WorldWideScience

Sample records for thermodynamic measurementsand structural

  1. RNA Thermodynamic Structural Entropy.

    Science.gov (United States)

    Garcia-Martin, Juan Antonio; Clote, Peter

    2015-01-01

    Conformational entropy for atomic-level, three dimensional biomolecules is known experimentally to play an important role in protein-ligand discrimination, yet reliable computation of entropy remains a difficult problem. Here we describe the first two accurate and efficient algorithms to compute the conformational entropy for RNA secondary structures, with respect to the Turner energy model, where free energy parameters are determined from UV absorption experiments. An algorithm to compute the derivational entropy for RNA secondary structures had previously been introduced, using stochastic context free grammars (SCFGs). However, the numerical value of derivational entropy depends heavily on the chosen context free grammar and on the training set used to estimate rule probabilities. Using data from the Rfam database, we determine that both of our thermodynamic methods, which agree in numerical value, are substantially faster than the SCFG method. Thermodynamic structural entropy is much smaller than derivational entropy, and the correlation between length-normalized thermodynamic entropy and derivational entropy is moderately weak to poor. In applications, we plot the structural entropy as a function of temperature for known thermoswitches, such as the repression of heat shock gene expression (ROSE) element, we determine that the correlation between hammerhead ribozyme cleavage activity and total free energy is improved by including an additional free energy term arising from conformational entropy, and we plot the structural entropy of windows of the HIV-1 genome. Our software RNAentropy can compute structural entropy for any user-specified temperature, and supports both the Turner'99 and Turner'04 energy parameters. It follows that RNAentropy is state-of-the-art software to compute RNA secondary structure conformational entropy. Source code is available at https://github.com/clotelab/RNAentropy/; a full web server is available at http

  2. RNA Thermodynamic Structural Entropy.

    Directory of Open Access Journals (Sweden)

    Juan Antonio Garcia-Martin

    Full Text Available Conformational entropy for atomic-level, three dimensional biomolecules is known experimentally to play an important role in protein-ligand discrimination, yet reliable computation of entropy remains a difficult problem. Here we describe the first two accurate and efficient algorithms to compute the conformational entropy for RNA secondary structures, with respect to the Turner energy model, where free energy parameters are determined from UV absorption experiments. An algorithm to compute the derivational entropy for RNA secondary structures had previously been introduced, using stochastic context free grammars (SCFGs. However, the numerical value of derivational entropy depends heavily on the chosen context free grammar and on the training set used to estimate rule probabilities. Using data from the Rfam database, we determine that both of our thermodynamic methods, which agree in numerical value, are substantially faster than the SCFG method. Thermodynamic structural entropy is much smaller than derivational entropy, and the correlation between length-normalized thermodynamic entropy and derivational entropy is moderately weak to poor. In applications, we plot the structural entropy as a function of temperature for known thermoswitches, such as the repression of heat shock gene expression (ROSE element, we determine that the correlation between hammerhead ribozyme cleavage activity and total free energy is improved by including an additional free energy term arising from conformational entropy, and we plot the structural entropy of windows of the HIV-1 genome. Our software RNAentropy can compute structural entropy for any user-specified temperature, and supports both the Turner'99 and Turner'04 energy parameters. It follows that RNAentropy is state-of-the-art software to compute RNA secondary structure conformational entropy. Source code is available at https://github.com/clotelab/RNAentropy/; a full web server is available at http

  3. Stochastic deformation of a thermodynamic symplectic structure

    OpenAIRE

    Kazinski, P. O.

    2008-01-01

    A stochastic deformation of a thermodynamic symplectic structure is studied. The stochastic deformation procedure is analogous to the deformation of an algebra of observables like deformation quantization, but for an imaginary deformation parameter (the Planck constant). Gauge symmetries of thermodynamics and corresponding stochastic mechanics, which describes fluctuations of a thermodynamic system, are revealed and gauge fields are introduced. A physical interpretation to the gauge transform...

  4. Structure and thermodynamics of molten salts

    International Nuclear Information System (INIS)

    Papatheodorou, G.N.

    1983-01-01

    This chapter investigates single-component molten salts and multicomponent salt mixtures. Molten salts provide an important testing ground for theories of liquids, solutions, and plasmas. Topics considered include molten salts as liquids (the pair potential, the radial distribution function, methods of characterization), single salts (structure, thermodynamic correlations), and salt mixtures (the thermodynamics of mixing; spectroscopy and structure). Neutron and X-ray scattering techniques are used to determine the structure of molten metal halide salts. The corresponding-states theory is used to obtain thermodynamic correlations on single salts. Structural information on salt mixtures is obtained by using vibrational (Raman) and electronic absorption spectroscopy. Charge-symmetrical systems and charge-unsymmetrical systems are used to examine the thermodynamics of salt mixtures

  5. Thermodynamics and the structure of quantum theory

    International Nuclear Information System (INIS)

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

    2017-01-01

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

  6. Organogels thermodynamics, structure, solvent role, and properties

    CERN Document Server

    Guenet, Jean-Michel

    2016-01-01

    This book provides a physics-oriented introduction to organogels with a comparison to polymer thermoreversible gels whenever relevant. The past decade has seen the development of a wide variety of newly-synthesized molecules that can spontaneously self-assemble or crystallize from their organic or aqueous solutions to produce fibrillar networks, namely organogels, with potential applications in organic electronics, light harvesting, bio-imaging, non-linear optics, and the like. This compact volume presents a detailed outlook of these novel molecular systems with special emphasis upon their thermodynamics, morphology, molecular structure, and rheology. The definition of these complex systems is also tackled, as well as the role of the solvent. The text features numerous temperature-phase diagrams for a variety of organogels as well as illustrations of their structures at the microscopic, mesoscopic and macroscopic level. A review of some potential applications is provided including hybrid functional materials ...

  7. Thermodynamic and structural properties in complexing media

    International Nuclear Information System (INIS)

    Di Giandomenico, M.V.

    2007-10-01

    Protactinium is experiencing a renewal of interest in the frame of long-term energy production. Modelling the behaviour of this element in the geosphere requires thermodynamic and structural data relevant to environmental conditions. Now deep clayey formation are considered for the disposal of radioactive waste and high values of natural sulphate contents have been determined in pore water in equilibrium with clay surface. Because of its tendency to polymerisation, hydrolysis and sorption on all solid supports, the equilibria constants relative to monomer species were determined at tracer scale (ca. 10 - 12 M) with 233 Pa. The complexation constants of Pa(V) and sulphate ions were calculated starting from a systematic study of the apparent distribution coefficient D in the system TTA/Toluene/H 2 O/Na 2 SO 4 /HClO 4 /NaClO 4 and as a function of ionic strength, temperature, free sulphate, protons and chelatant concentration. First of all, the interaction between free species H + , SO 4 - , Na + leads to the formation of HSO 4 - and NaSO 4 - , for which concentrations depend upon the related thermodynamic constants. For this purpose a computer code was developed in order to determine all free species concentration. This iterative code takes into account the influence of temperature and ionic strength (SIT modelling) on thermodynamic constants. The direct measure of Pa(V) in the organic and aqueous phase by g-spectrometry had conducted to estimate the apparent distribution coefficient D as function of free sulphate ions. Complexation constants have been determined after a mathematical treatment of D. The extrapolation of these constants at zero ionic strength have been realized by SIT modelling at different temperatures. Besides, enthalpy and entropy values were calculated. Parallelly, the structural study of Pa(V) was performed using 231 Pa. XANES and EXAFS spectra show unambiguously the absence of the trans di-oxo bond that characterizes the other early actinide

  8. [Relationships between microscope structure and thermodynamic properties

    International Nuclear Information System (INIS)

    Wu, R.S.; Lee, L.L.; Cochran, D.

    1990-01-01

    This paper exhibits on the molecular level, the relationships between the microscopic structure and thermodynamic properties of dilute supercritical solutions by application of the integral equation theories for molecular distribution functions. To solve the integral equations, the authors use Baxter's Wiener-Hopf factorization of the Ornstein-Zernike equations and then apply this method to binary Lennard-Jones mixtures. A number of closure relations have been used: such as the Percus-Yevick (PY), the reference hypernetted chain (RHNC), the hybrid mean spherical approximation (HMSA), and the reference interaction-site (RISM) methods. The authors examine the microstructures of several important classes of supercritical mixtures, including the usual attractive-type and the less known repulsive-type solutions. The clustering of solvent molecules for solvent-solute structures in the attractive mixtures and, correspondingly, the solvent cavitation in the repulsive mixtures are clearly demonstrated. These are shown to be responsible for the large negative growth of the solute partial molar volumes in the attractive case and the positive growth in the repulsive case

  9. Modern thermodynamics from heat engines to dissipative structures

    CERN Document Server

    Kondepudi, Dilip

    2014-01-01

    Modern Thermodynamics: From Heat Engines to Dissipative Structures, Second Edition presents a comprehensive introduction to 20th century thermodynamics that can be applied to both equilibrium and non-equilibrium systems, unifying what was traditionally divided into 'thermodynamics' and 'kinetics' into one theory of irreversible processes. This comprehensive text, suitable for introductory as well as advanced courses on thermodynamics, has been widely used by chemists, physicists, engineers and geologists.  Fully revised and expanded, this new edition includes the following updates and featur

  10. Thermodynamical properties and thermoelastic coupling of complex macroscopic structure

    International Nuclear Information System (INIS)

    Fabbri, M.; Sacripanti, A.

    1996-11-01

    Gross qualitative/quantitative analysis about thermodynamical properties and thermoelastic coupling (or elastocaloric effect) of complex macroscopic structure (running shoes) is performed by infrared camera. The experimental results showed the achievability of a n industrial research project

  11. Thermodynamic and structural characteristics of cement minerals at elevated temperature

    International Nuclear Information System (INIS)

    Bruton, C.J.; Meike, A.; Viani, B.E.; Martin, S.; Phillips, B.L.

    1994-05-01

    We have instituted an experimental and including program designed to elucidate the structural and thermodynamic response of cement minerals to elevated temperature. Components of the program involve: (a) synthesis of hydrated Ca-silicates; (b) structural analysis of cement phases induced by heating and dehydration/rehydration; (c) mechanistic and thermodynamic descriptions of the hydration/dehydration behavior of hydrated Ca-silicates as a function of temperature, pressure and relative humidity; (d) study of naturally occurring hydrated Ca-silicates; and (e) measurements of thermodynamic data for hydrated Ca-silicates

  12. GENERIC Integrators: Structure Preserving Time Integration for Thermodynamic Systems

    Science.gov (United States)

    Öttinger, Hans Christian

    2018-04-01

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

  13. Thermodynamics

    CERN Document Server

    Fermi, Enrico

    1956-01-01

    Indisputably, this is a modern classic of science. Based on a course of lectures delivered by the author at Columbia University, the text is elementary in treatment and remarkable for its clarity and organization. Although it is assumed that the reader is familiar with the fundamental facts of thermometry and calorimetry, no advanced mathematics beyond calculus is assumed.Partial contents: thermodynamic systems, the first law of thermodynamics (application, adiabatic transformations), the second law of thermodynamics (Carnot cycle, absolute thermodynamic temperature, thermal engines), the entr

  14. Molecular dynamics of the structure and thermodynamics of dusty ...

    African Journals Online (AJOL)

    The static structure and thermodynamic properties of two-dimensional dusty plasma are analyzed for some typical values of coupling and screening parameters using classical molecular dynamics. Radial distribution function and static structure factor are computed. The radial distribution functions display the typical ...

  15. Coal surface structure and thermodynamics. Final report

    Energy Technology Data Exchange (ETDEWEB)

    Larsen, J.W.; Wernett, P.C.; Glass, A.S.; Quay, D.; Roberts, J.

    1994-05-01

    Coals surfaces were studied using static surface adsorption measurements, low angle x-ray scattering (LAXS), inverse gas chromatography (IGC) and a new {sup 13}C NMR relaxation technique. A comparison of surface areas determined by hydrocarbon gas adsorption and LAXS led to the twin conclusions that the hydrocarbons had to diffuse through the solid to reach isolated pores and that the coal pores do not form interconnected networks, but are largely isolated. This conclusion was confirmed when IGC data for small hydrocarbons showed no discontinuities in their size dependence as usually observed with porous solids. IGC is capable of providing adsorption thermodynamics of gases on coal surfaces. The interactions of non-polar molecules and coal surfaces are directly proportioned to the gas molecular polarizability. For bases, the adsorption enthalpy is equal to the polarizability interaction plus the heat of hydrogen bond formation with phenol. Amphoteric molecules have more complex interactions. Mineral matter can have highly specific effects on surface interactions, but with most of the molecules studied is not an important factor.

  16. Thermodynamic behavior of glassy state of structurally related compounds.

    Science.gov (United States)

    Kaushal, Aditya Mohan; Bansal, Arvind Kumar

    2008-08-01

    Thermodynamic properties of amorphous pharmaceutical forms are responsible for enhanced solubility as well as poor physical stability. The present study was designed to investigate the differences in thermodynamic parameters arising out of disparate molecular structures and associations for four structurally related pharmaceutical compounds--celecoxib, valdecoxib, rofecoxib, and etoricoxib. Conventional and modulated temperature differential scanning calorimetry were employed to study glass forming ability and thermodynamic behavior of the glassy state of model compounds. Glass transition temperature of four glassy compounds was in a close range of 327.6-331.8 K, however, other thermodynamic parameters varied considerably. Kauzmann temperature, strength parameter and fragility parameter showed rofecoxib glass to be most fragile of the four compounds. Glass forming ability of the compounds fared similar in the critical cooling rate experiments, suggesting that different factors were determining the glass forming ability and subsequent behavior of the compounds in glassy state. A comprehensive understanding of such thermodynamic facets of amorphous form would help in rationalizing the approaches towards development of stable glassy pharmaceuticals.

  17. Entropy, related thermodynamic properties, and structure of methylisocyanate

    International Nuclear Information System (INIS)

    Davis, Phil S.; Kilpatrick, John E.

    2013-01-01

    Highlights: ► The thermodynamic properties of methylisocyanate have been determined by isothermal calorimetry from 15 to 298.15 K. ► The third law entropy has been compared with the entropy calculated by statistical thermodynamics. ► The comparisons are consistent with selected proposed molecular structures and vibrational frequencies. -- Abstract: The entropy and related thermodynamic properties of methylisocyanate, CH 3 NCO, have been determined by isothermal calorimetry. The entropy in the ideal gas state at 298.15 K and 1 atmosphere is S m o = 284.3 ± 0.6 J/K · mol. Other thermodynamic properties determined include: the heat capacity from 15 to 300 K, the temperature of fusion (T fus = 178.461 ± 0.024 K), the enthalpy of fusion (ΔH fus = 7455.2 ± 14.0 J/mol), the enthalpy of vaporization at 298.15 K (ΔH vap = 28768 ± 54 J/mol), and the vapor pressure from fusion to 300 K. Using statistical thermodynamics, the entropy in this same state has been calculated for various assumed structures for methylisocyante which have been proposed based on several spectroscopic and ab initio results. Comparisons between the experimental and calculated entropy have led to the following conclusions concerning historical differences among problematic structural properties: (1) The CNC/CNO angles can have the paired values of 140/180° or 135/173° respectively. It is not possible to distinguish between the two by this thermodynamic analysis. (2) The methyl group functions as a free rotor or near free rotor against the NCO rigid frame. The barrier to internal rotation is less than 2100 J/mol. (3) The CNC vibrational bending frequency is consistent with the more recently observed assignments at 165 and 172 cm −1 with some degree of anharmonicity or with a pure harmonic at about 158 cm −1

  18. Thermodynamic Upper Bound on Broadband Light Coupling with Photonic Structures

    KAUST Repository

    Yu, Zongfu; Raman, Aaswath; Fan, Shanhui

    2012-01-01

    to an upper bound dictated by the second law of thermodynamics. Such bound limits how efficient light can be coupled to any photonic structure. As one example of application, we use this upper bound to derive the limit of light absorption in broadband solar

  19. Thermodynamic structure of the marine atmosphere over the region ...

    Indian Academy of Sciences (India)

    R. Narasimhan (Krishtel eMaging) 1461 1996 Oct 15 13:05:22

    course of observations the ship moved from an open ... Marine boundary layer; thermodynamic structure; saturation point; Bay of Bengal Monsoon Experiment; .... when the low-pressure area is close to the ship the pressure is low and as the system moves away, the .... over oceanic regions to characterize the differences.

  20. Simulation of Cu-Mg metallic glass: Thermodynamics and structure

    DEFF Research Database (Denmark)

    Bailey, Nicholas; Schiøtz, Jakob; Jacobsen, Karsten Wedel

    2004-01-01

    We have obtained effective medium theory interatomic potential parameters suitable for studying Cu-Mg metallic glasses. We present thermodynamic and structural results from simulations of such glasses over a range of compositions. We have produced low-temperature configurations by cooling from...... the melt at as slow a rate as practical, using constant temperature and pressure molecular dynamics. During the cooling process we have carried out thermodynamic analyses based on the temperature dependence of the enthalpy and its derivative, the specific heat, from which the glass transition temperature...

  1. Perspective: Structural fluctuation of protein and Anfinsen's thermodynamic hypothesis

    Science.gov (United States)

    Hirata, Fumio; Sugita, Masatake; Yoshida, Masasuke; Akasaka, Kazuyuki

    2018-01-01

    The thermodynamics hypothesis, casually referred to as "Anfinsen's dogma," is described theoretically in terms of a concept of the structural fluctuation of protein or the first moment (average structure) and the second moment (variance and covariance) of the structural distribution. The new theoretical concept views the unfolding and refolding processes of protein as a shift of the structural distribution induced by a thermodynamic perturbation, with the variance-covariance matrix varying. Based on the theoretical concept, a method to characterize the mechanism of folding (or unfolding) is proposed. The transition state, if any, between two stable states is interpreted as a gap in the distribution, which is created due to an extensive reorganization of hydrogen bonds among back-bone atoms of protein and with water molecules in the course of conformational change. Further perspective to applying the theory to the computer-aided drug design, and to the material science, is briefly discussed.

  2. Structure, thermodynamics, and crystallization of amorphous hafnia

    International Nuclear Information System (INIS)

    Luo, Xuhui; Demkov, Alexander A.

    2015-01-01

    We investigate theoretically amorphous hafnia using the first principles melt and quench method. We identify two types of amorphous structures of hafnia. Type I and type II are related to tetragonal and monoclinic hafnia, respectively. We find type II structure to show stronger disorder than type I. Using the phonon density of states, we calculate the specific heat capacity for type II amorphous hafnia. Using the nudged elastic band method, we show that the averaged transition barrier between the type II amorphous hafnia and monoclinic phase is approximately 0.09 eV/HfO 2 . The crystallization temperature is estimated to be 421 K. The calculations suggest an explanation for the low thermal stability of amorphous hafnia

  3. Thermodynamics

    International Nuclear Information System (INIS)

    Zanchini, E.

    1988-01-01

    The definition of energy, in thermodynamics, is dependent by starting operative definitions of the basic concepts of physics on which it rests, such as those of isolated systems, ambient of a system, separable system and set of separable states. Then the definition of energy is rigorously extended to open systems. The extension gives a clear physical meaning to the concept of energy difference between two states with arbitrary different compositions

  4. Thermodynamic Upper Bound on Broadband Light Coupling with Photonic Structures

    KAUST Repository

    Yu, Zongfu

    2012-10-01

    The coupling between free space radiation and optical media critically influences the performance of optical devices. We show that, for any given photonic structure, the sum of the external coupling rates for all its optical modes are subject to an upper bound dictated by the second law of thermodynamics. Such bound limits how efficient light can be coupled to any photonic structure. As one example of application, we use this upper bound to derive the limit of light absorption in broadband solar absorbers. © 2012 American Physical Society.

  5. Thermodynamic and structural basis for electrochemical response of Cu–Zr based metallic glass

    International Nuclear Information System (INIS)

    Zhang, Chunzhi; Qiu, Nannan; Kong, Lingliang; Yang, Xiaodan; Li, Huiping

    2015-01-01

    Highlights: • Thermodynamic and structural basis for electrochemical response were proposed. • La improves the corrosion resistance by inhibition of the selective dissolution. • Corrosion of the MG responses well with thermodynamic and structural parameters. - Abstract: Cu–Zr based metallic glasses were prepared by hyperquenching strategy to explore the thermodynamic and structural basis for electrochemical response. The thermodynamic parameters and the local atomic structure were obtained. Corrosion resistance in seawater was investigated via potentiodynamic polarization curve. The results indicate that increasing thermodynamic parameter values improves the corrosion resistance. The topological instability represented by the nearest neighbor atomic distance yields same tendency as the corrosion resistance with La addition

  6. Predicting structural properties of fluids by thermodynamic extrapolation

    Science.gov (United States)

    Mahynski, Nathan A.; Jiao, Sally; Hatch, Harold W.; Blanco, Marco A.; Shen, Vincent K.

    2018-05-01

    We describe a methodology for extrapolating the structural properties of multicomponent fluids from one thermodynamic state to another. These properties generally include features of a system that may be computed from an individual configuration such as radial distribution functions, cluster size distributions, or a polymer's radius of gyration. This approach is based on the principle of using fluctuations in a system's extensive thermodynamic variables, such as energy, to construct an appropriate Taylor series expansion for these structural properties in terms of intensive conjugate variables, such as temperature. Thus, one may extrapolate these properties from one state to another when the series is truncated to some finite order. We demonstrate this extrapolation for simple and coarse-grained fluids in both the canonical and grand canonical ensembles, in terms of both temperatures and the chemical potentials of different components. The results show that this method is able to reasonably approximate structural properties of such fluids over a broad range of conditions. Consequently, this methodology may be employed to increase the computational efficiency of molecular simulations used to measure the structural properties of certain fluid systems, especially those used in high-throughput or data-driven investigations.

  7. On the application of thermodynamics of corrosion for service life design of concrete structures

    DEFF Research Database (Denmark)

    Küter, Andre; Geiker, Mette Rica; Møller, Per

    2010-01-01

    There are unexploited possibilities in the application of thermodynamics of corrosion for service life design (SLD) of concrete structures. Thermodynamics provides means for insightful descriptions of corrosion mechanisms and of corrosion protection mechanisms. Strategies for corrosion protection...... of the application of thermodynamics for SLD and gives examples of two applications: description of corrosion processes and design of countermeasures. Emphasis is set on chloride induced corrosion....... can be based on thermodynamically consistent corrosion mechanisms and evaluation of existing and design of new countermeasures can be performed using thermodynamics. Similarly, materials concepts for embedded electrodes can be designed using thermodynamics. The present paper provides a brief outline...

  8. Course 12: Proteins: Structural, Thermodynamic and Kinetic Aspects

    Science.gov (United States)

    Finkelstein, A. V.

    1 Introduction 2 Overview of protein architectures and discussion of physical background of their natural selection 2.1 Protein structures 2.2 Physical selection of protein structures 3 Thermodynamic aspects of protein folding 3.1 Reversible denaturation of protein structures 3.2 What do denatured proteins look like? 3.3 Why denaturation of a globular protein is the first-order phase transition 3.4 "Gap" in energy spectrum: The main characteristic that distinguishes protein chains from random polymers 4 Kinetic aspects of protein folding 4.1 Protein folding in vivo 4.2 Protein folding in vitro (in the test-tube) 4.3 Theory of protein folding rates and solution of the Levinthal paradox

  9. Simulation of Cu-Mg metallic glass: Thermodynamics and structure

    International Nuclear Information System (INIS)

    Bailey, Nicholas P.; Schioetz, Jakob; Jacobsen, Karsten W.

    2004-01-01

    We have obtained effective medium theory interatomic potential parameters suitable for studying Cu-Mg metallic glasses. We present thermodynamic and structural results from simulations of such glasses over a range of compositions. We have produced low-temperature configurations by cooling from the melt at as slow a rate as practical, using constant temperature and pressure molecular dynamics. During the cooling process we have carried out thermodynamic analyses based on the temperature dependence of the enthalpy and its derivative, the specific heat, from which the glass transition temperature may be determined. We have also carried out structural analyses using the radial distribution function (RDF) and common neighbor analysis (CNA). Our analysis suggests that the splitting of the second peak, commonly associated with metallic glasses, in fact, has little to do with the glass transition itself, but is simply a consequence of the narrowing of peaks associated with structural features present in the liquid state. In fact, the splitting temperature for the Cu-Cu RDF is well above T g . The CNA also highlights a strong similarity between the structure of the intermetallic alloys and the amorphous alloys of similar composition. We have also investigated the diffusivity in the supercooled regime. Its temperature dependence indicates fragile-liquid behavior, typical of binary metallic glasses. On the other hand, the relatively low specific-heat jump of around 1.5k B /atom indicates apparent strong-liquid behavior, but this can be explained by the width of the transition due to the high cooling rates

  10. Influence of thermodynamically unfavorable secondary structures on DNA hybridization kinetics

    Science.gov (United States)

    Hata, Hiroaki; Kitajima, Tetsuro

    2018-01-01

    Abstract Nucleic acid secondary structure plays an important role in nucleic acid–nucleic acid recognition/hybridization processes, and is also a vital consideration in DNA nanotechnology. Although the influence of stable secondary structures on hybridization kinetics has been characterized, unstable secondary structures, which show positive ΔG° with self-folding, can also form, and their effects have not been systematically investigated. Such thermodynamically unfavorable secondary structures should not be ignored in DNA hybridization kinetics, especially under isothermal conditions. Here, we report that positive ΔG° secondary structures can change the hybridization rate by two-orders of magnitude, despite the fact that their hybridization obeyed second-order reaction kinetics. The temperature dependence of hybridization rates showed non-Arrhenius behavior; thus, their hybridization is considered to be nucleation limited. We derived a model describing how ΔG° positive secondary structures affect hybridization kinetics in stopped-flow experiments with 47 pairs of oligonucleotides. The calculated hybridization rates, which were based on the model, quantitatively agreed with the experimental rate constant. PMID:29220504

  11. The vitreous state thermodynamics, structure, rheology, and crystallization

    CERN Document Server

    Gutzow, Ivan S

    2013-01-01

    This book summarizes the experimental evidence and modern classical and theoretical approaches in understanding the vitreous state, from structural problems, over equilibrium and non-equilibrium thermodynamics, to statistical physics. Glasses, and especially silicate glasses, are only the best known representatives of this particular physical state of matter. Other typical representatives include organic polymer glasses, and many other easily vitrifying organic and inorganic substances, technically important materials, amidst them vitreous water and vitrified aqueous solutions, and also many metallic alloy systems. Some of these systems only form glasses under particular conditions, e.g. through ultra-rapid cooling. This book describes the properties and the formation of both every-day technical glasses and especially of such more exotic forms of vitreous matter. It is a unique source of knowledge and new ideas for materials scientists, engineers and researchers working on condensed matter. The new edition e...

  12. Structure and thermodynamics of core-softened models for alcohols

    International Nuclear Information System (INIS)

    Munaò, Gianmarco; Urbic, Tomaz

    2015-01-01

    The phase behavior and the fluid structure of coarse-grain models for alcohols are studied by means of reference interaction site model (RISM) theory and Monte Carlo simulations. Specifically, we model ethanol and 1-propanol as linear rigid chains constituted by three (trimers) and four (tetramers) partially fused spheres, respectively. Thermodynamic properties of these models are examined in the RISM context, by employing closed formulæ for the calculation of free energy and pressure. Gas-liquid coexistence curves for trimers and tetramers are reported and compared with already existing data for a dimer model of methanol. Critical temperatures slightly increase with the number of CH 2 groups in the chain, while critical pressures and densities decrease. Such a behavior qualitatively reproduces the trend observed in experiments on methanol, ethanol, and 1-propanol and suggests that our coarse-grain models, despite their simplicity, can reproduce the essential features of the phase behavior of such alcohols. The fluid structure of these models is investigated by computing radial distribution function g ij (r) and static structure factor S ij (k); the latter shows the presence of a low−k peak at intermediate-high packing fractions and low temperatures, suggesting the presence of aggregates for both trimers and tetramers

  13. Structure and thermodynamic properties of molten strontium chloride

    International Nuclear Information System (INIS)

    Pastore, G.; Ballone, P.; Tosi, M.P.; Trieste Univ.

    1985-05-01

    Self-consistent calculations of pair distribution functions and thermodynamic properties are presented for a pair-potentials model of molten strontium chloride. The calculations extend to a strongly asymmetric ionic liquid an earlier assessment of bridge diagrams in a modified hypernetted chain approach to the liquid structure of alkali halides. Good agreement is found with computer simulation data obtained by de Leeuw with the same set of pair potentials, showing that the present approach incorporates genuine general features of liquid structure theory for multicomponent liquids with strong relative ordering of the component species. It is further shown that the strong correlations between the divalent cations, both in the model and in real molten strontium chloride, can be approximately reproduced on the basis of a simple one-component-plasma model, provided that dielectric screening is allowed for in the real liquid. This allows us to tentatively attribute the significant level of disagreement between a pair potentials model of this liquid and the neutron diffraction data of McGreevy and Mitchell to many-body distortions of the electronic shells of the ions. (author)

  14. Life as Thermodynamic Evidence of Algorithmic Structure in Natural Environments

    Directory of Open Access Journals (Sweden)

    David A. Rosenblueth

    2012-11-01

    Full Text Available In evolutionary biology, attention to the relationship between stochastic organisms and their stochastic environments has leaned towards the adaptability and learning capabilities of the organisms rather than toward the properties of the environment. This article is devoted to the algorithmic aspects of the environment and its interaction with living organisms. We ask whether one may use the fact of the existence of life to establish how far nature is removed from algorithmic randomness. The paper uses a novel approach to behavioral evolutionary questions, using tools drawn from information theory, algorithmic complexity and the thermodynamics of computation to support an intuitive assumption about the near optimal structure of a physical environment that would prove conducive to the evolution and survival of organisms, and sketches the potential of these tools, at present alien to biology, that could be used in the future to address different and deeper questions. We contribute to the discussion of the algorithmic structure of natural environments and provide statistical and computational arguments for the intuitive claim that living systems would not be able to survive in completely unpredictable environments, even if adaptable and equipped with storage and learning capabilities by natural selection (brain memory or DNA.

  15. Structure and thermodynamic properties of molten alkali chlorides

    International Nuclear Information System (INIS)

    Ballone, P.; Pastore, G.; Tosi, M.P.; Trieste Univ.

    1984-03-01

    Self-consistent calculations of partial pair distribution functions and thermodynamic properties are presented for molten alkali chlorides in a non-polarizable-ion model. The theory starts from the hypernetted chain approximation and analyzes the role of bridge diagrams both for a two-component ionic plasma on a neutralizing background and for a binary ionic liquid of cations and anions. A simple account of excluded-volume effects suffices for a good description of the pair distribution functions in the two-component plasma, in analogy with earlier work on one-component fluids. The interplay of Coulomb attractions and repulsions in the molten salt requires, on the other hand, the inclusion of (i) excluded-volume effects for the various ion pairs as in a mixture of hard spheres with non-additive radii and (ii) medium-range Coulomb effects reflected mainly in the like-ion correlations. All these effects are included approximately in an empirical evaluation of the bridge functions, with numerical results which compare very well with computer simulation data. A detailed discussion of the results against experimental structural data is then given in the case of molten sodium chloride. (author)

  16. Structure and thermodynamic properties of molten rubidium chloride

    International Nuclear Information System (INIS)

    Ballone, P.; Pastore, G.; Tosi, M.P.; Trieste Univ.

    1984-02-01

    Self-consistent calculations of partial pair distribution functions and thermodynamic properties are presented for molten RbCl in a non-polarizable-ion model and compared with computer simulation data. The theory, which is quantitatively very successful, hinges on an empirical evaluation of bridge diagrams including both excluded-volume effects and long-range Coulomb effects. (author)

  17. Thermodynamic formalism the mathematical structures of equilibrium statistical mechanics

    CERN Document Server

    Ruelle, David

    2004-01-01

    Reissued in the Cambridge Mathematical Library, this classic book outlines the theory of thermodynamic formalism which was developed to describe the properties of certain physical systems consisting of a large number of subunits. Background material on physics has been collected in appendices to help the reader. Supplementary work is provided in the form of exercises and problems that were "open" at the original time of writing.

  18. Thermodynamics and structure of liquid alkali metals from the charged-hard-sphere reference fluid

    International Nuclear Information System (INIS)

    Lai, S.K.; Akinlade, O.; Tosi, M.P.

    1989-12-01

    The evaluation of thermodynamic properties of liquid alkali metals is re-examined in the approach based on the Gibbs-Bogoliubov inequality and using the fluid of charged hard spheres in the mean spherical approximation as reference system, with a view to achieving consistency with the liquid structure factor. The perturbative variational calculation of the Helmholtz free energy is based on an ab initio and highly reliable nonlocal pseudopotential. Only limited improvement is found in the calculated thermodynamic functions, even when full advantage is taken of the two variational parameters inherent in this approach. The role of thermodynamic self-consistency between the equations of state of the reference fluid derived from the routes of the internal energy and of the virial theorem is then discussed, using previous results by Hoye and Stell. An approximate evaluation of the corresponding contribution to the free energy of liquid alkali metals yields appreciable improvements in both the thermodynamic functions and the liquid structure factor. It thus appears that an accurate treatment of thermodynamic self-consistency in the charged-hard-sphere system may help to resolve some of the difficulties that are commonly met in the evaluation of thermodynamic and structural properties of liquid metals. (author). 55 refs, 4 figs, 4 tabs

  19. Using Structured Examples and Prompting Reflective Questions to Correct Misconceptions about Thermodynamic Concepts

    Science.gov (United States)

    Olakanmi, E. O.; Doyoyo, M.

    2014-01-01

    This paper explores the effectiveness of using "structured examples in concert with prompting reflective questions" to address misconceptions held by mechanical engineering students about thermodynamic principles by employing pre-test and post-test design, a structured questionnaire, lecture room observation, and participants'…

  20. First Principles Prediction of Structure, Structure Selectivity, and Thermodynamic Stability under Realistic Conditions

    Energy Technology Data Exchange (ETDEWEB)

    Ceder, Gerbrand [Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States). Dept. of Materials and Engineering

    2018-01-28

    Novel materials are often the enabler for new energy technologies. In ab-initio computational materials science, method are developed to predict the behavior of materials starting from the laws of physics, so that properties can be predicted before compounds have to be synthesized and tested. As such, a virtual materials laboratory can be constructed, saving time and money. The objectives of this program were to develop first-principles theory to predict the structure and thermodynamic stability of materials. Since its inception the program focused on the development of the cluster expansion to deal with the increased complexity of complex oxides. This research led to the incorporation of vibrational degrees of freedom in ab-initio thermodynamics, developed methods for multi-component cluster expansions, included the explicit configurational degrees of freedom of localized electrons, developed the formalism for stability in aqueous environments, and culminated in the first ever approach to produce exact ground state predictions of the cluster expansion. Many of these methods have been disseminated to the larger theory community through the Materials Project, pymatgen software, or individual codes. We summarize three of the main accomplishments.

  1. Study of thermodynamic and structural properties of a flexible homopolymer chain using advanced Monte Carlo methods

    Directory of Open Access Journals (Sweden)

    Hammou Amine Bouziane

    2013-03-01

    Full Text Available We study the thermodynamic and structural properties of a flexible homopolymer chain using both multi canonical Monte Carlo method and Wang-Landau method. In this work, we focus on the coil-globule transition. Starting from a completely random chain, we have obtained a globule for different sizes of the chain. The implementation of these advanced Monte Carlo methods allowed us to obtain a flat histogram in energy space and calculate various thermodynamic quantities such as the density of states, the free energy and the specific heat. Structural quantities such as the radius of gyration where also calculated.

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

    Science.gov (United States)

    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.

  3. Structure, thermodynamics, and dynamical properties of supercooled liquids

    International Nuclear Information System (INIS)

    Kambayashi, Shaw

    1992-12-01

    The equilibrium properties of supercooled liquids with repulsive soft-sphere potentials, u(r) = ε(σ/r) n , have been obtained by solving the integral equation of the theory of liquids and by performing constant-temperature molecular dynamics (MD) simulations. A thermodynamically consistent approximation, proposed recently by Rogers and Young (RY), has been examined for the supercooled soft-sphere fluids. Then, a new approximation for the integral equation, called MHNCS (modified hypernetted-chain integral equation for highly supercooled soft-sphere fluids) approximation, is proposed. The solution of the MHNCS integral equation for highly supercooled liquid states agrees well with the results of computer simulations. The MHNCS integral equation has also been applied for binary soft-sphere mixtures. Dynamical properties of soft-sphere fluids have been investigated by molecular dynamics (MD) simulations. The reduced diffusion constant is found to be insensitive to the choice of the softness of the potential. On the other hand, the spectrum of the velocity autocorrelation function shows a pronounced dependence on the softness of the potential. These significant dynamical properties dependent on the softness parameter (n) are consistent to dynamical behavior observed in liquid alkali metals and liquefied inert gases. The self-part of the density-density autocorrelation function obtained shows a clear nonexponential decay in intermediate time, as the liquid-glass transition is approached. (J.P.N.) 105 refs

  4. Thermodynamics and structure of liquid metals from a consistent optimized random phase approximation

    International Nuclear Information System (INIS)

    Akinlade, O.; Badirkhan, Z.; Pastore, G.

    2000-05-01

    We study thermodynamics and structural properties of several liquid metals to assess the validity of the generalized non-local model potential (GNMP) of Li et. al. [J.Phys. F16,309 (1986)]. By using a new thermodynamically consistent version of the optimized random phase approximation (ORPA), especially adapted to continuous reference potentials, we improve our previous results obtained within the variational approach based on the Gibbs - Bogoliubov inequality. Hinging on the unified and very accurate evaluation of structure factors and thermodynamic quantities provided by the ORPA, we find that the GNMP yields satisfactory results for the alkali metals, however, those for the polyvalent metals point to a substantial inadequacy of the GNMP for high valence systems. (author)

  5. Thermodynamically self-consistent integral equations and the structure of liquid metals

    International Nuclear Information System (INIS)

    Pastore, G.; Kahl, G.

    1987-01-01

    We discuss the application of the new thermodynamically self-consistent integral equations for the determination of the structural properties of liquid metals. We present a detailed comparison of the structure (S(q) and g(r)) for models of liquid alkali metals as obtained from two thermodynamically self-consistent integral equations and some published exact computer simulation results; the range of states extends from the triple point to the expanded metal. The theories which only impose thermodynamic self-consistency without any fitting of external data show an excellent agreement with the simulation results, thus demonstrating that this new type of integral equation is definitely superior to the conventional ones (hypernetted chain, Percus-Yevick, mean spherical approximation, etc). (author)

  6. Student Oriented Approaches in the Teaching of Thermodynamics at Universities--Developing an Effective Course Structure

    Science.gov (United States)

    Partanen, Lauri

    2016-01-01

    The aim of this study was to apply current pedagogical research in order to develop an effective course and exercise structure for a physical chemistry thermodynamics course intended for second or third year university students of chemistry. A mixed-method approach was used to measure the impact the changes had on student learning. In its final…

  7. Coherent application of a contact structure to formulate Classical Non-Equilibrium Thermodynamics

    NARCIS (Netherlands)

    Knobbe, E; Roekaerts, D.J.E.M.

    2017-01-01

    This contribution presents an outline of a new mathematical formulation for
    Classical Non-Equilibrium Thermodynamics (CNET) based on a contact
    structure in differential geometry. First a non-equilibrium state space is introduced as the third key element besides the first and second law of

  8. The Influence of Content Organization on Student's Cognitive Structure in Thermodynamics.

    Science.gov (United States)

    Moreira, Marco A.; Santos, Carlos A.

    1981-01-01

    Two approaches to the content of thermodynamics were used in an introductory college physics course: traditional organization and organization based on Ausubel's learning theory. The influence of these organizations on engineering student's (N=58) cognitive structure was investigated using a word association test analyzed through hierarchical…

  9. Structure of water and the thermodynamics of aqueous solutions

    Energy Technology Data Exchange (ETDEWEB)

    Nemethy, G.

    1970-10-26

    This report represents the summary of a series of lectures held at the Istituto Superiore di Sanita, Laboratori di Fisica, from 18 September to 26 October 1970. The topics discussed were: Intermolecular forces, the individual water molecule and the hydrogen bond, the structures of the solid phases of water, experimental information on the strucuture of liquid water, theoretical models of water structure, experimental properties and theoretical models of aqueous solutions of nonpolar solutes, polar solutes, and electrolytes, the conformational stability of biological macromolecules.

  10. Model of the thermodynamic properties and structure of the non-stoichiometric plutonium and cerium oxides

    International Nuclear Information System (INIS)

    Manes, L.; Mari, C.; Ray, I.

    1979-01-01

    The tetrahedral defect consisting of one oxygen vacancy bonded to two reduced cations - is an important concept, which, as shown in the present work, can explain both the thermodynamic properties and the structures of the phases of the PuO 2 -x and CeO 2 -x systems. Based on this concept a statistical thermodynamic model has been developed and this model is described along with some preliminary calculations. A relatively good agreement with experimental thermodynamic data was obtained in this calculation. Using the exclusion principle, defect complexes each containing one tetrahedral defect are derived and it is shown that a systematic packing of these gives a good description both of the non-stoichiometric and the ordered phases observed for these oxide systems. (orig.) [de

  11. Advancing viral RNA structure prediction: measuring the thermodynamics of pyrimidine-rich internal loops.

    Science.gov (United States)

    Phan, Andy; Mailey, Katherine; Saeki, Jessica; Gu, Xiaobo; Schroeder, Susan J

    2017-05-01

    Accurate thermodynamic parameters improve RNA structure predictions and thus accelerate understanding of RNA function and the identification of RNA drug binding sites. Many viral RNA structures, such as internal ribosome entry sites, have internal loops and bulges that are potential drug target sites. Current models used to predict internal loops are biased toward small, symmetric purine loops, and thus poorly predict asymmetric, pyrimidine-rich loops with >6 nucleotides (nt) that occur frequently in viral RNA. This article presents new thermodynamic data for 40 pyrimidine loops, many of which can form UU or protonated CC base pairs. Uracil and protonated cytosine base pairs stabilize asymmetric internal loops. Accurate prediction rules are presented that account for all thermodynamic measurements of RNA asymmetric internal loops. New loop initiation terms for loops with >6 nt are presented that do not follow previous assumptions that increasing asymmetry destabilizes loops. Since the last 2004 update, 126 new loops with asymmetry or sizes greater than 2 × 2 have been measured. These new measurements significantly deepen and diversify the thermodynamic database for RNA. These results will help better predict internal loops that are larger, pyrimidine-rich, and occur within viral structures such as internal ribosome entry sites. © 2017 Phan et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

  12. Thermodynamics, maximum power, and the dynamics of preferential river flow structures at the continental scale

    Directory of Open Access Journals (Sweden)

    A. Kleidon

    2013-01-01

    Full Text Available The organization of drainage basins shows some reproducible phenomena, as exemplified by self-similar fractal river network structures and typical scaling laws, and these have been related to energetic optimization principles, such as minimization of stream power, minimum energy expenditure or maximum "access". Here we describe the organization and dynamics of drainage systems using thermodynamics, focusing on the generation, dissipation and transfer of free energy associated with river flow and sediment transport. We argue that the organization of drainage basins reflects the fundamental tendency of natural systems to deplete driving gradients as fast as possible through the maximization of free energy generation, thereby accelerating the dynamics of the system. This effectively results in the maximization of sediment export to deplete topographic gradients as fast as possible and potentially involves large-scale feedbacks to continental uplift. We illustrate this thermodynamic description with a set of three highly simplified models related to water and sediment flow and describe the mechanisms and feedbacks involved in the evolution and dynamics of the associated structures. We close by discussing how this thermodynamic perspective is consistent with previous approaches and the implications that such a thermodynamic description has for the understanding and prediction of sub-grid scale organization of drainage systems and preferential flow structures in general.

  13. Extended thermodynamics

    CERN Document Server

    Müller, Ingo

    1993-01-01

    Physicists firmly believe that the differential equations of nature should be hyperbolic so as to exclude action at a distance; yet the equations of irreversible thermodynamics - those of Navier-Stokes and Fourier - are parabolic. This incompatibility between the expectation of physicists and the classical laws of thermodynamics has prompted the formulation of extended thermodynamics. After describing the motifs and early evolution of this new branch of irreversible thermodynamics, the authors apply the theory to mon-atomic gases, mixtures of gases, relativistic gases, and "gases" of phonons and photons. The discussion brings into perspective the various phenomena called second sound, such as heat propagation, propagation of shear stress and concentration, and the second sound in liquid helium. The formal mathematical structure of extended thermodynamics is exposed and the theory is shown to be fully compatible with the kinetic theory of gases. The study closes with the testing of extended thermodynamics thro...

  14. Structural and thermodynamic analysis of modified nucleosides in self-assembled DNA cross-tiles.

    Science.gov (United States)

    Hakker, Lauren; Marchi, Alexandria N; Harris, Kimberly A; LaBean, Thomas H; Agris, Paul F

    2014-01-01

    DNA Holliday junctions are important natural strand-exchange structures that form during homologous recombination. Immobile four-arm junctions, analogs to Holliday junctions, have been designed to self-assemble into cross-tile structures by maximizing Watson-Crick base pairing and fixed crossover points. The cross-tiles, self-assembled from base pair recognition between designed single-stranded DNAs, form higher order lattice structures through cohesion of self-associating sticky ends. These cross-tiles have 16 unpaired nucleosides in the central loop at the junction of the four duplex stems. The importance of the centralized unpaired nucleosides to the structure's thermodynamic stability and self-assembly is unknown. Cross-tile DNA nanostructures were designed and constructed from nine single-stranded DNAs with four shell strands, four arms, and a central loop containing 16 unpaired bases. The 16 unpaired bases were either 2'-deoxyribothymidines, 2'-O-methylribouridines, or abasic 1',2'-dideoxyribonucleosides. Thermodynamic profiles and structural base-stacking contributions were assessed using UV absorption spectroscopy during thermal denaturation and circular dichroism spectroscopy, respectively, and the resulting structures were observed by atomic force microscopy. There were surprisingly significant changes in the thermodynamic and structural properties of lattice formation as a result of altering only the 16 unpaired, centralized nucleosides. The 16 unpaired 2'-O-methyluridines were stabilizing and produced uniform tubular structures. In contrast, the abasic nucleosides were destabilizing producing a mixture of structures. These results strongly indicate the importance of a small number of centrally located unpaired nucleosides within the structures. Since minor modifications lead to palpable changes in lattice formation, DNA cross-tiles present an easily manipulated structure convenient for applications in biomedical and biosensing devices.

  15. Thermodynamics and local structure of vinyl polymer melts

    International Nuclear Information System (INIS)

    Yethiraj, A.; Curro, J.G.; Rajasekaran, J.J.

    1995-01-01

    Monte Carlo simulation results are reported for the site-site pair correlations and equation of state of model vinyl polymer melts. The molecules are freely jointed hard chains with a hard sphere side-group attached to every other backbone bead. The local structure and pressure are investigated as a function of the diameter of the side group for melt-like densities. The intramolecular correlation functions are well represented by a single chain model where excluded volume interactions are included for beads separated by four bonds or less and neglected otherwise. The intermolecular correlation functions show interesting packing effects. The side group shields the backbone beads from approaching each other, to a degree that increases with increasing diameter of the side group. The polymer reference interaction site model integral equation theory is in good agreement with the simulation results for the pair correlation functions. At fixed volume fraction, the pressure is found to be a non-monotonic function of the size of the side group. copyright 1995 American Institute of Physics

  16. A statistical-thermodynamic model for ordering phenomena in thin film intermetallic structures

    International Nuclear Information System (INIS)

    Semenova, Olga; Krachler, Regina

    2008-01-01

    Ordering phenomena in bcc (110) binary thin film intermetallics are studied by a statistical-thermodynamic model. The system is modeled by an Ising approach that includes only nearest-neighbor chemical interactions and is solved in a mean-field approximation. Vacancies and anti-structure atoms are considered on both sublattices. The model describes long-range ordering and simultaneously short-range ordering in the thin film. It is applied to NiAl thin films with B2 structure. Vacancy concentrations, thermodynamic activity profiles and the virtual critical temperature of order-disorder as a function of film composition and thickness are presented. The results point to an important role of vacancies in near-stoichiometric and Ni-rich NiAl thin films

  17. Thermodynamic properties and static structure factor for a Yukawa fluid in the mean spherical approximation.

    Science.gov (United States)

    Montes-Perez, J; Cruz-Vera, A; Herrera, J N

    2011-12-01

    This work presents the full analytic expressions for the thermodynamic properties and the static structure factor for a hard sphere plus 1-Yukawa fluid within the mean spherical approximation. To obtain these properties of the fluid type Yukawa analytically it was necessary to solve an equation of fourth order for the scaling parameter on a large scale. The physical root of this equation was determined by imposing physical conditions. The results of this work are obtained from seminal papers of Blum and Høye. We show that is not necessary the use the series expansion to solve the equation for the scaling parameter. We applied our theoretical result to find the thermodynamic and the static structure factor for krypton. Our results are in good agreement with those obtained in an experimental form or by simulation using the Monte Carlo method.

  18. Structural, Mechanical and Thermodynamic Properties under Pressure Effect of Rubidium Telluride: First Principle Calculations

    Directory of Open Access Journals (Sweden)

    Bidai K.

    2017-06-01

    Full Text Available First-principles density functional theory calculations have been performed to investigate the structural, elastic and thermodynamic properties of rubidium telluride in cubic anti-fluorite (anti-CaF2-type structure. The calculated ground-state properties of Rb2Te compound such as equilibrium lattice parameter and bulk moduli are investigated by generalized gradient approximation (GGA-PBE that are based on the optimization of total energy. The elastic constants, Young’s and shear modulus, Poisson ratio, have also been calculated. Our results are in reasonable agreement with the available theoretical and experimental data. The pressure dependence of elastic constant and thermodynamic quantities under high pressure are also calculated and discussed.

  19. Application of a Thermodynamic Concept for the Analysis of Structural Degradation of Soap Thickened Lubricating Greases

    Directory of Open Access Journals (Sweden)

    Erik Kuhn

    2018-01-01

    Full Text Available Lubricating greases are special lubricants with a wide range of application. The tribologically stressed grease is used as tribological system and finally modeled as an open thermodynamic system. This study investigated the phenomenon of self-optimization and applied to the process of shearing a grease. The conditions for self-optimization and the consequences of created dissipative structures are investigated according to the interpreted literature.

  20. Thermodynamic Stability of Structure H Hydrates Based on the Molecular Properties of Large Guest Molecules

    OpenAIRE

    Tezuka, Kyoichi; Taguchi, Tatsuhiko; Alavi, Saman; Sum, Amadeu K.; Ohmura, Ryo

    2012-01-01

    This paper report analyses of thermodynamic stability of structure-H clathrate hydrates formed with methane and large guest molecules in terms of their gas phase molecular sizes and molar masses for the selection of a large guest molecule providing better hydrate stability. We investigated the correlation among the gas phase molecular sizes, the molar masses of large molecule guest substances, and the equilibrium pressures. The results suggest that there exists a molecular-size value for the ...

  1. A thermodynamical analysis of the π and K meson valence structure functions

    International Nuclear Information System (INIS)

    Angelini, C.; Pazzi, R.

    1982-01-01

    The π and K meson valance structure functions are analysed in the framework of a thermodynamical model already applied to the nucleon. We obtain a simple expression which reproduces quite well the data for chi > 0.3. The effective temperatures are found to be of the order of 20 MeV for the pion and 65 MeV for the kaon. (orig.)

  2. Statistical properties of thermodynamically predicted RNA secondary structures in viral genomes

    Science.gov (United States)

    Spanò, M.; Lillo, F.; Miccichè, S.; Mantegna, R. N.

    2008-10-01

    By performing a comprehensive study on 1832 segments of 1212 complete genomes of viruses, we show that in viral genomes the hairpin structures of thermodynamically predicted RNA secondary structures are more abundant than expected under a simple random null hypothesis. The detected hairpin structures of RNA secondary structures are present both in coding and in noncoding regions for the four groups of viruses categorized as dsDNA, dsRNA, ssDNA and ssRNA. For all groups, hairpin structures of RNA secondary structures are detected more frequently than expected for a random null hypothesis in noncoding rather than in coding regions. However, potential RNA secondary structures are also present in coding regions of dsDNA group. In fact, we detect evolutionary conserved RNA secondary structures in conserved coding and noncoding regions of a large set of complete genomes of dsDNA herpesviruses.

  3. Interfacial structures - Thermodynamical and experimental studies of the interfacial mass transfer

    International Nuclear Information System (INIS)

    Morel, Jean-Emile

    1972-01-01

    In the first section, we put forward hypotheses concerning the structure of the interfacial regions between two immiscible liquid phases. It appears that the longitudinal structure is comparable with that of a crystallized solid and that the transversal structure is nearest of that of a liquid. In the second section, we present a thermodynamical treatment of the irreversible phenomena in the interfacial region. The equation of evolution of a system consisting of two immiscible liquid phases are deduced. The third part allows an experimental verification of the theoretical relations. We also make clear, in certain cases, the appearance of a great 'interfacial resistance' which slows down the interfacial mass transfer. (author) [fr

  4. Thermodynamic analysis on an anisotropically superhydrophobic surface with a hierarchical structure

    Energy Technology Data Exchange (ETDEWEB)

    Zhao, Jieliang [Division of Intelligent and Biomechanical Systems, State Key Laboratory of Tribology, Tsinghua University, Room 3407, Building 9003, 100084 Beijing (China); Su, Zhengliang [Division of Intelligent and Biomechanical Systems, State Key Laboratory of Tribology, Tsinghua University, Room 3407, Building 9003, 100084 Beijing (China); Department of Automotive Engineering, Tsinghua University, Beijing 100084 (China); Yan, Shaoze, E-mail: yansz@mail.tsinghua.edu.cn [Division of Intelligent and Biomechanical Systems, State Key Laboratory of Tribology, Tsinghua University, Room 3407, Building 9003, 100084 Beijing (China)

    2015-12-01

    Graphical abstract: - Highlights: • We model the superhydrophobic surface with anisotropic and hierarchical structure. • Anisotropic wetting only shows in noncomposite state (not in composite state). • Transition from noncomposite to composite state on dual-scale structure is hard. • Droplets tend to roll in the particular direction. • Droplets tend to stably remain in one preferred thermodynamic state. - Abstract: Superhydrophobic surfaces, which refer to the surfaces with contact angle higher than 150° and hysteresis less than 10°, have been reported in various studies. However, studies on the superhydrophobicity of anisotropic, hierarchical surfaces are limited and the corresponding thermodynamic mechanisms could not be explained thoroughly. Here we propose a simplified surface model of anisotropic patterned surface with dual scale roughness. Based on the thermodynamic method, we calculate the equilibrium contact angle (ECA) and the contact angle hysteresis (CAH) on the given surface. We show here that the hierarchical structure has much better anisotropic wetting properties than the single-scale one, and the results shed light on the potential application in controllable micro-/nano-fluidic systems. Our studies can be potentially applied for the fabrication of anisotropically superhydrophobic surfaces.

  5. Role of thermodynamic, kinetic and structural factors in the recrystallization behavior of amorphous erythromycin salts

    Energy Technology Data Exchange (ETDEWEB)

    Nanakwani, Kapil; Modi, Sameer R.; Kumar, Lokesh; Bansal, Arvind K., E-mail: akbansal@niper.ac.in

    2014-04-01

    Graphical abstract: - Highlights: • Crystallization kinetics of amorphous erythromycin salts was assessed. • Contribution of thermodynamic, kinetic and structural factors was evaluated. • Role of counterions on physical stability of amorphous salts was investigated. • Implications of the study: In rationalizing stabilization approach for amorphous form. - Abstract: Amorphous form has become an important drug delivery strategy for poorly water soluble drugs. However, amorphous form has inherent physical instability due to its tendency to recrystallize to stable crystalline form. In the present study, amorphous forms of erythromycin free base (ED) and its salts namely, stearate (ES), phosphate (EP) and thiocyanate (ET) were generated by in situ melt quenching and evaluated for their crystallization tendency. Salts were characterized for kinetic, thermodynamic and structural factors to understand crystallization behavior. Kinetics of crystallization followed the order as ES > EP > ET > ED. Fragility and molecular mobility does not completely explain these findings. However, configurational entropy (S{sub conf}), indicative of entropic barrier to crystallization, followed the order as ET > EP > ES > ED. Lower crystallization tendency of ED can be explained by its lower thermodynamic driving force for crystallization (H{sub conf}). This correlated well with different structural parameters for the counter ions.

  6. Thermodynamic analysis on an anisotropically superhydrophobic surface with a hierarchical structure

    International Nuclear Information System (INIS)

    Zhao, Jieliang; Su, Zhengliang; Yan, Shaoze

    2015-01-01

    Graphical abstract: - Highlights: • We model the superhydrophobic surface with anisotropic and hierarchical structure. • Anisotropic wetting only shows in noncomposite state (not in composite state). • Transition from noncomposite to composite state on dual-scale structure is hard. • Droplets tend to roll in the particular direction. • Droplets tend to stably remain in one preferred thermodynamic state. - Abstract: Superhydrophobic surfaces, which refer to the surfaces with contact angle higher than 150° and hysteresis less than 10°, have been reported in various studies. However, studies on the superhydrophobicity of anisotropic, hierarchical surfaces are limited and the corresponding thermodynamic mechanisms could not be explained thoroughly. Here we propose a simplified surface model of anisotropic patterned surface with dual scale roughness. Based on the thermodynamic method, we calculate the equilibrium contact angle (ECA) and the contact angle hysteresis (CAH) on the given surface. We show here that the hierarchical structure has much better anisotropic wetting properties than the single-scale one, and the results shed light on the potential application in controllable micro-/nano-fluidic systems. Our studies can be potentially applied for the fabrication of anisotropically superhydrophobic surfaces.

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

    Science.gov (United States)

    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.

  8. Structural and Thermodynamic Properties of Amyloid-β Peptides: Impact of Fragment Size

    Science.gov (United States)

    Kitahara, T.; Wise-Scira, O.; Coskuner, O.

    2010-10-01

    Alzheimer's disease is a progressive neurodegenerative disease whose physiological characteristics include the accumulation of amyloid-containing deposits in the brain and consequent synapse and neuron loss. Unfortunately, most widely used drugs for the treatment can palliate the outer symptoms but cannot cure the disease itself. Hence, developing a new drug that can cure it. Most recently, the ``early aggregation and monomer'' hypothesis has become popular and a few drugs have been developed based on this hypothesis. Detailed understanding of the amyloid-β peptide structure can better help us to determine more effective treatment strategies; indeed, the structure of Amyloid has been studied extensively employing experimental and theoretical tools. Nevertheless, those studies have employed different fragment sizes of Amyloid and characterized its conformational nature in different media. Thus, the structural properties might be different from each other and provide a reason for the existing debates in the literature. Here, we performed all-atom MD simulations and present the structural and thermodynamic properties of Aβ1-16, Aβ1-28, and Aβ1-42 in the gas phase and in aqueous solution. Our studies show that the overall structures, secondary structures, and the calculated thermodynamic properties change with increasing peptide size. In addition, we find that the structural properties of those peptides are different from each other in the gas phase and in aqueous solution.

  9. Dynamics, thermodynamics and structure of liquids and supercritical fluids: crossover at the Frenkel line

    Science.gov (United States)

    Fomin, Yu D.; Ryzhov, V. N.; Tsiok, E. N.; Proctor, J. E.; Prescher, C.; Prakapenka, V. B.; Trachenko, K.; Brazhkin, V. V.

    2018-04-01

    We review recent work aimed at understanding dynamical and thermodynamic properties of liquids and supercritical fluids. The focus of our discussion is on solid-like transverse collective modes, whose evolution in the supercritical fluids enables one to discuss the main properties of the Frenkel line separating rigid liquid-like and non-rigid gas-like supercritical states. We subsequently present recent experimental evidence of the Frenkel line showing that structural and dynamical crossovers are seen at a pressure and temperature corresponding to the line as predicted by theory and modelling. Finally, we link dynamical and thermodynamic properties of liquids and supercritical fluids by the new calculation of liquid energy governed by the evolution of solid-like transverse modes. The disappearance of those modes at high temperature results in the observed decrease of heat capacity.

  10. Thermodynamic heuristics with case-based reasoning: combined insights for RNA pseudoknot secondary structure.

    Science.gov (United States)

    Al-Khatib, Ra'ed M; Rashid, Nur'Aini Abdul; Abdullah, Rosni

    2011-08-01

    The secondary structure of RNA pseudoknots has been extensively inferred and scrutinized by computational approaches. Experimental methods for determining RNA structure are time consuming and tedious; therefore, predictive computational approaches are required. Predicting the most accurate and energy-stable pseudoknot RNA secondary structure has been proven to be an NP-hard problem. In this paper, a new RNA folding approach, termed MSeeker, is presented; it includes KnotSeeker (a heuristic method) and Mfold (a thermodynamic algorithm). The global optimization of this thermodynamic heuristic approach was further enhanced by using a case-based reasoning technique as a local optimization method. MSeeker is a proposed algorithm for predicting RNA pseudoknot structure from individual sequences, especially long ones. This research demonstrates that MSeeker improves the sensitivity and specificity of existing RNA pseudoknot structure predictions. The performance and structural results from this proposed method were evaluated against seven other state-of-the-art pseudoknot prediction methods. The MSeeker method had better sensitivity than the DotKnot, FlexStem, HotKnots, pknotsRG, ILM, NUPACK and pknotsRE methods, with 79% of the predicted pseudoknot base-pairs being correct.

  11. Molecular structure and thermodynamic predictions to create highly sensitive microRNA biosensors

    International Nuclear Information System (INIS)

    Larkey, Nicholas E.; Brucks, Corinne N.; Lansing, Shan S.; Le, Sophia D.; Smith, Natasha M.; Tran, Victoria; Zhang, Lulu; Burrows, Sean M.

    2016-01-01

    Many studies have established microRNAs (miRNAs) as post-transcriptional regulators in a variety of intracellular molecular processes. Abnormal changes in miRNA have been associated with several diseases. However, these changes are sometimes subtle and occur at nanomolar levels or lower. Several biosensing hurdles for in situ cellular/tissue analysis of miRNA limit detection of small amounts of miRNA. Of these limitations the most challenging are selectivity and sensor degradation creating high background signals and false signals. Recently we developed a reporter+probe biosensor for let-7a that showed potential to mitigate false signal from sensor degradation. Here we designed reporter+probe biosensors for miR-26a-2-3p and miR-27a-5p to better understand the effect of thermodynamics and molecular structures of the biosensor constituents on the analytical performance. Signal changes from interactions between Cy3 and Cy5 on the reporters were used to understand structural aspects of the reporter designs. Theoretical thermodynamic values, single stranded conformations, hetero- and homodimerization structures, and equilibrium concentrations of the reporters and probes were used to interpret the experimental observations. Studies of the sensitivity and selectivity revealed 5–9 nM detection limits in the presence and absence of interfering off-analyte miRNAs. These studies will aid in determining how to rationally design reporter+probe biosensors to overcome hurdles associated with highly sensitive miRNA biosensing. - Highlights: • Challenges facing highly sensitive miRNA biosensor designs are addressed. • Thermodynamic and molecular structure design metrics for reporter+probe biosensors are proposed. • The influence of ideal and non-ideal reporter hairpin structures on reporter+probe formation and signal change are discussed. • 5–9 nM limits of detection were observed with no interference from off-analytes.

  12. Molecular structure and thermodynamic predictions to create highly sensitive microRNA biosensors

    Energy Technology Data Exchange (ETDEWEB)

    Larkey, Nicholas E.; Brucks, Corinne N.; Lansing, Shan S.; Le, Sophia D.; Smith, Natasha M.; Tran, Victoria; Zhang, Lulu; Burrows, Sean M., E-mail: sean.burrows@oregonstate.edu

    2016-02-25

    Many studies have established microRNAs (miRNAs) as post-transcriptional regulators in a variety of intracellular molecular processes. Abnormal changes in miRNA have been associated with several diseases. However, these changes are sometimes subtle and occur at nanomolar levels or lower. Several biosensing hurdles for in situ cellular/tissue analysis of miRNA limit detection of small amounts of miRNA. Of these limitations the most challenging are selectivity and sensor degradation creating high background signals and false signals. Recently we developed a reporter+probe biosensor for let-7a that showed potential to mitigate false signal from sensor degradation. Here we designed reporter+probe biosensors for miR-26a-2-3p and miR-27a-5p to better understand the effect of thermodynamics and molecular structures of the biosensor constituents on the analytical performance. Signal changes from interactions between Cy3 and Cy5 on the reporters were used to understand structural aspects of the reporter designs. Theoretical thermodynamic values, single stranded conformations, hetero- and homodimerization structures, and equilibrium concentrations of the reporters and probes were used to interpret the experimental observations. Studies of the sensitivity and selectivity revealed 5–9 nM detection limits in the presence and absence of interfering off-analyte miRNAs. These studies will aid in determining how to rationally design reporter+probe biosensors to overcome hurdles associated with highly sensitive miRNA biosensing. - Highlights: • Challenges facing highly sensitive miRNA biosensor designs are addressed. • Thermodynamic and molecular structure design metrics for reporter+probe biosensors are proposed. • The influence of ideal and non-ideal reporter hairpin structures on reporter+probe formation and signal change are discussed. • 5–9 nM limits of detection were observed with no interference from off-analytes.

  13. Grid inhomogeneous solvation theory: hydration structure and thermodynamics of the miniature receptor cucurbit[7]uril.

    Science.gov (United States)

    Nguyen, Crystal N; Young, Tom Kurtzman; Gilson, Michael K

    2012-07-28

    The displacement of perturbed water upon binding is believed to play a critical role in the thermodynamics of biomolecular recognition, but it is nontrivial to unambiguously define and answer questions about this process. We address this issue by introducing grid inhomogeneous solvation theory (GIST), which discretizes the equations of inhomogeneous solvation theory (IST) onto a three-dimensional grid situated in the region of interest around a solute molecule or complex. Snapshots from explicit solvent simulations are used to estimate localized solvation entropies, energies, and free energies associated with the grid boxes, or voxels, and properly summing these thermodynamic quantities over voxels yields information about hydration thermodynamics. GIST thus provides a smoothly varying representation of water properties as a function of position, rather than focusing on hydration sites where solvent is present at high density. It therefore accounts for full or partial displacement of water from sites that are highly occupied by water, as well as for partly occupied and water-depleted regions around the solute. GIST can also provide a well-defined estimate of the solvation free energy and therefore enables a rigorous end-states analysis of binding. For example, one may not only use a first GIST calculation to project the thermodynamic consequences of displacing water from the surface of a receptor by a ligand, but also account, in a second GIST calculation, for the thermodynamics of subsequent solvent reorganization around the bound complex. In the present study, a first GIST analysis of the molecular host cucurbit[7]uril is found to yield a rich picture of hydration structure and thermodynamics in and around this miniature receptor. One of the most striking results is the observation of a toroidal region of high water density at the center of the host's nonpolar cavity. Despite its high density, the water in this toroidal region is disfavored energetically and

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

    Science.gov (United States)

    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.

  15. Magnetic and thermodynamic properties of Ising model with borophene structure in a longitudinal magnetic field

    Science.gov (United States)

    Shi, Kaile; Jiang, Wei; Guo, Anbang; Wang, Kai; Wu, Chuang

    2018-06-01

    The magnetic and thermodynamic properties of borophene structure have been studied for the first time by Monte Carlo simulation. Two-dimensional borophene structure consisting of seven hexagonal B36 units is described by Ising model. Each B36 basic unit includes three benzene-like with spin-3/2. The general formula for the borophene structure is given. The numerical results of the magnetization, the magnetic susceptibility, the internal energy and the specific heat are studied with various parameters. The possibility to test the predicted magnetism in experiment are illustrated, for instance, the maximum on the magnetization curve. The multiple hysteresis loops and the magnetization plateaus are sensitive to the ferromagnetic or ferrimagnetic exchange coupling in borophene structure. The results show the borophene structure could have applications in spintronics, which deserves further studies in experiments.

  16. Vfold: a web server for RNA structure and folding thermodynamics prediction.

    Science.gov (United States)

    Xu, Xiaojun; Zhao, Peinan; Chen, Shi-Jie

    2014-01-01

    The ever increasing discovery of non-coding RNAs leads to unprecedented demand for the accurate modeling of RNA folding, including the predictions of two-dimensional (base pair) and three-dimensional all-atom structures and folding stabilities. Accurate modeling of RNA structure and stability has far-reaching impact on our understanding of RNA functions in human health and our ability to design RNA-based therapeutic strategies. The Vfold server offers a web interface to predict (a) RNA two-dimensional structure from the nucleotide sequence, (b) three-dimensional structure from the two-dimensional structure and the sequence, and (c) folding thermodynamics (heat capacity melting curve) from the sequence. To predict the two-dimensional structure (base pairs), the server generates an ensemble of structures, including loop structures with the different intra-loop mismatches, and evaluates the free energies using the experimental parameters for the base stacks and the loop entropy parameters given by a coarse-grained RNA folding model (the Vfold model) for the loops. To predict the three-dimensional structure, the server assembles the motif scaffolds using structure templates extracted from the known PDB structures and refines the structure using all-atom energy minimization. The Vfold-based web server provides a user friendly tool for the prediction of RNA structure and stability. The web server and the source codes are freely accessible for public use at "http://rna.physics.missouri.edu".

  17. Structural, elastic, mechanical and thermodynamic properties of Terbium oxide: First-principles investigations

    Directory of Open Access Journals (Sweden)

    Samah Al-Qaisi

    Full Text Available First-principles investigations of the Terbium oxide TbO are performed on structural, elastic, mechanical and thermodynamic properties. The investigations are accomplished by employing full potential augmented plane wave FP-LAPW method framed within density functional theory DFT as implemented in the WIEN2k package. The exchange-correlation energy functional, a part of the total energy functional, is treated through Perdew Burke Ernzerhof scheme of the Generalized Gradient Approximation PBEGGA. The calculations of the ground state structural parameters, like lattice constants a0, bulk moduli B and their pressure derivative B′ values, are done for the rock-salt RS, zinc-blende ZB, cesium chloride CsCl, wurtzite WZ and nickel arsenide NiAs polymorphs of the TbO compound. The elastic constants (C11, C12, C13, C33, and C44 and mechanical properties (Young’s modulus Y, Shear modulus S, Poisson’s ratio σ, Anisotropic ratio A and compressibility β, were also calculated to comprehend its potential for valuable applications. From our calculations, the RS phase of TbO compound was found strongest one mechanically amongst the studied cubic structures whereas from hexagonal phases, the NiAs type structure was found stronger than WZ phase of the TbO. To analyze the ductility of the different structures of the TbO, Pugh’s rule (B/SH and Cauchy pressure (C12–C44 approaches are used. It was found that ZB, CsCl and WZ type structures of the TbO were of ductile nature with the obvious dominance of the ionic bonding while RS and NiAs structures exhibited brittle nature with the covalent bonding dominance. Moreover, Debye temperature was calculated for both cubic and hexagonal structures of TbO in question by averaging the computed sound velocities. Keywords: DFT, TbO, Elastic properties, Thermodynamic properties

  18. Effect of secondary structure on the thermodynamics and kinetics of PNA hybridization to DNA hairpins

    DEFF Research Database (Denmark)

    Kushon, S A; Jordan, J P; Seifert, J L

    2001-01-01

    The binding of a series of PNA and DNA probes to a group of unusually stable DNA hairpins of the tetraloop motif has been observed using absorbance hypochromicity (ABS), circular dichroism (CD), and a colorimetric assay for PNA/DNA duplex detection. These results indicate that both stable PNA...... structures in both target and probe molecules are shown to depress the melting temperatures and free energies of the probe-target duplexes. Kinetic analysis of hybridization yields reaction rates that are up to 160-fold slower than hybridization between two unstructured strands. The thermodynamic and kinetic...

  19. Formation and thermodynamic stability of (polymer + porphyrin) supramolecular structures in aqueous solutions

    International Nuclear Information System (INIS)

    Costa, Viviana C.P. da; Hwang, Barrington J.; Eggen, Spencer E.; Wallace, Megan J.; Annunziata, Onofrio

    2014-01-01

    Highlights: • Thermodynamic stability of a (polymer + porphyrin) supramolecular structure was characterized. • Isothermal titration calorimetry provided two ways to determine reaction enthalpies. • Exothermic (polymer + porphyrin) binding competes with porphyrin self-association. • (Polymer + porphyrin) binding is entropically favored with respect to porphyrin self-association. • Spectral shifts show importance of porphyrin central hydrogens in polymer binding. - Abstract: Optical properties of porphyrins can be tuned through (polymer + porphyrin) (host + guest) binding in solution. This gives rise to the formation of supramolecular structures. In this paper, the formation, thermodynamic stability and spectroscopic properties of (polymer + porphyrin) supramolecular structures and their competition with porphyrin self-association were investigated by both isothermal titration calorimetry (ITC) and absorption spectroscopy. Specifically, reaction enthalpies and equilibrium constants were measured for meso-tetrakis(4-sulfonatophenyl) porphyrin (TPPS) self-association and TPPS binding to the polymer poly(vinylpyrrolidone) (PVP, 40 kg/mol) in aqueous solutions at pH 7 and three different temperatures (12, 25 and 37 °C). ITC, compared to spectroscopic techniques, provides two independent means to determine reaction enthalpies: direct measurements and Van’t Hoff plot. This was used as a criterion to assess that (1) self-association of TPPS is limited to the formation of dimers and (2) TPPS binds to PVP in its monomeric state only. The formation of TPPS dimers and (PVP + TPPS) supramolecular structures are both enthalpically driven. However, (polymer + porphyrin) binding was found to be entropically favored compared to dimerization. Furthermore, the reaction enthalpies of these two processes significantly depend on temperature. This behavior was attributed to hydrophobic interactions. Finally, the limiting absorption spectra of monomeric, dimeric and polymer

  20. Soft matter in hard confinement: phase transition thermodynamics, structure, texture, diffusion and flow in nanoporous media

    Science.gov (United States)

    Huber, Patrick

    2015-03-01

    Spatial confinement in nanoporous media affects the structure, thermodynamics and mobility of molecular soft matter often markedly. This article reviews thermodynamic equilibrium phenomena, such as physisorption, capillary condensation, crystallisation, self-diffusion, and structural phase transitions as well as selected aspects of the emerging field of spatially confined, non-equilibrium physics, i.e. the rheology of liquids, capillarity-driven flow phenomena, and imbibition front broadening in nanoporous materials. The observations in the nanoscale systems are related to the corresponding bulk phenomenologies. The complexity of the confined molecular species is varied from simple building blocks, like noble gas atoms, normal alkanes and alcohols to liquid crystals, polymers, ionic liquids, proteins and water. Mostly, experiments with mesoporous solids of alumina, gold, carbon, silica, and silicon with pore diameters ranging from a few up to 50 nm are presented. The observed peculiarities of nanopore-confined condensed matter are also discussed with regard to applications. A particular emphasis is put on texture formation upon crystallisation in nanoporous media, a topic both of high fundamental interest and of increasing nanotechnological importance, e.g. for the synthesis of organic/inorganic hybrid materials by melt infiltration, the usage of nanoporous solids in crystal nucleation or in template-assisted electrochemical deposition of nano structures.

  1. First principal studya of structural, electronic and thermodynamic properties of KTaO3-perovskite.

    Directory of Open Access Journals (Sweden)

    Hiadsi S.

    2013-03-01

    Full Text Available The results of first-principles theoretical study of structural, elastic, electronic and thermodynamic properties of KTaO3 compound, have been performed using the full-potential linear augmented plane-wave method plus local orbitals (FP-APW+lo as implemented in the Wien2k code. The exchange-correlation energy, is treated in generalized gradient approximation (GGA using the Perdew–Burke–Ernzerhof (PBE96 and PBEsol, Perdew 2008 parameterization. Also we have used the Engel-Vosko GGA optimizes the corresponding potential for band structure calculations. The calculated equilibrium parameter is in good agreement with other works. The elastic constants were calculated by using the Mehl method. The electronic band structure of this compound has been calculated using the Angel-Vosko (EV generalized gradient approximation (GGA for the exchange correlation potential. We deduced that KTaO3-perovskite exhibit an indirect from R to Γ point. To complete the fundamental characterization of KTaO3 material we have analyzed the thermodynamic properties using the quasi-harmonic Debye model.

  2. Energy effects on the structure and thermodynamic properties of nanoconfined fluids (a density functional theory study).

    Science.gov (United States)

    Keshavarzi, Ezat; Kamalvand, Mohammad

    2009-04-23

    The structure and properties of fluids confined in nanopores may show a dramatic departure from macroscopic bulk fluids. The main reason for this difference lies in the influence of system walls. In addition to the entropic wall effect, system walls can significantly change the energy of the confined fluid compared to macroscopic bulk fluids. The energy effect of the walls on a nanoconfined fluid appears in two forms. The first effect is the cutting off of the intermolecular interactions by the walls, which appears for example in the integrals for calculation of the thermodynamic properties. The second wall effect involves the wall-molecule interactions. In such confined fluids, the introduction of wall forces and the competition between fluid-wall and fluid-fluid forces could lead to interesting thermodynamic properties, including new kinds of phase transitions not observed in the macroscopic fluid systems. In this article, we use the perturbative fundamental measure density functional theory to study energy effects on the structure and properties of a hard core two-Yukawa fluid confined in a nanoslit. Our results show the changes undergone by the structure and phase transition of the nanoconfined fluids as a result of energy effects.

  3. Surface adsorption of lattice HP proteins: Thermodynamics and structural transitions using Wang-Landau sampling

    International Nuclear Information System (INIS)

    Li Yingwai; Landau, David P; Wüst, Thomas

    2012-01-01

    Wang-Landau sampling has been applied to investigate the thermodynamics and structural properties of a lattice hydrophobic-polar heteropolymer (the HP protein model) interacting with an attractive substrate. For simplicity, we consider a short HP sequence consisting of only 36 monomers interacting with a substrate which attracts all monomers in the sequence. The conformational “phase transitions” have been identified by a canonical analysis of the specific heat and suitable structural observables. Three major “transitions”, namely, adsorption, hydrophobic core formation and “flattening” of adsorbed structures, are observed. Depending on the surface attractive strength relative to the intra-protein attraction among the H monomers, these processes take place in different sequences upon cooling.

  4. Thermodynamic and structural models compared with the initial dissolution rates of SON glass samples

    International Nuclear Information System (INIS)

    Tovena, I.; Advocat, T.; Ghaleb, D.; Vernaz, E.

    1993-01-01

    The experimentally determined initial dissolution rate R 0 of nuclear glass was correlated with thermodynamic parameters and structural parameters. The initial corrosion rates of six ''R7T7'' glass samples measured at 100 deg C in a Soxhlet device were correlated with the glass free hydration energy and the glass formation enthalpy. These correlations were then tested with a group of 26 SON glasses selected for their wide diversity of compositions. The thermodynamic models provided a satisfactory approximation of the initial dissolution rate determined under Soxhlet conditions for SON glass samples that include up to 15 wt% of boron and some alumina. Conversely, these models are inaccurate if the boron concentration exceeds 15 wt% and the glass contains no alumina. Possible correlations between R 0 and structural parameters, such as the boron coordination number and the number of nonbridging oxygen atoms, were also investigated. The authors show that R 0 varies inversely with the number of 4-coordinate boron atoms; conversely, the results do not substantiate published reports of a correlation between R 0 and the number of nonbridging oxygen atoms. (authors). 13 refs., 2 figs., 4 tabs

  5. Stochastic and information-thermodynamic structures of population dynamics in a fluctuating environment

    Science.gov (United States)

    Kobayashi, Tetsuya J.; Sughiyama, Yuki

    2017-07-01

    Adaptation in a fluctuating environment is a process of fueling environmental information to gain fitness. Living systems have gradually developed strategies for adaptation from random and passive diversification of the phenotype to more proactive decision making, in which environmental information is sensed and exploited more actively and effectively. Understanding the fundamental relation between fitness and information is therefore crucial to clarify the limits and universal properties of adaptation. In this work, we elucidate the underlying stochastic and information-thermodynamic structure in this process, by deriving causal fluctuation relations (FRs) of fitness and information. Combined with a duality between phenotypic and environmental dynamics, the FRs reveal the limit of fitness gain, the relation of time reversibility with the achievability of the limit, and the possibility and condition for gaining excess fitness due to environmental fluctuation. The loss of fitness due to causal constraints and the limited capacity of real organisms is shown to be the difference between time-forward and time-backward path probabilities of phenotypic and environmental dynamics. Furthermore, the FRs generalize the concept of the evolutionary stable state (ESS) for fluctuating environment by giving the probability that the optimal strategy on average can be invaded by a suboptimal one owing to rare environmental fluctuation. These results clarify the information-thermodynamic structures in adaptation and evolution.

  6. Kinetic, Thermodynamic and Structural Studies of Native and N-Bromosuccinimide-Modified Mushroom Tyrosinase

    Directory of Open Access Journals (Sweden)

    Saeed Emami

    2016-10-01

    Full Text Available Background Mushroom tyrosinase (MT as a metalloenzyme is a good model for mechanistic studies of melanogenesis. To recognize the mechanism of MT action, it is important to investigate its inhibition, activation, mutation, and modification properties. Objectives In this study, the chemical modification of MT tryptophan residues was carried out by using N-bromosuccinimide (NBS and then, the activity, stability, and structure of the native and modified enzymes were compared. Methods Chemical modification of MT tryptophan residues was accomplished by enzyme incubation with different concentrations of NBS. The relative activity of native and modified MT was investigated through catecholase enzyme reaction in presence of dihydroxyphenylalanine (L-Dopa as substrate. Thermodynamic parameters including standard Gibbs free energy change (∆G25°C and Melting temperature (Tm were obtained from thermal denaturation of the native and modified enzymes. The circular dichroism and intrinsic fluorescence techniques were used to study secondary and tertiary structure of MT, respectively. All experiments were conducted in 2015 in biophysical laboratory of Qazvin University of Medical Sciences and Islamic Azad University, Science and Research Branch, Tehran. Results The relative activity reduced from 100% for native enzyme to 10%, 7.9%, and 6.4% for modified MT with different NBS of concentrations 2, 10, and 20 mM, respectively. Thermal instability of modified enzyme was confirmed by decreased Tm and ∆G25°C values after modification. In accordance with kinetic and thermodynamic results, the lower stability of modified MT was observed from the changes occurred on its secondary and tertiary structures. Conclusions Chemical modification of tryptophan residues with NBS reduces the activity and stability of MT simultaneously with its structural change. Thus, this study emphasizes the crucial role of tryptophan residues in the structure-function relationship of MT

  7. Linking landscape structure and rainfall runoff behaviour in a thermodynamic optimality context

    Science.gov (United States)

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

    2015-04-01

    gradients, and thus a faster relaxation back towards local thermodynamic equilibrium. Thermodynamic optimality principles allow for a priory optimization of the resistance field at a given gradient, not in the sense how they exactly look like but in the sense how they function with respect to export and dissipation of free energy associated with rainfall runoff processes. Based on this framework we explored the possibility of independent predictions of rainfall runoff, in the sense that the a-priory optimum model structures should match independent observations. We found that spatially organized patterns of soils and macropores observed in two distinctly different landscapes are in close accordance with thermodynamic optima expressed either by minimized relaxation times towards local thermodynamic equilibrium in cohesive soils or as steady state in the potential energy of soil water in non-cohesive soils. Predicted rainfall runoff based on the two optimized model structures was in both catchments in acceptable accordance with independent discharge observations. However, the nature of these optima suggests there might be two distinctly different thermodynamically optimal regimes of rainfall runoff behaviour. In the capillary- or c--regime, free energy dynamics of soil water is dominated by changes in its capillary binding energy, which is the case for cohesive soils. Soil wetting during rainfall in the c-regime implies pushing the system back towards LTE, especially after long dry spells. Dead ended macropores (roots, worm burrows which end in the soil matrix) 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 during rainfall runoff. In the c-regime several optimum macropore densities with respect to maximization of net reduction of free energy exist. This is because the governing equation is a second

  8. Quark–hadron phase structure, thermodynamics, and magnetization of QCD matter

    Science.gov (United States)

    Nasser Tawfik, Abdel; Magied Diab, Abdel; Hussein, M. T.

    2018-05-01

    The SU(3) Polyakov linear-sigma model (PLSM) is systematically implemented to characterize the quark-hadron phase structure and to determine various thermodynamic quantities and the magnetization of quantum chromodynamic (QCD) matter. Using mean-field approximation, the dependence of the chiral order parameter on a finite magnetic field is also calculated. Under a wide range of temperatures and magnetic field strengths, various thermodynamic quantities including trace anomaly, speed of sound squared, entropy density, and specific heat are presented, and some magnetic properties are described as well. Where available these results are compared to recent lattice QCD calculations. The temperature dependence of these quantities confirms our previous finding that the transition temperature is reduced with the increase in the magnetic field strength, i.e. QCD matter is characterized by an inverse magnetic catalysis. Furthermore, the temperature dependence of the magnetization showing that QCD matter has paramagnetic properties slightly below and far above the pseudo-critical temperature is confirmed as well. The excellent agreement with recent lattice calculations proves that our QCD-like approach (PLSM) seems to possess the correct degrees of freedom in both the hadronic and partonic phases and describes well the dynamics deriving confined hadrons to deconfined quark-gluon plasma.

  9. Structural and thermodynamic characterization of doxycycline/β-cyclodextrin supramolecular complex and its bacterial membrane interactions.

    Science.gov (United States)

    Suárez, Diego F; Consuegra, Jessika; Trajano, Vivianne C; Gontijo, Sávio M L; Guimarães, Pedro P G; Cortés, Maria E; Denadai, Ângelo L; Sinisterra, Rubén D

    2014-06-01

    Doxycycline is a semi-synthetic antibiotic commonly used for the treatment of many aerobic and anaerobic bacteria. It inhibits the activity of matrix metalloproteinases (MMPs) and affects cell proliferation. In this study, the structural and thermodynamic parameters of free DOX and a DOX/βCD complex were investigated, as well as their interactions and effects on Staphylococcus aureus cells and cellular cytotoxicity. Complexation of DOX and βCD was confirmed to be an enthalpy- and entropy-driven process, and a low equilibrium constant was obtained. Treatment of S. aureus with higher concentrations of DOX or DOX/βCD resulted in an exponential decrease in S. aureus cell size, as well as a gradual neutralization of zeta potential. These thermodynamic profiles suggest that ion-pairing and hydrogen bonding interactions occur between DOX and the membrane of S. aureus. In addition, the adhesion of βCD to the cell membrane via hydrogen bonding is hypothesized to mediate a synergistic effect which accounts for the higher activity of DOX/βCD against S. aureus compared to pure DOX. Lower cytotoxicity and induction of osteoblast proliferation was also associated with DOX/βCD compared with free DOX. These promising findings demonstrate the potential for DOX/βCD to mediate antimicrobial activity at lower concentrations, and provides a strategy for the development of other antimicrobial formulations. Copyright © 2014. Published by Elsevier B.V.

  10. Mesoscopic modeling of structural and thermodynamic properties of fluids confined by rough surfaces.

    Science.gov (United States)

    Terrón-Mejía, Ketzasmin A; López-Rendón, Roberto; Gama Goicochea, Armando

    2015-10-21

    The interfacial and structural properties of fluids confined by surfaces of different geometries are studied at the mesoscopic scale using dissipative particle dynamics simulations in the grand canonical ensemble. The structure of the surfaces is modeled by a simple function, which allows us to simulate readily different types of surfaces through the choice of three parameters only. The fluids we have modeled are confined either by two smooth surfaces or by symmetrically and asymmetrically structured walls. We calculate structural and thermodynamic properties such as the density, temperature and pressure profiles, as well as the interfacial tension profiles for each case and find that a structural order-disorder phase transition occurs as the degree of surface roughness increases. However, the magnitude of the interfacial tension is insensitive to the structuring of the surfaces and depends solely on the magnitude of the solid-fluid interaction. These results are important for modern nanotechnology applications, such as in the enhanced recovery of oil, and in the design of porous materials with specifically tailored properties.

  11. Optical, structural and thermodynamic properties of the interaction between tradimefon and serum albumin

    Science.gov (United States)

    Zhang, Hua-xin; Mei, Ping; Yang, Xi-xiong

    2009-04-01

    The biological toxicity of a chloric pesticide, tradimefon to bovine serum albumin (BSA) were studied by fluorescence and absorption spectroscopy. The fluorescence quenching mechanism analysis indicates the quenching of BSA by TDF was caused by BSA-TDF complex formation and electrostatic interaction played major role in the reaction. The number of binding sites n and observed binding constant Kb was measured by fluorescence quenching method. The thermodynamic parameters Δ Hθ, Δ Gθ, Δ Sθ at different temperatures were calculated, and the distance r between donor (BSA) and acceptor (TDF) was obtained according to Förster theory of non-radiation energy transfer. Three-dimensional fluorescence spectra, circular dichroism (CD) spectra and synchronous fluorescence spectra were used to investigate the structural change of BSA molecules with addition of TDF and the mechanism of binding reaction was analyzed at molecular level.

  12. Structural and thermodynamic basis of a frontometaphyseal dysplasia mutation in filamin A.

    Science.gov (United States)

    Ithychanda, Sujay S; Dou, Kevin; Robertson, Stephen P; Qin, Jun

    2017-05-19

    Filamin-mediated linkages between transmembrane receptors (TR) and the actin cytoskeleton are crucial for regulating many cytoskeleton-dependent cellular processes such as cell shape change and migration. A major TR binding site in the immunoglobulin repeat 21 (Ig21) of filamin is masked by the adjacent repeat Ig20, resulting in autoinhibition. The TR binding to this site triggers the relief of Ig20 and protein kinase A (PKA)-mediated phosphorylation of Ser-2152, thereby dynamically regulating the TR-actin linkages. A P2204L mutation in Ig20 reportedly cause frontometaphyseal dysplasia, a skeletal disorder with unknown pathogenesis. We show here that the P2204L mutation impairs a hydrophobic core of Ig20, generating a conformationally fluctuating molten globule-like state. Consequently, unlike in WT filamin, where PKA-mediated Ser-2152 phosphorylation is ligand-dependent, the P2204L mutant is readily accessible to PKA, promoting ligand-independent phosphorylation on Ser-2152. Strong TR peptide ligands from platelet GP1bα and G-protein-coupled receptor MAS effectively bound Ig21 by displacing Ig20 from autoinhibited WT filamin, but surprisingly, the capacity of these ligands to bind the P2204L mutant was much reduced despite the mutation-induced destabilization of the Ig20 structure that supposedly weakens the autoinhibition. Thermodynamic analysis indicated that compared with WT filamin, the conformationally fluctuating state of the Ig20 mutant makes Ig21 enthalpically favorable to bind ligand but with substantial entropic penalty, resulting in total higher free energy and reduced ligand affinity. Overall, our results reveal an unusual structural and thermodynamic basis for the P2204L-induced dysfunction of filamin and frontometaphyseal dysplasia disease. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  13. First-principles study of lattice dynamics, structural phase transition, and thermodynamic properties of barium titanate

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Huai-Yong; Zhao, Ying-Qin; Lu, Qing [Sichuan Univ., Chengdu (China). Inst. of Atomic and Molecular Physics; Zeng, Zhao-Yi [Chongqing Normal Univ. (China). College of Physics and Electronic Engineering; Chinese Academy of Engineering Physics, Mianyang (China). National Key Laboratory for Shock Wave and Detonation Physics Research; Cheng, Yan [Sichuan Univ., Chengdu (China). Inst. of Atomic and Molecular Physics; Sichuan Univ., Chengdu (China). Key Laboratory of High Energy Density Physics and Technology of Ministry of Education

    2016-11-01

    Lattice dynamics, structural phase transition, and the thermodynamic properties of barium titanate (BaTiO{sub 3}) are investigated by using first-principles calculations within the density functional theory (DFT). It is found that the GGA-WC exchange-correlation functional can produce better results. The imaginary frequencies that indicate structural instability are observed for the cubic, tetragonal, and orthorhombic phases of BaTiO{sub 3} and no imaginary frequencies emerge in the rhombohedral phase. By examining the partial phonon density of states (PDOSs), we find that the main contribution to the imaginary frequencies is the distortions of the perovskite cage (Ti-O). On the basis of the site-symmetry consideration and group theory, we give the comparative phonon symmetry analysis in four phases, which is useful to analyze the role of different atomic displacements in the vibrational modes of different symmetry. The calculated optical phonon frequencies at Γ point for the four phases are in good agreement with other theoretical and experimental data. The pressure-induced phase transition of BaTiO{sub 3} among four phases and the thermodynamic properties of BaTiO{sub 3} in rhombohedral phase have been investigated within the quasi-harmonic approximation (QHA). The sequence of the pressure-induced phase transition is rhombohedral → orthorhombic → tetragonal → cubic, and the corresponding transition pressure is 5.17, 5.92, 6.65 GPa, respectively. At zero pressure, the thermal expansion coefficient α{sub V}, heat capacity C{sub V}, Grueneisen parameter γ, and bulk modulus B of the rhombohedral phase BaTiO{sub 3} are estimated from 0 K to 200 K.

  14. Insight into the microscopic structure of an AdS black hole from a thermodynamical phase transition.

    Science.gov (United States)

    Wei, Shao-Wen; Liu, Yu-Xiao

    2015-09-11

    Comparing with an ordinary thermodynamic system, we investigate the possible microscopic structure of a charged anti-de Sitter black hole completely from the thermodynamic viewpoint. The number density of the black hole molecules is introduced to measure the microscopic degrees of freedom of the black hole. We found that the number density suffers a sudden change accompanied by a latent heat when the black hole system crosses the small-large black hole coexistence curve, while when the system passes the critical point, it encounters a second-order phase transition with a vanishing latent heat due to the continuous change of the number density. Moreover, the thermodynamic scalar curvature suggests that there is a weak attractive interaction between two black hole molecules. These phenomena might cast new insight into the underlying microscopic structure of a charged anti-de Sitter black hole.

  15. Structural domains and conformational changes in nuclear chromatin: a quantitative thermodynamic approach by differential scanning calorimetry.

    Science.gov (United States)

    Balbi, C; Abelmoschi, M L; Gogioso, L; Parodi, S; Barboro, P; Cavazza, B; Patrone, E

    1989-04-18

    A good deal of information on the thermodynamic properties of chromatin was derived in the last few years from optical melting experiments. The structural domains of the polynucleosomal chain, the linker, and the core particle denature as independent units. The differential scanning calorimetry profile of isolated chromatin is made up of three endotherms, at approximately 74, 90, and 107 degrees C, having an almost Gaussian shape. Previous work on this matter, however, was mainly concerned with the dependence of the transition enthalpy on external parameters, such as the ionic strength, or with the melting of nuclei from different sources. In this paper we report the structural assignment of the transitions of rat liver nuclei, observed at 58, 66, 75, 92, and 107 degrees C. They are representative of the quiescent state of the cell. The strategy adopted in this work builds on the method developed for the investigation of complex biological macromolecules. The heat absorption profile of the nucleus was related to the denaturation of isolated nuclear components; electron microscopy and electrophoretic techniques were used for their morphological and molecular characterization. The digestion of chromatin by endogenous nuclease mimics perfectly the decondensation of the higher order structure and represented the source of several misinterpretations. This point was carefully examined in order to define unambiguously the thermal profile of native nuclei. The low-temperature transitions, centered around 58 and 66 degrees C, arise from the melting of scaffolding structures and of the proteins associated with heterogeneous nuclear RNA.(ABSTRACT TRUNCATED AT 250 WORDS)

  16. Thermodynamics and Structure of Actinide(IV) Complexes with Nitrilotriacetic Acid

    Energy Technology Data Exchange (ETDEWEB)

    Bonin, L.; Guillaumont, D.; Jeanson, A.; Den Auwer, C.; Moisy, Ph. [CEA Marcoule, DEN, DRCP, SCPS, F-30207 Bagnols Sur Ceze (France); Grigoriev, M. [RAS, AN Frumkin Inst Phys Chem and Electrochem, Moscow 119991 (Russian Federation); Berthet, J.C. [CEA Saclay, DSM, IRAMIS, URA 331, Serv Chim Mol, CNRS, F-91191 Gif Sur Yvette (France); Hennig, C.; Scheinost, A. [Forschungszentrum Dresden Rossendorf, Inst Radiochem, D-01314 Dresden (Germany)

    2009-05-15

    Nitrilotriacetic acid, commonly known as NITA (N(CH{sub 2}CO{sub 2}H){sub 3}), can be considered a representative of the polyamino-carboxylic family. The results presented in this paper describe the thermodynamical complexation and structural investigation of An(IV) complexes with NTA in aqueous solution. In the first part, the stability constants of the An(IV) complexes (An = Pu, Np, U, and Th) have been determined by spectrophotometry. In the second part, the coordination spheres of the actinide cation in these complexes have been described using extended X-ray absorption fine structure spectroscopy and compared to the solid-state structure of (Hpy){sub 2}[U(NTA){sub 2}].H{sub 2}O. These data are further compared to quantum chemical calculations, and their evolution across the actinide series is discussed. In particular, an interpretation of the role of the nitrogen atom in the coordination mode is proposed. These results are considered to be model behavior of polyamino-carboxylic ligands such as diethylenetriamine pentaacetic acid, which is nowadays the best candidate for a chelating agent in the framework of actinide decorporation for the human body. (authors)

  17. Structural, electronic, and thermodynamic properties of curium dioxide: Density functional theory calculations

    Science.gov (United States)

    Hou, Ling; Li, Wei-Dong; Wang, Fangwei; Eriksson, Olle; Wang, Bao-Tian

    2017-12-01

    We present a systematic investigation of the structural, magnetic, electronic, mechanical, and thermodynamic properties of CmO2 with the local density approximation (LDA)+U and the generalized gradient approximation (GGA)+U approaches. The strong Coulomb repulsion and the spin-orbit coupling (SOC) effects on the lattice structures, electronic density of states, and band gaps are carefully studied, and compared with other A O2 (A =U , Np, Pu, and Am). The ferromagnetic configuration with half-metallic character is predicted to be energetically stable while a charge-transfer semiconductor is predicted for the antiferromagnetic configuration. The elastic constants and phonon spectra show that the fluorite structure is mechanically and dynamically stable. Based on the first-principles phonon density of states, the lattice vibrational energy is calculated using the quasiharmonic approximation. Then, the Gibbs free energy, thermal expansion coefficient, specific heat, and entropy are obtained and compared with experimental data. The mode Grüneisen parameters are presented to analyze the anharmonic properties. The Slack relation is applied to obtain the lattice thermal conductivity in temperature range of 300-1600 K. The phonon group velocities are also calculated to investigate the heat transfer. For all these properties, if available, we compare the results of CmO2 with other A O2 .

  18. Solution structure, dynamics and thermodynamics of the three SH3 domains of CD2AP

    Energy Technology Data Exchange (ETDEWEB)

    Roldan, Jose L. Ortega [Universidad de Granada, Departamento de Quimica Fisica e Instituto de Biotecnologia, Facultad de Ciencias (Spain); Blackledge, Martin [Institut de Biologie Structurale Jean-Pierre Ebel, CEA, CNRS, UJF UMR 5075, Protein Dynamics and Flexibility by NMR (France); Nuland, Nico A. J. van, E-mail: nvnuland@vub.ac.be [Vrije Universiteit Brussel, Structural Biology Brussels (Belgium); Azuaga, Ana I. [Universidad de Granada, Departamento de Quimica Fisica e Instituto de Biotecnologia, Facultad de Ciencias (Spain)

    2011-06-15

    CD2 associated protein (CD2AP) is an adaptor protein that plays an important role in cell to cell union needed for the kidney function. It contains three N-terminal SH3 domains that are able to interact among others with CD2, ALIX, c-Cbl and Ubiquitin. To understand the role of the individual SH3 domains of this adaptor protein we have performed a complete structural, thermodynamic and dynamic characterization of the separate domains using NMR and DSC. The energetic contributions to the stability and the backbone dynamics have been related to the structural features of each domain using the structure-based FoldX algorithm. We have found that the N-terminal SH3 domain of both adaptor proteins CD2AP and CIN85 are the most stable SH3 domains that have been studied until now. This high stability is driven by a more extensive network of intra-molecular interactions. We believe that this increased stabilization of N-terminal SH3 domains in adaptor proteins is crucial to maintain the necessary conformation to establish the proper interactions critical for the recruitment of their natural targets.

  19. Thermodynamics of dilute 3He-4He solid solutions with hcp structure

    Science.gov (United States)

    Chishko, K. A.

    2018-02-01

    To interpret the anomalies in heat capacity CV(T) and temperature-dependent pressure P(T) of solid hexagonal close-packed (hcp) 4He we exploit the model of hcp crystalline polytype with specific lattice degrees of freedom and describe the thermodynamics of impurity-free 4He solid as superposition of phononic and polytypic contributions. The hcp-based polytype is a stack of 2D basal atomic monolayers on triangular lattice packed with arbitrary long (up to infinity) spatial period along the hexagonal c axis perpendicular to the basal planes. It is a crystal with perfect ordering along the layers, but without microscopic translational symmetry in perpendicular direction (which remains, nevertheless, the rotational crystallographic axis of third order, so that the polytype can be considered as semidisordered system). Each atom of the hcp polytype has twelve crystallographic neighbors in both first and second coordination spheres at any arbitrary packing order. It is shown that the crystal of such structure behaves as anisotropic elastic medium with specific dispersion law of phonon excitations along c axis. The free energy and the heat capacity consist of two terms: one of them is a normal contribution [with CV(T) ˜ T3] from phonon excitations in an anisotropic lattice of hexagonal symmetry, and another term (an "excessive" heat) is a contribution resulted by packing entropy from quasi-one-dimensional system of 2D basal planes on triangular lattice stacked randomly along c axis without braking the closest pack between neighboring atomic layers. The excessive part of the free energy has been treated within 1D quasi-Ising (lattice gas) model using the transfer matrix approach. This model makes us possible to interpret successfully the thermodynamic anomaly (heat capacity peak in hcp 4He) observed experimentally.

  20. Selectivity in Ligand Binding to Uranyl Compounds: A Synthetic, Structural, Thermodynamic and Computational Study

    Energy Technology Data Exchange (ETDEWEB)

    Arnold, John [Univ. of California, Berkeley, CA (United States)

    2017-12-06

    The uranyl cation (UO22+) is the most abundant form of uranium on the planet. It is estimated that 4.5 billion tons of uranium in this form exist in sea water. The ability to bind and extract the uranyl cation from aqueous solution while separating it from other elements would provide a limitless source of nuclear fuel. A large body of research concerns the selective recognition and extraction of uranyl. A stable molecule, the cation has a linear O=U=O geometry. The short U-O bonds (1.78 Å) arise from the combination of uranium 5f/6d and oxygen 2p orbitals. Due to the oxygen moieties being multiply bonded, these sites were not thought to be basic enough for Lewis acidic coordination to be a viable approach to sequestration. We believe that the goal of developing a practical system for uranium separation from seawater will not be attained without new insights into our existing fundamental knowledge of actinide chemistry. We posit that detailed studies of the kinetic and thermodynamic factors that influence interactions between f-elements and ligands with a range of donor atoms is essential to any major advance in this important area. The goal of this research is thus to broaden the coordination chemistry of the uranyl ion by studying new ligand systems via synthetic, structural, thermodynamic and computational methods. We anticipate that this fundamental science will find use beyond actinide separation technologies in areas such as nuclear waste remediation and nuclear materials.

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

    Science.gov (United States)

    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...

  2. Electronic band structure, optical, dynamical and thermodynamic properties of cesium chloride (CsCl from first-principles

    Directory of Open Access Journals (Sweden)

    Bingol Suat

    2015-01-01

    Full Text Available The geometric structural optimization, electronic band structure, total density of states for valence electrons, density of states for phonons, optical, dynamical, and thermodynamical features of cesium chloride have been investigated by linearized augmented plane wave method using the density functional theory under the generalized gradient approximation. Ground state properties of cesium chloride are studied. The calculated ground state properties are consistent with experimental results. Calculated band structure indicates that the cesium chloride structure has an indirect band gap value of 5.46 eV and is an insulator. From the obtained phonon spectra, the cesium chloride structure is dynamically stable along the various directions in the Brillouin zone. Temperature dependent thermodynamic properties are studied using the harmonic approximation model.

  3. Crystal structures and thermodynamics/kinetics of Zn(II) coordination polymers with helical chains

    Energy Technology Data Exchange (ETDEWEB)

    He, Tian [Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi’an 710069 (China); Yue, Ke-Fen, E-mail: ykflyy@nwu.edu.cn [Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi’an 710069 (China); Zhao, Yi-xing; Chen, San-Ping [Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi’an 710069 (China); Zhou, Chun-sheng, E-mail: slzhoucs@126.com.cn [Shaanxi Key Laboratory of Comprehensive Utilization of Tailings Resources, College of Chemical Engineering and Modern Materials, Shangluo University, Shangluo 726000 (China); Yan, Ni [Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi’an 710069 (China)

    2016-07-15

    Solvothermal reactions of Zn(II) acetates and four V-shaped carboxylates ligands in the presence of 1,4-Bis(2-methyl-imidazol-1-yl)butane afforded four interesting Zn(II) coordination polymers with helical chains, namely, {[Zn(bib)(atibdc)]·2H_2O}{sub n} (1), {[Zn(bib)(atbip)]·H_2O}{sub n} (2), {[Zn(bib)(2,2′-tda)]}{sub n} (3) and {[Zn(bib)(5-tbipa)]·EtOH}{sub n} (4), (H{sub 2}atibdc=5-amino-2,4,6-triiodoisophthalic acid, H{sub 2}atbip=5-amino-2,4,6-tribromoisophthalic acid, 2,2′-H{sub 2}tad=2,2′-thiodiacetic acid, 5-H{sub 2}tbipa=5-tert-butyl-isophthalic acid). 1 reveals a 3D chiral framework with three kinds of helical chains along a, b and c axis. 2 shows a 2D step-type chiral framework with right-handed helical chains. 3 displays a wavelike 2D layer network possessing alternate left- and right-handed helical chains. 4 presents a four-connected 3D framework with zigzag and meso-helical chains. The different spacers and substituent group of carboxylic acid ligands may lead to the diverse network structures of 1–4. The fluorescent properties of complexes 1−4 were studied. In addition, the thermal decompositions properties of 1–4 were investigated by simultaneous TG/DTG–DSC technique. The apparent activation energy E and the pre-exponential factor (A) of skeleton collapse for the complexes 1–4 are calculated by the integral Kissinger's method and Ozawa–Doyle's method. The activation energy E (E{sub 1}=209.658 kJ·mol{sup −1}, E{sub 2}=250.037 kJ mol{sup −1}, E{sub 3}=225.300 kJ mol{sup −1}, E{sub 4}=186.529 kJ·mol{sup −1}) demonstrates that the reaction rate of the melting decomposition is slow. The thermodynamic parameters (ΔH{sup ‡}, ΔG{sup ‡} and ΔS{sup ‡}) at the peak temperatures of the DTG curves were also calculated. ΔG{sup ‡}>0 indicates that the skeleton collapse is not spontaneous. ΔH{sub d}>0 suggests that the skeleton collapse is endothermic, corresponding to the intense endothermic peak of the DSC

  4. Thermodynamic and structure-property study of liquid-vapor equilibrium for aroma compounds.

    Science.gov (United States)

    Tromelin, Anne; Andriot, Isabelle; Kopjar, Mirela; Guichard, Elisabeth

    2010-04-14

    Thermodynamic parameters (T, DeltaH degrees , DeltaS degrees , K) were collected from the literature and/or calculated for five esters, four ketones, two aldehydes, and three alcohols, pure compounds and compounds in aqueous solution. Examination of correlations between these parameters and the range values of DeltaH degrees and DeltaS degrees puts forward the key roles of enthalpy for vaporization of pure compounds and of entropy in liquid-vapor equilibrium of compounds in aqueous solution. A structure-property relationship (SPR) study was performed using molecular descriptors on aroma compounds to better understand their vaporization behavior. In addition to the role of polarity for vapor-liquid equilibrium of compounds in aqueous solution, the structure-property study points out the role of chain length and branching, illustrated by the correlation between the connectivity index CHI-V-1 and the difference between T and log K for vaporization of pure compounds and compounds in aqueous solution. Moreover, examination of the esters' enthalpy values allowed a probable conformation adopted by ethyl octanoate in aqueous solution to be proposed.

  5. Enzyme stability, thermodynamics and secondary structures of α-amylase as probed by the CD spectroscopy.

    Science.gov (United States)

    Kikani, B A; Singh, S P

    2015-11-01

    An amylase of a thermophilic bacterium, Bacillus sp. TSSC-3 (GenBank Number, EU710557) isolated from the Tulsi Shyam hot spring reservoir (Gujarat, India) was purified to the homogeneity in a single step on phenyl sepharose 6FF. The molecular weight of the enzyme was 25kD, while the temperature and pH optima for the enzyme catalysis were 80°C and 7, respectively. The purified enzyme was highly thermostable with broad pH stability and displayed remarkable resistance against surfactants, chelators, urea, guanidine HCl and various solvents as well. The stability and changes in the secondary structure of the enzyme under various extreme conditions were determined by the circular dichroism (CD) spectroscopy. The stability trends and the changes in the α-helices and β-sheets were analyzed by Mean Residual Ellipticity (MRE) and K2D3. The CD data confirmed the structural stability of the enzyme under various harsh conditions, yet it indicated reduced α-helix content and increased β-sheets upon denaturation. The thermodynamic parameters; deactivation rate constant, half-life, changes in entropy, enthalpy, activation energy and Gibb's free energy indicated that the enzyme-substrate reactions were highly stable. The overall profile of the enzyme: high thermostability, alkalitolerance, calcium independent nature, dextrose equivalent values and resistance against chemical denaturants, solvents and surfactants suggest its commercial applications. Copyright © 2015 Elsevier B.V. All rights reserved.

  6. Statistical thermodynamics

    International Nuclear Information System (INIS)

    Hwang, Jeong Ui; Jang, Jong Jae; Jee, Jong Gi

    1987-01-01

    The contents of this book are thermodynamics on the law of thermodynamics, classical thermodynamics and molecule thermodynamics, basics of molecule thermodynamics, molecule and assembly partition function, molecule partition function, classical molecule partition function, thermodynamics function for ideal assembly in fixed system, thermodynamics function for ideal assembly in running system, Maxwell-Boltzmann's law of distribution, chemical equilibrium like calculation of equilibrium constant and theory of absolute reaction rate.

  7. Structural and Thermodynamic Analysis of the First Mononuclear Aqueous Aluminum Citrate Complex Using DFT Calculations.

    Science.gov (United States)

    de Noronha, Antonio Luiz Oliveira; Guimarães, Luciana; Duarte, Hélio Anderson

    2007-05-01

    Structural and thermodynamic properties of the mononuclear Al/citrate complexes have been theoretically investigated aiming to understand the coordination mechanism at an atomic level. GGA-DFT/PCM calculations have been performed for the different conformations and tautomers arising from the Al(3+) and citric acid (H3L) interaction in aqueous solution. The Gibbs reaction energies were estimated based on the reaction of the trigonal planar Al(OH)3 and H3L to form different Al-citrate complexes. The estimated Gibbs free reaction energies for the [AlL], [AlHL](+), and [Al(OH)L](-) species are in good agreement with the experimental values. In these species, the Al(3+) center is coordinated by two carboxylic and the tertiary hydroxyl groups of the citrate. Conversely to what has been proposed based on the experiments, the present theoretical calculations indicate that the citric acid hydroxyl group remains protonated upon the coordination of Al(3+). In fact, our model turns out to be more consistent with the relative pKa values of citrate protonation groups and with the hydrolysis constant of the H2O bound to Al(3+) leading to better agreement with the available experimental data.

  8. Co-assembly in chitosan-surfactant mixtures: thermodynamics, structures, interfacial properties and applications.

    Science.gov (United States)

    Chiappisi, Leonardo; Gradzielski, Michael

    2015-06-01

    In this review, different aspects characterizing chitosan-surfactant mixtures are summarized and compared. Chitosan is a bioderived cationic polysaccharide that finds wide-ranged applications in various field, e.g., medical or food industry, in which synergistic effects with surfactant can play a fundamental role. In particular, the behavior of chitosan interacting with strong and weak anionic, nonionic as well as cationic surfactants is reviewed. We put a focus on oppositely charged systems, as they exhibit the most interesting features. In that context, we discuss the thermodynamic description of the interaction and in particular the structural changes as they occur as a function of the mixed systems and external parameters. Moreover, peculiar properties of chitosan coated phospholipid vesicles are summarized. Finally, their co-assembly at interfaces is briefly reviewed. Despite the behavior of the mentioned systems might strongly differ, resulting in a high variety of properties, few general rules can be pointed out which improve the understanding of such complex systems. Copyright © 2015 Elsevier B.V. All rights reserved.

  9. Varying the charge of small cations in liquid water: Structural, transport, and thermodynamical properties

    Science.gov (United States)

    Martelli, Fausto; Vuilleumier, Rodolphe; Simonin, Jean-Pierre; Spezia, Riccardo

    2012-10-01

    In this work, we show how increasing the charge of small cations affects the structural, thermodynamical, and dynamical properties of these ions in liquid water. We have studied the case of lanthanoid and actinoid ions, for which we have recently developed accurate polarizable force fields, and the ionic radius is in the 0.995-1.250 Å range, and explored the valency range from 0 to 4+. We found that the ion charge strongly structures the neighboring water molecules and that, in this range of charges, the hydration enthalpies exhibit a quadratic dependence with respect to the charge, in line with the Born model. The diffusion process follows two main regimes: a hydrodynamical regime for neutral or low charges, and a dielectric friction regime for high charges in which the contraction of the ionic radius along the series of elements causes a decrease of the diffusion coefficient. This latter behavior can be qualitatively described by theoretical models, such as the Zwanzig and the solvated ion models. However, these models need be modified in order to obtain agreement with the observed behavior in the full charge range. We have thus modified the solvated ion model by introducing a dependence of the bare ion radius as a function of the ionic charge. Besides agreement between theory and simulation this modification allows one to obtain an empirical unified model. Thus, by analyzing the contributions to the drag coefficient from the viscous and the dielectric terms, we are able to explain the transition from a regime in which the effect of viscosity dominates to one in which dielectric friction governs the motion of ions with radii of ca. 1 Å.

  10. Noncanonical structures and their thermodynamics of DNA and RNA under molecular crowding: beyond the Watson-Crick double helix.

    Science.gov (United States)

    Sugimoto, Naoki

    2014-01-01

    How does molecular crowding affect the stability of nucleic acid structures inside cells? Water is the major solvent component in living cells, and the properties of water in the highly crowded media inside cells differ from that in buffered solution. As it is difficult to measure the thermodynamic behavior of nucleic acids in cells directly and quantitatively, we recently developed a cell-mimicking system using cosolutes as crowding reagents. The influences of molecular crowding on the structures and thermodynamics of various nucleic acid sequences have been reported. In this chapter, we discuss how the structures and thermodynamic properties of nucleic acids differ under various conditions such as highly crowded environments, compartment environments, and in the presence of ionic liquids, and the major determinants of the crowding effects on nucleic acids are discussed. The effects of molecular crowding on the activities of ribozymes and riboswitches on noncanonical structures of DNA- and RNA-like quadruplexes that play important roles in transcription and translation are also described. © 2014 Elsevier Inc. All rights reserved.

  11. Structure-thermodynamics-antioxidant activity relationships of selected natural phenolic acids and derivatives: an experimental and theoretical evaluation.

    Science.gov (United States)

    Chen, Yuzhen; Xiao, Huizhi; Zheng, Jie; Liang, Guizhao

    2015-01-01

    Phenolic acids and derivatives have potential biological functions, however, little is known about the structure-activity relationships and the underlying action mechanisms of these phenolic acids to date. Herein we investigate the structure-thermodynamics-antioxidant relationships of 20 natural phenolic acids and derivatives using DPPH• scavenging assay, density functional theory calculations at the B3LYP/6-311++G(d,p) levels of theory, and quantitative structure-activity relationship (QSAR) modeling. Three main working mechanisms (HAT, SETPT and SPLET) are explored in four micro-environments (gas-phase, benzene, water and ethanol). Computed thermodynamics parameters (BDE, IP, PDE, PA and ETE) are compared with the experimental radical scavenging activities against DPPH•. Available theoretical and experimental investigations have demonstrated that the extended delocalization and intra-molecular hydrogen bonds are the two main contributions to the stability of the radicals. The C = O or C = C in COOH, COOR, C = CCOOH and C = CCOOR groups, and orthodiphenolic functionalities are shown to favorably stabilize the specific radical species to enhance the radical scavenging activities, while the presence of the single OH in the ortho position of the COOH group disfavors the activities. HAT is the thermodynamically preferred mechanism in the gas phase and benzene, whereas SPLET in water and ethanol. Furthermore, our QSAR models robustly represent the structure-activity relationships of these explored compounds in polar media.

  12. Monte Carlo thermodynamic and structural properties of the TIP4P water model: dependence on the computational conditions

    Directory of Open Access Journals (Sweden)

    João Manuel Marques Cordeiro

    1998-11-01

    Full Text Available Classical Monte Carlo simulations were carried out on the NPT ensemble at 25°C and 1 atm, aiming to investigate the ability of the TIP4P water model [Jorgensen, Chandrasekhar, Madura, Impey and Klein; J. Chem. Phys., 79 (1983 926] to reproduce the newest structural picture of liquid water. The results were compared with recent neutron diffraction data [Soper; Bruni and Ricci; J. Chem. Phys., 106 (1997 247]. The influence of the computational conditions on the thermodynamic and structural results obtained with this model was also analyzed. The findings were compared with the original ones from Jorgensen et al [above-cited reference plus Mol. Phys., 56 (1985 1381]. It is notice that the thermodynamic results are dependent on the boundary conditions used, whereas the usual radial distribution functions g(O/O(r and g(O/H(r do not depend on them.

  13. Selectivity in ligand binding to uranyl compounds: A synthetic, structural, thermodynamic and computational study

    Energy Technology Data Exchange (ETDEWEB)

    Arnold, John [Univ. of California, Berkeley, CA (United States)

    2015-01-21

    The uranyl cation (UO₂²⁺) is the most abundant form of uranium on the planet. It is estimated that 4.5 billion tons of uranium in this form exist in sea water. The ability to bind and extract the uranyl cation from aqueous solution while separating it from other elements would provide a limitless source of nuclear fuel. A large body of research concerns the selective recognition and extraction of uranyl. A stable molecule, the cation has a linear O=U=O geometry. The short U-O bonds (1.78 Å) arise from the combination of uranium 5f/6d and oxygen 2p orbitals. Due to the oxygen moieties being multiply bonded, these sites were not thought to be basic enough for Lewis acidic coordination to be a viable approach to sequestration. The goal of this research is thus to broaden the coordination chemistry of the uranyl ion by studying new ligand systems via synthetic, structural, thermodynamic and computational methods. It is anticipated that this fundamental science will find use beyond actinide separation technologies in areas such as nuclear waste remediation and nuclear materials. The focus of this study is to synthesize uranyl complexes incorporating amidinate and guanidinate ligands. Both synthetic and computational methods are used to investigate novel equatorial ligand coordination and how this affects the basicity of the oxo ligands. Such an understanding will later apply to designing ligands incorporating functionalities that can bind uranyl both equatorially and axially for highly selective sequestration. Efficient and durable chromatography supports for lanthanide separation will be generated by (1) identifying robust peptoid-based ligands capable of binding different lanthanides with variable affinities, and (2) developing practical synthetic methods for the attachment of these ligands to Dowex ion exchange resins.

  14. Selectivity in ligand binding to uranyl compounds: A synthetic, structural, thermodynamic and computational study

    International Nuclear Information System (INIS)

    Arnold, John

    2015-01-01

    The uranyl cation (UO 2 2+ ) is the most abundant form of uranium on the planet. It is estimated that 4.5 billion tons of uranium in this form exist in sea water. The ability to bind and extract the uranyl cation from aqueous solution while separating it from other elements would provide a limitless source of nuclear fuel. A large body of research concerns the selective recognition and extraction of uranyl. A stable molecule, the cation has a linear O=U=O geometry. The short U-O bonds (1.78 Å) arise from the combination of uranium 5f/6d and oxygen 2p orbitals. Due to the oxygen moieties being multiply bonded, these sites were not thought to be basic enough for Lewis acidic coordination to be a viable approach to sequestration. The goal of this research is thus to broaden the coordination chemistry of the uranyl ion by studying new ligand systems via synthetic, structural, thermodynamic and computational methods. It is anticipated that this fundamental science will find use beyond actinide separation technologies in areas such as nuclear waste remediation and nuclear materials. The focus of this study is to synthesize uranyl complexes incorporating amidinate and guanidinate ligands. Both synthetic and computational methods are used to investigate novel equatorial ligand coordination and how this affects the basicity of the oxo ligands. Such an understanding will later apply to designing ligands incorporating functionalities that can bind uranyl both equatorially and axially for highly selective sequestration. Efficient and durable chromatography supports for lanthanide separation will be generated by (1) identifying robust peptoid-based ligands capable of binding different lanthanides with variable affinities, and (2) developing practical synthetic methods for the attachment of these ligands to Dowex ion exchange resins.

  15. Ganymede's internal structure including thermodynamics of magnesium sulfate oceans in contact with ice

    Science.gov (United States)

    Vance, Steve; Bouffard, Mathieu; Choukroun, Mathieu; Sotin, Christophe

    2014-06-01

    The large icy moons of Jupiter contain vast quantities of liquid water, a key ingredient for life. Ganymede and Callisto are weaker candidates for habitability than Europa, in part because of the model-based assumption that high-pressure ice layers cover their seafloors and prevent significant water-rock interaction. Water-rock interactions may occur, however, if heating at the rock-ice interface melts the high pressure ice. Highly saline fluids would be gravitationally stable, and might accumulate under the ice due to upward migration, refreezing, and fractionation of salt from less concentrated liquids. To assess the influence of salinity on Ganymede's internal structure, we use available phase-equilibrium data to calculate activity coefficients and predict the freezing of water ice in the presence of aqueous magnesium sulfate. We couple this new equation of state with thermal profiles in Ganymede's interior-employing recently published thermodynamic data for the aqueous phase-to estimate the thicknesses of layers of ice I, III, V, and VI. We compute core and silicate mantle radii consistent with available constraints on Ganymede's mass and gravitational moment of inertia. Mantle radii range from 800 to 900 km for the values of salt and heat flux considered here (4-44 mW m-2 and 0 to 10 wt% MgSO4). Ocean concentrations with salinity higher than 10 wt% have little high pressure ice. Even in a Ganymede ocean that is mostly liquid, achieving such high ocean salinity is permissible for the range of likely S/Si ratios. However, elevated salinity requires a smaller silicate mantle radius to satisfy mass and moment-of-inertia constraints, so ice VI is always present in Ganymede's ocean. For lower values of heat flux, oceans with salinity as low as 3 wt% can co-exist with ice III. Available experimental data indicate that ice phases III and VI become buoyant for salinity higher than 5 wt% and 10 wt%, respectively. Similar behavior probably occurs for ice V at salinities

  16. Vacancy formation energies in close-packed crystals correlated with melting temperature via thermodynamics and liquid structure

    International Nuclear Information System (INIS)

    Rashid, R.I.M.A.; March, N.H.

    1988-08-01

    In earlier work, the vacancy formation energy E v in close-packed crystals, in units of the thermal energy k B T m at the melting temperature T m , has been connected with compressibility and specific heats, plus terms dependent on the liquid structure at T m . Here, this connection has been examined quantitatively for (a) the insulating condensed rare gases Ne, Ar and Kr, and (b) a variety of close-packed metals. For case (a), E v /k B T m can be calculated directly from thermodynamic data to obtain agreement with experiment for Ar and Kr, though not for Ne. A 'residual' contribution is estimated for Ar and Kr from diffraction and computer experiments on the density dependence of the liquid pair correlation function and is shown to be very small. Agreement is less impressive for case (b) for the eight close-packed metals for which all data required is known, the thermodynamic formula giving an average value E v /k B T m =7.8+-1.1 whereas experiment yields 9.4+-1.8. However, for the body-centred cubic alkalis the thermodynamic average value of 4.5+-0.5 is much lower than the experimental value 11.5+-2.0 consistent with the known role of ionic relaxation round the vacancy in such open structures. (author). 16 refs, 2 tabs

  17. Structural characterization of Am(III) formate complexes. Combining EXAFS spectroscopy with DFT and thermodynamical calculations

    Energy Technology Data Exchange (ETDEWEB)

    Rossberg, Andre [Helmholtz-Zentrum Dresden-Rossendorf e.V., Dresden (Germany). Molecular Structures; Froehlich, D.R. [Heidelberg Univ. (Germany). Physikalisch-Chemisches Inst.

    2017-06-01

    We used iterative transformation factor analysis (ITFA) in order to isolate the EXAFS spectral contributions of the complexing ligand from a Am(III)/formate pH-series. Thermodynamic calculations were used as constraint for ITFA and for density functional theory (DFT) calculations to identify the coordination mode within the formed complexes.

  18. Effects of chemical structure on the thermodynamic efficiency of radical chain carriers for organic synthesis.

    Science.gov (United States)

    Lin, Ching Yeh; Peh, Jessie; Coote, Michelle L

    2011-03-18

    The chain carrier index (CCI), defined as the ratio of the bond dissociation free energies (BDFE) of corresponding chain carrier halides and hydrides, is proposed as a measure of the thermodynamic efficiency of chain carriers for radical dehalogenation. The larger this value is relative to the corresponding value of the organic substrate, the more thermodynamically efficient the process. The chloride and bromide CCIs were evaluated at the G3(MP2)-RAD(+) level of theory for 120 different R-groups, covering a broad range of carbon-centered and noncarbon-centered species; the effects of solvent and temperature have also been studied. The broad finding from this work is that successful chain carriers generally maximize the strength of their halide (versus hydride bonds) through charge-shift bonding. As a result, the thermodynamic efficiency of a chain carrier tends to increase down the periodic table, and also with the inclusion of stronger electron donating substituents. The CCIs of carbon-centered species fall into a relatively narrow range so that, even when the CCI is maximized through inclusion of lone pair donor OMe or NMe(2) groups, the thermodynamic driving force for dehalogenation of other organic substrates is modest at best, and the process is likely to be kinetically hampered. Among the noncarbon-centered species studied, bismuth- and borane-centered compounds have some of the highest CCI values and, although their kinetics requires further optimization, these classes of compounds would be worth further investigation as tin-free radical reducing agents.

  19. Thermodynamic properties and atomic structure of Ca-based liquid alloys

    Science.gov (United States)

    Poizeau, Sophie

    To identify the most promising positive electrodes for Ca-based liquid metal batteries, the thermodynamic properties of diverse Ca-based liquid alloys were investigated. The thermodynamic properties of Ca-Sb alloys were determined by emf measurements. It was found that Sb as positive electrode would provide the highest voltage for Ca-based liquid metal batteries (1 V). The price of such a battery would be competitive for the grid-scale energy storage market. The impact of Pb, a natural impurity of Sb, was predicted successfully and confirmed via electrochemical measurements. It was shown that the impact on the open circuit voltage would be minor. Indeed, the interaction between Ca and Sb was demonstrated to be much stronger than between Ca and Pb using thermodynamic modeling, which explains why the partial thermodynamic properties of Ca would not vary much with the addition of Pb to Sb. However, the usage of the positive electrode would be reduced, which would limit the interest of a Pb-Sb positive electrode. Throughout this work, the molecular interaction volume model (MIVM) was used for the first time for alloys with thermodynamic properties showing strong negative deviation from ideality. This model showed that systems such as Ca-Sb have strong short-range order: Ca is most stable when its first nearest neighbors are Sb. This is consistent with what the more traditional thermodynamic model, the regular association model, would predict. The advantages of the MIVM are the absence of assumption regarding the composition of an associate, and the reduced number of fitting parameters (2 instead of 5). Based on the parameters derived from the thermodynamic modeling using the MIVM, a new potential of mixing for liquid alloys was defined to compare the strength of interaction in different Ca-based alloys. Comparing this trend with the strength of interaction in the solid state of these systems (assessed by the energy of formation of the intermetallics), the systems with

  20. Basic Thermodynamics

    International Nuclear Information System (INIS)

    Duthil, P

    2014-01-01

    The goal of this paper is to present a general thermodynamic basis that is useable in the context of superconductivity and particle accelerators. The first part recalls the purpose of thermodynamics and summarizes its important concepts. Some applications, from cryogenics to magnetic systems, are covered. In the context of basic thermodynamics, only thermodynamic equilibrium is considered

  1. Basic Thermodynamics

    Energy Technology Data Exchange (ETDEWEB)

    Duthil, P [Orsay, IPN (France)

    2014-07-01

    The goal of this paper is to present a general thermodynamic basis that is useable in the context of superconductivity and particle accelerators. The first part recalls the purpose of thermodynamics and summarizes its important concepts. Some applications, from cryogenics to magnetic systems, are covered. In the context of basic thermodynamics, only thermodynamic equilibrium is considered.

  2. Theoretical investigation of the structural stabilities, optoelectronic properties and thermodynamic characteristics of GaPxSb1-x ternary alloys

    Science.gov (United States)

    Oumelaz, F.; Nemiri, O.; Boumaza, A.; Ghemid, S.; Meradji, H.; Bin Omran, S.; El Haj Hassan, F.; Rai, D. P.; Khenata, R.

    2018-06-01

    In this theoretical study, we have investigated the structural, phase transition, electronic, thermodynamic and optical properties of GaPxSb1-x ternary alloys. Our calculations are performed with the WIEN2k code based on density functional theory using the full-potential linearized augmented plane wave method. For the electron exchange-correlation potential, a generalized gradient approximation within Wu-Cohen scheme is considered. The recently developed Tran-Blaha modified Becke-Johnson potential has also been used to improve the underestimated band gap. The structural properties, including the lattice constants, the bulk moduli and their pressure derivatives are in very good agreement with the available experimental data and theoretical results. Several structural phase transitions were studied here to establish the stable structure and to predict the phase transition under hydrostatic pressure. The computed transition pressure (Pt) of the material of our interest from the zinc blende (B3) to the rock salt (B1) phase has been determined and found to agree well with the experimental and theoretical data. The calculated band structure shows that GaSb binary compound and the ternary alloys are direct band gap semiconductors. Optical parameters such as the dielectric constants and the refractive indices are calculated and analyzed. The thermodynamic results are also interpreted and analyzed.

  3. Statistical thermodynamics

    International Nuclear Information System (INIS)

    Lim, Gyeong Hui

    2008-03-01

    This book consists of 15 chapters, which are basic conception and meaning of statistical thermodynamics, Maxwell-Boltzmann's statistics, ensemble, thermodynamics function and fluctuation, statistical dynamics with independent particle system, ideal molecular system, chemical equilibrium and chemical reaction rate in ideal gas mixture, classical statistical thermodynamics, ideal lattice model, lattice statistics and nonideal lattice model, imperfect gas theory on liquid, theory on solution, statistical thermodynamics of interface, statistical thermodynamics of a high molecule system and quantum statistics

  4. Electronic, elastic, thermodynamic properties and structure disorder of {gamma}-AlON solid solution from ab initio calculations

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Yuezhong, E-mail: wyzphysics@163.com [Department of Physics and Key Laboratory for Radiation Physics and Technology of Ministry of Education, Sichuan University, Chengdu 610064 (China); Tianjin Jinhang Institute of Technical Physics, Tianjin 300192 (China); Lu, Tiecheng, E-mail: lutiecheng@scu.edu.cn [Department of Physics and Key Laboratory for Radiation Physics and Technology of Ministry of Education, Sichuan University, Chengdu 610064 (China); International Center for Material Physics, Chinese Academy of Sciences, Shenyang 110015 (China); Zhang, Rongshi [Tianjin Jinhang Institute of Technical Physics, Tianjin 300192 (China); Jiang, Shengli; Qi, Jianqi; Wang, Ying [Department of Physics and Key Laboratory for Radiation Physics and Technology of Ministry of Education, Sichuan University, Chengdu 610064 (China); Chen, Qingyun [Department of Physics and Key Laboratory for Radiation Physics and Technology of Ministry of Education, Sichuan University, Chengdu 610064 (China); National Defense Key Discipline Laboratory of Nuclear Waste and Environmental Safety, Southwest University of Science and Technology, Mianyang 621010 (China); Miao, Naihua [Physique Theorique des Materiaux, Universite de Liege, Sart Tilman B-4000 (Belgium); He, Duanwei [Institute of Atomic and Molecular Physics, Sichuan University, Chengdu 610064 (China)

    2013-01-25

    Highlights: Black-Right-Pointing-Pointer We reassess the chemical bonding character of {gamma}-AlON which shows strong ionicity. Black-Right-Pointing-Pointer {gamma}-AlON single-crystals exhibit highly elastic anisotropy. Black-Right-Pointing-Pointer The thermodynamic properties are investigated in a wider temperature/pressure range. Black-Right-Pointing-Pointer {gamma}-AlON is an O/N partially disordered structure. - Abstract: Spinel aluminium oxynitride ({gamma}-AlON), as a kind of transparent ceramic material expectable, is studied using the ab initio density functional method, in terms of electronic, elastic, thermodynamic properties and structure disorder. The results show that {gamma}-AlON exhibits strong ionicity, as quantitatively expressed by (Al{sub O}{sup 2.43+}){sub 15}(Al{sub T}{sup 2.41+}){sub 8}(O{sup 1.64-}){sub 27}(N{sup 2.27-}){sub 5} from our reassessment of the ionic character. We summarize and speculate that the considered oxynitride single-crystals exhibit highly elastic anisotropy. The interpretation of the thermodynamic properties of {gamma}-AlON according to quasi-harmonic Debye model confirm the available experiments and are extended to a wider temperature/pressure range. This material holds high elastic strength under extreme environments, where dB/dT absolute value is less than 0.03 GPa/K, independent of the pressure. Finally, we study the O/N structure disorder character of {gamma}-AlON solid solution by investigating nine possible crystal structures. It is found that {gamma}-AlON should be partially disordered, and in fact, the O/N ordering has a significant effect on the properties.

  5. Electronic, elastic, thermodynamic properties and structure disorder of γ-AlON solid solution from ab initio calculations

    International Nuclear Information System (INIS)

    Wang, Yuezhong; Lu, Tiecheng; Zhang, Rongshi; Jiang, Shengli; Qi, Jianqi; Wang, Ying; Chen, Qingyun; Miao, Naihua; He, Duanwei

    2013-01-01

    Highlights: ► We reassess the chemical bonding character of γ-AlON which shows strong ionicity. ► γ-AlON single-crystals exhibit highly elastic anisotropy. ► The thermodynamic properties are investigated in a wider temperature/pressure range. ► γ-AlON is an O/N partially disordered structure. - Abstract: Spinel aluminium oxynitride (γ-AlON), as a kind of transparent ceramic material expectable, is studied using the ab initio density functional method, in terms of electronic, elastic, thermodynamic properties and structure disorder. The results show that γ-AlON exhibits strong ionicity, as quantitatively expressed by (Al O 2.43+ ) 15 (Al T 2.41+ ) 8 (O 1.64- ) 27 (N 2.27- ) 5 from our reassessment of the ionic character. We summarize and speculate that the considered oxynitride single-crystals exhibit highly elastic anisotropy. The interpretation of the thermodynamic properties of γ-AlON according to quasi-harmonic Debye model confirm the available experiments and are extended to a wider temperature/pressure range. This material holds high elastic strength under extreme environments, where dB/dT absolute value is less than 0.03 GPa/K, independent of the pressure. Finally, we study the O/N structure disorder character of γ-AlON solid solution by investigating nine possible crystal structures. It is found that γ-AlON should be partially disordered, and in fact, the O/N ordering has a significant effect on the properties.

  6. Pressure effect on structural, elastic, and thermodynamic properties of tetragonal B4C4

    Directory of Open Access Journals (Sweden)

    Baobing Zheng

    2015-03-01

    Full Text Available The compressibility, elastic anisotropy, and thermodynamic properties of the recently proposed tetragonal B4C4 (t-B4C4 are investigated under high temperature and high pressure by using of first-principles calculations method. The elastic constants, bulk modulus, shear modulus, Young’s modulus, Vickers hardness, Pugh’s modulus ratio, and Poisson’s ratio for t-B4C4 under various pressures are systematically explored, the obtained results indicate that t-B4C4 is a stiffer material. The elastic anisotropies of t-B4C4 are discussed in detail under pressure from 0 GPa to 100 GPa. The thermodynamic properties of t-B4C4, such as Debye temperature, heat capacity, and thermal expansion coefficient are investigated by the quasi-harmonic Debye model.

  7. Molecular structures and thermodynamic properties of monohydrated gaseous iodine compounds: Modelling for severe accident simulation

    Science.gov (United States)

    Sudolská, Mária; Cantrel, Laurent; Budzák, Šimon; Černušák, Ivan

    2014-03-01

    Monohydrated complexes of iodine species (I, I2, HI, and HOI) have been studied by correlated ab initio calculations. The standard enthalpies of formation, Gibbs free energy and the temperature dependence of the heat capacities at constant pressure were calculated. The values obtained have been implemented in ASTEC nuclear accident simulation software to check the thermodynamic stability of hydrated iodine compounds in the reactor coolant system and in the nuclear containment building of a pressurised water reactor during a severe accident. It can be concluded that iodine complexes are thermodynamically unstable by means of positive Gibbs free energies and would be represented by trace level concentrations in severe accident conditions; thus it is well justified to only consider pure iodine species and not hydrated forms.

  8. Ab initio study of thermodynamic, electronic, magnetic, structural, and elastic properties of Ni4N allotropes

    Czech Academy of Sciences Publication Activity Database

    Hemzalová, P.; Friák, Martin; Šob, Mojmír; Ma, D.; Udyansky, A.; Raabe, D.; Neugebauer, J.

    2013-01-01

    Roč. 88, č. 17 (2013), Art. no. 174103 ISSN 1098-0121 R&D Projects: GA ČR(CZ) GAP108/12/0311; GA ČR GD106/09/H035; GA AV ČR IAA100100920 Institutional support: RVO:68081723 Keywords : nitrides * ab initio * thermodynamics * elasticity Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 3.664, year: 2013

  9. Studies on Pidotimod Enantiomers With Chiralpak-IA: Crystal Structure, Thermodynamic Parameters and Molecular Docking.

    Science.gov (United States)

    Dou, Xiaorui; Su, Xin; Wang, Yue; Chen, Yadong; Shen, Weiyang

    2015-11-01

    Pidotimod, a synthetic dipeptide, has two chiral centers with biological and immunological activity. Its enantiomers were characterized by x-ray crystallographic analysis. A chiral stationary phase (CSP) Chiralpak-IA based on amylose derivatized with tris-(3, 5-dimethylphenyl carbamate) was used to separate pidotimod enantiomers. The mobile phase was prepared in a ratio of 35:65:0.2 of methyl-tert-butyl-ether and acetonitrile trifluoroaceticacid. In addition, thermodynamics and molecular docking methods were used to explain the enantioseparation mechanism by Chiralpak-IA. Thermodynamic studies were carried out from 10 to 45 °C. In general, both retention and enantioselectivity decreased as the temperature increased. Thermodynamic parameters indicate that the interaction force between the pidotimod enantiomer (4S, 2'R) and IA CSP is stronger and their complex model is more stable. According to GOLD molecular docking simulation, Van der Waals force is the leading cause of pidotimod enantiomers separation by IA CSP. © 2015 Wiley Periodicals, Inc.

  10. Correlation between structural and thermodynamic properties of some selenium based phase-change materials

    Science.gov (United States)

    Chandel, Namrata; Mehta, Neeraj

    2018-04-01

    In this study, we prepared novel selenium rich multi-component glasses by incorporating In, Cd and Sb as foreign elements in an Sn containing Sesbnd Te system in order to study their metal-induced effects on the thermal properties of the parent ternary glass. In particular, we determined the thermodynamic parameters of Se80Te18Sn2 and Se80Te8Sn2M10 (M = Cd, In, Sb) glassy semiconductors in a non-isothermal environment using the differential scanning calorimetry. Calorimetric measurements were obtained in the glass transition regions for Se80Te18Sn2 and Se80Te8Sn2M10 (M = Cd, In, Sb) glasses to determine their thermodynamic parameters such as the specific heat, enthalpy, and entropy during glass transition. We analyzed the variation in the specific heat before and after the heat capacity jump in these alloys. The metal-induced effects of foreign elements on the thermodynamic properties of the parent glass were also investigated in terms of the influence of the elemental specific heat of the added elemental metal as well as the thermal stability and glass-forming ability of the glasses.

  11. Thermodynamic and structural signatures of water-driven methane-methane attraction in coarse-grained mW water.

    Science.gov (United States)

    Song, Bin; Molinero, Valeria

    2013-08-07

    Hydrophobic interactions are responsible for water-driven processes such as protein folding and self-assembly of biomolecules. Microscopic theories and molecular simulations have been used to study association of a pair of methanes in water, the paradigmatic example of hydrophobic attraction, and determined that entropy is the driving force for the association of the methane pair, while the enthalpy disfavors it. An open question is to which extent coarse-grained water models can still produce correct thermodynamic and structural signatures of hydrophobic interaction. In this work, we investigate the hydrophobic interaction between a methane pair in water at temperatures from 260 to 340 K through molecular dynamics simulations with the coarse-grained monatomic water model mW. We find that the coarse-grained model correctly represents the free energy of association of the methane pair, the temperature dependence of free energy, and the positive change in entropy and enthalpy upon association. We investigate the relationship between thermodynamic signatures and structural order of water through the analysis of the spatial distribution of the density, energy, and tetrahedral order parameter Qt of water. The simulations reveal an enhancement of tetrahedral order in the region between the first and second hydration shells of the methane molecules. The increase in tetrahedral order, however, is far from what would be expected for a clathrate-like or ice-like shell around the solutes. This work shows that the mW water model reproduces the key signatures of hydrophobic interaction without long ranged electrostatics or the need to be re-parameterized for different thermodynamic states. These characteristics, and its hundred-fold increase in efficiency with respect to atomistic models, make mW a promising water model for studying water-driven hydrophobic processes in more complex systems.

  12. The pressure dependence of structural, electronic, mechanical, vibrational, and thermodynamic properties of palladium-based Heusler alloys

    Energy Technology Data Exchange (ETDEWEB)

    Coban, Cansu [Balikesir Univ. (Turkey). Dept. of Physics

    2017-07-01

    The pressure dependent behaviour of the structural, electronic, mechanical, vibrational, and thermodynamic properties of Pd{sub 2}TiX (X=Ga, In) Heusler alloys was investigated by ab initio calculations. The lattice constant, the bulk modulus and its first pressure derivative, the electronic band structure and the density of states (DOS), mechanical properties such as elastic constants, anisotropy factor, Young's modulus, etc., the phonon dispersion curves and phonon DOS, entropy, heat capacity, and free energy were obtained under pressure. It was determined that the calculated lattice parameters are in good agreement with the literature, the elastic constants obey the stability criterion, and the phonon dispersion curves have no negative frequency which shows that the compounds are stable. The band structures at 0, 50, and 70 GPa showed valence instability at the L point which explains the superconductivity in Pd{sub 2}TiX (X=Ga, In).

  13. Thermodynamic and structural models compared with the initial dissolution rates of open-quotes SONclose quotes glass samples

    International Nuclear Information System (INIS)

    Tovena, I.; Advocat, T.; Ghaleb, D.; Vernaz, E.; Larche, F.

    1994-01-01

    The experimentally determined initial dissolution rate R 0 of nuclear glass was correlated with thermodynamic parameters and structural parameters. The initial corrosion rates of six open-quotes R7T7close quotes glass samples measured at 100 degrees C in a Soxhlet device were correlated with the glass free hydration energy and the glass formation enthalpy. These correlations were then tested with a group of 26 SON glasses selected for their wide diversity of compositions. The thermodynamic models provided a satisfactory approximation of the initial dissolution rate determined under Soxhlet conditions for SON glass samples that include up to 15 wt% of boron and some alumina. Conversely, these models are inaccurate if the boron concentration exceeds 15 wt% and the glass contains no alumina. Possible correlations between R 0 and structural parameters, such as the boron coordination number and the number of nonbridging oxygen atoms, were also investigated. The authors show that R 0 varies inversely with the number of 4-coordinate boron atoms; conversely, the results do not substantiate published reports of a correlation between R 0 and the number of nonbridging oxygen atoms

  14. Surface thermodynamics

    International Nuclear Information System (INIS)

    Garcia-Moliner, F.

    1975-01-01

    Basic thermodynamics of a system consisting of two bulk phases with an interface. Solid surfaces: general. Discussion of experimental data on surface tension and related concepts. Adsorption thermodynamics in the Gibbsian scheme. Adsorption on inert solid adsorbents. Systems with electrical charges: chemistry and thermodynamics of imperfect crystals. Thermodynamics of charged surfaces. Simple models of charge transfer chemisorption. Adsorption heat and related concepts. Surface phase transitions

  15. Correlation between sequence conservation and structural thermodynamics of microRNA precursors from human, mouse, and chicken genomes

    Directory of Open Access Journals (Sweden)

    Wang Shengqi

    2010-10-01

    Full Text Available Abstract Background Previous studies have shown that microRNA precursors (pre-miRNAs have considerably more stable secondary structures than other native RNAs (tRNA, rRNA, and mRNA and artificial RNA sequences. However, pre-miRNAs with ultra stable secondary structures have not been investigated. It is not known if there is a tendency in pre-miRNA sequences towards or against ultra stable structures? Furthermore, the relationship between the structural thermodynamic stability of pre-miRNA and their evolution remains unclear. Results We investigated the correlation between pre-miRNA sequence conservation and structural stability as measured by adjusted minimum folding free energies in pre-miRNAs isolated from human, mouse, and chicken. The analysis revealed that conserved and non-conserved pre-miRNA sequences had structures with similar average stabilities. However, the relatively ultra stable and unstable pre-miRNAs were more likely to be non-conserved than pre-miRNAs with moderate stability. Non-conserved pre-miRNAs had more G+C than A+U nucleotides, while conserved pre-miRNAs contained more A+U nucleotides. Notably, the U content of conserved pre-miRNAs was especially higher than that of non-conserved pre-miRNAs. Further investigations showed that conserved and non-conserved pre-miRNAs exhibited different structural element features, even though they had comparable levels of stability. Conclusions We proposed that there is a correlation between structural thermodynamic stability and sequence conservation for pre-miRNAs from human, mouse, and chicken genomes. Our analyses suggested that pre-miRNAs with relatively ultra stable or unstable structures were less favoured by natural selection than those with moderately stable structures. Comparison of nucleotide compositions between non-conserved and conserved pre-miRNAs indicated the importance of U nucleotides in the pre-miRNA evolutionary process. Several characteristic structural elements were

  16. First principle study of structural, electronic and thermodynamic behavior of ternary intermetallic compound: CeMgTl

    Directory of Open Access Journals (Sweden)

    R.P. Singh

    2014-12-01

    Full Text Available To study the structural, electronic and thermodynamic behavior of CeMgTl, full-potential linear augmented plane wave plus local orbital (FP-LAPW + lo method has been used. The lattice parameters (a0, c0, bulk modulus (B0 and its first order pressure derivative (B0′ have been calculated for CeMgTl. Band structure and density of states histograms depicts that “5d” orbital electrons of Tl have dominant character in the electronic contribution to CeMgTl. Impact of the temperature and pressure on unit cell volume, bulk modulus, Debye temperature, Grüneisen parameter, specific heat and thermal expansion coefficient (α have been studied in wide temperature range (0–300 K and pressure range (0–15 GPa.

  17. Reactive-site hydrolyzed Cucurbita maxima trypsin inhibitor-V: function, thermodynamic stability, and NMR solution structure.

    Science.gov (United States)

    Cai, M; Gong, Y; Prakash, O; Krishnamoorthi, R

    1995-09-26

    Reactive-site (Lys44-Asp45 peptide bond) hydrolyzed Cucurbita maxima trypsin inhibitor-V (CMTI-V*) was prepared and characterized: In comparison to the intact form, CMTI-V* exhibited markedly reduced inhibitory properties and binding affinities toward trypsin and human blood coagulation factor XIIa. The equilibrium constant of trypsin-catalyzed hydrolysis, Khyd, defined as [CMTI-V*]/[CMTI-V], was measured to be approximately 9.4 at 25 degrees C (delta G degrees = -1.3 kcal.mol-1). From the temperature dependence of delta G degrees, the following thermodynamic parameters were estimated: delta H degrees = 1.6 kcal.mol-1 and delta S degrees = 9.8 eu. In order to understand the functional and thermodynamic differences between the two forms, the three-dimensional solution structure of CMTI-V* was determined by a combined approach of NMR, distance geometry, and simulated annealing methods. Thus, following sequence-specific and stereospecific resonance assignments, including those of beta-, gamma-, delta-, and epsilon-hydrogens and valine methyl hydrogens, 809 interhydrogen distances and 123 dihedral angle constraints were determined, resulting in the computation and energy-minimization of 20 structures for CMTI-V*. The average root mean squared deviation in position for equivalent atoms between the 20 individual structures and the mean structure obtained by averaging their coordinates is 0.67 +/- 0.15 A for the main chain atoms and 1.19 +/- 0.23 A for all the non-hydrogen atoms of residues 5-40 and residues 48-67.(ABSTRACT TRUNCATED AT 250 WORDS)

  18. First-principles study of the structural, phonon, elastic, and thermodynamic properties of Al_3Ta compound under high pressure

    Directory of Open Access Journals (Sweden)

    W. Leini

    2018-03-01

    Full Text Available We have investigated the phonon, elastic and thermodynamic properties of L1_2 phase Al_3Ta by density functional theory approach combining with quasi-harmonic approximation model. The results of phonon band structure shows that L1_2 phase Al_3Ta possesses dynamical stability in the pressure range from 0 to 80 GPa due to the absence of imaginary frequencies. The pressure dependences of the elastic constants C_ij, bulk modulus B, shear modulus G, Young's modulus Y, B/G and Poisson's ratio ν have been analysed. The elastic constants are satisfied with mechanical stability criteria up to the external pressure of 80 GPa. The results of the elastic properties studies show that Al_3Ta compound possesses a higher hardness, improved ductility and plasticity under higher pressures. Further, we systematically investigate the thermodynamic properties, such as the Debye temperature Θ, heat capacity C_p, and thermal expansion coefficient α, and provide the relationships between thermal parameters and pressure.

  19. Theoretical investigation of the structural, electronic, and thermodynamic properties of CdS1-xSex alloys

    Science.gov (United States)

    Long, Debing; Li, Mingkai; Meng, Dongxue; Ahuja, Rajeev; He, Yunbin

    2018-03-01

    In this work, the structural, electronic, and thermodynamic properties of wurtzite (WZ) and zincblende (ZB) CdS1-xSex alloys are investigated using the density functional theory (DFT) and the cluster expansion method. A special quasirandom structure containing 16 atoms is constructed to calculate the band structures of random alloys. The band gaps of CdS1-xSex alloys are direct and decrease as the Se content increases. The delta self-consistent-field method is applied to correct band gaps that are underestimated by DFT. The band offsets clearly reflect the variation in valence band maxima and conduction band minima, thus providing information useful to the design of relevant quantum well structures. The positive formation enthalpies of both phases imply that CdS1-xSex is an immiscible system and tends to phase separate. The influence of lattice vibrations on the phase diagram is investigated by calculating the phonon density of states. Lattice vibration effects can reduce the critical temperature Tc and increase alloy solid solubilities. This influence is especially significant in the ZB structure. When only chemical interactions are present, the Tc values for WZ- and ZB-CdS1-xSex are 260 K and 249 K, respectively. The lattice vibration enthalpy and entropy lower the Tc to 255 K and 233 K, respectively.

  20. Thermodynamic Characterization of Humic Acid-surfactant Interaction: New Insights into the Characteristics and Structure of Humic Acids

    Directory of Open Access Journals (Sweden)

    Leonardus Vergütz

    2015-12-01

    Full Text Available ABSTRACT Humic acids (HA are a component of humic substances (HS, which are found in nearly all soils, sediments, and waters. They play a key role in many, if not most, chemical and physical properties in their environment. Despite the importance of HA, their high complexity makes them a poorly understood system. Therefore, understanding the physicochemical properties and interactions of HA is crucial for determining their fundamental role and obtaining structural details. Cationic surfactants are known to interact electrostatically and hydrophobically with HA. Because they are a very well-known and characterized system, they offer a good choice as molecular probes for studying HA. The objective of this study was to evaluate the interaction between cationic surfactants and HA through isothermal titration calorimetry in a thermodynamic manner, aiming to obtain information about the basic structure of HA, the nature of this interaction, and if HA from different origins show different basic structures. Contrary to what the supramolecular model asserts, HA structure is not loosely held, though it may separate depending on the conditions the HA are subjected to in their milieu. It did not show any division or conformational change when interacting with surfactants. The basic structure of the HA remains virtually the same regardless of the different sources and compositions of these HA.

  1. Use of state-dependent pair potentials in describing the structural and thermodynamic properties of noble gases

    Energy Technology Data Exchange (ETDEWEB)

    Jakse, Noel; Bretonnet, Jean-Louis [Laboratoire de Theorie de la Matiere Condensee, Universite de Metz, 1 Boulevard FD Arago, 57078 Metz Cedex 3 (France)

    2003-12-08

    Understanding the interatomic interactions in noble gases remains one of the fundamental problems not completely solved to date. From small-angle neutron scattering experiments it is well-known that three-body forces exist and cannot be neglected. On the theoretical side, semi-analytic and simulation methods have been used to reveal the nature of these many-body interactions. The purpose of the present work is to provide an overview of the different three-body contributions to the interactions and their relative importance in describing the structural and thermodynamic properties for noble gases by means of the integral equation theory and molecular dynamics simulations. We examine the relevance of the effective state-dependent pair potential in this framework, as well as the self-consistency problem that we are faced with in the integral equation theory.

  2. Thermodynamic and structural properties in complexing media; Comportement chimique du protactinium (V) en presence d'ions sulfate

    Energy Technology Data Exchange (ETDEWEB)

    Di Giandomenico, M.V

    2007-10-15

    Protactinium is experiencing a renewal of interest in the frame of long-term energy production. Modelling the behaviour of this element in the geosphere requires thermodynamic and structural data relevant to environmental conditions. Now deep clayey formation are considered for the disposal of radioactive waste and high values of natural sulphate contents have been determined in pore water in equilibrium with clay surface. Because of its tendency to polymerisation, hydrolysis and sorption on all solid supports, the equilibria constants relative to monomer species were determined at tracer scale (ca. 10 - 12 M) with {sup 233}Pa. The complexation constants of Pa(V) and sulphate ions were calculated starting from a systematic study of the apparent distribution coefficient D in the system TTA/Toluene/H{sub 2}O/Na{sub 2}SO{sub 4}/HClO{sub 4}/NaClO{sub 4} and as a function of ionic strength, temperature, free sulphate, protons and chelatant concentration. First of all, the interaction between free species H{sup +}, SO{sub 4}{sup -}, Na{sup +} leads to the formation of HSO{sub 4}{sup -} and NaSO{sub 4}{sup -}, for which concentrations depend upon the related thermodynamic constants. For this purpose a computer code was developed in order to determine all free species concentration. This iterative code takes into account the influence of temperature and ionic strength (SIT modelling) on thermodynamic constants. The direct measure of Pa(V) in the organic and aqueous phase by g-spectrometry had conducted to estimate the apparent distribution coefficient D as function of free sulphate ions. Complexation constants have been determined after a mathematical treatment of D. The extrapolation of these constants at zero ionic strength have been realized by SIT modelling at different temperatures. Besides, enthalpy and entropy values were calculated. Parallelly, the structural study of Pa(V) was performed using 231 Pa. XANES and EXAFS spectra show unambiguously the absence of the

  3. Structure, thermodynamic and electronic properties of carbon-nitrogen cubanes and protonated polynitrogen cations

    Science.gov (United States)

    Chaban, Vitaly V.; Andreeva, Nadezhda A.

    2017-12-01

    Energy generation and storage are at the center of modern civilization. Energetic materials constitute quite a large class of compounds with a high amount of stored chemical energy that can be released. We hereby use a combination of quantum chemistry methods to investigate feasibility and properties of carbon-nitrogen cubanes and multi-charged polynitrogen cations in the context of their synthesis and application as unprecedented energetic materials. We show that the stored energy increases gradually with the nitrogen content increase. Nitrogen-poor cubanes retain their stabilities in vacuum, even at elevated temperatures. Such molecules will be probably synthesized at some point. In turn, polynitrogen cations are highly unstable, except N8H+, despite they are isoelectronic to all-carbon cubane. Kinetic stability of the cation decays drastically as its total charge increases. High-level thermodynamic calculations revealed that large amounts of energy are liberated upon decompositions of polynitrogen cations, which produce molecular nitrogen, acetylene, and protons. The present results bring a substantial insights to the design of novel high-energy compounds.

  4. Importance of van der Waals interaction on structural, vibrational, and thermodynamic properties of NaCl

    Science.gov (United States)

    Marcondes, Michel L.; Wentzcovitch, Renata M.; Assali, Lucy V. C.

    2018-05-01

    Thermal equations of state (EOS) are essential in several scientific domains. However, experimental determination of EOS parameters may be limited at extreme conditions, therefore, ab initio calculations have become an important method to obtain them. Density functional theory (DFT) and its extensions with various degrees of approximations for the exchange and correlation (XC) energy is the method of choice, but large errors in the EOS parameters are still common. The alkali halides have been problematic from the onset of this field and the quest for appropriate DFT functionals for such ionic and relatively weakly bonded systems has remained an active topic of research. Here we use DFT + van der Waals functionals to calculate vibrational properties, thermal EOS, thermodynamic properties, and the B1 to B2 phase boundary of NaCl with high precision. Our results reveal a remarkable improvement over the performance of standard local density approximation and generalized gradient approximation functionals for all these properties and phase transition boundary, as well as great sensitivity of anharmonic effects on the choice of XC functional.

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

    Science.gov (United States)

    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.

  6. Theoretical simulations of the structural stabilities, elastic, thermodynamic and electronic properties of Pt3Sc and Pt3Y compounds

    Science.gov (United States)

    Boulechfar, R.; Khenioui, Y.; Drablia, S.; Meradji, H.; Abu-Jafar, M.; Omran, S. Bin; Khenata, R.; Ghemid, S.

    2018-05-01

    Ab-initio calculations based on density functional theory have been performed to study the structural, electronic, thermodynamic and mechanical properties of intermetallic compounds Pt3Sc and Pt3Y using the full-potential linearized augmented plane wave(FP-LAPW) method. The total energy calculations performed for L12, D022 and D024 structures confirm the experimental phase stability. Using the generalized gradient approximation (GGA), the values of enthalpies formation are -1.23 eV/atom and -1.18 eV/atom for Pt3Sc and Pt3Y, respectively. The densities of states (DOS) spectra show the existence of a pseudo-gap at the Fermi level for both compounds which indicate the strong spd hybridization and directing covalent bonding. Furthermore, the density of states at the Fermi level N(EF), the electronic specific heat coefficient (γele) and the number of bonding electrons per atom are predicted in addition to the elastic constants (C11, C12 and C44). The shear modulus (GH), Young's modulus (E), Poisson's ratio (ν), anisotropy factor (A), ratio of B/GH and Cauchy pressure (C12-C44) are also estimated. These parameters show that the Pt3Sc and Pt3Y are ductile compounds. The thermodynamic properties were calculated using the quasi-harmonic Debye model to account for their lattice vibrations. In addition, the influence of the temperature and pressure was analyzed on the heat capacities (Cp and Cv), thermal expansion coefficient (α), Debye temperature (θD) and Grüneisen parameter (γ).

  7. Phase structures of the black Dp-D(p+4)-brane system in various ensembles II: electrical and thermodynamic stability

    International Nuclear Information System (INIS)

    Xiao, Zhiguang; Zhou, Da

    2015-01-01

    By incorporating the electrical stability condition into the discussion, we continue the study on the thermodynamic phase structures of the Dp-D(p+4) black brane in GG, GC, CG, CC ensembles defined in our previous paper http://dx.doi.org/10.1007/JHEP07(2015)134. We find that including the electrical stability conditions in addition to the thermal stability conditions does not modify the phase structure of the GG ensemble but puts more constraints on the parameter space where black branes can stably exist in GC, CG, CC ensembles. In particular, the van der Waals-like phase structure which was supposed to be present in these ensembles when only thermal stability condition is considered would no longer be visible, since the phase of the small black brane is unstable under electrical fluctuations. However, the symmetry of the phase structure by interchanging the two kinds of brane charges and potentials is still preserved, which is argued to be the result of T-duality.

  8. Generalization of Gibbs Entropy and Thermodynamic Relation

    OpenAIRE

    Park, Jun Chul

    2010-01-01

    In this paper, we extend Gibbs's approach of quasi-equilibrium thermodynamic processes, and calculate the microscopic expression of entropy for general non-equilibrium thermodynamic processes. Also, we analyze the formal structure of thermodynamic relation in non-equilibrium thermodynamic processes.

  9. Electronic structure, thermodynamic properties and hydrogenation of LaPtIn and CePtIn compounds by ab-initio methods

    International Nuclear Information System (INIS)

    Jezierski, Andrzej; Szytuła, Andrzej

    2016-01-01

    The electronic structures and thermodynamic properties of LaPtIn and CePtIn are studied by means of ab-initio full-relativistic full-potential local orbital basis (FPLO) method within densities functional (DFT) methodologies. We have also examined the influence of hydrogen on the electronic structure and stability of CePtInH and LaPtInH systems. The positions of the hydrogen atoms have been found from the minimum of the total energy. Our calculations have shown that band structure and topology of the Fermi surfaces changed significantly during the hydrogenation. The thermodynamic properties (bulk modulus, Debye temperatures, constant pressure heat capacity) calculated in quasi-harmonic Debye-Grüneisen model are in a good agreement with the experimental data. We have applied different methods of the calculation of the equation of states (EOS) (Murnaghan, Birch-Murnaghan, Poirier–Tarantola, Vinet). The thermodynamic properties are presented for the pressure 0< P<9 GPa and the temperature range 0< T<300 K. - Highlights: • Full relativistic band structure of LaPtIn and CePtIn. • Fermi surface of LaPtIn, LaPtInH, CePtIn, CePtInH. • Effect of hydrogenation on the electronic structure of LaPtIn and CePtIn. • Thermodynamic properties in the quasi-harmonic Debye-Grüneisen model.

  10. Self-assembled materials and supramolecular chemistry within microfluidic environments: from common thermodynamic states to non-equilibrium structures.

    Science.gov (United States)

    Sevim, S; Sorrenti, A; Franco, C; Furukawa, S; Pané, S; deMello, A J; Puigmartí-Luis, J

    2018-05-01

    Self-assembly is a crucial component in the bottom-up fabrication of hierarchical supramolecular structures and advanced functional materials. Control has traditionally relied on the use of encoded building blocks bearing suitable moieties for recognition and interaction, with targeting of the thermodynamic equilibrium state. On the other hand, nature leverages the control of reaction-diffusion processes to create hierarchically organized materials with surprisingly complex biological functions. Indeed, under non-equilibrium conditions (kinetic control), the spatio-temporal command of chemical gradients and reactant mixing during self-assembly (the creation of non-uniform chemical environments for example) can strongly affect the outcome of the self-assembly process. This directly enables a precise control over material properties and functions. In this tutorial review, we show how the unique physical conditions offered by microfluidic technologies can be advantageously used to control the self-assembly of materials and of supramolecular aggregates in solution, making possible the isolation of intermediate states and unprecedented non-equilibrium structures, as well as the emergence of novel functions. Selected examples from the literature will be used to confirm that microfluidic devices are an invaluable toolbox technology for unveiling, understanding and steering self-assembly pathways to desired structures, properties and functions, as well as advanced processing tools for device fabrication and integration.

  11. Thermodynamic properties of nonstoichiometric H-Nb2 Osub(5-x) derived from a statistical model of its defect structure

    International Nuclear Information System (INIS)

    Schilling, O.F.

    1986-01-01

    A statistical method for the treatment of the defect structure of oxides is applied to H-Nb 2 Osub(5-x) and its thermodynamic properties are derived as a function of x and temperature. The results based on a model of Nb O 3 vacancy clusters located at the tetrahedral columns of the structure presented very good agreement with experimental data in the literature [2]. Further, the predicted arrangement of the clusters of vacancies along the columns at the limiting composition of the H-Nb 2 O 5 phase indicates, according to recent electron microscopy experiments [18, 19], that the initial step of the transformation is the collapse of the structure around rows of defective sites along the columns, involving Andersson and Wadsley's [20] cooperative migration of atoms. The limiting compositions of the H-Nb 2 O 5 and Nb 53 O 132 phases are also correctly predicted on the basis of electrostatic interactions among defect units only. Thus elastic interactions among planar defects appear to affect only the arrangement of such defects, and not the compositions of the initial and final compounds. (author)

  12. Effect of spin-orbit interactions on the structural stability, thermodynamic properties, and transport properties of lead under pressure

    Science.gov (United States)

    Smirnov, N. A.

    2018-03-01

    The paper investigates the role of spin-orbit interaction in the prediction of structural stability, lattice dynamics, elasticity, thermodynamic and transport properties (electrical resistivity and thermal conductivity) of lead under pressure with the FP-LMTO (full-potential linear-muffin-tin orbital) method for the first-principles band structure calculations. Our calculations were carried out for three polymorphous lead modifications (fcc, hcp, and bcc) in generalized gradient approximation with the exchange-correlation functional PBEsol. They suggest that compared to the scalar-relativistic calculation, the account for the SO effects insignificantly influences the compressibility of Pb. At the same time, in the calculation of phonon spectra and transport properties, the role of SO interaction is important, at least, for P ≲150 GPa. At higher pressures, the contribution from SO interaction reduces but not vanishes. As for the relative structural stability, our studies show that SO effects influence weakly the pressure of the fcc →hcp transition and much higher the pressure of the hcp →bcc transition.

  13. Intrinsic Thermodynamics and Structures of 2,4- and 3,4-Substituted Fluorinated Benzenesulfonamides Binding to Carbonic Anhydrases.

    Science.gov (United States)

    Zubrienė, Asta; Smirnov, Alexey; Dudutienė, Virginija; Timm, David D; Matulienė, Jurgita; Michailovienė, Vilma; Zakšauskas, Audrius; Manakova, Elena; Gražulis, Saulius; Matulis, Daumantas

    2017-01-20

    The goal of rational drug design is to understand structure-thermodynamics correlations in order to predict the chemical structure of a drug that would exhibit excellent affinity and selectivity for a target protein. In this study we explored the contribution of added functionalities of benzenesulfonamide inhibitors to the intrinsic binding affinity, enthalpy, and entropy for recombinant human carbonic anhydrases (CA) CA I, CA II, CA VII, CA IX, CA XII, and CA XIII. The binding enthalpies of compounds possessing similar chemical structures and affinities were found to be very different, spanning a range from -90 to +10 kJ mol -1 , and are compensated by a similar opposing entropy contribution. The intrinsic parameters of binding were determined by subtracting the linked protonation reactions. The sulfonamide group pK a values of the compounds were measured spectrophotometrically, and the protonation enthalpies were measured by isothermal titration calorimetry (ITC). Herein we describe the development of meta- or ortho-substituted fluorinated benzenesulfonamides toward the highly potent compound 10 h, which exhibits an observed dissociation constant value of 43 pm and an intrinsic dissociation constant value of 1.1 pm toward CA IX, an anticancer target that is highly overexpressed in various tumors. Fluorescence thermal shift assays, ITC, and X-ray crystallography were all applied in this work. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  14. Structure and thermodynamic properties of molten rare earth-alkali chloride mixtures

    International Nuclear Information System (INIS)

    Okamoto, Y.; Ogawa, T.

    1999-01-01

    The dependence of the enthalpy of mixing on the structure of molten rare earth-alkali chloride mixtures has been investigated by molecular dynamics simulation. The experimental enthalpy of the mixing with its negative and its dependence on the cation size was qualitatively reproduced. It became clear that the enthalpy of mixing depends on the structural features of short and medium range. (orig.)

  15. Denatured states of yeast cytochrome c induced by heat and guanidinium chloride are structurally and thermodynamically different.

    Science.gov (United States)

    Zaidi, Sobia; Haque, Md Anzarul; Ubaid-Ullah, Shah; Prakash, Amresh; Hassan, Md Imtaiyaz; Islam, Asimul; Batra, Janendra K; Ahmad, Faizan

    2017-05-01

    A sequence alignment of mammalian cytochromes c with yeast iso-1-cytochrome c (y-cyt-c) shows that the yeast protein contains five extra N-terminal residues. We have been interested in understanding the question: What is the role of these five extra N-terminal residues in folding and stability of the protein? To answer this question we have prepared five deletants of y-cyt-c by sequentially removing these extra residues. During our studies on the wild type (WT) protein and its deletants, we observed that the amount of secondary structure in the guanidinium chloride (GdmCl)-induced denatured (D) state of each protein is different from that of the heat-induced denatured (H) state. This finding is confirmed by the observation of an additional cooperative transition curve of optical properties between H and D states on the addition of different concentrations of GdmCl to the already heat denatured WT y-cyt-c and its deletants at pH 6.0 and 68°C. For each protein, analysis of transition curves representing processes, native (N) state ↔ D state, N state ↔ H state, and H state ↔ D state, was done to obtain Gibbs free energy changes associated with all the three processes. This analysis showed that, for each protein, thermodynamic cycle accommodates Gibbs free energies associated with transitions between N and D states, N and H states, and H and D states, the characteristics required for a thermodynamic function. All these experimental observations have been supported by our molecular dynamics simulation studies.

  16. General thermodynamics

    CERN Document Server

    Olander, Donald

    2007-01-01

    The book’s methodology is unified, concise, and multidisciplinary, allowing students to understand how the principles of thermodynamics apply to all technical fields that touch upon this most fundamental of scientific theories. It also offers a rigorous approach to the quantitative aspects of thermodynamics, accompanied by clear explanations to help students transition smoothly from the physical concepts to their mathematical representations

  17. Structural, electronic, elastic, and thermodynamic properties of CaSi, Ca2Si, and CaSi2 phases from first-principles calculations

    Science.gov (United States)

    Li, X. D.; Li, K.; Wei, C. H.; Han, W. D.; Zhou, N. G.

    2018-06-01

    The structural, electronic, elastic, and thermodynamic properties of CaSi, Ca2Si, and CaSi2 are systematically investigated by using first-principles calculations method based on density functional theory (DFT). The calculated formation enthalpies and cohesive energies show that CaSi2 possesses the greatest structural stability and CaSi has the strongest alloying ability. The structural stability of the three phases is compared according to electronic structures. Further analysis on electronic structures indicates that the bonding of these phases exhibits the combinations of metallic, covalent, and ionic bonds. The elastic constants are calculated, and the bulk modulus, shear modulus, Young's modulus, Poisson's ratio, and anisotropy factor of polycrystalline materials are deduced. Additionally, the thermodynamic properties were theoretically predicted and discussed.

  18. Microemulsions and Aggregation Formation in Extraction Processes for Used Nuclear Fuel: Thermodynamic and Structural Studies

    Energy Technology Data Exchange (ETDEWEB)

    Nilsson, Mikael [Univ. of California, Irvine, CA (United States)

    2016-05-04

    Advanced nuclear fuel cycles rely on successful chemical separation of various elements in the used fuel. Numerous solvent extraction (SX) processes have been developed for the recovery and purification of metal ions from this used material. However, the predictability of process operations has been challenged by the lack of a fundamental understanding of the chemical interactions in several of these separation systems. For example, gaps in the thermodynamic description of the mechanism and the complexes formed will make predictions very challenging. Recent studies of certain extraction systems under development and a number of more established SX processes have suggested that aggregate formation in the organic phase results in a transformation of its selectivity and efficiency. Aggregation phenomena have consistently been interfering in SX process development, and have, over the years, become synonymous with an undesirable effect that must be prevented. This multiyear, multicollaborative research effort was carried out to study solvation and self-organization in non-aqueous solutions at conditions promoting aggregation phenomena. Our approach to this challenging topic was to investigate extraction systems comprising more than one extraction reagent where synergy of the metal ion could be observed. These systems were probed for the existence of stable microemulsions in the organic phase, and a number of high-end characterization tools were employed to elucidate the role of the aggregates in metal ion extraction. The ultimate goal was to find connections between synergy of metal ion extraction and reverse micellar formation. Our main accomplishment for this project was the expansion of the understanding of metal ion complexation in the extraction system combining tributyl phosphate (TBP) and dibutyl phosphoric acid (HDBP). We have found that for this system no direct correlation exists for the metal ion extraction and the formation of aggregates, meaning that the

  19. Microemulsions and Aggregation Formation in Extraction Processes for Used Nuclear Fuel: Thermodynamic and Structural Studies

    International Nuclear Information System (INIS)

    Nilsson, Mikael

    2016-01-01

    Advanced nuclear fuel cycles rely on successful chemical separation of various elements in the used fuel. Numerous solvent extraction (SX) processes have been developed for the recovery and purification of metal ions from this used material. However, the predictability of process operations has been challenged by the lack of a fundamental understanding of the chemical interactions in several of these separation systems. For example, gaps in the thermodynamic description of the mechanism and the complexes formed will make predictions very challenging. Recent studies of certain extraction systems under development and a number of more established SX processes have suggested that aggregate formation in the organic phase results in a transformation of its selectivity and efficiency. Aggregation phenomena have consistently been interfering in SX process development, and have, over the years, become synonymous with an undesirable effect that must be prevented. This multiyear, multicollaborative research effort was carried out to study solvation and self-organization in non-aqueous solutions at conditions promoting aggregation phenomena. Our approach to this challenging topic was to investigate extraction systems comprising more than one extraction reagent where synergy of the metal ion could be observed. These systems were probed for the existence of stable microemulsions in the organic phase, and a number of high-end characterization tools were employed to elucidate the role of the aggregates in metal ion extraction. The ultimate goal was to find connections between synergy of metal ion extraction and reverse micellar formation. Our main accomplishment for this project was the expansion of the understanding of metal ion complexation in the extraction system combining tributyl phosphate (TBP) and dibutyl phosphoric acid (HDBP). We have found that for this system no direct correlation exists for the metal ion extraction and the formation of aggregates, meaning that the

  20. Correlation of RNA secondary structure statistics with thermodynamic stability and applications to folding.

    Science.gov (United States)

    Wu, Johnny C; Gardner, David P; Ozer, Stuart; Gutell, Robin R; Ren, Pengyu

    2009-08-28

    The accurate prediction of the secondary and tertiary structure of an RNA with different folding algorithms is dependent on several factors, including the energy functions. However, an RNA higher-order structure cannot be predicted accurately from its sequence based on a limited set of energy parameters. The inter- and intramolecular forces between this RNA and other small molecules and macromolecules, in addition to other factors in the cell such as pH, ionic strength, and temperature, influence the complex dynamics associated with transition of a single stranded RNA to its secondary and tertiary structure. Since all of the factors that affect the formation of an RNAs 3D structure cannot be determined experimentally, statistically derived potential energy has been used in the prediction of protein structure. In the current work, we evaluate the statistical free energy of various secondary structure motifs, including base-pair stacks, hairpin loops, and internal loops, using their statistical frequency obtained from the comparative analysis of more than 50,000 RNA sequences stored in the RNA Comparative Analysis Database (rCAD) at the Comparative RNA Web (CRW) Site. Statistical energy was computed from the structural statistics for several datasets. While the statistical energy for a base-pair stack correlates with experimentally derived free energy values, suggesting a Boltzmann-like distribution, variation is observed between different molecules and their location on the phylogenetic tree of life. Our statistical energy values calculated for several structural elements were utilized in the Mfold RNA-folding algorithm. The combined statistical energy values for base-pair stacks, hairpins and internal loop flanks result in a significant improvement in the accuracy of secondary structure prediction; the hairpin flanks contribute the most.

  1. Thermodynamic properties of Al-Mn, Al-Cu, and Al-Fe-Cu melts and their relations to liquid and quasicrystal structure

    International Nuclear Information System (INIS)

    Zaitsev, A I; Zaitseva, N E; Shimko, R Yu; Arutyunyan, N A; Dunaev, S F; Kraposhin, V S; Lam, Ha Thanh

    2008-01-01

    Thermodynamic properties of molten Al-Mn, Al-Cu and Al-Fe-Cu alloys in a wide temperature range of 1123-1878 K and the whole range of concentrations have been studied using the integral effusion method and Knudsen mass spectrometry. Thermodynamic functions of melts were described by the associated solution model. The possibility of icosahedral quasicrystal (i-QC) precipitation from liquid Al-Mn and Al-Cu-Fe alloys was found to be a consequence of the existence in liquid associates (clusters). A geometric model is suggested for the structure of associates in liquid

  2. Structural study and thermodynamic characterization of inhibitor binding to lumazine synthase from Bacillus anthracis

    Energy Technology Data Exchange (ETDEWEB)

    Morgunova, Ekaterina [Karolinska Institutet NOVUM, Center of Structural Biochemistry, Hälsovägen 7-9, 141 57 Huddinge (Sweden); Illarionov, Boris; Saller, Sabine [Institut für Lebensmittelchemie, Universität Hamburg, Grindelallee 117, 20146 Hamburg (Germany); Popov, Aleksander [European Synchrotron Radiation Facility, BP 220, F-38043 Grenoble CEDEX 09 (France); Sambaiah, Thota [Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University (United States); Bacher, Adelbert [Chemistry Department, Technical University of Munich, 85747 Garching (Germany); Cushman, Mark [Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University (United States); Fischer, Markus [Institut für Lebensmittelchemie, Universität Hamburg, Grindelallee 117, 20146 Hamburg (Germany); Ladenstein, Rudolf, E-mail: rudolf.ladenstein@ki.se [Karolinska Institutet NOVUM, Center of Structural Biochemistry, Hälsovägen 7-9, 141 57 Huddinge (Sweden)

    2010-09-01

    Crystallographic studies of lumazine synthase, the penultimate enzyme of the riboflavin-biosynthetic pathway in B. anthracis, provide a structural framework for the design of antibiotic inhibitors, together with calorimetric and kinetic investigations of inhibitor binding. The crystal structure of lumazine synthase from Bacillus anthracis was solved by molecular replacement and refined to R{sub cryst} = 23.7% (R{sub free} = 28.4%) at a resolution of 3.5 Å. The structure reveals the icosahedral symmetry of the enzyme and specific features of the active site that are unique in comparison with previously determined orthologues. The application of isothermal titration calorimetry in combination with enzyme kinetics showed that three designed pyrimidine derivatives bind to lumazine synthase with micromolar dissociation constants and competitively inhibit the catalytic reaction. Structure-based modelling suggested the binding modes of the inhibitors in the active site and allowed an estimation of the possible contacts formed upon binding. The results provide a structural framework for the design of antibiotics active against B. anthracis.

  3. Applicability of special quasi-random structure models in thermodynamic calculations using semi-empirical Debye–Grüneisen theory

    International Nuclear Information System (INIS)

    Kim, Jiwoong

    2015-01-01

    In theoretical calculations, expressing the random distribution of atoms in a certain crystal structure is still challenging. The special quasi-random structure (SQS) model is effective for depicting such random distributions. The SQS model has not been applied to semi-empirical thermodynamic calculations; however, Debye–Grüneisen theory (DGT), a semi-empirical method, was used here for that purpose. The model reliability was obtained by comparing supercell models of various sizes. The results for chemical bonds, pair correlation, and elastic properties demonstrated the reliability of the SQS models. Thermodynamic calculations using density functional perturbation theory (DFPT) and DGT assessed the applicability of the SQS models. DGT and DFPT led to similar variations of the mixing and formation energies. This study provides guidelines for theoretical assessments to obtain the reliable SQS models and to calculate the thermodynamic properties of numerous materials with a random atomic distribution. - Highlights: • Various material properties are used to examine reliability of special quasi-random structures. • SQS models are applied to thermodynamic calculations by semi-empirical methods. • Basic calculation guidelines for materials with random atomic distribution are given.

  4. First-principles prediction of structural, elastic, electronic and thermodynamic properties of the cubic SrUO{sub 3}-Perovskite

    Energy Technology Data Exchange (ETDEWEB)

    Sahli, B. [Laboratoire de Génie Physique, Université Ibn Khaldoun, Tiaret, 14000 (Algeria); Laboratoire des Matériaux Magnétiques, Université Djillali Liabés, Sidi Bel-Abbes 22000 (Algeria); Bouafia, H., E-mail: hamza.tssm@gmail.com [Laboratoire de Génie Physique, Université Ibn Khaldoun, Tiaret, 14000 (Algeria); Abidri, B.; Abdellaoui, A. [Laboratoire des Matériaux Magnétiques, Université Djillali Liabés, Sidi Bel-Abbes 22000 (Algeria); Hiadsi, S.; Akriche, A. [Laboratoire de Microscope Electronique et Sciences des Matériaux, Université des Sciences et de la Technologie Mohamed Boudiaf, département de Génie Physique, BP1505 El m’naouar, Oran (Algeria); Benkhettou, N.; Rached, D. [Laboratoire des Matériaux Magnétiques, Université Djillali Liabés, Sidi Bel-Abbes 22000 (Algeria)

    2015-06-25

    Highlights: • The ground state properties of SrUO{sub 3}-Perovskite were investigated. • Elastic constants and their related parameters were calculated. • Electronic properties are treated using GGA-PBEsol + U approach. - Abstract: In this paper, we investigate bulk properties of the cubic SrUO{sub 3}-Perovskite in their nonmagnetic (NM), antiferromagnetic (AFM) and ferromagnetic (FM) states using all-electron self consistent Full Potential Augmented Plane Waves plus local orbital (FP-(L)APW + lo) method within PBEsol Generalized Gradiant density approximations. Our calculation allowed us to predict that the more stable magnetic state of the cubic SrUO{sub 3}-Perovskite is that of the ferromagnetic (FM). This work is the first prediction of elastic constants and their related parameters (Young modulus, shear modulus, Poisson ratio, Zener anisotropy and the Debye temperature) for this cubic compound using Mehl method. We have employed the GGA(PBEsol) and GGA(PBEsol) + U to investigate the electronic band structure, density of states and electronic charge density of SrUO{sub 3}-Perovskite. The electronic band structure calculations revealed that SrUO{sub 3} exhibits metallic behavior. On the other hand the charge density plots for [1 1 0] direction indicates a strong ionic character along the Sr–O bond while the U–O bond has strong covalent character. Finally, we have analyzed the thermodynamic properties using the quasi-harmonic Debye model to complete the fundamental characterization of cubic SrUO{sub 3}-Perovskite.

  5. A thermodynamical and structural study on the complexation of trivalent lanthanides with a polycarboxylate based concrete superplasticizer.

    Science.gov (United States)

    Fröhlich, Daniel R; Maiwald, Martin M; Taube, Franziska; Plank, Johann; Panak, Petra J

    2017-03-21

    The complexation of trivalent lanthanides with a commercial polycarboxylate based concrete superplasticizer (Glenium® 51) is investigated using different spectroscopic techniques. Time-resolved laser fluorescence spectroscopy (TRLFS) in combination with a charge neutralization model is used to determine temperature dependent conditional stability constants (log β'(T)) for the complexation of Eu(iii) with Glenium® 51 in 0.1 mol kg -1 NaCl solution in the temperature range of 20-90 °C. Only one complex species is observed, and log β'(T) (given in kg per mol eq) shows a very slight increase with temperature from 7.5 to 7.9. The related conditional molar reaction enthalpy (Δ r H' m ) and entropy (Δ r S' m ) obtained using the Van't Hoff equation show that the complexation reaction is slightly endothermic and entropy driven. The thermodynamic investigations are complemented by structural data for complexes formed with Gd(iii) or Tb(iii) and Glenium® 51 using extended X-ray absorption fine structure (EXAFS) spectroscopy. The results imply a non-chelate coordination of the trivalent metals through approximately three carboxylic functions of the polycarboxylate comb polymer which are attached predominantly in a bidentate fashion to the lanthanide under the given experimental conditions.

  6. Effect of conditioners upon the thermodynamics and kinetics of methane hydrate formation. A preliminary structure-properties relationship study

    Energy Technology Data Exchange (ETDEWEB)

    Di Profio, Pietro; Arca, Simone; Germani, Raimondo; Savelli, Gianfranco

    2005-07-01

    The synthesis and stability of gas hydrates was found to be heavily affected by the presence of small quantities of additives, or conditioners, particularly surfactants. In a recent work, we showed that the enhancement of hydrate formation, both from previously described and newly synthesized surfactants, is probably due to surfactant monomers, rather than micelles, and that the features of hydrate induction time should not be used as a measure of critical micelle concentration. In the present paper, we discuss the results of a structure-properties relationship study in which a preliminary attempt to relate the structural features of several amphiphilic additives to some kinetic and thermodynamic parameters of methane hydrate formation - e.g., induction times, rate of formation, occupancy, etc. - is conducted. According to the present study, it is found that, for a particular conditioner, a reduction of induction time does not correlate to an increase of the formation rate and occupancy, and vice versa. This may be related to the nature of chemical moieties forming a particular amphiphile (e.g., the hydrophobic tail, head group, counterion, etc.). The understanding of the mechanisms by which those moieties play their differential role may be the key tool to the design and synthesis of tailored conditioners. (Author)

  7. Interaction between bradykinin potentiating nonapeptide (BPP9a) and {beta}-cyclodextrin: A structural and thermodynamic study

    Energy Technology Data Exchange (ETDEWEB)

    Lula, Ivana; De Sousa, Frederico B. [Departamento de Quimica, Instituto de Ciencias Exatas, Universidade Federal de Minas Gerais, Av. Antonio Carlos, 6627, 31270-901, Belo Horizonte, MG (Brazil); Denadai, Angelo M.L. [Centro Federal de Educacao Tecnologica de Minas Gerais, CEFET-MG, Campus VII, 35.183-006, Timoteo, MG (Brazil); Ferreira de Lima, Guilherme; Duarte, Helio Anderson [Departamento de Quimica, Instituto de Ciencias Exatas, Universidade Federal de Minas Gerais, Av. Antonio Carlos, 6627, 31270-901, Belo Horizonte, MG (Brazil); Mares Guia, Thiago R. dos [Departamento de Bioquimica e Imunologia, ICB, Universidade Federal de Minas Gerais, 31270-901, Belo Horizonte, MG (Brazil); Faljoni-Alario, Adelaide [Departamento de Bioquimica, Instituto de Quimica, Universidade de Sao Paulo, 05508-900, Sao Paulo, SP (Brazil); Santoro, Marcelo M. [Departamento de Bioquimica e Imunologia, ICB, Universidade Federal de Minas Gerais, 31270-901, Belo Horizonte, MG (Brazil); Camargo, Antonio C.M. de [Center for Applied Toxinology CAT-CEPID, Laboratorio Especial de Toxicologia Aplicada, Instituto Butantan, 05503-900, Sao Paulo, SP (Brazil); Santos, Robson A.S. dos [Departamento de Fisiologia e Biofisica, ICB, Universidade Federal de Minas Gerais, 31270-901, Belo Horizonte, MG (Brazil); and others

    2012-02-01

    Herein, we demonstrate the physical and chemical characterizations of the supramolecular complex formed between {beta}-cyclodextrin ({beta}CD) and bradykinin potentiating nonapeptide (BPP9a), an endogenous toxin found in Bothrops jararaca. Circular dichroism results indicate a conformational change in the BPP9a secondary structure upon its complexation with {beta}CD. Nuclear magnetic resonance results, mainly from NOESY experiments, and theoretical calculations showed a favorable interaction between the tryptophan residue of BPP9a and the {beta}CD cavity. Thermodynamic inclusion parameters were investigated by isothermal titration calorimetry, demonstrating that {beta}CD/BPP9a complex formation is an exothermic process that results in a reduction in entropy. Additionally, in vitro degradation study of BPP9a against trypsin (37 Degree-Sign C, pH 7.2) showed higher stability of peptide in presence of {beta}CD. This {beta}CD/BPP9a complex, which presents new chemical properties arising from the peptide inclusion process, may be useful as an antihypertensive drug in oral pharmaceutical formulations. Highlights: Black-Right-Pointing-Pointer Cd and NMR showed evidences for the existence of more than one structure in solution. Black-Right-Pointing-Pointer Complexation with {beta}CD reduces the conformational rigidity of the peptide. Black-Right-Pointing-Pointer {beta}CD cavity recognize Trp and/or Pro segments of BPP9a. Black-Right-Pointing-Pointer Interactions involving disaggregation of BPP9a assemblies and binding with {beta}CD.

  8. Modeling of structural and thermodynamics properties of sigma-phase for the Fe-Cr system

    Directory of Open Access Journals (Sweden)

    Udovskya A.

    2012-01-01

    Full Text Available The three- sub-lattice model (3SLM for description of atom’s distribution of two components with different coordination numbers (12, 14 and 15, into s-phase structure depended on composition and temperature is depictured in this paper. Energetic parameters of 3SLM were calculated by fitting procedure fixed to results obtained by ab-initio calculations conducted for paramagnetic states of differently ordered complexes stayed at the sigma-phase’s crystal structure for Fe-Cr system at 0 K. Respective algorithm and computer program have allowed to calculate an atom distribution of components upon the sub-lattices of s-phase at 300 - 1100 K. There is satisfactory agreement between calculated results and the experimental data obtained by neutron and structural research methods. Obtained results demonstrate satisfactory agreement between calculated and experimental data of BCC solutions and sigma - phase of the Fe-Cr system stayed at an equilibrium state.

  9. Thermodynamic and real-space structural evidence of a 2D critical point in phospholipid monolayers

    DEFF Research Database (Denmark)

    Nielsen, Lars K.; Bjørnholm, Thomas; Mouritsen, Ole G.

    2007-01-01

    The two-dimensional phase diagram of phospholipid monolayers at air-water interfaces has been constructed from Langmuir compression isotherms. The coexistence region between the solid and fluid phases of the monolayer ends at the critical temperature of the transition. The small-scale lateral...... structure of the monolayers has been imaged by atomic force microscopy in the nm to mu m range at distinct points in the phase diagram. The lateral structure is immobilized by transferring the monolayer from an air-water interface to a solid mica support using Langmuir-Blodgett techniques. A transfer...

  10. Steric structure and thermodynamic aspects of Dy3+ complexes with aminobenzoic acids in aqueous solutions

    International Nuclear Information System (INIS)

    Kondrashina, Yu.G.; Mustafina, A.R.; Vul'fson, S.G.

    1994-01-01

    Stability and structure of dysprosium(3) aminobenzoate complexes with molar ratios Dy:L 1:1 and 1:2 (HL-aminobenzoic acid) in aqueous solutions are determined on the basis of pH-metric and paramagnetic birefringence data. The increase of conjugation effect in the series of benzoic, meta- ortho-, and para-aminobenzoic acid results in the increase of stability of 1:1 and 1:2 complexes. Features of the structure and coordination of ligands in dysprosium complexes with meta-, ortho-, and para-aminobenzoic acid are considered. 11 refs.; 4 figs.; 2 tabs

  11. Seismic and Thermal Structure of the Arctic Lithosphere, From Waveform Tomography and Thermodynamic Modelling

    Science.gov (United States)

    Lebedev, S.; Schaeffer, A. J.; Fullea, J.; Pease, V.

    2015-12-01

    Thermal structure of the lithosphere is reflected in the values of seismic velocities within it. Our new tomographic models of the crust and upper mantle of the Arctic are constrained by an unprecedentedly large global waveform dataset and provide substantially improved resolution, compared to previous models. The new tomography reveals lateral variations in the temperature and thickness of the lithosphere and defines deep boundaries between tectonic blocks with different lithospheric properties and age. The shape and evolution of the geotherm beneath a tectonic unit depends on both crustal and mantle-lithosphere structure beneath it: the lithospheric thickness and its changes with time (these determine the supply of heat from the deep Earth), the crustal thickness and heat production (the supply of heat from within the crust), and the thickness and thermal conductivity of the sedimentary cover (the insulation). Detailed thermal structure of the basins can be modelled by combining seismic velocities from tomography with data on the crustal structure and heat production, in the framework of computational petrological modelling. The most prominent lateral contrasts across the Arctic are between the cold, thick lithospheres of the cratons (in North America, Greenland and Eurasia) and the warmer, non-cratonic blocks. The lithosphere of the Canada Basin is cold and thick, similar to old oceanic lithosphere elsewhere around the world; its thermal structure offers evidence on its lithospheric age and formation mechanism. At 150-250 km depth, the central Arctic region shows a moderate low-velocity anomaly, cooler than that beneath Iceland and N Atlantic. An extension of N Atlantic low-velocity anomaly into the Arctic through the Fram Strait may indicate an influx of N Atlantic asthenosphere under the currently opening Eurasia Basin.

  12. Structural, electronic, optical and thermodynamic properties of cubic REGa{sub 3} (RE = Sc or Lu) compounds: Ab initio study

    Energy Technology Data Exchange (ETDEWEB)

    Murtaza, G., E-mail: murtaza@icp.edu.pk [Materials Modeling Laboratory, Department of Physics, Islamia College Peshawar (Pakistan); Gupta, S.K. [Department of Physics, Michigan Technological University, Houghton, MI 49931 (United States); Seddik, T. [Laboratoire de Physique Quantique et de Modélisation Mathématique, Université de Mascara, 29000 Mascara (Algeria); Khenata, R., E-mail: khenata_rabah@yahoo.fr [Laboratoire de Physique Quantique et de Modélisation Mathématique, Université de Mascara, 29000 Mascara (Algeria); Alahmed, Z.A. [Department of Physics and Astronomy, College of Science, King Saud University, Riyadh 11451 (Saudi Arabia); Ahmed, R. [Department of Physics, Faculty of Science, Universiti Teknologi Malaysia, UTM Skudai, 81310 Johor (Malaysia); Khachai, H. [Physics Department, Djillali Liabes University of Sidi Bel-Abbes (Algeria); Jha, P.K. [Department of Physics, Maharaja Krishnakumarsinhji Bhavnagar University, Bhavnagar 364001 (India); Bin Omran, S. [Department of Physics and Astronomy, College of Science, King Saud University, Riyadh 11451 (Saudi Arabia)

    2014-06-01

    Highlights: • REGa{sub 3} (RE = Sc or Lu) compounds are mechanical stabile. • Both ScGa{sub 3} and LuGa{sub 3} exhibit metallic behavior just like other REGa{sub 3} compounds. • Melting temperature T{sub m} (K) for ScGa{sub 3} and LuGa{sub 3} are 1244.2 and 1143.8. • High absorption observed in the visible energy region. • The present study would be helpful for future experimental/theoretical explorations. - Abstract: Structural, elastic, optoelectronic and thermodynamic properties of REGa{sub 3} (RE = Sc and Lu) compounds have been studied self consistently by employing state of the art full potential (FP) linearized (L) approach of augmented plane wave (APW) plus local orbitals method. Calculations were executed at the level of Perdew–Burke and Ernzerhof (PBE) parameterized generalized gradient approximation (GGA) for exchange correlation functional in addition to modified Becke–Johnson (mBJ) potential. Our obtained results of lattice parameters show reasonable agreement to the previously reported experimental and other theoretical studies. Analysis of the calculated band structure of ScGa{sub 3} and LuGa{sub 3} compounds demonstrates their metallic character. Moreover, a positive value of calculated Cauchy pressure, in addition to reflecting their ductile nature, endorses their metallic character as well. To understand optical behavior calculations related to the important optical parameters; real and imaginary parts of the dielectric function, reflectivity R(ω), refractive index n(ω) and electron energy-loss function L(ω) have also been performed. In the present work, thermodynamically properties are also investigated by employing lattice vibrations integrated in quasi harmonic Debye model. Obtained results of volume, heat capacity and Debye temperature as a function of temperature for both compounds, at different values of pressure, are found to be consistent. The calculated value of melting temperature for both compounds (ScGa{sub 3} and Lu

  13. Contact symmetries and Hamiltonian thermodynamics

    International Nuclear Information System (INIS)

    Bravetti, A.; Lopez-Monsalvo, C.S.; Nettel, F.

    2015-01-01

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

  14. Structure-property relationships in halogenbenzoic acids: Thermodynamics of sublimation, fusion, vaporization and solubility.

    Science.gov (United States)

    Zherikova, Kseniya V; Svetlov, Aleksey A; Kuratieva, Natalia V; Verevkin, Sergey P

    2016-10-01

    Temperature dependences of vapor pressures for 2-, 3-, and 4-bromobenzoic acid, as well as for five isomeric bromo-methylbenzoic acids were studied by the transpiration method. Melting temperatures and enthalpies of fusion for all isomeric bromo-methylbenzoic acids and 4-bromobenzoic acid were measured with a DSC. The molar enthalpies of sublimation and vaporization were derived. These data together with results available in the literature were collected and checked for internal consistency using a group-additivity procedure and results from X-ray structural diffraction studies. Specific (hydrogen bonding) interactions in the liquid and in the crystal phase of halogenbenzoic acids were quantified based on experimental values of vaporization and sublimation enthalpies. Structure-property correlations of solubilities of halogenobenzoic acids with sublimation pressures and sublimation enthalpies were developed and solubilities of bromo-benzoic acids were estimated. These new results resolve much of the ambiguity in the available thermochemical and solubility data on bromobenzoic acids. The approach based on structure property correlations can be applied for the assessment of water solubility of sparingly soluble drugs. Copyright © 2016 Elsevier Ltd. All rights reserved.

  15. Intrinsic point defects in zinc oxide. Modeling of structural, electronic, thermodynamic and kinetic properties

    Energy Technology Data Exchange (ETDEWEB)

    Erhart, P.

    2006-07-01

    The present dissertation deals with the modeling of zinc oxide on the atomic scale employing both quantum mechanical as well as atomistic methods. The first part describes quantum mechanical calculations based on density functional theory of intrinsic point defects in ZnO. To begin with, the geometric and electronic structure of vacancies and oxygen interstitials is explored. In equilibrium oxygen interstitials are found to adopt dumbbell and split interstitial configurations in positive and negative charge states, respectively. Semi-empirical self-interaction corrections allow to improve the agreement between the experimental and the calculated band structure significantly; errors due to the limited size of the supercells can be corrected by employing finite-size scaling. The effect of both band structure corrections and finite-size scaling on defect formation enthalpies and transition levels is explored. Finally, transition paths and barriers for the migration of zinc as well as oxygen vacancies and interstitials are determined. The results allow to interpret diffusion experiments and provide a consistent basis for developing models for device simulation. In the second part an interatomic potential for zinc oxide is derived. To this end, the Pontifix computer code is developed which allows to fit analytic bond-order potentials. The code is subsequently employed to obtain interatomic potentials for Zn-O, Zn-Zn, and O-O interactions. To demonstrate the applicability of the potentials, simulations on defect production by ion irradiation are carried out. (orig.)

  16. Atmospheric thermodynamics

    CERN Document Server

    Iribarne, J V

    1973-01-01

    The thermodynamics of the atmosphere is the subject of several chapters in most textbooks on dynamic meteorology, but there is no work in English to give the subject a specific and more extensive treatment. In writing the present textbook, we have tried to fill this rather remarkable gap in the literature related to atmospheric sciences. Our aim has been to provide students of meteorology with a book that can playa role similar to the textbooks on chemical thermodynamics for the chemists. This implies a previous knowledge of general thermodynamics, such as students acquire in general physics courses; therefore, although the basic principles are reviewed (in the first four chapters), they are only briefly discussed, and emphasis is laid on those topics that will be useful in later chapters, through their application to atmospheric problems. No attempt has been made to introduce the thermodynamics of irreversible processes; on the other hand, consideration of heterogeneous and open homogeneous systems permits a...

  17. Thermodynamic holography

    Science.gov (United States)

    Wei, Bo-Bo; Jiang, Zhan-Feng; Liu, Ren-Bao

    2015-01-01

    The holographic principle states that the information about a volume of a system is encoded on the boundary surface of the volume. Holography appears in many branches of physics, such as optics, electromagnetism, many-body physics, quantum gravity, and string theory. Here we show that holography is also an underlying principle in thermodynamics, a most important foundation of physics. The thermodynamics of a system is fully determined by its partition function. We prove that the partition function of a finite but arbitrarily large system is an analytic function on the complex plane of physical parameters, and therefore the partition function in a region on the complex plane is uniquely determined by its values along the boundary. The thermodynamic holography has applications in studying thermodynamics of nano-scale systems (such as molecule engines, nano-generators and macromolecules) and provides a new approach to many-body physics. PMID:26478214

  18. Structural Properties and Thermodynamic Stability of Metastable Phases in the Zr-Nb and Ti-V Systems

    International Nuclear Information System (INIS)

    Aurelio, Gabriela

    2003-01-01

    The structural properties and relative stability of metastable phases have been studied in the Zr-Nb and Ti-V systems.The first part of this Thesis is connected to a previous work performed in our Group (G. Grad, PhD Thesis, Instituto Balseiro, Argentina, 1999).It presents a phenomenological analysis of the systematics of interatomic distances in the omega (Ω ) and bcc (β) phases of the transition metals, which concerns a parameter entering into Pauling's resonating-valence- bond-theory and the structural and bonding properties of the Ω and β phases.Neutron diffraction experiments in Zr-Nb and Ti-V alloys are reported, aimed at studying possible atomic ordering in the Ω phase and the composition dependence of its interatomic distances.An extensive neutron diffraction study was performed on a series of Zr-Nb and Ti-V alloys quenched from high temperatures, where β is the stable phase.Upon quenching, three metastable structures are formed, viz., the hcp (∝ q ) phase, the Ω q phase, and the untransformed β q phase.The structural properties of these metastable phases were determined as a function of the Nb and V contents to generate a reliable experimental database.With such data, a series of issues are discussed related to the structure, relative stability, and phase relations in the alloys and its constitutive elements.The effect of composition upon the lattice parameters of the metastable β q and Ω q phases was combined in a consistent way with a critical analysis of structural and thermophysical data on the metastable phases of Ti and Zr.The relative stability of the metastable ∝ q , Ω q and β q phases in Zr-Nb alloys, and its evolution towards thermodynamic equilibrium, were studied combining neutron thermodiffraction and analytical electron microscopy techniques.During isothermal heat treatments performed at high temperature, the structural properties of the alloys were determined as a function of temperature, time and composition.A method of

  19. Sequence dependent structure and thermodynamics of DNA oligonucleotides and polynucleotides: uv melting and NMR (nuclear magnetic resonance) studies

    Energy Technology Data Exchange (ETDEWEB)

    Aboul-ela, F.M.

    1987-12-01

    Thermodynamic parameters for double strand formation have been measured for the twenty-five DNA double helices made by mixing deoxyoligonucleotides of the sequence dCA/sub 3/XA/sub 3/G with the complement dCT/sub 3/YT/sub 3/G. Each of the bases A, C, G, T, and I (I = hypoxanthine) have been substituted at the positions labeled X and Y. The results are analyzed in terms of nearest neighbors. At higher temperatures the sequences containing a G)centerreverse arrowdot)C base pair become more stable than those containing only A)centerreverse arrowdot)T. All molecules containing mismatcher are destabilized with respect to those with only Watson-Crick pairing, but there is a wide range of destabilization. Large neighboring base effects upon stability were observed. For example, when (X, Y) = (I, A), the duplex is eightfold more stable than when (X, Y) = (A, I). Independent of sequence effects the order of stabilities is: I)centerreverse arrowdot)C )succ) I)centerreverse arrowdot) A)succ) I)centerreverse arrowdot)T approx. I)centerreverse arrowdot)G. All of these results are discussed within the context of models for sequence dependent DNA secondary structure, replication fidelity and mechanisms of mismatch repair, and implications for probe design. The duplex deoxyoligonucleotide d(GGATGGGAG))centerreverse arrowdot)d(CTCCCATCC) is a portion of the gene recognition sequence of the protein transcription factor IIIA. The crystal structure of this oligonucleotide was shown to be A-form The present study employs Nuclear Magnetic Resonance, optical, chemical and enzymatic techniques to investigate the solution structure of this DNA 9-mer. (157 refs., 19 figs., 10 tabs.

  20. Electronic band structure, magnetic, transport and thermodynamic properties of In-filled skutterudites InxCo4Sb12

    International Nuclear Information System (INIS)

    Leszczynski, J; Da Ros, V; Lenoir, B; Dauscher, A; Candolfi, C; Masschelein, P; Hejtmanek, J; Kutorasinski, K; Tobola, J; Smith, R I; Stiewe, C; Müller, E

    2013-01-01

    The thermoelectric and thermodynamic properties of polycrystalline In x Co 4 Sb 12 (0.0 ⩽ x ⩽ 0.26) skutterudites were investigated and analysed between 2 and 800 K by means of electrical resistivity, thermopower, thermal conductivity and specific heat measurements. Hall effect, sound velocity and thermal expansion measurements were also made in order to gain insights into the transport and elastic properties of these compounds. The impact of the In filling on the crystal structure as well as the thermal dynamics of the In atoms were tracked down to 4 K using powder neutron diffraction experiments. Analyses of the transport data were compared with the evolution of the electronic band structure with x determined theoretically within the Korringa–Kohn–Rostoker method with the coherent potential approximation. These calculations indicate that In gives rise to a remarkably large p-like density of states located at the conduction band edge. The electrical properties show typical trends of heavily doped semiconductors regardless of the In content. The thermal transport in CoSb 3 is strongly influenced by the presence of In in the voids of the crystal structure resulting in a drop in the lattice thermal conductivity values in the whole temperature range. The low value of the Grüneisen parameter suggests that this decrease mainly originates from enhanced mass-fluctuations and point-defect scattering mechanisms. The highest thermoelectric figure of merit ZT ∼ 1.0 at 750 K was achieved at the maximum In filling fraction, i.e. for x = 0.26. (paper)

  1. Sequence dependent structure and thermodynamics of DNA oligonucleotides and polynucleotides: uv melting and NMR (nuclear magnetic resonance) studies

    International Nuclear Information System (INIS)

    Aboul-ela, F.M.

    1987-12-01

    Thermodynamic parameters for double strand formation have been measured for the twenty-five DNA double helices made by mixing deoxyoligonucleotides of the sequence dCA 3 XA 3 G with the complement dCT 3 YT 3 G. Each of the bases A, C, G, T, and I (I = hypoxanthine) have been substituted at the positions labeled X and Y. The results are analyzed in terms of nearest neighbors. At higher temperatures the sequences containing a G/center dot/C base pair become more stable than those containing only A/center dot/T. All molecules containing mismatcher are destabilized with respect to those with only Watson-Crick pairing, but there is a wide range of destabilization. Large neighboring base effects upon stability were observed. For example, when (X, Y) = (I, A), the duplex is eightfold more stable than when (X, Y) = (A, I). Independent of sequence effects the order of stabilities is: I/center dot/C /succ/ I/center dot/ A/succ/ I/center dot/T ∼ I/center dot/G. All of these results are discussed within the context of models for sequence dependent DNA secondary structure, replication fidelity and mechanisms of mismatch repair, and implications for probe design. The duplex deoxyoligonucleotide d(GGATGGGAG)/center dot/d(CTCCCATCC) is a portion of the gene recognition sequence of the protein transcription factor IIIA. The crystal structure of this oligonucleotide was shown to be A-form The present study employs Nuclear Magnetic Resonance, optical, chemical and enzymatic techniques to investigate the solution structure of this DNA 9-mer. (157 refs., 19 figs., 10 tabs.)

  2. Thermodynamics and Structural Evolution during a Reversible Vesicle-Micelle Transition of a Vitamin-Derived Bolaamphiphile Induced by Sodium Cholate.

    Science.gov (United States)

    Tian, Jun-Nan; Ge, Bing-Qiang; Shen, Yun-Feng; He, Yu-Xuan; Chen, Zhong-Xiu

    2016-03-09

    Interaction of endogenous sodium cholate (SC) with dietary amphiphiles would induce structural evolution of the self-assembled aggregates, which inevitably affects the hydrolysis of fat in the gut. Current work mainly focused on the interaction of bile salts with classical double-layered phospholipid vesicles. In this paper, the thermodynamics and structural evolution during the interaction of SC with novel unilamellar vesicles formed from vitamin-derived zwitterionic bolaamphiphile (DDO) were characterized. It was revealed that an increased temperature and the presence of NaCl resulted in narrowed micelle-vesicle coexistence and enlarged the vesicle region. The coexistence of micelles and vesicles mainly came from the interaction of monomeric SC with DDO vesicles, whereas micellar SC contributed to the total solubilization of DDO vesicles. This research may enrich the thermodynamic mechanism behind the structure transition of the microaggregates formed by amphiphiles in the gut. It will also contribute to the design of food formulation and drug delivery system.

  3. Thermodynamic and Structure Guided Design of Statin Based Inhibitors of 3-Hydroxy-3-Methylglutaryl Coenzyme A Reductase

    Energy Technology Data Exchange (ETDEWEB)

    Sarver, Ronald W.; Bills, Elizabeth; Bolton, Gary; Bratton, Larry D.; Caspers, Nicole L.; Dunbar, James B.; Harris, Melissa S.; Hutchings, Richard H.; Kennedy, Robert M.; Larsen, Scott D.; Pavlovsky, Alexander; Pfefferkorn, Jeffrey A.; Bainbridge, Graeme (Pfizer)

    2008-10-02

    Clinical studies have demonstrated that statins, 3-hydroxy-3-methylglutaryl coenzyme A reductase (HMGR) inhibitors, are effective at lowering mortality levels associated with cardiovascular disease; however, 2--7% of patients may experience statin-induced myalgia that limits compliance with a treatment regimen. High resolution crystal structures, thermodynamic binding parameters, and biochemical data were used to design statin inhibitors with improved HMGR affinity and therapeutic index relative to statin-induced myalgia. These studies facilitated the identification of imidazole 1 as a potent (IC{sub 50} = 7.9 nM) inhibitor with excellent hepatoselectivity (>1000-fold) and good in vivo efficacy. The binding of 1 to HMGR was found to be enthalpically driven with a {Delta}H of -17.7 kcal/M. Additionally, a second novel series of bicyclic pyrrole-based inhibitors was identified that induced order in a protein flap of HMGR. Similar ordering was detected in a substrate complex, but has not been reported in previous statin inhibitor complexes with HMGR.

  4. A critical appraisal of the zero-multipole method: Structural, thermodynamic, dielectric, and dynamical properties of a water system

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Han, E-mail: wang-han@iapcm.ac.cn [CAEP Software Center for High Performance Numerical Simulation, Huayuan Road 6, 100088 Beijing, China and Zuse Institute Berlin (ZIB), Berlin (Germany); Nakamura, Haruki [Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871 (Japan); Fukuda, Ikuo, E-mail: ifukuda@protein.osaka-u.ac.jp [Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871 (Japan); RIKEN (The Institute of Physical and Chemical Research), 2-1 Hirosawa, Wako, Saitama 351-0198 (Japan)

    2016-03-21

    We performed extensive and strict tests for the reliability of the zero-multipole (summation) method (ZMM), which is a method for estimating the electrostatic interactions among charged particles in a classical physical system, by investigating a set of various physical quantities. This set covers a broad range of water properties, including the thermodynamic properties (pressure, excess chemical potential, constant volume/pressure heat capacity, isothermal compressibility, and thermal expansion coefficient), dielectric properties (dielectric constant and Kirkwood-G factor), dynamical properties (diffusion constant and viscosity), and the structural property (radial distribution function). We selected a bulk water system, the most important solvent, and applied the widely used TIP3P model to this test. In result, the ZMM works well for almost all cases, compared with the smooth particle mesh Ewald (SPME) method that was carefully optimized. In particular, at cut-off radius of 1.2 nm, the recommended choices of ZMM parameters for the TIP3P system are α ≤ 1 nm{sup −1} for the splitting parameter and l = 2 or l = 3 for the order of the multipole moment. We discussed the origin of the deviations of the ZMM and found that they are intimately related to the deviations of the equilibrated densities between the ZMM and SPME, while the magnitude of the density deviations is very small.

  5. A critical appraisal of the zero-multipole method: Structural, thermodynamic, dielectric, and dynamical properties of a water system.

    Science.gov (United States)

    Wang, Han; Nakamura, Haruki; Fukuda, Ikuo

    2016-03-21

    We performed extensive and strict tests for the reliability of the zero-multipole (summation) method (ZMM), which is a method for estimating the electrostatic interactions among charged particles in a classical physical system, by investigating a set of various physical quantities. This set covers a broad range of water properties, including the thermodynamic properties (pressure, excess chemical potential, constant volume/pressure heat capacity, isothermal compressibility, and thermal expansion coefficient), dielectric properties (dielectric constant and Kirkwood-G factor), dynamical properties (diffusion constant and viscosity), and the structural property (radial distribution function). We selected a bulk water system, the most important solvent, and applied the widely used TIP3P model to this test. In result, the ZMM works well for almost all cases, compared with the smooth particle mesh Ewald (SPME) method that was carefully optimized. In particular, at cut-off radius of 1.2 nm, the recommended choices of ZMM parameters for the TIP3P system are α ≤ 1 nm(-1) for the splitting parameter and l = 2 or l = 3 for the order of the multipole moment. We discussed the origin of the deviations of the ZMM and found that they are intimately related to the deviations of the equilibrated densities between the ZMM and SPME, while the magnitude of the density deviations is very small.

  6. Response of the dynamic and thermodynamic structure of the stratosphere to the solar cycle in the boreal winter

    Science.gov (United States)

    Shi, Chunhua; Gao, Yannan; Cai, Juan; Guo, Dong; Lu, Yan

    2018-04-01

    The response of the dynamic and thermodynamic structure of the stratosphere to the solar cycle in the boreal winter is investigated based on measurements of the solar cycle by the Spectral Irradiance Monitor onboard the SORCE satellite, monthly ERA-Interim Reanalysis data from the European Center for Medium-Range Weather Forecasts, the radiative transfer scheme of the Beijing Climate Center (BCC-RAD) and a multiple linear regression model. The results show that during periods of strong solar activity, the solar shortwave heating anomaly from the climatology in the tropical upper stratosphere triggers a local warm anomaly and strong westerly winds in mid-latitudes, which strengthens the upward propagation of planetary wave 1 but prevents that of wave 2. The enhanced westerly jet makes a slight adjustment to the propagation path of wave 1, but prevents wave 2 from propagating upward, decreases the dissipation of wave 2 in the extratropical upper stratosphere and hence weakens the Brewer-Dobson circulation. The adiabatic heating term in relation to the Brewer-Dobson circulation shows anomalous warming in the tropical lower stratosphere and anomalous cooling in the mid-latitude upper stratosphere.

  7. Applications in environmental bioinorganic: Nutritional and ultrastructural evaluation and calculus of thermodynamic and structural properties of metal-oxalate complexes.

    Science.gov (United States)

    Tolentino, Terezinha Alves; Bertoli, Alexandre Carvalho; dos Santos Pires, Maíra; Carvalho, Ruy; Labory, Claudia Regina Gontijo; Nunes, Janaira Santana; Bastos, Ana Rosa Ribeiro; de Freitas, Matheus Puggina

    2015-01-01

    Lead (Pb) is known by its toxicity both for animals and plants. In order to evaluate its toxicity, plants of Brachiaria brizantha were cultivated on nutritive solution of Hoagland during 90 days and submitted to different concentrations of Pb. The content of macro and micronutrients was evaluated and there was a reduction on root content of Ca, besides the lowest dosages of Pb had induced an increase of N, S, Mn, Cu, Zn and Fe. The cell ultrastructure of leaves and roots were analyzed by transmission electronic microscopy (TEM). Among the main alterations occurred there were invaginations on cell walls, the presence of crystals on the root cells, accumulation of material on the interior of cells and vacuolar compartmentalization. On the leaves the degradation of chloroplasts was observed, as well as the increase of vacuoles. Structures for the formation of oxalate crystals were proposed through molecular modeling and thermodynamic stability. Calculi suggest the formation of highly stable metal-oxalate complexes. Copyright © 2015 Elsevier B.V. All rights reserved.

  8. A novel pressure variation study on electronic structure, mechanical stability and thermodynamic properties of potassium based fluoroperovskite

    Science.gov (United States)

    Erum, Nazia; Azhar Iqbal, Muhammad

    2017-09-01

    The effect of pressure variation on stability, structural parameters, elastic constants, mechanical, electronic and thermodynamic properties of cubic SrKF3 fluoroperovskite have been investigated by using the full-potential linearized augmented plane wave (FP-LAPW) method combined with Quasi-harmonic Debye model in which the phonon effects are considered. The calculated lattice parameters show a prominent decrease in lattice constant and bonds length with the increase in pressure. The application of pressure from 0 to 25 GPa reveals a predominant characteristic associated with widening of bandgap with GGA and GGA plus Tran-Blaha modified Becke-Johnson (TB-mBJ) potential. The influence of pressure on elastic constants and their related mechanical parameters have been discussed in detail. Apart of linear dependence of elastic coefficients, transition from brittle to ductile behavior is also observed at elevated pressure ranges. We have successfully computed variation of lattice constant, volume expansion, bulk modulus, Debye temperature and specific heat capacities at pressure and temperature in the range of 0-25 GPa and 0-600 K.

  9. Complexation thermodynamics and structural studies of trivalent actinide and lanthanide complexes with DTPA, MS-325 and HMDTPA

    Energy Technology Data Exchange (ETDEWEB)

    Thakur, P.; Choppin, G.R. [Florida State Univ., Tallahassee, FL (United States). Dept. of Chemistry and Biochemistry; Conca, J.L. [RJ Lee Group, Inc., Pasco, WA (United States). Center for Lab. Sciences; Dodge, C.J. [Brookhaven National Laboratory, Upton, NY (United States); Francis, A.J. [Brookhaven National Laboratory, Upton, NY (United States); Pohang Univ. of Science and Technology (Korea, Republic of). Div. of Advanced Nuclear Engineering

    2013-05-01

    The protonation constants of DTPA (diethylenetriaminepentaacetic acid) and two derivatives of DTPA, 1-R(4,4-diphenyl cyclohexyl-phosphonyl-methyl diethylenentriaminepentaacetic acid) (MS-325) and (R)-hydroxymethyl-diethylenentriaminepentaacetic acid (HMDTPA) were determined by potentiometric titration in 0.1 M NaClO{sub 4}. The formation of 1: 1 complexes of Am{sup 3+}, Cm{sup 3+} and Ln{sup 3+} cations with these three ligands were investigated by potentiometric titration with competition by ethylenediaminetetraacetic acid (EDTA) and the solvent extraction method in aqueous solutions of I=0.10 M NaClO{sub 4}. The thermodynamic data of complexation were determined by the temperature dependence of the stability constants and by calorimetry. The complexation is exothermic and becomes weaker with increase in temperature. The complexation strength of these ligands follows the order: DTPA {approx} HMDTPA > MS-325. Eu{sup 3+}/Cm{sup 3+} luminescence, EXAFS (Extended X-ray Absorption Fine Structure) and DFT (Density Functional Theory) calculations suggest that all three ligands are octadentate in the complex. In the complex, M(L){sup 2-} (L = DTPA, MS-325 and HMDTPA). The M{sup 3+} binds via five carboxylates oxygen atoms, three nitrogen atoms, and the complex contains one water of hydration. (orig.)

  10. Long-term prediction of reinforced concrete structures - Use of thermodynamic data to assess steel corrosion in carbonated concrete

    Energy Technology Data Exchange (ETDEWEB)

    Huet, Bruno [Laboratoire d' Etude du Comportement des Betons et Argiles, DEN/DPC/SCCME/LECBA, Bat. 158, CEA Saclay, 91191 Gif sur Yvette cedex (France)]|[Laboratoire de Physico-Chimie Industrielle, LPCI, INSA de Lyon, Bat. Leonard de Vinci, 20 av. Albert Einstein, 69621 Villeurbanne cedex (France); L' Hostis, Valerie; Le Bescop, Patrick [Laboratoire d' Etude du Comportement des Betons et Argiles, DEN/DPC/SCCME/LECBA, Bat. 158, CEA Saclay, 91191 Gif sur Yvette cedex (France); Idrissi, Hassane [Laboratoire de Physico-Chimie Industrielle, LPCI, INSA de Lyon, Bat. Leonard de Vinci, 20 av. Albert Einstein, 69621 Villeurbanne cedex (France)

    2004-07-01

    In the context of the prediction of the long-term behaviour of reinforced concrete structures involved in the nuclear waste storage, the corrosion mechanisms of the steels have to be assessed and modelled. When nuclear wastes are embedded in reinforced concrete containers, the chemical environment of the reinforcement is progressively modified, due to the diffusion of the carbonation front inside the concrete matrix. This modification leads to the variation of the properties of the iron oxides formed at the steel/concrete interface, and the active corrosion can be initiated. In order to understand and modelled the mechanisms of steel corrosion in concrete, the equilibrium of two main systems must be separately described with the help of thermodynamic data issued from the literature: - The mineral phases, lime and calcium silicate hydrate (C-S-H), in equilibrium with the pore solution during the propagation of the carbonation front; - The iron oxides in equilibrium with the aqueous solution. For this purpose, the nature of aqueous species present in the pore solution was calculated in the whole range of pH encountered during the cement paste degradation by carbonation. As a matter of fact, as the pH decreases, calcium concentration decreases and silicates concentration increases due to the calcium carbonate formation and C-S-H dissolution. The pH of a carbonated concrete ranges between 8.3 and 10, depending on the partial pressure of carbon dioxide in the porosity and the conversion degree of carbonation. In this pH range, the iron oxides equilibria were analysed as a function of the redox potential and aqueous species (carbonates and sulphates present in the solution) present inside the solution. In a reductive solution and in presence of carbonates, the high solubility of iron oxides may prevent passivation or generate the dissolution of the passive film. Moreover, the relevance of thermodynamics calculations has been confirmed by corrosion tests of mild steel

  11. Long-term prediction of reinforced concrete structures - Use of thermodynamic data to assess steel corrosion in carbonated concrete

    International Nuclear Information System (INIS)

    Huet, Bruno; L'Hostis, Valerie; Le Bescop, Patrick; Idrissi, Hassane

    2004-01-01

    In the context of the prediction of the long-term behaviour of reinforced concrete structures involved in the nuclear waste storage, the corrosion mechanisms of the steels have to be assessed and modelled. When nuclear wastes are embedded in reinforced concrete containers, the chemical environment of the reinforcement is progressively modified, due to the diffusion of the carbonation front inside the concrete matrix. This modification leads to the variation of the properties of the iron oxides formed at the steel/concrete interface, and the active corrosion can be initiated. In order to understand and modelled the mechanisms of steel corrosion in concrete, the equilibrium of two main systems must be separately described with the help of thermodynamic data issued from the literature: - The mineral phases, lime and calcium silicate hydrate (C-S-H), in equilibrium with the pore solution during the propagation of the carbonation front; - The iron oxides in equilibrium with the aqueous solution. For this purpose, the nature of aqueous species present in the pore solution was calculated in the whole range of pH encountered during the cement paste degradation by carbonation. As a matter of fact, as the pH decreases, calcium concentration decreases and silicates concentration increases due to the calcium carbonate formation and C-S-H dissolution. The pH of a carbonated concrete ranges between 8.3 and 10, depending on the partial pressure of carbon dioxide in the porosity and the conversion degree of carbonation. In this pH range, the iron oxides equilibria were analysed as a function of the redox potential and aqueous species (carbonates and sulphates present in the solution) present inside the solution. In a reductive solution and in presence of carbonates, the high solubility of iron oxides may prevent passivation or generate the dissolution of the passive film. Moreover, the relevance of thermodynamics calculations has been confirmed by corrosion tests of mild steel

  12. A density functional reactivity theory (DFRT) based approach to understand the effect of symmetry of fullerenes on the kinetic, thermodynamic and structural aspects of carbon NanoBuds

    Energy Technology Data Exchange (ETDEWEB)

    Sarmah, Amrit; Roy, Ram Kinkar, E-mail: rkroy2@rediffmail.com

    2016-06-15

    Highlights: • Kinetic and thermodynamic aspects of the interaction between fullerene (C{sub 32}) and SWCNT using CDASE scheme. • Role of symmetry of fullerenes as well as the site of covalent attachment to the SWCNT in the structural stability of the NanoBud structure. • Increase in the fullerene symmetry improves the relative stability of hybrid NanoBud structure. - Abstract: In the present study, we have rationalized the effect of variation in the symmetry of relatively smaller fullerene (C{sub 32}) on the mode of its interaction with semi-conducting Single-Walled Carbon Nanotubes (SWCNTs) in the process of formation of stable hybrid carbon NanoBuds. Thermodynamic and kinetic parameters, along with the charge transfer values associated with the interaction between fullerene and SWCNTs, have been evaluated using an un-conventional and computationally cost–effective method based on density functional reactivity theory (DFRT). In addition to this, conventional DFT based studies are also performed to substantiate the growth of NanoBud structures formed by the interaction between fullerene and SWCNTs. The findings of the present study suggest that the kinetic, thermodynamic and structural aspects of hybrid carbon NanoBuds are significantly influenced by both the symmetry of C{sub 32} fullerene and its site of covalent attachment to the SWCNT.

  13. Thermodynamics and structure of liquid surfaces investigated directly with surface analytical tools

    Energy Technology Data Exchange (ETDEWEB)

    Andersson, Gunther [Flinders Univ., Adelaide, SA (Australia). Centre for NanoScale Science and Technology; Morgner, Harald [Leipzig Univ. (Germany). Wilhelm Ostwald Inst. for Physical and Theoretical Chemistry

    2017-06-15

    Measuring directly the composition, the distribution of constituents as function of the depth and the orientation of molecules at liquid surfaces is essential for determining physicochemical properties of liquid surfaces. While the experimental tools that have been developed for analyzing solid surfaces can in principal be applied to liquid surfaces, it turned out that they had to be adjusted to the particular challenges imposed by liquid samples, e.g. by the unavoidable vapor pressure and by the mobility of the constituting atoms/molecules. In the present work it is shown, how electron spectroscopy and ion scattering spectroscopy have been used for analyzing liquid surfaces. The emphasis of this review is on using the structural information gained for determining the physicochemical properties of liquid surfaces. (copyright 2017 by WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  14. Structure, stability, and thermodynamics of a short intermolecular purine-purine-pyrimidine triple helix

    International Nuclear Information System (INIS)

    Pilch, D.S.; Shafer, R.H.; Levenson, C.

    1991-01-01

    The authors have investigated the structure and physical chemistry of the d(C 3 T 4 C 3 )·2[d(G 3 A 4 G 3 )] triple helix by polyacrylamide gel electrophoresis (PAGE), 1 H NMR, and ultraviolet (UV) absorption spectroscopy. The triplex was stabilized with MgCl 2 at neutral pH. PAGE studies verify the stoichiometry of the strands comprising the triplex and indicate that the orientation of the third strand in purine-purine-pyrimidine (pur-pur-pyr) triplexes is antiparallel with respect to the purine strand of the underlying duplex. Imino proton NMR spectra provide evidence for the existence of new purine-purine (pur·pur) hydrogen bonds, in addition to those of the Watson-Crick (W-C) base pairs, in the triplex structure. These new hydrogen bonds are likely to correspond to the interaction between third-strand guanine NH1 imino protons and the N7 atoms of guanine residues on the puring strand of the underlying duplex. Thermal denaturation of the triplex proceeds to single strands in one step, under the conditions used in this study. Binding of the third strand appears to enhance the thermal stability of the duplex by 1-3 C, depending on the DNA concentration. This marked enhancement in stability, coupled with the lack of an acidic pH requirement, suggests that pur-pur-pyr triplexes are appealing choices for use in applications involving oligonucleotide targeting of duplex DNA in vitro and in vivo

  15. Molecular simulation of the water-triolein-oleic acid mixture: Local structure and thermodynamic properties

    Science.gov (United States)

    Couallier, E.; Riaublanc, A.; David Briand, E.; Rousseau, B.

    2018-05-01

    An artificial oil-in-water emulsion analogous to those found in bioresources or food matrices is simulated and studied experimentally. It is composed of one of the major natural free fatty acids (the oleic acid, OA) and the corresponding triacylglyceride (trioleic glyceride, or triolein, GTO). Because of the large time and length scales involved, the molecular simulations are done with the Martini force field, a coarse-grained model. This allowed us to study the water-OA-GTO system at different compositions with more than 20 000 molecules and up to 2 μs. Interfacial tension was measured using the pendant drop method and compared with molecular simulation results. We observe very good agreement at high OA concentrations and deviations up to 15% at low OA concentrations. The water solubility in the lipid phase is in fair agreement with experiments, between 0.03 and 0.32 mol/l, rising with the OA content. The area occupied by OA and GTO at the interface between water and the pure product fitted with experimental data (AOA = 36.6 Å2 and AGTO = 152.1 Å2). The consistency between simulation and experimental results allowed a structural analysis of the interface. A bilayer structure of the lipids at the water/oil interface is proposed, containing preferentially oleic acid but also triolein. Through all these results, the usefulness of coarse-grained simulation for the description of water-oil interfacial organization is demonstrated. This method will be used later to bring local information on the organization of target compounds, necessary in biomass fractionation processes or food additive formulations, for example.

  16. The thermodynamic and structural properties of metallocenes-type random ethylene copolymers

    International Nuclear Information System (INIS)

    Simanke, Adriane G.; Mauler, Raquel S.; Galland, Griselda B.; Alamo, Rufina G.

    2001-01-01

    The properties of a series of random ethylene copolymers prepared with the metallocenes catalytic system rac-Et[Ind] 2 ZrCl 2 /MAO were studied for a large variety of comonomer types. These include the classical 1-alkene type with length up to 10 carbons and those of the cyclic type such as cyclopentadiene and dicyclopentadiene. Under rapid crystallization, the melting temperatures of the newly synthesized copolymers followed the relation of model random copolymers indicating a behavior that conforms to that predicted by Flory's phase equilibrium theory. The molar entropy of fusion is not significantly altered by the comonomer type including the dicyclopentadiene type. All types of comonomers studied showed, for a fixed comonomer content, the same change in properties during annealing, except the ethylene 1-butenes. These latter copolymers and the hydrogenated poly butadiene showed a faster rate of change in thermal properties. This is consistent with a higher molecular diffusion for the butene comonomer than for the rest of comonomers analyzed. The properties of the inter lamellar region were also studied as a function of comonomer type and content following the variation of the amorphous halo extracted from the WAXS diffractograms. The observed systematic decrease in the peak scattering angle with increasing comonomer content indicates a variation of the intermolecular liquid structure. (author)

  17. New Perspectives on Blowing Snow Transport, Sublimation, and Layer Thermodynamic Structure over Antarctica

    Science.gov (United States)

    Palm, Steve; Kayetha, Vinay; Yang, Yuekui; Pauly, Rebecca M.

    2017-01-01

    Blowing snow over Antarctica is a widespread and frequent event. Satellite remote sensing using lidar has shown that blowing snow occurs over 70% of the time over large areas of Antarctica in winter. The transport and sublimation of blowing snow are important terms in the ice sheet mass balance equation and the latter is also an important part of the hydrological cycle. Until now the only way to estimate the magnitude of these processes was through model parameterization. We present a technique that uses direct satellite observations of blowing snow and model (MERRA-2) temperature and humidity fields to compute both transport and sublimation of blowing snow over Antarctica for the period 2006 to 2016. The results show a larger annual continent-wide integrated sublimation than current published estimates and a significant transport of snow from continent to ocean. The talk will also include the lidar backscatter structure of blowing snow layers that often reach heights of 200 to 300 m as well as the first dropsonde measurements of temperature, moisture and wind through blowing snow layers.

  18. Structural and thermodynamic studies of the tobacco calmodulin-like rgs-CaM protein.

    Science.gov (United States)

    Makiyama, Rodrigo K; Fernandes, Carlos A H; Dreyer, Thiago R; Moda, Bruno S; Matioli, Fabio F; Fontes, Marcos R M; Maia, Ivan G

    2016-11-01

    The tobacco calmodulin-like protein rgs-CaM is involved in host defense against virus and is reported to possess an associated RNA silencing suppressor activity. Rgs-CaM is also believed to act as an antiviral factor by interacting and targeting viral silencing suppressors for autophagic degradation. Despite these functional data, calcium interplay in the modulation of rgs-CaM is still poorly understood. Here we show that rgs-CaM displays a prevalent alpha-helical conformation and possesses three functional Ca 2+ -binding sites. Using computational modeling and molecular dynamics simulation, we demonstrate that Ca 2+ binding to rgs-CaM triggers expansion of its tertiary structure with reorientation of alpha-helices within the EF-hands. This conformational change leads to the exposure of a large negatively charged region that may be implicated in the electrostatic interactions between rgs-CaM and viral suppressors. Moreover, the k d values obtained for Ca 2+ binding to the three functional sites are not within the affinity range of a typical Ca 2+ sensor. Copyright © 2016 Elsevier B.V. All rights reserved.

  19. Composition effects on chemical durability and viscosity of nuclear waste glasses - systematic studies and structural thermodynamic models

    International Nuclear Information System (INIS)

    Feng, X.

    1988-01-01

    Two of the primary criteria for the acceptability of nuclear waste glasses are their durability, i.e. chemical resistance to aqueous attack for 10 4 to 10 5 years, and processability, which requires their viscosity at the desired melt temperature to be sufficiently low. Chapter 3 presents the results of systematic composition variation studies around the preliminary reference glass composition WV205 and an atomistic interpretation of the effects of individual oxides. Chapter 4 is concerned with modifications of the Jantzen-Plodinec hydration model which takes into account formation of complex aluminosilicate compounds in the glass. Chapter 5 is devoted to the development and validation of the structural-thermodynamic model for both durability and viscosity. This model assumes the strength of bonds between atoms to be the controlling factor in the composition dependence of these glass properties. The binding strengths are derived from the known heats of formation and the structural roles of constituent oxides. Since the coordination state of various oxides in the glass is temperature dependent and cation size has opposite effects on the two properties, the correlation between melt viscosity and rate of corrosion at low temperature is not simply linear. Chapter 6 surveys the effects of aqueous phase composition on the leach behavior of glasses. These studies provide a comprehensive view of the effects of both glass composition and leachant composition on leaching. The models developed correlate both durability and viscosity with glass composition. A major implication is that these findings can be used in the systematic optimization of the properties of complex oxide glasses

  20. Structural, hydrogen storage and thermodynamic properties of some mischmetal-nickel alloys with partial substitutions for nickel

    Energy Technology Data Exchange (ETDEWEB)

    Kumar, E. Anil; Maiya, M. Prakash [Department of Mechanical Engineering, Indian Institute of Technology Madras, Chennai 600036 (India); Murthy, S. Srinivasa [Department of Mechanical Engineering, Indian Institute of Technology Madras, Chennai 600036 (India)], E-mail: ssmurthy@iitm.ac.in; Viswanathan, B. [National Centre for Catalysis Research, Indian Institute of Technology Madras, Chennai 600036 (India)

    2009-05-12

    Mischmetal-nickel (Mm-Ni) alloys with single (Al) and multiple (Al, Co, Mn, Fe) substitutions for Ni are studied for their structural, hydrogen storage and thermodynamic properties. The alloys considered are MmNi{sub 5}, MmNi{sub 4.7}Al{sub 0.3,} MmNi{sub 4.5}Al{sub 0.5}, MmNi{sub 4.2}Al{sub 0.8} and MmNi{sub 4}Al for single substitution, and MmNi{sub 3.9}Co{sub 0.8}Mn{sub 0.2}Al{sub 0.1}, MmNi{sub 3.8}Co{sub 0.7}Mn{sub 0.3}Al{sub 0.2}, MmNi{sub 3.7}Co{sub 0.7}Mn{sub 0.3}Al{sub 0.3}, MmNi{sub 3.6}Co{sub 0.6}Mn{sub 0.3}Al{sub 0.3}Fe{sub 0.2} and MmNi{sub 3.5}Co{sub 0.4}Mn{sub 0.4}Al{sub 0.4}Fe{sub 0.3} for multiple substitutions. The XRD patterns of all the alloys show single phase with the reflection peaks related to the CaCu{sub 5} hexagonal structure. All the multiple substituted alloys absorb and desorb hydrogen at sub-atmospheric pressures. The equilibrium pressure and hysteresis decrease, while enthalpy of formation ({delta}H) and plateau slope increase with increase in unit cell volume, indicating an increase in the stability of the alloys.

  1. Structural, Electronic, and Thermodynamic Properties of Tetragonal t-SixGe3−xN4

    Directory of Open Access Journals (Sweden)

    Chenxi Han

    2018-03-01

    Full Text Available The structural, mechanical, anisotropic, electronic, and thermal properties of t-Si3N4, t-Si2GeN4, t-SiGe2N4, and t-Ge3N4 in the tetragonal phase are systematically investigated in the present work. The mechanical stability is proved by the elastic constants of t-Si3N4, t-Si2GeN4, t-SiGe2N4, and t-Ge3N4. Moreover, they all demonstrate brittleness, because B/G < 1.75, and v < 0.26. The elastic anisotropy of t-Si3N4, t-Si2GeN4, t-SiGe2N4, and t-Ge3N4 is characterized by Poisson’s ratio, Young’s modulus, the percentage of elastic anisotropy for bulk modulus AB, the percentage of elastic anisotropy for shear modulus AG, and the universal anisotropic index AU. The electronic structures of t-Si3N4, t-Si2GeN4, t-SiGe2N4, and t-Ge3N4 are all wide band gap semiconductor materials, with band gaps of 4.26 eV, 3.94 eV, 3.83 eV, and 3.25 eV, respectively, when using the Heyd-Scuseria-Ernzerhof (HSE06 hybrid functional. Moreover, t-Ge3N4 is a quasi-direct gap semiconductor material. The thermodynamic properties of t-Si3N4, t-Si2GeN4, t-SiGe2N4, and t-Ge3N4 are investigated utilizing the quasi-harmonic Debye model. The effects of temperature and pressure on the thermal expansion coefficient, heat capacity, Debye temperature, and Grüneisen parameters are discussed in detail.

  2. Kinetic, thermodynamic and X-ray structural insights into the interaction of melatonin and analogues with quinone reductase 2

    Energy Technology Data Exchange (ETDEWEB)

    Calamini, Barbara; Santarsiero, Bernard D.; Boutin, Jean A.; Mesecar, Andrew D. (IdRS); (UIC)

    2008-09-12

    Melatonin exerts its biological effects through at least two transmembrane G-protein-coupled receptors, MT1 and MT2, and a lower-affinity cytosolic binding site, designated MT3. MT3 has recently been identified as QR2 (quinone reductase 2) (EC 1.10.99.2) which is of significance since it links the antioxidant effects of melatonin to a mechanism of action. Initially, QR2 was believed to function analogously to QR1 in protecting cells from highly reactive quinones. However, recent studies indicate that QR2 may actually transform certain quinone substrates into more highly reactive compounds capable of causing cellular damage. Therefore it is hypothesized that inhibition of QR2 in certain cases may lead to protection of cells against these highly reactive species. Since melatonin is known to inhibit QR2 activity, but its binding site and mode of inhibition are not known, we determined the mechanism of inhibition of QR2 by melatonin and a series of melatonin and 5-hydroxytryptamine (serotonin) analogues, and we determined the X-ray structures of melatonin and 2-iodomelatonin in complex with QR2 to between 1.5 and 1.8 {angstrom} (1 {angstrom} = 0.1 nm) resolution. Finally, the thermodynamic binding constants for melatonin and 2-iodomelatonin were determined by ITC (isothermal titration calorimetry). The kinetic results indicate that melatonin is a competitive inhibitor against N-methyldihydronicotinamide (K{sub i} = 7.2 {mu}M) and uncompetitive against menadione (K{sub i} = 92 {mu}M), and the X-ray structures shows that melatonin binds in multiple orientations within the active sites of the QR2 dimer as opposed to an allosteric site. These results provide new insights into the binding mechanisms of melatonin and analogues to QR2.

  3. First -principles calculations of the crystal structure, electronic structure, and thermodynamic stability of Be(BH4)2

    NARCIS (Netherlands)

    van Setten, Michiel J.; de Wijs, Gilles A.; Brocks, G.

    2008-01-01

    Alanates and boranates are intensively studied because of their potential use as hydrogen storage materials. In this paper, we present a first-principles study of the electronic structure and the energetics of beryllium boranate BeBH42. From total energy calculations, we show that—in contrast to the

  4. Boron-substitution and defects in B2-type AlNi compound: Site-preference and influence on structural, thermodynamic and electronic properties

    Energy Technology Data Exchange (ETDEWEB)

    Capaz, Rodrigo B. [Instituto de Física, Universidade Federal do Rio de Janeiro, Caixa Postal 68528, Rio de Janeiro, RJ 21941-972 (Brazil); ElMassalami, M., E-mail: massalam@if.ufrj.br [Instituto de Física, Universidade Federal do Rio de Janeiro, Caixa Postal 68528, Rio de Janeiro, RJ 21941-972 (Brazil); Terrazos, L.A. [Centro de Educação e Saúde, Universidade Federal de Campina Grande, Cuité, PB 58175-000 (Brazil); Elhadi, M. [Instituto de Física, Universidade Federal do Rio de Janeiro, Caixa Postal 68528, Rio de Janeiro, RJ 21941-972 (Brazil); Takeya, H. [National Institute for Materials Science, 1-2-1, Sengen, Tsukuba, 305-0047 (Japan); Ghivelder, L. [Instituto de Física, Universidade Federal do Rio de Janeiro, Caixa Postal 68528, Rio de Janeiro, RJ 21941-972 (Brazil)

    2016-06-05

    Using a combination of theoretical (first-principles total-energy and electronic structure calculations) as well as experimental (structural, thermodynamics) techniques, we systematically investigated the influence of B incorporation on the structural, electronic and thermodynamic properties of a series of technologically-important B-containing AlNi matrix. Special attention was paid to calculating the energy cost of placing B at various sites within the cubic unit cell. The most energetically favorable defects were identified to be, depending on initial stoichiometry, substitutional B at Al site (B{sub Al}), Ni vacancy (V{sub Ni}), or Ni antisite (Ni{sub Al}). We show that the induced variation in the lattice parameters can be correlated with the type and concentration of the involved defects: e.g. the surge of V{sub Ni} defects leads to a stronger lattice-parameter reduction, that of Ni{sub Al} ones to a relatively weaker reduction while that of B{sub Al} defects to a much weaker influence. Both electronic band structure calculations as well as thermodynamics measurements indicate that the 3d bands of Ni are fully occupied and magnetically unpolarized and that the resulting N(E{sub F}) is very small: all studied compounds are normal conductors with no trace of superconductivity or magnetic polarization.

  5. Thermodynamic and structural properties of ball-milled mixtures composed of nano-structural graphite and alkali(-earth) metal hydride

    International Nuclear Information System (INIS)

    Miyaoka, Hiroki; Ichikawa, Takayuki; Fujii, Hironobu

    2007-01-01

    Hydrogen desorption properties of mechanically milled materials composed of nano-structural hydrogenated-graphite (C nano H x ) and alkali(-earth) metal hydride (MH; M = Na, Mg and Ca) were investigated from the thermodynamic and structural points of view. The hydrogen desorption temperature for all the C nano H x and MH composites was obviously lower than that of the corresponding each hydride. In addition, the desorption of hydrocarbons from C nano H x was significantly suppressed by making composite of C nano H x with MH, even though C nano H x itself thermally desorbs a considerably large amount of hydrocarbons. These results indicate that an interaction exists between C nano H x and MH, and hydrogen in both the phases is destabilized by a close contact between polar C-H groups in C nano H x and the MH solid phase. Moreover, a new type of chemical bonding between the nano-structural carbon (C nano ) and the Li, Ca, or Mg metal atoms may be formed after hydrogen desorption. Thus, the above metal-C-H system would be recognized as a new family of H-storage materials

  6. A Systematic Transport and Thermodynamic Study of Heavy Transition Metal Oxides with Hexagonal Structure

    Science.gov (United States)

    Butrouna, Kamal

    There is no apparent, dominant interaction in heavy transition metal oxides (TMO), especially in 5d-TMO, where all relevant interactions are of comparable energy scales, and therefore strongly compete. In particular, the spin-orbit interaction (SOI) strongly competes with the electron-lattice and on-site Coulomb interaction (U). Therefore, any tool that allows one to tune the relative strengths of SOI and U is expected to offer an opportunity for the discovery and study of novel materials. BaIrO3 is a magnetic insulator driven by SOI, whereas the isostructural BaRuO3 is a paramagnetic metal. The contrasting ground states have been shown to result from the critical role of SOI in the iridate. This dissertation thoroughly examines a wide array of newly observed novel phenomena induced by adjusting the relative strengths of SOI and U via a systematic chemical substitution of the Ru4+(4d 4) ions for Ir4+(5d5) ions in BaIrO3, i.e., in high quality single crystals of BaIr1--x RuxO3(0.0 ≤ x ≤ 1.0). Our investigation of structural, magnetic, transport and thermal properties reveals that Ru substitution directly rebalances the competing energies so profoundly that it generates a rich phase diagram for BaIr 1--xRuxO 3 featuring two major effects: (1) Light Ru doping (0 ≤ x ≤ 0.15) prompts a simultaneous and precipitous drop in both the magnetic ordering temperature TC and the electrical resistivity, which exhibits metal-insulator transition at around TC. (2) Heavier Ru doping (0.41 ≤ x ≤ 0.82) induces a robust metallic and spin frustration state. For comparison and contrast, we also substituted Rh4+(4d 5) ions for Ir4+(5d5) ions in BaIrO3, i.e. in BaIr1--xRhxO 3(0.0 ≤ x ≤ 0.1), where Rh only reduces the SOI, but without altering the band filling. Hence, this system remains tuned at the Mott instability and is very susceptible to disorder scattering which gives rise to Anderson localization. KEYWORDS: spin-orbit interaction, heavy transition metal oxides

  7. Nuclear resonance scattering of synchrotron radiation as a unique electronic, structural and thermodynamic probe

    International Nuclear Information System (INIS)

    Alp, E. Ercan; Sturhahn, Wolfgang; Toellner, Thomas S.; Zhao, Jiyong; Leu, Bogdan M.

    2012-01-01

    (SMS). However, to place these two techniques into some perspective with respect to other methods that yield related information, they display their version of a frequently used map of momentum and energy transfer diagram in figure 17.1. Here, various probes like electrons, neutrons, or light, i.e., Brillouin or Raman, and relatively newer forms of X-ray scattering are placed according to their range of energy and momentum transfer taking place during the measurements. Accordingly, NRIXS is a method that needs to be considered as a complementary probe to inelastic neutron and X-ray scattering, while SMS occupies a unique space due to its sensitivity to magnetism, structural deformations, valence, and spin states.

  8. Molecular thermodynamics of nonideal fluids

    CERN Document Server

    Lee, Lloyd L

    2013-01-01

    Molecular Thermodynamics of Nonideal Fluids serves as an introductory presentation for engineers to the concepts and principles behind and the advances in molecular thermodynamics of nonideal fluids. The book covers related topics such as the laws of thermodynamics; entropy; its ensembles; the different properties of the ideal gas; and the structure of liquids. Also covered in the book are topics such as integral equation theories; theories for polar fluids; solution thermodynamics; and molecular dynamics. The text is recommended for engineers who would like to be familiarized with the concept

  9. Thermodynamics of Accelerating Black Holes.

    Science.gov (United States)

    Appels, Michael; Gregory, Ruth; Kubizňák, David

    2016-09-23

    We address a long-standing problem of describing the thermodynamics of an accelerating black hole. We derive a standard first law of black hole thermodynamics, with the usual identification of entropy proportional to the area of the event horizon-even though the event horizon contains a conical singularity. This result not only extends the applicability of black hole thermodynamics to realms previously not anticipated, it also opens a possibility for studying novel properties of an important class of exact radiative solutions of Einstein equations describing accelerated objects. We discuss the thermodynamic volume, stability, and phase structure of these black holes.

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

    Science.gov (United States)

    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.

  11. Structures of PEP–PEO Block Copolymer Micelles: Effects of Changing Solvent and PEO Length and Comparison to a Thermodynamic Model

    DEFF Research Database (Denmark)

    Jensen, Grethe Vestergaard; Shi, Qing; Deen, G. Roshan

    2012-01-01

    Structures of poly(ethylene propylene)–poly(ethylene oxide) (PEP–PEO) block copolymer micelles were determined from small-angle X-ray scattering and static light scattering and compared to predictions from a thermodynamic model. Both the corona block length and the solvent water–ethanol ratio were...... changed, leading to a thorough test of this model. With increasing ethanol fraction, the PEP core–solvent interfacial tension decreases, and the solvent quality for PEO changes. The weight-average block masses were 5.0 kDa for PEP and 2.8–49 kDa for PEO. For the lowest PEO molar mass and samples in pure...... water (except for the highest PEO molar mass), the micelles were cylindrical; for other conditions they were spherical. The structural parameters can be reasonably well described by the thermodynamic model by Zhulina et al. [Macromolecules2005, 38 (12), 5330–5351]; however, they have a stronger...

  12. Structural and thermodynamic properties of new pyrazolo[3,4-d]pyridazinones

    Energy Technology Data Exchange (ETDEWEB)

    Frizzo, Clarissa P., E-mail: clarissa.frizzo@yahoo.com.br [Núcleo de Química de Heterociclos (NUQUIMHE), Department of Chemistry, Federal University of Santa Maria, UFSM, CEP: 97105-900 Santa Maria, RS (Brazil); Villetti, Marcos A. [Department of Physics, Federal University of Santa Maria, UFSM, CEP: 97105-900 Santa Maria, RS (Brazil); Tier, Aniele Z.; Gindri, Izabelle M.; Buriol, Lilian; Rosa, Fernanda A. [Núcleo de Química de Heterociclos (NUQUIMHE), Department of Chemistry, Federal University of Santa Maria, UFSM, CEP: 97105-900 Santa Maria, RS (Brazil); Claramunt, Rosa M.; Sanz, Dionisia [Departamento de Química Orgánica y Bio-Orgánica, Facultad de Ciencias, UNED, Senda del Rey 9, E-28040 Madrid (Spain); Martins, Marcos A.P. [Núcleo de Química de Heterociclos (NUQUIMHE), Department of Chemistry, Federal University of Santa Maria, UFSM, CEP: 97105-900 Santa Maria, RS (Brazil)

    2013-12-20

    Highlights: • New 4-substituted-pyrazolo[3,4-d]pyridazinones were synthesized. • Kinetic parameters were determined by Friedmam and Ozawa–Flynn–Wall (OFW) methods. • Compound 2a was more stable than the 2d independent of the model used. • Degradation reaction of 2a and 2d occurs in a single-step. • Amorphous content of 2a and 2d was 48% and 74%, respectively. - Abstract: This work describes the synthesis of new 4-substituted-pyrazolo[3,4-d]pyridazinones (R = C{sub 6}H{sub 5}, 4-F-C{sub 6}H{sub 4}, benzofur-2-yl, CF{sub 3}, 4-NO{sub 2}-C{sub 6}H{sub 4}) from the reaction of dicarbonylpyrazoles with hydrazine hydrate. Solid and solution-state NMR were used to unequivocally assign the structure and identification of the byproduct formed when R = 4-NO{sub 2}-C{sub 6}H{sub 4}. Geometrical features and the intermolecular interactions of compounds were described using single crystal X-ray diffraction. The thermal behavior of the compounds was studied using differential scanning calorimetry (DSC) and thermogravimetric analysis (TGA). Kinetic parameters, such as the activation energy (E{sub a}) and pre-exponential factor (A), were determined as a function of the conversion degree for the thermal decomposition of two compounds, by using the isoconversional methods of Friedman and Ozawa–Flynn–Wall (OFW). The results showed that the E{sub a} for thermal decomposition of compound with R = CF{sub 3} is always higher than for compound with R = C{sub 6}H{sub 5}, independent of the model used (Friedman or OFW), indicating that the former is more stable than the latter. Furthermore, the E{sub a} values for compounds with R = C{sub 6}H{sub 5} and CF{sub 3} are practically constant for all α values from 0.1 to 0.9, indicating the existence of a single-step degradation reaction. The kinetics results also reveal the linear dependence of E{sub a} on the pre-exponential factor. In addition, the 4-substituted-pyrazolo[3,4-d]pyridazinones studied have two types of thermal

  13. Stochastic thermodynamics

    Science.gov (United States)

    Eichhorn, Ralf; Aurell, Erik

    2014-04-01

    'Stochastic thermodynamics as a conceptual framework combines the stochastic energetics approach introduced a decade ago by Sekimoto [1] with the idea that entropy can consistently be assigned to a single fluctuating trajectory [2]'. This quote, taken from Udo Seifert's [3] 2008 review, nicely summarizes the basic ideas behind stochastic thermodynamics: for small systems, driven by external forces and in contact with a heat bath at a well-defined temperature, stochastic energetics [4] defines the exchanged work and heat along a single fluctuating trajectory and connects them to changes in the internal (system) energy by an energy balance analogous to the first law of thermodynamics. Additionally, providing a consistent definition of trajectory-wise entropy production gives rise to second-law-like relations and forms the basis for a 'stochastic thermodynamics' along individual fluctuating trajectories. In order to construct meaningful concepts of work, heat and entropy production for single trajectories, their definitions are based on the stochastic equations of motion modeling the physical system of interest. Because of this, they are valid even for systems that are prevented from equilibrating with the thermal environment by external driving forces (or other sources of non-equilibrium). In that way, the central notions of equilibrium thermodynamics, such as heat, work and entropy, are consistently extended to the non-equilibrium realm. In the (non-equilibrium) ensemble, the trajectory-wise quantities acquire distributions. General statements derived within stochastic thermodynamics typically refer to properties of these distributions, and are valid in the non-equilibrium regime even beyond the linear response. The extension of statistical mechanics and of exact thermodynamic statements to the non-equilibrium realm has been discussed from the early days of statistical mechanics more than 100 years ago. This debate culminated in the development of linear response

  14. Modern thermodynamics

    CERN Document Server

    Ben-Naim, Arieh

    2017-01-01

    This textbook introduces thermodynamics with a modern approach, starting from four fundamental physical facts (the atomic nature of matter, the indistinguishability of atoms and molecules of the same species, the uncertainty principle, and the existence of equilibrium states) and analyzing the behavior of complex systems with the tools of information theory, in particular with Shannon's measure of information (or SMI), which can be defined on any probability distribution. SMI is defined and its properties and time evolution are illustrated, and it is shown that the entropy is a particular type of SMI, i.e. the SMI related to the phase-space distribution for a macroscopic system at equilibrium. The connection to SMI allows the reader to understand what entropy is and why isolated systems follow the Second Law of Thermodynamics. The Second Llaw is also formulated for other systems, not thermally isolated and even open with respect to the transfer of particles. All the fundamental aspects of thermodynamics are d...

  15. Lattice dynamical and thermodynamical properties of ReB2, RuB2, and OsB2 compounds in the ReB2 structure

    International Nuclear Information System (INIS)

    Deligoz, E.; Colakoglu, K.; Ciftci, Y. O.

    2012-01-01

    Structural and lattice dynamical properties of ReB 2 , RuB 2 , and OsB 2 in the ReB 2 structure are studied in the framework of density functional theory within the generalized gradient approximation. The present results show that these compounds are dynamically stable for the considered structure. The temperature-dependent behaviors of thermodynamical properties such as internal energy, free energy, entropy, and heat capacity are also presented. The obtained results are in good agreement with the available experimental and theoretical data

  16. Structural thermodynamics of alloys

    CERN Document Server

    Manenc, Jack

    1973-01-01

    Technical progress has for a very long time been directly dependent on progress in metallurgy, which is itself connected with improvements in the technology of alloys. Metals are most frequently used in the form of alloys for several reasons: the quantity of pure metal in its native state in the earth's crust is very limited; pure metals must be extracted from ores which are themselves impure. Finally, the methods of treatment used lead more easily to alloys than to pure metals. The most typical case is that of iron, where a pure ore may be found, but which is the starting point for cast iron or steel, alloys of iron and carbon. In addition, the properties of alloys are in general superior to those of pure metals and modem metallurgy consists of controlling these properties so as to make them conform to the requirements of the design office. Whilst the engineer was formerly compelled to adapt his designs and constructions to the materials available, such as wood, stone, bronze, iron, cast iron and ordinary st...

  17. On the electronic, structural, and thermodynamic properties of Au supported on α-Fe{sub 2}O{sub 3} surfaces and their interaction with CO

    Energy Technology Data Exchange (ETDEWEB)

    Nguyen, Manh-Thuong, E-mail: manhth.nguyen@gmail.com; Gebauer, Ralph [The Abdus Salam International Centre for Theoretical Physics, Strada Costiera 11, 34151 Trieste (Italy); Farnesi Camellone, Matteo, E-mail: mfarnesi@sissa.it [CNR-IOM DEMOCRITOS, Istituto Officina dei Materiali, Consiglio Nazionale delle Ricerche and SISSA Scuola Internazionale di Studi Superiori Avanzati, Via Bonomea 265, I-34136 Trieste (Italy)

    2015-07-21

    Extensive first principles calculations are carried out to investigate Au monomers and dimers supported on α-Fe{sub 2}O{sub 3}(0001) surfaces in terms of structure optimizations, electronic structure analyses, and ab initio thermodynamics calculations of surface phase diagrams. All computations rely on density functional theory in the generalized gradient approximation (Perdew-Burke-Ernzerhof (PBE)) and account for on-site Coulomb interactions via inclusion of a Hubbard correction (PBE+U). The relative stability of Au monomers/dimers on the stoichiometric termination of α-Fe{sub 2}O{sub 3}(0001) decorated with various vacancies (multiple oxygen vacancies, iron vacancy, and mixed iron-oxygen vacancies) has been computed as a function of the oxygen chemical potential. The charge rearrangement induced by Au at the oxide contact is analyzed in detail and discussed. On one hand, ab initio thermodynamics predicts that under O-rich conditions, structures obtained by replacing a surface Fe atom with a Au atom are thermodynamically stable over a wide range of temperatures. On the other hand, the complex of a CO molecule on a Au atom substituting surface Fe atoms is thermodynamically stable only in a much more narrow range of values of the O chemical potential under O-rich conditions. In the case of a Au dimer, under O-rich conditions, supported Au atoms at an O-Fe di-vacancy are more stable. However, upon CO adsorption, the complex of a CO molecule and 2 Au atoms located at a single Fe vacancy is more favorable.

  18. An analytical coarse-graining method which preserves the free energy, structural correlations, and thermodynamic state of polymer melts from the atomistic to the mesoscale.

    Science.gov (United States)

    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.

  19. Nonequilibrium thermodynamics of nucleation

    NARCIS (Netherlands)

    Schweizer, M.; Sagis, L.M.C.

    2014-01-01

    We present a novel approach to nucleation processes based on the GENERIC framework (general equation for the nonequilibrium reversible-irreversible coupling). Solely based on the GENERIC structure of time-evolution equations and thermodynamic consistency arguments of exchange processes between a

  20. On Teaching Thermodynamics

    Science.gov (United States)

    Debbasch, F.

    2011-01-01

    The logical structure of classical thermodynamics is presented in a modern, geometrical manner. The first and second law receive clear, operatively oriented statements and the Gibbs free energy extremum principle is fully discussed. Applications relevant to chemistry, such as phase transitions, dilute solutions theory and, in particular, the law…

  1. Statistical thermodynamics

    CERN Document Server

    Schrödinger, Erwin

    1952-01-01

    Nobel Laureate's brilliant attempt to develop a simple, unified standard method of dealing with all cases of statistical thermodynamics - classical, quantum, Bose-Einstein, Fermi-Dirac, and more.The work also includes discussions of Nernst theorem, Planck's oscillator, fluctuations, the n-particle problem, problem of radiation, much more.

  2. Structural and thermodynamic study of dicesium molybdate Cs2Mo2O7: Implications for fast neutron reactors

    Science.gov (United States)

    Smith, A. L.; Kauric, G.; van Eijck, L.; Goubitz, K.; Wallez, G.; Griveau, J.-C.; Colineau, E.; Clavier, N.; Konings, R. J. M.

    2017-09-01

    The structure of α-Cs2Mo2O7 (monoclinic in space group P21 / c), which can form during irradiation in fast breeder reactors in the space between nuclear fuel and cladding, has been refined in this work at room temperature from neutron diffraction data. Furthermore, the compounds' thermal expansion and polymorphism have been investigated using high temperature X-ray diffraction combined with high temperature Raman spectroscopy. A phase transition has been observed at Ttr(α → β)=(621.9±0.8) K using Differential Scanning Calorimetry, and the structure of the β-Cs2Mo2O7 phase, orthorhombic in space group Pbcm, has been solved ab initio from the high temperature X-ray diffraction data. Furthermore, the low temperature heat capacity of α-Cs2Mo2O7 has been measured in the temperature range T=(1.9-313.2) K using a Quantum Design PPMS (Physical Property Measurement System) calorimeter. The heat capacity and entropy values at T=298.15 K have been derived as Cp,mo (Cs2Mo2O7 , cr , 298.15 K) = (211.9 ± 2.1) J K-1mol-1 and Smo (Cs2Mo2O7 , cr , 298.15 K) = (317.4 ± 4.3) J K-1mol-1 . When combined with the enthalpy of formation reported in the literature, these data yield standard entropy and Gibbs energy of formation as Δf Smo (Cs2Mo2O7 , cr , 298.15 K) = - (628.2 ± 4.4) J K-1mol-1 and Δf Gmo (Cs2Mo2O7 , cr , 298.15 K) = - (2115.1 ± 2.5) kJmol-1 . Finally, the cesium partial pressure expected in the gap between fuel and cladding following the disproportionation reaction 2Cs2MoO4=Cs2Mo2O7+2Cs(g)+ 1/2 O2(g) has been calculated from the newly determined thermodynamic functions.

  3. Determination of structural, thermodynamic and phase properties in the Na2S-H2O system for application in a chemical heat pump

    International Nuclear Information System (INIS)

    Boer, R. de; Haije, W.G.; Veldhuis, J.B.J.

    2002-01-01

    Structural, thermodynamic and phase properties in the Na 2 S-H 2 O system for application in a chemical heat pump have been investigated using XRD, TG/DTA and melting point and vapour pressure determinations. Apart from the known crystalline phases Na 2 S·9H 2 O, Na 2 S·5H 2 O and Na 2 S a new phase Na 2 S·2H 2 O has been proven to exist. Na 2 S·((1)/(2))H 2 O is not a phase but a 3:1 mixture of Na 2 S and Na 2 S·2H 2 O, presumably stabilised by very slow dehydration kinetics. The vapour pressure-temperature equilibria of the sodium sulphide hydrates have been determined and a consistent set of thermodynamic functions for these compounds has been derived. XRD measurements indicate the topotactic character of the transitions between the hydration states

  4. Ab-initio study of structural, elastic, electronic and thermodynamic properties of BaxSr1−xS ternary alloys

    Directory of Open Access Journals (Sweden)

    Chelli S.

    2015-12-01

    Full Text Available The structural, elastic, electronic and thermodynamic properties of BaxSr1−xS ternary alloys have been investigated using the full-potential (linearized augmented plane wave method. The ground state properties, such as lattice constant, bulk modulus and elastic constants, are in good agreement with numerous experimental and theoretical data. The dependence of the lattice parameters, bulk modulus and band gap on the composition x was analyzed. Deviation of the lattice constant from Vegard’s law and the bulk modulus from linear concentration dependence (LCD was observed. The microscopic origins of the gap bowing were explained by using the approach of Zunger et al. The thermodynamic stability of BaxSr1−xS alloy was investigated by calculating the excess enthalpy of mixing, ΔHm and the calculated phase diagram showed a broad miscibility gap with a critical temperature.

  5. Structural and thermodynamic characterization of the Escherichia coli RelBE toxin-antitoxin system: indication for a functional role of differential stability

    DEFF Research Database (Denmark)

    Cherny, Izhack; Overgaard, Martin; Borch, Jonas

    2007-01-01

    on the folding and stability of the protein pair in solution. Here we structurally and thermodynamically characterize the RelBE system components from E. coli in solution, both separately and in their complexed state. The RelB antitoxin, an alpha-helical protein according to circular dichroism and infrared.......5 degrees C, and exhibits exceptional sensitivity to heat. Complex formation, accompanied by a structural transition, leads to a 12 degrees C increase in the TM and substantial heat resistance. Moreover, in vivo interaction and protein footprint experiments indicate that the C-terminal part of Rel...

  6. Modeling thermodynamic properties of propane or tetrahydrofuran mixed with carbon dioxide or methane in structure-II clathrate hydrates

    NARCIS (Netherlands)

    Fang, Bin; Ning, Fulong; Cao, Pinqiang; Peng, Li; Wu, Jianyang; Zhang, Zhun; Vlugt, T.J.H.; Kjelstrup, Signe

    2017-01-01

    A sound knowledge of thermodynamic properties of sII hydrates is of great importance to understand the stability of sII gas hydrates in petroleum pipelines and in natural settings. Here, we report direct molecular dynamics (MD) simulations of the thermal expansion coefficient, the

  7. Contact Geometry of Mesoscopic Thermodynamics and Dynamics

    Directory of Open Access Journals (Sweden)

    Miroslav Grmela

    2014-03-01

    Full Text Available The time evolution during which macroscopic systems reach thermodynamic equilibrium states proceeds as a continuous sequence of contact structure preserving transformations maximizing the entropy. This viewpoint of mesoscopic thermodynamics and dynamics provides a unified setting for the classical equilibrium and nonequilibrium thermodynamics, kinetic theory, and statistical mechanics. One of the illustrations presented in the paper is a new version of extended nonequilibrium thermodynamics with fluxes as extra state variables.

  8. Co-operative intra-protein structural response due to protein-protein complexation revealed through thermodynamic quantification: study of MDM2-p53 binding.

    Science.gov (United States)

    Samanta, Sudipta; Mukherjee, Sanchita

    2017-10-01

    The p53 protein activation protects the organism from propagation of cells with damaged DNA having oncogenic mutations. In normal cells, activity of p53 is controlled by interaction with MDM2. The well understood p53-MDM2 interaction facilitates design of ligands that could potentially disrupt or prevent the complexation owing to its emergence as an important objective for cancer therapy. However, thermodynamic quantification of the p53-peptide induced structural changes of the MDM2-protein remains an area to be explored. This study attempts to understand the conformational free energy and entropy costs due to this complex formation from the histograms of dihedral angles generated from molecular dynamics simulations. Residue-specific quantification illustrates that, hydrophobic residues of the protein contribute maximum to the conformational thermodynamic changes. Thermodynamic quantification of structural changes of the protein unfold the fact that, p53 binding provides a source of inter-element cooperativity among the protein secondary structural elements, where the highest affected structural elements (α2 and α4) found at the binding site of the protein affects faraway structural elements (β1 and Loop1) of the protein. The communication perhaps involves water mediated hydrogen bonded network formation. Further, we infer that in inhibitory F19A mutation of P53, though Phe19 is important in the recognition process, it has less prominent contribution in the stability of the complex. Collectively, this study provides vivid microscopic understanding of the interaction within the protein complex along with exploring mutation sites, which will contribute further to engineer the protein function and binding affinity.

  9. Co-operative intra-protein structural response due to protein-protein complexation revealed through thermodynamic quantification: study of MDM2-p53 binding

    Science.gov (United States)

    Samanta, Sudipta; Mukherjee, Sanchita

    2017-10-01

    The p53 protein activation protects the organism from propagation of cells with damaged DNA having oncogenic mutations. In normal cells, activity of p53 is controlled by interaction with MDM2. The well understood p53-MDM2 interaction facilitates design of ligands that could potentially disrupt or prevent the complexation owing to its emergence as an important objective for cancer therapy. However, thermodynamic quantification of the p53-peptide induced structural changes of the MDM2-protein remains an area to be explored. This study attempts to understand the conformational free energy and entropy costs due to this complex formation from the histograms of dihedral angles generated from molecular dynamics simulations. Residue-specific quantification illustrates that, hydrophobic residues of the protein contribute maximum to the conformational thermodynamic changes. Thermodynamic quantification of structural changes of the protein unfold the fact that, p53 binding provides a source of inter-element cooperativity among the protein secondary structural elements, where the highest affected structural elements (α2 and α4) found at the binding site of the protein affects faraway structural elements (β1 and Loop1) of the protein. The communication perhaps involves water mediated hydrogen bonded network formation. Further, we infer that in inhibitory F19A mutation of P53, though Phe19 is important in the recognition process, it has less prominent contribution in the stability of the complex. Collectively, this study provides vivid microscopic understanding of the interaction within the protein complex along with exploring mutation sites, which will contribute further to engineer the protein function and binding affinity.

  10. First principles thermodynamics of alloys

    International Nuclear Information System (INIS)

    Ducastelle, F.

    1993-01-01

    We present a brief report on the methods of solid state physics (electronic structure, statistical thermodynamics) that allow us to discuss the phase stability of alloys and to determine their phase diagrams. (orig.)

  11. Quantum Thermodynamics at Strong Coupling: Operator Thermodynamic Functions and Relations

    Directory of Open Access Journals (Sweden)

    Jen-Tsung Hsiang

    2018-05-01

    Full Text Available Identifying or constructing a fine-grained microscopic theory that will emerge under specific conditions to a known macroscopic theory is always a formidable challenge. Thermodynamics is perhaps one of the most powerful theories and best understood examples of emergence in physical sciences, which can be used for understanding the characteristics and mechanisms of emergent processes, both in terms of emergent structures and the emergent laws governing the effective or collective variables. Viewing quantum mechanics as an emergent theory requires a better understanding of all this. In this work we aim at a very modest goal, not quantum mechanics as thermodynamics, not yet, but the thermodynamics of quantum systems, or quantum thermodynamics. We will show why even with this minimal demand, there are many new issues which need be addressed and new rules formulated. The thermodynamics of small quantum many-body systems strongly coupled to a heat bath at low temperatures with non-Markovian behavior contains elements, such as quantum coherence, correlations, entanglement and fluctuations, that are not well recognized in traditional thermodynamics, built on large systems vanishingly weakly coupled to a non-dynamical reservoir. For quantum thermodynamics at strong coupling, one needs to reexamine the meaning of the thermodynamic functions, the viability of the thermodynamic relations and the validity of the thermodynamic laws anew. After a brief motivation, this paper starts with a short overview of the quantum formulation based on Gelin & Thoss and Seifert. We then provide a quantum formulation of Jarzynski’s two representations. We show how to construct the operator thermodynamic potentials, the expectation values of which provide the familiar thermodynamic variables. Constructing the operator thermodynamic functions and verifying or modifying their relations is a necessary first step in the establishment of a viable thermodynamics theory for

  12. Solvation thermodynamics

    CERN Document Server

    Ben-Naim, Arieh

    1987-01-01

    This book deals with a subject that has been studied since the beginning of physical chemistry. Despite the thousands of articles and scores of books devoted to solvation thermodynamics, I feel that some fundamen­ tal and well-established concepts underlying the traditional approach to this subject are not satisfactory and need revision. The main reason for this need is that solvation thermodynamics has traditionally been treated in the context of classical (macroscopic) ther­ modynamics alone. However, solvation is inherently a molecular pro­ cess, dependent upon local rather than macroscopic properties of the system. Therefore, the starting point should be based on statistical mechanical methods. For many years it has been believed that certain thermodynamic quantities, such as the standard free energy (or enthalpy or entropy) of solution, may be used as measures of the corresponding functions of solvation of a given solute in a given solvent. I first challenged this notion in a paper published in 1978 b...

  13. Ab initio investigation of thermodynamic stability and structure of cell molecules B3N4H8 and Be4O4H8

    International Nuclear Information System (INIS)

    Minyaev, R.M.

    2000-01-01

    Ab initio calculation methods (RHF/6-31G, MP2(full)/6-31G and MP2(full)/6-311++G) ) are used to investigate thermodynamic stability, energy and structural characteristics of different position isomers of isoelectron B 3 N 4 H 8 (1) and Be 4 O 4 H 8 (2) systems with cubane structure. High thermodynamic stability of these system is shown. Decomposition of structure (1) into two 1,3,2,4-diazadiborethidine molecules or four molecules of iminoborane HBNH is an endothermal process and needs 10.1 (RHF/6-31G), 39/6 (MP2(full)/6-31G) Cal/mol and 140.6 (RHF/6-31G), 161.4 (MP2(full)/6-31G) Cal/mol accordingly. Decomposition of structure (2) into two 1,3,2,4-dioxydiberyllotidine or four molecules of HBeOH is an endothermal process too and needs 22.1 (RHF/6-31G), 39.8 (MP2(full)/6-31G) Cal/mol and 127.1(RHF/6-31G), 155.2 MP2(full)/6-31G) Cal/mol accordingly. Geometrical characteristics of simple BeH 2 , Be 2 , Be 2 H 2 , Be 2 H 4 , BeO, Be 2 O 2 molecules are calculated [ru

  14. Synthesis, crystal structures and thermodynamic properties of two novel lanthanide complexes based on 3,4-diethoxybenzoic acid and 2,2′-bipyridine

    International Nuclear Information System (INIS)

    Jin, Cheng-Wei; Wang, Ye; Ren, Ning; Geng, Li-Na; Zhang, Jian-Jun

    2016-01-01

    Highlights: • Two novel complexes crystal structures are obtained. • The 1-D chain and 2D layer structures were formed via π–π stacking interactions. • The pathway of thermal decomposition for title complexes were investigated. • The molar heat capacities and thermodynamic functions were calculated. - Abstract: Two binuclear lanthanide complexes [Ln(3,4,-DEOBA) 3 DIPY] 2 DIPY (Ln = Tb (1), Dy (2); 3,4,-DEOBA = 3,4-diethoxybenzoate; DIPY = 2,2′-bipyridine) have been synthesized and characterized. The single crystals of complexes 1 and 2 were obtained. And the two complexes are isostructural with a coordination number of eight to form a distorted square antiprism. Carboxylic groups adopt two modes coordinating with Ln(III) ions: bidentate chelate, and bridging bidentate. Binuclear complexes 1 and 2 are stitched together via π–π stacking interactions to form 1D chain and 2D layer supramolecular structures. The two complexes were characterized by elemental analysis, IR spectra, and powder X-ray diffraction. The luminescence spectra of complexes 1 and 2 show the characteristic emissions of Tb 3+ ( 5 D 4 → 7 F 6-3 ) and Dy 3+ ( 4 F 9/2 → 6 H 15/2 , 6 H 13/2 ). The thermal decomposition mechanisms for title complexes were studied by the technology of TG-FTIR. And the heat capacities of two complexes were measured by DSC in the temperature range from 258.15 to 343.15 K. The smoothed heat capacities and thermodynamic functions for complexes 1 and 2 were calculated by fitted polynomial and thermodynamic equations.

  15. Investigations of structural, elastic, electronic and thermodynamic properties of lutetium filled skutterudite LuFe4P12 under pressure effect: FP-LMTO method

    Directory of Open Access Journals (Sweden)

    Boudia Keltouma

    2015-12-01

    Full Text Available Structural, elastic, electronic and thermodynamic properties of ternary cubic filled skutterudite compound were calculated. We have computed the elastic modulus and its pressure dependence. From the elastic parameter behavior, it is inferred that this compound is elastically stable and ductile in nature. Through the quasi-harmonic Debye model, in which phononic effects are considered, the effect of pressure P (0 to 50 GPa and temperature T (0 to 3000 °C on the lattice constant, elastic parameters, bulk modulus B, heat capacity, thermal expansion coefficient α, internal energy U, entropy S, Debye temperature θD, Helmholtz free energy A, and Gibbs free energy G are investigated.

  16. Microcanonical thermodynamics and statistical fragmentation of dissipative systems. The topological structure of the N-body phase space

    Science.gov (United States)

    Gross, D. H. E.

    1997-01-01

    This review is addressed to colleagues working in different fields of physics who are interested in the concepts of microcanonical thermodynamics, its relation and contrast to ordinary, canonical or grandcanonical thermodynamics, and to get a first taste of the wide area of new applications of thermodynamical concepts like hot nuclei, hot atomic clusters and gravitating systems. Microcanonical thermodynamics describes how the volume of the N-body phase space depends on the globally conserved quantities like energy, angular momentum, mass, charge, etc. Due to these constraints the microcanonical ensemble can behave quite differently from the conventional, canonical or grandcanonical ensemble in many important physical systems. Microcanonical systems become inhomogeneous at first-order phase transitions, or with rising energy, or with external or internal long-range forces like Coulomb, centrifugal or gravitational forces. Thus, fragmentation of the system into a spatially inhomogeneous distribution of various regions of different densities and/or of different phases is a genuine characteristic of the microcanonical ensemble. In these cases which are realized by the majority of realistic systems in nature, the microcanonical approach is the natural statistical description. We investigate this most fundamental form of thermodynamics in four different nontrivial physical cases: (I) Microcanonical phase transitions of first and second order are studied within the Potts model. The total energy per particle is a nonfluctuating order parameter which controls the phase which the system is in. In contrast to the canonical form the microcanonical ensemble allows to tune the system continuously from one phase to the other through the region of coexisting phases by changing the energy smoothly. The configurations of coexisting phases carry important informations about the nature of the phase transition. This is more remarkable as the canonical ensemble is blind against these

  17. Characterization of the Elusive Conformers of Glycine from State-of-the-Art Structural, Thermodynamic, and Spectroscopic Computations: Theory Complements Experiment.

    Science.gov (United States)

    Barone, Vincenzo; Biczysko, Malgorzata; Bloino, Julien; Puzzarini, Cristina

    2013-03-12

    A state-of-the-art computational strategy for the evaluation of accurate molecular structures as well as thermodynamic and spectroscopic properties along with the direct simulation of infrared (IR) and Raman spectra is established, validated (on the basis of the experimental data available for the Ip glycine conformer) and then used to provide a reliable and accurate characterization of the elusive IVn/gtt and IIIp/tct glycine conformers. The integrated theoretical model proposed is based on accurate post-Hartree-Fock computations (involving composite schemes) of energies, structures, properties, and harmonic force fields coupled to DFT corrections for the proper inclusion of vibrational effects at an anharmonic level (as provided by general second-order perturbative approach). It is shown that the approach presented here allows the evaluation of structural, thermodynamic, and spectroscopic properties with an overall accuracy of about, or better than, 0.001 Å, 20 MHz, 1 kJ·mol(-1), and 10 cm(-1) for bond distances, rotational constants, conformational enthalpies, and vibrational frequencies, respectively. The high accuracy of the computational results allows one to support and complement experimental studies, thus providing (i) an unequivocal identification of several conformers concomitantly present in the experimental mixture and (ii) data not available or difficult to experimentally derive.

  18. Intrinsic Thermodynamics and Structure Correlation of Benzenesulfonamides with a Pyrimidine Moiety Binding to Carbonic Anhydrases I, II, VII, XII, and XIII.

    Directory of Open Access Journals (Sweden)

    Miglė Kišonaitė

    Full Text Available The early stage of drug discovery is often based on selecting the highest affinity lead compound. To this end the structural and energetic characterization of the binding reaction is important. The binding energetics can be resolved into enthalpic and entropic contributions to the binding Gibbs free energy. Most compound binding reactions are coupled to the absorption or release of protons by the protein or the compound. A distinction between the observed and intrinsic parameters of the binding energetics requires the dissection of the protonation/deprotonation processes. Since only the intrinsic parameters can be correlated with molecular structural perturbations associated with complex formation, it is these parameters that are required for rational drug design. Carbonic anhydrase (CA isoforms are important therapeutic targets to treat a range of disorders including glaucoma, obesity, epilepsy, and cancer. For effective treatment isoform-specific inhibitors are needed. In this work we investigated the binding and protonation energetics of sixteen [(2-pyrimidinylthioacetyl]benzenesulfonamide CA inhibitors using isothermal titration calorimetry and fluorescent thermal shift assay. The compounds were built by combining four sulfonamide headgroups with four tailgroups yielding 16 compounds. Their intrinsic binding thermodynamics showed the limitations of the functional group energetic additivity approach used in fragment-based drug design, especially at the level of enthalpies and entropies of binding. Combined with high resolution crystal structural data correlations were drawn between the chemical functional groups on selected inhibitors and intrinsic thermodynamic parameters of CA-inhibitor complex formation.

  19. Intrinsic Thermodynamics and Structure Correlation of Benzenesulfonamides with a Pyrimidine Moiety Binding to Carbonic Anhydrases I, II, VII, XII, and XIII

    Science.gov (United States)

    Kišonaitė, Miglė; Zubrienė, Asta; Čapkauskaitė, Edita; Smirnov, Alexey; Smirnovienė, Joana; Kairys, Visvaldas; Michailovienė, Vilma; Manakova, Elena; Gražulis, Saulius; Matulis, Daumantas

    2014-01-01

    The early stage of drug discovery is often based on selecting the highest affinity lead compound. To this end the structural and energetic characterization of the binding reaction is important. The binding energetics can be resolved into enthalpic and entropic contributions to the binding Gibbs free energy. Most compound binding reactions are coupled to the absorption or release of protons by the protein or the compound. A distinction between the observed and intrinsic parameters of the binding energetics requires the dissection of the protonation/deprotonation processes. Since only the intrinsic parameters can be correlated with molecular structural perturbations associated with complex formation, it is these parameters that are required for rational drug design. Carbonic anhydrase (CA) isoforms are important therapeutic targets to treat a range of disorders including glaucoma, obesity, epilepsy, and cancer. For effective treatment isoform-specific inhibitors are needed. In this work we investigated the binding and protonation energetics of sixteen [(2-pyrimidinylthio)acetyl]benzenesulfonamide CA inhibitors using isothermal titration calorimetry and fluorescent thermal shift assay. The compounds were built by combining four sulfonamide headgroups with four tailgroups yielding 16 compounds. Their intrinsic binding thermodynamics showed the limitations of the functional group energetic additivity approach used in fragment-based drug design, especially at the level of enthalpies and entropies of binding. Combined with high resolution crystal structural data correlations were drawn between the chemical functional groups on selected inhibitors and intrinsic thermodynamic parameters of CA-inhibitor complex formation. PMID:25493428

  20. Ecosystem thermodynamics

    International Nuclear Information System (INIS)

    Gomez Palacio, German Rau

    1998-01-01

    Ecology is no more a descriptive and self-sufficient science. Many viewpoints are needed simultaneously to give a full coverage of such complex systems: ecosystems. These viewpoints come from physics, chemistry, and nuclear physics, without a new far from equilibrium thermodynamics and without new mathematical tools such as catastrophe theory, fractal theory, cybernetics and network theory, the development of ecosystem science would never have reached the point of today. Some ideas are presented about the importance that concept such as energy, entropy, exergy information and none equilibrium have in the analysis of processes taking place in ecosystems

  1. Chemical thermodynamics. An introduction

    Energy Technology Data Exchange (ETDEWEB)

    Keszei, Ernoe [Budapest Univ. (Hungary). Dept. of Physical Chemistry

    2012-07-01

    Eminently suitable as a required textbook comprising complete material for or an undergraduate chemistry major course in chemical thermodynamics. Clearly explains details of formal derivations that students can easily follow and so master applied mathematical operations. Offers problems and solutions at the end of each chapter for self-test and self- or group study. This course-derived undergraduate textbook provides a concise explanation of the key concepts and calculations of chemical thermodynamics. Instead of the usual 'classical' introduction, this text adopts a straightforward postulatory approach that introduces thermodynamic potentials such as entropy and energy more directly and transparently. Structured around several features to assist students' understanding, Chemical Thermodynamics: - Develops applications and methods for the ready treatment of equilibria on a sound quantitative basis. - Requires minimal background in calculus to understand the text and presents formal derivations to the student in a detailed but understandable way. - Offers end-of-chapter problems (and answers) for self-testing and review and reinforcement, of use for self- or group study. This book is suitable as essential reading for courses in a bachelor and master chemistry program and is also valuable as a reference or textbook for students of physics, biochemistry and materials science.

  2. Thermodynamic metrics and optimal paths.

    Science.gov (United States)

    Sivak, David A; Crooks, Gavin E

    2012-05-11

    A fundamental problem in modern thermodynamics is how a molecular-scale machine performs useful work, while operating away from thermal equilibrium without excessive dissipation. To this end, we derive a friction tensor that induces a Riemannian manifold on the space of thermodynamic states. Within the linear-response regime, this metric structure controls the dissipation of finite-time transformations, and bestows optimal protocols with many useful properties. We discuss the connection to the existing thermodynamic length formalism, and demonstrate the utility of this metric by solving for optimal control parameter protocols in a simple nonequilibrium model.

  3. Large-deviation principles, stochastic effective actions, path entropies, and the structure and meaning of thermodynamic descriptions

    International Nuclear Information System (INIS)

    Smith, Eric

    2011-01-01

    The meaning of thermodynamic descriptions is found in large-deviations scaling (Ellis 1985 Entropy, Large Deviations, and Statistical Mechanics (New York: Springer); Touchette 2009 Phys. Rep. 478 1-69) of the probabilities for fluctuations of averaged quantities. The central function expressing large-deviations scaling is the entropy, which is the basis both for fluctuation theorems and for characterizing the thermodynamic interactions of systems. Freidlin-Wentzell theory (Freidlin and Wentzell 1998 Random Perturbations in Dynamical Systems 2nd edn (New York: Springer)) provides a quite general formulation of large-deviations scaling for non-equilibrium stochastic processes, through a remarkable representation in terms of a Hamiltonian dynamical system. A number of related methods now exist to construct the Freidlin-Wentzell Hamiltonian for many kinds of stochastic processes; one method due to Doi (1976 J. Phys. A: Math. Gen. 9 1465-78; 1976 J. Phys. A: Math. Gen. 9 1479) and Peliti (1985 J. Physique 46 1469; 1986 J. Phys. A: Math. Gen. 19 L365, appropriate to integer counting statistics, is widely used in reaction-diffusion theory. Using these tools together with a path-entropy method due to Jaynes (1980 Annu. Rev. Phys. Chem. 31 579-601), this review shows how to construct entropy functions that both express large-deviations scaling of fluctuations, and describe system-environment interactions, for discrete stochastic processes either at or away from equilibrium. A collection of variational methods familiar within quantum field theory, but less commonly applied to the Doi-Peliti construction, is used to define a 'stochastic effective action', which is the large-deviations rate function for arbitrary non-equilibrium paths. We show how common principles of entropy maximization, applied to different ensembles of states or of histories, lead to different entropy functions and different sets of thermodynamic state variables. Yet the relations among all these levels of

  4. Molecular dynamics simulation of the ionic liquid N-octylpyridinium tetrafluoroborate and acetonitrile: Thermodynamic and structural properties

    Science.gov (United States)

    Zhou, Siwen; Zhu, Guanglai; Kang, Xianqu; Li, Qiang; Sha, Maolin; Cui, Zhifeng; Xu, Xinsheng

    2018-06-01

    Using molecular dynamics simulation, the research obtained the thermodynamic properties and microstructures of the mixture of N-octylpyridinium tetrafluoroborate and acetonitrile, including density, self-diffusion coefficients, excess properties, radial distribution functions (RDFs) and spatial distribution functions (SDFs). Both RDFs and SDFs indicate that the local microstructure of the polar region is different from the nonpolar region with different mole fraction of ionic liquids. Acetonitrile could increase the order of the polar regions. While with acetonitrile increasing, the orderliness of the nonpolar region increases firstly and then decreases. In relatively dilute solution, ionic liquids were dispersed to form small aggregates wrapped by acetonitrile.

  5. Solvation Structure and Thermodynamic Mapping (SSTMap): An Open-Source, Flexible Package for the Analysis of Water in Molecular Dynamics Trajectories.

    Science.gov (United States)

    Haider, Kamran; Cruz, Anthony; Ramsey, Steven; Gilson, Michael K; Kurtzman, Tom

    2018-01-09

    We have developed SSTMap, a software package for mapping structural and thermodynamic water properties in molecular dynamics trajectories. The package introduces automated analysis and mapping of local measures of frustration and enhancement of water structure. The thermodynamic calculations are based on Inhomogeneous Fluid Solvation Theory (IST), which is implemented using both site-based and grid-based approaches. The package also extends the applicability of solvation analysis calculations to multiple molecular dynamics (MD) simulation programs by using existing cross-platform tools for parsing MD parameter and trajectory files. SSTMap is implemented in Python and contains both command-line tools and a Python module to facilitate flexibility in setting up calculations and for automated generation of large data sets involving analysis of multiple solutes. Output is generated in formats compatible with popular Python data science packages. This tool will be used by the molecular modeling community for computational analysis of water in problems of biophysical interest such as ligand binding and protein function.

  6. Study of pressure variation effect on structural, opto-electronic, elastic, mechanical, and thermodynamic properties of SrLiF3

    Science.gov (United States)

    Erum, Nazia; Iqbal, Muhammad Azhar

    2017-11-01

    The structural, electronic, elastic, optical and thermodynamic properties of cubic fluoroperovskite SrLiF3 at ambient and high-pressure are investigated by using first-principles total energy calculations within the framework of Generalized Gradient Approximation (GGA), combined with Quasi-harmonic Debye model in which the phonon effects are considered. The pressure effects are determined in the range of 0-50 GPa, in which cubic stability of SrLiF3 fluoroperovskite remains valid. The computed lattice parameters agree well with experimental and previous theoretical results. Decrease in lattice constant and bonds length is observed with the increase in pressure from 0 to 50 GPa. The effect of increase in pressure on electronic 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 elastic constants and their related mechanical parameters have been discussed in detail. All the calculated optical properties such as the complex dielectric function Ԑ(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 neff, via sum rules shift towards the higher energies under the application of pressure. Moreover, important thermodynamic properties heat capacities (Cp and Cv), volume expansion coefficient (α), and Debye temperature (θD) are predicted successfully in the wide temperature and pressure ranges.

  7. An investigation on the structure, spectroscopy and thermodynamic aspects of Br2((-))(H2O)n clusters using a conjunction of stochastic and quantum chemical methods.

    Science.gov (United States)

    Naskar, Pulak; Chaudhury, Pinaki

    2016-06-28

    In this work we obtained global as well as local structures of Br2((-))(H2O)n clusters for n = 2 to 6 followed by the study of IR-spectral features and thermochemistry for the structures. The way adopted by us to obtain structures is not the conventional one used in most cases. Here we at first generated excellent quality pre-optimized structures by exploring the suitable empirical potential energy surface using stochastic optimizer simulated annealing. These structures are then further refined using quantum chemical calculations to obtain the final structures, and spectral and thermodynamic features. We clearly showed that our approach results in very quick and better convergence which reduces the computational cost and obviously using the strategy we are able to get one [i.e. global] or more than one [i.e. global and local(s)] energetically lower structures than those which are already reported for a given cluster size. Moreover, IR-spectral results and the evolutionary trends in interaction energy, solvation energy and vertical detachment energy for global structures of each size have also been presented to establish the utility of the procedure employed.

  8. Equilibrium thermodynamics

    CERN Document Server

    de Oliveira, Mário J

    2017-01-01

    This textbook provides an exposition of equilibrium thermodynamics and its applications to several areas of physics with particular attention to phase transitions and critical phenomena. The applications include several areas of condensed matter physics and include also a chapter on thermochemistry. Phase transitions and critical phenomena are treated according to the modern development of the field, based on the ideas of universality and on the Widom scaling theory. For each topic, a mean-field or Landau theory is presented to describe qualitatively the phase transitions. These theories include the van der Waals theory of the liquid-vapor transition, the Hildebrand-Heitler theory of regular mixtures, the Griffiths-Landau theory for multicritical points in multicomponent systems, the Bragg-Williams theory of order-disorder in alloys, the Weiss theory of ferromagnetism, the Néel theory of antiferromagnetism, the Devonshire theory for ferroelectrics and Landau-de Gennes theory of liquid crystals. This new edit...

  9. High-pressure structural, elastic, and thermodynamic properties of zircon-type HoPO4 and TmPO4

    International Nuclear Information System (INIS)

    Gomis, O; Lavina, B; Rodríguez-Hernández, P; Muñoz, A; Errandonea, R; Errandonea, D; Bettinelli, M

    2017-01-01

    Zircon-type holmium phosphate (HoPO 4 ) and thulium phosphate (TmPO 4 ) have been studied by single-crystal x-ray diffraction and ab initio calculations. We report on the influence of pressure on the crystal structure, and on the elastic and thermodynamic properties. The equation of state for both compounds is accurately determined. We have also obtained information on the polyhedral compressibility which is used to explain the anisotropic axial compressibility and the bulk compressibility. Both compounds are ductile and more resistive to volume compression than to shear deformation at all pressures. Furthermore, the elastic anisotropy is enhanced upon compression. Finally, the calculations indicate that the possible causes that make the zircon structure unstable are mechanical instabilities and the softening of a silent B 1u mode. (paper)

  10. Adsorptioin performance of modified nkalagu bentonite in dye removal: kinetics, equilibrium, thermodynamics and structureal properties of the modified samples

    International Nuclear Information System (INIS)

    Ajemba, R.O.

    2015-01-01

    The adsorption performance of modified Nkalagu bentonite in removing Congo red (CR) from solution was investigated. The raw bentonite was modified by three different physicochemical methods: thermal activation (TA), acid activation (AA), and combined acid and thermal activation (ATA). The Congo red adsorption increased with increase in contact time, initial dye concentration, adsorbent dosage, temperature, and pH change. The results of the kinetics analysis of the adsorption data revealed that adsorption follows pseudo second-order kinetics. Analysis of the equilibrium data showed that Langmuir isotherm provided a better fit to the data. Evaluation of the thermodynamic parameters revealed that adsorption process is spontaneous and endothermic. The results from this study suggest that a combination of thermal and acid activation is an effective modification method to improve adsorption capacity of bentonite and makes the bentonite as low-cost adsorbent for removal of water pollutants. (author)

  11. Idealized Simulations of a Squall Line from the MC3E Field Campaign Applying Three Bin Microphysics Schemes: Dynamic and Thermodynamic Structure

    Energy Technology Data Exchange (ETDEWEB)

    Xue, Lulin [National Center for Atmospheric Research, Boulder, Colorado; Fan, Jiwen [Pacific Northwest National Laboratory, Richland, Washington; Lebo, Zachary J. [University of Wyoming, Laramie, Wyoming; Wu, Wei [National Center for Atmospheric Research, Boulder, Colorado; University of Illinois at Urbana–Champaign, Urbana, Illinois; Morrison, Hugh [National Center for Atmospheric Research, Boulder, Colorado; Grabowski, Wojciech W. [National Center for Atmospheric Research, Boulder, Colorado; Chu, Xia [University of Wyoming, Laramie, Wyoming; Geresdi, István [University of Pécs, Pécs, Hungary; North, Kirk [McGill University, Montréal, Québec, Canada; Stenz, Ronald [University of North Dakota, Grand Forks, North Dakota; Gao, Yang [Pacific Northwest National Laboratory, Richland, Washington; Lou, Xiaofeng [Chinese Academy of Meteorological Sciences, Beijing, China; Bansemer, Aaron [National Center for Atmospheric Research, Boulder, Colorado; Heymsfield, Andrew J. [National Center for Atmospheric Research, Boulder, Colorado; McFarquhar, Greg M. [National Center for Atmospheric Research, Boulder, Colorado; University of Illinois at Urbana–Champaign, Urbana, Illinois; Rasmussen, Roy M. [National Center for Atmospheric Research, Boulder, Colorado

    2017-12-01

    The squall line event on May 20, 2011, during the Midlatitude Continental Convective Clouds (MC3E) field campaign has been simulated by three bin (spectral) microphysics schemes coupled into the Weather Research and Forecasting (WRF) model. Semi-idealized three-dimensional simulations driven by temperature and moisture profiles acquired by a radiosonde released in the pre-convection environment at 1200 UTC in Morris, Oklahoma show that each scheme produced a squall line with features broadly consistent with the observed storm characteristics. However, substantial differences in the details of the simulated dynamic and thermodynamic structure are evident. These differences are attributed to different algorithms and numerical representations of microphysical processes, assumptions of the hydrometeor processes and properties, especially ice particle mass, density, and terminal velocity relationships with size, and the resulting interactions between the microphysics, cold pool, and dynamics. This study shows that different bin microphysics schemes, designed to be conceptually more realistic and thus arguably more accurate than bulk microphysics schemes, still simulate a wide spread of microphysical, thermodynamic, and dynamic characteristics of a squall line, qualitatively similar to the spread of squall line characteristics using various bulk schemes. Future work may focus on improving the representation of ice particle properties in bin schemes to reduce this uncertainty and using the similar assumptions for all schemes to isolate the impact of physics from numerics.

  12. Structure and thermodynamics of a mixture of patchy and spherical colloids: A multi-body association theory with complete reference fluid information

    Energy Technology Data Exchange (ETDEWEB)

    Bansal, Artee; Asthagiri, D.; Cox, Kenneth R.; Chapman, Walter G., E-mail: wgchap@rice.edu [Department of Chemical and Biomolecular Engineering, Rice University, Houston, Texas 77251 (United States)

    2016-08-21

    A mixture of solvent particles with short-range, directional interactions and solute particles with short-range, isotropic interactions that can bond multiple times is of fundamental interest in understanding liquids and colloidal mixtures. Because of multi-body correlations, predicting the structure and thermodynamics of such systems remains a challenge. Earlier Marshall and Chapman [J. Chem. Phys. 139, 104904 (2013)] developed a theory wherein association effects due to interactions multiply the partition function for clustering of particles in a reference hard-sphere system. The multi-body effects are incorporated in the clustering process, which in their work was obtained in the absence of the bulk medium. The bulk solvent effects were then modeled approximately within a second order perturbation approach. However, their approach is inadequate at high densities and for large association strengths. Based on the idea that the clustering of solvent in a defined coordination volume around the solute is related to occupancy statistics in that defined coordination volume, we develop an approach to incorporate the complete information about hard-sphere clustering in a bulk solvent at the density of interest. The occupancy probabilities are obtained from enhanced sampling simulations but we also develop a concise parametric form to model these probabilities using the quasichemical theory of solutions. We show that incorporating the complete reference information results in an approach that can predict the bonding state and thermodynamics of the colloidal solute for a wide range of system conditions.

  13. The Structural, Dielectric, Lattice Dynamical and Thermodynamic Properties of Zinc-Blende CdX (X=S, Se, Te) from First-Principles Analysis

    International Nuclear Information System (INIS)

    Feng Shi-Quan; Li Jun-Yu; Cheng Xin-Lu

    2015-01-01

    The structural, dielectric, lattice dynamical and thermodynamic properties of zinc-blende CdX (X=S, Se, Te) are studied by using a plane-wave pseudopotential method within the density-functional theory. Our calculated lattice constants and bulk modulus are compared with the published experimental and theoretical data. In addition, the Born effective charges, electronic dielectric tensors, phonon frequencies, and longitudinal optical-transverse optical splitting are calculated by the linear-response approach. Some of the characteristics of the phonon-dispersion curves for zinc-blende CdX (X=S, Se, Te) are summarized. What is more, based on the lattice dynamical properties, we investigate the thermodynamic properties of CdX (X=S, Se, Te) and analyze the temperature dependences of the Helmholtz free energy F, the internal energy E, the entropy S and the constant-volume specific heat C_v. The results show that the heat capacities for CdTe, CdSe, and CdS approach approximately to the Petit-Dulong limit 6R. (paper)

  14. The effect of pressure on the structural, electronic, magnetic, and thermodynamic properties of the Mn{sub 2}RuGe inverse Heusler alloy

    Energy Technology Data Exchange (ETDEWEB)

    Song, Ting, E-mail: songting_lzjtu@163.com [State Key Laboratory of Advanced Processing and Recycling of Non-ferrous Metals, Lanzhou University of Technology, Lanzhou 730050 (China); College of Material Science and Engineering, Lanzhou University of Technology, Lanzhou 730050 (China); School of Mathematics and Physics, Lanzhou Jiaotong University, Lanzhou 730070 (China); Sun, Xiao-Wei [School of Mathematics and Physics, Lanzhou Jiaotong University, Lanzhou 730070 (China); Tian, Jun-Hong [School of Mathematics and Physics, Lanzhou Jiaotong University, Lanzhou 730070 (China); Institute of Atomic and Molecular Physics, Sichuan University, Chengdu 610065 (China); Wei, Xiao-Ping; Wan, Gui-Xin [School of Mathematics and Physics, Lanzhou Jiaotong University, Lanzhou 730070 (China); Ma, Qin, E-mail: maqin_lut@yeah.net [State Key Laboratory of Advanced Processing and Recycling of Non-ferrous Metals, Lanzhou University of Technology, Lanzhou 730050 (China); College of Material Science and Engineering, Lanzhou University of Technology, Lanzhou 730050 (China)

    2017-04-15

    In the frame of density functional theory, first-principles calculations based on generalized gradient approximation and quasi-harmonic Debye approximation model in which the phononic effects are taken into account have been carried out to investigate the structural, electronic, magnetic, and thermodynamic properties of full-Heusler alloy Mn{sub 2}RuGe in CuHg{sub 2}Ti-type structure in the pressure range of 0–50 GPa. Present calculations predict that Mn{sub 2}RuGe is a ferrimagnet with an optimized lattice parameter of 5.854 Å. The calculated total magnetic moment of 2.01 μ{sub B} per formula unit is very close to integer value and agree well with the Slater-Pauling rule, where the partial spin moments of Mn (A) and Mn (B) which mainly contribute to the total magnetic moment are 2.66 μ{sub B} and −0.90 μ{sub B}, respectively. In the study of the energy band structures and density of states, Mn{sub 2}RuGe exhibits half-metallicity with an indirect gap of 0.235 eV in the spin-down channels, and the shifting of bands towards higher energies in spin-down channel under high pressure. Meanwhile, the high-pressure thermodynamic properties of Mn{sub 2}RuGe, such as the pressure-volume-temperature relationship, bulk modulus, thermal expansivity, heat capacity, Debye temperature, and Grüneisen parameter are evaluated systematically in the temperature range of 0–900 K. This set of data is considered as the useful information to understand the high-pressure and high-temperature properties for the Mn{sub 2}RuZ-type Heusler alloy family.

  15. Structural, electronic, magnetic, half-metallic, mechanical, and thermodynamic properties of the quaternary Heusler compound FeCrRuSi: A first-principles study.

    Science.gov (United States)

    Wang, Xiaotian; Khachai, Houari; Khenata, Rabah; Yuan, Hongkuan; Wang, Liying; Wang, Wenhong; Bouhemadou, Abdelmadjid; Hao, Liyu; Dai, Xuefang; Guo, Ruikang; Liu, Guodong; Cheng, Zhenxiang

    2017-11-23

    In this paper, we have investigated the structural, electronic, magnetic, half-metallic, mechanical, and thermodynamic properties of the equiatomic quaternary Heusler (EQH) compound FeCrRuSi using the density functional theory (DFT) and the quasi-harmonic Debye model. Our results reveal that FeCrRuSi is a half-metallic material (HMM) with a total magnetic moment of 2.0 μ B in agreement with the well-known Slater-Pauling rule M t  = Z t  - 24. Furthermore, the origin of the half-metallic band gap in FeCrRuSi is well studied through a schematic diagram of the possible d-d hybridization between Fe, Cr and Ru elements. The half-metallic behavior of FeCrRuSi can be maintained in a relatively wide range of variations of the lattice constant (5.5-5.8 Å) under uniform strain and the c/a ratio (0.96-1.05) under tetragonal distortion. The calculated phonon dispersion, cohesive and formation energies, and mechanical properties reveal that FeCrRuSi is stable with an EQH structure. Importantly, the compound of interest has been prepared and is found to exist in an EQH type structure with the presence of some B2 disorder. Moreover, the thermodynamic properties, such as the thermal expansion coefficient α, the heat capacity C V , the Grüneisen constant γ, and the Debye temperature Θ D are calculated.

  16. Performance Evaluation of PBL Schemes of ARW Model in Simulating Thermo-Dynamical Structure of Pre-Monsoon Convective Episodes over Kharagpur Using STORM Data Sets

    Science.gov (United States)

    Madala, Srikanth; Satyanarayana, A. N. V.; Srinivas, C. V.; Tyagi, Bhishma

    2016-05-01

    In the present study, advanced research WRF (ARW) model is employed to simulate convective thunderstorm episodes over Kharagpur (22°30'N, 87°20'E) region of Gangetic West Bengal, India. High-resolution simulations are conducted using 1 × 1 degree NCEP final analysis meteorological fields for initial and boundary conditions for events. The performance of two non-local [Yonsei University (YSU), Asymmetric Convective Model version 2 (ACM2)] and two local turbulence kinetic energy closures [Mellor-Yamada-Janjic (MYJ), Bougeault-Lacarrere (BouLac)] are evaluated in simulating planetary boundary layer (PBL) parameters and thermodynamic structure of the atmosphere. The model-simulated parameters are validated with available in situ meteorological observations obtained from micro-meteorological tower as well has high-resolution DigiCORA radiosonde ascents during STORM-2007 field experiment at the study location and Doppler Weather Radar (DWR) imageries. It has been found that the PBL structure simulated with the TKE closures MYJ and BouLac are in better agreement with observations than the non-local closures. The model simulations with these schemes also captured the reflectivity, surface pressure patterns such as wake-low, meso-high, pre-squall low and the convective updrafts and downdrafts reasonably well. Qualitative and quantitative comparisons reveal that the MYJ followed by BouLac schemes better simulated various features of the thunderstorm events over Kharagpur region. The better performance of MYJ followed by BouLac is evident in the lesser mean bias, mean absolute error, root mean square error and good correlation coefficient for various surface meteorological variables as well as thermo-dynamical structure of the atmosphere relative to other PBL schemes. The better performance of the TKE closures may be attributed to their higher mixing efficiency, larger convective energy and better simulation of humidity promoting moist convection relative to non

  17. Thermodynamics of Radiation Modes

    Science.gov (United States)

    Pina, Eduardo; de la Selva, Sara Maria Teresa

    2010-01-01

    We study the equilibrium thermodynamics of the electromagnetic radiation in a cavity of a given volume and temperature. We found three levels of description, the thermodynamics of one mode, the thermodynamics of the distribution of frequencies in a band by summing over the frequencies in it and the global thermodynamics by summing over all the…

  18. Impact of structural modification of 1,2,4-thiadiazole derivatives on thermodynamics of solubility and solvation processes in 1-octanol and n-hexane

    International Nuclear Information System (INIS)

    Surov, Artem O.; Bui, Cong Trinh; Volkova, Tatyana V.; Proshin, Alexey N.; Perlovich, German L.

    2016-01-01

    Highlights: • Solubility processes of some 1,2,4-thiadiazoles in n-hexane and 1-octanol were investigated. • Solvation processes of some 1,2,4-thiadiazoles in n-hexane and 1-octanol were studied. • Transfer processes from n-hexane to 1-octanol were evaluated. • Impact of various substituents in 1,2,4-thiadiazoles on the mentioned processes was studied. - Abstract: Influence of a structural modification on thermodynamic aspects of solubility and solvation processes of the 1,2,4-thiadiazole drug-like compounds in pharmaceutically relevant solvents n-hexane and 1-octanol was investigated. The solubility of the compounds in 1-octanol does not substantially depend on the nature and position of the substituent in the phenyl moiety. In n-hexane, however, the introduction of any substituent in the phenyl ring of the 1,2,4-thiadiazole molecule reduces the solubility in the solvent. In order to rationalize the relationships between the structure of 1,2,4-thiadiazoles and their solubility, the latter was considered in terms of two fundamental processes: sublimation and solvation. It was found that for the most of the compounds the solubility change in both solvents is a consequence of competition between the sublimation and solvation contributions, i.e. the introduction of substituents leads to growth of the sublimation Gibbs energy and increase in the solvation Gibbs energy. Thermodynamic parameters of the transfer process of the compounds from n-hexane to 1-octanol, which is a model of the blood–brain barrier (BBB), were also analyzed.

  19. Mathematical foundations of thermodynamics

    CERN Document Server

    Giles, R; Stark, M; Ulam, S

    2013-01-01

    Mathematical Foundations of Thermodynamics details the core concepts of the mathematical principles employed in thermodynamics. The book discusses the topics in a way that physical meanings are assigned to the theoretical terms. The coverage of the text includes the mechanical systems and adiabatic processes; topological considerations; and equilibrium states and potentials. The book also covers Galilean thermodynamics; symmetry in thermodynamics; and special relativistic thermodynamics. The book will be of great interest to practitioners and researchers of disciplines that deal with thermodyn

  20. Thermodynamic properties of water molecules in the presence of cosolute depend on DNA structure: a study using grid inhomogeneous solvation theory

    Science.gov (United States)

    Nakano, Miki; Tateishi-Karimata, Hisae; Tanaka, Shigenori; Tama, Florence; Miyashita, Osamu; Nakano, Shu-ichi; Sugimoto, Naoki

    2015-01-01

    In conditions that mimic those of the living cell, where various biomolecules and other components are present, DNA strands can adopt many structures in addition to the canonical B-form duplex. Previous studies in the presence of cosolutes that induce molecular crowding showed that thermal stabilities of DNA structures are associated with the properties of the water molecules around the DNAs. To understand how cosolutes, such as ethylene glycol, affect the thermal stability of DNA structures, we investigated the thermodynamic properties of water molecules around a hairpin duplex and a G-quadruplex using grid inhomogeneous solvation theory (GIST) with or without cosolutes. Our analysis indicated that (i) cosolutes increased the free energy of water molecules around DNA by disrupting water–water interactions, (ii) ethylene glycol more effectively disrupted water–water interactions around Watson–Crick base pairs than those around G-quartets or non-paired bases, (iii) due to the negative electrostatic potential there was a thicker hydration shell around G-quartets than around Watson–Crick-paired bases. Our findings suggest that the thermal stability of the hydration shell around DNAs is one factor that affects the thermal stabilities of DNA structures under the crowding conditions. PMID:26538600

  1. Structural and Thermodynamic Insights into Chitooligosaccharide Binding to Human Cartilage Chitinase 3-like Protein 2 (CHI3L2 or YKL-39)*

    Science.gov (United States)

    Ranok, Araya; Wongsantichon, Jantana; Robinson, Robert C.; Suginta, Wipa

    2015-01-01

    Four crystal structures of human YKL-39 were solved in the absence and presence of chitooligosaccharides. The structure of YKL-39 comprises a major (β/α)8 triose-phosphate isomerase barrel domain and a small α + β insertion domain. Structural analysis demonstrates that YKL-39 interacts with chitooligosaccharides through hydrogen bonds and hydrophobic interactions. The binding of chitin fragments induces local conformational changes that facilitate tight binding. Compared with other GH-18 members, YKL-39 has the least extended chitin-binding cleft, containing five subsites for sugars, namely (−3)(−2)(−1)(+1)(+2), with Trp-360 playing a prominent role in the sugar-protein interactions at the center of the chitin-binding cleft. Evaluation of binding affinities obtained from isothermal titration calorimetry and intrinsic fluorescence spectroscopy suggests that YKL-39 binds to chitooligosaccharides with Kd values in the micromolar concentration range and that the binding energies increase with the chain length. There were no significant differences between the Kd values of chitopentaose and chitohexaose, supporting the structural evidence for the five binding subsite topology. Thermodynamic analysis indicates that binding of chitooligosaccharide to YKL-39 is mainly driven by enthalpy. PMID:25477513

  2. Structural and thermodynamic insights into chitooligosaccharide binding to human cartilage chitinase 3-like protein 2 (CHI3L2 or YKL-39).

    Science.gov (United States)

    Ranok, Araya; Wongsantichon, Jantana; Robinson, Robert C; Suginta, Wipa

    2015-01-30

    Four crystal structures of human YKL-39 were solved in the absence and presence of chitooligosaccharides. The structure of YKL-39 comprises a major (β/α)8 triose-phosphate isomerase barrel domain and a small α + β insertion domain. Structural analysis demonstrates that YKL-39 interacts with chitooligosaccharides through hydrogen bonds and hydrophobic interactions. The binding of chitin fragments induces local conformational changes that facilitate tight binding. Compared with other GH-18 members, YKL-39 has the least extended chitin-binding cleft, containing five subsites for sugars, namely (-3)(-2)(-1)(+1)(+2), with Trp-360 playing a prominent role in the sugar-protein interactions at the center of the chitin-binding cleft. Evaluation of binding affinities obtained from isothermal titration calorimetry and intrinsic fluorescence spectroscopy suggests that YKL-39 binds to chitooligosaccharides with Kd values in the micromolar concentration range and that the binding energies increase with the chain length. There were no significant differences between the Kd values of chitopentaose and chitohexaose, supporting the structural evidence for the five binding subsite topology. Thermodynamic analysis indicates that binding of chitooligosaccharide to YKL-39 is mainly driven by enthalpy. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

  3. Thermodynamics of Crystals

    Science.gov (United States)

    Navrotsky, Alexandra

    Thermodynamics of Crystals is a gold mine of a references bargain with more derivations of useful equations per dollar, or per page, than almost any other book I know. Useful to whom? To the solid state physicist, the solid state chemist working the geophysicist, the rock mechanic, the mineral physicist. Useful for what? For lattice dynamics, crystal potentials, band structure. For elegant, rigorous, and concise derivations of fundamental equations. For comparison of levels of approximation. For some data and physical insights, especially for metals and simple halides. This book is a reissue, with some changes and additions, of a 1970 treatise. It ages well, since the fundamentals do not change.

  4. Thermodynamic Studies for Drug Design and Screening

    Science.gov (United States)

    Garbett, Nichola C.; Chaires, Jonathan B.

    2012-01-01

    Introduction A key part of drug design and development is the optimization of molecular interactions between an engineered drug candidate and its binding target. Thermodynamic characterization provides information about the balance of energetic forces driving binding interactions and is essential for understanding and optimizing molecular interactions. Areas covered This review discusses the information that can be obtained from thermodynamic measurements and how this can be applied to the drug development process. Current approaches for the measurement and optimization of thermodynamic parameters are presented, specifically higher throughput and calorimetric methods. Relevant literature for this review was identified in part by bibliographic searches for the period 2004 – 2011 using the Science Citation Index and PUBMED and the keywords listed below. Expert opinion The most effective drug design and development platform comes from an integrated process utilizing all available information from structural, thermodynamic and biological studies. Continuing evolution in our understanding of the energetic basis of molecular interactions and advances in thermodynamic methods for widespread application are essential to realize the goal of thermodynamically-driven drug design. Comprehensive thermodynamic evaluation is vital early in the drug development process to speed drug development towards an optimal energetic interaction profile while retaining good pharmacological properties. Practical thermodynamic approaches, such as enthalpic optimization, thermodynamic optimization plots and the enthalpic efficiency index, have now matured to provide proven utility in design process. Improved throughput in calorimetric methods remains essential for even greater integration of thermodynamics into drug design. PMID:22458502

  5. Thermodynamic studies for drug design and screening.

    Science.gov (United States)

    Garbett, Nichola C; Chaires, Jonathan B

    2012-04-01

    A key part of drug design and development is the optimization of molecular interactions between an engineered drug candidate and its binding target. Thermodynamic characterization provides information about the balance of energetic forces driving binding interactions and is essential for understanding and optimizing molecular interactions. This review discusses the information that can be obtained from thermodynamic measurements and how this can be applied to the drug development process. Current approaches for the measurement and optimization of thermodynamic parameters are presented, specifically higher throughput and calorimetric methods. Relevant literature for this review was identified in part by bibliographic searches for the period 2004 - 2011 using the Science Citation Index and PUBMED and the keywords listed below. The most effective drug design and development platform comes from an integrated process utilizing all available information from structural, thermodynamic and biological studies. Continuing evolution in our understanding of the energetic basis of molecular interactions and advances in thermodynamic methods for widespread application are essential to realize the goal of thermodynamically driven drug design. Comprehensive thermodynamic evaluation is vital early in the drug development process to speed drug development toward an optimal energetic interaction profile while retaining good pharmacological properties. Practical thermodynamic approaches, such as enthalpic optimization, thermodynamic optimization plots and the enthalpic efficiency index, have now matured to provide proven utility in the design process. Improved throughput in calorimetric methods remains essential for even greater integration of thermodynamics into drug design. © 2012 Informa UK, Ltd.

  6. Structure, Stabilities, Thermodynamic Properties, and IR Spectra of Acetylene Clusters (C2H2)n=2-5.

    Science.gov (United States)

    Karthikeyan, S; Lee, Han Myoung; Kim, Kwang S

    2010-10-12

    There are no clear conclusions over the structures of the acetylene clusters. In this regard, we have carried out high-level calculations for acetylene clusters (C2H2)2-5 using dispersion-corrected density functional theory (DFT-D), Møller-Plesset second-order perturbation theory (MP2); and coupled-cluster theory with single, double, and perturbative triple excitations [CCSD(T)] at the complete basis set limit. The lowest energy structure of the acetylene dimer has a T-shaped structure of C2v symmetry, but it is nearly isoenergetic to the displaced stacked structure of C2h symmetry. We find that the structure shows the quantum statistical distribution for configurations between the T-shaped and displaced stacked structures for which the average angle (|θ̃|) between two acetylene molecules would be 53-78°, close to the T-shaped structure. The trimer has a triangular structure of C3h symmetry. The tetramer has two lowest energy isomers of S4 and C2h symmetry in zero-point energy (ZPE)-uncorrected energy (ΔEe), but one lowest energy isomer of C2v symmetry in ZPE-corrected energy (ΔE0). For the pentamer, the global minimum structure is C1 symmetry with eight sets of T-type π-H interactions and a set of π-π interactions. Our high-level ab initio calculations are consistent with available experimental data.

  7. Thermodynamic tables to accompany Modern engineering thermodynamics

    CERN Document Server

    Balmer, Robert T

    2011-01-01

    This booklet is provided at no extra charge with new copies of Balmer's Modern Engineering Thermodynamics. It contains two appendices. Appendix C contains 40 thermodynamic tables, and Appendix D consists of 6 thermodynamic charts. These charts and tables are provided in a separate booklet to give instructors the flexibility of allowing students to bring the tables into exams. The booklet may be purchased separately if needed.

  8. Classical and statistical thermodynamics

    CERN Document Server

    Rizk, Hanna A

    2016-01-01

    This is a text book of thermodynamics for the student who seeks thorough training in science or engineering. Systematic and thorough treatment of the fundamental principles rather than presenting the large mass of facts has been stressed. The book includes some of the historical and humanistic background of thermodynamics, but without affecting the continuity of the analytical treatment. For a clearer and more profound understanding of thermodynamics this book is highly recommended. In this respect, the author believes that a sound grounding in classical thermodynamics is an essential prerequisite for the understanding of statistical thermodynamics. Such a book comprising the two wide branches of thermodynamics is in fact unprecedented. Being a written work dealing systematically with the two main branches of thermodynamics, namely classical thermodynamics and statistical thermodynamics, together with some important indexes under only one cover, this treatise is so eminently useful.

  9. The validity of the potential model in predicting the structural, dynamical, thermodynamic properties of the unary and binary mixture of water-alcohol: Methanol-water case

    Science.gov (United States)

    Obeidat, Abdalla; Abu-Ghazleh, Hind

    2018-06-01

    Two intermolecular potential models of methanol (TraPPE-UA and OPLS-AA) have been used in order to examine their validity in reproducing the selected structural, dynamical, and thermodynamic properties in the unary and binary systems. These two models are combined with two water models (SPC/E and TIP4P). The temperature dependence of density, surface tension, diffusion and structural properties for the unary system has been computed over specific range of temperatures (200-300K). The very good performance of the TraPPE-UA potential model in predicting surface tension, diffusion, structure, and density of the unary system led us to examine its accuracy and performance in its aqueous solution. In the binary system the same properties were examined, using different mole fractions of methanol. The TraPPE-UA model combined with TIP4P-water shows a very good agreement with the experimental results for density and surface tension properties; whereas the OPLS-AA combined with SPCE-water shows a very agreement with experimental results regarding the diffusion coefficients. Two different approaches have been used in calculating the diffusion coefficient in the mixture, namely the Einstein equation (EE) and Green-Kubo (GK) method. Our results show the advantageous of applying GK over EE in reproducing the experimental results and in saving computer time.

  10. An Ab-initio study of structural, elastic, electronic and thermodynamic properties of triclinic Cu{sub 7}In{sub 3}

    Energy Technology Data Exchange (ETDEWEB)

    Yu, Ching-Feng [Department of Power Mechanical Engineering, National Tsing Hua University, Hsinchu 30013, Taiwan (China); Cheng, Hsien-Chie, E-mail: hccheng@fcu.edu.tw [Department of Aerospace and Systems Engineering, Feng Chia University, Taichung 40724, Taiwan (China); Chen, Wen-Hwa, E-mail: whchen@pme.nthu.edu.tw [Department of Power Mechanical Engineering, National Tsing Hua University, Hsinchu 30013, Taiwan (China)

    2016-05-01

    First principles density functional theory calculations within the generalized gradient approximation are performed to comprehensively study the structural, elastic, electronic and thermodynamic properties of triclinic single and polycrystalline Cu{sub 7}In{sub 3}. The polycrystalline elastic properties are predicted using the Voigt–Reuss–Hill approximation and the thermodynamic properties are evaluated based on the quasi-harmonic Debye model. Their temperature, hydrostatic pressure or crystal orientation dependences are also addressed, and the predicted physical properties are compared with the literature experimental and theoretical data and also with those of three other Cu–In compounds, i.e., CuIn, Cu{sub 2}In and Cu{sub 11}In{sub 9}. The present calculations show that in addition to being a much better conductor compared to Cu{sub 2}In and Cu{sub 11}In{sub 9}, Cu{sub 7}In{sub 3} crystal reveals weak elastic anisotropy, high ductility and low stiffness, and tends to become more elastically isotropic at very high hydrostatic pressure. Moreover, the Cu{sub 7}In{sub 3} holds the largest high-temperature heat capacity among the four Cu–In compounds. - Highlights: • The physical property of Cu{sub 7}In{sub 3} is reported by first-principles calculations. • Pressure effect on the physical property of Cu{sub 7}In{sub 3} is presented. • The calculated lattice constants of Cu{sub 7}In{sub 3} agree well with the experimental data. • Cu{sub 7}In{sub 3} tends to become more elastically isotropic at very high pressure. • The heat capacity of Cu{sub 7}In{sub 3} is much larger than that of CuIn, Cu{sub 2}In and Cu{sub 11}In{sub 9}.

  11. Tuning the nano/micro-structure and properties of melt-processed ternary composites of polypropylene/ethylene vinyl acetate blend and nanoclay: The influence of kinetic and thermodynamic parameters

    CSIR Research Space (South Africa)

    Mofokeng, Tladi G

    2017-09-01

    Full Text Available The present study reports the dependence of the nano/micro-structure and properties of polypropylene (PP)/ethylene vinyl acetate (EVA)/nanoclay ternary composites on the kinetics and thermodynamics of the melt-mixing process. The size of dispersed...

  12. Fundamentals for remote structural health monitoring of wind turbine blades - a preproject. Annex C. Fibre transducer for damage detection in adhesive layers of wind turbine blades

    DEFF Research Database (Denmark)

    Sendrup, P.

    2002-01-01

    displacement transducer for detection of damage in adhesive layers of wind turbine blades. It was chosen to base the transducer on the fibre optic micro-bend principle. The report contains the result of measurementsand optical simulations of light transmittance through optical fibres with micro......-bends and a suggestion for a micro-bend transducer design specifically suitable for detection of damage in adhesive layers between larger composite structures, as the shellsin a wind turbine blade. Such a damage will cause the joined parts to move slightly relative to each other, and the transducer is designed to change...... optic micro-bend transducer would be in the range between0.5%/um to 1 %/um depending on the number of bends on the fibre. A measurement on the final transducer showed that the sensitivity was 1.2 %/um. A large 50 % change in transmittance, that is easy to measure, is then obtained for displacements...

  13. Structural and thermodynamic characterization of modified cellulose fiber-based materials and related interactions with water vapor

    Energy Technology Data Exchange (ETDEWEB)

    Bedane, Alemayehu H., E-mail: Alemayehu.Bedane@unb.ca; Xiao, Huining, E-mail: hxiao@unb.ca; Eić, Mladen, E-mail: meic@unb.ca; Farmahini-Farahani, Madjid, E-mail: Madjid.Farahani@unb.ca

    2015-10-01

    Highlights: • Coating on paper increases the specific surface area but decreases the pore diameter. • Pore size reduction and decrease of hydrophilic property caused reduction in WVTRs. • The low monolayer moisture content of the sample is generally related to the low WVTR. • The net isosteric heats of adsorption decreased with increased sample moisture content. • FT-IR results reveal the formation of water clusters at higher relative humidities. - Abstract: In this study, the surface characteristics, water vapor interactions, and state of water adsorbed on unmodified and coated paper samples were investigated in an attempt to obtain a better understanding of the fundamental principles related to thermodynamics of this process, as well as to provide essential insight that could be used for further improvement of the papers’ barrier properties. Based on the BET measurement, the coated paper samples showed higher specific surface areas than unmodified paper; however, their mean pore diameters are smaller. The BJH method was used for pore size distribution analysis. Hydrophobic properties of the paper samples were determined from experimental isotherms, e.g., monolayer moisture content, and these results have been related to the water vapor transfer rates (WVTRs) showing a complex nature of these relations. The highest peak corresponding to the modified samples with smaller pore sizes was found to be in the range of 1–30 nm, while it was in the 30–100 nm pore size range for unmodified paper. The net isosteric heats of sorption for different unmodified and modified paper samples were determined from water vapor adsorption isotherms measured at 15, 25, and 35 °C. The net isosteric heats of sorption decreased with an increase of moisture content after reaching the maximum values at 12.53, 15.25, 14.71, 23.2, and 22.77 kJ/mol for unmodified, zein grafted, calendered coated, PLA, and PHBV coated papers, respectively. The state of adsorbed water and water

  14. UNRES server for physics-based coarse-grained simulations and prediction of protein structure, dynamics and thermodynamics.

    Science.gov (United States)

    Czaplewski, Cezary; Karczynska, Agnieszka; Sieradzan, Adam K; Liwo, Adam

    2018-04-30

    A server implementation of the UNRES package (http://www.unres.pl) for coarse-grained simulations of protein structures with the physics-based UNRES model, coined a name UNRES server, is presented. In contrast to most of the protein coarse-grained models, owing to its physics-based origin, the UNRES force field can be used in simulations, including those aimed at protein-structure prediction, without ancillary information from structural databases; however, the implementation includes the possibility of using restraints. Local energy minimization, canonical molecular dynamics simulations, replica exchange and multiplexed replica exchange molecular dynamics simulations can be run with the current UNRES server; the latter are suitable for protein-structure prediction. The user-supplied input includes protein sequence and, optionally, restraints from secondary-structure prediction or small x-ray scattering data, and simulation type and parameters which are selected or typed in. Oligomeric proteins, as well as those containing D-amino-acid residues and disulfide links can be treated. The output is displayed graphically (minimized structures, trajectories, final models, analysis of trajectory/ensembles); however, all output files can be downloaded by the user. The UNRES server can be freely accessed at http://unres-server.chem.ug.edu.pl.

  15. [Thermodynamics of the origin of life, evolution and aging].

    Science.gov (United States)

    Gladyshev, G P

    2014-01-01

    Briefly discusses the history of the search of thermodynamic approach to explain the origin of life, evolution and aging of living beings. The origin of life is the result of requirement by the quasi-equilibrium hierarchical thermodynamics, in particular, the supramolecular thermodynamics. The evolution and aging of living beings is accompanied with changes of chemical and supramolecular compositions of living bodies, as well as with changes in the composition and structure of all hierarchies of the living world. The thermodynamic principle of substance stability predicts the existence of a single genetic code in our universe. The thermodynamic theory optimizes physiology and medicine and recommends antiaging diets and medicines. Hierarchical thermodynamics forms the design diversity of culture and art. The thermodynamic theory of origin of life, evolution and aging is the development of Clausius-Gibbs thermodynamics. Hierarchical thermodynamics is the mirror of Darwin-Wallace's-theory.

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

    Science.gov (United States)

    Dunn, Nicholas J H; Noid, W G

    2016-05-28

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

  17. Thermodynamics in Einstein's thought

    International Nuclear Information System (INIS)

    Klein, M.J.

    1983-01-01

    The role of the thermodynamical approach in the Einstein's scientific work is analyzed. The Einstein's development of a notion about statistical fluctuations of thermodynamical systems that leads him to discovery of corpuscular-wave dualism is retraced

  18. Heat and thermodynamics

    CERN Document Server

    Saxena, A K

    2014-01-01

    Heat and thermodynamics aims to serve as a textbook for Physics, Chemistry and Engineering students. The book covers basic ideas of Heat and Thermodynamics, Kinetic Theory and Transport Phenomena, Real Gases, Liquafaction and Production and Measurement of very Low Temperatures, The First Law of Thermodynamics, The Second and Third Laws of Thermodynamics and Heat Engines and Black Body Radiation. KEY FEATURES Emphasis on concepts Contains 145 illustrations (drawings), 9 Tables and 48 solved examples At the end of chapter exercises and objective questions

  19. Structural and thermodynamic basis of the inhibition of Leishmania major farnesyl diphosphate synthase by nitrogen-containing bisphosphonates

    Energy Technology Data Exchange (ETDEWEB)

    Aripirala, Srinivas [Johns Hopkins University, 725 North Wolfe Street WBSB 605, Baltimore, MD 21210 (United States); Gonzalez-Pacanowska, Dolores [López-Neyra Institute of Parasitology and Biomedicine, 18001 Granada (Spain); Oldfield, Eric [University of Illinois at Urbana-Champaign, Urbana, IL 61801 (United States); Kaiser, Marcel [University of Basel, Petersplatz 1, CH-4003 Basel (Switzerland); Amzel, L. Mario, E-mail: mamzel@jhmi.edu [Johns Hopkins University School of Medicine, 725 N. Wolfe Street WBSB 604, Baltimore, MD 21205 (United States); Gabelli, Sandra B., E-mail: mamzel@jhmi.edu [Johns Hopkins University School of Medicine, 725 N. Wolfe Street WBSB 604, Baltimore, MD 21205 (United States); Johns Hopkins University School of Medicine, Baltimore, MD 21205 (United States); Johns Hopkins University, 725 North Wolfe Street WBSB 605, Baltimore, MD 21210 (United States)

    2014-03-01

    Structural insights into L. major farnesyl diphosphate synthase, a key enzyme in the mevalonate pathway, are described. Farnesyl diphosphate synthase (FPPS) is an essential enzyme involved in the biosynthesis of sterols (cholesterol in humans and ergosterol in yeasts, fungi and trypanosomatid parasites) as well as in protein prenylation. It is inhibited by bisphosphonates, a class of drugs used in humans to treat diverse bone-related diseases. The development of bisphosphonates as antiparasitic compounds targeting ergosterol biosynthesis has become an important route for therapeutic intervention. Here, the X-ray crystallographic structures of complexes of FPPS from Leishmania major (the causative agent of cutaneous leishmaniasis) with three bisphosphonates determined at resolutions of 1.8, 1.9 and 2.3 Å are reported. Two of the inhibitors, 1-(2-hydroxy-2,2-diphosphonoethyl)-3-phenylpyridinium (300B) and 3-butyl-1-(2,2-diphosphonoethyl)pyridinium (476A), co-crystallize with the homoallylic substrate isopentenyl diphosphate (IPP) and three Ca{sup 2+} ions. A third inhibitor, 3-fluoro-1-(2-hydroxy-2,2-diphosphonoethyl)pyridinium (46I), was found to bind two Mg{sup 2+} ions but not IPP. Calorimetric studies showed that binding of the inhibitors is entropically driven. Comparison of the structures of L. major FPPS (LmFPPS) and human FPPS provides new information for the design of bisphosphonates that will be more specific for inhibition of LmFPPS. The asymmetric structure of the LmFPPS–46I homodimer indicates that binding of the allylic substrate to both monomers of the dimer results in an asymmetric dimer with one open and one closed homoallylic site. It is proposed that IPP first binds to the open site, which then closes, opening the site on the other monomer, which closes after binding the second IPP, leading to the symmetric fully occupied FPPS dimer observed in other structures.

  20. The Thermodynamic Machinery of Life

    CERN Document Server

    Kurzynski, Michal

    2006-01-01

    Living organisms are open thermodynamic systems whose functional structure has developed and been kinetically frozen during the historical process of biological evolution. A thermodynamics of both nonequilibrium and complex systems is needed for their description. In this book, the foundations of such a thermodynamics are presented. Biological processes at the cellular level are considered as coupled chemical reactions and transport processes across internal and the cytoplasmic membrane. All these processes are catalyzed by specific enzymes hence the kinetics of enzymatic catalysis and its control are described here in detail. The coupling of several processes through a common enzyme is considered in the context of free energy or signal transduction. Special attention is paid to evidence for a rich stochastic internal dynamics of native proteins and its possible role in the control of enzyme activity and in the action of biological molecular machines.

  1. Advanced classical thermodynamics

    International Nuclear Information System (INIS)

    Emanuel, G.

    1987-01-01

    The theoretical and mathematical foundations of thermodynamics are presented in an advanced text intended for graduate engineering students. Chapters are devoted to definitions and postulates, the fundamental equation, equilibrium, the application of Jacobian theory to thermodynamics, the Maxwell equations, stability, the theory of real gases, critical-point theory, and chemical thermodynamics. Diagrams, graphs, tables, and sample problems are provided. 38 references

  2. Solubilisation of a host molecule in a surfactant film: thermodynamic and structural approach in the case of lindane

    International Nuclear Information System (INIS)

    Testard, Fabienne

    1996-01-01

    In this research thesis, the author aimed at understanding the main aspects of solubilisation in the specific case of a pesticide, the lindane, which is a hydrophobic molecule, poorly soluble in water. She first proposes a review of some existing models of solubilisation, and presents the only existing predictive model for the prediction of solubilisation in water-ionic surfactant binary systems. She addresses these systems and tries to characterise disruptions induced by the presence of the solute for lindane-saturated solutions (study of phase diagrams, of structure for different surfactant concentrations and different temperatures). Then she focuses on a part of the ternary diagram which allows micro emulsions to be reached at the point of spontaneous null curvature. She reports the study (by neutron and X ray scattering at small angles) of structural information on the surfactant film in different aggregates of ternary solutions in presence of solute. She finally proposes a more chemical approach to solubilisation [fr

  3. Kinetic, thermodynamic and structural analysis of tamiphosphor binding to neuraminidase of H1N1 (2009) pandemic influenza

    Czech Academy of Sciences Publication Activity Database

    Albinana, C. B.; Machara, A.; Řezáčová, Pavlína; Pachl, P.; Konvalinka, J.; Kožíšek, M.

    2016-01-01

    Roč. 121, OCT 4 (2016), s. 100-109 ISSN 0223-5234 R&D Projects: GA ČR GA13-19561S; GA MŠk LO1302; GA MŠk(CZ) LO1304 Institutional support: RVO:68378050 Keywords : Influenza neuraminidase * Oseltamivir * Tamiphosphor * Isothermal titration calorimetry * Crystal structure * Lattice-translocation defect Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 4.519, year: 2016

  4. Kinetic, thermodynamic and structural analysis of tamiphosphor binding to neuraminidase of H1N1 (2009) pandemic influenza

    Czech Academy of Sciences Publication Activity Database

    Albinana, C. B.; Machara, A.; Řezáčová, Pavlína; Pachl, Petr; Konvalinka, Jan; Kožíšek, Milan

    2016-01-01

    Roč. 121, Oct 4 (2016), s. 100-109 ISSN 0223-5234 R&D Projects: GA ČR GA13-19561S; GA MŠk LO1302; GA MŠk(CZ) LO1304 Institutional support: RVO:61388963 Keywords : influenza neuraminidase * oseltamivir * tamiphosphor * isothermal titration calorimetry * crystal structure * lattice-translocation defect Subject RIV: CE - Biochemistry Impact factor: 4.519, year: 2016

  5. Structural and thermodynamic aspects of the dissociation of cyclopentadienyl rings from homoleptic cyclopentadienyl early transition metal, cerium, and thorium derivatives

    International Nuclear Information System (INIS)

    Peng Bin; Cheng Feng; Li Qianshu; Xie Yaoming; King, R. Bruce; Schaefer, Henry F.

    2011-01-01

    Graphical abstract: Density functional theory indicates that for Cp 4 M the S 4 structures are saddle points and the minima have C 1 symmetry with all η 5 -Cp rings for M = Ce and Th, three η 5 -Cp rings and one η 5 -Cp ring for M = Zr, and two η 5 -Cp rings and two η 5 -Cp rings for M = Ti and Hf. The dissociation energies for Cp 4 M → Cp 3 M + Cp · increase in the sequence Ti 3h structures with all η 5 -Cp rings are genuine minima for most of the Cp 3 M compounds except for Cp 3 Ti, which has a Cs symmetry minimum with two η 5 -Cp rings and one η 2 -Cp ring. The dissociation energies for Cp 3 M → Cp 2 M + Cp · increase in the sequence V 4 M the S 4 structures are saddle points. → The minima for Cp 4 M have all η 5 -Cp rings for M = Ce and Th, three η 5 -Cp rings and one η 1 -Cp ring for M = Zr, and two η 5 -Cp rings and two η 5 -Cp rings for M = Ti and Hf. → The dissociation energies for Cp 4 M → Cp 3 M + Cp · increase in the sequence Ti 3h structures with all η 5 -Cp rings are genuine minima for all of the Cp 3 M compounds except for Cp 3 Ti. → The dissociation energies for Cp 3 M → Cp 2 M + Cp · increase in the sequence V 4 M (M = Ti, Zr, Ce, Hf, Th), Cp 3 M (M = Sc, Y, most lanthanides, Ti, Zr, Hf, Th), and Cp 2 M (M = Ti, V). Density functional theory shows that the Cp 4 M structures with unusual S 4 symmetry are saddle points for the d-block metals Ti, Zr, Hf but genuine minima for the f-block metals Ce and Th. The true equilibrium Cp 4 M geometries have C 1 symmetry with two η 5 -Cp rings and two η 1 -Cp rings for M = Ti and Hf but three η 5 -Cp rings and one η 1 -Cp ring for M = Zr. The dissociation energies for Cp 4 M → Cp 3 M + Cp · are substantial and in the order Ti 3h structures with all η 5 -Cp rings are genuine minima for most of the Cp 3 M compounds except for Cp 3 Ti, which has a C s symmetry minimum with two η 5 -Cp rings and one η 2 -Cp ring, and Cp 3 V, which has two η 5 -Cp rings and one η 1 -Cp ring

  6. Introduction to applied thermodynamics

    CERN Document Server

    Helsdon, R M; Walker, G E

    1965-01-01

    Introduction to Applied Thermodynamics is an introductory text on applied thermodynamics and covers topics ranging from energy and temperature to reversibility and entropy, the first and second laws of thermodynamics, and the properties of ideal gases. Standard air cycles and the thermodynamic properties of pure substances are also discussed, together with gas compressors, combustion, and psychrometry. This volume is comprised of 16 chapters and begins with an overview of the concept of energy as well as the macroscopic and molecular approaches to thermodynamics. The following chapters focus o

  7. Twenty lectures on thermodynamics

    CERN Document Server

    Buchdahl, H A

    2013-01-01

    Twenty Lectures on Thermodynamics is a course of lectures, parts of which the author has given various times over the last few years. The book gives the readers a bird's eye view of phenomenological and statistical thermodynamics. The book covers many areas in thermodynamics such as states and transition; adiabatic isolation; irreversibility; the first, second, third and Zeroth laws of thermodynamics; entropy and entropy law; the idea of the application of thermodynamics; pseudo-states; the quantum-static al canonical and grand canonical ensembles; and semi-classical gaseous systems. The text

  8. Thermodynamic and structural study of two-dimensional melting within monolayers or rare gases or methane physically adsorbed upon the surface of layer-like solids

    International Nuclear Information System (INIS)

    Tessier, Christine

    1983-01-01

    The 2D (two-dimensional) melting of monolayers of rare gases or methane physically adsorbed on the basal face of lamellar solids (graphite, boron nitride and lamellar halides) has been studied. Two different experimental measurements have been made: i) adsorption isotherms; ii) neutron diffraction spectra. The main part of this report deals with the 2D liquid-incommensurate solid transition within monolayers of rare gases or methane adsorbed on the basal face of lamellar halides. This transition is first order. It is observed only if certain conditions of dimensional incompatibility between the substrate and the absorbate are fulfilled. It is little affected by the structure of the underlying substrate. A number of thermodynamic parameters associated with it, are constants once properly scaled. These constants agree well with theoretical estimates for 6-12 Lennard Jones particles adsorbed on a smooth surface. For the monolayer of Xe adsorbed on graphite the temperature of the tricritical point above which melting becomes a continuous transition has been measured. The isotope effect associated with 2D melting has been investigated by comparing the behaviour of monolayers of CH 4 and CD 4 adsorbed on boron nitride. The vapor pressure of Xe has been determined in the temperature range 101-120 K. (author) [fr

  9. Theoretical investigations on the structural, spectroscopic, electronic and thermodynamic properties of (3-Oxo-3H-benzo[f]chromen-1yl methyl N,N-dimethylcarbamodithioate-1ex

    Directory of Open Access Journals (Sweden)

    Kara Mehmet

    2017-10-01

    Full Text Available Hartree-Fock and Density Functional Theory (B3LYP, B3PW91 calculations for the ground state of (3-Oxo-3Hbenzo[ f]chromen-1-yl methyl N,N-dimethylcarbamodithioate have been presented and the calculated structural parameters and energetic properties have been compared with the available X-ray diffraction data. The vibrational frequencies have been calculated using optimized geometry of the molecule. The conformational properties of the molecule have been determined by computing molecular energy properties, in which torsional angle varied from -180° to +180° in steps of 10°. Moreover, natural bond orbital analysis and atomic charge analysis have been performed. Besides, HOMO and LUMO energies have been calculated and their pictures have been presented. Finally, molecular electrostatic potential and thermodynamic properties have been calculated. It is seen that the obtained theoretical results agree well with the available experimental values. In all the calculations, except for optimization and vibrational calculations, B3LYP level of theory with 6-311++G(d,p basis set has been used.

  10. Kinetic and Thermodynamic Rationale for SAHA Being a Preferential Human HDAC8 Inhibitor as Compared to the Structurally Similar Ligand, TSA

    Science.gov (United States)

    Singh, Raushan K.; Lall, Naveena; Leedahl, Travis S.; McGillivray, Abigail; Mandal, Tanmay; Haldar, Manas; Mallik, Sanku; Cook, Gregory; Srivastava, D.K.

    2013-01-01

    Of the different hydroxamate-based histone deacetylase (HDAC) inhibitors, Suberoylanilide hydroxamic acid (SAHA) has been approved by the FDA for treatment of T-cell lymphoma. Interestingly, a structurally similar inhibitor, Trichostatin A (TSA), which has a higher in vitro inhibitory-potency against HDAC8, reportedly shows a poor efficacy in clinical settings. In order to gain the molecular insight into the above discriminatory feature, we performed transient kinetic and isothermal titration calorimetric studies for the interaction of SAHA and TSA to the recombinant form of human HDAC8. The transient kinetic data revealed that the binding of both the inhibitors to the enzyme showed the biphasic profiles, which represented an initial encounter of enzyme with the inhibitor followed by the isomerization of the transient enzyme-inhibitor complexes. The temperature-dependent transient kinetic studies with the above inhibitors revealed that the bimolecular process is primarily dominated by favorable enthalpic changes, as opposed to the isomerization step; which is solely contributed by entropic changes. The standard binding-enthalpy (ΔH0) of SAHA, deduced from the transient kinetic as well as the isothermal titration calorimetric experiments, was 2–3 kcal/mol higher as compared to TSA. The experimental data presented herein suggests that SAHA serves as a preferential (target-specific/selective) HDAC8 inhibitor as compared to TSA. Arguments are presented that the detailed kinetic and thermodynamic studies may guide in the rational design of HDAC inhibitors as therapeutic agents. PMID:24079912

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

    Energy Technology Data Exchange (ETDEWEB)

    Dunn, Nicholas J. H.; Noid, W. G., E-mail: wnoid@chem.psu.edu [Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802 (United States)

    2016-05-28

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

  12. Thermodynamics of Fluid Polyamorphism

    Directory of Open Access Journals (Sweden)

    Mikhail A. Anisimov

    2018-01-01

    Full Text Available Fluid polyamorphism is the existence of different condensed amorphous states in a single-component fluid. It is either found or predicted, usually at extreme conditions, for a broad group of very different substances, including helium, carbon, silicon, phosphorous, sulfur, tellurium, cerium, hydrogen, and tin tetraiodide. This phenomenon is also hypothesized for metastable and deeply supercooled water, presumably located a few degrees below the experimental limit of homogeneous ice formation. We present a generic phenomenological approach to describe polyamorphism in a single-component fluid, which is completely independent of the molecular origin of the phenomenon. We show that fluid polyamorphism may occur either in the presence or in the absence of fluid phase separation depending on the symmetry of the order parameter. In the latter case, it is associated with a second-order transition, such as in liquid helium or liquid sulfur. To specify the phenomenology, we consider a fluid with thermodynamic equilibrium between two distinct interconvertible states or molecular structures. A fundamental signature of this concept is the identification of the equilibrium fraction of molecules involved in each of these alternative states. However, the existence of the alternative structures may result in polyamorphic fluid phase separation only if mixing of these structures is not ideal. The two-state thermodynamics unifies all the debated scenarios of fluid polyamorphism in different areas of condensed-matter physics, with or without phase separation, and even goes beyond the phenomenon of polyamorphism by generically describing the anomalous properties of fluids exhibiting interconversion of alternative molecular states.

  13. Density functional theory study of the structural, electronic, lattice dynamical, and thermodynamic properties of Li4SiO4 and its capability for CO2 capture

    Energy Technology Data Exchange (ETDEWEB)

    Duan, Yuhua; Parlinski, K.

    2011-01-01

    The structural, electronic, lattice dynamical, optical, thermodynamic, and CO{sub 2} capture properties of monoclinic and triclinic phases of Li{sub 4}SiO{sub 4} are investigated by combining density functional theory with phonon lattice dynamics calculations. We found that these two phases have some similarities in their bulk and thermodynamic properties. The calculated bulk modulus and the cohesive energies of these two phases are close to each other. Although both of them are insulators, the monoclinic phase of Li{sub 4}SiO{sub 4} has a direct band gap of 5.24 eV while the triclinic Li{sub 4}SiO{sub 4} phase has an indirect band gap of 4.98 eV. In both phases of Li{sub 4}SiO{sub 4}, the s orbital of O mainly contributes to the lower-energy second valence band (VB{sub 2}) and the p orbitals contribute to the fist valence band (VB{sub 1}) and the conduction bands (CBs). The s orbital of Si mainly contributes to the lower portions of the VB1 and VB{sub 2}, and Si p orbitals mainly contribute to the higher portions of the VB{sub 1} and VB{sub 2}. The s and p orbitals of Li contribute to both VBs and to CBs, and Li p orbitals have a higher contribution than the Li s orbital. There is possibly a phonon soft mode existing in triclinic {gamma}-Li{sub 4}SiO{sub 4}; in the monoclinic Li{sub 4}SiO{sub 4}, there are three phonon soft modes, which correspond to the one type of Li disordered over a few sites. Their LO-TO splitting indicates that both phases of Li{sub 4}SiO{sub 4} are polar anisotropic materials. The calculated infrared absorption spectra for LO and TO modes are different for these two phases of Li{sub 4}SiO{sub 4}. The calculated relationships of the chemical potential versus temperature and CO{sub 2} pressure for reaction of Li{sub 4}SiO{sub 4} with CO{sub 2} shows that Li{sub 4}SiO{sub 4} could be a good candidate for a high-temperature CO{sub 2} sorbent while used for postcombustion capture technology.

  14. Rational extended thermodynamics

    CERN Document Server

    Müller, Ingo

    1998-01-01

    Ordinary thermodynamics provides reliable results when the thermodynamic fields are smooth, in the sense that there are no steep gradients and no rapid changes. In fluids and gases this is the domain of the equations of Navier-Stokes and Fourier. Extended thermodynamics becomes relevant for rapidly varying and strongly inhomogeneous processes. Thus the propagation of high­ frequency waves, and the shape of shock waves, and the regression of small-scale fluctuation are governed by extended thermodynamics. The field equations of ordinary thermodynamics are parabolic while extended thermodynamics is governed by hyperbolic systems. The main ingredients of extended thermodynamics are • field equations of balance type, • constitutive quantities depending on the present local state and • entropy as a concave function of the state variables. This set of assumptions leads to first order quasi-linear symmetric hyperbolic systems of field equations; it guarantees the well-posedness of initial value problems and f...

  15. Thermodynamics and structure of inclusion compounds of tauro- and glyco-conjugated bile salts and beta-cyclodextrin

    DEFF Research Database (Denmark)

    Holm, Rene; Shi, Wei; Andersen Hartvig, Rune

    2009-01-01

    The interaction between natural beta-cyclodextrin and bile salts common in rat, dog and man, taurocholate, tauro-beta-muricholate, taurodeoxycholate, taurochenodeoxycholate, glycocholate, glycodeoxycholate and glycochenodeoxycholate, was studied using isothermal titration calorimetry, and the str......The interaction between natural beta-cyclodextrin and bile salts common in rat, dog and man, taurocholate, tauro-beta-muricholate, taurodeoxycholate, taurochenodeoxycholate, glycocholate, glycodeoxycholate and glycochenodeoxycholate, was studied using isothermal titration calorimetry......, and the structural differences in the interaction were investigated by H-1-ROESY NMR and molecular modeling. The beta-cyclodextrin was selected based upon its frequent use in preformulation and drug formulation as oral excipients for the solubilization of drug substances with low aqueous solubility. All...

  16. Steady-state thermodynamic simulation and structural design of the dephlegmator used in mixed-refrigerant Joule-Thomson refrigerators

    International Nuclear Information System (INIS)

    Li, Mei; Gong, Maoqiong; Guo, Hao; Sun, Zhaohu; Wu, Jianfeng

    2016-01-01

    Highlights: • Good agreements and the feasibility of the MESH model were found. • Fine applicability and low energy consumption of the dephlegmator were addressed. • A clear and comprehensive three-dimensional dephlegmator model was shown. - Abstract: Dephlegmators can be used to reduce the energy consumption and simplify the layout of the mixed-refrigerant Joule–Thomson (MRJT) cycle. Heat-exchange characteristics and refrigeration design are currently based on highly simplified assumptions. Synthesis methods to efficiently solve all design issues of dephlegmators in MRJT cycle are insufficient. No suitable separation module is available for the simultaneous heat and mass transfer processes in Aspen Plus because the module should be programmed and incorporated into Aspen Plus as a user-defined unit. In this paper, a systematic steady-state method was proposed for the detailed design of dephlegmators for gas mixture separation, considering the simulation and heat exchanger design simultaneously. The material balance, vapor–liquid equilibrium, mole fraction summation and heat balance (MESH) model was programmed in FORTRAN language. Good agreements and the feasibility of the MESH model were found. Deviations between the simulation results and patent data were all within 5%. The errors in the predicted temperatures of vapor and liquid products were less than 2% and 10%, respectively. Fine applicability and low energy consumption of the dephlegmator were addressed. The mole fraction of n-butane in the liquid phase had high recovery ratio of 90%. The dephlegmator decreased more than 30% of energy consumption compared with the traditional distillation tower under similar separation effects. In the structural design process, the dephlegmator was divided into certain segments by baffle plates on the basis of segmented calculation. The heat transfer coefficient, heat transfer area, pressure drop, and structural parameters of the dephlegmator were evaluated. A clear

  17. Plasma out of thermodynamical equilibrium: influence of the plasma environment on atomic structure and collisional cross sections

    International Nuclear Information System (INIS)

    Belkhiri, Madeny

    2014-01-01

    In hot dense plasmas, the free-electron and ion spatial distribution may strongly affect the atomic structure. To account for such effects we have implemented a potential correction based on the uniform electron gas model and on a Thomas-Fermi Approach in the Flexible Atomic Code (FAC). This code has been applied to obtain energies, wave-functions and radiative rates modified by the plasma environment. In hydrogen-like ions, these numerical results have been successfully compared to an analytical calculation based on first-order perturbation theory. In the case of multi-electron ions, we observe level crossings in agreement with another recent model calculation. Various methods for the collision cross-section calculations are reviewed. The influence of plasma environment on these cross-sections is analyzed in detail. Some analytical expressions are proposed for hydrogen-like ions in the limit where Born or Lotz approximations apply and are compared to the numerical results from the FAC code. Finally, from this work, we study the influence of the plasma environment on our collisional-radiative model so-called Foch. Because of this environment, the mean charge state of the ions increases. The line shift is observed on the bound-bound emission spectra. A good agreement is found between our work and experimental data on a Titanium plasma. (author) [fr

  18. Thermodynamics of irreversible structural transformation in Raddlesden-Popper perovskite-like layered Li-containing phases

    International Nuclear Information System (INIS)

    Reznitskij, L.A.

    2001-01-01

    The parameters of crystal units of the perovskite-like layer La 2 La 0.833 Nb 1.5 Ti 0.5 O 7 , Li 2 La 1.78 Nb 0.66 Ti 2.34 O 10 , Li 2 Sr 1.5 Nb 3 O 10 and Li 2 La 2.25 Nb 1.25 Ti 2.75 O 13 compounds ranked among the Raddlesden-Popper phases of the general formula Li 2 La x Nb 2n-3x Ti 3x-n O 3n+1 (n = 2, 3, 4; x = 0.833, 1.78, 2.25 correspondingly) and Li 2 Sr 1.5 Nb 3-x Fe x O 10-x (n = 3, x = 0) are shown before and after investigation by means of high resolution electron microscopy. Calculated volumes of formula units, changes in volumes after transformation, evaluations of specific heat C p of the compounds are demonstrated. Changing of transformation entropies, enthalpies and Gibbs energies of monotropic structural transformation were calculated [ru

  19. Structure and thermodynamics of effector molecule binding to the nitrogen signal transduction PII protein GlnZ from Azospirillum brasilense.

    Science.gov (United States)

    Truan, Daphné; Bjelić, Saša; Li, Xiao-Dan; Winkler, Fritz K

    2014-07-29

    The trimeric PII signal transduction proteins regulate the function of a variety of target proteins predominantly involved in nitrogen metabolism. ATP, ADP and 2-oxoglutarate (2-OG) are key effector molecules influencing PII binding to targets. Studies of PII proteins have established that the 20-residue T-loop plays a central role in effector sensing and target binding. However, the specific effects of effector binding on T-loop conformation have remained poorly documented. We present eight crystal structures of the Azospirillum brasilense PII protein GlnZ, six of which are cocrystallized and liganded with ADP or ATP. We find that interaction with the diphosphate moiety of bound ADP constrains the N-terminal part of the T-loop in a characteristic way that is maintained in ADP-promoted complexes with target proteins. In contrast, the interactions with the triphosphate moiety in ATP complexes are much more variable and no single predominant interaction mode is apparent except for the ternary MgATP/2-OG complex. These conclusions can be extended to most investigated PII proteins of the GlnB/GlnK subfamily. Unlike reported for other PII proteins, microcalorimetry reveals no cooperativity between the three binding sites of GlnZ trimers for any of the three effectors under carefully controlled experimental conditions. Copyright © 2014 Elsevier Ltd. All rights reserved.

  20. Ab initio investigation of the thermodynamics of cation distribution and of the electronic and magnetic structures in the LiMn2O4 spinel

    Science.gov (United States)

    Santos-Carballal, David; Ngoepe, Phuti E.; de Leeuw, Nora H.

    2018-02-01

    The spinel-structured lithium manganese oxide (LiMn2O4 ) is a material currently used as cathode for secondary lithium-ion batteries, but whose properties are not yet fully understood. Here, we report a computational investigation of the inversion thermodynamics and electronic behavior of LiMn2O4 derived from spin-polarized density functional theory calculations with a Hubbard Hamiltonian and long-range dispersion corrections (DFT+U-D3). Based on the analysis of the configurational free energy, we have elucidated a partially inverse equilibrium cation distribution for the LiMn2O4 spinel. This equilibrium degree of inversion is rationalized in terms of the crystal field stabilization effects and the difference between the size of the cations. We compare the atomic charges with the oxidation numbers for each degree of inversion. We found segregation of the Mn charge once these ions occupy the tetrahedral and octahedral sites of the spinel. We have obtained the atomic projections of the electronic band structure and density of states, showing that the normal LiMn2O4 has half-metallic properties, while the fully inverse spinel is an insulator. This material is in the ferrimagnetic state for the inverse and partially inverse cation arrangement. The optimized lattice and oxygen parameters, as well as the equilibrium degree of inversion, are in agreement with the available experimental data. The partial equilibrium degree of inversion is important in the interpretation of the lithium ion migration and surface properties of the LiMn2O4 spinel.

  1. Crystal Structures and Thermodynamic Analysis Reveal Distinct Mechanisms of CD28 Phosphopeptide Binding to the Src Homology 2 (SH2) Domains of Three Adaptor Proteins*

    Science.gov (United States)

    Inaba, Satomi; Numoto, Nobutaka; Ogawa, Shuhei; Morii, Hisayuki; Ikura, Teikichi; Abe, Ryo; Ito, Nobutoshi; Oda, Masayuki

    2017-01-01

    Full activation of T cells and differentiation into effector T cells are essential for many immune responses and require co-stimulatory signaling via the CD28 receptor. Extracellular ligand binding to CD28 recruits protein-tyrosine kinases to its cytoplasmic tail, which contains a YMNM motif. Following phosphorylation of the tyrosine, the proteins growth factor receptor-bound protein 2 (Grb2), Grb2-related adaptor downstream of Shc (Gads), and p85 subunit of phosphoinositide 3-kinase may bind to pYMNM (where pY is phosphotyrosine) via their Src homology 2 (SH2) domains, leading to downstream signaling to distinct immune pathways. These three adaptor proteins bind to the same site on CD28 with variable affinity, and all are important for CD28-mediated co-stimulatory function. However, the mechanism of how these proteins recognize and compete for CD28 is unclear. To visualize their interactions with CD28, we have determined the crystal structures of Gads SH2 and two p85 SH2 domains in complex with a CD28-derived phosphopeptide. The high resolution structures obtained revealed that, whereas the CD28 phosphopeptide bound to Gads SH2 is in a bent conformation similar to that when bound to Grb2 SH2, it adopts a more extended conformation when bound to the N- and C-terminal SH2 domains of p85. These differences observed in the peptide-protein interactions correlated well with the affinity and other thermodynamic parameters for each interaction determined by isothermal titration calorimetry. The detailed insight into these interactions reported here may inform the development of compounds that specifically inhibit the association of CD28 with these adaptor proteins to suppress excessive T cell responses, such as in allergies and autoimmune diseases. PMID:27927989

  2. Crystal Structures and Thermodynamic Analysis Reveal Distinct Mechanisms of CD28 Phosphopeptide Binding to the Src Homology 2 (SH2) Domains of Three Adaptor Proteins.

    Science.gov (United States)

    Inaba, Satomi; Numoto, Nobutaka; Ogawa, Shuhei; Morii, Hisayuki; Ikura, Teikichi; Abe, Ryo; Ito, Nobutoshi; Oda, Masayuki

    2017-01-20

    Full activation of T cells and differentiation into effector T cells are essential for many immune responses and require co-stimulatory signaling via the CD28 receptor. Extracellular ligand binding to CD28 recruits protein-tyrosine kinases to its cytoplasmic tail, which contains a YMNM motif. Following phosphorylation of the tyrosine, the proteins growth factor receptor-bound protein 2 (Grb2), Grb2-related adaptor downstream of Shc (Gads), and p85 subunit of phosphoinositide 3-kinase may bind to pYMNM (where pY is phosphotyrosine) via their Src homology 2 (SH2) domains, leading to downstream signaling to distinct immune pathways. These three adaptor proteins bind to the same site on CD28 with variable affinity, and all are important for CD28-mediated co-stimulatory function. However, the mechanism of how these proteins recognize and compete for CD28 is unclear. To visualize their interactions with CD28, we have determined the crystal structures of Gads SH2 and two p85 SH2 domains in complex with a CD28-derived phosphopeptide. The high resolution structures obtained revealed that, whereas the CD28 phosphopeptide bound to Gads SH2 is in a bent conformation similar to that when bound to Grb2 SH2, it adopts a more extended conformation when bound to the N- and C-terminal SH2 domains of p85. These differences observed in the peptide-protein interactions correlated well with the affinity and other thermodynamic parameters for each interaction determined by isothermal titration calorimetry. The detailed insight into these interactions reported here may inform the development of compounds that specifically inhibit the association of CD28 with these adaptor proteins to suppress excessive T cell responses, such as in allergies and autoimmune diseases. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  3. Quantum molecular dynamics: Numerical methods and physical study of the structure, thermodynamics, stability and fragmentation of sodium metallic clusters

    International Nuclear Information System (INIS)

    Blaise, Philippe

    1998-01-01

    The aim of this thesis is to study metallic sodium clusters by numerical simulation. We have developed two ab initio molecular dynamics programs within the formalism of density functional theory. The first is based on the semi-classical extended Thomas-Fermi approach. We use a real-space grid and a Car-Parrinello-like scheme. The computational cost is O(N), and we have built a pseudopotential that speeds up the calculations. By neglecting quantum shell effects, we are able to study a very large set of clusters. We show that sodium cluster energies fit well a liquid drop formula, by adjusting a few parameters. We have investigated breathing modes, surface oscillations and the net charge density. We have shown that the surface energy varies strongly with temperature, and that clusters have a lower melting point than bulk material. We have calculated fission barriers by a constraint method. The second program is based on the quantum Kohn-Sham approach. We use a real-space grid, and combine a generalized Broyden scheme for assuring self-consistency with an iterative Davidson-Lanczos algorithm for solving the Eigen-problem. The cost of the method is much higher. First of all, we have calculated some stable structures for small clusters and their energetics. We obtained very good agreement with previous works. Then, we have investigated highly charged cluster dynamics. We have identified a chaotic fission process. For high fissility systems, we observe a multi-fragmentation dynamics and we find preferential emission of monomers on a characteristic time scale less than a pico-second. This has been simulated for the first time, with the help of our adaptive grid method which follows each fragment as they move apart during the fragmentation. (author)

  4. An introduction to equilibrium thermodynamics

    CERN Document Server

    Morrill, Bernard; Hartnett, James P; Hughes, William F

    1973-01-01

    An Introduction to Equilibrium Thermodynamics discusses classical thermodynamics and irreversible thermodynamics. It introduces the laws of thermodynamics and the connection between statistical concepts and observable macroscopic properties of a thermodynamic system. Chapter 1 discusses the first law of thermodynamics while Chapters 2 through 4 deal with statistical concepts. The succeeding chapters describe the link between entropy and the reversible heat process concept of entropy; the second law of thermodynamics; Legendre transformations and Jacobian algebra. Finally, Chapter 10 provides a

  5. Thermodynamics for scientists and engineers

    International Nuclear Information System (INIS)

    Lim, Gyeong Hui

    2011-02-01

    This book deals with thermodynamics for scientists and engineers. It consists of 11 chapters, which are concept and background of thermodynamics, the first law of thermodynamics, the second law of thermodynamics and entropy, mathematics related thermodynamics, properties of thermodynamics on pure material, equilibrium, stability of thermodynamics, the basic of compound, phase equilibrium of compound, excess gibbs energy model of compound and activity coefficient model and chemical equilibrium. It has four appendixes on properties of pure materials and thermal mass.

  6. Thermodynamics of Bioreactions.

    Science.gov (United States)

    Held, Christoph; Sadowski, Gabriele

    2016-06-07

    Thermodynamic principles have been applied to enzyme-catalyzed reactions since the beginning of the 1930s in an attempt to understand metabolic pathways. Currently, thermodynamics is also applied to the design and analysis of biotechnological processes. The key thermodynamic quantity is the Gibbs energy of reaction, which must be negative for a reaction to occur spontaneously. However, the application of thermodynamic feasibility studies sometimes yields positive Gibbs energies of reaction even for reactions that are known to occur spontaneously, such as glycolysis. This article reviews the application of thermodynamics in enzyme-catalyzed reactions. It summarizes the basic thermodynamic relationships used for describing the Gibbs energy of reaction and also refers to the nonuniform application of these relationships in the literature. The review summarizes state-of-the-art approaches that describe the influence of temperature, pH, electrolytes, solvents, and concentrations of reacting agents on the Gibbs energy of reaction and, therefore, on the feasibility and yield of biological reactions.

  7. Thermodynamically efficient solar concentrators

    Science.gov (United States)

    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.

  8. Black Holes and Thermodynamics

    OpenAIRE

    Wald, Robert M.

    1997-01-01

    We review the remarkable relationship between the laws of black hole mechanics and the ordinary laws of thermodynamics. It is emphasized that - in analogy with the laws of thermodynamics - the validity the laws of black hole mechanics does not appear to depend upon the details of the underlying dynamical theory (i.e., upon the particular field equations of general relativity). It also is emphasized that a number of unresolved issues arise in ``ordinary thermodynamics'' in the context of gener...

  9. Thermodynamic theory of equilibrium fluctuations

    International Nuclear Information System (INIS)

    Mishin, Y.

    2015-01-01

    The postulational basis of classical thermodynamics has been expanded to incorporate equilibrium fluctuations. The main additional elements of the proposed thermodynamic theory are the concept of quasi-equilibrium states, a definition of non-equilibrium entropy, a fundamental equation of state in the entropy representation, and a fluctuation postulate describing the probability distribution of macroscopic parameters of an isolated system. Although these elements introduce a statistical component that does not exist in classical thermodynamics, the logical structure of the theory is different from that of statistical mechanics and represents an expanded version of thermodynamics. Based on this theory, we present a regular procedure for calculations of equilibrium fluctuations of extensive parameters, intensive parameters and densities in systems with any number of fluctuating parameters. The proposed fluctuation formalism is demonstrated by four applications: (1) derivation of the complete set of fluctuation relations for a simple fluid in three different ensembles; (2) fluctuations in finite-reservoir systems interpolating between the canonical and micro-canonical ensembles; (3) derivation of fluctuation relations for excess properties of grain boundaries in binary solid solutions, and (4) derivation of the grain boundary width distribution for pre-melted grain boundaries in alloys. The last two applications offer an efficient fluctuation-based approach to calculations of interface excess properties and extraction of the disjoining potential in pre-melted grain boundaries. Possible future extensions of the theory are outlined.

  10. Influence of Secondary Interactions on the Structure, Sublimation Thermodynamics, and Solubility of Salicylate:4-Hydroxybenzamide Cocrystals. Combined Experimental and Theoretical Study.

    Science.gov (United States)

    Manin, Alex N; Voronin, Alexander P; Shishkina, Anastasia V; Vener, Mikhail V; Churakov, Andrei V; Perlovich, German L

    2015-08-20

    Cocrystal screening of 4-hydroxybenzamide with a number of salicylates (salicylic acid, SA; 4-aminosalicylic acid, PASA; acetylsalicylic acid, ASA; and salicylsalicylic acid, SSA) was conducted to confirm the formation of two cocrystals, [SA+4-OHBZA] (1:1) and [PASA+4-OHBZA] (1:1). Their structures were determined using single-crystal X-ray diffraction, and the hydrogen-bond network topology was studied. Thermodynamic characteristics of salicylic acid cocrystal sublimation were obtained experimentally. It was proved that PASA cocrystallization with 4-OHBZA makes the drug more stable and prevents the irreversible process of decarboxylation of PASA resulting in formation of toxic 3-aminophenol. The pattern of non-covalent interactions in the cocrystals is described quantitatively using solid-state density functional theory followed by Bader analysis of the periodic electron density. It has been found that the total energy of secondary interactions between synthon atoms and the side hydroxyl group of the acid molecule in [SA+4-OHBZA] (1:1) and [PASA+4-OHBZA] (1:1) cocrystals is comparable to the energy of the primary acid-amide heterosynthon. The theoretical value of the sublimation enthalpy of [SA+4-OHBZA], 231 kJ/mol, agrees fairly well with the experimental one, 272 kJ/mol. The dissolution experiments with [SA+4-OHBZA] have proved that the relatively large cocrystal stability in relation to the stability of its components has a negative effect on the dissolution rate and equilibrium solubility. The [PASA+4-OHBZA] (1:1) cocrystal showed an enhancement of apparent solubility compared to that of the corresponding pure active pharmaceutical ingredient, while their intrinsic dissolution rates are comparable.

  11. Hidden in Plain Sight: Subtle Effects of the 8-Oxoguanine Lesion on the Structure, Dynamics, and Thermodynamics of a 15-Base-Pair Oligodeoxynucleotide Duplex†

    Science.gov (United States)

    Crenshaw, Charisse M.; Wade, Jacqueline E.; Arthanari, Haribabu; Frueh, Dominique; Lane, Benjamin F.; Núñez, Megan E.

    2011-01-01

    The base lesion 8-oxoguanine is formed readily by oxidation of DNA, potentially leading to G→T transversion mutations. Despite the apparent similarity of 8-oxoguanine-cytosine base pairs to normal guanine-cytosine base pairs, cellular base excision repair systems effectively recognize the lesion base. Here we apply several techniques to examine a single 8-oxoguanine lesion at the center of a nonpalindromic 15-mer duplex oligonucleotide in an effort to determine what, if anything, distinguishes an 8-oxoguanine-cytosine base pair from a normal base pair. The lesion duplex is globally almost indistinguishable from the unmodified parent duplex using CD spectroscopy and UV melting thermodynamics. The DNA mismatch-detecting photocleavage agent Rh(bpy)2chrysi3+ cleaves only weakly and nonspecifically, revealing that the 8oxoG-C pair is locally stable at the level of the individual base pairs. NMR spectra are also consistent with a well-conserved B-form duplex structure. In the 2D NOESY spectra, base-sugar and imino-imino crosspeaks are strikingly similar between parent and lesion duplexes. Changes in chemical shift due to the 8oxoG lesion are localized to its complementary cytosine and to the 2–3 base pairs immediately flanking the lesion on the lesion strand. Residues further removed from the lesion are shown to be unperturbed by its presence. Notably, imino exchange experiments indicate that the 8-oxoguanine-cytosine pair is strong and stable, with an apparent equilibrium constant for opening equal to that of other internal guanine-cytosine base pairs, on the order of 10−6. This collection of experiments shows that the 8-oxoguanine-cytosine base pair is incredibly stable and similar to the native pair. PMID:21902242

  12. Methods of thermodynamics

    CERN Document Server

    Reiss, Howard

    1997-01-01

    Since there is no shortage of excellent general books on elementary thermodynamics, this book takes a different approach, focusing attention on the problem areas of understanding of concept and especially on the overwhelming but usually hidden role of ""constraints"" in thermodynamics, as well as on the lucid exposition of the significance, construction, and use (in the case of arbitrary systems) of the thermodynamic potential. It will be especially useful as an auxiliary text to be used along with any standard treatment.Unlike some texts, Methods of Thermodynamics does not use statistical m

  13. Thermodynamics of nuclear materials

    International Nuclear Information System (INIS)

    Rand, M.H.

    1975-01-01

    A report is presented of the Fourth International Symposium on Thermodynamics of Nuclear Materials held in Vienna, 21-25 October 1974. The technological theme of the Symposium was the application of thermodynamics to the understanding of the chemistry of irradiated nuclear fuels and to safety assessments for hypothetical accident conditions in reactors. The first four sessions were devoted to these topics and they were followed by four more sessions on the more basic thermodynamics, phase diagrams and the thermodynamic properties of a wide range of nuclear materials. Sixty-seven papers were presented

  14. Thermodynamic analysis of elastic-plastic deformation

    International Nuclear Information System (INIS)

    Lubarda, V.

    1981-01-01

    The complete set of constitutive equations which fully describes the behaviour of material in elastic-plastic deformation is derived on the basis of thermodynamic analysis of the deformation process. The analysis is done after the matrix decomposition of the deformation gradient is introduced into the structure of thermodynamics with internal state variables. The free energy function, is decomposed. Derive the expressions for the stress response, entropy and heat flux, and establish the evolution equation. Finally, we establish the thermodynamic restrictions of the deformation process. (Author) [pt

  15. Introduction to physics mechanics, hydrodynamics thermodynamics

    CERN Document Server

    Frauenfelder, P

    2013-01-01

    Introduction of Physics: Mechanics , Hydrodynamics, Thermodynamics covers the principles of matter and its motion through space and time, as well as the related concepts of energy and force. This book is composed of eleven chapters, and begins with an introduction to the basic principles of mechanics, hydrodynamics, and thermodynamics. The subsequent chapters deal with the statics of rigid bodies and the dynamics of particles and rigid bodies. These topics are followed by discussions on elasticity, mechanics of fluids, the basic concept of thermodynamic, kinetic theory, and crystal structure o

  16. Improved Estimates of Thermodynamic Parameters

    Science.gov (United States)

    Lawson, D. D.

    1982-01-01

    Techniques refined for estimating heat of vaporization and other parameters from molecular structure. Using parabolic equation with three adjustable parameters, heat of vaporization can be used to estimate boiling point, and vice versa. Boiling points and vapor pressures for some nonpolar liquids were estimated by improved method and compared with previously reported values. Technique for estimating thermodynamic parameters should make it easier for engineers to choose among candidate heat-exchange fluids for thermochemical cycles.

  17. Thermodynamic evolution far from equilibrium

    Science.gov (United States)

    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.

  18. Thermodynamic and Quantum Thermodynamic Analyses of Brownian Movement

    OpenAIRE

    Gyftopoulos, Elias P.

    2006-01-01

    Thermodynamic and quantum thermodynamic analyses of Brownian movement of a solvent and a colloid passing through neutral thermodynamic equilibrium states only. It is shown that Brownian motors and E. coli do not represent Brownian movement.

  19. Thermodynamics of nuclear materials

    International Nuclear Information System (INIS)

    1979-01-01

    Full text: The science of chemical thermodynamics has substantially contributed to the understanding of the many problems encountered in nuclear and reactor technology. These problems include reaction of materials with their surroundings and chemical and physical changes of fuels. Modern reactor technology, by its very nature, has offered new fields of investigations for the scientists and engineers concerned with the design of nuclear fuel elements. Moreover, thermodynamics has been vital in predicting the behaviour of new materials for fission as well as fusion reactors. In this regard, the Symposium was organized to provide a mechanism for review and discussion of recent thermodynamic investigations of nuclear materials. The Symposium was held in the Juelich Nuclear Research Centre, at the invitation of the Government of the Federal Republic of Germany. The International Atomic Energy Agency has given much attention to the thermodynamics of nuclear materials, as is evidenced by its sponsorship of four international symposia in 1962, 1965, 1967, and 1974. The first three meetings were primarily concerned with the fundamental thermodynamics of nuclear materials; as with the 1974 meeting, this last Symposium was primarily aimed at the thermodynamic behaviour of nuclear materials in actual practice, i.e., applied thermodynamics. Many advances have been made since the 1974 meeting, both in fundamental and applied thermodynamics of nuclear materials, and this meeting provided opportunities for an exchange of new information on this topic. The Symposium dealt in part with the thermodynamic analysis of nuclear materials under conditions of high temperatures and a severe radiation environment. Several sessions were devoted to the thermodynamic studies of nuclear fuels and fission and fusion reactor materials under adverse conditions. These papers and ensuing discussions provided a better understanding of the chemical behaviour of fuels and materials under these

  20. Reconciling structural and thermodynamic predictions using all-atom and coarse-grain force fields: the case of charged oligo-arginine translocation into DMPC bilayers.

    Science.gov (United States)

    Hu, Yuan; Sinha, Sudipta Kumar; Patel, Sandeep

    2014-10-16

    Using the translocation of short, charged cationic oligo-arginine peptides (mono-, di-, and triarginine) from bulk aqueous solution into model DMPC bilayers, we explore the question of the similarity of thermodynamic and structural predictions obtained from molecular dynamics simulations using all-atom and Martini coarse-grain force fields. Specifically, we estimate potentials of mean force associated with translocation using standard all-atom (CHARMM36 lipid) and polarizable and nonpolarizable Martini force fields, as well as a series of modified Martini-based parameter sets. We find that we are able to reproduce qualitative features of potentials of mean force of single amino acid side chain analogues into model bilayers. In particular, modifications of peptide-water and peptide-membrane interactions allow prediction of free energy minima at the bilayer-water interface as obtained with all-atom force fields. In the case of oligo-arginine peptides, the modified parameter sets predict interfacial free energy minima as well as free energy barriers in almost quantitative agreement with all-atom force field based simulations. Interfacial free energy minima predicted by a modified coarse-grained parameter set are -2.51, -4.28, and -5.42 for mono-, di-, and triarginine; corresponding values from all-atom simulations are -0.83, -3.33, and -3.29, respectively, all in units of kcal/mol. We found that a stronger interaction between oligo-arginine and the membrane components and a weaker interaction between oligo-arginine and water are crucial for producing such minima in PMFs using the polarizable CG model. The difference between bulk aqueous and bilayer center states predicted by the modified coarse-grain force field are 11.71, 14.14, and 16.53 kcal/mol, and those by the all-atom model are 6.94, 8.64, and 12.80 kcal/mol; those are of almost the same order of magnitude. Our simulations also demonstrate a remarkable similarity in the structural aspects of the ensemble of

  1. Structural and thermodynamic characteristics of X2MYH2 compounds (M Al, Ga, In; X = F, Cl, Br, I; Y = N, P, As) - the products of hydrohalogen elimination from X3MYH3 donor-acceptor complexes

    International Nuclear Information System (INIS)

    Timoshkin, A.Yu.; Suvorov, A.V.; Shefer, G.F.

    2001-01-01

    Geometrical and thermodynamic characteristics of complexes X 2 MYH 2 (M Al, Ga, In; X = F, Cl, Br, I; Y = N, P, As) were obtained by the method of density functional B3LYP. It is shown that nitrogen complexes X 2 MNH 2 have a plane structure, whereas phosphorus and arsenic complexes are pyramidal. In the process of HX elimination the dissociation energy of M-Y bond is strengthened essentially (by 150-270 kJ/mol), which makes dissociation of X 2 MYH 2 into components quite inefficient from thermodynamic viewpoint even at temperatures of about 1000 deg C. Dimerization enthalpies of X 2 MYH 2 lie in the range 40 (Y = P, As) - 260 (Y=N) kJ/mol. Thus, dimers [X 2 MNH 2 ] 2 can be intermediate products in the processes of nitrides chemical precipitation from gaseous phase of donor-acceptor complexes [ru

  2. Thermodynamics and heat power

    CERN Document Server

    Granet, Irving

    2014-01-01

    Fundamental ConceptsIntroductionThermodynamic SystemsTemperatureForce and MassElementary Kinetic Theory of GasesPressureReviewKey TermsEquations Developed in This ChapterQuestionsProblemsWork, Energy, and HeatIntroductionWorkEnergyInternal EnergyPotential EnergyKinetic EnergyHeatFlow WorkNonflow WorkReviewKey TermsEquations Developed in This ChapterQuestionsProblemsFirst Law of ThermodynamicsIntroductionFirst Law of ThermodynamicsNonflow SystemSteady-Flow SystemApplications of First Law of ThermodynamicsReviewKey TermsEquations Developed in This ChapterQuestionsProblemsThe Second Law of ThermodynamicsIntroductionReversibility-Second Law of ThermodynamicsThe Carnot CycleEntropyReviewKey TermsEquations Developed in This ChapterQuestionsProblemsProperties of Liquids and GasesIntroductionLiquids and VaporsThermodynamic Properties of SteamComputerized PropertiesThermodynamic DiagramsProcessesReviewKey TermsEquations Developed in This ChapterQuestionsProblemsThe Ideal GasIntroductionBasic ConsiderationsSpecific Hea...

  3. The thermodynamic solar energy

    International Nuclear Information System (INIS)

    Rivoire, B.

    2002-04-01

    The thermodynamic solar energy is the technic in the whole aiming to transform the solar radiation energy in high temperature heat and then in mechanical energy by a thermodynamic cycle. These technic are most often at an experimental scale. This paper describes and analyzes the research programs developed in the advanced countries, since 1980. (A.L.B.)

  4. Quasiparticles and thermodynamical consistency

    International Nuclear Information System (INIS)

    Shanenko, A.A.; Biro, T.S.; Toneev, V.D.

    2003-01-01

    A brief and simple introduction into the problem of the thermodynamical consistency is given. The thermodynamical consistency relations, which should be taken into account under constructing a quasiparticle model, are found in a general manner from the finite-temperature extension of the Hellmann-Feynman theorem. Restrictions following from these relations are illustrated by simple physical examples. (author)

  5. Equilibrium thermodynamics - Callen's postulational approach

    NARCIS (Netherlands)

    Jongschaap, R.J.J.; Öttinger, Hans Christian

    2001-01-01

    In order to provide the background for nonequilibrium thermodynamics, we outline the fundamentals of equilibrium thermodynamics. Equilibrium thermodynamics must not only be obtained as a special case of any acceptable nonequilibrium generalization but, through its shining example, it also elucidates

  6. Applied chemical engineering thermodynamics

    CERN Document Server

    Tassios, Dimitrios P

    1993-01-01

    Applied Chemical Engineering Thermodynamics provides the undergraduate and graduate student of chemical engineering with the basic knowledge, the methodology and the references he needs to apply it in industrial practice. Thus, in addition to the classical topics of the laws of thermodynamics,pure component and mixture thermodynamic properties as well as phase and chemical equilibria the reader will find: - history of thermodynamics - energy conservation - internmolecular forces and molecular thermodynamics - cubic equations of state - statistical mechanics. A great number of calculated problems with solutions and an appendix with numerous tables of numbers of practical importance are extremely helpful for applied calculations. The computer programs on the included disk help the student to become familiar with the typical methods used in industry for volumetric and vapor-liquid equilibria calculations.

  7. Thermodynamics an engineering approach

    CERN Document Server

    Cengel, Yunus A

    2014-01-01

    Thermodynamics, An Engineering Approach, eighth edition, covers the basic principles of thermodynamics while presenting a wealth of real-world engineering examples so students get a feel for how thermodynamics is applied in engineering practice. This text helps students develop an intuitive understanding by emphasizing the physics and physical arguments. Cengel and Boles explore the various facets of thermodynamics through careful explanations of concepts and use of numerous practical examples and figures, having students develop necessary skills to bridge the gap between knowledge and the confidence to properly apply their knowledge. McGraw-Hill is proud to offer Connect with the eighth edition of Cengel/Boles, Thermodynamics, An Engineering Approach. This innovative and powerful new system helps your students learn more efficiently and gives you the ability to assign homework problems simply and easily. Problems are graded automatically, and the results are recorded immediately. Track individual stude...

  8. THE EFFECT OF CHEMICAL-STRUCTURE UPON THE THERMODYNAMICS OF MICELLIZATION OF MODEL ALKYLARENESULPHONATES - PREDICTION OF MICELLAR PROPERTIES WITH THE POISSON-BOLTZMANN MODEL

    NARCIS (Netherlands)

    Bijma, K; Engberts, J B F N

    This paper describes how the theory of the ''dressed micelle'', which is based on the nonlinear Poisson-Boltzmann equation, can be used to calculate a number of thermodynamic quantities for micellization of sodium p-alkylbenzenesulphonates. From the Gibbs energy of micellization, the enthalpy of

  9. Thermodynamic estimation: Ionic materials

    International Nuclear Information System (INIS)

    Glasser, Leslie

    2013-01-01

    Thermodynamics establishes equilibrium relations among thermodynamic parameters (“properties”) and delineates the effects of variation of the thermodynamic functions (typically temperature and pressure) on those parameters. However, classical thermodynamics does not provide values for the necessary thermodynamic properties, which must be established by extra-thermodynamic means such as experiment, theoretical calculation, or empirical estimation. While many values may be found in the numerous collected tables in the literature, these are necessarily incomplete because either the experimental measurements have not been made or the materials may be hypothetical. The current paper presents a number of simple and relible estimation methods for thermodynamic properties, principally for ionic materials. The results may also be used as a check for obvious errors in published values. The estimation methods described are typically based on addition of properties of individual ions, or sums of properties of neutral ion groups (such as “double” salts, in the Simple Salt Approximation), or based upon correlations such as with formula unit volumes (Volume-Based Thermodynamics). - Graphical abstract: Thermodynamic properties of ionic materials may be readily estimated by summation of the properties of individual ions, by summation of the properties of ‘double salts’, and by correlation with formula volume. Such estimates may fill gaps in the literature, and may also be used as checks of published values. This simplicity arises from exploitation of the fact that repulsive energy terms are of short range and very similar across materials, while coulombic interactions provide a very large component of the attractive energy in ionic systems. Display Omitted - Highlights: • Estimation methods for thermodynamic properties of ionic materials are introduced. • Methods are based on summation of single ions, multiple salts, and correlations. • Heat capacity, entropy

  10. Statistical thermodynamics of nonequilibrium processes

    CERN Document Server

    Keizer, Joel

    1987-01-01

    The structure of the theory ofthermodynamics has changed enormously since its inception in the middle of the nineteenth century. Shortly after Thomson and Clausius enunciated their versions of the Second Law, Clausius, Maxwell, and Boltzmann began actively pursuing the molecular basis of thermo­ dynamics, work that culminated in the Boltzmann equation and the theory of transport processes in dilute gases. Much later, Onsager undertook the elucidation of the symmetry oftransport coefficients and, thereby, established himself as the father of the theory of nonequilibrium thermodynamics. Com­ bining the statistical ideas of Gibbs and Langevin with the phenomenological transport equations, Onsager and others went on to develop a consistent statistical theory of irreversible processes. The power of that theory is in its ability to relate measurable quantities, such as transport coefficients and thermodynamic derivatives, to the results of experimental measurements. As powerful as that theory is, it is linear and...

  11. Sorption of trivalent lanthanides and actinides onto montmorillonite: Macroscopic, thermodynamic and structural evidence for ternary hydroxo and carbonato surface complexes on multiple sorption sites.

    Science.gov (United States)

    Fernandes, M Marques; Scheinost, A C; Baeyens, B

    2016-08-01

    The credibility of long-term safety assessments of radioactive waste repositories may be greatly enhanced by a molecular level understanding of the sorption processes onto individual minerals present in the near- and far-fields. In this study we couple macroscopic sorption experiments to surface complexation modelling and spectroscopic investigations, including extended X-ray absorption fine structure (EXAFS) and time-resolved laser fluorescence spectroscopies (TRLFS), to elucidate the uptake mechanism of trivalent lanthanides and actinides (Ln/An(III)) by montmorillonite in the absence and presence of dissolved carbonate. Based on the experimental sorption isotherms for the carbonate-free system, the previously developed 2 site protolysis non electrostatic surface complexation and cation exchange (2SPNE SC/CE) model needed to be complemented with an additional surface complexation reaction onto weak sites. The fitting of sorption isotherms in the presence of carbonate required refinement of the previously published model by reducing the strong site capacity and by adding the formation of Ln/An(III)-carbonato complexes both on strong and weak sites. EXAFS spectra of selected Am samples and TRLFS spectra of selected Cm samples corroborate the model assumptions by showing the existence of different surface complexation sites and evidencing the formation of Ln/An(III) carbonate surface complexes. In the absence of carbonate and at low loadings, Ln/An(III) form strong inner-sphere complexes through binding to three Al(O,OH)6 octahedra, most likely by occupying vacant sites in the octahedral layers of montmorillonite, which are exposed on {010} and {110} edge faces. At higher loadings, Ln/An(III) binds to only one Al octahedron, forming a weaker, edge-sharing surface complex. In the presence of carbonate, we identified a ternary mono- or dicarbonato Ln/An(III) complex binding directly to one Al(O,OH)6 octahedron, revealing that type-A ternary complexes form with the one

  12. Thermodynamics and economics

    International Nuclear Information System (INIS)

    Mansson, B.A.

    1990-01-01

    Economics, as the social science most concerned with the use and distribution of natural resources, must start to make use of the knowledge at hand in the natural sciences about such resources. In this, thermodynamics is an essential part. In a physicists terminology, human economic activity may be described as a dissipative system which flourishes by transforming and exchanging resources, goods and services. All this involves complex networks of flows of energy and materials. This implies that thermodynamics, the physical theory of energy and materials flows, must have implications for economics. On another level, thermodynamics has been recognized as a physical theory of value, with value concepts similar to those of economic theory. This paper discusses some general aspects of the significance of non-equilibrium thermodynamics for economics. The role of exergy, probably the most important of the physical measures of value, is elucidated. Two examples of integration of thermodynamics with economic theory are reviewed. First, a simple model of a steady-state production system is sued to illustrate the effects of thermodynamic process constraints. Second, the framework of a simple macroeconomic growth model is used to illustrate how some thermodynamic limitations may be integrated in macroeconomic theory

  13. Advanced thermodynamics engineering

    CERN Document Server

    Annamalai, Kalyan; Jog, Milind A

    2011-01-01

    Thermolab Excel-Based Software for Thermodynamic Properties and Flame Temperatures of Fuels IntroductionImportance, Significance and LimitationsReview of ThermodynamicsMathematical BackgroundOverview of Microscopic/NanothermodynamicsSummaryAppendix: Stokes and Gauss Theorems First Law of ThermodynamicsZeroth LawFirst Law for a Closed SystemQuasi Equilibrium (QE) and Nonquasi-equilibrium (NQE) ProcessesEnthalpy and First LawAdiabatic Reversible Process for Ideal Gas with Constant Specific HeatsFirst Law for an Open SystemApplications of First Law for an Open SystemIntegral and Differential Form

  14. Thermodynamics I essentials

    CERN Document Server

    REA, The Editors of

    2012-01-01

    REA's Essentials provide quick and easy access to critical information in a variety of different fields, ranging from the most basic to the most advanced. As its name implies, these concise, comprehensive study guides summarize the essentials of the field covered. Essentials are helpful when preparing for exams, doing homework and will remain a lasting reference source for students, teachers, and professionals. Thermodynamics I includes review of properties and states of a pure substance, work and heat, energy and the first law of thermodynamics, entropy and the second law of thermodynamics

  15. Non-equilibrium thermodynamics

    CERN Document Server

    De Groot, Sybren Ruurds

    1984-01-01

    The study of thermodynamics is especially timely today, as its concepts are being applied to problems in biology, biochemistry, electrochemistry, and engineering. This book treats irreversible processes and phenomena - non-equilibrium thermodynamics.S. R. de Groot and P. Mazur, Professors of Theoretical Physics, present a comprehensive and insightful survey of the foundations of the field, providing the only complete discussion of the fluctuating linear theory of irreversible thermodynamics. The application covers a wide range of topics: the theory of diffusion and heat conduction, fluid dyn

  16. Thermodynamics of quantum strings

    CERN Document Server

    Morgan, M J

    1994-01-01

    A statistical mechanical analysis of an ideal gas of non-relativistic quantum strings is presented, in which the thermodynamic properties of the string gas are calculated from a canonical partition function. This toy model enables students to gain insight into the thermodynamics of a simple 'quantum field' theory, and provides a useful pedagogical introduction to the more complicated relativistic string theories. A review is also given of the thermodynamics of the open bosonic string gas and the type I (open) superstring gas. (author)

  17. Modern engineering thermodynamics

    CERN Document Server

    Balmer, Robert T

    2010-01-01

    Designed for use in a standard two-semester engineering thermodynamics course sequence. The first half of the text contains material suitable for a basic Thermodynamics course taken by engineers from all majors. The second half of the text is suitable for an Applied Thermodynamics course in mechanical engineering programs. The text has numerous features that are unique among engineering textbooks, including historical vignettes, critical thinking boxes, and case studies. All are designed to bring real engineering applications into a subject that can be somewhat abstract and mathematica

  18. First-principles calculations of the structural and thermodynamic properties of bcc, fcc and hcp solid solutions in the Al-TM (TM = Ti, Zr and Hf) systems: A comparison of cluster expansion and supercell methods

    International Nuclear Information System (INIS)

    Ghosh, G.; Walle, A. van de; Asta, M.

    2008-01-01

    The thermodynamic properties of solid solutions with body-centered cubic (bcc), face-centered cubic (fcc) and hexagonal close-packed (hcp) structures in the Al-TM (TM = Ti, Zr and Hf) systems are calculated from first-principles using cluster expansion (CE), Monte-Carlo simulation and supercell methods. The 32-atom special quasirandom structure (SQS) supercells are employed to compute properties at 25, 50 and 75 at.% TM compositions, and 64-atom supercells have been employed to compute properties of alloys in the dilute concentration limit (one solute and 63 solvent atoms). In general, the energy of mixing (Δ m E) calculated by CE and dilute supercells agree very well. In the concentrated region, the Δ m E values calculated by CE and SQS methods also agree well in many cases; however, noteworthy discrepancies are found in some cases, which we argue originate from inherent elastic and dynamic instabilities of the relevant parent lattice structures. The importance of short-range order on the calculated values of Δ m E for hcp Al-Ti alloys is demonstrated. We also present calculated results for the composition dependence of the atomic volumes in random solid solutions with bcc, fcc and hcp structures. The properties of solid solutions reported here may be integrated within the CALPHAD formalism to develop reliable thermodynamic databases in order to facilitate: (i) calculations of stable and metastable phase diagrams of binary and multicomponent systems, (ii) alloy design, and (iii) processing of Al-TM-based alloys

  19. Theoretical physics 5 thermodynamics

    CERN Document Server

    Nolting, Wolfgang

    2017-01-01

    This concise textbook offers a clear and comprehensive introduction to thermodynamics, one of the core components of undergraduate physics courses. It follows on naturally from the previous volumes in this series, defining macroscopic variables, such as internal energy, entropy and pressure,together with thermodynamic principles. The first part of the book introduces the laws of thermodynamics and thermodynamic potentials. More complex themes are covered in the second part of the book, which describes phases and phase transitions in depth. Ideally suited to undergraduate students with some grounding in classical mechanics, the book is enhanced throughout with learning features such as boxed inserts and chapter summaries, with key mathematical derivations highlighted to aid understanding. The text is supported by numerous worked examples and end of chapter problem sets. About the Theoretical Physics series Translated from the renowned and highly successful German editions, the eight volumes of this series cove...

  20. Elements of chemical thermodynamics

    CERN Document Server

    Nash, Leonard K

    2005-01-01

    This survey of purely thermal data in calculating the position of equilibrium in a chemical reaction highlights the physical content of thermodynamics, as distinct from purely mathematical aspects. 1970 edition.

  1. Elements of statistical thermodynamics

    CERN Document Server

    Nash, Leonard K

    2006-01-01

    Encompassing essentially all aspects of statistical mechanics that appear in undergraduate texts, this concise, elementary treatment shows how an atomic-molecular perspective yields new insights into macroscopic thermodynamics. 1974 edition.

  2. Electrochemical thermodynamic measurement system

    Science.gov (United States)

    Reynier, Yvan [Meylan, FR; Yazami, Rachid [Los Angeles, CA; Fultz, Brent T [Pasadena, CA

    2009-09-29

    The present invention provides systems and methods for accurately characterizing thermodynamic and materials properties of electrodes and electrochemical energy storage and conversion systems. Systems and methods of the present invention are configured for simultaneously collecting a suite of measurements characterizing a plurality of interconnected electrochemical and thermodynamic parameters relating to the electrode reaction state of advancement, voltage and temperature. Enhanced sensitivity provided by the present methods and systems combined with measurement conditions that reflect thermodynamically stabilized electrode conditions allow very accurate measurement of thermodynamic parameters, including state functions such as the Gibbs free energy, enthalpy and entropy of electrode/electrochemical cell reactions, that enable prediction of important performance attributes of electrode materials and electrochemical systems, such as the energy, power density, current rate and the cycle life of an electrochemical cell.

  3. Workshop on Teaching Thermodynamics

    CERN Document Server

    1985-01-01

    It seemed appropriate to arrange a meeting of teachers of thermodynamics in the United Kingdom, a meeting held in the pleasant surroundings of Emmanuel College, Cambridge, in Sept~mber, 1984. This volume records the ideas put forward by authors, the discussion generated and an account of the action that discussion has initiated. Emphasis was placed on the Teaching of Thermodynamics to degree-level students in their first and second years. The meeting, a workshop for practitioners in which all were expected to take part, was remarkably well supported. This was notable in the representation of essentially every UK university and polytechnic engaged in teaching engineering thermodynamics and has led to a stimulating spread of ideas. By intention, the emphasis for attendance was put on teachers of engineering concerned with thermodynamics, both mechanical and chemical engineering disciplines. Attendance from others was encouraged but limited as follows: non-engineering acad­ emics, 10%, industrialists, 10%. The ...

  4. Black-hole thermodynamics

    International Nuclear Information System (INIS)

    Bekenstein, J.D.

    1980-01-01

    Including black holes in the scheme of thermodynamics has disclosed a deep-seated connection between gravitation, heat and the quantum that may lead us to a synthesis of the corresponding branches of physics

  5. Polyelectrolytes thermodynamics and rheology

    CERN Document Server

    P M, Visakh; Picó, Guillermo Alfredo

    2014-01-01

    This book discusses current development of theoretical models and experimental findings on the thermodynamics of polyelectrolytes. Particular emphasis is placed on the rheological description of polyelectrolyte solutions and hydrogels.

  6. A New Perspective on Thermodynamics

    CERN Document Server

    Lavenda, Bernard H

    2010-01-01

    Dr. Bernard H. Lavenda has written A New Perspective on Thermodynamics to combine an old look at thermodynamics with a new foundation. The book presents a historical perspective, which unravels the current presentation of thermodynamics found in standard texts, and which emphasizes the fundamental role that Carnot played in the development of thermodynamics. A New Perspective on Thermodynamics will: Chronologically unravel the development of the principles of thermodynamics and how they were conceived by their discoverers Bring the theory of thermodynamics up to the present time and indicate areas of further development with the union of information theory and the theory of means and their inequalities. New areas include nonextensive thermodynamics, the thermodynamics of coding theory, multifractals, and strange attractors. Reintroduce important, yet nearly forgotten, teachings of N.L. Sardi Carnot Highlight conceptual flaws in timely topics such as endoreversible engines, finite-time thermodynamics, geometri...

  7. Gravity as a thermodynamic phenomenon

    OpenAIRE

    Moustos, Dimitris

    2017-01-01

    The analogy between the laws of black hole mechanics and the laws of thermodynamics led Bekenstein and Hawking to argue that black holes should be considered as real thermodynamic systems that are characterised by entropy and temperature. Black hole thermodynamics indicates a deeper connection between thermodynamics and gravity. We review and examine in detail the arguments that suggest an interpretation of gravity itself as a thermodynamic theory.

  8. Investigation on complex coacervation between fish skin gelatin from cold-water fish and gum arabic: Phase behavior, thermodynamic, and structural properties.

    Science.gov (United States)

    Li, Yong; Zhang, Xiyue; Zhao, Yu; Ding, Jie; Lin, Songyi

    2018-05-01

    The study is aimed to investigate phase behavior, thermodynamic, and structural properties based on complex coacervation between fish skin gelatin (FSG) from cold-water fish and gum arabic (GA). Phase separation behavior between FSG and GA was investigated as a function of pH through varying mixing ratios from 4:1 to 1:4 at 25 °C and 1.0 wt% of total biopolymer concentration. The turbidity of FSG-GA mixture reached the maximum (1.743) at the 1:2 of mixing ratio and pH opt 3.5, and stabilized at zero. Then physicochemical properties of FSG-GA coacervates at pH opt 3.5 and FSG-GA mixtures at pH 6.0 (>pH c ) were evaluated. Scanning electron microscope (SEM) and X-ray diffraction (XRD) showed that the interactions between FSG and GA occurred at pH opt 3.5 and were very weak at pH 6.0 (>pH c ). The isothermal titration calorimetry (ITC) results including the negative Gibbs free energy change (ΔG = -18.71 ± 1.300 kJ/mol), binding enthalpy (ΔH = -41.81 ± 1.300 kJ/mol) and binding entropy (TΔS = -23.10 kJ/mol) indicated that the complexation between FSG and GA was spontaneous and driven by negative enthalpy owing to the electrostatic interaction and hydrogen bondings. The zeta potential (ZP) of FSG-GA coacervates at pH opt 3.5 was -9.00 ± 0.79 mV that was not close to electrically neutral, indicating other interactions besides electronic interaction. Hydrogen bondings in FSG-GA mixtures at pH 6.0 and 3.5 were found to be stronger than pure FSG at pH 6.0 and 3.5 owing to that the amide II peaks shifted to high wavenumbers. Electronic interaction was proven to exist in FSG-GA mixtures at pH 6.0 through the vanishment of asymmetric COO - stretching. However, the electronic interaction in FSG-GA coacervates at pH opt 3.5 was obviously stronger than FSG-GA mixtures at pH 6.0, resulting from the vanishment of asymmetric and symmetric COO - stretching vibration and the positively charged FSG and GA. The intrinsic

  9. Thermodynamic basis for cluster kinetics

    DEFF Research Database (Denmark)

    Hu, Lina; Bian, Xiufang; Qin, Xubo

    2006-01-01

    Due to the inaccessibility of the supercooled region of marginal metallic glasses (MMGs) within the experimental time window, we study the cluster kinetics above the liquidus temperature, Tl, to acquire information on the fragility of the MMG systems. Thermodynamic basis for the stability...... of locally ordered structure in the MMG liquids is discussed in terms of the two-order-parameter model. It is found that the Arrhenius activation energy of clusters, h, is proportional to the chemical mixing enthalpy of alloys, Hchem. Fragility of the MMG forming liquids can be described by the ratio...

  10. Complexation of amidocarbamoyl phosphine oxides with Ln{sup +3} (Ln = La, Nd, Pm, Sm and Eu) cation series: structural and thermodynamical features

    Energy Technology Data Exchange (ETDEWEB)

    Hosseinnejad, Tayebeh; Kazemi, Tayebeh [Alzahra Univ., Tehran (Iran, Islamic Republic of). Dept. of Chemistry

    2016-05-01

    In the present study, we have mainly investigated the nature of interactions in Ln{sup 3+} (Ln = La, Nd, Pm, Sm, Eu) complexes with amidocarbamoyl methyl phosphine oxide (CMPO) and amidocarbamoyl propyl phosphine oxide (CPPO) ligands based on density functional theory (DFT) approaches. In the first step, thermodynamical properties for complexation of CMPO and CPPO ligands with Ln{sup 3+} cation series have been determined in the gas phase and with the presence of three solvents: n-hexane, chloroform and toluene, via polarized continuum model (PCM) computations. The trend of metal-ligand interaction strength has been analyzed and compared with the trend of ionic hardness within the series of lanthanide cations and different size of alkyl chain of amidocarbamoyl phosphine oxide ligand. The calculated thermochemical results in the gas and solution phases reveals that there is a consistency between increasing trend in the hardness of Ln{sup 3+} cation series and also electron-donating property of alkyl chain with increasing in thermodynamical stability of [Ln-CMPO]{sup 3+} and [Ln-CPPO]{sup 3+} complex series. We have also demonstrated that in the complexation reaction of all complex series, using n-hexane as solvent is more favorable thermodynamically than chloroform and toluene. It should be stated that this issue has been observed in many experiments. Finally, analysis of calculated deformation energies and also the variation in bond order of some selected key bonds in CMPO and CPPO ligands and their corresponded Ln{sup 3+} complexes series show a similar trend with increasing in the hardness of Ln{sup 3+} cation series and electron-donating of alkyl chain of amidocarbamoyl phosphine oxide ligand.

  11. Complexation of amidocarbamoyl phosphine oxides with Ln+3 (Ln = La, Nd, Pm, Sm and Eu) cation series: structural and thermodynamical features

    International Nuclear Information System (INIS)

    Hosseinnejad, Tayebeh; Kazemi, Tayebeh

    2016-01-01

    In the present study, we have mainly investigated the nature of interactions in Ln 3+ (Ln = La, Nd, Pm, Sm, Eu) complexes with amidocarbamoyl methyl phosphine oxide (CMPO) and amidocarbamoyl propyl phosphine oxide (CPPO) ligands based on density functional theory (DFT) approaches. In the first step, thermodynamical properties for complexation of CMPO and CPPO ligands with Ln 3+ cation series have been determined in the gas phase and with the presence of three solvents: n-hexane, chloroform and toluene, via polarized continuum model (PCM) computations. The trend of metal-ligand interaction strength has been analyzed and compared with the trend of ionic hardness within the series of lanthanide cations and different size of alkyl chain of amidocarbamoyl phosphine oxide ligand. The calculated thermochemical results in the gas and solution phases reveals that there is a consistency between increasing trend in the hardness of Ln 3+ cation series and also electron-donating property of alkyl chain with increasing in thermodynamical stability of [Ln-CMPO] 3+ and [Ln-CPPO] 3+ complex series. We have also demonstrated that in the complexation reaction of all complex series, using n-hexane as solvent is more favorable thermodynamically than chloroform and toluene. It should be stated that this issue has been observed in many experiments. Finally, analysis of calculated deformation energies and also the variation in bond order of some selected key bonds in CMPO and CPPO ligands and their corresponded Ln 3+ complexes series show a similar trend with increasing in the hardness of Ln 3+ cation series and electron-donating of alkyl chain of amidocarbamoyl phosphine oxide ligand.

  12. Thermodynamics of firms' growth

    Science.gov (United States)

    Zambrano, Eduardo; Hernando, Alberto; Hernando, Ricardo; Plastino, Angelo

    2015-01-01

    The distribution of firms' growth and firms' sizes is a topic under intense scrutiny. In this paper, we show that a thermodynamic model based on the maximum entropy principle, with dynamical prior information, can be constructed that adequately describes the dynamics and distribution of firms' growth. Our theoretical framework is tested against a comprehensive database of Spanish firms, which covers, to a very large extent, Spain's economic activity, with a total of 1 155 142 firms evolving along a full decade. We show that the empirical exponent of Pareto's law, a rule often observed in the rank distribution of large-size firms, is explained by the capacity of economic system for creating/destroying firms, and that can be used to measure the health of a capitalist-based economy. Indeed, our model predicts that when the exponent is larger than 1, creation of firms is favoured; when it is smaller than 1, destruction of firms is favoured instead; and when it equals 1 (matching Zipf's law), the system is in a full macroeconomic equilibrium, entailing ‘free’ creation and/or destruction of firms. For medium and smaller firm sizes, the dynamical regime changes, the whole distribution can no longer be fitted to a single simple analytical form and numerical prediction is required. Our model constitutes the basis for a full predictive framework regarding the economic evolution of an ensemble of firms. Such a structure can be potentially used to develop simulations and test hypothetical scenarios, such as economic crisis or the response to specific policy measures. PMID:26510828

  13. Thermodynamics of nuclear materials

    International Nuclear Information System (INIS)

    1962-01-01

    The first session of the symposium discussed in general the thermodynamic properties of actinides, including thorium, uranium and Plutonium which provide reactor fuel. The second session was devoted to applications of thermodynamic theory to the study of nuclear materials, while the experimental techniques for the determination of thermodynamic data were examined at the next session. The thermodynamic properties of alloys were considered at a separate session, and another session was concerned with solids other than alloys. Vaporization processes, which are of special interest in the development of high-temperature reactors, were discussed at a separate session. The discussions on the methods of developing the data and ascertaining their accuracy were especially useful in highlighting the importance of determining whether any given data are reliable before they can be put to practical application. Many alloys and refractory materials (i. e. materials which evaporate only at very high temperatures) are of great importance in nuclear technology, and some of these substances are extremely complex in their chemical composition. For example, until recently the phase composition of the oxides of thorium, uranium and plutonium had been only very imperfectly understood, and the same was true of the carbides of these elements. Recent developments in experimental techniques have made it possible to investigate the phase composition of these complex materials as well as the chemical species of these materials in the gaseous phase. Recent developments in measuring techniques, such as fluorine bomb calorimetry and Knudsen effusion technique, have greatly increased the accuracy of thermodynamic data

  14. First-Principles Investigations of the Structural, Anisotropic Mechanical, Thermodynamic and Electronic Properties of the AlNi2Ti Compound

    Directory of Open Access Journals (Sweden)

    Shuli Tang

    2018-02-01

    Full Text Available In this paper, the electronic, mechanical and thermodynamic properties of AlNi2Ti are studied by first-principles calculations in order to reveal the influence of AlNi2Ti as an interfacial phase on ZTA (zirconia toughened alumina/Fe. The results show that AlNi2Ti has relatively high mechanical properties, which will benefit the impact or wear resistance of the ZTA/Fe composite. The values of bulk, shear and Young’s modulus are 164.2, 63.2 and 168.1 GPa respectively, and the hardness of AlNi2Ti (4.4 GPa is comparable to common ferrous materials. The intrinsic ductile nature and strong metallic bonding character of AlNi2Ti are confirmed by B/G and Poisson’s ratio. AlNi2Ti shows isotropy bulk modulus and anisotropic elasticity in different crystallographic directions. At room temperature, the linear thermal expansion coefficient (LTEC of AlNi2Ti estimated by quasi-harmonic approximation (QHA based on Debye model is 10.6 × 10−6 K−1, close to LTECs of zirconia toughened alumina and iron. Therefore, the thermal matching of ZTA/Fe composite with AlNi2Ti interfacial phase can be improved. Other thermodynamic properties including Debye temperature, sound velocity, thermal conductivity and heat capacity, as well as electronic properties, are also calculated.

  15. Thermodynamic fluctuations and the monopole density of the early Universe

    International Nuclear Information System (INIS)

    Diosi, L.; Lukacs, B.

    1984-10-01

    The probability of thermodynamic fluctuations is calculated by explicitly using the Riemannian structure of the thermodynamic state space. By means of this probability distribution, a correlation volume can be defined. Identifying this volume with one domain in the GUT continuum at the symmetry breaking phase transition in the early Universe, a prediction can be obtained for the primordial monopole density. (author)

  16. Thermodynamics of complexity

    DEFF Research Database (Denmark)

    Westerhoff, Hans V.; Jensen, Peter Ruhdal; Snoep, Jacky L.

    1998-01-01

    -called emergent properties. Tendency towards increased entropy is an essential determinant for the behaviour of ideal gas mixtures, showing that even in the simplest physical/chemical systems, (dys)organisation of components is crucial for the behaviour of systems. This presentation aims at illustrating...... that the behaviour of two functionally interacting biological components (molecules, protein domains, pathways, organelles) differs from the behaviour these components would exhibit in isolation from one another, where the difference should be essential for the maintenance and growth of the living state, For a true...... understanding of this BioComplexity, modem thermodynamic concepts and methods (nonequilibrium thermodynamics, metabolic and hierarchical control analysis) will be needed. We shall propose to redefine nonequilibrium thermodynamics as: The science that aims at understanding the behaviour of nonequilibrium systems...

  17. Extended Irreversible Thermodynamics

    CERN Document Server

    Jou, David

    2010-01-01

    This is the 4th edition of the highly acclaimed monograph on Extended Irreversible Thermodynamics, a theory that goes beyond the classical theory of irreversible processes. In contrast to the classical approach, the basic variables describing the system are complemented by non-equilibrium quantities. The claims made for extended thermodynamics are confirmed by the kinetic theory of gases and statistical mechanics. The book covers a wide spectrum of applications, and also contains a thorough discussion of the foundations and the scope of the current theories on non-equilibrium thermodynamics. For this new edition, the authors critically revised existing material while taking into account the most recent developments in fast moving fields such as heat transport in micro- and nanosystems or fast solidification fronts in materials sciences. Several fundamental chapters have been revisited emphasizing physics and applications over mathematical derivations. Also, fundamental questions on the definition of non-equil...

  18. Statistical thermodynamics of alloys

    CERN Document Server

    Gokcen, N A

    1986-01-01

    This book is intended for scientists, researchers, and graduate students interested in solutions in general, and solutions of metals in particular. Readers are assumed to have a good background in thermodynamics, presented in such books as those cited at the end of Chapter 1, "Thermo­ dynamic Background." The contents of the book are limited to the solutions of metals + metals, and metals + metalloids, but the results are also appli­ cable to numerous other types of solutions encountered by metallurgists, materials scientists, geologists, ceramists, and chemists. Attempts have been made to cover each topic in depth with numerical examples whenever necessary. Chapter 2 presents phase equilibria and phase diagrams as related to the thermodynamics of solutions. The emphasis is on the binary diagrams since the ternary diagrams can be understood in terms of the binary diagrams coupled with the phase rule, and the Gibbs energies of mixing. The cal­ culation of thermodynamic properties from the phase diagrams is ...

  19. Thermodynamics of Crystalline States

    CERN Document Server

    Fujimoto, Minoru

    2010-01-01

    Thermodynamics is a well-established discipline of physics for properties of matter in thermal equilibrium surroundings. Applying to crystals, however, the laws encounter undefined properties of crystal lattices, which therefore need to be determined for a clear and well-defined description of crystalline states. Thermodynamics of Crystalline States explores the roles played by order variables and dynamic lattices in crystals in a wholly new way. This book is divided into three parts. The book begins by clarifying basic concepts for stable crystals. Next, binary phase transitions are discussed to study collective motion of order variables, as described mostly as classical phenomena. In the third part, the multi-electron system is discussed theoretically, as a quantum-mechanical example, for the superconducting state in metallic crystals. Throughout the book, the role played by the lattice is emphasized and examined in-depth. Thermodynamics of Crystalline States is an introductory treatise and textbook on meso...

  20. Concise chemical thermodynamics

    CERN Document Server

    Peters, APH

    2010-01-01

    EnergyThe Realm of ThermodynamicsEnergy BookkeepingNature's Driving ForcesSetting the Scene: Basic IdeasSystem and SurroundingsFunctions of StateMechanical Work and Expanding GasesThe Absolute Temperature Scale Forms of Energy and Their Interconversion Forms of Renewable Energy Solar Energy Wind Energy Hydroelectric Power Geothermal Energy Biomass Energy References ProblemsThe First Law of Thermodynamics Statement of the First Law Reversible Expansion of an Ideal GasConstant-Volume ProcessesConstant-Pressure ProcessesA New Function: EnthalpyRelationship between ?H and ?UUses and Conventions of

  1. Thermodynamics II essentials

    CERN Document Server

    REA, The Editors of

    2013-01-01

    REA's Essentials provide quick and easy access to critical information in a variety of different fields, ranging from the most basic to the most advanced. As its name implies, these concise, comprehensive study guides summarize the essentials of the field covered. Essentials are helpful when preparing for exams, doing homework and will remain a lasting reference source for students, teachers, and professionals. Thermodynamics II includes review of thermodynamic relations, power and refrigeration cycles, mixtures and solutions, chemical reactions, chemical equilibrium, and flow through nozzl

  2. Thermodynamics for engineers

    CERN Document Server

    Wong, Kaufui Vincent

    2011-01-01

    Praise for the First Edition from Students: "It is a great thermodynamics text…I loved it!-Mathew Walters "The book is comprehensive and easy to understand. I love the real world examples and problems, they make you feel like you are learning something very practical."-Craig Paxton"I would recommend the book to friends."-Faure J. Malo-Molina"The clear diction, as well as informative illustrations and diagrams, help convey the material clearly to the reader."-Paul C. Start"An inspiring and effective tool for any aspiring scientist or engineer. Definitely the best book on Classical Thermodynamics out."-Seth Marini.

  3. Mechanics, Waves and Thermodynamics

    Science.gov (United States)

    Ranjan Jain, Sudhir

    2016-05-01

    Figures; Preface; Acknowledgement; 1. Energy, mass, momentum; 2. Kinematics, Newton's laws of motion; 3. Circular motion; 4. The principle of least action; 5. Work and energy; 6. Mechanics of a system of particles; 7. Friction; 8. Impulse and collisions; 9. Central forces; 10. Dimensional analysis; 11. Oscillations; 12. Waves; 13. Sound of music; 14. Fluid mechanics; 15. Water waves; 16. The kinetic theory of gases; 17. Concepts and laws of thermodynamics; 18. Some applications of thermodynamics; 19. Basic ideas of statistical mechanics; Bibliography; Index.

  4. Statistical thermodynamics of alloys

    International Nuclear Information System (INIS)

    Gokcen, N.A.

    1986-01-01

    This book presents information on the following topics: consequences of laws of thermodynamics; Helmholtz and Gibbs energies; analytical forms of excess partial molar properties; single-component and multicomponent equilibria; phase rules and diagrams; lever rule; fermions, bosons, and Boltzons; approximate equations; enthalpy and heat capacity; Pd-H system; hydrogen-metal systems; limitations of Wagner model; energy of electrons and hols; dopants in semiconductors; derived thermodynamic properties; simple equivalent circuit; calculation procedure; multicompoent diagrams re; Engel-Brewer theories; p-n junctions; and solar cells

  5. Experimental thermodynamics experimental thermodynamics of non-reacting fluids

    CERN Document Server

    Neindre, B Le

    2013-01-01

    Experimental Thermodynamics, Volume II: Experimental Thermodynamics of Non-reacting Fluids focuses on experimental methods and procedures in the study of thermophysical properties of fluids. The selection first offers information on methods used in measuring thermodynamic properties and tests, including physical quantities and symbols for physical quantities, thermodynamic definitions, and definition of activities and related quantities. The text also describes reference materials for thermometric fixed points, temperature measurement under pressures, and pressure measurements. The publicatio

  6. Black Hole Thermodynamics in an Undergraduate Thermodynamics Course.

    Science.gov (United States)

    Parker, Barry R.; McLeod, Robert J.

    1980-01-01

    An analogy, which has been drawn between black hole physics and thermodynamics, is mathematically broadened in this article. Equations similar to the standard partial differential relations of thermodynamics are found for black holes. The results can be used to supplement an undergraduate thermodynamics course. (Author/SK)

  7. Correct thermodynamic forces in Tsallis thermodynamics: connection with Hill nanothermodynamics

    International Nuclear Information System (INIS)

    Garcia-Morales, Vladimir; Cervera, Javier; Pellicer, Julio

    2005-01-01

    The equivalence between Tsallis thermodynamics and Hill's nanothermodynamics is established. The correct thermodynamic forces in Tsallis thermodynamics are pointed out. Through this connection we also find a general expression for the entropic index q which we illustrate with two physical examples, allowing in both cases to relate q to the underlying dynamics of the Hamiltonian systems

  8. Electronic structure of Ge-2 and Ge-2 and thermodynamic properties of Ge-2 from all electron ab initio investigations and Knudsen effusion mass spectroscopic measurements

    DEFF Research Database (Denmark)

    Shim, Irene; Baba, M. Sai; Gingerich, K.A.

    2002-01-01

    The low-lying states of the molecule Ge-2 and of the ion Ge-2(-) have been investigated by all electron ab initio multiconfiguration self-consistent field (CASSCF) and multi-reference configuration interaction (MRCI) calculations. The relativistic corrections for the Darwin contact term and for t......The low-lying states of the molecule Ge-2 and of the ion Ge-2(-) have been investigated by all electron ab initio multiconfiguration self-consistent field (CASSCF) and multi-reference configuration interaction (MRCI) calculations. The relativistic corrections for the Darwin contact term...... excited states are presented. Thermal functions based on the theoretically determined molecular parameters were used to derive the thermodynamic properties of the Ge-2 molecule from new mass spectrometric equilibrium data. The literature value for the dissociation energy of Ge-2 has been re...

  9. Thermodynamics and statistical mechanics an integrated approach

    CERN Document Server

    Hardy, Robert J

    2014-01-01

    This textbook brings together the fundamentals of the macroscopic and microscopic aspects of thermal physics by presenting thermodynamics and statistical mechanics as complementary theories based on small numbers of postulates. The book is designed to give the instructor flexibility in structuring courses for advanced undergraduates and/or beginning graduate students and is written on the principle that a good text should also be a good reference. The presentation of thermodynamics follows the logic of Clausius and Kelvin while relating the concepts involved to familiar phenomena and the mod

  10. Thermodynamical, kinetic and structural properties of simple and mixed complexes of zirconium (IV) with the hydroxyl and carbonate ions. Study by potentiometry, Raman spectroscopy and NMR spectroscopy

    International Nuclear Information System (INIS)

    Veyland, A.

    1999-01-01

    Most of zirconium production is used by the nuclear industry for the cladding of nuclear fuels and for the storage of radioactive wastes. The aim of this work is the qualitative and quantitative study of the complexes made by zirconium with the hydroxyl and carbonate ions in order to evaluate the long-term pollution risks linked with the corrosion of confinement containers. The zirconium(IV)/hydroxyl system is studied by proto-metry and follows a protocol which reduces the local over-concentrations of reagent and the precipitation of zirconium hydroxide. In potassium nitrate environment and in a pH range of 1.5 to 3.5, three soluble species are evidenced: Zr(OH) 3 + , Zr 2 (OH) 7 + and Zr(OH) 4 . Their apparent constant of formation and the solubility product of zirconium hydroxide are determined with 4 ionic forces. Using these results, the corresponding thermodynamic constants are calculated by applying the theory of specific interactions. The formation of zirconium (IV) hydroxo-carbonate complexes is evidenced by proto-metry and 17 O and 13 C NMR. The number of carbonates fixed by zirconium varies from 0 to 4. The dialysis indicates that the degree of poly-condensation of species is an inverse function of the number of complex carbonates. The Raman polarized spectra and the 13 C NMR results demonstrate for all complexes the bidentate character of the complexation mode of the carbonates. The dynamical study made by 13 C NMR of the exchange between complexed carbonates of the tetra-carbonate-zirconate ion and free carbonates in solution allows to determine the kinetic constants and the corresponding velocity law. An associative mechanism is proposed, in agreement with the results obtained by mass spectroscopy with electro-spray ionization. These new thermodynamical and kinetic data allow to model the speciation of zirconium in natural waters. (J.S.)

  11. Thermodynamic structure of the Atmospheric Boundary Layer over the Arabian Sea and the Indian Ocean during pre-INDOEX and INDOEX-FFP campaigns

    Directory of Open Access Journals (Sweden)

    M. V. Ramana

    2004-09-01

    Full Text Available Spatial and temporal variability of the Marine Atmospheric Boundary Layer (MABL height for the Indian Ocean Experiment (INDOEX study period are examined using the data collected through Cross-chained LORAN (Long-Range Aid to Navigation Atmospheric Sounding System (CLASS launchings during the Northern Hemispheric winter monsoon period. This paper reports the results of the analyses of the data collected during the pre-INDOEX (1997 and the INDOEX-First Field Phase (FFP; 1998 in the latitude range 14°N to 20°S over the Arabian Sea and the Indian Ocean. Mixed layer heights are derived from thermodynamic profiles and they indicated the variability of heights ranging from 400m to 1100m during daytime depending upon the location. Mixed layer heights over the Indian Ocean are slightly higher during the INDOEX-FFP than the pre-INDOEX due to anomalous conditions prevailing during the INDOEX-FFP. The trade wind inversion height varied from 2.3km to 4.5km during the pre-INDOEX and from 0.4km to 2.5km during the INDOEX-FFP. Elevated plumes of polluted air (lofted aerosol plumes above the marine boundary layer are observed from thermodynamic profiles of the lower troposphere during the INDOEX-FFP. These elevated plumes are examined using 5-day back trajectory analysis and show that one group of air mass travelled a long way from Saudi Arabia and Iran/Iraq through India before reaching the location of measurement, while the other air mass originates from India and the Bay of Bengal.

  12. Fluctuating Thermodynamics for Biological Processes

    Science.gov (United States)

    Ham, Sihyun

    Because biomolecular processes are largely under thermodynamic control, dynamic extension of thermodynamics is necessary to uncover the mechanisms and driving factors of fluctuating processes. The fluctuating thermodynamics technology presented in this talk offers a practical means for the thermodynamic characterization of conformational dynamics in biomolecules. The use of fluctuating thermodynamics has the potential to provide a comprehensive picture of fluctuating phenomena in diverse biological processes. Through the application of fluctuating thermodynamics, we provide a thermodynamic perspective on the misfolding and aggregation of the various proteins associated with human diseases. In this talk, I will present the detailed concepts and applications of the fluctuating thermodynamics technology for elucidating biological processes. This work was supported by Samsung Science and Technology Foundation under Project Number SSTF-BA1401-13.

  13. A Hamiltonian approach to Thermodynamics

    Energy Technology Data Exchange (ETDEWEB)

    Baldiotti, M.C., E-mail: baldiotti@uel.br [Departamento de Física, Universidade Estadual de Londrina, 86051-990, Londrina-PR (Brazil); Fresneda, R., E-mail: rodrigo.fresneda@ufabc.edu.br [Universidade Federal do ABC, Av. dos Estados 5001, 09210-580, Santo André-SP (Brazil); Molina, C., E-mail: cmolina@usp.br [Escola de Artes, Ciências e Humanidades, Universidade de São Paulo, Av. Arlindo Bettio 1000, CEP 03828-000, São Paulo-SP (Brazil)

    2016-10-15

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

  14. A Hamiltonian approach to Thermodynamics

    International Nuclear Information System (INIS)

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

    2016-01-01

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

  15. New perspectives in thermodynamics

    International Nuclear Information System (INIS)

    Serrin, J.

    1986-01-01

    The last decade has seen a unity of method and approach in the foundations of thermodynamics and continuum mechanics, in which rigorous laws of thermodynamics have been combined with invariance notions of mechanics to produce new and deep understanding. Real progress has been made in finding a set of appropriate concepts for classical thermodynamics, by which energy conservation and the Clausius inequality can be given well-defined meanings for arbitrary processes and which allow an approach to the entropy concept which is free of traditional ambiguities. There has been, moreover, a careful scrutiny of long established but nevertheless not sharply defined concepts such as the Maxwell equal-area rule, the famous Gibbs phase rule, and the equivalence of work and heat. The thirteen papers in this volume accordingly gather together for the first time the many ideas and concepts which have raised classical thermodynamics from a heuristic and intuitive science to the level of precision presently demanded of other branches of mathematical physics

  16. Thermodynamics and statistical mechanics

    CERN Document Server

    Landsberg, Peter T

    1990-01-01

    Exceptionally articulate treatment combines precise mathematical style with strong physical intuition. Wide range of applications includes negative temperatures, negative heat capacities, special and general relativistic effects, black hole thermodynamics, gravitational collapse, more. Over 100 problems with worked solutions. Advanced undergraduate, graduate level. Table of applications. Useful formulas and other data.

  17. Thermodynamic stabilization of colloids

    NARCIS (Netherlands)

    Stol, R.J.; Bruyn, P.L. de

    An analysis is given of the conditions necessary for obtaining a thermodynamically stable dispersion (TSD) of solid particles in a continuous aqueous solution phase. The role of the adsorption of potential-determining ions at the planar interface in lowering the interfacial free energy (γ) to

  18. Thermodynamics applied. Where? Why?

    NARCIS (Netherlands)

    Hirs, Gerard

    2003-01-01

    In recent years, thermodynamics has been applied in a number of new fields leading to a greater societal impact. This paper gives a survey of these new fields and the reasons why these applications are important. In addition, it is shown that the number of fields could be even greater in the future

  19. Thermodynamics, applied. : Where? why?

    NARCIS (Netherlands)

    Hirs, Gerard

    1999-01-01

    In recent years thermodynamics has been applied in a number of new fields leading to a greater societal impact. The paper gives a survey of these new fields and the reasons why these applications are important. In addition it is shown that the number of fields could be even greater in the future and

  20. Black hole thermodynamical entropy

    International Nuclear Information System (INIS)

    Tsallis, Constantino; Cirto, Leonardo J.L.

    2013-01-01

    As early as 1902, Gibbs pointed out that systems whose partition function diverges, e.g. gravitation, lie outside the validity of the Boltzmann-Gibbs (BG) theory. Consistently, since the pioneering Bekenstein-Hawking results, physically meaningful evidence (e.g., the holographic principle) has accumulated that the BG entropy S BG of a (3+1) black hole is proportional to its area L 2 (L being a characteristic linear length), and not to its volume L 3 . Similarly it exists the area law, so named because, for a wide class of strongly quantum-entangled d-dimensional systems, S BG is proportional to lnL if d=1, and to L d-1 if d>1, instead of being proportional to L d (d ≥ 1). These results violate the extensivity of the thermodynamical entropy of a d-dimensional system. This thermodynamical inconsistency disappears if we realize that the thermodynamical entropy of such nonstandard systems is not to be identified with the BG additive entropy but with appropriately generalized nonadditive entropies. Indeed, the celebrated usefulness of the BG entropy is founded on hypothesis such as relatively weak probabilistic correlations (and their connections to ergodicity, which by no means can be assumed as a general rule of nature). Here we introduce a generalized entropy which, for the Schwarzschild black hole and the area law, can solve the thermodynamic puzzle. (orig.)

  1. Thermodynamics Far from the Thermodynamic Limit.

    Science.gov (United States)

    de Miguel, Rodrigo; Rubí, J Miguel

    2017-11-16

    Understanding how small systems exchange energy with a heat bath is important to describe how their unique properties can be affected by the environment. In this contribution, we apply Landsberg's theory of temperature-dependent energy levels to describe the progressive thermalization of small systems as their spectrum is perturbed by a heat bath. We propose a mechanism whereby the small system undergoes a discrete series of excitations and isentropic spectrum adjustments leading to a final state of thermal equilibrium. This produces standard thermodynamic results without invoking system size. The thermal relaxation of a single harmonic oscillator is analyzed as a model example of a system with a quantized spectrum than can be embedded in a thermal environment. A description of how the thermal environment affects the spectrum of a small system can be the first step in using environmental factors, such as temperature, as parameters in the design and operation of nanosystem properties.

  2. Thermodynamics for the practicing engineer

    CERN Document Server

    Theodore, Louis; Vanvliet, Timothy

    2009-01-01

    This book concentrates specifically on the applications of thermodynamics, rather than the theory. It addresses both technical and pragmatic problems in the field, and covers such topics as enthalpy effects, equilibrium thermodynamics, non-ideal thermodynamics and energy conversion applications. Providing the reader with a working knowledge of the principles of thermodynamics, as well as experience in their application, it stands alone as an easy-to-follow self-teaching aid to practical applications and contains worked examples.

  3. Choice of the thermodynamic variables

    International Nuclear Information System (INIS)

    Balian, R.

    1985-09-01

    Some basic ideas of thermodynamics and statistical mechanics, both at equilibrium and off equilibrium, are recalled. In particular, the selection of relevant variables which underlies any macroscopic description is discussed, together with the meaning of the various thermodynamic quantities, in order to set the thermodynamic approaches used in nuclear physics in a general prospect [fr

  4. Activation and thermodynamic parameter study of the heteronuclear C=O···H-N hydrogen bonding of diphenylurethane isomeric structures by FT-IR spectroscopy using the regularized inversion of an eigenvalue problem.

    Science.gov (United States)

    Spegazzini, Nicolas; Siesler, Heinz W; Ozaki, Yukihiro

    2012-08-02

    The doublet of the ν(C=O) carbonyl band in isomeric urethane systems has been extensively discussed in qualitative terms on the basis of FT-IR spectroscopy of the macromolecular structures. Recently, a reaction extent model was proposed as an inverse kinetic problem for the synthesis of diphenylurethane for which hydrogen-bonded and non-hydrogen-bonded C=O functionalities were identified. In this article, the heteronuclear C=O···H-N hydrogen bonding in the isomeric structure of diphenylurethane synthesized from phenylisocyanate and phenol was investigated via FT-IR spectroscopy, using a methodology of regularization for the inverse reaction extent model through an eigenvalue problem. The kinetic and thermodynamic parameters of this system were derived directly from the spectroscopic data. The activation and thermodynamic parameters of the isomeric structures of diphenylurethane linked through a hydrogen bonding equilibrium were studied. The study determined the enthalpy (ΔH = 15.25 kJ/mol), entropy (TΔS = 14.61 kJ/mol), and free energy (ΔG = 0.6 kJ/mol) of heteronuclear C=O···H-N hydrogen bonding by FT-IR spectroscopy through direct calculation from the differences in the kinetic parameters (δΔ(‡)H, -TδΔ(‡)S, and δΔ(‡)G) at equilibrium in the chemical reaction system. The parameters obtained in this study may contribute toward a better understanding of the properties of, and interactions in, supramolecular systems, such as the switching behavior of hydrogen bonding.

  5. Effect of ordered B-site cations on the structure, elastic and thermodynamic properties of KTa{sub 0.5}Nb{sub 0.5}O{sub 3} crystal

    Energy Technology Data Exchange (ETDEWEB)

    Yang, Wenlong; Han, Junsheng; Wang, Li; Yang, Yuqiang; Li, Haidong [Harbin University of Science and Technology, Department of Applied Science, Harbin (China); Shen, Yanqing [Harbin Institute of Technology, Department of Physics, Harbin (China); Li, Linjun [Heilongjiang Institute of Technology, Institute of Optoelectronic Technology, Harbin (China); Chen, Liangyu [Jiangsu University of Science and Technology, School of Material Science and Engineering, Zhenjiang (China)

    2017-07-15

    BO{sub 6} oxygen octahedral was considered as the key part in ABO{sub 3} perovskite structure, and the electro-optical, elastic and thermodynamic properties of potassium tantalate niobate (KTa{sub 0.5}Nb{sub 0.5}O{sub 3}, abbreviated as KTN) were closely depended on the B-site Ta/Nb ratio and ordering. The effect of [100]{sub NT}, [110]{sub NT}, and [111]{sub NT} B-site cations ordering (N means a pure Nb layer parallel to (h, k, l), T means a pure Ta layer parallel to (h, k, l)) on structure, elastic properties and Debye temperatures properties of KTN were investigated based on density functional theory (DFT). KTN with [111]{sub NT} B-site ordering presents an cubic phase structure with excellent stability from the view of lattice properties. The elastic properties include elastic stiffness coefficients C{sub ij}, bulk modulus B, shear modulus G, Young's modulus E and Poisson' ratio ν were calculated. The elastic stiffness coefficients C{sub 11} of KTN with B-site ordering have approached to maximum 485.506 GPa, indicating that KTN materials have better deformation ability along x axis compared with other perovskite materials. The calculated results of bulk modulus B and the shear modulus G show that KTN with [100 ]{sub NT} B-site ordering has stronger ability to resist fracture and plastic deformation. And the criteria B/G <1.75 suggests that KTN should be classified as a brittle material. The KTN with [100 ]{sub NT} B-site has excellent ductility properties compared with any other B-site arrangements. Debye temperatures of KTN with [100 ]{sub NT}, [110 ]{sub NT}, [111 ]{sub NT} are about 650 K, and KTN with [100 ]{sub NT} B-site has best thermodynamic stability. (orig.)

  6. Relationships between molecular structure and kinetic and thermodynamic controls in lipid systems. Part II: Phase behavior and transformation paths of SSS, PSS and PPS saturated triacylglycerols--effect of chain length mismatch.

    Science.gov (United States)

    Bouzidi, Laziz; Narine, Suresh S

    2012-01-01

    The kinetic phase behavior and phase transformation paths of purified tristearoylglycerol (SSS), 3-palmitoyl-1,2-distearoyl-sn-glycerol (PSS) and 1,2-dipalmitoyl-3-stearoyl-sn-glycerol (PPS) were investigated in terms of polymorphism, crystallization and melting. The details of the phase transformation paths were obtained using the heating cycles of two sets of experiments: (a) cooling rate was varied and heating rate fixed and (b) cooling rate was fixed and heating rate varied. Kinetic effects were manifest in all measured properties, underscoring the complexity of the phase transformation paths for each TAG, and the intricate thermodynamics-molecular relationships. For the first time, XRD data obtained for SSS, PSS and PPS TAGs, cooled at rates higher than 0.5°C/min, suggested the formation of a transient structure similar to the so-called α(2)-phase which has been observed in mixed saturated-unsaturated TAGs quenched from the melt. The more stable phases (β' in PSS and PPS, and β in SSS) were only observed for cooling rates lower than 1.0°C/min. The kinetic and thermodynamic differences observed in the crystallization, structure and melting of SSS, PSS and PPS are proposed to be mainly due to the disturbances introduced at the "terrace" level via methyl-end group interactions, i.e., the missing of two or four CH(2) groups compared to SSS. The symmetrical SSS with a relatively flat "terrace" crystallizes preferably in the most stable β-form. Two missing CH(2) groups at the sn-1 position (PSS) introduces enough structural disturbances to promote the relative prevalence and persistence of the β'-phase, and four missing CH(2) groups at the sn-1 and sn-2 positions (PPS) is relatively too large of a disturbance and therefore favors the α-form. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

  7. Thermodynamics of ionic processes in solutions

    International Nuclear Information System (INIS)

    Krestov, G.A.

    1984-01-01

    The present nitions about the mechanism of solvation of atomic-molecular particles and the structure of electrolyte and non electrolyte solutions are given. From common positions a wide range of interrelated problems (general and thermodynamic characteristic of ions, thermodynamic characteristic of ion solvation and various ionic reactions in solutions, structural changes of the solvent in the above processes etc...) is considered. The latest scientific data including those on the effect on the thermodynamio properties of low temperatures, various impurities (air, water), large ions, peculiarities of the structure of solvent molecules reflected. Considerable attention is given to new conceptions definitions, structural notions as well as theoretical and experimental methods of obtaining quantitative characteristics of ion solvation

  8. Thermodynamic properties and crystal structure refinement of ferricopiapite, coquimbite, rhomboclase, and Fe2(SO4)3(H2O)5

    Science.gov (United States)

    Majzlan, J.; Navrotsky, A.; McCleskey, R. Blaine; Alpers, Charles N.

    2006-01-01

    Enthalpies of formation of ferricopiapite [nominally Fe4.67(SO4)6(OH)2 (H2O)20]. coquimbite [Fe2(SO4)3(H2O)9], rhomboclase [(H3O)Fe(SO4)2 (H2O)3], and Fe2(SO4)3(H2O)5 were measured by acid (5 N HCl) solution calorimetry. The samples were characterized by wet chemical analyses and synchrotron powder X-ray diffraction (XRD). The refinement of XRD patterns gave lattice parameters, atomic positions, thermal factors, and occupancies of the sites. The calculated formulae differ slightly from the nominal compositions: Fe4.78(SO4)6 (OH)2.34(H2O)20.71 (ferricopiapite), (Fe1.47Al0.53)(SO4)3 (H2O)9.65 (coquimbite), (H3O)1.34Fe(SO4)2.17 (H2O)3.06 (rhomboclase), and Fe2(SO4)3 (H2O)5.03. All thermodynamic data are given per mole of these formulae. The measured standard enthalpies (in kJ/mol) of formation from the elements (crystalline Fe, Al, S, and ideal gases O2 and H2) at T = 298.15 K are -4115.8??4.1 [Fe2(SO4)3 (H2O)5.03], -12045.1??9.2 (ferricopiapite), -5738.4??3.3 (coquimbite), and -3201.1??2.6 (rhomboclase). Standard entropy (S??) was estimated as a sum of entropies of oxide, hydroxide, and sulfate components. The estimated S?? (in J/mol.K) values for the iron sulfates are 488.2 [Fe2(SO4)3 (H2O)5.03], 1449.2 (ferricopiapite), 638.3 (coquimbite), and 380.1 (rhomboclase). The calculated Gibbs free energies of formation (in kJ/mol) are -3499.7??4.2 [Fe2(SO4)3 (H2O)5.03], -10089.8??9.3 (ferricopiapite), -4845.6??3.3 (coquimbite), and -2688.0??2.7 (rhomboclase). These results combined with other available thermodynamic data allow construction of mineral stability diagrams in the FeIII2(SO4)3-FeII SO4-H2O system. One such diagram is provided, indicating that the order of stability of ferric sulfate minerals with decreasing pH in the range of 1.5 to -0.5 is: hydronium jarosite, ferricopiapite, and rhomboclase. ?? 2006 E. Schweizerbart'sche Verlagsbuchhandlung.

  9. Thermodynamic and transport properties of liquid gallium

    International Nuclear Information System (INIS)

    Park, H.Y.; Jhon, M.S.

    1982-01-01

    The significant structure theory of liquids has been successfully applied to liquid gallium. In this work, we have assumed that two structures exist simultaneously in liquid gallium. One is considerec as loosely close packed β-Ga-like structure and the other is remainder of solid α-Ga or α-Ga-like structure. This two structural model is introduced to construct the liquid partition function. Using the partition function, the thermodynamic and transport properties are calculated ever a wide temperature range. The calculated results are quite satisfactory when compared with the experimental results. (Author)

  10. Non-covalent conjugation of cutinase from Fusarium sp. ICT SAC1 with pectin for enhanced stability: Process minutiae, kinetics, thermodynamics and structural study.

    Science.gov (United States)

    Muley, Abhijeet B; Chaudhari, Sandeep A; Singhal, Rekha S

    2017-09-01

    Cutinase, a member of α/β-fold hydrolase family possess potentially diverse applications in several industrial processes and products. The present work aims towards thermo-stabilization of cutinase from novel source Fusarium sp. ICT SAC1 via non-covalent interaction with polysaccharides. Although all six polysaccharides chosen for study enhanced the thermal stability, pectin was found to be most promising. The interaction protocol for cutinase with pectin was optimized sequentially with respect to the ratio of enzyme to pectin, solution pH, and buffer strength. Cutinase-pectin conjugate under optimized conditions (1:12, pH-6.5, 50mM) showed enhanced thermal stability as evident from lower inactivation rate constant, higher half-life and D-value within the 40-55°C. A slender rise in K m and V max values and enhanced thermodynamic parameters of cutinase-pectin conjugate were observed after non-covalent interaction. Entropy values were 1.5-fold higher for cutinase-pectin conjugate at each temperature suggesting an upsurge in number of protein molecules in a transition activated state. Positive values of entropy for both forms of cutinase suggested a rise in disordered conformation. Noticeable conformational changes in cutinase after conjugation with pectin were confirmed by FTIR as well as fluorescence emission spectra. An increment in helix to turn conversion was observed in complexed cutinase vis-à-vis free cutinase. Copyright © 2017 Elsevier B.V. All rights reserved.

  11. Theoretical study of the elastic and thermodynamic properties of Pt_{3}Al with the L1_{2} structure under high pressure

    Directory of Open Access Journals (Sweden)

    N. Wei

    2015-12-01

    Full Text Available In this work, the elastic and thermodynamic properties of Pt_{3}Al under high pressure are investigated using density functional theory within the generalized gradient approximation. The results of bulk modulus and elastic constants at zero pressure are in good agreement with the available theoretical and experimental values. Under high pressure, all the elastic constants meet the corresponding mechanical stability criteria, meaning that Pt_{3}Al possesses mechanical stability. In addition, the elastic constants and elastic modulus increase linearly with the applied pressure. According to the Poisson's ratio ν and elastic modulus ratio (B/G, Pt_{3}Al alloy is found to be ductile, and higher pressure can significantly enhance the ductility. Those indicate that the elastic properties of Pt_{3}Al will be improved under high pressure. Through the quasi-harmonic Debye model, we first successfully report the variations of the Debye temperature Θ_{D}, specific heats C_{P}, thermal expansion coefficient α, and Grüneisen parameter γ under pressure range from 0 to 100 GPa and temperature range from 0 to 1000 K.

  12. Statistical Thermodynamics and Microscale Thermophysics

    Science.gov (United States)

    Carey, Van P.

    1999-08-01

    Many exciting new developments in microscale engineering are based on the application of traditional principles of statistical thermodynamics. In this text Van Carey offers a modern view of thermodynamics, interweaving classical and statistical thermodynamic principles and applying them to current engineering systems. He begins with coverage of microscale energy storage mechanisms from a quantum mechanics perspective and then develops the fundamental elements of classical and statistical thermodynamics. Subsequent chapters discuss applications of equilibrium statistical thermodynamics to solid, liquid, and gas phase systems. The remainder of the book is devoted to nonequilibrium thermodynamics of transport phenomena and to nonequilibrium effects and noncontinuum behavior at the microscale. Although the text emphasizes mathematical development, Carey includes many examples and exercises to illustrate how the theoretical concepts are applied to systems of scientific and engineering interest. In the process he offers a fresh view of statistical thermodynamics for advanced undergraduate and graduate students, as well as practitioners, in mechanical, chemical, and materials engineering.

  13. Fragile Thermodynamic Order

    International Nuclear Information System (INIS)

    Bernhoeft, N.; Lander, G.H.; Colineau, E.

    2003-01-01

    An asymmetric shift in the position of the magnetic Bragg peak with respect to the fiducial lattice has been observed by resonant X-ray scattering in a diverse series of antiferromagnetic compounds. This apparent violation of Bragg's law is interpreted in terms of a dynamically phased order parameter. We demonstrate the use of this effect as a novel probe of fragile or dynamic thermodynamic order in strongly correlated electronic systems. In particular, fresh light is shed on the paradoxical situation encountered in URu 2 Si 2 where the measured entropy gain on passing through T Neel is incompatible with the ground state moment estimated by neutron diffraction. The intrinsic space-time averaging of the probe used to characterise the thermodynamic macroscopic state may play a crucial and previously neglected role. In turn, this suggests the further use of resonant X-ray scattering in investigations of systems dominated by quantum fluctuations. (author)

  14. Mechanics and thermodynamics

    CERN Document Server

    Demtröder, Wolfgang

    2017-01-01

    This introduction to classical mechanics and thermodynamics provides an accessible and clear treatment of the fundamentals. Starting with particle mechanics and an early introduction to special relativity this textbooks enables the reader to understand the basics in mechanics. The text is written from the experimental physics point of view, giving numerous real life examples and applications of classical mechanics in technology. This highly motivating presentation deepens the knowledge in a very accessible way. The second part of the text gives a concise introduction to rotational motion, an expansion to rigid bodies, fluids and gases. Finally, an extensive chapter on thermodynamics and a short introduction to nonlinear dynamics with some instructive examples intensify the knowledge of more advanced topics. Numerous problems with detailed solutions are perfect for self study.

  15. Thermodynamical quantum information sharing

    International Nuclear Information System (INIS)

    Wiesniak, M.; Vedral, V.; Brukner, C.

    2005-01-01

    Full text: Thermodynamical properties fully originate from classical physics and can be easily measured for macroscopic systems. On the other hand, entanglement is a widely spoken feature of quantum physics, which allows to perform certain task with efficiency unavailable with any classical resource. Therefore an interesting question is whether we can witness entanglement in a state of a macroscopic sample. We show, that some macroscopic properties, in particular magnetic susceptibility, can serve as an entanglement witnesses. We also study a mutual relation between magnetic susceptibility and magnetisation. Such a complementarity exhibits quantum information sharing between these two thermodynamical quantities. Magnetization expresses properties of individual spins, while susceptibility might reveal non-classical correlations as a witness. Therefore, a rapid change of one of these two quantities may mean a phase transition also in terms of entanglement. The complementarity relation is demonstrated by an analytical solution of an exemplary model. (author)

  16. A commentary on thermodynamics

    CERN Document Server

    Day, William Alan

    1988-01-01

    The aim of this book is to comment on, and clarify, the mathematical aspects of the theory of thermodynamics. The standard presentations of the subject are often beset by a number of obscurities associated with the words "state", "reversible", "irreversible", and "quasi-static". This book is written in the belief that such obscurities are best removed not by the formal axiomatization of thermodynamics, but by setting the theory in the wider context of a genuine field theory which incorporates the effects of heat conduction and intertia, and proving appropriate results about the governing differential equations of this field theory. Even in the simplest one-dimensional case it is a nontrivial task to carry through the details of this program, and many challenging problems remain open.

  17. Thermodynamics of Crystalline States

    CERN Document Server

    Fujimoto, Minoru

    2013-01-01

    Thermodynamics is a well-established discipline of physics for properties of matter in thermal equilibrium with the surroundings. Applying to crystals, however, the laws encounter undefined properties of crystal lattice, which therefore need to be determined for a clear and well-defined description of crystalline states. Thermodynamics of Crystalline States explores the roles played by order variables and dynamic lattices in crystals in a wholly new way. The book begins by clarifying basic concepts for stable crystals. Next, binary phase transitions are discussed to study collective motion of order variables, as described mostly as classical phenomena. New to this edition is the examination of magnetic crystals, where magnetic symmetry is essential for magnetic phase transitions. The multi-electron system is also discussed  theoretically, as a quantum-mechanical example, for superconductivity in metallic crystals. Throughout the book, the role played by the lattice is emphasized and studied in-depth. Thermod...

  18. Thermodynamic geometry and phase transitions of AdS braneworld black holes

    Energy Technology Data Exchange (ETDEWEB)

    Chaturvedi, Pankaj, E-mail: cpankaj@iitk.ac.in; Sengupta, Gautam, E-mail: sengupta@iitk.ac.in

    2017-02-10

    The thermodynamics and phase transitions of charged RN–AdS and rotating Kerr–AdS black holes in a generalized Randall–Sundrum braneworld are investigated in the framework of thermodynamic geometry. A detailed analysis of the thermodynamics, stability and phase structures in the canonical and the grand canonical ensembles for these AdS braneworld black holes are described. The thermodynamic curvatures for both these AdS braneworld black holes are computed and studied as a function of the thermodynamic variables. Through this analysis we illustrate an interesting dependence of the phase structures on the braneworld parameter for these black holes.

  19. Thermodynamics of clan production

    International Nuclear Information System (INIS)

    Giovannini, Alberto; Lupia, Sergio; Ugoccioni, Roberto

    2002-01-01

    Scenarios for particle production in the GeV and TeV regions are reviewed. The expected increase with the c.m. energy of the average number of clans for the soft component and the decrease for the semihard one indicate possible classical and quantum behavior of gluons, respectively. Clan thermodynamics, discussed in the paper, appears as the natural framework to deal with such phenomena

  20. Work reservoirs in thermodynamics

    International Nuclear Information System (INIS)

    Anacleto, Joaquim

    2010-01-01

    We stress the usefulness of the work reservoir in the formalism of thermodynamics, in particular in the context of the first law. To elucidate its usefulness, the formalism is then applied to the Joule expansion and other peculiar and instructive experimental situations, clarifying the concepts of configuration and dissipative work. The ideas and discussions presented in this study are primarily intended for undergraduate students, but they might also be useful to graduate students, researchers and teachers.

  1. Work reservoirs in thermodynamics

    Science.gov (United States)

    Anacleto, Joaquim

    2010-05-01

    We stress the usefulness of the work reservoir in the formalism of thermodynamics, in particular in the context of the first law. To elucidate its usefulness, the formalism is then applied to the Joule expansion and other peculiar and instructive experimental situations, clarifying the concepts of configuration and dissipative work. The ideas and discussions presented in this study are primarily intended for undergraduate students, but they might also be useful to graduate students, researchers and teachers.

  2. Thermodynamics of chaos

    International Nuclear Information System (INIS)

    Bonasera, A.; Latora, V.; Ploszajczak, M.

    1996-07-01

    The maximal Lyapunov exponents (LE) are calculated, starting from concepts of hydrodynamics. Analytical expressions for the LE can be found in ergodic limit by using results of the classical thermodynamics for a Boltzmann gas and for systems undergoing a second order phase transition. A recipe is given to measure LE in systems which might have a critical behavior, such as a Bose-Einstein condensation or a transition to a quark-gluon plasma. (author)

  3. Advanced thermodynamic (exergetic) analysis

    International Nuclear Information System (INIS)

    Tsatsaronis, G; Morosuk, T

    2012-01-01

    Exergy analysis is a powerful tool for developing, evaluating and improving an energy conversion system. However, the lack of a formal procedure in using the results obtained by an exergy analysis is one of the reasons for exergy analysis not being very popular among energy practitioners. Such a formal procedure cannot be developed as long as the interactions among components of the overall system are not being taken properly into account. Splitting the exergy destruction into unavoidable and avoidable parts in a component provides a realistic measure of the potential for improving the thermodynamic efficiency of this component. Alternatively splitting the exergy destruction into endogenous and exogenous parts provides information on the interactions among system components. Distinctions between avoidable and unavoidable exergy destruction on one side and endogenous and exogenous exergy destruction on the other side allow the engineer to focus on the thermodynamic inefficiencies that can be avoided and to consider the interactions among system components. The avoidable endogenous and the avoidable exogenous exergy destruction provide the best guidance for improving the thermodynamic performance of energy conversion systems.

  4. The discovery of thermodynamics

    Science.gov (United States)

    Weinberger, Peter

    2013-07-01

    Based on the idea that a scientific journal is also an "agora" (Greek: market place) for the exchange of ideas and scientific concepts, the history of thermodynamics between 1800 and 1910 as documented in the Philosophical Magazine Archives is uncovered. Famous scientists such as Joule, Thomson (Lord Kelvin), Clausius, Maxwell or Boltzmann shared this forum. Not always in the most friendly manner. It is interesting to find out, how difficult it was to describe in a scientific (mathematical) language a phenomenon like "heat", to see, how long it took to arrive at one of the fundamental principles in physics: entropy. Scientific progress started from the simple rule of Boyle and Mariotte dating from the late eighteenth century and arrived in the twentieth century with the concept of probabilities. Thermodynamics was the driving intellectual force behind the industrial revolution, behind the enormous social changes caused by this revolution. The history of thermodynamics is a fascinating story, which also gives insights into the mechanism that seem to govern science.

  5. Thermodynamic forces in coarse-grained simulations

    Science.gov (United States)

    Noid, William

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

  6. Correlation of thermodynamics and grain growth kinetics in nanocrystalline metals

    International Nuclear Information System (INIS)

    Song Xiaoyan; Zhang Jiuxing; Li Lingmei; Yang Keyong; Liu Guoquan

    2006-01-01

    We investigated the correlation of thermodynamics and grain growth kinetics of nanocrystalline metals both theoretically and experimentally. A model was developed to describe the thermodynamic properties of nanograin boundaries, which could give reliable predictions in the destabilization characteristics of nanograin structures and the slowing down of grain growth kinetics at a constant temperature. Both the temperature-varying and isothermal nanograin growth behaviors in pure nanocrystalline Co were studied to verify the thermodynamic predictions. The experimental results showing that discontinuous nanograin growth takes place at a certain temperature and grain growth rate decreases monotonically with time confirm our thermodynamics-based description of nanograin growth characteristics. Therefore, we propose a thermodynamic viewpoint to explain the deviation of grain growth kinetics in nanocrystalline metals from those of polycrystalline materials

  7. Thermodynamical and structural properties of solid surfaces in the high temperature range by molecular dynamics solution: evidence for a roughening transition on the F.C.C. {110} surface

    International Nuclear Information System (INIS)

    Rosato, Vittorio

    1986-01-01

    We have studied by Molecular Dynamics simulation the thermodynamical and structural properties of the {110} solid Argon surface as a function of temperature up to T m . The following results have been obtained: 1) the Arrhenius plot indicates that for T> 0.7 T m the defect creation becomes a nearly athermal process. The measured surface diffusion coefficients are very high and are comparable with those observed in the liquid state. 2) the long range order is preserved at least up to T= 0.94 T m . The thermal disorder is related to the onset of a roughening transition on that surface at T ≅ 0.7 T m . Surface layers are not melted in the whole range of temperature we have studied. Furthermore we have investigated the influence of constraints on the surface structure for the same model system previously used at T = 0.48 T m . We have shown that both temperature and constraints induce disorder on surface: for constraints corresponding to elastic deformations of -5 pc applied along the dense axis {110}, the surface structure results to be very similar to that obtained, without constraints, at a higher temperature (T = 0.68 T m ). The implications of our bindings in several areas of Materials Science are briefly discussed. (author) [fr

  8. Thermodynamics: The Unique Universal Science

    Directory of Open Access Journals (Sweden)

    Wassim M. Haddad

    2017-11-01

    Full Text Available Thermodynamics is a physical branch of science that governs the thermal behavior of dynamical systems from those as simple as refrigerators to those as complex as our expanding universe. The laws of thermodynamics involving conservation of energy and nonconservation of entropy are, without a doubt, two of the most useful and general laws in all sciences. The first law of thermodynamics, according to which energy cannot be created or destroyed, merely transformed from one form to another, and the second law of thermodynamics, according to which the usable energy in an adiabatically isolated dynamical system is always diminishing in spite of the fact that energy is conserved, have had an impact far beyond science and engineering. In this paper, we trace the history of thermodynamics from its classical to its postmodern forms, and present a tutorial and didactic exposition of thermodynamics as it pertains to some of the deepest secrets of the universe.

  9. Thermodynamics of adaptive molecular resolution.

    Science.gov (United States)

    Delgado-Buscalioni, R

    2016-11-13

    A relatively general thermodynamic formalism for adaptive molecular resolution (AMR) is presented. The description is based on the approximation of local thermodynamic equilibrium and considers the alchemic parameter λ as the conjugate variable of the potential energy difference between the atomistic and coarse-grained model Φ=U (1) -U (0) The thermodynamic formalism recovers the relations obtained from statistical mechanics of H-AdResS (Español et al, J. Chem. Phys. 142, 064115, 2015 (doi:10.1063/1.4907006)) and provides relations between the free energy compensation and thermodynamic potentials. Inspired by this thermodynamic analogy, several generalizations of AMR are proposed, such as the exploration of new Maxwell relations and how to treat λ and Φ as 'real' thermodynamic variablesThis article is part of the themed issue 'Multiscale modelling at the physics-chemistry-biology interface'. © 2016 The Author(s).

  10. Chemical thermodynamics of uranium

    International Nuclear Information System (INIS)

    Grenthe, I.; Fuger, J.; Lemire, R.J.; Muller, A.B.; Nguyen-Trung Cregu, C.; Wanner, H.

    1992-01-01

    A comprehensive overview on the chemical thermodynamics of those elements that are of particular importance in the safety assessment of radioactive waste disposal systems is provided. This is the first volume in a series of critical reviews to be published on this subject. The book provides an extensive compilation of chemical thermodynamic data for uranium. A description of procedures for activity corrections and uncertainty estimates is given. A critical discussion of data needed for nuclear waste management assessments, including areas where significant gaps of knowledge exist is presented. A detailed inventory of chemical thermodynamic data for inorganic compounds and complexes of uranium is listed. Data and their uncertainty limits are recommended for 74 aqueous complexes and 199 solid and 31 gaseous compounds containing uranium, and on 52 aqueous and 17 solid auxiliary species containing no uranium. The data are internally consistent and compatible with the CODATA Key Values. The book contains a detailed discussion of procedures used for activity factor corrections in aqueous solution, as well as including methods for making uncertainty estimates. The recommended data have been prepared for use in environmental geochemistry. Containing contributions written by experts the chapters cover various subject areas such a s: oxide and hydroxide compounds and complexes, the uranium nitrides, the solid uranium nitrates and the arsenic-containing uranium compounds, uranates, procedures for consistent estimation of entropies, gaseous and solid uranium halides, gaseous uranium oxides, solid phosphorous-containing uranium compounds, alkali metal uranates, uncertainties, standards and conventions, aqueous complexes, uranium minerals dealing with solubility products and ionic strength corrections. The book is intended for nuclear research establishments and consulting firms dealing with uranium mining and nuclear waste disposal, as well as academic and research institutes

  11. Thermodynamics of phase transitions

    International Nuclear Information System (INIS)

    Cofta, H.

    1972-01-01

    The phenomenology of the phase transitions has been considered. The definitions of thermodynamic functions and parameters, as well as those of the phase transitions, are given and some of the relations between those quantities are discussed. The phase transitions classification proposed by Ehrenfest has been described. The most important features of phase transitions are discussed using the selected physical examples including the critical behaviour of ferromagnetic materials at the Curie temperature and antiferromagnetic materials at the Neel temperature. Some aspects of the Ehrenfest's equations, that have been derived, for the interfacial lines and surfaces are considered as well as the role the notion of interfaces. (S.B.)

  12. Thermodynamics of quark gas

    Energy Technology Data Exchange (ETDEWEB)

    Biswas, S. N.

    1980-07-01

    The application of quantum statistical mechanics to a system of particles consisting of quarks is considered. Realistic theoretical investigations have been underway to understand highly dense objects such as white dwarfs and neutron stars. The various possibilities in the case of very high densities such as 10/sup 15/ or 10/sup 16/ g/cm/sup 3/ are enumerated. The thermodynamics of a phase transition from neutron matter phase to quark matter phase is analysed. Preliminary results based on quantum chromodynamics and other phenomenological models are reported.

  13. Time and Thermodynamics

    CERN Document Server

    Kirkland, Kyle

    2007-01-01

    Temperature is vital to the health and welfare of all living beings, and Earth's temperature varies considerably from place to place. Early humans could only live in warm areas such as the tropics. Although modern humans have the technology to keep their houses and offices warm even in cold environments, the growth and development of civilization has created unintentional effects. Cities are warmer than their surrounding regions, and on a global scale, Earth is experiencing rising temperatures. Thus, the science of thermodynamics offers an important tool to study these effects. "Time and

  14. Interfacial solvation thermodynamics

    International Nuclear Information System (INIS)

    Ben-Amotz, Dor

    2016-01-01

    Previous studies have reached conflicting conclusions regarding the interplay of cavity formation, polarizability, desolvation, and surface capillary waves in driving the interfacial adsorptions of ions and molecules at air–water interfaces. Here we revisit these questions by combining exact potential distribution results with linear response theory and other physically motivated approximations. The results highlight both exact and approximate compensation relations pertaining to direct (solute–solvent) and indirect (solvent–solvent) contributions to adsorption thermodynamics, of relevance to solvation at air–water interfaces, as well as a broader class of processes linked to the mean force potential between ions, molecules, nanoparticles, proteins, and biological assemblies. (paper)

  15. Principles of thermodynamics

    CERN Document Server

    Kaufman, Myron

    2002-01-01

    Ideal for one- or two-semester courses that assume elementary knowledge of calculus, This text presents the fundamental concepts of thermodynamics and applies these to problems dealing with properties of materials, phase transformations, chemical reactions, solutions and surfaces. The author utilizes principles of statistical mechanics to illustrate key concepts from a microscopic perspective, as well as develop equations of kinetic theory. The book provides end-of-chapter question and problem sets, some using Mathcad™ and Mathematica™; a useful glossary containing important symbols, definitions, and units; and appendices covering multivariable calculus and valuable numerical methods.

  16. Gravitation, Thermodynamics, and Quantum Theory

    OpenAIRE

    Wald, Robert M.

    1999-01-01

    During the past 30 years, research in general relativity has brought to light strong hints of a very deep and fundamental relationship between gravitation, thermodynamics, and quantum theory. The most striking indication of such a relationship comes from black hole thermodynamics, where it appears that certain laws of black hole mechanics are, in fact, simply the ordinary laws of thermodynamics applied to a system containing a black hole. This article will review the present status of black h...

  17. On thermodynamic and microscopic reversibility

    International Nuclear Information System (INIS)

    Crooks, Gavin E

    2011-01-01

    The word 'reversible' has two (apparently) distinct applications in statistical thermodynamics. A thermodynamically reversible process indicates an experimental protocol for which the entropy change is zero, whereas the principle of microscopic reversibility asserts that the probability of any trajectory of a system through phase space equals that of the time reversed trajectory. However, these two terms are actually synonymous: a thermodynamically reversible process is microscopically reversible, and vice versa

  18. Experimental approaches to membrane thermodynamics

    DEFF Research Database (Denmark)

    Westh, Peter

    2009-01-01

    Thermodynamics describes a system on the macroscopic scale, yet it is becoming an important tool for the elucidation of many specific molecular aspects of membrane properties. In this note we discuss this application of thermodynamics, and give a number of examples on how thermodynamic measurements...... have contributed to the understanding of specific membrane phenomena. We mainly focus on non-specific interactions of bilayers and small molecules (water and solutes) in the surrounding solvent, and the changes in membrane properties they bring about. Differences between thermodynamic...

  19. Pressure-induced structural transition and thermodynamic properties of RhN2 and the effect of metallic bonding on its hardness

    International Nuclear Information System (INIS)

    Liu Jun; Kuang Xiao-Yu; Wang Zhen-Hua; Huang Xiao-Fen

    2012-01-01

    The elastic constant, structural phase transition, and effect of metallic bonding on the hardness of RhN 2 under high pressure are investigated through the first-principles calculation by means of the pseudopotential plane-wave method. Three structures are chosen to investigate for RhN 2 , namely, simple hexagonal P6/mmm (denoted as SH), orthorhombic Pnnm (marcasite), and simple tetragonal P4/mbm (denoted as ST). Our calculations show that the SH phase is energetically more stable than the other two phases at zero pressure. On the basis of the third-order Birch—Murnaghan equation of states, we find that the phase transition pressures from an SH to a marcasite structure and from a marcasite to an ST structure are 1.09 GPa and 354.57 GPa, respectively. Elastic constants, formation enthalpies, shear modulus, Young's modulus, and Debye temperature of RhN 2 are derived. The calculated values are, generally speaking, in good agreement with the previous theoretical results. Meanwhile, it is found that the pressure has an important influence on physical properties. Moreover, the effect of metallic bonding on the hardness of RhN 2 is investigated. This is a quantitative investigation on the structural properties of RhN 2 , and it still awaits experimental confirmation. (condensed matter: structural, mechanical, and thermal properties)

  20. Binding thermodynamics discriminates fragments from druglike compounds: a thermodynamic description of fragment-based drug discovery.

    Science.gov (United States)

    Williams, Glyn; Ferenczy, György G; Ulander, Johan; Keserű, György M

    2017-04-01

    Small is beautiful - reducing the size and complexity of chemical starting points for drug design allows better sampling of chemical space, reveals the most energetically important interactions within protein-binding sites and can lead to improvements in the physicochemical properties of the final drug. The impact of fragment-based drug discovery (FBDD) on recent drug discovery projects and our improved knowledge of the structural and thermodynamic details of ligand binding has prompted us to explore the relationships between ligand-binding thermodynamics and FBDD. Information on binding thermodynamics can give insights into the contributions to protein-ligand interactions and could therefore be used to prioritise compounds with a high degree of specificity in forming key interactions. Copyright © 2016 Elsevier Ltd. All rights reserved.

  1. Modeling the thermodynamics of QCD

    Energy Technology Data Exchange (ETDEWEB)

    Hell, Thomas

    2010-07-26

    Strongly interacting (QCD) matter is expected to exhibit a multifaceted phase structure: a hadron gas at low temperatures, a quark-gluon plasma at very high temperatures, nuclear matter in the low-temperature and high-density region, color superconductors at asymptotically high densities. Most of the conjectured phases cannot yet be scrutinized by experiments. Much of the present picture - particularly concerning the intermediate temperature and density area of the phase diagram of QCD matter - is based on model calculations. Further insights come from Lattice-QCD computations. The present thesis elaborates a nonlocal covariant extension of the Nambu and Jona-Lasinio (NJL) model with built-in constraints from the running coupling of QCD at high-momentum and instanton physics at low-momentum scales. We present this model for two and three quark flavors (in the latter case paying particular attention to the axial anomaly). At finite temperatures and densities, gluon dynamics is incorporated through a gluonic background field, expressed in terms of the Polyakov loop (P). The thermodynamics of this nonlocal PNJL model accounts for both chiral and deconfinement transitions. We obtain results in mean-field approximation and beyond, including additional pionic and kaonic contributions to the chiral condensate, the pressure and other thermodynamic quantities. Finally, the nonlocal PNJL model is applied to the finite-density region of the QCD phase diagram; for three quark flavors we investigate, in particular, the dependence of the critical point appearing in the models on the axial anomaly. The thesis closes with a derivation of the nonlocal PNJL model from first principles of QCD. (orig.)

  2. Nanoparticle shape, thermodynamics and kinetics

    International Nuclear Information System (INIS)

    Marks, L D; Peng, L

    2016-01-01

    Nanoparticles can be beautiful, as in stained glass windows, or they can be ugly as in wear and corrosion debris from implants. We estimate that there will be about 70 000 papers in 2015 with nanoparticles as a keyword, but only one in thirteen uses the nanoparticle shape as an additional keyword and research focus, and only one in two hundred has thermodynamics. Methods for synthesizing nanoparticles have exploded over the last decade, but our understanding of how and why they take their forms has not progressed as fast. This topical review attempts to take a critical snapshot of the current understanding, focusing more on methods to predict than a purely synthetic or descriptive approach. We look at models and themes which are largely independent of the exact synthetic method whether it is deposition, gas-phase condensation, solution based or hydrothermal synthesis. Elements are old dating back to the beginning of the 20th century—some of the pioneering models developed then are still relevant today. Others are newer, a merging of older concepts such as kinetic-Wulff constructions with methods to understand minimum energy shapes for particles with twins. Overall we find that while there are still many unknowns, the broad framework of understanding and predicting the structure of nanoparticles via diverse Wulff constructions, either thermodynamic, local minima or kinetic has been exceedingly successful. However, the field is still developing and there remain many unknowns and new avenues for research, a few of these being suggested towards the end of the review. (topical review)

  3. Thermodynamics of geothermal fluids

    Energy Technology Data Exchange (ETDEWEB)

    Rogers, P.S.Z.

    1981-03-01

    A model to predict the thermodynamic properties of geothermal brines, based on a minimum amount of experimental data on a few key systems, is tested. Volumetric properties of aqueous sodium chloride, taken from the literature, are represented by a parametric equation over the range 0 to 300{sup 0}C and 1 bar to 1 kbar. Density measurements at 20 bar needed to complete the volumetric description also are presented. The pressure dependence of activity and thermal properties, derived from the volumetric equation, can be used to complete an equation of state for sodium chloride solutions. A flow calorimeter, used to obtain heat capacity data at high temperatures and pressures, is described. Heat capacity measurements, from 30 to 200{sup 0}C and 1 bar to 200 bar, are used to derive values for the activity coefficient and other thermodynamic properties of sodium sulfate solutions as a function of temperature. Literature data on the solubility of gypsum in mixed electrolyte solutions have been used to evaluate model parameters for calculating gypsum solubility in seawater and natural brines. Predictions of strontium and barium sulfate solubility in seawater also are given.

  4. Thermodynamics of Error Correction

    Directory of Open Access Journals (Sweden)

    Pablo Sartori

    2015-12-01

    Full Text Available Information processing at the molecular scale is limited by thermal fluctuations. This can cause undesired consequences in copying information since thermal noise can lead to errors that can compromise the functionality of the copy. For example, a high error rate during DNA duplication can lead to cell death. Given the importance of accurate copying at the molecular scale, it is fundamental to understand its thermodynamic features. In this paper, we derive a universal expression for the copy error as a function of entropy production and work dissipated by the system during wrong incorporations. Its derivation is based on the second law of thermodynamics; hence, its validity is independent of the details of the molecular machinery, be it any polymerase or artificial copying device. Using this expression, we find that information can be copied in three different regimes. In two of them, work is dissipated to either increase or decrease the error. In the third regime, the protocol extracts work while correcting errors, reminiscent of a Maxwell demon. As a case study, we apply our framework to study a copy protocol assisted by kinetic proofreading, and show that it can operate in any of these three regimes. We finally show that, for any effective proofreading scheme, error reduction is limited by the chemical driving of the proofreading reaction.

  5. Chemical thermodynamic representation of

    International Nuclear Information System (INIS)

    Lindemer, T.B.; Besmann, T.M.

    1984-01-01

    The entire data base for the dependence of the nonstoichiometry, x, on temperature and chemical potential of oxygen (oxygen potential) was retrieved from the literature and represented. This data base was interpreted by least-squares analysis using equations derived from the classical thermodynamic theory for the solid solution of a solute in a solvent. For hyperstoichiometric oxide at oxygen potentials more positive than -266700 + 16.5T kJ/mol, the data were best represented by a [UO 2 ]-[U 3 O 7 ] solution. For O/U ratios above 2 and oxygen potentials below this boundary, a [UO 2 ]-[U 2 O 4 . 5 ] solution represented the data. The data were represented by a [UO 2 ]-[U 1 / 3 ] solution. The resulting equations represent the experimental ln(PO 2 ) - ln(x) behavior and can be used in thermodynamic calculations to predict phase boundary compositions consistent with the literature. Collectively, the present analysis permits a mathematical representation of the behavior of the total data base

  6. Light cone thermodynamics

    Science.gov (United States)

    De Lorenzo, Tommaso; Perez, Alejandro

    2018-02-01

    We show that null surfaces defined by the outgoing and infalling wave fronts emanating from and arriving at a sphere in Minkowski spacetime have thermodynamical properties that are in strict formal correspondence with those of black hole horizons in curved spacetimes. Such null surfaces, made of pieces of light cones, are bifurcate conformal Killing horizons for suitable conformally stationary observers. They can be extremal and nonextremal depending on the radius of the shining sphere. Such conformal Killing horizons have a constant light cone (conformal) temperature, given by the standard expression in terms of the generalization of surface gravity for conformal Killing horizons. Exchanges of conformally invariant energy across the horizon are described by a first law where entropy changes are given by 1 /(4 ℓp2) of the changes of a geometric quantity with the meaning of horizon area in a suitable conformal frame. These conformal horizons satisfy the zeroth to the third laws of thermodynamics in an appropriate way. In the extremal case they become light cones associated with a single event; these have vanishing temperature as well as vanishing entropy.

  7. Thermodynamic matchers for the construction of the cuckoo RNA family.

    Science.gov (United States)

    Reinkensmeier, Jan; Giegerich, Robert

    2015-01-01

    RNA family models describe classes of functionally related, non-coding RNAs based on sequence and structure conservation. The most important method for modeling RNA families is the use of covariance models, which are stochastic models that serve in the discovery of yet unknown, homologous RNAs. However, the performance of covariance models in finding remote homologs is poor for RNA families with high sequence conservation, while for families with high structure but low sequence conservation, these models are difficult to built in the first place. A complementary approach to RNA family modeling involves the use of thermodynamic matchers. Thermodynamic matchers are RNA folding programs, based on the established thermodynamic model, but tailored to a specific structural motif. As thermodynamic matchers focus on structure and folding energy, they unfold their potential in discovering homologs, when high structure conservation is paired with low sequence conservation. In contrast to covariance models, construction of thermodynamic matchers does not require an input alignment, but requires human design decisions and experimentation, and hence, model construction is more laborious. Here we report a case study on an RNA family that was constructed by means of thermodynamic matchers. It starts from a set of known but structurally different members of the same RNA family. The consensus secondary structure of this family consists of 2 to 4 adjacent hairpins. Each hairpin loop carries the same motif, CCUCCUCCC, while the stems show high variability in their nucleotide content. The present study describes (1) a novel approach for the integration of the structurally varying family into a single RNA family model by means of the thermodynamic matcher methodology, and (2) provides the results of homology searches that were conducted with this model in a wide spectrum of bacterial species.

  8. Heat pipe thermodynamic cycle and its applications

    International Nuclear Information System (INIS)

    Kobayashi, Y.

    1985-01-01

    A new type of thermodynamic cycle originating from extended application of the heat pipe principle is proposed and its thermal cycle is discussed from the viewpoint of theoretical thermal efficiency and Coefficient of Performance. An idealized structure that will meet the basic function for thermal systems is also suggested. A significant advantage of these systems is their use with lowtemperature energy sources found in nature or heat rejected from industrial sites

  9. Thermodynamics and statistical physics. 2. rev. ed.

    International Nuclear Information System (INIS)

    Schnakenberg, J.

    2002-01-01

    This textbook covers tthe following topics: Thermodynamic systems and equilibrium, irreversible thermodynamics, thermodynamic potentials, stability, thermodynamic processes, ideal systems, real gases and phase transformations, magnetic systems and Landau model, low temperature thermodynamics, canonical ensembles, statistical theory, quantum statistics, fermions and bosons, kinetic theory, Bose-Einstein condensation, photon gas

  10. Thermodynamic Properties and Thermodynamic Geometries of Black p-Branes

    International Nuclear Information System (INIS)

    Yi-Huan Wei; Xiao Cui; Jia-Xin Zhao

    2016-01-01

    The heat capacity and the electric capacitance of the black p-branes (BPB) are generally defined, then they are calculated for some special processes. It is found that the Ruppeiner thermodynamic geometry of BPB is flat. Finally, we give some discussions for the flatness of the Ruppeiner thermodynamic geometry of BPB and some black holes. (paper)

  11. Pressure effects on the structure, kinetic, and thermodynamic properties of heat-induced aggregation of protein studied by FT-IR spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Taniguchi, Y [Applied Chemistry Department, Ritsumeikan University, Kusatsu, Shiga 525-8577 (Japan); Okuno, A [Research Department 3, Central Research, Bridgestone Co. Kodaira, Tokyo 187-8531 (Japan); Kato, M, E-mail: taniguti@sk.ritsumei.ac.j [Pharmaceutical Sciences Department, Ritsumeikan University, Kusatsu, Shiga 525-8577 (Japan)

    2010-03-01

    Pressure can retrain the heat-induced aggregation and dissociate the heat-induced aggregates. We observed the aggregation-preventing pressure effect and the aggregates-dissociating pressure effect to characterize the heat-induced aggregation of equine serum albumin (ESA) by FT-IR spectroscopy. The results suggest the {alpha}-helical structure collapses at the beginning of heat-induced aggregation through the swollen structure, and then the rearrangement of structure to the intermolecular {beta}-sheet takes place through partially unfolded structure. We determined the activation volume for the heat-induced aggregation ({Delta}V'' = +93 ml/mol) and the partial molar volume difference between native state and heat-induced aggregates ({Delta}V=+32 ml/mol). This positive partial molar volume difference suggests that the heat-induced aggregates have larger internal voids than the native structure. Moreover, the positive volume change implies that the formation of the intermolecular {beta}-sheet is unfavorable under high pressure.

  12. Structural, elastic and thermodynamic properties under pressure and temperature effects of MgIn{sub 2}S{sub 4} and CdIn{sub 2}S{sub 4}

    Energy Technology Data Exchange (ETDEWEB)

    Bouhemadou, A., E-mail: a_bouhemadou@yahoo.fr [Laboratory for Developing New Materials and their Characterization, Department of Physics, Faculty of Science, University of Setif, 19000 Setif (Algeria); Haddadi, K. [Laboratory for Developing New Materials and their Characterization, Department of Physics, Faculty of Science, University of Setif, 19000 Setif (Algeria); Khenata, R. [Laboratoire de Physique Quantique et de Modelisation Mathematique (LPQ3M), Departement de Technologie, Universite de Mascara, 29000 Mascara (Algeria); Rached, D. [Department of Physics, Faculty of Science, University of Sidi-Bel-Abbes, 22000 (Algeria); Bin-Omran, S. [Department of Physics and Astronomy, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451 (Saudi Arabia)

    2012-06-15

    A density functional-based method is used to investigate the structural, elastic and thermodynamic properties of the cubic spinel semiconductors MgIn{sub 2}S{sub 4} and CdIn{sub 2}S{sub 4} at different pressures and temperatures. Computed ground structural parameters are in good agreement with the available experimental data. Single-crystal elastic parameters are calculated for pressure up to 10 GPa and temperature up to 1200 K. The obtained elastic constants values satisfy the requirement of mechanical stability, indicating that MgIn{sub 2}S{sub 4} and CdIn{sub 2}S{sub 4} compounds could be stable in the investigated pressure range. Isotropic elastic parameters for ideal polycrystalline MgIn{sub 2}S{sub 4} and CdIn{sub 2}S{sub 4} aggregates are computed in the framework of the Voigt-Reuss-Hill approximation. Pressure and thermal effects on some macroscopic properties such as lattice constant, volume expansion coefficient and heat capacities are predicted using the quasi-harmonic Debye model in which the lattice vibrations are taken into account.

  13. Thermodynamical and dynamical properties of charged BTZ black holes

    Energy Technology Data Exchange (ETDEWEB)

    Tang, Zi-Yu; Wang, Bin [Shanghai Jiao Tong University, Department of Physics and Astronomy, Center for Astronomy and Astrophysics, Shanghai (China); Zhang, Cheng-Yong [Peking University, Center for High-Energy Physics, Beijing (China); Kord Zangeneh, Mahdi [Shanghai Jiao Tong University, Department of Physics and Astronomy, Center for Astronomy and Astrophysics, Shanghai (China); Shahid Chamran University of Ahvaz, Physics Department, Faculty of Science, Ahvaz (Iran, Islamic Republic of); Research Institute for Astronomy and Astrophysics of Maragha (RIAAM)-Maragha, P. O. Box: 55134-441, Maragha (Iran, Islamic Republic of); Shiraz University, Physics Department and Biruni Observatory, College of Sciences, Shiraz (Iran, Islamic Republic of); Saavedra, Joel [Pontificia Universidad Catolica de Valparaiso, Instituto de Fisica, Valparaiso (Chile)

    2017-06-15

    We investigate the spacetime properties of BTZ black holes in the presence of the Maxwell field and Born-Infeld field and find rich properties in the spacetime structures when the model parameters are varied. Employing Landau-Lifshitz theory, we examine the thermodynamical phase transition in the charged BTZ black holes. We further study the dynamical perturbation in the background of the charged BTZ black holes and find different properties in the dynamics when the thermodynamical phase transition occurs. (orig.)

  14. Thermodynamics of the Earth

    International Nuclear Information System (INIS)

    Stacey, Frank D

    2010-01-01

    Applications of elementary thermodynamic principles to the dynamics of the Earth lead to robust, quantitative conclusions about the tectonic effects that arise from convection. The grand pattern of motion conveys deep heat to the surface, generating mechanical energy with a thermodynamic efficiency corresponding to that of a Carnot engine operating over the adiabatic temperature gradient between the heat source and sink. Referred to the total heat flux derived from the Earth's silicate mantle, the efficiency is 24% and the power generated, 7.7 x 10 12 W, causes all the material deformation apparent as plate tectonics and the consequent geological processes. About 3.5% of this is released in seismic zones but little more than 0.2% as seismic waves. Even major earthquakes are only localized hiccups in this motion. Complications that arise from mineral phase transitions can be used to illuminate details of the motion. There are two superimposed patterns of convection, plate subduction and deep mantle plumes, driven by sources of buoyancy, negative and positive respectively, at the top and bottom of the mantle. The patterns of motion are controlled by the viscosity contrasts (>10 4 : 1) at these boundaries and are self-selected as the least dissipative mechanisms of heat transfer for convection in a body with very strong viscosity variation. Both are subjects of the thermodynamic efficiency argument. Convection also drives the motion in the fluid outer core that generates the geomagnetic field, although in that case there is an important energy contribution by compositional separation, as light solute is rejected by the solidifying inner core and mixed into the outer core, a process referred to as compositional convection. Uncertainty persists over the core energy balance because thermal conduction is a drain on core energy that has been a subject of diverse estimates, with attendant debate over the need for radiogenic heat in the core. The geophysical approach to

  15. Fundamental functions in equilibrium thermodynamics

    NARCIS (Netherlands)

    Horst, H.J. ter

    In the standard presentations of the principles of Gibbsian equilibrium thermodynamics one can find several gaps in the logic. For a subject that is as widely used as equilibrium thermodynamics, it is of interest to clear up such questions of mathematical rigor. In this paper it is shown that using

  16. Thermodynamics of negative absolute pressures

    International Nuclear Information System (INIS)

    Lukacs, B.; Martinas, K.

    1984-03-01

    The authors show that the possibility of negative absolute pressure can be incorporated into the axiomatic thermodynamics, analogously to the negative absolute temperature. There are examples for such systems (GUT, QCD) processing negative absolute pressure in such domains where it can be expected from thermodynamical considerations. (author)

  17. Thermodynamic study of selected monoterpenes

    Czech Academy of Sciences Publication Activity Database

    Štejfa, V.; Fulem, Michal; Růžička, K.; Červinka, C.; Rocha, M.A.A.; Santos, L.M.N.B.F.; Schröder, B.

    2013-01-01

    Roč. 60, MAY (2013), 117-125 ISSN 0021-9614 Institutional support: RVO:68378271 Keywords : monoterpenes * pinene * vapor pressure * heat capacity * vaporization and sublimation enthalpy * ideal - gas thermodynamic Subject RIV: BJ - Thermodynamics Impact factor: 2.423, year: 2013

  18. Thermodynamic optimization of power plants

    NARCIS (Netherlands)

    Haseli, Y.

    2011-01-01

    Thermodynamic Optimization of Power Plants aims to establish and illustrate comparative multi-criteria optimization of various models and configurations of power plants. It intends to show what optimization objectives one may define on the basis of the thermodynamic laws, and how they can be applied

  19. Ch. 33 Modeling: Computational Thermodynamics

    International Nuclear Information System (INIS)

    Besmann, Theodore M.

    2012-01-01

    This chapter considers methods and techniques for computational modeling for nuclear materials with a focus on fuels. The basic concepts for chemical thermodynamics are described and various current models for complex crystalline and liquid phases are illustrated. Also included are descriptions of available databases for use in chemical thermodynamic studies and commercial codes for performing complex equilibrium calculations.

  20. Thermodynamics of urban population flows.

    Science.gov (United States)

    Hernando, A; Plastino, A

    2012-12-01

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

  1. Thermodynamics from Car to Kitchen

    Science.gov (United States)

    Auty, Geoff

    2014-01-01

    The historical background to the laws of thermodynamics is explained using examples we can all observe in the world around us, focusing on motorised transport, refrigeration and solar heating. This is not to be considered as an academic article. The purpose is to improve understanding of thermodynamics rather than impart new knowledge, and for…

  2. Applied thermodynamics: A new frontier for biotechnology

    DEFF Research Database (Denmark)

    Mollerup, Jørgen

    2006-01-01

    The scientific career of one of the most outstanding scientists in molecular thermodynamics, Professor John M. Prausnitz at Berkeley, reflects the change in the agenda of molecular thermodynamics, from hydrocarbon chemistry to biotechnology. To make thermodynamics a frontier for biotechnology...

  3. Thermodynamics in Loop Quantum Cosmology

    International Nuclear Information System (INIS)

    Li, L.F.; Zhu, J.Y.

    2009-01-01

    Loop quantum cosmology (LQC) is very powerful to deal with the behavior of early universe. Moreover, the effective loop quantum cosmology gives a successful description of the universe in the semiclassical region. We consider the apparent horizon of the Friedmann-Robertson-Walker universe as a thermodynamical system and investigate the thermodynamics of LQC in the semiclassical region. The effective density and effective pressure in the modified Friedmann equation from LQC not only determine the evolution of the universe in LQC scenario but also are actually found to be the thermodynamic quantities. This result comes from the energy definition in cosmology (the Misner-Sharp gravitational energy) and is consistent with thermodynamic laws. We prove that within the framework of loop quantum cosmology, the elementary equation of equilibrium thermodynamics is still valid.

  4. Thermodynamic properties of cryogenic fluids

    CERN Document Server

    Leachman, Jacob; Lemmon, Eric; Penoncello, Steven

    2017-01-01

    This update to a classic reference text provides practising engineers and scientists with accurate thermophysical property data for cryogenic fluids. The equations for fifteen important cryogenic fluids are presented in a basic format, accompanied by pressure-enthalpy and temperature-entropy charts and tables of thermodynamic properties. It begins with a chapter introducing the thermodynamic relations and functional forms for equations of state, and goes on to describe the requirements for thermodynamic property formulations, needed for the complete definition of the thermodynamic properties of a fluid. The core of the book comprises extensive data tables and charts for the most commonly-encountered cryogenic fluids. This new edition sees significant updates to the data presented for air, argon, carbon monoxide, deuterium, ethane, helium, hydrogen, krypton, nitrogen and xenon. The book supports and complements NIST’s REFPROP - an interactive database and tool for the calculation of thermodynamic propertie...

  5. Ab Initio Study of the Electronic Structure, Elastic Properties, Magnetic Feature and Thermodynamic Properties of the Ba2NiMoO6 Material

    Science.gov (United States)

    Deluque Toro, C. E.; Mosquera Polo, A. S.; Gil Rebaza, A. V.; Landínez Téllez, D. A.; Roa-Rojas, J.

    2018-04-01

    We report first-principles calculations of the elastic properties, electronic structure and magnetic behavior performed over the Ba2NiMoO6 double perovskite. Calculations are carried out through the full-potential linear augmented plane-wave method within the framework of the Density Functional Theory (DFT) with exchange and correlation effects in the Generalized Gradient and Local Density Approximations, including spin polarization. The elastic properties calculated are bulk modulus (B), the elastic constants (C 11, C 12 and C 44), the Zener anisotropy factor (A), the isotropic shear modulus (G), the Young modulus (Y) and the Poisson ratio (υ). Structural parameters, total energies and cohesive properties of the perovskite are studied by means of minimization of internal parameters with the Murnaghan equation, where the structural parameters are in good agreement with experimental data. Furthermore, we have explored different antiferromagnetic configurations in order to describe the magnetic ground state of this compound. The pressure and temperature dependence of specific heat, thermal expansion coefficient, Debye temperature and Grüneisen parameter were calculated by DFT from the state equation using the quasi-harmonic model of Debye. A specific heat behavior C V ≈ C P was found at temperatures below T = 400 K, with Dulong-Petit limit values, which is higher than those, reported for simple perovskites.

  6. Applied statistical thermodynamics

    CERN Document Server

    Lucas, Klaus

    1991-01-01

    The book guides the reader from the foundations of statisti- cal thermodynamics including the theory of intermolecular forces to modern computer-aided applications in chemical en- gineering and physical chemistry. The approach is new. The foundations of quantum and statistical mechanics are presen- ted in a simple way and their applications to the prediction of fluid phase behavior of real systems are demonstrated. A particular effort is made to introduce the reader to expli- cit formulations of intermolecular interaction models and to show how these models influence the properties of fluid sy- stems. The established methods of statistical mechanics - computer simulation, perturbation theory, and numerical in- tegration - are discussed in a style appropriate for newcom- ers and are extensively applied. Numerous worked examples illustrate how practical calculations should be carried out.

  7. Thermodynamic properties of vanadium

    International Nuclear Information System (INIS)

    Desai, P.D.

    1986-01-01

    This work reviews and discusses the data and information on the various thermodynamic properties of vanadium available through March 1985. These include the heat capacity and enthalpy, enthalpy of melting, vapor pressure, and enthalpy of vaporization. The existing data have been critically evaluated and analyzed, and the recommended values for heat capacity, enthalpy, entropy, and Gibbs energy function covering the temperature range from 1 to 3800 K have been generated. These values are referred to tempertures based on IPTS-1968. The units used for various properties are joules per mole (J. mol - 1 ). The estimated uncertainties in the heat capacity are +/-3% below 15 K, +/-10% from 15 to 150 K, +/-3% from 150 to 298.15 K, +/-2% from 298.15 to 1000 K, +/-3% from 1000 to the melting point (2202 K), and +/-5% in the liquid region

  8. Thermodynamics and energy conversion

    CERN Document Server

    Struchtrup, Henning

    2014-01-01

    This textbook gives a thorough treatment of engineering thermodynamics with applications to classical and modern energy conversion devices.   Some emphasis lies on the description of irreversible processes, such as friction, heat transfer and mixing, and the evaluation of the related work losses. Better use of resources requires high efficiencies, therefore the reduction of irreversible losses should be seen as one of the main goals of a thermal engineer. This book provides the necessary tools.   Topics include: car and aircraft engines,  including Otto, Diesel and Atkinson cycles, by-pass turbofan engines, ramjet and scramjet;  steam and gas power plants, including advanced regenerative systems, solar tower, and compressed air energy storage; mixing and separation, including reverse osmosis, osmotic powerplants, and carbon sequestration; phase equilibrium and chemical equilibrium, distillation, chemical reactors, combustion processes, and fuel cells; the microscopic definition of entropy.    The book i...

  9. Development of a thermodynamic data base for selected heavy metals

    International Nuclear Information System (INIS)

    Hageman, Sven; Scharge, Tina; Willms, Thomas

    2015-07-01

    The report on the development of a thermodynamic data base for selected heavy metals covers the description of experimental methods, the thermodynamic model for chromate, the thermodynamic model for dichromate, the thermodynamic model for manganese (II), the thermodynamic model for cobalt, the thermodynamic model for nickel, the thermodynamic model for copper (I), the thermodynamic model for copper(II), the thermodynamic model for mercury (0) and mercury (I), the thermodynamic model for mercury (III), the thermodynamic model for arsenate.

  10. Restricted primitive model for electrolyte solutions in slit-like pores with grafted chains: microscopic structure, thermodynamics of adsorption, and electric properties from a density functional approach.

    Science.gov (United States)

    Pizio, Orest; Sokołowski, Stefan

    2013-05-28

    We apply a density functional theory to describe properties of a restricted primitive model of an ionic fluid in slit-like pores. The pore walls are modified by grafted chains. The chains are built of uncharged or charged segments. We study the influence of modification of the pore walls on the structure, adsorption, ion selectivity, and the electric double layer capacitance of ionic fluid under confinement. The brush built of uncharged segments acts as a collection of obstacles in the walls vicinity. Consequently, separation of charges requires higher voltages, in comparison to the models without brushes. At high grafting densities the formation of crowding-type structure is inhibited. The double layer structure becomes more complex in various aspects, if the brushes are built of charged segments. In particular, the evolution of the brush height with the bulk fluid density and with the charge on the walls depends on the length of the blocks of charged spheres as well as on the distribution of charged species along chains. We also investigated how the dependence of the double layer capacitance on the electrostatic potential (or on the charge on the walls) changes with grafting density, the chain length, distribution of charges along the chain, the bulk fluid density, and, finally, with the pore width. The shape of the electric double layer capacitance vs. voltage changes from a camel-like to bell-like shape, if the bulk fluid density changes from low to moderate and high. If the bulk density is appropriately chosen, it is possible to alter the shape of this curve from the double hump to single hump by changing the grafting density. Moreover, in narrow pores one can observe the capacitance curve with even three humps for a certain set of parameters describing brush. This behavior illustrates how strong the influence of brushes on the electric double layer properties can be, particularly for ionic fluids in narrow pores.

  11. Structural and Thermodynamic Basis for Weak Interactions between Dihydrolipoamide Dehydrogenase and Subunit-binding Domain of the Branched-chain [alpha]-Ketoacid Dehydrogenase Complex

    Energy Technology Data Exchange (ETDEWEB)

    Brautigam, Chad A.; Wynn, R. Max; Chuang, Jacinta L.; Naik, Mandar T.; Young, Brittany B.; Huang, Tai-huang; Chuang, David T. (AS); (UTSMC)

    2012-02-27

    The purified mammalian branched-chain {alpha}-ketoacid dehydrogenase complex (BCKDC), which catalyzes the oxidative decarboxylation of branched-chain {alpha}-keto acids, is essentially devoid of the constituent dihydrolipoamide dehydrogenase component (E3). The absence of E3 is associated with the low affinity of the subunit-binding domain of human BCKDC (hSBDb) for hE3. In this work, sequence alignments of hSBDb with the E3-binding domain (E3BD) of the mammalian pyruvate dehydrogenase complex show that hSBDb has an arginine at position 118, where E3BD features an asparagine. Substitution of Arg-118 with an asparagine increases the binding affinity of the R118N hSBDb variant (designated hSBDb*) for hE3 by nearly 2 orders of magnitude. The enthalpy of the binding reaction changes from endothermic with the wild-type hSBDb to exothermic with the hSBDb* variant. This higher affinity interaction allowed the determination of the crystal structure of the hE3/hSBDb* complex to 2.4-{angstrom} resolution. The structure showed that the presence of Arg-118 poses a unique, possibly steric and/or electrostatic incompatibility that could impede E3 interactions with the wild-type hSBDb. Compared with the E3/E3BD structure, the hE3/hSBDb* structure has a smaller interfacial area. Solution NMR data corroborated the interactions of hE3 with Arg-118 and Asn-118 in wild-type hSBDb and mutant hSBDb*, respectively. The NMR results also showed that the interface between hSBDb and hE3 does not change significantly from hSBDb to hSBDb*. Taken together, our results represent a starting point for explaining the long standing enigma that the E2b core of the BCKDC binds E3 far more weakly relative to other {alpha}-ketoacid dehydrogenase complexes.

  12. Quartz: structural and thermodynamic analyses across the α ↔ β transition with origin of negative thermal expansion (NTE) in β quartz and calcite

    Energy Technology Data Exchange (ETDEWEB)

    Antao, Sytle M.

    2016-04-01

    The temperature variation,T, of the crystal structure of quartz, SiO2, from 298 to 1235 K was obtained with synchrotron powder X-ray diffraction data and Rietveld structure refinements. The polymorphic transformation fromP3221 (low-T, α quartz) toP6222 (high-T, β quartz) occurs at a transition temperature,Ttr= 847 K. TheTvariations of spontaneous strains and several structural parameters are fitted to an order parameter,Q, using Landau theory. The change in Si atom coordinate, Six, givesTtr-Tc= 0.49 K, which indicates an α ↔ β transition that is weakly first order and nearly tricritical in character (Q4T). Strains give higherTtr-Tcvalues (≃ 7 K). Other fitted parameters are the oxygen Ozcoordinate, Si—Si distance, Si—O—Si and φ angles, and intensity of the (111) reflection,I111. In α quartz, the Si—Si distance increases withTbecause of cation repulsion, so the Si—O—Si angle increases (and φ decreases) and causes the thermal expansion of the framework structure that consists of corner-sharing distorted rigid SiO4tetrahedra. The Si—Si distances contract withTand cause negative thermal expansion (NTE) in β quartz because of increasing thermal librations of the O atom in the Si—O—Si linkage that occur nearly perpendicular to the Si—Si contraction. In calcite, CaCO3, the short Ca—Ca distance expands withT, but the next-nearest Ca—Ca distance, which is of equal length to theaaxis, contracts withTand causes NTE along

  13. Structural, kinetic, and thermodynamic characterization of the interconverting isomers of MS-325, a gadolinium(III)-based magnetic resonance angiography contrast agent.

    Science.gov (United States)

    Tyeklar, Zoltan; Dunham, Stephen U; Midelfort, Katarina; Scott, Daniel M; Sajiki, Hirano; Ong, Karen; Lauffer, Randall B; Caravan, Peter; McMurry, Thomas J

    2007-08-06

    The amphiphilic gadolinium complex MS-325 ((trisodium-{(2-(R)-[(4,4-diphenylcyclohexyl) phosphonooxymethyl] diethylenetriaminepentaacetato) (aquo)gadolinium(III)}) is a contrast agent for magnetic resonance angiography (MRA). MS-325 comprises a GdDTPA core with an appended phosphodiester moiety linked to a diphenylcyclohexyl group to facilitate noncovalent binding to serum albumin and extension of the plasma half-life in vivo. The chiral DTPA ligand (R) was derived from L-serine, and upon complexation with gadolinium, forms two interconvertible diastereomers, denoted herein as isomers A and B. X-ray crystallography of the tris(ethylenediamine)cobalt(III) salt derivative of isomer A revealed a structure in the polar acentric space group P32. The structure consisted of three independent molecules of the gadolinium complex in the asymmetric unit along with three Delta-[Co(en)3]3+ cations, and it represents an unusual example of spontaneous Pasteur resolution of the cobalt cation. The geometry of the coordination core was best described as a distorted trigonal prism, and the final R factor was 5.6%. The configuration of the chiral central nitrogen of the DTPA core was S. The Gd-water (2.47-2.48 A), the Gd-acetate oxygens (2.34-2.42 A), and the Gd-N bond distances (central N, 2.59-2.63 A; terminal N, 2.74-2.80 A) were similar to other reported GdDTPA structures. The structurally characterized single crystal was one of two interconvertable diastereomers (isomers A and B) that equilibrated to a ratio of 1.81 to 1 at pH 7.4 and were separable at elevated pH by ion-exchange chromatography. The rate of isomerization was highly pH dependent: k1 = (1.45 +/- 0.08) x 102[H+] + (4.16 +/- 0.30) x 105[H+]2; k-1 = (2.57 +/- 0.17) x 102[H+] + (7.54 +/- 0.60) x 105[H+]2.

  14. Thermodynamic database for proteins: features and applications.

    Science.gov (United States)

    Gromiha, M Michael; Sarai, Akinori

    2010-01-01

    We have developed a thermodynamic database for proteins and mutants, ProTherm, which is a collection of a large number of thermodynamic data on protein stability along with the sequence and structure information, experimental methods and conditions, and literature information. This is a valuable resource for understanding/predicting the stability of proteins, and it can be accessible at http://www.gibk26.bse.kyutech.ac.jp/jouhou/Protherm/protherm.html . ProTherm has several features including various search, display, and sorting options and visualization tools. We have analyzed the data in ProTherm to examine the relationship among thermodynamics, structure, and function of proteins. We describe the progress on the development of methods for understanding/predicting protein stability, such as (i) relationship between the stability of protein mutants and amino acid properties, (ii) average assignment method, (iii) empirical energy functions, (iv) torsion, distance, and contact potentials, and (v) machine learning techniques. The list of online resources for predicting protein stability has also been provided.

  15. Hamiltonian and Thermodynamic Modeling of Quantum Turbulence

    Science.gov (United States)

    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.

  16. Classical or equilibrium thermodynamics: basic conceptual aspects

    Directory of Open Access Journals (Sweden)

    Luiz Augusto Calvo Tiritan

    2008-08-01

    Full Text Available The Classical or Equilibrium Thermodynamics is one of the most consolidated fields of Physics. It is synthesized by a well-known and self coherent knowledge structure. The essence of the Classical Thermodynamics theoretical structure consists of a set of natural laws that rule the macroscopic physical systems behavior. These laws were formulated based on observations generalizations and are mostly independent of any hypotheses concerning the microscopic nature of the matter. In general, the approaches established for the Classical Thermodynamics follow one of the following alternatives: the historical approach that describes chronologically the evolution of ideas, concepts and facts, and the postulational approach in which postulates are formulated but are not demonstrated a priori but can be confirmed a posteriori. In this work, a brief review of the pre-classical historical approach conceptual evolution is elaborated, from the beginning of the seventeenth century to the middle of the nineteenth century. As for this, the following themes are dealt with in an evolutionary and phenomenological way: heat nature, thermometry, calorimetry, Carnot’s heat engine, heat mechanical equivalent and the first and second laws. The Zeroth law that was formulated afterwards is included in the discussion.

  17. Simulant molecules with trivalent or pentavalent phosphorus atoms: bond dissociation energies and other thermodynamic and structural properties from quantum chemical models.

    Science.gov (United States)

    Hahn, David K; RaghuVeer, Krishans S; Ortiz, J V

    2011-08-04

    The CBS-QB3 and G4 thermochemical models have been used to generate energetic, structural, and spectroscopic data on a set of molecules with trivalent or pentavalent phosphorus atoms that can serve as simulants of chemical warfare agents. Based on structural data, the conformational stabilities of these molecules are explained in terms of the anomeric interaction within the OPOC and OPSC fragments. For those cases where experimental data are available, comparisons have been made between calculated and previously reported vibrational frequencies. All varieties of bond dissociation energies have been examined except those for C-H and P═O bonds. In trivalent phosphorus molecules, the O-C and S-C bonds have the lowest dissociation energies. In the pentavalent phosphorus set, the S-C bonds, followed by P-S bonds, have the lowest dissociation energies. In the fluorinated simulant molecules, the P-F bond is strongest, and the P-C or O-C bonds are weakest. © 2011 American Chemical Society

  18. First-principles study of structural phase transition, electronic, elastic and thermodynamic properties of C15-type Laves phase TiCr2 under pressure

    Science.gov (United States)

    He, Li-Zhi; Zhu, Jun; Zhang, Lin

    2018-02-01

    Phase transition of TiCr2 in C15 (MgCu2), C36 (MgNi2), C14 (MgZn2) structures have been studied by using the projector augmented wave method. It is found that C15-type is the most stable structure, which agrees with the results of Chen et al. At 0 K, the phase boundary of C15 to C36 is 207.79 GPa, and the phase transition from C36 to C14 is 265.61 GPa. Both the transition pressures decrease with increasing temperature. Phonon dispersion and elastic constants are calculated and found that C15-type TiCr2 is mechanically stable according to the elastic stability criteria and phonon dispersion analysis. Moreover, the pressure and temperature dependence of the specific heat, Debye temperature and thermal expansion coefficient are discussed, among them our calculated Debye temperature is consistent with the report of A. sari et al., however, it is far from the results of B. Mayer et al. and Chen et al.

  19. Nonequilibrium Thermodynamics of Driven Disordered Materials

    Science.gov (United States)

    Bouchbinder, Eran

    2011-03-01

    We present a nonequilibrium thermodynamic framework for describing the dynamics of driven disordered solids (noncrystalline solids near and below their glass temperature, soft glassy materials such as colloidal suspensions and heavily dislocated polycrystalline solids). A central idea in our approach is that the set of mechanically stable configurations, i.e. the part of the system that is described by inherent structures, evolves slowly as compared to thermal vibrations and is characterized by an effective disorder temperature. Our thermodynamics-motivated equations of motion for the flow of energy and entropy are supplemented by coarse-grained internal variables that carry information about the relevant microscopic physics. Applications of this framework to amorphous visco-plasticity (Shear-Transformation-Zone theory), glassy memory effects (the Kovacs effect) and dislocation-mediated polycrystalline plasticity will be briefly discussed.

  20. Thermodynamics for physicists, chemists and materials scientists

    CERN Document Server

    Hentschke, Reinhard

    2014-01-01

    Thermodynamics is the foundation of many-body physics and thus of physical chemistry and material science as well. Today new sources of useful energy, energy storage, transport and conversion, requiring development of novel technology, are of rapidly increasing importance. This development strongly affects modern industry. Thus thermodynamics will have to be given more prominence in the science curriculum in colleges and universities - something that is attempted in this book. The structure of this text is simple and transparent, enabling the easy mapping of the text onto a one-semester course syllabus and the attendant study. There are 8 chapters total and one three-part appendix. Throughout the text the student finds numerous examples (solved problems) reaching from cosmic to molecular evolution or from cloud formation to Bose condensation.

  1. Thermodynamics, kinetics and process control of nitriding

    DEFF Research Database (Denmark)

    Mittemeijer, Eric J.; Somers, Marcel A. J.

    1999-01-01

    As a prerequisite for predictability of properties obtained by a nitriding treatment of iron-based workpieces, the relation between the process parameters and the composition and structure of the surface layer produced must be known. At present (even) the description of thermodynamic equilibrium...... of pure iron-nitrogen phases has not been achieved fully. It has been shown that taking into account ordering of nitrogen in the epsilon and gamma' iron-nitride phases, leads to an improved understanding of the Fe-N phase diagram. Although thermodynamics indicate the state the system strives for......, the nitriding result is determined largely by the kinetics of the process. The nitriding kinetics have been shown to be characterised by the occurring local near-equilibria and stationary states at surfaces and interfaces, and the diffusion coefficient of nitrogen in the various phases, for which new data have...

  2. Thermodynamics, kinetics and process control of nitriding

    DEFF Research Database (Denmark)

    Mittemeijer, Eric J.; Somers, Marcel A. J.

    1997-01-01

    As a prerequisite for the predictability of properties obtained by a nitriding treatment of iron based workpieces, the relation between the process parameters and the composition and structure of the surface layer produced must be known. At present, even the description of thermodynamic equilibrium...... of pure Fe-N phases has not been fully achieved. It is shown that taking into account the ordering of nitrogen in the epsilon and gamma' iron nitride phases leads to an improved understanding of the Fe-N phase diagram. Although consideration of thermodynamics indicates the state the system strives for...... for process control of gaseous nitriding by monitoring the partial pressure of oxygen in the furnace using a solid state electrolyte is provided. At the time the work was carried out the authors were in the Laboratory of Materials Science, Delft University of Technology, Rotterdamseweg 137, 2628 AL Delft...

  3. A thermodynamic definition of protein domains.

    Science.gov (United States)

    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.

  4. TRLIFS study of Eu(III) spectroscopic properties to obtain structural and thermodynamic informations on lanthanide-malonamide complexes in the Eu(III)/NaNO3/tetraethylmalonamide system

    International Nuclear Information System (INIS)

    Couston, L.; Charbonnel, M.C.; Flandin, J.L.; Rancier, F.; Moulin, C.

    2004-01-01

    Improvement of the nuclear fuel reprocessing involves separating the minor actinides (Am(III) and Cm(III)) from the fission products. In the French strategy, the first step consists in the separation of the trivalent actinides and lanthanides from high-level liquid waste, for which malonamides RR'NCO(CHR '' )CONRR' are promising ligands. These molecules have been optimized for reprocessing but still require basic chemical studies to describe the complexation mechanisms at a molecular scale. This paper discusses a thermodynamic and structural study of a Ln(III)-malonamide complex formed with the hydrosoluble tetraethylmalonamide ligand (TEMA = (C 2 H 5 ) 2 NCOCH 2 CON(C 2 H 5 ) 2 ) dissolved in a nitrate medium. Despite the simplified chemical system obtained with TEMA, its weak chemical affinity and its physical properties pushed the analytical techniques to their limits. The sensitivity of time-resolved laser-induced fluorescence spectroscopy (TRLIFS) combined with the major luminescent spectroscopic properties of Eu(III) (hypersensitive band and fluorescence lifetime) were successfully used to determine the equilibrium constant and hydration number in the Eu(III), TEMA, and NO 3 - system. Fluorescence lifetimes, connected with the first coordination sphere of the solvated metal, clearly show the inner-sphere location of nitrate in the Eu(NO 3 ) 2+ complex, the outer-sphere location of TEMA in the Eu(TEMA) 3+ complex, and the outer-sphere location of both ligands in the Eu(NO 3 )(TEMA) 2+ complex. (orig.)

  5. Investigation on the structure, thermodynamic and electrochemical properties of the MmNi3.55Mn0.4Al0.3Fe0.75 compound used as negative electrode in Ni–MH batteries

    International Nuclear Information System (INIS)

    Ben Moussa, M.; Abdellaoui, M.; Lamloumi, J.; Percheron Guégan, A.

    2013-01-01

    Highlights: •The solid–gas capacity at room temperature is equal to 3.93 H/mol. •The value pressure equilibrium is 0.024 bar. •The average radius particles decrease with number of cycles. •The hydrogen diffusion coefficient D H , increase with number of cycles. -- Abstract: The structure, thermodynamic and electrochemical properties of the hydride poly-substituted MmNi 3.55 Mn 0.4 Al 0.3 Fe 0.75 alloy used as material for negative electrode in Ni–MH batteries investigated. The solid–gas capacity and pressure equilibrium measurement at room temperature are respectively 3.93 H/mol and 0.024 bars. The chronoamperometry method shows the size of the particles (a) participating in the electrochemical reaction decrease of cycle number. The hydrogen diffusion coefficient determined by electrochemical impedance spectroscopy (EIS) increase of the number of cycles from 3.5 × 10 −12 cm 2 s −1 before cycling to 7.29 × 10 −10 cm 2 s −1 after 13 cycles charge–decharge

  6. Molecular structure and conformational composition of 1,3-dihydroxyacetone studied by combined analysis of gas-phase electron diffraction data, rotational constants, and results of theoretical calculations. Ideal gas thermodynamic properties of 1,3-dihydroxyacetone.

    Science.gov (United States)

    Dorofeeva, Olga V; Vogt, Natalja; Vogt, Jürgen; Popik, Mikhail V; Rykov, Anatolii N; Vilkov, Lev V

    2007-07-19

    The molecular structure of 1,3-dihydroxyacetone (DHA) has been studied by gas-phase electron diffraction (GED), combined analysis of GED and microwave (MW) data, ab initio, and density functional theory calculations. The equilibrium re structure of DHA was determined by a joint analysis of the GED data and rotational constants taken from the literature. The anharmonic vibrational corrections to the internuclear distances (re-ra) and to the rotational constants (B(i)e-B(i)0) needed for the estimation of the re structure were calculated from the B3LYP/cc-pVTZ cubic force field. It was found that the experimental data are well reproduced by assuming that DHA consists of a mixture of three conformers. The most stable conformer of C2v symmetry has two hydrogen bonds, whereas the next two lowest energy conformers (Cs and C1 symmetry) have one hydrogen bond and their abundance is about 30% in total. A combined analysis of GED and MW data led to the following equilibrium structural parameters (re) of the most abundant conformer of DHA (the uncertainties in parentheses are 3 times the standard deviations): r(C=O)=1.215(2) A, r(C-C)=1.516(2) A, r(C-O)=1.393(2) A, r(C-H)=1.096(4) A, r(O-H)=0.967(4) A, angleC-C=O=119.9(2) degrees, angleC-C-O=111.0(2) degrees, angleC-C-H=108.2(7) degrees, angleC-O-H=106.5(7) degrees. These structural parameters reproduce the experimental B(i)0 values within 0.05 MHz. The experimental structural parameters are in good agreement with those obtained from theoretical calculations. Ideal gas thermodynamic functions (S degrees (T), C degrees p(T), and H degrees (T)-H degrees (0)) of DHA were calculated on the basis of experimental and theoretical molecular parameters obtained in this work. The enthalpy of formation of DHA, -523+/-4 kJ/mol, was calculated by the atomization procedure using the G3X method.

  7. Thermodynamics of hydrogen bonding and van der Waals interactions of organic solutes in solutions of imidazolium based ionic liquids: “Structure-property” relationships

    Energy Technology Data Exchange (ETDEWEB)

    Varfolomeev, Mikhail A., E-mail: vma.ksu@gmail.com; Khachatrian, Artashes A.; Akhmadeev, Bulat S.; Solomonov, Boris N.

    2016-06-10

    Highlights: • Solution enthalpies of organic solutes in imidazolium based ionic liquids were measured. • van der Waals interactions scale of imidazolium based ionic liquids was proposed. • Enthalpies of solvation of organic solutes in ionic liquids were determined. • Hydrogen bond enthalpies of organic solutes with ionic liquids were calculated. • Relationships between structure of ionic liquids and thermochemical data were obtained. - Abstract: In the present work thermochemistry of intermolecular interactions of organic compounds in solutions of imidazolium based ionic liquids (ILs) has been studied using solution calorimetry method. Enthalpies of solution at infinite dilution of non-polar (alkanes, aromatic hydrocarbons) and polar (alcohols, amides, and etc.) organic solutes in two ionic liquids 1-butyl-3-methylimidazolium tetrafluoroborate and 1-butyl-3-methylimidazolium trifluoromethanesulfonate were measured at 298.15 K. The scale of van der Waals interactions of imidazolium based ILs has been proposed on the basis of solution enthalpies of n-alkanes in their media. The effect of the cation and anion structure of ILs on the enthalpies of solvation was analyzed. Enthalpies of hydrogen bonding of organic solutes with imidazolium based ILs were determined. It has been shown that these values are close to zero for proton acceptor solutes. At the same time, enthalpies of hydrogen bonding of proton donor solutes with ionic liquids are increased depending the anion: tetrafluoroborate ≈ bis(trifluoromethylsulfonyl)imide < 2-(2-methoxyethoxy)ethyl sulfate < trifluoromethanesulfonate. Enthalpies of van der Waals interactions and hydrogen bonding in the solutions of imidazolium based ionic liquids were compared with the same data for molecular solvents.

  8. Thermodynamics of hydrogen bonding and van der Waals interactions of organic solutes in solutions of imidazolium based ionic liquids: “Structure-property” relationships

    International Nuclear Information System (INIS)

    Varfolomeev, Mikhail A.; Khachatrian, Artashes A.; Akhmadeev, Bulat S.; Solomonov, Boris N.

    2016-01-01

    Highlights: • Solution enthalpies of organic solutes in imidazolium based ionic liquids were measured. • van der Waals interactions scale of imidazolium based ionic liquids was proposed. • Enthalpies of solvation of organic solutes in ionic liquids were determined. • Hydrogen bond enthalpies of organic solutes with ionic liquids were calculated. • Relationships between structure of ionic liquids and thermochemical data were obtained. - Abstract: In the present work thermochemistry of intermolecular interactions of organic compounds in solutions of imidazolium based ionic liquids (ILs) has been studied using solution calorimetry method. Enthalpies of solution at infinite dilution of non-polar (alkanes, aromatic hydrocarbons) and polar (alcohols, amides, and etc.) organic solutes in two ionic liquids 1-butyl-3-methylimidazolium tetrafluoroborate and 1-butyl-3-methylimidazolium trifluoromethanesulfonate were measured at 298.15 K. The scale of van der Waals interactions of imidazolium based ILs has been proposed on the basis of solution enthalpies of n-alkanes in their media. The effect of the cation and anion structure of ILs on the enthalpies of solvation was analyzed. Enthalpies of hydrogen bonding of organic solutes with imidazolium based ILs were determined. It has been shown that these values are close to zero for proton acceptor solutes. At the same time, enthalpies of hydrogen bonding of proton donor solutes with ionic liquids are increased depending the anion: tetrafluoroborate ≈ bis(trifluoromethylsulfonyl)imide < 2-(2-methoxyethoxy)ethyl sulfate < trifluoromethanesulfonate. Enthalpies of van der Waals interactions and hydrogen bonding in the solutions of imidazolium based ionic liquids were compared with the same data for molecular solvents.

  9. Theoretical investigation of the thermodynamic properties of metallic thin films

    International Nuclear Information System (INIS)

    Hung, Vu Van; Phuong, Duong Dai; Hoa, Nguyen Thi; Hieu, Ho Khac

    2015-01-01

    The thermodynamic properties of metallic thin films with face-centered cubic structure at ambient conditions were investigated using the statistical moment method including the anharmonicity effects of thermal lattice vibrations. The analytical expressions of Helmholtz free energy, lattice parameter, linear thermal expansion coefficient, specific heats at the constant volume and constant pressure were derived in terms of the power moments of the atomic displacements. Numerical calculations of thermodynamic properties have been performed for Au and Al thin films and compared with those of bulk metals. This research proposes that thermodynamic quantities of thin films approach the values of bulk when the thickness of thin film is about 70 nm. - Highlights: • Thermodynamic properties of thin films were investigated using the moment method. • Expressions of Helmholtz energy, expansion coefficient, specific heats were derived. • Calculations for Au, Al thin films were performed and compared with those of bulks

  10. Theoretical investigation of the thermodynamic properties of metallic thin films

    Energy Technology Data Exchange (ETDEWEB)

    Hung, Vu Van [Vietnam Education Publishing House, 81 Tran Hung Dao, Hanoi (Viet Nam); Phuong, Duong Dai [Hanoi National University of Education, 136 Xuan Thuy, Hanoi (Viet Nam); Hoa, Nguyen Thi [University of Transport and Communications, Lang Thuong, Dong Da, Hanoi (Viet Nam); Hieu, Ho Khac, E-mail: hieuhk@duytan.edu.vn [Institute of Research and Development, Duy Tan University, K7/25 Quang Trung, Danang (Viet Nam)

    2015-05-29

    The thermodynamic properties of metallic thin films with face-centered cubic structure at ambient conditions were investigated using the statistical moment method including the anharmonicity effects of thermal lattice vibrations. The analytical expressions of Helmholtz free energy, lattice parameter, linear thermal expansion coefficient, specific heats at the constant volume and constant pressure were derived in terms of the power moments of the atomic displacements. Numerical calculations of thermodynamic properties have been performed for Au and Al thin films and compared with those of bulk metals. This research proposes that thermodynamic quantities of thin films approach the values of bulk when the thickness of thin film is about 70 nm. - Highlights: • Thermodynamic properties of thin films were investigated using the moment method. • Expressions of Helmholtz energy, expansion coefficient, specific heats were derived. • Calculations for Au, Al thin films were performed and compared with those of bulks.

  11. Statistical Thermodynamics of Disperse Systems

    DEFF Research Database (Denmark)

    Shapiro, Alexander

    1996-01-01

    Principles of statistical physics are applied for the description of thermodynamic equilibrium in disperse systems. The cells of disperse systems are shown to possess a number of non-standard thermodynamic parameters. A random distribution of these parameters in the system is determined....... On the basis of this distribution, it is established that the disperse system has an additional degree of freedom called the macro-entropy. A large set of bounded ideal disperse systems allows exact evaluation of thermodynamic characteristics. The theory developed is applied to the description of equilibrium...

  12. Thermodynamic light on black holes

    International Nuclear Information System (INIS)

    Davies, P.

    1977-01-01

    The existence of black holes and their relevance to our understanding of the nature of space and time are considered, with especial reference to the application of thermodynamic arguments which can reveal their energy-transfer processes in a new light. The application of thermodynamics to strongly gravitating systems promises some fascinating new insights into the nature of gravity. Situations can occur during gravitational collapse in which existing physics breaks down. Under these circumstances, the application of universal thermodynamical principles might be our only guide. (U.K.)

  13. Some aspects of plasma thermodynamics

    International Nuclear Information System (INIS)

    Gorgoraki, V.I.

    1986-01-01

    The objective reasons which have inhibited the development of a plasma-thermodynamics theory are discussed and the authors formulate the fundamental principles which can be the basis of a common plasma-thermodynamics theory. Two kinds of thermodynamic equilibrium plasmas are discussed, an isothermal plasma and a nonisothermal plasma. An isothermal plasma is a high-temperature plasma; the Saha-Eggert equation describes its behavior. A nonisothermal plasma is a low-temperature plasma, and the reactions taking place therein are purely plasma-chemical. The ionization equilibrium and the composition of such a plasma can be found with the aid of the equations presented in this paper

  14. Practical chemical thermodynamics for geoscientists

    CERN Document Server

    Fegley, Bruce, Jr

    2012-01-01

    Practical Chemical Thermodynamics for Geoscientists covers classical chemical thermodynamics and focuses on applications to practical problems in the geosciences, environmental sciences, and planetary sciences. This book will provide a strong theoretical foundation for students, while also proving beneficial for earth and planetary scientists seeking a review of thermodynamic principles and their application to a specific problem. Strong theoretical foundation and emphasis on applications Numerous worked examples in each chapter Brief historical summaries and biographies of key thermodynamicists-including their fundamental research and discoveries Extensive references to relevant literature.

  15. Thermodynamic analysis of biochemical systems

    International Nuclear Information System (INIS)

    Yuan, Y.; Fan, L.T.; Shieh, J.H.

    1989-01-01

    Introduction of the concepts of the availability (or exergy), datum level materials, and the dead state has been regarded as some of the most significant recent developments in classical thermodynamics. Not only the available energy balance but also the material and energy balances of a biological system may be established in reference to the datum level materials in the dead state or environment. In this paper these concepts are illustrated with two examples of fermentation and are shown to be useful in identifying sources of thermodynamic inefficiency, thereby leading naturally to the rational definition of thermodynamic efficiency of a biochemical process

  16. Extremely large magnetoresistance and Kohler's rule in PdSn4: A complete study of thermodynamic, transport, and band-structure properties

    Science.gov (United States)

    Jo, Na Hyun; Wu, Yun; Wang, Lin-Lin; Orth, Peter P.; Downing, Savannah S.; Manni, Soham; Mou, Dixiang; Johnson, Duane D.; Kaminski, Adam; Bud'ko, Sergey L.; Canfield, Paul C.

    2017-10-01

    The recently discovered material PtSn4 is known to exhibit extremely large magnetoresistance (XMR) that also manifests Dirac arc nodes on the surface. PdSn4 is isostructural to PtSn4 with the same electron count. We report on the physical properties of high-quality single crystals of PdSn4 including specific heat, temperature- and magnetic-field-dependent resistivity and magnetization, and electronic band-structure properties obtained from angle-resolved photoemission spectroscopy (ARPES). We observe that PdSn4 has physical properties that are qualitatively similar to those of PtSn4, but find also pronounced differences. Importantly, the Dirac arc node surface state of PtSn4 is gapped out for PdSn4. By comparing these similar compounds, we address the origin of the extremely large magnetoresistance in PdSn4 and PtSn4; based on detailed analysis of the magnetoresistivity ρ (H ,T ) , we conclude that neither the carrier compensation nor the Dirac arc node surface state are the primary reason for the extremely large magnetoresistance. On the other hand, we find that, surprisingly, Kohler's rule scaling of the magnetoresistance, which describes a self-similarity of the field-induced orbital electronic motion across different length scales and is derived for a simple electronic response of metals to an applied magnetic field is obeyed over the full range of temperatures and field strengths that we explore.

  17. Thermodynamic and structural studies of mixed monolayers: Mutual mixing of DPPC and DPPG with DoTAP at the air-water interface

    International Nuclear Information System (INIS)

    Panda, Amiya Kumar; Vasilev, Krasimir; Orgeig, Sandra; Prestidge, Clive A.

    2010-01-01

    Phospholipid monomolecular films at the air-water interface are useful model membranes to understand miscibility among various components. Surface pressure (π)-area (A) isotherms of pure and mixed monolayers of dioleoyltrimethylammonium propane (DoTAP)-dipalmitoylphosphatidylcholine (DPPC) and DoTAP-dipalmitoyphosphatidylglycerol (DPPG) were constructed using a surface balance. DPPC and DPPG produced isotherms as expected and reported earlier. DoTAP, an unsaturated lipid, demonstrated a continuous π-A isotherm. Associative interactions were identified in DPPC-DoTAP mixtures compared to the pure components, while DPPG-DoTAP mixtures showed repulsive interaction up to an equimolar ratio. Compression moduli of the monolayers revealed that DPPC-DoTAP mixtures had increasing stability with increasing surface pressure, but addition of DoTAP to DPPG showed instability at low and intermediate concentrations. In both cases increased stability was returned at higher X DoTAP values and surface pressures. Lipid monolayer film thickness values, determined on a gold coated glass substrate by surface plasmon resonance spectroscopy (SPR), indicated a systematic change in height profile for DPPC-DoTAP mixtures with increasing X DoTAP . However, DPPG-DoTAP mixed monolayer systems demonstrated a biphasic response. The SPR data were in excellent agreement with our interpretation of the structure of solid supported lipid monolayers.

  18. Thermodynamic and structural studies of mixed monolayers: Mutual mixing of DPPC and DPPG with DoTAP at the air-water interface

    Energy Technology Data Exchange (ETDEWEB)

    Panda, Amiya Kumar, E-mail: akpanda1@yahoo.com [Department of Chemistry, University of North Bengal, Darjeeling-734 013, West Bengal (India); Vasilev, Krasimir [Mawson Institute for Advanced Manufacturing, Mawson Lakes, University of South Australia, SA-5095 (Australia); Orgeig, Sandra [Sansom Institute for Health Research and School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, SA 5000 (Australia); Prestidge, Clive A. [Ian Wark Research Institute, University of South Australia, Mawson Lakes, SA 5095 (Australia)

    2010-05-10

    Phospholipid monomolecular films at the air-water interface are useful model membranes to understand miscibility among various components. Surface pressure ({pi})-area (A) isotherms of pure and mixed monolayers of dioleoyltrimethylammonium propane (DoTAP)-dipalmitoylphosphatidylcholine (DPPC) and DoTAP-dipalmitoyphosphatidylglycerol (DPPG) were constructed using a surface balance. DPPC and DPPG produced isotherms as expected and reported earlier. DoTAP, an unsaturated lipid, demonstrated a continuous {pi}-A isotherm. Associative interactions were identified in DPPC-DoTAP mixtures compared to the pure components, while DPPG-DoTAP mixtures showed repulsive interaction up to an equimolar ratio. Compression moduli of the monolayers revealed that DPPC-DoTAP mixtures had increasing stability with increasing surface pressure, but addition of DoTAP to DPPG showed instability at low and intermediate concentrations. In both cases increased stability was returned at higher X{sub DoTAP} values and surface pressures. Lipid monolayer film thickness values, determined on a gold coated glass substrate by surface plasmon resonance spectroscopy (SPR), indicated a systematic change in height profile for DPPC-DoTAP mixtures with increasing X{sub DoTAP}. However, DPPG-DoTAP mixed monolayer systems demonstrated a biphasic response. The SPR data were in excellent agreement with our interpretation of the structure of solid supported lipid monolayers.

  19. Three-dimensional quantitative structure-property relationship (3D-QSPR) models for prediction of thermodynamic properties of polychlorinated biphenyls (PCBs): enthalpy of vaporization.

    Science.gov (United States)

    Puri, Swati; Chickos, James S; Welsh, William J

    2002-01-01

    Three-dimensional Quantitative Structure-Property Relationship (QSPR) models have been derived using Comparative Molecular Field Analysis (CoMFA) to correlate the vaporization enthalpies of a representative set of polychlorinated biphenyls (PCBs) at 298.15 K with their CoMFA-calculated physicochemical properties. Various alignment schemes, such as inertial, as is, and atom fit, were employed in this study. The CoMFA models were also developed using different partial charge formalisms, namely, electrostatic potential (ESP) charges and Gasteiger-Marsili (GM) charges. The most predictive model for vaporization enthalpy (Delta(vap)H(m)(298.15 K)), with atom fit alignment and Gasteiger-Marsili charges, yielded r2 values 0.852 (cross-validated) and 0.996 (conventional). The vaporization enthalpies of PCBs increased with the number of chlorine atoms and were found to be larger for the meta- and para-substituted isomers. This model was used to predict Delta(vap)H(m)(298.15 K) of the entire set of 209 PCB congeners.

  20. Extremely large magnetoresistance and Kohler's rule in PdSn4 : A complete study of thermodynamic, transport, and band-structure properties

    International Nuclear Information System (INIS)

    Jo, Na Hyun; Wu, Yun; Wang, Lin-Lin; Orth, Peter P.; Downing, Savannah S.

    2017-01-01

    The recently discovered material PtSn 4 is known to exhibit extremely large magnetoresistance (XMR) that also manifests Dirac arc nodes on the surface. PdSn 4 is isostructural to PtSn 4 with the same electron count. Here, we report on the physical properties of high-quality single crystals of PdSn 4 including specific heat, temperature- and magnetic-field-dependent resistivity and magnetization, and electronic band-structure properties obtained from angle-resolved photoemission spectroscopy (ARPES). We observe that PdSn 4 has physical properties that are qualitatively similar to those of PtSn 4 , but find also pronounced differences. Importantly, the Dirac arc node surface state of PtSn 4 is gapped out for PdSn 4 . By comparing these similar compounds, we address the origin of the extremely large magnetoresistance in PdSn 4 and PtSn 4 ; based on detailed analysis of the magnetoresistivity ρ (H , T) , we conclude that neither the carrier compensation nor the Dirac arc node surface state are the primary reason for the extremely large magnetoresistance. On the other hand, we also find that, surprisingly, Kohler's rule scaling of the magnetoresistance, which describes a self-similarity of the field-induced orbital electronic motion across different length scales and is derived for a simple electronic response of metals to an applied magnetic field is obeyed over the full range of temperatures and field strengths that we explore.

  1. Thermodynamics of quantum spacetime histories

    Science.gov (United States)

    Smolin, Lee

    2017-11-01

    We show that the simplicity constraints, which define the dynamics of spin foam models, imply, and are implied by, the first law of thermodynamics, when the latter is applied to causal diamonds in the quantum spacetime. This result reveals an intimate connection between the holographic nature of gravity, as reflected by the Bekenstein entropy, and the fact that general relativity and other gravitational theories can be understood as constrained topological field theories. To state and derive this correspondence we describe causal diamonds in the causal structure of spin foam histories and generalize arguments given for the near horizon region of black holes by Frodden, Gosh and Perez [Phys. Rev. D 87, 121503 (2013); , 10.1103/PhysRevD.87.121503Phys. Rev. D 89, 084069 (2014); , 10.1103/PhysRevD.89.084069Phys. Rev. Lett. 107, 241301 (2011); , 10.1103/PhysRevLett.107.241301Phys. Rev. Lett.108, 169901(E) (2012)., 10.1103/PhysRevLett.108.169901] and Bianchi [arXiv:1204.5122.]. This allows us to apply a recent argument of Jacobson [Phys. Rev. Lett. 116, 201101 (2016).10.1103/PhysRevLett.116.201101] to show that if a spin foam history has a semiclassical limit described in terms of a smooth metric geometry, that geometry satisfies the Einstein equations. These results suggest also a proposal for a quantum equivalence principle.

  2. Thermodynamical string fragmentation

    Energy Technology Data Exchange (ETDEWEB)

    Fischer, Nadine [Theoretical Particle Physics, Department of Astronomy and Theoretical Physics, Lund University,Sölvegatan 14A, Lund, SE-223 62 (Sweden); School of Physics and Astronomy, Monash University,Wellington Road, Clayton, VIC-3800 (Australia); Sjöstrand, Torbjörn [Theoretical Particle Physics, Department of Astronomy and Theoretical Physics, Lund University,Sölvegatan 14A, Lund, SE-223 62 (Sweden)

    2017-01-31

    The observation of heavy-ion-like behaviour in pp collisions at the LHC suggests that more physics mechanisms are at play than traditionally assumed. The introduction e.g. of quark-gluon plasma or colour rope formation can describe several of the observations, but as of yet there is no established paradigm. In this article we study a few possible modifications to the Pythia event generator, which describes a wealth of data but fails for a number of recent observations. Firstly, we present a new model for generating the transverse momentum of hadrons during the string fragmentation process, inspired by thermodynamics, where heavier hadrons naturally are suppressed in rate but obtain a higher average transverse momentum. Secondly, close-packing of strings is taken into account by making the temperature or string tension environment-dependent. Thirdly, a simple model for hadron rescattering is added. The effect of these modifications is studied, individually and taken together, and compared with data mainly from the LHC. While some improvements can be noted, it turns out to be nontrivial to obtain effects as big as required, and further work is called for.

  3. Thermodynamics of mixtures containing amines. IX. Application of the concentration-concentration structure factor to the study of binary mixtures containing pyridines

    Energy Technology Data Exchange (ETDEWEB)

    Gonzalez, Juan Antonio, E-mail: jagl@termo.uva.es [G.E.T.E.F. Dpto Termodinamica y Fisica Aplicada, Facultad de Ciencias, Universidad de Valladolid, Valladolid 47071 (Spain); Cobos, Jose Carlos; Garcia de la Fuente, Isaias; Mozo, Ismael [G.E.T.E.F. Dpto Termodinamica y Fisica Aplicada, Facultad de Ciencias, Universidad de Valladolid, Valladolid 47071 (Spain)

    2009-10-10

    Binary mixtures formed by a pyridine base and an alkane, or an aromatic hydrocarbon, or a 1-alkanol have been studied in the framework of the concentration-concentration structure factor, S{sub CC}(0), formalism. Deviations between experimental data and those provided by the DISQUAC model are discussed. Systems containing alkanes are characterized by homocoordination. In pyridine + alkane mixtures, S{sub CC}(0) decreases with the chain length of the longer alkanes, due to size effects. For a given alkane, S{sub CC}(0) also decreases with the number of CH{sub 3}- groups in the pyridine base. This has been interpreted assuming that the number of amine-amine interactions available to be broken upon mixing also decreases similarly, probably as steric hindrances exerted by the methyl groups of the aromatic amine increase with the number of these groups. Homocoordination is higher in mixtures with 3,5-dimethylpyridine than in those with 2,6-dimethylpyridine. That is, steric effects exerted by methyl groups in positions 3 and 5 are stronger than when they are in positions 2 and 6. Similarly, from the application of the DISQUAC (dispersive-quasichemical) model, it is possible to conclude that homocoordination is higher in systems with 3- or 4-methylpyridine than in those involving 2-methylpyridine. Systems including aromatic hydrocarbons are nearly ideal, which seems to indicate that there is no specific interaction in such solutions. Mixtures with 1-alkanols show heterocoordination. This reveals the existence of interactions between unlike molecules, characteristic of alkanol + amine mixtures. Methanol systems show the lowest S{sub CC}(0) values due, partially, to size effects. This explains the observed decrease of homocoordination in such solutions in the order: pyridine > 2-methylpyridine > 2,6-dimethylpyridine. Moreover, as the energies of the OH-N hydrogen bonds are practically independent of the pyridine base considered when mixed with methanol, it suggests that

  4. Thermodynamic Calculations for Systems Biocatalysis

    DEFF Research Database (Denmark)

    Abu, Rohana; Gundersen, Maria T.; Woodley, John M.

    2015-01-01

    the transamination of a pro-chiral ketone into a chiral amine (interesting in many pharmaceutical applications). Here, the products are often less energetically stable than the reactants, meaning that the reaction may be thermodynamically unfavourable. As in nature, such thermodynamically-challenged reactions can...... on the basis of kinetics. However, many of the most interesting non-natural chemical reactions which could potentially be catalysed by enzymes, are thermodynamically unfavourable and are thus limited by the equilibrium position of the reaction. A good example is the enzyme ω-transaminase, which catalyses...... be altered by coupling with other reactions. For instance, in the case of ω-transaminase, such a coupling could be with alanine dehydrogenase. Herein, the aim of this work is to identify thermodynamic bottlenecks within a multi-enzyme process, using group contribution method to calculate the Gibbs free...

  5. Shock Thermodynamic Applied Research Facility

    Data.gov (United States)

    Federal Laboratory Consortium — The Shock Thermodynamic Applied Research Facility (STAR) facility, within Sandia’s Solid Dynamic Physics Department, is one of a few institutions in the world with a...

  6. Thermodynamic analysis of PBMR plant

    International Nuclear Information System (INIS)

    Sen, S.; Kadiroglu, O.K.

    2002-01-01

    The thermodynamic analysis of a PBMR is presented for various pressures and temperatures values. The design parameters of the components of the power plant are calculated and an optimum cycle for the maximum thermal efficiency is sought for. (author)

  7. Thermodynamic efficiency of solar concentrators.

    Science.gov (United States)

    Shatz, Narkis; Bortz, John; Winston, Roland

    2010-04-26

    The optical thermodynamic efficiency is a comprehensive metric that takes into account all loss mechanisms associated with transferring flux from the source to the target phase space, which may include losses due to inadequate design, non-ideal materials, fabrication errors, and less than maximal concentration. We discuss consequences of Fermat's principle of geometrical optics and review étendue dilution and optical loss mechanisms associated with nonimaging concentrators. We develop an expression for the optical thermodynamic efficiency which combines the first and second laws of thermodynamics. As such, this metric is a gold standard for evaluating the performance of nonimaging concentrators. We provide examples illustrating the use of this new metric for concentrating photovoltaic systems for solar power applications, and in particular show how skewness mismatch limits the attainable optical thermodynamic efficiency.

  8. Thermodynamic origin of nonimaging optics

    Science.gov (United States)

    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.

  9. Thermodynamic approach to biomass gasification

    International Nuclear Information System (INIS)

    Boissonnet, G.; Seiler, J.M.

    2003-01-01

    The document presents an approach of biomass transformation in presence of steam, hydrogen or oxygen. Calculation results based on thermodynamic equilibrium are discussed. The objective of gasification techniques is to increase the gas content in CO and H 2 . The maximum content in these gases is obtained when thermodynamic equilibrium is approached. Any optimisation action of a process. will, thus, tend to approach thermodynamic equilibrium conditions. On the other hand, such calculations can be used to determine the conditions which lead to an increase in the production of CO and H 2 . An objective is also to determine transformation enthalpies that are an important input for process calculations. Various existing processes are assessed, and associated thermodynamic limitations are evidenced. (author)

  10. [Thermodynamic theory of evolution and aging].

    Science.gov (United States)

    Gladyshev, G P

    2012-01-01

    Life in the Universe emerges and develops under certain conditions in accordance with the general laws of nature, in particular, in accordance with the law of temporal hierarchies, the second law of thermodynamics and the principle of stability of matter. Biological evolution and organism's aging are accompanied by a change in the chemical and supramolecular compositions of living bodies. As shown by the author in 1977 these well-known changes have the thermodynamic nature (origin). Phenomenological hierarchical thermodynamics of near-equilibrium quasi-closed systems allows us to explain and predict the evolutionary transformation in the living world. From a viewpoint of power-consuming substance of biological objects the phenomenon of life, first, is the struggle for power-consuming chemicals. The accumulation of this substance in biological systems is associated with the aspiration of the specific Gibbs function of formation of supramolecular structures of living organisms to a minimum. The development of classical science opens up new horizons to explore the real world and contributes to the success of gerontology and geriatrics. This paper is a brief review containing new results.

  11. Thermodynamics from concepts to applications

    CERN Document Server

    Shavit, Arthur

    2008-01-01

    The book presents a logical methodology for solving problems in the context of conservation laws and property tables or equations. The authors elucidate the terms around which thermodynamics has historically developed, such as work, heat, temperature, energy, and entropy. Using a pedagogical approach that builds from basic principles to laws and eventually corollaries of the laws, the text enables students to think in clear and correct thermodynamic terms as well as solve real engineering problems.

  12. First-principles prediction of the structural, elastic, thermodynamic, electronic and optical properties of Li{sub 4}Sr{sub 3}Ge{sub 2}N{sub 6} quaternary nitride

    Energy Technology Data Exchange (ETDEWEB)

    Boudrifa, O. [Laboratory for Developing New Materials and their Characterization, University of Setif 1, 19000 Setif (Algeria); Bouhemadou, A., E-mail: a_bouhemadou@yahoo.fr [Laboratory for Developing New Materials and their Characterization, University of Setif 1, 19000 Setif (Algeria); Guechi, N. [Department of Physics, Faculty of Science, University of Setif 1, 19000 Setif (Algeria); Bin-Omran, S. [Department of Physics and Astronomy, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451 (Saudi Arabia); Department of Physics, Faculty of Science and Humanitarian Studies, Salman Bin Abdalaziz University, Alkharj 11942 (Saudi Arabia); Al-Douri, Y. [Institute of Nano Electronic Engineering, Universiti Malaysia Perlis, 01000 Kangar, Perlis (Malaysia); Khenata, R. [Laboratoire de Physique Quantique et de Modélisation Mathématique (LPQ3M), Département de Technologie, Université de Mascara, 29000 Mascara (Algeria)

    2015-01-05

    Highlights: • Some physical properties of the quaternary nitride Li{sub 4}Sr{sub 3}Ge{sub 2}N{sub 6} have been predicted. • Elastic parameters reveal that Li{sub 4}Sr{sub 3}Ge{sub 2}N{sub 6} is mechanically stable but anisotropi. • Li{sub 4}Sr{sub 3}Ge{sub 2}N{sub 6} is an indirect semiconductor. • The fundamental indirect band gap changes to direct one under pressure effect. • The optical properties exhibit noticeable anisotropy. - Abstract: Structural parameters, elastic constants, thermodynamic properties, electronic structure and optical properties of the monoclinic Li{sub 4}Sr{sub 3}Ge{sub 2}N{sub 6} quaternary nitride are investigated theoretically for the first time using the pseudopotential plane-wave based first-principles calculations. The calculated structural parameters are in excellent agreement with the experimental data. This serves as a proof of reliability of the used theoretical method and gives confidence in the predicted results on aforementioned properties of Li{sub 4}Sr{sub 3}Ge{sub 2}N{sub 6}. The predicted elastic constants C{sub ij} reveal that Li{sub 4}Sr{sub 3}Ge{sub 2}N{sub 6} is mechanically stable but anisotropic. The elastic anisotropy is further illustrated by the direction-dependent of the linear compressibility and Young’s modulus. Macroscopic elastic parameters, including the bulk and shear moduli, the Young’s modulus, the Poisson ratio, the velocities of elastic waves and the Debye temperature are numerically estimated. The pressure and temperature dependence of the unit cell volume, isothermal bulk modulus, volume expansion coefficient, specific heat and Debye temperature are investigated through the quasiharmonic Debye model. The band structure and the density of states of Li{sub 4}Sr{sub 3}Ge{sub 2}N{sub 6} are analyzed, which reveals the semiconducting character of Li{sub 4}Sr{sub 3}Ge{sub 2}N{sub 6}. The complex dielectric function, refractive index, extinction coefficient, absorption coefficient, reflectivity

  13. Understanding Mn-Based Intercalation Cathodes from Thermodynamics and Kinetics

    Directory of Open Access Journals (Sweden)

    Yin Xie

    2017-07-01

    Full Text Available A series of Mn-based intercalation compounds have been applied as the cathode materials of Li-ion batteries, such as LiMn2O4, LiNi1−x−yCoxMnyO2, etc. With open structures, intercalation compounds exhibit a wide variety of thermodynamic and kinetic properties depending on their crystal structures, host chemistries, etc. Understanding these materials from thermodynamic and kinetic points of view can facilitate the exploration of cathodes with better electrochemical performances. This article reviews the current available thermodynamic and kinetic knowledge on Mn-based intercalation compounds, including the thermal stability, structural intrinsic features, involved redox couples, phase transformations as well as the electrical and ionic conductivity.

  14. Thermodynamic properties of vitamin B2

    International Nuclear Information System (INIS)

    Knyazev, A.V.; Letyanina, I.A.; Plesovskikh, A.S.; Smirnova, N.N.; Knyazeva, S.S.

    2014-01-01

    Graphical abstract: - Highlights: • Temperature dependence of heat capacity of vitamin B 2 has been measured by precision adiabatic vacuum calorimetry. • The thermodynamic functions of the vitamin B 2 have been determined for the range from T → 0 to 322 K. • The energy of combustion of the riboflavin has been measured at 298.15 K. • The enthalpy of combustion Δ c H° and the thermodynamic parameters Δ f H°, Δ f S°, Δ f G° have been calculated. - Abstract: In the present work temperature dependence of heat capacity of vitamin B 2 (riboflavin) has been measured for the first time in the range from 6 to 322 K by precision adiabatic vacuum calorimetry. Based on the experimental data, the thermodynamic functions of the vitamin B 2 , namely, the heat capacity, enthalpy H°(T) − H°(0), entropy S°(T) − S°(0) and Gibbs function G°(T) − H°(0) have been determined for the range from T → 0 to 322 K. The value of the fractal dimension D in the function of multifractal generalization of Debye's theory of the heat capacity of solids was estimated and the character of heterodynamics of structure was detected. In a calorimeter with a static bomb and an isothermal shield, the energy of combustion of the riboflavin has been measured at 298.15 K. The enthalpy of combustion Δ c H° and the thermodynamic parameters Δ f H°, Δ f S°, Δ f G° and of reaction of formation of the riboflavin from simple substances at T = 298.15 K and p = 0.1 MPa have been calculated

  15. Thermodynamic fingerprints of ligand binding to human telomeric G-quadruplexes

    OpenAIRE

    Bon?ina, Matja?; Podlipnik, ?rtomir; Piantanida, Ivo; Eilmes, Julita; Teulade-Fichou, Marie-Paule; Vesnaver, Gorazd; Lah, Jurij

    2015-01-01

    Thermodynamic studies of ligand binding to human telomere (ht) DNA quadruplexes, as a rule, neglect the involvement of various ht-DNA conformations in the binding process. Therefore, the thermodynamic driving forces and the mechanisms of ht-DNA G-quadruplex-ligand recognition remain poorly understood. In this work we characterize thermodynamically and structurally binding of netropsin (Net), dibenzotetraaza[14]annulene derivatives (DP77, DP78), cationic porphyrin (TMPyP4) and two bisquinolini...

  16. The pH-sensitive structure of the C-terminal domain of voltage-gated proton channel and the thermodynamic characteristics of Zn{sup 2+} binding to this domain

    Energy Technology Data Exchange (ETDEWEB)

    Zhao, Qing; Li, Chuanyong; Li, Shu Jie, E-mail: shujieli@nankai.edu.cn

    2015-01-02

    Highlights: • The α-helical content of the C-terminus is decreased with a pH increase. • The thermostability of the C-terminus is decreased with a pH increase. • Zn{sup 2+} binds to His{sup 244} and His{sup 266} residues within the C-terminal domain. • The binding of Zn{sup 2+} to His{sup 244} residue is an endothermic heat reaction. • The binding of Zn{sup 2+} to His{sup 266} residue is an exothermic heat reaction. - Abstract: The voltage-gated proton channel Hv1 is strongly sensitive to Zn{sup 2+}. The H{sup +} conduction is decreased at a high concentration of Zn{sup 2+} and Hv1 channel closing is slowed by the internal application of Zn{sup 2+}. Although the recent studies demonstrated that Zn{sup 2+} interacts with the intracellular C-terminal domain, the binding sites and details of the interaction remain unknown. Here, we studied the pH-dependent structural stability of the intracellular C-terminal domain of human Hv1 and showed that Zn{sup 2+} binds to His{sup 244} and His{sup 266} residues. The thermodynamics signature of Zn{sup 2+} binding to the two sites was investigated by isothermal titration calorimetry. The binding of Zn{sup 2+} to His{sup 244} (mutant H266A) and His{sup 266} (mutant H244A) were an endothermic heat reaction and an exothermic heat reaction, respectively.

  17. Thermodynamic and structural study of two-dimensional phase transitions and orientational order in films of linear molecules with a large quadrupole moment, physi-sorbed on lamellar substrates

    International Nuclear Information System (INIS)

    Terlain, Anne

    1984-01-01

    The 2D (two-dimensional) phase transitions and orientational order in N 2 O, CO 2 , C 2 N 2 and C 2 D 2 films physi-sorbed on the (0001) face of graphite or lamellar halides, were studied experimentally by adsorption isotherm measurements and neutron diffraction. The thermodynamic functions derived from sets of isotherms suggest that crystal monolayers of N 2 O, CO 2 , and C 2 N 2 adsorbed on graphite are orientationally ordered and that the quadrupolar interaction stabilizes the 2D crystal with respect to the 2D liquid. This stabilization leads to an increase in the 2D triple point temperature, T 2t as compared with the 2D critical temperature T 2c . For C 2 N 2 this stabilization is so pronounced that T 2t becomes virtually higher than T 2c , and the phase diagram qualitatively different, having no gas-liquid coexistence domain. From a neutron diffraction experiment we have determined the crystal structure of the C 2 N 2 monolayer. It supports our interpretation of the monolayer phase diagram. In N 2 O, CO 2 , C 2 N 2 films adsorbed on graphite the molecules lie flat on the surface and their orientational order hence differs from that in the bulk crystals resulting in a loss of adsorbate-adsorbate interaction energy. Beyond a given film thickness this loss will not be compensated by the adsorbate-substrate interaction and the film will stop growing. For most of the films studied a partial wetting transition is observed at which the film thickness increases discontinuously with temperature. Although C 2 N 2 and C 2 D 2 monolayers on graphite have comparable adsorption energies, only C 2 D 2 is adsorbed on lamellar halides. This adsorption is possible only because the monolayer has a large entropy due to orientational disorder. For C 2 N 2 , which has a higher moment of inertia, such an orientational disorder cannot exist. (author) [fr

  18. Superionic conductors with the fluorite structure: a) Measurement of the ionic conductivity of SrF2 at high temperatures, b) Study of the thermodynamic properties at CaF2 by numerical simulation

    International Nuclear Information System (INIS)

    Evangelakis, Georges

    1989-01-01

    In this work we present the results of an experimental study concerning the superionic conductivity of SrF 2 and those obtained by an investigation of the thermodynamical properties of CaF 2 using molecular dynamics simulation in the superionic region. The conductivity measurements in SrF 2 have been performed at high temperatures (700-1350 K) and various frequencies (10 Hz-10 MHz). At each temperature a frequency dependence of the conductivity has been detected. The analysis of the results using complex impedance diagrams revealed that this dependence is not an intrinsic property of the material but is related to electrodes effects. The apparent activation energies associated to the different parts of the intrinsic and extrinsic conductivity regions have been determined. Unfortunately no clear conclusion relative to the conduction mechanism can be made there from. Computer simulations by molecular dynamics have been performed in CaF 2 modeled using a rigid ion potential. The diffusion coefficient, the specific heat, structure factors, mean square displacements of both anions and cations, as well as the temperature dependence of these quantities have been calculated. The good agreement found between calculated quantities and experimental results justified us in using the crude approximation of a rigid on potential. A direct computation of the superionic conductivity has been obtained for the first time using non-equilibrium molecular dynamics in the linear response regime. From the independent calculation of the diffusion coefficient and the conductivity, the Havens ratio has been deduced, Hr 0.34, in the superionic region. Its value suggests that the superionic conductivity of CaF 2 is due to a collective and correlated mechanism, a fact which has been confirmed by the MD trajectory analysis. (author) [fr

  19. Ab initio thermodynamic model for magnesium carbonates and hydrates.

    Science.gov (United States)

    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.

  20. Thermodynamic and structural properties of the specific binding between Ag⁺ ion and C:C mismatched base pair in duplex DNA to form C-Ag-C metal-mediated base pair.

    Science.gov (United States)

    Torigoe, Hidetaka; Okamoto, Itaru; Dairaku, Takenori; Tanaka, Yoshiyuki; Ono, Akira; Kozasa, Tetsuo

    2012-11-01

    Metal ion-nucleic acid interactions have attracted considerable interest for their involvement in structure formation and catalytic activity of nucleic acids. Although interactions between metal ion and mismatched base pair duplex are important to understand mechanism of gene mutations related to heavy metal ions, they have not been well-characterized. We recently found that the Ag(+) ion stabilized a C:C mismatched base pair duplex DNA. A C-Ag-C metal-mediated base pair was supposed to be formed by the binding between the Ag(+) ion and the C:C mismatched base pair to stabilize the duplex. Here, we examined specificity, thermodynamics and structure of possible C-Ag-C metal-mediated base pair. UV melting indicated that only the duplex with the C:C mismatched base pair, and not of the duplexes with the perfectly matched and other mismatched base pairs, was specifically stabilized on adding the Ag(+) ion. Isothermal titration calorimetry demonstrated that the Ag(+) ion specifically bound with the C:C base pair at 1:1 molar ratio with a binding constant of 10(6) M(-1), which was significantly larger than those for nonspecific metal ion-DNA interactions. Electrospray ionization mass spectrometry also supported the specific 1:1 binding between the Ag(+) ion and the C:C base pair. Circular dichroism spectroscopy and NMR revealed that the Ag(+) ion may bind with the N3 positions of the C:C base pair without distorting the higher-order structure of the duplex. We conclude that the specific formation of C-Ag-C base pair with large binding affinity would provide a binding mode of metal ion-DNA interactions, similar to that of the previously reported T-Hg-T base pair. The C-Ag-C base pair may be useful not only for understanding of molecular mechanism of gene mutations related to heavy metal ions but also for wide variety of potential applications of metal-mediated base pairs in various fields, such as material, life and environmental sciences. Copyright © 2012 Elsevier