stochastic simulation approach to predict the metabolite levels, material flux, and thermodynamic profiles of the oxidative TCA cycles found in E. coli and Synechococcus sp. PCC 7002, and in the reductive TCA cycle typical of chemolithoautotrophs and phototrophic green sulfur bacteria such as Chlorobaculum tepidum. The simulation approach is based on modeling states using statistical thermodynamics and employs an assumption similar to that used in transition state theory. The ability to evaluate the thermodynamics of metabolic pathways allows one to understand the relationship between coupling of energy and material gradients in the environment and the self-organization of stable biological systems, and it is shown that each cycle operates in the direction expected due to its environmental niche. The simulations predict changes in metabolite levels and flux in response to changes in cofactor concentrations that would be hard to predict without an elaborate model based on the law of mass action. In fact, we show that a thermodynamically unfavorable reaction can still have flux in the forward direction when it is part of a reaction network. The ability to predict metabolite levels, energy flow, and material flux should be significant for understanding the dynamics of natural systems and for understanding principles for engineering organisms for production of specialty chemicals.

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.

Thermal fluctuations of dilaton black holes in gravity's rainbow

NASA Astrophysics Data System (ADS)

Dehghani, M.

2018-06-01

In this work, thermodynamics and phase transition of some new dilaton black hole solutions have been explored in the presence of the rainbow functions. By introducing an energy dependent space time, the dilaton potential has been obtained as the linear combination of two Liouville-type potentials and three new classes of black hole solutions have been constructed. The conserved and thermodynamic quantities of the new dilaton black holes have been calculated in the energy dependent space times. It has been shown that, even if some of the thermodynamic quantities are affected by the rainbow functions, the thermodynamical first law still remains valid. Also, the impacts of rainbow functions on the stability or phase transition of the new black hole solutions have been investigated. Finally, the quantum gravitational effects on the thermodynamics and phase transition of the solutions have been studied through consideration of the thermal fluctuations.

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.

Anisotropy and temperature dependence of structural, thermodynamic, and elastic properties of crystalline cellulose Iβ: a first-principles investigation

Treesearch

ShunLi Shang; Louis G. Hector Jr.; Paul Saxe; Zi-Kui Liu; Robert J. Moon; Pablo D. Zavattieri

2014-01-01

Anisotropy and temperature dependence of structural, thermodynamic and elastic properties of crystalline cellulose Iβ were computed with first-principles density functional theory (DFT) and a semi-empirical correction for van der Waals interactions. Specifically, we report the computed temperature variation (up to 500...

The Evolution of Metallicity and Metallicity Gradients from z = 2.7 to 0.6 with KMOS3D

NASA Astrophysics Data System (ADS)

Wuyts, Eva; Wisnioski, Emily; Fossati, Matteo; Förster Schreiber, Natascha M.; Genzel, Reinhard; Davies, Ric; Mendel, J. Trevor; Naab, Thorsten; Röttgers, Bernhard; Wilman, David J.; Wuyts, Stijn; Bandara, Kaushala; Beifiori, Alessandra; Belli, Sirio; Bender, Ralf; Brammer, Gabriel B.; Burkert, Andreas; Chan, Jeffrey; Galametz, Audrey; Kulkarni, Sandesh K.; Lang, Philipp; Lutz, Dieter; Momcheva, Ivelina G.; Nelson, Erica J.; Rosario, David; Saglia, Roberto P.; Seitz, Stella; Tacconi, Linda J.; Tadaki, Ken-ichi; Übler, Hannah; van Dokkum, Pieter

2016-08-01

We present measurements of the [N II]/Hα ratio as a probe of gas-phase oxygen abundance for a sample of 419 star-forming galaxies at z = 0.6-2.7 from the KMOS3D near-IR multi-integral field unit (IFU) survey. The mass-metallicity relation (MZR) is determined consistently with the same sample selection, metallicity tracer, and methodology over the wide redshift range probed by the survey. We find good agreement with long-slit surveys in the literature, except for the low-mass slope of the relation at z˜ 2.3, where this sample is less biased than previous samples based on optical spectroscopic redshifts. In this regime we measure a steeper slope than some literature results. Excluding the contribution from active galactic nuclei from the MZR reduces sensitivity at the high-mass end, but produces otherwise consistent results. There is no significant dependence of the [N II]/Hα ratio on star formation rate at fixed redshift and stellar mass. The IFU data allow spatially resolved measurements of [N II]/Hα, from which we can infer abundance gradients for 180 galaxies, thus tripling the current sample in the literature. The observed gradients are on average flat, with only 15 gradients statistically offset from zero at \\gt 3σ . We have modeled the effect of beam smearing, assuming a smooth intrinsic radial gradient and known seeing, inclination, and effective radius for each galaxy. Our seeing-limited observations can recover up to 70% of the intrinsic gradient for the largest, face-on disks, but only 30% for the smaller, more inclined galaxies. We do not find significant trends between observed or corrected gradients and any stellar population, dynamical, or structural galaxy parameters, mostly in agreement with existing studies with much smaller sample sizes. In cosmological simulations, strong feedback is generally required to produce flat gradients at high redshift.

Nonlocal thermoelectric effects and nonlocal Onsager relations in a three-terminal proximity-coupled superconductor-ferromagnet device.

PubMed

Machon, P; Eschrig, M; Belzig, W

2013-01-25

We study thermal and charge transport in a three-terminal setup consisting of one superconducting and two ferromagnetic contacts. We predict that the simultaneous presence of spin filtering and of spin-dependent scattering phase shifts at each of the two interfaces will lead to very large nonlocal thermoelectric effects both in clean and in disordered systems. The symmetries of thermal and electric transport coefficients are related to fundamental thermodynamic principles by the Onsager reciprocity. Our results show that a nonlocal version of the Onsager relations for thermoelectric currents holds in a three-terminal quantum coherent ferromagnet-superconductor heterostructure including a spin-dependent crossed Andreev reflection and coherent electron transfer processes.

Development of a thermodynamic model for a cold cycle 3He-4He dilution refrigerator

NASA Astrophysics Data System (ADS)

Mueller, B. W.; Miller, F. K.

2016-10-01

A thermodynamic model of a 3He-4He cold cycle dilution refrigerator with no actively-driven mechanical components is developed and investigated. The refrigerator employs a reversible superfluid magnetic pump, passive check valves, a phase separation chamber, and a series of recuperative heat exchangers to continuously circulate 3He-4He and maintain a 3He concentration gradient across the mixing chamber. The model predicts cooling power and mixing chamber temperature for a range of design and operating parameters, allowing an evaluation of feasibility for potential 3He-4He cold cycle dilution refrigerator prototype designs. Model simulations for a prototype refrigerator design are presented.

3D theory of a high-gain free-electron laser based on a transverse gradient undulator

NASA Astrophysics Data System (ADS)

Baxevanis, Panagiotis; Ding, Yuantao; Huang, Zhirong; Ruth, Ronald

2014-02-01

The performance of a free-electron laser (FEL) depends significantly on the various parameters of the driving electron beam. In particular, a large energy spread in the beam results in a substantial reduction of the FEL gain, an effect which is especially relevant when one considers FELs driven by plasma accelerators or ultimate storage rings. For such cases, one possible solution is to use a transverse gradient undulator (TGU). In this concept, the energy spread problem is mitigated by properly dispersing the electron beam and introducing a linear, transverse field dependence in the undulator. This paper presents a self-consistent theoretical analysis of a TGU-based, high-gain FEL which takes into account three-dimensional (3D) effects, including beam size variations along the undulator. The results of our theory compare favorably with simulation and are used in fast optimization studies of various x-ray FEL configurations.

The conversion process of hydrocarbon hydrates into CO2 hydrates and vice versa: thermodynamic considerations.

PubMed

Schicks, J M; Luzi, M; Beeskow-Strauch, B

2011-11-24

Microscopy, confocal Raman spectroscopy and powder X-ray diffraction (PXRD) were used for in situ investigations of the CO(2)-hydrocarbon exchange process in gas hydrates and its driving forces. The study comprises the exposure of simple structure I CH(4) hydrate and mixed structure II CH(4)-C(2)H(6) and CH(4)-C(3)H(8) hydrates to gaseous CO(2) as well as the reverse reaction, i.e., the conversion of CO(2)-rich structure I hydrate into structure II mixed hydrate. In the case of CH(4)-C(3)H(8) hydrates, a conversion in the presence of gaseous CO(2) from a supposedly more stable structure II hydrate to a less stable structure I CO(2)-rich hydrate was observed. PXRD data show that the reverse process requires longer initiation times, and structural changes seem to be less complete. Generally, the exchange process can be described as a decomposition and reformation process, in terms of a rearrangement of molecules, and is primarily induced by the chemical potential gradient between hydrate phase and the provided gas phase. The results show furthermore the dependency of the conversion rate on the surface area of the hydrate phase, the thermodynamic stability of the original and resulting hydrate phase, as well as the mobility of guest molecules and formation kinetics of the resulting hydrate phase.

Leo Szilard In Physics and Information

NASA Astrophysics Data System (ADS)

Garwin, Richard

2014-03-01

The excellent biography by William Lanouette, ``Genius in the Shadows,'' tells it the way it was, incredible though it may seem. The 1972 ``Collected Works of Leo Szilard: Scientific Papers'' Bernard T. Feld and Getrude W. Szilard, Editors, gives the source material both published and unpublished. Szilard's path-breaking but initially little-noticed 1929 paper, ``On the Decrease of Entropy in a Thermodynamic System by the Intervention of Intelligent Beings'' spawned much subsequent research. It connected what we now call a bit of information with a quantity k ln 2 of entropy, and showed that the process of acquiring, exploiting, and resetting this information in a one-molecule engine must dissipate at least kT ln 2 of energy at temperature T. His 1925 paper, ``On the Extension of Phenomenological Thermodynamics to Fluctuation Phenomena,'' showed that fluctuations were consistent with and predicted from equilibrium thermodynamics and did not depend on atomistic theories. His work on physics and technology, demonstrated an astonishing range of interest, ingenuity, foresight, and practical sense. I illustrate this with several of his fundamental contributions nuclear physics, to the neutron chain reaction and to nuclear reactors, and also to electromagnetic pumping of liquid metals.

Analysis of the statistical thermodynamic model for nonlinear binary protein adsorption equilibria.

PubMed

Zhou, Xiao-Peng; Su, Xue-Li; Sun, Yan

2007-01-01

The statistical thermodynamic (ST) model was used to study nonlinear binary protein adsorption equilibria on an anion exchanger. Single-component and binary protein adsorption isotherms of bovine hemoglobin (Hb) and bovine serum albumin (BSA) on DEAE Spherodex M were determined by batch adsorption experiments in 10 mM Tris-HCl buffer containing a specific NaCl concentration (0.05, 0.10, and 0.15 M) at pH 7.40. The ST model was found to depict the effect of ionic strength on the single-component equilibria well, with model parameters depending on ionic strength. Moreover, the ST model gave acceptable fitting to the binary adsorption data with the fitted single-component model parameters, leading to the estimation of the binary ST model parameter. The effects of ionic strength on the model parameters are reasonably interpreted by the electrostatic and thermodynamic theories. The effective charge of protein in adsorption phase can be separately calculated from the two categories of the model parameters, and the values obtained from the two methods are consistent. The results demonstrate the utility of the ST model for describing nonlinear binary protein adsorption equilibria.

Thermodynamic scaling in ionically conducting glasses and melts

NASA Astrophysics Data System (ADS)

Habasaki, Junko

2013-02-01

Molecular dynamics simulations have been performed to learn temperature, composition, pressure dependencies of the diffusivity and structures in the system having ion channels and network formers. Validity of the thermodynamic scaling in the lithium silicate glasses and melts is shown, where the scaling concept is extended with an aid of a percolation aspect of the ion channels. All diffusion coefficients of ions of different compositions, temperatures, pressures are successfully represented by a single master curve as a function of system volumes, temperatures and volume fraction of M2O part. It enables us to predict the diffusivity in different conditions. Furthermore, it suggests an applicability of scaling concept for the sub-structures in more complex systems. Nearby points on the master curve have the comparable MSD as well as self-part of the van Hove functions. Similarity is observed from an early term region. This observation is consistent to our previous claims [K. L. Ngai, J. Habasaki, D. Prevosto, S. Capaccioli, Marian Paluch, J. Chem. Phys. 137, 034511 (2012)] that the thermodynamic scaling of α-Relaxation time stems from the Johari-Goldstein β-relaxation or the primitive relaxation of the coupling model.

Ion channels versus ion pumps: the principal difference, in principle.

PubMed

Gadsby, David C

2009-05-01

The incessant traffic of ions across cell membranes is controlled by two kinds of border guards: ion channels and ion pumps. Open channels let selected ions diffuse rapidly down electrical and concentration gradients, whereas ion pumps labour tirelessly to maintain the gradients by consuming energy to slowly move ions thermodynamically uphill. Because of the diametrically opposed tasks and the divergent speeds of channels and pumps, they have traditionally been viewed as completely different entities, as alike as chalk and cheese. But new structural and mechanistic information about both of these classes of molecular machines challenges this comfortable separation and forces its re-evaluation.

Thermodynamics, Diffusion, and Structure of Mg2SiO4 forsterite grain boundaries from atomistic modeling

NASA Astrophysics Data System (ADS)

Adjaoud, O.; Marquardt, K.; Jahn, S.

2011-12-01

Most materials are not single crystals but consist of crystalline grains of various sizes, misorientated with respect to each other and joint by grain boundaries. The latter influence many of the material properties. For instance, grain boundaries are short circuits for diffusion and thus they strongly influence transport properties of materials such as electrical conductivity, or mineral growth rates, creep, or phase transform. Olivine is a major component of the Earth's upper mantle and therefore it is of considerable importance to study its physical and thermodynamic polycrystalline properties. In the present study, we have used molecular dynamics simulations to model thermodynamics, self-diffusion and structure of a series of [100] symmetric tilt grain boundaries in forsterite. The interactions between the atoms are modeled by an advanced ionic interaction potential (Jahn and Madden, 2007). The parameters of the potential are fitted to ab initio results. The model was optimized for the Ca-Mg-Al-Si-O system and shows good transferability in a wide range of pressures, temperatures, and compositions. Thermodynamics and structure were simulated at ambient conditions, and self-diffusion coefficients were determined at ambient pressure and temperatures of 1250, 1500, 1750, and 2000 K. We find that the energy and excess free volume of the grain boundaries in forsterite depend significantly on the misorientation angle of the grain boundary. One of our modeled structures is compared with an high-resolution transmission electron micrograph (HRTEM) (Heinemann et al., 2005). We relate our findings to previous studies of grain boundaries in ionic materials and in metals. For small misorientation angles (up to 22.1°), grain boundary structures consist of an array of c-edge dislocations as suggested by Heinemann et al. (2005) and their energies can be readily fit with the Read-Shockley dislocation model for grain boundaries. For high misorientation angles (32.1° and 60.8°), the cores of dislocations overlap and form repeated structural units. Similar to energies and excess free volumes, the self-diffusion coefficients of Mg and O depend significantly on the misorientation angle of the grain boundaries and they are well fitted with Arrhenius law. We compare our results to MgO grain boundary diffusion in forsterite derived from reaction rim growth experiments (Gardés and Heinrich, 2010).

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.

On the dominant impact of vertical moisture gradient on mesoscale cloud cellular organization of stratocumulus

NASA Astrophysics Data System (ADS)

Zhou, X.; Ackerman, A. S.; Fridlind, A. M.; Kollias, P.

2016-12-01

Large-eddy simulations are performed to study the mechanisms of stratocumulus organization. Precipitation tends to increase horizontal cloud scales, but is not required for cloud mesoscale organization. A study of the terms in the prognostic equation for total water mixing ratio variance shows the critical impact of vertical moisture gradient on cloud scale. For precipitating clouds, the organization originates from the negative moisture gradient in the boundary layer resulting from evaporation of precipitation. This hypothesis is supported by simulations in which thermodynamics profiles are nudged to their initial well-mixed state, which reduces cloud scales. Cold pools effect are surprisingly found to respond to rather than determine the cloud mesoscale variability. For non-precipitating clouds, organization results from turbulent transport of moisture variance originating primarily from cloud top, where dry air is entrained into the boundary layer through convection driven by cloud top longwave (LW) cooling. Both LW cooling and a moisture gradient above cloud top are essential for the growth of mesoscale fluctuations.

Aspects of Supercritical Turbulence: Direct Numerical Simulation of O2/H2 and C7H16/N2 Temporal Mixing Layers

NASA Technical Reports Server (NTRS)

Bellan, J.; Okongo, N. A.; Harstad, K. G.; Hutt, John (Technical Monitor)

2002-01-01

Results from Direct Numerical Simulations of temporal, supercritical mixing layers for two species systems are analyzed to elucidate species-specific turbulence aspects. The two species systems, O2/H2 and C7HG16/N2, have different thermodynamic characteristics; thus, although the simulations are performed at similar reduced pressure (ratio of the pressure to the critical pressure), the former system is dose to mixture ideality and has a relatively high solubility with respect to the latter, which exhibits strong departures from mixture ideality Due to the specified, smaller initial density stratification, the C7H16/N2 layers display higher growth and increased global molecular mixing as well as larger turbulence levels. However, smaller density gradients at the transitional state for the O2/H2 system indicate that on a local basis, the layer exhibits an enhanced mixing, this being attributed to the increased solubility and to mixture ideality. These thermodynamic features are shown to affect the irreversible entropy production (i.e. the dissipation), which is larger for the O2/H2 layer and is primarily concentrated in high density-gradient magnitude regions that are distortions of the initial density stratification boundary. In contrast, the regions of largest dissipation in the C7H16/N2 layer are located in high density-gradient magnitude regions resulting from the mixing of the two fluids.

Modeling the thermostability of surface functionalisation by oxygen, hydroxyl, and water on nanodiamonds.

PubMed

Lai, Lin; Barnard, Amanda S

2011-06-01

Understanding nanodiamond functionalisation is of great importance for biological and medical applications. Here we examine the stabilities of oxygen, hydroxyl, and water functionalisation of the nanodiamonds using the self-consistent charge density functional tight-binding simulations. We find that the oxygen and hydroxyl termination are thermodynamically favourable and form strong C–O covalent bonds on the nanodiamond surface in an O2 and H2 gas reservoir, which confirms previous experiments. Yet, the thermodynamic stabilities of oxygen and hydroxyl functionalisation decrease dramatically in a water vapour reservoir. In contrast, H2O molecules are found to be physically adsorbed on the nanodiamond surface, and forced chemical adsorption results in decomposition of H2O. Moreover, the functionalisation efficiency is found to be facet dependent. The oxygen functionalisation prefers the {100} facets as opposed to alternative facets in an O2 and H2 gas reservoir. The hydroxyl functionalisation favors the {111} surfaces in an O2 and H2 reservoir and the {100} facets in a water vapour reservoir, respectively. This facet selectivity is found to be largely dependent upon the environmental temperature, chemical reservoir, and morphology of the nanodiamonds.

Chemistry and Photochemistry of Anthocyanins and Related Compounds: A Thermodynamic and Kinetic Approach.

PubMed

Basílio, Nuno; Pina, Fernando

2016-11-10

Anthocyanins are identified by the respective flavylium cation, which is only one species of a multistate of different molecules reversibly interconverted by external inputs such as pH, light and temperature. The flavylium cation (acidic form) is involved in an apparent acid-base reaction, where the basic species is the sum of quinoidal base, hemiketal and cis - and trans -chalcones, their relative fraction depending on the substitution pattern of the flavylium cation. The full comprehension of this complex system requires a thermodynamic and kinetic approach. The first consists in drawing an energy level diagram where the relative positions of the different species are represented as a function of pH. On the other hand, the kinetic approach allows measuring the rates of the reactions that interconnect reversibly the multistate species. The kinetics is greatly dependent on the existence or not of a high cis - trans isomerization barrier. In this work, the procedure to obtain the energy level diagram and the rates of inter-conversion in the multistate in both cases (low or high isomerization barrier) are described. Practical examples of this approach are presented to illustrate the theory, and recently reported applications based on host-guest complexes are reviewed.

Thermophoresis of dissolved molecules and polymers: Consideration of the temperature-induced macroscopic pressure gradient

NASA Astrophysics Data System (ADS)

Semenov, Semen; Schimpf, Martin

2004-01-01

The movement of molecules and homopolymer chains dissolved in a nonelectrolyte solvent in response to a temperature gradient is considered a consequence of temperature-induced pressure gradients in the solvent layer surrounding the solute molecules. Local pressure gradients are produced by nonuniform London van der Waals interactions, established by gradients in the concentration (density) of solvent molecules. The density gradient is produced by variations in solvent thermal expansion within the nonuniform temperature field. The resulting expression for the velocity of the solute contains the Hamaker constants for solute-solvent and solute-solute interactions, the radius of the solute molecule, and the viscosity and cubic coefficient of thermal expansion of the solvent. In this paper we consider an additional force that arises from directional asymmetry in the interaction between solvent molecules. In a closed cell, the resulting macroscopic pressure gradient gives rise to a volume force that affects the motion of dissolved solutes. An expression for this macroscopic pressure gradient is derived and the resulting force is incorporated into the expression for the solute velocity. The expression is used to calculate thermodiffusion coefficients for polystyrene in several organic solvents. When these values are compared to those measured in the laboratory, the consistency is better than that found in previous reports, which did not consider the macroscopic pressure gradient that arises in a closed thermodiffusion cell. The model also allows for the movement of solute in either direction, depending on the relative values of the solvent and solute Hamaker constants.

Optical and thermodynamic properties of MgO from radiative shock temperature and sound speed measurements on samples preheated to 2300 K

NASA Astrophysics Data System (ADS)

Fatýanov, O. V.; Asimow, P. D.

2013-12-01

Thermodynamic properties of MgO, one of the major end-members of deep planetary interiors, play a significant role in the processes inside the Earth's lower mantle. Of particular importance in geophysics and geochemistry is the MgO melting behavior at high pressure. Despite considerable theoretical and experimental efforts over decades, it remains essentially unknown. The melting temperature predictions for MgO at 135 GPa, the Earth's core-mantle boundary pressure, range from 5 to 9 kK. In a continuous effort to resolve this inconsistency and to probe the P-T region previously unexplored, we developed a technique for radiative shock temperature measurements in single-crystal MgO preheated to 2300 K. Large ventilated Mo capsules were employed to hold ~20 mm long MgO crystals with controlled longitudinal thermal gradients. These hot targets were impacted by 0.8 mm thick Ta flyers launched at 6.5 to 7.5 km/s on the Caltech two-stage light-gas gun. Six spectral radiance histories from MgO shock front were recorded in every shot with 3 ns time resolution over 440-750 nm or 500-830 nm spectral range. The majority of our experiments showed smooth pressure dependence of MgO shock temperature and sound speed consistent with the solid phase at 197-243 GPa. Although most observed temperatures are ~700 K lower and sound speeds ~1 km/s higher than the model predictions, the pressure slopes for both parameters are in close agreement with those calculated for the solid phase. Unconfirmed data from a single experiment at 239 GPa and 8.3 kK showed correlated temperature and sound speed anomalies (both values lower than expected) that may be explained by partial melting. Our past and recent data on shock-compressed preheated MgO suggest its melting curve above 200 GPa is higher than the extrapolation of the experiments of Zerr & Boehler or the theoretical calculation by Strachan et. al. These results, features of shock experiments with 2300 K pre-heat temperatures, data analysis, and future plans will be discussed.

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…

A minimal dissipation type-based classification in irreversible thermodynamics and microeconomics

NASA Astrophysics Data System (ADS)

Tsirlin, A. M.; Kazakov, V.; Kolinko, N. A.

2003-10-01

We formulate the problem of finding classes of kinetic dependencies in irreversible thermodynamic and microeconomic systems for which minimal dissipation processes belong to the same type. We show that this problem is an inverse optimal control problem and solve it. The commonality of this problem in irreversible thermodynamics and microeconomics is emphasized.

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…

Variable stoichiometry in active ion transport: theoretical analysis of physiological consequences.

PubMed

Johnson, E A; Tanford, C; Reynolds, J A

1985-08-01

Active ion transport systems with fixed stoichiometry are subject to a thermodynamic limit on the ion concentration gradients that they can generate and maintain, and their net rates of transport must inevitably decrease as this limit is approached. The capability to vary stoichiometry might thus be physiologically advantageous: a shift to lower stoichiometry (fewer ions pumped per reaction cycle) at increasing thermodynamic load could increase the limit on the supportable concentration gradient and could accelerate the rate of transport under high-load conditions. Here we present a theoretical and numerical analysis of this possibility, using the sarcoplasmic reticulum ATP-driven Ca pump as the example. It is easy to introduce alternate pathways into the reaction cycle for this system to shift the stoichiometry (Ca2+/ATP) from the normal value of 2:1 to 1:1, but it cannot be done without simultaneous generation of a pathway for uncoupled leak of Ca2+ across the membrane. This counteracts the advantageous effect of the change in transport stoichiometry and a physiologically useful rate acceleration cannot be obtained. This result is likely to be generally applicable to most active transport systems.

Variable stoichiometry in active ion transport: theoretical analysis of physiological consequences.

PubMed Central

Johnson, E A; Tanford, C; Reynolds, J A

1985-01-01

Active ion transport systems with fixed stoichiometry are subject to a thermodynamic limit on the ion concentration gradients that they can generate and maintain, and their net rates of transport must inevitably decrease as this limit is approached. The capability to vary stoichiometry might thus be physiologically advantageous: a shift to lower stoichiometry (fewer ions pumped per reaction cycle) at increasing thermodynamic load could increase the limit on the supportable concentration gradient and could accelerate the rate of transport under high-load conditions. Here we present a theoretical and numerical analysis of this possibility, using the sarcoplasmic reticulum ATP-driven Ca pump as the example. It is easy to introduce alternate pathways into the reaction cycle for this system to shift the stoichiometry (Ca2+/ATP) from the normal value of 2:1 to 1:1, but it cannot be done without simultaneous generation of a pathway for uncoupled leak of Ca2+ across the membrane. This counteracts the advantageous effect of the change in transport stoichiometry and a physiologically useful rate acceleration cannot be obtained. This result is likely to be generally applicable to most active transport systems. PMID:3860866

Efficiency at Maximum Power Output of a Quantum-Mechanical Brayton Cycle

NASA Astrophysics Data System (ADS)

Yuan, Yuan; He, Ji-Zhou; Gao, Yong; Wang, Jian-Hui

2014-03-01

The performance in finite time of a quantum-mechanical Brayton engine cycle is discussed, without introduction of temperature. The engine model consists of two quantum isoenergetic and two quantum isobaric processes, and works with a single particle in a harmonic trap. Directly employing the finite-time thermodynamics, the efficiency at maximum power output is determined. Extending the harmonic trap to a power-law trap, we find that the efficiency at maximum power is independent of any parameter involved in the model, but depends on the confinement of the trapping potential.

Solid-phase equilibria on Pluto's surface

NASA Astrophysics Data System (ADS)

Tan, Sugata P.; Kargel, Jeffrey S.

2018-03-01

Pluto's surface is covered by volatile ices that are in equilibrium with the atmosphere. Multicomponent phase equilibria may be calculated using a thermodynamic equation of state and, without additional assumptions, result in methane-rich and nitrogen-rich solid phases. The former is formed at temperature range between the atmospheric pressure-dependent sublimation and condensation points, while the latter is formed at temperatures lower than the sublimation point. The results, calculated for the observed 11 μbar atmospheric pressure and composition, are consistent with recent work derived from observations by New Horizons.

A mesh gradient technique for numerical optimization

NASA Technical Reports Server (NTRS)

Willis, E. A., Jr.

1973-01-01

A class of successive-improvement optimization methods in which directions of descent are defined in the state space along each trial trajectory are considered. The given problem is first decomposed into two discrete levels by imposing mesh points. Level 1 consists of running optimal subarcs between each successive pair of mesh points. For normal systems, these optimal two-point boundary value problems can be solved by following a routine prescription if the mesh spacing is sufficiently close. A spacing criterion is given. Under appropriate conditions, the criterion value depends only on the coordinates of the mesh points, and its gradient with respect to those coordinates may be defined by interpreting the adjoint variables as partial derivatives of the criterion value function. In level 2, the gradient data is used to generate improvement steps or search directions in the state space which satisfy the boundary values and constraints of the given problem.

Molecular determinants for the thermodynamic and functional divergence of uniporter GLUT1 and proton symporter XylE

PubMed Central

Ke, Meng; Jiang, Xin; Yan, Nieng

2017-01-01

GLUT1 facilitates the down-gradient translocation of D-glucose across cell membrane in mammals. XylE, an Escherichia coli homolog of GLUT1, utilizes proton gradient as an energy source to drive uphill D-xylose transport. Previous studies of XylE and GLUT1 suggest that the variation between an acidic residue (Asp27 in XylE) and a neutral one (Asn29 in GLUT1) is a key element for their mechanistic divergence. In this work, we combined computational and biochemical approaches to investigate the mechanism of proton coupling by XylE and the functional divergence between GLUT1 and XylE. Using molecular dynamics simulations, we evaluated the free energy profiles of the transition between inward- and outward-facing conformations for the apo proteins. Our results revealed the correlation between the protonation state and conformational preference in XylE, which is supported by the crystal structures. In addition, our simulations suggested a thermodynamic difference between XylE and GLUT1 that cannot be explained by the single residue variation at the protonation site. To understand the molecular basis, we applied Bayesian network models to analyze the alteration in the architecture of the hydrogen bond networks during conformational transition. The models and subsequent experimental validation suggest that multiple residue substitutions are required to produce the thermodynamic and functional distinction between XylE and GLUT1. Despite the lack of simulation studies with substrates, these computational and biochemical characterizations provide unprecedented insight into the mechanistic difference between proton symporters and uniporters. PMID:28617850

Features of self-organized plasma physics in tokamaks

NASA Astrophysics Data System (ADS)

Razumova, K. A.

2018-01-01

The history of investigations the role of self-organization processes in tokamak plasma confinement is presented. It was experimentally shown that the normalized pressure profile is the same for different tokamaks. Instead of the conventional Fick equation, where the thermal flux is proportional to a pressure gradient, processes in the plasma are well described by the Dyabilanin’s energy balance equation, in which the heat flux is proportional to the difference of normalized gradients for self-consistent and real pressure profiles. The transport coefficient depends on the values of heat flux, which compensates distortion of the pressure profile with external impacts. Radiative cooling of the plasma edge decreases the heat flux and improves the confinement.

Demonstration of Nonlinearity Bias in the Measurement of the Apparent Diffusion Coefficient in Multicenter Trials

PubMed Central

Malyarenko, Dariya; Newitt, David; Wilmes, Lisa; Tudorica, Alina; Helmer, Karl G.; Arlinghaus, Lori R.; Jacobs, Michael A.; Jajamovich, Guido; Taouli, Bachir; Yankeelov, Thomas E.; Huang, Wei; Chenevert, Thomas L.

2015-01-01

Purpose Characterize system-specific bias across common magnetic resonance imaging (MRI) platforms for quantitative diffusion measurements in multicenter trials. Methods Diffusion weighted imaging (DWI) was performed on an ice-water phantom along the superior-inferior (SI) and right-left (RL) orientations spanning ±150 mm. The same scanning protocol was implemented on 14 MRI systems at seven imaging centers. The bias was estimated as a deviation of measured from known apparent diffusion coefficient (ADC) along individual DWI directions. The relative contributions of gradient nonlinearity, shim errors, imaging gradients and eddy currents were assessed independently. The observed bias errors were compared to numerical models. Results The measured systematic ADC errors scaled quadratically with offset from isocenter, and ranged between −55% (SI) and 25% (RL). Nonlinearity bias was dependent on system design and diffusion gradient direction. Consistent with numerical models, minor ADC errors (±5%) due to shim, imaging and eddy currents were mitigated by double echo DWI and image co-registration of individual gradient directions. Conclusion The analysis confirms gradient nonlinearity as a major source of spatial DW bias and variability in off-center ADC measurements across MRI platforms, with minor contributions from shim, imaging gradients and eddy currents. The developed protocol enables empiric description of systematic bias in multicenter quantitative DWI studies. PMID:25940607

Demonstration of nonlinearity bias in the measurement of the apparent diffusion coefficient in multicenter trials.

PubMed

Malyarenko, Dariya I; Newitt, David; J Wilmes, Lisa; Tudorica, Alina; Helmer, Karl G; Arlinghaus, Lori R; Jacobs, Michael A; Jajamovich, Guido; Taouli, Bachir; Yankeelov, Thomas E; Huang, Wei; Chenevert, Thomas L

2016-03-01

Characterize system-specific bias across common magnetic resonance imaging (MRI) platforms for quantitative diffusion measurements in multicenter trials. Diffusion weighted imaging (DWI) was performed on an ice-water phantom along the superior-inferior (SI) and right-left (RL) orientations spanning ± 150 mm. The same scanning protocol was implemented on 14 MRI systems at seven imaging centers. The bias was estimated as a deviation of measured from known apparent diffusion coefficient (ADC) along individual DWI directions. The relative contributions of gradient nonlinearity, shim errors, imaging gradients, and eddy currents were assessed independently. The observed bias errors were compared with numerical models. The measured systematic ADC errors scaled quadratically with offset from isocenter, and ranged between -55% (SI) and 25% (RL). Nonlinearity bias was dependent on system design and diffusion gradient direction. Consistent with numerical models, minor ADC errors (± 5%) due to shim, imaging and eddy currents were mitigated by double echo DWI and image coregistration of individual gradient directions. The analysis confirms gradient nonlinearity as a major source of spatial DW bias and variability in off-center ADC measurements across MRI platforms, with minor contributions from shim, imaging gradients and eddy currents. The developed protocol enables empiric description of systematic bias in multicenter quantitative DWI studies. © 2015 Wiley Periodicals, Inc.

Bulk viscosity of strongly interacting matter in the relaxation time approximation

DOE PAGES

Czajka, Alina; Hauksson, Sigtryggur; Shen, Chun; ...

2018-04-24

Here, we show how thermal mean field effects can be incorporated consistently in the hydrodynamical modeling of heavy-ion collisions. The nonequilibrium correction to the distribution function resulting from a temperature-dependent mass is obtained in a procedure which automatically satisfies the Landau matching condition and is thermodynamically consistent. The physics of the bulk viscosity is studied here for Boltzmann and Bose-Einstein gases within the Chapman-Enskog and 14-moment approaches in the relaxation time approximation. Constant and temperature-dependent masses are considered in turn. It is shown that, in the small mass limit, both methods lead to the same value of the ratio ofmore » the bulk viscosity to its relaxation time. The inclusion of a temperature-dependent mass leads to the emergence of the β λ function in that ratio, and it is of the expected parametric form for the Boltzmann gas, while for the Bose-Einstein case it is affected by the infrared cutoff. This suggests that the relaxation time approximation may be too crude to obtain a reliable form of ς/τ R for gases obeying Bose-Einstein statistics.« less

Bulk viscosity of strongly interacting matter in the relaxation time approximation

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

Czajka, Alina; Hauksson, Sigtryggur; Shen, Chun

Here, we show how thermal mean field effects can be incorporated consistently in the hydrodynamical modeling of heavy-ion collisions. The nonequilibrium correction to the distribution function resulting from a temperature-dependent mass is obtained in a procedure which automatically satisfies the Landau matching condition and is thermodynamically consistent. The physics of the bulk viscosity is studied here for Boltzmann and Bose-Einstein gases within the Chapman-Enskog and 14-moment approaches in the relaxation time approximation. Constant and temperature-dependent masses are considered in turn. It is shown that, in the small mass limit, both methods lead to the same value of the ratio ofmore » the bulk viscosity to its relaxation time. The inclusion of a temperature-dependent mass leads to the emergence of the β λ function in that ratio, and it is of the expected parametric form for the Boltzmann gas, while for the Bose-Einstein case it is affected by the infrared cutoff. This suggests that the relaxation time approximation may be too crude to obtain a reliable form of ς/τ R for gases obeying Bose-Einstein statistics.« less

Bulk viscosity of strongly interacting matter in the relaxation time approximation

NASA Astrophysics Data System (ADS)

Czajka, Alina; Hauksson, Sigtryggur; Shen, Chun; Jeon, Sangyong; Gale, Charles

2018-04-01

We show how thermal mean field effects can be incorporated consistently in the hydrodynamical modeling of heavy-ion collisions. The nonequilibrium correction to the distribution function resulting from a temperature-dependent mass is obtained in a procedure which automatically satisfies the Landau matching condition and is thermodynamically consistent. The physics of the bulk viscosity is studied here for Boltzmann and Bose-Einstein gases within the Chapman-Enskog and 14-moment approaches in the relaxation time approximation. Constant and temperature-dependent masses are considered in turn. It is shown that, in the small mass limit, both methods lead to the same value of the ratio of the bulk viscosity to its relaxation time. The inclusion of a temperature-dependent mass leads to the emergence of the βλ function in that ratio, and it is of the expected parametric form for the Boltzmann gas, while for the Bose-Einstein case it is affected by the infrared cutoff. This suggests that the relaxation time approximation may be too crude to obtain a reliable form of ζ /τR for gases obeying Bose-Einstein statistics.

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.

Thermodynamics of information processing based on enzyme kinetics: An exactly solvable model of an information pump

NASA Astrophysics Data System (ADS)

Cao, Yuansheng; Gong, Zongping; Quan, H. T.

2015-06-01

Motivated by the recent proposed models of the information engine [Proc. Natl. Acad. Sci. USA 109, 11641 (2012), 10.1073/pnas.1204263109] and the information refrigerator [Phys. Rev. Lett. 111, 030602 (2013), 10.1103/PhysRevLett.111.030602], we propose a minimal model of the information pump and the information eraser based on enzyme kinetics. This device can either pump molecules against the chemical potential gradient by consuming the information to be encoded in the bit stream or (partially) erase the information initially encoded in the bit stream by consuming the Gibbs free energy. The dynamics of this model is solved exactly, and the "phase diagram" of the operation regimes is determined. The efficiency and the power of the information machine is analyzed. The validity of the second law of thermodynamics within our model is clarified. Our model offers a simple paradigm for the investigating of the thermodynamics of information processing involving the chemical potential in small systems.

Local thermodynamic equilibrium for globally disequilibrium open systems under stress

NASA Astrophysics Data System (ADS)

Podladchikov, Yury

2016-04-01

Predictive modeling of far and near equilibrium processes is essential for understanding of patterns formation and for quantifying of natural processes that are never in global equilibrium. Methods of both equilibrium and non-equilibrium thermodynamics are needed and have to be combined. For example, predicting temperature evolution due to heat conduction requires simultaneous use of equilibrium relationship between internal energy and temperature via heat capacity (the caloric equation of state) and disequilibrium relationship between heat flux and temperature gradient. Similarly, modeling of rocks deforming under stress, reactions in system open for the porous fluid flow, or kinetic overstepping of the equilibrium reaction boundary necessarily needs both equilibrium and disequilibrium material properties measured under fundamentally different laboratory conditions. Classical irreversible thermodynamics (CIT) is the well-developed discipline providing the working recipes for the combined application of mutually exclusive experimental data such as density and chemical potential at rest under constant pressure and temperature and viscosity of the flow under stress. Several examples will be presented.

Theoretical study of phonon dispersion, elastic, mechanical and thermodynamic properties of barium chalcogenides

NASA Astrophysics Data System (ADS)

Musari, A. A.; Orukombo, S. A.

2018-03-01

Barium chalcogenides are known for their high-technological importance and great scientific interest. Detailed studies of their elastic, mechanical, dynamical and thermodynamic properties were carried out using density functional theory and plane-wave pseudo potential method within the generalized gradient approximation. The optimized lattice constants were in good agreement when compared with experimental data. The independent elastic constants, calculated from a linear fit of the computed stress-strain function, were used to determine the Young’s modulus (E), bulk modulus (B), shear modulus (G), Poisson’s ratio (σ) and Zener’s anisotropy factor (A). Also, the Debye temperature and sound velocities for barium chalcogenides were estimated from the three independent elastic constants. The calculations of phonon dispersion showed that there are no negative frequencies throughout the Brillouin zone. Hence barium chalcogenides have dynamically stable NaCl-type crystal structure. Finally, their thermodynamic properties were calculated in the temperature range of 0-1000 K and their constant-volume specific heat capacities at room-temperature were reported.

Vibrational and thermodynamic properties of β-HMX: a first-principles investigation.

PubMed

Wu, Zhongqing; Kalia, Rajiv K; Nakano, Aiichiro; Vashishta, Priya

2011-05-28

Thermodynamic properties of β-HMX crystal are investigated using the quasi-harmonic approximation and density functional theory within the local density approximation (LDA), generalized gradient approximation (GGA), and GGA + empirical van der Waals (vdW) correction. It is found that GGA well describes the thermal expansion coefficient and heat capacity but fails to produce correct bulk modulus and equilibrium volume. The vdW correction improves the bulk modulus and volume, but worsens the thermal expansion coefficient and heat capacity. In contrast, LDA describes all thermodynamic properties with reasonable accuracy, and overall is a good exchange-correlation functional for β-HMX molecular crystal. The results also demonstrate significant contributions of phonons to the equation of state. The static calculation of equilibrium volume for β-HMX differs from the room-temperature value incorporating lattice vibrations by over 5%. Therefore, for molecular crystals, it is essential to include phonon contributions when calculated equation of state is compared with experimental data at ambient condition. © 2011 American Institute of Physics

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.

Self-organization, preferential flow and rainfall runoff behavior - is there a connection?

NASA Astrophysics Data System (ADS)

Zehe, Erwin; Blume, Theresa; Kleidon, Axel; Ehret, Uwe; Scherer, Ulrike; Westhoff, Martijn

2013-04-01

In line with the studies of Kleidon et al. (2012) and Zehe et al. (2010) the proposed study analyzes mass flow related flows of free energy in open hydrological systems - hillslopes and small catchments - using thermodynamics methods. Why a thermodynamic treatment? A small part of the kinetic energy input from incoming rainfall is dissipated into heat and to break up soil aggregates. Depending on the partitioning of the incoming rainfall into overland flow and soil water, the remaining part of the incoming kinetic energy is partly transformed into potential energy of surface water and subsequently partly exported as kinetic energy of overland flow from the system; the rest is dissipated by frictional losses. The other part of rainfall infiltrates thereby increasing potential energy of soil water but depleting at the same time (gradients in) capillary binding energy of soil water, which again comprises energy dissipation into heat of immersion. Although, these mass fluxes are not associated with large heat fluxes, they reflect the overall conservation of energy as well as the second law of thermodynamics. They require thus a thermodynamic treatment, because tiny amounts of kinetic energy, surface energy and potential energy are dissipated into heat: this implies irreversibility and explains why water does not flow uphill. Soil hydraulic equilibrium (HE), arising from a balance in potential and capillary binding energy in soil, can be interpreted as a state of maximum entropy in soil. Soil water potential, defined as sum of matric potential and gravity potential, is in HE equal to zero along the soil profile. This corresponds to a state of maximum entropy due to a zero potential gradient, which implies due to Zehe et al. (2010) a state of minimum (Helmholtz) free energy. Our first main objective is to quantify to which extent connected preferential flow path, in our case vertical macropores and the river network enhance flow velocities at a given driving gradient and thus power in the associated mass fluxes. This implies either an enhanced export of free energy in form of kinetic energy in case of the river net, or an accelerated reduction of potential energy of infiltrating surface water which implies a reduction free energy in form of capillary binding energy of soil water. We hypothesize (H1) that network like structures act as dissipative structures "serving the purpose" of reducing the relaxation time to a state of lower "free" energy in the entire system. This is because they minimize dissipative losses of kinetic energy along their extent. This faster relaxation towards a state of smaller free energy is deemed to be favorable for mechanic stability of the entire hydrological system because a) mass flows perform due to the enhanced export of kinetic energy less work on the system itself and b) mechanical stress from ponded surface water is quickly reduced by fast infiltration and preferential flow. Our second main objective is, in line with the study of Zehe et al. (2010), the search for thermodynamic optimal hillslope architectures both with respect to the surface density of vertical macropores in soil and with respect to the spatial arrangement of soil types and macropores at the hillslope scale. In line with H1 we suggest (H2) that a hydro-geo-ecosystem is closer to a functional optimum than other possible configurations if it dissipates and exports more of the kinetic energy input from incoming rainfall by redistributing water against internal gradients and exporting water against macroscale geo-potential gradients. Note that H2 does not postulate that functionally optimal hillslope architectures necessarily exist, if they exist H2 implies however that they maximize entropy production and thus reduction of total free energy of the system at a "wisely" selected time scale. The surface density of apparent macropores does for instance control the tradeoff between Hortonian overland flow formation and infiltration, which implies a tradeoff between the amount of kinetic energy input from rainfall that is converted in to power associated with overland flow and power associated with soil water flows depleting gradients in soil water potential. Does this tradeoff imply an optimum surface density of macropores at the hillslope scale in the sense that power in soil water flow is maximized or reduction of free energy is maximized? In case such an optimum hillslope architecture existed, and in case that the evolution of the hydrological systems of interested was indeed in accordance with hypothesis H2, this optimal architecture should allow an acceptable uncalibrated simulation of the systems rainfall -runoff behavior (if the selected model structure can properly represent this architecture). We will address these questions and test the main implications of our hypotheses by means of numerical experiments with the physically based hydrological model CATFLOW. We use behavioral model structures as basic model setup, which have been shown to closely portray system behavior and its architecture in a sense that they reproduce distributed observations of soil moisture and catchment scale discharge and represent the observed structural and textural signatures of soils, flow networks and vegetation. Our test areas are the Weiherbach (Germany) and the Malalcahuello research headwaters (Chile), which are located in distinctly different hydro-climatic and hydro-pedological settings. Within the numerical experiments we will simulate the full concert of hydrological processes at the hillslope and headwater scales for meaningful perturbations of the behavioral model structure and compare them with respect to dynamics of free energy and production of power. These perturbations affect a) the river network and the geomorphology of the Weiherbach catchment, b) surface density of macropores in both catchments c) the spatial arrangement of soils and preferential pathways at the hillslope scale in the Weiherbach catchment. References: Kleidon, A., Zehe, E., Ehret, U., and Scherer, U.: Thermodynamics, maximum power, and the dynamics of preferential river flow structures on continents, Hydrol. Earth Syst. Sci. Discuss., 9, 7317-7378, 10.5194/hessd-9-7317-2012, 2012. Zehe, E., Blume, T., and Blöschl, G.: The principle of 'maximum energy dissipation': a novel thermodynamic perspective on rapid water flow in connected soil structures, Phil. Trans. R. Soc. B, 1-10, doi:10.1098/rstb.2009.0308, 2010.

Statistical-thermodynamic model for light scattering from eye lens protein mixtures

NASA Astrophysics Data System (ADS)

Bell, Michael M.; Ross, David S.; Bautista, Maurino P.; Shahmohamad, Hossein; Langner, Andreas; Hamilton, John F.; Lahnovych, Carrie N.; Thurston, George M.

2017-02-01

We model light-scattering cross sections of concentrated aqueous mixtures of the bovine eye lens proteins γB- and α-crystallin by adapting a statistical-thermodynamic model of mixtures of spheres with short-range attractions. The model reproduces measured static light scattering cross sections, or Rayleigh ratios, of γB-α mixtures from dilute concentrations where light scattering intensity depends on molecular weights and virial coefficients, to realistically high concentration protein mixtures like those of the lens. The model relates γB-γB and γB-α attraction strengths and the γB-α size ratio to the free energy curvatures that set light scattering efficiency in tandem with protein refractive index increments. The model includes (i) hard-sphere α-α interactions, which create short-range order and transparency at high protein concentrations, (ii) short-range attractive plus hard-core γ-γ interactions, which produce intense light scattering and liquid-liquid phase separation in aqueous γ-crystallin solutions, and (iii) short-range attractive plus hard-core γ-α interactions, which strongly influence highly non-additive light scattering and phase separation in concentrated γ-α mixtures. The model reveals a new lens transparency mechanism, that prominent equilibrium composition fluctuations can be perpendicular to the refractive index gradient. The model reproduces the concave-up dependence of the Rayleigh ratio on α/γ composition at high concentrations, its concave-down nature at intermediate concentrations, non-monotonic dependence of light scattering on γ-α attraction strength, and more intricate, temperature-dependent features. We analytically compute the mixed virial series for light scattering efficiency through third order for the sticky-sphere mixture, and find that the full model represents the available light scattering data at concentrations several times those where the second and third mixed virial contributions fail. The model indicates that increased γ-γ attraction can raise γ-α mixture light scattering far more than it does for solutions of γ-crystallin alone, and can produce marked turbidity tens of degrees celsius above liquid-liquid separation.

Thermodynamic evaluation of mass diffusion in ionic mixtures

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

Kagan, Grigory; Tang, Xian-Zhu

2014-02-15

The thermodynamic technique of Landau and Lifshitz originally developed for inter-species diffusion in a binary neutral gas mixture is extended to a quasi-neutral plasma with two ion species. It is shown that, while baro- and electro-diffusion coefficients depend on the choice of the thermodynamic system, prediction for the total diffusive mass flux is invariant.

Context-dependent interactions and the regulation of species richness in freshwater fish.

PubMed

MacDougall, Andrew S; Harvey, Eric; McCune, Jenny L; Nilsson, Karin A; Bennett, Joseph; Firn, Jennifer; Bartley, Timothy; Grace, James B; Kelly, Jocelyn; Tunney, Tyler D; McMeans, Bailey; Matsuzaki, Shin-Ichiro S; Kadoya, Taku; Esch, Ellen; Cazelles, Kevin; Lester, Nigel; McCann, Kevin S

2018-03-06

Species richness is regulated by a complex network of scale-dependent processes. This complexity can obscure the influence of limiting species interactions, making it difficult to determine if abiotic or biotic drivers are more predominant regulators of richness. Using integrative modeling of freshwater fish richness from 721 lakes along an 11 o latitudinal gradient, we find negative interactions to be a relatively minor independent predictor of species richness in lakes despite the widespread presence of predators. Instead, interaction effects, when detectable among major functional groups and 231 species pairs, were strong, often positive, but contextually dependent on environment. These results are consistent with the idea that negative interactions internally structure lake communities but do not consistently 'scale-up' to regulate richness independently of the environment. The importance of environment for interaction outcomes and its role in the regulation of species richness highlights the potential sensitivity of fish communities to the environmental changes affecting lakes globally.

Context-dependent interactions and the regulation of species richness in freshwater fish

USGS Publications Warehouse

MacDougall, Andrew S.; Harvey, Eric; McCune, Jenny L.; Nilsson, Karin A.; Bennett, Joseph; Firn, Jennifer; Bartley, Timothy; Grace, James B.; Kelly, Jocelyn; Tunney, Tyler D.; McMeans, Bailey; Matsuzaki, Shin-Ichiro S.; Kadoya, Taku; Esch, Ellen; Cazelles, Kevin; Lester, Nigel; McCann, Kevin S.

2018-01-01

Species richness is regulated by a complex network of scale-dependent processes. This complexity can obscure the influence of limiting species interactions, making it difficult to determine if abiotic or biotic drivers are more predominant regulators of richness. Using integrative modeling of freshwater fish richness from 721 lakes along an 11olatitudinal gradient, we find negative interactions to be a relatively minor independent predictor of species richness in lakes despite the widespread presence of predators. Instead, interaction effects, when detectable among major functional groups and 231 species pairs, were strong, often positive, but contextually dependent on environment. These results are consistent with the idea that negative interactions internally structure lake communities but do not consistently ‘scale-up’ to regulate richness independently of the environment. The importance of environment for interaction outcomes and its role in the regulation of species richness highlights the potential sensitivity of fish communities to the environmental changes affecting lakes globally.

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.

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.

A Tractable Disequilbrium Framework for Integrating Computational Thermodynamics and Geodynamics

NASA Astrophysics Data System (ADS)

Spiegelman, M. W.; Tweed, L. E. L.; Evans, O.; Kelemen, P. B.; Wilson, C. R.

2017-12-01

The consistent integration of computational thermodynamics and geodynamics is essential for exploring and understanding a wide range of processes from high-PT magma dynamics in the convecting mantle to low-PT reactive alteration of the brittle crust. Nevertheless, considerable challenges remain for coupling thermodynamics and fluid-solid mechanics within computationally tractable and insightful models. Here we report on a new effort, part of the ENKI project, that provides a roadmap for developing flexible geodynamic models of varying complexity that are thermodynamically consistent with established thermodynamic models. The basic theory is derived from the disequilibrium thermodynamics of De Groot and Mazur (1984), similar to Rudge et. al (2011, GJI), but extends that theory to include more general rheologies, multiple solid (and liquid) phases and explicit chemical reactions to describe interphase exchange. Specifying stoichiometric reactions clearly defines the compositions of reactants and products and allows the affinity of each reaction (A = -Δ/Gr) to be used as a scalar measure of disequilibrium. This approach only requires thermodynamic models to return chemical potentials of all components and phases (as well as thermodynamic quantities for each phase e.g. densities, heat capacity, entropies), but is not constrained to be in thermodynamic equilibrium. Allowing meta-stable phases mitigates some of the computational issues involved with the introduction and exhaustion of phases. Nevertheless, for closed systems, these problems are guaranteed to evolve to the same equilibria predicted by equilibrium thermodynamics. Here we illustrate the behavior of this theory for a range of simple problems (constructed with our open-source model builder TerraFERMA) that model poro-viscous behavior in the well understood Fo-Fa binary phase loop. Other contributions in this session will explore a range of models with more petrologically interesting phase diagrams as well as other rheologies.

Thermodynamic understanding of Sn whisker growth on the Cu surface in Cu(top)-Sn(bottom) bilayer system upon room temperature aging

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

Huang, Lin; Jian, Wei; Lin, Bing

2015-06-07

Sn whiskers are observed by scanning electron microscope on the Cu surface in Cu(top)-Sn(bottom) bilayer system upon room temperature aging. Only Cu{sub 6}Sn{sub 5} phase appears in the X-ray diffraction patterns and no Sn element is detected in the Cu sublayer by scanning transmission electron microscopy. Based on the interfacial thermodynamics, the intermetallic Cu{sub 6}Sn{sub 5} compound phase may form directly at the Sn grain boundary. Driven by the stress gradient during the formation of Cu{sub 6}Sn{sub 5} compound at Sn grain boundaries, Sn atoms segregate onto the Cu surface and accumulate to form Sn whisker.

A thermodynamic definition of protein domains.

PubMed

Porter, Lauren L; Rose, George D

2012-06-12

Protein domains are conspicuous structural units in globular proteins, and their identification has been a topic of intense biochemical interest dating back to the earliest crystal structures. Numerous disparate domain identification algorithms have been proposed, all involving some combination of visual intuition and/or structure-based decomposition. Instead, we present a rigorous, thermodynamically-based approach that redefines domains as cooperative chain segments. In greater detail, most small proteins fold with high cooperativity, meaning that the equilibrium population is dominated by completely folded and completely unfolded molecules, with a negligible subpopulation of partially folded intermediates. Here, we redefine structural domains in thermodynamic terms as cooperative folding units, based on m-values, which measure the cooperativity of a protein or its substructures. In our analysis, a domain is equated to a contiguous segment of the folded protein whose m-value is largely unaffected when that segment is excised from its parent structure. Defined in this way, a domain is a self-contained cooperative unit; i.e., its cooperativity depends primarily upon intrasegment interactions, not intersegment interactions. Implementing this concept computationally, the domains in a large representative set of proteins were identified; all exhibit consistency with experimental findings. Specifically, our domain divisions correspond to the experimentally determined equilibrium folding intermediates in a set of nine proteins. The approach was also proofed against a representative set of 71 additional proteins, again with confirmatory results. Our reframed interpretation of a protein domain transforms an indeterminate structural phenomenon into a quantifiable molecular property grounded in solution thermodynamics.

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.

Direct Determination of the Dependence of the Surface Shear and Dilatational Viscosities on the Thermodynamic State of the Interface: Theoretical Foundations.

PubMed

Lopez; Hirsa

1998-10-01

Recent developments in nonlinear optical techniques for noninvasive probing of a surfactant influenced gas/liquid interface allow for the measurement of the surfactant surface concentration, c, and thus provide new opportunities for the direct determination of its intrinsic viscosities. Here, we present the theoretical foundations, based on the Boussinesq-Scriven surface model without the usual simplification of constant viscosities, for an experimental technique to directly measure the surface shear (µs) and dilatational (kappas) viscosities of a Newtonian interface as functions of the surfactant surface concentration. This ability to directly measure the surfactant concentration permits the use of a simple surface flow for the measurement of the surface viscosities. The requirements are that the interface must be nearly flat, and the flow steady, axisymmetric, and swirling; these flow conditions can be achieved in the deep-channel viscometer driven at relatively fast rates. The tangential stress balance on such an interface leads to two equations; the balance in the azimuthal direction involves only µs and its gradients, and the balance in the radial direction involves both µs and kappas and their gradients. By further exploiting recent developments in laser-based flow measuring techniques, the surface velocities and their gradients which appear in the two equations can be measured directly. The surface tension gradient, which appears in the radial balance equation, is incorporated from the equation of state for the surfactant system and direct measurements of the surfactant surface concentration distribution. The stress balance equations are then ordinary differential equations in the surface viscosities as functions of radial position, which can be readily integrated. Since c is measured as a function of radial position, we then have a direct measurement of µs and kappas as functions of c. Numerical computations of the Navier-Stokes equations are performed to determine the appropriate conditions to achieve the requisite secondary flow. Copyright 1998 Academic Press.

Landau levels from neutral Bogoliubov particles in two-dimensional nodal superconductors under strain and doping gradients

NASA Astrophysics Data System (ADS)

Nica, Emilian M.; Franz, Marcel

2018-02-01

Motivated by recent work on strain-induced pseudomagnetic fields in Dirac and Weyl semimetals, we analyze the possibility of analogous fields in two-dimensional nodal superconductors. We consider the prototypical case of a d -wave superconductor, a representative of the cuprate family, and find that the presence of weak, spatially varying strain leads to pseudomagnetic fields and Landau quantization of Bogoliubov quasiparticles in the low-energy sector. A similar effect is induced by the presence of generic, weak doping gradients. In contrast to genuine magnetic fields in superconductors, the strain- and doping-gradient-induced pseudomagnetic fields couple in a way that preserves time-reversal symmetry and is not subject to the screening associated with the Meissner effect. These effects can be probed by tuning weak applied supercurrents which lead to shifts in the energies of the Landau levels and hence to quantum oscillations in thermodynamic and transport quantities.

Protonation free energy levels in complex molecular systems.

PubMed

Antosiewicz, Jan M

2008-04-01

All proteins, nucleic acids, and other biomolecules contain residues capable of exchanging protons with their environment. These proton transfer phenomena lead to pH sensitivity of many molecular processes underlying biological phenomena. In the course of biological evolution, Nature has invented some mechanisms to use pH gradients to regulate biomolecular processes inside cells or in interstitial fluids. Therefore, an ability to model protonation equilibria in molecular systems accurately would be of enormous value for our understanding of biological processes and for possible rational influence on them, like in developing pH dependent drugs to treat particular diseases. This work presents a derivation, by thermodynamic and statistical mechanical methods, of an expression for the free energy of a complex molecular system at arbitrary ionization state of its titratable residues. This constitutes one of the elements of modeling protonation equilibria. Starting from a consideration of a simple acid-base equilibrium of a model compound with a single tritratable group, we arrive at an expression which is of general validity for complex systems. The only approximation used in this derivation is the postulating that the interaction energy between any pair of titratable sites does not depend on the protonation states of all the remaining ionizable groups.

GGA + U studies of the early actinide mononitrides and dinitrides

NASA Astrophysics Data System (ADS)

Obodo, K. O.; Chetty, N.

2013-11-01

We present a detailed comparative study of the electronic and mechanical properties of the early actinide mononitrides and dinitrides within the framework of the Perdew-Burke-Ernzerhof generalized gradient approximation (GGA [PBE]) and GGA + U implementations of density functional theory with the inclusion of spin-orbit coupling. The dependence of selected observables of these materials on the effective U-parameter is investigated in detail. The properties include the lattice constant, bulk modulus, charge density distribution, hybridization of the atomic orbitals, energy of formation and the lattice dynamics. The inclusion of the Hubbard U parameter results in a proper description of the 5f electrons, and is subsequently used in the determination of the structural and electronic properties of these compounds. The mononitrides and dinitrides of the early actinides are metallic except for UN2, which is a semiconductor. These actinide nitrides are non-magnetic with the exception of UN, NpN, PuN, NpN2 and PuN2 that are magnetic systems with orbital-dependent magnetic moments oriented in the z-axis. We observed that ThN2 is elastically unstable to isotropic pressure. We discovered that UN2 is thermodynamically unstable, but may be stabilized by N vacancy formation.

Kinetics and thermodynamics of DNA polymerases with exonuclease proofreading

NASA Astrophysics Data System (ADS)

Gaspard, Pierre

2016-04-01

Kinetic theory and thermodynamics are applied to DNA polymerases with exonuclease activity, taking into account the dependence of the rates on the previously incorporated nucleotide. The replication fidelity is shown to increase significantly thanks to this dependence at the basis of the mechanism of exonuclease proofreading. In particular, this dependence can provide up to a 100-fold lowering of the error probability under physiological conditions. Theory is compared with numerical simulations for the DNA polymerases of T7 viruses and human mitochondria.

Hurricane genesis: on the breaking African easterly waves and critical layers

NASA Astrophysics Data System (ADS)

Asaadi, Ali; Brunet, Gilbert; Yau, Peter

2015-04-01

This study bring new understanding on the decades-old hurricane genesis problem that starts with westward travelling African easterly waves that can evolve into coherent cyclonic vortices depending on their strength and other nonlinear wave breaking processes. In general, observations indicate that only a small fraction of the African easterly waves that occur in a single hurricane season contribute to tropical cyclogenesis. However, this small fraction includes a large portion of named storms. In addition, a recent study by Dunkerton et al. (2009) has shown that named storms in the Atlantic and eastern Pacific basins are almost all associated with a cyclonic Kelvin "cat's eye" of a tropical easterly wave typical of critical layers, located equatorward of the easterly jet axis. To better understand the dynamics involved in hurricane genesis, the flow characteristics and the physical and dynamical mechanisms by which easterly waves form cat's eyes are investigated with the help of atmospheric reanalyzes and numerical simulations. We perform a climatological study of developing easterly waves covering the 1998-2001 hurricane seasons using ERA-Interim 6-hourly reanalysis data. Composite analyses for all named storms show a monotonic potential vorticity (PV) profile with weak meridional PV gradient and a cyclonic (i.e., south of the easterly jet axis) critical line for time periods of several days preceding the cat's eye formation. In addition, the developing PV anomaly composite shows a statistically significant companion wave-packet of non-developing easterly waves. A barotropic shallow water model is used to study the initial value and forced problems of disturbances on a parabolic jet and realistic profiles associated with weak basic state meridional PV gradients, leading to Kelvin cat's eye formation around the jet axis. The results highlight the synergy of the dynamical mechanisms, including wave breaking and PV redistribution within the nonlinear critical layer characterized by weak PV gradients, and the thermodynamical mechanisms such as convectively generated PV anomalies in the cat's eye formation in tropical cyclogenesis. These findings are consistent with the analytical theory of free and forced disturbances to an easterly parabolic jet (Brunet and Warn, 1990; Brunet and Haynes, 1995; Choboter et al., 2000). 1) Dunkerton, T. J., M. T. Montgomery, and Z. Wang, 2009: Tropical cyclogenesis in a tropical wave critical layer: Easterly waves. Atmos. Chem. Phys., 9, 5587-5646. 2) Brunet, G., and T. Warn, 1990: Rossby Wave Critical Layers on a Jet. J. Atmos. Sci., 47, 1173-1178. 3) Brunet, and P. H. Haynes, 1995: The Nonlinear Evolution of Disturbances to a Parabolic Jet. J. Atmos. Sci., 52, 464-477. 4) Choboter, P. F., G. Brunet, and S. A. Maslowe, 2000: Forced Disturbances in a Zero Absolute Vorticity Gradient Environment. J. Atmos. Sci., 57, 1406-1419.

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

Biological proton pumping in an oscillating electric field.

PubMed

Kim, Young C; Furchtgott, Leon A; Hummer, Gerhard

2009-12-31

Time-dependent external perturbations provide powerful probes of the function of molecular machines. Here we study biological proton pumping in an oscillating electric field. The protein cytochrome c oxidase is the main energy transducer in aerobic life, converting chemical energy into an electric potential by pumping protons across a membrane. With the help of master-equation descriptions that recover the key thermodynamic and kinetic properties of this biological "fuel cell," we show that the proton pumping efficiency and the electronic currents in steady state depend significantly on the frequency and amplitude of the applied field, allowing us to distinguish between different microscopic mechanisms of the machine. A spectral analysis reveals dominant reaction steps consistent with an electron-gated pumping mechanism.

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.

Nanoscale multiphase phase field approach for stress- and temperature-induced martensitic phase transformations with interfacial stresses at finite strains

NASA Astrophysics Data System (ADS)

Basak, Anup; Levitas, Valery I.

2018-04-01

A thermodynamically consistent, novel multiphase phase field approach for stress- and temperature-induced martensitic phase transformations at finite strains and with interfacial stresses has been developed. The model considers a single order parameter to describe the austenite↔martensitic transformations, and another N order parameters describing N variants and constrained to a plane in an N-dimensional order parameter space. In the free energy model coexistence of three or more phases at a single material point (multiphase junction), and deviation of each variant-variant transformation path from a straight line have been penalized. Some shortcomings of the existing models are resolved. Three different kinematic models (KMs) for the transformation deformation gradient tensors are assumed: (i) In KM-I the transformation deformation gradient tensor is a linear function of the Bain tensors for the variants. (ii) In KM-II the natural logarithms of the transformation deformation gradient is taken as a linear combination of the natural logarithm of the Bain tensors multiplied with the interpolation functions. (iii) In KM-III it is derived using the twinning equation from the crystallographic theory. The instability criteria for all the phase transformations have been derived for all the kinematic models, and their comparative study is presented. A large strain finite element procedure has been developed and used for studying the evolution of some complex microstructures in nanoscale samples under various loading conditions. Also, the stresses within variant-variant boundaries, the sample size effect, effect of penalizing the triple junctions, and twinned microstructures have been studied. The present approach can be extended for studying grain growth, solidifications, para↔ferro electric transformations, and diffusive phase transformations.

Direct mapping of the temperature and velocity gradients in discs. Imaging the vertical CO snow line around IM Lupi

NASA Astrophysics Data System (ADS)

Pinte, C.; Ménard, F.; Duchêne, G.; Hill, T.; Dent, W. R. F.; Woitke, P.; Maret, S.; van der Plas, G.; Hales, A.; Kamp, I.; Thi, W. F.; de Gregorio-Monsalvo, I.; Rab, C.; Quanz, S. P.; Avenhaus, H.; Carmona, A.; Casassus, S.

2018-01-01

Accurate measurements of the physical structure of protoplanetary discs are critical inputs for planet formation models. These constraints are traditionally established via complex modelling of continuum and line observations. Instead, we present an empirical framework to locate the CO isotopologue emitting surfaces from high spectral and spatial resolution ALMA observations. We apply this framework to the disc surrounding IM Lupi, where we report the first direct, i.e. model independent, measurements of the radial and vertical gradients of temperature and velocity in a protoplanetary disc. The measured disc structure is consistent with an irradiated self-similar disc structure, where the temperature increases and the velocity decreases towards the disc surface. We also directly map the vertical CO snow line, which is located at about one gas scale height at radii between 150 and 300 au, with a CO freeze-out temperature of 21 ± 2 K. In the outer disc (>300 au), where the gas surface density transitions from a power law to an exponential taper, the velocity rotation field becomes significantly sub-Keplerian, in agreement with the expected steeper pressure gradient. The sub-Keplerian velocities should result in a very efficient inward migration of large dust grains, explaining the lack of millimetre continuum emission outside of 300 au. The sub-Keplerian motions may also be the signature of the base of an externally irradiated photo-evaporative wind. In the same outer region, the measured CO temperature above the snow line decreases to ≈15 K because of the reduced gas density, which can result in a lower CO freeze-out temperature, photo-desorption, or deviations from local thermodynamic equilibrium.

Mantle discontinuities mapped by inversion of global surface wave data

NASA Astrophysics Data System (ADS)

Khan, A.; Boschi, L.; Connolly, J.

2009-12-01

We invert global observations of fundamental and higher order Love and Rayleigh surface-wave dispersion data jointly at selected locations for 1D radial profiles of Earth's mantle composition, thermal state and anisotropic structure using a stochastic sampling algorithm. Considering mantle compositions as equilibrium assemblages of basalt and harzburgite, we employ a self-consistent thermodynamic method to compute their phase equilibria and bulk physical properties (P, S wave velocity and density). Combining these with locally varying anisotropy profiles, we determine anisotropic P and S wave velocities to calculate dispersion curves for comparison with observations. Models fitting data within uncertainties, provide us with a range of profiles of composition, temperature and anisotropy. This methodology presents an important complement to conventional seismic tomograpy methods. Our results indicate radial and lateral gradients in basalt fraction, with basalt depletion in the upper and enrichment of the upper part of the lower mantle, in agreement with results from geodynamical calculations, melting processes at mid-ocean ridges and subduction of chemically stratified lithosphere. Compared with PREM and seismic tomography models, our velocity models are generally faster in the upper transition zone (TZ), and slower in the lower TZ, implying a steeper velocity gradient. While less dense than PREM, density gradients in the TZ are also steeper. Mantle geotherms are generally adiabatic in the TZ, whereas in the upper part of the lower mantle stronger lateral variations are observed. The TZ structure, and thus location of the phase transitions in the Olivine system as well as their physical properties, are found to be controlled to a large degree by thermal rather than compositional variations. The retrieved anistropy structure agrees with previous studies indicating positive as well as laterally varying upper mantle anisotropy, while there is little evidence for anisotropy in and below the TZ.

On mantle chemical and thermal heterogeneities and anisotropy as mapped by inversion of global surface wave data

NASA Astrophysics Data System (ADS)

Khan, A.; Boschi, L.; Connolly, J. A. D.

2009-09-01

We invert global observations of fundamental and higher-order Love and Rayleigh surface wave dispersion data jointly at selected locations for 1-D radial profiles of Earth's mantle composition, thermal state, and anisotropic structure using a stochastic sampling algorithm. Considering mantle compositions as equilibrium assemblages of basalt and harzburgite, we employ a self-consistent thermodynamic method to compute their phase equilibria and bulk physical properties (P, S wave velocity and density). Combining these with locally varying anisotropy profiles, we determine anisotropic P and S wave velocities to calculate dispersion curves for comparison with observations. Models fitting data within uncertainties provide us with a range of profiles of composition, temperature, and anisotropy. This methodology presents an important complement to conventional seismic tomography methods. Our results indicate radial and lateral gradients in basalt fraction, with basalt depletion in the upper and enrichment of the upper part of the lower mantle, in agreement with results from geodynamical calculations, melting processes at mid-ocean ridges, and subduction of chemically stratified lithosphere. Compared with preliminary reference Earth model (PREM) and seismic tomography models, our velocity models are generally faster in the upper transition zone (TZ) and slower in the lower TZ, implying a steeper velocity gradient. While less dense than PREM, density gradients in the TZ are also steeper. Mantle geotherms are generally adiabatic in the TZ, whereas in the upper part of the lower mantle, stronger lateral variations are observed. The retrieved anisotropy structure agrees with previous studies indicating positive as well as laterally varying upper mantle anisotropy, while there is little evidence for anisotropy in and below the TZ.

Environmental Effects on the Metallicities of Early-Type Galaxies

NASA Technical Reports Server (NTRS)

Jones, Christine; Oliversen, Ronald (Technical Monitor)

2004-01-01

We completed and published two papers in the Astrophysical Journal based on research from grant. In the first paper we analyzed nine X-ray-bright Virgo early-type galaxies observed by both ASCA and ROSAT. Through spatially resolved spectroscopy, we determined the radial temperature profiles and abundances of Mg, Si, and Fe for six galaxies. The temperature profiles are consistent with isothermal temperatures outside of cooler regions at the galaxies' centers. We present new evidence for iron abundance gradients in NGC 4472 and NGC 4649 and confirm the previous results on NGC 4636. Mg and Si abundance gradients on average are flatter than those of iron and correspond to an underabundance of α-process elements at high Fe values, while at low iron the element ratios favor enrichment by Type II supernovae (SNe). We explain the observed trend using the metallicity dependence of SN Ia metal production and present constraints on the available theoretical modeling for low-metallicity inhibition of SNe Ia. In the second paper We analyzed nine X-ray-bright Virgo early-type galaxies observed by both ASCA and ROSAT. Through spatially resolved spectroscopy, we determined the radial temperature profiles and abundances of Mg, Si, and Fe for six galaxies. The temperature profiles are consistent with isothermal temperatures outside of cooler regions at the galaxies' centers. We present new evidence for iron abundance gradients in NGC 4472 and NGC 4649 and confirm the previous results on NGC 4636. Mg and Si abundance gradients on average are flatter than those of iron and correspond to an underabundance of α-process elements at high Fe values, while at low iron the element ratios favor enrichment by Type I1 supernovae (SNe). We explain the observed trend using the metallicity dependence of SN Ia metal production and present constraints on the available theoretical modeling for low-metallicity inhibition of SNe Ia.

Fabrication and microstructures of functional gradient SiBCN–Nb composite by hot pressing

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

Sun, Min, E-mail: lcxsunmin@163.com; Fu, Ruoyu; Chen, Jun

2016-04-15

A functional gradient material with five layers composed of SiBCN ceramic and niobium (Nb) was prepared successfully by hot pressing. The phase composition, morphology features and microstructures were investigated in each layer of the gradient material. The Nb-containing compounds involving NbC, Nb{sub 6}C{sub 5}, Nb{sub 4}C{sub 3}, Nb{sub 5}Si{sub 3} and NbN increase with the volume fraction of Nb increasing in the sub-layer. They are randomly scattered (≤ 25 vol.% Nb), then strip-like, and finally distribute continuously (≥ 75 vol.% Nb). The size of BN(C) and SiC grains in Nb-containing layers is larger than in 100% SiBCN layer due tomore » the loss of the capsule-like structures. No distinct interfaces form in the transition regions indicating the gradual changes in phase composition and microstructures. - Highlights: • A functional gradient SiBCN–Nb material was prepared successfully by hot pressing. • Phase composition, morphology features and microstructures were investigated. • Thermodynamic calculation was used to aid in the phase analysis. • No distinct interfaces form typical of the functional gradient material.« less

Additive manufacturing of complex-shaped graded TiC/steel composites

DOE PAGES

Levy, Asaf; Miriyev, Aslan; Elliott, Amy; ...

2017-01-12

Complex-shaped TiCx ceramic preforms with a gradient of carbon content in the titanium carbide phase (x changes from 0.7 to 0.98) were fabricated for the first time by Binder jet 3D printing technology. The complex-shaped preforms were infiltrated with molten carbon steel (0.7 wt.%C). Thermodynamic considerations showed that carbon could be transferred from titanium carbide to steel and vice versa according to the initial concentration of carbon (activity) in both phases. After infiltration, solidification and slow cooling, a microstructural gradient was obtained throughout the steel matrix from ferrite, in the region where the steel was in contact with titanium carbidemore » of low carbon content (x=0.7), to pearlite, in the region where the steel underwent interactions with stoichiometric titanium carbide (x=0.98). After annealing at 900°C and quenching in oil, a structural gradient in the steel matrix from ferrite to martensite was obtained, resulting in a hardness gradient of 700-1600 HV. The suggested processing approach allows for fabrication of complex-shaped graded composites with the desired property gradient suitable for a wide range of practical applications.« less

Additive manufacturing of complex-shaped graded TiC/steel composites

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

Levy, Asaf; Miriyev, Aslan; Elliott, Amy

Complex-shaped TiCx ceramic preforms with a gradient of carbon content in the titanium carbide phase (x changes from 0.7 to 0.98) were fabricated for the first time by Binder jet 3D printing technology. The complex-shaped preforms were infiltrated with molten carbon steel (0.7 wt.%C). Thermodynamic considerations showed that carbon could be transferred from titanium carbide to steel and vice versa according to the initial concentration of carbon (activity) in both phases. After infiltration, solidification and slow cooling, a microstructural gradient was obtained throughout the steel matrix from ferrite, in the region where the steel was in contact with titanium carbidemore » of low carbon content (x=0.7), to pearlite, in the region where the steel underwent interactions with stoichiometric titanium carbide (x=0.98). After annealing at 900°C and quenching in oil, a structural gradient in the steel matrix from ferrite to martensite was obtained, resulting in a hardness gradient of 700-1600 HV. The suggested processing approach allows for fabrication of complex-shaped graded composites with the desired property gradient suitable for a wide range of practical applications.« less

Thermodiffusion as a means to manipulate liquid film dynamics on chemically patterned surfaces

PubMed Central

Kalpathy, Sreeram K.; Shreyes, Amrita Ravi

2017-01-01

The model problem examined here is the stability of a thin liquid film consisting of two miscible components, resting on a chemically patterned solid substrate and heated from below. In addition to surface tension gradients, the temperature variations also induce gradients in the concentration of the film by virtue of thermodiffusion/Soret effects. We study the stability and dewetting behaviour due to the coupled interplay between thermal gradients, Soret effects, long-range van der Waals forces, and wettability gradient-driven flows. Linear stability analysis is first employed to predict growth rates and the critical Marangoni number for chemically homogeneous surfaces. Then, nonlinear simulations are performed to unravel the interfacial dynamics and possible locations of the film rupture on chemically patterned substrates. Results suggest that appropriate tuning of the Soret parameter and its direction, in conjunction with either heating or cooling, can help manipulate the location and time scales of the film rupture. The Soret effect can either potentially aid or oppose film instability depending on whether the thermal and solutal contributions to flow are cooperative or opposed to each other. PMID:28595391

A constitutive model for magnetostriction based on thermodynamic framework

NASA Astrophysics Data System (ADS)

Ho, Kwangsoo

2016-08-01

This work presents a general framework for the continuum-based formulation of dissipative materials with magneto-mechanical coupling in the viewpoint of irreversible thermodynamics. The thermodynamically consistent model developed for the magnetic hysteresis is extended to include the magnetostrictive effect. The dissipative and hysteretic response of magnetostrictive materials is captured through the introduction of internal state variables. The evolution rate of magnetostrictive strain as well as magnetization is derived from thermodynamic and dissipative potentials in accordance with the general principles of thermodynamics. It is then demonstrated that the constitutive model is competent to describe the magneto-mechanical behavior by comparing simulation results with the experimental data reported in the literature.

Reconstructing thermal properties of firn at Summit, Greenland from a temperature profile

NASA Astrophysics Data System (ADS)

Giese, A. L.; Hawley, R. L.

2013-12-01

Thermodynamic properties of firn are important factors when considering energy balance and temperature-dependent physical processes in the near-surface of glaciers. Of particular interest is thermal diffusivity, which can take a range of values and which governs both the temperature gradient and its evolution through time. Given that temperature is a well-established driver of firn densification, a better understanding of heat transfer will permit greater accuracy in the compaction models essential for interpreting inter-annual and seasonal ice surface elevation changes detected by airborne and satellite altimetry. Due to its dependence on microstructure, diffusivity can vary significantly by location. Rather than directly measuring diffusivity or one of its proxies (e.g. density, hardness, shear strength), this study inverts the heat equation to reconstruct diffusivity values. This is a less logistically-intensive approach which circumvents many of the challenges associated with imperfect proxies and snow metamorphism during measurement. Hourly records (May 2004 - July 2008) from 8 thermistors placed in the top 10 m at Summit, Greenland provide temperature values for Summit's firn, which is broadly representative of firn across the ice sheet's dry snow zone. In this study, we use both physical analysis and a finite-difference numerical model to determine a diffusivity magnitude and gradient; we find that diffusivity of Summit firn falls in the lower end of the range expected from local density and temperature conditions alone (i.e. 15 - 36 m^2/a for firn at -30C). Further, we assess the utility of our modeling approach, explore the validity of assuming bulk conductive heat transfer when modeling temperature changes in non-homogeneous firn, and investigate the implications of a low-end diffusivity value for surface compaction modeling in Greenland.

Mass transport in morphogenetic processes: A second gradient theory for volumetric growth and material remodeling

NASA Astrophysics Data System (ADS)

Ciarletta, P.; Ambrosi, D.; Maugin, G. A.

2012-03-01

In this work, we derive a novel thermo-mechanical theory for growth and remodeling of biological materials in morphogenetic processes. This second gradient hyperelastic theory is the first attempt to describe both volumetric growth and mass transport phenomena in a single-phase continuum model, where both stress- and shape-dependent growth regulations can be investigated. The diffusion of biochemical species (e.g. morphogens, growth factors, migration signals) inside the material is driven by configurational forces, enforced in the balance equations and in the set of constitutive relations. Mass transport is found to depend both on first- and on second-order material connections, possibly withstanding a chemotactic behavior with respect to diffusing molecules. We find that the driving forces of mass diffusion can be written in terms of covariant material derivatives reflecting, in a purely geometrical manner, the presence of a (first-order) torsion and a (second-order) curvature. Thermodynamical arguments show that the Eshelby stress and hyperstress tensors drive the rearrangement of the first- and second-order material inhomogeneities, respectively. In particular, an evolution law is proposed for the first-order transplant, extending a well-known result for inelastic materials. Moreover, we define the first stress-driven evolution law of the second-order transplant in function of the completely material Eshelby hyperstress. The theory is applied to two biomechanical examples, showing how an Eshelbian coupling can coordinate volumetric growth, mass transport and internal stress state, both in physiological and pathological conditions. Finally, possible applications of the proposed model are discussed for studying the unknown regulation mechanisms in morphogenetic processes, as well as for optimizing scaffold architecture in regenerative medicine and tissue engineering.

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).

Energy conservation by oxidation of formate to carbon dioxide and hydrogen via a sodium ion current in a hyperthermophilic archaeon

PubMed Central

Lim, Jae Kyu; Mayer, Florian; Kang, Sung Gyun; Müller, Volker

2014-01-01

Thermococcus onnurineus NA1 is known to grow by the anaerobic oxidation of formate to CO2 and H2, a reaction that operates near thermodynamic equilibrium. Here we demonstrate that this reaction is coupled to ATP synthesis by a transmembrane ion current. Formate oxidation leads to H+ translocation across the cytoplasmic membrane that then drives Na+ translocation. The ion-translocating electron transfer system is rather simple, consisting of only a formate dehydrogenase module, a membrane-bound hydrogenase module, and a multisubunit Na+/H+ antiporter module. The electrochemical Na+ gradient established then drives ATP synthesis. These data give a mechanistic explanation for chemiosmotic energy conservation coupled to formate oxidation to CO2 and H2. Because it is discussed that the membrane-bound hydrogenase with the Na+/H+ antiporter module are ancestors of complex I of mitochondrial and bacterial electron transport these data also shed light on the evolution of ion transport in complex I-like electron transport chains. PMID:25049407

Energy conservation by oxidation of formate to carbon dioxide and hydrogen via a sodium ion current in a hyperthermophilic archaeon.

PubMed

Lim, Jae Kyu; Mayer, Florian; Kang, Sung Gyun; Müller, Volker

2014-08-05

Thermococcus onnurineus NA1 is known to grow by the anaerobic oxidation of formate to CO2 and H2, a reaction that operates near thermodynamic equilibrium. Here we demonstrate that this reaction is coupled to ATP synthesis by a transmembrane ion current. Formate oxidation leads to H(+) translocation across the cytoplasmic membrane that then drives Na(+) translocation. The ion-translocating electron transfer system is rather simple, consisting of only a formate dehydrogenase module, a membrane-bound hydrogenase module, and a multisubunit Na(+)/H(+) antiporter module. The electrochemical Na(+) gradient established then drives ATP synthesis. These data give a mechanistic explanation for chemiosmotic energy conservation coupled to formate oxidation to CO2 and H2. Because it is discussed that the membrane-bound hydrogenase with the Na(+)/H(+) antiporter module are ancestors of complex I of mitochondrial and bacterial electron transport these data also shed light on the evolution of ion transport in complex I-like electron transport chains.

Optimal Control of Thermo--Fluid Phenomena in Variable Domains

NASA Astrophysics Data System (ADS)

Volkov, Oleg; Protas, Bartosz

2008-11-01

This presentation concerns our continued research on adjoint--based optimization of viscous incompressible flows (the Navier--Stokes problem) coupled with heat conduction involving change of phase (the Stefan problem), and occurring in domains with variable boundaries. This problem is motivated by optimization of advanced welding techniques used in automotive manufacturing, where the goal is to determine an optimal heat input, so as to obtain a desired shape of the weld pool surface upon solidification. We argue that computation of sensitivities (gradients) in such free--boundary problems requires the use of the shape--differential calculus as a key ingredient. We also show that, with such tools available, the computational solution of the direct and inverse (optimization) problems can in fact be achieved in a similar manner and in a comparable computational time. Our presentation will address certain mathematical and computational aspects of the method. As an illustration we will consider the two--phase Stefan problem with contact point singularities where our approach allows us to obtain a thermodynamically consistent solution.

Concentrations and speciation of arsenic along a groundwater flow-path in the Upper Floridan aquifer, Florida, USA

NASA Astrophysics Data System (ADS)

Haque, S. E.; Johannesson, K. H.

2006-05-01

Arsenic (As) concentrations and speciation were determined in groundwaters along a flow-path in the Upper Floridan aquifer (UFA) to investigate the biogeochemical “evolution“ of As in this relatively pristine aquifer. Dissolved inorganic As species were separated in the field using anion-exchange chromatography and subsequently analyzed by inductively coupled plasma mass spectrometry. Total As concentrations are higher in the recharge area groundwaters compared to down-gradient portions of UFA. Redox conditions vary from relatively oxic to anoxic along the flow-path. Mobilization of As species in UFA groundwaters is influenced by ferric iron reduction and subsequent dissolution, sulfate reduction, and probable pyrite precipitation that are inferred from the data to occur along distinct regions of the flow-path. In general, the distribution of As species are consistent with equilibrium thermodynamics, such that arsenate dominates in more oxidizing waters near the recharge area, and arsenite predominates in the progressively reducing groundwaters beyond the recharge area.

Ultrafast Chemistry under Nonequilibrium Conditions and the Shock to Deflagration Transition at the Nanoscale

DOE PAGES

Wood, Mitchell A.; Cherukara, Mathew J.; Kober, Edward M.; ...

2015-06-13

We use molecular dynamics simulations to describe the chemical reactions following shock-induced collapse of cylindrical pores in the high-energy density material RDX. For shocks with particle velocities of 2 km/s we find that the collapse of a 40 nm diameter pore leads to a deflagration wave. Molecular collisions during the collapse lead to ultrafast, multistep chemical reactions that occur under nonequilibrium conditions. WE found that exothermic products formed during these first few picoseconds prevent the nanoscale hotspot from quenching. Within 30 ps, a local deflagration wave develops. It propagates at 0.25 km/s and consists of an ultrathin reaction zone ofmore » only ~5 nm, thus involving large temperature and composition gradients. Contrary to the assumptions in current models, a static thermal hotspot matching the dynamical one in size and thermodynamic conditions fails to produce a deflagration wave indicating the importance of nonequilibrium loading in the criticality of nanoscale hot spots. These results provide insight into the initiation of reactive decomposition.« less

Development of Computational Tools for Modeling Thermal and Radiation Effects on Grain Boundary Segregation and Precipitation in Fe-Cr-Ni-based Alloys

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

Yang, Ying

This work aims at developing computational tools for modeling thermal and radiation effects on solute segregation at grain boundaries (GBs) and precipitation. This report described two major efforts. One is the development of computational tools on integrated modeling of thermal equilibrium segregation (TES) and radiation-induced segregation (RIS), from which synergistic effects of thermal and radiation, pre-existing GB segregation have been taken into consideration. This integrated modeling was used in describing the Cr and Ni segregation in the Fe-Cr-Ni alloys. The other effort is thermodynamic modeling on the Fe-Cr-Ni-Mo system which includes the major alloying elements in the investigated alloys inmore » the Advanced Radiation Resistant Materials (ARRM) program. Through thermodynamic calculation, we provide baseline thermodynamic stability of the hardening phase Ni2(Cr,Mo) in selected Ni-based super alloys, and contribute knowledge on mechanistic understanding on the formation of Ni2(Cr,Mo) in the irradiated materials. The major outcomes from this work are listed in the following: 1) Under the simultaneous thermal and irradiation conditions, radiation-induced segregation played a dominant role in the GB segregation. The pre-existing GB segregation only affects the subsequent radiation-induced segregation in the short time. For the same element, the segregation tendency of Cr and Ni due to TES is opposite to it from RIS. The opposite tendency can lead to the formation of W-shape profile. These findings are consistent with literature observation of the transitory W-shape profile. 2) While TES only affects the distance of one or two atomic layers from GBs, the RIS can affect a broader distance from GB. Therefore, the W-shape due to pre-existing GB segregation is much narrower than that due to composition gradient formed during the transient state. Considering the measurement resolution of Auger or STEM analysis, the segregation tendency due to RIS should play a dominant role in the measured values. However, The GB segregation due to pre-existing GB segregation may affect the chemical potential of element at GB, and subsequently the corrosion resistance. 3) Based on the newly developed thermodynamic database of Fe-Cr-Ni-Mo, we predicted the Ni2(Cr,Mo) as a thermodynamically stable phase in all investigated low Fe-content Ni-based alloys. The calculated phase amount decreases with the increasing Fe content, being consistent with that observed in the irradiated materials. 4) The formation of the Ni2(Cr,Mo) phase in irradiated materials is due to irradiation enhanced diffusion. The calculated equilibrium Ni2(Cr,Mo) amount is more than that observed in the irradiated materials, suggesting that the amount of Ni2(Cr,Mo) is likely to increase more with further irradiation.« less

SDSS-IV MaNGA: modelling the metallicity gradients of gas and stars - radially dependent metal outflow versus IMF

NASA Astrophysics Data System (ADS)

Lian, Jianhui; Thomas, Daniel; Maraston, Claudia; Goddard, Daniel; Parikh, Taniya; Fernández-Trincado, J. G.; Roman-Lopes, Alexandre; Rong, Yu; Tang, Baitian; Yan, Renbin

2018-05-01

In our previous work, we found that only two scenarios are capable of reproducing the observed integrated mass-metallicity relations for the gas and stellar components of local star-forming galaxies simultaneously. One scenario invokes a time-dependent metal outflow loading factor with stronger outflows at early times. The other scenario uses a time-dependent initial mass function (IMF) slope with a steeper IMF at early times. In this work, we extend our study to investigate the radial profile of gas and stellar metallicity in local star-forming galaxies using spatially resolved spectroscopic data from the SDSS-IV MaNGA survey. We find that most galaxies show negative gradients in both gas and stellar metallicity with steeper gradients in stellar metallicity. The stellar metallicity gradients tend to be mass dependent with steeper gradients in more massive galaxies while no clear mass dependence is found for the gas metallicity gradient. Then we compare the observations with the predictions from a chemical evolution model of the radial profiles of gas and stellar metallicities. We confirm that the two scenarios proposed in our previous work are also required to explain the metallicity gradients. Based on these two scenarios, we successfully reproduce the radial profiles of gas metallicity, stellar metallicity, stellar mass surface density, and star formation rate surface density simultaneously. The origin of the negative gradient in stellar metallicity turns out to be driven by either radially dependent metal outflow or IMF slope. In contrast, the radial dependence of the gas metallicity is less constrained because of the degeneracy in model parameters.

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).

Interactions between solidification and compositional convection in mushy layers

NASA Technical Reports Server (NTRS)

Worster, M. Grae

1994-01-01

Mushy layers are ubiquitous during the solidification of alloys. They are regions of mixed phase wherein solid crystals are bathed in the melt from which they grew. The matrix of crystals forms a porous medium through which the melt can flow, driven either by external forces or by its own buoyancy in a gravitational field. Buoyancy-driven convection of the melt depends both on temperature gradients, which are necessary for solidification, and on compositional gradients, which are generated as certain components of the alloy are preferentially incorporated in the solid phase and the remaining components are expelled into the melt. In fully liquid regions, the combined action of temperature and concentration on the density of the liquid can cause various forms of double-diffusive convection. However, in the interior of mushy regions the temperature and concentration are thermodynamically coupled so only single-diffusive convection can occur. Typically, the effect of composition on the buoyancy of the melt is much greater than the effect of temperature, and thus convection in mushy layers in driven primarily by the computational gradients within them. The rising interstitial liquid is relatively dilute, having come from colder regions of the mushy layer, where the liquidus concentration is lower, and can dissolve the crystal matrix through which it flows. This is the fundamental process by which chimneys are formed. It is a nonlinear process that requires the convective velocities to be sufficiently large, so fully fledged chimneys (narrow channels) might be avoided by means that weaken the flow. Better still would be to prevent convection altogether, since even weak convection will cause lateral, compositional inhomogeneities in castings. This report outlines three studies that examine the onset of convection within mushy layers.

Limits of predictions in thermodynamic systems: a review

NASA Astrophysics Data System (ADS)

Marsland, Robert, III; England, Jeremy

2018-01-01

The past twenty years have seen a resurgence of interest in nonequilibrium thermodynamics, thanks to advances in the theory of stochastic processes and in their thermodynamic interpretation. Fluctuation theorems provide fundamental constraints on the dynamics of systems arbitrarily far from thermal equilibrium. Thermodynamic uncertainty relations bound the dissipative cost of precision in a wide variety of processes. Concepts of excess work and excess heat provide the basis for a complete thermodynamics of nonequilibrium steady states, including generalized Clausius relations and thermodynamic potentials. But these general results carry their own limitations: fluctuation theorems involve exponential averages that can depend sensitively on unobservably rare trajectories; steady-state thermodynamics makes use of a dual dynamics that lacks any direct physical interpretation. This review aims to present these central results of contemporary nonequilibrium thermodynamics in such a way that the power of each claim for making physical predictions can be clearly assessed, using examples from current topics in soft matter and biophysics.

Implicit constitutive models with a thermodynamic basis: a study of stress concentration

NASA Astrophysics Data System (ADS)

Bridges, C.; Rajagopal, K. R.

2015-02-01

Motivated by the recent generalization of the class of elastic bodies by Rajagopal (Appl Math 48:279-319, 2003), there have been several recent studies that have been carried out within the context of this new class. Rajagopal and Srinivasa (Proc R Soc Ser A 463:357-367, 2007, Proc R Soc Ser A: Math Phys Eng Sci 465:493-500, 2009) provided a thermodynamic basis for such models and appealing to the idea that rate of entropy production ought to be maximized they developed nonlinear rate equations of the form where T is the Cauchy stress and D is the stretching tensor as well as , where S is the Piola-Kirchhoff stress tensor and E is the Green-St. Venant strain tensor. We follow a similar procedure by utilizing the Gibb's potential and the left stretch tensor V from the Polar Decomposition of the deformation gradient, and we show that when the displacement gradient is small one arrives at constitutive relations of the form . This is, of course, in stark contrast to traditional elasticity wherein one obtains a single model, Hooke's law, when the displacement gradient is small. By solving a classical boundary value problem, with a particular form for f( T), we show that when the stresses are small, the strains are also small which is in agreement with traditional elasticity. However, within the context of our model, when the stress blows up the strains remain small, unlike the implications of Hooke's law. We use this model to study boundary value problems in annular domains to illustrate its efficacy.

Nonlinear Impedance Analysis of La 0.4Sr 0.6Co 0.2Fe 0.8O 3-δ Thin Film Oxygen Electrodes

DOE PAGES

Geary, Tim C.; Lee, Dongkyu; Shao-Horn, Yang; ...

2016-07-23

Here, linear and nonlinear electrochemical impedance spectroscopy (EIS, NLEIS) were used to study 20 nm thin film La 0.6Sr 0.4Co 0.2Fe 0.8O 3-δ (LSCF-6428) electrodes at 600°C in oxygen environments. LSCF films were epitaxially deposited on single crystal yttria-stabilized zirconia (YSZ) with a 5 nm gadolinium-doped ceria (GDC) protective interlayer. Impedance measurements reveal an oxygen storage capacity similar to independent thermogravimetry measurements on semi-porous pellets. However, the impedance data fail to obey a homogeneous semiconductor point-defect model. Two consistent scenarios were considered: a homogeneous film with non-ideal thermodynamics (constrained by thermogravimetry measurements), or an inhomogeneous film (constrained by a semiconductormore » point-defect model with a Sr maldistribution). The latter interpretation suggests that gradients in Sr composition would have to extend beyond the space-charge region of the gas-electrode interface. While there is growing evidence supporting an equilibrium Sr segregation at the LSCF surface monolayer, a long-range, non-equilibrium Sr stratification caused by electrode processing conditions offers a possible explanation for the large volume of highly reducible LSCF. Additionally, all thin films exhibited fluctuations in both linear and nonlinear impedance over the hundred-hour measurement period. This behavior is inconsistent with changes solely in the surface rate coefficient and possibly caused by variations in the surface thermodynamics over exposure time.« less

A stratocumulus thermodynamic analysis: July 5 case study

NASA Technical Reports Server (NTRS)

Austin, Philip

1990-01-01

On July 5 (NCAR Electra flight 4, Mission 186-G) the Electra flew a single aircraft mission which consisted of cross and along-wind legs at 6 different altitudes between 10:43 to 16:00 PDT (17:43 to 23:00 GMT). The leg length was kept short (8 to 10 minutes) to permit maximum vertical resolution, and there were 8 soundings. Observer notes report a thin, solid stratocumulus cloud deck which gradually became more broken in the afternoon. Winds were from the north at 10 to 13/ms throughout the night. Sea surface temperature measurements and conservative variable analyses for several of the July 5 legs are presented. These results are preliminary to a study of the thermodynamic budget on July 5; they indicate that: the sea surface temperature dropped more than 1 K (from 17.3 to 15.9 C) over the course of the flight (18:01 and at 21:51 GMT); mixing lines for each of the horizontal subcloud legs show the effect of a strong north-south gradient in SST; and there is a clear demarcation over a transition of 5 to 10 km between air to the south and cooler, moister air to the north. The FSSP measurements indicate there are small clouds/scud 250 m below cloud base on the cold northern side of this transition. The transition is seen in the saturation point diagrams at 984, 959, and 946 mb. There is no corresponding change in the horizontal wind across the transition regions.

Size-dependent pressure-induced amorphization: a thermodynamic panorama.

PubMed

Machon, Denis; Mélinon, Patrice

2015-01-14

Below a critical particle size, some pressurized compounds (e.g. TiO2, Y2O3, PbTe) undergo a crystal-to-amorphous transformation instead of a polymorphic transition. This effect reflects the greater propensity of nanomaterials for amorphization. In this work, a panorama of thermodynamic interpretations is given: first, a descriptive analysis based on the energy landscape concept gives a general comprehension of the balance between thermodynamics and kinetics to obtain an amorphous state. Then, a formal approach based on Gibbs energy to describe the thermodynamics and phase transitions in nanoparticles gives a basic explanation of size-dependent pressure-induced amorphization. The features of this transformation (amorphization occurs at pressures lower than the polymorphic transition pressure!) and the nanostructuration can be explained in an elaborated model based on the Ginzburg-Landau theory of phase transition and on percolation theory. It is shown that the crossover between polymorphic transition and amorphization is highly dependent on the defect density and interfacial energy, i.e., on the synthesis process. Their behavior at high pressure is a quality control test for the nanoparticles.

Differential invariants for spherical flows of a viscid fluid

NASA Astrophysics Data System (ADS)

Duyunova, Anna; Lychagin, Valentin; Tychkov, Sergey

2018-01-01

Symmetries and the corresponding algebras of differential invariants of viscid fluids on a sphere are given. Their dependence on thermodynamical states of media is studied, and a classification of thermodynamical states is given.

Microbial Preference for Soil Organic Carbon Changes Along Redox Gradients as a Function of the Energetic Cost of Respiration

NASA Astrophysics Data System (ADS)

Naughton, H.; Keiluweit, M.; Fendorf, S. E.; Farrant, D. N.

2016-12-01

Soil organic carbon (SOC) chemistry is known to impact carbon preservation via mineral associations and physical protection, which chemically or physically block SOC from microbial enzymatic access for decomposition. However, SOC decay models that include these processes do not reliably predict SOC dynamics. We propose that the energetics of respiration additionally regulate SOC cycling. Specifically, organic carbon will only be respired if the available electron acceptors yield enough energy for microbial growth when metabolically coupled to the SOC. To test this hypothesis, we constructed dual pore domain reactors in which water flows normal to a column of packed soil, allowing oxygen to diffuse from the upper channel through the soil and establish a redox gradient. With increasing depth into the soil column, the soil experiences a typical redox profile indicative of anaerobic respiration processes: after oxygen is consumed, nitrate, Mn, Fe, and sulfate serve as electron acceptors. We measure porewater and effluent for nitrate, sulfate, Fe(II) and Mn(II) and take microsensor profiles of dissolved oxygen and H2S to characterize the redox gradient and respiration pathways. To this we couple incubations of solid material at each depth post-experiment and quantify CO2 and CH4 production to assess respiration potential along the redox gradient. Porewater SOC chemistry is analyzed via spectroscopy and mass spectrometry to interpret SOC oxidation state and composition and thus test thermodynamic predictions on SOC stability given the available redox acceptors at a given depth in the reactor. Within 0.5 cm of the soil surface, oxygen concentrations drop below detection and signs of anaerobic respiration (Fe(II) production, loss of nitrate) initiate while respiration rates drops precipitously. More oxidized SOC is preferentially utilized with progression along the redox gradient, supporting thermodynamic predictions. This work highlights the potential of SOC chemistry within specific redox metabolic zones of soils and sediments to drive carbon utilization. An improved understanding on organic carbon utliization is critical to predict SOC dynamics under changing hydrology (e.g. saltwater intrusion, permafrost melting), temperature, and other factors impacting microbial respiration energetics.

On the thermomechanical coupling in dissipative materials: A variational approach for generalized standard materials

NASA Astrophysics Data System (ADS)

Bartels, A.; Bartel, T.; Canadija, M.; Mosler, J.

2015-09-01

This paper deals with the thermomechanical coupling in dissipative materials. The focus lies on finite strain plasticity theory and the temperature increase resulting from plastic deformation. For this type of problem, two fundamentally different modeling approaches can be found in the literature: (a) models based on thermodynamical considerations and (b) models based on the so-called Taylor-Quinney factor. While a naive straightforward implementation of thermodynamically consistent approaches usually leads to an over-prediction of the temperature increase due to plastic deformation, models relying on the Taylor-Quinney factor often violate fundamental physical principles such as the first and the second law of thermodynamics. In this paper, a thermodynamically consistent framework is elaborated which indeed allows the realistic prediction of the temperature evolution. In contrast to previously proposed frameworks, it is based on a fully three-dimensional, finite strain setting and it naturally covers coupled isotropic and kinematic hardening - also based on non-associative evolution equations. Considering a variationally consistent description based on incremental energy minimization, it is shown that the aforementioned problem (thermodynamical consistency and a realistic temperature prediction) is essentially equivalent to correctly defining the decomposition of the total energy into stored and dissipative parts. Interestingly, this decomposition shows strong analogies to the Taylor-Quinney factor. In this respect, the Taylor-Quinney factor can be well motivated from a physical point of view. Furthermore, certain intervals for this factor can be derived in order to guarantee that fundamental physically principles are fulfilled a priori. Representative examples demonstrate the predictive capabilities of the final constitutive modeling framework.

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.

Nonideal Solute Chemical Potential Equation and the Validity of the Grouped Solute Approach for Intracellular Solution Thermodynamics.

PubMed

Zielinski, Michal W; McGann, Locksley E; Nychka, John A; Elliott, Janet A W

2017-11-22

The prediction of nonideal chemical potentials in aqueous solutions is important in fields such as cryobiology, where models of water and solute transport-that is, osmotic transport-are used to help develop cryopreservation protocols and where solutions contain many varied solutes and are generally highly concentrated and thus thermodynamically nonideal. In this work, we further the development of a nonideal multisolute solution theory that has found application across a broad range of aqueous systems. This theory is based on the osmotic virial equation and does not depend on multisolute data. Specifically, we derive herein a novel solute chemical potential equation that is thermodynamically consistent with the existing model, and we establish the validity of a grouped solute model for the intracellular space. With this updated solution theory, it is now possible to model cellular osmotic behavior in nonideal solutions containing multiple permeating solutes, such as those commonly encountered by cells during cryopreservation. In addition, because we show here that for the osmotic virial equation the grouped solute approach is mathematically equivalent to treating each solute separately, multisolute solutions in other applications with fixed solute mass ratios can now be treated rigorously with such a model, even when all of the solutes cannot be enumerated.

Folding thermodynamics of model four-strand antiparallel beta-sheet proteins.

PubMed Central

Jang, Hyunbum; Hall, Carol K; Zhou, Yaoqi

2002-01-01

The thermodynamic properties for three different types of off-lattice four-strand antiparallel beta-strand protein models interacting via a hybrid Go-type potential have been investigated. Discontinuous molecular dynamic simulations have been performed for different sizes of the bias gap g, an artificial measure of a model protein's preference for its native state. The thermodynamic transition temperatures are obtained by calculating the squared radius of gyration R(g)(2), the root-mean-squared pair separation fluctuation Delta(B), the specific heat C(v), the internal energy of the system E, and the Lindemann disorder parameter Delta(L). Despite these models' simplicity, they exhibit a complex set of protein transitions, consistent with those observed in experimental studies on real proteins. Starting from high temperature, these transitions include a collapse transition, a disordered-to-ordered globule transition, a folding transition, and a liquid-to-solid transition. The high temperature transitions, i.e., the collapse transition and the disordered-to-ordered globule transition, exist for all three beta-strand proteins, although the native-state geometry of the three model proteins is different. However the low temperature transitions, i.e., the folding transition and the liquid-to-solid transition, strongly depend on the native-state geometry of the model proteins and the size of the bias gap. PMID:11806908

Steepest entropy ascent model for far-nonequilibrium thermodynamics: Unified implementation of the maximum entropy production principle

NASA Astrophysics Data System (ADS)

Beretta, Gian Paolo

2014-10-01

By suitable reformulations, we cast the mathematical frameworks of several well-known different approaches to the description of nonequilibrium dynamics into a unified formulation valid in all these contexts, which extends to such frameworks the concept of steepest entropy ascent (SEA) dynamics introduced by the present author in previous works on quantum thermodynamics. Actually, the present formulation constitutes a generalization also for the quantum thermodynamics framework. The analysis emphasizes that in the SEA modeling principle a key role is played by the geometrical metric with respect to which to measure the length of a trajectory in state space. In the near-thermodynamic-equilibrium limit, the metric tensor is directly related to the Onsager's generalized resistivity tensor. Therefore, through the identification of a suitable metric field which generalizes the Onsager generalized resistance to the arbitrarily far-nonequilibrium domain, most of the existing theories of nonequilibrium thermodynamics can be cast in such a way that the state exhibits the spontaneous tendency to evolve in state space along the path of SEA compatible with the conservation constraints and the boundary conditions. The resulting unified family of SEA dynamical models is intrinsically and strongly consistent with the second law of thermodynamics. The non-negativity of the entropy production is a general and readily proved feature of SEA dynamics. In several of the different approaches to nonequilibrium description we consider here, the SEA concept has not been investigated before. We believe it defines the precise meaning and the domain of general validity of the so-called maximum entropy production principle. Therefore, it is hoped that the present unifying approach may prove useful in providing a fresh basis for effective, thermodynamically consistent, numerical models and theoretical treatments of irreversible conservative relaxation towards equilibrium from far nonequilibrium states. The mathematical frameworks we consider are the following: (A) statistical or information-theoretic models of relaxation; (B) small-scale and rarefied gas dynamics (i.e., kinetic models for the Boltzmann equation); (C) rational extended thermodynamics, macroscopic nonequilibrium thermodynamics, and chemical kinetics; (D) mesoscopic nonequilibrium thermodynamics, continuum mechanics with fluctuations; and (E) quantum statistical mechanics, quantum thermodynamics, mesoscopic nonequilibrium quantum thermodynamics, and intrinsic quantum thermodynamics.

Minimization of a free-energy-like potential for non-equilibrium flow systems at steady state

PubMed Central

Niven, Robert K.

2010-01-01

This study examines a new formulation of non-equilibrium thermodynamics, which gives a conditional derivation of the ‘maximum entropy production’ (MEP) principle for flow and/or chemical reaction systems at steady state. The analysis uses a dimensionless potential function ϕst for non-equilibrium systems, analogous to the free energy concept of equilibrium thermodynamics. Spontaneous reductions in ϕst arise from increases in the ‘flux entropy’ of the system—a measure of the variability of the fluxes—or in the local entropy production; conditionally, depending on the behaviour of the flux entropy, the formulation reduces to the MEP principle. The inferred steady state is also shown to exhibit high variability in its instantaneous fluxes and rates, consistent with the observed behaviour of turbulent fluid flow, heat convection and biological systems; one consequence is the coexistence of energy producers and consumers in ecological systems. The different paths for attaining steady state are also classified. PMID:20368250

Dynamic Covalent Synthesis of Aryleneethynylene Cages through Alkyne Metathesis: Dimer, Tetramer, or Interlocked Complex?

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

Wang, Qi; Yu, Chao; Zhang, Chenxi

A dynamic covalent approach towards rigid aryleneethynylene covalent organic polyhedrons (COPs) was explored. Our study on the relationship of the COP structures and the geometry of their building blocks reveals that the topology of aryleneethynylene COPs strongly depends on the size of the building blocks. A tetramer (D2h symmetric), dimer, or interlocked complex can be formed from monomers with the same face-to-edge angle but in different sizes. As alkyne metathesis is a self-exchange reaction and non-directional, the cyclooligomerization of multi-alkyne monomers involves both intramolecular cyclization and intermolecular metathesis reaction, resulting in complicated thermodynamic process disturbed by kinetic competition. Although amore » tetrahedron-shaped tetramer (Td symmetric) has comparable thermodynamic stability to a D2h symmetric tetramer, its formation is kinetically disfavored and was not observed experimentally. Aryleneethynylene COPs consist of purely unsaturated carbon backbones and exhibit large internal cavities, which would have interesting applications in host-guest chemistry and development of porous materials.« less

Dynamical and thermodynamical modulations of future changes in landfalling atmospheric rivers over North America

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

Gao, Yang; Lu, Jian; Leung, Lai-Yung R.

This study examines the changes of landfalling atmospheric rivers (ARs) over the west coast of North America in response to future warming using model outputs from the Coupled Model Intercomparison Project phase 5 (CMIP5). The result reveals a strikingly large magnitude of increase of AR days by the end of the 21st century in the RCP8.5 climate change scenario, with fractional increases ranging between ~50% and 600%, depending on the seasons and the landfall locations. These increases are predominantly controlled by the super-Clausius-Clapeyron rate of increase of atmospheric water vapor with warming, while changes of winds that transport moisture inmore » the ARs, or dynamical effect, mostly counter the thermodynamical effect of increasing water vapor, limiting the increase of AR events in the future. The consistent negative effect of wind changes on AR days during spring and fall can be further linked to the robust poleward shift of the subtropical jet in the North Pacific basin.« less

Optimisation of driver actions in RWD race car including tyre thermodynamics

NASA Astrophysics Data System (ADS)

Maniowski, Michal

2016-04-01

The paper presents an innovative method for a lap time minimisation by using genetic algorithms for a multi objective optimisation of a race driver-vehicle model. The decision variables consist of 16 parameters responsible for actions of a professional driver (e.g. time traces for brake, accelerator and steering wheel) on a race track part with RH corner. Purpose-built, high fidelity, multibody vehicle model (called 'miMa') is described by 30 generalised coordinates and 440 parameters, crucial in motorsport. Focus is put on modelling of the tyre tread thermodynamics and its influence on race vehicle dynamics. Numerical example considers a Rear Wheel Drive BMW E36 prepared for track day events. In order to improve the section lap time (by 5%) and corner exit velocity (by 4%) a few different driving strategies are found depending on thermal conditions of semi-slick tyres. The process of the race driver adaptation to initially cold or hot tyres is explained.

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.

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.

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

Ukita, Masaya, E-mail: uktia.masaya@f.mbox.nagoya-u.ac.jp; Toyoura, Kazuaki; Nakamura, Atsutomo

The thermodynamic phase stabilities of calcite and aragonite have been investigated from lattice vibrational analyses based on first-principles calculations. Different pressure dependences in phonon feature were found between the two polymorphs, suggesting different physical origins of the pressure-induced phase transitions. In the most stable phase in calcite (calcite I), an imaginary phonon mode consisting of rotation of CO{sub 3} ions with slight displacement of Ca ions appears at the F point in the Brillouin zone above 0.8 GPa. Such a soft mode means that external pressure induces the lattice-dynamical instability of calcite I leading to the phase transition to calcite II.more » On the other hand, the origin of the phase transition in aragonite is not due to such a lattice-dynamical instability. The estimated thermodynamical properties indicate that a first-order phase transition occurs between aragonite and post-aragonite at 34.7 GPa, coinciding with the reported experimental value at room temperature (35 GPa).« less

Refined gradient theory of scale-dependent superthin rods

NASA Astrophysics Data System (ADS)

Lurie, S. A.; Kuznetsova, E. L.; Rabinskii, L. N.; Popova, E. I.

2015-03-01

A version of the refined nonclassical theory of thin beams whose thickness is comparable with the scale characteristic of the material structure is constructed on the basis of the gradient theory of elasticity which, in contrast to the classical theory, contains some additional physical characteristics depending on the structure scale parameters and is therefore most appropriate for modeling the strains of scale-dependent systems. The fundamental conditions for the well-posedness of the gradient theories are obtained for the first time, and it is shown that some of the known applied gradient theories do not generally satisfy the well-posedness criterion. A version of the well-posed gradient strain theory which satisfies the symmetry condition is proposed. The well-posed gradient theory is then used to implement the method of kinematic hypotheses for constructing a refined theory of scale-dependent beams. The equilibrium equations of the refined theory of scale-dependent Timoshenko and Bernoulli beams are obtained. It is shown that the scale effects are localized near the beam ends, and therefore, taking the scale effects into account does not give any correction to the bending rigidity of long beams as noted in the previously published papers dealing with the scale-dependent beams.

Energetics of sodium transport in toad urinary bladder.

PubMed Central

Canessa, M; Labarca, P; DiBona, D R; Leaf, A

1978-01-01

The ratio of the rate of transepithelial sodium transport, JNa, across the isolated toad urinary bladder to the simultaneously measured rate of transport-dependent metabolism, JsbCO2, has been measured as a function of the transepithelial electrical voltage, deltapsi. The ratio remains constant with a mean value of 18 to 20 over the range of imposed voltages of 0 to +70 mV. With increasing hyperpolarization of the bladder, JNa decreases and the calculated electromotive force or apparent "ENa" of the sodium pump increases. From thermodynamic and kinetic arguments it is shown that the apparent "ENa" approaches the maximal electrochemical potential gradient, ENa, against which sodium can be transported by this tissue only when JNa approximately 0. At this unique condition F ENa (in which F is the Faraday constant) is the maximal free energy of the chemical reaction driving sodium transport and thus equal to the maximal extramitochondrial phosphorylation potential and the maximal free energy of the mitochondrial respiratory chain within the transporting cells. PMID:100789

A thermodynamical model for the surface tension of silicate melts in contact with H2O gas

USGS Publications Warehouse

Colucci, Simone; Battaglia, Maurizio; Trigila, Raffaello

2016-01-01

Surface tension plays an important role in the nucleation of H2O gas bubbles in magmatic melts and in the time-dependent rheology of bubble-bearing magmas. Despite several experimental studies, a physics based model of the surface tension of magmatic melts in contact with H2O is lacking. This paper employs gradient theory to develop a thermodynamical model of equilibrium surface tension of silicate melts in contact with H2O gas at low to moderate pressures. In the last decades, this approach has been successfully applied in studies of industrial mixtures but never to magmatic systems. We calibrate and verify the model against literature experimental data, obtained by the pendant drop method, and by inverting bubble nucleation experiments using the Classical Nucleation Theory (CNT). Our model reproduces the systematic decrease in surface tension with increased H2O pressure observed in the experiments. On the other hand, the effect of temperature is confirmed by the experiments only at high pressure. At atmospheric pressure, the model shows a decrease of surface tension with temperature. This is in contrast with a number of experimental observations and could be related to microstructural effects that cannot be reproduced by our model. Finally, our analysis indicates that the surface tension measured inverting the CNT may be lower than the value measured by the pendant drop method, most likely because of changes in surface tension controlled by the supersaturation.

Time dependent inflow-outflow boundary conditions for 2D acoustic systems

NASA Technical Reports Server (NTRS)

Watson, Willie R.; Myers, Michael K.

1989-01-01

An analysis of the number and form of the required inflow-outflow boundary conditions for the full two-dimensional time-dependent nonlinear acoustic system in subsonic mean flow is performed. The explicit predictor-corrector method of MacCormack (1969) is used. The methodology is tested on both uniform and sheared mean flows with plane and nonplanar sources. Results show that the acoustic system requires three physical boundary conditions on the inflow and one on the outflow boundary. The most natural choice for the inflow boundary conditions is judged to be a specification of the vorticity, the normal acoustic impedance, and a pressure gradient-density gradient relationship normal to the boundary. Specification of the acoustic pressure at the outflow boundary along with these inflow boundary conditions is found to give consistent reliable results. A set of boundary conditions developed earlier, which were intended to be nonreflecting is tested using the current method and is shown to yield unstable results for nonplanar acoustic waves.

Functional characteristics of pyruvate transport in Phycomyces blakesleeanus.

PubMed

Marcos, J A; de Arriaga, D; Busto, F; Soler, J

1998-12-01

A saturable and accumulative transport system for pyruvate has been detected in Phycomyces blakesleeanus NRRL 1555(-) mycelium. It was strongly inhibited by alpha-cyano-4-hydroxycinnamate. l-Lactate and acetate were competitive inhibitors of pyruvate transport. The initial pyruvate uptake velocity and accumulation ratio was dependent on the external pH. The Vmax of transport greatly decreased with increasing pH, whereas the affinity of the carrier for pyruvate was not affected. The pyruvate transport system mediated its homologous exchange, which was essentially pH independent, and efflux, which increased with increasing external pH. The uptake of pyruvate was energy dependent and was strongly inhibited by inhibitors of oxidative phosphorylation and of the formation of proton gradients. Glucose counteracted the inhibitory effect of the pyruvate transport produced by inhibitors of mitochondrial ATP synthesis. Our results are consistent with a pyruvate/proton cotransport in P. blakesleeanus probably driven by an electrochemical gradient of H+ generated by a plasma membrane H+-ATPase. Copyright 1998 Academic Press.

Thermodynamic properties of lanthanum in gallium-zinc alloys

NASA Astrophysics Data System (ADS)

Dedyukhin, A. S.; Shepin, I. E.; Kharina, E. A.; Shchetinskiy, A. V.; Volkovich, V. A.; Yamshchikov, L. F.

2016-09-01

Thermodynamic properties of lanthanum were determined in gallium-zinc alloys of the eutectic and over-eutectic compositions. The electromotive force measurements were used to determine thermodynamic activity and sedimentation technique to measure solubility of lanthanum in liquid metal alloys. Temperature dependencies of lanthanum activity, solubility and activity coefficients in alloys with Ga-Zn mixtures containing 3.64, 15 and 50 wt. % zinc were obtained.

Frictional behaviour of sandstone: A sample-size dependent triaxial investigation

NASA Astrophysics Data System (ADS)

Roshan, Hamid; Masoumi, Hossein; Regenauer-Lieb, Klaus

2017-01-01

Frictional behaviour of rocks from the initial stage of loading to final shear displacement along the formed shear plane has been widely investigated in the past. However the effect of sample size on such frictional behaviour has not attracted much attention. This is mainly related to the limitations in rock testing facilities as well as the complex mechanisms involved in sample-size dependent frictional behaviour of rocks. In this study, a suite of advanced triaxial experiments was performed on Gosford sandstone samples at different sizes and confining pressures. The post-peak response of the rock along the formed shear plane has been captured for the analysis with particular interest in sample-size dependency. Several important phenomena have been observed from the results of this study: a) the rate of transition from brittleness to ductility in rock is sample-size dependent where the relatively smaller samples showed faster transition toward ductility at any confining pressure; b) the sample size influences the angle of formed shear band and c) the friction coefficient of the formed shear plane is sample-size dependent where the relatively smaller sample exhibits lower friction coefficient compared to larger samples. We interpret our results in terms of a thermodynamics approach in which the frictional properties for finite deformation are viewed as encompassing a multitude of ephemeral slipping surfaces prior to the formation of the through going fracture. The final fracture itself is seen as a result of the self-organisation of a sufficiently large ensemble of micro-slip surfaces and therefore consistent in terms of the theory of thermodynamics. This assumption vindicates the use of classical rock mechanics experiments to constrain failure of pressure sensitive rocks and the future imaging of these micro-slips opens an exciting path for research in rock failure mechanisms.

Turnstiles and bifurcators: the disequilibrium converting engines that put metabolism on the road.

PubMed

Branscomb, Elbert; Russell, Michael J

2013-02-01

The Submarine Hydrothermal Alkaline Spring Theory for the emergence of life holds that it is the ordered delivery of hydrogen and methane in alkaline hydrothermal solutions at a spontaneously precipitated inorganic osmotic and catalytic membrane to the carbon dioxide and other electron acceptors in the earliest acidulous cool ocean that, through these gradients, drove life into being. That such interactions between hydrothermal fuels and potential oxidants have so far not been accomplished in the lab is because some steps along the necessary metabolic pathways are endergonic and must therefore be driven by being coupled to thermodynamically larger exergonic processes. But coupling of this kind is far from automatic and it is not enough to merely sum the ΔGs of two supposedly coupled reactions and show their combined thermodynamic viability. An exergonic reaction will not drive an endergonic one unless 'forced' to do so by being tied to it mechanistically via an organized "engine" of "Free Energy Conversion" (FEC). Here we discuss the thermodynamics of FEC and advance proposals regarding the nature and roles of the FEC devices that could, in principle, have arisen spontaneously in the alkaline hydrothermal context and have forced the onset of a protometabolism. The key challenge is to divine what these initial engines of life were in physicochemical terms and as part of that, what structures provided the first "turnstile-like" mechanisms needed to couple the partner processes in free energy conversion; in particular to couple the dissipation of geochemically given gradients to, say, the reduction of CO(2) to formate and the generation of a pyrophosphate disequilibrium. This article is part of a Special Issue entitled: The evolutionary aspects of bioenergetic systems. Copyright © 2012 Elsevier B.V. All rights reserved.

On the biophysics and kinetics of toehold-mediated DNA strand displacement

PubMed Central

Srinivas, Niranjan; Ouldridge, Thomas E.; Šulc, Petr; Schaeffer, Joseph M.; Yurke, Bernard; Louis, Ard A.; Doye, Jonathan P. K.; Winfree, Erik

2013-01-01

Dynamic DNA nanotechnology often uses toehold-mediated strand displacement for controlling reaction kinetics. Although the dependence of strand displacement kinetics on toehold length has been experimentally characterized and phenomenologically modeled, detailed biophysical understanding has remained elusive. Here, we study strand displacement at multiple levels of detail, using an intuitive model of a random walk on a 1D energy landscape, a secondary structure kinetics model with single base-pair steps and a coarse-grained molecular model that incorporates 3D geometric and steric effects. Further, we experimentally investigate the thermodynamics of three-way branch migration. Two factors explain the dependence of strand displacement kinetics on toehold length: (i) the physical process by which a single step of branch migration occurs is significantly slower than the fraying of a single base pair and (ii) initiating branch migration incurs a thermodynamic penalty, not captured by state-of-the-art nearest neighbor models of DNA, due to the additional overhang it engenders at the junction. Our findings are consistent with previously measured or inferred rates for hybridization, fraying and branch migration, and they provide a biophysical explanation of strand displacement kinetics. Our work paves the way for accurate modeling of strand displacement cascades, which would facilitate the simulation and construction of more complex molecular systems. PMID:24019238

On the biophysics and kinetics of toehold-mediated DNA strand displacement.

PubMed

Srinivas, Niranjan; Ouldridge, Thomas E; Sulc, Petr; Schaeffer, Joseph M; Yurke, Bernard; Louis, Ard A; Doye, Jonathan P K; Winfree, Erik

2013-12-01

Dynamic DNA nanotechnology often uses toehold-mediated strand displacement for controlling reaction kinetics. Although the dependence of strand displacement kinetics on toehold length has been experimentally characterized and phenomenologically modeled, detailed biophysical understanding has remained elusive. Here, we study strand displacement at multiple levels of detail, using an intuitive model of a random walk on a 1D energy landscape, a secondary structure kinetics model with single base-pair steps and a coarse-grained molecular model that incorporates 3D geometric and steric effects. Further, we experimentally investigate the thermodynamics of three-way branch migration. Two factors explain the dependence of strand displacement kinetics on toehold length: (i) the physical process by which a single step of branch migration occurs is significantly slower than the fraying of a single base pair and (ii) initiating branch migration incurs a thermodynamic penalty, not captured by state-of-the-art nearest neighbor models of DNA, due to the additional overhang it engenders at the junction. Our findings are consistent with previously measured or inferred rates for hybridization, fraying and branch migration, and they provide a biophysical explanation of strand displacement kinetics. Our work paves the way for accurate modeling of strand displacement cascades, which would facilitate the simulation and construction of more complex molecular systems.

Theory of the milieu dependent isomerisation dynamics of reducing sugars applied to d-erythrose.

PubMed

Kaufmann, Martin; Mügge, Clemens; Kroh, Lothar W

2015-12-11

Quantitative (1)H selective saturation transfer NMR spectroscopy ((1)H SST qNMR) was used to fully describe the milieu dependent dynamics of the isomeric system of d-erythrose. Thermodynamic activation parameters are calculated for acidic as well as for basic catalysis combining McConnell's modified Bloch equations for the chemical exchange solved for the constraint of saturating the non-hydrated acyclic isomer, the Eyring equation and Hudson's equation for pH dependent catalysis. A detailed mathematical examination describing the milieu dependent dynamics of sugar isomerisation is provided. Thermodynamic data show evidence that photo-catalysed sugar isomerisation as well as degradation has to be considered. Approximations describing the pH and temperature dependence of thermodynamic activation parameters are derived that indicate the possibility of photo-affecting equilibrium constants. Moreover, the results show that isomerisation dynamics are closely related to degradation kinetics and that sugars' reactivities are altered by the concentration of acyclic carbonyl isomer and the sum of its ring closing rate constants. Additionally, it is concluded that sugar solutions show a limited self-stabilising behaviour. Copyright © 2015 Elsevier Ltd. All rights reserved.

Combining Step Gradients and Linear Gradients in Density.

PubMed

Kumar, Ashok A; Walz, Jenna A; Gonidec, Mathieu; Mace, Charles R; Whitesides, George M

2015-06-16

Combining aqueous multiphase systems (AMPS) and magnetic levitation (MagLev) provides a method to produce hybrid gradients in apparent density. AMPS—solutions of different polymers, salts, or surfactants that spontaneously separate into immiscible but predominantly aqueous phases—offer thermodynamically stable steps in density that can be tuned by the concentration of solutes. MagLev—the levitation of diamagnetic objects in a paramagnetic fluid within a magnetic field gradient—can be arranged to provide a near-linear gradient in effective density where the height of a levitating object above the surface of the magnet corresponds to its density; the strength of the gradient in effective density can be tuned by the choice of paramagnetic salt and its concentrations and by the strength and gradient in the magnetic field. Including paramagnetic salts (e.g., MnSO4 or MnCl2) in AMPS, and placing them in a magnetic field gradient, enables their use as media for MagLev. The potential to create large steps in density with AMPS allows separations of objects across a range of densities. The gradients produced by MagLev provide resolution over a continuous range of densities. By combining these approaches, mixtures of objects with large differences in density can be separated and analyzed simultaneously. Using MagLev to add an effective gradient in density also enables tuning the range of densities captured at an interface of an AMPS by simply changing the position of the container in the magnetic field. Further, by creating AMPS in which phases have different concentrations of paramagnetic ions, the phases can provide different resolutions in density. These results suggest that combining steps in density with gradients in density can enable new classes of separations based on density.

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

Non-convex dissipation potentials in multiscale non-equilibrium thermodynamics

NASA Astrophysics Data System (ADS)

Janečka, Adam; Pavelka, Michal

2018-04-01

Reformulating constitutive relation in terms of gradient dynamics (being derivative of a dissipation potential) brings additional information on stability, metastability and instability of the dynamics with respect to perturbations of the constitutive relation, called CR-stability. CR-instability is connected to the loss of convexity of the dissipation potential, which makes the Legendre-conjugate dissipation potential multivalued and causes dissipative phase transitions that are not induced by non-convexity of free energy, but by non-convexity of the dissipation potential. CR-stability of the constitutive relation with respect to perturbations is then manifested by constructing evolution equations for the perturbations in a thermodynamically sound way (CR-extension). As a result, interesting experimental observations of behavior of complex fluids under shear flow and supercritical boiling curve can be explained.

Nonequilibrium thermodynamics and boundary conditions for reaction and transport in heterogeneous media

NASA Astrophysics Data System (ADS)

Gaspard, Pierre; Kapral, Raymond

2018-05-01

Nonequilibrium interfacial thermodynamics is formulated in the presence of surface reactions for the study of diffusiophoresis in isothermal systems. As a consequence of microreversibility and Onsager-Casimir reciprocal relations, diffusiophoresis, i.e., the coupling of the tangential components of the pressure tensor to the concentration gradients of solute species, has a reciprocal effect where the interfacial currents of solutes are coupled to the slip velocity. The presence of surface reactions is shown to modify the diffusiophoretic and reciprocal effects at the fluid-solid interface. The thin-layer approximation is used to describe the solution flowing near a reactive solid interface. Analytic formulas describing the diffusiophoretic and reciprocal effects are deduced in the thin-layer approximation and tested numerically for the Poiseuille flow of a solution between catalytic planar surfaces.

Direct measurement of a nonequilibrium system entropy using a feedback trap

NASA Astrophysics Data System (ADS)

Gavrilov, Momčilo; Bechhoefer, John

2017-08-01

Feedback traps are tools for trapping single charged objects in solution. They periodically measure an object's position and apply a feedback force to counteract Brownian motion. The feedback force can be calculated as a gradient of a potential function, effectively creating a "virtual potential." Its flexibility regarding the choice of form of the potential gives an opportunity to explore various fundamental questions in stochastic thermodynamics. Here, we review the theory behind feedback traps and apply it to measuring the average work required to erase a fraction of a bit of information. The results agree with predictions based on the nonequilibrium system entropy. With this example, we also show how a feedback trap can easily implement the complex erasure protocols required to reach ultimate thermodynamic limits.

Continuum mechanics and thermodynamics in the Hamilton and the Godunov-type formulations

NASA Astrophysics Data System (ADS)

Peshkov, Ilya; Pavelka, Michal; Romenski, Evgeniy; Grmela, Miroslav

2018-01-01

Continuum mechanics with dislocations, with the Cattaneo-type heat conduction, with mass transfer, and with electromagnetic fields is put into the Hamiltonian form and into the form of the Godunov-type system of the first-order, symmetric hyperbolic partial differential equations (SHTC equations). The compatibility with thermodynamics of the time reversible part of the governing equations is mathematically expressed in the former formulation as degeneracy of the Hamiltonian structure and in the latter formulation as the existence of a companion conservation law. In both formulations the time irreversible part represents gradient dynamics. The Godunov-type formulation brings the mathematical rigor (the local well posedness of the Cauchy initial value problem) and the possibility to discretize while keeping the physical content of the governing equations (the Godunov finite volume discretization).

The effect of water on thermal stresses in polymer composites

NASA Technical Reports Server (NTRS)

Sullivan, Roy M.

1994-01-01

The fundamentals of the thermodynamic theory of mixtures and continuum thermochemistry are reviewed for a mixture of condensed water and polymer. A specific mixture which is mechanically elastic with temperature and water concentration gradients present is considered. An expression for the partial pressure of water in the mixture is obtained based on certain assumptions regarding the thermodynamic state of the water in the mixture. Along with a simple diffusion equation, this partial pressure expression may be used to simulate the thermostructural behavior of polymer composite materials due to water in the free volumes of the polymer. These equations are applied to a specific polymer composite material during isothermal heating conditions. The thermal stresses obtained by the application of the theory are compared to measured results to verify the accuracy of the approach.

Zero-G Thermodynamic Venting System (TVS) Performance Prediction Program

NASA Technical Reports Server (NTRS)

Nguyen, Han

1994-01-01

This report documents the Zero-g Thermodynamic Venting System (TVS) performance prediction computer program. The zero-g TVS is a device that destratifies and rejects environmentally induced zero-g thermal gradients in the LH2 storage transfer system. A recirculation pump and spray injection manifold recirculates liquid throughout the length of the tank thereby destratifying both the ullage gas and liquid bulk. Heat rejection is accomplished by the opening of the TVS control valve which allows a small flow rate to expand to a low pressure thereby producing a low temperature heat sink which is used to absorb heat from the recirculating liquid flow. The program was written in FORTRAN 77 language on the HP-9000 and IBM PC computers. It can be run on various platforms with a FORTRAN compiler.

Slip-Flow and Heat Transfer of a Non-Newtonian Nanofluid in a Microtube

PubMed Central

Niu, Jun; Fu, Ceji; Tan, Wenchang

2012-01-01

The slip-flow and heat transfer of a non-Newtonian nanofluid in a microtube is theoretically studied. The power-law rheology is adopted to describe the non-Newtonian characteristics of the flow, in which the fluid consistency coefficient and the flow behavior index depend on the nanoparticle volume fraction. The velocity profile, volumetric flow rate and local Nusselt number are calculated for different values of nanoparticle volume fraction and slip length. The results show that the influence of nanoparticle volume fraction on the flow of the nanofluid depends on the pressure gradient, which is quite different from that of the Newtonian nanofluid. Increase of the nanoparticle volume fraction has the effect to impede the flow at a small pressure gradient, but it changes to facilitate the flow when the pressure gradient is large enough. This remarkable phenomenon is observed when the tube radius shrinks to micrometer scale. On the other hand, we find that increase of the slip length always results in larger flow rate of the nanofluid. Furthermore, the heat transfer rate of the nanofluid in the microtube can be enhanced due to the non-Newtonian rheology and slip boundary effects. The thermally fully developed heat transfer rate under constant wall temperature and constant heat flux boundary conditions is also compared. PMID:22615961

Numerical Implementation of a Multiple-ISV Thermodynamically-Based Work Potential Theory for Modeling Progressive Damage and Failure in Fiber-Reinforced Laminates

NASA Technical Reports Server (NTRS)

Pineda, Evan J.; Waas, Anthony M.

2011-01-01

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, enhanced Schapery theory (EST), utilizes separate ISVs for modeling the effects of damage and failure. Damage is considered to be the effect of any structural changes in a material that manifest as pre-peak non-linearity in the stress versus strain response. Conversely, failure is taken to be the effect of the evolution of any mechanisms that results in post-peak strain softening. It is assumed that matrix microdamage is the dominant damage mechanism in continuous fiber-reinforced polymer matrix laminates, and its evolution is controlled with a single ISV. Three additional ISVs are introduced to account for failure due to mode I transverse cracking, mode II transverse cracking, and mode I axial failure. Typically, failure evolution (i.e., post-peak strain softening) results in pathologically mesh dependent solutions within a finite element method (FEM) setting. Therefore, consistent character element lengths are introduced into the formulation of the evolution of the three 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 is derived. The theory is implemented into commercial FEM software. Objectivity of total energy dissipated during the failure process, with regards to refinements in the FEM mesh, is demonstrated. The model is also 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 to the experiments.

A Thermodynamically-Based Mesh Objective Work Potential Theory for Predicting Intralaminar Progressive Damage and Failure in Fiber-Reinforced Laminates

NASA Technical Reports Server (NTRS)

Pineda, Evan J.; Waas, Anthony M.

2012-01-01

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, enhanced Schapery theory (EST), utilizes separate ISVs for modeling the effects of damage and failure. Damage is considered to be the effect of any structural changes in a material that manifest as pre-peak non-linearity in the stress versus strain response. Conversely, failure is taken to be the effect of the evolution of any mechanisms that results in post-peak strain softening. It is assumed that matrix microdamage is the dominant damage mechanism in continuous fiber-reinforced polymer matrix laminates, and its evolution is controlled with a single ISV. Three additional ISVs are introduced to account for failure due to mode I transverse cracking, mode II transverse cracking, and mode I axial failure. Typically, failure evolution (i.e., post-peak strain softening) results in pathologically mesh dependent solutions within a finite element method (FEM) setting. Therefore, consistent character element lengths are introduced into the formulation of the evolution of the three 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 is derived. The theory is implemented into commercial FEM software. Objectivity of total energy dissipated during the failure process, with regards to refinements in the FEM mesh, is demonstrated. The model is also 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 to the experiments.

Quantum Fluctuations and Thermodynamic Processes in the Presence of Closed Timelike Curves

NASA Astrophysics Data System (ADS)

Tanaka, Tsunefumi

1997-10-01

A closed timelike curve (CTC) is a closed loop in spacetime whose tangent vector is everywhere timelike. A spacetime which contains CTC's will allow time travel. One of these spacetimes is Grant space. It can be constructed from Minkowski space by imposing periodic boundary conditions in spatial directions and making the boundaries move toward each other. If Hawking's chronology protection conjecture is correct, there must be a physical mechanism preventing the formation of CTC's. Currently the most promising candidate for the chronology protection mechanism is the back reaction of the metric to quantum vacuum fluctuations. In this thesis the quantum fluctuations for a massive scalar field, a self-interacting field, and for a field at nonzero temperature are calculated in Grant space. The stress-energy tensor is found to remain finite everywhere in Grant space for the massive scalar field with sufficiently large field mass. Otherwise it diverges on chronology horizons like the stress-energy tensor for a massless scalar field. If CTC's exist they will have profound effects on physical processes. Causality can be protected even in the presence of CTC's if the self-consistency condition is imposed on all processes. Simple classical thermodynamic processes of a box filled with ideal gas in the presence of CTC's are studied. If a system of boxes is closed, its state does not change as it travels through a region of spacetime with CTC's. But if the system is open, the final state will depend on the interaction with the environment. The second law of thermodynamics is shown to hold for both closed and open systems. A similar problem is investigated at a statistical level for a gas consisting of multiple selves of a single particle in a spacetime with CTC's.

Radiative transfer in a plane stratified dielectric

NASA Technical Reports Server (NTRS)

Wilheit, T. T., Jr.

1975-01-01

A model is developed for calculating radiative transfer in a stratified dielectric. This model is used to show that the reflectivity of a stratified dielectric is primarily determined by gradients in the real part of the refractive index over distances on the order of 1/10 wavelength in the medium. The effective temperature of the medium is determined by the thermodynamic temperature profile over distances of the order delta T.

Characteristics of gradient-interface-structured ZnCdSSe quantum dots with modified interface and its application to quantum-dot-sensitized solar cells

NASA Astrophysics Data System (ADS)

Jeong, Da-Woon; Kim, Jae-Yup; Seo, Han Wook; Lim, Kyoung-Mook; Ko, Min Jae; Seong, Tae-Yeon; Kim, Bum Sung

2018-01-01

Colloidal quantum dots (QDs) are attractive materials for application in photovoltaics, LEDs, displays, and bio devices owing to their unique properties. In this study, we synthesized gradient-interface-structured ZnCdSSe QDs and modified the interface based on a thermodynamic simulation to investigate its optical and physical properties. In addition, the interface was modified by increasing the molar concentration of Se. QDs at the modified interface were applied to QD-sensitized solar cells, which showed a 25.5% increase in photoelectric conversion efficiency owing to the reduced electron confinement effect. The increase seems to be caused by the excited electrons being relatively easily transferred to the level of TiO2 owing to the reduced electron confinement effect. Consequently, the electron confinement effect was observed to be reduced by increasing the ZnSe (or Zn1-xCdxSe)-rich phase at the interface. This means that, based on the thermodynamic simulation, the interface between the core QDs and the surface of the QDs can be controlled. The improvement of optical and electronic properties by controlling interfaces and surfaces during the synthesis of QDs, as reported in this work, can be useful for many applications beyond solar cells.

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.

Nonlocal effects in nonisothermal hydrodynamics from the perspective of beyond-equilibrium thermodynamics.

PubMed

Hütter, Markus; Brader, Joseph M

2009-06-07

We examine the origins of nonlocality in a nonisothermal hydrodynamic formulation of a one-component fluid of particles that exhibit long-range correlations, e.g., due to a spherically symmetric, long-range interaction potential. In order to furnish the continuum modeling with physical understanding of the microscopic interactions and dynamics, we make use of systematic coarse graining from the microscopic to the continuum level. We thus arrive at a thermodynamically admissible and closed set of evolution equations for the densities of momentum, mass, and internal energy. From the consideration of an illustrative special case, the following main conclusions emerge. There are two different source terms in the momentum balance. The first is a body force, which in special circumstances can be related to the functional derivative of a nonlocal Helmholtz free energy density with respect to the mass density. The second source term is proportional to the temperature gradient, multiplied by the nonlocal entropy density. These two source terms combine into a pressure gradient only in the absence of long-range effects. In the irreversible contributions to the time evolution, the nonlocal contributions arise since the self-correlations of the stress tensor and heat flux, respectively, are nonlocal as a result of the microscopic nonlocal correlations. Finally, we point out specific points that warrant further discussions.

First-principles investigation of thermodynamic, elastic and electronic properties of Al{sub 3}V and Al{sub 3}Nb intermetallics under pressures

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

Chen, Zhe; Zhang, Peng; Chen, Dong

2015-02-28

The thermodynamic, elastic, and electronic properties of D0{sub 22}-type Al{sub 3}V and Al{sub 3}Nb intermetallics were studied using the first-principle method. The results showed the pressure has profound effects on the structural, mechanical and electronic properties in both Al{sub 3}V and Al{sub 3}Nb. Thermodynamically, the formation enthalpies for Al{sub 3}V and Al{sub 3}Nb were derived, which agreed well with available experimental and theoretical values. Comparably, Al{sub 3}Nb was a more stable phase with the more negative H{sub f} than Al{sub 3}V. Mechanically, the calculated elastic constants showed linearly increasing tendencies, and satisfied the Born's criteria from 0–20 GPa, indicating the mechanicallymore » stability of Al{sub 3}V and Al{sub 3}Nb under this pressure range. Further, the mechanical parameters (i.e., bulk modulus (B), shear modulus (G), and Young's modulus (E)) were derived using the Voigt-Reuss-Hill (VRH) method, and in good agreement with available experimental results at the ground state. All these parameters presented the linearly increasing dependences on the external pressure. The B/G ratios and Poisson's ratio indicated that the Al{sub 3}V and Al{sub 3}Nb crystals should exhibit brittle behavior at 0–20 GPa. Additionally, the bulk modulus can be obtained through fitting the Birch-Murnaghan equation (B{sub 0}), computing by VRH method (B{sub H}), and deriving from the elastic theory (B{sub relax}) in both intermetallics. The uniformity of these calculated bulk moduli in each compound exhibited the excellent reliability and self-consistency. In addition, Debye temperature was estimated from the average sound velocity. The Debye temperature showed an increasing dependence on the pressures. Finally, through density of states analysis, Al{sub 3}V and Al{sub 3}Nb were suggested to possess naturally metallic behavior. Under pressures, it was noted that the shapes of peaks and pseudogaps exhibited relative few changes, suggesting Al{sub 3}V and Al{sub 3}Nb has kept structurally stable up to 20 GPa. At zero pressure, Al{sub 3}Nb was considered as a more structurally stable phase with the more number of bonding electrons per atom than Al{sub 3}V. This conclusion was in consistent with the one drawn from the thermodynamic analysis.« less

A non-linear irreversible thermodynamic perspective on organic pigment proliferation and biological evolution

NASA Astrophysics Data System (ADS)

Michaelian, K.

2013-12-01

The most important thermodynamic work performed by life today is the dissipation of the solar photon flux into heat through organic pigments in water. From this thermodynamic perspective, biological evolution is thus just the dispersal of organic pigments and water throughout Earth's surface, while adjusting the gases of Earth's atmosphere to allow the most intense part of the solar spectrum to penetrate the atmosphere and reach the surface to be intercepted by these pigments. The covalent bonding of atoms in organic pigments provides excited levels compatible with the energies of these photons. Internal conversion through vibrational relaxation to the ground state of these excited molecules when in water leads to rapid dissipation of the solar photons into heat, and this is the major source of entropy production on Earth. A non-linear irreversible thermodynamic analysis shows that the proliferation of organic pigments on Earth is a direct consequence of the pigments catalytic properties in dissipating the solar photon flux. A small part of the energy of the photon goes into the production of more organic pigments and supporting biomass, while most of the energy is dissipated and channeled into the hydrological cycle through the latent heat of vaporization of surface water. By dissipating the surface to atmosphere temperature gradient, the hydrological cycle further increases the entropy production of Earth. This thermodynamic perspective of solar photon dissipation by life has implications to the possibility of finding extra-terrestrial life in our solar system and the Universe.

Thermodynamics of membrane insertion and refolding of the diphtheria toxin T-domain

PubMed Central

Vargas-Uribe, Mauricio; Rodnin, Mykola V.; Öjemalm, Karin; Holgado, Aurora; Kyrychenko, Alexander; Nilsson, IngMarie; Posokhov, Yevgen O.; Makhatadze, George; von Heijne, Gunnar; Ladokhin, Alexey S.

2014-01-01

The diphtheria toxin translocation (T) domain inserts into the endosomal membrane in response to the endosomal acidification and enables the delivery of the catalytic domain into the cell. The insertion pathway consists of a series of conformational changes that occur in solution and in the membrane and leads to the conversion of a water-soluble state into a transmembrane state. In this work, we utilize various biophysical techniques to characterize the insertion pathway from the thermodynamic perspective. Thermal and chemical unfolding measured by differential scanning calorimetry, circular dichroism and tryptophan fluorescence reveal that the free energy of unfolding of the T-domain at neutral and mildly acidic pH differ by 3–5 kcal/mol, depending on the experimental conditions. Fluorescence correlation spectroscopy measurements show that the free energy change from the membrane-competent state to the interfacial state is approximately −8 kcal/mol and is pH-independent, while that from the membrane-competent state to the transmembrane state ranges between −9.5 to −12 kcal/mol, depending on the membrane lipid composition and pH. Finally, the thermodynamics of transmembrane insertion of individual helices was tested using an in vitro assay that measures the translocon-assisted integration of test sequences into the microsomal membrane. These experiments suggest that even the most hydrophobic helix TH8 has only a small favorable free energy of insertion. The free energy for the insertion of the consensus insertion unit TH8-TH9 is slightly more favorable, yet less favorable than that measured for the entire protein, suggesting a cooperative effect for the membrane insertion of the helices of the T-domain. PMID:25281329

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

Thermodynamics and phase transition of charged AdS black holes with a global monopole

NASA Astrophysics Data System (ADS)

Deng, Gao-Ming; Fan, Jinbo; Li, Xinfei; Huang, Yong-Chang

2018-01-01

Thermodynamical properties of charged AdS black holes with a global monopole still remain obscure. In this paper, we investigate the thermodynamics and phase transition of the black holes in the extended phase space. It is shown that thermodynamical quantities of the black holes exhibit an interesting dependence on the internal global monopole, and they perfectly satisfy both the first law of thermodynamics and Smarr relation. Furthermore, analysis of the local and the global thermodynamical stability manifests that the charged AdS black hole undergoes an elegant phase transition at critical point. Of special interest, critical behaviors of the black holes resemble a Van der Waals liquid-gas system. Our results not only reveal the effect of a global monopole on thermodynamics of AdS black holes, but also further support that Van der Waals-like behavior of the black holes is a universal phenomenon.

Biological proton pumping in an oscillating electric field

PubMed Central

Kim, Young C.; Furchtgott, Leon A.; Hummer, Gerhard

2010-01-01

Time-dependent external perturbations provide powerful probes of the function of molecular machines. Here we study biological proton pumping in an oscillating electric field. The protein cytochrome c oxidase is the main energy transducer in aerobic life, converting chemical energy into an electric potential by pumping protons across a membrane. With the help of master-equation descriptions that recover the key thermodynamic and kinetic properties of this biological “fuel cell,” we show that the proton pumping efficiency and the electronic currents in steady state both depend significantly and distinctly on the frequency and amplitude of the applied field, allowing us to distinguish between different microscopic mechanisms of the machine. A spectral analysis reveals dominant kinetic modes that show reaction steps consistent with an electron-gated pumping mechanism. PMID:20366348

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.

Observations of the scale-dependent turbulence and evaluation of the flux–gradient relationship for sensible heat for a closed Douglas-fir canopy in very weak wind conditions

DOE PAGES

Vickers, D.; Thomas, C. K.

2014-09-16

Observations of the scale-dependent turbulent fluxes, variances, and the bulk transfer parameterization for sensible heat above, within, and beneath a tall closed Douglas-fir canopy in very weak winds are examined. The daytime sub-canopy vertical velocity spectra exhibit a double-peak structure with peaks at timescales of 0.8 s and 51.2 s. A double-peak structure is also observed in the daytime sub-canopy heat flux co-spectra. The daytime momentum flux co-spectra in the upper bole space and in the sub-canopy are characterized by a relatively large cross-wind component, likely due to the extremely light and variable winds, such that the definition of amore » mean wind direction, and subsequent partitioning of the momentum flux into along- and cross-wind components, has little physical meaning. Positive values of both momentum flux components in the sub-canopy contribute to upward transfer of momentum, consistent with the observed sub-canopy secondary wind speed maximum. For the smallest resolved scales in the canopy at nighttime, we find increasing vertical velocity variance with decreasing timescale, consistent with very small eddies possibly generated by wake shedding from the canopy elements that transport momentum, but not heat. Unusually large values of the velocity aspect ratio within the canopy were observed, consistent with enhanced suppression of the horizontal wind components compared to the vertical by the very dense canopy. The flux–gradient approach for sensible heat flux is found to be valid for the sub-canopy and above-canopy layers when considered separately in spite of the very small fluxes on the order of a few W m −2 in the sub-canopy. However, single-source approaches that ignore the canopy fail because they make the heat flux appear to be counter-gradient when in fact it is aligned with the local temperature gradient in both the sub-canopy and above-canopy layers. While sub-canopy Stanton numbers agreed well with values typically reported in the literature, our estimates for the above-canopy Stanton number were much larger, which likely leads to underestimated modeled sensible heat fluxes above dark warm closed canopies.« less

Observations of the scale-dependent turbulence and evaluation of the flux–gradient relationship for sensible heat for a closed Douglas-fir canopy in very weak wind conditions

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

Vickers, D.; Thomas, C. K.

Observations of the scale-dependent turbulent fluxes, variances, and the bulk transfer parameterization for sensible heat above, within, and beneath a tall closed Douglas-fir canopy in very weak winds are examined. The daytime sub-canopy vertical velocity spectra exhibit a double-peak structure with peaks at timescales of 0.8 s and 51.2 s. A double-peak structure is also observed in the daytime sub-canopy heat flux co-spectra. The daytime momentum flux co-spectra in the upper bole space and in the sub-canopy are characterized by a relatively large cross-wind component, likely due to the extremely light and variable winds, such that the definition of amore » mean wind direction, and subsequent partitioning of the momentum flux into along- and cross-wind components, has little physical meaning. Positive values of both momentum flux components in the sub-canopy contribute to upward transfer of momentum, consistent with the observed sub-canopy secondary wind speed maximum. For the smallest resolved scales in the canopy at nighttime, we find increasing vertical velocity variance with decreasing timescale, consistent with very small eddies possibly generated by wake shedding from the canopy elements that transport momentum, but not heat. Unusually large values of the velocity aspect ratio within the canopy were observed, consistent with enhanced suppression of the horizontal wind components compared to the vertical by the very dense canopy. The flux–gradient approach for sensible heat flux is found to be valid for the sub-canopy and above-canopy layers when considered separately in spite of the very small fluxes on the order of a few W m −2 in the sub-canopy. However, single-source approaches that ignore the canopy fail because they make the heat flux appear to be counter-gradient when in fact it is aligned with the local temperature gradient in both the sub-canopy and above-canopy layers. While sub-canopy Stanton numbers agreed well with values typically reported in the literature, our estimates for the above-canopy Stanton number were much larger, which likely leads to underestimated modeled sensible heat fluxes above dark warm closed canopies.« less

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.

Probing of molecular replication and accumulation in shallow heat gradients through numerical simulations.

PubMed

Keil, Lorenz; Hartmann, Michael; Lanzmich, Simon; Braun, Dieter

2016-07-27

How can living matter arise from dead matter? All known living systems are built around information stored in RNA and DNA. To protect this information against molecular degradation and diffusion, the second law of thermodynamics imposes the need for a non-equilibrium driving force. Following a series of successful experiments using thermal gradients, we have shown that heat gradients across sub-millimetre pores can drive accumulation, replication, and selection of ever longer molecules, implementing all the necessary parts for Darwinian evolution. For these lab experiments to proceed with ample speed, however, the temperature gradients have to be quite steep, reaching up to 30 K per 100 μm. Here we use computer simulations based on experimental data to show that 2000-fold shallower temperature gradients - down to 100 K over one metre - can still drive the accumulation of protobiomolecules. This finding opens the door for various environments to potentially host the origins of life: volcanic, water-vapour, or hydrothermal settings. Following the trajectories of single molecules in simulation, we also find that they are subjected to frequent temperature oscillations inside these pores, facilitating e.g. template-directed replication mechanisms. The tilting of the pore configuration is the central strategy to achieve replication in a shallow temperature gradient. Our results suggest that shallow thermal gradients across porous rocks could have facilitated the formation of evolutionary machines, significantly increasing the number of potential sites for the origin of life on young rocky planets.

Quantum mechanical/molecular mechanical/continuum style solvation model: linear response theory, variational treatment, and nuclear gradients.

PubMed

Li, Hui

2009-11-14

Linear response and variational treatment are formulated for Hartree-Fock (HF) and Kohn-Sham density functional theory (DFT) methods and combined discrete-continuum solvation models that incorporate self-consistently induced dipoles and charges. Due to the variational treatment, analytic nuclear gradients can be evaluated efficiently for these discrete and continuum solvation models. The forces and torques on the induced point dipoles and point charges can be evaluated using simple electrostatic formulas as for permanent point dipoles and point charges, in accordance with the electrostatic nature of these methods. Implementation and tests using the effective fragment potential (EFP, a polarizable force field) method and the conductorlike polarizable continuum model (CPCM) show that the nuclear gradients are as accurate as those in the gas phase HF and DFT methods. Using B3LYP/EFP/CPCM and time-dependent-B3LYP/EFP/CPCM methods, acetone S(0)-->S(1) excitation in aqueous solution is studied. The results are close to those from full B3LYP/CPCM calculations.

Mass flow and velocity profiles in Neurospora hyphae: partial plug flow dominates intra-hyphal transport.

PubMed

Abadeh, Aryan; Lew, Roger R

2013-11-01

Movement of nuclei, mitochondria and vacuoles through hyphal trunks of Neurospora crassa were vector-mapped using fluorescent markers and green fluorescent protein tags. The vectorial movements of all three were strongly correlated, indicating the central role of mass (bulk) flow in cytoplasm movements in N. crassa. Profiles of velocity versus distance from the hyphal wall did not match the parabolic shape predicted by the ideal Hagen-Poiseuille model of flow at low Reynolds number. Instead, the profiles were flat, consistent with a model of partial plug flow due to the high concentration of organelles in the flowing cytosol. The intra-hyphal pressure gradients were manipulated by localized external osmotic treatments to demonstrate the dependence of velocity (and direction) on pressure gradients within the hyphae. The data support the concept that mass transport, driven by pressure gradients, dominates intra-hyphal transport. The transport occurs by partial plug flow due to the organelles in the cytosol.

Fluid Dynamics and Thermodynamics of Vapor Phase Crystal Growth

NASA Technical Reports Server (NTRS)

Wiedemeier, H.

1985-01-01

The ground-based research effort under this program is concerned with systematic studies of the effects of variations: (1) of the relative importance of buoyancy-driven convection, and (2) of diffusion and viscosity conditions on crystal properties. These experimental studies are supported by thermodynamic characterizations of the systems, based on which fluid dynamic parameters can be determined. The specific materials under investigation include: the GeSe-GeI4, Ge-GeI4, HgTe-HgI2, and Hg sub (1-x)Cd sub (x) Te-HgI2 systems. Mass transport rate studies of the GeSe-GeI system as a function of orientation of the density gradient relative to the gravity vector demonstrated the validity of flux anomalies observed in earlier space experiments. The investigation of the effects of inert gases on mass flux yielded the first experimental evidence for the existence of a boundary layer in closed ampoules. Combined with a thorough thermodynamic analysis, a transport model for diffusive flow including chemical vapor transport, sublimation, and Stefan flow was developed.

Lattice Rotation Patterns and Strain Gradient Effects in Face-Centered-Cubic Single Crystals Under Spherical Indentation

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

Gao, Y. F.; Larson, B. C.; Lee, J. H.

Strain gradient effects are commonly modeled as the origin of the size dependence of material strength, such as the dependence of indentation hardness on contact depth and spherical indenter radius. However, studies on the microstructural comparisons of experiments and theories are limited. First, we have extended a strain gradient Mises-plasticity model to its crystal plasticity version and implemented a finite element method to simulate the load-displacement response and the lattice rotation field of Cu single crystals under spherical indentation. The strain gradient simulations demonstrate that the forming of distinct sectors of positive and negative angles in the lattice rotation fieldmore » is governed primarily by the slip geometry and crystallographic orientations, depending only weakly on strain gradient effects, although hardness depends strongly on strain gradients. Second, the lattice rotation simulations are compared quantitatively with micron resolution, three-dimensional X-ray microscopy (3DXM) measurements of the lattice rotation fields under 100mN force, 100 mu m radius spherical indentations in < 111 >, < 110 >, and < 001 > oriented Cu single crystals. Third, noting the limitation of continuum strain gradient crystal plasticity models, two-dimensional discrete dislocation simulation results suggest that the hardness in the nanocontact regime is governed synergistically by a combination of strain gradients and source-limited plasticity. However, the lattice rotation field in the discrete dislocation simulations is found to be insensitive to these two factors but to depend critically on dislocation obstacle densities and strengths.« less

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.

The Thermodynamic Structure of Arctic Coastal Fog Occurring During the Melt Season over East Greenland

NASA Astrophysics Data System (ADS)

Gilson, Gaëlle F.; Jiskoot, Hester; Cassano, John J.; Gultepe, Ismail; James, Timothy D.

2018-05-01

An automated method to classify Arctic fog into distinct thermodynamic profiles using historic in-situ surface and upper-air observations is presented. This classification is applied to low-resolution Integrated Global Radiosonde Archive (IGRA) soundings and high-resolution Arctic Summer Cloud Ocean Study (ASCOS) soundings in low- and high-Arctic coastal and pack-ice environments. Results allow investigation of fog macrophysical properties and processes in coastal East Greenland during melt seasons 1980-2012. Integrated with fog observations from three synoptic weather stations, 422 IGRA soundings are classified into six fog thermodynamic types based on surface saturation ratio, type of temperature inversion, fog-top height relative to inversion-base height and stability using the virtual potential temperature gradient. Between 65-80% of fog observations occur with a low-level inversion, and statically neutral or unstable surface layers occur frequently. Thermodynamic classification is sensitive to the assigned dew-point depression threshold, but categorization is robust. Despite differences in the vertical resolution of radiosonde observations, IGRA and ASCOS soundings yield the same six fog classes, with fog-class distribution varying with latitude and environmental conditions. High-Arctic fog frequently resides within an elevated inversion layer, whereas low-Arctic fog is more often restricted to the mixed layer. Using supplementary time-lapse images, ASCOS microwave radiometer retrievals and airmass back-trajectories, we hypothesize that the thermodynamic classes represent different stages of advection fog formation, development, and dissipation, including stratus-base lowering and fog lifting. This automated extraction of thermodynamic boundary-layer and inversion structure can be applied to radiosonde observations worldwide to better evaluate fog conditions that affect transportation and lead to improvements in numerical models.

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).

Temperature effect on the small-to-large crossover lengthscale of hydrophobic hydration

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

Djikaev, Y. S., E-mail: idjikaev@buffalo.edu; Ruckenstein, E.

2013-11-14

The thermodynamics of hydration is expected to change gradually from entropic for small solutes to enthalpic for large ones. The small-to-large crossover lengthscale of hydrophobic hydration depends on the thermodynamic conditions of the solvent such as temperature, pressure, presence of additives, etc. We attempt to shed some light on the temperature dependence of the crossover lengthscale by using a probabilistic approach to water hydrogen bonding that allows one to obtain an analytic expression for the number of bonds per water molecule as a function of both its distance to a solute and solute radius. Incorporating that approach into the densitymore » functional theory, one can examine the solute size effects on its hydration over the entire small-to-large lengthscale range at a series of different temperatures. Knowing the dependence of the hydration free energy on the temperature and solute size, one can also obtain its enthalpic and entropic contributions as functions of both temperature and solute size. These functions can provide some interesting insight into the temperature dependence of the crossover lengthscale of hydrophobic hydration. The model was applied to the hydration of spherical particles of various radii in water in the temperature range from T = 293.15 K to T = 333.15 K. The model predictions for the temperature dependence of the hydration free energy of small hydrophobes are consistent with the experimental and simulational data on the hydration of simple molecular solutes. Three alternative definitions for the small-to-large crossover length-scale of hydrophobic hydration are proposed, and their temperature dependence is obtained. Depending on the definition and temperature, the small-to-large crossover in the hydration mechanism is predicted to occur for hydrophobes of radii from one to several nanometers. Independent of its definition, the crossover length-scale is predicted to decrease with increasing temperature.« less

Size- and shape-dependent surface thermodynamic properties of nanocrystals

NASA Astrophysics Data System (ADS)

Fu, Qingshan; Xue, Yongqiang; Cui, Zixiang

2018-05-01

As the fundamental properties, the surface thermodynamic properties of nanocrystals play a key role in the physical and chemical changes. However, it remains ambiguous about the quantitative influence regularities of size and shape on the surface thermodynamic properties of nanocrystals. Thus by introducing interface variables into the Gibbs energy and combining Young-Laplace equation, relations between the surface thermodynamic properties (surface Gibbs energy, surface enthalpy, surface entropy, surface energy and surface heat capacity), respectively, and size of nanocrystals with different shapes were derived. Theoretical estimations of the orders of the surface thermodynamic properties of nanocrystals agree with available experimental values. Calculated results of the surface thermodynamic properties of Au, Bi and Al nanocrystals suggest that when r > 10 nm, the surface thermodynamic properties linearly vary with the reciprocal of particle size, and when r < 10 nm, the effect of particle size on the surface thermodynamic properties becomes greater and deviates from linear variation. For nanocrystals with identical equivalent diameter, the more the shape deviates from sphere, the larger the surface thermodynamic properties (absolute value) are.

THERMODYNAMIC PROPERTIES OF MC (M = V, Nb, Ta): FIRST-PRINCIPLES CALCULATIONS

NASA Astrophysics Data System (ADS)

Cao, Yong; Zhu, Jingchuan; Liu, Yong; Long, Zhishen

2013-07-01

Through the quasi-harmonic Debye model, the pressure and temperature dependences of linear expansion coefficient, bulk modulus, Debye temperature and heat capacity have been investigated. The calculated thermodynamic properties were compared with experimental data and satisfactory agreement is reached.

A Chemically Relevant Model for Teaching the Second Law of Thermodynamics.

ERIC Educational Resources Information Center

Williamson, Bryce E.; Morikawa, Tetsuo

2002-01-01

Introduces a chemical model illustrating the aspects of the second law of thermodynamics which explains concepts such as reversibility, path dependence, and extrapolation in terms of electrochemistry and calorimetry. Presents a thought experiment using an ideal galvanic electrochemical cell. (YDS)

The application of the thermodynamic perturbation theory to study the hydrophobic hydration.

PubMed

Mohoric, Tomaz; Urbic, Tomaz; Hribar-Lee, Barbara

2013-07-14

The thermodynamic perturbation theory was tested against newly obtained Monte Carlo computer simulations to describe the major features of the hydrophobic effect in a simple 3D-Mercedes-Benz water model: the temperature and hydrophobe size dependence on entropy, enthalpy, and free energy of transfer of a simple hydrophobic solute into water. An excellent agreement was obtained between the theoretical and simulation results. Further, the thermodynamic perturbation theory qualitatively correctly (with respect to the experimental data) describes the solvation thermodynamics under conditions where the simulation results are difficult to obtain with good enough accuracy, e.g., at high pressures.

The application of the thermodynamic perturbation theory to study the hydrophobic hydration

NASA Astrophysics Data System (ADS)

Mohorič, Tomaž; Urbic, Tomaz; Hribar-Lee, Barbara

2013-07-01

The thermodynamic perturbation theory was tested against newly obtained Monte Carlo computer simulations to describe the major features of the hydrophobic effect in a simple 3D-Mercedes-Benz water model: the temperature and hydrophobe size dependence on entropy, enthalpy, and free energy of transfer of a simple hydrophobic solute into water. An excellent agreement was obtained between the theoretical and simulation results. Further, the thermodynamic perturbation theory qualitatively correctly (with respect to the experimental data) describes the solvation thermodynamics under conditions where the simulation results are difficult to obtain with good enough accuracy, e.g., at high pressures.

Thermodynamic properties of rare earth elements in La-RE-Ga-In alloys (RE = Nd, Y)

NASA Astrophysics Data System (ADS)

Raguzina, Ekaterina V.; Maltsev, Dmitry S.; Volkovich, Vladimir A.; Yamshchikov, Leonid F.; Chukin, Andrey V.

2017-09-01

Thermodynamic properties of La, Nd, and Y were studied in pseudo-quaternary systems La-Nd-(Ga-In)eut and La-Y-(Ga-In)eut. Temperature dependences of lanthanum, neodymium, and yttrium activity in the alloys were determined at 300-800 °C employing the e.m.f. method. Partial thermodynamic functions of lanthanum in the alloys studied were calculated on the basis of the experimental data.

Consistent Temperature Coupling with Thermal Fluctuations of Smooth Particle Hydrodynamics and Molecular Dynamics

PubMed Central

Ganzenmüller, Georg C.; Hiermaier, Stefan; Steinhauser, Martin O.

2012-01-01

We propose a thermodynamically consistent and energy-conserving temperature coupling scheme between the atomistic and the continuum domain. The coupling scheme links the two domains using the DPDE (Dissipative Particle Dynamics at constant Energy) thermostat and is designed to handle strong temperature gradients across the atomistic/continuum domain interface. The fundamentally different definitions of temperature in the continuum and atomistic domain – internal energy and heat capacity versus particle velocity – are accounted for in a straightforward and conceptually intuitive way by the DPDE thermostat. We verify the here-proposed scheme using a fluid, which is simultaneously represented as a continuum using Smooth Particle Hydrodynamics, and as an atomistically resolved liquid using Molecular Dynamics. In the case of equilibrium contact between both domains, we show that the correct microscopic equilibrium properties of the atomistic fluid are obtained. As an example of a strong non-equilibrium situation, we consider the propagation of a steady shock-wave from the continuum domain into the atomistic domain, and show that the coupling scheme conserves both energy and shock-wave dynamics. To demonstrate the applicability of our scheme to real systems, we consider shock loading of a phospholipid bilayer immersed in water in a multi-scale simulation, an interesting topic of biological relevance. PMID:23300586

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

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

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.

Enviromental Effects on Internal Color Gradients of Early-Type Galaxies

NASA Astrophysics Data System (ADS)

La Barbera, F.; de Carvalho, R. R.; Gal, R. R.; Busarello, G.; Haines, C. P.; Mercurio, A.; Merluzzi, P.; Capaccioli, M.; Djorgovski, S. G.

2007-05-01

One of the most debated issues of observational and theoretical cosmology is that of how the environment affects the formation and evolution of galaxies. To gain new insight into this subject, we have derived surface photometry for a sample of 3,000 early-type galaxies belonging to 163 clusters with different richness, spanning a redshift range of 0.05 to 0.25. This large data-set is used to analyze how the color distribution inside galaxies depends on several parameters, such as cluster richness, local galaxy density, galaxy luminosity and redshift. We find that the internal color profile of galaxies strongly depends on the environment where galaxies reside. Galaxies in poor and rich clusters are found to follow two distinct trends in the color gradient vs. redshift diagram, with color gradients beeing less steep in rich rather than in poor clusters. No dependence of color gradients on galaxy luminosity is detected both for poor and rich clusters. We find that color gradients strongly depend on local galaxy density, with more shallow gradients in high density regions. Interestingly, this result holds only for low richness clusters, with color gradients of galaxies in rich clusters showing no dependence on local galaxy density. Our results support a reasonable picture whereby young early-type galaxies form in a dissipative collapse process, and then undergo increased (either major or minor) merging activity in richer rather than in poor clusters.

Study of the Pressure and Velocity Across the Aortic Valve

NASA Astrophysics Data System (ADS)

Kyung, Seo Young; Chung, Erica Soyun; Lee, Joo Hee; Kyung, Hayoung; Choi, Si Young

Biomechanics of the heart, requiring an extensive understanding of the complexity of the heart, have become the interests of many biomedical engineers in cardiology today. In order to study aortic valve disease, engineers have focused on the data obtained through bio-fluid flow analysis. To further this study, physical and computational analysis on the biomechanical determinants of blood flow in the stenosed aortic valve have been examined. These observations, along with the principles of cardiovascular physiology, confirm that when blood flows through the valve opening, pressure gradient across the valve is produced as a result of stenosis of the aortic valve. The aortic valve gradient is used to interpret the increase and decrease on each side of the defective valve. To compute different pressure gradients across the aortic valve, this paper analyzes Aortic Valve Areas (AVA) using simulations based on the continuity equation and Gorlin equation. The data obtained from such analysis consist of patients in the AS category that display mild Aortic Valve Velocity (AVV) and pressure gradient. Such correlation results in the construction of a dependent relationship between severe AS causing LV systolic dysfunction and the transaortic velocity.

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

Ahn, Cheol Hyoun; Hee Kim, So; Gu Yun, Myeong

In this study, we proposed the artificially designed channel structure in oxide thin-film transistors (TFTs) called a “step-composition gradient channel.” We demonstrated Al step-composition gradient Al-Zn-O (AZO) channel structures consisting of three AZO layers with different Al contents. The effects of stacking sequence in the step-composition gradient channel on performance and electrical stability of bottom-gate TFT devices were investigated with two channels of inverse stacking order (ascending/descending step-composition). The TFT with ascending step-composition channel structure (5 → 10 → 14 at. % Al composition) showed relatively negative threshold voltage (−3.7 V) and good instability characteristics with a reduced threshold voltage shift (Δmore » 1.4 V), which was related to the alignment of the conduction band off-set within the channel layer depending on the Al contents. Finally, the reduced Al composition in the initial layer of ascending step-composition channel resulted in the best field effect mobility of 4.5 cm{sup 2}/V s. We presented a unique active layer of the “step-composition gradient channel” in the oxide TFTs and explained the mechanism of adequate channel design.« less

Bicarbonate diffusion through mucus.

PubMed

Livingston, E H; Miller, J; Engel, E

1995-09-01

The mucus layer overlying duodenal epithelium maintains a pH gradient against high luminal acid concentrations. Despite these adverse conditions, epithelial surface pH remains close to neutrality. The exact nature of the gradient-forming barrier remains unknown. The barrier consists of mucus into which HCO3- is secreted. Quantification of the ability of HCO3- to establish and maintain the gradient depends on accurate measurement of this ion's diffusion coefficient through mucus. We describe new experimental and mathematical methods for diffusion measurement and report diffusion coefficients for HCO3- diffusion through saline, 5% mucin solutions, and rat duodenal mucus. The diffusion coefficients were 20.2 +/- 0.10, 3.02 +/- 0.31, and 1.81 +/- 0.12 x 10(-6) cm2/s, respectively. Modeling of the mucobicarbonate layer with this latter value suggests that for conditions of high luminal acid strength the neutralization of acid by HCO3- occurs just above the epithelial surface. Under these conditions the model predicts that fluid convection toward the lumen could be important in maintaining the pH gradient. In support of this hypothesis we were able to demonstrate a net luminal fluid flux of 5 microliters.min-1.cm-2 after perfusion of 0.15 N HCl in the rat duodenum.

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!

Impacts of chemical gradients on microbial community structure

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

Chen, Jianwei; Hanke, Anna; Tegetmeyer, Halina E.

Succession of redox processes is sometimes assumed to define a basic microbial community structure for ecosystems with oxygen gradients. In this paradigm, aerobic respiration, denitrification, fermentation and sulfate reduction proceed in a thermodynamically determined order, known as the ‘redox tower’. Here, we investigated whether redox sorting of microbial processes explains microbial community structure at low-oxygen concentrations. We subjected a diverse microbial community sampled from a coastal marine sediment to 100 days of tidal cycling in a laboratory chemostat. Oxygen gradients (both in space and time) led to the assembly of a microbial community dominated by populations that each performed aerobicmore » and anaerobic metabolism in parallel. This was shown by metagenomics, transcriptomics, proteomics and stable isotope incubations. Effective oxygen consumption combined with the formation of microaggregates sustained the activity of oxygen-sensitive anaerobic enzymes, leading to braiding of unsorted redox processes, within and between populations. Analyses of available metagenomic data sets indicated that the same ecological strategies might also be successful in some natural ecosystems.« less

Effects of copper vapour on thermophysical properties of CO2-N2 plasma

NASA Astrophysics Data System (ADS)

Zhong, Linlin; Wang, Xiaohua; Rong, Mingzhe; Cressault, Yann

2016-10-01

CO2-N2 mixtures are often used as arc quenching medium (to replace SF6) in circuit breakers and shielding gas in arc welding. In such applications, copper vapour resulting from electrode surfaces can modify characteristics of plasmas. This paper therefore presents an investigation of the effects of copper on thermophysical properties of CO2-N2 plasma. The equilibrium compositions, thermodynamic properties (including mass density, specific enthalpy, and specific heat), transport coefficients (including electrical conductivity, viscosity, and thermal conductivity), and four kinds of combined diffusion coefficients due to composition gradients, applied electric fields, temperature gradients, and pressure gradients respectively, were calculated and discussed for CO2-N2 (mixing ratio 7:3) plasma contaminated by different proportions of copper vapour. The significant influences of copper were observed on all the properties of CO2-N2-Cu mixtures. The better ionization ability and larger molar mass of copper and larger collision integrals related to copper, should be responsible for such influences.

Impacts of chemical gradients on microbial community structure

DOE PAGES

Chen, Jianwei; Hanke, Anna; Tegetmeyer, Halina E.; ...

2017-01-17

Succession of redox processes is sometimes assumed to define a basic microbial community structure for ecosystems with oxygen gradients. In this paradigm, aerobic respiration, denitrification, fermentation and sulfate reduction proceed in a thermodynamically determined order, known as the ‘redox tower’. Here, we investigated whether redox sorting of microbial processes explains microbial community structure at low-oxygen concentrations. We subjected a diverse microbial community sampled from a coastal marine sediment to 100 days of tidal cycling in a laboratory chemostat. Oxygen gradients (both in space and time) led to the assembly of a microbial community dominated by populations that each performed aerobicmore » and anaerobic metabolism in parallel. This was shown by metagenomics, transcriptomics, proteomics and stable isotope incubations. Effective oxygen consumption combined with the formation of microaggregates sustained the activity of oxygen-sensitive anaerobic enzymes, leading to braiding of unsorted redox processes, within and between populations. Analyses of available metagenomic data sets indicated that the same ecological strategies might also be successful in some natural ecosystems.« less

Impacts of chemical gradients on microbial community structure

PubMed Central

Chen, Jianwei; Hanke, Anna; Tegetmeyer, Halina E; Kattelmann, Ines; Sharma, Ritin; Hamann, Emmo; Hargesheimer, Theresa; Kraft, Beate; Lenk, Sabine; Geelhoed, Jeanine S; Hettich, Robert L; Strous, Marc

2017-01-01

Succession of redox processes is sometimes assumed to define a basic microbial community structure for ecosystems with oxygen gradients. In this paradigm, aerobic respiration, denitrification, fermentation and sulfate reduction proceed in a thermodynamically determined order, known as the ‘redox tower'. Here, we investigated whether redox sorting of microbial processes explains microbial community structure at low-oxygen concentrations. We subjected a diverse microbial community sampled from a coastal marine sediment to 100 days of tidal cycling in a laboratory chemostat. Oxygen gradients (both in space and time) led to the assembly of a microbial community dominated by populations that each performed aerobic and anaerobic metabolism in parallel. This was shown by metagenomics, transcriptomics, proteomics and stable isotope incubations. Effective oxygen consumption combined with the formation of microaggregates sustained the activity of oxygen-sensitive anaerobic enzymes, leading to braiding of unsorted redox processes, within and between populations. Analyses of available metagenomic data sets indicated that the same ecological strategies might also be successful in some natural ecosystems. PMID:28094795

Impacts of chemical gradients on microbial community structure.

PubMed

Chen, Jianwei; Hanke, Anna; Tegetmeyer, Halina E; Kattelmann, Ines; Sharma, Ritin; Hamann, Emmo; Hargesheimer, Theresa; Kraft, Beate; Lenk, Sabine; Geelhoed, Jeanine S; Hettich, Robert L; Strous, Marc

2017-04-01

Succession of redox processes is sometimes assumed to define a basic microbial community structure for ecosystems with oxygen gradients. In this paradigm, aerobic respiration, denitrification, fermentation and sulfate reduction proceed in a thermodynamically determined order, known as the 'redox tower'. Here, we investigated whether redox sorting of microbial processes explains microbial community structure at low-oxygen concentrations. We subjected a diverse microbial community sampled from a coastal marine sediment to 100 days of tidal cycling in a laboratory chemostat. Oxygen gradients (both in space and time) led to the assembly of a microbial community dominated by populations that each performed aerobic and anaerobic metabolism in parallel. This was shown by metagenomics, transcriptomics, proteomics and stable isotope incubations. Effective oxygen consumption combined with the formation of microaggregates sustained the activity of oxygen-sensitive anaerobic enzymes, leading to braiding of unsorted redox processes, within and between populations. Analyses of available metagenomic data sets indicated that the same ecological strategies might also be successful in some natural ecosystems.

Stirling Engine With Radial Flow Heat Exchangers

NASA Technical Reports Server (NTRS)

Vitale, N.; Yarr, George

1993-01-01

Conflict between thermodynamical and structural requirements resolved. In Stirling engine of new cylindrical configuration, regenerator and acceptor and rejector heat exchangers channel flow of working gas in radial direction. Isotherms in regenerator ideally concentric cylinders, and gradient of temperature across regenerator radial rather than axial. Acceptor and rejector heat exchangers located radially inward and outward of regenerator, respectively. Enables substantial increase in power of engine without corresponding increase in diameter of pressure vessel.

Curvature and bow of bulk GaN substrates

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

Foronda, Humberto M.; Young, Erin C.; Robertson, Christian A.

2016-07-21

We investigate the bow of free standing (0001) oriented hydride vapor phase epitaxy grown GaN substrates and demonstrate that their curvature is consistent with a compressive to tensile stress gradient (bottom to top) present in the substrates. The origin of the stress gradient and the curvature is attributed to the correlated inclination of edge threading dislocation (TD) lines away from the [0001] direction. A model is proposed and a relation is derived for bulk GaN substrate curvature dependence on the inclination angle and the density of TDs. The model is used to analyze the curvature for commercially available GaN substratesmore » as determined by high resolution x-ray diffraction. The results show a close correlation between the experimentally determined parameters and those predicted from theoretical model.« less

Thermal infrared properties of Titan's stratospheric aerosol

NASA Technical Reports Server (NTRS)

Samuelson, Robert E.; Mayo, Louis A.

1991-01-01

The monotonic increase with wavenumber of stratospheric IR opacities in the north polar neighborhood of Titan, in the 250-600/cm bandpass, becomes more extreme with decreasing altitude, consistent with an opacity that is primarily dependent on a high altitude photochemical aerosol, on the one hand, but which is moderated by condensed organics at lower altitudes. Because condensates exhibit a wavenumber dependence for opacity which is the opposite of that required, it is suggested that condensed nitriles may be prominent; either of these condensates may be acceptable for sufficiently large particles. While comparisons with low-latitude data indicate no clear dependence of vertically-integrated opacity on latitude above 80 km, indications of a particle size and/or composition gradient with latitude in the lower stratosphere are noted.

How does the Earth system generate and maintain thermodynamic disequilibrium and what does it imply for the future of the planet?

PubMed

Kleidon, Axel

2012-03-13

The Earth's chemical composition far from chemical equilibrium is unique in our Solar System, and this uniqueness has been attributed to the presence of widespread life on the planet. Here, I show how this notion can be quantified using non-equilibrium thermodynamics. Generating and maintaining disequilibrium in a thermodynamic variable requires the extraction of power from another thermodynamic gradient, and the second law of thermodynamics imposes fundamental limits on how much power can be extracted. With this approach and associated limits, I show that the ability of abiotic processes to generate geochemical free energy that can be used to transform the surface-atmosphere environment is strongly limited to less than 1 TW. Photosynthetic life generates more than 200 TW by performing photochemistry, thereby substantiating the notion that a geochemical composition far from equilibrium can be a sign for strong biotic activity. Present-day free energy consumption by human activity in the form of industrial activity and human appropriated net primary productivity is of the order of 50 TW and therefore constitutes a considerable term in the free energy budget of the planet. When aiming to predict the future of the planet, we first note that since global changes are closely related to this consumption of free energy, and the demands for free energy by human activity are anticipated to increase substantially in the future, the central question in the context of predicting future global change is then how human free energy demands can increase sustainably without negatively impacting the ability of the Earth system to generate free energy. This question could be evaluated with climate models, and the potential deficiencies in these models to adequately represent the thermodynamics of the Earth system are discussed. Then, I illustrate the implications of this thermodynamic perspective by discussing the forms of renewable energy and planetary engineering that would enhance the overall free energy generation and, thereby 'empower' the future of the planet.

Energy-dependent topological anti-de Sitter black holes in Gauss-Bonnet Born-Infeld gravity

NASA Astrophysics Data System (ADS)

Hendi, S. H.; Behnamifard, H.; Bahrami-Asl, B.

2018-03-01

Employing higher-curvature corrections to Einstein-Maxwell gravity has garnered a great deal of attention motivated by the high-energy regime in the quantum nature of black hole physics. In addition, one may employ gravity's rainbow to encode quantum gravity effects into black hole solutions. In this paper, we regard an energy-dependent static spacetime with various topologies and study its black hole solutions in the context of Gauss-Bonnet Born-Infeld (GB-BI) gravity. We study the thermodynamic properties and examine the first law of thermodynamics. Using a suitable local transformation, we endow the Ricci-flat black hole solutions with a global rotation and study the effects of rotation on thermodynamic quantities. We also investigate thermal stability in a canonical ensemble by calculating the heat capacity. We obtain the effects of various parameters on the horizon radius of stable black holes. Finally, we discuss a second-order phase transition in the extended phase space thermodynamics and investigate the critical behavior.

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.

Thermodynamics of anisotropic antiferromagnetic Heisenberg chain in the presence of longitudinal magnetic field

NASA Astrophysics Data System (ADS)

Rezania, H.

2018-07-01

We have addressed the specific heat and magnetization of one dimensional spin-1/2 anisotropic antiferromagnetic Heisenberg chain at finite magnetic field. We have investigated the thermodynamic properties by means of excitation spectrum in terms of a hard core Bosonic representation. The effect of in-plane anisotropy thermodynamic properties has also been studied via the Bosonic model by Green's function approach. This anisotropy is considered for exchange constants that couple spin components perpendicular to magnetic field direction. We have found the temperature dependence of the specific heat and longitudinal magnetization in the gapped field induced spin-polarized phase for various magnetic fields and anisotropy parameters. Furthermore we have studied the magnetic field dependence of specific heat and magnetization for various anisotropy parameters. Our results show temperature dependence of specific heat includes a peak so that its temperature position goes to higher temperature with increase of magnetic field. We have found the magnetic field dependence of specific heat shows a monotonic decreasing behavior for various magnetic fields due to increase of energy gap in the excitation spectrum. Also we have studied the temperature dependence of magnetization for different magnetic fields and various anisotropy parameters.

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.

First-principles study of elastic and thermodynamic properties of orthorhombic OsB4 under high pressure

NASA Astrophysics Data System (ADS)

Yan, Hai-Yan; Zhang, Mei-Guang; Huang, Duo-Hui; Wei, Qun

2013-04-01

The first-principles study on the elastic properties, elastic anisotropy and thermodynamic properties of the orthorhombic OsB4 is reported using density functional theory method with the ultrasoft pseudopotential scheme in the frame of the generalized gradient approximation. The calculated equilibrium parameters are in good agreement with the available theoretical data. A complete elastic tensor and crystal anisotropies of the ultra-incompressible OsB4 are determined in the pressure range of 0-50 GPa. By the elastic stability criteria, it is predicted that the orthorhombic OsB4 is stable below 50 GPa. By using the quasi-harmonic Debye model, the heat capacity, the coefficient of thermal expansion, and the Grüneisen parameter of OsB4 are also successfully obtained in the present work.

The Use of Thermal Remote Sensing to Study Thermodynamics of Ecosystem Development

NASA Technical Reports Server (NTRS)

Luvall, Jeffrey C.; Rickman, Doug L.; Arnold, James E. (Technical Monitor)

2000-01-01

Thermal remote sensing can provide environmental measuring tools with capabilities for measuring ecosystem development and integrity. Recent advances in applying principles of nonequilibrium thermodynamics to ecology provide fundamental insights into energy partitioning in ecosystems. Ecosystems are nonequilibrium systems, open to material and energy flows, which grow and develop structures and processes to increase energy degradation. More developed terrestrial ecosystems will be more effective at dissipating the solar gradient (degrading its energy content). This can be measured by the effective surface temperature of the ecosystem on a landscape scale. A series of airborne thermal infrared multispectral scanner data were collected from several forested ecosystems ranging from a western US douglas-fir forest to a tropical rain forest in Costa Rica. These data were used to develop measures of ecosystem development and integrity based on surface temperature.

Thermal Remote Sensing and the Thermodynamics of Ecosystems Development

NASA Technical Reports Server (NTRS)

Luvall, Jeffrey C.; Kay, James J.; Fraser, Roydon F.; Goodman, H. Michael (Technical Monitor)

2001-01-01

Thermal remote sensing can provide environmental measuring tools with capabilities for measuring ecosystem development and integrity. Recent advances in applying principles of nonequilibrium thermodynamics to ecology provide fundamental insights into energy partitioning in ecosystems. Ecosystems are nonequilibrium systems, open to material and energy flows, which grow and develop structures and processes to increase energy degradation. More developed terrestrial ecosystems will be more effective at dissipating the solar gradient (degrading its energy content). This can be measured by the effective surface temperature of the ecosystem on a landscape scale. A series of airborne thermal infrared multispectral scanner data were collected from several forested ecosystems ranging from a western US douglas-fir forest to a tropical rain forest in Costa Rica. Also measured were agriculture systems. These data were used to develop measures of ecosystem development and integrity based on surface temperature.

SDSS-IV MaNGA: The Spatially Resolved Stellar Initial Mass Function in ˜400 Early-Type Galaxies

NASA Astrophysics Data System (ADS)

Parikh, Taniya; Thomas, Daniel; Maraston, Claudia; Westfall, Kyle B.; Goddard, Daniel; Lian, Jianhui; Meneses-Goytia, Sofia; Jones, Amy; Vaughan, Sam; Andrews, Brett H.; Bershady, Matthew; Bizyaev, Dmitry; Brinkmann, Jonathan; Brownstein, Joel R.; Bundy, Kevin; Drory, Niv; Emsellem, Eric; Law, David R.; Newman, Jeffrey A.; Roman-Lopes, Alexandre; Wake, David; Yan, Renbin; Zheng, Zheng

2018-03-01

MaNGA provides the opportunity to make precise spatially resolved measurements of the IMF slope in galaxies owing to its unique combination of spatial resolution, wavelength coverage and sample size. We derive radial gradients in age, element abundances and IMF slope analysing optical and near-infrared absorption features from stacked spectra out to the half-light radius of 366 early-type galaxies with masses 9.9 - 10.8 log M/M⊙. We find flat gradients in age and [α/Fe] ratio, as well as negative gradients in metallicity, consistent with the literature. We further derive significant negative gradients in the [Na/Fe] ratio with galaxy centres being well enhanced in Na abundance by up to 0.5 dex. Finally, we find a gradient in IMF slope with a bottom-heavy IMF in the centre (typical mass excess factor of 1.5) and a Milky Way-type IMF at the half-light radius. This pattern is mass-dependent with the lowest mass galaxies in our sample featuring only a shallow gradient around a Milky Way IMF. Our results imply the local IMF-σ relation within galaxies to be even steeper than the global relation and hint towards the local metallicity being the dominating factor behind the IMF variations. We also employ different stellar population models in our analysis and show that a radial IMF gradient is found independently of the stellar population model used. A similar analysis of the Wing-Ford band provides inconsistent results and further evidence of the difficulty in measuring and modelling this particular feature.

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.

Thermodynamic evaluation of transonic compressor rotors using the finite volume approach

NASA Technical Reports Server (NTRS)

Moore, J.; Nicholson, S.; Moore, J. G.

1985-01-01

Research at NASA Lewis Research Center gave the opportunity to incorporate new control volumes in the Denton 3-D finite-volume time marching code. For duct flows, the new control volumes require no transverse smoothing and this allows calculations with large transverse gradients in properties without significant numerical total pressure losses. Possibilities for improving the Denton code to obtain better distributions of properties through shocks were demonstrated. Much better total pressure distributions through shocks are obtained when the interpolated effective pressure, needed to stabilize the solution procedure, is used to calculate the total pressure. This simple change largely eliminates the undershoot in total pressure down-stream of a shock. Overshoots and undershoots in total pressure can then be further reduced by a factor of 10 by adopting the effective density method, rather than the effective pressure method. Use of a Mach number dependent interpolation scheme for pressure then removes the overshoot in static pressure downstream of a shock. The stability of interpolation schemes used for the calculation of effective density is analyzed and a Mach number dependent scheme is developed, combining the advantages of the correct perfect gas equation for subsonic flow with the stability of 2-point and 3-point interpolation schemes for supersonic flow.

TEMPO/viologen electrochemical heterojunction for diffusion-controlled redox mediation: a highly rectifying bilayer-sandwiched device based on cross-reaction at the interface between dissimilar redox polymers.

PubMed

Tokue, Hiroshi; Oyaizu, Kenichi; Sukegawa, Takashi; Nishide, Hiroyuki

2014-03-26

A couple of totally reversible redox-active molecules, which are different in redox potentials, 2,2,6,6-tetramethylpiperidin-1-oxyl (TEMPO) and viologen (V(2+)), were employed to give rise to a rectified redox conduction effect. Single-layer and bilayer devices were fabricated using polymers containing these sites as pendant groups per repeating unit. The devices were obtained by sandwiching the redox polymer layer(s) with indium tin oxide (ITO)/glass and Pt foil electrodes. Electrochemical measurements of the single-layer device composed of polynorbornene-bearing TEMPO (PTNB) exhibited a diffusion-limited current-voltage response based on the TEMPO(+)/TEMPO exchange reaction, which was almost equivalent to a redox gradient through the PTNB layer depending upon the thickness. The bilayer device gave rise to the current rectification because of the thermodynamically favored cross-reaction between TEMPO(+) and V(+) at the polymer/polymer interface. A current-voltage response obtained for the bilayer device demonstrated a two-step diffusion-limited current behavior as a result of the concurrent V(2+)/V(+) and V(+)/V(0) exchange reactions according to the voltage and suggested that the charge transport process through the device was most likely to be rate-determined by a redox gradient in the polymer layer. Current collection experiments revealed a charge transport balance throughout the device, as a result of the electrochemical stability and robustness of the polymers in both redox states.

Quantum refrigerators and the third law of thermodynamics.

PubMed

Levy, Amikam; Alicki, Robert; Kosloff, Ronnie

2012-06-01

The rate of temperature decrease of a cooled quantum bath is studied as its temperature is reduced to absolute zero. The third law of thermodynamics is then quantified dynamically by evaluating the characteristic exponent ζ of the cooling process dT(t)/dt∼-T^{ζ} when approaching absolute zero, T→0. A continuous model of a quantum refrigerator is employed consisting of a working medium composed either by two coupled harmonic oscillators or two coupled two-level systems. The refrigerator is a nonlinear device merging three currents from three heat baths: a cold bath to be cooled, a hot bath as an entropy sink, and a driving bath which is the source of cooling power. A heat-driven refrigerator (absorption refrigerator) is compared to a power-driven refrigerator. When optimized, both cases lead to the same exponent ζ, showing a lack of dependence on the form of the working medium and the characteristics of the drivers. The characteristic exponent is therefore determined by the properties of the cold reservoir and its interaction with the system. Two generic heat bath models are considered: a bath composed of harmonic oscillators and a bath composed of ideal Bose/Fermi gas. The restrictions on the interaction Hamiltonian imposed by the third law are discussed. In the Appendices, the theory of periodically driven open systems and its implication for thermodynamics are outlined.

An equation of state for partially ionized plasmas: The Coulomb contribution to the free energy

NASA Astrophysics Data System (ADS)

Kilcrease, D. P.; Colgan, J.; Hakel, P.; Fontes, C. J.; Sherrill, M. E.

2015-09-01

We have previously developed an equation of state (EOS) model called ChemEOS (Hakel and Kilcrease, Atomic Processes in Plasmas, Eds., J. Cohen et al., AIP, 2004) for a plasma of interacting ions, atoms and electrons. It is based on a chemical picture of the plasma and is derived from an expression for the Helmholtz free energy of the interacting species. All other equilibrium thermodynamic quantities are then obtained by minimizing this free energy subject to constraints, thus leading to a thermodynamically consistent EOS. The contribution to this free energy from the Coulomb interactions among the particles is treated using the method of Chabrier and Potekhin (Phys. Rev. E 58, 4941 (1998)) which we have adapted for partially ionized plasmas. This treatment is further examined and is found to give rise to unphysical behavior for various elements at certain values of the density and temperature where the Coulomb coupling begins to become significant and the atoms are partially ionized. We examine the source of this unphysical behavior and suggest corrections that produce acceptable results. The sensitivity of the thermodynamic properties and frequency-dependent opacity of iron is examined with and without these corrections. The corrected EOS is used to determine the fractional ion populations and level populations for a new generation of OPLIB low-Z opacity tables currently being prepared at Los Alamos National Laboratory with the ATOMIC code.

Protein folding thermodynamics applied to the photocycle of the photoactive yellow protein.

PubMed Central

Van Brederode, M E; Hoff, W D; Van Stokkum, I H; Groot, M L; Hellingwerf, K J

1996-01-01

Two complementary aspects of the thermodynamics of the photoactive yellow protein (PYP), a new type of photoreceptor that has been isolated from Ectothiorhodospira halophila, have been investigated. First, the thermal denaturation of PYP at pH 3.4 has been examined by global analysis of the temperature-induced changes in the UV-VIS absorbance spectrum of this chromophoric protein. Subsequently, a thermodynamic model for protein (un)folding processes, incorporating heat capacity changes, has been applied to these data. The second aspect of PYP that has been studied is the temperature dependence of its photocycle kinetics, which have been reported to display an unexplained deviation from normal Arrhenius behavior. We have extended these measurements in two solvents with different hydrophobicities and have analyzed the number of rate constants needed to describe these data. Here we show that the resulting temperature dependence of the rate constants can be quantitatively explained by the application of a thermodynamic model which assumes that heat capacity changes are associated with the two transitions in the photocycle of PYP. This result is the first example of an enzyme catalytic cycle being described by a thermodynamic model including heat capacity changes. It is proposed that a strong link exists between the processes occurring during the photocycle of PYP and protein (un)folding processes. This permits a thermodynamic analysis of the light-induced, physiologically relevant, conformational changes occurring in this photoreceptor protein. PMID:8804619

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

Wu, Wei; Wang, Jin, E-mail: jin.wang.1@stonybrook.edu; State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, 130022 Changchun, China and College of Physics, Jilin University, 130021 Changchun

We have established a general non-equilibrium thermodynamic formalism consistently applicable to both spatially homogeneous and, more importantly, spatially inhomogeneous systems, governed by the Langevin and Fokker-Planck stochastic dynamics with multiple state transition mechanisms, using the potential-flux landscape framework as a bridge connecting stochastic dynamics with non-equilibrium thermodynamics. A set of non-equilibrium thermodynamic equations, quantifying the relations of the non-equilibrium entropy, entropy flow, entropy production, and other thermodynamic quantities, together with their specific expressions, is constructed from a set of dynamical decomposition equations associated with the potential-flux landscape framework. The flux velocity plays a pivotal role on both the dynamic andmore » thermodynamic levels. On the dynamic level, it represents a dynamic force breaking detailed balance, entailing the dynamical decomposition equations. On the thermodynamic level, it represents a thermodynamic force generating entropy production, manifested in the non-equilibrium thermodynamic equations. The Ornstein-Uhlenbeck process and more specific examples, the spatial stochastic neuronal model, in particular, are studied to test and illustrate the general theory. This theoretical framework is particularly suitable to study the non-equilibrium (thermo)dynamics of spatially inhomogeneous systems abundant in nature. This paper is the second of a series.« less

Measurement and Analysis of the Temperature Gradient of Blackbody Cavities, for Use in Radiation Thermometry

NASA Astrophysics Data System (ADS)

De Lucas, Javier; Segovia, José Juan

2018-05-01

Blackbody cavities are the standard radiation sources widely used in the fields of radiometry and radiation thermometry. Its effective emissivity and uncertainty depend to a large extent on the temperature gradient. An experimental procedure based on the radiometric method for measuring the gradient is followed. Results are applied to particular blackbody configurations where gradients can be thermometrically estimated by contact thermometers and where the relationship between both basic methods can be established. The proposed procedure may be applied to commercial blackbodies if they are modified allowing secondary contact temperature measurement. In addition, the established systematic may be incorporated as part of the actions for quality assurance in routine calibrations of radiation thermometers, by using the secondary contact temperature measurement for detecting departures from the real radiometrically obtained gradient and the effect on the uncertainty. On the other hand, a theoretical model is proposed to evaluate the effect of temperature variations on effective emissivity and associated uncertainty. This model is based on a gradient sample chosen following plausible criteria. The model is consistent with the Monte Carlo method for calculating the uncertainty of effective emissivity and complements others published in the literature where uncertainty is calculated taking into account only geometrical variables and intrinsic emissivity. The mathematical model and experimental procedure are applied and validated using a commercial type three-zone furnace, with a blackbody cavity modified to enable a secondary contact temperature measurement, in the range between 400 °C and 1000 °C.

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.

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.

A thermodynamic counterpart of the Axelrod model of social influence: The one-dimensional case

NASA Astrophysics Data System (ADS)

Gandica, Y.; Medina, E.; Bonalde, I.

2013-12-01

We propose a thermodynamic version of the Axelrod model of social influence. In one-dimensional (1D) lattices, the thermodynamic model becomes a coupled Potts model with a bonding interaction that increases with the site matching traits. We analytically calculate thermodynamic and critical properties for a 1D system and show that an order-disorder phase transition only occurs at T=0 independent of the number of cultural traits q and features F. The 1D thermodynamic Axelrod model belongs to the same universality class of the Ising and Potts models, notwithstanding the increase of the internal dimension of the local degree of freedom and the state-dependent bonding interaction. We suggest a unifying proposal to compare exponents across different discrete 1D models. The comparison with our Hamiltonian description reveals that in the thermodynamic limit the original out-of-equilibrium 1D Axelrod model with noise behaves like an ordinary thermodynamic 1D interacting particle system.

Strain Rate Dependant Material Model for Orthotropic Metals

NASA Astrophysics Data System (ADS)

Vignjevic, Rade

2016-08-01

In manufacturing processes anisotropic metals are often exposed to the loading with high strain rates in the range from 102 s-1 to 106 s-1 (e.g. stamping, cold spraying and explosive forming). These types of loading often involve generation and propagation of shock waves within the material. The material behaviour under such a complex loading needs to be accurately modelled, in order to optimise the manufacturing process and achieve appropriate properties of the manufactured component. The presented research is related to development and validation of a thermodynamically consistent physically based constitutive model for metals under high rate loading. The model is capable of modelling damage, failure and formation and propagation of shock waves in anisotropic metals. The model has two main parts: the strength part which defines the material response to shear deformation and an equation of state (EOS) which defines the material response to isotropic volumetric deformation [1]. The constitutive model was implemented into the transient nonlinear finite element code DYNA3D [2] and our in house SPH code. Limited model validation was performed by simulating a number of high velocity material characterisation and validation impact tests. The new damage model was developed in the framework of configurational continuum mechanics and irreversible thermodynamics with internal state variables. The use of the multiplicative decomposition of deformation gradient makes the model applicable to arbitrary plastic and damage deformations. To account for the physical mechanisms of failure, the concept of thermally activated damage initially proposed by Tuller and Bucher [3], Klepaczko [4] was adopted as the basis for the new damage evolution model. This makes the proposed damage/failure model compatible with the Mechanical Threshold Strength (MTS) model Follansbee and Kocks [5], 1988; Chen and Gray [6] which was used to control evolution of flow stress during plastic deformation. In addition the constitutive model is coupled with a vector shock equation of state which allows for modelling of shock wave propagation in orthotropic the material. Parameters for the new constitutive model are typically derived on the basis of the tensile tests (performed over a range of temperatures and strain rates), plate impact tests and Taylor anvil tests. The model was applied to simulate explosively driven fragmentation, blast loading and cold spraying impacts.

Thermodynamics of stoichiometric biochemical networks in living systems far from equilibrium.

PubMed

Qian, Hong; Beard, Daniel A

2005-04-22

The principles of thermodynamics apply to both equilibrium and nonequilibrium biochemical systems. The mathematical machinery of the classic thermodynamics, however, mainly applies to systems in equilibrium. We introduce a thermodynamic formalism for the study of metabolic biochemical reaction (open, nonlinear) networks in both time-dependent and time-independent nonequilibrium states. Classical concepts in equilibrium thermodynamics-enthalpy, entropy, and Gibbs free energy of biochemical reaction systems-are generalized to nonequilibrium settings. Chemical motive force, heat dissipation rate, and entropy production (creation) rate, key concepts in nonequilibrium systems, are introduced. Dynamic equations for the thermodynamic quantities are presented in terms of the key observables of a biochemical network: stoichiometric matrix Q, reaction fluxes J, and chemical potentials of species mu without evoking empirical rate laws. Energy conservation and the Second Law are established for steady-state and dynamic biochemical networks. The theory provides the physiochemical basis for analyzing large-scale metabolic networks in living organisms.

Large Eddy Simulation Study for Fluid Disintegration and Mixing

NASA Technical Reports Server (NTRS)

Bellan, Josette; Taskinoglu, Ezgi

2011-01-01

A new modeling approach is based on the concept of large eddy simulation (LES) within which the large scales are computed and the small scales are modeled. The new approach is expected to retain the fidelity of the physics while also being computationally efficient. Typically, only models for the small-scale fluxes of momentum, species, and enthalpy are used to reintroduce in the simulation the physics lost because the computation only resolves the large scales. These models are called subgrid (SGS) models because they operate at a scale smaller than the LES grid. In a previous study of thermodynamically supercritical fluid disintegration and mixing, additional small-scale terms, one in the momentum and one in the energy conservation equations, were identified as requiring modeling. These additional terms were due to the tight coupling between dynamics and real-gas thermodynamics. It was inferred that if these terms would not be modeled, the high density-gradient magnitude regions, experimentally identified as a characteristic feature of these flows, would not be accurately predicted without the additional term in the momentum equation; these high density-gradient magnitude regions were experimentally shown to redistribute turbulence in the flow. And it was also inferred that without the additional term in the energy equation, the heat flux magnitude could not be accurately predicted; the heat flux to the wall of combustion devices is a crucial quantity that determined necessary wall material properties. The present work involves situations where only the term in the momentum equation is important. Without this additional term in the momentum equation, neither the SGS-flux constant-coefficient Smagorinsky model nor the SGS-flux constant-coefficient Gradient model could reproduce in LES the pressure field or the high density-gradient magnitude regions; the SGS-flux constant- coefficient Scale-Similarity model was the most successful in this endeavor although not totally satisfactory. With a model for the additional term in the momentum equation, the predictions of the constant-coefficient Smagorinsky and constant-coefficient Scale-Similarity models were improved to a certain extent; however, most of the improvement was obtained for the Gradient model. The previously derived model and a newly developed model for the additional term in the momentum equation were both tested, with the new model proving even more successful than the previous model at reproducing the high density-gradient magnitude regions. Several dynamic SGS-flux models, in which the SGS-flux model coefficient is computed as part of the simulation, were tested in conjunction with the new model for this additional term in the momentum equation. The most successful dynamic model was a "mixed" model combining the Smagorinsky and Gradient models. This work is directly applicable to simulations of gas turbine engines (aeronautics) and rocket engines (astronautics).

Minimizing inner product data dependencies in conjugate gradient iteration

NASA Technical Reports Server (NTRS)

Vanrosendale, J.

1983-01-01

The amount of concurrency available in conjugate gradient iteration is limited by the summations required in the inner product computations. The inner product of two vectors of length N requires time c log(N), if N or more processors are available. This paper describes an algebraic restructuring of the conjugate gradient algorithm which minimizes data dependencies due to inner product calculations. After an initial start up, the new algorithm can perform a conjugate gradient iteration in time c*log(log(N)).

Thermal Remote Sensing and the Thermodynamics of Ecosystem Development

NASA Technical Reports Server (NTRS)

Luvall, Jeffrey C.; Rickman, Doug; Fraser, Roydon F.

2013-01-01

Thermal remote sensing can provide environmental measuring tools with capabilities for measuring ecosystem development and integrity. Recent advances in applying principles of nonequilibrium thermodynamics to ecology provide fundamental insights into energy partitioning in ecosystems. Ecosystems are nonequilibrium systems, open to material and energy flows, which grow and develop structures and processes to increase energy degradation. More developed terrestrial ecosystems will be more effective at dissipating the solar gradient (degrading its exergy content) and can be measured by the effective surface temperature of the ecosystem on a landscape scale. Ecosystems are viewed as open thermodynamic systems with a large gradient impressed on them by the exergy flux from the sun. Ecosystems, according to the restated second law, develop in ways that systematically increases their ability to degrade the incoming solar exergy, hence negating it's ability to set up even larger gradients. Thus it should be expected that more mature ecosystems degrade the exergy they capture more completely than a less developed ecosystem. The degree to which incoming solar exergy is degraded is a function of the surface temperature of the ecosystem. If a group of ecosystems receives the same amount of incoming radiation, we would expect that the most mature ecosystem would reradiate its energy at the lowest quality level and thus would have the lowest surface temperature (coldest black body temperature). Initial development work was done using NASA's airborne Thermal Infrared Multispectral Scanner (TIMS) followed by the use of a multispectral visible and thermal scanner-Airborne Thermal and Land Applications Sensor (ATLAS). Luvall and his coworkers have documented ecosystem energy budgets, including tropical forests, midlatitude varied ecosystems, and semiarid ecosystems. These data show that under similar environmental conditions (air temperature, relative humidity, winds, and solar irradiance) and within a given biome type, the more developed the ecosystem, the cooler it's surface temperature and the more degraded the quality of it's reradiated energy. HyspIRI is a hyperspectral visible/Near IR and multispectral thermal future global satellite mission that will collect data to study the world's ecosystems and will provide a benchmark on the state of the worlds ecosystems against which future changes can be assessed. HyspIRI will provide global data sets that will provide a means for measuring ecosystem development and integrity.

Thermal Remote Sensing and the Thermodynamics of Ecosystem Development

NASA Technical Reports Server (NTRS)

Luvall, Jeffrey C.; Rickman, Doug.; Fraser, Roydon F.

2013-01-01

Thermal remote sensing can provide environmental measuring tools with capabilities for measuring ecosystem development and integrity. Recent advances in applying principles of nonequilibrium thermodynamics to ecology provide fundamental insights into energy partitioning in ecosystems. Ecosystems are nonequilibrium systems, open to material and energy flows, which grow and develop structures and processes to increase energy degradation. More developed terrestrial ecosystems will be more effective at dissipating the solar gradient (degrading its exergy content) and can be measured by the effective surface temperature of the ecosystem on a landscape scale. Ecosystems are viewed as open thermodynamic systems with a large gradient impressed on them by the exergy flux from the sun. Ecosystems, according to the restated second law, develop in ways that systematically increases their ability to degrade the incoming solar exergy, hence negating it's ability to set up even larger gradients. Thus it should be expected that more mature ecosystems degrade the exergy they capture more completely than a less developed ecosystem. The degree to which incoming solar exergy is degraded is a function of the surface temperature of the ecosystem. If a group of ecosystems receives the same amount of incoming radiation, we would expect that the most mature ecosystem would reradiate its energy at the lowest quality level and thus would have the lowest surface temperature (coldest black body temperature). Initial development work was done using NASA's airborne Thermal Infrared Multispectral Scanner (TIMS) followed by the use of a multispectral visible and thermal scanner- Airborne Thermal and Land Applications Sensor (ATLAS). Luvall and his coworkers have documented ecosystem energy budgets, including tropical forests, midlatitude varied ecosystems, and semiarid ecosystems. These data show that under similar environmental conditions (air temperature, relative humidity, winds, and solar irradiance) and within a given biome type, the more developed the ecosystem, the cooler it's surface temperature and the more degraded the quality of it's reradiated energy. HyspIRI is a hyperspectral visible/Near IR and multispectral thermal future global satellite mission that will collect data to study the world's ecosystems and will provide a benchmark on the state of the worlds ecosystems against which future changes can be assessed. HyspIRI will provide global data sets that will provide a means for measuring ecosystem development and integrity.

Diffusion pore imaging with generalized temporal gradient profiles.

PubMed

Laun, Frederik B; Kuder, Tristan A

2013-09-01

In porous material research, one main interest of nuclear magnetic resonance diffusion (NMR) experiments is the determination of the shape of pores. While it has been a longstanding question if this is in principle achievable, it has been shown recently that it is indeed possible to perform NMR-based diffusion pore imaging. In this work we present a generalization of these previous results. We show that the specific temporal gradient profiles that were used so far are not unique as more general temporal diffusion gradient profiles may be used. These temporal gradient profiles may consist of any number of "short" gradient pulses, which fulfil the short-gradient approximation. Additionally, "long" gradient pulses of small amplitude may be present, which can be used to fulfil the rephasing condition for the complete profile. Some exceptions exist. For example, classical q-space gradients consisting of two short gradient pulses of opposite sign cannot be used as the phase information is lost due to the temporal antisymmetry of this profile. Copyright © 2013 Elsevier Inc. All rights reserved.

Thermodynamic Study on Plasma Expansion along a Divergent Magnetic Field.

PubMed

Zhang, Yunchao; Charles, Christine; Boswell, Rod

2016-01-15

Thermodynamic properties are revisited for electrons that are governed by nonlocal electron energy probability functions in a plasma of low collisionality. Measurements in a laboratory helicon double layer experiment have shown that the effective electron temperature and density show a polytropic correlation with an index of γ_{e}=1.17±0.02 along the divergent magnetic field, implying a nearly isothermal plasma (γ_{e}=1) with heat being brought into the system. However, the evolution of electrons along the divergent magnetic field is essentially an adiabatic process, which should have a γ_{e}=5/3. The reason for this apparent contradiction is that the nearly collisionless plasma is very far from local thermodynamic equilibrium and the electrons behave nonlocally. The corresponding effective electron enthalpy has a conservation relation with the potential energy, which verifies that there is no heat transferred into the system during the electron evolution. The electrons are shown in nonlocal momentum equilibrium under the electric field and the gradient of the effective electron pressure. The convective momentum of ions, which can be assumed as a cold species, is determined by the effective electron pressure and the effective electron enthalpy is shown to be the source for ion acceleration. For these nearly collisionless plasmas, the use of traditional thermodynamic concepts can lead to very erroneous conclusions regarding the thermal conductivity.

Thermodynamic properties of pressurized PH3 superconductor

NASA Astrophysics Data System (ADS)

Koka, S.; Rao, G. Venugopal

2018-05-01

The paper presents the superconducting thermodynamic functions determined for pressurized phosphorus trihydride (PH3). In particular, free energy difference ΔF, thermodynamic critical field Hc, specific heat etc. have been calculated using analytical expressions. The calculations were performed in the frame work of the strong-coupling formalism. The obtained dimensionless parameters: RΔ ≡ 2Δ(0)/kBTc, RC ≡ ΔC(Tc)/CN(Tc) and RH≡TcCN(Tc)/Hc2(0) are 4.05, 1.96 and 0.156 respectively, which significantly differ from the values arising from the BCS theory of superconductivity. The thermodynamic properties strongly depend on the depairing electron correlations and retardation effects.

The application of the thermodynamic perturbation theory to study the hydrophobic hydration

PubMed Central

Mohorič, Tomaž; Urbic, Tomaz; Hribar-Lee, Barbara

2013-01-01

The thermodynamic perturbation theory was tested against newly obtained Monte Carlo computer simulations to describe the major features of the hydrophobic effect in a simple 3D-Mercedes-Benz water model: the temperature and hydrophobe size dependence on entropy, enthalpy, and free energy of transfer of a simple hydrophobic solute into water. An excellent agreement was obtained between the theoretical and simulation results. Further, the thermodynamic perturbation theory qualitatively correctly (with respect to the experimental data) describes the solvation thermodynamics under conditions where the simulation results are difficult to obtain with good enough accuracy, e.g., at high pressures. PMID:23862923

Variation in the composition of corals, fishes, sponges, echinoderms, ascidians, molluscs, foraminifera and macroalgae across a pronounced in-to-offshore environmental gradient in the Jakarta Bay-Thousand Islands coral reef complex.

PubMed

Cleary, D F R; Polónia, A R M; Renema, W; Hoeksema, B W; Rachello-Dolmen, P G; Moolenbeek, R G; Budiyanto, A; Yahmantoro; Tuti, Y; Giyanto; Draisma, S G A; Prud'homme van Reine, W F; Hariyanto, R; Gittenberger, A; Rikoh, M S; de Voogd, N J

2016-09-30

Substrate cover, water quality parameters and assemblages of corals, fishes, sponges, echinoderms, ascidians, molluscs, benthic foraminifera and macroalgae were sampled across a pronounced environmental gradient in the Jakarta Bay-Thousand Islands reef complex. Inshore sites mainly consisted of sand, rubble and turf algae with elevated temperature, dissolved oxygen, pH and chlorophyll concentrations and depauperate assemblages of all taxa. Live coral cover was very low inshore and mainly consisted of sparse massive coral heads and a few encrusting species. Faunal assemblages were more speciose and compositionally distinct mid- and offshore compared to inshore. There were, however, small-scale differences among taxa. Certain midshore sites, for example, housed assemblages resembling those typical of the inshore environment but this differed depending on the taxon. Substrate, water quality and spatial variables together explained from 31% (molluscs) to 72% (foraminifera) of the variation in composition. In general, satellite-derived parameters outperformed locally measured parameters. Copyright © 2016 Elsevier Ltd. All rights reserved.

Remote sensing of wetland parameters related to carbon cycling

NASA Technical Reports Server (NTRS)

Bartlett, David S.; Johnson, Robert W.

1985-01-01

Measurement of the rates of important biogeochemical fluxes on regional or global scales is vital to understanding the geochemical and climatic consequences of natural biospheric processes and of human intervention in those processes. Remote data gathering and interpretation techniques were used to examine important cycling processes taking place in wetlands over large geographic expanses. Large area estimation of vegetative biomass and productivity depends upon accurate, consistent measurements of canopy spectral reflectance and upon wide applicability of algorithms relating reflectance to biometric parameters. Results of the use of airborne multispectral scanner data to map above-ground biomass in a Delaware salt marsh are shown. The mapping uses an effective algorithm linking biomass to measured spectral reflectance and a means to correct the scanner data for large variations in the angle of observation of the canopy. The consistency of radiometric biomass algorithms for marsh grass when they are applied over large latitudinal and tidal range gradients were also examined. Results of a 1 year study of methane emissions from tidal wetlands along a salinity gradient show marked effects of temperature, season, and pore-water chemistry in mediating flux to the atmosphere.

A thermodynamic study of electroneutral K-Cl cotransport in pH- and volume-clamped low K sheep erythrocytes with normal and low internal magnesium.

PubMed

Lauf, P K; Adragna, N C

1996-10-01

Swelling-induced human erythrocyte K-Cl cotransport is membrane potential independent and capable of uphill transport. However, a complete thermodynamic analysis of basal and stimulated K-Cl cotransport, at constant cell volume, is missing. This study was performed in low K sheep red blood cells before and after reducing cellular free Mg into the nanomolar range with the divalent cation ionophore A23187 and a chelator, an intervention known to stimulate K-Cl cotransport. The anion exchange inhibitor 4,4'diisothiocyanato-2,2'disulfonic stilbene was used to clamp intracellular pH and Cl or NO3 concentrations. Cell volume was maintained constant as external and internal pH differed by more than two units. K-Cl cotransport was calculated from the K effluxes and Rb (as K congener) influxes measured in Cl and NO3, at constant internal K and external anions, and variable concentrations of extracellular Rb and internal anions, respectively. The external Rb concentration at which net K-Cl cotransport is zero was defined as flux reversal point which changed with internal pH and hence Cl. Plots of the ratio of external Rb concentrations corresponding to the flux reversal points and the internal K concentration versus the ratio of the internal and external Cl concentrations (i.e., the Donnan ratio of the transported ions) yielded slopes near unity for both control and low internal Mg cells. Thus, basal as well as low internal Mg-stimulated net K-Cl cotransport depends on the electrochemical potential gradient of KCl.

Non LTE Effects in Laser Plasmas

NASA Astrophysics Data System (ADS)

Klapisch, Marcel

1997-11-01

Laser produced plasmas are not in Local Thermodynamical Equilibrium(LTE) because of the strong gradients and the escaping radiation. Departure from LTE changes the average charge state Z^*, and through it the electron temperature and other thermodynamical variables. Hydrodynamic simulations using LTE and non LTE modes show that in some cases the temperatures can change by an order of magnitude. Several rad/hydro models have solved the approximate atomic rate equations in-line within the average atom model(W. A. Lokke and W. H. Grasburger, LLNL, Report UCRL-52276 (1977),G. Pollack, LANL, Report LA-UR-90-2423 (1990)), or with global rates(M. Busquet, J. P. Raucourt and J. C. Gauthier, J. Quant. Spectrosc. Radiat. Transfer, 54, 81 (1995)). A new technique developed by Busquet, the Radiation Dependent Ionization Model (RADIOM)(M. Busquet, Phys. Fluids B, 5, 4191 (1993)) has been implemented in the NRL hydro-code. It uses an ionization temperature Tz to obtain the opacities and EOS in table look-ups. A very elaborate LTE atomic physics such as the STA code( A. Bar-Shalom and J. Oreg, Phys. Rev. E, 54, 1850 (1996), and ref. therein), or OPAL, can then be used off-line for generating the tables. The algorithm for Tz is very simple and quick. RADIOM has recently been benchmarked with a new detailed collisional radiative model SCROLL(A. Bar-Shalom, J. Oreg and M. Klapisch, Phys. Rev. E, to appear in July (1997)) on a range of temperatures, densities and atomic numbers. RADIOM has been surprisingly successful in calculations of non-LTE opacities.

Energetics of Amino Acid Synthesis in Alkaline Hydrothermal Environments

NASA Astrophysics Data System (ADS)

Kitadai, Norio

2015-12-01

Alkaline hydrothermal systems have received considerable attention as candidates for the origin and evolution of life on the primitive Earth. Nevertheless, sufficient information has not yet been obtained for the thermodynamic properties of amino acids, which are necessary components for life, at high temperatures and alkaline pH. These properties were estimated using experimental high-temperature volume and heat capacity data reported in the literature for several amino acids, together with correlation algorithms and the revised Helgeson-Kirkham-Flowers (HKF) equations of state. This approach enabled determination of a complete set of the standard molal thermodynamic data and the revised HKF parameters for the 20 protein amino acids in their zwitterionic and ionization states. The obtained dataset was then used to evaluate the energetics of amino acid syntheses from simple inorganic precursors (CO2, H2, NH3 and H2S) in a simulated alkaline hydrothermal system on the Hadean Earth. Results show that mixing between CO2-rich seawater and the H2-rich hydrothermal fluid can produce energetically favorable conditions for amino acid syntheses, particularly in the lower-temperature region of such systems. Together with data related to the pH and temperature dependences of the energetics of amino acid polymerizations presented in earlier reports, these results suggest the following. Hadean alkaline hydrothermal settings, where steep pH and temperature gradients may have existed between cool, slightly acidic Hadean ocean water and hot, alkaline hydrothermal fluids at the vent-ocean interface, may be energetically the most suitable environment for the synthesis and polymerization of amino acids.

A thermodynamic study of electroneutral K-Cl cotransport in pH- and volume-clamped low K sheep erythrocytes with normal and low internal magnesium

PubMed Central

1996-01-01

Swelling-induced human erythrocyte K-Cl cotransport is membrane potential independent and capable of uphill transport. However, a complete thermodynamic analysis of basal and stimulated K-Cl cotransport, at constant cell volume, is missing. This study was performed in low K sheep red blood cells before and after reducing cellular free Mg into the nanomolar range with the divalent cation ionophore A23187 and a chelator, an intervention known to stimulate K- Cl cotransport. The anion exchange inhibitor 4,4'diisothiocyanato- 2,2'disulfonic stilbene was used to clamp intracellular pH and Cl or NO3 concentrations. Cell volume was maintained constant as external and internal pH differed by more than two units. K-Cl cotransport was calculated from the K effluxes and Rb (as K congener) influxes measured in Cl and NO3, at constant internal K and external anions, and variable concentrations of extracellular Rb and internal anions, respectively. The external Rb concentration at which net K-Cl cotransport is zero was defined as flux reversal point which changed with internal pH and hence Cl. Plots of the ratio of external Rb concentrations corresponding to the flux reversal points and the internal K concentration versus the ratio of the internal and external Cl concentrations (i.e., the Donnan ratio of the transported ions) yielded slopes near unity for both control and low internal Mg cells. Thus, basal as well as low internal Mg-stimulated net K-Cl cotransport depends on the electrochemical potential gradient of KCl. PMID:8894982

Energetics of Amino Acid Synthesis in Alkaline Hydrothermal Environments.

PubMed

Kitadai, Norio

2015-12-01

Alkaline hydrothermal systems have received considerable attention as candidates for the origin and evolution of life on the primitive Earth. Nevertheless, sufficient information has not yet been obtained for the thermodynamic properties of amino acids, which are necessary components for life, at high temperatures and alkaline pH. These properties were estimated using experimental high-temperature volume and heat capacity data reported in the literature for several amino acids, together with correlation algorithms and the revised Helgeson-Kirkham-Flowers (HKF) equations of state. This approach enabled determination of a complete set of the standard molal thermodynamic data and the revised HKF parameters for the 20 protein amino acids in their zwitterionic and ionization states. The obtained dataset was then used to evaluate the energetics of amino acid syntheses from simple inorganic precursors (CO2, H2, NH3 and H2S) in a simulated alkaline hydrothermal system on the Hadean Earth. Results show that mixing between CO2-rich seawater and the H2-rich hydrothermal fluid can produce energetically favorable conditions for amino acid syntheses, particularly in the lower-temperature region of such systems. Together with data related to the pH and temperature dependences of the energetics of amino acid polymerizations presented in earlier reports, these results suggest the following. Hadean alkaline hydrothermal settings, where steep pH and temperature gradients may have existed between cool, slightly acidic Hadean ocean water and hot, alkaline hydrothermal fluids at the vent-ocean interface, may be energetically the most suitable environment for the synthesis and polymerization of amino acids.