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)

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)

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.

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.

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

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...

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.

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.

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

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)

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

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.

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.

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.

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)

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.

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.

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.

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.

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.)

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.)

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

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.

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.

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.

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.

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

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.)

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

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

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.

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.

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.

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.

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.

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

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.

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...

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…

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.

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.

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.

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…

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)

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

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.

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

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)

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…

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

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.

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...

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

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.

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.

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…

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).

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.

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.

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

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.

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.

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.

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.

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.

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.

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.

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.

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%.

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…

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.

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.

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...

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.

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.)

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).

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.

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 ...

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

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

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

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

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)

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

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

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)

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.

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.

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.

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.

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.

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.

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.

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

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

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.

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.

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.

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.

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

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.

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.

Thermo-chemistry of nuclear waste glasses: a new approach

International Nuclear Information System (INIS)

Linard, Y.; Neuville, D.R.; Richet, P.

1997-01-01

Understanding of the stability and weathering of glasses used for storing fission products is hampered by a general lack of basic thermochemical information. Models have been setup to predict Gibbs free energies of dissolution of glasses, but ascertaining their accuracy is made difficult by the very lack of reliable experimental data with which model results should be compared. As enthalpies of formation can in principle be determined from usual solution calorimetry experiments, the lack of Gibbs-free energy data for glasses mainly stems from the fact that, as disordered substances, glasses do not obey the third principle and have indeed large configurational entropies. These entropies can be determined from thermochemical measurements only when there exist a congruently melting crystalline compound with the same composition. Using available data, we have calculated the Gibbs-free energies of formation of a series of silicate glasses for which such a calorimetric determination is possible. With these results, we assess the predictions of Paul's model (1977) for calculating Gibbs-free energies of dissolution. As the complex compositions of the borosilicate glasses used for nuclear waste storage prevent determining configurational entropies by calorimetric methods, we point out how these can be determined instead from viscosity measurements. We finally discuss the implications of this approach for modeling of water-glass interactions. (authors)

Fabrication of nanocrystalline alloys Cu–Cr–Mo super satured solid solution by mechanical alloying

Energy Technology Data Exchange (ETDEWEB)

Aguilar, C., E-mail: claudio.aguilar@usm.cl [Departamento de Ingeniería Metalúrgica y Materiales, Universidad Técnica Federico Santa María, Av. España 1680, Valparaíso (Chile); Guzmán, D. [Departamento de Ingeniería en Metalurgia, Facultad de Ingeniería, Universidad de Atacama y Centro Regional de Investigación y Desarrollo Sustentable de Atacama (CRIDESAT), Av. Copayapu 485, Copiapó (Chile); Castro, F.; Martínez, V.; Cuevas, F. de las [Centro de Estudios e Investigaciones Técnicas de Gipuzkoa, Paseo de Manuel Lardizábal, N° 15, 20018 San Sebastián (Spain); Lascano, S. [Departamento de Ingeniería Mecánica, Universidad Técnica Federico Santa María, Av. España 1680, Valparaíso (Chile); Muthiah, T. [Departamento de Ingeniería Metalúrgica y Materiales, Universidad Técnica Federico Santa María, Av. España 1680, Valparaíso (Chile)

2014-08-01

This work discusses the extension of solid solubility of Cr and Mo in Cu processed by mechanical alloying. Three alloys processed, Cu–5Cr–5Mo, Cu–10Cr–10Mo and Cu–15Cr–15Mo (weight%) using a SPEX mill. Gibbs free energy of mixing values 10, 15 and 20 kJ mol{sup −1} were calculated for these three alloys respectively by using the Miedema's model. The crystallite size decreases and dislocation density increases when the milling time increases, so Gibbs free energy storage in powders increases by the presence of crystalline defects. The energy produced by crystallite boundaries and strain dislocations were estimated and compared with Gibbs free energy of mixing values. The energy storage values by the presence of crystalline defects were higher than Gibbs free energy of mixing at 120 h for Cu–5Cr–5Mo, 130 h for Cu–10Cr–10Mo and 150 h for Cu–15Cr–15Mo. During milling, crystalline defects are produced that increases the Gibbs free energy storage and thus the Gibbs free energy curves are moved upwards and hence the solubility limit changes. Therefore, the three alloys form solid solutions after these milling time, which are supported with the XRD results. - Highlights: • Extension of solid solution Cr and Mo in Cu achieved by mechanical alloying. • X-ray characterization of Cu–Cr–Mo system processed by mechanical alloying. • Thermodynamics analysis of formation of solid solution of the Cu–Cr–Mo system.

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)

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...

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.

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

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

Phase equilibrium of PuO2-x - Pu2O3 based on first-principles calculations and configurational entropy change

International Nuclear Information System (INIS)

Minamoto, Satoshi; Kato, Masato; Konashi, Kenji

2011-01-01

Combination of an oxygen vacancy formation energy calculated using first-principles approach and the configurational entropy change treated within the framework of statistical mechanics gives an expression of the Gibbs free energy at large deviation from stoichiometry of plutonium oxide PuO 2 . An oxygen vacancy formation energy 4.20 eV derived from our previously first-principles calculation was used to evaluate the Gibbs free energy change due to oxygen vacancies in the crystal. The oxygen partial pressures then can be evaluated from the change of the free energy with two fitting parameters (a vacancy-vacancy interaction energy and vibration entropy change due to induced vacancies). Derived thermodynamic expression for the free energy based on the SGTE thermodynamic data for the stoichiometric PuO 2 and the Pu 2 O 3 compounds was further incorporated into the CALPHAD modeling, then phase equilibrium between the stoichiometric Pu 2 O 3 and non-stoichiometric PuO 2-x were reproduced.

Phase equilibrium of PuO{sub 2-x} - Pu{sub 2}O{sub 3} based on first-principles calculations and configurational entropy change

Energy Technology Data Exchange (ETDEWEB)

Minamoto, Satoshi, E-mail: satoshi.minamoto@ctc-g.co.jp [ITOCHU Techno-Solutions Corporation, Kasumigaseki, 2-5, Kasumigaseki 3-chome, Chiyoda-ku, Tokyo 100-6080 (Japan); Kato, Masato [Japan Atomic Energy Agency, Tokai-mura, Naka-gun, Ibaraki (Japan); Konashi, Kenji [Institute for Materials Research, Tohoku University, Oarai-chou, Ibaraki (Japan)

2011-05-31

Combination of an oxygen vacancy formation energy calculated using first-principles approach and the configurational entropy change treated within the framework of statistical mechanics gives an expression of the Gibbs free energy at large deviation from stoichiometry of plutonium oxide PuO{sub 2}. An oxygen vacancy formation energy 4.20 eV derived from our previously first-principles calculation was used to evaluate the Gibbs free energy change due to oxygen vacancies in the crystal. The oxygen partial pressures then can be evaluated from the change of the free energy with two fitting parameters (a vacancy-vacancy interaction energy and vibration entropy change due to induced vacancies). Derived thermodynamic expression for the free energy based on the SGTE thermodynamic data for the stoichiometric PuO{sub 2} and the Pu{sub 2}O{sub 3} compounds was further incorporated into the CALPHAD modeling, then phase equilibrium between the stoichiometric Pu{sub 2}O{sub 3} and non-stoichiometric PuO{sub 2-x} were reproduced.

Thermo-chemistry of nuclear waste glasses: a new approach; Thermochimie des verres de stockage de dechets nucleaires: une nouvelle approche

Energy Technology Data Exchange (ETDEWEB)

Linard, Y.; Neuville, D.R.; Richet, P. [Institut de Physique du Globe, Lab. de Physique des Geomateriaux, URA CNRS 734, 75 - Paris (France)

1997-07-01

Understanding of the stability and weathering of glasses used for storing fission products is hampered by a general lack of basic thermochemical information. Models have been setup to predict Gibbs free energies of dissolution of glasses, but ascertaining their accuracy is made difficult by the very lack of reliable experimental data with which model results should be compared. As enthalpies of formation can in principle be determined from usual solution calorimetry experiments, the lack of Gibbs-free energy data for glasses mainly stems from the fact that, as disordered substances, glasses do not obey the third principle and have indeed large configurational entropies. These entropies can be determined from thermochemical measurements only when there exist a congruently melting crystalline compound with the same composition. Using available data, we have calculated the Gibbs-free energies of formation of a series of silicate glasses for which such a calorimetric determination is possible. With these results, we assess the predictions of Paul's model (1977) for calculating Gibbs-free energies of dissolution. As the complex compositions of the borosilicate glasses used for nuclear waste storage prevent determining configurational entropies by calorimetric methods, we point out how these can be determined instead from viscosity measurements. We finally discuss the implications of this approach for modeling of water-glass interactions. (authors)

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.

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.

Thermodynamic properties of soddyite from solubility and calorimetry measurements

International Nuclear Information System (INIS)

Gorman-Lewis, Drew; Mazeina, Lena; Fein, Jeremy B.; Szymanowski, Jennifer E.S.; Burns, Peter C.; Navrotsky, Alexandra

2007-01-01

The release of uranium from geologic nuclear waste repositories under oxidizing conditions can only be modeled if the thermodynamic properties of the secondary uranyl minerals that form in the repository setting are known. Toward this end, we synthesized soddyite ((UO 2 ) 2 (SiO 4 )(H 2 O) 2 ), and performed solubility measurements from both undersaturation and supersaturation. The solubility measurements rigorously constrain the value of the solubility product of synthetic soddyite, and consequently its standard-state Gibbs free energy of formation. The log solubility product (lg K sp ) with its error (1σ) is (6.43 + 0.20/-0.37), and the standard-state Gibbs free energy of formation is (-3652.2 ± 4.2 (2σ)) kJ mol -1 . High-temperature drop solution calorimetry was conducted, yielding a calculated standard-state enthalpy of formation of soddyite of (-4045.4 ± 4.9 (2σ)) kJ . mol -1 . The standard-state Gibbs free energy and enthalpy of formation yield a calculated standard-state entropy of formation of soddyite of (-1318.7 ± 21.7 (2σ)) J . mol -1 . K -1 . The measurements and associated thermodynamic calculations not only describe the T = 298 K stability and solubility of soddyite, but they also can be used in predictions of repository performance through extrapolation of these properties to repository temperatures

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

Thermodynamic Study of the Nickel Addition in Zinc Hot-Dip Galvanizing Baths

Science.gov (United States)

Pistofidis, N.; Vourlias, G.

2010-01-01

A usual practice during zinc hot-dip galvanizing is the addition of nickel in the liquid zinc which is used to inhibit the Sandelin effect. Its action is due to the fact that the ζ (zeta) phase of the Fe-Zn system is replaced by the Τ (tau) phase of the Fe-Zn-Ni system. In the present work an attempt is made to explain the formation of the Τ phase with thermodynamics. For this reason the Gibbs free energy changes for Τ and ζ phases were calculated. The excess free energy for the system was calculated with the Redlich-Kister polyonyme. From this calculation it was deduced that the Gibbs energy change for the tau phase is negative. As a result its formation is spontaneous.

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.

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.

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

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)

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.

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 ...

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.

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.

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

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.

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.

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.

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

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.)

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.

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.

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

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.

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

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.

The calculation of thermodynamic properties of molecules

DEFF Research Database (Denmark)

van Speybroeck, Veronique; Gani, Rafiqul; Meier, Robert Johan

2010-01-01

Thermodynamic data are key in the understanding and design of chemical processes. Next to the experimental evaluation of such data, computational methods are valuable and sometimes indispensable tools in obtaining heats of formation and Gibbs free energies. The major toolboxes to obtain such quan......Thermodynamic data are key in the understanding and design of chemical processes. Next to the experimental evaluation of such data, computational methods are valuable and sometimes indispensable tools in obtaining heats of formation and Gibbs free energies. The major toolboxes to obtain...... molecules the combination of group contribution methods with group additive values that are determined with the best available computational ab initio methods seems to be a viable alternative to obtain thermodynamic properties near chemical accuracy. New developments and full use of existing tools may lead...

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.

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...

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)

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

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.

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...

Reflections on Gibbs: From Statistical Physics to the Amistad V3.0

Science.gov (United States)

Kadanoff, Leo P.

2014-07-01

This note is based upon a talk given at an APS meeting in celebration of the achievements of J. Willard Gibbs. J. Willard Gibbs, the younger, was the first American physical sciences theorist. He was one of the inventors of statistical physics. He introduced and developed the concepts of phase space, phase transitions, and thermodynamic surfaces in a remarkably correct and elegant manner. These three concepts form the basis of different areas of physics. The connection among these areas has been a subject of deep reflection from Gibbs' time to our own. This talk therefore celebrated Gibbs by describing modern ideas about how different parts of physics fit together. I finished with a more personal note. Our own J. Willard Gibbs had all his many achievements concentrated in science. His father, also J. Willard Gibbs, also a Professor at Yale, had one great non-academic achievement that remains unmatched in our day. I describe it.

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

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

Science.gov (United States)

Yip, Ngai Yin; Elimelech, Menachem

2012-05-01

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

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.

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.

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.

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]).

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

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,…

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...

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

Science.gov (United States)

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

2014-03-01

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

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

Thermokinetic comparison of trypan blue decolorization by free laccase and fungal biomass.

Science.gov (United States)

Razak, N N A; Annuar, M S M

2014-03-01

Free laccase and fungal biomass from white-rot fungi were compared in the thermokinetics study of the laccase-catalyzed decolorization of an azo dye, i.e., Trypan Blue. The decolorization in both systems followed a first-order kinetics. The apparent first-order rate constant, k1', value increases with temperature. Apparent activation energy of decolorization was similar for both systems at ∼ 22 kJ mol(-1), while energy for laccase inactivation was 18 kJ mol(-1). Although both systems were endothermic, fungal biomass showed higher enthalpy, entropy, and Gibbs free energy changes for the decolorization compared to free laccase. On the other hand, free laccase showed reaction spontaneity over a wider range of temperature (ΔT = 40 K) as opposed to fungal biomass (ΔT = 15 K). Comparison of entropy change (ΔS) values indicated metabolism of the dye by the biomass.

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

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

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)

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.

Molten salt e.m.f. cell measurements on U-Ga alloys

International Nuclear Information System (INIS)

Prabhakara Reddy, B.; Kandan, R.; Nagarajan, K.; Vasudeva Rao, P.R.

2000-01-01

The Gibbs free energy of formation of intermetallic compounds, UGa 3 , UGa 2 and U 2 Ga 3 were determined by using high temperature molten salt galvanic cell measurements in the temperature range of 644-988 K, 751-947 K and 800-950 K, respectively. (author)

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)

Dynamical predictive power of the generalized Gibbs ensemble revealed in a second quench.

Science.gov (United States)

Zhang, J M; Cui, F C; Hu, Jiangping

2012-04-01

We show that a quenched and relaxed completely integrable system is hardly distinguishable from the corresponding generalized Gibbs ensemble in a dynamical sense. To be specific, the response of the quenched and relaxed system to a second quench can be accurately reproduced by using the generalized Gibbs ensemble as a substitute. Remarkably, as demonstrated with the transverse Ising model and the hard-core bosons in one dimension, not only the steady values but even the transient, relaxation dynamics of the physical variables can be accurately reproduced by using the generalized Gibbs ensemble as a pseudoinitial state. This result is an important complement to the previously established result that a quenched and relaxed system is hardly distinguishable from the generalized Gibbs ensemble in a static sense. The relevance of the generalized Gibbs ensemble in the nonequilibrium dynamics of completely integrable systems is then greatly strengthened.

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.

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.

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.

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.

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.

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.

The speciation of Si and other alloying elements in the oxide surface film of galvanically corroded weld fusion zone of laser welded AA6061 aluminium alloy

Energy Technology Data Exchange (ETDEWEB)

Mujibur Rahman, A.B.M.; Kumar, Sunil [Ian Wark Research Institute, University of South Australia, Mawson Lakes Campus, Mawson Lakes, South Australia 5095 (Australia); Gerson, Andrea R. [Applied Centre for Structural and Synchrotron Studies, University of South Australia, Mawson Lakes Campus, Mawson Lakes, South Australia 5095 (Australia)], E-mail: Andrea.Gerson@unisa.edu.au

2008-05-15

It has recently been proposed that on galvanic corrosion of laser weldments of AA6061 aluminium alloy the temporal increase in galvanic corrosion resulted from either the build up of intermetallic phases in the surface oxide layer and/or a significant increase in the surface area of the cathodic weld fusion zone due to the porous nature of the surface layer. This proposition has motivated a comprehensive surface analytical study of the incorporation of alloying elements into the oxide surface film, which is composed predominately of alumina. Si is found to be present as silicate and silicides. The Gibbs free energy of formation, per cation, of silicate is more negative than that for alumina and hence silicate formation is thermodynamically, relatively, favourable. In contrast the Gibbs free energy for oxide formation, per cation, for the other alloying elements is less negative and hence relatively unfavourable compared to the formation of alumina. We propose therefore that Fe, Cu and Cr are present in the metallic form, possibly as silicides, within the oxide surface layer. Magnesium is found to be depleted relative to the weld fusion zone presumably due to dissolution within the electrolyte.

The speciation of Si and other alloying elements in the oxide surface film of galvanically corroded weld fusion zone of laser welded AA6061 aluminium alloy

International Nuclear Information System (INIS)

Mujibur Rahman, A.B.M.; Kumar, Sunil; Gerson, Andrea R.

2008-01-01

It has recently been proposed that on galvanic corrosion of laser weldments of AA6061 aluminium alloy the temporal increase in galvanic corrosion resulted from either the build up of intermetallic phases in the surface oxide layer and/or a significant increase in the surface area of the cathodic weld fusion zone due to the porous nature of the surface layer. This proposition has motivated a comprehensive surface analytical study of the incorporation of alloying elements into the oxide surface film, which is composed predominately of alumina. Si is found to be present as silicate and silicides. The Gibbs free energy of formation, per cation, of silicate is more negative than that for alumina and hence silicate formation is thermodynamically, relatively, favourable. In contrast the Gibbs free energy for oxide formation, per cation, for the other alloying elements is less negative and hence relatively unfavourable compared to the formation of alumina. We propose therefore that Fe, Cu and Cr are present in the metallic form, possibly as silicides, within the oxide surface layer. Magnesium is found to be depleted relative to the weld fusion zone presumably due to dissolution within the electrolyte

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.

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].

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.

The effect of reinforcement percentages on properties of copper matrix composites reinforced with TiC particles

Energy Technology Data Exchange (ETDEWEB)

Bagheri, GH.A., E-mail: Gh.a.bagheri65@gmail.com

2016-08-15

In this research, copper matrix composites reinforced with different amounts of titanium carbide particles were produced by mechanical milling and in-situ formation of reinforcements. Morphology and size of milled powders were inspected by scanning electron microscopy (SEM) several times during milling process. Changes in lattice parameter, crystallite size, lattice strain, dislocation density and Gibbs free energy changes (due to increasing in dislocation densities and grain boundaries) in different samples (with different TiC particles contents) were studied by X-Ray Diffraction technique with Cu-kα radiation and using Nelson–Riley method and Williamson–Hall equation. Microstructure of samples after sintering was investigated by FESEM. Finally, densitometry, hardness, determination of electrical resistance and pin on disk wear test were performed and effect of reinforcement percentages on the physical and mechanical properties of composites was studied. Results show incredible improvement in mechanical properties with increasing in TiC value, even though, electrical conductivity dropped off considerably. - Highlights: • Microstructures, mechanical and physical properties of composites have been studied. • Stored Gibbs free energy of dislocations and grain boundaries has been calculated. • Gibbs free energy increased with increasing in titanium percent. • Higher TiC percentage led to better mechanical and unfavorable physical properties.

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.

Rapidly Mixing Gibbs Sampling for a Class of Factor Graphs Using Hierarchy Width.

Science.gov (United States)

De Sa, Christopher; Zhang, Ce; Olukotun, Kunle; Ré, Christopher

2015-12-01

Gibbs sampling on factor graphs is a widely used inference technique, which often produces good empirical results. Theoretical guarantees for its performance are weak: even for tree structured graphs, the mixing time of Gibbs may be exponential in the number of variables. To help understand the behavior of Gibbs sampling, we introduce a new (hyper)graph property, called hierarchy width . We show that under suitable conditions on the weights, bounded hierarchy width ensures polynomial mixing time. Our study of hierarchy width is in part motivated by a class of factor graph templates, hierarchical templates , which have bounded hierarchy width-regardless of the data used to instantiate them. We demonstrate a rich application from natural language processing in which Gibbs sampling provably mixes rapidly and achieves accuracy that exceeds human volunteers.

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.

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.

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

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.

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

Standard molar enthalpies of formation of 1- and 2-cyanonaphthalene

International Nuclear Information System (INIS)

Ribeiro da Silva, Manuel A.V.; Lobo Ferreira, Ana I.M.C.; Barros, Ana L.M.; Bessa, Ana R.C.; Brito, Barbara C.S.A.; Vieira, Joana A.S.; Martins, Silvia A.P.

2011-01-01

Highlights: → Enthalpies of formation of 1- and 2-cyanonaphthalene were measured by combustion calorimetry. → Vapor pressures of crystalline 1- and 2-cyanonaphthalene obtained by Knudsen effusion mass loss technique. → Enthalpies, entropies and Gibbs functions of sublimation at T = 298.15 K were calculated. - Abstract: The standard (p o = 0.1 MPa) molar enthalpies of formation, in the crystalline state, of the 1- and 2-cyanonaphthalene were derived from the standard molar energies of combustion, in oxygen, at T = 298.15 K, measured by static-bomb combustion calorimetry. Vapor pressure measurements at different temperatures, using the Knudsen mass loss effusion technique, enabled the determination of the enthalpy, entropy, and Gibbs energy of sublimation, at T = 298.15 K, for both isomers. The standard molar enthalpies of sublimation, at T = 298.15 K, for 1- and 2-cyanonaphthalene, were also measured by high-temperature Calvet microcalorimetry. (table) Combining these two experimental values, the gas-phase standard molar enthalpies, at T = 298.15 K, were derived and compared with those estimated by employing two different methodologies: one based on the Cox scheme and the other one based on G3MP2B3 calculations. The calculated values show a good agreement with the experimental values obtained in this work.

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.

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.

Crystallization of glass-forming liquids: Specific surface energy

International Nuclear Information System (INIS)

Schmelzer, Jürn W. P.; Abyzov, Alexander S.

2016-01-01

A generalization of the Stefan-Skapski-Turnbull relation for the melt-crystal specific interfacial energy is developed in terms of the generalized Gibbs approach extending its standard formulation to thermodynamic non-equilibrium states. With respect to crystal nucleation, this relation is required in order to determine the parameters of the critical crystal clusters being a prerequisite for the computation of the work of critical cluster formation. As one of its consequences, a relation for the dependence of the specific surface energy of critical clusters on temperature and pressure is derived applicable for small and moderate deviations from liquid-crystal macroscopic equilibrium states. Employing the Stefan-Skapski-Turnbull relation, general expressions for the size and the work of formation of critical crystal clusters are formulated. The resulting expressions are much more complex as compared to the respective relations obtained via the classical Gibbs theory. Latter relations are retained as limiting cases of these more general expressions for moderate undercoolings. By this reason, the formulated, here, general relations for the specification of the critical cluster size and the work of critical cluster formation give a key for an appropriate interpretation of a variety of crystallization phenomena occurring at large undercoolings which cannot be understood in terms of the Gibbs’ classical treatment.

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

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.

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

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...

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

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.

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

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

Continuous spin mean-field models : Limiting kernels and Gibbs properties of local transforms

NARCIS (Netherlands)

Kulske, Christof; Opoku, Alex A.

2008-01-01

We extend the notion of Gibbsianness for mean-field systems to the setup of general (possibly continuous) local state spaces. We investigate the Gibbs properties of systems arising from an initial mean-field Gibbs measure by application of given local transition kernels. This generalizes previous

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

Numerical implementation and oceanographic application of the Gibbs potential of ice

Directory of Open Access Journals (Sweden)

R. Feistel

2005-01-01

Full Text Available The 2004 Gibbs thermodynamic potential function of naturally abundant water ice is based on much more experimental data than its predecessors, is therefore significantly more accurate and reliable, and for the first time describes the entire temperature and pressure range of existence of this ice phase. It is expressed in the ITS-90 temperature scale and is consistent with the current scientific pure water standard, IAPWS-95, and the 2003 Gibbs potential of seawater. The combination of these formulations provides sublimation pressures, freezing points, and sea ice properties covering the parameter ranges of oceanographic interest. This paper provides source code examples in Visual Basic, Fortran and C++ for the computation of the Gibbs function of ice and its partial derivatives. It reports the most important related thermodynamic equations for ice and sea ice properties.

Study of phase equilibrium of Pu2O3-PuO2 system by the first-principles calculation and CALPHAD approach

International Nuclear Information System (INIS)

Minamoto, Satoshi; Kato, Masato; Konashi, Kenji

2010-01-01

A combination of a first-principles calculation, lattice dynamics and CALPHAD (CALculation of PHAse Diagrams) modeling is proven as a powerful tool so as to evaluate the Gibbs free energy and a phase equilibrium between compounds including large amount of vacancies. In this work, non-stoichiometric PuO 2-x (dioxide) and Pu 2 O 3 (sesquioxide) has been studied. An electron cohesive energy was evaluated from a first-principles calculations to estimate total energy of the compounds and a vacancy formation energy, and the theory of statistical mechanics was applied to evaluate enthalpy/entropy change due to oxygen vacancies for the non-stoichiometry of the PuO 2 (i.e. PuO 2-x ). Then a vacancy-vacancy interaction energy was determined by fitting to the experimental data of a quantity of non-stoichiometry of the PuO 2 compounds as a function of oxygen potentials at large deviation from stoichiometry. The resulting Gibbs free energy yields phase boundary between the phases with good agreement with to the experimental data.

Study of phase equilibrium of Pu{sub 2}O{sub 3}-PuO{sub 2} system by the first-principles calculation and CALPHAD approach

Energy Technology Data Exchange (ETDEWEB)

Minamoto, Satoshi [ITOCHU Techno-Solutions Corporation, Kasumigaseki 3, Chiyoda-ku, Tokyo, Energy and Industrial Systems Department (Japan); Kato, Masato [Japan Atomic Energy Agency, Tokai-mura, Naka-gun, Ibaraki (Japan); Konashi, Kenji, E-mail: satoshi.minamoto@ctc-g.co.jp, E-mail: masato.kato@jaea.go.jp, E-mail: konashi@imr.tohoku-u.ac.jp [Institute for Materials Research, Tohoku University, Oarai-chou, Ibaraki (Japan)

2010-03-15

A combination of a first-principles calculation, lattice dynamics and CALPHAD (CALculation of PHAse Diagrams) modeling is proven as a powerful tool so as to evaluate the Gibbs free energy and a phase equilibrium between compounds including large amount of vacancies. In this work, non-stoichiometric PuO{sub 2-x} (dioxide) and Pu{sub 2}O{sub 3} (sesquioxide) has been studied. An electron cohesive energy was evaluated from a first-principles calculations to estimate total energy of the compounds and a vacancy formation energy, and the theory of statistical mechanics was applied to evaluate enthalpy/entropy change due to oxygen vacancies for the non-stoichiometry of the PuO{sub 2} (i.e. PuO{sub 2-x}). Then a vacancy-vacancy interaction energy was determined by fitting to the experimental data of a quantity of non-stoichiometry of the PuO{sub 2} compounds as a function of oxygen potentials at large deviation from stoichiometry. The resulting Gibbs free energy yields phase boundary between the phases with good agreement with to the experimental data.

Large scale inference in the Infinite Relational Model: Gibbs sampling is not enough

DEFF Research Database (Denmark)

Albers, Kristoffer Jon; Moth, Andreas Leon Aagard; Mørup, Morten

2013-01-01

. We find that Gibbs sampling can be computationally scaled to handle millions of nodes and billions of links. Investigating the behavior of the Gibbs sampler for different sizes of networks we find that the mixing ability decreases drastically with the network size, clearly indicating a need...

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)

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...

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

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.

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.

On P-Adic Quasi Gibbs Measures for Q + 1-State Potts Model on the Cayley Tree

International Nuclear Information System (INIS)

Mukhamedov, Farrukh

2010-06-01

In the present paper we introduce a new class of p-adic measures, associated with q +1-state Potts model, called p-adic quasi Gibbs measure, which is totally different from the p-adic Gibbs measure. We establish the existence p-adic quasi Gibbs measures for the model on a Cayley tree. If q is divisible by p, then we prove the occurrence of a strong phase transition. If q and p are relatively prime, then there is a quasi phase transition. These results are totally different from the results of [F.M.Mukhamedov, U.A. Rozikov, Indag. Math. N.S. 15(2005) 85-100], since q is divisible by p, which means that q + 1 is not divided by p, so according to a main result of the mentioned paper, there is a unique and bounded p-adic Gibbs measure (different from p-adic quasi Gibbs measure). (author)

An Introduction to the DA-T Gibbs Sampler for the Two-Parameter Logistic (2PL Model and Beyond

Directory of Open Access Journals (Sweden)

Gunter Maris

2005-01-01

Full Text Available The DA-T Gibbs sampler is proposed by Maris and Maris (2002 as a Bayesian estimation method for a wide variety of Item Response Theory (IRT models. The present paper provides an expository account of the DAT Gibbs sampler for the 2PL model. However, the scope is not limited to the 2PL model. It is demonstrated how the DA-T Gibbs sampler for the 2PL may be used to build, quite easily, Gibbs samplers for other IRT models. Furthermore, the paper contains a novel, intuitive derivation of the Gibbs sampler and could be read for a graduate course on sampling.

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.

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.

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.

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.

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.

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

Numerical implementation and oceanographic application of the Gibbs thermodynamic potential of seawater

Directory of Open Access Journals (Sweden)

R. Feistel

2005-01-01

Full Text Available The 2003 Gibbs thermodynamic potential function represents a very accurate, compact, consistent and comprehensive formulation of equilibrium properties of seawater. It is expressed in the International Temperature Scale ITS-90 and is fully consistent with the current scientific pure water standard, IAPWS-95. Source code examples in FORTRAN, C++ and Visual Basic are presented for the numerical implementation of the potential function and its partial derivatives, as well as for potential temperature. A collection of thermodynamic formulas and relations is given for possible applications in oceanography, from density and chemical potential over entropy and potential density to mixing heat and entropy production. For colligative properties like vapour pressure, freezing points, and for a Gibbs potential of sea ice, the equations relating the Gibbs function of seawater to those of vapour and ice are presented.

An update on the thermodynamics of Ta2O5

International Nuclear Information System (INIS)

Jacob, K.T.; Shekhar, Chander; Waseda, Y.

2009-01-01

Using a solid-state electrochemical cell incorporating yttria-doped thoria (YDT) as the electrolyte and a mixture of (Mn + MnO) as the reference electrode, standard Gibbs free energy of formation of β-Ta 2 O 5 has been determined as a function of temperature in the range (1000 to 1300) K. The solid-state electrochemical cell used can be represented as (-)Pt,Ta+Ta 2 O 5 //(Y 2 O 3 )ThO 2 //Mn+MnO,Pt(+) Combining the reversible e.m.f. of the cell with recent data on the free energy of formation of MnO, standard Gibbs free energy of formation of Ta 2 O 5 from Ta metal and diatomic oxygen gas (O 2 ) in the temperature range (1000 to 1300) K is obtained: Δ f G 0 ±0.35/(kJ.mol -1 )=-2004.376+0.40445(T/K). Because of the significant solid solubility of oxygen in tantalum, a small correction for the activity of Ta in the metal phase in equilibrium with Ta 2 O 5 is applied. An analysis of the results obtained in this study and other free energy data reported in the literature by the 'third law' method suggests the need for refining data for Ta 2 O 5 reported in thermodynamic compilations. Used in the analysis is a revised value for standard entropy of Ta 2 O 5 based on more recent low-temperature heat capacity measurements. An improved set of thermodynamic properties of ditantalum pentoxide (Ta 2 O 5 ) are presented in the temperature range (298.15 to 2200) K.

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.

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.

Liquid phase stabilization versus bubble formation at a nanoscale curved interface

Science.gov (United States)

Schiffbauer, Jarrod; Luo, Tengfei

2018-03-01

We investigate the nature of vapor bubble formation near a nanoscale-curved convex liquid-solid interface using two models: an equilibrium Gibbs model for homogenous nucleation, and a nonequilibrium dynamic van der Waals-diffuse-interface model for phase change in an initially cool liquid. Vapor bubble formation is shown to occur for sufficiently large radius of curvature and is suppressed for smaller radii. Solid-fluid interactions are accounted for and it is shown that liquid-vapor interfacial energy, and hence Laplace pressure, has limited influence over bubble formation. The dominant factor is the energetic cost of creating the solid-vapor interface from the existing solid-liquid interface, as demonstrated via both equilibrium and nonequilibrium arguments.

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.

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.)

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

Periodic p-adic Gibbs Measures of q-State Potts Model on Cayley Trees I: The Chaos Implies the Vastness of the Set of p-Adic Gibbs Measures

Science.gov (United States)

Ahmad, Mohd Ali Khameini; Liao, Lingmin; Saburov, Mansoor

2018-06-01

We study the set of p-adic Gibbs measures of the q-state Potts model on the Cayley tree of order three. We prove the vastness of the set of the periodic p-adic Gibbs measures for such model by showing the chaotic behavior of the corresponding Potts-Bethe mapping over Q_p for the prime numbers p≡1 (mod 3). In fact, for 0< |θ -1|_p< |q|_p^2 < 1 where θ =\\exp _p(J) and J is a coupling constant, there exists a subsystem that is isometrically conjugate to the full shift on three symbols. Meanwhile, for 0< |q|_p^2 ≤ |θ -1|_p< |q|_p < 1, there exists a subsystem that is isometrically conjugate to a subshift of finite type on r symbols where r ≥ 4. However, these subshifts on r symbols are all topologically conjugate to the full shift on three symbols. The p-adic Gibbs measures of the same model for the prime numbers p=2,3 and the corresponding Potts-Bethe mapping are also discussed. On the other hand, for 0< |θ -1|_p< |q|_p < 1, we remark that the Potts-Bethe mapping is not chaotic when p=3 and p≡ 2 (mod 3) and we could not conclude the vastness of the set of the periodic p-adic Gibbs measures. In a forthcoming paper with the same title, we will treat the case 0< |q|_p ≤ |θ -1|_p < 1 for all prime numbers p.

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.

Modeling adsorption of cationic surfactants at air/water interface without using the Gibbs equation.

Science.gov (United States)

Phan, Chi M; Le, Thu N; Nguyen, Cuong V; Yusa, Shin-ichi

2013-04-16

The Gibbs adsorption equation has been indispensable in predicting the surfactant adsorption at the interfaces, with many applications in industrial and natural processes. This study uses a new theoretical framework to model surfactant adsorption at the air/water interface without the Gibbs equation. The model was applied to two surfactants, C14TAB and C16TAB, to determine the maximum surface excesses. The obtained values demonstrated a fundamental change, which was verified by simulations, in the molecular arrangement at the interface. The new insights, in combination with recent discoveries in the field, expose the limitations of applying the Gibbs adsorption equation to cationic surfactants at the air/water interface.

Theoretical Understanding the Relations of Melting-point Determination Methods from Gibbs Thermodynamic Surface and Applications on Melting Curves of Lower Mantle Minerals

Science.gov (United States)

Yin, K.; Belonoshko, A. B.; Zhou, H.; Lu, X.

2016-12-01

The melting temperatures of materials in the interior of the Earth has significant implications in many areas of geophysics. The direct calculations of the melting point by atomic simulations would face substantial hysteresis problem. To overcome the hysteresis encountered in the atomic simulations there are a few different melting-point determination methods available nowadays, which are founded independently, such as the free energy method, the two-phase or coexistence method, and the Z method, etc. In this study, we provide a theoretical understanding the relations of these methods from a geometrical perspective based on a quantitative construction of the volume-entropy-energy thermodynamic surface, a model first proposed by J. Willard Gibbs in 1873. Then combining with an experimental data and/or a previous melting-point determination method, we apply this model to derive the high-pressure melting curves for several lower mantle minerals with less computational efforts relative to using previous methods only. Through this way, some polyatomic minerals at extreme pressures which are almost unsolvable before are calculated fully from first principles now.

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.

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.

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.

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.

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.

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.

Hydrolysis, formation and ionization constants at 250C, and at high temperature-high ionic strength

International Nuclear Information System (INIS)

Phillips, S.L.; Phillips, C.A.; Skeen, J.

1985-02-01

Thermochemical data for nuclear waste disposal are compiled. The resulting computerized database consists of critically evaluated data on Gibbs energy of formation, enthalpy of formation, entropy and heat capacity of selected substances for about 16 elements at 25 0 C and zero ionic strength. Elements covered are Am, As, Br, C, Cl, F, I, Mo, Np, N, O, P, Pu, Si, Sr, S, and U. Values of these thermodynamic properties were used to calculate equilibrium quotients for hydrolysis, complexation and ionization reactions up to 300 0 C and 3 ionic strength, for selected chemical reactions

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.

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.

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…

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.

The MaxEnt extension of a quantum Gibbs family, convex geometry and geodesics

International Nuclear Information System (INIS)

Weis, Stephan

2015-01-01

We discuss methods to analyze a quantum Gibbs family in the ultra-cold regime where the norm closure of the Gibbs family fails due to discontinuities of the maximum-entropy inference. The current discussion of maximum-entropy inference and irreducible correlation in the area of quantum phase transitions is a major motivation for this research. We extend a representation of the irreducible correlation from finite temperatures to absolute zero

Microhydration of caesium compounds: Cs, CsOH, CsI and Cs₂I₂ complexes with one to three H₂O molecules of nuclear safety interest.

Science.gov (United States)

Sudolská, Mária; Cantrel, Laurent; Cernušák, Ivan

2014-04-01

Structure and thermodynamic properties (standard enthalpies of formation and Gibbs free energies) of hydrated caesium species of nuclear safety interest, Cs, CsOH, CsI and its dimer Cs₂I₂, with one up to three water molecules, are calculated to assess their possible existence in severe accident occurring to a pressurized water reactor. The calculations were performed using the coupled cluster theory including single, double and non-iterative triple substitutions (CCSD(T)) in conjunction with the basis sets (ANO-RCC) developed for scalar relativistic calculations. The second-order spin-free Douglas-Kroll-Hess Hamiltonian was used to account for the scalar relativistic effects. Thermodynamic properties obtained by these correlated ab initio calculations (entropies and thermal capacities at constant pressure as a function of temperature) are used in nuclear accident simulations using ASTEC/SOPHAEROS software. Interaction energies, standard enthalpies and Gibbs free energies of successive water molecules addition determine the ordering of the complexes. CsOH forms the most hydrated stable complexes followed by CsI, Cs₂I₂, and Cs. CsOH still exists in steam atmosphere even at quite high temperature, up to around 1100 K.

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.

Threshold oxygen levels in Na(I) for the formation of NaCrO 2(s) on 18-8 stainless steels from accurate thermodynamic measurements

Science.gov (United States)

Sreedharan, O. M.; Madan, B. S.; Gnanamoorthy, J. B.

1983-12-01

The compound NaCrO 2(s) is an important corrosion product in sodium-cooled LMFBRs. The standard Gibbs energy of formation of NaCrO 2(s) is required for the computation of threshold oxygen levels in Na(1) for the formation of NaCrO 2(s) on 18-8 stainless steels. For this purpose the emf of the galvanic cell: Pt, NaCrO 2, Cr 2O 3, Na 2CrO 4/15 YSZ/O 2 ( P O 2 = 0.21 atm, air), Pt was measured over 784-1012 K to be: (E±4.4)(mV) = 483.67-0.34155 T(K). From this, the standard Gibbs energy of formation of NaCrO 2(s) from the elements ( ΔG f,T0) and from the oxides ( ΔG f,OX,T0) was calculated to be: [ΔG f,T0(NaCrO 2, s)±1.86] (kJ/mol) =-869.98 + 0.18575 T(K) , [ΔG f,OX,T0(NaCr0 2, s)±4.8] (kJ/mol) = -104.25-0.00856 T(K) . The molar heat capacity, C P0, of NaCrO 2(s) was measured by DSC to be (350-600 K): C P0(NaCrO 2, s) (J/K mol) = 27.15 + 0.1247 T (K) , From these data, values of -99.3 kJ/mol and 91.6 J/K mol were computed for ΔH f,2980 and S 2980 of NaCrO 2(s). The internal consistency was checked with the use of enthalpy data on Na 2CrO 4(s). From the standard Gibbs energy of formation of NaCrO 2(s) the equation logC 0(wppm) = 3.9905-3147.6 T(K) was derived, where C 0 is the threshold oxygen level for the formation of NaCrO 2(s) on 18-8 stainless steels.

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.

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...

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...

Amine-free reversible hydrogen storage in formate salts catalyzed by ruthenium pincer complex without pH control or solvent change.

Science.gov (United States)

Kothandaraman, Jotheeswari; Czaun, Miklos; Goeppert, Alain; Haiges, Ralf; Jones, John-Paul; May, Robert B; Prakash, G K Surya; Olah, George A

2015-04-24

Due to the intermittent nature of most renewable energy sources, such as solar and wind, energy storage is increasingly required. Since electricity is difficult to store, hydrogen obtained by electrochemical water splitting has been proposed as an energy carrier. However, the handling and transportation of hydrogen in large quantities is in itself a challenge. We therefore present here a method for hydrogen storage based on a CO2 (HCO3 (-) )/H2 and formate equilibrium. This amine-free and efficient reversible system (>90 % yield in both directions) is catalyzed by well-defined and commercially available Ru pincer complexes. The formate dehydrogenation was triggered by simple pressure swing without requiring external pH control or the change of either the solvent or the catalyst. Up to six hydrogenation-dehydrogenation cycles were performed and the catalyst performance remained steady with high selectivity (CO free H2 /CO2 mixture was produced). © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Existence and uniqueness of Gibbs states for a statistical mechanical polyacetylene model

International Nuclear Information System (INIS)

Park, Y.M.

1987-01-01

One-dimensional polyacetylene is studied as a model of statistical mechanics. In a semiclassical approximation the system is equivalent to a quantum XY model interacting with unbounded classical spins in one-dimensional lattice space Z. By establishing uniform estimates, an infinite-volume-limit Hilbert space, a strongly continuous time evolution group of unitary operators, and an invariant vector are constructed. Moreover, it is proven that any infinite-limit state satisfies Gibbs conditions. Finally, a modification of Araki's relative entropy method is used to establish the uniqueness of Gibbs states

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.

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.

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…

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.

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)

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.

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.

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.

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.

Thermodynamic modeling of the stacking fault energy of austenitic steels

International Nuclear Information System (INIS)

Curtze, S.; Kuokkala, V.-T.; Oikari, A.; Talonen, J.; Haenninen, H.

2011-01-01

The stacking fault energies (SFE) of 10 austenitic steels were determined in the temperature range 50 ≤ T ≤ 600 K by thermodynamic modeling of the Fe-Cr-Ni-Mn-Al-Si-Cu-C-N system using a modified Olson and Cohen modeling approach (Olson GB, Cohen M. Metall Trans 1976;7A:1897 ). The applied model accounts for each element's contribution to the Gibbs energy, the first-order excess free energies, magnetic contributions and the effect of interstitial nitrogen. Experimental SFE values from X-ray diffraction measurements were used for comparison. The effect of SFE on deformation mechanisms was also studied by electron backscatter diffraction.

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)

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

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...

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

Discrete tomographic reconstruction of 2D polycrystal orientation maps from X-ray diffraction projections using Gibbs priors

DEFF Research Database (Denmark)

Rodek, L.; Knudsen, E.; Poulsen, H.F.

2005-01-01

discrete tomographic algorithm, applying image-modelling Gibbs priors and a homogeneity condition. The optimization of the objective function is accomplished via the Gibbs Sampler in conjunction with simulated annealing. In order to express the structure of the orientation map, the similarity...

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

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

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

WATEQ3 geochemical model: thermodynamic data for several additional solids

International Nuclear Information System (INIS)

Krupka, K.M.; Jenne, E.A.

1982-09-01

Geochemical models such as WATEQ3 can be used to model the concentrations of water-soluble pollutants that may result from the disposal of nuclear waste and retorted oil shale. However, for a model to competently deal with these water-soluble pollutants, an adequate thermodynamic data base must be provided that includes elements identified as important in modeling these pollutants. To this end, several minerals and related solid phases were identified that were absent from the thermodynamic data base of WATEQ3. In this study, the thermodynamic data for the identified solids were compiled and selected from several published tabulations of thermodynamic data. For these solids, an accepted Gibbs free energy of formation, ΔG 0 /sub f,298/, was selected for each solid phase based on the recentness of the tabulated data and on considerations of internal consistency with respect to both the published tabulations and the existing data in WATEQ3. For those solids not included in these published tabulations, Gibbs free energies of formation were calculated from published solubility data (e.g., lepidocrocite), or were estimated (e.g., nontronite) using a free-energy summation method described by Mattigod and Sposito (1978). The accepted or estimated free energies were then combined with internally consistent, ancillary thermodynamic data to calculate equilibrium constants for the hydrolysis reactions of these minerals and related solid phases. Including these values in the WATEQ3 data base increased the competency of this geochemical model in applications associated with the disposal of nuclear waste and retorted oil shale. Additional minerals and related solid phases that need to be added to the solubility submodel will be identified as modeling applications continue in these two programs

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

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.

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

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.

Solid Oxide Galvanic Cell to determine thermochemical data of Dy6UO12(s)

International Nuclear Information System (INIS)

Sahu, Manjulata; Dash, Smruti; Sen, B.K.; Venugopal, V.

2010-01-01

The rare earth elements such as Sm, Eu, Gd, and Dy have very high thermal neutron absorption cross sections and their oxides are utilized as burnable poisons in nuclear reactor to maintain constant reactivity of the core. These oxides form solid solution with urania as their ionic radii are within 20% of that of urania. Rare earth oxides-urania solid solutions are also beneficial in preventing oxidation of UO 2 (s). RE 6 UO I2 (s) (RE = rare earth) type of compounds are known to exist in RE-U-O system and their formation cannot be ruled out under transient conditions. The data on Gibbs energy of formation of compounds in RE-U-O system is therefore essential to predict the feasibility. Theoretically, the measurement of the e.m.f. of a suitable galvanic cell is one of the most accurate methods to obtain Gibbs energy of formation of compounds if e.m.f cell operates reversibly. In this study, the standard molar Gibbs energy of formation of Dy 6 UO I2 (s) was determined using solid oxide galvanic cell technique. The Gibbs energy of formation of Dy 6 UO 12 (s) is reported for the first time

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,

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.

Free radical scavenging potency of quercetin catecholic colonic metabolites: Thermodynamics of 2H+/2e- processes.

Science.gov (United States)

Amić, Ana; Lučić, Bono; Stepanić, Višnja; Marković, Zoran; Marković, Svetlana; Dimitrić Marković, Jasmina M; Amić, Dragan

2017-03-01

Reaction energetics of the double (2H + /2e - ), i.e., the first 1H + /1e - (catechol→ phenoxyl radical) and the second 1H + /1e - (phenoxyl radical→ quinone) free radical scavenging mechanisms of quercetin and its six colonic catecholic metabolites (caffeic acid, hydrocaffeic acid, homoprotocatechuic acid, protocatechuic acid, 4-methylcatechol, and catechol) were computationally studied using density functional theory, with the aim to estimate the antiradical potency of these molecules. We found that second hydrogen atom transfer (HAT) and second sequential proton loss electron transfer (SPLET) mechanisms are less energy demanding than the first ones indicating 2H + /2e - processes as inherent to catechol moiety. The Gibbs free energy change for reactions of inactivation of selected free radicals indicate that catecholic colonic metabolites constitute an efficient group of more potent scavengers than quercetin itself, able to deactivate various free radicals, under different biological conditions. They could be responsible for the health benefits associated with regular intake of flavonoid-rich diet. Copyright © 2016 Elsevier Ltd. All rights reserved.

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.

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.

Influence of lipophilicity on drug-cyclodextrin interactions: A calorimetric study

International Nuclear Information System (INIS)

Waters, Laura J.; Bedford, Susan; Parkes, Gareth M.B.; Mitchell, J.C.

2010-01-01

This study presents a systematic investigation of the interaction of three functionally related drugs, ibuprofen, ketoprofen and flurbiprofen, with two distinct forms of cyclodextrin at three specific temperatures, 298, 303 and 310 K using isothermal titration calorimetry (ITC). Although all three pharmaceutical compounds have similar pKa values, they exhibit widely differing lipophilicities. While previous authors have presented data regarding the binding of flurbiprofen and ibuprofen with β-cyclodextrin, this is the first report of the interaction of all three drug substances with β-cyclodextrin and 2-(hydroxypropyl)-β-cyclodextrin at controlled pH and temperature. For all scenarios, the associated changes in Gibbs free energy, enthalpy and entropy are presented alongside the stoichiometry and binding constants concerned. In all cases the binding was found to occur at a 1:1 ratio with an associated negative enthalpy and Gibbs free energy with the formation of the complex enthalpically, rather than entropically driven. The data further demonstrates a clear relationship between the thermodynamic behaviour and log P of the drug molecules. This work confirms the suitability of ITC to determine thermodynamic data for drug-cyclodextrin complex formations and provides an insight into the selection of appropriate cyclodextrins for bespoke pharmaceutical formulations.

Influence of lipophilicity on drug-cyclodextrin interactions: A calorimetric study

Energy Technology Data Exchange (ETDEWEB)

Waters, Laura J., E-mail: l.waters@hud.ac.uk [School of Applied Sciences, University of Huddersfield, Queensgate, Huddersfield, HD1 3DH (United Kingdom); Bedford, Susan; Parkes, Gareth M.B. [School of Applied Sciences, University of Huddersfield, Queensgate, Huddersfield, HD1 3DH (United Kingdom); Mitchell, J.C. [Medway Sciences, School of Science, University of Greenwich at Medway, Chatham Maritime, Kent ME4 4TB (United Kingdom)

2010-11-20

This study presents a systematic investigation of the interaction of three functionally related drugs, ibuprofen, ketoprofen and flurbiprofen, with two distinct forms of cyclodextrin at three specific temperatures, 298, 303 and 310 K using isothermal titration calorimetry (ITC). Although all three pharmaceutical compounds have similar pKa values, they exhibit widely differing lipophilicities. While previous authors have presented data regarding the binding of flurbiprofen and ibuprofen with {beta}-cyclodextrin, this is the first report of the interaction of all three drug substances with {beta}-cyclodextrin and 2-(hydroxypropyl)-{beta}-cyclodextrin at controlled pH and temperature. For all scenarios, the associated changes in Gibbs free energy, enthalpy and entropy are presented alongside the stoichiometry and binding constants concerned. In all cases the binding was found to occur at a 1:1 ratio with an associated negative enthalpy and Gibbs free energy with the formation of the complex enthalpically, rather than entropically driven. The data further demonstrates a clear relationship between the thermodynamic behaviour and log P of the drug molecules. This work confirms the suitability of ITC to determine thermodynamic data for drug-cyclodextrin complex formations and provides an insight into the selection of appropriate cyclodextrins for bespoke pharmaceutical formulations.

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

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.

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.

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.

Formation of amorphous layers by irradiation

International Nuclear Information System (INIS)

Bourgoin, J.C.

1979-01-01

When an ordered solid is irradiated with heavy energy particles, disorder is produced. When the irradiation dose exceeds a so-called critical dose, the irradiated area of the solid becomes uniformly disordered. Mention is first made of the nature, concentration and distribution of the defects created by a heavy energy particle. The description is then given -solely with respect to semiconductors- of the effect of the various parameters on the critical dose energy and nature of the ion, nature and temperature of the solid, irradiation flux. The physical properties (electronic and thermodynamic types) and the uniformly disordered areas are briefly discussed and these properties are compared with those of amorphous semiconductor layers fabricated by evaporation. It is concluded that the evaporated and irradiated layers are similar in nature. It is suggested that the transformation of an irradiated crystalline area into an amorphous one occurs when the Gibbs energy of the crystal become greater than the Gibbs energy of the amorphous one [fr

Free energy calculations give insight into the stereoselective hydroxylation of α-ionones by engineered cytochrome P450 BM3 mutants.

Science.gov (United States)

de Beer, Stephanie B A; Venkataraman, Harini; Geerke, Daan P; Oostenbrink, Chris; Vermeulen, Nico P E

2012-08-27

Previously, stereoselective hydroxylation of α-ionone by Cytochrome P450 BM3 mutants M01 A82W and M11 L437N was observed. While both mutants hydroxylate α-ionone in a regioselective manner at the C3 position, M01 A82W catalyzes formation of trans-3-OH-α-ionone products whereas M11 L437N exhibits opposite stereoselectivity, producing trans-(3S,6S)-OH-α-ionone and cis-(3S,6R)-OH-α-ionone. Here, we explore the stereoselective C3 hydroxylation of α-ionone by Cytochrome P450 BM3 mutants M01 A82W and M11 L437N using molecular dynamics-based free energy calculations to study the interaction between the enzyme and both the substrates and the products. The one-step perturbation approach is applied using an optimized reference state for substrates and products. While the free energy differences between the substrates free in solution amount to ~0 kJ mol(-1), the differences in mutant M01 A82W agree with the experimentally obtained dissociation constants K(d). Moreover, a correlation with experimentally observed trends in product formation is found in both mutants. The trans isomers show the most favorable relative binding free energy in the range of all four possible hydroxylated diastereomers for mutant M01 A82W, while the trans product from (6S)-α-ionone and the cis product from (6R)-α-ionone show highest affinity for mutant M11 L437N. Marcus theory is subsequently used to relate the thermodynamic stability to transition state energies and rates of formation.

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

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.

A Gibbs potential expansion with a quantic system made up of a large number of particles; Un developpement du potentiel de Gibbs d'un systeme compose d'un grand nombre de particules

Energy Technology Data Exchange (ETDEWEB)

Bloch, Claude; Dominicis, Cyrano de [Commissariat a l' energie atomique et aux energies alternatives - CEA, Centre d' Etudes Nucleaires de Saclay, Gif-sur-Yvette (France)

1959-07-01

Starting from an expansion derived in a previous work, we study the contribution to the Gibbs potential of the two-body dynamical correlations, taking into account the statistical correlations. Such a contribution is of interest for low density systems at low temperature. In the zero density limit, it reduces to the Beth Uhlenbeck expression of the second virial coefficient. For a system of fermions in the zero temperature limit, it yields the contribution of the Brueckner reaction matrix to the ground state energy, plus, under certain conditions, additional terms of the form exp. (β |Δ|), where the Δ are the binding energies of 'bound states' of the type first discussed by L. Cooper. Finally, we study the wave function of two particles immersed in a medium (defined by its temperature and chemical potential). lt satisfies an equation generalizing the Bethe Goldstone equation for an arbitrary temperature. Reprint of a paper published in 'Nuclear Physics' 10, 1959, p. 181-196 [French] Partant d'un developpement extrait d'un precedent travail, nous etudions la contribution au potentiel de Gibbs des relations dynamiques du systeme de deux corps, en tenant compte des relations statistiques. Une telle contribution presente de l'interet pour les systemes a densite faible et a basse temperature. A la densite limite zero, elle se ramene a l'expression de Beth Uhlenbeck du second coefficient virial. Pour un systeme de fermions a la temperature limite zero, il produit la contribution de la matrice de reaction de Brueckner au niveau fondamental, plus, dans certaines conditions, des termes additionnels de la forme exp. (β |Δ|), ou les Δ sont les energies de liaison des 'etats lies' du premier type, discutes auparavant par L. Cooper. Finalement, on etudie la fonction d'onde de deux particules immerges dans un milieu (definie par sa temperature et son potentiel chimique). Il satisfait a une equation generalisant l'equation de Bethe Goldstone pour une temperature arbitraire

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.

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.)

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.)

One of Gibbs's ideas that has gone unnoticed (comment on chapter IX of his classic book)

International Nuclear Information System (INIS)

Sukhanov, Alexander D; Rudoi, Yurii G

2006-01-01

We show that contrary to the commonly accepted view, Chapter IX of Gibbs's book [1] contains the prolegomena to a macroscopic statistical theory that is qualitatively different from his own microscopic statistical mechanics. The formulas obtained by Gibbs were the first results in the history of physics related to the theory of fluctuations in any macroparameters, including temperature. (from the history of physics)

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.

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

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

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.

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.

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.

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 .

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

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 ...

The Gibbs-Thomson equation for a spherical coherent precipitate with applications to nucleation

International Nuclear Information System (INIS)

Rottman, C.; Voorhees, P.W.; Johnson, W.C.

1988-01-01

The conditions for interfacial thermodynamic equilibrium form the basis for the derivation of a number of basic equations in materials science, including the various forms of the Gibbs-Thomson equation. The equilibrium conditions pertaining to a curved interface in a two-phase fluid system are well-known. In contrast, the conditions for thermodynamic equilibrium at a curved interface in nonhydrostatically stressed solids have only recently been examined. These conditions can be much different from those at a fluid interface and, as a result, the Gibbs-Thomson equation appropriate to coherent solids is likely to be considerably different from that for fluids. In this paper, the authors first derive the conditions necessary for thermodynamic equilibrium at the precipitate-matrix interface of a coherent spherical precipitate. The authors' derivation of these equilibrium conditions includes a correction to the equilibrium conditions of Johnson and Alexander for a spherical precipitate in an isotropic matrix. They then use these conditions to derive the dependence of the interfacial precipitate and matrix concentrations on precipitate radius (Gibbs-Thomson equation) for a such a precipitate. In addition, these relationships are then used to calculate the critical radius for the nucleation of a coherent misfitting precipitate

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

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

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

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.

Modeling and Simulation on NOx and N2O Formation in Co-combustion of Low-rank Coal and Palm Kernel Shell

Directory of Open Access Journals (Sweden)

Mahidin Mahidin

2012-12-01

Full Text Available NOx and N2O emissions from coal combustion are claimed as the major contributors for the acid rain, photochemical smog, green house and ozone depletion problems. Based on the facts, study on those emissions formation is interest topic in the combustion area. In this paper, theoretical study by modeling and simulation on NOx and N2O formation in co-combustion of low-rank coal and palm kernel shell has been done. Combustion model was developed by using the principle of chemical-reaction equilibrium. Simulation on the model in order to evaluate the composition of the flue gas was performed by minimization the Gibbs free energy. The results showed that by introduced of biomass in coal combustion can reduce the NOx concentration in considerably level. Maximum NO level in co-combustion of low-rank coal and palm kernel shell with fuel composition 1:1 is 2,350 ppm, low enough compared to single low-rank coal combustion up to 3,150 ppm. Moreover, N2O is less than 0.25 ppm in all cases. Keywords: low-rank coal, N2O emission, NOx emission, palm kernel shell

LA CASA GIBBS Y EL MONOPOLIO SALITRERO PERUANO: 1876-1878

Directory of Open Access Journals (Sweden)

Manuel Ravest Mora

2008-06-01

Full Text Available El objeto de este breve trabajo es mostrar la disposición de Anthony Gibbs & Sons, y de sus filiales, a apoyar el proyecto monopólico salitrero del Perú con recursos monetarios y los manejos de sus directores en la única empresa que, dada su capacidad de elaboración, podía hacerlo fracasar: la Compañía de Salitres y Ferrocarril de Antofagasta, de la que Gibbs era el segundo mayor accionista. Para el gobierno chileno la causa primaria de la guerra de 1879 fue el intento del Perú por monopolizar la producción salitrera. Bolivia, su aliada secreta desde 1873, colaboró arrendándole y vendiéndole sus depósitos de nitrato, e imponiendo a la exportación del salitre un tributo que infringió la condición -estipulada en un Tratado de Límites- bajo la cual Chile le cedió territorio. Su recuperación manu militari inició el conflicto. A partir de la segunda mitad del siglo pasado esta tesis economicista-legalista fue cuestionada en Chile y en el exterior, desplazando el acento causal al reordenamiento de los mercados de materias primas -de las que los beligerantes eran exportadores- a consecuencia de la crisis mundial de la década de 1870.This brief study aims at showing Anthony Gibbs & Sons disposition in supporting the Peruvian monopolistic nitrate project with monetary resources and its Director's influences in the only company which, due its production's capacity, could make the project fail: the Chilean Antofagasta Nitrate and Railway Co. in which Gibbs was the second most important stockholder. According to Chilean government the primary cause of 1879's war was Peru's attempt to monopolize nitrate production. Bolivia, its secret allied since 1873, helped renting and selling him her nitrate fields and imposing a tax on the nitrate exports of the Chilean company in Antofagasta, thus violating the condition stated in a Border Treaty by which Chile had ceded territory. Its recovery through the use of military forcé was the first act

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.

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

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.

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.

An assessment of the thermodynamic behaviour of neptunium in water and model groundwaters from 25 to 150 degrees C

International Nuclear Information System (INIS)

Lemire, R.J.

1984-03-01

Standard molal Gibbs energy of formation and entropy data for simple neptunium solids and aqueous neptunium complexes with OH - , Cl - , F - , CO 3 2- , PO 4 3- , SO-4 2- and Na + have been critically reviewed. Selected values are used with estimated heat capacity values to derive self-consistent analytical expressions for the temperature dependence of the standard molal Gibbs energies of formation of the species from 25 to 150 degrees C. The Gibbs energies have been used to evaluate the effect of different concentrations of ligands on the solubility of neptunium solids as a function of temperature. Potential-pH diagrams are given for neptunium in pure water and in two model groundwaters. Important deficiencies in the available thermodynamic data for neptunium species are discussed

Statistical mechanics and the description of the early universe II. Principle of detailed balance and primordial 4He formation

DEFF Research Database (Denmark)

Pessah, Martin Elias; F. Torres, Diego

2001-01-01

If the universe is slightly non-extensive, and the distribution functions are not exactly given by those of Boltzmann-Gibbs, the primordial production of light elements will be non-trivially modified. In particular, the principle of detailed balance (PDB), of fundamental importance in the standard...... the formation of Helium and Deuterium, and study the kind of deviation one could expect from the standard regime. The correction to the capture time, the moment in which Deuterium can no longer be substantially photo-disintegrated, is also presented. This allows us to take into account the process of the free...

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.

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.)

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....

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.

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.

Improved modification for the density-functional theory calculation of thermodynamic properties for C-H-O composite compounds.

Science.gov (United States)

Liu, Min Hsien; Chen, Cheng; Hong, Yaw Shun

2005-02-08

A three-parametric modification equation and the least-squares approach are adopted to calibrating hybrid density-functional theory energies of C(1)-C(10) straight-chain aldehydes, alcohols, and alkoxides to accurate enthalpies of formation DeltaH(f) and Gibbs free energies of formation DeltaG(f), respectively. All calculated energies of the C-H-O composite compounds were obtained based on B3LYP6-311++G(3df,2pd) single-point energies and the related thermal corrections of B3LYP6-31G(d,p) optimized geometries. This investigation revealed that all compounds had 0.05% average absolute relative error (ARE) for the atomization energies, with mean value of absolute error (MAE) of just 2.1 kJ/mol (0.5 kcal/mol) for the DeltaH(f) and 2.4 kJ/mol (0.6 kcal/mol) for the DeltaG(f) of formation.

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.

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.

Simultaneous alignment and clustering of peptide data using a Gibbs sampling approach

DEFF Research Database (Denmark)

Andreatta, Massimo; Lund, Ole; Nielsen, Morten

2013-01-01

Motivation: Proteins recognizing short peptide fragments play a central role in cellular signaling. As a result of high-throughput technologies, peptide-binding protein specificities can be studied using large peptide libraries at dramatically lower cost and time. Interpretation of such large...... peptide datasets, however, is a complex task, especially when the data contain multiple receptor binding motifs, and/or the motifs are found at different locations within distinct peptides.Results: The algorithm presented in this article, based on Gibbs sampling, identifies multiple specificities...... of unaligned peptide datasets of variable length. Example applications described in this article include mixtures of binders to different MHC class I and class II alleles, distinct classes of ligands for SH3 domains and sub-specificities of the HLA-A*02:01 molecule.Availability: The Gibbs clustering method...

Mechanical alloying of Cu-xCr (x = 3, 5 and 8 wt.%) alloys

International Nuclear Information System (INIS)

Aguilar, C.; Ordonez, S.; Guzman, D.; Rojas, P.A.

2010-01-01

This work studies the structural evolution of Cu-xCr (x = 3, 5 and 8 wt.%) alloys processed by mechanical alloying using X-ray diffraction profiles, scanning microscopy and microhardness analysis. X-ray diffraction analysis using the modified Williamson-Hall and Warren-Averbach methods were used to determine structural properties, such as crystallite size, stacking fault probability and energy, dislocation density, lattice parameters and crystallite size distribution of metallic powder as a function of Cr amount and milling time. Lattice defects increase the Gibbs free energy and the Gibbs free energy curves shift upward, therefore the solubility limit change.

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.

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.)

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.

Relation between the characteristic molecular volume and hydrophobicity of nonpolar molecules

Energy Technology Data Exchange (ETDEWEB)

Sedov, Igor A., E-mail: igor_sedov@inbox.ru; Solomonov, Boris N., E-mail: boris.solomonov@ksu.r

2010-09-15

Experimental values of the Gibbs free energies of hydration for a set of nonpolar or very slightly polar compounds are analyzed in order to investigate how does the hydrophobic effect depend on molecular structure and shape. The contribution due to the hydrophobic effect is evaluated using a method we suggested previously. A number of values of the Gibbs free energies of solvation in dimethyl sulfoxide and in hexadecane, which are required for calculation, were determined by gas chromatographic headspace analysis. It is found that the Gibbs hydrophobic effect energy is linearly dependent on characteristic molecular volume for a large variety of solutes with branched and unbranched carbon chains, different functional groups and atomic composition. Molecular structure and shape do not significantly affect the hydrophobicity of chemical species, and molecular volume is a main factor determining it.

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

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.

Thermodynamics of solvation and solvophobic effect in formamide

International Nuclear Information System (INIS)

Sedov, I.A.; Stolov, M.A.; Solomonov, B.N.

2013-01-01

Highlights: • Enthalpies of solution of apolar organic compounds in formamide were measured. • Gibbs free energies of solution were experimentally determined. • Influence of the solvophobic effect on solvation thermodynamics was studied. • Thermodynamic features of solutions in formamide resemble those of aqueous solutions. -- Abstract: Using semi-adiabatic calorimetry, we measured the enthalpies of solution for various low-polar compounds including alkanes, aromatic hydrocarbons and their halogenated derivatives in formamide at temperature of 298 K. For the same compounds, the values of limiting activity coefficients in formamide were determined using GC headspace analysis at 298 K, and Gibbs free energies of solution and solvation were calculated. Based on these data and the available literature values of the Gibbs free energy of solvation in formamide for a number of other low-polar solutes, a study of the solvophobic effect in this solvent is performed, and its resemblance to the hydrophobic effect in aqueous solutions is demonstrated. It is shown that the contribution of the solvophobic effect into the solvation Gibbs free energy in formamide is much higher than that in aliphatic alcohols, but lower than that in water. Like in water, the magnitude of this contribution for different solutes linearly increases with the solute molecular volume. Solvophobic effect also significantly affects the enthalpies of dissolution in formamide, causing them to be more negative in the case of alkanes and more positive in the case of arenes

Uniqueness of Gibbs Measure for Models with Uncountable Set of Spin Values on a Cayley Tree

International Nuclear Information System (INIS)

Eshkabilov, Yu. Kh.; Haydarov, F. H.; Rozikov, U. A.

2013-01-01

We consider models with nearest-neighbor interactions and with the set [0, 1] of spin values, on a Cayley tree of order K ≥ 1. It is known that the ‘splitting Gibbs measures’ of the model can be described by solutions of a nonlinear integral equation. For arbitrary k ≥ 2 we find a sufficient condition under which the integral equation has unique solution, hence under the condition the corresponding model has unique splitting Gibbs measure.

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.

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.

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

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.

Enhanced free energy of extraction of Eu3+ and Am3+ ions towards diglycolamide appended calix[4]arene: insights from DFT-D3 and COSMO-RS solvation models.

Science.gov (United States)

Ali, Sk Musharaf

2017-08-22

Density functional theory in conjunction with COSMO and COSMO-RS solvation models employing dispersion correction (DFT-D3) has been applied to gain an insight into the complexation of Eu 3+ /Am 3+ with diglycolamide (DGA) and calix[4]arene appended diglycolamide (CAL4DGA) in ionic liquids by studying structures, energetics, thermodynamics and population analysis. The calculated Gibbs free energy for both Eu 3+ and Am 3+ ions with DGA was found to be smaller than that with CAL4DGA. The entropy of complexation was also found to be reduced to a large extent with DGA compared to complexation with CAL4DGA. The solution phase free energy was found to be negative and was higher for Eu 3+ ion. The entropy of complexation was not only found to be further reduced but also became negative in the case of DGA alone. Though the entropy was found to be negative it could not outweigh the high negative enthalpic contribution. The same trend was observed in the solution where the free energy of extraction, ΔG, for Eu 3+ ions was shown to be higher than that for Am 3+ ions towards free DGA. But the values of ΔG and ΔΔG(= ΔG Eu -ΔG Am ) were found to be much higher with CAL4DGA (-12.58 kcal mol -1 ) in the presence of nitrate ions compared to DGA (-1.69 kcal mol -1 ) due to enhanced electronic interaction and positive entropic contribution. Furthermore, both the COSMO and COSMO-RS models predict very close values of ΔΔΔG (= ΔΔG CAL4DGA - ΔΔG nDGA ), indicating that both solvation models could be applied for evaluating the metal ion selectivity. The value of the reaction free energy was found to be higher after dispersion correction. The charge on the Eu and Am atoms for the complexes with DGA and CAL4DGA indicates the charge-dipole type interaction leading to strong binding energy. The present theoretical results support the experimental findings and thus might be of importance in the design of functionalized ligands.

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

Molecular interaction of pinic acid with sulfuric acid

DEFF Research Database (Denmark)

Elm, Jonas; Kurtén, Theo; Bilde, Merete

2014-01-01

We investigate the molecular interactions between the semivolatile α-pinene oxidation product pinic acid and sulfuric acid using computational methods. The stepwise Gibbs free energies of formation have been calculated utilizing the M06-2X functional, and the stability of the clusters is evaluated...... cluster. The involvement of more than one pinic acid molecule in a single cluster is observed to lead to the formation of favorable (pinic acid)2(H2SO4) and (pinic acid)2(H2SO4)2 clusters. The identified most favorable growth paths starting from a single pinic acid molecule lead to closed structures...

Solid-state e.m.f. and calorimetric measurements on Cs2Cr2O7(I)

International Nuclear Information System (INIS)

Venugopal, V.; Iyer, V.S.; Agarwal, R.; Roy, K.N.; Prasad, R.; Sood, D.D.

1987-01-01

The standard molar Gibbs free energy of formation of Cs 2 Cr 2 O 7 (1) has been determined in the temperature range 797 to 874 K, using a solid-oxide-electrolyte galvanic cell. The melting and transition temperatures, molar enthalpies of fusion and of transition of the same caesium compound were determined in the temperature range 662 to 826 K, using a high temperature Calvet microcalorimeter. Results on the standard molar enthalpy of formation of Cs 2 Cr 2 O 7 at 298.15 K are in good agreement with those reported by other workers. (U.K.)

The effect of different oxygen exchange layers on TaO x based RRAM devices

Science.gov (United States)

Alamgir, Zahiruddin; Holt, Joshua; Beckmann, Karsten; Cady, Nathaniel C.

2018-01-01

In this work, we investigated the effect of the oxygen exchange layer (OEL) on the resistive switching properties of TaO x based memory cells. It was found that the forming voltage, SET-RESET voltage, R off, R on and retention properties are strongly correlated with the oxygen scavenging ability of the OEL, and the resulting oxygen vacancy formation ability of this layer. Higher forming voltage was observed for OELs having lower electronegativity/lower Gibbs free energy for oxide formation, and devices fabricated with these OELs exhibited an increased memory window, when using similar SET-RESET voltage range.

Theoretical study of the possibility of glycin with thiotriazoline complexes formation

Directory of Open Access Journals (Sweden)

L. I. Kucherenko

2017-10-01

Full Text Available Brain strokes are widely spread all over the world and are among the most dangerous for the population. Often it leads to death, complete or partial loss of ability to work. The correction of imbalance of Excitatory and inhibitory neurotransmitter systems by activation of natural inhibitory processes is a promising direction of primary neuroprotection in cerebral ischemia. Particular attention is drawn to the natural inhibitory neurotransmitter – glycine and its role in the mechanisms of acute cerebral ischemia. There are data on the ability of the thiotriazoline antioxidant to potentiate the therapeutic effect of neurometabolic cerebroprotectors. Therefore, the creation of new combined preparation based on glycine with thiotriazoline is important today. Objective: to study the structure, and estimate the energy of formation and geometric characteristics of the intermolecular hydrogen bonds for complexes which are formed with glycine, 3-methyl-1,2,4-triazolyl-5-thioacetate (MTTA and morpholine. Method of calculation. The initial approximation to the structure of the complexes was obtained with the help of molecular docking procedure using the AutoDock Vina program. The resulting three-component complexes were preliminarily optimized by the semiempirical PM7 method, taking into account the outward influences, which was simulated by the COSMO method. The calculations were carried out using the MOPAC2012 program. The complexes were optimized using the density functional method with the empirical dispersion correction B97-D3/SVP+COSMO (Water using geometric correction for the incompleteness of the gCP basic set. A more accurate calculation of the solvation energy was carried out by SMD method. Calculations by the density functional method were carried out using the ORCA 3.0.3 program. The energy of formation of complexes in solution was calculated as the difference between the free Gibbs energies of the solvated complex and its individual solvated

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.

Biochemical thermodynamics: applications of Mathematica.

Science.gov (United States)

Alberty, Robert A

2006-01-01

The most efficient way to store thermodynamic data on enzyme-catalyzed reactions is to use matrices of species properties. Since equilibrium in enzyme-catalyzed reactions is reached at specified pH values, the thermodynamics of the reactions is discussed in terms of transformed thermodynamic properties. These transformed thermodynamic properties are complicated functions of temperature, pH, and ionic strength that can be calculated from the matrices of species values. The most important of these transformed thermodynamic properties is the standard transformed Gibbs energy of formation of a reactant (sum of species). It is the most important because when this function of temperature, pH, and ionic strength is known, all the other standard transformed properties can be calculated by taking partial derivatives. The species database in this package contains data matrices for 199 reactants. For 94 of these reactants, standard enthalpies of formation of species are known, and so standard transformed Gibbs energies, standard transformed enthalpies, standard transformed entropies, and average numbers of hydrogen atoms can be calculated as functions of temperature, pH, and ionic strength. For reactions between these 94 reactants, the changes in these properties can be calculated over a range of temperatures, pHs, and ionic strengths, and so can apparent equilibrium constants. For the other 105 reactants, only standard transformed Gibbs energies of formation and average numbers of hydrogen atoms at 298.15 K can be calculated. The loading of this package provides functions of pH and ionic strength at 298.15 K for standard transformed Gibbs energies of formation and average numbers of hydrogen atoms for 199 reactants. It also provides functions of temperature, pH, and ionic strength for the standard transformed Gibbs energies of formation, standard transformed enthalpies of formation, standard transformed entropies of formation, and average numbers of hydrogen atoms for 94

Solvation thermodynamics of L-cystine, L-tyrosine, and L-leucine in aqueous-electrolyte media

Science.gov (United States)

Roy, Sanjay; Guin, Partha Sarathi; Mahali, Kalachand; Dolui, Bijoy Krishna

2017-12-01

Solubilities of L-cystine, L-tyrosine, and L-leucine in aqueous NaCl media at 298.15 K have been studied. Indispensable and related solvent parameters such as molar mass, molar volume, etc., were also determined. The results are used to evaluate the standard transfer Gibbs free energy, cavity forming enthalpy of transfer, cavity forming transfer Gibbs free energy and dipole-dipole interaction effects during the course of solvation. Various weak interactions involving solute-solvent or solvent-solvent molecules were characterized in order to find their role on the solvation of these amino acids.

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.

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.

The Energetics of Streptococcal Enolase Octamer Formation: The Quantitative Contributions of the Last Eight Amino Acids at the Carboxy-Terminus.

Directory of Open Access Journals (Sweden)

Jack A Kornblatt

Full Text Available The enolase produced by Streptococcus pyogenes is a homo-octamer whose overall shape resembles that of a donut. The octamer is best described as a tetramer of dimers. As such, it contains two types of interfaces. The first is common to almost all enolases as most enolases that have been studied are dimers. The second is unique to the octamers and includes residues near the carboxy-terminus. The primary sequence of the enolase contains 435 residues with an added 19 as an N-terminal hexahistine tag. We have systematically truncated the carboxy-terminus, individually removing the first 8 residues. This gave rise to a series of eight structures containing respectively, 435, 434, 433, 432, 431, 430, 429 and 427 residues. The truncations cause the protein to gradually dissociate from octamers to enzymatically inactive monomers with very small amounts of intermediate tetramers and dimers. We have evaluated the contributions of the missing residues to the monomer/octamer equilibrium using a combination of analytical ultracentrifugation and activity assays. For the dissociation reaction, octamer 8 monomer truncation of all eight C-terminal residues resulted in a diminution in the standard Gibbs energy of dissociation of about 59 kJ/mole of octamer relative to the full length protein. Considering that this change is spread over eight subunits, this translates to a change in standard Gibbs interaction energy of less than 8 kJ/mole of monomer distributed over the eight monomers. The resulting proteins, containing 434, 433, 432, 431, 430, 429 and 427 residues per monomer, showed intermediate free energies of dissociation. Finally, three other mutations were introduced into our reference protein to establish how they influenced the equilibrium. The main importance of this work is it shows that for homo-multimeric proteins a small change in the standard Gibbs interaction energy between subunits can have major physiological effects.

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

Inverse problems with non-trivial priors: efficient solution through sequential Gibbs sampling

DEFF Research Database (Denmark)

Hansen, Thomas Mejer; Cordua, Knud Skou; Mosegaard, Klaus

2012-01-01

Markov chain Monte Carlo methods such as the Gibbs sampler and the Metropolis algorithm can be used to sample solutions to non-linear inverse problems. In principle, these methods allow incorporation of prior information of arbitrary complexity. If an analytical closed form description of the prior...... is available, which is the case when the prior can be described by a multidimensional Gaussian distribution, such prior information can easily be considered. In reality, prior information is often more complex than can be described by the Gaussian model, and no closed form expression of the prior can be given....... We propose an algorithm, called sequential Gibbs sampling, allowing the Metropolis algorithm to efficiently incorporate complex priors into the solution of an inverse problem, also for the case where no closed form description of the prior exists. First, we lay out the theoretical background...

Uniqueness of Gibbs states and global Markov property for Euclidean fields

International Nuclear Information System (INIS)

Albeverio, S.; Hoeegh-Krohn, R.

1981-01-01

The authors briefly discuss the proof of the uniqueness of solutions of the DLR equations (uniqueness of Gibbs states) in the class of regular generalized random fields (in the sense of having second moments bounded by those of some Euclidean field), for the Euclidean fields with trigonometric interaction. (Auth.)

Thermodynamical modeling of nuclear glasses: coexistence of amorphous phases

International Nuclear Information System (INIS)

Adjanor, G.

2007-11-01

Investigating the stability of borosilicate glasses used in the nuclear industry with respect to phase separation requires to estimate the Gibbs free energies of the various phases appearing in the material. In simulation, using current computational resources, a direct state-sampling of a glassy system with respect to its ensemble statistics is not ergodic and the estimated ensemble averages are not reliable. Our approach consists in generating, at a given cooling rate, a series of quenches, or paths connecting states of the liquid to states of the glass, and then in taking into account the probability to generate the paths leading to the different glassy states in ensembles averages. In this way, we introduce a path ensemble formalism and calculate a Landau free energy associated to a glassy meta-basin. This method was validated by accurately mapping the free energy landscape of a 38-atom glassy cluster. We then applied this approach to the calculation of the Gibbs free energies of binary amorphous Lennard-Jones alloys, and checked the correlation between the observed tendencies to order or to phase separate and the computed Gibbs free energies. We finally computed the driving force to phase separation in a simplified three-oxide nuclear glass modeled by a Born-Mayer-Huggins potential that includes a three-body term, and we compared the estimated quantities to the available experimental data. (author)

Thermodynamical modeling of nuclear glasses: coexistence of amorphous phases; Modelisation thermodynamique des verres nucleaires: coexistence entre phases amorphes

Energy Technology Data Exchange (ETDEWEB)

Adjanor, G

2007-11-15

Investigating the stability of borosilicate glasses used in the nuclear industry with respect to phase separation requires to estimate the Gibbs free energies of the various phases appearing in the material. In simulation, using current computational resources, a direct state-sampling of a glassy system with respect to its ensemble statistics is not ergodic and the estimated ensemble averages are not reliable. Our approach consists in generating, at a given cooling rate, a series of quenches, or paths connecting states of the liquid to states of the glass, and then in taking into account the probability to generate the paths leading to the different glassy states in ensembles averages. In this way, we introduce a path ensemble formalism and calculate a Landau free energy associated to a glassy meta-basin. This method was validated by accurately mapping the free energy landscape of a 38-atom glassy cluster. We then applied this approach to the calculation of the Gibbs free energies of binary amorphous Lennard-Jones alloys, and checked the correlation between the observed tendencies to order or to phase separate and the computed Gibbs free energies. We finally computed the driving force to phase separation in a simplified three-oxide nuclear glass modeled by a Born-Mayer-Huggins potential that includes a three-body term, and we compared the estimated quantities to the available experimental data. (author)

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.

Formation of vacancy clusters in tungsten crystals under hydrogen-rich condition

Energy Technology Data Exchange (ETDEWEB)

Kato, Daiji, E-mail: kato.daiji@nifs.ac.jp [National Institute for Fusion Science, 322-6 Oroshi-cho, Toki, Gifu 509-5292 (Japan); Iwakiri, Hirotomo, E-mail: iwakiri@edu.u-ryukyu.ac.jp [University of the Ryukyus, Okinawa 903-0213 (Japan); Morishita, Kazunori, E-mail: morishita@iae.kyoto-u.ac.jp [Institute of Advanced Energy, Kyoto University, Kyoto 611-0011 (Japan)

2011-10-01

Di-vacancy formation assisted by hydrogen trapping is studied in terms of nucleation free-energies evaluated with density functional theory. Calculations give binding energies for single hydrogen atom as first- and second-nearest-neighbor of di-vacancies of 1.80 and 2.15 eV, respectively, which are significantly larger than that for mono-vacancies. At elevated atomic concentrations of interstitial hydrogen atoms, evaluated nucleation free-energies indicate that the hydrogen assisted di-vacancy formation becomes more favorable. It is suggested that the formation would be preceded by VH cluster formation.

Formation of vacancy clusters in tungsten crystals under hydrogen-rich condition

International Nuclear Information System (INIS)

Kato, Daiji; Iwakiri, Hirotomo; Morishita, Kazunori

2011-01-01

Di-vacancy formation assisted by hydrogen trapping is studied in terms of nucleation free-energies evaluated with density functional theory. Calculations give binding energies for single hydrogen atom as first- and second-nearest-neighbor of di-vacancies of 1.80 and 2.15 eV, respectively, which are significantly larger than that for mono-vacancies. At elevated atomic concentrations of interstitial hydrogen atoms, evaluated nucleation free-energies indicate that the hydrogen assisted di-vacancy formation becomes more favorable. It is suggested that the formation would be preceded by VH cluster formation.

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…

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.

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).

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).

Thermochemical properties of lanthanoid-iron-perovskite at high temperatures. [La, Nd, Sm, Eu, Gd, Tb, Dy

Energy Technology Data Exchange (ETDEWEB)

Katsura, T; Kitayama, K; Sugihara, T [Tokyo Inst. of Tech. (Japan). Faculty of Science; Kimizuka, N

1975-06-01

The standard Gibbs energy of formation of C/sup -/FeO/sub 3/(C/sup -/=La, Nd, Sm, Eu, Gd, Tb, and Dy) from metallic iron, C/sub 2//sup -/O/sub 3/, and oxygen has been determined at temperatures from 1473 to 1673 K. Based on the free-energy data, the heat of reaction and the entropy change resulting from the reaction have been calculated. The values of the heat of reaction of LaFeO/sub 3/, NdFeO/sub 3/, SmFeO/sub 3/, EuFeO/sub 3/, and GdFeO/sub 3/ (the first group) were identical, - 107 kcal/mol, at the present temperature interval. However, the values of the heat of reaction of TbFeO/sub 3/ and DyFeO/sub 3/ (the second group) decreased with an increase in the temperature. The entropy change of each reaction in the first group was constant, independent of the temperature, and each value decreased in the sequence from LaFeO/sub 3/ to GdFeO/sub 3/. The entropy change of the second group decreased with an increase in the temperature. The change of the standard Gibbs energy was intimately related to the ionic radii of C/sup -/-ions, and the relationship between the Gibbs energy and the tolerance factor has been clarified.

Study on the Formation and Precipitation Mechanism of Mn5Si3 Phase in the MBA-2 Brass Alloy

Science.gov (United States)

Li, Hang; Jie, Jinchuan; Zhang, Pengchao; Jia, Chunxu; Wang, Tongmin; Li, Tingju

2016-06-01

Mn5Si3 is an attractive dispersion in the special brass, owing to its high hardness and high wear resistance. In the present study, synchrotron X-ray radiography and rapid cooling were applied to investigate the formation mechanism of Mn5Si3 phase in the MBA-2 brass alloy. The primary Mn5Si3 phase is proved to exist stably in the alloy melt and nucleate from the melt at temperatures above 1373 K (1100 °C). In addition, the precipitation mechanism of Mn5Si3 phase is addressed systematically by the isothermal heat treatment. The Mn5Si3 particles are observed to precipitate from the matrix at temperatures above 1023 K (750 °C), and a crystallographic orientation relationship is found between the precipitated Mn5Si3 particle and β phase: (110)_{β } //(1overline{1} 00)_{{{{Mn}}5 {{Si}}3 }} and [overline{1} 11]_{β } //[11overline{2} overline{2} ]_{{{{Mn}}5 {{Si}}3 }} . However, the precipitation of Mn5Si3 phase is thermodynamically inhibited at lower temperatures, which can be ascribed to the increase in the Gibbs free energy of formation of Mn5Si3 with decreasing the temperature.

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

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.

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.

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)...

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.

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.

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.

Gaussian free turbulence: structures and relaxation in plasma models

International Nuclear Information System (INIS)

Gruzinov, A.V.

1993-01-01

Free-turbulent relaxation in two-dimensional MHD, the degenerate Hasegawa-Mima equation and a two-dimensional microtearing model are studied. The Gibbs distributions of these three systems can be completely analyzed, due to the special structure of their invariants and due to the existence of ultraviolet catastrophe. The free-turbulent field is seen to be a sum of a certain coherent structure (statistical attractor) and Gaussian random noise. Two-dimensional current layers are shown to be statistical attractors in 2D MHD. (author)

Determination of formation enthalpies of incongruently fusing compounds

Energy Technology Data Exchange (ETDEWEB)

Kesler, Ya.A.; Cheshnitskij, S.M.; Fotiev, A.A.; Tret' yakov, Yu.D.

1985-04-01

Using the method of drop-calorimetry i.e. drop into the calorimeter cell being at the specified temperature of the specimen thermostated at 298 K, for studying reactions of peritectic decomposition of compounds for determining their formation enthalpies is considered. The measurements have been performed at 973 K using high temperature double microcalorimeter. The values ..delta..H/sub 1/=(367.0 +- 2.8) kJ/mol and ..delta..H/sub 2/=)343.9 +- 3.1) kJ/mol are obtained as a result of two series of measurements (6 experiments in each). The advantage of the described technique consists in the fact that the value of enthalpy of compound formation is obtained as a result of direct calorimetric measurements while in the e.m.f. method this value is determined as a coefficient in the Gibbs energy temperature dependence. The method is simple and does not require much time (one measurement takes 30-40 min).

Determination of formation enthalpies of incongruently fusing compounds

International Nuclear Information System (INIS)

Kesler, Ya.A.; Cheshnitskij, S.M.; Fotiev, A.A.; Tret'yakov, Yu.D.

1985-01-01

Using the method of drop-calorimetry i.e. drop into the calorimeter cell being at the specified temperature of the specimen thermostated at 298 K, for studying reactions of peritectic decomposition of compounds for determining their formation enthalpies is considered. The measurements have been performed at 973 K using high temperature double microcalorimeter. The values ΔH 1 =(367.0+-2.8) kJ/mol and ΔH 2 =)343.9+-3.1) kJ/mol are obtained as a result of two series of measurements (6 experiments in each). The advantage of the described technique consists in the fact that the value of enthalpy of compound formation is obtained as a result of direct calorimetric measurements while in the e.m.f. method this value is determined as a coefficient in the Gibbs energy temperature dependence. The method is simple and does not require much time (one measurement takes 30-40 min)

The importance of the photosynthetic Gibbs effect in the elucidation of the Calvin-Benson-Bassham cycle.

Science.gov (United States)

Ebenhöh, Oliver; Spelberg, Stephanie

2018-02-19

The photosynthetic carbon reduction cycle, or Calvin-Benson-Bassham (CBB) cycle, is now contained in every standard biochemistry textbook. Although the cycle was already proposed in 1954, it is still the subject of intense research, and even the structure of the cycle, i.e. the exact series of reactions, is still under debate. The controversy about the cycle's structure was fuelled by the findings of Gibbs and Kandler in 1956 and 1957, when they observed that radioactive 14 CO 2 was dynamically incorporated in hexoses in a very atypical and asymmetrical way, a phenomenon later termed the 'photosynthetic Gibbs effect'. Now, it is widely accepted that the photosynthetic Gibbs effect is not in contradiction to the reaction scheme proposed by CBB, but the arguments given have been largely qualitative and hand-waving. To fully appreciate the controversy and to understand the difficulties in interpreting the Gibbs effect, it is illustrative to illuminate the history of the discovery of the CBB cycle. We here give an account of central scientific advances and discoveries, which were essential prerequisites for the elucidation of the cycle. Placing the historic discoveries in the context of the modern textbook pathway scheme illustrates the complexity of the cycle and demonstrates why especially dynamic labelling experiments are far from easy to interpret. We conclude by arguing that it requires sound theoretical approaches to resolve conflicting interpretations and to provide consistent quantitative explanations. © 2018 The Author(s).

Carbohydrates in thermophile metabolism: calculation of the standard molal thermodynamic properties of aqueous pentoses and hexoses at elevated temperatures and pressures

Science.gov (United States)

Amend, Jan P.; Plyasunov, Andrey V.

2001-11-01

Experimental thermodynamic data for aqueous organic compounds can be combined with the revised Helgeson-Kirkham-Flowers (HKF) equations of state to generate parameters that can be used to estimate standard molal properties as functions of temperature and pressure. In this study, we regressed thermodynamic data for aqueous carbohydrates at temperatures up to 393 K reported in the literature to permit the calculation of the apparent standard molal Gibbs free energies and enthalpies of formation (ΔGo and ΔHo, respectively) and the standard molal entropies (S2o), heat capacities (CP,2o), and volumes (V2o) to 423 K and several hundred MPa of aqueous C5 aldoses (ribose, arabinose, xylose, lyxose) and C5 ketoses (ribulose, xylulose) as well as C6 aldoses (glucose, mannose, galactose) and C6 ketoses (fructose, sorbose). Values of ΔGo for these 11 aqueous carbohydrates are given as a function of temperature at the saturated water vapor pressure (PSAT) and at 50 MPa. Values of ΔGo for aqueous glucose are then combined with those of other aqueous organic and inorganic compounds to calculate values of the standard molal Gibbs free energies of 13 fermentation and respiration reactions (ΔGro) known or likely to be carried out by thermophilic microorganisms. Finally, values of the overall Gibbs free energies of these reactions (ΔGr) are calculated at the temperature, pressure, and chemical composition that obtain in the hydrothermal fluids of Vulcano Island, southern Italy, a site that is widely known for its tremendous diversity of organisms able to live at high temperatures. At likely activities of aqueous glucose, it is shown that thermophiles in the hot springs of Vulcano at 373 K and ∼0.1 MPa can gain between 400 and 3000 kJ per mole of glucose fermented or respired.

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.

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.

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.

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

Gibbs paradox of entropy of mixing experimental facts. Its rejection, and the theoretical consequences

International Nuclear Information System (INIS)

Lin, Shu-Kun

1996-01-01

Gibbs paradox statement of entropy of mixing has been regarded as the theoretical foundation of statistical mechanics, quantum theory and biophysics. However, all the relevant chemical experimental observations and logical analyses indicate that the Gibbs paradox statement is false. I prove that this statement is wrong: Gibbs paradox statement implies that entropy decreases with the increase in symmetry (as represented by a symmetry number σ; see any statistical mechanics textbook). From group theory any system has at least a symmetry number σ=1 which is the identity operation for a strictly asymmetric system. It follows that the entropy of a system is equal to, or less than, zero. However, from either von Neumann-Shannon entropy formula (S(w) =-Σ ω in p 1 ) or the Boltzmann entropy formula (S = in w) and the original definition, entropy is non-negative. Therefore, this statement is false. It should not be a surprise that for the first time, many outstanding problems such as the validity of Pauling's resonance theory, the explanation of second order phase transition phenomena, the biophysical problem of protein folding and the related hydrophobic effect, etc., can be solved. Empirical principles such as Pauli principle (and Hund's rule) and HSAB principle, etc., can also be given a theoretical explanation

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

Improved prediction of MHC class I and class II epitopes using a novel Gibbs sampling approach

DEFF Research Database (Denmark)

Nielsen, Morten; Lundegaard, Claus; Worning, Peder

2004-01-01

Prediction of which peptides will bind a specific major histocompatibility complex (MHC) constitutes an important step in identifying potential T-cell epitopes suitable as vaccine candidates. MHC class II binding peptides have a broad length distribution complicating such predictions. Thus......, identifying the correct alignment is a crucial part of identifying the core of an MHC class II binding motif. In this context, we wish to describe a novel Gibbs motif sampler method ideally suited for recognizing such weak sequence motifs. The method is based on the Gibbs sampling method, and it incorporates...

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).

Ion-specific weak adsorption of salts and water/octanol transfer free energy of a model amphiphilic hexa-peptide

International Nuclear Information System (INIS)

Dejugnat, Ch.; Dufreche, J.F.; Zemb, Th.; Dejugnat, Ch.

2011-01-01

An amphiphilic hexa-peptide 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 hexa-peptide 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. (authors)

Thermodynamic investigations of oxyfluoride of thorium and uranium

International Nuclear Information System (INIS)

Mukherjee, Sumanta; Dash, Smruti; Mukerjee, S.K.; Ramakumar, K.L.

2015-01-01

The standard molar Gibbs energy of formation of ThOF_2(s) and UO_2F_2(s) has been determined using an e.m.f. technique. For this purpose, separate fluoride cell has been constructed using CaF_2(s) as the solid electrolyte. From the measured e.m.f. values and required Gibbs energy data available in the literature, Δ_fG"o_m(T) for these oxyfluorides has been calculated. The enthalpy of formation of ThOF_2(s) and UO_2F_2(s) at 298.15 K has been calculated from the experimentally measured Gibbs energy data using the second and the third law methods. To determine the stability domains of ThOF_2(s) and UO_2F_2(s), the phase diagram and chemical potential diagrams of Th–F–O and U–F–O systems were calculated by the CALPHAD method and FactSage software. These calculations can be used to predict the oxygen partial pressures and the temperature domains in which thorium and uranium oxyfluorides might be formed in the molten salt medium. - Highlights: • The Gibbs energies of formation of ThOF_2(s) and UO_2F_2(s) have been measured using e.m.f. technique. • The Δ_fH"o_m(UO_2F_2,s,298.15 K) derived from the measured Gibbs energy data is reasonably agreeing with that directly measured from that of solution calorimeter. • The chemical potential diagram of Th–F–O and U–F–O systems have been calculated. • The oxygen impurity in the fuel coolant salt mixture will first form thorium oxyfluoride. • The formation of UO_2F_2(s) in the molten salt can be prevented by keeping Δμ_O_2 is greater – 293.2 kJ mol"−"1 at 800 K.