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Sample records for gibbs formation free energy

  1. Gibbs free energy of formation of UPb(s) compound

    International Nuclear Information System (INIS)

    Samui, Pradeep; Agarwal, Renu; Mishra, Ratikanta

    2012-01-01

    Liquid lead and lead-bismuth eutectic (LBE) are being explored as primary candidates for coolants in accelerator driven systems and in advanced nuclear reactors due to their favorable thermo-physical and chemical properties. They are also proposed to be used as spallation neutron source in ADS Reactor Systems. However, corrosion of structural materials (i.e. steel) presents a critical challenge for the use of liquid lead or LBE in advanced nuclear reactors. The interactions of liquid lead or LBE with clad and fuel is of great scientific and technological importance in the development of advanced nuclear reactors. Clad failure/breach can lead to reaction of coolant elements with fuel components. Thus the study of fuel-coolant interaction of U with Pb/Bi is important. The paper deals with the determination of Gibbs free energy of formation of U-rich phase i.e. UPb in Pb-U system, employing Knudsen effusion mass loss technique

  2. Gibbs free energy of formation of liquid lanthanide-bismuth alloys

    International Nuclear Information System (INIS)

    Sheng Jiawei; Yamana, Hajimu; Moriyama, Hirotake

    2001-01-01

    The linear free energy relationship developed by Sverjensky and Molling provides a way to predict Gibbs free energies of liquid Ln-Bi alloys formation from the known thermodynamic properties of aqueous trivalent lanthanides (Ln 3(5(6+ ). The Ln-Bi alloys are divided into two isostructural families named as the LnBi 2 (Ln=La, Ce, Pr, Nd and Pm) and LnBi (Ln=Sm, Eu, Gd, Tb, Dy, Ho, Er, Tm and Yb). The calculated Gibbs free energy values are well agreed with experimental data

  3. Estimates of Gibbs free energies of formation of chlorinated aliphatic compounds

    NARCIS (Netherlands)

    Dolfing, Jan; Janssen, Dick B.

    1994-01-01

    The Gibbs free energy of formation of chlorinated aliphatic compounds was estimated with Mavrovouniotis' group contribution method. The group contribution of chlorine was estimated from the scarce data available on chlorinated aliphatics in the literature, and found to vary somewhat according to the

  4. Gibbs free energy of formation of lanthanum rhodate by quadrupole mass spectrometer

    International Nuclear Information System (INIS)

    Prasad, R.; Banerjee, Aparna; Venugopal, V.

    2003-01-01

    The ternary oxide in the system La-Rh-O is of considerable importance because of its application in catalysis. Phase equilibria in the pseudo-binary system La 2 O 3 -Rh 2 O 3 has been investigated by Shevyakov et. al. Gibbs free energy of LaRhO 3 (s) was determined by Jacob et. al. using a solid state Galvanic cell in the temperature range 890 to 1310 K. No other thermodynamic data were available in the literature. Hence it was decided to determine Gibbs free energy of formation of LaRhO 3 (s) by an independent technique, viz. quadrupole mass spectrometer (QMS) coupled with a Knudsen effusion cell and the results are presented

  5. Gibbs Free Energy of Formation for Selected Platinum Group Minerals (PGM

    Directory of Open Access Journals (Sweden)

    Spiros Olivotos

    2016-01-01

    Full Text Available Thermodynamic data for platinum group (Os, Ir, Ru, Rh, Pd and Pt minerals are very limited. The present study is focused on the calculation of the Gibbs free energy of formation (ΔfG° for selected PGM occurring in layered intrusions and ophiolite complexes worldwide, applying available experimental data on their constituent elements at their standard state (ΔG = G(species − ΔG(elements, using the computer program HSC Chemistry software 6.0. The evaluation of the accuracy of the calculation method was made by the calculation of (ΔGf of rhodium sulfide phases. The calculated values were found to be ingood agreement with those measured in the binary system (Rh + S as a function of temperature by previous authors (Jacob and Gupta (2014. The calculated Gibbs free energy (ΔfG° followed the order RuS2 < (Ir,OsS2 < (Pt, PdS < (Pd, PtTe2, increasing from compatible to incompatible noble metals and from sulfides to tellurides.

  6. Standard molar Gibbs free energy of formation of URh3(s)

    International Nuclear Information System (INIS)

    Prasad, Rajendra; Sayi, Y.S.; Radhakrishna, J.; Yadav, C.S.; Shankaran, P.S.; Chhapru, G.C.

    1992-01-01

    Equilibrium partial pressures of CO(g) over the system (UO 2 (s) + C(s) + Rh(s) + URh 3 (s)) were measured in the temperature range 1327 - 1438 K. Standard Gibbs molar free energy of formation of URh 3 (Δ f G o m ) in the above temperature range can be expressed as Δ f G o m (URh 3 ,s,T)+-3.0(kJ/mol)= -348.165 + 0.03144 T(K). The second and third law enthalpy of formation, ΔfH o m (URh 3 ,s,298.15 K) are (-318.4 +- 3.0) and (298.3 +- 2.5) kJ/mol respectively. (author). 7 refs., 3 tabs

  7. Use of linear free energy relationship to predict Gibbs free energies of formation of pyrochlore phases (CaMTi2O7)

    International Nuclear Information System (INIS)

    Xu, H.; Wang, Y.

    1999-01-01

    In this letter, a linear free energy relationship is used to predict the Gibbs free energies of formation of crystalline phases of pyrochlore and zirconolite families with stoichiometry of MCaTi 2 O 7 (or, CaMTi 2 O 7 ,) from the known thermodynamic properties of aqueous tetravalent cations (M 4+ ). The linear free energy relationship for tetravalent cations is expressed as ΔG f,M v X 0 =a M v X ΔG n,M 4+ 0 +b M v X +β M v X r M 4+ , where the coefficients a M v X , b M v X , and β M v X characterize a particular structural family of M v X, r M 4+ is the ionic radius of M 4+ cation, ΔG f,M v X 0 is the standard Gibbs free energy of formation of M v X, and ΔG n,M 4+ 0 is the standard non-solvation energy of cation M 4+ . The coefficients for the structural family of zirconolite with the stoichiometry of M 4+ CaTi 2 O 7 are estimated to be: a M v X =0.5717, b M v X =-4284.67 (kJ/mol), and β M v X =27.2 (kJ/mol nm). The coefficients for the structural family of pyrochlore with the stoichiometry of M 4+ CaTi 2 O 7 are estimated to be: a M v X =0.5717, b M v X =-4174.25 (kJ/mol), and β M v X =13.4 (kJ/mol nm). Using the linear free energy relationship, the Gibbs free energies of formation of various zirconolite and pyrochlore phases are calculated. (orig.)

  8. Standard enthalpy, entropy and Gibbs free energy of formation of «A» type carbonate phosphocalcium hydroxyapatites

    International Nuclear Information System (INIS)

    Jebri, Sonia; Khattech, Ismail; Jemal, Mohamed

    2017-01-01

    Highlights: • A-type carbonate hydroxyapatites with 0 ⩽ x ⩽ 1 were prepared and characterized by DRX, IR spectroscopy and CHN analysis. • The heat of solution was measured in 9 wt% HNO 3 using an isoperibol calorimeter. • The standard enthalpy of formation was determined by thermochemical cycle. • Gibbs free energy has been deduced by estimating standard entropy of formation. • Carbonatation increases the stability till x = 0.6 mol. - Abstract: « A » type carbonate phosphocalcium hydroxyapatites having the general formula Ca 10 (PO 4 ) 6 (OH) (2-2x) (CO 3 ) x with 0 ⩽ x ⩽ 1, were prepared by solid gas reaction in the temperature range of 700–1000 °C. The obtained materials were characterized by X-ray diffraction and infrared spectroscopy. The carbonate content has been determined by C–H–N analysis. The heat of solution of these products was measured at T = 298 K in 9 wt% nitric acid solution using an isoperibol calorimeter. A thermochemical cycle was proposed and complementary experiences were performed in order to access to the standard enthalpies of formation of these phosphates. The results were compared to those previously obtained on apatites containing strontium and barium and show a decrease with the carbonate amount introduced in the lattice. This quantity becomes more negative as the ratio of substitution increases. Estimation of the entropy of formation allowed the determination of standard Gibbs free energy of formation of these compounds. The study showed that the substitution of hydroxyl by carbonate ions contributes to the stabilisation of the apatite structure.

  9. The standard Gibbs free energy of formation of lithium manganese oxides at the temperatures of (680, 740 and 800) K

    International Nuclear Information System (INIS)

    Rog, G.; Kucza, W.; Kozlowska-Rog, A.

    2004-01-01

    The standard Gibbs free energy of formation of LiMnO 2 and LiMn 2 O 4 at the temperatures of (680, 740 and 800) K has been determined with the help of the solid-state galvanic cells involving lithium-β-alumina electrolyte. The equilibrium electrical potentials of cathode containing Li x Mn 2 O 4 spinel, in the composition ranges 0≤x≤1 and 1≤x≤2, vs. metallic lithium in the reversible intercalation galvanic cell have been calculated. The existence of two-voltage plateaus which appeared during charging and discharging processes in reversible intercalation of lithium into Li x Mn 2 O 4 spinel, has been discussed

  10. Use of linear free energy relationship to predict Gibbs free energies of formation of zirconolite phases (MZrTi2O7 and MHfTi2O7)

    International Nuclear Information System (INIS)

    Xu, H.

    1999-01-01

    In this letter, the Sverjensky-Molling equation derived from a linear free energy relationship is used to calculate the Gibbs free energies of formation of zirconolite crystalline phases (MZrTi 2 O 7 and MHfTi 2 O 7 ) from the known thermodynamic properties of the corresponding aqueous divalent cations (M 2+ ). Sverjensky-Molling equation is expressed as ΔG 0 f,M v X =a M v X ΔG 0 n,M 2+ +b M v X +β M v X r M 2+ , where the coefficients a M v X , b M v X , and β M v X characterize a particular structural family of M v X, r M 2+ is the ionic radius of M 2+ cation, ΔG f,M v X 0 is the standard Gibbs free energy of formation of M v X, and ΔG 0 n,M 2+ is the standard non-solvation energy of cation M 2+ . This relationship can be used to predict the Gibbs free energies of formation of various fictive phases (such as BaZrTi 2 O 7 , SrZrTi 2 O 7 , PbZrTi 2 O 7 , etc.) that may form solid solution with CaZrTi 2 O 7 in actual Synroc-based nuclear waste forms. Based on obtained linear free energy relationships, it is predicted that large cations (e.g., Ba and Ra) prefer to be in perovskite structure, and small cations (e.g., Ca, Zn, and Cd) prefer to be in zirconolite structure. (orig.)

  11. Inference with minimal Gibbs free energy in information field theory

    International Nuclear Information System (INIS)

    Ensslin, Torsten A.; Weig, Cornelius

    2010-01-01

    Non-linear and non-Gaussian signal inference problems are difficult to tackle. Renormalization techniques permit us to construct good estimators for the posterior signal mean within information field theory (IFT), but the approximations and assumptions made are not very obvious. Here we introduce the simple concept of minimal Gibbs free energy to IFT, and show that previous renormalization results emerge naturally. They can be understood as being the Gaussian approximation to the full posterior probability, which has maximal cross information with it. We derive optimized estimators for three applications, to illustrate the usage of the framework: (i) reconstruction of a log-normal signal from Poissonian data with background counts and point spread function, as it is needed for gamma ray astronomy and for cosmography using photometric galaxy redshifts, (ii) inference of a Gaussian signal with unknown spectrum, and (iii) inference of a Poissonian log-normal signal with unknown spectrum, the combination of (i) and (ii). Finally we explain how Gaussian knowledge states constructed by the minimal Gibbs free energy principle at different temperatures can be combined into a more accurate surrogate of the non-Gaussian posterior.

  12. Chemical Disequilibria and Sources of Gibbs Free Energy Inside Enceladus

    Science.gov (United States)

    Zolotov, M. Y.

    2010-12-01

    Non-photosynthetic organisms use chemical disequilibria in the environment to gain metabolic energy from enzyme catalyzed oxidation-reduction (redox) reactions. The presence of carbon dioxide, ammonia, formaldehyde, methanol, methane and other hydrocarbons in the eruptive plume of Enceladus [1] implies diverse redox disequilibria in the interior. In the history of the moon, redox disequilibria could have been activated through melting of a volatile-rich ice and following water-rock-organic interactions. Previous and/or present aqueous processes are consistent with the detection of NaCl and Na2CO3/NaHCO3-bearing grains emitted from Enceladus [2]. A low K/Na ratio in the grains [2] and a low upper limit for N2 in the plume [3] indicate low temperature (possibly enzymes if organisms were (are) present. The redox conditions in aqueous systems and amounts of available Gibbs free energy should have been affected by the production, consumption and escape of hydrogen. Aqueous oxidation of minerals (Fe-Ni metal, Fe-Ni phosphides, etc.) accreted on Enceladus should have led to H2 production, which is consistent with H2 detection in the plume [1]. Numerical evaluations based on concentrations of plume gases [1] reveal sufficient energy sources available to support metabolically diverse life at a wide range of activities (a) of dissolved H2 (log aH2 from 0 to -10). Formaldehyde, carbon dioxide [c.f. 4], HCN (if it is present), methanol, acetylene and other hydrocarbons have the potential to react with H2 to form methane. Aqueous hydrogenations of acetylene, HCN and formaldehyde to produce methanol are energetically favorable as well. Both favorable hydrogenation and hydration of HCN lead to formation of ammonia. Condensed organic species could also participate in redox reactions. Methane and ammonia are the final products of these putative redox transformations. Sulfates may have not formed in cold and/or short-term aqueous environments with a limited H2 escape. In contrast to

  13. Determination of Gibbs energies of formation in aqueous solution using chemical engineering tools.

    Science.gov (United States)

    Toure, Oumar; Dussap, Claude-Gilles

    2016-08-01

    Standard Gibbs energies of formation are of primary importance in the field of biothermodynamics. In the absence of any directly measured values, thermodynamic calculations are required to determine the missing data. For several biochemical species, this study shows that the knowledge of the standard Gibbs energy of formation of the pure compounds (in the gaseous, solid or liquid states) enables to determine the corresponding standard Gibbs energies of formation in aqueous solutions. To do so, using chemical engineering tools (thermodynamic tables and a model enabling to predict activity coefficients, solvation Gibbs energies and pKa data), it becomes possible to determine the partial chemical potential of neutral and charged components in real metabolic conditions, even in concentrated mixtures. Copyright © 2016 Elsevier Ltd. All rights reserved.

  14. Determination of standard Gibbs free energy of formation for Ca2P2O7 and Ca(PO3)2 from solid-state EMF measurements using yttria stabilised zirconia as solid electrolyte

    International Nuclear Information System (INIS)

    Sandstroem, Malin Hannah; Bostroem, Dan; Rosen, Erik

    2006-01-01

    The equilibrium reactions: 3Ca 2 P 2 O 7 (s)+6Ni(s)-bar 2Ca 3 (PO 4 ) 2 (s)+2Ni 3 P(s)+52O 2 (g) and 2Ca(PO 3 ) 2 (s)+6Ni(s)-bar Ca 2 P 2 O 7 (s)+2Ni 3 P(s)+52O 2 (g) were studied in the temperature range 890K to 1140K. The oxygen equilibrium pressures were determined using galvanic cells incorporating yttria stabilized zirconia as solid electrolyte. From the measured data and using the literature values of standard Gibbs free energy of formation for Ca 3 (PO 4 ) 2 and Ni 3 P, the following relationship of the standard Gibbs free energy of formation for Ca 2 P 2 O 7 and Ca(PO 3 ) 2 were calculated:Δ f G o (Ca 2 P 2 O 7 )+/-11/(kJ.mol -1 )=-3475.9+1.5441(T/K)-0.1051(T/K).ln(T/K)andΔ f G o (Ca(PO 3 ) 2 )+/-12/(kJ.mol -1 )=-3334.8+6.1561(T/K)-0.6950(T/K).ln(T/K)

  15. Specification and comparative calculation of enthalpies and Gibbs formation energies of anhydrous lanthanide nitrates

    International Nuclear Information System (INIS)

    Del' Pino, Kh.; Chukurov, P.M.; Drakin, S.I.

    1980-01-01

    Analyzed are the results of experimental depermination of formation enthalpies of waterless nitrates of lanthane cerium, praseodymium, neodymium and samarium. Using method of comparative calculation computed are enthalpies of formation of waterless lanthanide and yttrium nitrates. Calculated values of enthalpies and Gibbs energies of waterless lanthanide nitrate formation are tabulated

  16. Experimental Determination of Third Derivative of the Gibbs Free Energy, G II

    DEFF Research Database (Denmark)

    Koga, Yoshikata; Westh, Peter; Inaba, Akira

    2010-01-01

    We have been evaluating third derivative quantities of the Gibbs free energy, G, by graphically differentiating the second derivatives that are accessible experimentally, and demonstrated their power in elucidating the mixing schemes in aqueous solutions. Here we determine directly one of the third...

  17. Determination of standard molar Gibbs energy of formation of Sm6UO12(s)

    International Nuclear Information System (INIS)

    Sahu, Manjulata; Dash, Smruti

    2015-01-01

    The standard molar Gibbs energies of formation of Sm 6 UO 12 (s) have been measured using an oxygen concentration cell with yttria stabilized zirconia as solid electrolyte. Δ f G o m (T) for Sm 6 UO 12 (s) has been calculated using the measured and required thermodynamic data from the literature. The calculated Gibbs energy expression in the temperature range 899 to 1127 K can be given as: Δ f G o m (Nd 6 UO 12 , s,T)/(±2.3) kJ∙ mol -1 = -6681 +1.099 (T/K) (899-1127 K)(T/K). (author)

  18. The thermodynamic properties of the upper continental crust: Exergy, Gibbs free energy and enthalpy

    International Nuclear Information System (INIS)

    Valero, Alicia; Valero, Antonio; Vieillard, Philippe

    2012-01-01

    This paper shows a comprehensive database of the thermodynamic properties of the most abundant minerals of the upper continental crust. For those substances whose thermodynamic properties are not listed in the literature, their enthalpy and Gibbs free energy are calculated with 11 different estimation methods described in this study, with associated errors of up to 10% with respect to values published in the literature. Thanks to this procedure we have been able to make a first estimation of the enthalpy, Gibbs free energy and exergy of the bulk upper continental crust and of each of the nearly 300 most abundant minerals contained in it. Finally, the chemical exergy of the continental crust is compared to the exergy of the concentrated mineral resources. The numbers obtained indicate the huge chemical exergy wealth of the crust: 6 × 10 6 Gtoe. However, this study shows that approximately only 0.01% of that amount can be effectively used by man.

  19. Direct measurements of the Gibbs free energy of OH using a CW tunable laser

    Science.gov (United States)

    Killinger, D. K.; Wang, C. C.

    1979-01-01

    The paper describes an absorption measurement for determining the Gibbs free energy of OH generated in a mixture of water and oxygen vapor. These measurements afford a direct verification of the accuracy of thermochemical data of H2O at high temperatures and pressures. The results indicate that values for the heat capacity of H2O obtained through numerical computations are correct within an experimental uncertainty of 0.15 cal/mole K.

  20. Standard Gibbs free energies for transfer of actinyl ions at the aqueous/organic solution interface

    International Nuclear Information System (INIS)

    Kitatsuji, Yoshihiro; Okugaki, Tomohiko; Kasuno, Megumi; Kubota, Hiroki; Maeda, Kohji; Kimura, Takaumi; Yoshida, Zenko; Kihara, Sorin

    2011-01-01

    Research highlights: → Standard Gibbs free energies for ion-transfer of tri- to hexavalent actinide ions. → Determination is based on distribution method combined with ion-transfer voltammetry. → Organic solvents examined are nitrobenzene, DCE, benzonitrile, acetophenone and NPOE. → Gibbs free energies of U(VI), Np(VI) and Pu(VI) are similar to each other. → Gibbs free energies of Np(V) is very large, comparing with ordinary monovalent cations. - Abstract: Standard Gibbs free energies for transfer (ΔG tr 0 ) of actinyl ions (AnO 2 z+ ; z = 2 or 1; An: U, Np, or Pu) between an aqueous solution and an organic solution were determined based on distribution method combined with voltammetry for ion transfer at the interface of two immiscible electrolyte solutions. The organic solutions examined were nitrobenzene, 1,2-dichloroethane, benzonitrile, acetophenone, and 2-nitrophenyl octyl ether. Irrespective of the type of organic solutions, ΔG tr 0 of UO 2 2+ ,NpO 2 2+ , and PuO 2 2+ were nearly equal to each other and slightly larger than that of Mg 2+ . The ΔG tr 0 of NpO 2 + was extraordinary large compared with those of ordinary monovalent cations. The dependence of ΔG tr 0 of AnO 2 z+ on the type of organic solutions was similar to that of H + or Mg 2+ . The ΔG tr 0 of An 3+ and An 4+ were also discussed briefly.

  1. Prediction of Gibbs energies of formation and stability constants of some secondary uranium minerals containing the uranyl group

    International Nuclear Information System (INIS)

    Genderen, A.C.G. van; Weijden, C.H. van der

    1984-01-01

    For a group of minerals containing a common anion there exists a linear relationship between two parameters called ΔO and ΔF.ΔO is defined as the difference between the Gibbs energy of formation of a solid oxide and the Gibbs energy of formation of its aqueous cation, while ΔF is defined as the Gibbs energy of reaction of the formation of a mineral from the constituting oxide(s) and the acid. Using the Gibbs energies of formation of a number of known minerals the corresponding ΔO's and ΔF's were calculated and with the resulting regression equation it is possible to predict values for the Gibbs energies of formation of other minerals containing the same anion. This was done for 29 minerals containing the uranyl-ion together with phosphate, vanadate, arsenate or carbonate. (orig.)

  2. Size and shape dependent Gibbs free energy and phase stability of titanium and zirconium nanoparticles

    International Nuclear Information System (INIS)

    Xiong Shiyun; Qi Weihong; Huang Baiyun; Wang Mingpu; Li Yejun

    2010-01-01

    The Debye model of Helmholtz free energy for bulk material is generalized to Gibbs free energy (GFE) model for nanomaterial, while a shape factor is introduced to characterize the shape effect on GFE. The structural transitions of Ti and Zr nanoparticles are predicted based on GFE. It is further found that GFE decreases with the shape factor and increases with decreasing of the particle size. The critical size of structural transformation for nanoparticles goes up as temperature increases in the absence of change in shape factor. For specified temperature, the critical size climbs up with the increase of shape factor. The present predictions agree well with experiment values.

  3. The Role of Shearing Energy and Interfacial Gibbs Free Energy in the Emulsification Mechanism of Waxy Crude Oil

    Directory of Open Access Journals (Sweden)

    Zhihua Wang

    2017-05-01

    Full Text Available Crude oil is generally produced with water, and the water cut produced by oil wells is increasingly common over their lifetime, so it is inevitable to create emulsions during oil production. However, the formation of emulsions presents a costly problem in surface process particularly, both in terms of transportation energy consumption and separation efficiency. To deal with the production and operational problems which are related to crude oil emulsions, especially to ensure the separation and transportation of crude oil-water systems, it is necessary to better understand the emulsification mechanism of crude oil under different conditions from the aspects of bulk and interfacial properties. The concept of shearing energy was introduced in this study to reveal the driving force for emulsification. The relationship between shearing stress in the flow field and interfacial tension (IFT was established, and the correlation between shearing energy and interfacial Gibbs free energy was developed. The potential of the developed correlation model was validated using the experimental and field data on emulsification behavior. It was also shown how droplet deformation could be predicted from a random deformation degree and orientation angle. The results indicated that shearing energy as the energy produced by shearing stress working in the flow field is the driving force activating the emulsification behavior. The deformation degree and orientation angle of dispersed phase droplet are associated with the interfacial properties, rheological properties and the experienced turbulence degree. The correlation between shearing stress and IFT can be quantified if droplet deformation degree vs. droplet orientation angle data is available. When the water cut is close to the inversion point of waxy crude oil emulsion, the interfacial Gibbs free energy change decreased and the shearing energy increased. This feature is also presented in the special regions where

  4. Extrapolation procedures for calculating high-temperature gibbs free energies of aqueous electrolytes

    International Nuclear Information System (INIS)

    Tremaine, P.R.

    1979-01-01

    Methods for calculating high-temprature Gibbs free energies of mononuclear cations and anions from room-temperature data are reviewed. Emphasis is given to species required for oxide solubility calculations relevant to mass transport situations in the nuclear industry. Free energies predicted by each method are compared to selected values calculated from recently reported solubility studies and other literature data. Values for monatomic ions estimated using the assumption anti C 0 p(T) = anti C 0 p(298) agree best with experiment to 423 K. From 423 K to 523 K, free energies from an electrostatic model for ion hydration are more accurate. Extrapolations for hydrolyzed species are limited by a lack of room-temperature entropy data and expressions for estimating these entropies are discussed. (orig.) [de

  5. Solid oxide galvanic cell for determination of Gibbs energy of formation of Tb6UO12(s)

    International Nuclear Information System (INIS)

    Sahu, Manjulata; Dash, Smruti

    2013-01-01

    Citrate-nitrate combustion method was used to synthesise Tb 6 UO 12 (s). Gibbs energy of formation of Tb 6 UO 12 (s) was measured using solid oxide galvanic cell in the temperature range 957-1175 K. (author)

  6. The Gibbs free energy of homogeneous nucleation: From atomistic nuclei to the planar limit.

    Science.gov (United States)

    Cheng, Bingqing; Tribello, Gareth A; Ceriotti, Michele

    2017-09-14

    In this paper we discuss how the information contained in atomistic simulations of homogeneous nucleation should be used when fitting the parameters in macroscopic nucleation models. We show how the number of solid and liquid atoms in such simulations can be determined unambiguously by using a Gibbs dividing surface and how the free energy as a function of the number of solid atoms in the nucleus can thus be extracted. We then show that the parameters (the chemical potential, the interfacial free energy, and a Tolman correction) of a model based on classical nucleation theory can be fitted using the information contained in these free-energy profiles but that the parameters in such models are highly correlated. This correlation is unfortunate as it ensures that small errors in the computed free energy surface can give rise to large errors in the extrapolated properties of the fitted model. To resolve this problem we thus propose a method for fitting macroscopic nucleation models that uses simulations of planar interfaces and simulations of three-dimensional nuclei in tandem. We show that when the chemical potentials and the interface energy are pinned to their planar-interface values, more precise estimates for the Tolman length are obtained. Extrapolating the free energy profile obtained from small simulation boxes to larger nuclei is thus more reliable.

  7. Reduction efficiency prediction of CENIBRA's recovery boiler by direct minimization of gibbs free energy

    Directory of Open Access Journals (Sweden)

    W. L. Silva

    2008-09-01

    Full Text Available The reduction efficiency is an important variable during the black liquor burning process in the Kraft recovery boiler. This variable value is obtained by slow experimental routines and the delay of this measure disturbs the pulp and paper industry customary control. This paper describes an optimization approach for the reduction efficiency determination in the furnace bottom of the recovery boiler based on the minimization of the Gibbs free energy. The industrial data used in this study were directly obtained from CENIBRA's data acquisition system. The resulting approach is able to predict the steady state behavior of the chemical composition of the furnace recovery boiler, - especially the reduction efficiency when different operational conditions are used. This result confirms the potential of this approach in the analysis of the daily operation of the recovery boiler.

  8. Gibbs Free-Energy Gradient along the Path of Glucose Transport through Human Glucose Transporter 3.

    Science.gov (United States)

    Liang, Huiyun; Bourdon, Allen K; Chen, Liao Y; Phelix, Clyde F; Perry, George

    2018-06-11

    Fourteen glucose transporters (GLUTs) play essential roles in human physiology by facilitating glucose diffusion across the cell membrane. Due to its central role in the energy metabolism of the central nervous system, GLUT3 has been thoroughly investigated. However, the Gibbs free-energy gradient (what drives the facilitated diffusion of glucose) has not been mapped out along the transport path. Some fundamental questions remain. Here we present a molecular dynamics study of GLUT3 embedded in a lipid bilayer to quantify the free-energy profile along the entire transport path of attracting a β-d-glucose from the interstitium to the inside of GLUT3 and, from there, releasing it to the cytoplasm by Arrhenius thermal activation. From the free-energy profile, we elucidate the unique Michaelis-Menten characteristics of GLUT3, low K M and high V MAX , specifically suitable for neurons' high and constant demand of energy from their low-glucose environments. We compute GLUT3's binding free energy for β-d-glucose to be -4.6 kcal/mol in agreement with the experimental value of -4.4 kcal/mol ( K M = 1.4 mM). We also compute the hydration energy of β-d-glucose, -18.0 kcal/mol vs the experimental data, -17.8 kcal/mol. In this, we establish a dynamics-based connection from GLUT3's crystal structure to its cellular thermodynamics with quantitative accuracy. We predict equal Arrhenius barriers for glucose uptake and efflux through GLUT3 to be tested in future experiments.

  9. A simple approach to the solvent reorganisation Gibbs free energy in electron transfer reactions of redox metalloproteins

    DEFF Research Database (Denmark)

    Ulstrup, Jens

    1999-01-01

    We discuss a simple model for the environmental reorganisation Gibbs free energy, E-r, in electron transfer between a metalloprotein and a small reaction partner. The protein is represented as a dielectric globule with low dielectric constant, the metal centres as conducting spheres, all embedded...

  10. Standard Gibbs free energies of reactions of ozone with free radicals in aqueous solution: quantum-chemical calculations.

    Science.gov (United States)

    Naumov, Sergej; von Sonntag, Clemens

    2011-11-01

    Free radicals are common intermediates in the chemistry of ozone in aqueous solution. Their reactions with ozone have been probed by calculating the standard Gibbs free energies of such reactions using density functional theory (Jaguar 7.6 program). O(2) reacts fast and irreversibly only with simple carbon-centered radicals. In contrast, ozone also reacts irreversibly with conjugated carbon-centered radicals such as bisallylic (hydroxycylohexadienyl) radicals, with conjugated carbon/oxygen-centered radicals such as phenoxyl radicals, and even with nitrogen- oxygen-, sulfur-, and halogen-centered radicals. In these reactions, further ozone-reactive radicals are generated. Chain reactions may destroy ozone without giving rise to products other than O(2). This may be of importance when ozonation is used in pollution control, and reactions of free radicals with ozone have to be taken into account in modeling such processes.

  11. The Concentration Dependence of the (Delta)s Term in the Gibbs Free Energy Function: Application to Reversible Reactions in Biochemistry

    Science.gov (United States)

    Gary, Ronald K.

    2004-01-01

    The concentration dependence of (delta)S term in the Gibbs free energy function is described in relation to its application to reversible reactions in biochemistry. An intuitive and non-mathematical argument for the concentration dependence of the (delta)S term in the Gibbs free energy equation is derived and the applicability of the equation to…

  12. Comment on "Inference with minimal Gibbs free energy in information field theory".

    Science.gov (United States)

    Iatsenko, D; Stefanovska, A; McClintock, P V E

    2012-03-01

    Enßlin and Weig [Phys. Rev. E 82, 051112 (2010)] have introduced a "minimum Gibbs free energy" (MGFE) approach for estimation of the mean signal and signal uncertainty in Bayesian inference problems: it aims to combine the maximum a posteriori (MAP) and maximum entropy (ME) principles. We point out, however, that there are some important questions to be clarified before the new approach can be considered fully justified, and therefore able to be used with confidence. In particular, after obtaining a Gaussian approximation to the posterior in terms of the MGFE at some temperature T, this approximation should always be raised to the power of T to yield a reliable estimate. In addition, we show explicitly that MGFE indeed incorporates the MAP principle, as well as the MDI (minimum discrimination information) approach, but not the well-known ME principle of Jaynes [E.T. Jaynes, Phys. Rev. 106, 620 (1957)]. We also illuminate some related issues and resolve apparent discrepancies. Finally, we investigate the performance of MGFE estimation for different values of T, and we discuss the advantages and shortcomings of the approach.

  13. Oxygen concentration cell for the measurements of the standard molar Gibbs energy of formation of Nd6UO12(s)

    International Nuclear Information System (INIS)

    Sahu, Manjulata; Dash, Smruti

    2011-01-01

    The standard molar Gibbs energies of formation of Nd 6 UO 12 (s) have been measured using an oxygen concentration cell with yttria stabilized zirconia as solid electrolyte. Δ f G m o (T) for Nd 6 UO 12 (s) has been calculated using the measured and required thermodynamic data from the literature. The calculated Gibbs energy expression can be given as: Δ f G m o (Nd 6 UO 12 , s,T)/(± 2.3) kJmol -1 = -6660.1+1.0898 (T/K). (author)

  14. Gibbs Sampler-Based λ-Dynamics and Rao-Blackwell Estimator for Alchemical Free Energy Calculation.

    Science.gov (United States)

    Ding, Xinqiang; Vilseck, Jonah Z; Hayes, Ryan L; Brooks, Charles L

    2017-06-13

    λ-dynamics is a generalized ensemble method for alchemical free energy calculations. In traditional λ-dynamics, the alchemical switch variable λ is treated as a continuous variable ranging from 0 to 1 and an empirical estimator is utilized to approximate the free energy. In the present article, we describe an alternative formulation of λ-dynamics that utilizes the Gibbs sampler framework, which we call Gibbs sampler-based λ-dynamics (GSLD). GSLD, like traditional λ-dynamics, can be readily extended to calculate free energy differences between multiple ligands in one simulation. We also introduce a new free energy estimator, the Rao-Blackwell estimator (RBE), for use in conjunction with GSLD. Compared with the current empirical estimator, the advantage of RBE is that RBE is an unbiased estimator and its variance is usually smaller than the current empirical estimator. We also show that the multistate Bennett acceptance ratio equation or the unbinned weighted histogram analysis method equation can be derived using the RBE. We illustrate the use and performance of this new free energy computational framework by application to a simple harmonic system as well as relevant calculations of small molecule relative free energies of solvation and binding to a protein receptor. Our findings demonstrate consistent and improved performance compared with conventional alchemical free energy methods.

  15. The thermodynamic approach to boron chemical vapour deposition based on a computer minimization of the total Gibbs free energy

    International Nuclear Information System (INIS)

    Naslain, R.; Thebault, J.; Hagenmuller, P.; Bernard, C.

    1979-01-01

    A thermodynamic approach based on the minimization of the total Gibbs free energy of the system is used to study the chemical vapour deposition (CVD) of boron from BCl 3 -H 2 or BBr 3 -H 2 mixtures on various types of substrates (at 1000 < T< 1900 K and 1 atm). In this approach it is assumed that states close to equilibrium are reached in the boron CVD apparatus. (Auth.)

  16. Development of Bi-phase sodium-oxygen-hydrogen chemical equilibrium calculation program (BISHOP) using Gibbs free energy minimization method

    International Nuclear Information System (INIS)

    Okano, Yasushi

    1999-08-01

    In order to analyze the reaction heat and compounds due to sodium combustion, the multiphase chemical equilibrium calculation program for chemical reaction among sodium, oxygen and hydrogen is developed in this study. The developed numerical program is named BISHOP; which denotes Bi-Phase, Sodium - Oxygen - Hydrogen, Chemical Equilibrium Calculation Program'. Gibbs free energy minimization method is used because of the special merits that easily add and change chemical species, and generally deal many thermochemical reaction systems in addition to constant temperature and pressure one. Three new methods are developed for solving multi-phase sodium reaction system in this study. One is to construct equation system by simplifying phase, and the other is to expand the Gibbs free energy minimization method into multi-phase system, and the last is to establish the effective searching method for the minimum value. Chemical compounds by the combustion of sodium in the air are calculated using BISHOP. The Calculated temperature and moisture conditions where sodium-oxide and hydroxide are formed qualitatively agree with the experiments. Deformation of sodium hydride is calculated by the program. The estimated result of the relationship between the deformation temperature and pressure closely agree with the well known experimental equation of Roy and Rodgers. It is concluded that BISHOP can be used for evaluated the combustion and deformation behaviors of sodium and its compounds. Hydrogen formation condition of the dump-tank room at the sodium leak event of FBR is quantitatively evaluated by BISHOP. It can be concluded that to keep the temperature of dump-tank room lower is effective method to suppress the formation of hydrogen. In case of choosing the lower inflammability limit of 4.1 mol% as the hydrogen concentration criterion, formation reaction of sodium hydride from sodium and hydrogen is facilitated below the room temperature of 800 K, and concentration of hydrogen

  17. Size Fluctuations of Near Critical Nuclei and Gibbs Free Energy for Nucleation of BDA on Cu(001)

    Science.gov (United States)

    Schwarz, Daniel; van Gastel, Raoul; Zandvliet, Harold J. W.; Poelsema, Bene

    2012-07-01

    We present a low-energy electron microscopy study of nucleation and growth of BDA on Cu(001) at low supersaturation. At sufficiently high coverage, a dilute BDA phase coexists with c(8×8) crystallites. The real-time microscopic information allows a direct visualization of near-critical nuclei, determination of the supersaturation and the line tension of the crystallites, and, thus, derivation of the Gibbs free energy for nucleation. The resulting critical nucleus size nicely agrees with the measured value. Nuclei up to 4-6 times larger still decay with finite probability, urging reconsideration of the classic perception of a critical nucleus.

  18. Gibbs free-energy difference between the glass and crystalline phases of a Ni-Zr alloy

    Science.gov (United States)

    Ohsaka, K.; Trinh, E. H.; Holzer, J. C.; Johnson, W. L.

    1993-01-01

    The heats of eutectic melting and devitrification, and the specific heats of the crystalline, glass, and liquid phases have been measured for a Ni24Zr76 alloy. The data are used to calculate the Gibbs free-energy difference, Delta G(AC), between the real glass and the crystal on an assumption that the liquid-glass transition is second order. The result shows that Delta G(AC) continuously increases as the temperature decreases in contrast to the ideal glass case where Delta G(AC) is assumed to be independent of temperature.

  19. Gibbs free energy difference between the undercooled liquid and the beta phase of a Ti-Cr alloy

    Science.gov (United States)

    Ohsaka, K.; Trinh, E. H.; Holzer, J. C.; Johnson, W. L.

    1992-01-01

    The heat of fusion and the specific heats of the solid and liquid have been experimentally determined for a Ti60Cr40 alloy. The data are used to evaluate the Gibbs free energy difference, delta-G, between the liquid and the beta phase as a function of temperature to verify a reported spontaneous vitrification (SV) of the beta phase in Ti-Cr alloys. The results show that SV of an undistorted beta phase in the Ti60Cr40 alloy at 873 K is not feasible because delta-G is positive at the temperature. However, delta-G may become negative with additional excess free energy to the beta phase in the form of defects.

  20. Determination of standard Ghibbs free energy of formation of NiW sub 2 B sub 2 and activity of Ni-W binary system by EMF measurement. Kidenryokuho ni yoru NiW sub 2 B sub 2 no hyojun seisei Gibbs jiyu energy to Ni-W 2 seibunkei no katsuryo no sokutei

    Energy Technology Data Exchange (ETDEWEB)

    Kayama, Koichiro; Hashimoto, Yasuhiko; Suzuki, Kenji; Matsuo, Hideki (Himeji Inst. of Tech., Hyogo (Japan) Fukushin Electric Co., Ltd., Hyogo (Japan))

    1989-12-25

    NiW {sub 2} B {sub 2} (M phase), existing in trinary Ni-W-B system, was measured in standard Gibbs free energy (GF) of formation in the temperature range from 1273K to 1423K by an electromotive force method (EMF) with use of solid oxide electrolyte. First, oxide phase in equilibrium with three-phase M-W-Ni solid solution region was confirmed to be B {sub 2} O {sub 3}. Binary Ni-W system solid solution in equilibrium with M phase and W phase is constant in composition with Ni-16.4mo1%W in the above temperature range. WO {sub 2} and WO {sub 2.72} were actually measured in GF. As Ni-W solid solution is in equilibrium with WO {sub 2} and WO {sub 2.72}, binary Ni-W system was measured in activity by the EMF, and Ni-16.4mo1%W solid solution was calculated in GF of mixing by use of the above measured GF of WO {sub 2} and WO {sub 2.72}. Finally with use of sample in M-W-Ni solid solution region, M phase was calculated in GF by the EMF. The result of those calculations were expressed with experimental formulas. 19 refs., 10 figs., 3 tabs.

  1. Strand Analysis, a free online program for the computational identification of the best RNA interference (RNAi targets based on Gibbs free energy

    Directory of Open Access Journals (Sweden)

    Tiago Campos Pereira

    2007-01-01

    Full Text Available The RNA interference (RNAi technique is a recent technology that uses double-stranded RNA molecules to promote potent and specific gene silencing. The application of this technique to molecular biology has increased considerably, from gene function identification to disease treatment. However, not all small interfering RNAs (siRNAs are equally efficient, making target selection an essential procedure. Here we present Strand Analysis (SA, a free online software tool able to identify and classify the best RNAi targets based on Gibbs free energy (deltaG. Furthermore, particular features of the software, such as the free energy landscape and deltaG gradient, may be used to shed light on RNA-induced silencing complex (RISC activity and RNAi mechanisms, which makes the SA software a distinct and innovative tool.

  2. THE PREDICTION OF pH BY GIBBS FREE ENERGY MINIMIZATION IN THE SUMP SOLUTION UNDER LOCA CONDITION OF PWR

    Directory of Open Access Journals (Sweden)

    HYOUNGJU YOON

    2013-02-01

    Full Text Available It is required that the pH of the sump solution should be above 7.0 to retain iodine in a liquid phase and be within the material compatibility constraints under LOCA condition of PWR. The pH of the sump solution can be determined by conventional chemical equilibrium constants or by the minimization of Gibbs free energy. The latter method developed as a computer code called SOLGASMIX-PV is more convenient than the former since various chemical components can be easily treated under LOCA conditions. In this study, SOLGASMIX-PV code was modified to accommodate the acidic and basic materials produced by radiolysis reactions and to calculate the pH of the sump solution. When the computed pH was compared with measured by the ORNL experiment to verify the reliability of the modified code, the error between two values was within 0.3 pH. Finally, two cases of calculation were performed for the SKN 3&4 and UCN 1&2. As results, pH of the sump solution for the SKN 3&4 was between 7.02 and 7.45, and for the UCN 1&2 plant between 8.07 and 9.41. Furthermore, it was found that the radiolysis reactions have insignificant effects on pH because the relative concentrations of HCl, HNO3, and Cs are very low.

  3. Gibbs free energy of reactions involving SiC, Si3N4, H2, and H2O as a function of temperature and pressure

    Science.gov (United States)

    Isham, M. A.

    1992-01-01

    Silicon carbide and silicon nitride are considered for application as structural materials and coating in advanced propulsion systems including nuclear thermal. Three-dimensional Gibbs free energy were constructed for reactions involving these materials in H2 and H2/H2O. Free energy plots are functions of temperature and pressure. Calculations used the definition of Gibbs free energy where the spontaneity of reactions is calculated as a function of temperature and pressure. Silicon carbide decomposes to Si and CH4 in pure H2 and forms a SiO2 scale in a wet atmosphere. Silicon nitride remains stable under all conditions. There was no apparent difference in reaction thermodynamics between ideal and Van der Waals treatment of gaseous species.

  4. Thermodynamics of Micellar Systems : Comparison of Mass Action and Phase Equilibrium Models for the Calculation of Standard Gibbs Energies of Micelle Formation

    NARCIS (Netherlands)

    Blandamer, Michael J.; Cullis, Paul M.; Soldi, L. Giorgio; Engberts, Jan B.F.N.; Kacperska, Anna; Os, Nico M. van

    1995-01-01

    Micellar colloids are distinguished from other colloids by their association-dissociation equilibrium in solution between monomers, counter-ions and micelles. According to classical thermodynamics, the standard Gibbs energy of formation of micelles at fixed temperature and pressure can be related to

  5. Size fluctuations of near critical and Gibbs free energy for nucleation of BDA on Cu(001)

    NARCIS (Netherlands)

    Schwarz, Daniel; van Gastel, Raoul; Zandvliet, Henricus J.W.; Poelsema, Bene

    2012-01-01

    We present a low-energy electron microscopy study of nucleation and growth of BDA on Cu(001) at low supersaturation. At sufficiently high coverage, a dilute BDA phase coexists with c(8×8) crystallites. The real-time microscopic information allows a direct visualization of near-critical nuclei,

  6. Enzyme Catalysis and the Gibbs Energy

    Science.gov (United States)

    Ault, Addison

    2009-01-01

    Gibbs-energy profiles are often introduced during the first semester of organic chemistry, but are less often presented in connection with enzyme-catalyzed reactions. In this article I show how the Gibbs-energy profile corresponds to the characteristic kinetics of a simple enzyme-catalyzed reaction. (Contains 1 figure and 1 note.)

  7. Gibbs free energy of transfer of a methylene group on {UCON + (sodium or potassium) phosphate salts} aqueous two-phase systems: Hydrophobicity effects

    International Nuclear Information System (INIS)

    Silverio, Sara C.; Rodriguez, Oscar; Teixeira, Jose A.; Macedo, Eugenia A.

    2010-01-01

    The Gibbs free energy of transfer of a suitable hydrophobic probe can be regarded as a measure of the relative hydrophobicity of the different phases. The methylene group (CH 2 ) can be considered hydrophobic, and thus be a suitable probe for hydrophobicity. In this work, the partition coefficients of a series of five dinitrophenylated-amino acids were experimentally determined, at 23 o C, in three different tie-lines of the biphasic systems: (UCON + K 2 HPO 4 ), (UCON + potassium phosphate buffer, pH 7), (UCON + KH 2 PO 4 ), (UCON + Na 2 HPO 4 ), (UCON + sodium phosphate buffer, pH 7), and (UCON + NaH 2 PO 4 ). The Gibbs free energy of transfer of CH 2 units were calculated from the partition coefficients and used to compare the relative hydrophobicity of the equilibrium phases. The largest relative hydrophobicity was found for the ATPS formed by dihydrogen phosphate salts.

  8. Using self-consistent Gibbs free energy surfaces to calculate size distributions of neutral and charged clusters for the sulfuric acid-water binary system

    Science.gov (United States)

    Smith, J. A.; Froyd, K. D.; Toon, O. B.

    2012-12-01

    We construct tables of reaction enthalpies and entropies for the association reactions involving sulfuric acid vapor, water vapor, and the bisulfate ion. These tables are created from experimental measurements and quantum chemical calculations for molecular clusters and a classical thermodynamic model for larger clusters. These initial tables are not thermodynamically consistent. For example, the Gibbs free energy of associating a cluster consisting of one acid molecule and two water molecules depends on the order in which the cluster was assembled: add two waters and then the acid or add an acid and a water and then the second water. We adjust the values within the tables using the method of Lagrange multipliers to minimize the adjustments and produce self-consistent Gibbs free energy surfaces for the neutral clusters and the charged clusters. With the self-consistent Gibbs free energy surfaces, we calculate size distributions of neutral and charged clusters for a variety of atmospheric conditions. Depending on the conditions, nucleation can be dominated by growth along the neutral channel or growth along the ion channel followed by ion-ion recombination.

  9. Gibbs Free Energy of Hydrolytic Water Molecule in Acyl-Enzyme Intermediates of a Serine Protease: A Potential Application for Computer-Aided Discovery of Mechanism-Based Reversible Covalent Inhibitors.

    Science.gov (United States)

    Masuda, Yosuke; Yamaotsu, Noriyuki; Hirono, Shuichi

    2017-01-01

    In order to predict the potencies of mechanism-based reversible covalent inhibitors, the relationships between calculated Gibbs free energy of hydrolytic water molecule in acyl-trypsin intermediates and experimentally measured catalytic rate constants (k cat ) were investigated. After obtaining representative solution structures by molecular dynamics (MD) simulations, hydration thermodynamics analyses using WaterMap™ were conducted. Consequently, we found for the first time that when Gibbs free energy of the hydrolytic water molecule was lower, logarithms of k cat were also lower. The hydrolytic water molecule with favorable Gibbs free energy may hydrolyze acylated serine slowly. Gibbs free energy of hydrolytic water molecule might be a useful descriptor for computer-aided discovery of mechanism-based reversible covalent inhibitors of hydrolytic enzymes.

  10. Standard Gibbs energies of formation and equilibrium constants from ab-initio calculations: Covalent dimerization of NO2 and synthesis of NH3

    International Nuclear Information System (INIS)

    Awasthi, Neha; Ritschel, Thomas; Lipowsky, Reinhard; Knecht, Volker

    2013-01-01

    Highlights: • ΔG and K eq for NO 2 dimerization and NH 3 synthesis calculated via ab-initio methods. • Vis-á-vis experiments, W1 and CCSD(T) are accurate and G3B3 also does quite well. • CBS-APNO most accurate for NH 3 reaction but shows limitations in modeling NO 2 . • Temperature dependence of ΔG and K eq is calculated for the NH 3 reaction. • Good agreement of calculated K eq with experiments and the van’t Hoff approximation. -- Abstract: Standard quantum chemical methods are used for accurate calculation of thermochemical properties such as enthalpies of formation, entropies and Gibbs energies of formation. Equilibrium reactions are widely investigated and experimental measurements often lead to a range of reaction Gibbs energies and equilibrium constants. It is useful to calculate these equilibrium properties from quantum chemical methods in order to address the experimental differences. Furthermore, most standard calculation methods differ in accuracy and feasibility of the system size. Hence, a systematic comparison of equilibrium properties calculated with different numerical algorithms would provide a useful reference. We select two well-known gas phase equilibrium reactions with small molecules: covalent dimer formation of NO 2 (2NO 2 ⇌ N 2 O 4 ) and the synthesis of NH 3 (N 2 + 3 H 2 ⇌ 2NH 3 ). We test four quantum chemical methods denoted by G3B3, CBS-APNO, W1 and CCSD(T) with aug-cc-pVXZ basis sets (X = 2, 3, and 4), to obtain thermochemical data for NO 2 , N 2 O 4 , and NH 3 . The calculated standard formation Gibbs energies Δ f G° are used to calculate standard reaction Gibbs energies Δ r G° and standard equilibrium constants K eq for the two reactions. Standard formation enthalpies Δ f H° are calculated in a more reliable way using high-level methods such as W1 and CCSD(T). Standard entropies S° for the molecules are calculated well within the range of experiments for all methods, however, the values of standard formation

  11. Gibbs energies of formation of zircon (ZrSiO4), thorite (ThSiO4), and phenacite (Be2SiO4)

    International Nuclear Information System (INIS)

    Schuiling, R.D.; Vergouwen, L.; Rijst, H. van der

    1976-01-01

    Zircon, thorite, and phenacite are very refractory compounds which do not yield to solution calorimetry. In In order to obtain approximate Gibbs energies of formation for these minerals, their reactions with a number of silica-undersaturated compounds (silicates or oxides) were studied. Conversely baddeleyite (ZrO 2 ), thorianite (ThO 2 ), and bromellite (BeO) were reacted with the appropriate silicates. As the Gibbs energies of reaction of the undersaturated compounds with SiO 2 are known, the experiments yield the following data: Δ G 298 , 1 /sub bar/ 0 = -459.02 +- 1.04 kcal for zircon, -489.67 +- 1.04 for thorite, and -480.20 +- 1.01 for phenacite

  12. Activity coefficients and excess Gibbs' free energy of some binary mixtures formed by p-cresol at 95.23 kPa

    Energy Technology Data Exchange (ETDEWEB)

    Prasad, T.E. Vittal [Properties Group, Chemical Engineering Laboratory, Indian Institute of Chemical Technology, Hyderabad 500 007 (India); Venkanna, N. [Swamy Ramanandateertha Institute of Science and Technology, Hyderabad 508 004 (India); Kumar, Y. Naveen [Swamy Ramanandateertha Institute of Science and Technology, Hyderabad 508 004 (India); Ashok, K. [Swamy Ramanandateertha Institute of Science and Technology, Hyderabad 508 004 (India); Sirisha, N.M. [Swamy Ramanandateertha Institute of Science and Technology, Hyderabad 508 004 (India); Prasad, D.H.L. [Properties Group, Chemical Engineering Laboratory, Indian Institute of Chemical Technology, Hyderabad 500 007 (India)]. E-mail: dasika@iict.res.in

    2007-07-15

    Bubble point temperatures at 95.23 kPa, over the entire composition range are measured for the binary mixtures formed by p-cresol with 1,2-dichloroethane, 1,1,2,2-tetrachloroethane trichloroethylene, tetrachloroethylene, and o- , m- , and p-xylenes, making use of a Swietoslawski-type ebulliometer. Liquid phase mole fraction (x {sub 1}) versus bubble point temperature (T) measurements are found to be well represented by the Wilson model. The optimum Wilson parameters are used to calculate the vapor phase composition, activity coefficients, and excess Gibbs free energy. The results are discussed.

  13. Gibb's energy and intermolecular free length of 'Borassus Flabellifier' (BF) and Adansonia digitata (AnD) aqueous binary mixture

    International Nuclear Information System (INIS)

    Phadke, Sushil; Shrivastava, Bhakt Darshan; Ujle, S K; Mishra, Ashutosh; Dagaonkar, N

    2014-01-01

    One of the potential driving forces behind a chemical reaction is favourable a new quantity known as the Gibbs free energy (G) of the system, which reflects the balance between these forces. Ultrasonic velocity and absorption measurements in liquids and liquid mixtures find extensive application to study the nature of intermolecular forces. Ultrasonic velocity measurements have been successfully employed to detect weak and strong molecular interactions present in binary and ternary liquid mixtures. After measuring the density and ultrasonic velocity of aqueous solution of 'Borassus Flabellifier' BF and Adansonia digitata And, we calculated Gibb's energy and intermolecular free length. The velocity of ultrasonic waves was measured, using a multi-frequency ultrasonic interferometer with a high degree of accuracy operating Model M-84 by M/s Mittal Enterprises, New Delhi, at a fixed frequency of 2 MHz. Natural sample 'Borassus Flabellifier' BF fruit pulp and Adansonia digitata AnD powder was collected from Dhar, District of MP, India for this study.

  14. Free energy of formation of lanthanum nickelate

    International Nuclear Information System (INIS)

    Sreedharan, O.M.; Chandrasekharaiah, M.S.; Karkhanavala, M.D.

    1976-01-01

    The ΔG 0 /sub f/ of La 2 NiO 4 (s) was determined from the measured emf in the range 1123 to 1373 0 K of the solid oxide electrolyte galvanic cell. The emf data were fitted to a linear equation by the method of least squares. From these data, the standard free-energy change, ΔG 0 , for the reaction NiO(s) + La 2 O 3 (s) = La 2 NiO 4 (s) was calculated. Combining these emf data with the best available free energy of formation data for NiO(s) and La 2 O 3 (s), the following expression for ΔG 0 /sub f/(La 2 NiO 4 (s)) was derived as ΔG 0 /sub f/(La 2 NiO 4 (s)/kJ mole -1 = -2057.0 + 322.8 x 10 -3 T +- 17.30

  15. Illustrating Enzyme Inhibition Using Gibbs Energy Profiles

    Science.gov (United States)

    Bearne, Stephen L.

    2012-01-01

    Gibbs energy profiles have great utility as teaching and learning tools because they present students with a visual representation of the energy changes that occur during enzyme catalysis. Unfortunately, most textbooks divorce discussions of traditional kinetic topics, such as enzyme inhibition, from discussions of these same topics in terms of…

  16. Comparative study of solute trapping and Gibbs free energy changes at the phase interface during alloy solidification under local nonequilibrium conditions

    Energy Technology Data Exchange (ETDEWEB)

    Sobolev, S. L., E-mail: sobolev@icp.ac.ru [Russian Academy of Sciences, Institute of Problems of Chemical Physics (Russian Federation)

    2017-03-15

    An analytical model has been developed to describe the influence of solute trapping during rapid alloy solidification on the components of the Gibbs free energy change at the phase interface with emphasis on the solute drag energy. For relatively low interface velocity V < V{sub D}, where V{sub D} is the characteristic diffusion velocity, all the components, namely mixing part, local nonequilibrium part, and solute drag, significantly depend on solute diffusion and partitioning. When V ≥ V{sub D}, the local nonequilibrium effects lead to a sharp transition to diffusionless solidification. The transition is accompanied by complete solute trapping and vanishing solute drag energy, i.e. partitionless and “dragless” solidification.

  17. Vapour pressure and excess Gibbs free energy of binary mixtures of hydrogen sulphide with ethane, propane, and n-butane at temperature of 182.33K

    International Nuclear Information System (INIS)

    Lobo, L.Q.; Ferreira, A.G.M.; Fonseca, I.M.A.; Senra, A.M.P.

    2006-01-01

    The vapour pressure of binary mixtures of hydrogen sulphide with ethane, propane, and n-butane was measured at T=182.33K covering most of the composition range. The excess Gibbs free energy of these mixtures has been derived from the measurements made. For the equimolar mixtures G m E (x 1 =0.5)=(835.5+/-5.8)J.mol -1 for (H 2 S+C 2 H 6 ) (820.1+/-2.4)J.mol -1 for (H 2 S+C 3 H 8 ), and (818.6+/-0.9)J.mol -1 for (H 2 S+n-C 4 H 10 ). The binary mixtures of H 2 S with ethane and with propane exhibit azeotropes, but that with n-butane does not

  18. Equilibrium modeling of gasification: Gibbs free energy minimization approach and its application to spouted bed and spout-fluid bed gasifiers

    International Nuclear Information System (INIS)

    Jarungthammachote, S.; Dutta, A.

    2008-01-01

    Spouted beds have been found in many applications, one of which is gasification. In this paper, the gasification processes of conventional and modified spouted bed gasifiers were considered. The conventional spouted bed is a central jet spouted bed, while the modified spouted beds are circular split spouted bed and spout-fluid bed. The Gibbs free energy minimization method was used to predict the composition of the producer gas. The major six components, CO, CO 2 , CH 4 , H 2 O, H 2 and N 2 , were determined in the mixture of the producer gas. The results showed that the carbon conversion in the gasification process plays an important role in the model. A modified model was developed by considering the carbon conversion in the constraint equations and in the energy balance calculation. The results from the modified model showed improvements. The higher heating values (HHV) were also calculated and compared with the ones from experiments. The agreements of the calculated and experimental values of HHV, especially in the case of the circular split spouted bed and the spout-fluid bed were observed

  19. Vapor pressures and standard molar enthalpies, entropies, and Gibbs free energies of sublimation of 2,4- and 3,4-dinitrobenzoic acids

    International Nuclear Information System (INIS)

    Vecchio, Stefano; Brunetti, Bruno

    2009-01-01

    The vapor pressures of the solid and liquid 2,4- and 3,4-dinitrobenzoic acids were determined by torsion-effusion and thermogravimetry under both isothermal and non-isothermal conditions, respectively. From the temperature dependence of vapor pressure derived by the experimental torsion-effusion and thermogravimetry data the molar enthalpies of sublimation Δ cr g H m 0 ( ) and vaporization Δ l g H m 0 ( ) were determined, respectively, at the middle of the respective temperature intervals. The melting temperatures and the molar enthalpies of fusion of these compounds were measured by d.s.c. Finally, the results obtained by all the methods proposed were corrected at the reference temperature of 298.15 K using the estimated heat capacity differences between gas and liquid for vaporization experiments and the estimated heat capacity differences between gas and solid for sublimation experiments. Therefore, the averages of the standard (p o = 0.1 MPa) molar enthalpies, entropies and Gibbs free energies of sublimation at 298.15 K, have been derived.

  20. Standard free energy of formation of iron iodide

    Science.gov (United States)

    Khandkar, A.; Tare, V. B.; Wagner, J. B., Jr.

    1983-01-01

    An experiment is reported where silver iodide is used to determine the standard free energy of formation of iron iodide. By using silver iodide as a solid electrolyte, a galvanic cell, Ag/AgI/Fe-FeI2, is formulated. The standard free energy of formation of AgI is known, and hence it is possible to estimate the standard free energy of formation of FeI2 by measuring the open-circuit emf of the above cell as a function of temperature. The free standard energy of formation of FeI2 determined by this method is -38784 + 24.165T cal/mol. It is estimated that the maximum error associated with this method is plus or minus 2500 cal/mol.

  1. Oxidation potentials, Gibbs energies, enthalpies and entropies of actinide ions in aqueous solutions

    International Nuclear Information System (INIS)

    1977-01-01

    The values of the Gibbs energy, enthalpy, and entropy of different actinide ions, thermodynamic characteristics of the processes of hydration of these ions, and the presently known ionization potentials of actinides are given. The enthalpy and entropy components of the oxidation potentials of actinide elements are considered. The curves of the dependence of the Gibbs energy of ion formation on the atomic number of the element and the Frost diagrams are analyzed. The diagram proposed by Frost represents the graphical dependence of the Gibbs energy of hydrated ions on the degree of oxidation of the element. Using the Frost diagram it is easy to establish whether a given ion is stable to disproportioning

  2. First-Year University Chemistry Textbooks' Misrepresentation of Gibbs Energy

    Science.gov (United States)

    Quilez, Juan

    2012-01-01

    This study analyzes the misrepresentation of Gibbs energy by college chemistry textbooks. The article reports the way first-year university chemistry textbooks handle the concepts of spontaneity and equilibrium. Problems with terminology are found; confusion arises in the meaning given to [delta]G, [delta][subscript r]G, [delta]G[degrees], and…

  3. Consistent estimation of Gibbs energy using component contributions.

    Directory of Open Access Journals (Sweden)

    Elad Noor

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

  4. From quantum chemical formation free energies to evaporation rates

    Directory of Open Access Journals (Sweden)

    I. K. Ortega

    2012-01-01

    Full Text Available Atmospheric new particle formation is an important source of atmospheric aerosols. Large efforts have been made during the past few years to identify which molecules are behind this phenomenon, but the actual birth mechanism of the particles is not yet well known. Quantum chemical calculations have proven to be a powerful tool to gain new insights into the very first steps of particle formation. In the present study we use formation free energies calculated by quantum chemical methods to estimate the evaporation rates of species from sulfuric acid clusters containing ammonia or dimethylamine. We have found that dimethylamine forms much more stable clusters with sulphuric acid than ammonia does. On the other hand, the existence of a very deep local minimum for clusters with two sulfuric acid molecules and two dimethylamine molecules hinders their growth to larger clusters. These results indicate that other compounds may be needed to make clusters grow to larger sizes (containing more than three sulfuric acid molecules.

  5. Excess Gibbs Energy for Ternary Lattice Solutions of Nonrandom Mixing

    Energy Technology Data Exchange (ETDEWEB)

    Jung, Hae Young [DukSung Womens University, Seoul (Korea, Republic of)

    2008-12-15

    It is assumed for three components lattice solution that the number of ways of arranging particles randomly on the lattice follows a normal distribution of a linear combination of N{sub 12}, N{sub 23}, N{sub 13} which are the number of the nearest neighbor interactions between different molecules. It is shown by random number simulations that this assumption is reasonable. From this distribution, an approximate equation for the excess Gibbs energy of three components lattice solution is derived. Using this equation, several liquid-vapor equilibria are calculated and compared with the results from other equations.

  6. From slump loss to Gibbs' free energy

    DEFF Research Database (Denmark)

    Jensen, Ole Mejlhede; Diamond, Sidney

    2006-01-01

    In its classical form, the science of construction materials is a descriptive, empirical discipline related to certain types of materials, e.g. the study of the properties of wood, steel, concrete and plastics. This traditional division of the science into the separate study of the different...

  7. The MgO-Al2O3-SiO2 system - Free energy of pyrope and Al2O3-enstatite. [in earth mantle formation

    Science.gov (United States)

    Saxena, S. K.

    1981-01-01

    The model of fictive ideal components is used to determine Gibbs free energies of formation of pyrope and Al2O3-enstatite from the experimental data on coexisting garnet and orthopyroxene and orthopyroxene and spinel in the temperature range 1200-1600 K. It is noted that Al2O3 forms an ideal solution with MgSiO3. These thermochemical data are found to be consistent with the Al2O3 isopleths that could be drawn using most recent experimental data and with the reversed experimental data on the garnet-spinel field boundary.

  8. A Simple Method to Calculate the Temperature Dependence of the Gibbs Energy and Chemical Equilibrium Constants

    Science.gov (United States)

    Vargas, Francisco M.

    2014-01-01

    The temperature dependence of the Gibbs energy and important quantities such as Henry's law constants, activity coefficients, and chemical equilibrium constants is usually calculated by using the Gibbs-Helmholtz equation. Although, this is a well-known approach and traditionally covered as part of any physical chemistry course, the required…

  9. A comparison of various Gibbs energy dissipation correlations for predicting microbial growth yields

    Energy Technology Data Exchange (ETDEWEB)

    Liu, J.-S. [Laboratory of Chemical and Biochemical Engineering, Swiss Federal Institute of Technology, EPFL, CH-1015 Lausanne (Switzerland); Vojinovic, V. [Laboratory of Chemical and Biochemical Engineering, Swiss Federal Institute of Technology, EPFL, CH-1015 Lausanne (Switzerland); Patino, R. [Cinvestav-Merida, Departamento de Fisica Aplicada, Km. 6 carretera antigua a Progreso, AP 73 Cordemex, 97310 Merida, Yucatan (Mexico); Maskow, Th. [UFZ Centre for Environmental Research, Department of Environmental Microbiology, Permoserstrasse 15, D-04318 Leipzig (Germany); Stockar, U. von [Laboratory of Chemical and Biochemical Engineering, Swiss Federal Institute of Technology, EPFL, CH-1015 Lausanne (Switzerland)]. E-mail: urs.vonStockar@epfl.ch

    2007-06-25

    Thermodynamic analysis may be applied in order to predict microbial growth yields roughly, based on an empirical correlation of the Gibbs energy of the overall growth reaction or Gibbs energy dissipation. Due to the well-known trade-off between high biomass yield and high Gibbs energy dissipation necessary for fast growth, an optimal range of Gibbs energy dissipation exists and it can be correlated to physical characteristics of the growth substrates. A database previously available in the literature has been extended significantly in order to test such correlations. An analysis of the relationship between biomass yield and Gibbs energy dissipation reveals that one does not need a very precise estimation of the latter to predict the former roughly. Approximating the Gibbs energy dissipation with a constant universal value of -500 kJ C-mol{sup -1} of dry biomass grown predicts many experimental growth yields nearly as well as a carefully designed, complex correlation available from the literature, even though a number of predictions are grossly out of range. A new correlation for Gibbs energy dissipation is proposed which is just as accurate as the complex literature correlation despite its dramatically simpler structure.

  10. A comparison of various Gibbs energy dissipation correlations for predicting microbial growth yields

    International Nuclear Information System (INIS)

    Liu, J.-S.; Vojinovic, V.; Patino, R.; Maskow, Th.; Stockar, U. von

    2007-01-01

    Thermodynamic analysis may be applied in order to predict microbial growth yields roughly, based on an empirical correlation of the Gibbs energy of the overall growth reaction or Gibbs energy dissipation. Due to the well-known trade-off between high biomass yield and high Gibbs energy dissipation necessary for fast growth, an optimal range of Gibbs energy dissipation exists and it can be correlated to physical characteristics of the growth substrates. A database previously available in the literature has been extended significantly in order to test such correlations. An analysis of the relationship between biomass yield and Gibbs energy dissipation reveals that one does not need a very precise estimation of the latter to predict the former roughly. Approximating the Gibbs energy dissipation with a constant universal value of -500 kJ C-mol -1 of dry biomass grown predicts many experimental growth yields nearly as well as a carefully designed, complex correlation available from the literature, even though a number of predictions are grossly out of range. A new correlation for Gibbs energy dissipation is proposed which is just as accurate as the complex literature correlation despite its dramatically simpler structure

  11. Acquisition of rheological and calorimetric properties of borosilicate glass to determine the free energy of formation

    International Nuclear Information System (INIS)

    Linard, Y.; Advocat, Th.

    2000-01-01

    measure low viscosities at up to 1700 K. The Adam-Gibbs theory of the entropy of relaxation processes allowed the calculation of S conf (T g ) from the various viscosity measurements. The enthalpy of formation for each glass composition was determined from experimental measurements of the enthalpy of dissolution Δ s H(T s ) of a glass sample in a molten salt ( 2 PbO.B 2 O 3 ) at 970 K using a Tian-Calvet calorimeter. Figure 3 shows some of the results obtained with simple glass compositions. The heat capacity C p , measured within 0.7% uncertainty, gradually increased with temperature, with a sharp rise at the glass transition point T g , and then remained constant at higher temperatures. The measured viscosities are shown in Figure 4, revealing the strong influence of the composition on the viscosity at temperatures near T g between 800 and 1000 K. The temperature plot does not follow a classic Arrhenius relation-hence the use of (Eqn(5)) to calculate S conf (T g ), which ranged from 10 to 17 J.mol-1 K -1 (±3 5%) for the test compositions. A narrow range of values was obtained for the enthalpy of glass dissolution in lead borate at 970 K: -0.62 to 0.37 kJ.moL -1 with relatively high (50-100%) uncertainty. All the basic parameters needed to determine the free energy of formation Δ f G T) are thus available; the results calculated using Eqns (3), (4,) and (1) are given in Table I at room temperature (298 K). In the final step, the free energy of dissolution in water was calculated for the glass compositions by integrating the thermodynamic properties obtained from the previously described experimental methods. Major differences were observed with respect to the free energy of dissolution determined by a simple model from the sum of the thermodynamic properties of simple binary silicates. These experimental determinations will allow an assessment of glass thermodynamic stability in water. This step will notably involve the correlation of aqueous leaching results with the

  12. Diagrams of the variations in the free energy of formation of metallic compounds (1960)

    International Nuclear Information System (INIS)

    Darras, R.; Loriers, H.

    1960-01-01

    The variations in the standard free energy ΔG produced during the formation of the principal simple metallic compounds have been calculated as a function of the temperature from recently published data, and are presented in convenient diagram form. Their usefulness in metallurgy is illustrated by some possible applications. (author) [fr

  13. Proposed Empirical Entropy and Gibbs Energy Based on Observations of Scale Invariance in Open Nonequilibrium Systems.

    Science.gov (United States)

    Tuck, Adrian F

    2017-09-07

    There is no widely agreed definition of entropy, and consequently Gibbs energy, in open systems far from equilibrium. One recent approach has sought to formulate an entropy and Gibbs energy based on observed scale invariances in geophysical variables, particularly in atmospheric quantities, including the molecules constituting stratospheric chemistry. The Hamiltonian flux dynamics of energy in macroscopic open nonequilibrium systems maps to energy in equilibrium statistical thermodynamics, and corresponding equivalences of scale invariant variables with other relevant statistical mechanical variables such as entropy, Gibbs energy, and 1/(k Boltzmann T), are not just formally analogous but are also mappings. Three proof-of-concept representative examples from available adequate stratospheric chemistry observations-temperature, wind speed and ozone-are calculated, with the aim of applying these mappings and equivalences. Potential applications of the approach to scale invariant observations from the literature, involving scales from molecular through laboratory to astronomical, are considered. Theoretical support for the approach from the literature is discussed.

  14. Gibbs Energy Modeling of Digenite and Adjacent Solid-State Phases

    Science.gov (United States)

    Waldner, Peter

    2017-08-01

    All sulfur potential and phase diagram data available in the literature for solid-state equilibria related to digenite have been assessed. Thorough thermodynamic analysis at 1 bar total pressure has been performed. A three-sublattice approach has been developed to model the Gibbs energy of digenite as a function of composition and temperature using the compound energy formalism. The Gibbs energies of the adjacent solid-state phases covelitte and high-temperature chalcocite are also modeled treating both sulfides as stoichiometric compounds. The novel model for digenite offers new interpretation of experimental data, may contribute from a thermodynamic point of view to the elucidation of the role of copper species within the crystal structure and allows extrapolation to composition regimes richer in copper than stoichiometric digenite Cu2S. Preliminary predictions into the ternary Cu-Fe-S system at 1273 K (1000 °C) using the Gibbs energy model of digenite for calculating its iron solubility are promising.

  15. The Gibbs Energy Basis and Construction of Boiling Point Diagrams in Binary Systems

    Science.gov (United States)

    Smith, Norman O.

    2004-01-01

    An illustration of how excess Gibbs energies of the components in binary systems can be used to construct boiling point diagrams is given. The underlying causes of the various types of behavior of the systems in terms of intermolecular forces and the method of calculating the coexisting liquid and vapor compositions in boiling point diagrams with…

  16. Enhanced conformational sampling to visualize a free-energy landscape of protein complex formation.

    Science.gov (United States)

    Iida, Shinji; Nakamura, Haruki; Higo, Junichi

    2016-06-15

    We introduce various, recently developed, generalized ensemble methods, which are useful to sample various molecular configurations emerging in the process of protein-protein or protein-ligand binding. The methods introduced here are those that have been or will be applied to biomolecular binding, where the biomolecules are treated as flexible molecules expressed by an all-atom model in an explicit solvent. Sampling produces an ensemble of conformations (snapshots) that are thermodynamically probable at room temperature. Then, projection of those conformations to an abstract low-dimensional space generates a free-energy landscape. As an example, we show a landscape of homo-dimer formation of an endothelin-1-like molecule computed using a generalized ensemble method. The lowest free-energy cluster at room temperature coincided precisely with the experimentally determined complex structure. Two minor clusters were also found in the landscape, which were largely different from the native complex form. Although those clusters were isolated at room temperature, with rising temperature a pathway emerged linking the lowest and second-lowest free-energy clusters, and a further temperature increment connected all the clusters. This exemplifies that the generalized ensemble method is a powerful tool for computing the free-energy landscape, by which one can discuss the thermodynamic stability of clusters and the temperature dependence of the cluster networks. © 2016 The Author(s).

  17. Calculation of the surface free energy of fcc copper nanoparticles

    International Nuclear Information System (INIS)

    Jia Ming; Lai Yanqing; Tian Zhongliang; Liu Yexiang

    2009-01-01

    Using molecular dynamics simulations with the modified analytic embedded-atom method we calculate the Gibbs free energy and surface free energy for fcc Cu bulk, and further obtain the Gibbs free energy of nanoparticles. Based on the Gibbs free energy of nanoparticles, we have investigated the heat capacity of copper nanoparticles. Calculation results indicate that the Gibbs free energy and the heat capacity of nanoparticles can be divided into two parts: bulk quantity and surface quantity. The molar heat capacity of the bulk sample is lower compared with the molar heat capacity of nanoparticles, and this difference increases with the decrease in the particle size. It is also observed that the size effect on the thermodynamic properties of Cu nanoparticles is not really significant until the particle is less than about 20 nm. It is the surface atoms that decide the size effect on the thermodynamic properties of nanoparticles

  18. Unified interpretation of exciplex formation and marcus electron transfer on the basis of two-dimensional free energy surfaces.

    Science.gov (United States)

    Murata, Shigeo; Tachiya, M

    2007-09-27

    The mechanism of exciplex formation proposed in a previous paper has been refined to show how exciplex formation and Marcus electron transfer (ET) in fluorescence quenching are related to each other. This was done by making simple calculations of the free energies of the initial (DA*) and final (D+A-) states of ET. First it was shown that the decrease in D-A distance can induce intermolecular ET even in nonpolar solvents where solvent orientational polarization is absent, and that it leads to exciplex formation. This is consistent with experimental results that exciplex is most often observed in nonpolar solvents. The calculation was then extended to ET in polar solvents where the free energies are functions of both D-A distance and solvent orientational polarization. This enabled us to discuss both exciplex formation and Marcus ET in the same D-A pair and solvent on the basis of 2-dimensional free energy surfaces. The surfaces contain more information about the rates of these reactions, the mechanism of fluorescence quenching by ET, etc., than simple reaction schemes. By changing the parameters such as the free energy change of reaction, solvent dielectric constants, etc., one can construct the free energy surfaces for various systems. The effects of free energy change of reaction and of solvent polarity on the mechanism and relative importance of exciplex formation and Marcus ET in fluorescence quenching can be well explained. The free energy surface will also be useful for discussion of other phenomena related to ET reactions.

  19. Molar Surface Gibbs Energy of the Aqueous Solution of Ionic Liquid [C4mim][Oac

    Institute of Scientific and Technical Information of China (English)

    TONG Jing; ZHENG Xu; TONG Jian; QU Ye; LIU Lu; LI Hui

    2017-01-01

    The values of density and surface tension for aqueous solution of ionic liquid(IL) 1-butyl-3-methylimidazolium acetate([C4mim][OAc]) with various molalities were measured in the range of 288.15-318.15 K at intervals of 5 K.On the basis of thermodynamics,a semi-empirical model-molar surface Gibbs energy model of the ionic liquid solution that could be used to predict the surface tension or molar volume of solutions was put forward.The predicted values of the surface tension for aqueous [C4im][OAc] and the corresponding experimental ones were highly correlated and extremely similar.In terms of the concept of the molar Gibbs energy,a new E(o)tv(o)s equation was obtained and each parameter of the new equation has a clear physical meaning.

  20. Ionic Strength Modulation of the Free Energy Landscape of Aβ40 Peptide Fibril Formation.

    Science.gov (United States)

    Abelein, Axel; Jarvet, Jüri; Barth, Andreas; Gräslund, Astrid; Danielsson, Jens

    2016-06-01

    Protein misfolding and formation of cross-β structured amyloid fibrils are linked to many neurodegenerative disorders. Although recently developed quantitative approaches have started to reveal the molecular nature of self-assembly and fibril formation of proteins and peptides, it is yet unclear how these self-organization events are precisely modulated by microenvironmental factors, which are known to strongly affect the macroscopic aggregation properties. Here, we characterize the explicit effect of ionic strength on the microscopic aggregation rates of amyloid β peptide (Aβ40) self-association, implicated in Alzheimer's disease. We found that physiological ionic strength accelerates Aβ40 aggregation kinetics by promoting surface-catalyzed secondary nucleation reactions. This promoted catalytic effect can be assigned to shielding of electrostatic repulsion between monomers on the fibril surface or between the fibril surface itself and monomeric peptides. Furthermore, we observe the formation of two different β-structured states with similar but distinct spectroscopic features, which can be assigned to an off-pathway immature state (Fβ*) and a mature stable state (Fβ), where salt favors formation of the Fβ fibril morphology. Addition of salt to preformed Fβ* accelerates transition to Fβ, underlining the dynamic nature of Aβ40 fibrils in solution. On the basis of these results we suggest a model where salt decreases the free-energy barrier for Aβ40 folding to the Fβ state, favoring the buildup of the mature fibril morphology while omitting competing, energetically less favorable structural states.

  1. Variación de la energía libre de Gibbs de la caolinita en función de la cristalinidad y tamaño de partícula

    OpenAIRE

    La Iglesia, A.

    1989-01-01

    The effect of grinding on crystallinity, particle size and solubility of two samples of kaolinite was studied. The standard Gibbs free energies of formation of different ground samples were calculated from solubility measurements, and show a direct relationship between Gibbs free energy and particle size-crystallinity variation. Values of -3752.2 and -3776.4 KJ/mol. were determinated for ΔGºl (am) and ΔGºl (crys) of kaolinite, respectively. A new th...

  2. Using Graphs of Gibbs Energy versus Temperature in General Chemistry Discussions of Phase Changes and Colligative Properties

    Science.gov (United States)

    Hanson, Robert M.; Riley, Patrick; Schwinefus, Jeff; Fischer, Paul J.

    2008-01-01

    The use of qualitative graphs of Gibbs energy versus temperature is described in the context of chemical demonstrations involving phase changes and colligative properties at the general chemistry level. (Contains 5 figures and 1 note.)

  3. Phase relations and Gibbs energies of spinel phases and solid solutions in the system Mg-Rh-O

    Energy Technology Data Exchange (ETDEWEB)

    Jacob, K.T., E-mail: katob@materials.iisc.ernet.in [Department of Materials Engineering, Indian Institute of Science, Bangalore 560 012 (India); Prusty, Debadutta [Department of Materials Engineering, Indian Institute of Science, Bangalore 560 012 (India); Kale, G.M. [Institute for Materials Research, University of Leeds, Leeds, LS2 9JT (United Kingdom)

    2012-02-05

    Highlights: Black-Right-Pointing-Pointer Refinement of phase diagram for the system Mg-Rh-O and thermodynamic data for spinel compounds MgRh{sub 2}O{sub 4} and Mg{sub 2}RhO{sub 4} is presented. Black-Right-Pointing-Pointer A solid-state electrochemical cell is used for thermodynamic measurement. Black-Right-Pointing-Pointer An advanced design of the solid-state electrochemical cell incorporating buffer electrodes is deployed to minimize polarization of working electrode. Black-Right-Pointing-Pointer Regular solution model for the spinel solid solution MgRh{sub 2}O{sub 4} - Mg{sub 2}RhO{sub 4} based on ideal mixing of cations on the octahedral site is proposed. Black-Right-Pointing-Pointer Factors responsible for stabilization of tetravalent rhodium in spinel compounds are identified. - Abstract: Pure stoichiometric MgRh{sub 2}O{sub 4} could not be prepared by solid state reaction from an equimolar mixture of MgO and Rh{sub 2}O{sub 3} in air. The spinel phase formed always contained excess of Mg and traces of Rh or Rh{sub 2}O{sub 3}. The spinel phase can be considered as a solid solution of Mg{sub 2}RhO{sub 4} in MgRh{sub 2}O{sub 4}. The compositions of the spinel solid solution in equilibrium with different phases in the ternary system Mg-Rh-O were determined by electron probe microanalysis. The oxygen potential established by the equilibrium between Rh + MgO + Mg{sub 1+x}Rh{sub 2-x}O{sub 4} was measured as a function of temperature using a solid-state cell incorporating yttria-stabilized zirconia as an electrolyte and pure oxygen at 0.1 MPa as the reference electrode. To avoid polarization of the working electrode during the measurements, an improved design of the cell with a buffer electrode was used. The standard Gibbs energies of formation of MgRh{sub 2}O{sub 4} and Mg{sub 2}RhO{sub 4} were deduced from the measured electromotive force (e.m.f.) by invoking a model for the spinel solid solution. The parameters of the model were optimized using the measured

  4. Phase relations and gibbs energies in the system Mn-Rh-O

    Science.gov (United States)

    Jacob, K. T.; Sriram, M. V.

    1994-07-01

    Phase relations in the system Mn-Rh-O are established at 1273 K by equilibrating different compositions either in evacuated quartz ampules or in pure oxygen at a pressure of 1.01 × 105 Pa. The quenched samples are examined by optical microscopy, X-ray diffraction, and energy-dispersive X-ray analysis (EDAX). The alloys and intermetallics in the binary Mn-Rh system are found to be in equilibrium with MnO. There is only one ternary compound, MnRh2O4, with normal spinel structure in the system. The compound Mn3O4 has a tetragonal structure at 1273 K. A solid solution is formed between MnRh2O4 and Mn3O4. The solid solution has the cubic structure over a large range of composition and coexists with metallic rhodium. The partial pressure of oxygen corresponding to this two-phase equilibrium is measured as a function of the composition of the spinel solid solution and temperature. A new solid-state cell, with three separate electrode compartments, is designed to measure accurately the chemical potential of oxygen in the two-phase mixture, Rh + Mn3-2xRh2xO4, which has 1 degree of freedom at constant temperature. From the electromotive force (emf), thermodynamic mixing properties of the Mn3O4-MnRh2O4 solid solution and Gibbs energy of formation of MnRh2O4 are deduced. The activities exhibit negative deviations from Raoult’s law for most of the composition range, except near Mn3O4, where a two-phase region exists. In the cubic phase, the entropy of mixing of the two Rh3+ and Mn3+ ions on the octahedral site of the spinel is ideal, and the enthalpy of mixing is positive and symmetric with respect to composition. For the formation of the spinel (sp) from component oxides with rock salt (rs) and orthorhombic (orth) structures according to the reaction, MnO (rs) + Rh2O3 (orth) → MnRh2O4 (sp), ΔG° = -49,680 + 1.56T (±500) J mol-1 The oxygen potentials corresponding to MnO + Mn3O4 and Rh + Rh2O3 equilibria are also obtained from potentiometric measurements on galvanic

  5. Diagrams of the variations in the free energy of formation of metallic compounds (1960); Diagrammes de variations d'energie libre de formation des composes metalliques (1960)

    Energy Technology Data Exchange (ETDEWEB)

    Darras, R; Loriers, H [Commissariat a l' Energie Atomique, Saclay (France).Centre d' Etudes Nucleaires

    1960-07-01

    The variations in the standard free energy {delta}G produced during the formation of the principal simple metallic compounds have been calculated as a function of the temperature from recently published data, and are presented in convenient diagram form. Their usefulness in metallurgy is illustrated by some possible applications. (author) [French] Les variations d'energie libre standard {delta}G intervenant lors de la formation des principaux composes metalliques simples ont ete calculees, en fonction de la temperature, d'apres les donnees recentes de la litterature et rassemblees sous forme de diagrammes d'utilisation commode. Leur interet certain en metallurgie est concretise par quelques exemples d'applications possibles. (auteur)

  6. Excess Gibbs energy for six binary solid solutions of molecularly simple substances

    Energy Technology Data Exchange (ETDEWEB)

    Lobo, L J; Staveley, L A.K.

    1985-01-01

    In this paper we apply the method developed in a previous study of Ar + CH/sub 4/ to the evaluation of the excess Gibbs energy G /SUP E.S/ for solid solutions of two molecularly simple components. The method depends on combining information on the excess Gibbs energy G /SUP E.L/ for the liquid mixture of the two components with a knowledge of the (T, x) solid-liquid phase diagram. Certain thermal properties o the pure substances are also needed. G /SUP E.S/ has been calculated for binary mixtures of Ar + Kr, Kr + CH/sub 4/, CO + N/sub 2/, Kr + Xe, Ar + N/sub 2/, and Ar + CO. In general, but not always, the solid mixtures are more non-ideal than the liquid mixtures of the same composition at the same temperature. Except for the Kr + CH/sub 4/ system, the ratio r = G /SUP E.S/ /G /SUP E.L/ is larger the richer the solution in the component with the smaller molecules.

  7. Determination of the free enthalpies of formation of borosilicate glasses

    International Nuclear Information System (INIS)

    Linard, Y.

    2000-01-01

    This work contributes to the study of the thermochemical properties of nuclear waste glasses. Results are used to discuss mechanisms and parameters integrated in alteration models of conditioning materials. Glass is a disordered material defined thermodynamically as a non-equilibrium state. Taking into account one order parameter to characterise its configurational state, the metastable equilibrium for the glass was considered and the main thermochemical properties were determined. Calorimetric techniques were used to measure heat capacities and formation enthalpies of borosilicate glasses (from 3 to 8 constitutive oxides). Formation Entropies were measured too, using the entropy theory of relaxation processes proposed by Adam and Gibbs (1965). The configurational entropy contribution were determined from viscosity measurements. This set of data has allowed the calculation of Gibb's free energies of dissolution of glasses in pure water. By comparison with leaching experiments, it has been demonstrated that the decreasing of the dissolution rate at high reaction progress cannot be associated to the approach of an equilibrium between the sound glass and the aqueous solution. The composition changes of the reaction area at the glass surface need to be considered too. To achieve a complete description of the thermodynamic stability, the equilibrium between hydrated de-alkalinized glass and/or the gel layer with the aqueous solution should also be evaluated. (author)

  8. Solubility and Standard Gibb's energies of transfer of alkali metal perchlorates, tetramethyl- and tetraethylammonium from water to aqua-acetone solvents

    International Nuclear Information System (INIS)

    Kireev, A.A.; Pak, T.G.; Bezuglyj, V.D.

    1996-01-01

    Solubilities of KClO 4 , RbClO 4 , CsClO 4 , (CH 3 ) 4 NClO 4 , (C 2 M 5 ) 4 NClO 4 in water and water-acetone mixtures are determined by the method of isothermal saturation at 298.15 K. Dissociation constants of alkali metal perchlorates are found by conductometric method. Solubility products and standard Gibbs energies of transfer of corresponding electrolytes from water into water-acetone solvents are calculated. The character of transfer Gibbs energy dependence on solvent composition is explained by preferred solvation of cations by acetone molecules and anions-by water molecules. Features of tetraalkyl ammonium ions are explained by large changes in energy of cavity formation for these ions

  9. Generalized Gibbs distribution and energy localization in the semiclassical FPU problem

    Science.gov (United States)

    Hipolito, Rafael; Danshita, Ippei; Oganesyan, Vadim; Polkovnikov, Anatoli

    2011-03-01

    We investigate dynamics of the weakly interacting quantum mechanical Fermi-Pasta-Ulam (qFPU) model in the semiclassical limit below the stochasticity threshold. Within this limit we find that initial quantum fluctuations lead to the damping of FPU oscillations and relaxation of the system to a slowly evolving steady state with energy localized within few momentum modes. We find that in large systems this state can be described by the generalized Gibbs ensemble (GGE), with the Lagrange multipliers being very weak functions of time. This ensembles gives accurate description of the instantaneous correlation functions, both quadratic and quartic. Based on these results we conjecture that GGE generically appears as a prethermalized state in weakly non-integrable systems.

  10. A Short Essay on the Uses of Free Energy

    Science.gov (United States)

    Koutandos, Spyridon

    2013-01-01

    In this article we examine cases of more classical and less classical nature compared to results found by quantum mechanics and attribute a form of Free Energy discontinuity for each case within a boundary layer. The concept of a boundary layer is broadened as to include areas of first or second variations of the Gibbs free energy. It is…

  11. Free energy

    International Nuclear Information System (INIS)

    Holm, Oeystein B.

    2006-01-01

    Norway has fallen behind in the development of district heating and use of solar energy compared to Sweden and Denmark. It is a myth that Norway has less hours of sun than its neighbours; southern and eastern Norway has equally good conditions as areas in Sweden and Denmark that have large solar collector installations used for district heating. Benefits of the solar energy technology are highlighted, especially environmental aspects (ml)

  12. Gibbs energy formation of Sr5Nb4O15

    International Nuclear Information System (INIS)

    Samui, Pradeep; Padhi, Anyuna; Agarwal, Renu; Kulkarni, S.G.

    2012-01-01

    Ternary oxides of strontium and niobium may form as fission product compounds in an operating nuclear reactor with oxide fuels under certain oxygen potential. Evaluations of thermodynamic stability of these ternary oxides are therefore important for assessment of fission product interactions. Furthermore, thermodynamic data of these oxides are also of relevance because of computation of phase diagram and phase stability of pseudo-ternary systems BaO-SrO-Nb 2 O 5 , SrO-Nb 2 O 5 -TaO 5 etc. in which some of the compounds are potential candidate materials for microwave ceramics with high dielectric constant, electro-optic, pyroelectric and piezoelectric devices. The system Sr-Nb-O contains many ternary oxides out of which we have investigated the thermodynamic parameters for the compound Sr 5 Nb 4 O 15 in the present study

  13. Free energy of formation of Mo2C and the thermodynamic properties of carbon in solid molybdenum

    Science.gov (United States)

    Seigle, L. L.; Chang, C. L.; Sharma, T. P.

    1979-01-01

    As part of a study of the thermodynamical properties of interstitial elements in refractory metals, the free energy of formation of Mo2C is determined, and the thermodynamical properties of C in solution in solid Mo evaluated. The activity of C in the two-phase region Mo + Mo2C is obtained from the C content of iron rods equilibrated with metal + carbide powder mixtures. The free energy of formation of alpha-Mo2C is determined from the activity data. The thermodynamic properties of C in the terminal solid solution are calculated from available data on the solid solubility of C in Mo. Lattice distortion due to misfit of the C atoms in the interstitial sites appears to play a significant role in determining the thermodynamic properties of C in solid Mo.

  14. Application of a linear free energy relationship to crystalline solids of MO2 and M(OH)4

    International Nuclear Information System (INIS)

    Xu Huifang; Barton, L.L.

    1999-01-01

    In this letter, a linear free energy relationship developed by Sverjensky and Molling is used to predict the Gibbs free energies of formation of crystalline phases of M 4+ O 2 and M 4+ (OH) 4 from the known thermodynamic properties of aqueous tetravalent cations (M 4+ ). The modified Sverjensky and Molling equation for tetravalent cations is expressed as ΔG 0 f,M v X = a M v X ΔG 0 n,M 4+ + b M v X + β M v X r M 4+ , where the coefficients a M v X , b M v X and β M v X characterize a particular structural family of M v X, r M 4+ is the ionic radius of M 4+ cation, ΔG 0 f,M v X is the standard Gibbs free energy of formation of M v X, and ΔG 0 n,M 4+ is the standard non-solvation energy of cation M 4+ . By fitting the equation to the existing thermodynamic data, the coefficients in the equation for the MO 2 family minerals are estimated to be: a M v X = 0.670, β M v X = 32 (kcal/mol A), and b = -430.02 (kcal/mol). The constrained relationship can be used to predict the standard Gibbs free energies of formation of crystalline phases and fictive phases (i.e., phases which are thermodynamically unstable and do not occur at standard conditions) within the isostructural families of M 4+ O 2 and M 4+ (OH) 4 if the standard Gibbs free energies of formation of the tetravalent cations are known. (orig.)

  15. Statistical mechanical estimation of the free energy of formation of E. coli biomass for use with macroscopic bioreactor balances.

    Science.gov (United States)

    Grosz, R; Stephanopoulos, G

    1983-09-01

    The need for the determination of the free energy of formation of biomass in bioreactor second law balances is well established. A statistical mechanical method for the calculation of the free energy of formation of E. coli biomass is introduced. In this method, biomass is modelled to consist of a system of biopolymer networks. The partition function of this system is proposed to consist of acoustic and optical modes of vibration. Acoustic modes are described by Tarasov's model, the parameters of which are evaluated with the aid of low-temperature calorimetric data for the crystalline protein bovine chymotrypsinogen A. The optical modes are described by considering the low-temperature thermodynamic properties of biological monomer crystals such as amino acid crystals. Upper and lower bounds are placed on the entropy to establish the maximum error associated with the statistical method. The upper bound is determined by endowing the monomers in biomass with ideal gas properties. The lower bound is obtained by limiting the monomers to complete immobility. On this basis, the free energy of formation is fixed to within 10%. Proposals are made with regard to experimental verification of the calculated value and extension of the calculation to other types of biomass.

  16. A procedure to compute equilibrium concentrations in multicomponent systems by Gibbs energy minimization on spreadsheets

    International Nuclear Information System (INIS)

    Lima da Silva, Aline; Heck, Nestor Cesar

    2003-01-01

    Equilibrium concentrations are traditionally calculated with the help of equilibrium constant equations from selected reactions. This procedure, however, is only useful for simpler problems. Analysis of the equilibrium state in a multicomponent and multiphase system necessarily involves solution of several simultaneous equations, and, as the number of system components grows, the required computation becomes more complex and tedious. A more direct and general method for solving the problem is the direct minimization of the Gibbs energy function. The solution for the nonlinear problem consists in minimizing the objective function (Gibbs energy of the system) subjected to the constraints of the elemental mass-balance. To solve it, usually a computer code is developed, which requires considerable testing and debugging efforts. In this work, a simple method to predict equilibrium composition in multicomponent systems is presented, which makes use of an electronic spreadsheet. The ability to carry out these calculations within a spreadsheet environment shows several advantages. First, spreadsheets are available 'universally' on nearly all personal computers. Second, the input and output capabilities of spreadsheets can be effectively used to monitor calculated results. Third, no additional systems or programs need to be learned. In this way, spreadsheets can be as suitable in computing equilibrium concentrations as well as to be used as teaching and learning aids. This work describes, therefore, the use of the Solver tool, contained in the Microsoft Excel spreadsheet package, on computing equilibrium concentrations in a multicomponent system, by the method of direct Gibbs energy minimization. The four phases Fe-Cr-O-C-Ni system is used as an example to illustrate the method proposed. The pure stoichiometric phases considered in equilibrium calculations are: Cr 2 O 3 (s) and FeO C r 2 O 3 (s). The atmosphere consists of O 2 , CO e CO 2 constituents. The liquid iron

  17. Ligand Conformational and Solvation/Desolvation Free Energy in Protein-Ligand Complex Formation

    Czech Academy of Sciences Publication Activity Database

    Kolář, Michal; Fanfrlík, Jindřich; Hobza, Pavel

    2011-01-01

    Roč. 115, č. 16 (2011), s. 4718-4724 ISSN 1520-6106 R&D Projects: GA MŠk LC512; GA ČR GAP208/11/0295 Grant - others:Korea Science and Engineering Foundation(KR) R32-2008-000-10180-0; European Science Fund(XE) CZ.1.05/2.1.00/03.0058 Institutional research plan: CEZ:AV0Z40550506 Keywords : solvation free energy * SMD * HIV protease inhibitors Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 3.696, year: 2011

  18. Room temperature chemical synthesis of highly oriented PbSe nanotubes based on negative free energy of formation

    Energy Technology Data Exchange (ETDEWEB)

    Sankapal, B.R., E-mail: brsankapal@rediffmail.com [Thin Film and Nano Science Laboratory, Department of Physics, School of Physical Sciences, North Maharashtra University, Jalgaon 425 001 (MS) (India); Ladhe, R.D.; Salunkhe, D.B.; Baviskar, P.K. [Thin Film and Nano Science Laboratory, Department of Physics, School of Physical Sciences, North Maharashtra University, Jalgaon 425 001 (MS) (India); Gupta, V.; Chand, S. [Organic and Hybrid Solar Cell, Physics of Energy Harvesting Division, Dr. K.S. Krishnan Marg, National Physical Laboratory, New Delhi 110012 (India)

    2011-10-13

    Highlights: > Simple, inexpensive and room temperature chemical synthesis route. > Highly oriented PbSe nanotubes from Cd(OH){sub 2} nanowires through lead hydroxination. > The process was template free without the use of any capping agent. > Reaction kinetics was accomplished due to more negative free energy of formation. > The ion exchange mechanism due to difference in the solubility products. - Abstract: The sacrificial template free chemical synthesis of PbSe nanotubes at room temperature has been performed by lead hydroxination from cadmium hydroxide nanowires. This process was based on the ion exchange reaction to replace Cd{sup 2+} with Pb{sup 2+} ions from hydroxyl group followed by replacement of hydroxyl group with selenium ions. The reaction kinetics was accomplished due to more negative free energy of formation and thus the difference in the solubility products. The formed nanotubes were inclusive of Pb and Se with proper inter-chemical bonds with preferred orientations having diameter in tens of nanometer. These nanotubes can have future applications in electronic, optoelectronics and photovoltaic's as well.

  19. Room temperature chemical synthesis of highly oriented PbSe nanotubes based on negative free energy of formation

    International Nuclear Information System (INIS)

    Sankapal, B.R.; Ladhe, R.D.; Salunkhe, D.B.; Baviskar, P.K.; Gupta, V.; Chand, S.

    2011-01-01

    Highlights: → Simple, inexpensive and room temperature chemical synthesis route. → Highly oriented PbSe nanotubes from Cd(OH) 2 nanowires through lead hydroxination. → The process was template free without the use of any capping agent. → Reaction kinetics was accomplished due to more negative free energy of formation. → The ion exchange mechanism due to difference in the solubility products. - Abstract: The sacrificial template free chemical synthesis of PbSe nanotubes at room temperature has been performed by lead hydroxination from cadmium hydroxide nanowires. This process was based on the ion exchange reaction to replace Cd 2+ with Pb 2+ ions from hydroxyl group followed by replacement of hydroxyl group with selenium ions. The reaction kinetics was accomplished due to more negative free energy of formation and thus the difference in the solubility products. The formed nanotubes were inclusive of Pb and Se with proper inter-chemical bonds with preferred orientations having diameter in tens of nanometer. These nanotubes can have future applications in electronic, optoelectronics and photovoltaic's as well.

  20. A Gibbs Energy Minimization Approach for Modeling of Chemical Reactions in a Basic Oxygen Furnace

    Science.gov (United States)

    Kruskopf, Ari; Visuri, Ville-Valtteri

    2017-12-01

    In modern steelmaking, the decarburization of hot metal is converted into steel primarily in converter processes, such as the basic oxygen furnace. The objective of this work was to develop a new mathematical model for top blown steel converter, which accounts for the complex reaction equilibria in the impact zone, also known as the hot spot, as well as the associated mass and heat transport. An in-house computer code of the model has been developed in Matlab. The main assumption of the model is that all reactions take place in a specified reaction zone. The mass transfer between the reaction volume, bulk slag, and metal determine the reaction rates for the species. The thermodynamic equilibrium is calculated using the partitioning of Gibbs energy (PGE) method. The activity model for the liquid metal is the unified interaction parameter model and for the liquid slag the modified quasichemical model (MQM). The MQM was validated by calculating iso-activity lines for the liquid slag components. The PGE method together with the MQM was validated by calculating liquidus lines for solid components. The results were compared with measurements from literature. The full chemical reaction model was validated by comparing the metal and slag compositions to measurements from industrial scale converter. The predictions were found to be in good agreement with the measured values. Furthermore, the accuracy of the model was found to compare favorably with the models proposed in the literature. The real-time capability of the proposed model was confirmed in test calculations.

  1. Free energies of formation of WC and WzC and the thermodynamic properties of carbon in solid tungsten

    Science.gov (United States)

    Gupta, D. K.; Seigle, L. L.

    1974-01-01

    The activity of carbon in the two-phase regions - W + WC and W + W2C was obtained from the carbon content of iron rods equilibrated with mixtures of metal plus carbide powders. From this activity data the standard free energies of formation of WC and W2C were calculated. The temperature of the invariant reaction W2C = W + WC was fixed at 1570 + or - 5K. Using available solubility data for C in solid W, the partial molar free energy of C in the dilute solid solution was also calculated. The heat of solution of C in W, and the excess entropy for the interstitial solid solution, were computed, assuming that the carbon atoms reside in the octahedral interstices of bcc W.

  2. Gibbs energy of the resolvation of glycylglycine and its anion in aqueous solutions of dimethylsulfoxide at 298.15 K

    Science.gov (United States)

    Naumov, V. V.; Isaeva, V. A.; Kuzina, E. N.; Sharnin, V. A.

    2012-12-01

    Gibbs energies for the transfer of glycylglycine and glycylglycinate ions from water to water-dimethylsulfoxide solvents are determined from the interface distribution of substances between immiscible phases in the composition range of 0.00 to 0.20 molar fractions of DMSO at 298.15 K. It is shown that with a rise in the concentration of nonaqueous components in solution, we observe the solvation of dipeptide and its anion, due mainly to the destabilization of the carboxyl group.

  3. Free energies of stable and metastable pores in lipid membranes under tension.

    Science.gov (United States)

    den Otter, Wouter K

    2009-11-28

    The free energy profile of pore formation in a lipid membrane, covering the entire range from a density fluctuation in an intact bilayer to a large tension-stabilized pore, has been calculated by molecular dynamics simulations with a coarse-grained lipid model. Several fixed elongations are used to obtain the Helmholtz free energy as a function of pore size for thermodynamically stable, metastable, and unstable pores, and the system-size dependence of these elongations is discussed. A link to the Gibbs free energy at constant tension, commonly known as the Litster model, is established by a Legendre transformation. The change of genus upon pore formation is exploited to estimate the saddle-splay modulus or Gaussian curvature modulus of the membrane leaflets. Details are provided of the simulation approach, which combines the potential of mean constraint force method with a reaction coordinate based on the local lipid density.

  4. Free-format RPG IV

    CERN Document Server

    Martin, Jim

    2013-01-01

    This how-to guide offers a concise and thorough introduction to the increased productivity, better readability, and easier program maintenance that comes with the free-format style of programming in RPG IV. Although free-format information is available in IBM manuals, it is not separated from everything else, thereby requiring hours of tedious research to track down the information needed. This book provides everything one needs to know to write RPG IV in the free-format style, and author Jim Martin not only teaches rules and syntax but also explains how this new style of coding has the pot

  5. Syntactic Formats for Free

    DEFF Research Database (Denmark)

    Klin, Bartek; Sobocinski, Pawel

    2003-01-01

    A framework of Plotkin and Turi’s, originally aimed at providing an abstract notion of bi-simulation, is modified to cover other operational equivalences and preorders. Combined with bi-algebraic methods, it yields a technique for the derivation of syntactic formats for transition system specific...

  6. Computation of free energy

    NARCIS (Netherlands)

    van Gunsteren, WF; Daura, [No Value; Mark, AE

    2002-01-01

    Many quantities that are standardly used to characterize a chemical system are related to free-energy differences between particular states of the system. By statistical mechanics, free-energy differences may be expressed in terms of averages over ensembles of atomic configurations for the molecular

  7. How Does the Gibbs Inequality Condition Affect the Stability and Detachment of Floating Spheres from the Free Surface of Water?

    Science.gov (United States)

    Feng, Dong-xia; Nguyen, Anh V

    2016-03-01

    Floating objects on the air-water interfaces are central to a number of everyday activities, from walking on water by insects to flotation separation of valuable minerals using air bubbles. The available theories show that a fine sphere can float if the force of surface tension and buoyancies can support the sphere at the interface with an apical angle subtended by the circle of contact being larger than the contact angle. Here we show that the pinning of the contact line at the sharp edge, known as the Gibbs inequality condition, also plays a significant role in controlling the stability and detachment of floating spheres. Specifically, we truncated the spheres with different angles and used a force sensor device to measure the force of pushing the truncated spheres from the interface into water. We also developed a theoretical modeling to calculate the pushing force that in combination with experimental results shows different effects of the Gibbs inequality condition on the stability and detachment of the spheres from the water surface. For small angles of truncation, the Gibbs inequality condition does not affect the sphere detachment, and hence the classical theories on the floatability of spheres are valid. For large truncated angles, the Gibbs inequality condition determines the tenacity of the particle-meniscus contact and the stability and detachment of floating spheres. In this case, the classical theories on the floatability of spheres are no longer valid. A critical truncated angle for the transition from the classical to the Gibbs inequality regimes of detachment was also established. The outcomes of this research advance our understanding of the behavior of floating objects, in particular, the flotation separation of valuable minerals, which often contain various sharp edges of their crystal faces.

  8. Free energy of hydration of niobium oxide

    International Nuclear Information System (INIS)

    Plodinec, M.J.

    1996-01-01

    Some of the glasses being formulated by SRTC researchers contain niobium oxide. In this report, the free energy of hydration of the oxide is calculated from the free energies of formation of the oxide, the hydroxide, and water. This value can be used in calculations of the free energy of hydration of glasses containing niobium

  9. Coefficients of interphase distribution and Gibbs energy of the transfer of nicotinic acid from water into aqueous solutions of ethanol and dimethylsulfoxide

    Science.gov (United States)

    Grazhdan, K. V.; Gamov, G. A.; Dushina, S. V.; Sharnin, V. A.

    2012-11-01

    Coefficients of the interphase distribution of nicotinic acid are determined in aqueous solution systems of ethanol-hexane and DMSO-hexane at 25.0 ± 0.1°C. They are used to calculate the Gibbs energy of the transfer of nicotinic acid from water into aqueous solutions of ethanol and dimethylsulfoxide. The Gibbs energy values for the transfer of the molecular and zwitterionic forms of nicotinic acid are obtained by means of UV spectroscopy. The diametrically opposite effect of the composition of binary solvents on the transfer of the molecular and zwitterionic forms of nicotinic acid is noted.

  10. Origin of the correlation between the standard Gibbs energies of ion transfer from water to a hydrophobic ionic liquid and to a molecular solvent

    Czech Academy of Sciences Publication Activity Database

    Langmaier, Jan; Záliš, Stanislav; Samec, Zdeněk; Bovtun, Viktor; Kempa, Martin

    2013-01-01

    Roč. 87, JAN 2013 (2013), s. 591-598 ISSN 0013-4686 R&D Projects: GA ČR GAP206/11/0707 Institutional support: RVO:61388955 ; RVO:68378271 Keywords : ionic liquid s * cyclic voltammetry * standard Gibbs energy of ion transfer Subject RIV: CG - Electrochemistry Impact factor: 4.086, year: 2013

  11. Thermodynamic analysis of ethanol/water system in a fuel cell reformer with the Gibbs energy minimization method

    International Nuclear Information System (INIS)

    Lima da Silva, Aline; De Fraga Malfatti, Celia; Heck, Nestor Cesar

    2003-01-01

    The use of fuel cells is a promising technology in the conversion of chemical to electrical energy. Due to environmental concerns related to the reduction of atmospheric pollution and greenhouse gases emissions such as CO 2 , NO x and hydrocarbons, there have been many researches about fuel cells using hydrogen as fuel. Hydrogen gas can be produced by several routes; a promising one is the steam reforming of ethanol. This route may become an important industrial process, especially for sugarcane producing countries. Ethanol is renewable energy and presents several advantages over other sources related to natural availability, storage and handling safety. In order to contribute to the understanding of the steam reforming of ethanol inside the reformer, this work displays a detailed thermodynamic analysis of the ethanol/water system, in the temperature range of 500-1200K, considering different H 2 O/ethanol reforming ratios. The equilibrium determinations were done with the help of the Gibbs energy minimization method using the Generalized Reduced Gradient algorithm (GRG). Based on literature data, the species considered in calculations were: H 2 , H 2 O, CO, CO 2 , CH 4 , C 2 H 4 , CH 3 CHO, C 2 H 5 OH (gas phase) and C gr . (graphite phase). The thermodynamic conditions for carbon deposition (probably soot) on catalyst during gas reforming were analyzed, in order to establish temperature ranges and H 2 O/ethanol ratios where carbon precipitation is not thermodynamically feasible. Experimental results from literature show that carbon deposition causes catalyst deactivation during reforming. This deactivation is due to encapsulating carbon that covers active phases on a catalyst substrate, e.g. Ni over Al 2 O 3 . In the present study, a mathematical relationship between Lagrange multipliers and the carbon activity (with reference to the graphite phase) was deduced, unveiling the carbon activity in the reformer atmosphere. From this, it is possible to foreseen if soot

  12. Reply to Comment on 'On the importance of the free energy for elasticity under pressure'

    International Nuclear Information System (INIS)

    Marcus, P M; Qiu, S L

    2004-01-01

    All criticisms by Steinle-Neumann and Cohen of the correctness of our calculations of equilibrium structure and elastic constants under pressure from the Gibbs free energy are answered and the criticisms are rejected. The difference between the free energy and the internal energy as functions of structure is described to clarify the use of the free energy. The meaning of elastic constants in a system under pressure is discussed in order to derive the basic quadratic expansion of the free energy in the strains. The coefficients in the expansion are the elastic constants under pressure and are in agreement with well-known work. We give reasons why calculations based on the Gibbs free energy are simpler and more accurate than the usual calculations based on minima of the energy at constant volume. (reply)

  13. Detection of non-coding RNAs on the basis of predicted secondary structure formation free energy change

    Directory of Open Access Journals (Sweden)

    Uzilov Andrew V

    2006-03-01

    Full Text Available Abstract Background Non-coding RNAs (ncRNAs have a multitude of roles in the cell, many of which remain to be discovered. However, it is difficult to detect novel ncRNAs in biochemical screens. To advance biological knowledge, computational methods that can accurately detect ncRNAs in sequenced genomes are therefore desirable. The increasing number of genomic sequences provides a rich dataset for computational comparative sequence analysis and detection of novel ncRNAs. Results Here, Dynalign, a program for predicting secondary structures common to two RNA sequences on the basis of minimizing folding free energy change, is utilized as a computational ncRNA detection tool. The Dynalign-computed optimal total free energy change, which scores the structural alignment and the free energy change of folding into a common structure for two RNA sequences, is shown to be an effective measure for distinguishing ncRNA from randomized sequences. To make the classification as a ncRNA, the total free energy change of an input sequence pair can either be compared with the total free energy changes of a set of control sequence pairs, or be used in combination with sequence length and nucleotide frequencies as input to a classification support vector machine. The latter method is much faster, but slightly less sensitive at a given specificity. Additionally, the classification support vector machine method is shown to be sensitive and specific on genomic ncRNA screens of two different Escherichia coli and Salmonella typhi genome alignments, in which many ncRNAs are known. The Dynalign computational experiments are also compared with two other ncRNA detection programs, RNAz and QRNA. Conclusion The Dynalign-based support vector machine method is more sensitive for known ncRNAs in the test genomic screens than RNAz and QRNA. Additionally, both Dynalign-based methods are more sensitive than RNAz and QRNA at low sequence pair identities. Dynalign can be used as a

  14. A Short Essay on the Uses of Free Energy

    OpenAIRE

    Koutandos, Spyridon

    2013-01-01

    In this article we examine cases of more classical and less classical nature compared to results found by quantum mechanics and attribute a form of Free Energy discontinuity for each case within a boundary layer. The concept of a boundary layer is broadened as to include areas of first or second variations of the Gibbs free energy. It is constructive to think not only of implosions like boundary layers but also of explosion like ones. Situations such as boiling and the passage of electric cur...

  15. The Relationship of Dynamical Heterogeneity to the Adam-Gibbs and Random First-Order Transition Theories of Glass Formation

    OpenAIRE

    Starr, Francis W.; Douglas, Jack F.; Sastry, Srikanth

    2013-01-01

    We carefully examine common measures of dynamical heterogeneity for a model polymer melt and test how these scales compare with those hypothesized by the Adam and Gibbs (AG) and random first-order transition (RFOT) theories of relaxation in glass-forming liquids. To this end, we first analyze clusters of highly mobile particles, the string-like collective motion of these mobile particles, and clusters of relative low mobility. We show that the time scale of the high-mobility clusters and stri...

  16. Unifying hydrotropy under Gibbs phase rule.

    Science.gov (United States)

    Shimizu, Seishi; Matubayasi, Nobuyuki

    2017-09-13

    The task of elucidating the mechanism of solubility enhancement using hydrotropes has been hampered by the wide variety of phase behaviour that hydrotropes can exhibit, encompassing near-ideal aqueous solution, self-association, micelle formation, and micro-emulsions. Instead of taking a field guide or encyclopedic approach to classify hydrotropes into different molecular classes, we take a rational approach aiming at constructing a unified theory of hydrotropy based upon the first principles of statistical thermodynamics. Achieving this aim can be facilitated by the two key concepts: (1) the Gibbs phase rule as the basis of classifying the hydrotropes in terms of the degrees of freedom and the number of variables to modulate the solvation free energy; (2) the Kirkwood-Buff integrals to quantify the interactions between the species and their relative contributions to the process of solubilization. We demonstrate that the application of the two key concepts can in principle be used to distinguish the different molecular scenarios at work under apparently similar solubility curves observed from experiments. In addition, a generalization of our previous approach to solutes beyond dilution reveals the unified mechanism of hydrotropy, driven by a strong solute-hydrotrope interaction which overcomes the apparent per-hydrotrope inefficiency due to hydrotrope self-clustering.

  17. Gibbs energy calculation of electrolytic plasma channel with inclusions of copper and copper oxide with Al-base

    Science.gov (United States)

    Posuvailo, V. M.; Klapkiv, M. D.; Student, M. M.; Sirak, Y. Y.; Pokhmurska, H. V.

    2017-03-01

    The oxide ceramic coating with copper inclusions was synthesized by the method of plasma electrolytic oxidation (PEO). Calculations of the Gibbs energies of reactions between the plasma channel elements with inclusions of copper and copper oxide were carried out. Two methods of forming the oxide-ceramic coatings on aluminum base in electrolytic plasma with copper inclusions were established. The first method - consist in the introduction of copper into the aluminum matrix, the second - copper oxide. During the synthesis of oxide ceramic coatings plasma channel does not react with copper and copper oxide-ceramic included in the coating. In the second case is reduction of copper oxide in interaction with elements of the plasma channel. The content of oxide-ceramic layer was investigated by X-ray and X-ray microelement analysis. The inclusions of copper, CuAl2, Cu9Al4 in the oxide-ceramic coatings were found. It was established that in the spark plasma channels alongside with the oxidation reaction occurs also the reaction aluminothermic reduction of the metal that allows us to dope the oxide-ceramic coating by metal the isobaric-isothermal potential oxidation of which is less negative than the potential of the aluminum oxide.

  18. A Free Energy Barrier Caused by the Refolding of an Oligomeric Intermediate Controls the Lag Time of Amyloid Formation by hIAPP.

    Science.gov (United States)

    Serrano, Arnaldo L; Lomont, Justin P; Tu, Ling-Hsien; Raleigh, Daniel P; Zanni, Martin T

    2017-11-22

    Transiently populated oligomers formed en route to amyloid fibrils may constitute the most toxic aggregates associated with many amyloid-associated diseases. Most nucleation theories used to describe amyloid aggregation predict low oligomer concentrations and do not take into account free energy costs that may be associated with structural rearrangements between the oligomer and fiber states. We have used isotope labeling and two-dimensional infrared spectroscopy to spectrally resolve an oligomeric intermediate during the aggregation of the human islet amyloid protein (hIAPP or amylin), the protein associated with type II diabetes. A structural rearrangement includes the F 23 G 24 A 25 I 26 L 27 region of hIAPP, which starts from a random coil structure, evolves into ordered β-sheet oligomers containing at least 5 strands, and then partially disorders in the fibril structure. The supercritical concentration is measured to be between 150 and 250 μM, which is the thermodynamic parameter that sets the free energy of the oligomers. A 3-state kinetic model fits the experimental data, but only if it includes a concentration independent free energy barrier >3 kcal/mol that represents the free energy cost of refolding the oligomeric intermediate into the structure of the amyloid fibril; i.e., "oligomer activation" is required. The barrier creates a transition state in the free energy landscape that slows fibril formation and creates a stable population of oligomers during the lag phase, even at concentrations below the supercritical concentration. Largely missing in current kinetic models is a link between structure and kinetics. Our experiments and modeling provide evidence that protein structural rearrangements during aggregation impact the populations and kinetics of toxic oligomeric species.

  19. Vapor pressures and standard molar enthalpies, entropies and Gibbs energies of sublimation of two hexachloro herbicides using a TG unit

    International Nuclear Information System (INIS)

    Vecchio, Stefano

    2010-01-01

    The vapor pressures above the solid hexachlorobenzene (HCB) and above both the solid and liquid 1,2,3,4,5,6-hexachlorocyclohexane (lindane) were determined in the ranges 332-450 K and 347-429 K, respectively, by measuring the mass loss rates recorded by thermogravimetry under both isothermal and nonisothermal conditions. The results obtained were compared with those taken from literature. From the temperature dependence of vapor pressure derived by the experimental thermogravimetry data the molar enthalpies of sublimation Δ cr g H m o ( ) were selected for HCB and lindane as well as the molar enthalpy of vaporization Δ l g H m o ( ) for lindane only, at the middle of the respective temperature intervals. The melting temperatures and the molar enthalpies of fusion Δ cr l H m o (T fus ) of lindane were measured by differential scanning calorimetry. Finally, the standard molar enthalpies of sublimation Δ cr g H m o (298.15 K) were obtained for both chlorinated compounds at the reference temperature of 298.15 K using the Δ cr g H m o ( ), Δ l g H m o ( ) and Δ cr l H m o (T fus ) values, as well as the heat capacity differences between gas and liquid and the heat capacity differences between gas and solid, Δ l g C p,m o and Δ cr g C p,m o , respectively, both estimated by applying a group additivity procedure. Therefore, the averages of the standard (p o = 0.1 MPa) molar enthalpies, entropies and Gibbs energies of sublimation at 298.15 K, have been derived.

  20. Linear free energy relationship applied to trivalent cations with lanthanum and actinium oxide and hydroxide structure

    International Nuclear Information System (INIS)

    Ragavan, Anpalaki J.

    2006-01-01

    Linear free energy relationships for trivalent cations with crystalline M 2 O 3 and, M(OH) 3 phases of lanthanides and actinides were developed from known thermodynamic properties of the aqueous trivalent cations, modifying the Sverjensky and Molling equation. The linear free energy relationship for trivalent cations is as ΔG f,MvX 0 =a MvX ΔG n,M 3+ 0 +b MvX +β MvX r M 3+ , where the coefficients a MvX , b MvX , and β MvX characterize a particular structural family of MvX, r M 3+ is the ionic radius of M 3+ cation, ΔG f,MvX 0 is the standard Gibbs free energy of formation of MvX and ΔG n,M 3+ 0 is the standard non-solvation free energy of the cation. The coefficients for the oxide family are: a MvX =0.2705, b MvX =-1984.75 (kJ/mol), and β MvX =197.24 (kJ/molnm). The coefficients for the hydroxide family are: a MvX =0.1587, b MvX =-1474.09 (kJ/mol), and β MvX =791.70 (kJ/molnm).

  1. Josiah Willard Gibbs

    Indian Academy of Sciences (India)

    The younger Gibbs grew up in the liberal and academic atmos- phere at Yale, where .... research in the premier European universities at the time when a similar culture ... tion in obscure journals, Gibbs' work did not receive wide recognition in ...

  2. The relationship of dynamical heterogeneity to the Adam-Gibbs and random first-order transition theories of glass formation.

    Science.gov (United States)

    Starr, Francis W; Douglas, Jack F; Sastry, Srikanth

    2013-03-28

    We carefully examine common measures of dynamical heterogeneity for a model polymer melt and test how these scales compare with those hypothesized by the Adam and Gibbs (AG) and random first-order transition (RFOT) theories of relaxation in glass-forming liquids. To this end, we first analyze clusters of highly mobile particles, the string-like collective motion of these mobile particles, and clusters of relative low mobility. We show that the time scale of the high-mobility clusters and strings is associated with a diffusive time scale, while the low-mobility particles' time scale relates to a structural relaxation time. The difference of the characteristic times for the high- and low-mobility particles naturally explains the well-known decoupling of diffusion and structural relaxation time scales. Despite the inherent difference of dynamics between high- and low-mobility particles, we find a high degree of similarity in the geometrical structure of these particle clusters. In particular, we show that the fractal dimensions of these clusters are consistent with those of swollen branched polymers or branched polymers with screened excluded-volume interactions, corresponding to lattice animals and percolation clusters, respectively. In contrast, the fractal dimension of the strings crosses over from that of self-avoiding walks for small strings, to simple random walks for longer, more strongly interacting, strings, corresponding to flexible polymers with screened excluded-volume interactions. We examine the appropriateness of identifying the size scales of either mobile particle clusters or strings with the size of cooperatively rearranging regions (CRR) in the AG and RFOT theories. We find that the string size appears to be the most consistent measure of CRR for both the AG and RFOT models. Identifying strings or clusters with the "mosaic" length of the RFOT model relaxes the conventional assumption that the "entropic droplets" are compact. We also confirm the

  3. Free Energy in Introductory Physics

    Science.gov (United States)

    Prentis, Jeffrey J.; Obsniuk, Michael J.

    2016-01-01

    Energy and entropy are two of the most important concepts in science. For all natural processes where a system exchanges energy with its environment, the energy of the system tends to decrease and the entropy of the system tends to increase. Free energy is the special concept that specifies how to balance the opposing tendencies to minimize energy…

  4. Thermodynamic description of the Al–Mg–Si system using a new formulation for the temperature dependence of the excess Gibbs energy

    International Nuclear Information System (INIS)

    Tang, Ying; Du, Yong; Zhang, Lijun; Yuan, Xiaoming; Kaptay, George

    2012-01-01

    Highlights: ► An exponential formulation to describe ternary excess Gibbs energy is proposed. ► Theoretical analysis is performed to verify stability of phase using new formulation. ► Al–Mg–Si system and its boundary binaries have been assessed by the new formulation. ► Present calculations for Al–Mg–Si system are more reasonable than previous ones. - Abstract: An exponential formulation was proposed to replace the linear interaction parameter in the Redlich–Kister (R–K) polynomial for the excess Gibbs energy of ternary solution phase. The theoretical analysis indicates that the proposed new exponential formulation can not only avoid the artificial miscibility gap at high temperatures but also describe the ternary system well. A thermodynamic description for the Al–Mg–Si system and its boundary binaries was then performed by using both R–K linear and exponential formulations. The inverted miscibility gaps occurring in the Mg–Si and the Al–Mg–Si systems at high temperatures due to the use of R–K linear polynomials are avoided by using the new formulation. Besides, the thermodynamic properties predicted with the new formulation confirm the general thermodynamic belief that the solution phase approaches to the ideal solution at infinite temperatures, which cannot be described with the traditional R–K linear polynomials.

  5. SOCIAL EQUIVALENT OF FREE ENERGY

    Directory of Open Access Journals (Sweden)

    Josip Stepanic

    2004-06-01

    Full Text Available Characterisation of unbounded resources of a social system within the sociological interpretation has resulted in a large number of different notions, which are relevant in different situations. From the view point of statistical mechanics, these notions resemble free energy. In this paper the concept of social free energy is introduced and first steps toward its development presented. The social free energy is a function equal to physical free energy appropriately determined for the social system, with intrinsically sociological interpretation as a measure of social action obtainable in a given social system without changes in its structure. Its construction is a consequence of response of a social system to recognised parts of environment dynamics. It is argued that development of a social system response resembles exciting the normal modes of a general, physical system.

  6. Determination of the free enthalpies of formation of borosilicate glasses; Determination des enthalpies libres de formation des verres borosilicates. Application a l'etude de l'alteration des verres de confinement de dechets radioactifs

    Energy Technology Data Exchange (ETDEWEB)

    Linard, Y

    2000-07-01

    This work contributes to the study of the thermochemical properties of nuclear waste glasses. Results are used to discuss mechanisms and parameters integrated in alteration models of conditioning materials. Glass is a disordered material defined thermodynamically as a non-equilibrium state. Taking into account one order parameter to characterise its configurational state, the metastable equilibrium for the glass was considered and the main thermochemical properties were determined. Calorimetric techniques were used to measure heat capacities and formation enthalpies of borosilicate glasses (from 3 to 8 constitutive oxides). Formation Entropies were measured too, using the entropy theory of relaxation processes proposed by Adam and Gibbs (1965). The configurational entropy contribution were determined from viscosity measurements. This set of data has allowed the calculation of Gibb's free energies of dissolution of glasses in pure water. By comparison with leaching experiments, it has been demonstrated that the decreasing of the dissolution rate at high reaction progress cannot be associated to the approach of an equilibrium between the sound glass and the aqueous solution. The composition changes of the reaction area at the glass surface need to be considered too. To achieve a complete description of the thermodynamic stability, the equilibrium between hydrated de-alkalinized glass and/or the gel layer with the aqueous solution should also be evaluated. (author)

  7. Free-format RPG IV the express guide to learning free format

    CERN Document Server

    Martin, Jim

    2015-01-01

    Focusing strictly on teaching free-format RPG programming methods, this book will help programmers wishing to upgrade their skills   This how-to guide offers a concise and thorough introduction to the increased productivity, better readability, and easier program maintenance that comes with the free-format style of programming in RPG IV. Although free-format information is available in IBM manuals, it is not separated from everything else, requiring hours of tedious research to track down the information needed. This book provides everything you need to know to write RPG IV in the free-format

  8. Gibbs-non-Gibbs transitions and vector-valued integration

    NARCIS (Netherlands)

    Zuijlen, van W.B.

    2016-01-01

    This thesis consists of two distinct topics. The first part of the thesis con- siders Gibbs-non-Gibbs transitions. Gibbs measures describe the macro- scopic state of a system of a large number of components that is in equilib- rium. It may happen that when the system is transformed, for example, by

  9. The Ideal Ionic Liquid Salt Bridge for the Direct Determination of Gibbs Energies of Transfer of Single Ions, Part I: The Concept.

    Science.gov (United States)

    Radtke, Valentin; Ermantraut, Andreas; Himmel, Daniel; Koslowski, Thorsten; Leito, Ivo; Krossing, Ingo

    2018-02-23

    Described is a procedure for the thermodynamically rigorous, experimental determination of the Gibbs energy of transfer of single ions between solvents. The method is based on potential difference measurements between two electrochemical half cells with different solvents connected by an ideal ionic liquid salt bridge (ILSB). Discussed are the specific requirements for the IL with regard to the procedure, thus ensuring that the liquid junction potentials (LJP) at both ends of the ILSB are mostly canceled. The remaining parts of the LJPs can be determined by separate electromotive force measurements. No extra-thermodynamic assumptions are necessary for this procedure. The accuracy of the measurements depends, amongst others, on the ideality of the IL used, as shown in our companion paper Part II. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  10. Gibbs energy modelling of the driving forces and calculation of the fcc/hcp martensitic transformation temperatures in Fe-Mn and Fe-Mn-Si alloys

    International Nuclear Information System (INIS)

    Cotes, S.; Fernandez Guillermet, A.; Sade, M.

    1999-01-01

    Very recent, accurate dilatometric measurements of the fcc hcp martensitic transformation (MT) temperatures are used to develop a new thermodynamic description of the fcc and hcp phases in the Fe-Mn-Si system, based on phenomenological models for the Gibbs energy function. The composition dependence of the driving forces for the fcc→hcp and the hcp→fcc MTs is established. Detailed calculations of the MT temperatures are reported, which are used to investigate the systematic effects of Si additions upon the MT temperatures of Fe-Mn alloys. A critical comparison with one of the most recent thermodynamic analyses of the Fe-Mn-Si system, which is due to Forsberg and Agren, is also presented. (orig.)

  11. Functions in Free-Format RPG IV

    CERN Document Server

    Martin, Jim

    2009-01-01

    Written especially for programmers adopting a free-format style, this manual explores the role of functions in writing RPG IV programs. Demonstrating the potential of functions, many topics are explored such as details about existing RPG IV built-in functions, writing new functions, using ILE concepts to use C functions, and utilizing IBM API's functions. Explaining how to write small programs, either as sub-procedures or modules, and how to gather those parts together to make programs that are easy to write and maintain, this is a natural next step for programmers familiar with a free-format

  12. Free energy and heat capacity

    International Nuclear Information System (INIS)

    Kurata, M.; Devanathan, R.

    2015-01-01

    Free energy and heat capacity of actinide elements and compounds are important properties for the evaluation of the safety and reliable performance of nuclear fuel. They are essential inputs for models that describe complex phenomena that govern the behaviour of actinide compounds during nuclear fuels fabrication and irradiation. This chapter introduces various experimental methods to measure free energy and heat capacity to serve as inputs for models and to validate computer simulations. This is followed by a discussion of computer simulation of these properties, and recent simulations of thermophysical properties of nuclear fuel are briefly reviewed. (authors)

  13. Calculation of Gibbs energy of Zr-Al-Ni, Zr-Al-Cu, Al-Ni-Cu and Zr-Al-Ni-Cu liquid alloys based on quasiregular solution model

    International Nuclear Information System (INIS)

    Li, H.Q.; Yang, Y.S.; Tong, W.H.; Wang, Z.Y.

    2007-01-01

    With the effects of electronic structure and atomic size being introduced, the mixing enthalpy as well as the Gibbs energy of the ternary Zr-Al-Cu, Ni-Al-Cu, Zr-Ni-Al and quaternary Zr-Al-Ni-Cu systems are calculated based on quasiregular solution model. The computed results agree well with the experimental data. The sequence of Gibbs energies of different systems is: G Zr-Al-Ni-Cu Zr-Al-Ni Zr-Al-Cu Cu-Al-Ni . To Zr-Al-Cu, Ni-Al-Cu and Zr-Ni-Al, the lowest Gibbs energy locates in the composition range of X Zr 0.39-0.61, X Al = 0.38-0.61; X Ni = 0.39-0.61, X Al = 0.38-0.60 and X Zr = 0.32-0.67, X Al = 0.32-0.66, respectively. And to the Zr-Ni-Al-Cu system with 66.67% Zr, the lowest Gibbs energy is obtained in the region of X Al = 0.63-0.80, X Ni = 0.14-0.24

  14. Gibbs energies of protonation and complexation of platinum and vanadate metal ions with naringenin and phenolic acids: Theoretical calculations associated with experimental values

    International Nuclear Information System (INIS)

    Fazary, Ahmed E.; Alshihri, Ayed S.; Alfaifi, Mohammad Y.; Saleh, Kamel A.; Elbehairi, Serag Eldin I.; Fawy, Khaled F.; Abd-Rabboh, Hisham S.M.

    2016-01-01

    Highlights: • The experimental thermodynamic equilibrium and stability constants of vanadium and platinum complexes involving naringin, ferulic acid, p-coumaric acid, caffeic acid, vanillic acid, sinapic acid, and gallic acid were determined. • The theoretical calculations of the free energy changes associated with the ligand protonation, and metal ion–ligand complex formation equilibria using density function theory calculations, providing a complete picture of the microscopic equilibria of the studied complex systems. - Abstract: The Experimental thermodynamic equilibrium (pK_a values) and stability (log β) constants of vanadium and platinum binary and mixed ligand complexes involving naringenin, ferulic acid, p-coumaric acid, caffeic acid, vanillic acid, sinapic acid, and gallic acid were determined at 310.15 K in 0.16 mol·dm"−"3 KCl aqueous solutions using pH-potentiometric technique and by means of two estimation models (HYPERQUAD 2008 and Bjerrum–Calvin). The theoretical calculations of overall protonation and stability constants of the metal complex species in solution were predicted as the free energy change associated with the ligand protonation, and metal ion–ligand complex formation equilibria (species solvation/de-solvation) using ab initio and density function theory (DFT) calculations. The usage of the experimental potentiometry technique and theoretical predictions provides a complete picture of the microscopic equilibria of the studied systems (vanadium/platinum–naringenin–phenolic acid). Specifically, this theoretically DFT predications would be useful to determine the most real protonation constants of the studied bioligands in which the binding sites changes due to the ligand protonation/deprotonation equilibria. Also, the complexing capacities of vanadium and platinum towards naringenin, ferulic acid, p-coumaric acid, caffeic acid, vanillic acid, sinapic acid, and gallic acid in solutions were evaluated and discussed. From the

  15. Grain-boundary free energy in an assembly of elastic disks.

    Science.gov (United States)

    Lusk, Mark T; Beale, Paul D

    2004-02-01

    Grain-boundary free energy is estimated as a function of misoriention for symmetric tilt boundaries in an assembly of nearly hard disks. Fluctuating cell theory is used to accomplish this since the most common techniques for calculating interfacial free energy cannot be applied to such assemblies. The results are analogous to those obtained using a Leonard-Jones potential, but in this case the interfacial energy is dominated by an entropic contribution. Disk assemblies colorized with free and specific volume elucidate differences between these two characteristics of boundary structure. Profiles are also provided of the Helmholtz and Gibbs free energies as a function of distance from the grain boundaries. Low angle grain boundaries are shown to follow the classical relationship between dislocation orientation/spacing and misorientation angle.

  16. Algunas Precisiones en torno a las funciones termodinámicas energía libre de Gibbs

    OpenAIRE

    Solaz Portolés, Joan Josep; Quílez Pardo, Juan

    2001-01-01

    The aim of this study is to elucidate some didactic misundertandings related with the use and the appli cability of the delta functions ∆G, ∆rG and ∆rG0, which derive from the thermodynamic potential Gibbs Free Energy, G.

  17. Using reweighting and free energy surface interpolation to predict solid-solid phase diagrams

    Science.gov (United States)

    Schieber, Natalie P.; Dybeck, Eric C.; Shirts, Michael R.

    2018-04-01

    Many physical properties of small organic molecules are dependent on the current crystal packing, or polymorph, of the material, including bioavailability of pharmaceuticals, optical properties of dyes, and charge transport properties of semiconductors. Predicting the most stable crystalline form at a given temperature and pressure requires determining the crystalline form with the lowest relative Gibbs free energy. Effective computational prediction of the most stable polymorph could save significant time and effort in the design of novel molecular crystalline solids or predict their behavior under new conditions. In this study, we introduce a new approach using multistate reweighting to address the problem of determining solid-solid phase diagrams and apply this approach to the phase diagram of solid benzene. For this approach, we perform sampling at a selection of temperature and pressure states in the region of interest. We use multistate reweighting methods to determine the reduced free energy differences between T and P states within a given polymorph and validate this phase diagram using several measures. The relative stability of the polymorphs at the sampled states can be successively interpolated from these points to create the phase diagram by combining these reduced free energy differences with a reference Gibbs free energy difference between polymorphs. The method also allows for straightforward estimation of uncertainties in the phase boundary. We also find that when properly implemented, multistate reweighting for phase diagram determination scales better with the size of the system than previously estimated.

  18. Dark Energy and Structure Formation

    International Nuclear Information System (INIS)

    Singh, Anupam

    2010-01-01

    We study the gravitational dynamics of dark energy configurations. We report on the time evolution of the dark energy field configurations as well as the time evolution of the energy density to demonstrate the gravitational collapse of dark energy field configurations. We live in a Universe which is dominated by Dark Energy. According to current estimates about 75% of the Energy Density is in the form of Dark Energy. Thus when we consider gravitational dynamics and Structure Formation we expect Dark Energy to play an important role. The most promising candidate for dark energy is the energy density of fields in curved space-time. It therefore become a pressing need to understand the gravitational dynamics of dark energy field configurations. We develop and describe the formalism to study the gravitational collapse of fields given any general potential for the fields. We apply this formalism to models of dark energy motivated by particle physics considerations. We solve the resulting evolution equations which determine the time evolution of field configurations as well as the dynamics of space-time. Our results show that gravitational collapse of dark energy field configurations occurs and must be considered in any complete picture of our universe.

  19. Thermodynamics of metabolic pathways for penicillin production: Analysis of thermodynamic feasibility and free energy changes during fed-batch cultivation

    DEFF Research Database (Denmark)

    Pissarra, P.D.; Nielsen, Jens Bredal

    1997-01-01

    This paper describes the thermodynamic analysis of pathways related to penicillin production in Penicillium chrysogenum. First a thermodynamic feasibility analysis is performed of the L-lysine pathway of which one of the precursors for penicillin biosynthesis (alpha-aminoadipic acid......) is an intermediate. It is found that the L-lysine pathway in P. chrysogenum is thermodynamically feasible and that the calculated standard Gibbs free energy values of the two enzymes controlling the pathway flux indicate that they operate far from equilibrium. It is therefore proposed that the regulation of alpha......-aminoadipate reductase by lysine is important to maintain a high concentration of alpha-aminoadipate in order to direct the carbon flux to penicillin production. Secondly the changes in Gibbs free energy in the penicillin biosynthetic pathway during fed-batch cultivation were studied. The analysis showed that all...

  20. Exploring the ab initio/classical free energy perturbation method: The hydration free energy of water

    International Nuclear Information System (INIS)

    Sakane, Shinichi; Yezdimer, Eric M.; Liu, Wenbin; Barriocanal, Jose A.; Doren, Douglas J.; Wood, Robert H.

    2000-01-01

    The ab initio/classical free energy perturbation (ABC-FEP) method proposed previously by Wood et al. [J. Chem. Phys. 110, 1329 (1999)] uses classical simulations to calculate solvation free energies within an empirical potential model, then applies free energy perturbation theory to determine the effect of changing the empirical solute-solvent interactions to corresponding interactions calculated from ab initio methods. This approach allows accurate calculation of solvation free energies using an atomistic description of the solvent and solute, with interactions calculated from first principles. Results can be obtained at a feasible computational cost without making use of approximations such as a continuum solvent or an empirical cavity formation energy. As such, the method can be used far from ambient conditions, where the empirical parameters needed for approximate theories of solvation may not be available. The sources of error in the ABC-FEP method are the approximations in the ab initio method, the finite sample of configurations, and the classical solvent model. This article explores the accuracy of various approximations used in the ABC-FEP method by comparing to the experimentally well-known free energy of hydration of water at two state points (ambient conditions, and 973.15 K and 600 kg/m3). The TIP4P-FQ model [J. Chem. Phys. 101, 6141 (1994)] is found to be a reliable solvent model for use with this method, even at supercritical conditions. Results depend strongly on the ab initio method used: a gradient-corrected density functional theory is not adequate, but a localized MP2 method yields excellent agreement with experiment. Computational costs are reduced by using a cluster approximation, in which ab initio pair interaction energies are calculated between the solute and up to 60 solvent molecules, while multi-body interactions are calculated with only a small cluster (5 to 12 solvent molecules). Sampling errors for the ab initio contribution to

  1. Reaction Mechanisms for the Electrochemical Reduction of CO2 to CO and Formate on the Cu(100) Surface at 298K from Quantum Mechanics Free Energy Calculations with Explicit Water.

    Science.gov (United States)

    Cheng, Tao; Xiao, Hai; Goddard, William A

    2016-10-11

    Copper is the only elemental metal that reduces a significant fraction of CO 2 to hydrocarbons and alcohols, but the atomistic reaction mechanism that controls the product distributions are not known because it has not been possible to detect the reaction intermediates on the electrode surface experimentally, or carry out Quantum Mechanics (QM) calculations with a realistic description of the electrolyte (water). Here, we carry out Quantum Mechanics (QM) calculations with an explicit description of water on the Cu(100) surface (experimentally shown to be stable under CO2RR conditions) to examine the initial reaction pathways to form CO and formate (HCOO - ) from CO 2 through free energy calculations at 298K and pH 7. We find that CO formation proceeds from physisorbed CO 2 to chemisorbed CO 2 (*CO 2 δ- ), with a free energy barrier of ΔG ‡ =0.43 eV, the rate determining step (RDS). The subsequent barriers of protonating *CO 2 δ- to form COOH* and then dissociating COOH* to form *CO are 0.37 eV and 0.30 eV, respectively. HCOO - formation proceeds through a very different pathway in which physisorbed CO 2 reacts directly with a surface H* (along with electron transfer), leading to ΔG ‡ = 0.80 eV. Thus, the competition between CO formation and HCOO - formation occurs in the first electron transfer step. On Cu(100), the RDS for CO formation is lower, making CO the predominant product. Thus, to alter the product distribution we need to control this first step of CO 2 binding, which might involve alloying or changing the structure at the nanoscale.

  2. Microscopically derived free energy of dislocations

    NARCIS (Netherlands)

    Kooiman, M.; Hütter, M.; Geers, M.G.D.

    2015-01-01

    The dynamics of large amounts of dislocations is the governing mechanism in metal plasticity. The free energy of a continuous dislocation density profile plays a crucial role in the description of the dynamics of dislocations, as free energy derivatives act as the driving forces of dislocation

  3. Uncertainty Quantification in Alchemical Free Energy Methods.

    Science.gov (United States)

    Bhati, Agastya P; Wan, Shunzhou; Hu, Yuan; Sherborne, Brad; Coveney, Peter V

    2018-05-02

    Alchemical free energy methods have gained much importance recently from several reports of improved ligand-protein binding affinity predictions based on their implementation using molecular dynamics simulations. A large number of variants of such methods implementing different accelerated sampling techniques and free energy estimators are available, each claimed to be better than the others in its own way. However, the key features of reproducibility and quantification of associated uncertainties in such methods have barely been discussed. Here, we apply a systematic protocol for uncertainty quantification to a number of popular alchemical free energy methods, covering both absolute and relative free energy predictions. We show that a reliable measure of error estimation is provided by ensemble simulation-an ensemble of independent MD simulations-which applies irrespective of the free energy method. The need to use ensemble methods is fundamental and holds regardless of the duration of time of the molecular dynamics simulations performed.

  4. Mechanism of active transport: free energy dissipation and free energy transduction.

    OpenAIRE

    Tanford, C

    1982-01-01

    The thermodynamic pathway for "chemiosmotic" free energy transduction in active transport is discussed with an ATP-driven Ca2+ pump as an illustrative example. Two innovations are made in the analysis. (i) Free energy dissipated as heat is rigorously excluded from overall free energy bookkeeping by focusing on the dynamic equilibrium state of the chemiosmotic process. (ii) Separate chemical potential terms for free energy donor and transported ions are used to keep track of the thermodynamic ...

  5. The role of the concentration scale in the definition of transfer free energies.

    Science.gov (United States)

    Moeser, Beate; Horinek, Dominik

    2015-01-01

    The Gibbs free energy of transferring a solute at infinite dilution between two solvents quantifies differences in solute-solvent interactions - if the transfer takes place at constant molarity of the solute. Yet, many calculation formulae and measuring instructions that are commonly used to quantify solute-solvent interactions correspond to transfer processes in which not the molarity of the solute but its concentration measured in another concentration scale is constant. Here, we demonstrate that in this case, not only the change in solute-solvent interactions is quantified but also the entropic effect of a volume change during the transfer. Consequently, the "phenomenon" which is known as "concentration-scale dependence" of transfer free energies is simply explained by a volume-entropy effect. Our explanations are of high importance for the study of cosolvent effects on protein stability. Copyright © 2014 Elsevier B.V. All rights reserved.

  6. Thermodynamics, Gibbs Method and Statistical Physics of Electron Gases Gibbs Method and Statistical Physics of Electron Gases

    CERN Document Server

    Askerov, Bahram M

    2010-01-01

    This book deals with theoretical thermodynamics and the statistical physics of electron and particle gases. While treating the laws of thermodynamics from both classical and quantum theoretical viewpoints, it posits that the basis of the statistical theory of macroscopic properties of a system is the microcanonical distribution of isolated systems, from which all canonical distributions stem. To calculate the free energy, the Gibbs method is applied to ideal and non-ideal gases, and also to a crystalline solid. Considerable attention is paid to the Fermi-Dirac and Bose-Einstein quantum statistics and its application to different quantum gases, and electron gas in both metals and semiconductors is considered in a nonequilibrium state. A separate chapter treats the statistical theory of thermodynamic properties of an electron gas in a quantizing magnetic field.

  7. The free-energy cost of interaction between DNA loops.

    Science.gov (United States)

    Huang, Lifang; Liu, Peijiang; Yuan, Zhanjiang; Zhou, Tianshou; Yu, Jianshe

    2017-10-03

    From the viewpoint of thermodynamics, the formation of DNA loops and the interaction between them, which are all non-equilibrium processes, result in the change of free energy, affecting gene expression and further cell-to-cell variability as observed experimentally. However, how these processes dissipate free energy remains largely unclear. Here, by analyzing a mechanic model that maps three fundamental topologies of two interacting DNA loops into a 4-state model of gene transcription, we first show that a longer DNA loop needs more mean free energy consumption. Then, independent of the type of interacting two DNA loops (nested, side-by-side or alternating), the promotion between them always consumes less mean free energy whereas the suppression dissipates more mean free energy. More interestingly, we find that in contrast to the mechanism of direct looping between promoter and enhancer, the facilitated-tracking mechanism dissipates less mean free energy but enhances the mean mRNA expression, justifying the facilitated-tracking hypothesis, a long-standing debate in biology. Based on minimal energy principle, we thus speculate that organisms would utilize the mechanisms of loop-loop promotion and facilitated tracking to survive in complex environments. Our studies provide insights into the understanding of gene expression regulation mechanism from the view of energy consumption.

  8. Free Energy and Internal Combustion Engine Cycles

    OpenAIRE

    Harris, William D.

    2012-01-01

    The performance of one type (Carnot) of Internal Combustion Engine (ICE) cycle is analyzed within the framework of thermodynamic free energies. ICE performance is different from that of an External Combustion Engine (ECE) which is dictated by Carnot's rule.

  9. Inquiries into the Nature of Free Energy and Entropy in Respect to Biochemical Thermodynamics

    Directory of Open Access Journals (Sweden)

    Clinton D. Stoner

    2000-08-01

    Full Text Available Free energy and entropy are examined in detail from the standpoint of classical thermodynamics. The approach is logically based on the fact that thermodynamic work is mediated by thermal energy through the tendency for nonthermal energy to convert spontaneously into thermal energy and for thermal energy to distribute spontaneously and uniformly within the accessible space. The fact that free energy is a Second-Law, expendable energy that makes it possible for thermodynamic work to be done at finite rates is emphasized. Entropy, as originally defined, is pointed out to be the capacity factor for thermal energy that is hidden with respect to temperature; it serves to evaluate the practical quality of thermal energy and to account for changes in the amounts of latent thermal energies in systems maintained at constant temperature. With entropy thus operationally defined, it is possible to see that TDS° of the Gibbs standard free energy relation DG°= DH°-TDS° serves to account for differences or changes in nonthermal energies that do not contribute to DG° and that, since DH° serves to account for differences or changes in total energy, complete enthalpy-entropy (DH° - TDS° compensation must invariably occur in isothermal processes for which TDS° is finite. A major objective was to clarify the means by which free energy is transferred and conserved in sequences of biological reactions coupled by freely diffusible intermediates. In achieving this objective it was found necessary to distinguish between a 'characteristic free energy' possessed by all First-Law energies in amounts equivalent to the amounts of the energies themselves and a 'free energy of concentration' that is intrinsically mechanical and relatively elusive in that it can appear to be free of First-Law energy. The findings in this regard serve to clarify the fact that the transfer of chemical potential energy from one

  10. Formate as an energy source for microbial metabolism in chemosynthetic zones of hydrothermal ecosystems.

    Science.gov (United States)

    Windman, Todd; Zolotova, Natalya; Schwandner, Florian; Shock, Everett L

    2007-12-01

    Formate, a simple organic acid known to support chemotrophic hyperthermophiles, is found in hot springs of varying temperature and pH. However, it is not yet known how metabolic strategies that use formate could contribute to primary productivity in hydrothermal ecosystems. In an effort to provide a quantitative framework for assessing the role of formate metabolism, concentration data for dissolved formate and many other solutes in samples from Yellowstone hot springs were used, together with data for coexisting gas compositions, to evaluate the overall Gibbs energy for many reactions involving formate oxidation or reduction. The result is the first rigorous thermodynamic assessment of reactions involving formate oxidation to bicarbonate and reduction to methane coupled with various forms of iron, nitrogen, sulfur, hydrogen, and oxygen for hydrothermal ecosystems. We conclude that there are a limited number of reactions that can yield energy through formate reduction, in contrast to numerous formate oxidation reactions that can yield abundant energy for chemosynthetic microorganisms. Because the energy yields are so high, these results challenge the notion that hydrogen is the primary energy source of chemosynthetic microbes in hydrothermal ecosystems.

  11. Breakdown of the Arrhenius Law in Describing Vacancy Formation Energies: The Importance of Local Anharmonicity Revealed by Ab initio Thermodynamics

    Directory of Open Access Journals (Sweden)

    A. Glensk

    2014-02-01

    Full Text Available We study the temperature dependence of the Gibbs energy of vacancy formation in Al and Cu from T=0  K up to the melting temperature, fully taking into account anharmonic contributions. Our results show that the formation entropy of vacancies is not constant as often assumed but increases almost linearly with temperature. The resulting highly nonlinear temperature dependence in the Gibbs formation energy naturally explains the differences between positron annihilation spectroscopy and differential dilatometry data and shows that nonlinear thermal corrections are crucial to extrapolate high-temperature experimental data to T=0  K. Employing these corrections—rather than the linear Arrhenius extrapolation that is commonly assumed in analyzing experimental data—revised formation enthalpies are obtained that differ up to 20% from the previously accepted ones. Using the revised experimental formation enthalpies, we show that a large part of the discrepancies between DFT-GGA and unrevised experimental vacancy formation energies disappears. The substantial shift between previously accepted and the newly revised T=0  K formation enthalpies also has severe consequences in benchmarking ab initio methods against experiments, e.g., in deriving corrections that go beyond commonly used LDA and GGA exchange-correlation functionals such as the AM05 functional.

  12. Good Practices in Free-energy Calculations

    Science.gov (United States)

    Pohorille, Andrew; Jarzynski, Christopher; Chipot, Christopher

    2013-01-01

    As access to computational resources continues to increase, free-energy calculations have emerged as a powerful tool that can play a predictive role in drug design. Yet, in a number of instances, the reliability of these calculations can be improved significantly if a number of precepts, or good practices are followed. For the most part, the theory upon which these good practices rely has been known for many years, but often overlooked, or simply ignored. In other cases, the theoretical developments are too recent for their potential to be fully grasped and merged into popular platforms for the computation of free-energy differences. The current best practices for carrying out free-energy calculations will be reviewed demonstrating that, at little to no additional cost, free-energy estimates could be markedly improved and bounded by meaningful error estimates. In energy perturbation and nonequilibrium work methods, monitoring the probability distributions that underlie the transformation between the states of interest, performing the calculation bidirectionally, stratifying the reaction pathway and choosing the most appropriate paradigms and algorithms for transforming between states offer significant gains in both accuracy and precision. In thermodynamic integration and probability distribution (histogramming) methods, properly designed adaptive techniques yield nearly uniform sampling of the relevant degrees of freedom and, by doing so, could markedly improve efficiency and accuracy of free energy calculations without incurring any additional computational expense.

  13. Free energy analysis of cell spreading.

    Science.gov (United States)

    McEvoy, Eóin; Deshpande, Vikram S; McGarry, Patrick

    2017-10-01

    In this study we present a steady-state adaptation of the thermodynamically motivated stress fiber (SF) model of Vigliotti et al. (2015). We implement this steady-state formulation in a non-local finite element setting where we also consider global conservation of the total number of cytoskeletal proteins within the cell, global conservation of the number of binding integrins on the cell membrane, and adhesion limiting ligand density on the substrate surface. We present a number of simulations of cell spreading in which we consider a limited subset of the possible deformed spread-states assumed by the cell in order to examine the hypothesis that free energy minimization drives the process of cell spreading. Simulations suggest that cell spreading can be viewed as a competition between (i) decreasing cytoskeletal free energy due to strain induced assembly of cytoskeletal proteins into contractile SFs, and (ii) increasing elastic free energy due to stretching of the mechanically passive components of the cell. The computed minimum free energy spread area is shown to be lower for a cell on a compliant substrate than on a rigid substrate. Furthermore, a low substrate ligand density is found to limit cell spreading. The predicted dependence of cell spread area on substrate stiffness and ligand density is in agreement with the experiments of Engler et al. (2003). We also simulate the experiments of Théry et al. (2006), whereby initially circular cells deform and adhere to "V-shaped" and "Y-shaped" ligand patches. Analysis of a number of different spread states reveals that deformed configurations with the lowest free energy exhibit a SF distribution that corresponds to experimental observations, i.e. a high concentration of highly aligned SFs occurs along free edges, with lower SF concentrations in the interior of the cell. In summary, the results of this study suggest that cell spreading is driven by free energy minimization based on a competition between decreasing

  14. The new view of hydrophobic free energy.

    Science.gov (United States)

    Baldwin, Robert L

    2013-04-17

    In the new view, hydrophobic free energy is measured by the work of solute transfer of hydrocarbon gases from vapor to aqueous solution. Reasons are given for believing that older values, measured by solute transfer from a reference solvent to water, are not quantitatively correct. The hydrophobic free energy from gas-liquid transfer is the sum of two opposing quantities, the cavity work (unfavorable) and the solute-solvent interaction energy (favorable). Values of the interaction energy have been found by simulation for linear alkanes and are used here to find the cavity work, which scales linearly with molar volume, not accessible surface area. The hydrophobic free energy is the dominant factor driving folding as judged by the heat capacity change for transfer, which agrees with values for solvating hydrocarbon gases. There is an apparent conflict with earlier values of hydrophobic free energy from studies of large-to-small mutations and an explanation is given. Copyright © 2013 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

  15. Free energy of superfluid 3He

    International Nuclear Information System (INIS)

    Rainer, D.; Serene, J.W.

    1976-01-01

    A systematic scheme is presented for calculating the free energy of superfluid Fermi liquids by an asymptotic expansion in the small parameter T/subc//T/subF/. This scheme is used to evaluate the strong-coupling corrections to the free energy of superfluid 3 He. It is shown that the leading corrections can be expressed in terms of the normal-state quasiparticle scattering amplitude, and the strong-coupling results are discussed using the s-p approximation for the scattering amplitude

  16. Free energy barriers to evaporation of water in hydrophobic confinement.

    Science.gov (United States)

    Sharma, Sumit; Debenedetti, Pablo G

    2012-11-08

    We use umbrella sampling Monte Carlo and forward and reverse forward flux sampling (FFS) simulation techniques to compute the free energy barriers to evaporation of water confined between two hydrophobic surfaces separated by nanoscopic gaps, as a function of the gap width, at 1 bar and 298 K. The evaporation mechanism for small (1 × 1 nm(2)) surfaces is found to be fundamentally different from that for large (3 × 3 nm(2)) surfaces. In the latter case, the evaporation proceeds via the formation of a gap-spanning tubular cavity. The 1 × 1 nm(2) surfaces, in contrast, are too small to accommodate a stable vapor cavity. Accordingly, the associated free energy barriers correspond to the formation of a critical-sized cavity for sufficiently large confining surfaces, and to complete emptying of the gap region for small confining surfaces. The free energy barriers to evaporation were found to be of O(20kT) for 14 Å gaps, and to increase by approximately ~5kT with every 1 Å increase in the gap width. The entropy contribution to the free energy of evaporation was found to be independent of the gap width.

  17. Quantum Gibbs Samplers: The Commuting Case

    Science.gov (United States)

    Kastoryano, Michael J.; Brandão, Fernando G. S. L.

    2016-06-01

    We analyze the problem of preparing quantum Gibbs states of lattice spin Hamiltonians with local and commuting terms on a quantum computer and in nature. Our central result is an equivalence between the behavior of correlations in the Gibbs state and the mixing time of the semigroup which drives the system to thermal equilibrium (the Gibbs sampler). We introduce a framework for analyzing the correlation and mixing properties of quantum Gibbs states and quantum Gibbs samplers, which is rooted in the theory of non-commutative {mathbb{L}_p} spaces. We consider two distinct classes of Gibbs samplers, one of them being the well-studied Davies generator modelling the dynamics of a system due to weak-coupling with a large Markovian environment. We show that their spectral gap is independent of system size if, and only if, a certain strong form of clustering of correlations holds in the Gibbs state. Therefore every Gibbs state of a commuting Hamiltonian that satisfies clustering of correlations in this strong sense can be prepared efficiently on a quantum computer. As concrete applications of our formalism, we show that for every one-dimensional lattice system, or for systems in lattices of any dimension at temperatures above a certain threshold, the Gibbs samplers of commuting Hamiltonians are always gapped, giving an efficient way of preparing the associated Gibbs states on a quantum computer.

  18. Thermodynamic analysis of (Ni, Fe)3Al formation by mechanical alloying

    International Nuclear Information System (INIS)

    Adabavazeh, Z.; Karimzadeh, F.; Enayati, M.H.

    2012-01-01

    Highlights: ► (Ni, Fe) 3 Al intermetallic compound was synthesized by mechanical alloying. ► We use a thermodynamic analysis to predict the more stable phase. ► We calculate the Gibbs free-energy changes by using extended Miedema model. ► The results of MA compared with thermodynamic analysis and showed a good agreement with it. - Abstract: (Ni, Fe) 3 Al intermetallic compound was synthesized by mechanical alloying (MA) of Ni, Fe and Al elemental powder mixtures of composition Ni 50 Fe 25 Al 25 . Phase transformation and microstructure characteristics of the alloy powders were investigated by X-ray diffraction (XRD). The results show that mechanical alloying resulted in a Ni (Al, Fe) solid solution. By continued milling, this structure transformed to the disordered (Ni, Fe) 3 Al intermetallic compound. A thermodynamic model developed on the basis of extended theory of Miedema is used to calculate the Gibbs free-energy changes. Final product of MA is a phase having minimal Gibbs free energy compared with other competing phases in Ni–Fe–Al system. However in Ni–Fe–Al system, the most stable phase at all compositions is intermetallic compound (not amorphous phase or solid solution). The results of MA were compared with thermodynamic analysis and revealed the leading role of thermodynamic on the formation of MA product prediction.

  19. The free energy principle, negative energy modes, and stability

    International Nuclear Information System (INIS)

    Morrison, P.J.; Kotschenreuther, M.

    1990-01-01

    This paper is concerned with instability of equilibria of Hamiltonian, fluid and plasma dynamical systems. Usually the dynamical equilibrium of interest is not the state of thermodynamic equilibrium, and does not correspond to a free energy minimum. The relaxation of this type of equilibrium is conventionally considered to be initiated by linear instability. However, there are many cases where linear instability is not present, but the equilibrium is nonlinearly unstable to arbitrarily small perturbations. This paper is about general free energy expressions for determining the presence of linear or nonlinear instabilities. These expressions are simple and practical, and can be obtained for all equilibria of all ideal fluid and plasma models. By free energy, we mean the energy change upon perturbations of the equilibrium that respect dynamical phase space constraints. This quantity is measured by a self-adjoint quadratic form, called δ 2 F. The free energy can result in instability when δ 2 F is indefinite; i.e. there exist accessible perturbations that lower the free energy of the system. A primary purpose of this paper is to tie together three manifestations of what we will refer to as negative energy modes. The first is the conventional plasma physics notion of negative energy mode that is based on the definition of the energy in a homogeneous dielectric medium. A negative energy mode is a normal mode of the medium (plasma) that possesses negative dielectric energy. The second manifestation occurs in finite degree-of-freedom Hamiltonian normal form theory. The quadratic part of a Hamiltonian in the vicinity of an equilibrium point, which possesses only distinct oscillatory eigenvalues, has an invariant signature. Thus in cases where the quadratic form is indefinite, it is natural to refer to the modes corresponding to the negative signature as negative energy modes

  20. The Bogoliubov free energy functional II

    DEFF Research Database (Denmark)

    Napiórkowski, Marcin; Reuvers, Robin; Solovej, Jan Philip

    2018-01-01

    We analyse the canonical Bogoliubov free energy functional at low temperatures in the dilute limit. We prove existence of a first order phase transition and, in the limit $a_0\\to a$, we determine the critical temperature to be $T_{\\rm{c}}=T_{\\rm{fc}}(1+1.49(\\rho^{1/3}a))$ to leading order. Here, $T......_{\\rm{fc}}$ is the critical temperature of the free Bose gas, $\\rho$ is the density of the gas, $a$ is the scattering length of the pair-interaction potential $V$, and $a_0=(8\\pi)^{-1}\\widehat{V}(0)$ its first order approximation. We also prove asymptotic expansions for the free energy. In particular, we recover the Lee...

  1. Calculating Free Energies Using Average Force

    Science.gov (United States)

    Darve, Eric; Pohorille, Andrew; DeVincenzi, Donald L. (Technical Monitor)

    2001-01-01

    A new, general formula that connects the derivatives of the free energy along the selected, generalized coordinates of the system with the instantaneous force acting on these coordinates is derived. The instantaneous force is defined as the force acting on the coordinate of interest so that when it is subtracted from the equations of motion the acceleration along this coordinate is zero. The formula applies to simulations in which the selected coordinates are either unconstrained or constrained to fixed values. It is shown that in the latter case the formula reduces to the expression previously derived by den Otter and Briels. If simulations are carried out without constraining the coordinates of interest, the formula leads to a new method for calculating the free energy changes along these coordinates. This method is tested in two examples - rotation around the C-C bond of 1,2-dichloroethane immersed in water and transfer of fluoromethane across the water-hexane interface. The calculated free energies are compared with those obtained by two commonly used methods. One of them relies on determining the probability density function of finding the system at different values of the selected coordinate and the other requires calculating the average force at discrete locations along this coordinate in a series of constrained simulations. The free energies calculated by these three methods are in excellent agreement. The relative advantages of each method are discussed.

  2. Analysis of the Bogoliubov free energy functional

    DEFF Research Database (Denmark)

    Reuvers, Robin

    In this thesis, we analyse a variational reformulation of the Bogoliubov approximation that is used to describe weakly-interacting translationally-invariant Bose gases. For the resulting model, the `Bogoliubov free energy functional', we demonstrate existence of minimizers as well as the presence...

  3. Applications for Energy Recovering Free Electron Lasers

    Energy Technology Data Exchange (ETDEWEB)

    George Neil

    2007-08-01

    The availability of high-power, high-brilliance sources of tunable photons from energy-recovered Free Electron Lasers is opening up whole new fields of application of accelerators in industry. This talk will review some of the ideas that are already being put into production, and some of the newer ideas that are still under development.

  4. Nucleation theory - Is replacement free energy needed?. [error analysis of capillary approximation

    Science.gov (United States)

    Doremus, R. H.

    1982-01-01

    It has been suggested that the classical theory of nucleation of liquid from its vapor as developed by Volmer and Weber (1926) needs modification with a factor referred to as the replacement free energy and that the capillary approximation underlying the classical theory is in error. Here, the classical nucleation equation is derived from fluctuation theory, Gibb's result for the reversible work to form a critical nucleus, and the rate of collision of gas molecules with a surface. The capillary approximation is not used in the derivation. The chemical potential of small drops is then considered, and it is shown that the capillary approximation can be derived from thermodynamic equations. The results show that no corrections to Volmer's equation are needed.

  5. Geometric and Texture Inpainting by Gibbs Sampling

    DEFF Research Database (Denmark)

    Gustafsson, David Karl John; Pedersen, Kim Steenstrup; Nielsen, Mads

    2007-01-01

    . In this paper we use the well-known FRAME (Filters, Random Fields and Maximum Entropy) for inpainting. We introduce a temperature term in the learned FRAME Gibbs distribution. By sampling using different temperature in the FRAME Gibbs distribution, different contents of the image are reconstructed. We propose...... a two step method for inpainting using FRAME. First the geometric structure of the image is reconstructed by sampling from a cooled Gibbs distribution, then the stochastic component is reconstructed by sample froma heated Gibbs distribution. Both steps in the reconstruction process are necessary...

  6. Formation fracturing by energy waves

    Energy Technology Data Exchange (ETDEWEB)

    Brandon, C W

    1966-11-28

    A method described for recovering oil from an oil strata penetrated by a well bore includes a step of applying fluid pressure to the interior of the well bore across the face of the stratum, and alternately varying the applied fluid pressure, first above and then below the reservoir pressure. This is in order to fracture and break up the face of the strata from internal pressure exerted on the strata. The pressure is affected using liquefied gas at low pressure across the formation.

  7. The Magnetic Free Energy in Active Regions

    Science.gov (United States)

    Metcalf, Thomas R.; Mickey, Donald L.; LaBonte, Barry J.

    2001-01-01

    The magnetic field permeating the solar atmosphere governs much of the structure, morphology, brightness, and dynamics observed on the Sun. The magnetic field, especially in active regions, is thought to provide the power for energetic events in the solar corona, such as solar flares and Coronal Mass Ejections (CME) and is believed to energize the hot coronal plasma seen in extreme ultraviolet or X-rays. The question remains what specific aspect of the magnetic flux governs the observed variability. To directly understand the role of the magnetic field in energizing the solar corona, it is necessary to measure the free magnetic energy available in active regions. The grant now expiring has demonstrated a new and valuable technique for observing the magnetic free energy in active regions as a function of time.

  8. Is the Free Vacuum Energy Infinite?

    International Nuclear Information System (INIS)

    Shirazi, S. M.; Razmi, H.

    2015-01-01

    Considering the fundamental cutoff applied by the uncertainty relations’ limit on virtual particles’ frequency in the quantum vacuum, it is shown that the vacuum energy density is proportional to the inverse of the fourth power of the dimensional distance of the space under consideration and thus the corresponding vacuum energy automatically regularized to zero value for an infinitely large free space. This can be used in regularizing a number of unwanted infinities that happen in the Casimir effect, the cosmological constant problem, and so on without using already known mathematical (not so reasonable) techniques and tricks

  9. The Formation of GM-free and GM Coasean Clubs

    NARCIS (Netherlands)

    Punt, Maarten J.; Wesseler, Justus

    2017-01-01

    The unintended presence of traces of genetically modified (GM) crops in the harvests of non-GM crops plays a prominent role in the debate over the coexistence of GM and non-GM crops. One way to address the issue is the formation of GM-free or GM-only clubs. We model the decisions of individual

  10. Holographic free energy and thermodynamic geometry

    Science.gov (United States)

    Ghorai, Debabrata; Gangopadhyay, Sunandan

    2016-12-01

    We obtain the free energy and thermodynamic geometry of holographic superconductors in 2+1 dimensions. The gravitational theory in the bulk dual to this 2+1-dimensional strongly coupled theory lives in the 3+1 dimensions and is that of a charged AdS black hole together with a massive charged scalar field. The matching method is applied to obtain the nature of the fields near the horizon using which the holographic free energy is computed through the gauge/gravity duality. The critical temperature is obtained for a set of values of the matching point of the near horizon and the boundary behaviour of the fields in the probe limit approximation which neglects the back reaction of the matter fields on the background spacetime geometry. The thermodynamic geometry is then computed from the free energy of the boundary theory. From the divergence of the thermodynamic scalar curvature, the critical temperature is obtained once again. We then compare this result for the critical temperature with that obtained from the matching method.

  11. Holographic free energy and thermodynamic geometry

    International Nuclear Information System (INIS)

    Ghorai, Debabrata; Gangopadhyay, Sunandan

    2016-01-01

    We obtain the free energy and thermodynamic geometry of holographic superconductors in 2 + 1 dimensions. The gravitational theory in the bulk dual to this 2 + 1-dimensional strongly coupled theory lives in the 3 + 1 dimensions and is that of a charged AdS black hole together with a massive charged scalar field. The matching method is applied to obtain the nature of the fields near the horizon using which the holographic free energy is computed through the gauge/gravity duality. The critical temperature is obtained for a set of values of the matching point of the near horizon and the boundary behaviour of the fields in the probe limit approximation which neglects the back reaction of the matter fields on the background spacetime geometry. The thermodynamic geometry is then computed from the free energy of the boundary theory. From the divergence of the thermodynamic scalar curvature, the critical temperature is obtained once again. We then compare this result for the critical temperature with that obtained from the matching method. (orig.)

  12. Holographic free energy and thermodynamic geometry

    Energy Technology Data Exchange (ETDEWEB)

    Ghorai, Debabrata [S.N. Bose National Centre for Basic Sciences, Kolkata (India); Gangopadhyay, Sunandan [Indian Institute of Science Education and Research, Kolkata, Nadia (India); West Bengal State University, Department of Physics, Barasat (India); Inter University Centre for Astronomy and Astrophysics, Pune (India)

    2016-12-15

    We obtain the free energy and thermodynamic geometry of holographic superconductors in 2 + 1 dimensions. The gravitational theory in the bulk dual to this 2 + 1-dimensional strongly coupled theory lives in the 3 + 1 dimensions and is that of a charged AdS black hole together with a massive charged scalar field. The matching method is applied to obtain the nature of the fields near the horizon using which the holographic free energy is computed through the gauge/gravity duality. The critical temperature is obtained for a set of values of the matching point of the near horizon and the boundary behaviour of the fields in the probe limit approximation which neglects the back reaction of the matter fields on the background spacetime geometry. The thermodynamic geometry is then computed from the free energy of the boundary theory. From the divergence of the thermodynamic scalar curvature, the critical temperature is obtained once again. We then compare this result for the critical temperature with that obtained from the matching method. (orig.)

  13. Enthalpy and interfacial free energy changes of water capillary condensed in mesoporous silica, MCM-41 and SBA-15.

    Science.gov (United States)

    Kittaka, Shigeharu; Ishimaru, Shinji; Kuranishi, Miki; Matsuda, Tomoko; Yamaguchi, Toshio

    2006-07-21

    The effect of confinement on the solid-liquid phase transitions of water was studied by using DSC and FT-IR measurements. Enthalpy changes upon melting of frozen water in MCM-41 and SBA-15 were determined as a function of pore size and found to decrease with decreasing pore size. The melting point also decreased almost monotonically with a decrease in pore size. Analysis of the Gibbs-Thomson relation on the basis of the thermodynamic data showed that there were two stages of interfacial free energy change after the constant region, i.e., below a pore size of 6.0 nm: a gradual decrease down to 3.4 nm and another decrease after a small jump upward. This fact demonstrates that the simple Gibbs-Thomson relation, i.e., a linear relation between the melting point change and the inverse pore size, is limited to the range not far from the melting point of bulk water. FT-IR measurements suggest that the decrease in enthalpy change and interfacial free energy change with decreasing pore size reflect the similarity of the structures of both liquid and solid phases of water in smaller pores at lower temperatures.

  14. Arbitrage-free valuation of energy derivatives

    International Nuclear Information System (INIS)

    Amin, K.; Ng, V.; Pirrong, C.

    1999-01-01

    This chapter focuses on techniques available for valuing energy-contingent claims and develops an arbitrage-free framework to value energy derivatives. The relationship between the spot, forward and futures prices is explained. Option valuation with deterministic convenience yields is discussed using an extension of the Black (1976) framework, and details of the risk-neutral valuation of European options, and valuation of American and European-style options are given. Option valuations with stochastic convenience yields, the evolution of the term structure of convenience yield, and a tree approach to valuing American and other options are discussed. Applications and limitations of the models for pricing energy derivative products are considered. The stochastic differential equation for the futures prices when the convenience yields are stochastic is presented in an appendix

  15. Assessment of CO2 free energy options

    International Nuclear Information System (INIS)

    Cavlina, N.; Raseta, D.; Matutinovic, I.

    2014-01-01

    One of the European Union climate and energy targets is to significantly reduce CO 2 emissions, at least 20% by 2020, compared to 1990. In the power industry, most popular solution is use of solar and wind power. Since their production varies significantly during the day, for the purpose of base-load production they can be paired with gas-fired power plant. Other possible CO 2 -free solution is nuclear power plant. This article compared predicted cost of energy production for newly built nuclear power plant and newly built combination of wind or solar and gas-fired power plant. Comparison was done using Levelized Unit of Energy Cost (LUEC). Calculations were performed using the Monte Carlo method. For input parameters that have biggest uncertainty (gas cost, CO 2 emission fee) those uncertainties were addressed not only through probability distribution around predicted value, but also through different scenarios. Power plants were compared based on their economic lifetime. (authors)

  16. Free energy landscape and molecular pathways of gas hydrate nucleation

    International Nuclear Information System (INIS)

    Bi, Yuanfei; Porras, Anna; Li, Tianshu

    2016-01-01

    Despite the significance of gas hydrates in diverse areas, a quantitative knowledge of hydrate formation at a molecular level is missing. The impediment to acquiring this understanding is primarily attributed to the stochastic nature and ultra-fine scales of nucleation events, posing a great challenge for both experiment and simulation to explore hydrate nucleation. Here we employ advanced molecular simulation methods, including forward flux sampling (FFS), p B histogram analysis, and backward flux sampling, to overcome the limit of direct molecular simulation for exploring both the free energy landscape and molecular pathways of hydrate nucleation. First we test the half-cage order parameter (H-COP) which we developed for driving FFS, through conducting the p B histogram analysis. Our results indeed show that H-COP describes well the reaction coordinates of hydrate nucleation. Through the verified order parameter, we then directly compute the free energy landscape for hydrate nucleation by combining both forward and backward flux sampling. The calculated stationary distribution density, which is obtained independently of nucleation theory, is found to fit well against the classical nucleation theory (CNT). Subsequent analysis of the obtained large ensemble of hydrate nucleation trajectories show that although on average, hydrate formation is facilitated by a two-step like mechanism involving a gradual transition from an amorphous to a crystalline structure, there also exist nucleation pathways where hydrate crystallizes directly, without going through the amorphous stage. The CNT-like free energy profile and the structural diversity suggest the existence of multiple active transition pathways for hydrate nucleation, and possibly also imply the near degeneracy in their free energy profiles among different pathways. Our results thus bring a new perspective to the long standing question of how hydrates crystallize.

  17. Free energy landscape and molecular pathways of gas hydrate nucleation.

    Science.gov (United States)

    Bi, Yuanfei; Porras, Anna; Li, Tianshu

    2016-12-07

    Despite the significance of gas hydrates in diverse areas, a quantitative knowledge of hydrate formation at a molecular level is missing. The impediment to acquiring this understanding is primarily attributed to the stochastic nature and ultra-fine scales of nucleation events, posing a great challenge for both experiment and simulation to explore hydrate nucleation. Here we employ advanced molecular simulation methods, including forward flux sampling (FFS), p B histogram analysis, and backward flux sampling, to overcome the limit of direct molecular simulation for exploring both the free energy landscape and molecular pathways of hydrate nucleation. First we test the half-cage order parameter (H-COP) which we developed for driving FFS, through conducting the p B histogram analysis. Our results indeed show that H-COP describes well the reaction coordinates of hydrate nucleation. Through the verified order parameter, we then directly compute the free energy landscape for hydrate nucleation by combining both forward and backward flux sampling. The calculated stationary distribution density, which is obtained independently of nucleation theory, is found to fit well against the classical nucleation theory (CNT). Subsequent analysis of the obtained large ensemble of hydrate nucleation trajectories show that although on average, hydrate formation is facilitated by a two-step like mechanism involving a gradual transition from an amorphous to a crystalline structure, there also exist nucleation pathways where hydrate crystallizes directly, without going through the amorphous stage. The CNT-like free energy profile and the structural diversity suggest the existence of multiple active transition pathways for hydrate nucleation, and possibly also imply the near degeneracy in their free energy profiles among different pathways. Our results thus bring a new perspective to the long standing question of how hydrates crystallize.

  18. Free energy landscape and molecular pathways of gas hydrate nucleation

    Energy Technology Data Exchange (ETDEWEB)

    Bi, Yuanfei; Porras, Anna; Li, Tianshu, E-mail: tsli@gwu.edu [Department of Civil and Environmental Engineering, George Washington University, Washington DC 20052 (United States)

    2016-12-07

    Despite the significance of gas hydrates in diverse areas, a quantitative knowledge of hydrate formation at a molecular level is missing. The impediment to acquiring this understanding is primarily attributed to the stochastic nature and ultra-fine scales of nucleation events, posing a great challenge for both experiment and simulation to explore hydrate nucleation. Here we employ advanced molecular simulation methods, including forward flux sampling (FFS), p{sub B} histogram analysis, and backward flux sampling, to overcome the limit of direct molecular simulation for exploring both the free energy landscape and molecular pathways of hydrate nucleation. First we test the half-cage order parameter (H-COP) which we developed for driving FFS, through conducting the p{sub B} histogram analysis. Our results indeed show that H-COP describes well the reaction coordinates of hydrate nucleation. Through the verified order parameter, we then directly compute the free energy landscape for hydrate nucleation by combining both forward and backward flux sampling. The calculated stationary distribution density, which is obtained independently of nucleation theory, is found to fit well against the classical nucleation theory (CNT). Subsequent analysis of the obtained large ensemble of hydrate nucleation trajectories show that although on average, hydrate formation is facilitated by a two-step like mechanism involving a gradual transition from an amorphous to a crystalline structure, there also exist nucleation pathways where hydrate crystallizes directly, without going through the amorphous stage. The CNT-like free energy profile and the structural diversity suggest the existence of multiple active transition pathways for hydrate nucleation, and possibly also imply the near degeneracy in their free energy profiles among different pathways. Our results thus bring a new perspective to the long standing question of how hydrates crystallize.

  19. ON A PARABOLIC FREE BOUNDARY EQUATION MODELING PRICE FORMATION

    KAUST Repository

    MARKOWICH, P. A.

    2009-10-01

    We discuss existence and uniqueness of solutions for a one-dimensional parabolic evolution equation with a free boundary. This problem was introduced by Lasry and Lions as description of the dynamical formation of the price of a trading good. Short time existence and uniqueness is established by a contraction argument. Then we discuss the issue of global-in-time-extension of the local solution which is closely related to the regularity of the free boundary. We also present numerical results. © 2009 World Scientific Publishing Company.

  20. ON A PARABOLIC FREE BOUNDARY EQUATION MODELING PRICE FORMATION

    KAUST Repository

    MARKOWICH, P. A.; MATEVOSYAN, N.; PIETSCHMANN, J.-F.; WOLFRAM, M.-T.

    2009-01-01

    We discuss existence and uniqueness of solutions for a one-dimensional parabolic evolution equation with a free boundary. This problem was introduced by Lasry and Lions as description of the dynamical formation of the price of a trading good. Short time existence and uniqueness is established by a contraction argument. Then we discuss the issue of global-in-time-extension of the local solution which is closely related to the regularity of the free boundary. We also present numerical results. © 2009 World Scientific Publishing Company.

  1. Local thermodynamics and the generalized Gibbs-Duhem equation in systems with long-range interactions.

    Science.gov (United States)

    Latella, Ivan; Pérez-Madrid, Agustín

    2013-10-01

    The local thermodynamics of a system with long-range interactions in d dimensions is studied using the mean-field approximation. Long-range interactions are introduced through pair interaction potentials that decay as a power law in the interparticle distance. We compute the local entropy, Helmholtz free energy, and grand potential per particle in the microcanonical, canonical, and grand canonical ensembles, respectively. From the local entropy per particle we obtain the local equation of state of the system by using the condition of local thermodynamic equilibrium. This local equation of state has the form of the ideal gas equation of state, but with the density depending on the potential characterizing long-range interactions. By volume integration of the relation between the different thermodynamic potentials at the local level, we find the corresponding equation satisfied by the potentials at the global level. It is shown that the potential energy enters as a thermodynamic variable that modifies the global thermodynamic potentials. As a result, we find a generalized Gibbs-Duhem equation that relates the potential energy to the temperature, pressure, and chemical potential. For the marginal case where the power of the decaying interaction potential is equal to the dimension of the space, the usual Gibbs-Duhem equation is recovered. As examples of the application of this equation, we consider spatially uniform interaction potentials and the self-gravitating gas. We also point out a close relationship with the thermodynamics of small systems.

  2. Equilibrium Crystal Shape of BaZrO{sub 3} and Space Charge Formation in the (011) Surface by Using Ab-Initio Thermodynamics

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Ji-Su; Kim, Yeong-Cheol [Korea University of Technology and Education, Cheonan (Korea, Republic of)

    2017-01-15

    We investigated the equilibrium crystal shape of BaZrO{sub 3} and the space charge formation in an O-terminated (011) surface by using ab-initio thermodynamics. Twenty-two low-indexed (001), (011), and (111) surfaces were calculated to analyze their surface Gibbs-free energy under the stable condition of BaZrO{sub 3}. Based on the Gibbs-Wulff theorem, the equilibrium crystal shape of BaZrO{sub 3} changed from cubic to decaoctahedral with decreasing Ba chemical potential. The dominant facets of BaZrO{sub 3} were {001} and {011}, which were well consistent with experimental observations. The space charge formation in the (011) surface was evaluated using the space-charge model. We found that the (011) surface was even more resistive than the (001) surface.

  3. Development of a group contribution method for estimating free energy of peptides in a dodecane-water system via molecular dynamic simulations.

    Science.gov (United States)

    Mora Osorio, Camilo Andrés; González Barrios, Andrés Fernando

    2016-12-07

    Calculation of the Gibbs free energy changes of biological molecules at the oil-water interface is commonly performed with Molecular Dynamics simulations (MD). It is a process that could be performed repeatedly in order to find some molecules of high stability in this medium. Here, an alternative method of calculation has been proposed: a group contribution method (GCM) for peptides based on MD of the twenty classic amino acids to obtain free energy change during the insertion of any peptide chain in water-dodecane interfaces. Multiple MD of the twenty classic amino acids located at the interface of rectangular simulation boxes with a dodecane-water medium were performed. A GCM to calculate the free energy of entire peptides is then proposed. The method uses the summation of the Gibbs free energy of each amino acid adjusted in function of its presence or absence in the chain as well as its hydrophobic characteristics. Validation of the equation was performed with twenty-one peptides all simulated using MD in dodecane-water rectangular boxes in previous work, obtaining an average relative error of 16%.

  4. Exploration, Novelty, Surprise and Free Energy Minimisation

    Directory of Open Access Journals (Sweden)

    Philipp eSchwartenbeck

    2013-10-01

    Full Text Available This paper reviews recent developments under the free energy principle that introduce a normative perspective on classical economic (utilitarian decision-making based on (active Bayesian inference. It has been suggested that the free energy principle precludes novelty and complexity, because it assumes that biological systems – like ourselves - try to minimise the long-term average of surprise to maintain their homeostasis. However, recent formulations show that minimising surprise leads naturally to concepts such as exploration and novelty bonuses. In this approach, agents infer a policy that minimises surprise by minimising the difference (or relative entropy between likely and desired outcomes, which involves both pursuing the goal-state that has the highest expected utility (often termed ‘exploitation’ and visiting a number of different goal-states (‘exploration’. Crucially, the opportunity to visit new states increases the value of the current state. Casting decision-making problems within a variational framework, therefore, predicts that our behaviour is governed by both the entropy and expected utility of future states. This dissolves any dialectic between minimising surprise and exploration or novelty seeking.

  5. Calculation of liquid-liquid equilibrium of aqueous two-phase systems using a chemical-theory-based excess Gibbs energy model

    Directory of Open Access Journals (Sweden)

    Pessôa Filho P. A.

    2004-01-01

    Full Text Available Mixtures containing compounds that undergo hydrogen bonding show large deviations from ideal behavior. These deviations can be accounted for through chemical theory, according to which the formation of a hydrogen bond can be treated as a chemical reaction. This chemical equilibrium needs to be taken into account when applying stability criteria and carrying out phase equilibrium calculations. In this work, we illustrate the application of the stability criteria to establish the conditions under which a liquid-phase split may occur and the subsequent calculation of liquid-liquid equilibrium using a chemical-theory-modified Flory-Huggins equation to describe the non ideality of aqueous two-phase systems composed of poly(ethylene glycol and dextran. The model was found to be able to correlate ternary liquid-liquid diagrams reasonably well by simple adjustment of the polymer-polymer binary interaction parameter.

  6. The Limit of Free Magnetic Energy in Active Regions

    Science.gov (United States)

    Moore, Ron; Falconer, David; Sterling, Alphonse

    2012-01-01

    By measuring from active-region magnetograms a proxy of the free energy in the active region fs magnetic field, it has been found previously that (1) there is an abrupt upper limit to the free energy the field can hold that increases with the amount of magnetic field in the active region, the active region fs magnetic flux content, and (2) the free energy is usually near its limit when the field explodes in a CME/flare eruption. That is, explosive active regions are concentrated in a main-sequence path bordering the free-energy ]limit line in (flux content, free-energy proxy) phase space. Here, from measurement of Marshall Space Flight Center vector magnetograms, we find the magnetic condition that underlies the free ]energy limit and the accompanying main sequence of explosive active regions. Using a suitable free ]energy proxy measured from vector magnetograms of 44 active regions, we find that (1) in active regions at and near their free ]energy limit, the ratio of magnetic-shear free energy to the non ]free magnetic energy the potential field would have is approximately 1 in the core field, the field rooted along the neutral line, and (2) this ratio is progressively less in active regions progressively farther below their free ]energy limit. This shows that most active regions in which this core-field energy ratio is much less than 1 cannot be triggered to explode; as this ratio approaches 1, most active regions become capable of exploding; and when this ratio is 1 or greater, most active regions are compelled to explode. From these results we surmise the magnetic condition that determines the free ]energy limit is the ratio of the free magnetic energy to the non-free energy the active region fs field would have were it completely relaxed to its potential ]field configuration, and that this ratio is approximately 1 at the free-energy limit and in the main sequence of explosive active regions.

  7. Generalized formulation of free energy and application to photosynthesis

    Science.gov (United States)

    Zhang, Hwe Ik; Choi, M. Y.

    2018-03-01

    The origin of free energy on the earth is solar radiation. However, the amount of free energy it contains has seldom been investigated, because the free energy concept was believed to be inappropriate for a system of photons. Instead, the origin of free energy has been sought in the process of photosynthesis, imposing a limit of conversion given by the Carnot efficiency. Here we present a general formulation, capable of not only assessing accurately the available amount of free energy in the photon gas but also explaining the primary photosynthetic process more succinctly. In this formulation, the problem of "photosynthetic conversion of the internal energy of photons into the free energy of chlorophyll" is replaced by simple "free energy transduction" between the photons and chlorophyll. An analytic expression for the photosynthetic efficiency is derived and shown to deviate from the Carnot efficiency. Some predictions verifiable possibly by observation are also suggested.

  8. Gibbs' theorem for open systems with incomplete statistics

    International Nuclear Information System (INIS)

    Bagci, G.B.

    2009-01-01

    Gibbs' theorem, which is originally intended for canonical ensembles with complete statistics has been generalized to open systems with incomplete statistics. As a result of this generalization, it is shown that the stationary equilibrium distribution of inverse power law form associated with the incomplete statistics has maximum entropy even for open systems with energy or matter influx. The renormalized entropy definition given in this paper can also serve as a measure of self-organization in open systems described by incomplete statistics.

  9. Extension of Gibbs-Duhem equation including influences of external fields

    Science.gov (United States)

    Guangze, Han; Jianjia, Meng

    2018-03-01

    Gibbs-Duhem equation is one of the fundamental equations in thermodynamics, which describes the relation among changes in temperature, pressure and chemical potential. Thermodynamic system can be affected by external field, and this effect should be revealed by thermodynamic equations. Based on energy postulate and the first law of thermodynamics, the differential equation of internal energy is extended to include the properties of external fields. Then, with homogeneous function theorem and a redefinition of Gibbs energy, a generalized Gibbs-Duhem equation with influences of external fields is derived. As a demonstration of the application of this generalized equation, the influences of temperature and external electric field on surface tension, surface adsorption controlled by external electric field, and the derivation of a generalized chemical potential expression are discussed, which show that the extended Gibbs-Duhem equation developed in this paper is capable to capture the influences of external fields on a thermodynamic system.

  10. Free Magnetic Energy and Coronal Heating

    Science.gov (United States)

    Winebarger, Amy; Moore, Ron; Falconer, David

    2012-01-01

    Previous work has shown that the coronal X-ray luminosity of an active region increases roughly in direct proportion to the total photospheric flux of the active region's magnetic field (Fisher et al. 1998). It is also observed, however, that the coronal luminosity of active regions of nearly the same flux content can differ by an order of magnitude. In this presentation, we analyze 10 active regions with roughly the same total magnetic flux. We first determine several coronal properties, such as X-ray luminosity (calculated using Hinode XRT), peak temperature (calculated using Hinode EIS), and total Fe XVIII emission (calculated using SDO AIA). We present the dependence of these properties on a proxy of the free magnetic energy of the active region

  11. Postselection-free energy-time entanglement

    International Nuclear Information System (INIS)

    Strekalov, D.V.; Pittman, T.B.; Sergienko, A.V.; Shih, Y.H.; Kwiat, P.G.

    1996-01-01

    We report a two-photon interference experiment that realizes a postselection-free test of Bell close-quote s inequality based on energy-time entanglement. In contrast with all previous experiments of this type, the employed entangled states are obtained without the use of a beam splitter or a short coincidence window to open-quote open-quote throw away close-quote close-quote unwanted amplitudes. A (95.0±1.4)% interference fringe visibility is observed, implying a strong violation of the Bell inequality. The scheme is very compact and has demonstrated excellent stability, suggesting that it may be useful, for example, in practical quantum cryptography. copyright 1996 The American Physical Society

  12. Crystal-free Formation of Non-Oxide Optical Fiber

    Science.gov (United States)

    Nabors, Sammy A.

    2015-01-01

    Researchers at NASA Marshall Space Flight Center have devised a method for the creation of crystal-free nonoxide optical fiber preforms. Non-oxide fiber optics are extensively used in infrared transmitting applications such as communication systems, chemical sensors, and laser fiber guides for cutting, welding and medical surgery. However, some of these glasses are very susceptible to crystallization. Even small crystals can lead to light scatter and a high attenuation coefficient, limiting their usefulness. NASA has developed a new method of non-oxide fiber formation that uses axial magnetic fields to suppress crystallization. The resulting non-oxide fibers are crystal free and have lower signal attenuation rates than silica based optical fibers.

  13. Free energy landscape of a minimalist salt bridge model.

    Science.gov (United States)

    Li, Xubin; Lv, Chao; Corbett, Karen M; Zheng, Lianqing; Wu, Dongsheng; Yang, Wei

    2016-01-01

    Salt bridges are essential to protein stability and dynamics. Despite the importance, there has been scarce of detailed discussion on how salt bridge partners interact with each other in distinct solvent exposed environments. In this study, employing a recent generalized orthogonal space tempering (gOST) method, we enabled efficient molecular dynamics simulation of repetitive breaking and reforming of salt bridge structures within a minimalist salt-bridge model, the Asp-Arg dipeptide and thereby were able to map its detailed free energy landscape in aqueous solution. Free energy surface analysis shows that although individually-solvated states are more favorable, salt-bridge states still occupy a noticeable portion of the overall population. Notably, the competing forces, e.g. intercharge attractions that drive the formation of salt bridges and solvation forces that pull the charged groups away from each other, are energetically comparable. As the result, the salt bridge stability is highly tunable by local environments; for instance when local water molecules are perturbed to interact more strongly with each other, the population of the salt-bridge states is likely to increase. Our results reveal the critical role of local solvent structures in modulating salt-bridge partner interactions and imply the importance of water fluctuations on conformational dynamics that involves solvent accessible salt bridge formations. © 2015 The Protein Society.

  14. The Formation of GM-free and GM Coasean Clubs

    DEFF Research Database (Denmark)

    Punt, Maarten J.; Wesseler, Justus

    2018-01-01

    The unintended presence of traces of genetically modified (GM) crops in the harvests of non-GM crops plays a prominent role in the debate over the coexistence of GM and non-GM crops. One way to address the issue is the formation of GM-free or GM-only clubs. We model the decisions of individual...... farmers to cultivate either GM or non-GM crops and combine this with a game theoretic model of club formation to investigate the feasibility of such clubs. We consider two liability regimes: GM farmers are liable or they are not.We consider two benchmarks: Nash equilibrium without negotiations......, they reach 95% of an efficient allocation. This holds independent of the property rights system and provides strong support for coexistence policies based on ex-post liability such as in the US and Spain....

  15. Towards a fossil free energy future. The next energy transition

    Energy Technology Data Exchange (ETDEWEB)

    Lazarus, M.; Greber, L.; Hall, J.; Bartels, C.; Bernow, S.; Hansen, E.; Raskin, P.; Von Hippel, D. (Stockholm Environment Institute, Boston, MA (United States))

    1993-04-01

    The report provides technical analysis and documentation as input to the Greenpeace project 'Towards a fossil free energy future'. It presents a main scenario and several variants for reducing greenhouse gas emissions, and the technical methods and assumptions used to develop them. The goal is to investigate the technical, economic and policy feasibility to phasing out fossil fuels over the next century as part of a strategy to avert unacceptably high levels or rates of global warming. 209 refs., 42 figs., 27 tabs.

  16. Evaluation of potential reaction mechanisms leading to the formation of coniferyl alcohol α-linkages in lignin: a density functional theory study.

    Science.gov (United States)

    Watts, Heath D; Mohamed, Mohamed Naseer Ali; Kubicki, James D

    2011-12-21

    Five potential reaction mechanisms, each leading to the formation of an α-O-4-linked coniferyl alcohol dimer, and one scheme leading to the formation of a recently proposed free-radical coniferyl alcohol trimer were assessed using density functional theory (DFT) calculations. These potential reaction mechanisms were evaluated using both the calculated Gibbs free energies, to predict the spontaneity of the constituent reactions, and the electron-density mapped Fukui function, to determine the most reactive sites of each intermediate species. The results indicate that each reaction in one of the six mechanisms is thermodynamically favorable to those in the other mechanisms; what is more, the Fukui function for each free radical intermediate corroborates with the thermochemical results for this mechanism. This mechanism proceeds via the formation of two distinct free-radical intermediates, which then react to produce the four α-O-4 stereoisomers.

  17. A Carbon-Free Energy Future

    Science.gov (United States)

    Linden, H. R.; Singer, S. F.

    2001-12-01

    It is generally agreed that hydrogen is an ideal energy source, both for transportation and for the generation of electric power. Through the use of fuel cells, hydrogen becomes a high-efficiency carbon-free power source for electromotive transport; with the help of regenerative braking, cars should be able to reach triple the current mileage. Many have visualized a distributed electric supply network with decentralized generation based on fuel cells. Fuel cells can provide high generation efficiencies by overcoming the fundamental thermodynamic limitation imposed by the Carnot cycle. Further, by using the heat energy of the high-temperature fuel cell in co-generation, one can achieve total thermal efficiencies approaching 100 percent, as compared to present-day average power-plant efficiencies of around 35 percent. In addition to reducing CO2 emissions, distributed generation based on fuel cells also eliminates the tremendous release of waste heat into the environment, the need for cooling water, and related limitations on siting. Manufacture of hydrogen remains a key problem, but there are many technical solutions that come into play whenever the cost equations permit . One can visualize both central and local hydrogen production. Initially, reforming of abundant natural gas into mixtures of 80% H2 and 20% CO2 provides a relatively low-emission source of hydrogen. Conventional fossil-fuel plants and nuclear plants can become hydrogen factories using both high-temperature topping cycles and electrolysis of water. Hydro-electric plants can manufacture hydrogen by electrolysis. Later, photovoltaic and wind farms could be set up at favorable locations around the world as hydrogen factories. If perfected, photovoltaic hydrogen production through catalysis would use solar photons most efficiently . For both wind and PV, hydrogen production solves some crucial problems: intermittency of wind and of solar radiation, storage of energy, and use of locations that are not

  18. Notes on the development of the gibbs potential; Sur le developpement du potentiel de gibbs

    Energy Technology Data Exchange (ETDEWEB)

    Bloch, C; Dominicis, C de [Commissariat a l' Energie Atomique, Saclay (France).Centre d' Etudes Nucleaires

    1959-07-01

    A short account is given of some recent work on the perturbation expansion of the Gibbs potential of quantum statistical mechanics. (author) [French] Expose en resume de quelques travaux sur le developpement dans la theorie des perturbations du potentiel de Gibbs de la Mecanique Statistique. (auteur)

  19. Variación de la energía libre de Gibbs de la caolinita en función de la cristalinidad y tamaño de partícula

    Directory of Open Access Journals (Sweden)

    La Iglesia, A.

    1989-12-01

    Full Text Available The effect of grinding on crystallinity, particle size and solubility of two samples of kaolinite was studied. The standard Gibbs free energies of formation of different ground samples were calculated from solubility measurements, and show a direct relationship between Gibbs free energy and particle size-crystallinity variation. Values of -3752.2 and -3776.4 KJ/mol. were determinated for ΔGºl (am and ΔGºl (crys of kaolinite, respectively. A new thermodinamic equation that relates ΔGºl to particle size is proposed. This equation can probably be extended to clay mineals.Se estudia el efecto de la molienda prolongada sobre la cristalinidad, tamaño de partícula y solubilidad de dos muestras de caolinita. Se ha calculado la energía libre estandar de formación del mineral a partir de medidas de solubilidad, encontrando una relación directa entre ΔGºl, y las variaciones de tamaño de partícula y cristalinidad de las muestras. Por extrapolación, se han obtenido los valores de -3752,0 y -3776,4 KJ/mol. para ΔGºl caolinita amorfa y cristalina. Se propone una ecuación termodinámica que relaciona ΔGºl y el tamaño de partícula de la caolinita; esta ecuación puede aplicarse también a otros minerales de la arcilla.

  20. Free energy change of a dislocation due to a Cottrell atmosphere

    Science.gov (United States)

    Sills, R. B.; Cai, W.

    2018-06-01

    The free energy reduction of a dislocation due to a Cottrell atmosphere of solutes is computed using a continuum model. We show that the free energy change is composed of near-core and far-field components. The far-field component can be computed analytically using the linearized theory of solid solutions. Near the core the linearized theory is inaccurate, and the near-core component must be computed numerically. The influence of interactions between solutes in neighbouring lattice sites is also examined using the continuum model. We show that this model is able to reproduce atomistic calculations of the nickel-hydrogen system, predicting hydride formation on dislocations. The formation of these hydrides leads to dramatic reductions in the free energy. Finally, the influence of the free energy change on a dislocation's line tension is examined by computing the equilibrium shape of a dislocation shear loop and the activation stress for a Frank-Read source using discrete dislocation dynamics.

  1. Temperature dependence of grain boundary free energy and elastic constants

    International Nuclear Information System (INIS)

    Foiles, Stephen M.

    2010-01-01

    This work explores the suggestion that the temperature dependence of the grain boundary free energy can be estimated from the temperature dependence of the elastic constants. The temperature-dependent elastic constants and free energy of a symmetric Σ79 tilt boundary are computed for an embedded atom method model of Ni. The grain boundary free energy scales with the product of the shear modulus times the lattice constant for temperatures up to about 0.75 the melting temperature.

  2. Evolution algebras generated by Gibbs measures

    International Nuclear Information System (INIS)

    Rozikov, Utkir A.; Tian, Jianjun Paul

    2009-03-01

    In this article we study algebraic structures of function spaces defined by graphs and state spaces equipped with Gibbs measures by associating evolution algebras. We give a constructive description of associating evolution algebras to the function spaces (cell spaces) defined by graphs and state spaces and Gibbs measure μ. For finite graphs we find some evolution subalgebras and other useful properties of the algebras. We obtain a structure theorem for evolution algebras when graphs are finite and connected. We prove that for a fixed finite graph, the function spaces have a unique algebraic structure since all evolution algebras are isomorphic to each other for whichever Gibbs measures are assigned. When graphs are infinite graphs then our construction allows a natural introduction of thermodynamics in studying of several systems of biology, physics and mathematics by theory of evolution algebras. (author)

  3. A Free Energy Model for Hysteresis Ferroelectric Materials

    National Research Council Canada - National Science Library

    Smith, Ralph C; Ounaies, Zoubeida; Seelecke, Stefan; Smith, Joshua

    2003-01-01

    This paper provides a theory for quantifying the hysteresis and constitutive nonlinearities inherent to piezoceramic compounds through a combination of free energy analysis and stochastic homogenization techniques...

  4. Simulations of Skin Barrier Function: Free Energies of Hydrophobic and Hydrophilic Transmembrane Pores in Ceramide Bilayers

    OpenAIRE

    Notman, Rebecca; Anwar, Jamshed; Briels, W. J.; Noro, Massimo G.; den Otter, Wouter K.

    2008-01-01

    Transmembrane pore formation is central to many biological processes such as ion transport, cell fusion, and viral infection. Furthermore, pore formation in the ceramide bilayers of the stratum corneum may be an important mechanism by which penetration enhancers such as dimethylsulfoxide (DMSO) weaken the barrier function of the skin. We have used the potential of mean constraint force (PMCF) method to calculate the free energy of pore formation in ceramide bilayers in both the innate gel pha...

  5. Free-Energy Calculations. A Mathematical Perspective

    Science.gov (United States)

    Pohorille, Andrzej

    2015-01-01

    conductance, defined as the ratio of ionic current through the channel to applied voltage, can be calculated in MD simulations by way of applying an external electric field to the system and counting the number of ions that traverse the channel per unit time. If the current is small, a voltage significantly higher than the experimental one needs to be applied to collect sufficient statistics of ion crossing events. Then, the calculated conductance has to be extrapolated to the experimental voltage using procedures of unknown accuracy. Instead, we propose an alternative approach that applies if ion transport through channels can be described with sufficient accuracy by the one-dimensional diffusion equation in the potential given by the free energy profile and applied voltage. Then, it is possible to test the assumptions of the equation, recover the full voltage/current dependence, determine the reliability of the calculated conductance and reconstruct the underlying (equilibrium) free energy profile, all from MD simulations at a single voltage. We will present the underlying theory, model calculations that test this theory and simulations on ion conductance through a channel that has been extensively studied experimentally. To our knowledge this is the first case in which the complete, experimentally measured dependence of the current on applied voltage has been reconstructed from MD simulations.

  6. Diabat Interpolation for Polymorph Free-Energy Differences.

    Science.gov (United States)

    Kamat, Kartik; Peters, Baron

    2017-02-02

    Existing methods to compute free-energy differences between polymorphs use harmonic approximations, advanced non-Boltzmann bias sampling techniques, and/or multistage free-energy perturbations. This work demonstrates how Bennett's diabat interpolation method ( J. Comput. Phys. 1976, 22, 245 ) can be combined with energy gaps from lattice-switch Monte Carlo techniques ( Phys. Rev. E 2000, 61, 906 ) to swiftly estimate polymorph free-energy differences. The new method requires only two unbiased molecular dynamics simulations, one for each polymorph. To illustrate the new method, we compute the free-energy difference between face-centered cubic and body-centered cubic polymorphs for a Gaussian core solid. We discuss the justification for parabolic models of the free-energy diabats and similarities to methods that have been used in studies of electron transfer.

  7. Universal Scaling Relations in Scale-Free Structure Formation

    Science.gov (United States)

    Guszejnov, Dávid; Hopkins, Philip F.; Grudić, Michael Y.

    2018-04-01

    A large number of astronomical phenomena exhibit remarkably similar scaling relations. The most well-known of these is the mass distribution dN/dM∝M-2 which (to first order) describes stars, protostellar cores, clumps, giant molecular clouds, star clusters and even dark matter halos. In this paper we propose that this ubiquity is not a coincidence and that it is the generic result of scale-free structure formation where the different scales are uncorrelated. We show that all such systems produce a mass function proportional to M-2 and a column density distribution with a power law tail of dA/d lnΣ∝Σ-1. In the case where structure formation is controlled by gravity the two-point correlation becomes ξ2D∝R-1. Furthermore, structures formed by such processes (e.g. young star clusters, DM halos) tend to a ρ∝R-3 density profile. We compare these predictions with observations, analytical fragmentation cascade models, semi-analytical models of gravito-turbulent fragmentation and detailed "full physics" hydrodynamical simulations. We find that these power-laws are good first order descriptions in all cases.

  8. Catholyte-Free Electrocatalytic CO2 Reduction to Formate.

    Science.gov (United States)

    Lee, Wonhee; Kim, Young Eun; Youn, Min Hye; Jeong, Soon Kwan; Park, Ki Tae

    2018-04-16

    Electrochemical reduction of carbon dioxide (CO 2 ) into value-added chemicals is a promising strategy to reduce CO 2 emission and mitigate climate change. One of the most serious problems in electrocatalytic CO 2 reduction (CO 2 R) is the low solubility of CO 2 in an aqueous electrolyte, which significantly limits the cathodic reaction rate. This paper proposes a facile method of catholyte-free electrocatalytic CO 2 reduction to avoid the solubility limitation using commercial tin nanoparticles as a cathode catalyst. Interestingly, as the reaction temperature rises from 303 K to 363 K, the partial current density (PCD) of formate improves more than two times with 52.9 mA cm -2 , despite the decrease in CO 2 solubility. Furthermore, a significantly high formate concentration of 41.5 g L -1 is obtained as a one-path product at 343 K with high PCD (51.7 mA cm -2 ) and high Faradaic efficiency (93.3 %) via continuous operation in a full flow cell at a low cell voltage of 2.2 V. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  9. 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.

  10. Finite Cycle Gibbs Measures on Permutations of

    Science.gov (United States)

    Armendáriz, Inés; Ferrari, Pablo A.; Groisman, Pablo; Leonardi, Florencia

    2015-03-01

    We consider Gibbs distributions on the set of permutations of associated to the Hamiltonian , where is a permutation and is a strictly convex potential. Call finite-cycle those permutations composed by finite cycles only. We give conditions on ensuring that for large enough temperature there exists a unique infinite volume ergodic Gibbs measure concentrating mass on finite-cycle permutations; this measure is equal to the thermodynamic limit of the specifications with identity boundary conditions. We construct as the unique invariant measure of a Markov process on the set of finite-cycle permutations that can be seen as a loss-network, a continuous-time birth and death process of cycles interacting by exclusion, an approach proposed by Fernández, Ferrari and Garcia. Define as the shift permutation . In the Gaussian case , we show that for each , given by is an ergodic Gibbs measure equal to the thermodynamic limit of the specifications with boundary conditions. For a general potential , we prove the existence of Gibbs measures when is bigger than some -dependent value.

  11. Gibbs equilibrium averages and Bogolyubov measure

    International Nuclear Information System (INIS)

    Sankovich, D.P.

    2011-01-01

    Application of the functional integration methods in equilibrium statistical mechanics of quantum Bose-systems is considered. We show that Gibbs equilibrium averages of Bose-operators can be represented as path integrals over a special Gauss measure defined in the corresponding space of continuous functions. We consider some problems related to integration with respect to this measure

  12. Is the Bakken Formation the Answer to our Energy Independence?

    Science.gov (United States)

    Waggoner, E. G.; Hall, C.

    2012-12-01

    The Bakken Formation has garnered substantial attention due to an unprecedented surge in US domestic oil production, much of it from shale oil from the Bakken. The sheer size of the formation coupled with technological advances in horizontal drilling and hydraulic fracking have led many, including the former head of BP, to speculate that domestic shale oil will free the US from its dependence upon foreign oil entirely. Shale oil is indeed likely to provide a significant contribution to our domestic energy portfolio, but real problems exist in the form of physical limitations. Our preliminary analysis indicates that the most important fields in the Bakken Formation are depleting rapidly. Mckenzie and Mountrail Counties, the two largest oil producing counties in North Dakota, account for over 50% of North Dakota's total oil production. However, Mountrail County appears to have hit peak production between the months of March and April 2012. The decline is especially apparent in the Mountrail County's two largest producing fields, suggesting that much of production occurs in concentrated areas and many of these fields with high profitability are undergoing rapid production declines. In order to maintain a consistent level of production and offset these growing declines, an increasing number of wells must be drilled throughout the lifetime of a field. Energy Return on Investment (EROI), the ratio of energy outputs over energy inputs, can be utilized to determine the profitability of resource base. Preliminary EROI analysis indicates that newly developed fields in the Bakken are less profitable and yield far less energy than the larger producing predecessors such as those in Mountrail County. Will the smaller fields ultimately compensate for the steep declines witnessed in the larger fields? If current trends continue, ultimate production from the Bakken will be far less than predicted. This poses significant financial implications for the future of shale oil and US

  13. Free-energy coarse-grained potential for C60

    International Nuclear Information System (INIS)

    Edmunds, D. M.; Tangney, P.; Vvedensky, D. D.; Foulkes, W. M. C.

    2015-01-01

    We propose a new deformable free energy method for generating a free-energy coarse-graining potential for C 60 . Potentials generated from this approach exhibit a strong temperature dependence and produce excellent agreement with benchmark fully atomistic molecular dynamics simulations. Parameter sets for analytical fits to this potential are provided at four different temperatures

  14. Cosmological constant versus free energy for heterotic strings

    International Nuclear Information System (INIS)

    Alvarez, E.; Osorio, M.A.R.

    1988-01-01

    A detailed analysis is made of the modular-invariant formulation of the free energy of heterotic strings. Several instances are pointed out in which a duality formula can be obtained, and its physical implications are discussed. The interplay between the free energy of a given heterotic string and the cosmological constant of the toroidal compactification of another heterotic string is emphasized. (orig.)

  15. Calculation of molecular free energies in classical potentials

    International Nuclear Information System (INIS)

    Farhi, Asaf; Singh, Bipin

    2016-01-01

    Free energies of molecules can be calculated by quantum chemistry computations or by normal mode classical calculations. However, the first can be computationally impractical for large molecules and the second is based on the assumption of harmonic dynamics. We present a novel, accurate and complete calculation of molecular free energies in standard classical potentials. In this method we transform the molecule by relaxing potential terms which depend on the coordinates of a group of atoms in that molecule and calculate the free energy difference associated with the transformation. Then, since the transformed molecule can be treated as non-interacting systems, the free energy associated with these atoms is analytically or numerically calculated. This two-step calculation can be applied to calculate free energies of molecules or free energy difference between (possibly large) molecules in a general environment. We demonstrate the method in free energy calculations for methanethiol and butane molecules in vacuum and solvent. We suggest the potential application of free energy calculation of chemical reactions in classical molecular simulations. (paper)

  16. Free energy from molecular dynamics with multiple constraints

    NARCIS (Netherlands)

    den Otter, Wouter K.; Briels, Willem J.

    2000-01-01

    In molecular dynamics simulations of reacting systems, the key step to determining the equilibrium constant and the reaction rate is the calculation of the free energy as a function of the reaction coordinate. Intuitively the derivative of the free energy is equal to the average force needed to

  17. Alternative Energy: A Guide to Free Information for Educators.

    Science.gov (United States)

    White, Janet A.

    This guide was compiled to help teachers and students locate free educational materials (both lessons and nontechnical background references) on renewable energy resources and energy conservation. The 214 entries are arranged by these topic areas: (1) energy efficiency and renewables; (2) biomass; (3) hydropower; (4) solar thermal energy; (5)…

  18. Free energy profiles from single-molecule pulling experiments.

    Science.gov (United States)

    Hummer, Gerhard; Szabo, Attila

    2010-12-14

    Nonequilibrium pulling experiments provide detailed information about the thermodynamic and kinetic properties of molecules. We show that unperturbed free energy profiles as a function of molecular extension can be obtained rigorously from such experiments without using work-weighted position histograms. An inverse Weierstrass transform is used to relate the system free energy obtained from the Jarzynski equality directly to the underlying molecular free energy surface. An accurate approximation for the free energy surface is obtained by using the method of steepest descent to evaluate the inverse transform. The formalism is applied to simulated data obtained from a kinetic model of RNA folding, in which the dynamics consists of jumping between linker-dominated folded and unfolded free energy surfaces.

  19. Opinion formation on multiplex scale-free networks

    Science.gov (United States)

    Nguyen, Vu Xuan; Xiao, Gaoxi; Xu, Xin-Jian; Li, Guoqi; Wang, Zhen

    2018-01-01

    Most individuals, if not all, live in various social networks. The formation of opinion systems is an outcome of social interactions and information propagation occurring in such networks. We study the opinion formation with a new rule of pairwise interactions in the novel version of the well-known Deffuant model on multiplex networks composed of two layers, each of which is a scale-free network. It is found that in a duplex network composed of two identical layers, the presence of the multiplexity helps either diminish or enhance opinion diversity depending on the relative magnitudes of tolerance ranges characterizing the degree of openness/tolerance on both layers: there is a steady separation between different regions of tolerance range values on two network layers where multiplexity plays two different roles, respectively. Additionally, the two critical tolerance ranges follow a one-sum rule; that is, each of the layers reaches a complete consensus only if the sum of the tolerance ranges on the two layers is greater than a constant approximately equaling 1, the double of the critical bound on a corresponding isolated network. A further investigation of the coupling between constituent layers quantified by a link overlap parameter reveals that as the layers are loosely coupled, the two opinion systems co-evolve independently, but when the inter-layer coupling is sufficiently strong, a monotonic behavior is observed: an increase in the tolerance range of a layer causes a decline in the opinion diversity on the other layer regardless of the magnitudes of tolerance ranges associated with the layers in question.

  20. Probing Free-Energy Surfaces with Differential Scanning Calorimetry

    Science.gov (United States)

    Sanchez-Ruiz, Jose M.

    2011-05-01

    Many aspects of protein folding can be understood in terms of projections of the highly dimensional energy landscape onto a few (or even only one) particularly relevant coordinates. These free-energy surfaces can be probed conveniently from experimental differential scanning calorimetry (DSC) thermograms, as DSC provides a direct relation with the protein partition function. Free-energy surfaces thus obtained are consistent with two fundamental scenarios predicted by the energy-landscape perspective: (a) well-defined macrostates separated by significant free-energy barriers, in some cases, and, in many other cases, (b) marginal or even vanishingly small barriers, which furthermore show a good correlation with kinetics for fast- and ultrafast-folding proteins. Overall, the potential of DSC to assess free-energy surfaces for a wide variety of proteins makes it possible to address fundamental issues, such as the molecular basis of the barrier modulations produced by natural selection in response to functional requirements or to ensure kinetic stability.

  1. The elastic free energy of a tandem modular protein under force.

    Science.gov (United States)

    Valle-Orero, Jessica; Eckels, Edward C; Stirnemann, Guillaume; Popa, Ionel; Berkovich, Ronen; Fernandez, Julio M

    2015-05-01

    Recent studies have provided a theoretical framework for including entropic elasticity in the free energy landscape of proteins under mechanical force. Accounting for entropic elasticity using polymer physics models has helped explain the hopping behavior seen in single molecule experiments in the low force regime. Here, we expand on the construction of the free energy of a single protein domain under force proposed by Berkovich et al. to provide a free energy landscape for N tandem domains along a continuous polypeptide. Calculation of the free energy of individual domains followed by their concatenation provides a continuous free energy landscape whose curvature is dominated by the worm-like chain at forces below 20 pN. We have validated our free energy model using Brownian dynamics and reproduce key features of protein folding. This free energy model can predict the effects of changes in the elastic properties of a multidomain protein as a consequence of biological modifications such as phosphorylation or the formation of disulfide bonds. This work lays the foundations for the modeling of tissue elasticity, which is largely determined by the properties of tandem polyproteins. Copyright © 2015. Published by Elsevier Inc.

  2. Free Magnetic Energy in Solar Active Regions above the Minimum-Energy Relaxed State

    OpenAIRE

    Regnier, S.; Priest, E. R.

    2008-01-01

    To understand the physics of solar flares, including the local reorganization of the magnetic field and the acceleration of energetic particles, we have first to estimate the free magnetic energy available for such phenomena, which can be converted into kinetic and thermal energy. The free magnetic energy is the excess energy of a magnetic configuration compared to the minimum-energy state, which is a linear force-free field if the magnetic helicity of the configuration is conserved. We inves...

  3. Guidelines for the analysis of free energy calculations.

    Science.gov (United States)

    Klimovich, Pavel V; Shirts, Michael R; Mobley, David L

    2015-05-01

    Free energy calculations based on molecular dynamics simulations show considerable promise for applications ranging from drug discovery to prediction of physical properties and structure-function studies. But these calculations are still difficult and tedious to analyze, and best practices for analysis are not well defined or propagated. Essentially, each group analyzing these calculations needs to decide how to conduct the analysis and, usually, develop its own analysis tools. Here, we review and recommend best practices for analysis yielding reliable free energies from molecular simulations. Additionally, we provide a Python tool, alchemical-analysis.py, freely available on GitHub as part of the pymbar package (located at http://github.com/choderalab/pymbar), that implements the analysis practices reviewed here for several reference simulation packages, which can be adapted to handle data from other packages. Both this review and the tool covers analysis of alchemical calculations generally, including free energy estimates via both thermodynamic integration and free energy perturbation-based estimators. Our Python tool also handles output from multiple types of free energy calculations, including expanded ensemble and Hamiltonian replica exchange, as well as standard fixed ensemble calculations. We also survey a range of statistical and graphical ways of assessing the quality of the data and free energy estimates, and provide prototypes of these in our tool. We hope this tool and discussion will serve as a foundation for more standardization of and agreement on best practices for analysis of free energy calculations.

  4. From free energy to expected energy: Improving energy-based value function approximation in reinforcement learning.

    Science.gov (United States)

    Elfwing, Stefan; Uchibe, Eiji; Doya, Kenji

    2016-12-01

    Free-energy based reinforcement learning (FERL) was proposed for learning in high-dimensional state and action spaces. However, the FERL method does only really work well with binary, or close to binary, state input, where the number of active states is fewer than the number of non-active states. In the FERL method, the value function is approximated by the negative free energy of a restricted Boltzmann machine (RBM). In our earlier study, we demonstrated that the performance and the robustness of the FERL method can be improved by scaling the free energy by a constant that is related to the size of network. In this study, we propose that RBM function approximation can be further improved by approximating the value function by the negative expected energy (EERL), instead of the negative free energy, as well as being able to handle continuous state input. We validate our proposed method by demonstrating that EERL: (1) outperforms FERL, as well as standard neural network and linear function approximation, for three versions of a gridworld task with high-dimensional image state input; (2) achieves new state-of-the-art results in stochastic SZ-Tetris in both model-free and model-based learning settings; and (3) significantly outperforms FERL and standard neural network function approximation for a robot navigation task with raw and noisy RGB images as state input and a large number of actions. Copyright © 2016 The Author(s). Published by Elsevier Ltd.. All rights reserved.

  5. Free energy evaluation in polymer translocation via Jarzynski equality

    Energy Technology Data Exchange (ETDEWEB)

    Mondaini, Felipe, E-mail: fmondaini@if.ufrj.br [Centro Federal de Educação Tecnológica Celso Suckow da Fonseca, Petrópolis, 25.620-003, RJ (Brazil); Moriconi, L., E-mail: moriconi@if.ufrj.br [Instituto de Física, Universidade Federal do Rio de Janeiro, C.P. 68528, 21945-970, Rio de Janeiro, RJ (Brazil)

    2014-05-01

    We perform, with the help of cloud computing resources, extensive Langevin simulations, which provide free energy estimates for unbiased three-dimensional polymer translocation. We employ the Jarzynski equality in its rigorous setting, to compute the variation of the free energy in single monomer translocation events. In our three-dimensional Langevin simulations, the excluded-volume and van der Waals interactions between beads (monomers and membrane atoms) are modeled through a repulsive Lennard-Jones (LJ) potential and consecutive monomers are subject to the Finite-Extension Nonlinear Elastic (FENE) potential. Analysing data for polymers with different lengths, the free energy profile is noted to have interesting finite-size scaling properties.

  6. Free energy evaluation in polymer translocation via Jarzynski equality

    International Nuclear Information System (INIS)

    Mondaini, Felipe; Moriconi, L.

    2014-01-01

    We perform, with the help of cloud computing resources, extensive Langevin simulations, which provide free energy estimates for unbiased three-dimensional polymer translocation. We employ the Jarzynski equality in its rigorous setting, to compute the variation of the free energy in single monomer translocation events. In our three-dimensional Langevin simulations, the excluded-volume and van der Waals interactions between beads (monomers and membrane atoms) are modeled through a repulsive Lennard-Jones (LJ) potential and consecutive monomers are subject to the Finite-Extension Nonlinear Elastic (FENE) potential. Analysing data for polymers with different lengths, the free energy profile is noted to have interesting finite-size scaling properties.

  7. Surface free energy for systems with integrable boundary conditions

    International Nuclear Information System (INIS)

    Goehmann, Frank; Bortz, Michael; Frahm, Holger

    2005-01-01

    The surface free energy is the difference between the free energies for a system with open boundary conditions and the same system with periodic boundary conditions. We use the quantum transfer matrix formalism to express the surface free energy in the thermodynamic limit of systems with integrable boundary conditions as a matrix element of certain projection operators. Specializing to the XXZ spin-1/2 chain we introduce a novel 'finite temperature boundary operator' which characterizes the thermodynamical properties of surfaces related to integrable boundary conditions

  8. Information-to-free-energy conversion: Utilizing thermal fluctuations.

    Science.gov (United States)

    Toyabe, Shoichi; Muneyuki, Eiro

    2013-01-01

    Maxwell's demon is a hypothetical creature that can convert information to free energy. A debate that has lasted for more than 100 years has revealed that the demon's operation does not contradict the laws of thermodynamics; hence, the demon can be realized physically. We briefly review the first experimental demonstration of Maxwell's demon of Szilard's engine type that converts information to free energy. We pump heat from an isothermal environment by using the information about the thermal fluctuations of a Brownian particle and increase the particle's free energy.

  9. Regeneralized London free energy for high-Tc vortex lattices

    Directory of Open Access Journals (Sweden)

    M. A. Shahzamanian

    2006-09-01

    Full Text Available   The London free-energy is regeneralized by the Ginsburg-Landau free-energy density in the presence of both d and s order parameters. We have shown that the strength of the s-d coupling, makes an important rule to determine the form of the lattice vortex. Appearance of the ratios of the coherence length to penetration depth in the higher order corrections of the free-energy density will truncate these corrections for even large values of .

  10. Implicit ligand theory for relative binding free energies

    Science.gov (United States)

    Nguyen, Trung Hai; Minh, David D. L.

    2018-03-01

    Implicit ligand theory enables noncovalent binding free energies to be calculated based on an exponential average of the binding potential of mean force (BPMF)—the binding free energy between a flexible ligand and rigid receptor—over a precomputed ensemble of receptor configurations. In the original formalism, receptor configurations were drawn from or reweighted to the apo ensemble. Here we show that BPMFs averaged over a holo ensemble yield binding free energies relative to the reference ligand that specifies the ensemble. When using receptor snapshots from an alchemical simulation with a single ligand, the new statistical estimator outperforms the original.

  11. Turbulent kinetic energy equation and free mixing

    Science.gov (United States)

    Morel, T.; Torda, T. P.; Bradshaw, P.

    1973-01-01

    Calculation of free shear flows was carried out to investigate the usefulness of several concepts which were previously successfully applied to wall flows. The method belongs to the class of differential approaches. The turbulence is taken into account by the introduction of one additional partial differential equation, the transport equation for the turbulent shear stress. The structure of turbulence is modeled after Bradshaw et al. This model was used successfully in boundary layers and its applicability to other flows is demonstrated. The work reported differs substantially from that of an earlier attempt to use this approach for calculation of free flows. The most important difference is that the region around the center line is treated by invoking the interaction hypothesis (concerning the structure of turbulence in the regions separated by the velocity extrema). The compressibility effects on shear layer spreading at low and moderate Mach numbers were investigated. In the absence of detailed experiments in free flows, the evidence from boundary layers that at low Mach numbers the structure of turbulence is unaffected by the compressibility was relied on. The present model was tested over a range of self-preserving and developing flows including pressure gradients using identical empirical input. The dependence of the structure of turbulence on the spreading rate of the shear layer was established.

  12. High-energy components of 'designer gasoline and designer diesel fuel' I. Heat capacities, enthalpy increments, vapor pressures, critical properties, and derived thermodynamic functions for bicyclopentyl between the T=(10 and 600) K

    International Nuclear Information System (INIS)

    Chirico, R.D.; Steele, W.V.

    2004-01-01

    Measurements leading to the calculation of the standard thermodynamic properties for gaseous bicyclopentyl (Chemicals Abstracts registry number [1636-39-1]) are reported. Experimental methods include adiabatic heat-capacity calorimetry, comparative ebulliometry, and differential-scanning calorimetry (d.s.c.). The critical temperature was determined by d.s.c. and the critical pressure and critical density were estimated. Standard molar entropies, standard molar enthalpies, and standard molar Gibbs free energies of formation are reported at selected temperatures between T=(298.15 and 600) K. Formation properties were calculated with a literature value for the enthalpy of combustion in the liquid phase. All results are compared with available literature values

  13. Gibbs sampling on large lattice with GMRF

    Science.gov (United States)

    Marcotte, Denis; Allard, Denis

    2018-02-01

    Gibbs sampling is routinely used to sample truncated Gaussian distributions. These distributions naturally occur when associating latent Gaussian fields to category fields obtained by discrete simulation methods like multipoint, sequential indicator simulation and object-based simulation. The latent Gaussians are often used in data assimilation and history matching algorithms. When the Gibbs sampling is applied on a large lattice, the computing cost can become prohibitive. The usual practice of using local neighborhoods is unsatisfying as it can diverge and it does not reproduce exactly the desired covariance. A better approach is to use Gaussian Markov Random Fields (GMRF) which enables to compute the conditional distributions at any point without having to compute and invert the full covariance matrix. As the GMRF is locally defined, it allows simultaneous updating of all points that do not share neighbors (coding sets). We propose a new simultaneous Gibbs updating strategy on coding sets that can be efficiently computed by convolution and applied with an acceptance/rejection method in the truncated case. We study empirically the speed of convergence, the effect of choice of boundary conditions, of the correlation range and of GMRF smoothness. We show that the convergence is slower in the Gaussian case on the torus than for the finite case studied in the literature. However, in the truncated Gaussian case, we show that short scale correlation is quickly restored and the conditioning categories at each lattice point imprint the long scale correlation. Hence our approach enables to realistically apply Gibbs sampling on large 2D or 3D lattice with the desired GMRF covariance.

  14. An efficient estimator for Gibbs random fields

    Czech Academy of Sciences Publication Activity Database

    Janžura, Martin

    2014-01-01

    Roč. 50, č. 6 (2014), s. 883-895 ISSN 0023-5954 R&D Projects: GA ČR(CZ) GBP402/12/G097 Institutional support: RVO:67985556 Keywords : Gibbs random field * efficient estimator * empirical estimator Subject RIV: BA - General Mathematics Impact factor: 0.541, year: 2014 http://library.utia.cas.cz/separaty/2015/SI/janzura-0441325.pdf

  15. Surface free energy of alkali and transition metal nanoparticles

    International Nuclear Information System (INIS)

    Aqra, Fathi; Ayyad, Ahmed

    2014-01-01

    Graphical abstract: Size dependent surface free energy of spherical, cubic and disk Au nanoparticles. - Highlights: • A model to account for the surface free energy of metallic nanoparticles is described. • The model requires only the cohesive energy of the nanoparticle. • The surface free energy of a number of metallic nanoparticles has been calculated, and the obtained values agree well with existing data. • Surface energy falls down very fast when the number of atoms is less than hundred. • The model is applicable to any metallic nanoparticle. - Abstract: This paper addresses an interesting issue on the surface free energy of metallic nanoparticles as compared to the bulk material. Starting from a previously reported equation, a theoretical model, that involves a specific term for calculating the cohesive energy of nanoparticle, is established in a view to describe the behavior of surface free energy of metallic nanoparticles (using different shapes of particle: sphere, cube and disc). The results indicate that the behavior of surface energy is very appropriate for spherical nanoparticle, and thus, it is the most realistic shape of a nanoparticle. The surface energy of copper, silver, gold, platinum, tungsten, molybdenum, tantalum, paladium and alkali metallic nanoparticles is only prominent in the nanoscale size, and it decreases with the decrease of nanoparticle size. Thus, the surface free energy plays a more important role in determining the properties of nanoparticles than in bulk materials. It differs from shape to another, and falls down as the number of atoms (nanoparticle size) decreases. In the case of spherical nanoparticles, the onset of the sharp decrease in surface energy is observed at about 110 atom. A decrease of 16% and 45% in surface energy is found by moving from bulk to 110 atom and from bulk to 5 atom, respectively. The predictions are consistent with the reported data

  16. Accurate calculation of conformational free energy differences in explicit water: the confinement-solvation free energy approach.

    Science.gov (United States)

    Esque, Jeremy; Cecchini, Marco

    2015-04-23

    The calculation of the free energy of conformation is key to understanding the function of biomolecules and has attracted significant interest in recent years. Here, we present an improvement of the confinement method that was designed for use in the context of explicit solvent MD simulations. The development involves an additional step in which the solvation free energy of the harmonically restrained conformers is accurately determined by multistage free energy perturbation simulations. As a test-case application, the newly introduced confinement/solvation free energy (CSF) approach was used to compute differences in free energy between conformers of the alanine dipeptide in explicit water. The results are in excellent agreement with reference calculations based on both converged molecular dynamics and umbrella sampling. To illustrate the general applicability of the method, conformational equilibria of met-enkephalin (5 aa) and deca-alanine (10 aa) in solution were also analyzed. In both cases, smoothly converged free-energy results were obtained in agreement with equilibrium sampling or literature calculations. These results demonstrate that the CSF method may provide conformational free-energy differences of biomolecules with small statistical errors (below 0.5 kcal/mol) and at a moderate computational cost even with a full representation of the solvent.

  17. Star-Formation in Free-Floating Evaporating Gaseous Globules

    Science.gov (United States)

    Sahai, Raghvendra

    2017-08-01

    We propose to study the stellar embryos in select members of a newly recognized class of Free-floating Evaporating Gaseous Globules (frEGGS) embedded in HII regions and having head-tail shapes. We discovered two of these in the Cygnus massive star-forming region (MSFR) with HST, including one of the most prominent members of this class (IRAS20324). Subsequent archival searches of Spitzer imaging of MSFRs has allowed us to build a statistical sample of frEGGs. Our molecular-line observations show the presence of dense molecular cores with total gas masses of (0.5-few) Msun in these objects, and our radio continuum images and Halpha images (from the IPHAS survey) reveal bright photo-ionized peripheries around these objects. We hypothesize that frEGGs are density concentrations originating in giant molecular clouds, that, when subject to the sculpting and compression by strong winds and UV radiation from massive stars, become active star-forming cores. For the 4 frEGGs with HST or near-IR AO images showing young stars and bipolar cavities produced by their jets or collimated outflows, the symmetry axis points roughly toward the external ionizing star or star cluster - exciting new evidence for our overpressure-induced star formation hypothesis. We propose to test this hypothesis by imaging 24 frEGGs in two nearby MSFRs that represent different radiation-dominated environments. Using ACS imaging with filters F606W, F814W, & F658N (Ha+[NII]), we will search for jets and outflow-excavated cavities, investigate the stellar nurseries inside frEGGs, and determine whether the globules are generally forming multiple star systems or small clusters, as in IRAS20324.

  18. Free energies of stable and metastable pores in lipid membranes under tension

    NARCIS (Netherlands)

    den Otter, Wouter K.

    2009-01-01

    The free energy profile of pore formation in a lipid membrane, covering the entire range from a density fluctuation in an intact bilayer to a large tension-stabilized pore, has been calculated by molecular dynamics simulations with a coarse-grained lipid model. Several fixed elongations are used to

  19. Free energy distribution function of a random Ising ferromagnet

    International Nuclear Information System (INIS)

    Dotsenko, Victor; Klumov, Boris

    2012-01-01

    We study the free energy distribution function of a weakly disordered Ising ferromagnet in terms of the D-dimensional random temperature Ginzburg–Landau Hamiltonian. It is shown that besides the usual Gaussian 'body' this distribution function exhibits non-Gaussian tails both in the paramagnetic and in the ferromagnetic phases. Explicit asymptotic expressions for these tails are derived. It is demonstrated that the tails are strongly asymmetric: the left tail (for large negative values of the free energy) is much slower than the right one (for large positive values of the free energy). It is argued that at the critical point the free energy of the random Ising ferromagnet in dimensions D < 4 is described by a non-trivial universal distribution function which is non-self-averaging

  20. The free-energy principle: a unified brain theory?

    Science.gov (United States)

    Friston, Karl

    2010-02-01

    A free-energy principle has been proposed recently that accounts for action, perception and learning. This Review looks at some key brain theories in the biological (for example, neural Darwinism) and physical (for example, information theory and optimal control theory) sciences from the free-energy perspective. Crucially, one key theme runs through each of these theories - optimization. Furthermore, if we look closely at what is optimized, the same quantity keeps emerging, namely value (expected reward, expected utility) or its complement, surprise (prediction error, expected cost). This is the quantity that is optimized under the free-energy principle, which suggests that several global brain theories might be unified within a free-energy framework.

  1. Free energy surfaces in the superconducting mixed state

    Science.gov (United States)

    Finnemore, D. K.; Fang, M. M.; Bansal, N. P.; Farrell, D. E.

    1989-01-01

    The free energy surface for Tl2Ba2Ca2Cu3O1O has been measured as a function of temperature and magnetic field to determine the fundamental thermodynamic properties of the mixed state. The change in free energy, G(H)-G(O), is found to be linear in temperature over a wide range indicating that the specific heat is independent of field.

  2. Free-market approach to energy proposed in new study

    International Nuclear Information System (INIS)

    Anon.

    1992-01-01

    This paper reports that a free-market approach to energy use, intensified R and D and an emphasis on conservation and clean fuels such as natural gas can result in significant reductions in emissions of greenhouse gases, without any major new federal policy initiatives, according to a new study, An Alternative Energy Future, sponsored by Alliance to Save Energy, AGA and Solar Energy Industries Assn

  3. QM/MM free energy simulations: recent progress and challenges

    Science.gov (United States)

    Lu, Xiya; Fang, Dong; Ito, Shingo; Okamoto, Yuko; Ovchinnikov, Victor

    2016-01-01

    Due to the higher computational cost relative to pure molecular mechanical (MM) simulations, hybrid quantum mechanical/molecular mechanical (QM/MM) free energy simulations particularly require a careful consideration of balancing computational cost and accuracy. Here we review several recent developments in free energy methods most relevant to QM/MM simulations and discuss several topics motivated by these developments using simple but informative examples that involve processes in water. For chemical reactions, we highlight the value of invoking enhanced sampling technique (e.g., replica-exchange) in umbrella sampling calculations and the value of including collective environmental variables (e.g., hydration level) in metadynamics simulations; we also illustrate the sensitivity of string calculations, especially free energy along the path, to various parameters in the computation. Alchemical free energy simulations with a specific thermodynamic cycle are used to probe the effect of including the first solvation shell into the QM region when computing solvation free energies. For cases where high-level QM/MM potential functions are needed, we analyze two different approaches: the QM/MM-MFEP method of Yang and co-workers and perturbative correction to low-level QM/MM free energy results. For the examples analyzed here, both approaches seem productive although care needs to be exercised when analyzing the perturbative corrections. PMID:27563170

  4. Learning free energy landscapes using artificial neural networks.

    Science.gov (United States)

    Sidky, Hythem; Whitmer, Jonathan K

    2018-03-14

    Existing adaptive bias techniques, which seek to estimate free energies and physical properties from molecular simulations, are limited by their reliance on fixed kernels or basis sets which hinder their ability to efficiently conform to varied free energy landscapes. Further, user-specified parameters are in general non-intuitive yet significantly affect the convergence rate and accuracy of the free energy estimate. Here we propose a novel method, wherein artificial neural networks (ANNs) are used to develop an adaptive biasing potential which learns free energy landscapes. We demonstrate that this method is capable of rapidly adapting to complex free energy landscapes and is not prone to boundary or oscillation problems. The method is made robust to hyperparameters and overfitting through Bayesian regularization which penalizes network weights and auto-regulates the number of effective parameters in the network. ANN sampling represents a promising innovative approach which can resolve complex free energy landscapes in less time than conventional approaches while requiring minimal user input.

  5. Hierarchical Protein Free Energy Landscapes from Variationally Enhanced Sampling.

    Science.gov (United States)

    Shaffer, Patrick; Valsson, Omar; Parrinello, Michele

    2016-12-13

    In recent work, we demonstrated that it is possible to obtain approximate representations of high-dimensional free energy surfaces with variationally enhanced sampling ( Shaffer, P.; Valsson, O.; Parrinello, M. Proc. Natl. Acad. Sci. , 2016 , 113 , 17 ). The high-dimensional spaces considered in that work were the set of backbone dihedral angles of a small peptide, Chignolin, and the high-dimensional free energy surface was approximated as the sum of many two-dimensional terms plus an additional term which represents an initial estimate. In this paper, we build on that work and demonstrate that we can calculate high-dimensional free energy surfaces of very high accuracy by incorporating additional terms. The additional terms apply to a set of collective variables which are more coarse than the base set of collective variables. In this way, it is possible to build hierarchical free energy surfaces, which are composed of terms that act on different length scales. We test the accuracy of these free energy landscapes for the proteins Chignolin and Trp-cage by constructing simple coarse-grained models and comparing results from the coarse-grained model to results from atomistic simulations. The approach described in this paper is ideally suited for problems in which the free energy surface has important features on different length scales or in which there is some natural hierarchy.

  6. Learning free energy landscapes using artificial neural networks

    Science.gov (United States)

    Sidky, Hythem; Whitmer, Jonathan K.

    2018-03-01

    Existing adaptive bias techniques, which seek to estimate free energies and physical properties from molecular simulations, are limited by their reliance on fixed kernels or basis sets which hinder their ability to efficiently conform to varied free energy landscapes. Further, user-specified parameters are in general non-intuitive yet significantly affect the convergence rate and accuracy of the free energy estimate. Here we propose a novel method, wherein artificial neural networks (ANNs) are used to develop an adaptive biasing potential which learns free energy landscapes. We demonstrate that this method is capable of rapidly adapting to complex free energy landscapes and is not prone to boundary or oscillation problems. The method is made robust to hyperparameters and overfitting through Bayesian regularization which penalizes network weights and auto-regulates the number of effective parameters in the network. ANN sampling represents a promising innovative approach which can resolve complex free energy landscapes in less time than conventional approaches while requiring minimal user input.

  7. Accelerated weight histogram method for exploring free energy landscapes

    Energy Technology Data Exchange (ETDEWEB)

    Lindahl, V.; Lidmar, J.; Hess, B. [Department of Theoretical Physics and Swedish e-Science Research Center, KTH Royal Institute of Technology, 10691 Stockholm (Sweden)

    2014-07-28

    Calculating free energies is an important and notoriously difficult task for molecular simulations. The rapid increase in computational power has made it possible to probe increasingly complex systems, yet extracting accurate free energies from these simulations remains a major challenge. Fully exploring the free energy landscape of, say, a biological macromolecule typically requires sampling large conformational changes and slow transitions. Often, the only feasible way to study such a system is to simulate it using an enhanced sampling method. The accelerated weight histogram (AWH) method is a new, efficient extended ensemble sampling technique which adaptively biases the simulation to promote exploration of the free energy landscape. The AWH method uses a probability weight histogram which allows for efficient free energy updates and results in an easy discretization procedure. A major advantage of the method is its general formulation, making it a powerful platform for developing further extensions and analyzing its relation to already existing methods. Here, we demonstrate its efficiency and general applicability by calculating the potential of mean force along a reaction coordinate for both a single dimension and multiple dimensions. We make use of a non-uniform, free energy dependent target distribution in reaction coordinate space so that computational efforts are not wasted on physically irrelevant regions. We present numerical results for molecular dynamics simulations of lithium acetate in solution and chignolin, a 10-residue long peptide that folds into a β-hairpin. We further present practical guidelines for setting up and running an AWH simulation.

  8. Levy-free part in energy tax is not wanted

    International Nuclear Information System (INIS)

    Gilijamse, W.

    1995-01-01

    The Dutch government proposed to implement an energy levy for small-scale consumers in 1996. The yields will be reimbursed by means of a reduction of the tax burden. By applying a levy-free tax allowance the tax reduction can be limited. However, it appears that this allowance does not work: it reduces the energy saving impact of the energy levy, because it does not stimulate investments in energy saving housing construction and energy saving heat supply. It also interferes with a just compensation of income. It is recommended to cancel the levy-free tax allowance and to realize compensation by raising the tax free allowance in the income tax. 2 figs., 1 tab., 6 refs

  9. Using the fast fourier transform in binding free energy calculations.

    Science.gov (United States)

    Nguyen, Trung Hai; Zhou, Huan-Xiang; Minh, David D L

    2018-04-30

    According to implicit ligand theory, the standard binding free energy is an exponential average of the binding potential of mean force (BPMF), an exponential average of the interaction energy between the unbound ligand ensemble and a rigid receptor. Here, we use the fast Fourier transform (FFT) to efficiently evaluate BPMFs by calculating interaction energies when rigid ligand configurations from the unbound ensemble are discretely translated across rigid receptor conformations. Results for standard binding free energies between T4 lysozyme and 141 small organic molecules are in good agreement with previous alchemical calculations based on (1) a flexible complex ( R≈0.9 for 24 systems) and (2) flexible ligand with multiple rigid receptor configurations ( R≈0.8 for 141 systems). While the FFT is routinely used for molecular docking, to our knowledge this is the first time that the algorithm has been used for rigorous binding free energy calculations. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

  10. Measuring excess free energies of self-assembled membrane structures.

    Science.gov (United States)

    Norizoe, Yuki; Daoulas, Kostas Ch; Müller, Marcus

    2010-01-01

    Using computer simulation of a solvent-free, coarse-grained model for amphiphilic membranes, we study the excess free energy of hourglass-shaped connections (i.e., stalks) between two apposed bilayer membranes. In order to calculate the free energy by simulation in the canonical ensemble, we reversibly transfer two apposed bilayers into a configuration with a stalk in three steps. First, we gradually replace the intermolecular interactions by an external, ordering field. The latter is chosen such that the structure of the non-interacting system in this field closely resembles the structure of the original, interacting system in the absence of the external field. The absence of structural changes along this path suggests that it is reversible; a fact which is confirmed by expanded-ensemble simulations. Second, the external, ordering field is changed as to transform the non-interacting system from the apposed bilayer structure to two-bilayers connected by a stalk. The final external field is chosen such that the structure of the non-interacting system resembles the structure of the stalk in the interacting system without a field. On the third branch of the transformation path, we reversibly replace the external, ordering field by non-bonded interactions. Using expanded-ensemble techniques, the free energy change along this reversible path can be obtained with an accuracy of 10(-3)k(B)T per molecule in the n VT-ensemble. Calculating the chemical potential, we obtain the free energy of a stalk in the grandcanonical ensemble, and employing semi-grandcanonical techniques, we calculate the change of the excess free energy upon altering the molecular architecture. This computational strategy can be applied to compute the free energy of self-assembled phases in lipid and copolymer systems, and the excess free energy of defects or interfaces.

  11. Conformational Transitions and Convergence of Absolute Binding Free Energy Calculations

    Science.gov (United States)

    Lapelosa, Mauro; Gallicchio, Emilio; Levy, Ronald M.

    2011-01-01

    The Binding Energy Distribution Analysis Method (BEDAM) is employed to compute the standard binding free energies of a series of ligands to a FK506 binding protein (FKBP12) with implicit solvation. Binding free energy estimates are in reasonably good agreement with experimental affinities. The conformations of the complexes identified by the simulations are in good agreement with crystallographic data, which was not used to restrain ligand orientations. The BEDAM method is based on λ -hopping Hamiltonian parallel Replica Exchange (HREM) molecular dynamics conformational sampling, the OPLS-AA/AGBNP2 effective potential, and multi-state free energy estimators (MBAR). Achieving converged and accurate results depends on all of these elements of the calculation. Convergence of the binding free energy is tied to the level of convergence of binding energy distributions at critical intermediate states where bound and unbound states are at equilibrium, and where the rate of binding/unbinding conformational transitions is maximal. This finding mirrors similar observations in the context of order/disorder transitions as for example in protein folding. Insights concerning the physical mechanism of ligand binding and unbinding are obtained. Convergence for the largest FK506 ligand is achieved only after imposing strict conformational restraints, which however require accurate prior structural knowledge of the structure of the complex. The analytical AGBNP2 model is found to underestimate the magnitude of the hydrophobic driving force towards binding in these systems characterized by loosely packed protein-ligand binding interfaces. Rescoring of the binding energies using a numerical surface area model corrects this deficiency. This study illustrates the complex interplay between energy models, exploration of conformational space, and free energy estimators needed to obtain robust estimates from binding free energy calculations. PMID:22368530

  12. Connecting free energy surfaces in implicit and explicit solvent: an efficient method to compute conformational and solvation free energies.

    Science.gov (United States)

    Deng, Nanjie; Zhang, Bin W; Levy, Ronald M

    2015-06-09

    The ability to accurately model solvent effects on free energy surfaces is important for understanding many biophysical processes including protein folding and misfolding, allosteric transitions, and protein–ligand binding. Although all-atom simulations in explicit solvent can provide an accurate model for biomolecules in solution, explicit solvent simulations are hampered by the slow equilibration on rugged landscapes containing multiple basins separated by barriers. In many cases, implicit solvent models can be used to significantly speed up the conformational sampling; however, implicit solvent simulations do not fully capture the effects of a molecular solvent, and this can lead to loss of accuracy in the estimated free energies. Here we introduce a new approach to compute free energy changes in which the molecular details of explicit solvent simulations are retained while also taking advantage of the speed of the implicit solvent simulations. In this approach, the slow equilibration in explicit solvent, due to the long waiting times before barrier crossing, is avoided by using a thermodynamic cycle which connects the free energy basins in implicit solvent and explicit solvent using a localized decoupling scheme. We test this method by computing conformational free energy differences and solvation free energies of the model system alanine dipeptide in water. The free energy changes between basins in explicit solvent calculated using fully explicit solvent paths agree with the corresponding free energy differences obtained using the implicit/explicit thermodynamic cycle to within 0.3 kcal/mol out of ∼3 kcal/mol at only ∼8% of the computational cost. We note that WHAM methods can be used to further improve the efficiency and accuracy of the implicit/explicit thermodynamic cycle.

  13. Free energy of the Lennard-Jones solid

    NARCIS (Netherlands)

    Hoef, van der M.A.

    2000-01-01

    We have determined a simple expression for the absolute Helmholtz free energy of the fcc Lennard-Jones solid from molecular dynamics simulations. The pressure and energy data from these simulations have been fitted to a simple functional form (18 parameters) for densities ranging from around

  14. Low energy quasi free scattering on nuclear surface

    Energy Technology Data Exchange (ETDEWEB)

    Shiyuan, S.

    1983-05-01

    The result of RGM calculation of low energy /sup 3/He(n, n)/sup 3/ He total elastic cross section does not agree well with experimental data for E/sub n/<1 MeV. This discrepancy can be improved by assuming lwo energy quasi-free scattering of particles beyond the nuclear surface.

  15. Aromatic Side Chain Water-to-Lipid Transfer Free Energies Show a Depth Dependence across the Membrane Normal.

    Science.gov (United States)

    McDonald, Sarah K; Fleming, Karen G

    2016-06-29

    Quantitating and understanding the physical forces responsible for the interactions of biomolecules are fundamental to the biological sciences. This is especially challenging for membrane proteins because they are embedded within cellular bilayers that provide a unique medium in which hydrophobic sequences must fold. Knowledge of the energetics of protein-lipid interactions is thus vital to understand cellular processes involving membrane proteins. Here we used a host-guest mutational strategy to calculate the Gibbs free energy changes of water-to-lipid transfer for the aromatic side chains Trp, Tyr, and Phe as a function of depth in the membrane. This work reveals an energetic gradient in the transfer free energies for Trp and Tyr, where transfer was most favorable to the membrane interfacial region and comparatively less favorable into the bilayer center. The transfer energetics follows the concentration gradient of polar atoms across the bilayer normal that naturally occurs in biological membranes. Additional measurements revealed nearest-neighbor coupling in the data set are influenced by a network of aromatic side chains in the host protein. Taken together, these results show that aromatic side chains contribute significantly to membrane protein stability through either aromatic-aromatic interactions or placement at the membrane interface.

  16. Free-Format RPG IV How to Bring Your RPG Programs Into the 21st Century

    CERN Document Server

    Martin, Jim

    2005-01-01

    Traditional-format style RPG IV programmers who need information on the free-format style of coding will find everything they need in this free format how-to guide. The rules and syntax of free format RPG IV are explained as is how this new style of coding has the potential to improve overall programmer productivity from initial development through maintenance stages. Many style issues, such as named indicators and built in functions are covered, as well as such issues as program flow, data manipulation, math operations, and input and output.

  17. Energy buildup in sheared force-free magnetic fields

    Science.gov (United States)

    Wolfson, Richard; Low, Boon C.

    1992-01-01

    Photospheric displacement of the footpoints of solar magnetic field lines results in shearing and twisting of the field, and consequently in the buildup of electric currents and magnetic free energy in the corona. The sudden release of this free energy may be the origin of eruptive events like coronal mass ejections, prominence eruptions, and flares. An important question is whether such an energy release may be accompanied by the opening of magnetic field lines that were previously closed, for such open field lines can provide a route for matter frozen into the field to escape the sun altogether. This paper presents the results of numerical calculations showing that opening of the magnetic field is permitted energetically, in that it is possible to build up more free energy in a sheared, closed, force-free magnetic field than is in a related magnetic configuration having both closed and open field lines. Whether or not the closed force-free field attains enough energy to become partially open depends on the form of the shear profile; the results presented compare the energy buildup for different shear profiles. Implications for solar activity are discussed briefly.

  18. Free-energy minimization and the dark-room problem.

    Science.gov (United States)

    Friston, Karl; Thornton, Christopher; Clark, Andy

    2012-01-01

    Recent years have seen the emergence of an important new fundamental theory of brain function. This theory brings information-theoretic, Bayesian, neuroscientific, and machine learning approaches into a single framework whose overarching principle is the minimization of surprise (or, equivalently, the maximization of expectation). The most comprehensive such treatment is the "free-energy minimization" formulation due to Karl Friston (see e.g., Friston and Stephan, 2007; Friston, 2010a,b - see also Fiorillo, 2010; Thornton, 2010). A recurrent puzzle raised by critics of these models is that biological systems do not seem to avoid surprises. We do not simply seek a dark, unchanging chamber, and stay there. This is the "Dark-Room Problem." Here, we describe the problem and further unpack the issues to which it speaks. Using the same format as the prolog of Eddington's Space, Time, and Gravitation (Eddington, 1920) we present our discussion as a conversation between: an information theorist (Thornton), a physicist (Friston), and a philosopher (Clark).

  19. Computation of Hemagglutinin Free Energy Difference by the Confinement Method

    Science.gov (United States)

    2017-01-01

    Hemagglutinin (HA) mediates membrane fusion, a crucial step during influenza virus cell entry. How many HAs are needed for this process is still subject to debate. To aid in this discussion, the confinement free energy method was used to calculate the conformational free energy difference between the extended intermediate and postfusion state of HA. Special care was taken to comply with the general guidelines for free energy calculations, thereby obtaining convergence and demonstrating reliability of the results. The energy that one HA trimer contributes to fusion was found to be 34.2 ± 3.4kBT, similar to the known contributions from other fusion proteins. Although computationally expensive, the technique used is a promising tool for the further energetic characterization of fusion protein mechanisms. Knowledge of the energetic contributions per protein, and of conserved residues that are crucial for fusion, aids in the development of fusion inhibitors for antiviral drugs. PMID:29151344

  20. Converging ligand-binding free energies obtained with free-energy perturbations at the quantum mechanical level.

    Science.gov (United States)

    Olsson, Martin A; Söderhjelm, Pär; Ryde, Ulf

    2016-06-30

    In this article, the convergence of quantum mechanical (QM) free-energy simulations based on molecular dynamics simulations at the molecular mechanics (MM) level has been investigated. We have estimated relative free energies for the binding of nine cyclic carboxylate ligands to the octa-acid deep-cavity host, including the host, the ligand, and all water molecules within 4.5 Å of the ligand in the QM calculations (158-224 atoms). We use single-step exponential averaging (ssEA) and the non-Boltzmann Bennett acceptance ratio (NBB) methods to estimate QM/MM free energy with the semi-empirical PM6-DH2X method, both based on interaction energies. We show that ssEA with cumulant expansion gives a better convergence and uses half as many QM calculations as NBB, although the two methods give consistent results. With 720,000 QM calculations per transformation, QM/MM free-energy estimates with a precision of 1 kJ/mol can be obtained for all eight relative energies with ssEA, showing that this approach can be used to calculate converged QM/MM binding free energies for realistic systems and large QM partitions. © 2016 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc. © 2016 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.

  1. Efficient free energy calculations for compounds with multiple stable conformations separated by high energy barriers

    NARCIS (Netherlands)

    Hritz, J.; Oostenbrink, C.

    2009-01-01

    Compounds with high intramolecular energy barriers represent challenging targets for free energy calculations because of the difficulty to obtain sufficient conformational sampling. Existing approaches are therefore computationally very demanding, thus preventing practical applications for such

  2. Parabolic Free Boundary Price Formation Models Under Market Size Fluctuations

    KAUST Repository

    Markowich, Peter A.

    2016-10-04

    In this paper we propose an extension of the Lasry-Lions price formation model which includes uctuations of the numbers of buyers and vendors. We analyze the model in the case of deterministic and stochastic market size uctuations and present results on the long time asymptotic behavior and numerical evidence and conjectures on periodic, almost periodic, and stochastic uctuations. The numerical simulations extend the theoretical statements and give further insights into price formation dynamics.

  3. Energy budgets’ formation based on incomplete data

    Directory of Open Access Journals (Sweden)

    Litvak Valery

    2017-01-01

    Full Text Available The universal technique of the current energy budget calculation is recommended for several periods of time. Basing on the data of annual energy budget and considering the plant’s features, social, climatic and other conditions, correcting factors are calculated to estimate energy resources consumption for the day, week, month and year. Shortterm current energy budget supports important financial, trade, logistic, organizational and other control directions. The developed technique is applicable for subnational entities and industrial enterprises in order to increase level of energy resources consumption planning and forecasting as well as bills’ optimization.

  4. Free energy calculations along entropic pathways. III. Nucleation of capillary bridges and bubbles

    Science.gov (United States)

    Desgranges, Caroline; Delhommelle, Jerome

    2017-05-01

    Using molecular simulation, we analyze the capillary condensation and evaporation processes for argon confined in a cylindrical nanopore. For this purpose, we define the entropy of the adsorbed fluid as a reaction coordinate and determine the free energy associated with both processes along entropic pathways. For capillary condensation, we identify a complex free energy profile resulting from the multi-stage nature of this phenomenon. We find capillary condensation to proceed through the nucleation of a liquid bridge across the nanopore, followed by its expansion throughout the pore to give rise to the stable phase of high density. In the case of capillary evaporation, the free energy profile along the entropy pathway also exhibits different regimes, corresponding to the initial destabilization of the layered structure of the fluid followed by the formation, and subsequent expansion, of a bubble across the nanopore.

  5. A Variational Approach to Enhanced Sampling and Free Energy Calculations

    Science.gov (United States)

    Parrinello, Michele

    2015-03-01

    The presence of kinetic bottlenecks severely hampers the ability of widely used sampling methods like molecular dynamics or Monte Carlo to explore complex free energy landscapes. One of the most popular methods for addressing this problem is umbrella sampling which is based on the addition of an external bias which helps overcoming the kinetic barriers. The bias potential is usually taken to be a function of a restricted number of collective variables. However constructing the bias is not simple, especially when the number of collective variables increases. Here we introduce a functional of the bias which, when minimized, allows us to recover the free energy. We demonstrate the usefulness and the flexibility of this approach on a number of examples which include the determination of a six dimensional free energy surface. Besides the practical advantages, the existence of such a variational principle allows us to look at the enhanced sampling problem from a rather convenient vantage point.

  6. Variational Approach to Enhanced Sampling and Free Energy Calculations

    Science.gov (United States)

    Valsson, Omar; Parrinello, Michele

    2014-08-01

    The ability of widely used sampling methods, such as molecular dynamics or Monte Carlo simulations, to explore complex free energy landscapes is severely hampered by the presence of kinetic bottlenecks. A large number of solutions have been proposed to alleviate this problem. Many are based on the introduction of a bias potential which is a function of a small number of collective variables. However constructing such a bias is not simple. Here we introduce a functional of the bias potential and an associated variational principle. The bias that minimizes the functional relates in a simple way to the free energy surface. This variational principle can be turned into a practical, efficient, and flexible sampling method. A number of numerical examples are presented which include the determination of a three-dimensional free energy surface. We argue that, beside being numerically advantageous, our variational approach provides a convenient and novel standpoint for looking at the sampling problem.

  7. Unsupervised Calculation of Free Energy Barriers in Large Crystalline Systems

    Science.gov (United States)

    Swinburne, Thomas D.; Marinica, Mihai-Cosmin

    2018-03-01

    The calculation of free energy differences for thermally activated mechanisms in the solid state are routinely hindered by the inability to define a set of collective variable functions that accurately describe the mechanism under study. Even when possible, the requirement of descriptors for each mechanism under study prevents implementation of free energy calculations in the growing range of automated material simulation schemes. We provide a solution, deriving a path-based, exact expression for free energy differences in the solid state which does not require a converged reaction pathway, collective variable functions, Gram matrix evaluations, or probability flux-based estimators. The generality and efficiency of our method is demonstrated on a complex transformation of C 15 interstitial defects in iron and double kink nucleation on a screw dislocation in tungsten, the latter system consisting of more than 120 000 atoms. Both cases exhibit significant anharmonicity under experimentally relevant temperatures.

  8. The formation of intermetallic compounds during interdiffusion of Mg–Al/Mg–Ce diffusion couples

    International Nuclear Information System (INIS)

    Dai, Jiahong; Jiang, Bin; Li, Xin; Yang, Qingshan; Dong, Hanwu; Xia, Xiangsheng; Pan, Fusheng

    2015-01-01

    Graphical abstract: Al–Ce intermetallic compounds (IMCs) formed in Mg–Al/Mg–Ce diffusion couples. During the whole diffusion process, Al was the dominant diffusing species, and it substituted for Mg atoms of the Mg–Ce substrate. Five Al–Ce IMCs of Al 4 Ce, Al 11 Ce 3 , Al 3 Ce, Al 2 Ce, and AlCe were formed via the reaction of Al and Ce. - Highlights: • Al–Ce IMCs formation in the Mg–Al/Mg–Ce diffusion couples was studied. • Formation of Al 4 Ce as the first phase was rationalized using the Gibbs free energy. • The activation energy for the growth of the diffusion reaction zones was 36.6 kJ/mol. - Abstract: The formation of Al–Ce intermetallic compounds (IMCs) during interdiffusion of Mg–Al/Mg–Ce diffusion couples prepared by solid–liquid contact method was investigated at 623 K, 648 K and 673 K for 24 h, 48 h and 72 h, respectively. During the whole diffusion process, Al was the dominant diffusing species, and it substituted for Mg of the Mg–Ce substrate. Five Al–Ce IMCs of Al 4 Ce, Al 11 Ce 3 , Al 3 Ce, Al 2 Ce and AlCe were formed via the reaction of Al and Ce. The formation of Al 4 Ce as the first kind of IMC was rationalized on the basis of an effective Gibbs free energy model. The activation energy for the growth of the total diffusion reaction layer was 36.6 kJ/mol

  9. Virtual substitution scan via single-step free energy perturbation.

    Science.gov (United States)

    Chiang, Ying-Chih; Wang, Yi

    2016-02-05

    With the rapid expansion of our computing power, molecular dynamics (MD) simulations ranging from hundreds of nanoseconds to microseconds or even milliseconds have become increasingly common. The majority of these long trajectories are obtained from plain (vanilla) MD simulations, where no enhanced sampling or free energy calculation method is employed. To promote the 'recycling' of these trajectories, we developed the Virtual Substitution Scan (VSS) toolkit as a plugin of the open-source visualization and analysis software VMD. Based on the single-step free energy perturbation (sFEP) method, VSS enables the user to post-process a vanilla MD trajectory for a fast free energy scan of substituting aryl hydrogens by small functional groups. Dihedrals of the functional groups are sampled explicitly in VSS, which improves the performance of the calculation and is found particularly important for certain groups. As a proof-of-concept demonstration, we employ VSS to compute the solvation free energy change upon substituting the hydrogen of a benzene molecule by 12 small functional groups frequently considered in lead optimization. Additionally, VSS is used to compute the relative binding free energy of four selected ligands of the T4 lysozyme. Overall, the computational cost of VSS is only a fraction of the corresponding multi-step FEP (mFEP) calculation, while its results agree reasonably well with those of mFEP, indicating that VSS offers a promising tool for rapid free energy scan of small functional group substitutions. This article is protected by copyright. All rights reserved. © 2016 Wiley Periodicals, Inc.

  10. Free energy surfaces from nonequilibrium processes without work measurement

    Science.gov (United States)

    Adib, Artur B.

    2006-04-01

    Recent developments in statistical mechanics have allowed the estimation of equilibrium free energies from the statistics of work measurements during processes that drive the system out of equilibrium. Here a different class of processes is considered, wherein the system is prepared and released from a nonequilibrium state, and no external work is involved during its observation. For such "clamp-and-release" processes, a simple strategy for the estimation of equilibrium free energies is offered. The method is illustrated with numerical simulations and analyzed in the context of tethered single-molecule experiments.

  11. Computational scheme for pH-dependent binding free energy calculation with explicit solvent.

    Science.gov (United States)

    Lee, Juyong; Miller, Benjamin T; Brooks, Bernard R

    2016-01-01

    We present a computational scheme to compute the pH-dependence of binding free energy with explicit solvent. Despite the importance of pH, the effect of pH has been generally neglected in binding free energy calculations because of a lack of accurate methods to model it. To address this limitation, we use a constant-pH methodology to obtain a true ensemble of multiple protonation states of a titratable system at a given pH and analyze the ensemble using the Bennett acceptance ratio (BAR) method. The constant pH method is based on the combination of enveloping distribution sampling (EDS) with the Hamiltonian replica exchange method (HREM), which yields an accurate semi-grand canonical ensemble of a titratable system. By considering the free energy change of constraining multiple protonation states to a single state or releasing a single protonation state to multiple states, the pH dependent binding free energy profile can be obtained. We perform benchmark simulations of a host-guest system: cucurbit[7]uril (CB[7]) and benzimidazole (BZ). BZ experiences a large pKa shift upon complex formation. The pH-dependent binding free energy profiles of the benchmark system are obtained with three different long-range interaction calculation schemes: a cutoff, the particle mesh Ewald (PME), and the isotropic periodic sum (IPS) method. Our scheme captures the pH-dependent behavior of binding free energy successfully. Absolute binding free energy values obtained with the PME and IPS methods are consistent, while cutoff method results are off by 2 kcal mol(-1) . We also discuss the characteristics of three long-range interaction calculation methods for constant-pH simulations. © 2015 The Protein Society.

  12. Free energy functionals for polarization fluctuations: Pekar factor revisited.

    Science.gov (United States)

    Dinpajooh, Mohammadhasan; Newton, Marshall D; Matyushov, Dmitry V

    2017-02-14

    The separation of slow nuclear and fast electronic polarization in problems related to electron mobility in polarizable media was considered by Pekar 70 years ago. Within dielectric continuum models, this separation leads to the Pekar factor in the free energy of solvation by the nuclear degrees of freedom. The main qualitative prediction of Pekar's perspective is a significant, by about a factor of two, drop of the nuclear solvation free energy compared to the total (electronic plus nuclear) free energy of solvation. The Pekar factor enters the solvent reorganization energy of electron transfer reactions and is a significant mechanistic parameter accounting for the solvent effect on electron transfer. Here, we study the separation of the fast and slow polarization modes in polar molecular liquids (polarizable dipolar liquids and polarizable water force fields) without relying on the continuum approximation. We derive the nonlocal free energy functional and use atomistic numerical simulations to obtain nonlocal, reciprocal space electronic and nuclear susceptibilities. A consistent transition to the continuum limit is introduced by extrapolating the results of finite-size numerical simulation to zero wavevector. The continuum nuclear susceptibility extracted from the simulations is numerically close to the Pekar factor. However, we derive a new functionality involving the static and high-frequency dielectric constants. The main distinction of our approach from the traditional theories is found in the solvation free energy due to the nuclear polarization: the anticipated significant drop of its magnitude with increasing liquid polarizability does not occur. The reorganization energy of electron transfer is either nearly constant with increasing the solvent polarizability and the corresponding high-frequency dielectric constant (polarizable dipolar liquids) or actually noticeably increases (polarizable force fields of water).

  13. Free energy functionals for polarization fluctuations: Pekar factor revisited

    International Nuclear Information System (INIS)

    Dinpajooh, Mohammadhasan; Newton, Marshall D.; Matyushov, Dmitry V.

    2017-01-01

    The separation of slow nuclear and fast electronic polarization in problems related to electron mobility in polarizable media was considered by Pekar 70 years ago. This separation leads to the Pekar factor in the free energy of solvation by the nuclear degrees of freedom, within dielectric continuum models. The main qualitative prediction of Pekar’s perspective is a significant, by about a factor of two, drop of the nuclear solvation free energy compared to the total (electronic plus nuclear) free energy of solvation. The Pekar factor enters the solvent reorganization energy of electron transfer reactions and is a significant mechanistic parameter accounting for the solvent effect on electron transfer. We study the separation of the fast and slow polarization modes in polar molecular liquids (polarizable dipolar liquids and polarizable water force fields) without relying on the continuum approximation. We derive the nonlocal free energy functional and use atomistic numerical simulations to obtain nonlocal, reciprocal space electronic and nuclear susceptibilities. A consistent transition to the continuum limit is introduced by extrapolating the results of finite-size numerical simulation to zero wavevector. The continuum nuclear susceptibility extracted from the simulations is numerically close to the Pekar factor. But, we derive a new functionality involving the static and high-frequency dielectric constants. The main distinction of our approach from the traditional theories is found in the solvation free energy due to the nuclear polarization: the anticipated significant drop of its magnitude with increasing liquid polarizability does not occur. The reorganization energy of electron transfer is either nearly constant with increasing the solvent polarizability and the corresponding high-frequency dielectric constant (polarizable dipolar liquids) or actually noticeably increases (polarizable force fields of water).

  14. Parabolic Free Boundary Price Formation Models Under Market Size Fluctuations

    KAUST Repository

    Markowich, Peter A.; Teichmann, Josef; Wolfram, Marie Therese

    2016-01-01

    In this paper we propose an extension of the Lasry-Lions price formation model which includes uctuations of the numbers of buyers and vendors. We analyze the model in the case of deterministic and stochastic market size uctuations and present

  15. Work and entropy production in generalised Gibbs ensembles

    International Nuclear Information System (INIS)

    Perarnau-Llobet, Martí; Riera, Arnau; Gallego, Rodrigo; Wilming, Henrik; Eisert, Jens

    2016-01-01

    Recent years have seen an enormously revived interest in the study of thermodynamic notions in the quantum regime. This applies both to the study of notions of work extraction in thermal machines in the quantum regime, as well as to questions of equilibration and thermalisation of interacting quantum many-body systems as such. In this work we bring together these two lines of research by studying work extraction in a closed system that undergoes a sequence of quenches and equilibration steps concomitant with free evolutions. In this way, we incorporate an important insight from the study of the dynamics of quantum many body systems: the evolution of closed systems is expected to be well described, for relevant observables and most times, by a suitable equilibrium state. We will consider three kinds of equilibration, namely to (i) the time averaged state, (ii) the Gibbs ensemble and (iii) the generalised Gibbs ensemble, reflecting further constants of motion in integrable models. For each effective description, we investigate notions of entropy production, the validity of the minimal work principle and properties of optimal work extraction protocols. While we keep the discussion general, much room is dedicated to the discussion of paradigmatic non-interacting fermionic quantum many-body systems, for which we identify significant differences with respect to the role of the minimal work principle. Our work not only has implications for experiments with cold atoms, but also can be viewed as suggesting a mindset for quantum thermodynamics where the role of the external heat baths is instead played by the system itself, with its internal degrees of freedom bringing coarse-grained observables to equilibrium. (paper)

  16. Interface-driven alloying and metallic glass formation in nano-multilayers in an immiscible Y-Nb system

    International Nuclear Information System (INIS)

    Chen, Y.G.; Liu, B.X.; Nanjing Univ.

    1999-01-01

    Several new amorphous alloys were obtained in an immiscible Y-Nb system by room temperature 190 keV xenon ion mixing of Y-Nb multilayered films, which were designed to include a sufficient fraction of interfacial atoms and thus possessed a high free energy comparable to that of the amorphous state. In addition, two metastable f.c.c. phases were formed in Y-rich and Nb-rich multilayered films, respectively. The growth kinetics of the f.c.c. phases and their effect on the composition range of amorphization are also discussed. To understand the observed unusual alloying behaviors, a Gibbs free-energy diagram was constructed based on Miedema's model. The diagram included the free-energy curves of all the involved phases as well as that of the Y-Nb multilayered films including the extra interfacial free energy and thus gave a qualitative and reasonable interpretation to the formation of metastable alloys upon ion mixing. Furthermore, some multilayered films with a sufficient fraction of interfacial atoms were subjected to steady-state thermal annealing, which also resulted in the formation of the Y-Nb amorphous phases, suggesting that alloying in this immiscible system was actually driven by the interfacial free energy

  17. Peptide Free Energy Landscapes Calibrated by Molecular Orbital Calculations

    OpenAIRE

    Ono, S.; Kuroda, M.; Higo, J.; Kamiya, N.; Nakajima, N.; Nakamura, H.

    2002-01-01

    Free energy landscapes of peptide conformations werecalibrated by ab initiomolecular orbital calculations, after enhancedconformational sampling using the multicanonical molecular dynamicssimulations. Three different potentials of mean force for an isolateddipeptide were individually obtained using the conventional force fields,AMBER parm94, AMBER parm96, and CHARMm22. Each potential ofmean force was calibrated based on the umbrella sampling algorithm fromthe adiabatic energy map that was cal...

  18. Estimation of formation enthalpies of vanadates by Born-Gaber cycle method

    International Nuclear Information System (INIS)

    Golovkin, B.G.

    1993-01-01

    Principle possibility of calculating Gibbs energy of ionic compound formation as a function of thermochemical radii of component ions of temperature and pressure is shown. Formula for determination of thermochemical radii of polyatomic ions is suggested. Enthalpies of formation of 81 vanadates were estimated with the use of Kapustinsky equation and Born-Gaber cycle

  19. Relationship between wave energy and free energy from pickup ions in the Comet Halley environment

    Science.gov (United States)

    Huddleston, D. E.; Johnstone, A. D.

    1992-01-01

    The free energy available from the implanted heavy ion population at Comet Halley is calculated by assuming that the initial unstable velocity space ring distribution of the ions evolves toward a bispherical shell. Ultimately this free energy adds to the turbulence in the solar wind. Upstream and downstream free energies are obtained separately for the conditions observed along the Giotto spacecraft trajectory. The results indicate that the waves are mostly upstream propagating in the solar wind frame. The total free energy density always exceeds the measured wave energy density because, as expected in the nonlinear process of ion scattering, the available energy is not all immediately released. An estimate of the amount which has been released can be obtained from the measured oxygen ion distributions and again it exceeds that observed. The theoretical analysis is extended to calculate the k spectrum of the cometary-ion-generated turbulence.

  20. Funnel metadynamics as accurate binding free-energy method

    Science.gov (United States)

    Limongelli, Vittorio; Bonomi, Massimiliano; Parrinello, Michele

    2013-01-01

    A detailed description of the events ruling ligand/protein interaction and an accurate estimation of the drug affinity to its target is of great help in speeding drug discovery strategies. We have developed a metadynamics-based approach, named funnel metadynamics, that allows the ligand to enhance the sampling of the target binding sites and its solvated states. This method leads to an efficient characterization of the binding free-energy surface and an accurate calculation of the absolute protein–ligand binding free energy. We illustrate our protocol in two systems, benzamidine/trypsin and SC-558/cyclooxygenase 2. In both cases, the X-ray conformation has been found as the lowest free-energy pose, and the computed protein–ligand binding free energy in good agreement with experiments. Furthermore, funnel metadynamics unveils important information about the binding process, such as the presence of alternative binding modes and the role of waters. The results achieved at an affordable computational cost make funnel metadynamics a valuable method for drug discovery and for dealing with a variety of problems in chemistry, physics, and material science. PMID:23553839

  1. The Free Energy in the Derrida-Retaux Recursive Model

    Science.gov (United States)

    Hu, Yueyun; Shi, Zhan

    2018-05-01

    We are interested in a simple max-type recursive model studied by Derrida and Retaux (J Stat Phys 156:268-290, 2014) in the context of a physics problem, and find a wide range for the exponent in the free energy in the nearly supercritical regime.

  2. Calculating zeros: Non-equilibrium free energy calculations

    International Nuclear Information System (INIS)

    Oostenbrink, Chris; Gunsteren, Wilfred F. van

    2006-01-01

    Free energy calculations on three model processes with theoretically known free energy changes have been performed using short simulation times. A comparison between equilibrium (thermodynamic integration) and non-equilibrium (fast growth) methods has been made in order to assess the accuracy and precision of these methods. The three processes have been chosen to represent processes often observed in biomolecular free energy calculations. They involve a redistribution of charges, the creation and annihilation of neutral particles and conformational changes. At very short overall simulation times, the thermodynamic integration approach using discrete steps is most accurate. More importantly, reasonable accuracy can be obtained using this method which seems independent of the overall simulation time. In cases where slow conformational changes play a role, fast growth simulations might have an advantage over discrete thermodynamic integration where sufficient sampling needs to be obtained at every λ-point, but only if the initial conformations do properly represent an equilibrium ensemble. From these three test cases practical lessons can be learned that will be applicable to biomolecular free energy calculations

  3. Molecular dynamics simulations and free energy profile of ...

    Indian Academy of Sciences (India)

    aDepartment of Chemical Engineering, bDepartment of Chemistry, Amirkabir University of Technology,. 15875-4413 ... Lipid bilayers; Paracetamol; free energy; molecular dynamics simulation; membrane. 1. ..... bilayer is less favourable due to the hydrophobic nature .... Orsi M and Essex J W 2010 Soft Matter 6 3797. 54.

  4. On the number of free energy extremums of a solid solution with two long-range order parameters

    International Nuclear Information System (INIS)

    Dateshidze, N.A.; Ratishvili, I.G.

    1977-01-01

    The free energy of ordering f.c.c. lattice solid solution is investigated. The ordering is regarded as homogeneous in the whole bulk of the crystal (i.e. resistant towards formation of antiphase domains). It is described by one of the appropriate distribution functions which contains two long-range order parameters. The calculations have revealed the extrema of the free energy function, and their shape and behaviour upon variations of temperature are analyzed. It is shown that under certain circumstances the system can display more than one minimum of free energy within the ordered phase

  5. Evaluation of the accuracy of the free-energy-minimization method

    International Nuclear Information System (INIS)

    Najafabadi, R.; Srolovitz, D.J.

    1995-01-01

    We have made a detailed comparison between three competing methods for determining the free energies of solids and their defects: the thermodynamic integration of Monte Carlo (TIMC) data, the quasiharmonic (QH) model, and the free-energy-minimization (FEM) method. The accuracy of these methods decreases from the TIMC to QH to FEM method, while the computational efficiency improves in that order. All three methods yield perfect crystal lattice parameters and free energies at finite temperatures which are in good agreement for three different Cu interatomic potentials [embedded atom method (EAM), Morse and Lennard-Jones]. The FEM error (relative to the TIMC) in the (001) surface free energy and in the vacancy formation energy were found to be much larger for the EAM potential than for the other two potentials. Part of the errors in the FEM determination of the free energies are associated with anharmonicities in the interatomic potentials, with the remainder attributed to decoupling of the atomic vibrations. The anharmonicity of the EAM potential was found to be unphysically large compared with experimental vacancy formation entropy determinations. Based upon these results, we show that the FEM method provides a reasonable compromise between accuracy and computational demands. However, the accuracy of this approach is sensitive to the choice of interatomic potential and the nature of the defect to which it is being applied. The accuracy of the FEM is best in high-symmetry environments (perfect crystal, high-symmetry defects, etc.) and when used to describe materials where the anharmonicity is not too large

  6. Concentration inequalities for functions of Gibbs fields with application to diffraction and random Gibbs measures

    CERN Document Server

    Külske, C

    2003-01-01

    We derive useful general concentration inequalities for functions of Gibbs fields in the uniqueness regime. We also consider expectations of random Gibbs measures that depend on an additional disorder field, and prove concentration w.r.t the disorder field. Both fields are assumed to be in the uniqueness regime, allowing in particular for non-independent disorder field. The modification of the bounds compared to the case of an independent field can be expressed in terms of constants that resemble the Dobrushin contraction coefficient, and are explicitly computable. On the basis of these inequalities, we obtain bounds on the deviation of a diffraction pattern created by random scatterers located on a general discrete point set in the Euclidean space, restricted to a finite volume. Here we also allow for thermal dislocations of the scatterers around their equilibrium positions. Extending recent results for independent scatterers, we give a universal upper bound on the probability of a deviation of the random sc...

  7. Free neutron-proton analyzing power at medium energies

    International Nuclear Information System (INIS)

    Newsom, C.R.

    1980-01-01

    In recent years, increasing efforts have been made to measure the nucleon-nucleon polarization parameters. To date, no free neutron-proton spin correlated parameters have been published in the energy range 500 to 800 MeV. Existing analyzing power data is of low precision and in most cases was obtained by quasi-free proton scattering. As a first step in determining the neutron-proton scattering matrix, the free neutron-proton analyzing power has been measured at the Los Alamos Physics Facility as a function of energy and angle. The experiment was performed by scattering a neutron beam from a polarized proton target. The neutron beam was generated by scattering 800 MeV protons from a Beryllium target and using the neutrons produced at 0 degrees. The incident energy ranged from 300 MeV to 800 MeV. The energy spread of the neutron beam made it possible to measure the analyzing power at different energies simultaneously. Angular distributions were taken from 60 to 170 degrees in the center of mass system (c.m.)

  8. Adriamycin and derivatives interaction with the mitochondrial membrane: O2 consumption and free radicals formation

    NARCIS (Netherlands)

    Pollakis, G.; Goormaghtigh, E.; Delmelle, M.; Lion, Y.; Ruysschaert, J. M.

    1984-01-01

    Adriamycin induces the formation of semiquinone free radicals, O(2) and OH. species, in beef heart intact mitochondria, submitochondrial particles and complex I-III containing proteoliposomes. Free radicals were detected by the use of Electron Spin Resonance (ESR) spectroscopy with the spin trapping

  9. A brief critique of the Adam-Gibbs entropy model

    DEFF Research Database (Denmark)

    Dyre, J. C.; Hecksher, Tina; Niss, Kristine

    2009-01-01

    This paper critically discusses the entropy model proposed by Adam and Gibbs in 1965 for the dramatic temperature dependence of glass-forming liquids' average relaxation time, which is one of the most influential models during the last four decades. We discuss the Adam-Gibbs model's theoretical...

  10. Simulations of skin barrier function: free energies of hydrophobic and hydrophilic transmembrane pores in ceramide bilayers.

    Science.gov (United States)

    Notman, Rebecca; Anwar, Jamshed; Briels, W J; Noro, Massimo G; den Otter, Wouter K

    2008-11-15

    Transmembrane pore formation is central to many biological processes such as ion transport, cell fusion, and viral infection. Furthermore, pore formation in the ceramide bilayers of the stratum corneum may be an important mechanism by which penetration enhancers such as dimethylsulfoxide (DMSO) weaken the barrier function of the skin. We have used the potential of mean constraint force (PMCF) method to calculate the free energy of pore formation in ceramide bilayers in both the innate gel phase and in the DMSO-induced fluidized state. Our simulations show that the fluid phase bilayers form archetypal water-filled hydrophilic pores similar to those observed in phospholipid bilayers. In contrast, the rigid gel-phase bilayers develop hydrophobic pores. At the relatively small pore diameters studied here, the hydrophobic pores are empty rather than filled with bulk water, suggesting that they do not compromise the barrier function of ceramide membranes. A phenomenological analysis suggests that these vapor pores are stable, below a critical radius, because the penalty of creating water-vapor and tail-vapor interfaces is lower than that of directly exposing the strongly hydrophobic tails to water. The PMCF free energy profile of the vapor pore supports this analysis. The simulations indicate that high DMSO concentrations drastically impair the barrier function of the skin by strongly reducing the free energy required for pore opening.

  11. Possible Lead Free Nanocomposite Dielectrics for High Energy Storage Applications

    Directory of Open Access Journals (Sweden)

    Srinivas Kurpati

    2017-03-01

    Full Text Available There is an increasing demand to improve the energy density of dielectric capacitors for satisfying the next generation material systems. One effective approach is to embed high dielectric constant inclusions such as lead zirconia titanate in polymer matrix. However, with the increasing concerns on environmental safety and biocompatibility, the need to expel lead (Pb from modern electronics has been receiving more attention. Using high aspect ratio dielectric inclusions such as nanowires could lead to further enhancement of energy density. Therefore, the present brief review work focuses on the feasibility of development of a lead-free nanowire reinforced polymer matrix capacitor for energy storage application. It is expected that Lead-free sodium Niobate nanowires (NaNbO3 and Boron nitride will be a future candidate to be synthesized using simple hydrothermal method, followed by mixing them with polyvinylidene fluoride (PVDF/ divinyl tetramethyl disiloxanebis (benzocyclobutene matrix using a solution-casting method for Nanocomposites fabrication. The energy density of NaNbO3 and BN based composites are also be compared with that of lead-containing (PbTiO3/PVDF Nano composites to show the feasibility of replacing lead-containing materials from high-energy density dielectric capacitors. Further, this paper explores the feasibility of these materials for space applications because of high energy storage capacity, more flexibility and high operating temperatures. This paper is very much useful researchers who would like to work on polymer nanocomposites for high energy storage applications.

  12. Calculating solution redox free energies with ab initio quantum mechanical/molecular mechanical minimum free energy path method

    International Nuclear Information System (INIS)

    Zeng Xiancheng; Hu Hao; Hu Xiangqian; Yang Weitao

    2009-01-01

    A quantum mechanical/molecular mechanical minimum free energy path (QM/MM-MFEP) method was developed to calculate the redox free energies of large systems in solution with greatly enhanced efficiency for conformation sampling. The QM/MM-MFEP method describes the thermodynamics of a system on the potential of mean force surface of the solute degrees of freedom. The molecular dynamics (MD) sampling is only carried out with the QM subsystem fixed. It thus avoids 'on-the-fly' QM calculations and thus overcomes the high computational cost in the direct QM/MM MD sampling. In the applications to two metal complexes in aqueous solution, the new QM/MM-MFEP method yielded redox free energies in good agreement with those calculated from the direct QM/MM MD method. Two larger biologically important redox molecules, lumichrome and riboflavin, were further investigated to demonstrate the efficiency of the method. The enhanced efficiency and uncompromised accuracy are especially significant for biochemical systems. The QM/MM-MFEP method thus provides an efficient approach to free energy simulation of complex electron transfer reactions.

  13. Comparative exploration of hydrogen sulfide and water transmembrane free energy surfaces via orthogonal space tempering free energy sampling.

    Science.gov (United States)

    Lv, Chao; Aitchison, Erick W; Wu, Dongsheng; Zheng, Lianqing; Cheng, Xiaolin; Yang, Wei

    2016-03-05

    Hydrogen sulfide (H2 S), a commonly known toxic gas compound, possesses unique chemical features that allow this small solute molecule to quickly diffuse through cell membranes. Taking advantage of the recent orthogonal space tempering (OST) method, we comparatively mapped the transmembrane free energy landscapes of H2 S and its structural analogue, water (H2 O), seeking to decipher the molecular determinants that govern their drastically different permeabilities. As revealed by our OST sampling results, in contrast to the highly polar water solute, hydrogen sulfide is evidently amphipathic, and thus inside membrane is favorably localized at the interfacial region, that is, the interface between the polar head-group and nonpolar acyl chain regions. Because the membrane binding affinity of H2 S is mainly governed by its small hydrophobic moiety and the barrier height inbetween the interfacial region and the membrane center is largely determined by its moderate polarity, the transmembrane free energy barriers to encounter by this toxic molecule are very small. Moreover when H2 S diffuses from the bulk solution to the membrane center, the above two effects nearly cancel each other, so as to lead to a negligible free energy difference. This study not only explains why H2 S can quickly pass through cell membranes but also provides a practical illustration on how to use the OST free energy sampling method to conveniently analyze complex molecular processes. © 2015 Wiley Periodicals, Inc. © 2015 Wiley Periodicals, Inc.

  14. Free energy landscape and transition pathways from Watson–Crick to Hoogsteen base pairing in free duplex DNA

    Science.gov (United States)

    Yang, Changwon; Kim, Eunae; Pak, Youngshang

    2015-01-01

    Houghton (HG) base pairing plays a central role in the DNA binding of proteins and small ligands. Probing detailed transition mechanism from Watson–Crick (WC) to HG base pair (bp) formation in duplex DNAs is of fundamental importance in terms of revealing intrinsic functions of double helical DNAs beyond their sequence determined functions. We investigated a free energy landscape of a free B-DNA with an adenosine–thymine (A–T) rich sequence to probe its conformational transition pathways from WC to HG base pairing. The free energy landscape was computed with a state-of-art two-dimensional umbrella molecular dynamics simulation at the all-atom level. The present simulation showed that in an isolated duplex DNA, the spontaneous transition from WC to HG bp takes place via multiple pathways. Notably, base flipping into the major and minor grooves was found to play an important role in forming these multiple transition pathways. This finding suggests that naked B-DNA under normal conditions has an inherent ability to form HG bps via spontaneous base opening events. PMID:26250116

  15. Free energy landscape and transition pathways from Watson-Crick to Hoogsteen base pairing in free duplex DNA.

    Science.gov (United States)

    Yang, Changwon; Kim, Eunae; Pak, Youngshang

    2015-09-18

    Houghton (HG) base pairing plays a central role in the DNA binding of proteins and small ligands. Probing detailed transition mechanism from Watson-Crick (WC) to HG base pair (bp) formation in duplex DNAs is of fundamental importance in terms of revealing intrinsic functions of double helical DNAs beyond their sequence determined functions. We investigated a free energy landscape of a free B-DNA with an adenosine-thymine (A-T) rich sequence to probe its conformational transition pathways from WC to HG base pairing. The free energy landscape was computed with a state-of-art two-dimensional umbrella molecular dynamics simulation at the all-atom level. The present simulation showed that in an isolated duplex DNA, the spontaneous transition from WC to HG bp takes place via multiple pathways. Notably, base flipping into the major and minor grooves was found to play an important role in forming these multiple transition pathways. This finding suggests that naked B-DNA under normal conditions has an inherent ability to form HG bps via spontaneous base opening events. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  16. Free-Free Transitions in the Presence of Laser Fields at Very Low Incident Electron Energy

    Science.gov (United States)

    Bhatia, A. K.; Sinha, Chandana

    2010-01-01

    We study the free-free transition in electron-hydrogenic systems in ground state in presence of an external laser field at very loud incident energies. The laser field is treated classically while the collision dynamics is treated quantum mechanically. The laser field is chosen to be monochromatic, linearly polarized and homogeneous. The incident electron is considered to be dressed by the laser in a nonperturbative manner by choosing a Volkov wave function for it. The scattering weave function for the electron is solved numerically by taking into account the effect of the electron exchange, short-range as well as of the long-range interactions to get the S and P wave phase shifts while for the higher angular momentum phase shifts the exchange approximation has only been considered. We calculate the laser assisted differential cross sections (LADCS) for the aforesaid free-free transition process for single photon absorption/emission. The laser intensity is chosen to be much less than the atomic field intensity. A strong suppression is noted in the LADCS as compared to the field free (FF) cross sections. Unlike the FF ones, the LADCS exhibit some oscillations having a distinct maximum at a low value of the scattering angle depending on the laser parameters as well as on the incident energies.

  17. Professional Formation in Hong Kong: Yin & Yang in a Free-Market Economy?

    Science.gov (United States)

    Forrester, Victor

    2007-01-01

    The relationship between the professional formation of beginning teachers, education reforms and Hong Kong's free-market economy is explored. An overview of educational change and then beginning teachers' professional formation within the context of economic cycles provides a contextual background against which two research projects are…

  18. A new energy transfer model for turbulent free shear flow

    Science.gov (United States)

    Liou, William W.-W.

    1992-01-01

    A new model for the energy transfer mechanism in the large-scale turbulent kinetic energy equation is proposed. An estimate of the characteristic length scale of the energy containing large structures is obtained from the wavelength associated with the structures predicted by a weakly nonlinear analysis for turbulent free shear flows. With the inclusion of the proposed energy transfer model, the weakly nonlinear wave models for the turbulent large-scale structures are self-contained and are likely to be independent flow geometries. The model is tested against a plane mixing layer. Reasonably good agreement is achieved. Finally, it is shown by using the Liapunov function method, the balance between the production and the drainage of the kinetic energy of the turbulent large-scale structures is asymptotically stable as their amplitude saturates. The saturation of the wave amplitude provides an alternative indicator for flow self-similarity.

  19. Free Electron Laser as Energy Driver for Inertial Confinement Fusion

    International Nuclear Information System (INIS)

    Saldin, E.L.; Shnejdmiller, E.A.; Ul'yanov, Yu.N.; Sarantsev, V.P.; Yurkov, M.V.

    1994-01-01

    A FEL based energy driver for Inertial Confinement Fusion (ICF) is proposed. The key element of the scheme is free electron laser system. Novel technical solutions reveal a possibility to construct the FEL system operating at radiation wavelength λ = 0.5 μm and providing flash energy E = 1 MJ and brightness 4 x 10 22 W cm -2 sr -1 within steering pulse duration 0.1-2 ns. Total energy efficiency of the proposed ICF energy driver is about of 11% and repetition rate is 40 Hz. Dimensions of such an ICF driver are comparable with those of heavy-ion ICF driver, while the problem of technical realization seems to be more realistic. It is shown that the FEL based ICF energy driver may be constructed at the present level of accelerator technique R and D. 27 refs., 10 figs., 3 tabs

  20. Designing molecular complexes using free-energy derivatives from liquid-state integral equation theory

    International Nuclear Information System (INIS)

    Mrugalla, Florian; Kast, Stefan M

    2016-01-01

    Complex formation between molecules in solution is the key process by which molecular interactions are translated into functional systems. These processes are governed by the binding or free energy of association which depends on both direct molecular interactions and the solvation contribution. A design goal frequently addressed in pharmaceutical sciences is the optimization of chemical properties of the complex partners in the sense of minimizing their binding free energy with respect to a change in chemical structure. Here, we demonstrate that liquid-state theory in the form of the solute–solute equation of the reference interaction site model provides all necessary information for such a task with high efficiency. In particular, computing derivatives of the potential of mean force (PMF), which defines the free-energy surface of complex formation, with respect to potential parameters can be viewed as a means to define a direction in chemical space toward better binders. We illustrate the methodology in the benchmark case of alkali ion binding to the crown ether 18-crown-6 in aqueous solution. In order to examine the validity of the underlying solute–solute theory, we first compare PMFs computed by different approaches, including explicit free-energy molecular dynamics simulations as a reference. Predictions of an optimally binding ion radius based on free-energy derivatives are then shown to yield consistent results for different ion parameter sets and to compare well with earlier, orders-of-magnitude more costly explicit simulation results. This proof-of-principle study, therefore, demonstrates the potential of liquid-state theory for molecular design problems. (paper)

  1. Water droplet excess free energy determined by cluster mitosis using guided molecular dynamics

    Science.gov (United States)

    Lau, Gabriel V.; Hunt, Patricia A.; Müller, Erich A.; Jackson, George; Ford, Ian J.

    2015-12-01

    Atmospheric aerosols play a vital role in affecting climate by influencing the properties and lifetimes of clouds and precipitation. Understanding the underlying microscopic mechanisms involved in the nucleation of aerosol droplets from the vapour phase is therefore of great interest. One key thermodynamic quantity in nucleation is the excess free energy of cluster formation relative to that of the saturated vapour. In our current study, the excess free energy is extracted for clusters of pure water modelled with the TIP4P/2005 intermolecular potential using a method based on nonequilibrium molecular dynamics and the Jarzynski relation. The change in free energy associated with the "mitosis" or division of a cluster of N water molecules into two N/2 sub-clusters is evaluated. This methodology is an extension of the disassembly procedure used recently to calculate the excess free energy of argon clusters [H. Y. Tang and I. J. Ford, Phys. Rev. E 91, 023308 (2015)]. Our findings are compared to the corresponding excess free energies obtained from classical nucleation theory (CNT) as well as internally consistent classical theory (ICCT). The values of the excess free energy that we obtain with the mitosis method are consistent with CNT for large cluster sizes but for the smallest clusters, the results tend towards ICCT; for intermediate sized clusters, we obtain values between the ICCT and CNT predictions. Furthermore, the curvature-dependent surface tension which can be obtained by regarding the clusters as spherical droplets of bulk density is found to be a monotonically increasing function of cluster size for the studied range. The data are compared to other values reported in the literature, agreeing qualitatively with some but disagreeing with the values determined by Joswiak et al. [J. Phys. Chem. Lett. 4, 4267 (2013)] using a biased mitosis approach; an assessment of the differences is the main motivation for our current study.

  2. Water droplet excess free energy determined by cluster mitosis using guided molecular dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Lau, Gabriel V.; Müller, Erich A.; Jackson, George [Department of Chemical Engineering, Imperial College London, South Kensington Campus, London SW7 2AZ (United Kingdom); Hunt, Patricia A. [Department of Chemistry, Imperial College London, South Kensington Campus, London SW7 2AZ (United Kingdom); Ford, Ian J. [Department of Physics and Astronomy and London Centre for Nanotechnology, University College London, Gower Street, London WC1E 6BT (United Kingdom)

    2015-12-28

    Atmospheric aerosols play a vital role in affecting climate by influencing the properties and lifetimes of clouds and precipitation. Understanding the underlying microscopic mechanisms involved in the nucleation of aerosol droplets from the vapour phase is therefore of great interest. One key thermodynamic quantity in nucleation is the excess free energy of cluster formation relative to that of the saturated vapour. In our current study, the excess free energy is extracted for clusters of pure water modelled with the TIP4P/2005 intermolecular potential using a method based on nonequilibrium molecular dynamics and the Jarzynski relation. The change in free energy associated with the “mitosis” or division of a cluster of N water molecules into two N/2 sub-clusters is evaluated. This methodology is an extension of the disassembly procedure used recently to calculate the excess free energy of argon clusters [H. Y. Tang and I. J. Ford, Phys. Rev. E 91, 023308 (2015)]. Our findings are compared to the corresponding excess free energies obtained from classical nucleation theory (CNT) as well as internally consistent classical theory (ICCT). The values of the excess free energy that we obtain with the mitosis method are consistent with CNT for large cluster sizes but for the smallest clusters, the results tend towards ICCT; for intermediate sized clusters, we obtain values between the ICCT and CNT predictions. Furthermore, the curvature-dependent surface tension which can be obtained by regarding the clusters as spherical droplets of bulk density is found to be a monotonically increasing function of cluster size for the studied range. The data are compared to other values reported in the literature, agreeing qualitatively with some but disagreeing with the values determined by Joswiak et al. [J. Phys. Chem. Lett. 4, 4267 (2013)] using a biased mitosis approach; an assessment of the differences is the main motivation for our current study.

  3. Interfacial free energy and stiffness of aluminum during rapid solidification

    International Nuclear Information System (INIS)

    Brown, Nicholas T.; Martinez, Enrique; Qu, Jianmin

    2017-01-01

    Using molecular dynamics simulations and the capillary fluctuation method, we have calculated the anisotropic crystal-melt interfacial free energy and stiffness of aluminum in a rapid solidification system where a temperature gradient is applied to enforce thermal non-equilibrium. To calculate these material properties, the standard capillary fluctuation method typically used for systems in equilibrium has been modified to incorporate a second-order Taylor expansion of the interfacial free energy term. The result is a robust method for calculating interfacial energy, stiffness and anisotropy as a function of temperature gradient using the fluctuations in the defined interface height. This work includes the calculation of interface characteristics for temperature gradients ranging from 11 to 34 K/nm. The captured results are compared to a thermal equilibrium case using the same model and simulation technique with a zero gradient definition. We define the temperature gradient as the change in temperature over height perpendicular to the crystal-melt interface. The gradients are applied in MD simulations using defined thermostat regions on a stable solid-liquid interface initially in thermal equilibrium. The results of this work show that the interfacial stiffness and free energy for aluminum are dependent on the magnitude of the temperature gradient, however the anisotropic parameters remain independent of the non-equilibrium conditions applied in this analysis. As a result, the relationships of the interfacial free energy/stiffness are determined to be linearly related to the thermal gradient, and can be interpolated to find material characteristics at additional temperature gradients.

  4. Two-Dimensional Free Energy Surfaces for Electron Transfer Reactions in Solution

    Directory of Open Access Journals (Sweden)

    Shigeo Murata

    2008-01-01

    Full Text Available Change in intermolecular distance between electron donor (D and acceptor (A can induce intermolecular electron transfer (ET even in nonpolar solvent, where solvent orientational polarization is absent. This was shown by making simple calculations of the energies of the initial and final states of ET. In the case of polar solvent, the free energies are functions of both D-A distance and solvent orientational polarization. On the basis of 2-dimensional free energy surfaces, the relation of Marcus ET and exciplex formation is discussed. The transient effect in fluorescence quenching was measured for several D-A pairs in a nonpolar solvent. The results were analyzed by assuming a distance dependence of the ET rate that is consistent with the above model.

  5. Free energy option and its relevance to improve domestic energy demands in southern Nigeria

    Directory of Open Access Journals (Sweden)

    Moses Eterigho Emetere

    2016-11-01

    Full Text Available The aim of this paper is to seek an energy option that would benefit the growing energy demands. Domestic energy demands in southern Nigeria had increased greatly due to failing power programs and seasonal migrations. The fossil fuel option is gradually fading away due to environmental pollution and recent dynamic cost. The renewable energy option had been celebrated with little success in the coastal area of southern Nigeria. At the moment, the renewable energy option is very expensive with little guarantee on its efficiency with time. The data set used for this study was obtained from the Davis weather installation in Covenant University. The free energy option was considered. The cost and its environmental implication for domestic use were comparatively discussed alongside other energy options — using the Life cycle cost analysis. It was found out that free energy option is more affordable and efficient for domestic use.

  6. Calculation of total free energy yield as an alternative approach for predicting the importance of potential chemolithotrophic reactions in geothermal springs.

    Science.gov (United States)

    Dodsworth, Jeremy A; McDonald, Austin I; Hedlund, Brian P

    2012-08-01

    To inform hypotheses regarding the relative importance of chemolithotrophic metabolisms in geothermal environments, we calculated free energy yields of 26 chemical reactions potentially supporting chemolithotrophy in two US Great Basin hot springs, taking into account the effects of changing reactant and product activities on the Gibbs free energy as each reaction progressed. Results ranged from 1.2 × 10(-5) to 3.6 J kg(-1) spring water, or 3.7 × 10(-5) to 11.5 J s(-1) based on measured flow rates, with aerobic oxidation of CH(4) or NH4 + giving the highest average yields. Energy yields calculated without constraining pH were similar to those at constant pH except for reactions where H(+) was consumed, which often had significantly lower yields when pH was unconstrained. In contrast to the commonly used normalization of reaction chemical affinities per mole of electrons transferred, reaction energy yields for a given oxidant varied by several orders of magnitude and were more sensitive to differences in the activities of products and reactants. The high energy yield of aerobic ammonia oxidation is consistent with previous observations of significant ammonia oxidation rates and abundant ammonia-oxidizing archaea in sediments of these springs. This approach offers an additional lens through which to view the thermodynamic landscape of geothermal springs. © 2012 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

  7. Nonlocal Free Energy of a Spatially Inhomogeneous Superconductor

    International Nuclear Information System (INIS)

    Grigorishin, K.V.; Lev, B.I.

    2012-01-01

    The microscopic approach is developed for obtaining of the free energy of a superconductor based on direct calculation of the vacuum amplitude. The free energy functional of the spatially inhomogeneous superconductor in a magnetic field is obtained with help of the developed approach. The obtained functional is generalization of Ginzburg-Landau functionals for any temperature, for arbitrary spatial variations of the order parameter and for the nonlocality of a magnetic response and the order parameter. Moreover, the nonlocality of the magnetic response is the consequence of order parameter's nonlocality. The extremals of this functional are considered in the explicit form in the low- and high-temperature limit at the condition of slowness of spatial variations of the order parameter. (condensed matter: electronic structure, electrical, magnetic, and optical properties)

  8. Solid/liquid interfacial free energies in binary systems

    Science.gov (United States)

    Nason, D.; Tiller, W. A.

    1973-01-01

    Description of a semiquantitative technique for predicting the segregation characteristics of smooth interfaces between binary solid and liquid solutions in terms of readily available thermodynamic parameters of the bulk solutions. A lattice-liquid interfacial model and a pair-bonded regular solution model are employed in the treatment with an accommodation for liquid interfacial entropy. The method is used to calculate the interfacial segregation and the free energy of segregation for solid-liquid interfaces between binary solutions for the (111) boundary of fcc crystals. The zone of compositional transition across the interface is shown to be on the order of a few atomic layers in width, being moderately narrower for ideal solutions. The free energy of the segregated interface depends primarily upon the solid composition and the heats of fusion of the component atoms, the composition difference of the solutions, and the difference of the heats of mixing of the solutions.

  9. FESetup: Automating Setup for Alchemical Free Energy Simulations.

    Science.gov (United States)

    Loeffler, Hannes H; Michel, Julien; Woods, Christopher

    2015-12-28

    FESetup is a new pipeline tool which can be used flexibly within larger workflows. The tool aims to support fast and easy setup of alchemical free energy simulations for molecular simulation packages such as AMBER, GROMACS, Sire, or NAMD. Post-processing methods like MM-PBSA and LIE can be set up as well. Ligands are automatically parametrized with AM1-BCC, and atom mappings for a single topology description are computed with a maximum common substructure search (MCSS) algorithm. An abstract molecular dynamics (MD) engine can be used for equilibration prior to free energy setup or standalone. Currently, all modern AMBER force fields are supported. Ease of use, robustness of the code, and automation where it is feasible are the main development goals. The project follows an open development model, and we welcome contributions.

  10. EPR study of N+-ion-induced free radical formation in antibiotic-producers

    International Nuclear Information System (INIS)

    Xie Liqing; Zhang Yinfen; Chen Ruyi; Gao Juncheng; Zhang Peiling; Ying Hengfeng.

    1995-01-01

    Under the room temperature, electron paramagnetic resonance (EPR) spectrometer was used to study free radical formation in antibiotic-producers in order to investigate antibiotic-producer mutagenic breeding, which were induced by N + ion implanting into antibiotic-producers (e.g., Streptomyces ribosidificus, Streptomyces kanamyceticus and the phage-resistant culture of Streptomyces kanamyceticus). The results show that a lot of free radicals can be induced by N + ion implanting into antibiotic-producers, and the yields of the free radicals increase with implanting dose. The death rate of antibiotic-producers rises due to the increase of N + -ion-induced free radical yields. (author)

  11. Surface free energy analysis of adsorbents used for radioiodine adsorption

    International Nuclear Information System (INIS)

    González-García, C.M.; Román, S.; González, J.F.; Sabio, E.; Ledesma, B.

    2013-01-01

    In this work, the surface free energy of biomass-based activated carbons, both fresh and impregnated with triethylenediamine, has been evaluated. The contribution of Lifshitz van der Waals components was determined by the model proposed by van Oss et al. The results obtained allowed predicting the most probable configurations of the impregnant onto the carbon surface and its influence on the subsequent adsorption of radioactive methyl iodide.

  12. Optimized Free Energies from Bidirectional Single-Molecule Force Spectroscopy

    Science.gov (United States)

    Minh, David D. L.; Adib, Artur B.

    2008-05-01

    An optimized method for estimating path-ensemble averages using data from processes driven in opposite directions is presented. Based on this estimator, bidirectional expressions for reconstructing free energies and potentials of mean force from single-molecule force spectroscopy—valid for biasing potentials of arbitrary stiffness—are developed. Numerical simulations on a model potential indicate that these methods perform better than unidirectional strategies.

  13. Characterizing structural transitions using localized free energy landscape analysis.

    Directory of Open Access Journals (Sweden)

    Nilesh K Banavali

    Full Text Available Structural changes in molecules are frequently observed during biological processes like replication, transcription and translation. These structural changes can usually be traced to specific distortions in the backbones of the macromolecules involved. Quantitative energetic characterization of such distortions can greatly advance the atomic-level understanding of the dynamic character of these biological processes.Molecular dynamics simulations combined with a variation of the Weighted Histogram Analysis Method for potential of mean force determination are applied to characterize localized structural changes for the test case of cytosine (underlined base flipping in a GTCAGCGCATGG DNA duplex. Free energy landscapes for backbone torsion and sugar pucker degrees of freedom in the DNA are used to understand their behavior in response to the base flipping perturbation. By simplifying the base flipping structural change into a two-state model, a free energy difference of upto 14 kcal/mol can be attributed to the flipped state relative to the stacked Watson-Crick base paired state. This two-state classification allows precise evaluation of the effect of base flipping on local backbone degrees of freedom.The calculated free energy landscapes of individual backbone and sugar degrees of freedom expectedly show the greatest change in the vicinity of the flipping base itself, but specific delocalized effects can be discerned upto four nucleotide positions away in both 5' and 3' directions. Free energy landscape analysis thus provides a quantitative method to pinpoint the determinants of structural change on the atomic scale and also delineate the extent of propagation of the perturbation along the molecule. In addition to nucleic acids, this methodology is anticipated to be useful for studying conformational changes in all macromolecules, including carbohydrates, lipids, and proteins.

  14. Hydrogen role in a carbon-free energy mix

    International Nuclear Information System (INIS)

    2014-02-01

    Among the energy storage technologies under development today, there is today an increasing interest towards the hydrogen-based ones. Hydrogen generation allows to store electricity, while its combustion can supply electrical, mechanical or heat energy. The French Atomic Energy Commission (CEA) started to work on hydrogen technologies at the end of the 1990's in order to reinforce its economical interest. The development of these technologies is one of the 34 French industrial programs presented in September 2013 by the French Minister of productive recovery. This paper aims at identifying the hydrogen stakes in a carbon-free energy mix and at highlighting the remaining technological challenges to be met before reaching an industrial development level

  15. Computing conformational free energy differences in explicit solvent: An efficient thermodynamic cycle using an auxiliary potential and a free energy functional constructed from the end points.

    Science.gov (United States)

    Harris, Robert C; Deng, Nanjie; Levy, Ronald M; Ishizuka, Ryosuke; Matubayasi, Nobuyuki

    2017-06-05

    Many biomolecules undergo conformational changes associated with allostery or ligand binding. Observing these changes in computer simulations is difficult if their timescales are long. These calculations can be accelerated by observing the transition on an auxiliary free energy surface with a simpler Hamiltonian and connecting this free energy surface to the target free energy surface with free energy calculations. Here, we show that the free energy legs of the cycle can be replaced with energy representation (ER) density functional approximations. We compute: (1) The conformational free energy changes for alanine dipeptide transitioning from the right-handed free energy basin to the left-handed basin and (2) the free energy difference between the open and closed conformations of β-cyclodextrin, a "host" molecule that serves as a model for molecular recognition in host-guest binding. β-cyclodextrin contains 147 atoms compared to 22 atoms for alanine dipeptide, making β-cyclodextrin a large molecule for which to compute solvation free energies by free energy perturbation or integration methods and the largest system for which the ER method has been compared to exact free energy methods. The ER method replaced the 28 simulations to compute each coupling free energy with two endpoint simulations, reducing the computational time for the alanine dipeptide calculation by about 70% and for the β-cyclodextrin by > 95%. The method works even when the distribution of conformations on the auxiliary free energy surface differs substantially from that on the target free energy surface, although some degree of overlap between the two surfaces is required. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  16. Energy and the NAFTA [North American Free Trade Agreement

    International Nuclear Information System (INIS)

    Plourde, A.

    1993-01-01

    A review is presented of the implications of the North American Free Trade Agreement (NAFTA) for the energy industry. This agreement expands the coverage accorded to energy in the Canada-US Free Trade Agreement (FTA), and is of limited significance with respect to Canada-US relations, but is quite important to these two countries' energy trade with Mexico. With respect to Canada-US trade, the most important departure from the FTA is that NAFTA tends to ensure a greater degree of respect for the terms of negotiated contracts, in particular by requiring the parties to make efforts to secure compliance with the national treatment provisions of the NAFTA by subfederal regulatory entities. Mexico's constitution severely restricts foreign participation in the activities of its energy industries, including basic petrochemicals. While NAFTA accomodates these restrictions, Canadian and US companies will have opportunities to bid on contracts for goods and services and construction in the Mexican energy sector on an equal footing with their Mexican counterparts. NAFTA also provides expanded opportunities for foreign investment and control in electricity generation for own-use, cogeneration and public service purposes. The parties are explicitly allowed to extend activity incentives to their respective oil and gas industries. 9 refs

  17. Directionally independent energy gap formation due to the hyperfine interaction

    NARCIS (Netherlands)

    Miyashita, Seiji; Raedt, Hans De; Michielsen, Kristel

    We study energy gap formation at the level-crossing point due to the hyperfine interaction. In contrast to the energy gap induced by the Dzyaloshinskii-Moriya interaction, the gap induced by the hyperfine interaction is independent of the direction of the magnetic field. We also study the dynamics

  18. Psychoanalytic Interpretation of Blueberries by Susan Gibb

    Directory of Open Access Journals (Sweden)

    Maya Zalbidea Paniagua

    2014-06-01

    Full Text Available Blueberries (2009 by Susan Gibb, published in the ELO (Electronic Literature Organization, invites the reader to travel inside the protagonist’s mind to discover real and imaginary experiences examining notions of gender, sex, body and identity of a traumatised woman. This article explores the verbal and visual modes in this digital short fiction following semiotic patterns as well as interpreting the psychological states that are expressed through poetical and technological components. A comparative study of the consequences of trauma in the protagonist will be developed including psychoanalytic theories by Sigmund Freud, Jacques Lacan and the feminist psychoanalysts: Melanie Klein and Bracha Ettinger. The reactions of the protagonist will be studied: loss of reality, hallucinations and Electra Complex, as well as the rise of defence mechanisms and her use of the artistic creativity as a healing therapy. The interactivity of the hypermedia, multiple paths and endings will be analyzed as a literary strategy that increases the reader’s capacity of empathizing with the speaker.

  19. Free energy of activation. Definition, properties, and dependent variables with special reference to linear free energy relations

    International Nuclear Information System (INIS)

    Levine, R.D.

    1979-01-01

    The reaction rate constant is expressed as Z exp(-G/sub a//RT). Z is the binary collision frequency. G/sub a/, the free energy of activation, is shown to be the difference between the free energy of the reactive reactants and the free energy of all reactants. The results are derived from both a statistical mechanical and a collision theoretic point of view. While the later is more suitable for an ab-initio computation of the reaction rate, it is the former that lends itself to the search of systematics and of correlations and to compaction of data. Different thermodynamic-like routes to the characterization of G/sub a/ are thus explored. The two most promising ones appear to be the use of thermodynamic type cycles and the changes of dependent variables using the Legendre transform technique. The dependence of G/sub a/ on ΔG 0 , the standard free energy change in the reaction, is examined from the later point of view. It is shown that one can rigorously express this dependence as G/sub a/ = αΔG 0 + G/sub a/ 0 M(α). Here α is the Bronsted slope, α = -par. delta ln k(T)/par. delta(ΔG 0 /RT), G/sub a/ 0 is independent of ΔG 0 and M(α), the Legendre transform of G/sub a/, is a function only of α. For small changes in ΔG 0 , the general result reduces to the familiar ''linear'' free energy relation delta G/sub a/ = α delta ΔG 0 . It is concluded from general considerations that M(α) is a symmetric, convex function of α and hence that α is a monotonically increasing function of ΔG 0 . Experimental data appear to conform well to the form α = 1/[1 + exp(-ΔG 0 /G/sub s/ 0 )]. A simple interpretation of the ΔG 0 dependence of G/sub a/, based on an interpolation of the free energy from that of the reagents to that of the products, is offered. 4 figures, 69 references

  20. Calculating Free Energies Using Scaled-Force Molecular Dynamics Algorithm

    Science.gov (United States)

    Darve, Eric; Wilson, Micahel A.; Pohorille, Andrew

    2000-01-01

    One common objective of molecular simulations in chemistry and biology is to calculate the free energy difference between different states of the system of interest. Examples of problems that have such an objective are calculations of receptor-ligand or protein-drug interactions, associations of molecules in response to hydrophobic, and electrostatic interactions or partition of molecules between immiscible liquids. Another common objective is to describe evolution of the system towards a low energy (possibly the global minimum energy), 'native' state. Perhaps the best example of such a problem is folding of proteins or short RNA molecules. Both types of problems share the same difficulty. Often, different states of the system are separated by high energy barriers, which implies that transitions between these states are rare events. This, in turn, can greatly impede exploration of phase space. In some instances this can lead to 'quasi non-ergodicity', whereby a part of phase space is inaccessible on timescales of the simulation. A host of strategies has been developed to improve efficiency of sampling the phase space. For example, some Monte Carlo techniques involve large steps which move the system between low-energy regions in phase space without the need for sampling the configurations corresponding to energy barriers (J-walking). Most strategies, however, rely on modifying probabilities of sampling low and high-energy regions in phase space such that transitions between states of interest are encouraged. Perhaps the simplest implementation of this strategy is to increase the temperature of the system. This approach was successfully used to identify denaturation pathways in several proteins, but it is clearly not applicable to protein folding. It is also not a successful method for determining free energy differences. Finally, the approach is likely to fail for systems with co-existing phases, such as water-membrane systems, because it may lead to spontaneous

  1. Determination of partial molar volumes from free energy perturbation theory.

    Science.gov (United States)

    Vilseck, Jonah Z; Tirado-Rives, Julian; Jorgensen, William L

    2015-04-07

    Partial molar volume is an important thermodynamic property that gives insights into molecular size and intermolecular interactions in solution. Theoretical frameworks for determining the partial molar volume (V°) of a solvated molecule generally apply Scaled Particle Theory or Kirkwood-Buff theory. With the current abilities to perform long molecular dynamics and Monte Carlo simulations, more direct methods are gaining popularity, such as computing V° directly as the difference in computed volume from two simulations, one with a solute present and another without. Thermodynamically, V° can also be determined as the pressure derivative of the free energy of solvation in the limit of infinite dilution. Both approaches are considered herein with the use of free energy perturbation (FEP) calculations to compute the necessary free energies of solvation at elevated pressures. Absolute and relative partial molar volumes are computed for benzene and benzene derivatives using the OPLS-AA force field. The mean unsigned error for all molecules is 2.8 cm(3) mol(-1). The present methodology should find use in many contexts such as the development and testing of force fields for use in computer simulations of organic and biomolecular systems, as a complement to related experimental studies, and to develop a deeper understanding of solute-solvent interactions.

  2. Determination of partial molar volumes from free energy perturbation theory†

    Science.gov (United States)

    Vilseck, Jonah Z.; Tirado-Rives, Julian

    2016-01-01

    Partial molar volume is an important thermodynamic property that gives insights into molecular size and intermolecular interactions in solution. Theoretical frameworks for determining the partial molar volume (V°) of a solvated molecule generally apply Scaled Particle Theory or Kirkwood–Buff theory. With the current abilities to perform long molecular dynamics and Monte Carlo simulations, more direct methods are gaining popularity, such as computing V° directly as the difference in computed volume from two simulations, one with a solute present and another without. Thermodynamically, V° can also be determined as the pressure derivative of the free energy of solvation in the limit of infinite dilution. Both approaches are considered herein with the use of free energy perturbation (FEP) calculations to compute the necessary free energies of solvation at elevated pressures. Absolute and relative partial molar volumes are computed for benzene and benzene derivatives using the OPLS-AA force field. The mean unsigned error for all molecules is 2.8 cm3 mol−1. The present methodology should find use in many contexts such as the development and testing of force fields for use in computer simulations of organic and biomolecular systems, as a complement to related experimental studies, and to develop a deeper understanding of solute–solvent interactions. PMID:25589343

  3. Mass and free energy of Lovelock black holes

    International Nuclear Information System (INIS)

    Kastor, David; Traschen, Jennie; Ray, Sourya

    2011-01-01

    An explicit formula for the ADM mass of an asymptotically AdS black hole in a generic Lovelock gravity theory is presented, identical in form to that in Einstein gravity, but multiplied by a function of the Lovelock coupling constants and the AdS curvature radius. A Gauss' law-type formula relates the mass, which is an integral at infinity, to an expression depending instead on the horizon radius. This and other thermodynamic quantities, such as the free energy, are then analyzed in the limits of small and large horizon radius, yielding results that are independent of the detailed choice of Lovelock couplings. In even dimensions, the temperature diverges in both limits, implying the existence of a minimum temperature for black holes. The negative free energy of sufficiently large black holes implies the existence of a Hawking-Page transition. In odd dimensions, the temperature still diverges for large black holes, which again have negative free energy. However, the temperature vanishes as the horizon radius tends to zero and sufficiently small black holes have positive specific heat.

  4. Emotional valence and the free-energy principle.

    Science.gov (United States)

    Joffily, Mateus; Coricelli, Giorgio

    2013-01-01

    The free-energy principle has recently been proposed as a unified Bayesian account of perception, learning and action. Despite the inextricable link between emotion and cognition, emotion has not yet been formulated under this framework. A core concept that permeates many perspectives on emotion is valence, which broadly refers to the positive and negative character of emotion or some of its aspects. In the present paper, we propose a definition of emotional valence in terms of the negative rate of change of free-energy over time. If the second time-derivative of free-energy is taken into account, the dynamics of basic forms of emotion such as happiness, unhappiness, hope, fear, disappointment and relief can be explained. In this formulation, an important function of emotional valence turns out to regulate the learning rate of the causes of sensory inputs. When sensations increasingly violate the agent's expectations, valence is negative and increases the learning rate. Conversely, when sensations increasingly fulfil the agent's expectations, valence is positive and decreases the learning rate. This dynamic interaction between emotional valence and learning rate highlights the crucial role played by emotions in biological agents' adaptation to unexpected changes in their world.

  5. Emotional valence and the free-energy principle.

    Directory of Open Access Journals (Sweden)

    Mateus Joffily

    Full Text Available The free-energy principle has recently been proposed as a unified Bayesian account of perception, learning and action. Despite the inextricable link between emotion and cognition, emotion has not yet been formulated under this framework. A core concept that permeates many perspectives on emotion is valence, which broadly refers to the positive and negative character of emotion or some of its aspects. In the present paper, we propose a definition of emotional valence in terms of the negative rate of change of free-energy over time. If the second time-derivative of free-energy is taken into account, the dynamics of basic forms of emotion such as happiness, unhappiness, hope, fear, disappointment and relief can be explained. In this formulation, an important function of emotional valence turns out to regulate the learning rate of the causes of sensory inputs. When sensations increasingly violate the agent's expectations, valence is negative and increases the learning rate. Conversely, when sensations increasingly fulfil the agent's expectations, valence is positive and decreases the learning rate. This dynamic interaction between emotional valence and learning rate highlights the crucial role played by emotions in biological agents' adaptation to unexpected changes in their world.

  6. Light fragment formation at intermediate energies

    International Nuclear Information System (INIS)

    Boal, D.H.

    1982-03-01

    This paper concerns itself mainly with the production of energetic protons and light fragments at wide angles. The experiments point to nucleon emission in proton-induced reactions as involving a mechanism in which the observed nucleon is directly knocked out of the nucleus. A similar feature seems to be required to explain (p,F) and (e,F) reactions: an energetic nucleon is produced in one scattering of the projectile, and the struck nucleon subsequently loses some of its energy as it traverses the remaining part of the nucleus, gathering up other nucleons as it goes, to become a fragment. This is what one might call the extreme snowball model, and a more accurate description probably involves multiple scattering of the projectile in addition to the extreme snowball contribution. This will be particularly true for fragments in the mass 6 to 9 region. This scenario also appears to apply to deuteron-induced fragment production. However, for alpha-induced reactions it would appear that the nucleons forming a fragment can originate from collisions involving different incident nucleons in the projectile. For heavy ions, this effect is even stronger, and the snowball contribution is greatly reduced compared to that of the traditional coalescence model

  7. Distribution of nuclei in equilibrium stellar matter from the free-energy density in a Wigner-Seitz cell

    Science.gov (United States)

    Grams, G.; Giraud, S.; Fantina, A. F.; Gulminelli, F.

    2018-03-01

    The aim of the present study is to calculate the nuclear distribution associated at finite temperature to any given equation of state of stellar matter based on the Wigner-Seitz approximation, for direct applications in core-collapse simulations. The Gibbs free energy of the different configurations is explicitly calculated, with special care devoted to the calculation of rearrangement terms, ensuring thermodynamic consistency. The formalism is illustrated with two different applications. First, we work out the nuclear statistical equilibrium cluster distribution for the Lattimer and Swesty equation of state, widely employed in supernova simulations. Secondly, we explore the effect of including shell structure, and consider realistic nuclear mass tables from the Brussels-Montreal Hartree-Fock-Bogoliubov model (specifically, HFB-24). We show that the whole collapse trajectory is dominated by magic nuclei, with extremely spread and even bimodal distributions of the cluster probability around magic numbers, demonstrating the importance of cluster distributions with realistic mass models in core-collapse simulations. Simple analytical expressions are given, allowing further applications of the method to any relativistic or nonrelativistic subsaturation equation of state.

  8. Formation of a superhigh energy electron spectrum in the Galaxy

    International Nuclear Information System (INIS)

    Agaronyan, F.A.; Ambartsumyan, A.S.

    1985-01-01

    The formation of superhigh energy electron spectrum in the disk of the galaxy and halo is considered. A different behaviour of the electron spectrum within the framework of capture models in disk or halo, in the energy region E> or approximately 10 5 GeV is revealed due to the account of relativistic corrections ir the energy losses of electrons during the inverse Compton scattering. A comparison with the existing experimental data is carried out

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

    Science.gov (United States)

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

    2016-06-01

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

  10. Gibbs perturbations of a two-dimensional gauge field

    International Nuclear Information System (INIS)

    Petrova, E.N.

    1981-01-01

    Small Gibbs perturbations of random fields have been investigated up to now for a few initial fields only. Among them there are independent fields, Gaussian fields and some others. The possibility for the investigation of Gibbs modifications of a random field depends essentially on the existence of good estimates for semiinvariants of this field. This is the reason why the class of random fields for which the investigation of Gibbs perturbations with arbitrary potential of bounded support is possible is rather small. The author takes as initial a well-known model: a two-dimensional gauge field. (Auth.)

  11. Assignment of Side-Chain Conformation Using Adiabatic Energy Mapping, Free Energy Perturbation, and Molecular Dynamic Simulations

    DEFF Research Database (Denmark)

    Frimurer, Thomas M.; Günther, Peter H.; Sørensen, Morten Dahl

    1999-01-01

    adiabatic mapping, conformational change, essentialdynamics, free energy simulations, Kunitz type inhibitor *ga3(VI)......adiabatic mapping, conformational change, essentialdynamics, free energy simulations, Kunitz type inhibitor *ga3(VI)...

  12. Relation between track structure and LET effect on free radical formation for ion beam-irradiated alanine dosimeter

    International Nuclear Information System (INIS)

    Krushev, V.V.; Koizumi, Hitoshi; Ichikawa, Tsuneki; Yoshida, Hiroshi; Shibata, Hiromi; Tagawa, Seiichi; Yoshida, Yoichi

    1994-01-01

    The yield and local concentration of free radicals generated from alanine (α-aminopropionic acid) by irradiation with 3 MeV H + and He + ions were examined by means of electron spin resonance (ESR) and ESR power saturation methods at room temperature. The G-value of the radical formation showed a marked dependence on linear energy transfer (LET) of the ions. The G-value for the H + ion (average LET: 28 eV/nm) was almost the same as that for γ-irradiation and it was smaller by a factor of 1/4.7 for the He + ion (average LET: 225eV/nm). Combining the local concentration of the free radicals along the ion tracks with the G-values and the reported ion range, the radius of a track filled with free radicals was estimated to be 4 ∼ 5 nm by assuming a simple rod-shaped track with a constant radius and homogeneous distribution of the free radicals in it. The track radius scarcely depends on the LET within the range examined. The radiation energy deposited in the core region of the ion track was concluded to spread over the rod to generate free radicals. (author)

  13. Linear free energy relationships between aqueous phase hydroxyl radical reaction rate constants and free energy of activation.

    Science.gov (United States)

    Minakata, Daisuke; Crittenden, John

    2011-04-15

    The hydroxyl radical (HO(•)) is a strong oxidant that reacts with electron-rich sites on organic compounds and initiates complex radical chain reactions in aqueous phase advanced oxidation processes (AOPs). Computer based kinetic modeling requires a reaction pathway generator and predictions of associated reaction rate constants. Previously, we reported a reaction pathway generator that can enumerate the most important elementary reactions for aliphatic compounds. For the reaction rate constant predictor, we develop linear free energy relationships (LFERs) between aqueous phase literature-reported HO(•) reaction rate constants and theoretically calculated free energies of activation for H-atom abstraction from a C-H bond and HO(•) addition to alkenes. The theoretical method uses ab initio quantum mechanical calculations, Gaussian 1-3, for gas phase reactions and a solvation method, COSMO-RS theory, to estimate the impact of water. Theoretically calculated free energies of activation are found to be within approximately ±3 kcal/mol of experimental values. Considering errors that arise from quantum mechanical calculations and experiments, this should be within the acceptable errors. The established LFERs are used to predict the HO(•) reaction rate constants within a factor of 5 from the experimental values. This approach may be applied to other reaction mechanisms to establish a library of rate constant predictions for kinetic modeling of AOPs.

  14. Improved free-energy landscape reconstruction of bacteriorhodopsin highlights local variations in unfolding energy.

    Science.gov (United States)

    Heenan, Patrick R; Yu, Hao; Siewny, Matthew G W; Perkins, Thomas T

    2018-03-28

    Precisely quantifying the energetics that drive the folding of membrane proteins into a lipid bilayer remains challenging. More than 15 years ago, atomic force microscopy (AFM) emerged as a powerful tool to mechanically extract individual membrane proteins from a lipid bilayer. Concurrently, fluctuation theorems, such as the Jarzynski equality, were applied to deduce equilibrium free energies (ΔG 0 ) from non-equilibrium single-molecule force spectroscopy records. The combination of these two advances in single-molecule studies deduced the free-energy of the model membrane protein bacteriorhodopsin in its native lipid bilayer. To elucidate this free-energy landscape at a higher resolution, we applied two recent developments. First, as an input to the reconstruction, we used force-extension curves acquired with a 100-fold higher time resolution and 10-fold higher force precision than traditional AFM studies of membrane proteins. Next, by using an inverse Weierstrass transform and the Jarzynski equality, we removed the free energy associated with the force probe and determined the molecular free-energy landscape of the molecule under study, bacteriorhodopsin. The resulting landscape yielded an average unfolding free energy per amino acid (aa) of 1.0 ± 0.1 kcal/mol, in agreement with past single-molecule studies. Moreover, on a smaller spatial scale, this high-resolution landscape also agreed with an equilibrium measurement of a particular three-aa transition in bacteriorhodopsin that yielded 2.7 kcal/mol/aa, an unexpectedly high value. Hence, while average unfolding ΔG 0 per aa is a useful metric, the derived high-resolution landscape details significant local variation from the mean. More generally, we demonstrated that, as anticipated, the inverse Weierstrass transform is an efficient means to reconstruct free-energy landscapes from AFM data.

  15. Drift-free solar sail formations in elliptical Sun-synchronous orbits

    Science.gov (United States)

    Parsay, Khashayar; Schaub, Hanspeter

    2017-10-01

    To study the spatial and temporal variations of plasma in the highly dynamic environment of the magnetosphere, multiple spacecraft must fly in a formation. The objective for this study is to investigate the feasibility of solar sail formation flying in the Earth-centered, Sun-synchronous orbit regime. The focus of this effort is to enable formation flying for a group of solar sails that maintain a nominally fixed Sun-pointing attitude during formation flight, solely for the purpose of precessing their orbit apse lines Sun-synchronously. A fixed-attitude solar sail formation is motivated by the difficulties in the simultaneous control of orbit and attitude in flying solar sails. First, the secular rates of the orbital elements resulting from the effects of solar radiation pressure (SRP) are determined using averaging theory for a Sun-pointing attitude sail. These averaged rates are used to analytically derive the first-order necessary conditions for a drift-free solar sail formation in Sun-synchronous orbits, assuming a fixed Sun-pointing orientation for each sail in formation. The validity of the first-order necessary conditions are illustrated by designing quasi-periodic relative motions. Next, nonlinear programming is applied to design truly drift-free two-craft solar sail formations. Lastly, analytic expressions are derived to determine the long-term dynamics and sensitivity of the formation with respect to constant attitude errors, uncertainty in orbital elements, and uncertainty in a sail's characteristic acceleration.

  16. Exploring the free energy surfaces of clusters using reconnaissance metadynamics

    Science.gov (United States)

    Tribello, Gareth A.; Cuny, Jérôme; Eshet, Hagai; Parrinello, Michele

    2011-09-01

    A new approach is proposed for exploring the low-energy structures of small to medium-sized aggregates of atoms and molecules. This approach uses the recently proposed reconnaissance metadynamics method [G. A. Tribello, M. Ceriotti, and M. Parrinello. Proc. Natl. Acad. Sci. U.S.A. 107(41), 17509 (2010), 10.1073/pnas.1011511107] in tandem with collective variables that describe the average structure of the coordination sphere around the atoms/molecules. We demonstrate this method on both Lennard-Jones and water clusters and show how it is able to quickly find the global minimum in the potential energy surface, while exploring the finite temperature free energy surface.

  17. Variationally Optimized Free-Energy Flooding for Rate Calculation

    Science.gov (United States)

    McCarty, James; Valsson, Omar; Tiwary, Pratyush; Parrinello, Michele

    2015-08-01

    We propose a new method to obtain kinetic properties of infrequent events from molecular dynamics simulation. The procedure employs a recently introduced variational approach [Valsson and Parrinello, Phys. Rev. Lett. 113, 090601 (2014)] to construct a bias potential as a function of several collective variables that is designed to flood the associated free energy surface up to a predefined level. The resulting bias potential effectively accelerates transitions between metastable free energy minima while ensuring bias-free transition states, thus allowing accurate kinetic rates to be obtained. We test the method on a few illustrative systems for which we obtain an order of magnitude improvement in efficiency relative to previous approaches and several orders of magnitude relative to unbiased molecular dynamics. We expect an even larger improvement in more complex systems. This and the ability of the variational approach to deal efficiently with a large number of collective variables will greatly enhance the scope of these calculations. This work is a vindication of the potential that the variational principle has if applied in innovative ways.

  18. Approximate scaling properties of RNA free energy landscapes

    Science.gov (United States)

    Baskaran, S.; Stadler, P. F.; Schuster, P.

    1996-01-01

    RNA free energy landscapes are analysed by means of "time-series" that are obtained from random walks restricted to excursion sets. The power spectra, the scaling of the jump size distribution, and the scaling of the curve length measured with different yard stick lengths are used to describe the structure of these "time series". Although they are stationary by construction, we find that their local behavior is consistent with both AR(1) and self-affine processes. Random walks confined to excursion sets (i.e., with the restriction that the fitness value exceeds a certain threshold at each step) exhibit essentially the same statistics as free random walks. We find that an AR(1) time series is in general approximately self-affine on timescales up to approximately the correlation length. We present an empirical relation between the correlation parameter rho of the AR(1) model and the exponents characterizing self-affinity.

  19. Bifurcation-free design method of pulse energy converter controllers

    International Nuclear Information System (INIS)

    Kolokolov, Yury; Ustinov, Pavel; Essounbouli, Najib; Hamzaoui, Abdelaziz

    2009-01-01

    In this paper, a design method of pulse energy converter (PEC) controllers is proposed. This method develops a classical frequency domain design, based on the small signal modeling, by means of an addition of a nonlinear dynamics analysis stage. The main idea of the proposed method consists in fact that the PEC controller, designed with an application of the small signal modeling, is tuned after with taking into the consideration an essentially nonlinear nature of the PEC that makes it possible to avoid bifurcation phenomena in the PEC dynamics at the design stage (bifurcation-free design). Also application of the proposed method allows an improvement of the designed controller performance. The application of this bifurcation-free design method is demonstrated on an example of the controller design of direct current-direct current (DC-DC) buck converter with an input electromagnetic interference filter.

  20. Reflections on Gibbs: From Critical Phenomena to the Amistad

    Science.gov (United States)

    Kadanoff, Leo P.

    2003-03-01

    J. Willard Gibbs, the younger was the first American theorist. He was one of the inventors of statistical physics. His introduction and development of the concepts of phase space, phase transitions, and thermodynamic surfaces was remarkably correct and elegant. These three concepts form the basis of different but related areas of physics. The connection among these areas has been a subject of deep reflection from Gibbs' time to our own. I shall talk about these connections by using concepts suggested by the work of Michael Berry and explicitly put forward by the philosopher Robert Batterman. This viewpoint relates theory-connection to the applied mathematics concepts of asymptotic analysis and singular perturbations. J. Willard Gibbs, the younger, had all his achievements concentrated in science. His father, also J. Willard Gibbs, also a Professor at Yale, had one great achievement that remains unmatched in our day. I shall describe it.

  1. Boltzmann, Gibbs and Darwin-Fowler approaches in parastatistics

    International Nuclear Information System (INIS)

    Ponczek, R.L.; Yan, C.C.

    1976-01-01

    Derivations of the equilibrium values of occupation numbers are made using three approaches, namely, the Boltzmann 'elementary' one, the ensemble method of Gibbs, and that of Darwin and Fowler as well [pt

  2. Achieving Chemical Equilibrium: The Role of Imposed Conditions in the Ammonia Formation Reaction

    Science.gov (United States)

    Tellinghuisen, Joel

    2006-01-01

    Under conditions of constant temperature T and pressure P, chemical equilibrium occurs in a closed system (fixed mass) when the Gibbs free energy G of the reaction mixture is minimized. However, when chemical reactions occur under other conditions, other thermodynamic functions are minimized or maximized. For processes at constant T and volume V,…

  3. Generalized trends in the formation energies of perovskite oxides.

    Science.gov (United States)

    Zeng, ZhenHua; Calle-Vallejo, Federico; Mogensen, Mogens B; Rossmeisl, Jan

    2013-05-28

    Generalized trends in the formation energies of several families of perovskite oxides (ABO3) and plausible explanations to their existence are provided in this study through a combination of DFT calculations, solid-state physics analyses and simple physical/chemical descriptors. The studied elements at the A site of perovskites comprise rare-earth, alkaline-earth and alkaline metals, whereas 3d and 5d metals were studied at the B site. We also include ReO3-type compounds, which have the same crystal structure of cubic ABO3 perovskites except without A-site elements. From the observations we extract the following four conclusions for the perovskites studied in the present paper: for a given cation at the B site, (I) perovskites with cations of identical oxidation state at the A site possess close formation energies; and (II) perovskites with cations of different oxidation states at the A site usually have quite different but ordered formation energies. On the other hand, for a given A-site cation, (III) the formation energies of perovskites vary linearly with respect to the atomic number of the elements at the B site within the same period of the periodic table, and the slopes depend systematically on the oxidation state of the A-site cation; and (IV) the trends in formation energies of perovskites with elements from different periods at the B site depend on the oxidation state of A-site cations. Since the energetics of perovskites is shown to be the superposition of the individual contributions of their constituent oxides, the trends can be rationalized in terms of A-O and B-O interactions in the ionic crystal. These findings reveal the existence of general systematic trends in the formation energies of perovskites and provide further insight into the role of ion-ion interactions in the properties of ternary compounds.

  4. Free-energy landscape of a hyperstable RNA tetraloop.

    Science.gov (United States)

    Miner, Jacob C; Chen, Alan A; García, Angel E

    2016-06-14

    We report the characterization of the energy landscape and the folding/unfolding thermodynamics of a hyperstable RNA tetraloop obtained through high-performance molecular dynamics simulations at microsecond timescales. Sampling of the configurational landscape is conducted using temperature replica exchange molecular dynamics over three isochores at high, ambient, and negative pressures to determine the thermodynamic stability and the free-energy landscape of the tetraloop. The simulations reveal reversible folding/unfolding transitions of the tetraloop into the canonical A-RNA conformation and the presence of two alternative configurations, including a left-handed Z-RNA conformation and a compact purine Triplet. Increasing hydrostatic pressure shows a stabilizing effect on the A-RNA conformation and a destabilization of the left-handed Z-RNA. Our results provide a comprehensive description of the folded free-energy landscape of a hyperstable RNA tetraloop and highlight the significant advances of all-atom molecular dynamics in describing the unbiased folding of a simple RNA secondary structure motif.

  5. Overview of direct air free cooling and thermal energy storage potential energy savings in data centres

    International Nuclear Information System (INIS)

    Oró, Eduard; Depoorter, Victor; Pflugradt, Noah; Salom, Jaume

    2015-01-01

    In the last years the total energy demand of data centres has experienced a dramatic increase which is expected to continue. This is why data centres industry and researchers are working on implementing energy efficiency measures and integrating renewable energy to overcome energy dependence and to reduce operational costs and CO 2 emissions. The cooling system of these unique infrastructures can account for 40% of the total energy consumption. To reduce the energy consumption, free cooling strategies are used more and more, but so far there has been little research about the potential of thermal energy storage (TES) solutions to match energy demand and energy availability. Hence, this work intends to provide an overview of the potential of the integration of direct air free cooling strategy and TES systems into data centres located at different European locations. For each location, the benefit of using direct air free cooling is evaluated energetically and economically for a data centre of 1250 kW. The use of direct air free cooling is shown to be feasible. This does not apply the TES systems by itself. But when using TES in combination with an off-peak electricity tariff the operational cooling cost can be drastically reduced. - Highlights: • The total annual hours for direct air free cooling in data centres are calculated. • The potential of TES integration in data centres is evaluated. • The implementation of TES to store the ambient air cold is not recommended. • TES is feasible if combined with redundant chillers and off-peak electricity price. • The cooling electricity cost is being reduced up to 51%, depending on the location

  6. Gibbs phenomenon for dispersive PDEs on the line

    OpenAIRE

    Biondini, Gino; Trogdon, Thomas

    2014-01-01

    We investigate the Cauchy problem for linear, constant-coefficient evolution PDEs on the real line with discontinuous initial conditions (ICs) in the small-time limit. The small-time behavior of the solution near discontinuities is expressed in terms of universal, computable special functions. We show that the leading-order behavior of the solution of dispersive PDEs near a discontinuity of the ICs is characterized by Gibbs-type oscillations and gives exactly the Wilbraham-Gibbs constant.

  7. Electronic structure and formation energy of a vacancy in aluminum

    International Nuclear Information System (INIS)

    Chakraborty, B.; Siegel, R.W.

    1981-11-01

    The electronic structure of a vacancy in Al was calculated self-consistently using norm-conserving ionic pseudopotentials obtained from ab initio atomic calculations. A 27-atom-site supercell containing 1 vacancy and 26 atoms was used to simulate the environment of the vacancy. A vacancy formation energy of 1.5 eV was also calculated (cf. the experimental value of 0.66 eV). The effects of the supercell and the nature of the ionic potential on the resulting electronic structure and formation energy are discussed. Results for the electronic structure of a divacancy are also presented. 3 figures

  8. On a price formation free boundary model by Lasry and Lions

    KAUST Repository

    Caffarelli, Luis A.

    2011-06-01

    We discuss global existence and asymptotic behaviour of a price formation free boundary model introduced by Lasry and Lions in 2007. Our results are based on a construction which transforms the problem into the heat equation with specially prepared initial datum. The key point is that the free boundary present in the original problem becomes the zero level set of this solution. Using the properties of the heat operator we can show global existence, regularity and asymptotic results of the free boundary. 2011 Académie des sciences.

  9. On a price formation free boundary model by Lasry and Lions

    KAUST Repository

    Caffarelli, Luis A.; Markowich, Peter A.; Pietschmann, Jan-F.

    2011-01-01

    We discuss global existence and asymptotic behaviour of a price formation free boundary model introduced by Lasry and Lions in 2007. Our results are based on a construction which transforms the problem into the heat equation with specially prepared initial datum. The key point is that the free boundary present in the original problem becomes the zero level set of this solution. Using the properties of the heat operator we can show global existence, regularity and asymptotic results of the free boundary. 2011 Académie des sciences.

  10. Trp-cage: Folding free energy landscape in explicit water

    Science.gov (United States)

    Zhou, Ruhong

    2003-11-01

    Trp-cage is a 20-residue miniprotein, which is believed to be the fastest folder known so far. In this study, the folding free energy landscape of Trp-cage has been explored in explicit solvent by using an OPLSAA force field with periodic boundary condition. A highly parallel replica exchange molecular dynamics method is used for the conformation space sampling, with the help of a recently developed efficient molecular dynamics algorithm P3ME/RESPA (particle-particle particle-mesh Ewald/reference system propagator algorithm). A two-step folding mechanism is proposed that involves an intermediate state where two correctly formed partial hydrophobic cores are separated by an essential salt-bridge between residues Asp-9 and Arg-16 near the center of the peptide. This metastable intermediate state provides an explanation for the superfast folding process. The free energy landscape is found to be rugged at low temperatures, and then becomes smooth and funnel-like above 340 K. The lowest free energy structure at 300 K is only 1.50 Å C-RMSD (C-rms deviation) from the NMR structures. The simulated nuclear Overhauser effect pair distances are in excellent agreement with the raw NMR data. The temperature dependence of the Trp-cage population, however, is found to be significantly different from experiment, with a much higher melting transition temperature above 400 K (experimental 315 K), indicating that the current force fields, parameterized at room temperature, need to be improved to correctly predict the temperature dependence.

  11. Minimal Self-Models and the Free Energy Principle

    Directory of Open Access Journals (Sweden)

    Jakub eLimanowski

    2013-09-01

    Full Text Available The term "minimal phenomenal selfhood" describes the basic, pre-reflective experience of being a self (Blanke & Metzinger, 2009. Theoretical accounts of the minimal self have long recognized the importance and the ambivalence of the body as both part of the physical world, and the enabling condition for being in this world (Gallagher, 2005; Grafton, 2009. A recent account of minimal phenomenal selfhood (MPS, Metzinger, 2004a centers on the consideration that minimal selfhood emerges as the result of basic self-modeling mechanisms, thereby being founded on pre-reflective bodily processes. The free energy principle (FEP, Friston, 2010 is a novel unified theory of cortical function that builds upon the imperative that self-organizing systems entail hierarchical generative models of the causes of their sensory input, which are optimized by minimizing free energy as an approximation of the log-likelihood of the model. The implementation of the FEP via predictive coding mechanisms and in particular the active inference principle emphasizes the role of embodiment for predictive self-modeling, which has been appreciated in recent publications. In this review, we provide an overview of these conceptions and illustrate thereby the potential power of the FEP in explaining the mechanisms underlying minimal selfhood and its key constituents, multisensory integration, interoception, agency, perspective, and the experience of mineness. We conclude that the conceptualization of MPS can be well mapped onto a hierarchical generative model furnished by the free energy principle and may constitute the basis for higher-level, cognitive forms of self-referral, as well as the understanding of other minds.

  12. The interfacial free energy of solid Sn on the boundary interface with liquid Cd-Sn eutectic solution

    International Nuclear Information System (INIS)

    Saatci, B; Cimen, S; Pamuk, H; Guenduez, M

    2007-01-01

    Equilibrated grain boundary groove shapes for solid Sn in equilibrium with Cd-Sn liquid were directly observed after annealing a sample at the eutectic temperature for about 8 days. The thermal conductivities of the solid phase, K S , and the liquid phase, K L , for the groove shapes were measured. From the observed groove shapes, the Gibbs-Thomson coefficients were obtained with a numerical method, using the measured G, K S and K L values. The solid-liquid interfacial energy of solid Sn in equilibrium with Cd-Sn liquid was determined from the Gibbs-Thomson equation. The grain boundary energy for solid Sn was also calculated from the observed groove shapes

  13. Wettability and surface free energy of polarised ceramic biomaterials

    International Nuclear Information System (INIS)

    Nakamura, Miho; Hori, Naoko; Namba, Saki; Yamashita, Kimihiro; Toyama, Takeshi; Nishimiya, Nobuyuki

    2015-01-01

    The surface modification of ceramic biomaterials used for medical devices is expected to improve osteoconductivity through control of the interfaces between the materials and living tissues. Polarisation treatment induced surface charges on hydroxyapatite, β-tricalcium phosphate, carbonate-substituted hydroxyapatite and yttria-stabilized zirconia regardless of the differences in the carrier ions participating in the polarisation. Characterization of the surfaces revealed that the wettability of the polarised ceramic biomaterials was improved through the increase in the surface free energies compared with conventional ceramic surfaces. (note)

  14. Trivial constraints on orbital-free kinetic energy density functionals

    Science.gov (United States)

    Luo, Kai; Trickey, S. B.

    2018-03-01

    Approximate kinetic energy density functionals (KEDFs) are central to orbital-free density functional theory. Limitations on the spatial derivative dependencies of KEDFs have been claimed from differential virial theorems. We identify a central defect in the argument: the relationships are not true for an arbitrary density but hold only for the minimizing density and corresponding chemical potential. Contrary to the claims therefore, the relationships are not constraints and provide no independent information about the spatial derivative dependencies of approximate KEDFs. A simple argument also shows that validity for arbitrary v-representable densities is not restored by appeal to the density-potential bijection.

  15. Advancing Drug Discovery through Enhanced Free Energy Calculations.

    Science.gov (United States)

    Abel, Robert; Wang, Lingle; Harder, Edward D; Berne, B J; Friesner, Richard A

    2017-07-18

    A principal goal of drug discovery project is to design molecules that can tightly and selectively bind to the target protein receptor. Accurate prediction of protein-ligand binding free energies is therefore of central importance in computational chemistry and computer aided drug design. Multiple recent improvements in computing power, classical force field accuracy, enhanced sampling methods, and simulation setup have enabled accurate and reliable calculations of protein-ligands binding free energies, and position free energy calculations to play a guiding role in small molecule drug discovery. In this Account, we outline the relevant methodological advances, including the REST2 (Replica Exchange with Solute Temperting) enhanced sampling, the incorporation of REST2 sampling with convential FEP (Free Energy Perturbation) through FEP/REST, the OPLS3 force field, and the advanced simulation setup that constitute our FEP+ approach, followed by the presentation of extensive comparisons with experiment, demonstrating sufficient accuracy in potency prediction (better than 1 kcal/mol) to substantially impact lead optimization campaigns. The limitations of the current FEP+ implementation and best practices in drug discovery applications are also discussed followed by the future methodology development plans to address those limitations. We then report results from a recent drug discovery project, in which several thousand FEP+ calculations were successfully deployed to simultaneously optimize potency, selectivity, and solubility, illustrating the power of the approach to solve challenging drug design problems. The capabilities of free energy calculations to accurately predict potency and selectivity have led to the advance of ongoing drug discovery projects, in challenging situations where alternative approaches would have great difficulties. The ability to effectively carry out projects evaluating tens of thousands, or hundreds of thousands, of proposed drug candidates

  16. Free electron lasers for transmission of energy in space

    Science.gov (United States)

    Segall, S. B.; Hiddleston, H. R.; Catella, G. C.

    1981-01-01

    A one-dimensional resonant-particle model of a free electron laser (FEL) is used to calculate laser gain and conversion efficiency of electron energy to photon energy. The optical beam profile for a resonant optical cavity is included in the model as an axial variation of laser intensity. The electron beam profile is matched to the optical beam profile and modeled as an axial variation of current density. Effective energy spread due to beam emittance is included. Accelerators appropriate for a space-based FEL oscillator are reviewed. Constraints on the concentric optical resonator and on systems required for space operation are described. An example is given of a space-based FEL that would produce 1.7 MW of average output power at 0.5 micrometer wavelength with over 50% conversion efficiency of electrical energy to laser energy. It would utilize a 10 m-long amplifier centered in a 200 m-long optical cavity. A 3-amp, 65 meV electrostatic accelerator would provide the electron beam and recover the beam after it passes through the amplifier. Three to five shuttle flights would be needed to place the laser in orbit.

  17. Standard Glbbs Energy of Formation of the Hydroxyl Radical in Aqueous Solution. Rate Constants for the Reaction C102- -t O3 S 03- -t CIO,

    DEFF Research Database (Denmark)

    Klaning, U. K.; Sehested, Knud; Holcman, J.

    1985-01-01

    The rate constants of the following reactions were determined by pulse radiolysis and stopped-flow experiments: C102- + O3 + C102 + 03-(k f= (4 f 1) X lo6 dm3 mol-' s-', k, = (1.8 f 0.2) X lo5 dm3 mol-' s-]); C102 + OH - C103- + H+ (k = (4.0 * 0.4) X lo9 dm3 mol-' s-l); C102 + 0- - C103- (k = (2.......7 * 0.4) X lo9 dm3 mol-' s-l); and O3 + C102 - C103 + O2 (k = (1.05 f 0.10) X lo3 dm3 mol-l s-'), where kf is the forward rate of reaction and k, is the reverse rate of reaction. The standard Gibbs energy of formation of OH in aqueous solution A&O,,(OH) and the corresponding standard oxidation potential...

  18. Binding energy and formation heat of UO2

    International Nuclear Information System (INIS)

    Almeida, M.R. de; Veado, J.T.; Siqueira, M.L. de

    The Born-Haber cycle is utilized for the calculation of the heat of formation of UO 2 , on the assumption that the binding energy is predominantly ionic in character. The ionization potentials of U and the repulsion energy are two critical values that influence calculations. Calculations of the ionization potentials with non-relativistic Hartree-Fock-Gaspar-Kohn-Sham approximation are presented [pt

  19. High-throughput DFT calculations of formation energy, stability and oxygen vacancy formation energy of ABO3 perovskites

    Science.gov (United States)

    Emery, Antoine A.; Wolverton, Chris

    2017-10-01

    ABO3 perovskites are oxide materials that are used for a variety of applications such as solid oxide fuel cells, piezo-, ferro-electricity and water splitting. Due to their remarkable stability with respect to cation substitution, new compounds for such applications potentially await discovery. In this work, we present an exhaustive dataset of formation energies of 5,329 cubic and distorted perovskites that were calculated using first-principles density functional theory. In addition to formation energies, several additional properties such as oxidation states, band gap, oxygen vacancy formation energy, and thermodynamic stability with respect to all phases in the Open Quantum Materials Database are also made publicly available. This large dataset for this ubiquitous crystal structure type contains 395 perovskites that are predicted to be thermodynamically stable, of which many have not yet been experimentally reported, and therefore represent theoretical predictions. The dataset thus opens avenues for future use, including materials discovery in many research-active areas.

  20. Coarse-grained versus atomistic simulations : realistic interaction free energies for real proteins

    NARCIS (Netherlands)

    May, Ali; Pool, René; van Dijk, Erik; Bijlard, Jochem; Abeln, Sanne; Heringa, Jaap; Feenstra, K Anton

    2014-01-01

    MOTIVATION: To assess whether two proteins will interact under physiological conditions, information on the interaction free energy is needed. Statistical learning techniques and docking methods for predicting protein-protein interactions cannot quantitatively estimate binding free energies. Full

  1. Free energy minimization and information gain: The devil is in the details

    NARCIS (Netherlands)

    Kwisthout, J.H.P.; Rooij, I.J.E.I. van

    2015-01-01

    Contrary to Friston's previous work, this paper describes free energy minimization using categorical probability distributions over discrete states. This alternative mathematical framework exposes a fundamental, yet unnoticed challenge for the free energy principle. When considering discrete state

  2. Coarse-grained versus atomistic simulations: realistic interaction free energies for real proteins

    NARCIS (Netherlands)

    May, A.; Pool, R.; van Dijk, E.; Bijlard, J.; Abeln, S.; Heringa, J.; Feenstra, K.A.

    2014-01-01

    MOTIVATION: To assess whether two proteins will interact under physiological conditions, information on the interaction free energy is needed. Statistical learning techniques and docking methods for predicting protein-protein interactions cannot quantitatively estimate binding free energies. Full

  3. Low-energy electron inelastic mean free path in materials

    Energy Technology Data Exchange (ETDEWEB)

    Nguyen-Truong, Hieu T., E-mail: nguyentruongthanhhieu@tdt.edu.vn [Theoretical Physics Research Group & Faculty of Applied Sciences, Ton Duc Thang University, Ho Chi Minh City 756636 (Viet Nam)

    2016-04-25

    We show that the dielectric approach can determine electron inelastic mean free paths in materials with an accuracy equivalent to those from first-principle calculations in the GW approximation of many-body theory. The present approach is an alternative for calculating the hot-electron lifetime, which is an important quantity in ultrafast electron dynamics. This approach, applied here to solid copper for electron energies below 100 eV, yields results in agreement with experimental data from time-resolved two-photon photoemission, angle-resolved photoelectron spectroscopy, and X-ray absorption fine structure measurements in the energy ranges 2–3.5, 10–15, and 60–100 eV, respectively.

  4. Formation of defect-free 6FDA-DAM asymmetric hollow fiber membranes for gas separations

    KAUST Repository

    Xu, Liren

    2014-06-01

    This paper reports the formation of defect-free 6FDA-DAM asymmetric hollow fiber membranes. 6FDA-polyimides are of great interest for advanced gas separation membranes, and 6FDA-DAM polyimide is a representative polymer in this family with attractive dense film properties for several potential applications. The work reported here for the 6FDA-DAM polyimide provides insight for the challenging fabrication of defect-free asymmetric hollow fiber membranes for this class of 6FDA-polyimides, which behave rather different from lower free volume polymers. Specifically, the 6FDA based materials show relatively slow phase separation rate in water quench baths, which presents a challenge for fiber spinning. For convenience, we refer to the behavior as more "non-solvent resistant" in comparison to other lower free volume polymers, since the binodal phase boundary is displaced further from the conventional position near the pure polymer-solvent axis on a ternary phase diagram in conventional polymers like Matrimid® and Ultem®. The addition of lithium nitrate to promote phase separation has a useful impact on 6FDA-DAM asymmetric hollow fiber formation. 6FDA-DAM phase diagrams using ethanol and water as non-solvent are reported, and it was found that water is less desirable as a non-solvent dope additive for defect-free fiber spinning. Phase diagrams are also reported for 6FDA-DAM dope formulation with and without the addition of lithium nitrate, and defect-free asymmetric hollow fiber membranes are reported for both cases. The effect of polymer molecular weight on defect-free fiber spinning was also investigated. Gas transport properties and morphology of hollow fibers were characterized. With several thorough case studies, this work provides a systematic guideline for defect-free fiber formation from 6FDA-polymers. © 2014 Elsevier B.V.

  5. New theory of radiative energy transfer in free electromagnetic fields

    International Nuclear Information System (INIS)

    Wolf, E.

    1976-01-01

    A new theory of radiative energy transfer in free, statistically stationary electromagnetic fields is presented. It provides a model for energy transport that is rigorous both within the framework of the stochastic theory of the classical field as well as within the framework of the theory of the quantized field. Unlike the usual phenomenological model of radiative energy transfer that centers around a single scalar quantity (the specific intensity of radiation), our theory brings into evidence the need for characterizing the energy transport by means of two (related) quantities: a scalar and a vector that may be identified, in a well-defined sense, with ''angular components'' of the average electromagnetic energy density and of the average Poynting vector, respectively. Both of them are defined in terms of invariants of certain new electromagnetic correlation tensors. In the special case when the field is statistically homogeneous, our model reduces to the usual one and our angular component of the average electromagnetic energy density, when multiplied by the vacuum speed of light, then acquires all the properties of the specific intensity of radiation. When the field is not statistically homogeneous our model approximates to the usual phenomenological one, provided that the angular correlations between plane wave modes of the field extend over a sufficiently small solid angle of directions about the direction of propagation of each mode. It is tentatively suggested that, when suitably normalized, our angular component of the average electromagnetic energy density may be interpreted as a quasi-probability (general quantum-mechancial phase-space distribution function, such as Wigner's) for the position and the momentum of a photon

  6. Impact of Wire Geometry in Energy Extraction from Salinity Differences Using Capacitive Technology

    NARCIS (Netherlands)

    Sales, B.B.; Burheim, O.S.; Liu, F.; Schaetzle, O.; Buisman, C.J.N.; Hamelers, H.V.M.

    2012-01-01

    Energy extraction based on capacitive Donnan potential (CDP) is a recently suggested technique for sustainable power generation. CDP combines the use of ion-exchange membranes and porous carbon electrodes to convert the Gibbs free energy of mixing sea and river water into electric work. The

  7. Thermodynamic, energy efficiency, and power density analysis of reverse electrodialysis power generation with natural salinity gradients

    NARCIS (Netherlands)

    Yip, N.Y.; Vermaas, D.A.; Nijmeijer, K.; Elimelech, M.

    2014-01-01

    Reverse electrodialysis (RED) can harness the Gibbs free energy of mixing when fresh river water flows into the sea for sustainable power generation. In this study, we carry out a thermodynamic and energy efficiency analysis of RED power generation, and assess the membrane power density. First, we

  8. Formation of defect-free 6FDA-DAM asymmetric hollow fiber membranes for gas separations

    KAUST Repository

    Xu, Liren; Zhang, Chen; Rungta, Meha; Qiu, Wulin; Liu, Junqiang; Koros, William J.

    2014-01-01

    This paper reports the formation of defect-free 6FDA-DAM asymmetric hollow fiber membranes. 6FDA-polyimides are of great interest for advanced gas separation membranes, and 6FDA-DAM polyimide is a representative polymer in this family

  9. Non-Equilibrium Properties from Equilibrium Free Energy Calculations

    Science.gov (United States)

    Pohorille, Andrew; Wilson, Michael A.

    2012-01-01

    Calculating free energy in computer simulations is of central importance in statistical mechanics of condensed media and its applications to chemistry and biology not only because it is the most comprehensive and informative quantity that characterizes the eqUilibrium state, but also because it often provides an efficient route to access dynamic and kinetic properties of a system. Most of applications of equilibrium free energy calculations to non-equilibrium processes rely on a description in which a molecule or an ion diffuses in the potential of mean force. In general case this description is a simplification, but it might be satisfactorily accurate in many instances of practical interest. This hypothesis has been tested in the example of the electrodiffusion equation . Conductance of model ion channels has been calculated directly through counting the number of ion crossing events observed during long molecular dynamics simulations and has been compared with the conductance obtained from solving the generalized Nernst-Plank equation. It has been shown that under relatively modest conditions the agreement between these two approaches is excellent, thus demonstrating the assumptions underlying the diffusion equation are fulfilled. Under these conditions the electrodiffusion equation provides an efficient approach to calculating the full voltage-current dependence routinely measured in electrophysiological experiments.

  10. Diffusion in multicomponent systems: a free energy approach

    International Nuclear Information System (INIS)

    Emmanuel, Simon; Cortis, Andrea; Berkowitz, Brian

    2004-01-01

    This work examines diffusion in ternary non-ideal systems and derives coupled non-linear equations based on a non-equilibrium thermodynamic approach in which an explicit expression for the free energy is substituted into standard diffusion equations. For ideal solutions, the equations employ four mobility parameters (M aa , M ab , M ba , and M bb ), and uphill diffusion is predicted for certain initial conditions and combinations of mobilities. For the more complex case of ternary Simple Mixtures, two non-ideality parameters (χ ac and χ bc ) that are directly related to the excess free energy of mixing are introduced. The solution of the equations is carried out by means of two different numerical schemes: (1) spectral collocation and (2) finite element. An error minimization technique is coupled with the spectral collocation method and applied to diffusional profiles to extract the M and χ parameters. The model satisfactorily reproduces diffusional profiles from published data for silicate melts. Further improvements in numerical and experimental techniques are then suggested

  11. Flavour fields in steady state: stress tensor and free energy

    International Nuclear Information System (INIS)

    Banerjee, Avik; Kundu, Arnab; Kundu, Sandipan

    2016-01-01

    The dynamics of a probe brane in a given gravitational background is governed by the Dirac-Born-Infeld action. The corresponding open string metric arises naturally in studying the fluctuations on the probe. In Gauge-String duality, it is known that in the presence of a constant electric field on the worldvolume of the probe, the open string metric acquires an event horizon and therefore the fluctuation modes on the probe experience an effective temperature. In this article, we bring together various properties of such a system to a formal definition and a subsequent narration of the effective thermodynamics and the stress tensor of the corresponding flavour fields, also including a non-vanishing chemical potential. In doing so, we point out a potentially infinitely-degenerate scheme-dependence of regularizing the free energy, which nevertheless yields a universal contribution in certain cases. This universal piece appears as the coefficient of a log-divergence in free energy when a space-filling probe brane is embedded in AdS d+1 -background, for d=2,4, and is related to conformal anomaly. For the special case of d=2, the universal factor has a striking resemblance to the well-known heat current formula in (1+1)-dimensional conformal field theory in steady-state, which endows a plausible physical interpretation to it. Interestingly, we observe a vanishing conformal anomaly in d=6.

  12. Iterative free-energy optimization for recurrent neural networks (INFERNO)

    Science.gov (United States)

    2017-01-01

    The intra-parietal lobe coupled with the Basal Ganglia forms a working memory that demonstrates strong planning capabilities for generating robust yet flexible neuronal sequences. Neurocomputational models however, often fails to control long range neural synchrony in recurrent spiking networks due to spontaneous activity. As a novel framework based on the free-energy principle, we propose to see the problem of spikes’ synchrony as an optimization problem of the neurons sub-threshold activity for the generation of long neuronal chains. Using a stochastic gradient descent, a reinforcement signal (presumably dopaminergic) evaluates the quality of one input vector to move the recurrent neural network to a desired activity; depending on the error made, this input vector is strengthened to hill-climb the gradient or elicited to search for another solution. This vector can be learned then by one associative memory as a model of the basal-ganglia to control the recurrent neural network. Experiments on habit learning and on sequence retrieving demonstrate the capabilities of the dual system to generate very long and precise spatio-temporal sequences, above two hundred iterations. Its features are applied then to the sequential planning of arm movements. In line with neurobiological theories, we discuss its relevance for modeling the cortico-basal working memory to initiate flexible goal-directed neuronal chains of causation and its relation to novel architectures such as Deep Networks, Neural Turing Machines and the Free-Energy Principle. PMID:28282439

  13. Energy Pooling Upconversion in Free Space and Optical Cavities

    Science.gov (United States)

    LaCount, Michael D.

    energy pooling rate efficiency of 99%. This demonstrates that the energy pooling rate can be made faster than its competing processes. Based on the results of this study, a set of design rules was developed to optimize the rate efficiency of energy pooling. Prior to this research, no attempt had been made to determine if energy pooling could be made to out-pace competing processes--i.e. whether or not a molecular system could be designed to utilize energy pooling as an efficient means of upconversion. This initial investigation was part of a larger effort involving a team of researchers at the University of Colorado, Boulder and at the National Renewable Energy Laboratory. After establishing our computational proof-of-concept, we collectively used the new design rules to select an improved system for energy pooling. This consisted of rhodamine 6G and stilbene-420. These molecules were fabricated into a thin film, and the maximum internal quantum yield was measured to be 36% under sufficiently high intensity light. To further increase the efficiency of energy pooling, encapsulation within optical cavities was considered as a way of changing the rate of processes characterized by electric dipole-dipole coupling. This was carried out using a combination of classical electromagnetism, quantum electrodynamics, and perturbation theory. It was found that, in the near field, if the distance of the energy transfer is smaller than the distance from the energy transfer site and the cavity wall, then the electric dipole-dipole coupling tensor is not influenced by the cavity environment and the rates of energy transfer processes are the same as those in free space. Any increase in energy transfer efficiencies that are experimentally measured must therefore be caused by changing the rate of light absorption and emission. This is an important finding because earlier, less rigorous studies had concluded otherwise. It has been previously demonstrated that an optical cavity can be used to

  14. Structure formation in inhomogeneous Early Dark Energy models

    International Nuclear Information System (INIS)

    Batista, R.C.; Pace, F.

    2013-01-01

    We study the impact of Early Dark Energy fluctuations in the linear and non-linear regimes of structure formation. In these models the energy density of dark energy is non-negligible at high redshifts and the fluctuations in the dark energy component can have the same order of magnitude of dark matter fluctuations. Since two basic approximations usually taken in the standard scenario of quintessence models, that both dark energy density during the matter dominated period and dark energy fluctuations on small scales are negligible, are not valid in such models, we first study approximate analytical solutions for dark matter and dark energy perturbations in the linear regime. This study is helpful to find consistent initial conditions for the system of equations and to analytically understand the effects of Early Dark Energy and its fluctuations, which are also verified numerically. In the linear regime we compute the matter growth and variation of the gravitational potential associated with the Integrated Sachs-Wolf effect, showing that these observables present important modifications due to Early Dark Energy fluctuations, though making them more similar to the ΛCDM model. We also make use of the Spherical Collapse model to study the influence of Early Dark Energy fluctuations in the nonlinear regime of structure formation, especially on δ c parameter, and their contribution to the halo mass, which we show can be of the order of 10%. We finally compute how the number density of halos is modified in comparison to the ΛCDM model and address the problem of how to correct the mass function in order to take into account the contribution of clustered dark energy. We conclude that the inhomogeneous Early Dark Energy models are more similar to the ΛCDM model than its homogeneous counterparts

  15. Free energy landscapes of electron transfer system in dipolar environment below and above the rotational freezing temperature

    International Nuclear Information System (INIS)

    Suzuki, Yohichi; Tanimura, Yoshitaka

    2007-01-01

    Electron transfer reaction in a polar solvent is modeled by a solute dipole surrounded by dipolar molecules with simple rotational dynamics posted on the three-dimensional distorted lattice sites. The interaction energy between the solute and solvent dipoles as a reaction coordinate is adopted and free energy landscapes are calculated by generating all possible states for a 26 dipolar system and by employing Wang-Landau sampling algorithm for a 92 dipolar system. For temperatures higher than the energy scale of dipole-dipole interactions, the free energy landscapes for the small reaction coordinate region have quadratic shape as predicted by Marcus [Rev. Mod. Phys. 65, 599 (1993)] whereas for the large reaction coordinate region, the landscapes exhibit a nonquadratic shape. When the temperature drops, small notched structures appear on the free energy profiles because of the frustrated interactions among dipoles. The formation of notched structure is analyzed with statistical approach and it is shown that the amplitude of notched structure depend upon the segment size of the reaction coordinate and is characterized by the interaction energy among the dipoles. Using simulated free energy landscapes, the authors calculate the reaction rates as a function of the energy gap for various temperatures. At high temperature, the reactions rates follow a bell shaped (inverted parabolic) energy gap law in the small energy gap regions, while it becomes steeper than the parabolic shape in a large energy gap regions due to the nonquadratic shape of the free energy landscape. The peak position of parabola also changes as the function of temperature. At low temperature, the profile of the reaction rates is no longer smooth because of the many local minima of the free energy landscape

  16. Ab-initio calculation for cation vacancy formation energy in anti-fluorite structure

    Science.gov (United States)

    Saleel, V. P. Saleel Ahammad; Chitra, D.; Veluraja, K.; Eithiraj, R. D.

    2018-04-01

    Lithium oxide (Li2O) has been suggested as a suitable breeder blanket material for fusion reactors. Li+ vacancies are created by neutron irradiation, forming bulk defect complex whose extra character is experimentally unclear. We present a theoretical study of Li2O using density functional theory (DFT) with a plane-wave basis set. The generalized gradient approximation (GGA) and local-density approximation (LDA) were used for exchange and correlation. Here we address the total energy for defect free, cation defect, cation vacancy and vacancy formation energy in Li2O crystal in anti-fluorite structure.

  17. A free vein graft cap influences neuroma formation after nerve transection.

    Science.gov (United States)

    Galeano, Mariarosaria; Manasseri, Benedetto; Risitano, Giovanni; Geuna, Stefano; Di Scipio, Federica; La Rosa, Paola; Delia, Gabriele; D'Alcontres, Francesco Stagno; Colonna, Michele R

    2009-01-01

    : Neuroma formation is a major problem in nerve surgery and consensus about its prevention has not been reached. It has been suggested that vein covering can reduce neuroma formation in transected nerves. In this article, the Authors propose an easy and novel method of covering by nerve stump capping with a free vein graft. : Neuroma-like lesions were created on the rat thigh sectioning the femoral nerve above its division in 16 animals. The proximal nerve stump was invaginated into the lumen of a 1.5 cm long femoral free vein graft on the right side, and the vein was closed on itself by microsurgical sutures to form a cap for the nerve stump. On the left side acting as the control neuroma, the nerve was cut and left uncovered. Histological and immunohistochemical assessment was used to quantify the degree of neuroma formation. : Significant differences were found in both neuroma size and axon-glia organization between the treated and control sides indicating that free vein graft capping reduced neuroma formation in comparison to uncovered nerve stumps. : Our results confirm that vein-covering of a transected nerve stump can be effective in reducing neuroma formation. Moreover, unlike previous works that buried the nerve into an adjacent vein left in place, our experiments showed that also the use of a free vein graft cap can hinder neuroma formation. Although translation of rat experiments to the clinics should be dealt with caution, our data suggest a careful clinical use of the technique. (c) 2009 Wiley-Liss, Inc. Microsurgery, 2009.

  18. Formation of Lignans(-)-Secoisolariciresinol and (-)-Matairesinol with Forsythia intermedia Cell-Free Extracts

    Science.gov (United States)

    Umezawa, Toshiaki; Davin, Laurence B.; Lewis, Norman G.

    1991-01-01

    In vivo labeling experiments of Forsythia intermedia plant tissue with [8-(C-14)]- and [9,9-(2)H2,OC(2)H3]coniferyl alcohols revealed that the lignans, (-)-secoisolariciresinol and (-)-matairesinol, were derived from two coniferyl alcohol molecules; no evidence for the formation of the corresponding (+)-enantiomers was found. Administration of (+/-)-[Ar-(H-3)] secoisolariciresinols to excised shoots of F.intermedia resulted in a significant conversion into (-)-matairesinol; again, the (+)-antipode was not detected. Experiments using cell-free extracts of F.intermedia confirmed and extended these findings. In the presence of NAD(P)H and H2O2, the cell-free extracts catalyzed the formation of (-)- secoisolariciresinol, with either [8-(C-14)]- or [9,9-(2)H2,OC(2)H3]coniferyl alcohols as substrates. The (+)- enantiomer was not formed. Finally, when either (-)-[Ar-(H-3)] or (+/-)-[Ar-(H-2)]secoisolariciresinols were used as substrates, in the presence of NAD(P), only (-)- and not (+)-matairesinol formation occurred. The other antipode, (+)-secoisolariciresinol, did not serve as a substrate for the formation of either (+)- or (-)-matairesinol. Thus, in F.intermedia, the formation of the lignan, (-)-secoisolariciresinol, occurs under strict stereochemical control, in a reaction or reactions requiring NAD(P)H and H2O2 as cofactors. This stereoselectivity is retained in the subsequent conversion into (-)-matairesinol, since (+)-secoisolariciresinol is not a substrate. These are the first two enzymes to be discovered in lignan formation.

  19. Effect of flavoring chemicals on free radical formation in electronic cigarette aerosols.

    Science.gov (United States)

    Bitzer, Zachary T; Goel, Reema; Reilly, Samantha M; Elias, Ryan J; Silakov, Alexey; Foulds, Jonathan; Muscat, Joshua; Richie, John P

    2018-05-20

    Flavoring chemicals, or flavorants, have been used in electronic cigarettes (e-cigarettes) since their inception; however, little is known about their toxicological effects. Free radicals present in e-cigarette aerosols have been shown to induce oxidative stress resulting in damage to proliferation, survival, and inflammation pathways in the cell. Aerosols generated from e-liquid solvents alone contain high levels of free radicals but few studies have looked at how these toxins are modulated by flavorants. We investigated the effects of different flavorants on free radical production in e-cigarette aerosols. Free radicals generated from 49 commercially available e-liquid flavors were captured and analyzed using electron paramagnetic resonance (EPR). The flavorant composition of each e-liquid was analyzed by gas chromatography mass spectroscopy (GCMS). Radical production was correlated with flavorant abundance. Ten compounds were identified and analyzed for their impact on free radical generation. Nearly half of the flavors modulated free radical generation. Flavorants with strong correlations included β-damascone, δ-tetradecalactone, γ-decalactone, citral, dipentene, ethyl maltol, ethyl vanillin, ethyl vanillin PG acetal, linalool, and piperonal. Dipentene, ethyl maltol, citral, linalool, and piperonal promoted radical formation in a concentration-dependent manner. Ethyl vanillin inhibited the radical formation in a concentration dependent manner. Free radical production was closely linked with the capacity to oxidize biologically-relevant lipids. Our results suggest that flavoring agents play an important role in either enhancing or inhibiting the production of free radicals in flavored e-cigarette aerosols. This information is important for developing regulatory strategies aimed at reducing potential harm from e-cigarettes. Copyright © 2018 Elsevier Inc. All rights reserved.

  20. Examining ion channel properties using free-energy methods.

    Science.gov (United States)

    Domene, Carmen; Furini, Simone

    2009-01-01

    Recent advances in structural biology have revealed the architecture of a number of transmembrane channels, allowing for these complex biological systems to be understood in atomistic detail. Computational simulations are a powerful tool by which the dynamic and energetic properties, and thereby the function of these protein architectures, can be investigated. The experimentally observable properties of a system are often determined more by energetic than dynamics, and therefore understanding the underlying free energy (FE) of biophysical processes is of crucial importance. Critical to the accurate evaluation of FE values are the problems of obtaining accurate sampling of complex biological energy landscapes, and of obtaining accurate representations of the potential energy of a system, this latter problem having been addressed through the development of molecular force fields. While these challenges are common to all FE methods, depending on the system under study, and the questions being asked of it, one technique for FE calculation may be preferable to another, the choice of method and simulation protocol being crucial to achieve efficiency. Applied in a correct manner, FE calculations represent a predictive and affordable computational tool with which to make relevant contact with experiments. This chapter, therefore, aims to give an overview of the most widely implemented computational methods used to calculate the FE associated with particular biochemical or biophysical events, and to highlight their recent applications to ion channels. Copyright © 2009 Elsevier Inc. All rights reserved.

  1. Environmental protection through energy conservation: A free lunch at last?

    International Nuclear Information System (INIS)

    Ruff, L.E.

    1990-01-01

    A cautious analysis of demand-side management programs is presented. Utility demand-side management (DSM) programs deserve to be given full and careful consideration as a potential way to give consumers better end-use energy services for their money, utilities an edge in an increasingly competitive market, and society a way to reduce the environmental costs of energy production. But in each of these areas, DSM programs offer no free lunches and have no inherent advantages over supply-side programs. If energy conservation makes sense on economic and business grounds, it can meet the standard economic and business tests applied to most of the rest of the economy; it neither requires nor deserves to be exempt from market concepts and disciplines. If utility DSM programs make sense on environmental grounds, they should be able to demonstrate their cost-effectiveness relative to other, primarily supply-side measures society is willing to undertake in order to control environmental effects. Subsidizing DSM measures in the hope that something good will happen far upstream can waste much money and cause disappointment and frustration

  2. 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.

  3. Effect of Dark Energy Perturbation on Cosmic Voids Formation

    Science.gov (United States)

    Endo, Takao; Nishizawa, Atsushi J.; Ichiki, Kiyotomo

    2018-05-01

    In this paper, we present the effects of dark energy perturbation on the formation and abundance of cosmic voids. We consider dark energy to be a fluid with a negative pressure characterised by a constant equation of state w and speed of sound c_s^2. By solving fluid equations for two components, namely, dark matter and dark energy fluids, we quantify the effects of dark energy perturbation on the sizes of top-hat voids. We also explore the effects on the size distribution of voids based on the excursion set theory. We confirm that dark energy perturbation negligibly affects the size evolution of voids; c_s^2=0 varies the size only by 0.1% as compared to the homogeneous dark energy model. We also confirm that dark energy perturbation suppresses the void size when w -1 (Basse et al. 2011). In contrast to the negligible impact on the size, we find that the size distribution function on scales larger than 10 Mpc/h highly depends on dark energy perturbation; compared to the homogeneous dark energy model, the number of large voids of radius 30Mpc is 25% larger for the model with w = -0.9 and c_s^2=0 while they are 20% less abundant for the model with w = -1.3 and c_s^2=0.

  4. Crystal structure representations for machine learning models of formation energies

    Energy Technology Data Exchange (ETDEWEB)

    Faber, Felix [Department of Chemistry, Institute of Physical Chemistry and National Center for Computational Design and Discovery of Novel Materials, University of Basel Switzerland; Lindmaa, Alexander [Department of Physics, Chemistry and Biology, Linköping University, SE-581 83 Linköping Sweden; von Lilienfeld, O. Anatole [Department of Chemistry, Institute of Physical Chemistry and National Center for Computational Design and Discovery of Novel Materials, University of Basel Switzerland; Argonne Leadership Computing Facility, Argonne National Laboratory, 9700 S. Cass Avenue Lemont Illinois 60439; Armiento, Rickard [Department of Physics, Chemistry and Biology, Linköping University, SE-581 83 Linköping Sweden

    2015-04-20

    We introduce and evaluate a set of feature vector representations of crystal structures for machine learning (ML) models of formation energies of solids. ML models of atomization energies of organic molecules have been successful using a Coulomb matrix representation of the molecule. We consider three ways to generalize such representations to periodic systems: (i) a matrix where each element is related to the Ewald sum of the electrostatic interaction between two different atoms in the unit cell repeated over the lattice; (ii) an extended Coulomb-like matrix that takes into account a number of neighboring unit cells; and (iii) an ansatz that mimics the periodicity and the basic features of the elements in the Ewald sum matrix using a sine function of the crystal coordinates of the atoms. The representations are compared for a Laplacian kernel with Manhattan norm, trained to reproduce formation energies using a dataset of 3938 crystal structures obtained from the Materials Project. For training sets consisting of 3000 crystals, the generalization error in predicting formation energies of new structures corresponds to (i) 0.49, (ii) 0.64, and (iii) 0.37eV/atom for the respective representations.

  5. Free radical mediated formation of 3-monochloropropanediol (3-MCPD) fatty acid diesters.

    Science.gov (United States)

    Zhang, Xiaowei; Gao, Boyan; Qin, Fang; Shi, Haiming; Jiang, Yuangrong; Xu, Xuebing; Yu, Liangli Lucy

    2013-03-13

    The present study was conducted to test the hypothesis that a free radical was formed and mediated the formation of 3-monochloropropanediol (3-MCPD) fatty acid diesters, a group of food contaminants, from diacylglycerols at high temperature under a low-moisture condition for the first time. The presence of free radicals in a vegetable oil kept at 120 °C for 20 min was demonstrated using an electron spin resonance (ESR) spectroscopy examination with 5,5-dimethylpyrroline-N-oxide (DMPO) as the spin trap agent. ESR investigation also showed an association between thermal treatment degree and the concentration of free radicals. A Fourier transform infrared spectroscopy (FT-IR) analysis of sn-1,2-stearoylglycerol (DSG) at 25 and 120 °C suggested the possible involvement of an ester carbonyl group in forming 3-MCPD diesters. On the basis of these results, a novel free radical mediated chemical mechanism was proposed for 3-MCPD diester formation. Furthermore, a quadrupole-time of flight (Q-TOF) MS/MS investigation was performed and detected the DMPO adducts with the cyclic acyloxonium free radical (CAFR) and its product MS ions, proving the presence of CAFR. Furthermore, the free radical mechanism was validated by the formation of 3-MCPD diesters through reacting DSG with a number of organic and inorganic chlorine sources including chlorine gas at 120 and 240 °C. The findings of this study might lead to the improvement of oil and food processing conditions to reduce the level of 3-MCPD diesters in foods and enhance food safety.

  6. Ising model on tangled chain - 1: Free energy and entropy

    International Nuclear Information System (INIS)

    Mejdani, R.

    1993-04-01

    In this paper we have considered an Ising model defined on tangled chain, in which more bonds have been added to those of pure Ising chain. to understand their competition, particularly between ferromagnetic and antiferromagnetic bonds, we have studied, using the transfer matrix method, some simple analytical calculations and an iterative algorithm, the behaviour of the free energy and entropy, particularly in the zero-field and zero temperature limit, for different configurations of the ferromagnetic tangled chain and different types of addition interaction (ferromagnetic or antiferromagnetic). We found that the condition J=J' between the ferromagnetic interaction J along the chain and the antiferromagnetic interaction J' across the chain is somewhat as a ''transition-region'' condition for this behaviour. Our results indicate also the existence of non-zero entropy at zero temperature. (author). 17 refs, 8 figs

  7. The puckering free-energy surface of proline

    Directory of Open Access Journals (Sweden)

    Di Wu

    2013-03-01

    Full Text Available Proline has two preferred puckering states, which are often characterized by the pseudorotation phase angle and amplitude. Although proline's five endocyclic torsion angles can be utilized to calculate the phase angle and amplitude, it is not clear if there is any direct correlation between each torsion angle and the proline-puckering pathway. Here we have designed five proline puckering pathways utilizing each torsion angle χj (j = 1∼5 as the reaction coordinate. By examining the free-energy surfaces of the five puckering pathways, we find they can be categorized into two groups. The χ2 pathway (χ2 is about the Cβ—Cγ bond is especially meaningful in describing proline puckering: it changes linearly with the puckering amplitude and symmetrically with the phase angle. Our results show that this conclusion applies to both trans and cis proline conformations. We have also analyzed the correlations of proline puckering and its backbone torsion angles ϕ and ψ. We show proline has preferred puckering states at the specific regions of ϕ, ψ angles. Interestingly, the shapes of ψ-χ2 free-energy surfaces are similar among the trans proline in water, cis proline in water and cis proline in the gas phase, but they differ substantially from that of the trans proline in the gas phase. Our calculations are conducted using molecular simulations; we also verify our results using the proline conformations selected from the Protein Data Bank. In addition, we have compared our results with those calculated by the quantum mechanical methods.

  8. The Emissions-Free Energy (EFE) Working Group

    Energy Technology Data Exchange (ETDEWEB)

    Humphries, R., E-mail: Roger.Humphries@amec.com [AMEC NSS, Toronto, Ontario (Canada)

    2014-07-01

    There has been a growing international interest in smaller, simpler reactors for generating electricity and process heat. They incorporate modern technological advances in reactor design, reactor safety, modular construction, proliferation resistance, and risk reduction. The interest in these reactors has been driven by many factors, including the need to reduce greenhouse gas emissions and provide reliable power in 'off-grid' or 'edge-of-grid' locations. Licensing these new small reactors, particularly in Canada's resource rich remote northern regions, will raises issues in a wide variety of technical, institutional, socio-economic and regulatory policy areas. The first small reactor vendor to file a license application or to engage the CNSC in its pre-licensing vendor design review process is going to have to deal with these issues. However these issues affect the entire small reactor industry and it is essential that the industry as a whole address them. Accordingly, a small reactor industry-wide Working Group has been established to identify and prioritize the issues that need to be addressed and work with the CNSC and other interested stakeholders to agree on a resolution acceptable to all parties. The objective of the small reactor industry is to introduce an economical, emissions-free source of electrical and thermal energy. It is the opinion of the WG that our emphasis ought to be on the product rather than the technology, hence the name Emissions-Free Energy Working Group. The EFE WG has initiated contact with the CNSC and has started its review of CNSC draft regulatory and guidance documents. (author)

  9. Primary Formation Path of Formaldehyde in Hydrothermal Vents

    Science.gov (United States)

    Inaba, Satoshi

    2018-03-01

    Formaldehyde is abundant in the universe and one of the fundamental molecules for life. Hydrothermal vents produce a substantial amount of hydrogen molecules by serpentinization and promote reductive reactions of single carbon compounds. The abundance of formaldehyde is expected to be low due to the high Gibbs free energy in hydrothermal vents. We consider two competing formation pathways of formaldehyde: (1) the reduction of CO by H2 and (2) the reduction of HCOOH by H2 to form a methanediol, followed by the dehydration of the methanediol. We performed a number of quantum chemical simulations to examine the formation of formaldehyde in the gas phase as well as in aqueous solution. The energy barrier is significantly reduced by the catalytic effect of water molecules in aqueous solution and becomes lowest when a water cluster consisted of 5 water molecules catalyzes the reduction. The energy barrier to form a methanediol by the reduction of HCOOH is lower by 17.5 kcal/mol than that to form a formaldehyde by the reduction of CO. Considering the low energy barrier to dehydrate methanediol, the primary pathway to form formaldehyde in hydrothermal vents is concluded to be the reduction of HCOOH by H2, followed by the dehydration of methanediol.

  10. Exploration, Sampling, And Reconstruction of Free Energy Surfaces with Gaussian Process Regression.

    Science.gov (United States)

    Mones, Letif; Bernstein, Noam; Csányi, Gábor

    2016-10-11

    Practical free energy reconstruction algorithms involve three separate tasks: biasing, measuring some observable, and finally reconstructing the free energy surface from those measurements. In more than one dimension, adaptive schemes make it possible to explore only relatively low lying regions of the landscape by progressively building up the bias toward the negative of the free energy surface so that free energy barriers are eliminated. Most schemes use the final bias as their best estimate of the free energy surface. We show that large gains in computational efficiency, as measured by the reduction of time to solution, can be obtained by separating the bias used for dynamics from the final free energy reconstruction itself. We find that biasing with metadynamics, measuring a free energy gradient estimator, and reconstructing using Gaussian process regression can give an order of magnitude reduction in computational cost.

  11. Free Energy Landscape of the Dissolution of Gibbsite at High pH

    Energy Technology Data Exchange (ETDEWEB)

    Shen, Zhizhang; Kerisit, Sebastien N.; Stack, Andrew G.; Rosso, Kevin M.

    2018-03-26

    The individual elementary reactions involved in the dissolution of a solid into solution remain mostly speculative due to a lack of suitable, direct experimental probes. In this regard, we have applied atomistic simulations to map the free energy landscape of the dissolution of gibbsite from a step edge, as a model of metal hydroxide dissolution. The overall reaction combines kink site formation and kink site propagation. Two individual reactions were found to be rate-limiting for kink site formation, that is, the displacement of Al from a step site to a ledge adatom site and its detachment from ledge/terrace adatom sites into the solution. As a result, a pool of mobile and labile Al adsorbed species, or adatoms, exists before the release of Al into solution. Because of the quasi-hexagonal symmetry of gibbsite, kink site propagation can occur in multiple directions. Overall, the simulation results will enable the development of microscopic mechanistic models of metal oxide dissolution.

  12. Living systems do not minimize free energy. Comment on "Answering Schrödinger's question: A free-energy formulation" by Maxwell James Dèsormeau Ramstead et al.

    Science.gov (United States)

    Martyushev, Leonid M.

    2018-03-01

    processes occurring at constant temperatures and volumes. In physics, the minimum free energy corresponds to an equilibrium state to which an isochoric-isothermal system relaxes [4,5]. It is obvious that the biological systems considered by the authors are fundamentally non-equilibrium, do not seek equilibrium, and, in most cases, do not retain their volumes as they develop. For a biological system, the equilibrium means death, decay. Therefore, to base the idea of life on FEP is the same as to state that the pursuit of death is the purpose and meaning of life. In order to consider processes addressed by the authors, one needs functionals employed in non-equilibrium rather than equilibrium thermodynamics [6-8]. Specifically, I would like to draw their attention to the rate of change of the Gibbs energy with time, or entropy production (the maximum entropy production principle can be useful here [7,9-12]).

  13. Formation of the priority directions of innovative strategic energy management

    Science.gov (United States)

    Mottaeva, Asiiat; Minnullina, Anna

    2017-10-01

    Article is devoted to the matter of the ensuring long-term potential of dynamic growth of the Russian economy, its sustainable development in which the special role is assigned to the energy industry. Inclusion of the stage of management of the human capital, which becomes one of priority levers in the field of management of the industrial enterprises, into the in structure of strategy of planning subsequently represents one of innovative steps at the heart of power management. In work the algorithm of the development of the key performance indicators of the human capital on the basis of stage-by-stage problem definition of energy saving, search of the centers of responsibility in energy consumption and quality control of the involved productions is offered in the article. The application of the offered innovative algorithm might promote the formation of high culture of energy saving and the decrease in the level of resistance to organizational changes.

  14. Investigations on Cs-free alternative materials for negative hydrogen ion formation

    Energy Technology Data Exchange (ETDEWEB)

    Kurutz, Uwe

    2017-01-19

    Neutral beam injection (NBI) represents a main auxiliary heating and current drive system for thermonuclear fusion devices. For ITER, a total heating power of up to 33 MW will be delivered for up to one hour pulses at particle energies of up to 1 MeV by two NBI systems. The respective ion sources will therefore have to allow for the extraction and acceleration of negative hydrogen ions at a current density of 200 A/m{sup 2} from a low pressure low temperature hydrogen plasma. Also for the succeeding demonstration reactor DEMO the application of NBI is currently discussed. Respective systems will, however, have to fulfil even higher demands, like higher powers (up to 135 MW), longer pulse lengths (2 h or even cw operation), and more restrictive constrains regarding the reliability and stability. Today efficient NBI negative hydrogen ion sources are based mainly on the conversion of positive hydrogen ions and/or hydrogen atoms at a grid surface coated with caesium. Cs is used for reducing the grid's work function which significantly enhances the particle conversion probability. However, the alkali metal is chemically very reactive and easily forms compounds with residual gas impurities. Furthermore, complex redistribution dynamics of the deposited Cs layer is given. This inherently links the application of Cs with a temporal and spatial non-stability of the negative ion yield, which contradicts the required reliability of a DEMO NBI system. Thus, for DEMO, Cs-free alternative materials for negative ion formation are investigated within this work at a flexible laboratory experiment. An ECR discharge is used which provides comparable parameters (pressure, densities, particle fluxes and -energies) to the NBI ion sources. Negative ion formation is measured above different material samples via laser photodetachment together with global plasma parameters using a Langmuir probe and optical emission spectroscopy. The plasma parameters are used for modelling the

  15. Investigations on Cs-free alternative materials for negative hydrogen ion formation

    International Nuclear Information System (INIS)

    Kurutz, Uwe

    2017-01-01

    Neutral beam injection (NBI) represents a main auxiliary heating and current drive system for thermonuclear fusion devices. For ITER, a total heating power of up to 33 MW will be delivered for up to one hour pulses at particle energies of up to 1 MeV by two NBI systems. The respective ion sources will therefore have to allow for the extraction and acceleration of negative hydrogen ions at a current density of 200 A/m 2 from a low pressure low temperature hydrogen plasma. Also for the succeeding demonstration reactor DEMO the application of NBI is currently discussed. Respective systems will, however, have to fulfil even higher demands, like higher powers (up to 135 MW), longer pulse lengths (2 h or even cw operation), and more restrictive constrains regarding the reliability and stability. Today efficient NBI negative hydrogen ion sources are based mainly on the conversion of positive hydrogen ions and/or hydrogen atoms at a grid surface coated with caesium. Cs is used for reducing the grid's work function which significantly enhances the particle conversion probability. However, the alkali metal is chemically very reactive and easily forms compounds with residual gas impurities. Furthermore, complex redistribution dynamics of the deposited Cs layer is given. This inherently links the application of Cs with a temporal and spatial non-stability of the negative ion yield, which contradicts the required reliability of a DEMO NBI system. Thus, for DEMO, Cs-free alternative materials for negative ion formation are investigated within this work at a flexible laboratory experiment. An ECR discharge is used which provides comparable parameters (pressure, densities, particle fluxes and -energies) to the NBI ion sources. Negative ion formation is measured above different material samples via laser photodetachment together with global plasma parameters using a Langmuir probe and optical emission spectroscopy. The plasma parameters are used for modelling the inherently

  16. Pattern formation on Ge by low energy ion beam erosion

    International Nuclear Information System (INIS)

    Teichmann, Marc; Lorbeer, Jan; Frost, Frank; Rauschenbach, Bernd; Ziberi, Bashkim

    2013-01-01

    Modification of nanoscale surface topography is inherent to low-energy ion beam erosion processes and is one of the most important fields of nanotechnology. In this report a comprehensive study of surface smoothing and self-organized pattern formation on Ge(100) by using different noble gases ion beam erosion is presented. The investigations focus on low ion energies (⩽ 2000 eV) and include the entire range of ion incidence angles. It is found that for ions (Ne, Ar) with masses lower than the mass of the Ge target atoms, no pattern formation occurs and surface smoothing is observed for all angles of ion incidence. In contrast, for erosion with higher mass ions (Kr, Xe), ripple formation starts at incidence angles of about 65° depending on ion energy. At smaller incident angles surface smoothing occurs again. Investigations of the surface dynamics for specific ion incidence angles by changing the ion fluence over two orders of magnitude gives a clear evidence for coarsening and faceting of the surface pattern. Both observations indicate that gradient-dependent sputtering and reflection of primary ions play crucial role in the pattern evolution, just at the lowest accessible fluences. The results are discussed in relation to recently proposed redistributive or stress-induced models for pattern formation. In addition, it is argued that a large angular variation of the sputter yield and reflected primary ions can significantly contribute to pattern formation and evolution as nonlinear and non-local processes as supported by simulation of sputtering and ion reflection. (paper)

  17. Generalized trends in the formation energies of perovskite oxides

    DEFF Research Database (Denmark)

    Zeng, Zhenhua; Calle-Vallejo, Federico; Mogensen, Mogens Bjerg

    2013-01-01

    Generalized trends in the formation energies of several families of perovskite oxides (ABO3) and plausible explanations to their existence are provided in this study through a combination of DFT calculations, solid-state physics analyses and simple physical/chemical descriptors. The studied...... elements at the A site of perovskites comprise rare-earth, alkaline-earth and alkaline metals, whereas 3d and 5d metals were studied at the B site. We also include ReO3-type compounds, which have the same crystal structure of cubic ABO3 perovskites except without A-site elements. From the observations we...... extract the following four conclusions for the perovskites studied in the present paper: for a given cation at the B site, (I) perovskites with cations of identical oxidation state at the A site possess close formation energies; and (II) perovskites with cations of different oxidation states at the A site...

  18. Time-dependent generalized Gibbs ensembles in open quantum systems

    Science.gov (United States)

    Lange, Florian; Lenarčič, Zala; Rosch, Achim

    2018-04-01

    Generalized Gibbs ensembles have been used as powerful tools to describe the steady state of integrable many-particle quantum systems after a sudden change of the Hamiltonian. Here, we demonstrate numerically that they can be used for a much broader class of problems. We consider integrable systems in the presence of weak perturbations which break both integrability and drive the system to a state far from equilibrium. Under these conditions, we show that the steady state and the time evolution on long timescales can be accurately described by a (truncated) generalized Gibbs ensemble with time-dependent Lagrange parameters, determined from simple rate equations. We compare the numerically exact time evolutions of density matrices for small systems with a theory based on block-diagonal density matrices (diagonal ensemble) and a time-dependent generalized Gibbs ensemble containing only a small number of approximately conserved quantities, using the one-dimensional Heisenberg model with perturbations described by Lindblad operators as an example.

  19. Development of linear free energy relationships for aqueous phase radical-involved chemical reactions.

    Science.gov (United States)

    Minakata, Daisuke; Mezyk, Stephen P; Jones, Jace W; Daws, Brittany R; Crittenden, John C

    2014-12-02

    Aqueous phase advanced oxidation processes (AOPs) produce hydroxyl radicals (HO•) which can completely oxidize electron rich organic compounds. The proper design and operation of AOPs require that we predict the formation and fate of the byproducts and their associated toxicity. Accordingly, there is a need to develop a first-principles kinetic model that can predict the dominant reaction pathways that potentially produce toxic byproducts. We have published some of our efforts on predicting the elementary reaction pathways and the HO• rate constants. Here we develop linear free energy relationships (LFERs) that predict the rate constants for aqueous phase radical reactions. The LFERs relate experimentally obtained kinetic rate constants to quantum mechanically calculated aqueous phase free energies of activation. The LFERs have been applied to 101 reactions, including (1) HO• addition to 15 aromatic compounds; (2) addition of molecular oxygen to 65 carbon-centered aliphatic and cyclohexadienyl radicals; (3) disproportionation of 10 peroxyl radicals, and (4) unimolecular decay of nine peroxyl radicals. The LFERs correlations predict the rate constants within a factor of 2 from the experimental values for HO• reactions and molecular oxygen addition, and a factor of 5 for peroxyl radical reactions. The LFERs and the elementary reaction pathways will enable us to predict the formation and initial fate of the byproducts in AOPs. Furthermore, our methodology can be applied to other environmental processes in which aqueous phase radical-involved reactions occur.

  20. A Localization-Free Interference and Energy Holes Minimization Routing for Underwater Wireless Sensor Networks.

    Science.gov (United States)

    Khan, Anwar; Ahmedy, Ismail; Anisi, Mohammad Hossein; Javaid, Nadeem; Ali, Ihsan; Khan, Nawsher; Alsaqer, Mohammed; Mahmood, Hasan

    2018-01-09

    Interference and energy holes formation in underwater wireless sensor networks (UWSNs) threaten the reliable delivery of data packets from a source to a destination. Interference also causes inefficient utilization of the limited battery power of the sensor nodes in that more power is consumed in the retransmission of the lost packets. Energy holes are dead nodes close to the surface of water, and their early death interrupts data delivery even when the network has live nodes. This paper proposes a localization-free interference and energy holes minimization (LF-IEHM) routing protocol for UWSNs. The proposed algorithm overcomes interference during data packet forwarding by defining a unique packet holding time for every sensor node. The energy holes formation is mitigated by a variable transmission range of the sensor nodes. As compared to the conventional routing protocols, the proposed protocol does not require the localization information of the sensor nodes, which is cumbersome and difficult to obtain, as nodes change their positions with water currents. Simulation results show superior performance of the proposed scheme in terms of packets received at the final destination and end-to-end delay.

  1. A Localization-Free Interference and Energy Holes Minimization Routing for Underwater Wireless Sensor Networks

    Directory of Open Access Journals (Sweden)

    Anwar Khan

    2018-01-01

    Full Text Available Interference and energy holes formation in underwater wireless sensor networks (UWSNs threaten the reliable delivery of data packets from a source to a destination. Interference also causes inefficient utilization of the limited battery power of the sensor nodes in that more power is consumed in the retransmission of the lost packets. Energy holes are dead nodes close to the surface of water, and their early death interrupts data delivery even when the network has live nodes. This paper proposes a localization-free interference and energy holes minimization (LF-IEHM routing protocol for UWSNs. The proposed algorithm overcomes interference during data packet forwarding by defining a unique packet holding time for every sensor node. The energy holes formation is mitigated by a variable transmission range of the sensor nodes. As compared to the conventional routing protocols, the proposed protocol does not require the localization information of the sensor nodes, which is cumbersome and difficult to obtain, as nodes change their positions with water currents. Simulation results show superior performance of the proposed scheme in terms of packets received at the final destination and end-to-end delay.

  2. The regulated energy economy versus the free energy market - The West German experience

    International Nuclear Information System (INIS)

    Liesen, K.; Schwarz, H.O.

    1989-09-01

    The overall good performance of the West German energy industry in terms of energy policy objectives such as security of supplies, competitiveness, efficient use of energy and environmental protection, is attributable to an energy policy based on the principles of the market economy and steady application of these same principles. Today, though, a debate, at times controversial, on whether more market influence or more government intervention is required is underway in West Germany; in view of the successes of energy policy and the balance struck between free enterprise and the government in the past, this debate has met with little understanding in some quarters. It is generally agreed, though, that the quality of the challenges energy policy and the energy industry in West Germany will confront in the future will remain essentially unchanged. West German energy policy will have to deal with: reestablishing a consensus on coal and nuclear power policy; achieving a high standard of environmental protection in the European Communities, and strengthening the position of the energy industry as efforts are made to get moves underway to create a single European market for energy underway. No fundamental change in the course of energy policy in the Federal Republic of Germany is needed to solve current energy policy issues or to preserve the underlying goals of this policy. An energy policy which continues to give priority where possible to market mechanisms as a means of adjustment and provides energy suppliers and users with a stable and reliable framework in which to operate, offers the best promise for meeting the challenges of the future. (author). 2 figs

  3. A logistic regression estimating function for spatial Gibbs point processes

    DEFF Research Database (Denmark)

    Baddeley, Adrian; Coeurjolly, Jean-François; Rubak, Ege

    We propose a computationally efficient logistic regression estimating function for spatial Gibbs point processes. The sample points for the logistic regression consist of the observed point pattern together with a random pattern of dummy points. The estimating function is closely related to the p......We propose a computationally efficient logistic regression estimating function for spatial Gibbs point processes. The sample points for the logistic regression consist of the observed point pattern together with a random pattern of dummy points. The estimating function is closely related...

  4. Finite-size corrections to the free energies of crystalline solids

    NARCIS (Netherlands)

    Polson, J.M.; Trizac, E.; Pronk, S.; Frenkel, D.

    2000-01-01

    We analyze the finite-size corrections to the free energy of crystals with a fixed center of mass. When we explicitly correct for the leading (ln N/N) corrections, the remaining free energy is found to depend linearly on 1/N. Extrapolating to the thermodynamic limit (N → ∞), we estimate the free

  5. Wireless network interface energy consumption implications of popular streaming formats

    Science.gov (United States)

    Chandra, Surendar

    2001-12-01

    With the proliferation of mobile streaming multimedia, available battery capacity constrains the end-user experience. Since streaming applications tend to be long running, wireless network interface card's (WNIC) energy consumption is particularly an acute problem. In this work, we explore the WNIC energy consumption implications of popular multimedia streaming formats from Microsoft (Windows media), Real (Real media) and Apple (Quick Time). We investigate the energy consumption under varying stream bandwidth and network loss rates. We also explore history-based client-side strategies to reduce the energy consumed by transitioning the WNICs to a lower power consuming sleep state. We show that Microsoft media tends to transmit packets at regular intervals; streams optimized for 28.8 Kbps can save over 80% in energy consumption with 2% data loss. A high bandwidth stream (768 Kbps) can still save 57% in energy consumption with less than 0.3% data loss. For high bandwidth streams, Microsoft media exploits network-level packet fragmentation, which can lead to excessive packet loss (and wasted energy) in a lossy network. Real stream packets tend to be sent closer to each other, especially at higher bandwidths. Quicktime packets sometimes arrive in quick succession; most likely an application level fragmentation mechanism. Such packets are harder to predict at the network level without understanding the packet semantics.

  6. Evaluating conformational free energies: the colony energy and its application to the problem of loop prediction.

    Science.gov (United States)

    Xiang, Zhexin; Soto, Cinque S; Honig, Barry

    2002-05-28

    In this paper, we introduce a method to account for the shape of the potential energy curve in the evaluation of conformational free energies. The method is based on a procedure that generates a set of conformations, each with its own force-field energy, but adds a term to this energy that favors conformations that are close in structure (have a low rmsd) to other conformations. The sum of the force-field energy and rmsd-dependent term is defined here as the "colony energy" of a given conformation, because each conformation that is generated is viewed as representing a colony of points. The use of the colony energy tends to select conformations that are located in broad energy basins. The approach is applied to the ab initio prediction of the conformations of all of the loops in a dataset of 135 nonredundant proteins. By using an rmsd from a native criterion based on the superposition of loop stems, the average rmsd of 5-, 6-, 7-, and 8-residue long loops is 0.85, 0.92, 1.23, and 1.45 A, respectively. For 8-residue loops, 60 of 61 predictions have an rmsd of less than 3.0 A. The use of the colony energy is found to improve significantly the results obtained from the potential function alone. (The loop prediction program, "Loopy," can be downloaded at http://trantor.bioc.columbia.edu.)

  7. Formation of model-free motor memories during motor adaptation depends on perturbation schedule.

    Science.gov (United States)

    Orban de Xivry, Jean-Jacques; Lefèvre, Philippe

    2015-04-01

    Motor adaptation to an external perturbation relies on several mechanisms such as model-based, model-free, strategic, or repetition-dependent learning. Depending on the experimental conditions, each of these mechanisms has more or less weight in the final adaptation state. Here we focused on the conditions that lead to the formation of a model-free motor memory (Huang VS, Haith AM, Mazzoni P, Krakauer JW. Neuron 70: 787-801, 2011), i.e., a memory that does not depend on an internal model or on the size or direction of the errors experienced during the learning. The formation of such model-free motor memory was hypothesized to depend on the schedule of the perturbation (Orban de Xivry JJ, Ahmadi-Pajouh MA, Harran MD, Salimpour Y, Shadmehr R. J Neurophysiol 109: 124-136, 2013). Here we built on this observation by directly testing the nature of the motor memory after abrupt or gradual introduction of a visuomotor rotation, in an experimental paradigm where the presence of model-free motor memory can be identified (Huang VS, Haith AM, Mazzoni P, Krakauer JW. Neuron 70: 787-801, 2011). We found that relearning was faster after abrupt than gradual perturbation, which suggests that model-free learning is reduced during gradual adaptation to a visuomotor rotation. In addition, the presence of savings after abrupt introduction of the perturbation but gradual extinction of the motor memory suggests that unexpected errors are necessary to induce a model-free motor memory. Overall, these data support the hypothesis that different perturbation schedules do not lead to a more or less stabilized motor memory but to distinct motor memories with different attributes and neural representations. Copyright © 2015 the American Physiological Society.

  8. Free Radicals Formation of Irradiated Lyophilized Can-Cellous Human and Bovine Bone

    International Nuclear Information System (INIS)

    Abbas, Basril; Sudiro, Sutjipto; Hilmy, Nazly

    2000-01-01

    Radiation sterilization of lyophilized human and bovine bone as allograft and xenograft have been produced and used in orthopaedic practice in Indonesia routinely. It is well known from radio biologic studies that one of the most pronounce effects of ionizing radiation on biologic species produced the free radicals that influence the physico-chemical as well as the mechanical properties of irradiated bone. The aim of our study is to investigate the free radicals formation of irradiated lyophilized cancellous triple A bone (Autolyzed Antigen-Extracted Allograft) produced by Batan Research Tissue Bank in Jakarta. The cancellous triple A were prepared according to AATB (American Association of Tissue Bank) method. Gamma Irradiations was done at doses of 10, 20 and 30 kGy with a dose rate of 7,5 kGy/h at room temperature (30 o C± 2 o C). Measurements of free radicals was done at 24 o C ±1 o C within 30 minutes after irradiational and measurement were continued up to 9 months of storage using a JES-REIX ESR Spectrophotometer (JEOL) with Mn exp. ++ standard. Parameters measured, were the effects of mechanical grinding, water immersion and irradiation dose on free radicals formation in the bone. Results show that the signal area of ESR spectra from irradiated bovine bone of 30 kGy was higher than those of human bone I.e. 1,4 x 10 exp. 7 dan 6,4 x 10 exp. 6 Au (arbitrary unit)/g samples respectively. The signal of ESR spectra increased linearly with increasing dose in the range of 10-30 kGy and it will reduce about 30% caused by water immersion. The ESR signal reduced sharply after 2 days and gradually decreased up to 14 days and then became constant up to 9 months of storage at room temperature. A certain method of crushing can produce free radicals. Key Words: free radical, irradiation, allograft, xenograft, mechanical-grinding

  9. On the TAP Free Energy in the Mixed p-Spin Models

    Science.gov (United States)

    Chen, Wei-Kuo; Panchenko, Dmitry

    2018-05-01

    Thouless et al. (Phys Mag 35(3):593-601, 1977), derived a representation for the free energy of the Sherrington-Kirkpatrick model, called the TAP free energy, written as the difference of the energy and entropy on the extended configuration space of local magnetizations with an Onsager correction term. In the setting of mixed p-spin models with Ising spins, we prove that the free energy can indeed be written as the supremum of the TAP free energy over the space of local magnetizations whose Edwards-Anderson order parameter (self-overlap) is to the right of the support of the Parisi measure. Furthermore, for generic mixed p-spin models, we prove that the free energy is equal to the TAP free energy evaluated on the local magnetization of any pure state.

  10. Optimization of sources for focusing wave energy in targeted formations

    KAUST Repository

    Jeong, C

    2010-06-08

    We discuss a numerical approach for identifying the surface excitation that is necessary to maximize the response of a targeted subsurface formation. The motivation stems from observations in the aftermath of earthquakes, and from limited field experiments, whereby increased oil production rates were recorded and were solely attributable to the induced reservoir shaking. The observations suggest that focusing wave energy to the reservoir could serve as an effective low-cost enhanced oil recovery method. In this paper, we report on a general method that allows the determination of the source excitation, when provided with a desired maximization outcome at the targeted formation. We discuss, for example, how to construct the excitation that will maximize the kinetic energy in the target zone, while keeping silent the neighbouring zones. To this end, we cast the problem as an inverse-source problem, and use a partial-differential- equation-constrained optimization approach to arrive at an optimized source signal. We seek to satisfy stationarity of an augmented functional, which formally leads to a triplet of state, adjoint and control problems. We use finite elements to resolve the state and adjoint problems, and an iterative scheme to satisfy the control problem to converge to the sought source signal. We report on one-dimensional numerical experiments in the time domain involving a layered medium of semi-infinite extent. The numerical results show that the targeted formation\\'s kinetic energy resulting from an optimized wave source could be several times greater than the one resulting from a blind source choice, and could overcome the mobility threshold of entrapped reservoir oil. © 2010 Nanjing Geophysical Research Institute.

  11. Interfacial wave theory of pattern formation in solidification dendrites, fingers, cells and free boundaries

    CERN Document Server

    Xu, Jian-Jun

    2017-01-01

    This comprehensive work explores interfacial instability and pattern formation in dynamic systems away from the equilibrium state in solidification and crystal growth. Further, this significantly expanded 2nd edition introduces and reviews the progress made during the last two decades. In particular, it describes the most prominent pattern formation phenomena commonly observed in material processing and crystal growth in the framework of the previously established interfacial wave theory, including free dendritic growth from undercooled melt, cellular growth and eutectic growth in directional solidification, as well as viscous fingering in Hele-Shaw flow. It elucidates the key problems, systematically derives their mathematical solutions by pursuing a unified, asymptotic approach, and finally carefully examines these results by comparing them with the available experimental results. The asymptotic approach described here will be useful for the investigation of pattern formation phenomena occurring in a much b...

  12. Contributions of stress and oxidation on the formation of whiskers in Pb-free solders

    Energy Technology Data Exchange (ETDEWEB)

    Duncan, A. J. [Savannah River Site (SRS), Aiken, SC (United States). Savannah River National Lab. (SRNL); Hoffman, E. N. [Savannah River Site (SRS), Aiken, SC (United States). Savannah River National Lab. (SRNL)

    2016-01-01

    Understanding the environmental factors influencing formation of tin whiskers on electrodeposited lead free, tin coatings over copper (or copper containing) substrates is the topic of this study . An interim report* summarized initial observations as to the role of stress and oxide formation on whisker growth. From the initial results, two main areas were chosen to be the focus of additional research: the demonstration of effects of elastic stress state in the nucleation of whiskers and the confirmation of the effect of oxygen content in the formation of whiskers. Different levels of elastic stress were induced with the incorporation of a custom designed fixture that loaded the sample in a four-point bending configuration and were maintained in an environmental chamber under conditions deemed favorable for whisker growth. The effects of oxygen content were studied by aging substrates in gas vials of varying absolute pressure and different oxygen partial pressure.

  13. Characteristics of Methane Hydrate Formation in Artificial and Natural Media

    Directory of Open Access Journals (Sweden)

    Qingbai Wu

    2013-03-01

    Full Text Available The formation of methane hydrate in two significantly different media was investigated, using silica gel as an artificial medium and loess as a natural medium. The methane hydrate formation was observed through the depletion of water in the matrix, measured via the matrix potential and the relationship between the matrix potential and the water content was determined using established equations. The velocity of methane hydrate nucleation slowed over the course of the reaction, as it relied on water transfer to the hydrate surfaces with lower Gibbs free energy after nucleation. Significant differences in the reactions in the two types of media arose from differences in the water retention capacity and lithology of media due to the internal surface area and pore size distributions. Compared with methane hydrate formation in silica gel, the reaction in loess was much slower and formed far less methane hydrate. The results of this study will advance the understanding of how the properties of the environment affect the formation of gas hydrates in nature.

  14. Heavy-quark free energies, internal-energy and entropy contributions

    International Nuclear Information System (INIS)

    Kaczmarek, O.

    2009-01-01

    We present lattice QCD results on heavy-quark free energies, extract from its temperature dependence the entropy and internal-energy contributions, and discuss the onset of medium effects that lead to screening of static quark-antiquark sources in a thermal medium. The detailed analysis of the temperature and distance dependence of the different contributions indicate the complex non-perturbative nature of strongly interacting matter. We shall discuss the necessity to include those effects in studies on the behavior of heavy quarks, heavy-quark bound states and their dissociation in the quark-gluon plasma phase. (orig.)

  15. Impact of domain knowledge on blinded predictions of binding energies by alchemical free energy calculations

    Science.gov (United States)

    Mey, Antonia S. J. S.; Jiménez, Jordi Juárez; Michel, Julien

    2018-01-01

    The Drug Design Data Resource (D3R) consortium organises blinded challenges to address the latest advances in computational methods for ligand pose prediction, affinity ranking, and free energy calculations. Within the context of the second D3R Grand Challenge several blinded binding free energies predictions were made for two congeneric series of Farsenoid X Receptor (FXR) inhibitors with a semi-automated alchemical free energy calculation workflow featuring FESetup and SOMD software tools. Reasonable performance was observed in retrospective analyses of literature datasets. Nevertheless, blinded predictions on the full D3R datasets were poor due to difficulties encountered with the ranking of compounds that vary in their net-charge. Performance increased for predictions that were restricted to subsets of compounds carrying the same net-charge. Disclosure of X-ray crystallography derived binding modes maintained or improved the correlation with experiment in a subsequent rounds of predictions. The best performing protocols on D3R set1 and set2 were comparable or superior to predictions made on the basis of analysis of literature structure activity relationships (SAR)s only, and comparable or slightly inferior, to the best submissions from other groups.

  16. The global mean energy balance under cloud-free conditions

    Science.gov (United States)

    Wild, Martin; Hakuba, Maria; Folini, Dois; Ott, Patricia; Long, Charles

    2017-04-01

    A long standing problem of climate models is their overestimation of surface solar radiation not only under all-sky, but also under clear-sky conditions (Wild et al. 1995, Wild et al. 2006). This overestimation reduced over time in consecutive model generations due to the simulation of stronger atmospheric absorption. Here we analyze the clear sky fluxes of the latest climate model generation from the Coupled Model Intercomparison Project Phase 5 (CMIP5) against an expanded and updated set of direct observations from the Baseline Surface Radiation Network (BSRN). Clear sky climatologies from these sites have been composed based on the Long and Ackermann (2000) clear sky detection algorithm (Hakuba et al. 2017), and sampling issues when comparing with model simulated clear sky fluxes have been analyzed in Ott (2017). Overall, the overestimation of clear sky insolation in the CMIP5 models is now merely 1-2 Wm-2 in the multimodel mean, compared to 4 Wm-2 in CMIP3 and 6 Wm-2 in AMIPII (Wild et al. 2006). Still a considerable spread in the individual model biases is apparent, ranging from -2 Wm-2 to 10 Wm-2 when averaged over 53 globally distributed BSRN sites. This bias structure is used to infer best estimates for present day global mean clear sky insolation, following an approach developped in Wild et al. (2013, 2015, Clim. Dyn.) for all sky fluxes. Thereby the flux biases in the various models are linearly related to their respective global means. A best estimate can then be inferred from the linear regression at the intersect where the bias against the surface observations becomes zero. This way we obtain a best estimate of 247 Wm-2 for the global mean insolation at the Earth surface under cloud free conditions, and a global mean absorbed solar radiation of 214 Wm-2 in the cloud-free atmosphere, assuming a global mean surface albedo of 13.5%. Combined with a best estimate for the net influx of solar radiation at the Top of Atmosphere under cloud free conditions

  17. Virial theorem and Gibbs thermodynamic potential for Coulomb systems

    International Nuclear Information System (INIS)

    Bobrov, V. B.; Trigger, S. A.

    2014-01-01

    Using the grand canonical ensemble and the virial theorem, we show that the Gibbs thermodynamic potential of the non-relativistic system of charged particles is uniquely defined by single-particle Green functions of electrons and nuclei. This result is valid beyond the perturbation theory with respect to the interparticle interaction

  18. Virial theorem and Gibbs thermodynamic potential for Coulomb systems

    OpenAIRE

    Bobrov, V. B.; Trigger, S. A.

    2013-01-01

    Using the grand canonical ensemble and the virial theorem, we show that the Gibbs thermodynamic potential of the non-relativistic system of charged particles is uniquely defined by single-particle Green functions of electrons and nuclei. This result is valid beyond the perturbation theory with respect to the interparticle interaction.

  19. Inverse Gaussian model for small area estimation via Gibbs sampling

    African Journals Online (AJOL)

    We present a Bayesian method for estimating small area parameters under an inverse Gaussian model. The method is extended to estimate small area parameters for finite populations. The Gibbs sampler is proposed as a mechanism for implementing the Bayesian paradigm. We illustrate the method by application to ...

  20. Exploring Fourier Series and Gibbs Phenomenon Using Mathematica

    Science.gov (United States)

    Ghosh, Jonaki B.

    2011-01-01

    This article describes a laboratory module on Fourier series and Gibbs phenomenon which was undertaken by 32 Year 12 students. It shows how the use of CAS played the role of an "amplifier" by making higher level mathematical concepts accessible to students of year 12. Using Mathematica students were able to visualise Fourier series of…

  1. Thermodynamic fluctuations within the Gibbs and Einstein approaches

    International Nuclear Information System (INIS)

    Rudoi, Yurii G; Sukhanov, Alexander D

    2000-01-01

    A comparative analysis of the descriptions of fluctuations in statistical mechanics (the Gibbs approach) and in statistical thermodynamics (the Einstein approach) is given. On this basis solutions are obtained for the Gibbs and Einstein problems that arise in pressure fluctuation calculations for a spatially limited equilibrium (or slightly nonequilibrium) macroscopic system. A modern formulation of the Gibbs approach which allows one to calculate equilibrium pressure fluctuations without making any additional assumptions is presented; to this end the generalized Bogolyubov - Zubarev and Hellmann - Feynman theorems are proved for the classical and quantum descriptions of a macrosystem. A statistical version of the Einstein approach is developed which shows a fundamental difference in pressure fluctuation results obtained within the context of two approaches. Both the 'genetic' relation between the Gibbs and Einstein approaches and the conceptual distinction between their physical grounds are demonstrated. To illustrate the results, which are valid for any thermodynamic system, an ideal nondegenerate gas of microparticles is considered, both classically and quantum mechanically. Based on the results obtained, the correspondence between the micro- and macroscopic descriptions is considered and the prospects of statistical thermodynamics are discussed. (reviews of topical problems)

  2. Quantitative Experimental Determination of Primer-Dimer Formation Risk by Free-Solution Conjugate Electrophoresis

    Science.gov (United States)

    Desmarais, Samantha M.; Leitner, Thomas; Barron, Annelise E.

    2012-01-01

    DNA barcodes are short, unique ssDNA primers that “mark” individual biomolecules. To gain better understanding of biophysical parameters constraining primer-dimer formation between primers that incorporate barcode sequences, we have developed a capillary electrophoresis method that utilizes drag-tag-DNA conjugates to quantify dimerization risk between primer-barcode pairs. Results obtained with this unique free-solution conjugate electrophoresis (FSCE) approach are useful as quantitatively precise input data to parameterize computation models of dimerization risk. A set of fluorescently labeled, model primer-barcode conjugates were designed with complementary regions of differing lengths to quantify heterodimerization as a function of temperature. Primer-dimer cases comprised two 30-mer primers, one of which was covalently conjugated to a lab-made, chemically synthesized poly-N-methoxyethylglycine drag-tag, which reduced electrophoretic mobility of ssDNA to distinguish it from ds primer-dimers. The drag-tags also provided a shift in mobility for the dsDNA species, which allowed us to quantitate primer-dimer formation. In the experimental studies, pairs of oligonucleotide primer-barcodes with fully or partially complementary sequences were annealed, and then separated by free-solution conjugate CE at different temperatures, to assess effects on primer-dimer formation. When less than 30 out of 30 basepairs were bonded, dimerization was inversely correlated to temperature. Dimerization occurred when more than 15 consecutive basepairs formed, yet non-consecutive basepairs did not create stable dimers even when 20 out of 30 possible basepairs bonded. The use of free-solution electrophoresis in combination with a peptoid drag-tag and different fluorophores enabled precise separation of short DNA fragments to establish a new mobility shift assay for detection of primer-dimer formation. PMID:22331820

  3. Multivariable extrapolation of grand canonical free energy landscapes

    Science.gov (United States)

    Mahynski, Nathan A.; Errington, Jeffrey R.; Shen, Vincent K.

    2017-12-01

    We derive an approach for extrapolating the free energy landscape of multicomponent systems in the grand canonical ensemble, obtained from flat-histogram Monte Carlo simulations, from one set of temperature and chemical potentials to another. This is accomplished by expanding the landscape in a Taylor series at each value of the order parameter which defines its macrostate phase space. The coefficients in each Taylor polynomial are known exactly from fluctuation formulas, which may be computed by measuring the appropriate moments of extensive variables that fluctuate in this ensemble. Here we derive the expressions necessary to define these coefficients up to arbitrary order. In principle, this enables a single flat-histogram simulation to provide complete thermodynamic information over a broad range of temperatures and chemical potentials. Using this, we also show how to combine a small number of simulations, each performed at different conditions, in a thermodynamically consistent fashion to accurately compute properties at arbitrary temperatures and chemical potentials. This method may significantly increase the computational efficiency of biased grand canonical Monte Carlo simulations, especially for multicomponent mixtures. Although approximate, this approach is amenable to high-throughput and data-intensive investigations where it is preferable to have a large quantity of reasonably accurate simulation data, rather than a smaller amount with a higher accuracy.

  4. Estimating Atomic Contributions to Hydration and Binding Using Free Energy Perturbation.

    Science.gov (United States)

    Irwin, Benedict W J; Huggins, David J

    2018-05-08

    We present a general method called atom-wise free energy perturbation (AFEP), which extends a conventional molecular dynamics free energy perturbation (FEP) simulation to give the contribution to a free energy change from each atom. AFEP is derived from an expansion of the Zwanzig equation used in the exponential averaging method by defining that the system total energy can be partitioned into contributions from each atom. A partitioning method is assumed and used to group terms in the expansion to correspond to individual atoms. AFEP is applied to six example free energy changes to demonstrate the method. Firstly, the hydration free energies of methane, methanol, methylamine, methanethiol, and caffeine in water. AFEP highlights the atoms in the molecules that interact favorably or unfavorably with water. Finally AFEP is applied to the binding free energy of human immunodeficiency virus type 1 protease to lopinavir, and AFEP reveals the contribution of each atom to the binding free energy, indicating candidate areas of the molecule to improve to produce a more strongly binding inhibitor. FEP gives a single value for the free energy change and is already a very useful method. AFEP gives a free energy change for each "part" of the system being simulated, where part can mean individual atoms, chemical groups, amino acids, or larger partitions depending on what the user is trying to measure. This method should have various applications in molecular dynamics studies of physical, chemical, or biochemical phenomena, specifically in the field of computational drug discovery.

  5. Direct measurement of the free energy of aging hard sphere colloidal glasses.

    Science.gov (United States)

    Zargar, Rojman; Nienhuis, Bernard; Schall, Peter; Bonn, Daniel

    2013-06-21

    The nature of the glass transition is one of the most important unsolved problems in condensed matter physics. The difference between glasses and liquids is believed to be caused by very large free energy barriers for particle rearrangements; however, so far it has not been possible to confirm this experimentally. We provide the first quantitative determination of the free energy for an aging hard sphere colloidal glass. The determination of the free energy allows for a number of new insights in the glass transition, notably the quantification of the strong spatial and temporal heterogeneity in the free energy. A study of the local minima of the free energy reveals that the observed variations are directly related to the rearrangements of the particles. Our main finding is that the probability of particle rearrangements shows a power law dependence on the free energy changes associated with the rearrangements similar to the Gutenberg-Richter law in seismology.

  6. An ab initio approach to free-energy reconstruction using logarithmic mean force dynamics

    International Nuclear Information System (INIS)

    Nakamura, Makoto; Obata, Masao; Morishita, Tetsuya; Oda, Tatsuki

    2014-01-01

    We present an ab initio approach for evaluating a free energy profile along a reaction coordinate by combining logarithmic mean force dynamics (LogMFD) and first-principles molecular dynamics. The mean force, which is the derivative of the free energy with respect to the reaction coordinate, is estimated using density functional theory (DFT) in the present approach, which is expected to provide an accurate free energy profile along the reaction coordinate. We apply this new method, first-principles LogMFD (FP-LogMFD), to a glycine dipeptide molecule and reconstruct one- and two-dimensional free energy profiles in the framework of DFT. The resultant free energy profile is compared with that obtained by the thermodynamic integration method and by the previous LogMFD calculation using an empirical force-field, showing that FP-LogMFD is a promising method to calculate free energy without empirical force-fields

  7. Ion-specific weak adsorption of salts and water/octanol transfer free energy of a model amphiphilic hexapeptide.

    Science.gov (United States)

    Déjugnat, Christophe; Dufrêche, Jean-François; Zemb, Thomas

    2011-04-21

    An amphiphilic hexapeptide has been used as a model to quantify how specific ion effects induced by addition of four salts tune the hydrophilic/hydrophobic balance and induce temperature-dependant coacervate formation from aqueous solution. The hexapeptide chosen is present as a dimer with low transfer energy from water to octanol. Taking sodium chloride as the reference state in the Hofmeister scale, we identify water activity effects and therefore measure the free energy of transfer from water to octanol and separately the free energy associated to the adsorption of chaotropic ions or the desorption of kosmotropic ions for the same amphiphilic peptide. These effects have the same order of magnitude: therefore, both energies of solvation as well as transfer into octanol strongly depend on the nature of the electrolytes used to formulate any buffer. Model peptides could be used on separation processes based on criteria linked to "Hofmeister" but different from volume and valency.

  8. Variational energy principle for compressible, baroclinic flow. 2: Free-energy form of Hamilton's principle

    Science.gov (United States)

    Schmid, L. A.

    1977-01-01

    The first and second variations are calculated for the irreducible form of Hamilton's Principle that involves the minimum number of dependent variables necessary to describe the kinetmatics and thermodynamics of inviscid, compressible, baroclinic flow in a specified gravitational field. The form of the second variation shows that, in the neighborhood of a stationary point that corresponds to physically stable flow, the action integral is a complex saddle surface in parameter space. There exists a form of Hamilton's Principle for which a direct solution of a flow problem is possible. This second form is related to the first by a Friedrichs transformation of the thermodynamic variables. This introduces an extra dependent variable, but the first and second variations are shown to have direct physical significance, namely they are equal to the free energy of fluctuations about the equilibrium flow that satisfies the equations of motion. If this equilibrium flow is physically stable, and if a very weak second order integral constraint on the correlation between the fluctuations of otherwise independent variables is satisfied, then the second variation of the action integral for this free energy form of Hamilton's Principle is positive-definite, so the action integral is a minimum, and can serve as the basis for a direct trail and error solution. The second order integral constraint states that the unavailable energy must be maximum at equilibrium, i.e. the fluctuations must be so correlated as to produce a second order decrease in the total unavailable energy.

  9. Optimization of sources for focusing wave energy in targeted formations

    International Nuclear Information System (INIS)

    Jeong, C; Kallivokas, L F; Huh, C; Lake, L W

    2010-01-01

    We discuss a numerical approach for identifying the surface excitation that is necessary to maximize the response of a targeted subsurface formation. The motivation stems from observations in the aftermath of earthquakes, and from limited field experiments, whereby increased oil production rates were recorded and were solely attributable to the induced reservoir shaking. The observations suggest that focusing wave energy to the reservoir could serve as an effective low-cost enhanced oil recovery method. In this paper, we report on a general method that allows the determination of the source excitation, when provided with a desired maximization outcome at the targeted formation. We discuss, for example, how to construct the excitation that will maximize the kinetic energy in the target zone, while keeping silent the neighbouring zones. To this end, we cast the problem as an inverse-source problem, and use a partial-differential-equation-constrained optimization approach to arrive at an optimized source signal. We seek to satisfy stationarity of an augmented functional, which formally leads to a triplet of state, adjoint and control problems. We use finite elements to resolve the state and adjoint problems, and an iterative scheme to satisfy the control problem to converge to the sought source signal. We report on one-dimensional numerical experiments in the time domain involving a layered medium of semi-infinite extent. The numerical results show that the targeted formation's kinetic energy resulting from an optimized wave source could be several times greater than the one resulting from a blind source choice, and could overcome the mobility threshold of entrapped reservoir oil

  10. Formation of free round jets with long laminar regions at large Reynolds numbers

    Science.gov (United States)

    Zayko, Julia; Teplovodskii, Sergey; Chicherina, Anastasia; Vedeneev, Vasily; Reshmin, Alexander

    2018-04-01

    The paper describes a new, simple method for the formation of free round jets with long laminar regions by a jet-forming device of ˜1.5 jet diameters in size. Submerged jets of 0.12 m diameter at Reynolds numbers of 2000-12 560 are experimentally studied. It is shown that for the optimal regime, the laminar region length reaches 5.5 diameters for Reynolds number ˜10 000 which is not achievable for other methods of laminar jet formation. To explain the existence of the optimal regime, a steady flow calculation in the forming unit and a stability analysis of outcoming jet velocity profiles are conducted. The shortening of the laminar regions, compared with the optimal regime, is explained by the higher incoming turbulence level for lower velocities and by the increase of perturbation growth rates for larger velocities. The initial laminar regions of free jets can be used for organising air curtains for the protection of objects in medicine and technologies by creating the air field with desired properties not mixed with ambient air. Free jets with long laminar regions can also be used for detailed studies of perturbation growth and transition to turbulence in round jets.

  11. Catalase expression is modulated by vancomycin and ciprofloxacin and influences the formation of free radicals in Staphylococcus aureus cultures

    DEFF Research Database (Denmark)

    Wang, Ying; Hougaard, Anni Bygvrå; Paulander, Wilhelm Erik Axel

    2015-01-01

    Detection of free radicals in biological systems is challenging due to their short half-lives. We have applied electron spin resonance (ESR) spectroscopy combined with spin traps using the probes PBN (N-tert-butyl-α-phenylnitrone) and DMPO (5,5-dimethyl-1-pyrroline N-oxide) to assess free radical...... that in S. aureus, bactericidal antibiotics modulate catalase expression, which in turn influences the formation of free radicals in the surrounding broth medium. If similar regulation is found in other bacterial species, it might explain why bactericidal antibiotics are perceived as inducing formation...... of free radicals....

  12. Formation of Defect-Free Latex Films on Porous Fiber Supports

    KAUST Repository

    Lively, Ryan P.

    2011-09-28

    We present here the creation of a defect-free polyvinylidene chloride barrier layer on the lumen-side of a hollow fiber sorbent. Hollow fiber sorbents have previously been shown to be promising materials for enabling low-cost CO 2 capture, provided a defect-free lumen-side barrier layer can be created. Film experiments examined the effect of drying rate, latex age, substrate porosity (porous vs nonporous), and substrate hydrophobicity/ hydrophilicity. Film studies show that in ideal conditions (i.e., slow drying, fresh latex, and smooth nonporous substrate), a defect-free film can be formed, whereas the other permutations of the variables investigated led to defective films. These results were extended to hollow fiber sorbents, and despite using fresh latex and relatively slow drying conditions, a defective lumen-side layer resulted. XRD and DSC indicate that polyvinylidene chloride latex develops crystallinity over time, thereby inhibiting proper film formation as confirmed by SEM and gas permeation. This and other key additional challenges associated with the porous hollow fiber substrate vs the nonporous flat substrate were overcome. By employing a toluene-vapor saturated drying gas (a swelling solvent for polyvinylidene chloride) a defect-free lumen-side barrier layer was created, as investigated by gas and water vapor permeation. © 2011 American Chemical Society.

  13. Correcting for the free energy costs of bond or angle constraints in molecular dynamics simulations.

    Science.gov (United States)

    König, Gerhard; Brooks, Bernard R

    2015-05-01

    Free energy simulations are an important tool in the arsenal of computational biophysics, allowing the calculation of thermodynamic properties of binding or enzymatic reactions. This paper introduces methods to increase the accuracy and precision of free energy calculations by calculating the free energy costs of constraints during post-processing. The primary purpose of employing constraints for these free energy methods is to increase the phase space overlap between ensembles, which is required for accuracy and convergence. The free energy costs of applying or removing constraints are calculated as additional explicit steps in the free energy cycle. The new techniques focus on hard degrees of freedom and use both gradients and Hessian estimation. Enthalpy, vibrational entropy, and Jacobian free energy terms are considered. We demonstrate the utility of this method with simple classical systems involving harmonic and anharmonic oscillators, four-atomic benchmark systems, an alchemical mutation of ethane to methanol, and free energy simulations between alanine and serine. The errors for the analytical test cases are all below 0.0007kcal/mol, and the accuracy of the free energy results of ethane to methanol is improved from 0.15 to 0.04kcal/mol. For the alanine to serine case, the phase space overlaps of the unconstrained simulations range between 0.15 and 0.9%. The introduction of constraints increases the overlap up to 2.05%. On average, the overlap increases by 94% relative to the unconstrained value and precision is doubled. The approach reduces errors arising from constraints by about an order of magnitude. Free energy simulations benefit from the use of constraints through enhanced convergence and higher precision. The primary utility of this approach is to calculate free energies for systems with disparate energy surfaces and bonded terms, especially in multi-scale molecular mechanics/quantum mechanics simulations. This article is part of a Special Issue

  14. The free energy landscape of small molecule unbinding.

    Directory of Open Access Journals (Sweden)

    Danzhi Huang

    2011-02-01

    Full Text Available The spontaneous dissociation of six small ligands from the active site of FKBP (the FK506 binding protein is investigated by explicit water molecular dynamics simulations and network analysis. The ligands have between four (dimethylsulphoxide and eleven (5-diethylamino-2-pentanone non-hydrogen atoms, and an affinity for FKBP ranging from 20 to 0.2 mM. The conformations of the FKBP/ligand complex saved along multiple trajectories (50 runs at 310 K for each ligand are grouped according to a set of intermolecular distances into nodes of a network, and the direct transitions between them are the links. The network analysis reveals that the bound state consists of several subbasins, i.e., binding modes characterized by distinct intermolecular hydrogen bonds and hydrophobic contacts. The dissociation kinetics show a simple (i.e., single-exponential time dependence because the unbinding barrier is much higher than the barriers between subbasins in the bound state. The unbinding transition state is made up of heterogeneous positions and orientations of the ligand in the FKBP active site, which correspond to multiple pathways of dissociation. For the six small ligands of FKBP, the weaker the binding affinity the closer to the bound state (along the intermolecular distance are the transition state structures, which is a new manifestation of Hammond behavior. Experimental approaches to the study of fragment binding to proteins have limitations in temporal and spatial resolution. Our network analysis of the unbinding simulations of small inhibitors from an enzyme paints a clear picture of the free energy landscape (both thermodynamics and kinetics of ligand unbinding.

  15. The use of computational thermodynamics for the determination of surface tension and Gibbs-Thomson coefficient of multicomponent alloys

    Science.gov (United States)

    Ferreira, D. J. S.; Bezerra, B. N.; Collyer, M. N.; Garcia, A.; Ferreira, I. L.

    2018-04-01

    The simulation of casting processes demands accurate information on the thermophysical properties of the alloy; however, such information is scarce in the literature for multicomponent alloys. Generally, metallic alloys applied in industry have more than three solute components. In the present study, a general solution of Butler's formulation for surface tension is presented for multicomponent alloys and is applied in quaternary Al-Cu-Si-Fe alloys, thus permitting the Gibbs-Thomson coefficient to be determined. Such coefficient is a determining factor to the reliability of predictions furnished by microstructure growth models and by numerical computations of solidification thermal parameters, which will depend on the thermophysical properties assumed in the calculations. The Gibbs-Thomson coefficient for ternary and quaternary alloys is seldom reported in the literature. A numerical model based on Powell's hybrid algorithm and a finite difference Jacobian approximation has been coupled to a Thermo-Calc TCAPI interface to assess the excess Gibbs energy of the liquid phase, permitting liquidus temperature, latent heat, alloy density, surface tension and Gibbs-Thomson coefficient for Al-Cu-Si-Fe hypoeutectic alloys to be calculated, as an example of calculation capabilities for multicomponent alloys of the proposed method. The computed results are compared with thermophysical properties of binary Al-Cu and ternary Al-Cu-Si alloys found in the literature and presented as a function of the Cu solute composition.

  16. CaFE: a tool for binding affinity prediction using end-point free energy methods.

    Science.gov (United States)

    Liu, Hui; Hou, Tingjun

    2016-07-15

    Accurate prediction of binding free energy is of particular importance to computational biology and structure-based drug design. Among those methods for binding affinity predictions, the end-point approaches, such as MM/PBSA and LIE, have been widely used because they can achieve a good balance between prediction accuracy and computational cost. Here we present an easy-to-use pipeline tool named Calculation of Free Energy (CaFE) to conduct MM/PBSA and LIE calculations. Powered by the VMD and NAMD programs, CaFE is able to handle numerous static coordinate and molecular dynamics trajectory file formats generated by different molecular simulation packages and supports various force field parameters. CaFE source code and documentation are freely available under the GNU General Public License via GitHub at https://github.com/huiliucode/cafe_plugin It is a VMD plugin written in Tcl and the usage is platform-independent. tingjunhou@zju.edu.cn. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  17. The calculation of surface free energy based on embedded atom method for solid nickel

    International Nuclear Information System (INIS)

    Luo Wenhua; Hu Wangyu; Su Kalin; Liu Fusheng

    2013-01-01

    Highlights: ► A new solution for accurate prediction of surface free energy based on embedded atom method was proposed. ► The temperature dependent anisotropic surface energy of solid nickel was obtained. ► In isotropic environment, the approach does not change most predictions of bulk material properties. - Abstract: Accurate prediction of surface free energy of crystalline metals is a challenging task. The theory calculations based on embedded atom method potentials often underestimate surface free energy of metals. With an analytical charge density correction to the argument of the embedding energy of embedded atom method, an approach to improve the prediction for surface free energy is presented. This approach is applied to calculate the temperature dependent anisotropic surface energy of bulk nickel and surface energies of nickel nanoparticles, and the obtained results are in good agreement with available experimental data.

  18. Heavy quark free energies for three quark systems at finite temperature

    International Nuclear Information System (INIS)

    Huebner, Kay; Karsch, Frithjof; Kaczmarek, Olaf; Vogt, Oliver

    2008-01-01

    We study the free energy of static three quark systems in singlet, octet, decuplet, and average color channels in the quenched approximation and in 2-flavor QCD at finite temperature. We show that in the high temperature phase singlet and decuplet free energies of three quark systems are well described by the sum of the free energies of three diquark systems plus self-energy contributions of the three quarks. In the confining low temperature phase we find evidence for a Y-shaped flux tube in SU(3) pure gauge theory, which is less evident in 2-flavor QCD due to the onset of string breaking. We also compare the short distance behavior of octet and decuplet free energies to the free energies of single static quarks in the corresponding color representations.

  19. Cumulative approaches to track formation under swift heavy ion (SHI) irradiation: Phenomenological correlation with formation energies of Frenkel pairs

    Energy Technology Data Exchange (ETDEWEB)

    Crespillo, M.L., E-mail: mcrespil@utk.edu [Centro de Microanálisis de Materiales, CMAM-UAM, Cantoblanco, Madrid 28049 (Spain); Department of Materials Science & Engineering, University of Tennessee, Knoxville, TN 37996 (United States); Agulló-López, F., E-mail: fal@uam.es [Centro de Microanálisis de Materiales, CMAM-UAM, Cantoblanco, Madrid 28049 (Spain); Zucchiatti, A. [Centro de Microanálisis de Materiales, CMAM-UAM, Cantoblanco, Madrid 28049 (Spain)

    2017-03-01

    Highlights: • Extensive survey formation energies Frenkel pairs and electronic stopping thresholds. • Correlation: track formation thresholds and the energies for Frenkel pair formation. • Formation energies Frenkel pairs discussed in relation to the cumulative mechanisms. • Amorphous track formation mechanisms: defect accumulation models versus melting. • Advantages cumulative models to deal with new hot topics: nuclear-electronic synergy. - Abstract: An extensive survey for the formation energies of Frenkel pairs, as representative candidates for radiation-induced point defects, is presented and discussed in relation to the cumulative mechanisms (CM) of track formation in dielectric materials under swift heavy ion (SHI) irradiation. These mechanisms rely on the generation and accumulation of point defects during irradiation followed by collapse of the lattice once a threshold defect concentration is reached. The physical basis of those approaches has been discussed by Fecht as a defect-assisted transition to an amorphous phase. Although a first quantitative analysis of the CM model was previously performed for LiNbO{sub 3} crystals, we have, here, adopted a broader phenomenological approach. It explores the correlation between track formation thresholds and the energies for Frenkel pair formation for a broad range of materials. It is concluded that the threshold stopping powers can be roughly scaled with the energies required to generate a critical Frenkel pair concentration in the order of a few percent of the total atomic content. Finally, a comparison with the predictions of the thermal spike model is discussed within the analytical Szenes approximation.

  20. Formation and reactions of free radicals in the radiolysis of organic materials by ion beams

    International Nuclear Information System (INIS)

    Koizumi, H.

    2000-01-01

    High-energy heavy ions deposit energy along ion tracks with high density. Chemical effects of the heavy ions may hence differ from that of γ-rays and fast electrons. We can utilize these effects for material modification and fabrication of microstructure. It is necessary to know the dependence of the effects on ion beams and the variation of the effects on materials for developing new application of ion beams. We then studied radical formation in organic solids of alanine and of adipic acid by ion beams irradiation. (author)

  1. Renewable energy made easy free energy from solar, wind, hydropower, and other alternative energy sources

    CERN Document Server

    Craddock, David

    2008-01-01

    Studies have shown that the average North American family will spend more than a quarter of a million dollars on energy in a lifetime. What many other countries, including Germany, Spain, France, Denmark, China, Brazil, and even Iceland, have realized is that there is a better way to power our homes, businesses, and cars by using renewable energy sources. Recently, the United States has begun to understand the importance of reducing its reliance on coal, natural gas, nuclear power, and hydropower plants, which comprise the majority of the nation's electricity, due to increasing oil prices.

  2. The importance of dissolved free oxygen during formation of sandstone-type uranium deposits

    Science.gov (United States)

    Granger, Harry Clifford; Warren, C.G.

    1979-01-01

    One factor which distinguishes t, he genesis of roll-type uranium deposits from the Uravan Mineral Belt and other sandstone-type uranium deposits may be the presence and concentration of dissolved free oxygen in the ore-forming. solutions. Although dissolved oxygen is a necessary prerequisite for the formation of roll-type deposits, it is proposed that a lack of dissolved oxygen is a prerequisite for the Uravan deposits. Solutions that formed both types of deposits probably had a supergene origin and originated as meteoric water in approximate equilibrium with atmospheric oxygen. Roll-type deposits were formed where the Eh dropped abruptly following consumption of the oxygen by iron sulfide minerals and creation of kinetically active sulfur species that could reduce uranium. The solutions that formed the Uravan deposits, on the other hand, probably first equilibrated with sulfide-free ferrous-ferric detrital minerals and fossil organic matter in the host rock. That is, the uraniferous solutions lost their oxygen without lowering their Eh enough to precipitate uranium. Without oxygen, they then. became incapable of oxidizing iron sulfide minerals. Subsequent localization and formation of ore bodies from these oxygen-depleted solutions, therefore, was not necessarily dependent on large reducing capacities.

  3. Formation of Negative Metal Ions in a Field-Free Plasma

    Energy Technology Data Exchange (ETDEWEB)

    Larsson, E

    1969-02-15

    A field-free and homogeneous plasma of a large volume is formed by neutron irradiation of {sup 3}He at a density corresponding to NTP and at gas temperatures in the range 300-1600 deg K. The accuracy and ease by which the source density of free electrons can be varied and controlled offers special possibilities to study recombination and attachment phenomena in the absence of diffusion. These possibilities are described and utilized for the study of the effects of mixing the helium gas with metal vapours. Attachment of electrons to neutral metal atoms is found to be the dominant cause of electron removal for metal concentrations above certain limits. Negative metal ions are formed and the rate of their formation was determined to be about 10{sup -13} cm{sup 3}/s. Evidence is also presented, that for such conditions where formation of negative metal ions does not occur, the electrons are lost in electron-ion recombinations, in which the third body is not an electron. No molecular helium spectrum is observed from the plasma when it is very close to spectroscopic purity. Instead, between 3,000-7,000 A only one atomic helium line at 5875 A is observed. The recombination of He{sup +}{sub 2} may therefore be dissociative. A difference in recombination behaviour between {sup 3}He and {sup 4}He at high pressures may therefore exist considering results from previous work on {sup 4}He.

  4. Assessment of the full content of physique stereotypes with a free-response format.

    Science.gov (United States)

    Butler, J C; Ryckman, R M; Thornton, B; Bouchard, R L

    1993-04-01

    A major limitation of physique stereotyping research is that American subjects have used a restricted set of traits provided by the experimenter to evaluate endomorphs, mesomorphs, and ectomorphs. A free-response procedure was used in Study 1 to identify the full domain of traits associated with each physique. Although many of the traits identified were similar to those used in previous research, a number of new trait dimensions were uncovered. In Study 2, the large number of traits generated with the free-response format was reduced by combining synonyms. This new set of traits was placed in semantic differential format and given to a new sample of subjects to evaluate. The results paralleled those of the first study with the exception that ectomorphs were seen more favorably. This discrepancy, as well as the fact that raters listed trait antonyms within each of the three major physiques in Study 1, suggests the possibility of unique subtypes within the global stereotypes. Examples of these subtypes are proposed.

  5. Hierarchical formation of dark matter halos and the free streaming scale

    International Nuclear Information System (INIS)

    Ishiyama, Tomoaki

    2014-01-01

    The smallest dark matter halos are formed first in the early universe. According to recent studies, the central density cusp is much steeper in these halos than in larger halos and scales as ρ∝r –(1.5-1.3) . We present the results of very large cosmological N-body simulations of the hierarchical formation and evolution of halos over a wide mass range, beginning from the formation of the smallest halos. We confirmed early studies that the inner density cusps are steeper in halos at the free streaming scale. The cusp slope gradually becomes shallower as the halo mass increases. The slope of halos 50 times more massive than the smallest halo is approximately –1.3. No strong correlation exists between the inner slope and the collapse epoch. The cusp slope of halos above the free streaming scale seems to be reduced primarily due to major merger processes. The concentration, estimated at the present universe, is predicted to be 60-70, consistent with theoretical models and earlier simulations, and ruling out simple power law mass-concentration relations. Microhalos could still exist in the present universe with the same steep density profiles.

  6. Formation of Negative Metal Ions in a Field-Free Plasma

    International Nuclear Information System (INIS)

    Larsson, E.

    1969-02-01

    A field-free and homogeneous plasma of a large volume is formed by neutron irradiation of 3 He at a density corresponding to NTP and at gas temperatures in the range 300-1600 deg K. The accuracy and ease by which the source density of free electrons can be varied and controlled offers special possibilities to study recombination and attachment phenomena in the absence of diffusion. These possibilities are described and utilized for the study of the effects of mixing the helium gas with metal vapours. Attachment of electrons to neutral metal atoms is found to be the dominant cause of electron removal for metal concentrations above certain limits. Negative metal ions are formed and the rate of their formation was determined to be about 10 -13 cm 3 /s. Evidence is also presented, that for such conditions where formation of negative metal ions does not occur, the electrons are lost in electron-ion recombinations, in which the third body is not an electron. No molecular helium spectrum is observed from the plasma when it is very close to spectroscopic purity. Instead, between 3,000-7,000 A only one atomic helium line at 5875 A is observed. The recombination of He + 2 may therefore be dissociative. A difference in recombination behaviour between 3 He and 4 He at high pressures may therefore exist considering results from previous work on 4 He

  7. Free energy change of off-eutectic binary alloys on solidification

    Science.gov (United States)

    Ohsaka, K.; Trinh, E. H.; Lin, J.-C.; Perepezko, J. H.

    1991-01-01

    A formula for the free energy difference between the undercooled liquid phase and the stable solid phase is derived for off-eutectic binary alloys in which the equilibrium solid/liquid transition takes place over a certain temperature range. The free energy change is then evaluated numerically for a Bi-25 at. pct Cd alloy modeled as a sub-subregular solution.

  8. A simple free energy for the isotropic-nematic phase transition of rods

    NARCIS (Netherlands)

    Tuinier, R.

    2016-01-01

    A free energy expression is proposed that describes the isotropic-nematic binodal concentrations of hard rods. A simple analytical form for this free energy was yet only available using a Gaussian trial function for the orientation distribution function (ODF), leading, however, to a significant

  9. Constructing a multidimensional free energy surface like a spider weaving a web.

    Science.gov (United States)

    Chen, Changjun

    2017-10-15

    Complete free energy surface in the collective variable space provides important information of the reaction mechanisms of the molecules. But, sufficient sampling in the collective variable space is not easy. The space expands quickly with the number of the collective variables. To solve the problem, many methods utilize artificial biasing potentials to flatten out the original free energy surface of the molecule in the simulation. Their performances are sensitive to the definitions of the biasing potentials. Fast-growing biasing potential accelerates the sampling speed but decreases the accuracy of the free energy result. Slow-growing biasing potential gives an optimized result but needs more simulation time. In this article, we propose an alternative method. It adds the biasing potential to a representative point of the molecule in the collective variable space to improve the conformational sampling. And the free energy surface is calculated from the free energy gradient in the constrained simulation, not given by the negative of the biasing potential as previous methods. So the presented method does not require the biasing potential to remove all the barriers and basins on the free energy surface exactly. Practical applications show that the method in this work is able to produce the accurate free energy surfaces for different molecules in a short time period. The free energy errors are small in the cases of various biasing potentials. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

  10. Free energy on a cycle graph and trigonometric deformation of heat kernel traces on odd spheres

    Science.gov (United States)

    Kan, Nahomi; Shiraishi, Kiyoshi

    2018-01-01

    We consider a possible ‘deformation’ of the trace of the heat kernel on odd dimensional spheres, motivated by the calculation of the free energy of a scalar field on a discretized circle. By using an expansion in terms of the modified Bessel functions, we obtain the values of the free energies after a suitable regularization.

  11. Designed azurins show lower reorganization free energies for intraprotein electron transfer

    DEFF Research Database (Denmark)

    Farver, Ole; Marshall, Nicholas M; Wherland, Scot

    2013-01-01

    Low reorganization free energies are necessary for fast electron transfer (ET) reactions. Hence, rational design of redox proteins with lower reorganization free energies has been a long-standing challenge, promising to yield a deeper understanding of the underlying principles of ET reactivity...

  12. Incorporating the effect of ionic strength in free energy calculations using explicit ions

    NARCIS (Netherlands)

    Donnini, S; Mark, AE; Juffer, AH; Villa, Alessandra

    2005-01-01

    The incorporation of explicit ions to mimic the effect of ionic strength or to neutralize the overall charge on a system in free energy calculations using molecular dynamics simulations is investigated. The difference in the free energy of hydration between two triosephosphate isomerase inhibitors

  13. CAN THE STABILITY OF PROTEIN MUTANTS BE PREDICTED BY FREE-ENERGY CALCULATIONS

    NARCIS (Netherlands)

    YUNYU, S; MARK, AE; WANG, CX; HUANG, FH; BERENDSEN, HJC; VANGUNSTEREN, WF

    The use of free energy simulation techniques in the study of protein stability is critically evaluated. Results from two simulations of the thermostability mutation Asn218 to Ser218 in Subtilisin are presented. It is shown that components of the free energy change can be highly sensitive to the

  14. Direct evaluation of free energy for large system through structure integration approach.

    Science.gov (United States)

    Takeuchi, Kazuhito; Tanaka, Ryohei; Yuge, Koretaka

    2015-09-30

    We propose a new approach, 'structure integration', enabling direct evaluation of configurational free energy for large systems. The present approach is based on the statistical information of lattice. Through first-principles-based simulation, we find that the present method evaluates configurational free energy accurately in disorder states above critical temperature.

  15. Inferring the Gibbs state of a small quantum system

    International Nuclear Information System (INIS)

    Rau, Jochen

    2011-01-01

    Gibbs states are familiar from statistical mechanics, yet their use is not limited to that domain. For instance, they also feature in the maximum entropy reconstruction of quantum states from incomplete measurement data. Outside the macroscopic realm, however, estimating a Gibbs state is a nontrivial inference task, due to two complicating factors: the proper set of relevant observables might not be evident a priori; and whenever data are gathered from a small sample only, the best estimate for the Lagrange parameters is invariably affected by the experimenter's prior bias. I show how the two issues can be tackled with the help of Bayesian model selection and Bayesian interpolation, respectively, and illustrate the use of these Bayesian techniques with a number of simple examples.

  16. Computing the Free Energy along a Reaction Coordinate Using Rigid Body Dynamics.

    Science.gov (United States)

    Tao, Peng; Sodt, Alexander J; Shao, Yihan; König, Gerhard; Brooks, Bernard R

    2014-10-14

    The calculations of potential of mean force along complex chemical reactions or rare events pathways are of great interest because of their importance for many areas in chemistry, molecular biology, and material science. The major difficulty for free energy calculations comes from the great computational cost for adequate sampling of the system in high-energy regions, especially close to the reaction transition state. Here, we present a method, called FEG-RBD, in which the free energy gradients were obtained from rigid body dynamics simulations. Then the free energy gradients were integrated along a reference reaction pathway to calculate free energy profiles. In a given system, the reaction coordinates defining a subset of atoms (e.g., a solute, or the quantum mechanics (QM) region of a quantum mechanics/molecular mechanics simulation) are selected to form a rigid body during the simulation. The first-order derivatives (gradients) of the free energy with respect to the reaction coordinates are obtained through the integration of constraint forces within the rigid body. Each structure along the reference reaction path is separately subjected to such a rigid body simulation. The individual free energy gradients are integrated along the reference pathway to obtain the free energy profile. Test cases provided demonstrate both the strengths and weaknesses of the FEG-RBD method. The most significant benefit of this method comes from the fast convergence rate of the free energy gradient using rigid-body constraints instead of restraints. A correction to the free energy due to approximate relaxation of the rigid-body constraint is estimated and discussed. A comparison with umbrella sampling using a simple test case revealed the improved sampling efficiency of FEG-RBD by a factor of 4 on average. The enhanced efficiency makes this method effective for calculating the free energy of complex chemical reactions when the reaction coordinate can be unambiguously defined by a

  17. On the Tsallis Entropy for Gibbs Random Fields

    Czech Academy of Sciences Publication Activity Database

    Janžura, Martin

    2014-01-01

    Roč. 21, č. 33 (2014), s. 59-69 ISSN 1212-074X R&D Projects: GA ČR(CZ) GBP402/12/G097 Institutional research plan: CEZ:AV0Z1075907 Keywords : Tsallis entropy * Gibbs random fields * phase transitions * Tsallis entropy rate Subject RIV: BB - Applied Statistics, Operational Research http://library.utia.cas.cz/separaty/2014/SI/janzura-0441885.pdf

  18. Extensitivity of entropy and modern form of Gibbs paradox

    International Nuclear Information System (INIS)

    Home, D.; Sengupta, S.

    1981-01-01

    The extensivity property of entropy is clarified in the light of a critical examination of the entropy formula based on quantum statistics and the relevant thermodynamic requirement. The modern form of the Gibbs paradox, related to the discontinuous jump in entropy due to identity or non-identity of particles, is critically investigated. Qualitative framework of a new resolution of this paradox, which analyses the general effect of distinction mark on the Hamiltonian of a system of identical particles, is outlined. (author)

  19. GibbsCluster: unsupervised clustering and alignment of peptide sequences

    DEFF Research Database (Denmark)

    Andreatta, Massimo; Alvarez, Bruno; Nielsen, Morten

    2017-01-01

    motif characterizing each cluster. Several parameters are available to customize cluster analysis, including adjustable penalties for small clusters and overlapping groups and a trash cluster to remove outliers. As an example application, we used the server to deconvolute multiple specificities in large......-scale peptidome data generated by mass spectrometry. The server is available at http://www.cbs.dtu.dk/services/GibbsCluster-2.0....

  20. Free energy simulations with the AMOEBA polarizable force field and metadynamics on GPU platform.

    Science.gov (United States)

    Peng, Xiangda; Zhang, Yuebin; Chu, Huiying; Li, Guohui

    2016-03-05

    The free energy calculation library PLUMED has been incorporated into the OpenMM simulation toolkit, with the purpose to perform enhanced sampling MD simulations using the AMOEBA polarizable force field on GPU platform. Two examples, (I) the free energy profile of water pair separation (II) alanine dipeptide dihedral angle free energy surface in explicit solvent, are provided here to demonstrate the accuracy and efficiency of our implementation. The converged free energy profiles could be obtained within an affordable MD simulation time when the AMOEBA polarizable force field is employed. Moreover, the free energy surfaces estimated using the AMOEBA polarizable force field are in agreement with those calculated from experimental data and ab initio methods. Hence, the implementation in this work is reliable and would be utilized to study more complicated biological phenomena in both an accurate and efficient way. © 2015 Wiley Periodicals, Inc. © 2015 Wiley Periodicals, Inc.

  1. Free energies of binding from large-scale first-principles quantum mechanical calculations: application to ligand hydration energies.

    Science.gov (United States)

    Fox, Stephen J; Pittock, Chris; Tautermann, Christofer S; Fox, Thomas; Christ, Clara; Malcolm, N O J; Essex, Jonathan W; Skylaris, Chris-Kriton

    2013-08-15

    Schemes of increasing sophistication for obtaining free energies of binding have been developed over the years, where configurational sampling is used to include the all-important entropic contributions to the free energies. However, the quality of the results will also depend on the accuracy with which the intermolecular interactions are computed at each molecular configuration. In this context, the energy change associated with the rearrangement of electrons (electronic polarization and charge transfer) upon binding is a very important effect. Classical molecular mechanics force fields do not take this effect into account explicitly, and polarizable force fields and semiempirical quantum or hybrid quantum-classical (QM/MM) calculations are increasingly employed (at higher computational cost) to compute intermolecular interactions in free-energy schemes. In this work, we investigate the use of large-scale quantum mechanical calculations from first-principles as a way of fully taking into account electronic effects in free-energy calculations. We employ a one-step free-energy perturbation (FEP) scheme from a molecular mechanical (MM) potential to a quantum mechanical (QM) potential as a correction to thermodynamic integration calculations within the MM potential. We use this approach to calculate relative free energies of hydration of small aromatic molecules. Our quantum calculations are performed on multiple configurations from classical molecular dynamics simulations. The quantum energy of each configuration is obtained from density functional theory calculations with a near-complete psinc basis set on over 600 atoms using the ONETEP program.

  2. Smart Energy Choices Free Up Dollars for Capital Improvements.

    Science.gov (United States)

    Ritchey, David

    2003-01-01

    Describes several ways to design or renovate school building to save thousand of dollars of energy costs. Considers site design, energy-efficient building envelope, renewable energy systems, lighting and electrical systems, mechanical and ventilation systems, water conservation, and transportation. Describes how to obtain information about the…

  3. Effect of Particulate Matter Mineral Composition on Environmentally Persistent Free Radical (EPFR) Formation.

    Science.gov (United States)

    Feld-Cook, Elisabeth E; Bovenkamp-Langlois, Lisa; Lomnicki, Slawo M

    2017-09-19

    Environmentally Persistent Free Radicals (EPFRs) are newly discovered, long-lived surface bound radicals that form on particulate matter and combustion borne particulates, such as fly ash. Human exposure to such particulates lead to translocation into the lungs and heart resulting in cardio-vascular and respiratory disease through the production of reactive oxygen species. Analysis of some waste incinerator fly ashes revealed a significant difference between their EPFR contents. Although EPFR formation occurs on the metal domains, these differences were correlated with the altering concentration of calcium and sulfur. To analyze these phenomena, surrogate fly ashes were synthesized to mimic the presence of their major mineral components, including metal oxides, calcium, and sulfur. The results of this study led to the conclusion that the presence of sulfates limits formation of EPFRs due to inhibition or poisoning of the transition metal active sites necessary for their formation. These findings provide a pathway toward understanding differences in EPFR presence on particulate matter and uncover the possibility of remediating EPFRs from incineration and hazardous waste sites.

  4. Towards a Continental Energy Market: From the Energy Crisis to the Free Trade Agreement, 1970-88.

    Science.gov (United States)

    Bennett, Paul W.

    1989-01-01

    Discusses the impact the 1973 oil embargo and resulting energy crisis had on Canadian energy policies, which eventually led in 1987 to the enactment of the Free Trade Agreement between Canada and the United States. Includes excerpts of three documents which reveal much about the shift in Canadian policy toward a continental energy market. (LS)

  5. Free-Free Transitions in the Presence of Laser Fields and Debye Potential at Very Low Incident Electron Energies

    Science.gov (United States)

    Bhatia, Anand

    2012-01-01

    We study the free-free transition in electron-helium ion in the ground state and embedded in a Debye potential in the presence of an external laser field at very low incident electron energies. The laser field is treated classically while the collision dynamics is treated quantum mechanically. The laser field is chosen as monochromatic, linearly polarized and homogeneous. The incident electron is considered to be dressed by the laser field in a nonperturbative manner by choosing Volkov wave function for it. The scattering wave function for the incident electron on the target embedded in a Debye potential is solved numerically by taking into account the effect of electron exchange. We calculate the laser-assisted differential and total cross sections for free-free transition for absorption/emission of a single photon or no photon exchange. The results will be presented at the conference.

  6. Effect of inter-species selective interactions on the thermodynamics and nucleation free-energy barriers of a tessellating polyhedral compound

    International Nuclear Information System (INIS)

    Escobedo, Fernando A.

    2016-01-01

    The phase behavior and the homogeneous nucleation of an equimolar mixture of octahedra and cuboctahedra are studied using thermodynamic integration, Gibbs-Duhem integration, and umbrella sampling simulations. The components of this mixture are modeled as polybead objects of equal edge lengths so that they can assemble into a space-filling compound with the CsCl crystal structure. Taking as reference the hard-core system where the compound crystal does not spontaneously nucleate, we quantified the effect of inter-species selective interactions on facilitating the disorder-to-order transition. Facet selective and facet non-selective inter-species attractions were considered, and while the former was expectedly more favorable toward the target tessellating structure, the latter was found to be similarly effective in nucleating the crystal compound. Ranges for the strength of attractions and degree of supersaturation were identified where the nucleation free-energy barrier was small enough to foretell a fast process but large enough to prevent spinodal fluctuations that can trap the system in dense metastable states lacking long-range order. At those favorable conditions, the tendency toward the local orientational order favored by packing entropy is amplified and found to play a key role seeding nuclei with the CsCl structure.

  7. Low-energy positron-argon collisions by using parameter-free positron correlation polarization potentials

    International Nuclear Information System (INIS)

    Jain, A.

    1990-01-01

    We report differential, integral, and momentum-transfer cross sections and the scattering length (A 0 ) for positron (e + )-argon scattering at low energies below the positronium formation threshold. An optical-potential approach is employed in which the repulsive Coulombic interaction is calculated exactly at the Hartree-Fock level and the attractive polarization and correlation effects are included approximately via a parameter-free positron correlation polarization (PCP) potential recently proposed by us. The PCP model is based on the correlation energy var-epsilon corr of one positron in a homogeneous electron gas; in the outside region, the var-epsilon corr is joined smoothly with the correct asymptotic form of the polarization interaction (-α 0 /2r 4 , where α 0 is the target polarizability) where they cross each other for the first time. The total optical potential of the e + -argon system is treated exactly in a partial-wave analysis to extract the scattering parameters. It is found that the PCP potential gives much better qualitative results, particularly for the differential cross sections and the scattering length, than the corresponding results obtained from an electron polarization potential used as such for the positron case. We also discuss the ''critical'' points (representing the minima in the differential scattering) in the low-energy e + -Ar scattering. The present results involve no fitting procedure

  8. Energy Analysis in Combined Reforming of Propane

    Directory of Open Access Journals (Sweden)

    K. Moon

    2013-01-01

    Full Text Available Combined (steam and CO2 reforming is one of the methods to produce syngas for different applications. An energy requirement analysis of steam reforming to dry reforming with intermediate steps of steam reduction and equivalent CO2 addition to the feed fuel for syngas generation has been done to identify condition for optimum process operation. Thermodynamic equilibrium data for combined reforming was generated for temperature range of 400–1000°C at 1 bar pressure and combined oxidant (CO2 + H2O stream to propane (fuel ratio of 3, 6, and 9 by employing the Gibbs free energy minimization algorithm of HSC Chemistry software 5.1. Total energy requirement including preheating and reaction enthalpy calculations were done using the equilibrium product composition. Carbon and methane formation was significantly reduced in combined reforming than pure dry reforming, while the energy requirements were lower than pure steam reforming. Temperatures of minimum energy requirement were found in the data analysis of combined reforming which were optimum for the process.

  9. High Energy, Lead-Free Ignition Formulation for Thermate

    National Research Council Canada - National Science Library

    Tracy, Gene

    2002-01-01

    ... in the AN-Ml4 thermate grenade. This lead-free formulation has provided reliable ignition of the XM89 over a temperature range of -25 degrees F - 120 degrees F when using the M201 Al fuze as the initiator...

  10. Is free knowledge transfer history in the energy sector?

    International Nuclear Information System (INIS)

    Zewald, H.

    2000-01-01

    The European power industry is gradually changing from a government-controlled sector of monopolists to an internationally privatized free sector. Companies that used to cooperate are now competing with one another. The question is: can the international knowledge transfer institutes escape from this competitive climate or will they fall victim to it?

  11. Energy dissipation of free exciton polaritons in semiconducting films

    International Nuclear Information System (INIS)

    De Crescenzi, M.; Harbeke, G.; Tosatti, E.

    1978-08-01

    The effective (thickness-dependent) light absorption coefficient K(ω,d) is discussed for thin semiconducting films in the frequency range of free, spatially dispersive exciton polaritons. We find that (i) it oscillates strongly for small film thicknesses; (ii) it exhibits a slanted peak lineshape; (iii) its integrated strength also depends upon the exciton damping and extrapolates to zero for vanishing damping

  12. Multiscale Free Energy Simulations: An Efficient Method for Connecting Classical MD Simulations to QM or QM/MM Free Energies Using Non-Boltzmann Bennett Reweighting Schemes

    Science.gov (United States)

    2015-01-01

    The reliability of free energy simulations (FES) is limited by two factors: (a) the need for correct sampling and (b) the accuracy of the computational method employed. Classical methods (e.g., force fields) are typically used for FES and present a myriad of challenges, with parametrization being a principle one. On the other hand, parameter-free quantum mechanical (QM) methods tend to be too computationally expensive for adequate sampling. One widely used approach is a combination of methods, where the free energy difference between the two end states is computed by, e.g., molecular mechanics (MM), and the end states are corrected by more accurate methods, such as QM or hybrid QM/MM techniques. Here we report two new approaches that significantly improve the aforementioned scheme; with a focus on how to compute corrections between, e.g., the MM and the more accurate QM calculations. First, a molecular dynamics trajectory that properly samples relevant conformational degrees of freedom is generated. Next, potential energies of each trajectory frame are generated with a QM or QM/MM Hamiltonian. Free energy differences are then calculated based on the QM or QM/MM energies using either a non-Boltzmann Bennett approach (QM-NBB) or non-Boltzmann free energy perturbation (NB-FEP). Both approaches are applied to calculate relative and absolute solvation free energies in explicit and implicit solvent environments. Solvation free energy differences (relative and absolute) between ethane and methanol in explicit solvent are used as the initial test case for QM-NBB. Next, implicit solvent methods are employed in conjunction with both QM-NBB and NB-FEP to compute absolute solvation free energies for 21 compounds. These compounds range from small molecules such as ethane and methanol to fairly large, flexible solutes, such as triacetyl glycerol. Several technical aspects were investigated. Ultimately some best practices are suggested for improving methods that seek to connect

  13. Enzymatic and free radical formation of cis- and trans- epoxyeicosatrienoic acids in vitro and in vivo.

    Science.gov (United States)

    Aliwarga, Theresa; Raccor, Brianne S; Lemaitre, Rozenn N; Sotoodehnia, Nona; Gharib, Sina A; Xu, Libin; Totah, Rheem A

    2017-11-01

    Epoxyeicosatrienoic acids (EETs) are metabolites of arachidonic acid (AA) oxidation that have important cardioprotective and signaling properties. AA is an ω-6 polyunsaturated fatty acid (PUFA) that is prone to autoxidation. Although hydroperoxides and isoprostanes are major autoxidation products of AA, EETs are also formed from the largely overlooked peroxyl radical addition mechanism. While autoxidation yields both cis- and trans-EETs, cytochrome P450 (CYP) epoxygenases have been shown to exclusively catalyze the formation of all regioisomer cis-EETs, on each of the double bonds. In plasma and red blood cell (RBC) membranes, cis- and trans-EETs have been observed, and both have multiple physiological functions. We developed a sensitive ultra-performance liquid chromatography tandem mass spectrometry (UPLC-MS/MS) assay that separates cis- and trans- isomers of EETs and applied it to determine the relative distribution of cis- vs. trans-EETs in reaction mixtures of AA subjected to free radical oxidation in benzene and liposomes in vitro. We also determined the in vivo distribution of EETs in several tissues, including human and mouse heart, and RBC membranes. We then measured EET levels in heart and RBC of young mice compared to old. Formation of EETs in free radical reactions of AA in benzene and in liposomes exhibited time- and AA concentration-dependent increase and trans-EET levels were higher than cis-EETs under both conditions. In contrast, cis-EET levels were overall higher in biological samples. In general, trans-EETs increased with mouse age more than cis-EETs. We propose a mechanism for the non-enzymatic formation of cis- and trans-EETs involving addition of the peroxyl radical to one of AA's double bonds followed by bond rotation and intramolecular homolytic substitution (S H i). Enzymatic formation of cis-EETs by cytochrome P450 most likely occurs via a one-step concerted mechanism that does not allow bond rotation. The ability to accurately measure

  14. Computational Approach to Explore the B/A Junction Free Energy in DNA.

    Science.gov (United States)

    Kulkarni, Mandar; Mukherjee, Arnab

    2016-01-04

    Protein-DNA interactions induce conformational changes in DNA such as B- to A-form transitions at a local level. Such transitions are associated with a junction free energy cost at the boundary of two different conformations in a DNA molecule. In this study, we performed umbrella sampling simulations to find the free energy values of the B-A transition at the dinucleotide and trinucleotide level of DNA. Using a combination of dinucleotide and trinucleotide free energy costs obtained from simulations, we calculated the B/A junction free energy. Our study shows that the B/A junction free energy is 0.52 kcal mol(-1) for the A-philic GG step and 1.59 kcal mol(-1) for the B-philic AA step. This observation is in agreement with experimentally derived values. After excluding junction effects, we obtained an absolute free energy cost for the B- to A-form conversion for all the dinucleotide steps. These absolute free energies may be used for predicting the propensity of structural transitions in DNA. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  15. Free-energy analysis of spin models on hyperbolic lattice geometries.

    Science.gov (United States)

    Serina, Marcel; Genzor, Jozef; Lee, Yoju; Gendiar, Andrej

    2016-04-01

    We investigate relations between spatial properties of the free energy and the radius of Gaussian curvature of the underlying curved lattice geometries. For this purpose we derive recurrence relations for the analysis of the free energy normalized per lattice site of various multistate spin models in the thermal equilibrium on distinct non-Euclidean surface lattices of the infinite sizes. Whereas the free energy is calculated numerically by means of the corner transfer matrix renormalization group algorithm, the radius of curvature has an analytic expression. Two tasks are considered in this work. First, we search for such a lattice geometry, which minimizes the free energy per site. We conjecture that the only Euclidean flat geometry results in the minimal free energy per site regardless of the spin model. Second, the relations among the free energy, the radius of curvature, and the phase transition temperatures are analyzed. We found out that both the free energy and the phase transition temperature inherit the structure of the lattice geometry and asymptotically approach the profile of the Gaussian radius of curvature. This achievement opens new perspectives in the AdS-CFT correspondence theories.

  16. The inverted free energy landscape of an intrinsically disordered peptide by simulations and experiments.

    Science.gov (United States)

    Granata, Daniele; Baftizadeh, Fahimeh; Habchi, Johnny; Galvagnion, Celine; De Simone, Alfonso; Camilloni, Carlo; Laio, Alessandro; Vendruscolo, Michele

    2015-10-26

    The free energy landscape theory has been very successful in rationalizing the folding behaviour of globular proteins, as this representation provides intuitive information on the number of states involved in the folding process, their populations and pathways of interconversion. We extend here this formalism to the case of the Aβ40 peptide, a 40-residue intrinsically disordered protein fragment associated with Alzheimer's disease. By using an advanced sampling technique that enables free energy calculations to reach convergence also in the case of highly disordered states of proteins, we provide a precise structural characterization of the free energy landscape of this peptide. We find that such landscape has inverted features with respect to those typical of folded proteins. While the global free energy minimum consists of highly disordered structures, higher free energy regions correspond to a large variety of transiently structured conformations with secondary structure elements arranged in several different manners, and are not separated from each other by sizeable free energy barriers. From this peculiar structure of the free energy landscape we predict that this peptide should become more structured and not only more compact, with increasing temperatures, and we show that this is the case through a series of biophysical measurements.

  17. Calculation of free-energy differences from computer simulations of initial and final states

    International Nuclear Information System (INIS)

    Hummer, G.; Szabo, A.

    1996-01-01

    A class of simple expressions of increasing accuracy for the free-energy difference between two states is derived based on numerical thermodynamic integration. The implementation of these formulas requires simulations of the initial and final (and possibly a few intermediate) states. They involve higher free-energy derivatives at these states which are related to the moments of the probability distribution of the perturbation. Given a specified number of such derivatives, these integration formulas are optimal in the sense that they are exact to the highest possible order of free-energy perturbation theory. The utility of this approach is illustrated for the hydration free energy of water. This problem provides a quite stringent test because the free energy is a highly nonlinear function of the charge so that even fourth order perturbation theory gives a very poor estimate of the free-energy change. Our results should prove most useful for complex, computationally demanding problems where free-energy differences arise primarily from changes in the electrostatic interactions (e.g., electron transfer, charging of ions, protonation of amino acids in proteins). copyright 1996 American Institute of Physics

  18. Free radical formation in DNA: Some new aspects of an old problem

    International Nuclear Information System (INIS)

    Huettermann, J.; Gatzweiler, W.; Lange, M.; Weiland, B.

    1995-01-01

    Despite extensive efforts over the past three decades or more, there is a continuing debate about the number of different free radicals and their detailed chemical structure obtained from DNA irradiated under various conditions concerning, among others, hydration state, temperature of irradiation or measurement, base composition, and radiation dose or quality. The only proposal accepted unanimously is the 5-yl radical on the base thymine involving net H-gain at carbon C 6 denoted T(C 6 + H). Its octet spectrum which usually appears, after irradiation at e.g. 77 K, at elevated temperatures (ca. 200 K) provides for an unmistakable fingerprint in Electron Spin Resonance (ESR) spectroscopy, the method of choice for investigating free radicals in general. All other proposals of radical structures, nothing to say about details of their mechanism of formation or their subsequent reactions, have been challenged and are under debate. This apparently disturbing situation can, in the authors view, be traced back to several fundamental reasons which result from inherent limitations of both the sample itself and of the method of investigation

  19. Nuclear energy in a nuclear weapon free world

    Energy Technology Data Exchange (ETDEWEB)

    Pilat, Joseph [Los Alamos National Laboratory

    2009-01-01

    The prospect of a nuclear renaissance has revived a decades old debate over the proliferation and terrorism risks of the use of nuclear power. This debate in the last few years has taken on an added dimension with renewed attention to disarmament. Increasingly, concerns that proliferation risks may reduce the prospects for realizing the vision of a nuclear-weapon-free world are being voiced.

  20. Chemical Denaturants Smoothen Ruggedness on the Free Energy Landscape of Protein Folding.

    Science.gov (United States)

    Malhotra, Pooja; Jethva, Prashant N; Udgaonkar, Jayant B

    2017-08-08

    To characterize experimentally the ruggedness of the free energy landscape of protein folding is challenging, because the distributed small free energy barriers are usually dominated by one, or a few, large activation free energy barriers. This study delineates changes in the roughness of the free energy landscape by making use of the observation that a decrease in ruggedness is accompanied invariably by an increase in folding cooperativity. Hydrogen exchange (HX) coupled to mass spectrometry was used to detect transient sampling of local energy minima and the global unfolded state on the free energy landscape of the small protein single-chain monellin. Under native conditions, local noncooperative openings result in interconversions between Boltzmann-distributed intermediate states, populated on an extremely rugged "uphill" energy landscape. The cooperativity of these interconversions was increased by selectively destabilizing the native state via mutations, and further by the addition of a chemical denaturant. The perturbation of stability alone resulted in seven backbone amide sites exchanging cooperatively. The size of the cooperatively exchanging and/or unfolding unit did not depend on the extent of protein destabilization. Only upon the addition of a denaturant to a destabilized mutant variant did seven additional backbone amide sites exchange cooperatively. Segmentwise analysis of the HX kinetics of the mutant variants further confirmed that the observed increase in cooperativity was due to the smoothing of the ruggedness of the free energy landscape of folding of the protein by the chemical denaturant.

  1. Inequalities for magnetic-flux free energies and confinement in lattice gauge theories

    International Nuclear Information System (INIS)

    Yoneya, T.

    1982-01-01

    Rigorous inequalities among magnetic-flux free energies of tori with varying diameters are derived in lattice gauge theories. From the inequalities, it follows that if the magnetic-flux free energy vanishes in the limit of large uniform dilatation of a torus, the free energy must always decrease exponentially with the area of the cross section of the torus. The latter property is known to be sufficient for permanent confinement of static quarks. As a consequence of this property, a lower bound V(R) >= const x R for the static quark-antiquark potential is obtained in three-dimensional U(n) lattice gauge theory for sufficiently large R. (orig.)

  2. Magnetic energy dissipation in force-free jets

    Science.gov (United States)

    Choudhuri, Arnab Rai; Konigl, Arieh

    1986-01-01

    It is shown that a magnetic pressure-dominated, supersonic jet which expands or contracts in response to variations in the confining external pressure can dissipate magnetic energy through field-line reconnection as it relaxes to a minimum-energy configuration. In order for a continuous dissipation to occur, the effective reconnection time must be a fraction of the expansion time. The dissipation rate for the axisymmetric minimum-energy field configuration is analytically derived. The results indicate that the field relaxation process could be a viable mechanism for powering the synchrotron emission in extragalactic jets if the reconnection time is substantially shorter than the nominal resistive tearing time in the jet.

  3. ENERGY BUDGETS IN FREE-LIVING GREEN IGUANAS IN A SEASONAL ENVIRONMENT

    NARCIS (Netherlands)

    LICHTENBELT, WDV; WESSELINGH, RA; VOGEL, JT; ALBERS, KBM

    Using a variety of techniques we estimated energy expenditure and allocation of energy in free-living green iguanas (Iguana iguana) in a seasonal environment on Curacao, Netherlands Antilles. 1) Daily energy expenditure (DEE) was measured by means of the doubly labeled water (DLW) technique, using

  4. Effects of Energy Chirp on Echo-Enabled Harmonic Generation Free-Electron Lasers

    International Nuclear Information System (INIS)

    Huang, Z.

    2009-01-01

    We study effects of energy chirp on echo-enabled harmonic generation (EEHG). Analytical expressions are compared with numerical simulations for both harmonic and bunching factors. We also discuss the EEHG free-electron laser bandwidth increase due to an energy-modulated beam and its pulse length dependence on the electron energy chirp

  5. Concentrations of free amino acids and sugars in nine potato varieties: effects of storage and relationship with acrylamide formation.

    Science.gov (United States)

    Halford, Nigel G; Muttucumaru, Nira; Powers, Stephen J; Gillatt, Peter N; Hartley, Lee; Elmore, J Stephen; Mottram, Donald S

    2012-12-05

    Acrylamide forms during cooking and processing predominately from the reaction of free asparagine and reducing sugars in the Maillard reaction. The identification of low free asparagine and reducing sugar varieties of crops is therefore an important target. In this study, nine varieties of potato (French fry varieties Maris Piper (from two suppliers), Pentland Dell, King Edward, Daisy, and Markies; and chipping varieties Lady Claire, Lady Rosetta, Saturna, and Hermes) grown in the United Kingdom in 2009 were analyzed at monthly intervals through storage from November 2009 to July 2010. Acrylamide formation was measured in heated flour and chips fried in oil. Analysis of variance revealed significant interactions between varieties nested within type (French fry and chipping) and storage time for most free amino acids, glucose, fructose, and acrylamide formation. Acrylamide formed in chips correlated significantly with acrylamide formed in flour and with chip color. There were significant correlations between glucose or total reducing sugar concentration and acrylamide formation in both variety types, but with fructose the correlation was much stronger for chipping than for French fry varieties. Conversely, there were significant correlations with acrylamide formation for both total free amino acid and free asparagine concentration in the French fry but not chipping varieties. The study showed the potential of variety selection for preventing unacceptable levels of acrylamide formation in potato products and the variety-dependent effect of long-term storage on acrylamide risk. It also highlighted the complex relationship between precursor concentration and acrylamide risk in potatoes.

  6. Constraints on vacuum energy from structure formation and Nucleosynthesis

    Energy Technology Data Exchange (ETDEWEB)

    Adams, Fred C.; Grohs, Evan [Physics Department, University of Michigan, 450 Church Street, Ann Arbor, MI, 48109 (United States); Alexander, Stephon [Physics Department, Brown University, 6127 Wilder Laboratory, Providence, RI, 02912 (United States); Mersini-Houghton, Laura, E-mail: fca@umich.edu, E-mail: stephon_alexander@brown.edu, E-mail: egrohs@umich.edu, E-mail: mersini@physics.unc.edu [Physics Department, University of North Carolina, 120 E. Cameron Avenue, Chapel Hill, NC, 27599 (United States)

    2017-03-01

    This paper derives an upper limit on the density ρ{sub Λ} of dark energy based on the requirement that cosmological structure forms before being frozen out by the eventual acceleration of the universe. By allowing for variations in both the cosmological parameters and the strength of gravity, the resulting constraint is a generalization of previous limits. The specific parameters under consideration include the amplitude Q of the primordial density fluctuations, the Planck mass M {sub pl}, the baryon-to-photon ratio η, and the density ratio Ω {sub M} /Ω {sub b} . In addition to structure formation, we use considerations from stellar structure and Big Bang Nucleosynthesis (BBN) to constrain these quantities. The resulting upper limit on the dimensionless density of dark energy becomes ρ{sub Λ}/ M {sub pl}{sup 4} < 10{sup −90}, which is ∼30 orders of magnitude larger than the value in our universe ρ{sub Λ}/ M {sub pl}4 ∼ 10{sup −120}. This new limit is much less restrictive than previous constraints because additional parameters are allowed to vary. With these generalizations, a much wider range of universes can develop cosmic structure and support observers. To constrain the constituent parameters, new BBN calculations are carried out in the regime where η and G = M {sub pl}{sup −2} are much larger than in our universe. If the BBN epoch were to process all of the protons into heavier elements, no hydrogen would be left behind to make water, and the universe would not be viable. However, our results show that some hydrogen is always left over, even under conditions of extremely large η and G , so that a wide range of alternate universes are potentially habitable.

  7. GPU-accelerated Gibbs ensemble Monte Carlo simulations of Lennard-Jonesium

    Science.gov (United States)

    Mick, Jason; Hailat, Eyad; Russo, Vincent; Rushaidat, Kamel; Schwiebert, Loren; Potoff, Jeffrey

    2013-12-01

    This work describes an implementation of canonical and Gibbs ensemble Monte Carlo simulations on graphics processing units (GPUs). The pair-wise energy calculations, which consume the majority of the computational effort, are parallelized using the energetic decomposition algorithm. While energetic decomposition is relatively inefficient for traditional CPU-bound codes, the algorithm is ideally suited to the architecture of the GPU. The performance of the CPU and GPU codes are assessed for a variety of CPU and GPU combinations for systems containing between 512 and 131,072 particles. For a system of 131,072 particles, the GPU-enabled canonical and Gibbs ensemble codes were 10.3 and 29.1 times faster (GTX 480 GPU vs. i5-2500K CPU), respectively, than an optimized serial CPU-bound code. Due to overhead from memory transfers from system RAM to the GPU, the CPU code was slightly faster than the GPU code for simulations containing less than 600 particles. The critical temperature Tc∗=1.312(2) and density ρc∗=0.316(3) were determined for the tail corrected Lennard-Jones potential from simulations of 10,000 particle systems, and found to be in exact agreement with prior mixed field finite-size scaling calculations [J.J. Potoff, A.Z. Panagiotopoulos, J. Chem. Phys. 109 (1998) 10914].

  8. The application of computational thermodynamics and a numerical model for the determination of surface tension and Gibbs-Thomson coefficient of aluminum based alloys

    International Nuclear Information System (INIS)

    Jacome, Paulo A.D.; Landim, Mariana C.; Garcia, Amauri; Furtado, Alexandre F.; Ferreira, Ivaldo L.

    2011-01-01

    Highlights: → Surface tension and the Gibbs-Thomson coefficient are computed for Al-based alloys. → Butler's scheme and ThermoCalc are used to compute the thermophysical properties. → Predictive cell/dendrite growth models depend on accurate thermophysical properties. → Mechanical properties can be related to the microstructural cell/dendrite spacing. - Abstract: In this paper, a solution for Butler's formulation is presented permitting the surface tension and the Gibbs-Thomson coefficient of Al-based binary alloys to be determined. The importance of Gibbs-Thomson coefficient for binary alloys is related to the reliability of predictions furnished by predictive cellular and dendritic growth models and of numerical computations of solidification thermal variables, which will be strongly dependent on the thermophysical properties assumed for the calculations. A numerical model based on Powell hybrid algorithm and a finite difference Jacobian approximation was coupled to a specific interface of a computational thermodynamics software in order to assess the excess Gibbs energy of the liquid phase, permitting the surface tension and Gibbs-Thomson coefficient for Al-Fe, Al-Ni, Al-Cu and Al-Si hypoeutectic alloys to be calculated. The computed results are presented as a function of the alloy composition.

  9. The application of computational thermodynamics and a numerical model for the determination of surface tension and Gibbs-Thomson coefficient of aluminum based alloys

    Energy Technology Data Exchange (ETDEWEB)

    Jacome, Paulo A.D.; Landim, Mariana C. [Department of Mechanical Engineering, Fluminense Federal University, Av. dos Trabalhadores, 420-27255-125 Volta Redonda, RJ (Brazil); Garcia, Amauri, E-mail: amaurig@fem.unicamp.br [Department of Materials Engineering, University of Campinas, UNICAMP, PO Box 6122, 13083-970 Campinas, SP (Brazil); Furtado, Alexandre F.; Ferreira, Ivaldo L. [Department of Mechanical Engineering, Fluminense Federal University, Av. dos Trabalhadores, 420-27255-125 Volta Redonda, RJ (Brazil)

    2011-08-20

    Highlights: {yields} Surface tension and the Gibbs-Thomson coefficient are computed for Al-based alloys. {yields} Butler's scheme and ThermoCalc are used to compute the thermophysical properties. {yields} Predictive cell/dendrite growth models depend on accurate thermophysical properties. {yields} Mechanical properties can be related to the microstructural cell/dendrite spacing. - Abstract: In this paper, a solution for Butler's formulation is presented permitting the surface tension and the Gibbs-Thomson coefficient of Al-based binary alloys to be determined. The importance of Gibbs-Thomson coefficient for binary alloys is related to the reliability of predictions furnished by predictive cellular and dendritic growth models and of numerical computations of solidification thermal variables, which will be strongly dependent on the thermophysical properties assumed for the calculations. A numerical model based on Powell hybrid algorithm and a finite difference Jacobian approximation was coupled to a specific interface of a computational thermodynamics software in order to assess the excess Gibbs energy of the liquid phase, permitting the surface tension and Gibbs-Thomson coefficient for Al-Fe, Al-Ni, Al-Cu and Al-Si hypoeutectic alloys to be calculated. The computed results are presented as a function of the alloy composition.

  10. Temperature effects on the nuclear symmetry energy and symmetry free energy with an isospin and momentum dependent interaction

    International Nuclear Information System (INIS)

    Xu, Jun; Ma, Hong-Ru; Chen, Lie-Wen; Li, Bao-An

    2007-01-01

    Within a self-consistent thermal model using an isospin and momentum dependent interaction (MDI) constrained by the isospin diffusion data in heavy-ion collisions, we investigate the temperature dependence of the symmetry energy E sym (ρ,T) and symmetry free energy F sym (ρ,T) for hot, isospin asymmetric nuclear matter. It is shown that the symmetry energy E sym (ρ,T) generally decreases with increasing temperature while the symmetry free energy F sym (ρ,T) exhibits opposite temperature dependence. The decrement of the symmetry energy with temperature is essentially due to the decrement of the potential energy part of the symmetry energy with temperature. The difference between the symmetry energy and symmetry free energy is found to be quite small around the saturation density of nuclear matter. While at very low densities, they differ significantly from each other. In comparison with the experimental data of temperature dependent symmetry energy extracted from the isotopic scaling analysis of intermediate mass fragments (IMF's) in heavy-ion collisions, the resulting density and temperature dependent symmetry energy E sym (ρ,T) is then used to estimate the average freeze-out density of the IMF's

  11. Quasar Formation and Energy Emission in Black Hole Universe

    Directory of Open Access Journals (Sweden)

    Zhang T. X.

    2012-07-01

    Full Text Available Formation and energy emission of quasars are investigated in accord with the black hole universe, a new cosmological model recently developed by Zhang. According to this new cosmological model, the universe originated from a star-like black hole and grew through a supermassive black hole to the present universe by accreting ambient matter and merging with other black holes. The origin, structure, evolution, expansion, and cosmic microwave background radiation of the black hole universe have been fully ex- plained in Paper I and II. This study as Paper III explains how a quasar forms, ignites and releases energy as an amount of that emitted by dozens of galaxies. A main sequence star, after its fuel supply runs out, will, in terms of its mass, form a dwarf, a neutron star, or a black hole. A normal galaxy, after its most stars have run out of their fuels and formed dwarfs, neutron stars, and black holes, will eventually shrink its size and collapse towards the center by gravity to form a supermassive black hole with billions of solar masses. This collapse leads to that extremely hot stellar black holes merge each other and further into the massive black hole at the center and meantime release a huge amount of radiation energy that can be as great as that of a quasar. Therefore, when the stellar black holes of a galaxy collapse and merge into a supermassive black hole, the galaxy is activated and a quasar is born. In the black hole universe, the observed dis- tant quasars powered by supermassive black holes can be understood as donuts from the mother universe. They were actually formed in the mother universe and then swallowed into our universe. The nearby galaxies are still very young and thus quiet at the present time. They will be activated and further evolve into quasars after billions of years. At that time, they will enter the universe formed by the currently observed distant quasars as similar to the distant quasars entered our universe

  12. Formation Energies of Native Point Defects in Strained-Layer Superlattices (Postprint)

    Science.gov (United States)

    2017-06-05

    potential; bulk materials; total energy calculations; entropy; strained- layer superlattice (SLS) 16. SECURITY CLASSIFICATION OF: 17. LIMITATION OF...AFRL-RX-WP-JA-2017-0217 FORMATION ENERGIES OF NATIVE POINT DEFECTS IN STRAINED- LAYER SUPERLATTICES (POSTPRINT) Zhi-Gang Yu...2016 Interim 11 September 2013 – 5 November 2016 4. TITLE AND SUBTITLE FORMATION ENERGIES OF NATIVE POINT DEFECTS IN STRAINED- LAYER SUPERLATTICES

  13. First-principles calculations of the vacancy formation energy in transition and noble metals

    DEFF Research Database (Denmark)

    Korzhavyi, P.A.; Abrikosov, Igor A.; Johansson, Börje

    1999-01-01

    approach and include electrostatic multipole corrections to the atomic sphere approximation. The results are in excellent agreement with available full-potential calculations and with the vacancy formation energies obtained in positron annihilation measurements. The variation of the vacancy formation...

  14. Quantitative Boltzmann-Gibbs Principles via Orthogonal Polynomial Duality

    Science.gov (United States)

    Ayala, Mario; Carinci, Gioia; Redig, Frank

    2018-06-01

    We study fluctuation fields of orthogonal polynomials in the context of particle systems with duality. We thereby obtain a systematic orthogonal decomposition of the fluctuation fields of local functions, where the order of every term can be quantified. This implies a quantitative generalization of the Boltzmann-Gibbs principle. In the context of independent random walkers, we complete this program, including also fluctuation fields in non-stationary context (local equilibrium). For other interacting particle systems with duality such as the symmetric exclusion process, similar results can be obtained, under precise conditions on the n particle dynamics.

  15. Near-Optimal Detection in MIMO Systems using Gibbs Sampling

    DEFF Research Database (Denmark)

    Hansen, Morten; Hassibi, Babak; Dimakis, Georgios Alexandros

    2009-01-01

    In this paper we study a Markov Chain Monte Carlo (MCMC) Gibbs sampler for solving the integer least-squares problem. In digital communication the problem is equivalent to preforming Maximum Likelihood (ML) detection in Multiple-Input Multiple-Output (MIMO) systems. While the use of MCMC methods...... sampler provides a computationally efficient way of achieving approximative ML detection in MIMO systems having a huge number of transmit and receive dimensions. In fact, they further suggest that the Markov chain is rapidly mixing. Thus, it has been observed that even in cases were ML detection using, e...

  16. Binding free energy analysis of protein-protein docking model structures by evERdock.

    Science.gov (United States)

    Takemura, Kazuhiro; Matubayasi, Nobuyuki; Kitao, Akio

    2018-03-14

    To aid the evaluation of protein-protein complex model structures generated by protein docking prediction (decoys), we previously developed a method to calculate the binding free energies for complexes. The method combines a short (2 ns) all-atom molecular dynamics simulation with explicit solvent and solution theory in the energy representation (ER). We showed that this method successfully selected structures similar to the native complex structure (near-native decoys) as the lowest binding free energy structures. In our current work, we applied this method (evERdock) to 100 or 300 model structures of four protein-protein complexes. The crystal structures and the near-native decoys showed the lowest binding free energy of all the examined structures, indicating that evERdock can successfully evaluate decoys. Several decoys that show low interface root-mean-square distance but relatively high binding free energy were also identified. Analysis of the fraction of native contacts, hydrogen bonds, and salt bridges at the protein-protein interface indicated that these decoys were insufficiently optimized at the interface. After optimizing the interactions around the interface by including interfacial water molecules, the binding free energies of these decoys were improved. We also investigated the effect of solute entropy on binding free energy and found that consideration of the entropy term does not necessarily improve the evaluations of decoys using the normal model analysis for entropy calculation.

  17. High-energy inverse free-electron laser accelerator

    International Nuclear Information System (INIS)

    Courant, E.D.; Pellegrini, C.; Zakowicz, W.

    1985-01-01

    We study the inverse free electron laser (IFEL) accelerator and show that it can accelerate electrons to the few hundred GeV region with average acceleration rates of the order of 200 meV/m. Several possible accelerating structures are analyzed, and the effect of synchrotron radiation losses is studied. The longitudinal phase stability of accelerated particles is also analyzed. A Hamiltonian description, which takes into account the dissipative features of the IFEL accelerator, is introduced to study perturbations from the resonant acceleration. Adiabatic invariants are obtained and used to estimate the change of the electron phase space density during the acceleration process

  18. First-principles calculations of vacancy formation in In-free photovoltaic semiconductor Cu2ZnSnSe4

    International Nuclear Information System (INIS)

    Maeda, Tsuyoshi; Nakamura, Satoshi; Wada, Takahiro

    2011-01-01

    To quantitatively evaluate the formation energies of Cu, Zn, Sn, and Se vacancies in kesterite-type Cu 2 ZnSnSe 4 (CZTSe), first-principles pseudopotential calculations using plane-wave basis functions were performed. The formation energies of neutral Cu, Zn, Sn and Se vacancies were calculated as a function of the atomic chemical potentials of constituent elements. The obtained results were as follows: (1) the formation energy of Cu vacancy was generally smaller than those of the other Zn, Sn and Se vacancies, (2) under the Cu-poor and Zn-rich condition, the formation energy of Cu vacancy was particularly low, (3) the formation energy of Zn vacancy greatly depended on the chemical potentials of the constituent elements and under the Zn-poor and Se-rich condition, the formation energy of Zn vacancy was smaller than that of Cu vacancy, and (4) the formation energy of Sn vacancy did not greatly depend on the chemical potentials of the constituent elements and was much larger than those of Cu, Zn, and Se vacancies. These results indicate that Cu vacancy is easily formed under Cu-poor and Zn-rich conditions, but Zn vacancy is easily formed under the Zn-poor and Se-rich conditions.

  19. The free energies of partially open coronal magnetic fields

    Science.gov (United States)

    Low, B. C.; Smith, D. F.

    1993-01-01

    A simple model of the low corona is examined in terms of a static polytropic atmosphere in equilibrium with a global magnetic field. The question posed is whether magnetostatic states with partially open magnetic fields may contain magnetic energies in excess of those in fully open magnetic fields. Based on the analysis presented here, it is concluded that the cross-field electric currents in the pre-eruption corona are a viable source of the bulk of the energies in a mass ejection and its associated flare.

  20. The free energy of Maxwell-Vlasov equilibria

    International Nuclear Information System (INIS)

    Morrison, P.J.; Pfirsch, D.

    1989-10-01

    A previously derived expression for the energy of arbitrary perturbations about arbitrary Vlasov-Maxwell equilibria is transformed into a very compact form. The new form is also obtained by a canonical transformation method for solving Vlasov's equation, which is based on Lie group theory. This method is simpler than the one used before and provides better physical insight. Finally a procedure is presented for determining the existence of negative-energy modes. In this context the question of why there is an accessibility constraint for the particles, but not for the fields, is discussed. 16 refs