eQuilibrator--the biochemical thermodynamics calculator.

PubMed

Flamholz, Avi; Noor, Elad; Bar-Even, Arren; Milo, Ron

2012-01-01

The laws of thermodynamics constrain the action of biochemical systems. However, thermodynamic data on biochemical compounds can be difficult to find and is cumbersome to perform calculations with manually. Even simple thermodynamic questions like 'how much Gibbs energy is released by ATP hydrolysis at pH 5?' are complicated excessively by the search for accurate data. To address this problem, eQuilibrator couples a comprehensive and accurate database of thermodynamic properties of biochemical compounds and reactions with a simple and powerful online search and calculation interface. The web interface to eQuilibrator (http://equilibrator.weizmann.ac.il) enables easy calculation of Gibbs energies of compounds and reactions given arbitrary pH, ionic strength and metabolite concentrations. The eQuilibrator code is open-source and all thermodynamic source data are freely downloadable in standard formats. Here we describe the database characteristics and implementation and demonstrate its use.

eQuilibrator—the biochemical thermodynamics calculator

PubMed Central

Flamholz, Avi; Noor, Elad; Bar-Even, Arren; Milo, Ron

2012-01-01

The laws of thermodynamics constrain the action of biochemical systems. However, thermodynamic data on biochemical compounds can be difficult to find and is cumbersome to perform calculations with manually. Even simple thermodynamic questions like ‘how much Gibbs energy is released by ATP hydrolysis at pH 5?’ are complicated excessively by the search for accurate data. To address this problem, eQuilibrator couples a comprehensive and accurate database of thermodynamic properties of biochemical compounds and reactions with a simple and powerful online search and calculation interface. The web interface to eQuilibrator (http://equilibrator.weizmann.ac.il) enables easy calculation of Gibbs energies of compounds and reactions given arbitrary pH, ionic strength and metabolite concentrations. The eQuilibrator code is open-source and all thermodynamic source data are freely downloadable in standard formats. Here we describe the database characteristics and implementation and demonstrate its use. PMID:22064852

Development of a critically evaluated thermodynamic database for the systems containing alkaline-earth oxides

NASA Astrophysics Data System (ADS)

Shukla, Adarsh

In a thermodynamic system which contains several elements, the phase relationships among the components are usually very complex. Especially, systems containing oxides are generally very difficult to investigate owing to the very high experimental temperatures and corrosive action of slags. Due to such difficulties, large inconsistencies are often observed among the available experimental data. In order to investigate and understand the complex phase relationships effectively, it is very useful to develop thermodynamic databases containing optimized model parameters giving the thermodynamic properties of all phases as functions of temperature and composition. In a thermodynamic optimization, adjustable model parameters are calculated using, simultaneously, all available thermodynamic and phase-equilibrium data in order to obtain one set of model equations as functions of temperature and composition. Thermodynamic data, such as activities, can aid in the evaluation of the phase diagrams, and information on phase equilibria can be used to deduce thermodynamic properties. Thus, it is frequently possible to resolve discrepancies in the available data. From the model equations, all the thermodynamic properties and phase diagrams can be back-calculated, and interpolations and extrapolations can be made in a thermodynamically correct manner. The data are thereby rendered self-consistent and consistent with thermodynamic principles, and the available data are distilled into a small set of model parameters, ideal for computer storage. As part of a broader research project at the Centre de Recherche en Calcul Thermochimique (CRCT), Ecole Polytechnique to develop a thermodynamic database for multicomponent oxide systems, this thesis deals with the addition of components SrO and BaO to the existing multicomponent database of the SiO2-B2O3-Al2O 3-CaO-MgO system. Over the years, in collaboration with many industrial companies, a thermodynamic database for the SiO2-B2O 3-Al2O3-CaO-MgO system has been built quite satisfactorily. The aim of the present work was to improve the applicability of this five component database by adding SrO and BaO to it. The databases prepared in this work will be of special importance to the glass and steel industries. In the SiO2-B2O3-Al2O 3-CaO-MgO-BaO-SrO system there are 11 binary systems and 25 ternary systems which contain either BaO or SrO or both. For most of these binary systems, and for none of these ternary systems, is there a previous thermodynamic optimization available in the literature. In this thesis, thermodynamic evaluation and optimization for the 11 binary, 17 ternary and 5 quaternary BaO- and SrO- containing systems in the SiO2-B2O3-Al 2O3-CaO-MgO-BaO-SrO system is presented. All these thermodynamic optimizations were performed based on the experimental data available in the literature, except for the SrO-B2O3-SiO2 system. This latter system was optimized on the basis of a few experimental data points generated in the present work together with the data from the literature. In the present work, all the calculations were performed using the FactSage™ thermochemical software. The Modified Quasichemical Model (MQM), which is capable of taking short-range ordering into account, was used for the liquid phase. All the binary systems were critically evaluated and optimized using available phase equilibrium and thermodynamic data. The model parameters obtained as a result of this simultaneous optimization were used to represent the Gibbs energies of all phases as functions of temperature and composition. Optimized binary model parameters were used to estimate the thermodynamic properties of phases in the ternary systems. Proper “geometric” models were used for these estimations. Ternary phase diagram were calculated and compared with available experimental data. Wherever required, ternary interaction parameters were also added. The first part of this thesis comprises a general literature review on the subject of thermodynamic modeling and experimental techniques for phase diagram determination. The next chapters include the literature review and the thermodynamic optimizations of the various systems. The last part of the thesis is the presentation of experiments performed in the present work, by quenching and EPMA, in the SrO-B2O3-SiO2 system. The experiments were designed to generate the maximum amount of information with the minimum number of experiments using the thermodynamic optimization, based only on the data available in the literature, as a guide. These newly-obtained data improved the (preceding) thermodynamic optimization, based on the experimental data in the literature, of this ternary system.

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

NASA Astrophysics Data System (ADS)

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

2016-12-01

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

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

DOE PAGES

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

2016-12-01

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

Biofuel Database

National Institute of Standards and Technology Data Gateway

Biofuel Database (Web, free access)   This database brings together structural, biological, and thermodynamic data for enzymes that are either in current use or are being considered for use in the production of biofuels.

On the Future of Thermochemical Databases, the Development of Solution Models and the Practical Use of Computational Thermodynamics in Volcanology, Geochemistry and Petrology: Can Innovations of Modern Data Science Democratize an Oligarchy?

NASA Astrophysics Data System (ADS)

Ghiorso, M. S.

2014-12-01

Computational thermodynamics (CT) has now become an essential tool of petrologic and geochemical research. CT is the basis for the construction of phase diagrams, the application of geothermometers and geobarometers, the equilibrium speciation of solutions, the construction of pseudosections, calculations of mass transfer between minerals, melts and fluids, and, it provides a means of estimating materials properties for the evaluation of constitutive relations in fluid dynamical simulations. The practical application of CT to Earth science problems requires data. Data on the thermochemical properties and the equation of state of relevant materials, and data on the relative stability and partitioning of chemical elements between phases as a function of temperature and pressure. These data must be evaluated and synthesized into a self consistent collection of theoretical models and model parameters that is colloquially known as a thermodynamic database. Quantitative outcomes derived from CT reply on the existence, maintenance and integrity of thermodynamic databases. Unfortunately, the community is reliant on too few such databases, developed by a small number of research groups, and mostly under circumstances where refinement and updates to the database lag behind or are unresponsive to need. Given the increasing level of reliance on CT calculations, what is required is a paradigm shift in the way thermodynamic databases are developed, maintained and disseminated. They must become community resources, with flexible and assessable software interfaces that permit easy modification, while at the same time maintaining theoretical integrity and fidelity to the underlying experimental observations. Advances in computational and data science give us the tools and resources to address this problem, allowing CT results to be obtained at the speed of thought, and permitting geochemical and petrological intuition to play a key role in model development and calibration.

Thermodynamic database for the Co-Pr system.

PubMed

Zhou, S H; Kramer, M J; Meng, F Q; McCallum, R W; Ott, R T

2016-03-01

In this article, we describe data on (1) compositions for both as-cast and heat treated specimens were summarized in Table 1; (2) the determined enthalpy of mixing of liquid phase is listed in Table 2; (3) thermodynamic database of the Co-Pr system in TDB format for the research articled entitle Chemical partitioning for the Co-Pr system: First-principles, experiments and energetic calculations to investigate the hard magnetic phase W.

Thermodynamic database for the Co-Pr system

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

Zhou, S. H.; Kramer, M. J.; Meng, F. Q.

2016-01-21

In this article, we describe data on (1) compositions for both as-cast and heat treated specimens were summarized in Table 1; (2) the determined enthalpy of mixing of liquid phase is listed in Table 2; (3) thermodynamic database of the Co-Pr system in TDB format for the research articled entitle Chemical partitioning for the Co-Pr system: First-principles, experiments and energetic calculations to investigate the hard magnetic phase W.

Thermodynamic database for the Co-Pr system

DOE PAGES

Zhou, S. H.; Kramer, M. J.; Meng, F. Q.; ...

2016-03-01

In this article, we describe data on (1) compositions for both as-cast and heat treated specimens were summarized in Table 1; (2) the determined enthalpy of mixing of liquid phase is listed in Table 2; (3) thermodynamic database of the Co-Pr system in TDB format for the research articled entitled ''Chemical partitioning for the Co-Pr system: First-principles, experiments and energetic calculations to investigate the hard magnetic phase W.''

Numerical Mantle Convection Models With a Flexible Thermodynamic Interface

NASA Astrophysics Data System (ADS)

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

2001-12-01

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

Ablation Predictions for Carbonaceous Materials Using Two Databases for Species Thermodynamics

NASA Technical Reports Server (NTRS)

Milos, F. S.; Chen, Y.-K.

2013-01-01

During previous work at NASA Ames Research Center, most ablation predictions were obtained using a species thermodynamics database derived primarily from the JANAF thermochemical tables. However, the chemical equilibrium with applications thermodynamics database, also used by NASA, is considered more up to date. In this work, ablation analyses were performed for carbon and carbon phenolic materials using both sets of species thermodynamics. The ablation predictions are comparable at low and moderate heat fluxes, where the dominant mechanism is carbon oxidation. For high heat fluxes where sublimation is important, the predictions differ, with the chemical equilibrium with applications model predicting a lower ablation rate. The disagreement is greater for carbon phenolic than for carbon, and this difference is attributed to hydrocarbon species that may contribute to the ablation rate. Sample calculations for representative Orion and Stardust environments show significant differences only in the sublimation regime. For Stardust, if the calculations include a nominal environmental uncertainty for aeroheating, then the chemical equilibrium with applications model predicts a range of recession that is consistent with measurements for both heatshield cores.

Thermodynamic Modeling of Hydrogen Storage Capacity in Mg-Na Alloys

PubMed Central

Abdessameud, S.; Mezbahul-Islam, M.; Medraj, M.

2014-01-01

Thermodynamic modeling of the H-Mg-Na system is performed for the first time in this work in order to understand the phase relationships in this system. A new thermodynamic description of the stable NaMgH3 hydride is performed and the thermodynamic models for the H-Mg, Mg-Na, and H-Na systems are reassessed using the modified quasichemical model for the liquid phase. The thermodynamic properties of the ternary system are estimated from the models of the binary systems and the ternary compound using CALPHAD technique. The constructed database is successfully used to reproduce the pressure-composition isotherms for MgH2 + 10 wt.% NaH mixtures. Also, the pressure-temperature equilibrium diagram and reaction paths for the same composition are predicted at different temperatures and pressures. Even though it is proved that H-Mg-Na does not meet the DOE hydrogen storage requirements for onboard applications, the best working temperatures and pressures to benefit from its full catalytic role are given. Also, the present database can be used for thermodynamic assessments of higher order systems. PMID:25383361

Thermodynamic modeling of hydrogen storage capacity in Mg-Na alloys.

PubMed

Abdessameud, S; Mezbahul-Islam, M; Medraj, M

2014-01-01

Thermodynamic modeling of the H-Mg-Na system is performed for the first time in this work in order to understand the phase relationships in this system. A new thermodynamic description of the stable NaMgH3 hydride is performed and the thermodynamic models for the H-Mg, Mg-Na, and H-Na systems are reassessed using the modified quasichemical model for the liquid phase. The thermodynamic properties of the ternary system are estimated from the models of the binary systems and the ternary compound using CALPHAD technique. The constructed database is successfully used to reproduce the pressure-composition isotherms for MgH2 + 10 wt.% NaH mixtures. Also, the pressure-temperature equilibrium diagram and reaction paths for the same composition are predicted at different temperatures and pressures. Even though it is proved that H-Mg-Na does not meet the DOE hydrogen storage requirements for onboard applications, the best working temperatures and pressures to benefit from its full catalytic role are given. Also, the present database can be used for thermodynamic assessments of higher order systems.

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

NASA Astrophysics Data System (ADS)

Ghiorso, M. S.

2013-12-01

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

The thermodynamic scale of inorganic crystalline metastability

PubMed Central

Sun, Wenhao; Dacek, Stephen T.; Ong, Shyue Ping; Hautier, Geoffroy; Jain, Anubhav; Richards, William D.; Gamst, Anthony C.; Persson, Kristin A.; Ceder, Gerbrand

2016-01-01

The space of metastable materials offers promising new design opportunities for next-generation technological materials, such as complex oxides, semiconductors, pharmaceuticals, steels, and beyond. Although metastable phases are ubiquitous in both nature and technology, only a heuristic understanding of their underlying thermodynamics exists. We report a large-scale data-mining study of the Materials Project, a high-throughput database of density functional theory–calculated energetics of Inorganic Crystal Structure Database structures, to explicitly quantify the thermodynamic scale of metastability for 29,902 observed inorganic crystalline phases. We reveal the influence of chemistry and composition on the accessible thermodynamic range of crystalline metastability for polymorphic and phase-separating compounds, yielding new physical insights that can guide the design of novel metastable materials. We further assert that not all low-energy metastable compounds can necessarily be synthesized, and propose a principle of ‘remnant metastability’—that observable metastable crystalline phases are generally remnants of thermodynamic conditions where they were once the lowest free-energy phase. PMID:28138514

Technical Work Plan for: Thermodynamic Database for Chemical Modeling

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

C.F. Jovecolon

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

The Effect of Impurities on the Processing of Aluminum Alloys

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

Zi-Kui Liu; Shengjun Zhang; Qingyou Han

2007-04-23

For this Aluminum Industry of the Future (IOF) project, the effect of impurities on the processing of aluminum alloys was systematically investigated. The work was carried out as a collaborative effort between the Pennsylvania State University and Oak Ridge National Laboratory. Industrial support was provided by ALCOA and ThermoCalc, Inc. The achievements described below were made. A method that combines first-principles calculation and calculation of phase diagrams (CALPHAD) was used to develop the multicomponent database Al-Ca-K-Li-Mg-Na. This method was extensively used in this project for the development of a thermodynamic database. The first-principles approach provided some thermodynamic property data thatmore » are not available in the open literature. These calculated results were used in the thermodynamic modeling as experimental data. Some of the thermodynamic property data are difficult, if not impossible, to measure. The method developed and used in this project allows the estimation of these data for thermodynamic database development. The multicomponent database Al-Ca-K-Li-Mg-Na was developed. Elements such as Ca, Li, Na, and K are impurities that strongly affect the formability and corrosion behavior of aluminum alloys. However, these impurity elements are not included in the commercial aluminum alloy database. The process of thermodynamic modeling began from Al-Na, Ca-Li, Li-Na, K-Na, and Li-K sub-binary systems. Then ternary and higher systems were extrapolated because of the lack of experimental information. Databases for five binary alloy systems and two ternary systems were developed. Along with other existing binary and ternary databases, the full database of the multicomponent Al-Ca-K-Li-Mg-Na system was completed in this project. The methodology in integrating with commercial or other aluminum alloy databases can be developed. The mechanism of sodium-induced high-temperature embrittlement (HTE) of Al-Mg is now understood. Using the thermodynamic database developed in this project, thermodynamic simulations were carried out to investigate the effect of sodium on the HTE of Al-Mg alloys. The simulation results indicated that the liquid miscibility gap resulting from the dissolved sodium in the molten material plays an important role in HTE. A liquid phase forms from the solid face-centered cubic (fcc) phase (most likely at grain boundaries) during cooling, resulting in the occurrence of HTE. Comparison of the thermodynamic simulation results with experimental measurements on the high-temperature ductility of an Al-5Mg-Na alloy shows that HTE occurs in the temperature range at which the liquid phase exists. Based on this fundamental understanding of the HTE mechanism during processing of aluminum alloy, an HTE sensitive zone and a hot-rolling safe zone of the Al-Mg-Na alloys are defined as functions of processing temperature and alloy composition. The tendency of HTE was evaluated based on thermodynamic simulations of the fraction of the intergranular sodium-rich liquid phase. Methods of avoiding HTE during rolling/extrusion of Al-Mg-based alloys were suggested. Energy and environmental benefits from the results of this project could occur through a number of avenues: (1) energy benefits accruing from reduced rejection rates of the aluminum sheet and bar, (2) reduced dross formation during the remelting of the aluminum rejects, and (3) reduced CO2 emission related to the energy savings. The sheet and extruded bar quantities produced in the United States during 2000 were 10,822 and 4,546 million pounds, respectively. It is assumed that 50% of the sheet and 10% of the bar will be affected by implementing the results of this project. With the current process, the rejection rate of sheet and bar is estimated at 5%. Assuming that at least half of the 5% rejection of sheet and bar will be eliminated by using the results of this project and that 4% of the aluminum will be lost through dross (Al2O3) during remelting of the rejects, the full-scale industrial implementation of the project results would lead to energy savings in excess of 6.2 trillion Btu/year and cost savings of $42.7 million by 2020.« less

High-Throughput Thermodynamic Modeling and Uncertainty Quantification for ICME

NASA Astrophysics Data System (ADS)

Otis, Richard A.; Liu, Zi-Kui

2017-05-01

One foundational component of the integrated computational materials engineering (ICME) and Materials Genome Initiative is the computational thermodynamics based on the calculation of phase diagrams (CALPHAD) method. The CALPHAD method pioneered by Kaufman has enabled the development of thermodynamic, atomic mobility, and molar volume databases of individual phases in the full space of temperature, composition, and sometimes pressure for technologically important multicomponent engineering materials, along with sophisticated computational tools for using the databases. In this article, our recent efforts will be presented in terms of developing new computational tools for high-throughput modeling and uncertainty quantification based on high-throughput, first-principles calculations and the CALPHAD method along with their potential propagations to downstream ICME modeling and simulations.

DBCreate: A SUPCRT92-based program for producing EQ3/6, TOUGHREACT, and GWB thermodynamic databases at user-defined T and P

NASA Astrophysics Data System (ADS)

Kong, Xiang-Zhao; Tutolo, Benjamin M.; Saar, Martin O.

2013-02-01

SUPCRT92 is a widely used software package for calculating the standard thermodynamic properties of minerals, gases, aqueous species, and reactions. However, it is labor-intensive and error-prone to use it directly to produce databases for geochemical modeling programs such as EQ3/6, the Geochemist's Workbench, and TOUGHREACT. DBCreate is a SUPCRT92-based software program written in FORTRAN90/95 and was developed in order to produce the required databases for these programs in a rapid and convenient way. This paper describes the overall structure of the program and provides detailed usage instructions.

Recovery Act: An Integrated Experimental and Numerical Study: Developing a Reaction Transport Model that Couples Chemical Reactions of Mineral Dissolution/Precipitation with Spatial and Temporal Flow Variations.

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

Saar, Martin O.; Seyfried, Jr., William E.; Longmire, Ellen K.

2016-06-24

A total of 12 publications and 23 abstracts were produced as a result of this study. In particular, the compilation of a thermodynamic database utilizing consistent, current thermodynamic data is a major step toward accurately modeling multi-phase fluid interactions with solids. Existing databases designed for aqueous fluids did not mesh well with existing solid phase databases. Addition of a second liquid phase (CO2) magnifies the inconsistencies between aqueous and solid thermodynamic databases. Overall, the combination of high temperature and pressure lab studies (task 1), using a purpose built apparatus, and solid characterization (task 2), using XRCT and more developed technologies,more » allowed observation of dissolution and precipitation processes under CO2 reservoir conditions. These observations were combined with results from PIV experiments on multi-phase fluids (task 3) in typical flow path geometries. The results of the tasks 1, 2, and 3 were compiled and integrated into numerical models utilizing Lattice-Boltzmann simulations (task 4) to realistically model the physical processes and were ultimately folded into TOUGH2 code for reservoir scale modeling (task 5). Compilation of the thermodynamic database assisted comparisons to PIV experiments (Task 3) and greatly improved Lattice Boltzmann (Task 4) and TOUGH2 simulations (Task 5). PIV (Task 3) and experimental apparatus (Task 1) have identified problem areas in TOUGHREACT code. Additional lab experiments and coding work has been integrated into an improved numerical modeling code.« less

PROXiMATE: a database of mutant protein-protein complex thermodynamics and kinetics.

PubMed

Jemimah, Sherlyn; Yugandhar, K; Michael Gromiha, M

2017-09-01

We have developed PROXiMATE, a database of thermodynamic data for more than 6000 missense mutations in 174 heterodimeric protein-protein complexes, supplemented with interaction network data from STRING database, solvent accessibility, sequence, structural and functional information, experimental conditions and literature information. Additional features include complex structure visualization, search and display options, download options and a provision for users to upload their data. The database is freely available at http://www.iitm.ac.in/bioinfo/PROXiMATE/ . The website is implemented in Python, and supports recent versions of major browsers such as IE10, Firefox, Chrome and Opera. gromiha@iitm.ac.in. Supplementary data are available at Bioinformatics online. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

Thermodynamic database for proteins: features and applications.

PubMed

Gromiha, M Michael; Sarai, Akinori

2010-01-01

We have developed a thermodynamic database for proteins and mutants, ProTherm, which is a collection of a large number of thermodynamic data on protein stability along with the sequence and structure information, experimental methods and conditions, and literature information. This is a valuable resource for understanding/predicting the stability of proteins, and it can be accessible at http://www.gibk26.bse.kyutech.ac.jp/jouhou/Protherm/protherm.html . ProTherm has several features including various search, display, and sorting options and visualization tools. We have analyzed the data in ProTherm to examine the relationship among thermodynamics, structure, and function of proteins. We describe the progress on the development of methods for understanding/predicting protein stability, such as (i) relationship between the stability of protein mutants and amino acid properties, (ii) average assignment method, (iii) empirical energy functions, (iv) torsion, distance, and contact potentials, and (v) machine learning techniques. The list of online resources for predicting protein stability has also been provided.

Critical Evaluations and Thermodynamic Optimizations of the MnO-Mn2O3-SiO2 and FeO-Fe2O3-MnO-Mn2O3-SiO2 Systems

NASA Astrophysics Data System (ADS)

Kang, Youn-Bae; Jung, In-Ho

2017-06-01

A critical evaluation and thermodynamic modeling for thermodynamic properties of all oxide phases and phase diagrams in the Fe-Mn-Si-O system (MnO-Mn2O3-SiO2 and FeO-Fe2O3-MnO-Mn2O3-SiO2 systems) are presented. Optimized Gibbs energy parameters for the thermodynamic models of the oxide phases were obtained which reproduce all available and reliable experimental data within error limits from 298 K (25°C) to above the liquidus temperatures at all compositions covering from known oxide phases, and oxygen partial pressure from metal saturation to 0.21 bar. The optimized thermodynamic properties and phase diagrams are believed to be the best estimates presently available. Slag (molten oxide) was modeled using the modified quasichemical model in the pair approximation. Olivine (Fe2SiO4-Mn2SiO4) was modeled using two-sublattice model in the framework of the compound energy formalism (CEF), while rhodonite (MnSiO3-FeSiO3) and braunite (Mn7SiO_{12} with excess Mn2O3) were modeled as simple Henrian solutions. It is shown that the already developed models and databases of two spinel phases (cubic- and tetragonal-(Fe, Mn)3O4) using CEF [Kang and Jung, J. Phys. Chem. Solids (2016), vol. 98, pp. 237-246] can successfully be integrated into a larger thermodynamic database to be used in practically important higher order system such as silicate. The database of the model parameters can be used along with a software for Gibbs energy minimization in order to calculate any type of phase diagram section and thermodynamic properties.

Calculation of {alpha}/{gamma} equilibria in SA508 grade 3 steels for intercritical heat treatment

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

Lee, B.J.; Kim, H.D.; Hong, J.H.

1998-05-01

An attempt has been made to suggest an optimum temperature for intercritical heat treatment of an SA508 grade 3 steel for nuclear pressure vessels, based on thermodynamic calculation of the {alpha}/{gamma} phase equilibria. A thermodynamic database constructed for the Fe-Mn-Ni-Mo-Cr-Si-V-Al-C-N ten-component system and an empirical criterion that the amount of reformed austenite should be around 40 pct were used for thermodynamic calculation and derivation of the optimum heat-treatment temperature, respectively. The calculated optimum temperature, 720 C, was in good agreement with an experimentally determined temperature of 725 C obtained through an independent experimental investigation of the same steel. The agreementmore » between the calculated and measured fraction of reformed austenite during the intercritical heat treatment was also confirmed. Based on the agreement between calculation and experiment, it could be concluded that thermodynamic calculations can be successfully applied to the materials and/or process design as an additive tool to the already established technology, and that the currently constructed thermodynamic database for steel systems shows an accuracy that makes such applications possible.« less

Blending Education and Polymer Science: Semiautomated Creation of a Thermodynamic Property Database

ERIC Educational Resources Information Center

Tchoua, Roselyne B.; Qin, Jian; Audus, Debra J.; Chard, Kyle; Foster, Ian T.; de Pablo, Juan

2016-01-01

Structured databases of chemical and physical properties play a central role in the everyday research activities of scientists and engineers. In materials science, researchers and engineers turn to these databases to quickly query, compare, and aggregate various properties, thereby allowing for the development or application of new materials. The…

Ionic Liquids Database- (ILThermo)

National Institute of Standards and Technology Data Gateway

SRD 147 NIST Ionic Liquids Database- (ILThermo) (Web, free access)   IUPAC Ionic Liquids Database, ILThermo, is a free web research tool that allows users worldwide to access an up-to-date data collection from the publications on experimental investigations of thermodynamic, and transport properties of ionic liquids as well as binary and ternary mixtures containing ionic liquids.

Atomic Spectroscopic Databases at NIST

NASA Technical Reports Server (NTRS)

Reader, J.; Kramida, A. E.; Ralchenko, Yu.

2006-01-01

We describe recent work at NIST to develop and maintain databases for spectra, transition probabilities, and energy levels of atoms that are astrophysically important. Our programs to critically compile these data as well as to develop a new database to compare plasma calculations for atoms that are not in local thermodynamic equilibrium are also summarized.

Using Spreadsheets and Internally Consistent Databases to Explore Thermodynamics

NASA Astrophysics Data System (ADS)

Dasgupta, S.; Chakraborty, S.

2003-12-01

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

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

Wolery, Thomas J.; Tayne, Andrew; Jove-Colon, Carlos F.

Thermodynamic data are essential for understanding and evaluating geochemical processes, as by speciation-solubility calculations, reaction -path modeling, or reactive transport simulation. These data are required to evaluate both equilibrium states and the kinetic approach to such states (via the affinity term in rate laws). The development of thermodynamic databases for these purposes has a long history in geochemistry (e.g., Garrels and Christ, 1965; Helgeson et al., 1969; Helgeson et al., 1978, Johnson et al., 1992; Robie and Hemingway, 1995), paralleled by related and applicable work in the larger scientific community (e.g., Wagman et al., 1982, 1989; Cox et al., 1989;more » Barin and Platzki, 1995; Binneweis and Milke, 1999). The Yucca Mountain Project developed two qualified thermodynamic databases for to model geochemical processes, including ones involving repository components such as spent fuel. The first of the two (BSC, 2007a) was for systems containing dilute aqueous solutions only, the other (BSC, 2007b) for systems involving concentrated aqueous solutions and incorporating a model for such based on Pitzer’s (1991) equations . A 25°C-only database with similarities to the latter was also developed for WIPP (cf. Xiong, 2005). The YMP dilute systems database is widely used in the geochemistry community for a variety of applications involving rock/water interactions. The purpose of the present task is to improve these databases for work on the Used Fuel Disposition Project and maintain some semblance of order that will support qualification in support of the development of future underground high level nuclear waste disposal.« less

AntiJen: a quantitative immunology database integrating functional, thermodynamic, kinetic, biophysical, and cellular data

PubMed Central

Toseland, Christopher P; Clayton, Debra J; McSparron, Helen; Hemsley, Shelley L; Blythe, Martin J; Paine, Kelly; Doytchinova, Irini A; Guan, Pingping; Hattotuwagama, Channa K; Flower, Darren R

2005-01-01

AntiJen is a database system focused on the integration of kinetic, thermodynamic, functional, and cellular data within the context of immunology and vaccinology. Compared to its progenitor JenPep, the interface has been completely rewritten and redesigned and now offers a wider variety of search methods, including a nucleotide and a peptide BLAST search. In terms of data archived, AntiJen has a richer and more complete breadth, depth, and scope, and this has seen the database increase to over 31,000 entries. AntiJen provides the most complete and up-to-date dataset of its kind. While AntiJen v2.0 retains a focus on both T cell and B cell epitopes, its greatest novelty is the archiving of continuous quantitative data on a variety of immunological molecular interactions. This includes thermodynamic and kinetic measures of peptide binding to TAP and the Major Histocompatibility Complex (MHC), peptide-MHC complexes binding to T cell receptors, antibodies binding to protein antigens and general immunological protein-protein interactions. The database also contains quantitative specificity data from position-specific peptide libraries and biophysical data, in the form of diffusion co-efficients and cell surface copy numbers, on MHCs and other immunological molecules. The uses of AntiJen include the design of vaccines and diagnostics, such as tetramers, and other laboratory reagents, as well as helping parameterize the bioinformatic or mathematical in silico modeling of the immune system. The database is accessible from the URL: . PMID:16305757

Fundamentals of the NEA Thermochemical Database and its influence over national nuclear programs on the performance assessment of deep geological repositories.

PubMed

Ragoussi, Maria-Eleni; Costa, Davide

2017-03-14

For the last 30 years, the NEA Thermochemical Database (TDB) Project (www.oecd-nea.org/dbtdb/) has been developing a chemical thermodynamic database for elements relevant to the safety of radioactive waste repositories, providing data that are vital to support the geochemical modeling of such systems. The recommended data are selected on the basis of strict review procedures and are characterized by their consistency. The results of these efforts are freely available, and have become an international point of reference in the field. As a result, a number of important national initiatives with regard to waste management programs have used the NEA TDB as their basis, both in terms of recommended data and guidelines. In this article we describe the fundamentals and achievements of the project together with the characteristics of some databases developed in national nuclear waste disposal programs that have been influenced by the NEA TDB. We also give some insights on how this work could be seen as an approach to be used in broader areas of environmental interest. Copyright © 2017 Elsevier Ltd. All rights reserved.

Thermodynamic assessment of the LiF-NaF-BeF2-ThF4-UF4 system

NASA Astrophysics Data System (ADS)

Capelli, E.; Beneš, O.; Konings, R. J. M.

2014-06-01

The present study describes the full thermodynamic assessment of the LiF-NaF-BeF2-ThF4-UF4 system which is one of the key systems considered for a molten salt reactor fuel. The work is an extension of the previously assessed LiF-NaF-ThF4-UF4 system with addition of BeF2 which is characterized by very low neutron capture cross section and a relatively low melting point. To extend the database the binary BeF2-ThF4 and BeF2-UF4 systems were optimized and the novel data were used for the thermodynamic assessment of BeF2 containing ternary systems for which experimental data exist in the literature. The obtained database is used to optimize the molten salt reactor fuel composition and to assess its properties with the emphasis on the melting behaviour.

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

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

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

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

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

NASA Astrophysics Data System (ADS)

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

2017-09-01

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

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

DOE PAGES

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

2016-09-26

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

Applications of Protein Thermodynamic Database for Understanding Protein Mutant Stability and Designing Stable Mutants.

PubMed

Gromiha, M Michael; Anoosha, P; Huang, Liang-Tsung

2016-01-01

Protein stability is the free energy difference between unfolded and folded states of a protein, which lies in the range of 5-25 kcal/mol. Experimentally, protein stability is measured with circular dichroism, differential scanning calorimetry, and fluorescence spectroscopy using thermal and denaturant denaturation methods. These experimental data have been accumulated in the form of a database, ProTherm, thermodynamic database for proteins and mutants. It also contains sequence and structure information of a protein, experimental methods and conditions, and literature information. Different features such as search, display, and sorting options and visualization tools have been incorporated in the database. ProTherm is a valuable resource for understanding/predicting the stability of proteins and it can be accessed at http://www.abren.net/protherm/ . ProTherm has been effectively used to examine the relationship among thermodynamics, structure, and function of proteins. We describe the recent progress on the development of methods for understanding/predicting protein stability, such as (1) general trends on mutational effects on stability, (2) relationship between the stability of protein mutants and amino acid properties, (3) applications of protein three-dimensional structures for predicting their stability upon point mutations, (4) prediction of protein stability upon single mutations from amino acid sequence, and (5) prediction methods for addressing double mutants. A list of online resources for predicting has also been provided.

NIST/ASME Steam Properties Database

National Institute of Standards and Technology Data Gateway

SRD 10 NIST/ASME Steam Properties Database (PC database for purchase)   Based upon the International Association for the Properties of Water and Steam (IAPWS) 1995 formulation for the thermodynamic properties of water and the most recent IAPWS formulations for transport and other properties, this updated version provides water properties over a wide range of conditions according to the accepted international standards.

NIST Gas Hydrate Research Database and Web Dissemination Channel.

PubMed

Kroenlein, K; Muzny, C D; Kazakov, A; Diky, V V; Chirico, R D; Frenkel, M; Sloan, E D

2010-01-01

To facilitate advances in application of technologies pertaining to gas hydrates, a freely available data resource containing experimentally derived information about those materials was developed. This work was performed by the Thermodynamic Research Center (TRC) paralleling a highly successful database of thermodynamic and transport properties of molecular pure compounds and their mixtures. Population of the gas-hydrates database required development of guided data capture (GDC) software designed to convert experimental data and metadata into a well organized electronic format, as well as a relational database schema to accommodate all types of numerical and metadata within the scope of the project. To guarantee utility for the broad gas hydrate research community, TRC worked closely with the Committee on Data for Science and Technology (CODATA) task group for Data on Natural Gas Hydrates, an international data sharing effort, in developing a gas hydrate markup language (GHML). The fruits of these efforts are disseminated through the NIST Sandard Reference Data Program [1] as the Clathrate Hydrate Physical Property Database (SRD #156). A web-based interface for this database, as well as scientific results from the Mallik 2002 Gas Hydrate Production Research Well Program [2], is deployed at http://gashydrates.nist.gov.

A thermodynamic review of cryogenic refrigeration cycles for liquefaction of natural gas

NASA Astrophysics Data System (ADS)

Chang, Ho-Myung

2015-12-01

A thermodynamic review is presented on cryogenic refrigeration cycles for the liquefaction process of natural gas. The main purpose of this review is to examine the thermodynamic structure of various cycles and provide a theoretical basis for selecting a cycle in accordance with different needs and design criteria. Based on existing or proposed liquefaction processes, sixteen ideal cycles are selected and the optimal conditions to achieve their best thermodynamic performance are investigated. The selected cycles include standard and modified versions of Joule-Thomson (JT) cycle, Brayton cycle, and their combined cycle with pure refrigerants (PR) or mixed refrigerants (MR). Full details of the cycles are presented and discussed in terms of FOM (figure of merit) and thermodynamic irreversibility. In addition, a new method of nomenclature is proposed to clearly identify the structure of cycles by abbreviation.

Use of Tabulated Thermochemical Data for Pure Compounds

NASA Technical Reports Server (NTRS)

Jacobson, Nathan S.

1999-01-01

Thermodynamic data for inorganic compounds is found in a variety of tabulations and computer databases. An extensive listing of sources of inorganic thermodynamic data is provided. The three major tabulations are the JANAF tables. Thermodynamic Properties of Individual Substances, and the tabulation by Barin. The notation and choice of standard states is different in each of these tabulations, so combining data from the different tabulations is often a problem. By understanding the choice of standard states, it is possible to develop simple equations for conversion of the data from one form to another.

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

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

Carter, Robert; Seniow, Kendra

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

A thermodynamic database for tellurium-bearing systems relevant to nuclear technology

NASA Astrophysics Data System (ADS)

Chattopadhyay, G.; Juneja, J. M.

1993-06-01

A thermodynamic database for tellurium-bearing condensed phases and gaseous species which are relevant to nuclear technology is presented. It contains phase diagrams of the binary systems, PdTe, RhTe, PuTe, SmTe, CsTe, ZrTe, of the ternary systems, ZrTeO, MoTeO, AgTeO, UTeO, CsTeO, BaTeO as well as thermodynamic data for crystalline and liquid Te, for the solid phases Cs 2Te, Ag 2Te, SnTe, BaTe, CeTe, SmTe, RuTe 2, ZrTe 2, Fe 0.53Te 0.47, Mo 0.43Te 0.57, Cr 0.43Te 0.57, Ni 0.5Te 0.4, Cs 2TeO 3 and for the gaseous species, Te, Te 2, TeO, TeO 2, TeO(OH) 2, H 2Te, TeI, TeI 2, TeI 4, TeOI 2, SnTe, Sn 2Te 2, SnTe 2.

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

NASA Astrophysics Data System (ADS)

Chevalier, P. Y.; Fischer, E.

2001-02-01

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

Blending Education and Polymer Science: Semi Automated Creation of a Thermodynamic Property Database.

PubMed

Tchoua, Roselyne B; Qin, Jian; Audus, Debra J; Chard, Kyle; Foster, Ian T; de Pablo, Juan

2016-09-13

Structured databases of chemical and physical properties play a central role in the everyday research activities of scientists and engineers. In materials science, researchers and engineers turn to these databases to quickly query, compare, and aggregate various properties, thereby allowing for the development or application of new materials. The vast majority of these databases have been generated manually, through decades of labor-intensive harvesting of information from the literature; yet, while there are many examples of commonly used databases, a significant number of important properties remain locked within the tables, figures, and text of publications. The question addressed in our work is whether, and to what extent, the process of data collection can be automated. Students of the physical sciences and engineering are often confronted with the challenge of finding and applying property data from the literature, and a central aspect of their education is to develop the critical skills needed to identify such data and discern their meaning or validity. To address shortcomings associated with automated information extraction, while simultaneously preparing the next generation of scientists for their future endeavors, we developed a novel course-based approach in which students develop skills in polymer chemistry and physics and apply their knowledge by assisting with the semi-automated creation of a thermodynamic property database.

Blending Education and Polymer Science: Semiautomated Creation of a Thermodynamic Property Database

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

Tchoua, Roselyne B.; Qin, Jian; Audus, Debra J.

Structured databases of chemical and physical properties play a central role in the everyday research activities of scientists and engineers. In materials science, researchers and engineers turn to these databases to quickly query, compare, and aggregate various properties, thereby allowing for the development or application of new materials. The vast majority of these databases have been generated manually, through decades of labor-intensive harvesting of information from the literature, yet while there are many examples of commonly used databases, a significant number of important properties remain locked within the tables, figures, and text of publications. The question addressed in our workmore » is whether and to what extent the process of data collection can be automated. Students of the physical sciences and engineering are often confronted with the challenge of finding and applying property data from the literature, and a central aspect of their education is to develop the critical skills needed to identify such data and discern their meaning or validity. To address shortcomings associated with automated information extraction while simultaneously preparing the next generation of scientists for their future endeavors, we developed a novel course-based approach in which students develop skills in polymer chemistry and physics and apply their knowledge by assisting with the semiautomated creation of a thermodynamic property database.« less

Towards driving mantle convection by mineral physics

NASA Astrophysics Data System (ADS)

Piazzoni, A. S.; Bunge, H.; Steinle-Neumann, G.

2005-12-01

Models of mantle convection have become increasingly sophisticated over the past decade, accounting, for example, for 3 D spherical geometry, and changes in mantle rheology due to variations in temperature and stress. In light of such advances it is surprising that growing constraints on mantle structure derived from mineral physics have not yet been fully brought to bear on mantle convection models. In fact, despite much progress in our understanding of mantle mineralogy a partial description of the equation of state is often used to relate density changes to pressure and temperature alone, without taking into account compositional and mineralogical models of the mantle. Similarly, for phase transitions an incomplete description of thermodynamic constraints is often used, resulting in significant uncertainties in model behavior. While a number of thermodynamic models (some with limited scope) have been constructed recently, some lack the rigor in thermodynamics - for example with respect to the treatment of solid solution - that is needed to make predictions about mantle structure. Here we have constructed a new thermodynamic database for the mantle and have coupled the resulting density dynamically with mantle convection models. The database is build on a self-consistent Gibb's free energy minimization of the system MgO-FeO-SiO2-CaO-Al2O3 that is appropriate for standard (dry) chemical models of the Earth's mantle for relevant high pressure and temperature phases. We have interfaced the database with a high-resolution 2-D convection code (2DTERRA), dynamically coupling the thermodynamic model (density) with the conservation equations of mantle flow. The coupled model is run for different parameterizations of viscosity, initial temperature conditions, and varying the internal vs. external heating. We compare the resulting flow and temperature fields to cases with the Boussinesq approximation and other classical descriptions of the equation of state in mantle dynamics to assess the influence of realistic mineralogical density on mantle convection.

Development of models and software for liquidus temperatures of glasses of HWVP products. Final report

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

Hrma, P.R.; Vienna, J.D.; Pelton, A.D.

In an earlier report [92 Pel] was described the development of software and thermodynamic databases for the calculation of liquidus temperatures of glasses of HWVP products containing the components SiO{sub 2}-B{sub 2}O{sub 3}-Na{sub 2}O-Li{sub 2}O-CaO-MgO-Fe{sub 2}O{sub 3}-Al{sub 2}O{sub 3}-ZrO{sub 2}-{open_quotes}others{close_quotes}. The software package developed at that time consisted of the EQUILIB program of the F*A*C*T computer system with special input/output routines. Since then, Battelle has purchased the entire F*A*C*T computer system, and this fully replaces the earlier package. Furthermore, with the entire F*A*C*T system, additional calculations can be performed such as calculations at fixed O{sub 2}, SO{sub 2} etc. pressures,more » or graphing of output. Furthermore, the public F*A*C*T database of over 5000 gaseous species and condensed phases is now accessible. The private databases for the glass and crystalline phases were developed for Battelle by optimization of thermodynamic and phase diagram data. That is, all available data for 2- and 3-component sub-systems of the 9-component oxide system were collected, and parameters of model equations for the thermodynamic properties were found which best reproduce all the data. For representing the thermodynamic properties of the glass as a function of composition and temperature, the modified quasichemical model was used. This model was described in the earlier report [92 Pel] along with all the optimizations. With the model, it was possible to predict the thermodynamic properties of the 9-component glass, and thereby to calculate liquidus temperatures. Liquidus temperatures measured by Battelle for 123 CVS glass compositions were used to test the model and to refine the model by the addition of further parameters.« less

The GraVent DDT database

NASA Astrophysics Data System (ADS)

Boeck, Lorenz R.; Katzy, Peter; Hasslberger, Josef; Kink, Andreas; Sattelmayer, Thomas

2016-09-01

An open-access online platform containing data from experiments on deflagration-to-detonation transition conducted at the Institute of Thermodynamics, Technical University of Munich, has been developed and is accessible at http://www.td.mw.tum.de/ddt. The database provides researchers working on explosion dynamics with data for theoretical analyses and for the validation of numerical simulations.

Free Radical Halogenation, Selectivity, and Thermodynamics: The Polanyi Principle and Hammond's Postulate

ERIC Educational Resources Information Center

Scala, Alfred A.

2004-01-01

The underlying ideas of the Polanyi principle and Hammond's postulate in relation to the simple free halogenation reactions and their selectivity and thermodynamics is presented. The results indicate that the chlorine atom exhibits a slightly less selectivity in the liquid phase as compared to in the gas phase.

Is there a link between selectivity and binding thermodynamics profiles?

PubMed

Tarcsay, Ákos; Keserű, György M

2015-01-01

Thermodynamics of ligand binding is influenced by the interplay between enthalpy and entropy contributions of the binding event. The impact of these binding free energy components, however, is not limited to the primary target only. Here, we investigate the relationship between binding thermodynamics and selectivity profiles by combining publicly available data from broad off-target assay profiling and the corresponding thermodynamics measurements. Our analysis indicates that compounds binding their primary targets with higher entropy contributions tend to hit more off-targets compared with those ligands that demonstrated enthalpy-driven binding. Copyright © 2014 Elsevier Ltd. All rights reserved.

Development of a Knowledge Base of Ti-Alloys From First-Principles and Thermodynamic Modeling

NASA Astrophysics Data System (ADS)

Marker, Cassie

An aging population with an active lifestyle requires the development of better load-bearing implants, which have high levels of biocompatibility and a low elastic modulus. Titanium alloys, in the body centered cubic phase, are great implant candidates, due to their mechanical properties and biocompatibility. The present work aims at investigating the thermodynamic and elastic properties of bcc Tialloys, using the integrated first-principles based on Density Functional Theory (DFT) and the CALculation of PHAse Diagrams (CALPHAD) method. The use of integrated first-principles calculations based on DFT and CALPHAD modeling has greatly reduced the need for trial and error metallurgy, which is ineffective and costly. The phase stability of Ti-alloys has been shown to greatly affect their elastic properties. Traditionally, CALPHAD modeling has been used to predict the equilibrium phase formation, but in the case of Ti-alloys, predicting the formation of two metastable phases o and alpha" is of great importance as these phases also drastically effect the elastic properties. To build a knowledge base of Ti-alloys, for biomedical load-bearing implants, the Ti-Mo-Nb-Sn-Ta-Zr system was studied because of the biocompatibility and the bcc stabilizing effects of some of the elements. With the focus on bcc Ti-rich alloys, a database of thermodynamic descriptions of each phase for the pure elements, binary and Ti-rich ternary alloys was developed in the present work. Previous thermodynamic descriptions for the pure elements were adopted from the widely used SGTE database for global compatibility. The previous binary and ternary models from the literature were evaluated for accuracy and new thermodynamic descriptions were developed when necessary. The models were evaluated using available experimental data, as well as the enthalpy of formation of the bcc phase obtained from first-principles calculations based on DFT. The thermodynamic descriptions were combined into a database ensuring that the sublattice models are compatible with each other. For subsystems, such as the Sn-Ta system, where no thermodynamic description had been evaluated and minimal experimental data was available, first-principles calculations based on DFT were used. The Sn-Ta system has two intermetallic phases, TaSn2 and Ta3Sn, with three solution phases: bcc, body centered tetragonal (bct) and diamond. First-principles calculations were completed on the intermetallic and solution phases. Special quasirandom structures (SQS) were used to obtain information about the solution phases across the entire composition range. The Debye-Gruneisen approach, as well as the quasiharmonic phonon method, were used to obtain the finite-temperature data. Results from the first-principles calculations and experiments were used to complete the thermodynamic description. The resulting phase diagram reproduced the first-principles calculations and experimental data accurately. In order to determine the effect of alloying on the elastic properties, first-principles calculations based on DFT were systematically done on the pure elements, five Ti-X binary systems and Ti-X-Y ternary systems (X ≠ Y = Mo, Nb, Sn, Ta Zr) in the bcc phase. The first-principles calculations predicted the single crystal elastic stiffness constants cij 's. Correspondingly, the polycrystalline aggregate properties were also estimated from the cij's, including bulk modulus B, shear modulus G and Young's modulus E. The calculated results showed good agreement with experimental results. The CALPHAD method was then adapted to assist in the database development of the elastic properties as a function of composition. On average, the database predicted the elastic properties of higher order Ti-alloys within 5 GPa of the experimental results. Finally, the formation of the metastable phases, o and alpha" was studied in the Ti-Ta and Ti-Nb systems. The formation energy of these phases, calculated from first-principles at 0 K, showed that the phases have similar formation energies to the bcc and hcp phases. Inelastic neutron scattering was completed on four different Ti-Nb compositions to study the entropy of the phases as well as the transformations occurring when the phases form and the phase fractions. Ongoing work is being done to use the experimental information to introduce thermodynamic descriptions for these two phases in the Ti-Nb system in order to be able to predict the formation and phase fractions. DFT based first-principles were used to predict the effect these phases have on the elastic properties and a rule of mixtures was used to determine the elastic properties of multi-phase alloys. The results were compared with experiments and showed that if the ongoing modeling can predict the phase fraction, the elastic database can accurately predict the elastic properties of the o and alpha" phases. This thesis provides a knowledge base of the thermodynamic and elastic properties of Ti-alloys from computational thermodynamics. The databases created will impact research activities on Ti-alloys and specifically efforts focused on Ti-alloys for biomedical applications.

Characterization and Computational Modeling of Minor Phases in Alloy LSHR

NASA Technical Reports Server (NTRS)

Jou, Herng-Jeng; Olson, Gregory; Gabb, Timothy; Garg, Anita; Miller, Derek

2012-01-01

The minor phases of powder metallurgy disk superalloy LSHR were studied. Samples were consistently heat treated at three different temperatures for long times to approach equilibrium. Additional heat treatments were also performed for shorter times, to assess minor phase kinetics in non-equilibrium conditions. Minor phases including MC carbides, M23C6 carbides, M3B2 borides, and sigma were identified. Their average sizes and total area fractions were determined. CALPHAD thermodynamics databases and PrecipiCalc(TradeMark), a computational precipitation modeling tool, were employed with Ni-base thermodynamics and diffusion databases to model and simulate the phase microstructural evolution observed in the experiments with an objective to identify the model limitations and the directions of model enhancement.

Leveraging the contribution of thermodynamics in drug discovery with the help of fluorescence-based thermal shift assays.

PubMed

Hau, Jean Christophe; Fontana, Patrizia; Zimmermann, Catherine; De Pover, Alain; Erdmann, Dirk; Chène, Patrick

2011-06-01

The development of new drugs with better pharmacological and safety properties mandates the optimization of several parameters. Today, potency is often used as the sole biochemical parameter to identify and select new molecules. Surprisingly, thermodynamics, which is at the core of any interaction, is rarely used in drug discovery, even though it has been suggested that the selection of scaffolds according to thermodynamic criteria may be a valuable strategy. This poor integration of thermodynamics in drug discovery might be due to difficulties in implementing calorimetry experiments despite recent technological progress in this area. In this report, the authors show that fluorescence-based thermal shift assays could be used as prescreening methods to identify compounds with different thermodynamic profiles. This approach allows a reduction in the number of compounds to be tested in calorimetry experiments, thus favoring greater integration of thermodynamics in drug discovery.

A look at ligand binding thermodynamics in drug discovery.

PubMed

Claveria-Gimeno, Rafael; Vega, Sonia; Abian, Olga; Velazquez-Campoy, Adrian

2017-04-01

Drug discovery is a challenging endeavor requiring the interplay of many different research areas. Gathering information on ligand binding thermodynamics may help considerably in reducing the risk within a high uncertainty scenario, allowing early rejection of flawed compounds and pushing forward optimal candidates. In particular, the free energy, the enthalpy, and the entropy of binding provide fundamental information on the intermolecular forces driving such interaction. Areas covered: The authors review the current status and recent developments in the application of ligand binding thermodynamics in drug discovery. The thermodynamic binding profile (Gibbs energy, enthalpy, and entropy of binding) can be used for lead selection and optimization (binding enthalpy, selectivity, and adaptability). Expert opinion: Binding thermodynamics provides fundamental information on the forces driving the formation of the drug-target complex. It has been widely accepted that binding thermodynamics may be used as a decision criterion along the ligand optimization process in drug discovery and development. In particular, the binding enthalpy may be used as a guide when selecting and optimizing compounds over a set of potential candidates. However, this has been recently called into question by arguing certain difficulties and in the light of certain experimental examples.

Numeric Databases in Chemical Thermodynamics at the National Institute of Standards and Technology

PubMed Central

Chase, Malcolm W.

1989-01-01

During the past year the activities of the Chemical Thermodynamics Data Center and the JANAF Thermochemical Tables project have been combined to obtain an extensive collection of thermodynamic information for many chemical species, including the elements. Currently available are extensive bibliographic collections and data files of heat capacity, enthalpy, vapor pressure, phase transitions, etc. Future plans related to materials science are to improve the metallic oxide temperature dependent tabulations, upgrade the recommended values periodically, and maintain the bibliographic citations and the thermochemical data current. The recommended thermochemical information is maintained on-line, and tied to the calculational routines within the data center. Recent thermodynamic evaluations on the elements and oxides will be discussed, as well as studies in related activities at NIST. PMID:28053395

A thermodynamic approach for advanced fuels of gas-cooled reactors

NASA Astrophysics Data System (ADS)

Guéneau, C.; Chatain, S.; Gossé, S.; Rado, C.; Rapaud, O.; Lechelle, J.; Dumas, J. C.; Chatillon, C.

2005-09-01

For both high temperature reactor (HTR) and gas cooled fast reactor (GFR) systems, the high operating temperature in normal and accidental conditions necessitates the assessment of the thermodynamic data and associated phase diagrams for the complex system constituted of the fuel kernel, the inert materials and the fission products. A classical CALPHAD approach, coupling experiments and thermodynamic calculations, is proposed. Some examples of studies are presented leading with the CO and CO 2 gas formation during the chemical interaction of [UO 2± x/C] in the HTR particle, and the chemical compatibility of the couples [UN/SiC], [(U, Pu)N/SiC], [(U, Pu)N/TiN] for the GFR system. A project of constitution of a thermodynamic database for advanced fuels of gas-cooled reactors is proposed.

Implementation of equilibrium aqueous speciation and solubility (EQ3 type) calculations into Cantera for electrolyte solutions.

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

Moffat, Harry K.; Jove-Colon, Carlos F.

2009-06-01

In this report, we summarize our work on developing a production level capability for modeling brine thermodynamic properties using the open-source code Cantera. This implementation into Cantera allows for the application of chemical thermodynamics to describe the interactions between a solid and an electrolyte solution at chemical equilibrium. The formulations to evaluate the thermodynamic properties of electrolytes are based on Pitzer's model to calculate molality-based activity coefficients using a real equation-of-state (EoS) for water. In addition, the thermodynamic properties of solutes at elevated temperature and pressures are computed using the revised Helgeson-Kirkham-Flowers (HKF) EoS for ionic and neutral aqueous species.more » The thermodynamic data parameters for the Pitzer formulation and HKF EoS are from the thermodynamic database compilation developed for the Yucca Mountain Project (YMP) used with the computer code EQ3/6. We describe the adopted equations and their implementation within Cantera and also provide several validated examples relevant to the calculations of extensive properties of electrolyte solutions.« less

MMA-EoS: A Computational Framework for Mineralogical Thermodynamics

NASA Astrophysics Data System (ADS)

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

2017-12-01

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

JTHERGAS: Thermodynamic Estimation from 2D Graphical Representations of Molecules

PubMed Central

Blurock, Edward; Warth, V.; Grandmougin, X.; Bounaceur, R.; Glaude, P.A.; Battin-Leclerc, F.

2013-01-01

JTHERGAS is a versatile calculator (implemented in JAVA) to estimate thermodynamic information from two dimensional graphical representations of molecules and radicals involving covalent bonds based on the Benson additivity method. The versatility of JTHERGAS stems from its inherent philosophy that all the fundamental data used in the calculation should be visible, to see exactly where the final values came from, and modifiable, to account for new data that can appear in the literature. The main use of this method is within automatic combustion mechanism generation systems where fast estimation of a large number and variety of chemical species is needed. The implementation strategy is based on meta-atom definitions and substructure analysis allowing a highly extensible database without modification of the core algorithms. Several interfaces for the database and the calculations are provided from terminal line commands, to graphical interfaces to web-services. The first order estimation of thermodynamics is based summing up the contributions of each heavy atom bonding description. Second order corrections due to steric hindrance and ring strain are made. Automatic estimate of contributions due to internal, external and optical symmetries are also made. The thermodynamical data for radicals is calculated by taking the difference due to the lost of a hydrogen radical taking into account changes in symmetry, spin, rotations, vibrations and steric hindrances. The software is public domain and is based on standard libraries such as CDK and CML. PMID:23761949

NASA Glenn Coefficients for Calculating Thermodynamic Properties of Individual Species

NASA Technical Reports Server (NTRS)

McBride, Bonnie J.; Zehe, Michael J.; Gordon, Sanford

2002-01-01

This report documents the library of thermodynamic data used with the NASA Glenn computer program CEA (Chemical Equilibrium with Applications). This library, containing data for over 2000 solid, liquid, and gaseous chemical species for temperatures ranging from 200 to 20,000 K, is available for use with other computer codes as well. The data are expressed as least-squares coefficients to a seven-term functional form for C((sup o)(sub p)) (T) / R with integration constants for H (sup o) (T) / RT and S(sup o) (T) / R. The NASA Glenn computer program PAC (Properties and Coefficients) was used to calculate thermodynamic functions and to generate the least-squares coefficients. PAC input was taken from a variety of sources. A complete listing of the database is given along with a summary of thermodynamic properties at 0 and 298.15 K.

Contribution to the thermodynamic description of the corium - The U-Zr-O system

NASA Astrophysics Data System (ADS)

Quaini, A.; Guéneau, C.; Gossé, S.; Dupin, N.; Sundman, B.; Brackx, E.; Domenger, R.; Kurata, M.; Hodaj, F.

2018-04-01

In order to understand the stratification process that may occur in the late phase of the fuel degradation during a severe accident in a PWR, the thermodynamic knowledge of the U-Zr-O system is crucial. The presence of a miscibility gap in the U-Zr-O liquid phase may lead to a stratified configuration, which will impact the accidental scenario management. The aim of this work was to obtain new experimental data in the U-Zr-O liquid miscibility gap. New tie-line data were provided at 2567 ± 25 K. The related thermodynamic models were reassessed using present data and literature values. The reassessed model will be implemented in the TAF-ID international database. The composition and density of phases potentially formed during stratification will be predicted by coupling current thermodynamic model with thermal-hydraulics codes.

Bayesian Calibration of Thermodynamic Databases and the Role of Kinetics

NASA Astrophysics Data System (ADS)

Wolf, A. S.; Ghiorso, M. S.

2017-12-01

Self-consistent thermodynamic databases of geologically relevant materials (like Berman, 1988; Holland and Powell, 1998, Stixrude & Lithgow-Bertelloni 2011) are crucial for simulating geological processes as well as interpreting rock samples from the field. These databases form the backbone of our understanding of how fluids and rocks interact at extreme planetary conditions. Considerable work is involved in their construction from experimental phase reaction data, as they must self-consistently describe the free energy surfaces (including relative offsets) of potentially hundreds of interacting phases. Standard database calibration methods typically utilize either linear programming or least squares regression. While both produce a viable model, they suffer from strong limitations on the training data (which must be filtered by hand), along with general ignorance of many of the sources of experimental uncertainty. We develop a new method for calibrating high P-T thermodynamic databases for use in geologic applications. The model is designed to handle pure solid endmember and free fluid phases and can be extended to include mixed solid solutions and melt phases. This new calibration effort utilizes Bayesian techniques to obtain optimal parameter values together with a full family of statistically acceptable models, summarized by the posterior. Unlike previous efforts, the Bayesian Logistic Uncertain Reaction (BLUR) model directly accounts for both measurement uncertainties and disequilibrium effects, by employing a kinetic reaction model whose parameters are empirically determined from the experiments themselves. Thus, along with the equilibrium free energy surfaces, we also provide rough estimates of the activation energies, entropies, and volumes for each reaction. As a first application, we demonstrate this new method on the three-phase aluminosilicate system, illustrating how it can produce superior estimates of the phase boundaries by incorporating constraints from all available data, while automatically handling variable data quality due to a combination of measurement errors and kinetic effects.

High-Temperature Cast Aluminum for Efficient Engines

NASA Astrophysics Data System (ADS)

Bobel, Andrew C.

Accurate thermodynamic databases are the foundation of predictive microstructure and property models. An initial assessment of the commercially available Thermo-Calc TCAL2 database and the proprietary aluminum database of QuesTek demonstrated a large degree of deviation with respect to equilibrium precipitate phase prediction in the compositional region of interest when compared to 3-D atom probe tomography (3DAPT) and transmission electron microscopy (TEM) experimental results. New compositional measurements of the Q-phase (Al-Cu-Mg-Si phase) led to a remodeling of the Q-phase thermodynamic description in the CALPHAD databases which has produced significant improvements in the phase prediction capabilities of the thermodynamic model. Due to the unique morphologies of strengthening precipitate phases commonly utilized in high-strength cast aluminum alloys, the development of new microstructural evolution models to describe both rod and plate particle growth was critical for accurate mechanistic strength models which rely heavily on precipitate size and shape. Particle size measurements through both 3DAPT and TEM experiments were used in conjunction with literature results of many alloy compositions to develop a physical growth model for the independent prediction of rod radii and rod length evolution. In addition a machine learning (ML) model was developed for the independent prediction of plate thickness and plate diameter evolution as a function of alloy composition, aging temperature, and aging time. The developed models are then compared with physical growth laws developed for spheres and modified for ellipsoidal morphology effects. Analysis of the effect of particle morphology on strength enhancement has been undertaken by modification of the Orowan-Ashby equation for 〈110〉 alpha-Al oriented finite rods in addition to an appropriate version for similarly oriented plates. A mechanistic strengthening model was developed for cast aluminum alloys containing both rod and plate-like precipitates. The model accurately accounts for the temperature dependence of particle nucleation and growth, solid solution strengthening, Si eutectic strength, and base aluminum yield strength. Strengthening model predictions of tensile yield strength are in excellent agreement with experimental observations over a wide range of aluminum alloy systems, aging temperatures, and test conditions. The developed models enable the prediction of the required particle morphology and volume fraction necessary to achieve target property goals in the design of future aluminum alloys. The effect of partitioning elements to the Q-phase was also considered for the potential to control the nucleation rate, reduce coarsening, and control the evolution of particle morphology. Elements were selected based on density functional theory (DFT) calculations showing the prevalence of certain elements to partition to the Q-phase. 3DAPT experiments were performed on Q-phase containing wrought alloys with these additions and show segregation of certain elements to the Q-phase with relative agreement to DFT predictions.

Thermodynamically consistent model calibration in chemical kinetics

PubMed Central

2011-01-01

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

Thermodynamic characterization of the multivalent interactions underlying rapid and selective translocation through the nuclear pore complex

PubMed Central

Hayama, Ryo; Sparks, Samuel; Hecht, Lee M.; Dutta, Kaushik; Karp, Jerome M.; Cabana, Christina M.; Rout, Michael P.; Cowburn, David

2018-01-01

Intrinsically disordered proteins (IDPs) play important roles in many biological systems. Given the vast conformational space that IDPs can explore, the thermodynamics of the interactions with their partners is closely linked to their biological functions. Intrinsically disordered regions of Phe–Gly nucleoporins (FG Nups) that contain multiple phenylalanine–glycine repeats are of particular interest, as their interactions with transport factors (TFs) underlie the paradoxically rapid yet also highly selective transport of macromolecules mediated by the nuclear pore complex. Here, we used NMR and isothermal titration calorimetry to thermodynamically characterize these multivalent interactions. These analyses revealed that a combination of low per-FG motif affinity and the enthalpy–entropy balance prevents high-avidity interaction between FG Nups and TFs, whereas the large number of FG motifs promotes frequent FG–TF contacts, resulting in enhanced selectivity. Our thermodynamic model underlines the importance of functional disorder of FG Nups. It helps explain the rapid and selective translocation of TFs through the nuclear pore complex and further expands our understanding of the mechanisms of “fuzzy” interactions involving IDPs. PMID:29374059

Thermodynamic Functions of Yttrium Trifluoride and Its Dimer in the Gas Phase

NASA Astrophysics Data System (ADS)

Osina, E. L.; Kovtun, D. M.

2018-05-01

New calculations of the functions for YF3 and Y2F6 in the gas phase using quantum-chemical calculations by MP2 and CCSD(T) methods are performed in connection with the ongoing work on obtaining reliable thermodynamic data of yttrium halides. The obtained values are entered in the database of the IVTANTERMO software complex. Equations approximating the temperature dependence of the reduced Gibbs energy in the T = 298.15-6000 K range of temperatures are presented.

New developments of the CARTE thermochemical code: A two-phase equation of state for nanocarbons

NASA Astrophysics Data System (ADS)

Dubois, Vincent; Pineau, Nicolas

2016-01-01

We developed a new equation of state (EOS) for nanocarbons in the thermodynamic range of high explosives detonation products (up to 50 GPa and 4000 K). This EOS was fitted to an extensive database of thermodynamic properties computed by molecular dynamics simulations of nanodiamonds and nano-onions with the LCBOPII potential. We reproduced the detonation properties of a variety of high explosives with the CARTE thermochemical code, including carbon-poor and carbon-rich explosives, with excellent accuracy.

The VLab repository of thermodynamics and thermoelastic properties of minerals

NASA Astrophysics Data System (ADS)

Da Silveira, P. R.; Sarkar, K.; Wentzcovitch, R. M.; Shukla, G.; Lindemann, W.; Wu, Z.

2015-12-01

Thermodynamics and thermoelastic properties of minerals at planetary interior conditions are essential as input for geodynamics simulations and for interpretation of seismic tomography models. Precise experimental determination of these properties at such extreme conditions is very challenging. Therefore, ab initio calculations play an essential role in this context, but at the cost of great computational effort and memory use. Setting up a widely accessible and versatile mineral physics database can relax unnecessary repetition of such computationally intensive calculations. Access to such data facilitates transactional interaction across fields and can advance more quickly insights about deep Earth processes. Hosted by the Minnesota Supercomputing Institute, the Virtual Laboratory for Earth and Planetary Materials (VLab) was designed to develop and promote the theory of planetary materials using distributed, high-throughput quantum calculations. VLab hosts an interactive database of thermodynamics and thermoelastic properties or minerals computed by ab initio. Such properties can be obtained according to user's preference. The database is accompanied by interactive visualization tools, allowing users to repeat and build upon previously published results. Using VLab2015, we have evaluated thermoelastic properties, such as elastic coefficients (Cij), Voigt, Reuss, and Voigt-Reuss-Hill aggregate averages for bulk (K) and shear modulus (G), shear wave velocity (VS), longitudinal wave velocity (Vp), and bulk sound velocity (V0) for several important minerals. Developed web services are general and can be used for crystals of any symmetry. Results can be tabulated, plotted, or downloaded from the VLab website according to user's preference.

Simulations of Precipitate Microstructure Evolution during Heat Treatment

NASA Astrophysics Data System (ADS)

Wu, Kaisheng; Sterner, Gustaf; Chen, Qing; Jou, Herng-Jeng; Jeppsson, Johan; Bratberg, Johan; Engström, Anders; Mason, Paul

Precipitation, a major solid state phase transformation during heat treatment processes, has for more than one century been intensively employed to improve the strength and toughness of various high performance alloys. Recently, sophisticated precipitation reaction models, in assistance with well-developed CALPHAD databases, provide an efficient and cost-effective way to tailor precipitate microstructures that maximize the strengthening effect via the optimization of alloy chemistries and heat treatment schedules. In this presentation, we focus on simulating precipitate microstructure evolution in Nickel-base superalloys under arbitrary heat treatment conditions. The newly-developed TC-PRISMA program has been used for these simulations, with models refined especially for non-isothermal conditions. The effect of different cooling profiles on the formation of multimodal microstructures has been thoroughly examined in order to understand the underlying thermodynamics and kinetics. Meanwhile, validations against several experimental results have been carried out. Practical issues that are critical to the accuracy and applicability of the current simulations, such as modifications that overcome mean-field approximations, compatibility between CALPHAD databases, selection of key parameters (particularly interfacial energy and nucleation site densities), etc., are also addressed.

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

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

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

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

Extension of a Kolmogorov Atmospheric Turbulence Model for Time-Based Simulation Implementation

NASA Technical Reports Server (NTRS)

McMinn, John D.

1997-01-01

The development of any super/hypersonic aircraft requires the interaction of a wide variety of technical disciplines to maximize vehicle performance. For flight and engine control system design and development on this class of vehicle, realistic mathematical simulation models of atmospheric turbulence, including winds and the varying thermodynamic properties of the atmosphere, are needed. A model which has been tentatively selected by a government/industry group of flight and engine/inlet controls representatives working on the High Speed Civil Transport is one based on the Kolmogorov spectrum function. This report compares the Dryden and Kolmogorov turbulence forms, and describes enhancements that add functionality to the selected Kolmogorov model. These added features are: an altitude variation of the eddy dissipation rate based on Dryden data, the mapping of the eddy dissipation rate database onto a regular latitude and longitude grid, a method to account for flight at large vehicle attitude angles, and a procedure for transitioning smoothly across turbulence segments.

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

NASA Astrophysics Data System (ADS)

Jacobs, M.; Schmid-Fetzer, R.

2012-04-01

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

Compact acoustic refrigerator

DOEpatents

Bennett, G.A.

1992-11-24

A compact acoustic refrigeration system actively cools components, e.g., electrical circuits, in a borehole environment. An acoustic engine includes first thermodynamic elements for generating a standing acoustic wave in a selected medium. An acoustic refrigerator includes second thermodynamic elements located in the standing wave for generating a relatively cold temperature at a first end of the second thermodynamic elements and a relatively hot temperature at a second end of the second thermodynamic elements. A resonator volume cooperates with the first and second thermodynamic elements to support the standing wave. To accommodate the high heat fluxes required for heat transfer to/from the first and second thermodynamic elements, first heat pipes transfer heat from the heat load to the second thermodynamic elements and second heat pipes transfer heat from first and second thermodynamic elements to the borehole environment. 18 figs.

Laser engines operating by resonance absorption. [thermodynamic feasibility study

NASA Technical Reports Server (NTRS)

Garbuny, M.; Pechersky, M. J.

1976-01-01

Basic tutorial article on the thermodynamic feasibility of laser engines at the present state of the art. Three main options are considered: (1) laser power applied externally to a heat reservoir (boiler approach); (2) internal heating of working fluid by resonance absorption; and (3) direct conversion of selective excitation into work. Only (2) is considered practically feasible at present. Basic concepts and variants, efficiency relations, upper temperature limits of laser engines, selection of absorbing gases, engine walls, bleaching, thermodynamic cycles of optimized laser engines, laser-powered turbines, laser heat pumps are discussed. Photon engines and laser dissociation engines are also considered.

Thermodynamic guiding principles in selective synthesis of strontium iridate Ruddlesden-Popper epitaxial Films

DOE PAGES

Nishio, Kazunori; Hwang, Harold Y.; Hikita, Yasuyuki

2016-03-10

We demonstrate the selective fabrication of Ruddlesden-Popper (RP) type SrIrO 3, Sr 3Ir 2O 7, and Sr 2IrO 4 epitaxialthin films from a single SrIrO 3 target using pulsed laser deposition(PLD). We identified that the growth conditions stabilizing each phase directly map onto the phase diagram expected from thermodynamic equilibria. This approach allows precise cation stoichiometry control as evidenced by the stabilization of single phase Sr 3Ir 2O 7 for the first time, overcoming the close thermodynamic stability between neighboring RP phases. Furthermore, despite the non-equilibrium nature of PLD, these results highlight the importance of thermodynamic guiding principles to strategicallymore » synthesize the targeted phase in complex oxide thin films.« less

Fluorination utilizing thermodynamically unstable fluorides and fluoride salts thereof

DOEpatents

Bartlett, Neil; Whalen, J. Marc; Chacon, Lisa

2000-12-12

A method for fluorinating a carbon compound or cationic carbon compound utilizes a fluorination agent selected from thermodynamically unstable nickel fluorides and salts thereof in liquid anhydrous hydrogen fluoride. The desired carbon compound or cationic organic compound to undergo fluorination is selected and reacted with the fluorination agent by contacting the selected organic or cationic organic compound and the chosen fluorination agent in a reaction vessel for a desired reaction time period at room temperature or less.

Element Distribution in Silicon Refining: Thermodynamic Model and Industrial Measurements

NASA Astrophysics Data System (ADS)

Næss, Mari K.; Kero, Ida; Tranell, Gabriella; Tang, Kai; Tveit, Halvard

2014-11-01

To establish an overview of impurity elemental distribution among silicon, slag, and gas/fume in the refining process of metallurgical grade silicon (MG-Si), an industrial measurement campaign was performed at the Elkem Salten MG-Si plant in Norway. Samples of in- and outgoing mass streams, i.e., tapped Si, flux and cooling materials, refined Si, slag, and fume, were analyzed by high-resolution inductively coupled plasma mass spectrometry (HR-ICP-MS), with respect to 62 elements. The elemental distributions were calculated and the experimental data compared with equilibrium estimations based on commercial and proprietary, published databases and carried out using the ChemSheet software. The results are discussed in terms of boiling temperatures, vapor pressures, redox potentials, and activities of the elements. These model calculations indicate a need for expanded databases with more and reliable thermodynamic data for trace elements in general and fume constituents in particular.

Internet calculations of thermodynamic properties of substances: Some problems and results

NASA Astrophysics Data System (ADS)

Ustyuzhanin, E. E.; Ochkov, V. F.; Shishakov, V. V.; Rykov, S. V.

2016-11-01

Internet resources (databases, web sites and others) on thermodynamic properties R = (p,T,s,...) of technologically important substances are analyzed. These databases put online by a number of organizations (the Joint Institute for High Temperatures of the Russian Academy of Sciences, Standartinform, the National Institute of Standards and Technology USA, the Institute for Thermal Physics of the Siberian Branch of the Russian Academy of Sciences, etc) are investigated. Software codes are elaborated in the work in forms of “client functions” those have such characteristics: (i) they are placed on a remote server, (ii) they serve as open interactive Internet resources. A client can use them for a calculation of R properties of substances. “Complex client functions” are considered. They are focused on sharing (i) software codes elaborated to design of power plants (PP) and (ii) client functions those can calculate R properties of working fluids for PP.

Thermodynamic Database for the NdO(1.5)-YO(1.5)-YbO(1.5)-ScO(1.5)-ZrO2 System

NASA Technical Reports Server (NTRS)

Jacobson, Nathan S.; Copland, Evan H.; Kaufman, Larry

2001-01-01

A database for YO(1.5)-NdO(1.5)-YbO(1.5)-ScO(1.5)-ZrO2 for ThermoCalc (ThermoCalc AB, Stockholm, Sweden) has been developed. The basis of this work is the YO(1.5)-ZrO2 assessment by Y. Du, Z. Jin, and P. Huang, 'Thermodynamic Assessment of the ZrO2-YO(1.5) System'. Experimentally only the YO(1.5)-ZrO2 system has been well-studied. All other systems are only approximately known. The major simplification in this work is the treatment of each single cation unit as a component. The pure liquid oxides are taken as reference states and two term lattice stability descriptions are used for each of the components. The limited experimental phase diagrams are reproduced.

Scheil-Gulliver Constituent Diagrams

NASA Astrophysics Data System (ADS)

Pelton, Arthur D.; Eriksson, Gunnar; Bale, Christopher W.

2017-06-01

During solidification of alloys, conditions often approach those of Scheil-Gulliver cooling in which it is assumed that solid phases, once precipitated, remain unchanged. That is, they no longer react with the liquid or with each other. In the case of equilibrium solidification, equilibrium phase diagrams provide a valuable means of visualizing the effects of composition changes upon the final microstructure. In the present study, we propose for the first time the concept of Scheil-Gulliver constituent diagrams which play the same role as that in the case of Scheil-Gulliver cooling. It is shown how these diagrams can be calculated and plotted by the currently available thermodynamic database computing systems that combine Gibbs energy minimization software with large databases of optimized thermodynamic properties of solutions and compounds. Examples calculated using the FactSage system are presented for the Al-Li and Al-Mg-Zn systems, and for the Au-Bi-Sb-Pb system and its binary and ternary subsystems.

Thermodynamic scaling of the shear viscosity of Mie n-6 fluids and their binary mixtures

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

Delage-Santacreu, Stephanie; Galliero, Guillaume, E-mail: guillaume.galliero@univ-pau.fr; Hoang, Hai

2015-05-07

In this work, we have evaluated the applicability of the so-called thermodynamic scaling and the isomorph frame to describe the shear viscosity of Mie n-6 fluids of varying repulsive exponents (n = 8, 12, 18, 24, and 36). Furthermore, the effectiveness of the thermodynamic scaling to deal with binary mixtures of Mie n-6 fluids has been explored as well. To generate the viscosity database of these fluids, extensive non-equilibrium molecular dynamics simulations have been performed for various thermodynamic conditions. Then, a systematic approach has been used to determine the gamma exponent value (γ) characteristic of the thermodynamic scaling approach formore » each system. In addition, the applicability of the isomorph theory with a density dependent gamma has been confirmed in pure fluids. In both pure fluids and mixtures, it has been found that the thermodynamic scaling with a constant gamma is sufficient to correlate the viscosity data on a large range of thermodynamic conditions covering liquid and supercritical states as long as the density is not too high. Interestingly, it has been obtained that, in pure fluids, the value of γ is directly proportional to the repulsive exponent of the Mie potential. Finally, it has been found that the value of γ in mixtures can be deduced from those of the pure component using a simple logarithmic mixing rule.« less

Compact acoustic refrigerator

DOEpatents

Bennett, Gloria A.

1992-01-01

A compact acoustic refrigeration system actively cools components, e.g., electrical circuits (22), in a borehole environment. An acoustic engine (12, 14) includes first thermodynamic elements (12) for generating a standing acoustic wave in a selected medium. An acoustic refrigerator (16, 26, 28) includes second thermodynamic elements (16) located in the standing wave for generating a relatively cold temperature at a first end of the second thermodynamic elements (16) and a relatively hot temperature at a second end of the second thermodynamic elements (16). A resonator volume (18) cooperates with the first and second thermodynamic elements (12, 16) to support the standing wave. To accommodate the high heat fluxes required for heat transfer to/from the first and second thermodynamic elements (12, 16), first heat pipes (24, 26) transfer heat from the heat load (22) to the second thermodynamic elements (16) and second heat pipes (28, 32) transfer heat from first and second thermodynamic elements (12, 16) to the borehole environment.

Cyanide and antimony thermodynamic database for the aqueous species and solids for the EPA-MINTEQ geochemical code

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

Sehmel, G.A.

1989-05-01

Thermodynamic data for aqueous species and solids that contain cyanide and antimony were tabulated from several commonly accepted, published sources of thermodynamic data and recent journal article. The review does not include gases or organic complexes of either antimony or cyanide, nor does the review include the sulfur compounds of cyanide. The basic thermodynamic data, ..delta..G/sub f,298//sup o/, ..delta..H/sub f,298//sup o/, and S/sub f//sup o/ values, were chosen to represent each solid phase and aqueous species for which data were available in the appropriate standard state. From these data the equilibrium constants (log K/sub r,298//sup o/) and enthalpies of reactionmore » (..delta..H/sub r,298//sup o/) at 298 K (25/degree/C) were calculated for reactions involving the formation of these aqueous species and solids from the basic components. 34 refs., 14 tabs.« less

On a Thermodynamic Approach to Material Selection for Service in Aggressive Multi-Component Gaseous and/or Vapor Environments

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

Glazoff, Michael Vasily; Marschman, Steven Craig; Soelberg, Nicholas Ray

This report fulfills the M4 milestone, M4FT-15IN08020110 UNF Analysis Support, under Work Package Number FT-15IN080201. The issue of materials selection for many engineering applications represents an important problem, particularly in cases where material failure is possible as a result of corrosive environments. For example, 304 dual purpose or 316 stainless steel is used in the construction of many used nuclear fuel storage canisters. Deployed all over the world, these canisters are housed inside shielded enclosures and cooled passively by convective airflow. When located along seaboards or particular industrial areas, salt, other corrosive chemicals, and moisture can become entrained in themore » air that cools the canisters. It is important to develop an understanding of what impact, if any, that chemical environment will have on those canisters. In many cases of corrosion in aggressive gaseous environments, the material selection process is based on some general recommendations, anecdotal evidence, and/or the past experience of that particular project’s participants. For gaseous mixtures, the theoretical basis is practically limited to the construction of the so-called “Ellingham diagrams” for pure metals. These plots predict the equilibrium temperature between different individual metals, their respective oxides, and oxygen gas. Similar diagrams can be constructed for the reactions with sulfur, nitrogen, carbon, etc. In the generalization of this approach by Richardson and Jeffes, additional scales can be superimposed upon an Ellingham diagram that would correspond to different gaseous mixtures, e.g. CO/CO 2, or H 2/H 2O. However, while the general approach to predicting the stability of a multi-component heterogeneous alloy (e.g., steel or a superalloy) in a multi-component aggressive gaseous environment was developed in very general form, actual examples of its applications to concrete real-life problems are practically absent. This is related to alloy design, corrosion protection, and material selection for different applications. In this work, an effort was made to advance in that direction using modern computational thermodynamics methodology, software, and databases by Thermo-Calc Inc. The developed methodology is illustrated by the case study – a process of nuclear waste immobilization using a chemical engineering approach described below. The developed methodology can be considered a practical illustration of the Ellingham approach generalization and could be used for obtaining thermodynamic guidance on a given process’ feasibility using equipment/sensors made of a particular multicomponent heterogeneous metallic alloy.« less

Understanding AlN Obtaining Through Computational Thermodynamics Combined with Experimental Investigation

NASA Astrophysics Data System (ADS)

Florea, R. M.

2017-06-01

Basic material concept, technology and some results of studies on aluminum matrix composite with dispersive aluminum nitride reinforcement was shown. Studied composites were manufactured by „in situ” technique. Aluminum nitride (AlN) has attracted large interest recently, because of its high thermal conductivity, good dielectric properties, high flexural strength, thermal expansion coefficient matches that of Si and its non-toxic nature, as a suitable material for hybrid integrated circuit substrates. AlMg alloys are the best matrix for AlN obtaining. Al2O3-AlMg, AlN-Al2O3, and AlN-AlMg binary diagrams were thermodynamically modelled. The obtained Gibbs free energies of components, solution parameters and stoichiometric phases were used to build a thermodynamic database of AlN- Al2O3-AlMg system. Obtaining of AlN with Liquid-phase of AlMg as matrix has been studied and compared with the thermodynamic results. The secondary phase microstructure has a significant effect on the final thermal conductivity of the obtained AlN. Thermodynamic modelling of AlN-Al2O3-AlMg system provided an important basis for understanding the obtaining behavior and interpreting the experimental results.

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

PubMed Central

Phan, Andy; Mailey, Katherine; Saeki, Jessica; Gu, Xiaobo

2017-01-01

Accurate thermodynamic parameters improve RNA structure predictions and thus accelerate understanding of RNA function and the identification of RNA drug binding sites. Many viral RNA structures, such as internal ribosome entry sites, have internal loops and bulges that are potential drug target sites. Current models used to predict internal loops are biased toward small, symmetric purine loops, and thus poorly predict asymmetric, pyrimidine-rich loops with >6 nucleotides (nt) that occur frequently in viral RNA. This article presents new thermodynamic data for 40 pyrimidine loops, many of which can form UU or protonated CC base pairs. Uracil and protonated cytosine base pairs stabilize asymmetric internal loops. Accurate prediction rules are presented that account for all thermodynamic measurements of RNA asymmetric internal loops. New loop initiation terms for loops with >6 nt are presented that do not follow previous assumptions that increasing asymmetry destabilizes loops. Since the last 2004 update, 126 new loops with asymmetry or sizes greater than 2 × 2 have been measured. These new measurements significantly deepen and diversify the thermodynamic database for RNA. These results will help better predict internal loops that are larger, pyrimidine-rich, and occur within viral structures such as internal ribosome entry sites. PMID:28213527

Experimental study and thermodynamic modeling of the Al–Co–Cr–Ni system

DOE PAGES

Gheno, Thomas; Liu, Xuan L.; Lindwall, Greta; ...

2015-09-21

In this study, a thermodynamic database for the Al–Co–Cr–Ni system is built via the Calphad method by extrapolating re-assessed ternary subsystems. A minimum number of quaternary parameters are included, which are optimized using experimental phase equilibrium data obtained by electron probe micro-analysis and x-ray diffraction analysis of NiCoCrAlY alloys spanning a wide compositional range, after annealing at 900 °C, 1100 °C and 1200 °C, and water quenching. These temperatures are relevant to oxidation and corrosion resistant MCrAlY coatings, where M corresponds to some combination of nickel and cobalt. Comparisons of calculated and measured phase compositions show excellent agreement for themore » β–γ equilibrium, and good agreement for three-phase β–γ–σ and β–γ–α equilibria. An extensive comparison with existing Ni-base databases (TCNI6, TTNI8, NIST) is presented in terms of phase compositions.« less

Darwinian demons, evolutionary complexity, and information maximization.

PubMed

Krakauer, David C

2011-09-01

Natural selection is shown to be an extended instance of a Maxwell's demon device. A demonic selection principle is introduced that states that organisms cannot exceed the complexity of their selective environment. Thermodynamic constraints on error repair impose a fundamental limit to the rate that information can be transferred from the environment (via the selective demon) to the genome. Evolved mechanisms of learning and inference can overcome this limitation, but remain subject to the same fundamental constraint, such that plastic behaviors cannot exceed the complexity of reward signals. A natural measure of evolutionary complexity is provided by mutual information, and niche construction activity--the organismal contribution to the construction of selection pressures--might in principle lead to its increase, bounded by thermodynamic free energy required for error correction.

Electrochemistry of the Zinc-Silver Oxide System. Part 1: Thermodynamic Studies Using Commercial Miniature Cells.

ERIC Educational Resources Information Center

Smith, Michael J.; Vincent, Colin A.

1989-01-01

Uses reversible electrochemical cells near equilibrium to study basic thermodynamic concepts such as maximum work and free energy. Selects sealed, miniature, commercial cells to obtain accurate measurement of enthalpy, entropy, and Gibbs free energy. (MVL)

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

NASA Technical Reports Server (NTRS)

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

2003-01-01

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

An efficient and general approach for implementing thermodynamic phase equilibria information in geophysical and geodynamic studies

NASA Astrophysics Data System (ADS)

Afonso, Juan Carlos; Zlotnik, Sergio; Díez, Pedro

2015-10-01

We present a flexible, general, and efficient approach for implementing thermodynamic phase equilibria information (in the form of sets of physical parameters) into geophysical and geodynamic studies. The approach is based on Tensor Rank Decomposition methods, which transform the original multidimensional discrete information into a separated representation that contains significantly fewer terms, thus drastically reducing the amount of information to be stored in memory during a numerical simulation or geophysical inversion. Accordingly, the amount and resolution of the thermodynamic information that can be used in a simulation or inversion increases substantially. In addition, the method is independent of the actual software used to obtain the primary thermodynamic information, and therefore, it can be used in conjunction with any thermodynamic modeling program and/or database. Also, the errors associated with the decomposition procedure are readily controlled by the user, depending on her/his actual needs (e.g., preliminary runs versus full resolution runs). We illustrate the benefits, generality, and applicability of our approach with several examples of practical interest for both geodynamic modeling and geophysical inversion/modeling. Our results demonstrate that the proposed method is a competitive and attractive candidate for implementing thermodynamic constraints into a broad range of geophysical and geodynamic studies. MATLAB implementations of the method and examples are provided as supporting information and can be downloaded from the journal's website.

Prediction of precipitate evolution and martensite transformation in Ti-Ni-Cu shape memory alloys by computational thermodynamics

NASA Astrophysics Data System (ADS)

Povoden-Karadeniz, A.; Cirstea, D. C.; Kozeschnik, E.

2016-04-01

Ti-50Ni to Ti-55Ni (at.%) can be termed as the pioneer of shape memory alloys (SMA). Intermetallic precipitates play an important role for strengthening. Their influence on the start temperature of the martensitic transformation is a crucial property for the shape memory effect. Efforts for increasing the martensite start temperature include replacement of a part of Ni atoms by Cu. The influence of Cu-addition to Ti-Ni SMA on T0- temperatures and the character of the austenite-martensite transformation is evaluated using a new thermodynamic database for the Ti-Ni-system extended by Cu. Trends of precipitation of intermetallic phases are simulated by combining the assessed thermodynamics of the Ti-Ni-Cu system with assessed diffusion mobility data and kinetic models, as implemented in the solid-state transformation software MatCalc and are presented in the form of time-temperature-precipitation diagrams. Thermodynamic equilibrium considerations, complemented by predictive thermo-kinetic precipitation simulation, facilitates SMA alloy design and definition of optimized aging conditions.

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

PubMed

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

2017-05-01

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

The modelling routes for the chemical vapour deposition process: application to Si 1- xGe x deposition

NASA Astrophysics Data System (ADS)

Pons, M.; Bernard, C.; Rouch, H.; Madar, R.

1995-10-01

The purpose of this article is to present the modelling routes for the chemical vapour deposition process with a special emphasis on mass transport models with near local thermochemical equilibrium imposed in the gas-phase and at the deposition surface. The theoretical problems arising from the linking of the two selected approaches, thermodynamics and mass transport, are shown and a solution procedure is proposed. As an illustration, selected results of thermodynamic and mass transport analysis and of the coupled approach showed that, for the deposition of Si 1- xGe x solid solution at 1300 K (system SiGeClHAr), the thermodynamic heterogeneous stability of the reactive gases and the thermal diffusion led to the germanium depletion of the deposit.

Personalized anticancer therapy selection using molecular landscape topology and thermodynamics.

PubMed

Rietman, Edward A; Scott, Jacob G; Tuszynski, Jack A; Klement, Giannoula Lakka

2017-03-21

Personalized anticancer therapy requires continuous consolidation of emerging bioinformatics data into meaningful and accurate information streams. The use of novel mathematical and physical approaches, namely topology and thermodynamics can enable merging differing data types for improved accuracy in selecting therapeutic targets. We describe a method that uses chemical thermodynamics and two topology measures to link RNA-seq data from individual patients with academically curated protein-protein interaction networks to select clinically relevant targets for treatment of low-grade glioma (LGG). We show that while these three histologically distinct tumor types (astrocytoma, oligoastrocytoma, and oligodendroglioma) may share potential therapeutic targets, the majority of patients would benefit from more individualized therapies. The method involves computing Gibbs free energy of the protein-protein interaction network and applying a topological filtration on the energy landscape to produce a subnetwork known as persistent homology. We then determine the most likely best target for therapeutic intervention using a topological measure of the network known as Betti number. We describe the algorithm and discuss its application to several patients.

Thermodynamic analysis of steam-injected advanced gas turbine cycles

NASA Astrophysics Data System (ADS)

Pandey, Devendra; Bade, Mukund H.

2017-12-01

This paper deals with thermodynamic analysis of steam-injected gas turbine (STIGT) cycle. To analyse the thermodynamic performance of steam-injected gas turbine (STIGT) cycles, a methodology based on pinch analysis is proposed. This graphical methodology is a systematic approach proposed for a selection of gas turbine with steam injection. The developed graphs are useful for selection of steam-injected gas turbine (STIGT) for optimal operation of it and helps designer to take appropriate decision. The selection of steam-injected gas turbine (STIGT) cycle can be done either at minimum steam ratio (ratio of mass flow rate of steam to air) with maximum efficiency or at maximum steam ratio with maximum net work conditions based on the objective of plants designer. Operating the steam injection based advanced gas turbine plant at minimum steam ratio improves efficiency, resulting in reduction of pollution caused by the emission of flue gases. On the other hand, operating plant at maximum steam ratio can result in maximum work output and hence higher available power.

Competing Thermodynamic and Dynamic Factors Select Molecular Assemblies on a Gold Surface

NASA Astrophysics Data System (ADS)

Haxton, Thomas K.; Zhou, Hui; Tamblyn, Isaac; Eom, Daejin; Hu, Zonghai; Neaton, Jeffrey B.; Heinz, Tony F.; Whitelam, Stephen

2013-12-01

Controlling the self-assembly of surface-adsorbed molecules into nanostructures requires understanding physical mechanisms that act across multiple length and time scales. By combining scanning tunneling microscopy with hierarchical ab initio and statistical mechanical modeling of 1,4-substituted benzenediamine (BDA) molecules adsorbed on a gold (111) surface, we demonstrate that apparently simple nanostructures are selected by a subtle competition of thermodynamics and dynamics. Of the collection of possible BDA nanostructures mechanically stabilized by hydrogen bonding, the interplay of intermolecular forces, surface modulation, and assembly dynamics select at low temperature a particular subset: low free energy oriented linear chains of monomers and high free energy branched chains.

Silicate and Carbonatite Melts in the Mantle: Adding CO2 to the pMELTS Thermodynamic Model of Silicate Phase Equilibria

NASA Astrophysics Data System (ADS)

Antoshechkina, P. M.; Shorttle, O.

2016-12-01

The current rhyolite-MELTS algorithm includes a mixed H2O-CO2 vapor phase, and a self-consistent speciation model for CO2 and CaCO3 in the silicate liquid (Ghiorso & Gualda 2012; 2015). Although intended primarily to model crustal differentiation and degassing, GG15 captures much of the experimentally-observed melting behavior of CO2-rich mafic lithologies, including generation of small-degree carbonatite melts, a miscibility gap between carbonatite and silicate liquids at low P and a smooth transition to a single carbonated-silicate melt at high P (e.g. Dasgupta et al. 2007). However, solid and liquid carbonate phases were not used in calibration of GG15, and it is suitable only for P < 3 GPa. We present a preliminary model, based on pMELTS (Ghiorso et al. 2002), for melting of nominally-anhydrous carbonated peridotite and pyroxenite. In Antoshechkina et al. (2015; and references therein) we developed a scheme for calibration of molar volumes that directly interfaces with a MySQL database, adapted from LEPR (Hirschmann et al. 2008). Here, we further extend our database, e.g. to include multiple carbonate phases, and combine the calibration scheme with the libalphaMELTS interface to the rhyolite-MELTS, pMELTS, and H2O-CO2 fluid thermodynamic models (see magmasource.caltech.edu/alphamelts). We use a Monte-Carlo type calibration approach to fit the observed phases and compositions, though stop short of a fully Bayesian formulation. The CO2-fluid experimental database has been updated to include more recent and higher P studies, adding approximately 40 pure fluid plus liquid constraints that conform to the selection criteria used in GG15. To further expand the database, we plan to use some or all of: solid carbonate-bearing experiments; coexisting silicate and carbonatite liquids; phase-present, and phase-absent constraints. As a first approximation, we include four carbonate phases: pure calcite and aragonite, and binary solutions for dolomite-ankerite and magnesite-siderite. Following GG15, we have adopted the CO2 fluid model of Duan & Zhang (2006) and added CO2 and CaCO3 species to the pMELTS liquid model. A key question that we hope to address during calibration is whether a Na2CO3 liquid species is justified instead of, or in addition to, CaCO3 for the range over which pMELTS is calibrated (1 < P < 4 GPa).

Development of a component design tool for metal hydride heat pumps

NASA Astrophysics Data System (ADS)

Waters, Essene L.

Given current demands for more efficient and environmentally friendly energy sources, hydrogen based energy systems are an increasingly popular field of interest. Within the field, metal hydrides have become a prominent focus of research due to their large hydrogen storage capacity and relative system simplicity and safety. Metal hydride heat pumps constitute one such application, in which heat and hydrogen are transferred to and from metal hydrides. While a significant amount of work has been done to study such systems, the scope of materials selection has been quite limited. Typical studies compare only a few metal hydride materials and provide limited justification for the choice of those few. In this work, a metal hydride component design tool has been developed to enable the targeted down-selection of an extensive database of metal hydrides to identify the most promising materials for use in metal hydride thermal systems. The material database contains over 300 metal hydrides with various physical and thermodynamic properties included for each material. Sub-models for equilibrium pressure, thermophysical data, and default properties are used to predict the behavior of each material within the given system. For a given thermal system, this tool can be used to identify optimal materials out of over 100,000 possible hydride combinations. The selection tool described herein has been applied to a stationary combined heat and power system containing a high-temperature proton exchange membrane (PEM) fuel cell, a hot water tank, and two metal hydride beds used as a heat pump. A variety of factors can be used to select materials including efficiency, maximum and minimum system pressures, pressure difference, coefficient of performance (COP), and COP sensitivity. The targeted down-selection of metal hydrides for this system focuses on the system's COP for each potential pair. The values of COP and COP sensitivity have been used to identify pairs of highest interest for use in this application. The metal hydride component design tool developed in this work selects between metal hydride materials on an unprecedented scale. It can be easily applied to other hydrogen-based thermal systems, making it a powerful and versatile tool.

Thermodynamics of organic compounds

NASA Astrophysics Data System (ADS)

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

1982-11-01

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

A reduced basis approach for implementing thermodynamic phase-equilibria information in geophysical and geodynamic studies

NASA Astrophysics Data System (ADS)

Afonso, J. C.; Zlotnik, S.; Diez, P.

2015-12-01

We present a flexible, general and efficient approach for implementing thermodynamic phase equilibria information (in the form of sets of physical parameters) into geophysical and geodynamic studies. The approach is based on multi-dimensional decomposition methods, which transform the original multi-dimensional discrete information into a dimensional-separated representation. This representation has the property of increasing the number of coefficients to be stored linearly with the number of dimensions (opposite to a full multi-dimensional cube requiring exponential storage depending on the number of dimensions). Thus, the amount of information to be stored in memory during a numerical simulation or geophysical inversion is drastically reduced. Accordingly, the amount and resolution of the thermodynamic information that can be used in a simulation or inversion increases substantially. In addition, the method is independent of the actual software used to obtain the primary thermodynamic information, and therefore it can be used in conjunction with any thermodynamic modeling program and/or database. Also, the errors associated with the decomposition procedure are readily controlled by the user, depending on her/his actual needs (e.g. preliminary runs vs full resolution runs). We illustrate the benefits, generality and applicability of our approach with several examples of practical interest for both geodynamic modeling and geophysical inversion/modeling. Our results demonstrate that the proposed method is a competitive and attractive candidate for implementing thermodynamic constraints into a broad range of geophysical and geodynamic studies.

A computational study of diffusion in a glass-forming metallic liquid

DOE PAGES

Wang, T.; Zhang, F.; Yang, L.; ...

2015-06-09

In this study, liquid phase diffusion plays a critical role in phase transformations (e.g. glass transformation and devitrification) observed in marginal glass forming systems such as Al-Sm. Controlling transformation pathways in such cases requires a comprehensive description of diffusivity, including the associated composition and temperature dependencies. In our computational study, we examine atomic diffusion in Al-Sm liquids using ab initio molecular dynamics (AIMD) and determine the diffusivities of Al and Sm for selected alloy compositions. Non-Arrhenius diffusion behavior is observed in the undercooled liquids with an enhanced local structural ordering. Through assessment of our AIMD result, we construct a generalmore » formulation for Al-Sm liquid, involving a diffusion mobility database that includes composition and temperature dependence. A Volmer-Fulcher-Tammann (VFT) equation is adopted for describing the non-Arrhenius behavior observed in the undercooled liquid. Furthermore, the composition dependence of diffusivity is found quite strong, even for the Al-rich region contrary to the sole previous report on this binary system. The model is used in combination with the available thermodynamic database to predict specific diffusivities and compares well with reported experimental data for 0.6 at.% and 5.6 at.% Sm in Al-Sm alloys.« less

Probabilistic Analysis of Solid Oxide Fuel Cell Based Hybrid Gas Turbine System

NASA Technical Reports Server (NTRS)

Gorla, Rama S. R.; Pai, Shantaram S.; Rusick, Jeffrey J.

2003-01-01

The emergence of fuel cell systems and hybrid fuel cell systems requires the evolution of analysis strategies for evaluating thermodynamic performance. A gas turbine thermodynamic cycle integrated with a fuel cell was computationally simulated and probabilistically evaluated in view of the several uncertainties in the thermodynamic performance parameters. Cumulative distribution functions and sensitivity factors were computed for the overall thermal efficiency and net specific power output due to the uncertainties in the thermodynamic random variables. These results can be used to quickly identify the most critical design variables in order to optimize the design and make it cost effective. The analysis leads to the selection of criteria for gas turbine performance.

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

Ji, Yanzhou; Heo, Tae Wook; Zhang, Fan

Here we present our theoretical assessment of the kinetic pathways during phase transformations of multi-component Ti alloys. Employing the graphical thermodynamic approach and an integrated free energy function based on the realistic thermodynamic database and assuming that a displacive structural transformation occurs much faster than long-range diffusional processes, we analyze the phase stabilities of Ti-6Al -4V (Ti-6wt.%Al -4wt.%V). Our systematic analyses predict a variety of possible kinetic pathways for β to (α + β) transformations leading to different types of microstructures under various heat treatment conditions. In addition, the possibility of unconventional kinetic pathways is discussed. Lastly, we also brieflymore » discuss the application of our approach to general multicomponent/multiphase alloy systems.« less

The optical method for determining the thermodynamic parameters of hot gases

NASA Astrophysics Data System (ADS)

Egorov, O. V.; Voitsekhovskaya, O. K.; Kashirskii, D. E.; Tsvyk, R. Sh.; Sazanovich, V. M.; Sherstobitov, M. V.

2014-11-01

The research conducted on the thermodynamic parameters of a flame was based on its experimental transmission spectra in the 2.7 μm and 4.3 μm ranges. To produce the flame, alcohol was burned under atmospheric conditions. The hot gases resulting from the burning of ethanol (H2O, CO, and CO2) were accelerated and spun by the rotation of an impeller. The optical method developed by the authors was employed for predicting the temperature and partial pressure of the hot gases. The results demonstrate the practical significance of the method suggested. The spectroscopic database HITEMP 2010 was used for all line-by-line calculations presented in the article.

Nitrogen in chromium-manganese stainless steels: a review on the evaluation of stacking fault energy by computational thermodynamics.

PubMed

Mosecker, Linda; Saeed-Akbari, Alireza

2013-06-01

Nitrogen in austenitic stainless steels and its effect on the stacking fault energy (SFE) has been the subject of intense discussions in the literature. Until today, no generally accepted method for the SFE calculation exists that can be applied to a wide range of chemical compositions in these systems. Besides different types of models that are used from first-principle to thermodynamics-based approaches, one main reason is the general lack of experimentally measured SFE values for these steels. Moreover, in the respective studies, not only different alloying systems but also different domains of nitrogen contents were analyzed resulting in contrary conclusions on the effect of nitrogen on the SFE. This work gives a review on the current state of SFE calculation by computational thermodynamics for the Fe-Cr-Mn-N system. An assessment of the thermodynamic effective Gibbs free energy, [Formula: see text], model for the [Formula: see text] phase transformation considering existing data from different literature and commercial databases is given. Furthermore, we introduce the application of a non-constant composition-dependent interfacial energy, б γ / ε , required to consider the effect of nitrogen on SFE in these systems.

Nitrogen in chromium–manganese stainless steels: a review on the evaluation of stacking fault energy by computational thermodynamics

PubMed Central

Mosecker, Linda; Saeed-Akbari, Alireza

2013-01-01

Nitrogen in austenitic stainless steels and its effect on the stacking fault energy (SFE) has been the subject of intense discussions in the literature. Until today, no generally accepted method for the SFE calculation exists that can be applied to a wide range of chemical compositions in these systems. Besides different types of models that are used from first-principle to thermodynamics-based approaches, one main reason is the general lack of experimentally measured SFE values for these steels. Moreover, in the respective studies, not only different alloying systems but also different domains of nitrogen contents were analyzed resulting in contrary conclusions on the effect of nitrogen on the SFE. This work gives a review on the current state of SFE calculation by computational thermodynamics for the Fe–Cr–Mn–N system. An assessment of the thermodynamic effective Gibbs free energy, , model for the phase transformation considering existing data from different literature and commercial databases is given. Furthermore, we introduce the application of a non-constant composition-dependent interfacial energy, бγ/ε, required to consider the effect of nitrogen on SFE in these systems. PMID:27877573

Thermodynamic assessment and binary nucleation modeling of Sn-seeded InGaAs nanowires

NASA Astrophysics Data System (ADS)

Ghasemi, Masoomeh; Selleby, Malin; Johansson, Jonas

2017-11-01

We have performed a thermodynamic assessment of the As-Ga-In-Sn system based on the CALculation of PHAse Diagram (CALPHAD) method. This system is part of a comprehensive thermodynamic database that we are developing for nanowire materials. Specifically, the As-Ga-In-Sn can be used in modeling the growth of GaAs, InAs, and InxGa1-xAs nanowires assisted by Sn liquid seeds. In this work, the As-Sn binary, the As-Ga-Sn, As-In-Sn, and Ga-In-Sn ternary systems have been thermodynamically assessed using the CALPHAD method. We show the relevant phase diagrams and property diagrams. They all show good agreement with experimental data. Using our optimized description we have modeled the nucleation of InxGa1-xAs in the zinc blende phase from a Sn-based quaternary liquid alloy using binary nucleation modeling. We have linked the composition of the solid nucleus to the composition of the liquid phase. Eventually, we have predicted the critical size of the nucleus that forms from InAs and GaAs pairs under various conditions. We believe that our modeling can guide future experimental realization of Sn-seeded InxGa1-xAs nanowires.

Environmental and Molecular Science Laboratory Arrow

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

2016-06-24

Arrows is a software package that combines NWChem, SQL and NOSQL databases, email, and social networks (e.g. Twitter, Tumblr) that simplifies molecular and materials modeling and makes these modeling capabilities accessible to all scientists and engineers. EMSL Arrows is very simple to use. The user just emails chemical reactions to arrows@emsl.pnnl.gov and then an email is sent back with thermodynamic, reaction pathway (kinetic), spectroscopy, and other results. EMSL Arrows parses the email and then searches the database for the compounds in the reactions. If a compound isn't there, an NWChem calculation is setup and submitted to calculate it. Once themore » calculation is finished the results are entered into the database and then results are emailed back.« less

Correlation of water vapor adsorption behavior of wood with surface thermodynamic properties

Treesearch

Mandla A. Tshabalala; Agnes R. Denes; R. Sam Williams

1999-01-01

To improve the overall performance of wood-plastic composites, appropriate technologies are needed to control moisture sorption and to improve the interaction of wood fiber with selected hydrophobic matrices. The objective of this study was to determine the surface thermodynamic characteristics of a wood fiber and to correlate those characteristics with the fiberas...

Temperature Dependence of Mineral Solubility in Water. Part 3. Alkaline and Alkaline Earth Sulfates

NASA Astrophysics Data System (ADS)

Krumgalz, B. S.

2018-06-01

The databases of alkaline and alkaline earth sulfate solubilities in water at various temperatures were created using experimental data from the publications over about the last two centuries. Statistical critical evaluation of the created databases was produced since there were enough independent data sources to justify such evaluation. The reliable experimental data were adequately described by polynomial expressions over various temperature ranges. Using the Pitzer approach for ionic activity and osmotic coefficients, the thermodynamic solubility products for the discussed minerals have been calculated at various temperatures and represented by polynomial expressions.

Temperature Dependence of Mineral Solubility in Water. Part 2. Alkaline and Alkaline Earth Bromides

NASA Astrophysics Data System (ADS)

Krumgalz, B. S.

2018-03-01

Databases of alkaline and alkaline earth bromide solubilities in water at various temperatures were created using experimental data from publications over about the last two centuries. Statistical critical evaluation of the created databases was produced since there were enough independent data sources to justify such evaluation. The reliable experimental data were adequately described by polynomial expressions over various temperature ranges. Using the Pitzer approach for ionic activity and osmotic coefficients, the thermodynamic solubility products for the discussed bromide minerals have been calculated at various temperature intervals and also represented by polynomial expressions.

Thermodynamic assessment of the LiF-ThF4-PuF3-UF4 system

NASA Astrophysics Data System (ADS)

Capelli, E.; Beneš, O.; Konings, R. J. M.

2015-07-01

The LiF-ThF4-PuF3-UF4 system is the reference salt mixture considered for the Molten Salt Fast Reactor (MSFR) concept started with PuF3. In order to obtain the complete thermodynamic description of this quaternary system, two binary systems (ThF4-PuF3 and UF4-PuF3) and two ternary systems (LiF-ThF4-PuF3 and LiF-UF4-PuF3) have been assessed for the first time. The similarities between CeF3/PuF3 and ThF4/UF4 compounds have been taken into account for the presented optimization as well as in the experimental measurements performed, which have confirmed the temperatures predicted by the model. Moreover, the experimental results and the thermodynamic database developed have been used to identify potential compositions for the MSFR fuel and to evaluate the influence of partial substitution of ThF4 by UF4 in the salt.

A combined experimental and computational thermodynamic investigation of the U-Th-O system

DOE PAGES

McMurray, Jake Wesley; Voit, Stewart L.; Besmann, Theodore M.

2016-03-21

Here, the thermodynamics of the U–Th–O system have been assessed using the Calphad method. The compound energy formalism (CEF) and a partially ionic two-sublattice liquid model (TSLM) were used for the fluorite U 1–yTh yO 2±x, γ-(U,Th) 4O 9, and the U–Th–O melt. The O 2 activity of fluorite U 1–yTh yO 2±x with temperature and composition was determined by thermogravimetric analysis. Thermodynamic studies for the Th–O binary and U–Th–O ternary available in the open literature were critically reviewed. A self-consistent data set was selected and compiled with the equilibrium oxygen pressures determined by thermogravimetry in order to optimize themore » adjustable parameters of models selected to represent the phases in the Th–O and U–Th–O systems.« less

Statistical thermodynamics of clustered populations.

PubMed

Matsoukas, Themis

2014-08-01

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

dbAMEPNI: a database of alanine mutagenic effects for protein–nucleic acid interactions

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

Liu, Ling; Xiong, Yi; Gao, Hongyun

Protein–nucleic acid interactions play essential roles in various biological activities such as gene regulation, transcription, DNA repair and DNA packaging. Understanding the effects of amino acid substitutions on protein–nucleic acid binding affinities can help elucidate the molecular mechanism of protein–nucleic acid recognition. Until now, no comprehensive and updated database of quantitative binding data on alanine mutagenic effects for protein–nucleic acid interactions is publicly accessible. Thus, we developed a new database of Alanine Mutagenic Effects for Protein-Nucleic Acid Interactions (dbAMEPNI). dbAMEPNI is a manually curated, literature-derived database, comprising over 577 alanine mutagenic data with experimentally determined binding affinities for protein–nucleic acidmore » complexes. Here, it contains several important parameters, such as dissociation constant (Kd), Gibbs free energy change (ΔΔG), experimental conditions and structural parameters of mutant residues. In addition, the database provides an extended dataset of 282 single alanine mutations with only qualitative data (or descriptive effects) of thermodynamic information.« less

dbAMEPNI: a database of alanine mutagenic effects for protein–nucleic acid interactions

DOE PAGES

Liu, Ling; Xiong, Yi; Gao, Hongyun; ...

2018-04-02

Protein–nucleic acid interactions play essential roles in various biological activities such as gene regulation, transcription, DNA repair and DNA packaging. Understanding the effects of amino acid substitutions on protein–nucleic acid binding affinities can help elucidate the molecular mechanism of protein–nucleic acid recognition. Until now, no comprehensive and updated database of quantitative binding data on alanine mutagenic effects for protein–nucleic acid interactions is publicly accessible. Thus, we developed a new database of Alanine Mutagenic Effects for Protein-Nucleic Acid Interactions (dbAMEPNI). dbAMEPNI is a manually curated, literature-derived database, comprising over 577 alanine mutagenic data with experimentally determined binding affinities for protein–nucleic acidmore » complexes. Here, it contains several important parameters, such as dissociation constant (Kd), Gibbs free energy change (ΔΔG), experimental conditions and structural parameters of mutant residues. In addition, the database provides an extended dataset of 282 single alanine mutations with only qualitative data (or descriptive effects) of thermodynamic information.« less

Mechanical properties and leaching modeling of activated incinerator bottom ash in Portland cement blends

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

Onori, Roberta, E-mail: Roberta.onori@uniroma1.it; Polettini, Alessandra; Pomi, Raffaella

2011-02-15

In the present study the evolution of mechanical strength and the leaching behavior of major and trace elements from activated incinerator bottom ash/Portland cement mixtures were investigated. Chemical and mechanical activation were applied with the purpose of improving the reactivity of bottom ash in cement blends. Chemical activation made use of NaOH, KOH, CaCl{sub 2} or CaSO{sub 4}, which were selected for the experimental campaign on the basis of the results from previous studies. The results indicated that CaCl{sub 2} exhibited by far the best effects on the evolution of the hydration process in the mixtures; a positive effect onmore » mechanical strength was also observed when CaSO{sub 4} was used as the activator, while the gain in strength produced by KOH and NaOH was irrelevant. Geochemical modeling of the leaching solutions provided information on the mineral phases responsible for the release of major elements from the hardened materials and also indicated the important role played by surface sorption onto amorphous Fe and Al minerals in dictating the leaching of Pb. The leaching of the other trace metal cations investigated (Cu, Ni and Zn) could not be explained by any pure mineral included in the thermodynamic database used, suggesting they were present in the materials in the form of complex minerals or phase assemblages for which no consistent thermodynamic data are presently available in the literature.« less

Mechanical properties and leaching modeling of activated incinerator bottom ash in Portland cement blends.

PubMed

Onori, Roberta; Polettini, Alessandra; Pomi, Raffaella

2011-02-01

In the present study the evolution of mechanical strength and the leaching behavior of major and trace elements from activated incinerator bottom ash/Portland cement mixtures were investigated. Chemical and mechanical activation were applied with the purpose of improving the reactivity of bottom ash in cement blends. Chemical activation made use of NaOH, KOH, CaCl(2) or CaSO(4), which were selected for the experimental campaign on the basis of the results from previous studies. The results indicated that CaCl(2) exhibited by far the best effects on the evolution of the hydration process in the mixtures; a positive effect on mechanical strength was also observed when CaSO(4) was used as the activator, while the gain in strength produced by KOH and NaOH was irrelevant. Geochemical modeling of the leaching solutions provided information on the mineral phases responsible for the release of major elements from the hardened materials and also indicated the important role played by surface sorption onto amorphous Fe and Al minerals in dictating the leaching of Pb. The leaching of the other trace metal cations investigated (Cu, Ni and Zn) could not be explained by any pure mineral included in the thermodynamic database used, suggesting they were present in the materials in the form of complex minerals or phase assemblages for which no consistent thermodynamic data are presently available in the literature. Copyright © 2010 Elsevier Ltd. All rights reserved.

Proton donor acidity controls selectivity in nonaromatic nitrogen heterocycle synthesis.

PubMed

Duttwyler, Simon; Chen, Shuming; Takase, Michael K; Wiberg, Kenneth B; Bergman, Robert G; Ellman, Jonathan A

2013-02-08

Piperidines are prevalent in natural products and pharmaceutical agents and are important synthetic targets for drug discovery and development. We report on a methodology that provides highly substituted piperidine derivatives with regiochemistry selectively tunable by varying the strength of acid used in the reaction. Readily available starting materials are first converted to dihydropyridines via a cascade reaction initiated by rhodium-catalyzed carbon-hydrogen bond activation. Subsequent divergent regio- and diastereoselective protonation of the dihydropyridines under either kinetic or thermodynamic control provides two distinct iminium ion intermediates that then undergo highly diastereoselective nucleophilic additions. X-ray structural characterization of both the kinetically and thermodynamically favored iminium ions along with density functional theory calculations provide a theoretical underpinning for the high selectivities achieved for the reaction sequences.

Analysis of the Properties of Working Substances for the Organic Rankine Cycle based Database "REFPROP"

NASA Astrophysics Data System (ADS)

Galashov, Nikolay; Tsibulskiy, Svyatoslav; Serova, Tatiana

2016-02-01

The object of the study are substances that are used as a working fluid in systems operating on the basis of an organic Rankine cycle. The purpose of research is to find substances with the best thermodynamic, thermal and environmental properties. Research conducted on the basis of the analysis of thermodynamic and thermal properties of substances from the base "REFPROP" and with the help of numerical simulation of combined-cycle plant utilization triple cycle, where the lower cycle is an organic Rankine cycle. Base "REFPROP" describes and allows to calculate the thermodynamic and thermophysical parameters of most of the main substances used in production processes. On the basis of scientific publications on the use of working fluids in an organic Rankine cycle analysis were selected ozone-friendly low-boiling substances: ammonia, butane, pentane and Freon: R134a, R152a, R236fa and R245fa. For these substances have been identified and tabulated molecular weight, temperature of the triple point, boiling point, at atmospheric pressure, the parameters of the critical point, the value of the derivative of the temperature on the entropy of the saturated vapor line and the potential ozone depletion and global warming. It was also identified and tabulated thermodynamic and thermophysical parameters of the steam and liquid substances in a state of saturation at a temperature of 15 °C. This temperature is adopted as the minimum temperature of heat removal in the Rankine cycle when working on the water. Studies have shown that the best thermodynamic, thermal and environmental properties of the considered substances are pentane, butane and R245fa. For a more thorough analysis based on a gas turbine plant NK-36ST it has developed a mathematical model of combined cycle gas turbine (CCGT) triple cycle, where the lower cycle is an organic Rankine cycle, and is used as the air cooler condenser. Air condenser allows stating material at a temperature below 0 °C. Calculation of the parameters of all substances in the model are based on a base "REFPROP". Numerical investigations on this model showed that the highest net efficiency will be at work on pentane. Butane and R245fa have the same net efficiency, for 0.8% lower than pentane. Ammonia has a net efficiency of 2.5% is lower than pentane. CCP net efficiency strongly depends on the condensation temperature of the substance, as for pentane at lower temperature of condensation at 10 °C it is increased by 1%.

Data Qualification Report For: Thermodynamic Data File, DATA0.YMP.R0 For Geochemical Code, EQ3/6 

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

P.L. Cloke

The objective of this work is to evaluate the adequacy of chemical thermodynamic data provided by Lawrence Livermore National Laboratory (LLNL) as DataO.ymp.ROA in response to an input request submitted under AP-3.14Q. This request specified that chemical thermodynamic data available in the file, Data0.com.R2, be updated, improved, and augmented for use in geochemical modeling used in Process Model Reports (PMRs) for Engineered Barrier Systems, Waste Form, Waste Package, Unsaturated Zone, and Near Field Environment, as well as for Performance Assessment. The data are qualified in the temperature range 0 to 100 C. Several Data Tracking Numbers (DTNs) associated with Analysis/Modelmore » Reports (AMR) addressing various aspects of the post-closure chemical behavior of the waste package and the Engineered Barrier System that rely on EQ316 outputs to which these data are used as input, are Principal Factor affecting. This qualification activity was accomplished in accordance with the AP-SIII.2Q using the Technical Assessment method. A development plan, TDP-EBS-MD-000044, was prepared in accordance with AP-2.13Q and approved by the Responsible Manager. In addition, a Process Control Evaluation was performed in accordance with AP-SV.1Q. The qualification method, selected in accordance with AP-SIII.2Q, was Technical Assessment. The rationale for this approach is that the data in File Data0.com.R2 are considered Handbook data and therefore do not themselves require qualification. Only changes to Data0.com.R2 required qualification. A new file has been produced which contains the database Data0.ymp.R0, which is recommended for qualification as a result of this action. Data0.ymp.R0 will supersede Data0.com.R2 for all Yucca Mountain Project (YMP) activities.« less

Computational Thermochemistry of Jet Fuels and Rocket Propellants

NASA Technical Reports Server (NTRS)

Crawford, T. Daniel

2002-01-01

The design of new high-energy density molecules as candidates for jet and rocket fuels is an important goal of modern chemical thermodynamics. The NASA Glenn Research Center is home to a database of thermodynamic data for over 2000 compounds related to this goal, in the form of least-squares fits of heat capacities, enthalpies, and entropies as functions of temperature over the range of 300 - 6000 K. The chemical equilibrium with applications (CEA) program written and maintained by researchers at NASA Glenn over the last fifty years, makes use of this database for modeling the performance of potential rocket propellants. During its long history, the NASA Glenn database has been developed based on experimental results and data published in the scientific literature such as the standard JANAF tables. The recent development of efficient computational techniques based on quantum chemical methods provides an alternative source of information for expansion of such databases. For example, it is now possible to model dissociation or combustion reactions of small molecules to high accuracy using techniques such as coupled cluster theory or density functional theory. Unfortunately, the current applicability of reliable computational models is limited to relatively small molecules containing only around a dozen (non-hydrogen) atoms. We propose to extend the applicability of coupled cluster theory- often referred to as the 'gold standard' of quantum chemical methods- to molecules containing 30-50 non-hydrogen atoms. The centerpiece of this work is the concept of local correlation, in which the description of the electron interactions- known as electron correlation effects- are reduced to only their most important localized components. Such an advance has the potential to greatly expand the current reach of computational thermochemistry and thus to have a significant impact on the theoretical study of jet and rocket propellants.

Space Station Engineering and Technology Development. Proceedings of the Panel on Solar Thermodynamics Research and Technology Development, July 31, 1985

NASA Technical Reports Server (NTRS)

1985-01-01

Solar thermodynamics research and technology is reported. Comments on current program activity and future plans with regard to satisfying potential space station electric power generation requirements are provided. The proceedings contain a brief synopsis of the presentations to the panel, including panel comments, and a summary of the panel's observations. Selected presentation material is appended. Onboard maintainability and repair in space research and technology plan, solar thermodynamic research, program performance, onboard U.S. ground based mission control, and technology development rad maps from 10 C to the growth station are addressed.

A high-throughput approach to profile RNA structure.

PubMed

Delli Ponti, Riccardo; Marti, Stefanie; Armaos, Alexandros; Tartaglia, Gian Gaetano

2017-03-17

Here we introduce the Computational Recognition of Secondary Structure (CROSS) method to calculate the structural profile of an RNA sequence (single- or double-stranded state) at single-nucleotide resolution and without sequence length restrictions. We trained CROSS using data from high-throughput experiments such as Selective 2΄-Hydroxyl Acylation analyzed by Primer Extension (SHAPE; Mouse and HIV transcriptomes) and Parallel Analysis of RNA Structure (PARS; Human and Yeast transcriptomes) as well as high-quality NMR/X-ray structures (PDB database). The algorithm uses primary structure information alone to predict experimental structural profiles with >80% accuracy, showing high performances on large RNAs such as Xist (17 900 nucleotides; Area Under the ROC Curve AUC of 0.75 on dimethyl sulfate (DMS) experiments). We integrated CROSS in thermodynamics-based methods to predict secondary structure and observed an increase in their predictive power by up to 30%. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

pmx Webserver: A User Friendly Interface for Alchemistry.

PubMed

Gapsys, Vytautas; de Groot, Bert L

2017-02-27

With the increase of available computational power and improvements in simulation algorithms, alchemical molecular dynamics based free energy calculations have developed into routine usage. To further facilitate the usability of alchemical methods for amino acid mutations, we have developed a web based infrastructure for obtaining hybrid protein structures and topologies. The presented webserver allows amino acid mutation selection in five contemporary molecular mechanics force fields. In addition, a complete mutation scan with a user defined amino acid is supported. The output generated by the webserver is directly compatible with the Gromacs molecular dynamics engine and can be used with any of the alchemical free energy calculation setup. Furthermore, we present a database of input files and precalculated free energy differences for tripeptides approximating a disordered state of a protein, of particular use for protein stability studies. Finally, the usage of the webserver and its output is exemplified by performing an alanine scan and investigating thermodynamic stability of the Trp cage mini protein. The webserver is accessible at http://pmx.mpibpc.mpg.de.

Performance of a Kilowatt-Class Stirling Power Conversion System in a Thermodynamically Coupled Configuration

NASA Technical Reports Server (NTRS)

Geng, Steven M.; Briggs, Maxwell H.; Hervol, David S.

2011-01-01

A pair of 1-kWe free-piston Stirling power convertors has been modified into a thermodynamically coupled configuration, and performance map testing has been completed. This is the same configuration planned for the full-scale 12-kWe power conversion unit (PCU) that will be used in the Fission Power System Technology Demonstration Unit (TDU). The 1-kWe convertors were operated over a range of conditions to evaluate the effects of thermodynamic coupling on convertor performance and to identify any possible control challenges. The thermodynamically coupled convertor showed no measureable difference in performance from the baseline data collected when the engines were separate, and no major control issues were encountered during operation. The results of this test are guiding controller development and instrumentation selection for the TDU.

Performance of a Kilowatt-Class Stirling Power Conversion System in a Thermodynamically-Coupled Configuration

NASA Astrophysics Data System (ADS)

Geng, S. M.; Briggs, M. H.; Hervol, D. S.

A pair of 1kWe free-piston Stirling power convertors has been modified into a thermodynamically coupled configuration, and performance map testing has been completed. This is the same configuration planned for the full-scale 12 kWe power conversion unit (PCU) that will be used in the Fission Power System Technology Demonstration Unit (TDU). The 1-kWe convertors were operated over a range of conditions to evaluate the effects of thermodynamic coupling on convertor performance and to identify any possible control challenges. The thermodynamically coupled convertor showed no measurable difference in performance from the baseline data collected when the engines were separate and no major control issues were encountered during operation. The results of this test are guiding controller development and instrumentation selection for the TDU.

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

NASA Astrophysics Data System (ADS)

Halbach, Heiner; Chatterjee, Niranjan D.

1984-11-01

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

Extension of Generalized Fluid System Simulation Program's Fluid Property Database

NASA Technical Reports Server (NTRS)

Patel, Kishan

2011-01-01

This internship focused on the development of additional capabilities for the General Fluid Systems Simulation Program (GFSSP). GFSSP is a thermo-fluid code used to evaluate system performance by a finite volume-based network analysis method. The program was developed primarily to analyze the complex internal flow of propulsion systems and is capable of solving many problems related to thermodynamics and fluid mechanics. GFSSP is integrated with thermodynamic programs that provide fluid properties for sub-cooled, superheated, and saturation states. For fluids that are not included in the thermodynamic property program, look-up property tables can be provided. The look-up property tables of the current release version can only handle sub-cooled and superheated states. The primary purpose of the internship was to extend the look-up tables to handle saturated states. This involves a) generation of a property table using REFPROP, a thermodynamic property program that is widely used, and b) modifications of the Fortran source code to read in an additional property table containing saturation data for both saturated liquid and saturated vapor states. Also, a method was implemented to calculate the thermodynamic properties of user-fluids within the saturation region, given values of pressure and enthalpy. These additions required new code to be written, and older code had to be adjusted to accommodate the new capabilities. Ultimately, the changes will lead to the incorporation of this new capability in future versions of GFSSP. This paper describes the development and validation of the new capability.

Thermodynamics of soluble fission products cesium and iodine in the Molten Salt Reactor

NASA Astrophysics Data System (ADS)

Capelli, E.; Beneš, O.; Konings, R. J. M.

2018-04-01

The present study describes the full thermodynamic assessment of the Li,Cs,Th//F,I system. The existing database for the relevant fluoride salts considered as fuel for the Molten Salt Reactor (MSR) has been extended with two key fission products, cesium and iodine. A complete evaluation of all the common-ion binary and ternary sub-systems of the LiF-ThF4-CsF-LiI-ThI4-CsI system has been performed and the optimized parameters are presented in this work. New equilibrium data have been measured using Differential Scanning Calorimetry and were used to assess the reciprocal ternary systems and confirm the extrapolated phase diagrams. The developed database significantly contributes to the understanding of the behaviour of cesium and iodine in the MSR, which strongly depends on their concentration and chemical form. Cesium bonded with fluorine is well retained in the fuel mixture while in the form of CsI the solubility of these elements is very limited. Finally, the influence of CsI and CsF on the physico-chemical properties of the fuel mixture was calculated as function of composition.

Are We There Yet? Applying Thermodynamic and Kinetic Profiling on Embryonic Ectoderm Development (EED) Hit-to-Lead Program.

PubMed

Wang, Ying; Edalji, Rohinton P; Panchal, Sanjay C; Sun, Chaohong; Djuric, Stevan W; Vasudevan, Anil

2017-10-26

It is advocated that kinetic and thermodynamic profiling of bioactive compounds should be incorporated and utilized as complementary tools for hit and lead optimizations in drug discovery. To assess their applications in the EED hit-to-lead optimization process, large amount of thermodynamic and kinetic data were collected and analyzed via isothermal titration calorimetry (ITC) and surface plasmon resonance (SPR), respectively. Slower dissociation rates (k off ) of the lead compounds were observed as the program progressed. Analysis of the kinetic data indicated that compound cellular activity correlated with both K i and k off . Our analysis revealed that ITC data should be interpreted in the context of chiral purity of the compounds. The thermodynamic signatures of the EED aminopyrrolidine compounds were found to be mainly enthalpy driven with improved enthalpic contributions as the program progressed. Our study also demonstrated that significant challenges still exist in utilizing kinetic and thermodynamic parameters for hit selection.

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

NASA Astrophysics Data System (ADS)

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

2009-12-01

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

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

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

Bessinger, Brad; Apps, John A.

2003-03-23

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

Metal-organic frameworks as selectivity regulators for hydrogenation reactions

NASA Astrophysics Data System (ADS)

Zhao, Meiting; Yuan, Kuo; Wang, Yun; Li, Guodong; Guo, Jun; Gu, Lin; Hu, Wenping; Zhao, Huijun; Tang, Zhiyong

2016-11-01

Owing to the limited availability of natural sources, the widespread demand of the flavouring, perfume and pharmaceutical industries for unsaturated alcohols is met by producing them from α,β-unsaturated aldehydes, through the selective hydrogenation of the carbon-oxygen group (in preference to the carbon-carbon group). However, developing effective catalysts for this transformation is challenging, because hydrogenation of the carbon-carbon group is thermodynamically favoured. This difficulty is particularly relevant for one major category of heterogeneous catalyst: metal nanoparticles supported on metal oxides. These systems are generally incapable of significantly enhancing the selectivity towards thermodynamically unfavoured reactions, because only the edges of nanoparticles that are in direct contact with the metal-oxide support possess selective catalytic properties; most of the exposed nanoparticle surfaces do not. This has inspired the use of metal-organic frameworks (MOFs) to encapsulate metal nanoparticles within their layers or inside their channels, to influence the activity of the entire nanoparticle surface while maintaining efficient reactant and product transport owing to the porous nature of the material. Here we show that MOFs can also serve as effective selectivity regulators for the hydrogenation of α,β-unsaturated aldehydes. Sandwiching platinum nanoparticles between an inner core and an outer shell composed of an MOF with metal nodes of Fe3+, Cr3+ or both (known as MIL-101; refs 19, 20, 21) results in stable catalysts that convert a range of α,β-unsaturated aldehydes with high efficiency and with significantly enhanced selectivity towards unsaturated alcohols. Calculations reveal that preferential interaction of MOF metal sites with the carbon-oxygen rather than the carbon-carbon group renders hydrogenation of the former by the embedded platinum nanoparticles a thermodynamically favoured reaction. We anticipate that our basic design strategy will allow the development of other selective heterogeneous catalysts for important yet challenging transformations.

Metal-organic frameworks as selectivity regulators for hydrogenation reactions.

PubMed

Zhao, Meiting; Yuan, Kuo; Wang, Yun; Li, Guodong; Guo, Jun; Gu, Lin; Hu, Wenping; Zhao, Huijun; Tang, Zhiyong

2016-11-03

Owing to the limited availability of natural sources, the widespread demand of the flavouring, perfume and pharmaceutical industries for unsaturated alcohols is met by producing them from α,β-unsaturated aldehydes, through the selective hydrogenation of the carbon-oxygen group (in preference to the carbon-carbon group). However, developing effective catalysts for this transformation is challenging, because hydrogenation of the carbon-carbon group is thermodynamically favoured. This difficulty is particularly relevant for one major category of heterogeneous catalyst: metal nanoparticles supported on metal oxides. These systems are generally incapable of significantly enhancing the selectivity towards thermodynamically unfavoured reactions, because only the edges of nanoparticles that are in direct contact with the metal-oxide support possess selective catalytic properties; most of the exposed nanoparticle surfaces do not. This has inspired the use of metal-organic frameworks (MOFs) to encapsulate metal nanoparticles within their layers or inside their channels, to influence the activity of the entire nanoparticle surface while maintaining efficient reactant and product transport owing to the porous nature of the material. Here we show that MOFs can also serve as effective selectivity regulators for the hydrogenation of α,β-unsaturated aldehydes. Sandwiching platinum nanoparticles between an inner core and an outer shell composed of an MOF with metal nodes of Fe 3+ , Cr 3+ or both (known as MIL-101; refs 19, 20, 21) results in stable catalysts that convert a range of α,β-unsaturated aldehydes with high efficiency and with significantly enhanced selectivity towards unsaturated alcohols. Calculations reveal that preferential interaction of MOF metal sites with the carbon-oxygen rather than the carbon-carbon group renders hydrogenation of the former by the embedded platinum nanoparticles a thermodynamically favoured reaction. We anticipate that our basic design strategy will allow the development of other selective heterogeneous catalysts for important yet challenging transformations.

Thermodynamic properties of solvated peptides from selective integrated tempering sampling with a new weighting factor estimation algorithm

NASA Astrophysics Data System (ADS)

Shen, Lin; Xie, Liangxu; Yang, Mingjun

2017-04-01

Conformational sampling under rugged energy landscape is always a challenge in computer simulations. The recently developed integrated tempering sampling, together with its selective variant (SITS), emerges to be a powerful tool in exploring the free energy landscape or functional motions of various systems. The estimation of weighting factors constitutes a critical step in these methods and requires accurate calculation of partition function ratio between different thermodynamic states. In this work, we propose a new adaptive update algorithm to compute the weighting factors based on the weighted histogram analysis method (WHAM). The adaptive-WHAM algorithm with SITS is then applied to study the thermodynamic properties of several representative peptide systems solvated in an explicit water box. The performance of the new algorithm is validated in simulations of these solvated peptide systems. We anticipate more applications of this coupled optimisation and production algorithm to other complicated systems such as the biochemical reactions in solution.

Effect of the ionic strength of a mobile phase on the chromatographic retention and thermodynamic characteristics of the adsorption of enantiomers of α-phenylcarboxylic acids on a chiral adsorbent with grafted antibiotic eremomycin

NASA Astrophysics Data System (ADS)

Reshetova, E. N.

2017-01-01

The effect the ionic strength of an aqueous ethanol mobile phase containing buffer salt has the on retention and thermodynamics of adsorption of optical isomers of some α-phenylcarboxylic acids on chiral adsorbent Nautilus-E with grafted antibiotic eremomycin is investigated. It is shown that ion exchange processes participate in the adsorption of enantiomers of α-phenylcarboxylic acids. It is established that electrostatic interactions contribute to the retention of enantiomers of α-phenylcarboxylic acids and affect selectivity only slightly. The dependences of retention characteristics, selectivity, and thermodynamic parameters on the concentration of the buffer salt in the eluent are determined. A statistical analysis of enthalpy-entropy compensation is performed, and the compensation effect is shown to be true. It is found that the points corresponding to the investigated adsorbates are distributed over the compensation dependence according to the spatial structural characteristics of molecules.

Application of thermodynamics and Wagner model on two problems in continuous hot-dip galvanizing

NASA Astrophysics Data System (ADS)

Liu, Huachu; He, Yanlin; Li, Lin

2009-12-01

Firstly in this paper, the influence of H 2 and water vapor content on selective oxidation occurred in continuous hot-dip galvanizing has been studied by thermodynamics and Wagner model, then, the Gibbs energy of each possible aluminothermic reducing reaction in zinc bath was calculated in order to judge the possibility of these reactions. It was found that oxides' amounts and oxidation type were greatly related to the H 2 and water content in the annealing atmosphere. And from the view of thermodynamics, surface oxides (MnO, Cr 2O 3, SiO 2 etc.) can be reduced by the effective Al in Zn bath.

Thermodynamics of antibody-antigen interaction revealed by mutation analysis of antibody variable regions.

PubMed

Akiba, Hiroki; Tsumoto, Kouhei

2015-07-01

Antibodies (immunoglobulins) bind specific molecules (i.e. antigens) with high affinity and specificity. In order to understand their mechanisms of recognition, interaction analysis based on thermodynamic and kinetic parameters, as well as structure determination is crucial. In this review, we focus on mutational analysis which gives information about the role of each amino acid residue in antibody-antigen interaction. Taking anti-hen egg lysozyme antibodies and several anti-small molecule antibodies, the energetic contribution of hot-spot and non-hot-spot residues is discussed in terms of thermodynamics. Here, thermodynamics of the contribution from aromatic, charged and hydrogen bond-forming amino acids are discussed, and their different characteristics have been elucidated. The information gives fundamental understanding of the antibody-antigen interaction. Furthermore, the consequences of antibody engineering are analysed from thermodynamic viewpoints: humanization to reduce immunogenicity and rational design to improve affinity. Amino acid residues outside hot-spots in the interface play important roles in these cases, and thus thermodynamic and kinetic parameters give much information about the antigen recognition. Thermodynamic analysis of mutant antibodies thus should lead to advanced strategies to design and select antibodies with high affinity. © The Authors 2015. Published by Oxford University Press on behalf of the Japanese Biochemical Society. All rights reserved.

Self-association of plant wax components: a thermodynamic analysis.

PubMed

Casado, C G; Heredia, A

2001-01-01

Excess specific heat, C(p)()(E), of binary mixtures of selected components of plant cuticular waxes has been determined. This thermodynamic parameter gives an explanation of the special molecular arrangement in crystalline and amorphous zones of plant waxes. C(p)()(E) values indicate that hydrogen bonding between chains results in the formation of amorphous zones. Conclusions on the self-asembly process of plant waxes have been also made.

Thermodynamics of natural selection III: Landauer's principle in computation and chemistry.

PubMed

Smith, Eric

2008-05-21

This is the third in a series of three papers devoted to energy flow and entropy changes in chemical and biological processes, and their relations to the thermodynamics of computation. The previous two papers have developed reversible chemical transformations as idealizations for studying physiology and natural selection, and derived bounds from the second law of thermodynamics, between information gain in an ensemble and the chemical work required to produce it. This paper concerns the explicit mapping of chemistry to computation, and particularly the Landauer decomposition of irreversible computations, in which reversible logical operations generating no heat are separated from heat-generating erasure steps which are logically irreversible but thermodynamically reversible. The Landauer arrangement of computation is shown to produce the same entropy-flow diagram as that of the chemical Carnot cycles used in the second paper of the series to idealize physiological cycles. The specific application of computation to data compression and error-correcting encoding also makes possible a Landauer analysis of the somewhat different problem of optimal molecular recognition, which has been considered as an information theory problem. It is shown here that bounds on maximum sequence discrimination from the enthalpy of complex formation, although derived from the same logical model as the Shannon theorem for channel capacity, arise from exactly the opposite model for erasure.

Efficient affinity maturation of antibody variable domains requires co-selection of compensatory mutations to maintain thermodynamic stability

PubMed Central

Julian, Mark C.; Li, Lijuan; Garde, Shekhar; Wilen, Rebecca; Tessier, Peter M.

2017-01-01

The ability of antibodies to accumulate affinity-enhancing mutations in their complementarity-determining regions (CDRs) without compromising thermodynamic stability is critical to their natural function. However, it is unclear if affinity mutations in the hypervariable CDRs generally impact antibody stability and to what extent additional compensatory mutations are required to maintain stability during affinity maturation. Here we have experimentally and computationally evaluated the functional contributions of mutations acquired by a human variable (VH) domain that was evolved using strong selections for enhanced stability and affinity for the Alzheimer’s Aβ42 peptide. Interestingly, half of the key affinity mutations in the CDRs were destabilizing. Moreover, the destabilizing effects of these mutations were compensated for by a subset of the affinity mutations that were also stabilizing. Our findings demonstrate that the accumulation of both affinity and stability mutations is necessary to maintain thermodynamic stability during extensive mutagenesis and affinity maturation in vitro, which is similar to findings for natural antibodies that are subjected to somatic hypermutation in vivo. These findings for diverse antibodies and antibody fragments specific for unrelated antigens suggest that the formation of the antigen-binding site is generally a destabilizing process and that co-enrichment for compensatory mutations is critical for maintaining thermodynamic stability. PMID:28349921

First-Principles Prediction of Thermodynamically Stable Two-Dimensional Electrides

DOE PAGES

Ming, Wenmei; Yoon, Mina; Univ. of Tennessee, Knoxville, TN; ...

2016-10-21

Two-dimensional (2D) electrides, emerging as a new type of layered material whose electrons are confined in interlayer spaces instead of at atomic proximities, are receiving interest for their high performance in various (opto)electronics and catalytic applications. Experimentally, however, 2D electrides have been only found in a couple of layered nitrides and carbides. We report new thermodynamically stable alkaline-earth based 2D electrides by using a first-principles global structure optimization method, phonon spectrum analysis, and molecular dynamics simulation. The method was applied to binary compounds consisting of alkaline-earth elements as cations and group VA, VIA, or VIIA nonmetal elements as anions. Wemore » also revealed that the stability of a layered 2D electride structure is closely related to the cation/anion size ratio; stable 2D electrides possess a sufficiently large cation/anion size ratio to minimize electrostatic energy among cations, anions, and anionic electrons. This work demonstrates a new avenue to the discovery of thermodynamically stable 2D electrides beyond experimental material databases and provides new insight into the principles of electride design.« less

Boltzmann, Darwin and Directionality theory

NASA Astrophysics Data System (ADS)

Demetrius, Lloyd A.

2013-09-01

Boltzmann’s statistical thermodynamics is a mathematical theory which relates the macroscopic properties of aggregates of interacting molecules with the laws of their interaction. The theory is based on the concept thermodynamic entropy, a statistical measure of the extent to which energy is spread throughout macroscopic matter. Macroscopic evolution of material aggregates is quantitatively explained in terms of the principle: Thermodynamic entropy increases as the composition of the aggregate changes under molecular collision. Darwin’s theory of evolution is a qualitative theory of the origin of species and the adaptation of populations to their environment. A central concept in the theory is fitness, a qualitative measure of the capacity of an organism to contribute to the ancestry of future generations. Macroscopic evolution of populations of living organisms can be qualitatively explained in terms of a neo-Darwinian principle: Fitness increases as the composition of the population changes under variation and natural selection. Directionality theory is a quantitative model of the Darwinian argument of evolution by variation and selection. This mathematical theory is based on the concept evolutionary entropy, a statistical measure which describes the rate at which an organism appropriates energy from the environment and reinvests this energy into survivorship and reproduction. According to directionality theory, microevolutionary dynamics, that is evolution by mutation and natural selection, can be quantitatively explained in terms of a directionality principle: Evolutionary entropy increases when the resources are diverse and of constant abundance; but decreases when the resource is singular and of variable abundance. This report reviews the analytical and empirical support for directionality theory, and invokes the microevolutionary dynamics of variation and selection to delineate the principles which govern macroevolutionary dynamics of speciation and extinction. We also elucidate the relation between thermodynamic entropy, which pertains to the extent of energy spreading and sharing within inanimate matter, and evolutionary entropy, which refers to the rate of energy appropriation from the environment and allocation within living systems. We show that the entropic principle of thermodynamics is the limit as R→0, M→∞, (where R denote the resource production rate, and M denote population size) of the entropic principle of evolution. We exploit this relation between the thermodynamic and evolutionary tenets to propose a physico-chemical model of the transition from inanimate matter which is under thermodynamic selection, to living systems which are subject to evolutionary selection. Life history variation and the evolution of senescence The evolutionary dynamics of speciation and extinction Evolutionary trends in body size. The origin of sporadic forms of cancer and neurological diseases, and the evolution of cooperation are important recent applications of directionality theory. These applications, which draw from the medical sciences and sociobiology, appeal to methods which lie outside the formalism described in this report. A companion review, Demetrius and Gundlach (submitted for publication), gives an account of these applications.An important aspect of this report pertains to the connection between statistical mechanics and evolutionary theory and its implications towards understanding the processes which underlie the emergence of living systems from inanimate matter-a problem which has recently attracted considerable attention, Morowitz (1992), Eigen (1992), Dyson (2000), Pross (2012).The connection between the two disciplines can be addressed by appealing to certain extremal principles which are considered the mainstay of the respective theories.The extremal principle in statistical mechanics can be stated as follows:

Raman Scattering Study of Supercritical Bi-Component Mixtures Injected into a Subcritical Environment

DTIC Science & Technology

2007-09-01

Technology (NIST) [7]. SUPERTRAPP is an interactive computer database designed to predict the thermodynamic and transport properties of fluid mixtures...of liquid sprays. However, the potential core computation is done for all the Raman scattering injection conditions to compare the condensed phase...spaced from the Rayleigh component suggesting that they contain the same information about the vibrational quantum energy. The intensity

Nonequilibrium thermodynamics and information theory: basic concepts and relaxing dynamics

NASA Astrophysics Data System (ADS)

Altaner, Bernhard

2017-11-01

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

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

Miller, David L.; Schoof, Justin C.; Hobbs, Michael L.

This report presents plots of specific heat, enthalpy, entropy, and Gibbs free energy for 1439 species in the JCZS2i database. Included in this set of species are 496 condensed-phase species and 943 gas-phase species. The gas phase species contain 80 anions and 112 cations for a total of 192 ions. The JCZS2i database is used in conjunction with the TIGER thermochemical code to predict thermodynamic states from ambient conditions to high temperatures and pressures. Predictions from the TIGER code using the JCZS2i database can be used in shock physics codes where temperatures may be as high as 20,000 K andmore » ions may be present. Such high temperatures were not considered in the original JCZS database, and extrapolations made for these temperatures were unrealistic. For example, specific heat would sometimes go negative at high temperatures which fails the definition of specific heat. The JCZS2i database is a new version of the JCZS database that is being created to address these inaccuracies. The purpose of the current report is to visualize the high temperature extrapolations to insure that the specific heat, enthalpy, entropy, and Gibbs free energy predictions are reasonable up to 20,000 K.« less

Course 12: Proteins: Structural, Thermodynamic and Kinetic Aspects

NASA Astrophysics Data System (ADS)

Finkelstein, A. V.

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

77 FR 12234 - Changes in Hydric Soils Database Selection Criteria

Federal Register 2010, 2011, 2012, 2013, 2014

2012-02-29

... Conservation Service [Docket No. NRCS-2011-0026] Changes in Hydric Soils Database Selection Criteria AGENCY... Changes to the National Soil Information System (NASIS) Database Selection Criteria for Hydric Soils of the United States. SUMMARY: The National Technical Committee for Hydric Soils (NTCHS) has updated the...

On the Effectiveness of Nature-Inspired Metaheuristic Algorithms for Performing Phase Equilibrium Thermodynamic Calculations

PubMed Central

Fateen, Seif-Eddeen K.; Bonilla-Petriciolet, Adrian

2014-01-01

The search for reliable and efficient global optimization algorithms for solving phase stability and phase equilibrium problems in applied thermodynamics is an ongoing area of research. In this study, we evaluated and compared the reliability and efficiency of eight selected nature-inspired metaheuristic algorithms for solving difficult phase stability and phase equilibrium problems. These algorithms are the cuckoo search (CS), intelligent firefly (IFA), bat (BA), artificial bee colony (ABC), MAKHA, a hybrid between monkey algorithm and krill herd algorithm, covariance matrix adaptation evolution strategy (CMAES), magnetic charged system search (MCSS), and bare bones particle swarm optimization (BBPSO). The results clearly showed that CS is the most reliable of all methods as it successfully solved all thermodynamic problems tested in this study. CS proved to be a promising nature-inspired optimization method to perform applied thermodynamic calculations for process design. PMID:24967430

On the effectiveness of nature-inspired metaheuristic algorithms for performing phase equilibrium thermodynamic calculations.

PubMed

Fateen, Seif-Eddeen K; Bonilla-Petriciolet, Adrian

2014-01-01

The search for reliable and efficient global optimization algorithms for solving phase stability and phase equilibrium problems in applied thermodynamics is an ongoing area of research. In this study, we evaluated and compared the reliability and efficiency of eight selected nature-inspired metaheuristic algorithms for solving difficult phase stability and phase equilibrium problems. These algorithms are the cuckoo search (CS), intelligent firefly (IFA), bat (BA), artificial bee colony (ABC), MAKHA, a hybrid between monkey algorithm and krill herd algorithm, covariance matrix adaptation evolution strategy (CMAES), magnetic charged system search (MCSS), and bare bones particle swarm optimization (BBPSO). The results clearly showed that CS is the most reliable of all methods as it successfully solved all thermodynamic problems tested in this study. CS proved to be a promising nature-inspired optimization method to perform applied thermodynamic calculations for process design.

Thermodynamic model for solution behavior and solid-liquid equilibrium in Na-Al(III)-Fe(III)-Cr(III)-Cl-H2O system at 25°C

NASA Astrophysics Data System (ADS)

André, Laurent; Christov, Christomir; Lassin, Arnault; Azaroual, Mohamed

2018-03-01

The knowledge of the thermodynamic behavior of multicomponent aqueous electrolyte systems is of main interest in geo-, and environmental-sciences. The main objective of this study is the development of a high accuracy thermodynamic model for solution behavior, and highly soluble M(III)Cl3(s) (M= Al, Fe, Cr) minerals solubility in Na-Al(III)-Cr(III)-Fe(III)-Cl-H2O system at 25°C. Comprehensive thermodynamic models that accurately predict aluminium, chromium and iron aqueous chemistry and M(III) mineral solubilities as a function of pH, solution composition and concentration are critical for understanding many important geochemical and environmental processes involving these metals (e.g., mineral dissolution/alteration, rock formation, changes in rock permeability and fluid flow, soil formation, mass transport, toxic M(III) remediation). Such a model would also have many industrial applications (e.g., aluminium, chromium and iron production, and their corrosion, solve scaling problems in geothermal energy and oil production). Comparisons of solubility and activity calculations with the experimental data in binary and ternary systems indicate that model predictions are within the uncertainty of the data. Limitations of the model due to data insufficiencies are discussed. The solubility modeling approach, implemented to the Pitzer specific interaction equations is employed. The resulting parameterization was developed for the geochemical Pitzer formalism based PHREEQC database.

Working fluid selection for the Organic Rankine Cycle (ORC) exhaust heat recovery of an internal combustion engine power plant

NASA Astrophysics Data System (ADS)

Douvartzides, S.; Karmalis, I.

2016-11-01

Organic Rankine cycle technology is capable to efficiently convert low-grade heat into useful mechanical power. In the present investigation such a cycle is used for the recovery of heat from the exhaust gases of a four stroke V18 MAN 51/60DF internal combustion engine power plant operating with natural gas. Design is focused on the selection of the appropriate working fluid of the Rankine cycle in terms of thermodynamic, environmental and safety criteria. 37 candidate fluids have been considered and all Rankine cycles examined were subcritical. The thermodynamic analysis of all fluids has been comparatively undertaken and the effect of key operation conditions such as the evaporation pressure and the superheating temperature was taken into account. By appropriately selecting the working fluid and the Rankine cycle operation conditions the overall plant efficiency was improved by 5.52% and fuel consumption was reduced by 12.69%.

Theoretical Assessment on the Phase Transformation Kinetic Pathways of Multi-component Ti Alloys: Application to Ti-6Al- 4V

DOE PAGES

Ji, Yanzhou; Heo, Tae Wook; Zhang, Fan; ...

2015-12-21

Here we present our theoretical assessment of the kinetic pathways during phase transformations of multi-component Ti alloys. Employing the graphical thermodynamic approach and an integrated free energy function based on the realistic thermodynamic database and assuming that a displacive structural transformation occurs much faster than long-range diffusional processes, we analyze the phase stabilities of Ti-6Al -4V (Ti-6wt.%Al -4wt.%V). Our systematic analyses predict a variety of possible kinetic pathways for β to (α + β) transformations leading to different types of microstructures under various heat treatment conditions. In addition, the possibility of unconventional kinetic pathways is discussed. Lastly, we also brieflymore » discuss the application of our approach to general multicomponent/multiphase alloy systems.« less

EOSlib, Version 3

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

Woods, Nathan; Menikoff, Ralph

2017-02-03

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

International Shock-Wave Database: Current Status

NASA Astrophysics Data System (ADS)

Levashov, Pavel

2013-06-01

Shock-wave and related dynamic material response data serve for calibrating, validating, and improving material models over very broad regions of the pressure-temperature-density phase space. Since the middle of the 20th century vast amount of shock-wave experimental information has been obtained. To systemize it a number of compendiums of shock-wave data has been issued by LLNL, LANL (USA), CEA (France), IPCP and VNIIEF (Russia). In mid-90th the drawbacks of the paper handbooks became obvious, so the first version of the online shock-wave database appeared in 1997 (http://www.ficp.ac.ru/rusbank). It includes approximately 20000 experimental points on shock compression, adiabatic expansion, measurements of sound velocity behind the shock front and free-surface-velocity for more than 650 substances. This is still a useful tool for the shock-wave community, but it has a number of serious disadvantages which can't be easily eliminated: (i) very simple data format for points and references; (ii) minimalistic user interface for data addition; (iii) absence of history of changes; (iv) bad feedback from users. The new International Shock-Wave database (ISWdb) is intended to solve these and some other problems. The ISWdb project objectives are: (i) to develop a database on thermodynamic and mechanical properties of materials under conditions of shock-wave and other dynamic loadings, selected related quantities of interest, and the meta-data that describes the provenance of the measurements and material models; and (ii) to make this database available internationally through the Internet, in an interactive form. The development and operation of the ISWdb is guided by an advisory committee. The database will be installed on two mirrored web-servers, one in Russia and the other in USA (currently only one server is available). The database provides access to original experimental data on shock compression, non-shock dynamic loadings, isentropic expansion, measurements of sound speed in the Hugoniot state, and time-dependent free-surface or window-interface velocity profiles. Users are able to search the information in the database and obtain the experimental points in tabular or plain text formats directly via the Internet using common browsers. It is also possible to plot the experimental points for comparison with different approximations and results of equation-of-state calculations. The user can present the results of calculations in text or graphical forms and compare them with any experimental data available in the database. A short history of the shock-wave database will be presented and current possibilities of ISWdb will be demonstrated. Web-site of the project: http://iswdb.info. This work is supported by SNL contracts # 1143875, 1196352.

Thermodynamic Solubility Profile of Carbamazepine-Cinnamic Acid Cocrystal at Different pH.

PubMed

Keramatnia, Fatemeh; Shayanfar, Ali; Jouyban, Abolghasem

2015-08-01

Pharmaceutical cocrystal formation is a direct way to dramatically influence physicochemical properties of drug substances, especially their solubility and dissolution rate. Because of their instability in the solution, thermodynamic solubility of cocrystals could not be determined in the common way like other compounds; therefore, the thermodynamic solubility is calculated through concentration of their components in the eutectic point. The objective of this study is to investigate the effect of an ionizable coformer in cocrystal with a nonionizable drug at different pH. Carbamazepine (CBZ), a nonionizable drug with cinnamic acid (CIN), which is an acidic coformer, was selected to prepare CBZ-CIN cocrystal and its thermodynamic solubility was studied in pH range 2-7. Instead of HPLC that is a costly and time-consuming method, a chemometric-based approach, net analyte signal standard addition method, was selected for simultaneous determination of CBZ and CIN in solution. The result showed that, as pH increases, CIN ionization leads to change in CBZ-CIN cocrystal solubility and stability in solution. In addition, the results of this study indicated that there is no significant difference between intrinsic solubility of CBZ and cocrystal despite the higher ideal solubility of cocrystal. This verifies that ideal solubility is not good parameter to predict cocrystal solubility. © 2015 Wiley Periodicals, Inc. and the American Pharmacists Association.

Fuzzy and fast nuclear transport

PubMed Central

Mulder, Frans A. A.

2018-01-01

Exchange of macromolecules between the cytoplasm and the nucleus of all eukaryotic cells is controlled by nuclear pore complexes, which form a selective permeability barrier. The requirement for rapid but selective transport leads to a “transport paradox.” A new experimental study now provides a thermodynamic explanation. PMID:29572326

Energetics of phosphate binding to ammonium and guanidinium containing metallo-receptors in water.

PubMed

Tobey, Suzanne L; Anslyn, Eric V

2003-12-03

The design and synthesis of receptors containing a Cu(II) binding site with appended ammonium groups (1) and guanidinium groups (2), along with thermodynamics analyses of anion binding, are reported. Both receptors 1 and 2 show high affinities (10(4) M(-1)) and selectivities for phosphate over other anions in 98:2 water:methanol at biological pH. The binding of the host-guest pairs is proposed to proceed through ion-pairing interactions between the charged functional groups on both the host and the guest. The affinities and selectivities for oxyanions were determined using UV/vis titration techniques. Additionally, thermodynamic investigations indicate that the 1:phosphate complex is primarily entropy driven, while the 2:phosphate complex displays both favorable enthalpy and entropy changes. The thermodynamic data for binding provide a picture of the roles of the host, guest, counterions, and solvent. The difference in the entropy and enthalpy driving forces for the ammonium and guanidinium containing hosts are postulated to derive primarily from differences in the solvation shell of these two groups.

There goes the sea ice: following Arctic sea ice parcels and their properties.

NASA Astrophysics Data System (ADS)

Tschudi, M. A.; Tooth, M.; Meier, W.; Stewart, S.

2017-12-01

Arctic sea ice distribution has changed considerably over the last couple of decades. Sea ice extent record minimums have been observed in recent years, the distribution of ice age now heavily favors younger ice, and sea ice is likely thinning. This new state of the Arctic sea ice cover has several impacts, including effects on marine life, feedback on the warming of the ocean and atmosphere, and on the future evolution of the ice pack. The shift in the state of the ice cover, from a pack dominated by older ice, to the current state of a pack with mostly young ice, impacts specific properties of the ice pack, and consequently the pack's response to the changing Arctic climate. For example, younger ice typically contains more numerous melt ponds during the melt season, resulting in a lower albedo. First-year ice is typically thinner and more fragile than multi-year ice, making it more susceptible to dynamic and thermodynamic forcing. To investigate the response of the ice pack to climate forcing during summertime melt, we have developed a database that tracks individual Arctic sea ice parcels along with associated properties as these parcels advect during the summer. Our database tracks parcels in the Beaufort Sea, from 1985 - present, along with variables such as ice surface temperature, albedo, ice concentration, and convergence. We are using this database to deduce how these thousands of tracked parcels fare during summer melt, i.e. what fraction of the parcels advect through the Beaufort, and what fraction melts out? The tracked variables describe the thermodynamic and dynamic forcing on these parcels during their journey. This database will also be made available to all interested investigators, after it is published in the near future. The attached image shows the ice surface temperature of all parcels (right) that advected through the Beaufort Sea region (left) in 2014.

Method and apparatus for adapting steady flow with cyclic thermodynamics

DOEpatents

Swift, Gregory W.; Reid, Robert S.; Ward, William C.

2000-01-01

Energy transfer apparatus has a resonator for supporting standing acoustic waves at a selected frequency with a steady flow process fluid thermodynamic medium and a solid medium having heat capacity. The fluid medium and the solid medium are disposed within the resonator for thermal contact therebetween and for relative motion therebetween. The relative motion is produced by a first means for producing a steady velocity component and second means for producing an oscillating velocity component at the selected frequency and concomitant wavelength of the standing acoustic wave. The oscillating velocity and associated oscillating pressure component provide energy transfer between the steady flow process fluid and the solid medium as the steady flow process fluid moves through the resonator.

The thermodynamic characteristics of solution of L-α-histidine and L-α-phenylalanine in water at 273 373 K

NASA Astrophysics Data System (ADS)

Kustov, A. V.; Korolev, V. P.

2008-11-01

The solubility of L-phenylalanine and L-histidine in water at 298.15 and 318.15 K and the heat effects of solution of the amino acids at 328.15 K were determined. These results and the data obtained earlier were used to calculate all the standard thermodynamic functions of solution of the amino acids and the solubilities of L-phenylalanine and L-histidine over the temperature range 273 373 K. The selection of the form of the Δsol H o = f( T) dependence had a negligible effect on the free energies of solution and solubilities of the amino acids. This selection primarily influenced the entropy and heat capacity characteristics of the process.

Lunar base heat pump, phase 1

NASA Technical Reports Server (NTRS)

Goldman, Jeffrey H.; Harvey, A.; Lovell, T.; Walker, David H.

1994-01-01

This report describes the Phase 1 process and analysis used to select a refrigerant and thermodynamic cycle as the basis of a vapor compression heat pump requiring a high temperature lift, then to perform a preliminary design to implement the selected concept, including major component selection. Use of a vapor compression heat pump versus other types was based on prior work performed for the Electric Power Research Institute. A high lift heat pump is needed to enable a thermal control system to remove heat down to 275 K from a habitable volume when the external thermal environment is severe. For example, a long-term lunar base habitat will reject heat from a space radiator to a 325 K environment. The first step in the selection process was to perform an optimization trade study, quantifying the effect of radiator operating temperature and heat pump efficiency on total system mass; then, select the radiator operating temperature corresponding to the lowest system mass. Total system mass included radiators, all heat pump components, and the power supply system. The study showed that lunar night operation, with no temperature lift, dictated the radiator size. To operate otherwise would require a high mass penalty to store power. With the defined radiation surface, and heat pump performances assumed to be from 40 percent to 60 percent of the Carnot ideal, the optimum heat rejection temperature ranged from 387 K to 377 K, as a function of heat pump performance. Refrigerant and thermodynamic cycles were then selected to best meet the previously determined design conditions. The system was then adapted as a ground-based prototype lifting temperature to 360 K (versus 385 K for flight unit) and using readily available commercial-grade components. Over 40 refrigerants, separated into wet and dry compression behavioral types, were considered in the selection process. Refrigerants were initially screened for acceptable critical temperature. The acceptable refrigerants were analyzed in ideal single and two-stage thermodynamic cycles. Top candidates were analyzed assuming realistic component limits and system pressure drops, and were evaluated for other considerations such as safety, environmental impact, and commercial availability. A maximum coefficient of performance (COP) of 56 percent of the Carnot ideal was achievable for a three-stage CFC-11 cycle operating under the flight conditions above. The program was completed by defining a control scheme and by researching and selecting the major components, compressor and heat exchangers, that could be used to implement the thermodynamic cycle selected. Special attention was paid to using similar technologies for the SIRF and flight heat pumps resulting in the commercially available equivalent of the flight unit. A package concept was generated for the components selected and mass and volume estimated.

Modelling of clay diagenesis using a combined approach of crystalchemistry and thermochemistry: a case study in the smectite illitization.

NASA Astrophysics Data System (ADS)

Geloni, Claudio; Previde Massara, Elisabetta; Di Paola, Eleonora; Ortenzi, Andrea; Gherardi, Fabrizio; Blanc, Philippe

2017-04-01

Diagenetic transformations occurring in clayey and arenaceous sediments is investigated in a number of hydrocarbon reservoirs with an integrated approach that combines mineralogical analysis, crystalchemistry, estimation of thermochemical parameters of clay minerals, and geochemical modelling. Because of the extremely variable crystalchemistry of clays, especially in the smectite - illite compositional range, the estimation of thermochemical parameters of site-specific clay-rich rocks is crucial to investigate water-rock equilibria and to predict mineralogical evolutionary patterns at the clay-sandstone interface. The task of estimating the thermochemical properties of clay minerals and predicting diagenetic reactions in natural reservoirs is accomplished through the implementation of an informatized, procedure (IP) that consists of: (i) laboratory analysis of smectite, illite and mixed layers (I/S) for the determination of their textural characteristics and chemical composition; (ii) estimation of the thermodynamic and structural parameters (enthalpy, entropy, and free energy of formation, thermal capacity, molar volume, molar weight) with a MS Excel tool (XLS) specifically developed at the French Bureau of Geological and Mining Researches (BRGM); (iii) usage of the SUPCRT (Johnson et al., 1992) software package (thereinafter, SSP) to derive log K values to be incorporated in thermodynamic databases of the standard geochemical codes; (iv) check of the consistency of the stability domains calculated with these log K values with relevant predominance diagrams; (v) final application of geochemical and reactive transport models to investigate the reactive mechanisms under different thermal conditions (40-150°C). All the simulations consider pore waters having roughly the same chemical composition of reservoir pore waters, and are performed with The Geochemist Workbench (Bethke and Yeakel, 2015), PHREEQC (Parkhurst, 1999) and TOUGHREACT (Xu, 2006). The overall procedure benefits from: (i) (minor) improvements of the I/O structure of the SSP; (ii) the development of a suite of python scripts to automate the steps needed to augment the thermodynamic database by integrating the external information provided by potential users with the XLS tool and the SSP; (iii) the creation of specific outputs to allow for more convenient handling and inspection of computed parameters of the thermodynamic database. A case study focused on non-isothermal smectite-illite transformation is presented to show the capability of our numerical models to account for clay compaction under 1D geometry conditions. This model considers fluid flow driven by the compaction of a clay layer, and chemistry-fluid flow mutual feedback with the underlying sandstone during the advancement of the diagenesis. Due to this complex interaction, as a result of the smectite-illite transformation in the clays, significant quartz cementation affects the sandstone adjacent to the compacting clay.

Biochemical thermodynamics: applications of Mathematica.

PubMed

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 reactants. Thus loading this package makes available 774 mathematical functions for these properties. These functions can be added and subtracted to obtain changes in these properties in biochemical reactions and apparent equilibrium constants.

Evaporation rate-based selection of supramolecular chirality.

PubMed

Hattori, Shingo; Vandendriessche, Stefaan; Koeckelberghs, Guy; Verbiest, Thierry; Ishii, Kazuyuki

2017-03-09

We demonstrate the evaporation rate-based selection of supramolecular chirality for the first time. P-type aggregates prepared by fast evaporation, and M-type aggregates prepared by slow evaporation are kinetic and thermodynamic products under dynamic reaction conditions, respectively. These findings provide a novel solution reaction chemistry under the dynamic reaction conditions.

Contribution to the aluminum-tin-zinc ternary system

NASA Astrophysics Data System (ADS)

Drápala, J.; Kostiuková, G.; Losertová, M.

2017-11-01

The Sn-Zn-Al alloys are one of significant candidates in the proposal of alternative lead-free solders for higher temperature soldering. This paper deals with the study of the aluminum-tin-zinc system. Twenty Sn-Zn-Al alloys together with six binary Sn-Zn alloys were prepared and studied experimentally. Alloys were prepared from pure Sn, Zn and Al (melting and cooling in a vacuum resistance furnace). The specimens were studied metallographically including the micro-hardness measurements, complete chemical analysis (ICP-AES, OES), X-ray micro-analysis of alloys by SEM and EDX in order to determine the composition and identification of individual phases. Significant temperatures and enthalpies of phase transformations were determined by DTA. After long-term annealing of selected alloys in vacuum followed by quenching the structural and chemical microanalyses of the present phases and their limit concentrations were carried out. The achieved results were compared with the thermodynamic modelling of the ternary Sn-Zn-Al system (computer programs THERMOCALC, MTDATA, PANDAT and databases CALPHAD, COST). Electrical resistivity, density, magnetic susceptibility and wettability of Sn-Zn-Al solders were measured as well.

HomoTarget: a new algorithm for prediction of microRNA targets in Homo sapiens.

PubMed

Ahmadi, Hamed; Ahmadi, Ali; Azimzadeh-Jamalkandi, Sadegh; Shoorehdeli, Mahdi Aliyari; Salehzadeh-Yazdi, Ali; Bidkhori, Gholamreza; Masoudi-Nejad, Ali

2013-02-01

MiRNAs play an essential role in the networks of gene regulation by inhibiting the translation of target mRNAs. Several computational approaches have been proposed for the prediction of miRNA target-genes. Reports reveal a large fraction of under-predicted or falsely predicted target genes. Thus, there is an imperative need to develop a computational method by which the target mRNAs of existing miRNAs can be correctly identified. In this study, combined pattern recognition neural network (PRNN) and principle component analysis (PCA) architecture has been proposed in order to model the complicated relationship between miRNAs and their target mRNAs in humans. The results of several types of intelligent classifiers and our proposed model were compared, showing that our algorithm outperformed them with higher sensitivity and specificity. Using the recent release of the mirBase database to find potential targets of miRNAs, this model incorporated twelve structural, thermodynamic and positional features of miRNA:mRNA binding sites to select target candidates. Copyright © 2012 Elsevier Inc. All rights reserved.

Mapping uncharted territory in ice from zeolite networks to ice structures.

PubMed

Engel, Edgar A; Anelli, Andrea; Ceriotti, Michele; Pickard, Chris J; Needs, Richard J

2018-06-05

Ice is one of the most extensively studied condensed matter systems. Yet, both experimentally and theoretically several new phases have been discovered over the last years. Here we report a large-scale density-functional-theory study of the configuration space of water ice. We geometry optimise 74,963 ice structures, which are selected and constructed from over five million tetrahedral networks listed in the databases of Treacy, Deem, and the International Zeolite Association. All prior knowledge of ice is set aside and we introduce "generalised convex hulls" to identify configurations stabilised by appropriate thermodynamic constraints. We thereby rediscover all known phases (I-XVII, i, 0 and the quartz phase) except the metastable ice IV. Crucially, we also find promising candidates for ices XVIII through LI. Using the "sketch-map" dimensionality-reduction algorithm we construct an a priori, navigable map of configuration space, which reproduces similarity relations between structures and highlights the novel candidates. By relating the known phases to the tractably small, yet structurally diverse set of synthesisable candidate structures, we provide an excellent starting point for identifying formation pathways.

Thermodynamic constraints on fluctuation phenomena

NASA Astrophysics Data System (ADS)

Maroney, O. J. E.

2009-12-01

The relationships among reversible Carnot cycles, the absence of perpetual motion machines, and the existence of a nondecreasing globally unique entropy function form the starting point of many textbook presentations of the foundations of thermodynamics. However, the thermal fluctuation phenomena associated with statistical mechanics has been argued to restrict the domain of validity of this basis of the second law of thermodynamics. Here we demonstrate that fluctuation phenomena can be incorporated into the traditional presentation, extending rather than restricting the domain of validity of the phenomenologically motivated second law. Consistency conditions lead to constraints upon the possible spectrum of thermal fluctuations. In a special case this uniquely selects the Gibbs canonical distribution and more generally incorporates the Tsallis distributions. No particular model of microscopic dynamics need be assumed.

Thermodynamic constraints on fluctuation phenomena.

PubMed

Maroney, O J E

2009-12-01

The relationships among reversible Carnot cycles, the absence of perpetual motion machines, and the existence of a nondecreasing globally unique entropy function form the starting point of many textbook presentations of the foundations of thermodynamics. However, the thermal fluctuation phenomena associated with statistical mechanics has been argued to restrict the domain of validity of this basis of the second law of thermodynamics. Here we demonstrate that fluctuation phenomena can be incorporated into the traditional presentation, extending rather than restricting the domain of validity of the phenomenologically motivated second law. Consistency conditions lead to constraints upon the possible spectrum of thermal fluctuations. In a special case this uniquely selects the Gibbs canonical distribution and more generally incorporates the Tsallis distributions. No particular model of microscopic dynamics need be assumed.

Thermodynamic analysis and subscale modeling of space-based orbit transfer vehicle cryogenic propellant resupply

NASA Technical Reports Server (NTRS)

Defelice, David M.; Aydelott, John C.

1987-01-01

The resupply of the cryogenic propellants is an enabling technology for spacebased orbit transfer vehicles. As part of the NASA Lewis ongoing efforts in microgravity fluid management, thermodynamic analysis and subscale modeling techniques were developed to support an on-orbit test bed for cryogenic fluid management technologies. Analytical results have shown that subscale experimental modeling of liquid resupply can be used to validate analytical models when the appropriate target temperature is selected to relate the model to its prototype system. Further analyses were used to develop a thermodynamic model of the tank chilldown process which is required prior to the no-vent fill operation. These efforts were incorporated into two FORTRAN programs which were used to present preliminary analyticl results.

Influence of condensed species on thermo-physical properties of LTE and non-LTE SF6-Cu mixture

NASA Astrophysics Data System (ADS)

Chen, Zhexin; Wu, Yi; Yang, Fei; Sun, Hao; Rong, Mingzhe; Wang, Chunlin

2017-10-01

SF6-Cu mixture is frequently formed in high-voltage circuit breakers due to the electrode erosion and metal vapor diffusion. During the interruption process, the multiphase effect and deviation from local thermal equilibrium (non-LTE assumption) can both affect the thermo-physical of the arc plasma and further influence the performance of circuit breaker. In this paper, thermo-physical properties, namely composition, thermodynamic properties and transport coefficients are calculated for multiphase SF6-Cu mixture with and without LTE assumption. The composition is confirmed by combining classical two-temperature mass action law with phase equilibrium condition deduced from second law of thermodynamics. The thermodynamic properties and transport coefficients are calculated using the multiphase composition result. The influence of condensed species on thermo-physical properties is discussed at different temperature, pressure (0.1-10 atm), non-equilibrium degrees (1-10), and copper molar proportions (0-50%). It is found that the multiphase effect has significant influence on specific enthalpy, specific heat and heavy species thermal conductivity in both LTE and non-LTE SF6-Cu system. This paper provides a more accurate database for computational fluid dynamic calculation.

A robust and accurate numerical method for transcritical turbulent flows at supercritical pressure with an arbitrary equation of state

NASA Astrophysics Data System (ADS)

Kawai, Soshi; Terashima, Hiroshi; Negishi, Hideyo

2015-11-01

This paper addresses issues in high-fidelity numerical simulations of transcritical turbulent flows at supercritical pressure. The proposed strategy builds on a tabulated look-up table method based on REFPROP database for an accurate estimation of non-linear behaviors of thermodynamic and fluid transport properties at the transcritical conditions. Based on the look-up table method we propose a numerical method that satisfies high-order spatial accuracy, spurious-oscillation-free property, and capability of capturing the abrupt variation in thermodynamic properties across the transcritical contact surface. The method introduces artificial mass diffusivity to the continuity and momentum equations in a physically-consistent manner in order to capture the steep transcritical thermodynamic variations robustly while maintaining spurious-oscillation-free property in the velocity field. The pressure evolution equation is derived from the full compressible Navier-Stokes equations and solved instead of solving the total energy equation to achieve the spurious pressure oscillation free property with an arbitrary equation of state including the present look-up table method. Flow problems with and without physical diffusion are employed for the numerical tests to validate the robustness, accuracy, and consistency of the proposed approach.

A robust and accurate numerical method for transcritical turbulent flows at supercritical pressure with an arbitrary equation of state

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

Kawai, Soshi, E-mail: kawai@cfd.mech.tohoku.ac.jp; Terashima, Hiroshi; Negishi, Hideyo

2015-11-01

This paper addresses issues in high-fidelity numerical simulations of transcritical turbulent flows at supercritical pressure. The proposed strategy builds on a tabulated look-up table method based on REFPROP database for an accurate estimation of non-linear behaviors of thermodynamic and fluid transport properties at the transcritical conditions. Based on the look-up table method we propose a numerical method that satisfies high-order spatial accuracy, spurious-oscillation-free property, and capability of capturing the abrupt variation in thermodynamic properties across the transcritical contact surface. The method introduces artificial mass diffusivity to the continuity and momentum equations in a physically-consistent manner in order to capture themore » steep transcritical thermodynamic variations robustly while maintaining spurious-oscillation-free property in the velocity field. The pressure evolution equation is derived from the full compressible Navier–Stokes equations and solved instead of solving the total energy equation to achieve the spurious pressure oscillation free property with an arbitrary equation of state including the present look-up table method. Flow problems with and without physical diffusion are employed for the numerical tests to validate the robustness, accuracy, and consistency of the proposed approach.« less

The Einstein database of IPC x-ray observations of optically selected and radio-selected quasars, 1.

NASA Technical Reports Server (NTRS)

Wilkes, Belinda J.; Tananbaum, Harvey; Worrall, D. M.; Avni, Yoram; Oey, M. S.; Flanagan, Joan

1994-01-01

We present the first volume of the Einstein quasar database. The database includes estimates of the X-ray count rates, fluxes, and luminosities for 514 quasars and Seyfert 1 galaxies observed with the Imaging Proportional Counter (IPC) aboard the Einstein Observatory. All were previously known optically selected or radio-selected objects, and most were the targets of the X-ray observations. The X-ray properties of the Active Galactic Nuclei (AGNs) have been derived by reanalyzing the IPC data in a systematic manner to provide a uniform database for general use by the astronomical community. We use the database to extend earlier quasar luminosity studies which were made using only a subset of the currently available data. The database can be accessed on internet via the SAO Einstein on-line system ('Einline') and is available in ASCII format on magnetic tape and DOS diskette.

Incorporation of rapid thermodynamic data in fragment-based drug discovery.

PubMed

Kobe, Akihiro; Caaveiro, Jose M M; Tashiro, Shinya; Kajihara, Daisuke; Kikkawa, Masato; Mitani, Tomoya; Tsumoto, Kouhei

2013-03-14

Fragment-based drug discovery (FBDD) has enjoyed increasing popularity in recent years. We introduce SITE (single-injection thermal extinction), a novel thermodynamic methodology that selects high-quality hits early in FBDD. SITE is a fast calorimetric competitive assay suitable for automation that captures the essence of isothermal titration calorimetry but using significantly fewer resources. We describe the principles of SITE and identify a novel family of fragment inhibitors of the enzyme ketosteroid isomerase displaying high values of enthalpic efficiency.

Identification of thermodynamically stable ceramic reinforcement materials for iron aluminide matrices

NASA Technical Reports Server (NTRS)

Misra, Ajay K.

1990-01-01

Aluminide-base intermetallic matrix composites are currently being considered as potential high-temperature materials. One of the key factors in the selection of a reinforcement material is its chemical stability in the matrix. In this study, chemical interactions between iron aluminides and several potential reinforcement materials, which include carbides, oxides, borides, and nitrides, are analyzed from thermodynamic considerations. Several chemically compatible reinforcement materials are identified for the iron aluminides with Al concentrations ranging from 40 to 50 at. pct.

The Tübingen Model-Atom Database: A Revised Aluminum Model Atom and its Application for the Spectral Analysis of White Dwarfs

NASA Astrophysics Data System (ADS)

Löbling, L.

2017-03-01

Aluminum (Al) nucleosynthesis takes place during the asymptotic-giant-branch (AGB) phase of stellar evolution. Al abundance determinations in hot white dwarf stars provide constraints to understand this process. Precise abundance measurements require advanced non-local thermodynamic stellar-atmosphere models and reliable atomic data. In the framework of the German Astrophysical Virtual Observatory (GAVO), the Tübingen Model-Atom Database (TMAD) contains ready-to- use model atoms for elements from hydrogen to barium. A revised, elaborated Al model atom has recently been added. We present preliminary stellar-atmosphere models and emergent Al line spectra for the hot white dwarfs G191-B2B and RE 0503-289.

Descriptors and Thermodynamic Limitations of Electrocatalytic Carbon Dioxide Reduction on Rutile Oxide Surfaces.

PubMed

Bhowmik, Arghya; Vegge, Tejs; Hansen, Heine A

2016-11-23

A detailed understanding of the electrochemical reduction of CO 2 into liquid fuels on rutile metal oxide surfaces is developed by using DFT calculations. We consider oxide overlayer structures on RuO 2 (1 1 0) surfaces as model catalysts to elucidate the trends and limitations in the CO 2 reduction reaction (CO2RR) based on thermodynamic analysis. We aim to specify the requirements for CO2RR catalysts to establish adsorbate scaling relations and use these to derive activity volcanoes. Computational results show that the OH* binding free energy is a good descriptor of the thermodynamic limitations and it defines the left leg of the activity volcano for CO2RR. HCOOH* is a key intermediate for products formed through further reduction, for example, methanediol, methanol, and methane. The surfaces that do not bind HCOOH* are selective towards formic acid (HCOOH) production, but hydrogen evolution limits their suitability. We determine the ideal binding free energy for H* and OH* to facilitate selective CO2RR over H 2 /CO evolution to be ΔG B [H]>0.5 eV and -0.5 eV<ΔG B [OH]<0.1 eV. The Re-containing overlayers considered in this work display excellent promise for selectivity, although they are active at a highly reducing potential. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Computational designing and screening of solid materials for CO2capture

NASA Astrophysics Data System (ADS)

Duan, Yuhua

In this presentation, we will update our progress on computational designing and screening of solid materials for CO2 capture. By combining thermodynamic database mining with first principles density functional theory and phonon lattice dynamics calculations, a theoretical screening methodology to identify the most promising CO2 sorbent candidates from the vast array of possible solid materials have been proposed and validated at NETL. The advantage of this method is that it identifies the thermodynamic properties of the CO2 capture reaction as a function of temperature and pressure without any experimental input beyond crystallographic structural information of the solid phases involved. The calculated thermodynamic properties of different classes of solid materials versus temperature and pressure changes were further used to evaluate the equilibrium properties for the CO2 adsorption/desorption cycles. According to the requirements imposed by the pre- and post- combustion technologies and based on our calculated thermodynamic properties for the CO2 capture reactions by the solids of interest, we were able to identify only those solid materials for which lower capture energy costs are expected at the desired working conditions. In addition, we present a simulation scheme to increase and decrease the turnover temperature (Tt) of solid capturing CO2 reaction by mixing other solids. Our results also show that some solid sorbents can serve as bi-functional materials: CO2 sorbent and CO oxidation catalyst. Such dual functionality could be used for removing both CO and CO2 after water-gas-shift to obtain pure H2.

The Integration of Plant Sample Analysis, Laboratory Studies, and Thermodynamic Modeling to Predict Slag-Matte Equilibria in Nickel Sulfide Converting

NASA Astrophysics Data System (ADS)

Hidayat, Taufiq; Shishin, Denis; Grimsey, David; Hayes, Peter C.; Jak, Evgueni

2018-02-01

The Kalgoorlie Nickel Smelter (KNS) produces low Fe, low Cu nickel matte in its Peirce-Smith converter operations. To inform process development in the plant, new fundamental data are required on the effect of CaO in slag on the distribution of arsenic between slag and matte. A combination of plant sample analysis, high-temperature laboratory experiments, and thermodynamic modeling was carried out to identify process conditions in the converter and to investigate the effect of slag composition on the chemical behavior of the system. The high-temperature experiments involved re-equilibration of industrial matte-slag-lime samples at 1498 K (1225 °C) and P(SO2) = 0.12 atm on a magnetite/quartz substrate, rapid quenching in water, and direct measurement of phase compositions using electron probe X-ray microanalysis (EPMA) and laser ablation-inductively coupled plasma-mass spectrometry (LA-ICP-MS). A private thermodynamic database for the Ca-Cu-Fe-Mg-Ni-O-S-Si-(As) system was used together with the FactSage software package to assist in the analysis. Thermodynamic predictions combined with plant sample characterization and the present experimental data provide a quantitative basis for the analysis of the effect of CaO fluxing on the slag-matte thermochemistry during nickel sulfide converting, in particular on the spinel liquidus and the distribution of elements between slag and matte as a function of CaO addition.

DISSOLVED CONCENTRATION LIMITS OF RADIOACTIVE ELEMENTS

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

P. Bernot

The purpose of this study is to evaluate dissolved concentration limits (also referred to as solubility limits) of elements with radioactive isotopes under probable repository conditions, based on geochemical modeling calculations using geochemical modeling tools, thermodynamic databases, field measurements, and laboratory experiments. The scope of this activity is to predict dissolved concentrations or solubility limits for elements with radioactive isotopes (actinium, americium, carbon, cesium, iodine, lead, neptunium, plutonium, protactinium, radium, strontium, technetium, thorium, and uranium) relevant to calculated dose. Model outputs for uranium, plutonium, neptunium, thorium, americium, and protactinium are provided in the form of tabulated functions with pH andmore » log fCO{sub 2} as independent variables, plus one or more uncertainty terms. The solubility limits for the remaining elements are either in the form of distributions or single values. Even though selection of an appropriate set of radionuclides documented in Radionuclide Screening (BSC 2002 [DIRS 160059]) includes actinium, transport of Ac is not modeled in the total system performance assessment for the license application (TSPA-LA) model because of its extremely short half-life. Actinium dose is calculated in the TSPA-LA by assuming secular equilibrium with {sup 231}Pa (Section 6.10); therefore, Ac is not analyzed in this report. The output data from this report are fundamental inputs for TSPA-LA used to determine the estimated release of these elements from waste packages and the engineered barrier system. Consistent modeling approaches and environmental conditions were used to develop solubility models for the actinides discussed in this report. These models cover broad ranges of environmental conditions so they are applicable to both waste packages and the invert. Uncertainties from thermodynamic data, water chemistry, temperature variation, and activity coefficients have been quantified or otherwise addressed.« less

Hailstorm forecast from stability indexes in Southwestern France

NASA Astrophysics Data System (ADS)

Melcón, Pablo; Merino, Andrés; Sánchez, José Luis; Dessens, Jean; Gascón, Estíbaliz; Berthet, Claude; López, Laura; García-Ortega, Eduardo

2016-04-01

Forecasting hailstorms is a difficult task because of their small spatial and temporal scales. Over recent decades, stability indexes have been commonly used in operational forecasting to provide a simplified representation of different thermodynamic characteristics of the atmosphere, regarding the onset of convective events. However, they are estimated from vertical profiles obtained by radiosondes, which are usually available only twice a day and have limited spatial representativeness. Numerical models predictions can be used to overcome these drawbacks, providing vertical profiles with higher spatiotemporal resolution. The main objective of this study is to create a tool for hail prediction in the southwest of France, one of the European regions where hailstorms have a higher incidence. The Association Nationale d'Etude et de Lutte contre les Fleáux Atmosphériques (ANELFA) maintains there a dense hailpad network in continuous operation, which has created an extensive database of hail events, used in this study as ground truth. The new technique is aimed to classify the spatial distribution of different stability indexes on hail days. These indexes were calculated from vertical profiles at 1200 UTC provided by WRF numerical model, validated with radiosonde data from Bordeaux. Binary logistic regression is used to select those indexes that best represent thermodynamic conditions related to occurrence of hail in the zone. Then, they are combined in a single algorithm that surpassed the predictive power they have when used independently. Regression equation results in hail days are used in cluster analysis to identify different spatial patterns given by the probability algorithm. This new tool can be used in operational forecasting, in combination with synoptic and mesoscale techniques, to properly define hail probability and distribution. Acknowledgements The authors would like to thank the CEPA González Díez Foundation and the University of Leon for its financial support.

Analysis of the relationships between evolvability, thermodynamics, and the functions of intrinsically disordered proteins/regions.

PubMed

Huang, He; Sarai, Akinori

2012-12-01

The evolvability of proteins is not only restricted by functional and structural importance, but also by other factors such as gene duplication, protein stability, and an organism's robustness. Recently, intrinsically disordered proteins (IDPs)/regions (IDRs) have been suggested to play a role in facilitating protein evolution. However, the mechanisms by which this occurs remain largely unknown. To address this, we have systematically analyzed the relationship between the evolvability, stability, and function of IDPs/IDRs. Evolutionary analysis shows that more recently emerged IDRs have higher evolutionary rates with more functional constraints relaxed (or experiencing more positive selection), and that this may have caused accelerated evolution in the flanking regions and in the whole protein. A systematic analysis of observed stability changes due to single amino acid mutations in IDRs and ordered regions shows that while most mutations induce a destabilizing effect in proteins, mutations in IDRs cause smaller stability changes than in ordered regions. The weaker impact of mutations in IDRs on protein stability may have advantages for protein evolvability in the gain of new functions. Interestingly, however, an analysis of functional motifs in the PROSITE and ELM databases showed that motifs in IDRs are more conserved, characterized by smaller entropy and lower evolutionary rate, than in ordered regions. This apparently opposing evolutionary effect may be partly due to the flexible nature of motifs in IDRs, which require some key amino acid residues to engage in tighter interactions with other molecules. Our study suggests that the unique conformational and thermodynamic characteristics of IDPs/IDRs play an important role in the evolvability of proteins to gain new functions. Copyright © 2012 Elsevier Ltd. All rights reserved.

Modeling Complex Equilibria in ITC Experiments: Thermodynamic Parameters Estimation for a Three Binding Site Model

PubMed Central

Le, Vu H.; Buscaglia, Robert; Chaires, Jonathan B.; Lewis, Edwin A.

2013-01-01

Isothermal Titration Calorimetry, ITC, is a powerful technique that can be used to estimate a complete set of thermodynamic parameters (e.g. Keq (or ΔG), ΔH, ΔS, and n) for a ligand binding interaction described by a thermodynamic model. Thermodynamic models are constructed by combination of equilibrium constant, mass balance, and charge balance equations for the system under study. Commercial ITC instruments are supplied with software that includes a number of simple interaction models, for example one binding site, two binding sites, sequential sites, and n-independent binding sites. More complex models for example, three or more binding sites, one site with multiple binding mechanisms, linked equilibria, or equilibria involving macromolecular conformational selection through ligand binding need to be developed on a case by case basis by the ITC user. In this paper we provide an algorithm (and a link to our MATLAB program) for the non-linear regression analysis of a multiple binding site model with up to four overlapping binding equilibria. Error analysis demonstrates that fitting ITC data for multiple parameters (e.g. up to nine parameters in the three binding site model) yields thermodynamic parameters with acceptable accuracy. PMID:23262283

An EQT-based cDFT approach for thermodynamic properties of confined fluid mixtures

NASA Astrophysics Data System (ADS)

Motevaselian, M. H.; Aluru, N. R.

2017-04-01

We present an empirical potential-based quasi-continuum theory (EQT) to predict the structure and thermodynamic properties of confined fluid mixtures. The central idea in the EQT is to construct potential energies that integrate important atomistic details into a continuum-based model such as the Nernst-Planck equation. The EQT potentials can be also used to construct the excess free energy functional, which is required for the grand potential in the classical density functional theory (cDFT). In this work, we use the EQT-based grand potential to predict various thermodynamic properties of a confined binary mixture of hydrogen and methane molecules inside graphene slit channels of different widths. We show that the EQT-cDFT predictions for the structure, surface tension, solvation force, and local pressure tensor profiles are in good agreement with the molecular dynamics simulations. Moreover, we study the effect of different bulk compositions and channel widths on the thermodynamic properties. Our results reveal that the composition of methane in the mixture can significantly affect the ordering of molecules and thermodynamic properties under confinement. In addition, we find that graphene is selective to methane molecules.

Limited options for low-global-warming-potential refrigerants.

PubMed

McLinden, Mark O; Brown, J Steven; Brignoli, Riccardo; Kazakov, Andrei F; Domanski, Piotr A

2017-02-17

Hydrofluorocarbons, currently used as refrigerants in air-conditioning systems, are potent greenhouse gases, and their contribution to climate change is projected to increase. Future use of the hydrofluorocarbons will be phased down and, thus replacement fluids must be found. Here we show that only a few pure fluids possess the combination of chemical, environmental, thermodynamic, and safety properties necessary for a refrigerant and that these fluids are at least slightly flammable. We search for replacements by applying screening criteria to a comprehensive chemical database. For the fluids passing the thermodynamic and environmental screens (critical temperature and global warming potential), we simulate performance in small air-conditioning systems, including optimization of the heat exchangers. We show that the efficiency-versus-capacity trade-off that exists in an ideal analysis disappears when a more realistic system is considered. The maximum efficiency occurs at a relatively high volumetric refrigeration capacity, but there are few fluids in this range.

Reactive solute transport in acidic streams

USGS Publications Warehouse

Broshears, R.E.

1996-01-01

Spatial and temporal profiles of Ph and concentrations of toxic metals in streams affected by acid mine drainage are the result of the interplay of physical and biogeochemical processes. This paper describes a reactive solute transport model that provides a physically and thermodynamically quantitative interpretation of these profiles. The model combines a transport module that includes advection-dispersion and transient storage with a geochemical speciation module based on MINTEQA2. Input to the model includes stream hydrologic properties derived from tracer-dilution experiments, headwater and lateral inflow concentrations analyzed in field samples, and a thermodynamic database. Simulations reproduced the general features of steady-state patterns of observed pH and concentrations of aluminum and sulfate in St. Kevin Gulch, an acid mine drainage stream near Leadville, Colorado. These patterns were altered temporarily by injection of sodium carbonate into the stream. A transient simulation reproduced the observed effects of the base injection.

Limited options for low-global-warming-potential refrigerants

NASA Astrophysics Data System (ADS)

McLinden, Mark O.; Brown, J. Steven; Brignoli, Riccardo; Kazakov, Andrei F.; Domanski, Piotr A.

2017-02-01

Hydrofluorocarbons, currently used as refrigerants in air-conditioning systems, are potent greenhouse gases, and their contribution to climate change is projected to increase. Future use of the hydrofluorocarbons will be phased down and, thus replacement fluids must be found. Here we show that only a few pure fluids possess the combination of chemical, environmental, thermodynamic, and safety properties necessary for a refrigerant and that these fluids are at least slightly flammable. We search for replacements by applying screening criteria to a comprehensive chemical database. For the fluids passing the thermodynamic and environmental screens (critical temperature and global warming potential), we simulate performance in small air-conditioning systems, including optimization of the heat exchangers. We show that the efficiency-versus-capacity trade-off that exists in an ideal analysis disappears when a more realistic system is considered. The maximum efficiency occurs at a relatively high volumetric refrigeration capacity, but there are few fluids in this range.

Limited options for low-global-warming-potential refrigerants

PubMed Central

McLinden, Mark O.; Brown, J. Steven; Brignoli, Riccardo; Kazakov, Andrei F.; Domanski, Piotr A.

2017-01-01

Hydrofluorocarbons, currently used as refrigerants in air-conditioning systems, are potent greenhouse gases, and their contribution to climate change is projected to increase. Future use of the hydrofluorocarbons will be phased down and, thus replacement fluids must be found. Here we show that only a few pure fluids possess the combination of chemical, environmental, thermodynamic, and safety properties necessary for a refrigerant and that these fluids are at least slightly flammable. We search for replacements by applying screening criteria to a comprehensive chemical database. For the fluids passing the thermodynamic and environmental screens (critical temperature and global warming potential), we simulate performance in small air-conditioning systems, including optimization of the heat exchangers. We show that the efficiency-versus-capacity trade-off that exists in an ideal analysis disappears when a more realistic system is considered. The maximum efficiency occurs at a relatively high volumetric refrigeration capacity, but there are few fluids in this range. PMID:28211518

The role of stabilization centers in protein thermal stability

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

Magyar, Csaba; Gromiha, M. Michael; Sávoly, Zoltán

2016-02-26

The definition of stabilization centers was introduced almost two decades ago. They are centers of noncovalent long range interaction clusters, believed to have a role in maintaining the three-dimensional structure of proteins by preventing their decay due to their cooperative long range interactions. Here, this hypothesis is investigated from the viewpoint of thermal stability for the first time, using a large protein thermodynamics database. The positions of amino acids belonging to stabilization centers are correlated with available experimental thermodynamic data on protein thermal stability. Our analysis suggests that stabilization centers, especially solvent exposed ones, do contribute to the thermal stabilizationmore » of proteins. - Highlights: • Stabilization centers contribute to thermal stabilization of protein structures. • Stabilization center content correlates with melting temperature of proteins. • Exposed stabilization center content correlates with stability even in hyperthermophiles. • Stability changing mutations are frequently found at stabilization centers.« less

Experimental measurement of binding energy, selectivity, and allostery using fluctuation theorems.

PubMed

Camunas-Soler, Joan; Alemany, Anna; Ritort, Felix

2017-01-27

Thermodynamic bulk measurements of binding reactions rely on the validity of the law of mass action and the assumption of a dilute solution. Yet, important biological systems such as allosteric ligand-receptor binding, macromolecular crowding, or misfolded molecules may not follow these assumptions and may require a particular reaction model. Here we introduce a fluctuation theorem for ligand binding and an experimental approach using single-molecule force spectroscopy to determine binding energies, selectivity, and allostery of nucleic acids and peptides in a model-independent fashion. A similar approach could be used for proteins. This work extends the use of fluctuation theorems beyond unimolecular folding reactions, bridging the thermodynamics of small systems and the basic laws of chemical equilibrium. Copyright © 2017, American Association for the Advancement of Science.

Exergy analysis of helium liquefaction systems based on modified Claude cycle with two-expanders

NASA Astrophysics Data System (ADS)

Thomas, Rijo Jacob; Ghosh, Parthasarathi; Chowdhury, Kanchan

2011-06-01

Large-scale helium liquefaction systems, being energy-intensive, demand judicious selection of process parameters. An effective tool for design and analysis of thermodynamic cycles for these systems is exergy analysis, which is used to study the behavior of a helium liquefaction system based on modified Claude cycle. Parametric evaluation using process simulator Aspen HYSYS® helps to identify the effects of cycle pressure ratio and expander flow fraction on the exergetic efficiency of the liquefaction cycle. The study computes the distribution of losses at different refrigeration stages of the cycle and helps in selecting optimum cycle pressures, operating temperature levels of expanders and mass flow rates through them. Results from the analysis may help evolving guidelines for designing appropriate thermodynamic cycles for practical helium liquefaction systems.

Viral genome structures, charge, and sequences are optimal for capsid assembly

NASA Astrophysics Data System (ADS)

Hagan, Michael

2014-03-01

For many viruses, the spontaneous assembly of a capsid shell around the nu-cleic acid (NA) genome is an essential step in the viral life cycle. Capsid formation is a multicomponent, out-of-equilibrium assembly process for which kinetic effects and thermodynamic constraints compete to determine the outcome. Understand-ing how viral components drive highly efficient assembly under these constraints could promote biomedical efforts to block viral propagation, and would elucidate the factors controlling assembly in a wide range of systems containing proteins and polyelectrolytes. This talk will describe coarse-grained models of capsid proteins and NAs with which we investigate the dynamics and thermodynamics of virus assembly. In con-trast to recent theoretical models, we find that capsids spontaneously `overcharge' that is, the NA length which is kinetically and thermodynamically optimal possess-es a negative charge greater than the positive charge of the capsid. When applied to specific virus capsids, the calculated optimal NA lengths closely correspond to the natural viral genome lengths. These results suggest that the features included in this model (i.e. electrostatics, excluded volume, and NA tertiary structure) play key roles in determining assembly thermodynamics and consequently exert selec-tive pressure on viral evolution. I will then discuss mechanisms by which se-quence-specific interactions between NAs and capsid proteins promote selective encapsidation of the viral genome. This work was supported by NIH R01GM108021 and the Brandeis MRSEC NSF-MRSEC-0820492.

Improvement of the analog forecasting method by using local thermodynamic data. Application to autumn precipitation in Catalonia

NASA Astrophysics Data System (ADS)

Gibergans-Báguena, J.; Llasat, M. C.

2007-12-01

The objective of this paper is to present the improvement of quantitative forecasting of daily rainfall in Catalonia (NE Spain) from an analogues technique, taking into account synoptic and local data. This method is based on an analogues sorting technique: meteorological situations similar to the current one, in terms of 700 and 1000 hPa geopotential fields at 00 UTC, complemented with the inclusion of some thermodynamic parameters extracted from an historical data file. Thermodynamic analysis acts as a highly discriminating feature for situations in which the synoptic situation fails to explain either atmospheric phenomena or rainfall distribution. This is the case in heavy rainfall situations, where the existence of instability and high water vapor content is essential. With the objective of including these vertical thermodynamic features, information provided by the Palma de Mallorca radiosounding (Spain) has been used. Previously, a selection of the most discriminating thermodynamic parameters for the daily rainfall was made, and then the analogues technique applied to them. Finally, three analog forecasting methods were applied for the quantitative daily rainfall forecasting in Catalonia. The first one is based on analogies from geopotential fields to synoptic scale; the second one is exclusively based on the search of similarity from local thermodynamic information and the third method combines the other two methods. The results show that this last method provides a substantial improvement of quantitative rainfall estimation.

Thermodynamic data for biomass conversion and waste incineration

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

Domalski, E.S.; Jobe, T.L. Jr; Milne, T.A.

1986-09-01

The general purpose of this collection of thermodynamic data of selected materials is to make property information available to the engineering community on chemical mixtures, polymers, composite materials, solid wastes, biomass, and materials not easily identifiable by a single stoichiometric formula. More than 700 materials have been compiled covering properties such as specific heat, gross heat of combustion, heat of fusion, heat of vaporization, and vapor pressure. The information was obtained from the master files of the NBS Chemical Thermodynamics Data Center, the annual issues of the Bulletin of Chemical Thermodynamics, intermittent examinations of the Chemical Abstracts subject indexes, individualmore » articles by various authors, and other general reference sources. The compilation is organized into several broad categories; materials are listed alphabetically within each category. For each material, the physical state, information as to the composition or character of the material, the kind of thermodynamic property reported, the specific property values for the material, and citations to the reference list are given. In addition, appendix A gives an empirical formula that allows heats of combustion of carbonaceous materials to be predicted with surprising accuracy when the elemental composition is known. A spread sheet illustrates this predictability with examples from this report and elsewhere. Appendix B lists some reports containing heats of combustion not included in this publication. Appendix C contains symbols, units, conversion factors, and atomic weights used in evaluating and compiling the thermodynamic data.« less

Equilibrium studies of oxalate and aluminum containing solutions

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

Hay, M. S.; King, W. D.; Peters, T. B.

2015-11-01

The Savannah River National Laboratory (SRNL) was tasked to develop data on the solubility and conditions leading to precipitation of sodium oxalate, sodium nitrate, Bayerite (a polymorph of gibbsite, Al(OH) 3), and sodium aluminosilicate solids recently found in the Modular Caustic Side Solvent Extraction Unit (MCU). The data generated will be used to improve the OLI Systems thermodynamic database for these compounds allowing better prediction of solids formation by the modeling software in the future.

Optimization of the thermodynamic properties and phase diagrams of P2O5-containing systems

NASA Astrophysics Data System (ADS)

Hudon, Pierre; Jung, In-Ho

2014-05-01

P2O5 is an important oxide component in the late stage products of numerous igneous rocks such as granites and pegmatites. Typically, P2O5 combines with CaO and crystallizes in the form of apatite, while in volatile-free conditions, Ca-whitlockite is formed. In spite of their interest, the thermodynamic properties and phase diagrams of P2O5-containg systems are not well known yet. In the case of the pure P2O5 for example, no experimental thermodynamic data are available for the liquid and the O and O' solid phases. As a result, we re-evaluated all the thermodynamic and phase diagram data of the P2O5 unary system [1]. Optimization of the thermodynamic properties and phase diagrams of the binary P2O5 systems was then performed including the Li2O-, Na2O-, MgO-, CaO-, BaO-, MnO-, FeO-, Fe2O3-, ZnO-, Al2O3-, and SiO2-P2O5 [2] systems. All available thermodynamic and phase equilibrium data were simultaneously reproduced in order to obtain a set of model equations for the Gibbs energies of all phases as functions of temperature and composition. In particular, the Gibbs energy of the liquid solution was described using the Modified Quasichemical Model [3-5] implemented in the FactSage software [6]. Thermodynamic modeling of the Li2O-Na2O-K2O-MgO-CaO-FeO-Fe2O3-Al2O3-SiO2 system, which include many granite-forming minerals such as nepheline, leucite, pyroxene, melilite, feldspar and spinel is currently in progress. [1] Jung, I.-H., Hudon, P. (2012) Thermodynamic assessment of P2O5. J. Am. Ceram. Soc., 95 (11), 3665-3672. [2] Rahman, M., Hudon, P. and Jung, I.-H. (2013) A coupled experimental study and thermodynamic modeling of the SiO2-P2O5 system. Metall. Mater. Trans. B, 44 (4), 837-852. [3] Pelton, A.D. and Blander, M. (1984) Computer-assisted analysis of the thermodynamic properties and phase diagrams of slags. Proc. AIME Symp. Metall. Slags Fluxes, TMS-AIME, 281-294. [4] Pelton, A.D. and Blander, M. (1986) Thermodynamic analysis of ordered liquid solutions by a modified quasichemical approach application to silicate slags. Metall. Trans. B, 17, 805-815. [5] A.D. Pelton, S.A. Decterov, G. Eriksson, C. Robelin and Y. Dessureault (2000) The modified quasichemical model - I Binary solutions. Metall. Mater. Trans. B, 31, 651-660. [6] C.W. Bale, P. Chartrand, S.A. Decterov, G. Eriksson, K. Hack, R. Ben Mahfoud, J. Melançon, A.D. Pelton and S. Petersen. (2002) FactSage Thermochemical Software and Databases. Calphad, 26, 189-228.

Experimental and thermodynamic study of Co-Fe and Mn-Fe based mixed metal oxides for thermochemical energy storage application

NASA Astrophysics Data System (ADS)

André, Laurie; Abanades, Stéphane; Cassayre, Laurent

2017-06-01

Metal oxides are potential materials for thermochemical heat storage, and among them, cobalt oxide and manganese oxide are attracting attention. Furthermore, studies on mixed oxides are ongoing, as the synthesis of mixed oxides could be a way to answer the drawbacks of pure metal oxides, such as slow reaction kinetics, loss-in-capacity over cycles or sintering, selected for thermochemical heat storage application. The addition of iron oxide is under investigation and the obtained results are presented. This work proposes a comparison of thermodynamic modelling with experimental data in order to identify the impact of iron oxide addition to cobalt oxide and manganese oxide. Fe addition decreased the redox activity and energy storage capacity of Co3O4, whereas the cycling stability of Mn2O3 was significantly improved with added Fe amounts above 20 mol% while the energy storage capacity was unchanged. The thermodynamic modelling method to predict the behavior of the Mn-Fe-O and Co-Fe-O systems was validated, and the possibility to identify other mixed oxides becomes conceivable, by enabling the selection of transition metals additives for metal oxides destined for thermochemical energy storage applications.

Design of spatial oval plane mirror and its support structure

NASA Astrophysics Data System (ADS)

Chai, Wenyi; Hu, Yongming; Wang, Chenjie; Chen, Su; Feng, Song

2018-02-01

For the diameter of 150mm elliptical flat mirror that used in the space, selected the zerodur material and a lightweight design is conducted in the way of selected back-open-architecture with symmetrical axisymmetric arrangement, and in order to evaluate the effect of thermal stress from -10°C to 45°C on the mirror, a reflection mirror is designed based on the multipoint flexible support. The mirror component's mechanic and thermodynamic characteristics is analyzed with the simulation software, the support structure parameters are optimized, that can be used to evaluate the effect of gravity, assembly stress, and thermal stress load on mirror, while ensuring the component's stiffness and strength. According to the design condition developed a product and carried out mechanic and thermodynamic environment, the product could meet the shape accuracy PV λ/3, RMS λ/30 in the condition of thermodynamic environment, and the shape accuracy PV λ/5, RMS λ/40 in the condition of ground gravity and assembly stress (λ=632.8nm), while the product can withstand with the mechanical oscillation environment sinusoidal oscillation 10g, RMS random oscillation acceleration 14.4g.

Interactive FORTRAN IV computer programs for the thermodynamic and transport properties of selected cryogens (fluids pack)

NASA Technical Reports Server (NTRS)

Mccarty, R. D.

1980-01-01

The thermodynamic and transport properties of selected cryogens had programmed into a series of computer routines. Input variables are any two of P, rho or T in the single phase regions and either P or T for the saturated liquid or vapor state. The output is pressure, density, temperature, entropy, enthalpy for all of the fluids and in most cases specific heat capacity and speed of sound. Viscosity and thermal conductivity are also given for most of the fluids. The programs are designed for access by remote terminal; however, they have been written in a modular form to allow the user to select either specific fluids or specific properties for particular needs. The program includes properties for hydrogen, helium, neon, nitrogen, oxygen, argon, and methane. The programs include properties for gaseous and liquid states usually from the triple point to some upper limit of pressure and temperature which varies from fluid to fluid.

Predictive thermodynamics for ionic solids and liquids.

PubMed

Glasser, Leslie; Jenkins, H Donald Brooke

2016-08-21

The application of thermodynamics is simple, even if the theory may appear intimidating. We describe tools, developed over recent years, which make it easy to estimate often elusive thermodynamic parameter values, generally (but not exclusively) for ionic materials, both solid and liquid, as well as for their solid hydrates and solvates. The tools are termed volume-based thermodynamics (VBT) and thermodynamic difference rules (TDR), supplemented by the simple salt approximation (SSA) and single-ion values for volume, Vm, heat capacity, , entropy, , formation enthalpy, ΔfH°, and Gibbs formation energy, ΔfG°. These tools can be applied to provide values of thermodynamic and thermomechanical properties such as standard enthalpy of formation, ΔfH°, standard entropy, , heat capacity, Cp, Gibbs function of formation, ΔfG°, lattice potential energy, UPOT, isothermal expansion coefficient, α, and isothermal compressibility, β, and used to suggest the thermodynamic feasibility of reactions among condensed ionic phases. Because many of these methods yield results largely independent of crystal structure, they have been successfully extended to the important and developing class of ionic liquids as well as to new and hypothesised materials. Finally, these predictive methods are illustrated by application to K2SnCl6, for which known experimental results are available for comparison. A selection of applications of VBT and TDR is presented which have enabled input, usually in the form of thermodynamics, to be brought to bear on a range of topical problems. Perhaps the most significant advantage of VBT and TDR methods is their inherent simplicity in that they do not require a high level of computational expertise nor expensive high-performance computation tools - a spreadsheet will usually suffice - yet the techniques are extremely powerful and accessible to non-experts. The connection between formula unit volume, Vm, and standard thermodynamic parameters represents a major advance exploited by these techniques.

Synchronised Aerosol Mass Spectrometer Measurements across Europe

NASA Astrophysics Data System (ADS)

Nemitz, Eiko

2010-05-01

Up to twelve Aerodyne Aerosol Mass Spectrometers (AMSs) were operated simultaneously at rural and background stations (EMEP and EUSAAR sites) across Europe. Measurements took place during three intensive periods, in collaboration between the European EUCAARI IP and the EMEP monitoring activities under the UNECE Convention for Long-Range Transboundary Air Pollution (CLRTAP) during three contrasting months (May 2008, Sep/Oct 2008, Feb/Mar 2009). These measurements were conducted, analysed and quality controlled carefully using a unified protocol, providing the largest spatial database of aerosol chemical composition measured with a unified online technique to date, and a unique snapshots of the European non-refractory submicron aerosol climatology. As campaign averages over all active monitoring sites, organics represent 28 to 43%, sulphate 18 to 25%, ammonium 13 to 15% and nitrate 15 to 36% of the resolved aerosol mass, with the highest relative nitrate contribution during the Feb/Mar campaign. The measurements demonstrate that in NW Europe (e.g. Ireland, UK, The Netherlands, Germany, Switzerland) the regional submicron aerosol tends to be neutralised and here nitrates make a major contribution to the aerosol mass. By contrast, periods with low nitrate and acidic aerosol were observed at sites in S and E Europe (e.g. Greece, Finland), presumably due to a combination of larger SO2 point sources in Easter Europe, smaller local NH3 sources and, in the case of Greece, higher temperatures. While at the more marine and remote sites (Ireland, Scotland, Finland) nitrate concentrations were dominated by episodic transport phenomena, at continental sites (Switzerland, Germany, Hungary) nitrate followed a clear diurnal cycle, reflecting the thermodynamic behaviour of ammonium nitrate. The datasets clearly shows spatially co-ordinated, large-scale pollution episodes of organics, sulphate and nitrate, the latter being most pronounced during the Feb/Mar campaign. At selected sites concentrations of inorganic precursor gases (e.g. NH3, HNO3, SO2) were measured simultaneously, mainly with a denuder based wet chemistry technique. The database provides a powerful dataset against which to compare the performance of European scale Chemistry and Transport Models (CTMs) in reproducing transport patterns, thermodynamics (e.g. daytime vs. night-time concentrations and gas/aerosol partitioning) and organic aerosol partitioning (e.g. primary versus oxidised aerosol). Future analysis will include a detailed analysis of the organic aerosol composition, through statistical factor analysis and based on the high mass resolution data provided by a subset of the AMS instruments.

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

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

Yang, Ying

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

Simultaneous calibration of end-member thermodynamic data and solution properties with correlated uncertainties

NASA Astrophysics Data System (ADS)

Antoshechkina, P. M.; Wolf, A. S.; Hamecher, E. A.; Asimow, P. D.; Ghiorso, M. S.

2013-12-01

Community databases such as EarthChem, LEPR, and AMCSD both increase demand for quantitative petrological tools, including thermodynamic models like the MELTS family of algorithms, and are invaluable in development of such tools. The need to extend existing solid solution models to include minor components such as Cr and Na has been evident for years but as the number of components increases it becomes impossible to completely separate derivation of end-member thermodynamic data from calibration of solution properties. In Hamecher et al. (2012; 2013) we developed a calibration scheme that directly interfaces with a MySQL database based on LEPR, with volume data from AMCSD and elsewhere. Here we combine that scheme with a Bayesian approach, where independent constraints on parameter values (e.g. existence of miscibility gaps) are combined with uncertainty propagation to give a more reliable best-fit along with associated model uncertainties. We illustrate the scheme with a new model of molar volume for (Ca,Fe,Mg,Mn,Na)3(Al,Cr,Fe3+,Fe2+,Mg,Mn,Si,Ti)2Si3O12 cubic garnets. For a garnet in this chemical system, the model molar volume is obtained by adding excess volume terms to a linear combination of nine independent end-member volumes. The model calibration is broken into three main stages: (1) estimation of individual end-member thermodynamic properties; (2) calibration of standard state volumes for all available independent and dependent end members; (3) fitting of binary and mixed composition data. For each calibration step, the goodness-of-fit includes weighted residuals as well as χ2-like penalty terms representing the (not necessarily Gaussian) prior constraints on parameter values. Using the Bayesian approach, uncertainties are correctly propagated forward to subsequent steps, allowing determination of final parameter values and correlated uncertainties that account for the entire calibration process. For the aluminosilicate garnets, optimal values of the bulk modulus and its pressure derivative are obtained by fitting published compression data using the Vinet equation of state, with the Mie-Grüneisen-Debye thermal pressure formalism to model thermal expansion. End-member thermal parameters are obtained by fitting volume data while ensuring that the heat capacity is consistent with the thermodynamic database of Berman and co-workers. For other end members, data for related compositions are used where such data exist; otherwise ultrasonic data or density functional theory results are taken or, for thermal parameters, systematics in cation radii are used. In stages (2) and (3) the remaining data at ambient conditions are fit. Using this step-wise calibration scheme, most parameters are modified little by subsequent calibration steps but some, such as the standard state volume of the Ti-bearing end member, can vary within calculated uncertainties. The final model satisfies desired criteria and fits almost all the data (more than 1000 points); only excess parameters that are justified by the data are activated. The scheme can be easily extended to calibration of end-member and solution properties from experimental phase equilibria. As a first step we obtain the internally consistent standard state entropy and enthalpy of formation for knorringite and discuss differences between our results and those of Klemme and co-workers.

Examination of two methods of describing the thermodynamic properties of oxygen near the critical point

NASA Technical Reports Server (NTRS)

Rees, T. H.; Suttles, J. T.

1972-01-01

A computer study was conducted to compare the numerical behavior of two approaches to describing the thermodynamic properties of oxygen near the critical point. Data on the relative differences between values of specific heats at constant pressure (sub p) density, and isotherm and isochor derivatives of the equation of state are presented for selected supercritical pressures at temperatures in the range 100 to 300 K. The results of a more detailed study of the sub p representations afforded by the two methods are also presented.

Assessing cooperativity in supramolecular systems.

PubMed

von Krbek, Larissa K S; Schalley, Christoph A; Thordarson, Pall

2017-05-09

This tutorial review summarises different aspects of cooperativity in supramolecular complexes. We propose a systematic categorisation of cooperativity into cooperative aggregation, intermolecular (allosteric) cooperativity, intramolecular (chelate) cooperativity and interannular cooperativity and discuss approaches to quantify them thermodynamically using cooperativity factors. A brief summary of methods to determine the necessary thermodynamic data is given with emphasis on isothermal titration calorimetry (ITC), a method still underrepresented in supramolecular chemistry, which however offers some advantages over others. Finally, a discussion of very few selected examples, which highlight different aspects to illustrate why such an analysis is useful, rounds up this review.

Database Software Selection for the Egyptian National STI Network.

ERIC Educational Resources Information Center

Slamecka, Vladimir

The evaluation and selection of information/data management system software for the Egyptian National Scientific and Technical (STI) Network are described. An overview of the state-of-the-art of database technology elaborates on the differences between information retrieval and database management systems (DBMS). The desirable characteristics of…

Transport Coefficients for the NASA Lewis Chemical Equilibrium Program

NASA Technical Reports Server (NTRS)

Svehla, Roger A.

1995-01-01

The new transport property data that will be used in the NASA Lewis Research Center's Chemical Equilibrium and Applications Program (CEA) is presented. It complements a previous publication that documented the thermodynamic and transport property data then in use. Sources of the data and a brief description of the method by which the data were obtained are given. Coefficients to calculate the viscosity, thermal conductivity, and binary interactions are given for either one, or usually, two temperature intervals, typically 300 to 1000 K and 1000 to 5000 K. The form of the transport equation is the same as used previously. The number of species was reduced from the previous database. Many species for which the data were estimated were eliminated from the database. Some ionneutral interactions were added.

Calculation of Phase Equilibria in the Y2O3-Yb2O3-ZrO2 System

NASA Technical Reports Server (NTRS)

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

2001-01-01

Rare earth oxide stabilized zirconias find a wide range of applications. An understanding of phase equilibria is essential to all applications. In this study, the available phase boundary data and thermodynamic data is collected and assessed. Calphad-type databases are developed to completely describe the Y2O3-ZrO2, Yb2O3-ZrO2, and Y2O3-Yb2O3 systems. The oxide units are treated as components and regular and subregular solution models are used. The resultant calculated phase diagrams show good agreement with the experimental data. Then the binaries are combined to form the database for the Y2O3-Yb2O3-ZrO2 psuedo-ternary.

A simple model for solvation in mixed solvents. Applications to the stabilization and destabilization of macromolecular structures.

PubMed

Schellman, J A

1990-08-31

The properties of a simple model for solvation in mixed solvents are explored in this paper. The model is based on the supposition that solvent replacement is a simple one-for-one substitution reaction at macromolecular sites which are independent of one another. This leads to a new form for the binding polynomial in which all terms are associated with ligand interchange rather than ligand addition. The principal solvent acts as one of the ligands. Thermodynamic analysis then shows that thermodynamic binding (i.e., selective interaction) depends on the properties of K'-1, whereas stoichiometric binding (site occupation) depends on K'. K' is a 'practical' interchange equilibrium constant given by (f3/f1)K, where K is the true equilibrium constant for the interchange of components 3 and 1 on the site and f3 and f4 denote their respective activity coefficients on the mole fraction scale. Values of K' less than unity lead to negative selective interaction. It is selective interaction and not occupation number which determines the thermodynamic effects of solvation. When K' greater than 100 on the mole fraction scale or K' greater than 2 on the molality scale (in water), the differences between stoichiometric binding and selective interaction become less than 1%. The theory of this paper is therefore necessary only for very weak binding constants. When K'-1 is small, large concentrations of the added solvent component are required to produce a thermodynamic effect. Under these circumstances the isotherms for the selective interaction and for the excess (or transfer) free energy are strongly dependent on the behavior of the activity coefficients of both solvent components. Two classes of behavior are described depending on whether the components display positive or negative deviations from Raoult's law. Examples which are discussed are aqueous solutions of urea and guanidinium chloride for positive deviations and of sucrose and glucose for negative deviations. Examination of the few studies which have been reported in the literature shows that most of the qualitative features of the stabilization of proteins by sugars and their destabilization by urea and guanidinium chloride are faithfully represented with the model. This includes maxima in the free energy of stabilization and destabilization, decreased and zero selective interaction at high concentrations, etc. These phenomena had no prior explanation. Deficiencies in the model as a representation of solvation in aqueous solution are discussed in the appendix.

Thermodynamic System Drift in Protein Evolution

PubMed Central

Hart, Kathryn M.; Harms, Michael J.; Schmidt, Bryan H.; Elya, Carolyn; Thornton, Joseph W.; Marqusee, Susan

2014-01-01

Proteins from thermophiles are generally more thermostable than their mesophilic homologs, but little is known about the evolutionary process driving these differences. Here we attempt to understand how the diverse thermostabilities of bacterial ribonuclease H1 (RNH) proteins evolved. RNH proteins from Thermus thermophilus (ttRNH) and Escherichia coli (ecRNH) share similar structures but differ in melting temperature (Tm) by 20°C. ttRNH's greater stability is caused in part by the presence of residual structure in the unfolded state, which results in a low heat capacity of unfolding (ΔCp) relative to ecRNH. We first characterized RNH proteins from a variety of extant bacteria and found that Tm correlates with the species' growth temperatures, consistent with environmental selection for stability. We then used ancestral sequence reconstruction to statistically infer evolutionary intermediates along lineages leading to ecRNH and ttRNH from their common ancestor, which existed approximately 3 billion years ago. Finally, we synthesized and experimentally characterized these intermediates. The shared ancestor has a melting temperature between those of ttRNH and ecRNH; the Tms of intermediate ancestors along the ttRNH lineage increased gradually over time, while the ecRNH lineage exhibited an abrupt drop in Tm followed by relatively little change. To determine whether the underlying mechanisms for thermostability correlate with the changes in Tm, we measured the thermodynamic basis for stabilization—ΔCp and other thermodynamic parameters—for each of the ancestors. We observed that, while the Tm changes smoothly, the mechanistic basis for stability fluctuates over evolutionary time. Thus, even while overall stability appears to be strongly driven by selection, the proteins explored a wide variety of mechanisms of stabilization, a phenomenon we call “thermodynamic system drift.” This suggests that even on lineages with strong selection to increase stability, proteins have wide latitude to explore sequence space, generating biophysical diversity and potentially opening new evolutionary pathways. PMID:25386647

THERMODYNAMIC PROPERTIES OF SELECTED HFC REFRIGERANTS

EPA Science Inventory

Hydrofluorocarbon (HFC) refrigerants are possible alternatives to replace ozone-depleting chlorofluorocarbon and hydrochlorofluorocarbon (HCFC) refrigerants. The flammability of a proposed new refrigerant is a major consideration in assessing its utility for a particular applicat...

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

Zhao, Donghui; Key Lab of Inorganic Coating Materials, Shanghai Institute of Ceramics, Chinese Academy of Sciences, 1295 Dingxi, Changning, Shanghai 200050; Zhu, Yingchun, E-mail: yzhu@mail.sic.ac.cn

In this article, the polymorph selection of calcium carbonate has been successfully achieved in water-soluble carboxymethyl chitosan aqueous solution at different temperatures (25-95 {sup o}C). Vaterite is formed in carboxymethyl chitosan solution 25 {sup o}C accompanied with trace of calcite, whereas pure aragonite is obtained at 95 {sup o}C. Scanning electron microscopy and transmission electron microscopy analyses show that the products are formed from the recrystallization of nanometer crystallites. Thermodynamic and kinetic analyses reveal that the polymorph of calcium carbonate is controlled and selected by kinetics in various temperatures. As a heterogeneous nucleator and stabilizing agent, carboxymethyl chitosan changes themore » nucleation and growth of calcium carbonate from thermodynamic into kinetic control. Under kinetic limitation, the reaction rate of aragonite increases along with the elevating of temperature and surpasses the rate of vaterite above 327 K.« less

Doping Li and K into Na2ZrO3 Sorbent to Improve Its CO2 Capture Capability

NASA Astrophysics Data System (ADS)

Duan, Yuhua

Carbon dioxide is one of the major combustion products which once released into the air can contribute to global climate change. Solid sorbents have been reported in several previous studies to be promising candidates for CO2 sorbent applications due to their high CO2 absorption capacities at moderate working temperatures. However, at a given CO2 pressure, the turnover temperature (Tt) of an individual solid capture CO2 reaction is fixed and may be outside the operating temperature range (ΔTo) for a particularly capture technology. In order to shift such Tt for a solid into the range of ΔTo, its corresponding thermodynamic property must be changed by changing its structure by reacting (mixing) with other materials or doping with other elements. As an example, by combining thermodynamic database searching with ab initio thermodynamics calculations, in this work, we explored the Li- and K-doping effects on the Tt shifts of Na2ZrO3 at different doping levels. The obtained results showed that compared to pure Na2ZrO3, the Li- and K-doped mixtures Na2-αMαZrO3 (M =Li, K) have lower Tt and higher CO2 capture capacities.

Ab initio thermodynamic approach to identify mixed solid sorbents for CO 2 capture technology

DOE PAGES

Duan, Yuhua

2015-10-15

Because the current technologies for capturing CO 2 are still too energy intensive, new materials must be developed that can capture CO 2 reversibly with acceptable energy costs. At a given CO 2 pressure, the turnover temperature (T t) of the reaction of an individual solid that can capture CO 2 is fixed. Such T t may be outside the operating temperature range (ΔT o) for a practical capture technology. To adjust T t to fit the practical ΔT o, in this study, three scenarios of mixing schemes are explored by combining thermodynamic database mining with first principles density functionalmore » theory and phonon lattice dynamics calculations. Our calculated results demonstrate that by mixing different types of solids, it’s possible to shift T t to the range of practical operating temperature conditions. According to the requirements imposed by the pre- and post- combustion technologies and based on our calculated thermodynamic properties for the CO 2 capture reactions by the mixed solids of interest, we were able to identify the mixing ratios of two or more solids to form new sorbent materials for which lower capture energy costs are expected at the desired pressure and temperature conditions.« less

Does filler database size influence identification accuracy?

PubMed

Bergold, Amanda N; Heaton, Paul

2018-06-01

Police departments increasingly use large photo databases to select lineup fillers using facial recognition software, but this technological shift's implications have been largely unexplored in eyewitness research. Database use, particularly if coupled with facial matching software, could enable lineup constructors to increase filler-suspect similarity and thus enhance eyewitness accuracy (Fitzgerald, Oriet, Price, & Charman, 2013). However, with a large pool of potential fillers, such technologies might theoretically produce lineup fillers too similar to the suspect (Fitzgerald, Oriet, & Price, 2015; Luus & Wells, 1991; Wells, Rydell, & Seelau, 1993). This research proposes a new factor-filler database size-as a lineup feature affecting eyewitness accuracy. In a facial recognition experiment, we select lineup fillers in a legally realistic manner using facial matching software applied to filler databases of 5,000, 25,000, and 125,000 photos, and find that larger databases are associated with a higher objective similarity rating between suspects and fillers and lower overall identification accuracy. In target present lineups, witnesses viewing lineups created from the larger databases were less likely to make correct identifications and more likely to select known innocent fillers. When the target was absent, database size was associated with a lower rate of correct rejections and a higher rate of filler identifications. Higher algorithmic similarity ratings were also associated with decreases in eyewitness identification accuracy. The results suggest that using facial matching software to select fillers from large photograph databases may reduce identification accuracy, and provides support for filler database size as a meaningful system variable. (PsycINFO Database Record (c) 2018 APA, all rights reserved).

Evolution of the Tropical Cyclone Integrated Data Exchange And Analysis System (TC-IDEAS)

NASA Technical Reports Server (NTRS)

Turk, J.; Chao, Y.; Haddad, Z.; Hristova-Veleva, S.; Knosp, B.; Lambrigtsen, B.; Li, P.; Licata, S.; Poulsen, W.; Su, H.;

Thermodynamic design of 10 kW Brayton cryocooler for HTS cable

NASA Astrophysics Data System (ADS)

Chang, Ho-Myung; Park, C. W.; Yang, H. S.; Sohn, Song Ho; Lim, Ji Hyun; Oh, S. R.; Hwang, Si Dole

2012-06-01

Thermodynamic design of Brayton cryocooler is presented as part of an ongoing governmental project in Korea, aiming at 1 km HTS power cable in the transmission grid. The refrigeration requirement is 10 kW for continuously sub-cooling liquid nitrogen from 72 K to 65 K. An ideal Brayton cycle for this application is first investigated to examine the fundamental features. Then a practical cycle for a Brayton cryocooler is designed, taking into account the performance of compressor, expander, and heat exchangers. Commercial software (Aspen HYSYS) is used for simulating the refrigeration cycle with real fluid properties of refrigerant. Helium is selected as a refrigerant, as it is superior to neon in thermodynamic efficiency. The operating pressure and flow rate of refrigerant are decided with a constraint to avoid the freezing of liquid nitrogen

Thermodynamic properties of oxygen and nitrogen III

NASA Technical Reports Server (NTRS)

Stewart, R. B.; Jacobsen, R. T.; Myers, A. F.

1972-01-01

The final equation for nitrogen was determined. In the work on the equation of state for nitrogen, coefficients were determined by constraining the critical point to selected critical point parameters. Comparisons of this equation with all the P-density-T data were made, as well as comparisons to all other thermodynamic data reported in the literature. The extrapolation of the equation of state was studied for vapor to higher temperatures and lower temperatures, and for the liquid surface to the saturated liquid and the fusion lines. A new vapor pressure equation was also determined which was constrained to the same critical temperature, pressure, and slope (dP/dT) as the equation of state. Work on the equation of state for oxygen included studies for improving the equation at the critical point. Comparisons of velocity of sound data for oxygen were also made between values calculated with a preliminary equation of state and experimental data. Functions for the calculation of the derived thermodynamic properties using the equation of state are given, together with the derivative and integral functions for the calculation of the thermodynamic properties using the equations of state. Summary tables of the thermodynamic properties of nitrogen and oxygen are also included to serve as a check for those preparing computer programs using the equations of state.

Fluctuation relation based continuum model for thermoviscoplasticity in metals

NASA Astrophysics Data System (ADS)

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

2016-11-01

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

Bringing metabolic networks to life: convenience rate law and thermodynamic constraints

PubMed Central

Liebermeister, Wolfram; Klipp, Edda

2006-01-01

Background Translating a known metabolic network into a dynamic model requires rate laws for all chemical reactions. The mathematical expressions depend on the underlying enzymatic mechanism; they can become quite involved and may contain a large number of parameters. Rate laws and enzyme parameters are still unknown for most enzymes. Results We introduce a simple and general rate law called "convenience kinetics". It can be derived from a simple random-order enzyme mechanism. Thermodynamic laws can impose dependencies on the kinetic parameters. Hence, to facilitate model fitting and parameter optimisation for large networks, we introduce thermodynamically independent system parameters: their values can be varied independently, without violating thermodynamical constraints. We achieve this by expressing the equilibrium constants either by Gibbs free energies of formation or by a set of independent equilibrium constants. The remaining system parameters are mean turnover rates, generalised Michaelis-Menten constants, and constants for inhibition and activation. All parameters correspond to molecular energies, for instance, binding energies between reactants and enzyme. Conclusion Convenience kinetics can be used to translate a biochemical network – manually or automatically - into a dynamical model with plausible biological properties. It implements enzyme saturation and regulation by activators and inhibitors, covers all possible reaction stoichiometries, and can be specified by a small number of parameters. Its mathematical form makes it especially suitable for parameter estimation and optimisation. Parameter estimates can be easily computed from a least-squares fit to Michaelis-Menten values, turnover rates, equilibrium constants, and other quantities that are routinely measured in enzyme assays and stored in kinetic databases. PMID:17173669

Database Access Systems.

ERIC Educational Resources Information Center

Dalrymple, Prudence W.; Roderer, Nancy K.

1994-01-01

Highlights the changes that have occurred from 1987-93 in database access systems. Topics addressed include types of databases, including CD-ROMs; enduser interface; database selection; database access management, including library instruction and use of primary literature; economic issues; database users; the search process; and improving…

Thermodynamics of Micelle Formation and Membrane Fusion Modulate Antimicrobial Lipopeptide Activity

PubMed Central

Lin, Dejun; Grossfield, Alan

2015-01-01

Antimicrobial lipopeptides (AMLPs) are antimicrobial drug candidates that preferentially target microbial membranes. One class of AMLPs, composed of cationic tetrapeptides attached to an acyl chain, have minimal inhibitory concentrations in the micromolar range against a range of bacteria and fungi. Previously, we used coarse-grained molecular dynamics simulations and free energy methods to study the thermodynamics of their interaction with membranes in their monomeric state. Here, we extended the study to the biologically relevant micellar state, using, to our knowledge, a novel reaction coordinate based on hydrophobic contacts. Using umbrella sampling along this reaction coordinate, we identified the critical transition states when micelles insert into membranes. The results indicate that the binding of these AMLP micelles to membranes is thermodynamically favorable, but in contrast to the monomeric case, there are significant free energy barriers. The height of these free energy barriers depends on the membrane composition, suggesting that the AMLPs’ ability to selectively target bacterial membranes may be as much kinetic as thermodynamic. This mechanism highlights the importance of considering oligomeric state in solution as criterion when optimizing peptides or lipopeptides as antibiotic leads. PMID:26287627

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

NASA Astrophysics Data System (ADS)

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

2013-05-01

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

Calculating Water Thermodynamics in the Binding Site of Proteins - Applications of WaterMap to Drug Discovery.

PubMed

Cappel, Daniel; Sherman, Woody; Beuming, Thijs

2017-01-01

The ability to accurately characterize the solvation properties (water locations and thermodynamics) of biomolecules is of great importance to drug discovery. While crystallography, NMR, and other experimental techniques can assist in determining the structure of water networks in proteins and protein-ligand complexes, most water molecules are not fully resolved and accurately placed. Furthermore, understanding the energetic effects of solvation and desolvation on binding requires an analysis of the thermodynamic properties of solvent involved in the interaction between ligands and proteins. WaterMap is a molecular dynamics-based computational method that uses statistical mechanics to describe the thermodynamic properties (entropy, enthalpy, and free energy) of water molecules at the surface of proteins. This method can be used to assess the solvent contributions to ligand binding affinity and to guide lead optimization. In this review, we provide a comprehensive summary of published uses of WaterMap, including applications to lead optimization, virtual screening, selectivity analysis, ligand pose prediction, and druggability assessment. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Thermodynamics on Soluble Carbon Nanotubes: How Do DNA Molecules Replace Surfactants on Carbon Nanotubes?

PubMed Central

Kato, Yuichi; Inoue, Ayaka; Niidome, Yasuro; Nakashima, Naotoshi

2012-01-01

Here we represent thermodynamics on soluble carbon nanotubes that enables deep understanding the interactions between single-walled carbon nanotubes (SWNTs) and molecules. We selected sodium cholate and single-stranded cytosine oligo-DNAs (dCn (n = 4, 5, 6, 7, 8, 10, 15, and 20)), both of which are typical SWNT solubilizers, and successfully determined thermodynamic properties (ΔG, ΔH and ΔS values) for the exchange reactions of sodium cholate on four different chiralities of SWNTs ((n,m) = (6,5), (7,5), (10,2), and (8,6)) for the DNAs. Typical results contain i) the dC5 exhibited an exothermic exchange, whereas the dC6, 8, 10, 15, and 20 materials exhibited endothermic exchanges, and ii) the energetics of the dC4 and dC7 exchanges depended on the associated chiral indices and could be endothermic or exothermic. The presented method is general and is applicable to any molecule that interacts with nanotubes. The study opens a way for science of carbon nanotube thermodynamics. PMID:23066502

Characterization of the superconducting state in hafnium hydride under high pressure

NASA Astrophysics Data System (ADS)

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

2018-05-01

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

Thermodynamic Analysis of the Selectivity Enhancement Obtained by Using Smart Hydrogels That Are Zwitterionic When Detecting Glucose With Boronic Acid Moieties

PubMed Central

Horkay, F.; Cho, S. H.; Tathireddy, P.; Rieth, L.; Solzbacher, F.; Magda, J.

2011-01-01

Because the boronic acid moiety reversibly binds to sugar molecules and has low cytotoxicity, boronic acid-containing hydrogels are being used in a variety of implantable glucose sensors under development, including sensors based on optical, fluorescence, and swelling pressure measurements. However, some method of glucose selectivity enhancement is often necessary, because isolated boronic acid molecules have a binding constant with glucose that is some forty times smaller than their binding constant with fructose, the second most abundant sugar in the human body. In many cases, glucose selectivity enhancement is obtained by incorporating pendant tertiary amines into the hydrogel network, thereby giving rise to a hydrogel that is zwitterionic at physiological pH. However, the mechanism by which incorporation of tertiary amines confers selectivity enhancement is poorly understood. In order to clarify this mechanism, we use the osmotic deswelling technique to compare the thermodynamic interactions of glucose and fructose with a zwitterionic smart hydrogel containing boronic acid moieties. We also investigate the change in the structure of the hydrogel that occurs when it binds to glucose or to fructose using the technique of small angle neutron scattering. PMID:22190765

Understanding Ion Binding Affinity and Selectivity in β-Parvalbumin Using Molecular Dynamics and Mean Spherical Approximation Theory.

PubMed

Kucharski, Amir N; Scott, Caitlin E; Davis, Jonathan P; Kekenes-Huskey, Peter M

2016-08-25

Parvalbumin (PV) is a globular calcium (Ca(2+))-selective protein expressed in a variety of biological tissues. Our computational studies of the rat β-parvalbumin (β-PV) isoform seek to elucidate the molecular thermodynamics of Ca(2+) versus magnesium (Mg(2+)) binding at the protein's two EF-hand motifs. Specifically, we have utilized molecular dynamics (MD) simulations and a mean-field electrolyte model (mean spherical approximation (MSA) theory) to delineate how the EF-hand scaffold controls the "local" thermodynamics of Ca(2+) binding selectivity over Mg(2+). Our MD simulations provide the probability density of metal-chelating oxygens within the EF-hand scaffolds for both Ca(2+) and Mg(2+), as well the conformational strain induced by Mg(2+) relative to Ca(2+) binding. MSA theory utilizes the binding domain oxygen and charge distributions to predict the chemical potential of ion binding, as well as their corresponding concentrations within the binding domain. We find that the electrostatic and steric contributions toward ion binding were similar for Mg(2+) and Ca(2+), yet the latter was 5.5 kcal/mol lower in enthalpy when internal strain within the EF hand was considered. We therefore speculate that beyond differences in dehydration energies for the Ca(2+) versus Mg(2+), strain induced in the β-PV EF hand by cation binding significantly contributes to the nearly 10,000-fold difference in binding affinity reported in the literature. We further complemented our analyses of local factors governing cation binding selectivity with whole-protein (global) contributions, such as interhelical residue-residue contacts and solvent exposure of hydrophobic surface. These contributions were found to be comparable for both Ca(2+)- and Mg(2+)-bound β-PV, which may implicate local factors, EF-hand strain, and dehydration, in providing the primary means of selectivity. We anticipate these methods could be used to estimate metal binding thermodynamics across a broad range of PV sequence homologues and EF-hand-containing, Ca(2+) binding proteins.

Sensitivity of predicted scaling and permeability in Enhanced Geothermal Systems to Thermodynamic Data and Activity Models

NASA Astrophysics Data System (ADS)

Hingerl, Ferdinand F.; Wagner, Thomas; Kulik, Dmitrii A.; Kosakowski, Georg; Driesner, Thomas; Thomsen, Kaj

2010-05-01

A consortium of research groups from ETH Zurich, EPF Lausanne, the Paul Scherrer Institut and the University of Bonn collaborates in a comprehensive program of basic research on key aspects of the Enhanced Geothermal Systems (EGSs). As part of this GEOTHERM project (www.geotherm.ethz.ch), we concentrate on the fundamental investigation of thermodynamic models suitable for describing fluid-rock interactions at geothermal conditions. Predictions of the fluid-rock interaction in EGS still face several major challenges. Slight variations in the input thermodynamic and kinetic parameters may result in significant differences in the predicted mineral solubilities and stable assemblage. Realistic modeling of mineral precipitation in turn has implications onto our understanding of the permeability evolution of the geothermal reservoir, as well as the scaling in technical installations. In order to reasonably model an EGS, thermodynamic databases and activity models must be tailored to geothermal conditions. We therefore implemented in GEMS code the Pitzer formalism, which is the standard model used for computing thermodynamic excess properties of brines at elevated temperatures and pressures. This model, however, depends on a vast amount of interaction parameters, which are to a substantial extend unknown. Furthermore, a high order polynomial temperature interpolation makes extrapolation unreliable if not impossible. As an alternative we additionally implemented the EUNIQUAC activity model. EUNIQUAC requires fewer empirical fit parameters (only binary interaction parameters needed) and uses simpler and more stable temperature and pressure extrapolations. This results in an increase in computation speed, which is of crucial importance when performing coupled long term simulations of geothermal reservoirs. To achieve better performance under geothermal conditions, we are currently partly reformulating EUNIQUAC and refitting the existing parameter set. First results of the Pitzer-EUNIQUAC benchmark applied to relevant aqueous solutions at elevated temperature, pressure and ionic strength will be presented.

Data Science Innovations That Streamline Development, Documentation, Reproducibility, and Dissemination of Models in Computational Thermodynamics: An Application of Image Processing Techniques for Rapid Computation, Parameterization and Modeling of Phase Diagrams

NASA Astrophysics Data System (ADS)

Ghiorso, M. S.

2014-12-01

Computational thermodynamics (CT) represents a collection of numerical techniques that are used to calculate quantitative results from thermodynamic theory. In the Earth sciences, CT is most often applied to estimate the equilibrium properties of solutions, to calculate phase equilibria from models of the thermodynamic properties of materials, and to approximate irreversible reaction pathways by modeling these as a series of local equilibrium steps. The thermodynamic models that underlie CT calculations relate the energy of a phase to temperature, pressure and composition. These relationships are not intuitive and they are seldom well constrained by experimental data; often, intuition must be applied to generate a robust model that satisfies the expectations of use. As a consequence of this situation, the models and databases the support CT applications in geochemistry and petrology are tedious to maintain as new data and observations arise. What is required to make the process more streamlined and responsive is a computational framework that permits the rapid generation of observable outcomes from the underlying data/model collections, and importantly, the ability to update and re-parameterize the constitutive models through direct manipulation of those outcomes. CT procedures that take models/data to the experiential reference frame of phase equilibria involve function minimization, gradient evaluation, the calculation of implicit lines, curves and surfaces, contour extraction, and other related geometrical measures. All these procedures are the mainstay of image processing analysis. Since the commercial escalation of video game technology, open source image processing libraries have emerged (e.g., VTK) that permit real time manipulation and analysis of images. These tools find immediate application to CT calculations of phase equilibria by permitting rapid calculation and real time feedback between model outcome and the underlying model parameters.

Computer-aided solvent selection for multiple scenarios operation of limited-known properties solute

NASA Astrophysics Data System (ADS)

Anantpinijwatna, Amata

2017-12-01

Solvents have been applied for both production and separation of the complex chemical substance such as the pyrrolidine-2-carbonyl chloride (C5H8ClNO). Since the properties of the target substance itself are largely unknown, the selection of the solvent is limited by experiment only. However, the reaction carried out in conventional solvents are either afforded low yields or obtained slow reaction rates. Moreover, the solvents are also highly toxic and environmental unfriendly. Alternative solvents are required to enhance the production and lessen the harmful effect toward both organism and environment. A costly, time-consuming, and laborious experiments are required for acquiring a better solvent suite for production and separation of these complex compounds; whereas, a limited improvement can be obtained. On the other hand, the combination of the state-of-the-art thermodynamic models can provide faster and more robust solutions to this solvent selection problem. In this work, a framework for solvents selection in complex chemical production process is presented. The framework combines a group-contribution thermodynamic model and a segment activity coefficient model for predicting chemical properties and solubilities of the target chemical in newly formulated solvents. A guideline for solvent selection is also included. The potential of the selected solvents is then analysed and verified. The improvement toward the production yield, production rate, and product separation is then discussed.

Thermodynamic description of multicomponent nickel-base superalloys containing aluminum, chromium, ruthenium and platinum: A computational thermodynamic approach coupled with experiments

NASA Astrophysics Data System (ADS)

Zhu, Jun

Ru and Pt are candidate additional component for improving the high temperature properties of Ni-base superalloys. A thermodynamic description of the Ni-Al-Cr-Ru-Pt system, serving as an essential knowledge base for better alloy design and processing control, was developed in the present study by means of thermodynamic modeling coupled with experimental investigations of phase equilibria. To deal with the order/disorder transition occurring in the Ni-base superalloys, a physical sound model, Cluster/Site Approximation (CSA) was used to describe the fcc phases. The CSA offers computational advantages, without loss of accuracy, over the Cluster Variation Method (CVM) in the calculation of multicomponent phase diagrams. It has been successfully applied to fcc phases in calculating technologically important Ni-Al-Cr phase diagrams. Our effort in this study focused on the two key ternary systems: Ni-Al-Ru and Ni-Al-Pt. The CSA calculated Ni-Al-Ru ternary phase diagrams are in good agreement with the experimental results in the literature and from the current study. A thermodynamic description of quaternary Ni-Al-Cr-Ru was obtained based on the descriptions of the lower order systems and the calculated results agree with experimental data available in literature and in the current study. The Ni-Al-Pt system was thermodynamically modeled based on the limited experimental data available in the literature and obtained from the current study. With the help of the preliminary description, a number of alloy compositions were selected for further investigation. The information obtained was used to improve the current modeling. A thermodynamic description of the Ni-Al-Cr-Pt quaternary was then obtained via extrapolation from its constituent lower order systems. The thermodynamic description for Ni-base superalloy containing Al, Cr, Ru and Pt was obtained via extrapolation. It is believed to be reliable and useful to guide the alloy design and further experimental investigation.

Maximum entropy principle for stationary states underpinned by stochastic thermodynamics.

PubMed

Ford, Ian J

2015-11-01

The selection of an equilibrium state by maximizing the entropy of a system, subject to certain constraints, is often powerfully motivated as an exercise in logical inference, a procedure where conclusions are reached on the basis of incomplete information. But such a framework can be more compelling if it is underpinned by dynamical arguments, and we show how this can be provided by stochastic thermodynamics, where an explicit link is made between the production of entropy and the stochastic dynamics of a system coupled to an environment. The separation of entropy production into three components allows us to select a stationary state by maximizing the change, averaged over all realizations of the motion, in the principal relaxational or nonadiabatic component, equivalent to requiring that this contribution to the entropy production should become time independent for all realizations. We show that this recovers the usual equilibrium probability density function (pdf) for a conservative system in an isothermal environment, as well as the stationary nonequilibrium pdf for a particle confined to a potential under nonisothermal conditions, and a particle subject to a constant nonconservative force under isothermal conditions. The two remaining components of entropy production account for a recently discussed thermodynamic anomaly between over- and underdamped treatments of the dynamics in the nonisothermal stationary state.

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

PubMed

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

2018-04-30

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

Merits of full flow vs. conventional staged combustion cycles for reusable launch vehicle propulsion

NASA Astrophysics Data System (ADS)

Peery, Steven D.; Parsley, Randy C.

1996-03-01

This paper provides a comparison between full-flow and conventional staged combustion thermodynamic O2/H2 rocket engine cycles for Reusable Launch Vehicle, RLV, single-stage-to-orbit applications. The impact of the cycle thermodynamics, component configuration, and component operating parameters on engine performance and weight for the two approaches is presented. Both cycles were modeled with equivalent technology turbomachinery and chamber/nozzle RLV life requirements. The first order impact of cycle selection, pump exit pressure, and turbine temperature on the empty weight of an SSTO Reusable Launch Vehicle is presented.

Atmospheric environment for Space Shuttle (STS-3) launch

NASA Technical Reports Server (NTRS)

Johnson, D. L.; Brown, S. C.; Batts, G. W.

1982-01-01

Selected atmospheric conditions observed near Space Shuttle STS-3 launch time on March 22, 1982, at Kennedy Space Center, Florida are summarized. Values of ambient pressure, temperature, moisture, ground winds, visual observations (cloud), and winds aloft are included. The sequence of prlaunch Jimsphere measured vertical wind profiles and the wind and thermodynamic parameters measured at the surface and aloft in the SRB descent/impact ocean area are presented. Final meteorological tapes, which consist of wind and thermodynamic parameters versus altitude, for STS-3 vehicle ascent and SRB descent were constructed. The STS-3 ascent meteorological data tape is constructed.

Computational method and system for modeling, analyzing, and optimizing DNA amplification and synthesis

DOEpatents

Vandersall, Jennifer A.; Gardner, Shea N.; Clague, David S.

2010-05-04

A computational method and computer-based system of modeling DNA synthesis for the design and interpretation of PCR amplification, parallel DNA synthesis, and microarray chip analysis. The method and system include modules that address the bioinformatics, kinetics, and thermodynamics of DNA amplification and synthesis. Specifically, the steps of DNA selection, as well as the kinetics and thermodynamics of DNA hybridization and extensions, are addressed, which enable the optimization of the processing and the prediction of the products as a function of DNA sequence, mixing protocol, time, temperature and concentration of species.

Second law of thermodynamics in volume diffusion hydrodynamics in multicomponent gas mixtures

NASA Astrophysics Data System (ADS)

Dadzie, S. Kokou

2012-10-01

We presented the thermodynamic structure of a new continuum flow model for multicomponent gas mixtures. The continuum model is based on a volume diffusion concept involving specific species. It is independent of the observer's reference frame and enables a straightforward tracking of a selected species within a mixture composed of a large number of constituents. A method to derive the second law and constitutive equations accompanying the model is presented. Using the configuration of a rotating fluid we illustrated an example of non-classical flow physics predicted by new contributions in the entropy and constitutive equations.

A range of complex probabilistic models for RNA secondary structure prediction that includes the nearest-neighbor model and more.

PubMed

Rivas, Elena; Lang, Raymond; Eddy, Sean R

2012-02-01

The standard approach for single-sequence RNA secondary structure prediction uses a nearest-neighbor thermodynamic model with several thousand experimentally determined energy parameters. An attractive alternative is to use statistical approaches with parameters estimated from growing databases of structural RNAs. Good results have been reported for discriminative statistical methods using complex nearest-neighbor models, including CONTRAfold, Simfold, and ContextFold. Little work has been reported on generative probabilistic models (stochastic context-free grammars [SCFGs]) of comparable complexity, although probabilistic models are generally easier to train and to use. To explore a range of probabilistic models of increasing complexity, and to directly compare probabilistic, thermodynamic, and discriminative approaches, we created TORNADO, a computational tool that can parse a wide spectrum of RNA grammar architectures (including the standard nearest-neighbor model and more) using a generalized super-grammar that can be parameterized with probabilities, energies, or arbitrary scores. By using TORNADO, we find that probabilistic nearest-neighbor models perform comparably to (but not significantly better than) discriminative methods. We find that complex statistical models are prone to overfitting RNA structure and that evaluations should use structurally nonhomologous training and test data sets. Overfitting has affected at least one published method (ContextFold). The most important barrier to improving statistical approaches for RNA secondary structure prediction is the lack of diversity of well-curated single-sequence RNA secondary structures in current RNA databases.

Inverse Band Structure Design via Materials Database Screening: Application to Square Planar Thermoelectrics

DOE PAGES

Isaacs, Eric B.; Wolverton, Chris

2018-02-26

Electronic band structure contains a wealth of information on the electronic properties of a solid and is routinely computed. However, the more difficult problem of designing a solid with a desired band structure is an outstanding challenge. In order to address this inverse band structure design problem, we devise an approach using materials database screening with materials attributes based on the constituent elements, nominal electron count, crystal structure, and thermodynamics. Our strategy is tested in the context of thermoelectric materials, for which a targeted band structure containing both flat and dispersive components with respect to crystal momentum is highly desirable.more » We screen for thermodynamically stable or metastable compounds containing d 8 transition metals coordinated by anions in a square planar geometry in order to mimic the properties of recently identified oxide thermoelectrics with such a band structure. In doing so, we identify 157 compounds out of a total of over half a million candidates. After further screening based on electronic band gap and structural anisotropy, we explicitly compute the band structures for the several of the candidates in order to validate the approach. We successfully find two new oxide systems that achieve the targeted band structure. Electronic transport calculations on these two compounds, Ba 2PdO 3 and La 4PdO 7, confirm promising thermoelectric power factor behavior for the compounds. This methodology is easily adapted to other targeted band structures and should be widely applicable to a variety of design problems.« less

A range of complex probabilistic models for RNA secondary structure prediction that includes the nearest-neighbor model and more

PubMed Central

Rivas, Elena; Lang, Raymond; Eddy, Sean R.

2012-01-01

The standard approach for single-sequence RNA secondary structure prediction uses a nearest-neighbor thermodynamic model with several thousand experimentally determined energy parameters. An attractive alternative is to use statistical approaches with parameters estimated from growing databases of structural RNAs. Good results have been reported for discriminative statistical methods using complex nearest-neighbor models, including CONTRAfold, Simfold, and ContextFold. Little work has been reported on generative probabilistic models (stochastic context-free grammars [SCFGs]) of comparable complexity, although probabilistic models are generally easier to train and to use. To explore a range of probabilistic models of increasing complexity, and to directly compare probabilistic, thermodynamic, and discriminative approaches, we created TORNADO, a computational tool that can parse a wide spectrum of RNA grammar architectures (including the standard nearest-neighbor model and more) using a generalized super-grammar that can be parameterized with probabilities, energies, or arbitrary scores. By using TORNADO, we find that probabilistic nearest-neighbor models perform comparably to (but not significantly better than) discriminative methods. We find that complex statistical models are prone to overfitting RNA structure and that evaluations should use structurally nonhomologous training and test data sets. Overfitting has affected at least one published method (ContextFold). The most important barrier to improving statistical approaches for RNA secondary structure prediction is the lack of diversity of well-curated single-sequence RNA secondary structures in current RNA databases. PMID:22194308

Inverse Band Structure Design via Materials Database Screening: Application to Square Planar Thermoelectrics

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

Isaacs, Eric B.; Wolverton, Chris

Electronic band structure contains a wealth of information on the electronic properties of a solid and is routinely computed. However, the more difficult problem of designing a solid with a desired band structure is an outstanding challenge. In order to address this inverse band structure design problem, we devise an approach using materials database screening with materials attributes based on the constituent elements, nominal electron count, crystal structure, and thermodynamics. Our strategy is tested in the context of thermoelectric materials, for which a targeted band structure containing both flat and dispersive components with respect to crystal momentum is highly desirable.more » We screen for thermodynamically stable or metastable compounds containing d 8 transition metals coordinated by anions in a square planar geometry in order to mimic the properties of recently identified oxide thermoelectrics with such a band structure. In doing so, we identify 157 compounds out of a total of over half a million candidates. After further screening based on electronic band gap and structural anisotropy, we explicitly compute the band structures for the several of the candidates in order to validate the approach. We successfully find two new oxide systems that achieve the targeted band structure. Electronic transport calculations on these two compounds, Ba 2PdO 3 and La 4PdO 7, confirm promising thermoelectric power factor behavior for the compounds. This methodology is easily adapted to other targeted band structures and should be widely applicable to a variety of design problems.« less

The DREO Elint Browser Utility (DEBU) reference manual

NASA Astrophysics Data System (ADS)

Ford, Barbara; Jones, David

1992-04-01

An electronic intelligent database browsing tool called DEBU has been developed that allows databases such as ELP, Kilting, EWIR, and AFEWC to be reviewed and analyzed from a user-friendly environment on a personal computer. DEBU's basic function is to allow users to examine the contents of user-selected subfiles of user-selected emitters of user-selected databases. DEBU augments this functionality with support for selecting (filtering) and combining subsets of emitters by user-selected attributes such as name, parameter type, or parameter value. DEBU provides facilities for examining histograms and x-y plots of selected parameters, for doing ambiguity analysis and mode level analysis, and for generating and printing a variety of reports. A manual is provided for users of DEBU, including descriptions and illustrations of menus and windows.

Heating without heat: Thermodynamics of passive energy filters between finite systems

NASA Astrophysics Data System (ADS)

Muñoz-Tapia, R.; Brito, R.; Parrondo, J. M. R.

2017-09-01

Passive filters allowing the exchange of particles in a narrow band of energy are currently used in microrefrigerators and energy transducers. In this Rapid Communication, we analyze their thermal properties using linear irreversible thermodynamics and kinetic theory, and discuss a striking phenomenon: the possibility of simultaneously increasing or decreasing the temperatures of two systems without any supply of energy. This occurs when the filter induces a flow of particles whose energy is between the average energies of the two systems. Here we show that this selective transfer of particles does not need the action of any sort of Maxwell demon and can be carried out by passive filters without compromising the second law of thermodynamics. This phenomenon allows us to design cycles between two reservoirs at temperatures T1

Systems analysis of a closed loop ECLSS using the ASPEN simulation tool. Thermodynamic efficiency analysis of ECLSS components. M.S. Thesis

NASA Technical Reports Server (NTRS)

Chatterjee, Sharmista

1993-01-01

Our first goal in this project was to perform a systems analysis of a closed loop Environmental Control Life Support System (ECLSS). This pertains to the development of a model of an existing real system from which to assess the state or performance of the existing system. Systems analysis is applied to conceptual models obtained from a system design effort. For our modelling purposes we used a simulator tool called ASPEN (Advanced System for Process Engineering). Our second goal was to evaluate the thermodynamic efficiency of the different components comprising an ECLSS. Use is made of the second law of thermodynamics to determine the amount of irreversibility of energy loss of each component. This will aid design scientists in selecting the components generating the least entropy, as our penultimate goal is to keep the entropy generation of the whole system at a minimum.

Fractional watt Vuillemier cryogenic refrigerator program engineering notebook. Volume 1: Thermal analysis

NASA Technical Reports Server (NTRS)

Miller, W. S.

1974-01-01

The cryogenic refrigerator thermal design calculations establish design approach and basic sizing of the machine's elements. After the basic design is defined, effort concentrates on matching the thermodynamic design with that of the heat transfer devices (heat exchangers and regenerators). Typically, the heat transfer device configurations and volumes are adjusted to improve their heat transfer and pressure drop characteristics. These adjustments imply that changes be made to the active displaced volumes, compensating for the influence of the heat transfer devices on the thermodynamic processes of the working fluid. Then, once the active volumes are changed, the heat transfer devices require adjustment to account for the variations in flows, pressure levels, and heat loads. This iterative process is continued until the thermodynamic cycle parameters match the design of the heat transfer devices. By examing several matched designs, a near-optimum refrigerator is selected.

Comparisons of kinetics, thermodynamics and regeneration of tetramethylammonium hydroxide adsorption in aqueous solution with graphene oxide, zeolite and activated carbon

NASA Astrophysics Data System (ADS)

Chang, Shenteng; Lu, Chungsying; Lin, Kun-Yi Andrew

2015-01-01

Graphene oxide (GO), sodium Y-type zeolite (NaY) and granular activated carbon (GAC) are selected as adsorbents to study their kinetics, thermodynamics and regeneration of tetramethylammonium hydroxide (TMAH) adsorption from water. The adsorption kinetics follows the pseudo-second-order rate law while the adsorption thermodynamics shows an exothermic reaction with GO and GAC but displays an endothermic reaction with NaY. The adsorbed TMAH can be readily desorbed from the surface of GO and NaY by 0.05 M NaCl solution. A comparative study on the cyclic TMAH adsorption with GO, NaY and GAC is also conducted and the results reveal that GO exhibits the greatest TMAH adsorption capacity as well as superior reversibility of TMAH adsorption over 10 cycles of adsorption and desorption process. These features indicate that GO is a promising and efficient adsorbent for TMAH removal in wastewater treatment.

Progress report for the CCT-WG5 high temperature fixed point research plan

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

Machin, G.; Woolliams, E. R.; Anhalt, K.

2013-09-11

An overview of the progress in High Temperature Fixed Point (HTFP) research conducted under the auspices of the CCT-WG5 research plan is reported. In brief highlights are: Provisional long term stability of HTFPs has been demonstrated. Optimum construction methods for HTFPs have been established and high quality HTFPs of Co-C, Pt-C and Re-C have been constructed for thermodynamic temperature assignment. The major sources of uncertainty in the assignment of thermodynamic temperature have been identified and quantified. The status of absolute radiometric temperature measurement has been quantified through the circulation of a set of HTFPs. The measurement campaign to assign lowmore » uncertainty thermodynamic temperatures to a selected set of HTFPs will begin in mid-2012. It is envisaged that this will be complete by 2015 leading to HTFPs becoming routine reference standards for radiometry and high temperature metrology.« less

The 2006 Cape Canaveral Air Force Station Range Reference Atmosphere Model Validation Study and Sensitivity Analysis to the National Aeronautics and Space Administration's Space Shuttle

NASA Technical Reports Server (NTRS)

Decker, Ryan K.; Burns, Lee; Merry, Carl; Harrington, Brian

2008-01-01

Atmospheric parameters are essential in assessing the flight performance of aerospace vehicles. The effects of the Earth's atmosphere on aerospace vehicles influence various aspects of the vehicle during ascent ranging from its flight trajectory to the structural dynamics and aerodynamic heatmg on the vehicle. Atmospheric databases charactenzing the wind and thermodynamic environments, known as Range Reference Atmospheres (RRA), have been developed at space launch ranges by a governmental interagency working group for use by aerospace vehicle programs. The National Aeronantics and Space Administration's (NASA) Space Shuttle Program (SSP), which launches from Kennedy Space Center, utilizes atmosphenc statistics derived from the Cape Canaveral Air Force Station Range Reference Atmosphere (CCAFS RRA) database to evaluate environmental constraints on various aspects of the vehlcle during ascent.

Computationally Efficient Characterization of Potential Energy Surfaces Based on Fingerprint Distances

NASA Astrophysics Data System (ADS)

Schaefer, Bastian; Goedecker, Stefan; Goedecker Group Team

Based on Lennard-Jones, Silicon, Sodium-Chloride and Gold clusters, it was found that uphill barrier energies of transition states between directly connected minima tend to increase with increasing structural differences of the two minima. Based on this insight it also turned out that post-processing minima hopping data at a negligible computational cost allows to obtain qualitative topological information on potential energy surfaces that can be stored in so called qualitative connectivity databases. These qualitative connectivity databases are used for generating fingerprint disconnectivity graphs that allow to obtain a first qualitative idea on thermodynamic and kinetic properties of a system of interest. This research was supported by the NCCR MARVEL, funded by the Swiss National Science Foundation. Computer time was provided by the Swiss National Supercomputing Centre (CSCS) under Project ID No. s499.

Long-term modeling of glass waste in portland cement- and clay-based matrices

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

Stockman, H.W.; Nagy, K.L.; Morris, C.E.

A set of ``templates`` was developed for modeling waste glass interactions with cement-based and clay-based matrices. The templates consist of a modified thermodynamic database, and input files for the EQ3/6 reaction path code, containing embedded rate models and compositions for waste glass, cement, and several pozzolanic materials. Significant modifications were made in the thermodynamic data for Th, Pb, Ra, Ba, cement phases, and aqueous silica species. It was found that the cement-containing matrices could increase glass corrosion rates by several orders of magnitude (over matrixless or clay matrix systems), but they also offered the lowest overall solubility for Pb, Ra,more » Th and U. Addition of pozzolans to cement decreased calculated glass corrosion rates by up to a factor of 30. It is shown that with current modeling capabilities, the ``affinity effect`` cannot be trusted to passivate glass if nuclei are available for precipitation of secondary phases that reduce silica activity.« less

Coarse-Grained Models for Automated Fragmentation and Parametrization of Molecular Databases.

PubMed

Fraaije, Johannes G E M; van Male, Jan; Becherer, Paul; Serral Gracià, Rubèn

2016-12-27

We calibrate coarse-grained interaction potentials suitable for screening large data sets in top-down fashion. Three new algorithms are introduced: (i) automated decomposition of molecules into coarse-grained units (fragmentation); (ii) Coarse-Grained Reference Interaction Site Model-Hypernetted Chain (CG RISM-HNC) as an intermediate proxy for dissipative particle dynamics (DPD); and (iii) a simple top-down coarse-grained interaction potential/model based on activity coefficient theories from engineering (using COSMO-RS). We find that the fragment distribution follows Zipf and Heaps scaling laws. The accuracy in Gibbs energy of mixing calculations is a few tenths of a kilocalorie per mole. As a final proof of principle, we use full coarse-grained sampling through DPD thermodynamics integration to calculate log P OW for 4627 compounds with an average error of 0.84 log unit. The computational speeds per calculation are a few seconds for CG RISM-HNC and a few minutes for DPD thermodynamic integration.

Limited options for low-global-warming-potential refrigerants

DOE PAGES

McLinden, Mark O.; Brown, J. Steven; Brignoli, Riccardo; ...

2017-02-17

Hydrofluorocarbons, currently used as refrigerants in air-conditioning systems, are potent greenhouse gases, and their contribution to climate change is projected to increase. Future use of the hydrofluorocarbons will be phased down and, thus replacement fluids must be found. Here we show that only a few pure fluids possess the combination of chemical, environmental, thermodynamic, and safety properties necessary for a refrigerant and that these fluids are at least slightly flammable.We search for replacements by applying screening criteria to a comprehensive chemical database. For the fluids passing the thermodynamic and environmental screens (critical temperature and global warming potential), we simulate performancemore » in small air-conditioning systems, including optimization of the heat exchangers. We show that the efficiency-versus-capacity trade-off that exists in an ideal analysis disappears when a more realistic system is considered. Furthermore, the maximum efficiency occurs at a relatively high volumetric refrigeration capacity, but there are few fluids in this range.« less

Limited options for low-global-warming-potential refrigerants

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

McLinden, Mark O.; Brown, J. Steven; Brignoli, Riccardo

Hydrofluorocarbons, currently used as refrigerants in air-conditioning systems, are potent greenhouse gases, and their contribution to climate change is projected to increase. Future use of the hydrofluorocarbons will be phased down and, thus replacement fluids must be found. Here we show that only a few pure fluids possess the combination of chemical, environmental, thermodynamic, and safety properties necessary for a refrigerant and that these fluids are at least slightly flammable.We search for replacements by applying screening criteria to a comprehensive chemical database. For the fluids passing the thermodynamic and environmental screens (critical temperature and global warming potential), we simulate performancemore » in small air-conditioning systems, including optimization of the heat exchangers. We show that the efficiency-versus-capacity trade-off that exists in an ideal analysis disappears when a more realistic system is considered. Furthermore, the maximum efficiency occurs at a relatively high volumetric refrigeration capacity, but there are few fluids in this range.« less

Selecting polymers for two-phase partitioning bioreactors (TPPBs): Consideration of thermodynamic affinity, crystallinity, and glass transition temperature.

PubMed

Bacon, Stuart L; Peterson, Eric C; Daugulis, Andrew J; Parent, J Scott

2015-01-01

Two-phase partitioning bioreactor technology involves the use of a secondary immiscible phase to lower the concentration of cytotoxic solutes in the fermentation broth to subinhibitory levels. Although polymeric absorbents have attracted recent interest due to their low cost and biocompatibility, material selection requires the consideration of properties beyond those of small molecule absorbents (i.e., immiscible organic solvents). These include a polymer's (1) thermodynamic affinity for the target compound, (2) degree of crystallinity (wc ), and (3) glass transition temperature (Tg ). We have examined the capability of three thermodynamic models to predict the partition coefficient (PC) for n-butyric acid, a fermentation product, in 15 polymers. Whereas PC predictions for amorphous materials had an average absolute deviation (AAD) of ≥16%, predictions for semicrystalline polymers were less accurate (AAD ≥ 30%). Prediction errors were associated with uncertainties in determining the degree of crystallinity within a polymer and the effect of absorbed water on n-butyric acid partitioning. Further complications were found to arise for semicrystalline polymers, wherein strongly interacting solutes increased the polymer's absorptive capacity by actually dissolving the crystalline fraction. Finally, we determined that diffusion limitations may occur for polymers operating near their Tg , and that the Tg can be reduced by plasticization by water and/or solute. This study has demonstrated the impact of basic material properties that affects the performance of polymers as sequestering phases in TPPBs, and reflects the additional complexity of polymers that must be taken into account in material selection. © 2015 American Institute of Chemical Engineers.

Co-PylotDB - A Python-Based Single-Window User Interface for Transmitting Information to a Database

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

Barnette, Daniel W.

2012-01-05

Co-PylotDB, written completely in Python, provides a user interface (UI) with which to select user and data file(s), directories, and file content, and provide or capture various other information for sending data collected from running any computer program to a pre-formatted database table for persistent storage. The interface allows the user to select input, output, make, source, executable, and qsub files. It also provides fields for specifying the machine name on which the software was run, capturing compile and execution lines, and listing relevant user comments. Data automatically captured by Co-PylotDB and sent to the database are user, current directory,more » local hostname, current date, and time of send. The UI provides fields for logging into a local or remote database server, specifying a database and a table, and sending the information to the selected database table. If a server is not available, the UI provides for saving the command that would have saved the information to a database table for either later submission or for sending via email to a collaborator who has access to the desired database.« less

Selection of examples in case-based computer-aided decision systems

PubMed Central

Mazurowski, Maciej A.; Zurada, Jacek M.; Tourassi, Georgia D.

2013-01-01

Case-based computer-aided decision (CB-CAD) systems rely on a database of previously stored, known examples when classifying new, incoming queries. Such systems can be particularly useful since they do not need retraining every time a new example is deposited in the case base. The adaptive nature of case-based systems is well suited to the current trend of continuously expanding digital databases in the medical domain. To maintain efficiency, however, such systems need sophisticated strategies to effectively manage the available evidence database. In this paper, we discuss the general problem of building an evidence database by selecting the most useful examples to store while satisfying existing storage requirements. We evaluate three intelligent techniques for this purpose: genetic algorithm-based selection, greedy selection and random mutation hill climbing. These techniques are compared to a random selection strategy used as the baseline. The study is performed with a previously presented CB-CAD system applied for false positive reduction in screening mammograms. The experimental evaluation shows that when the development goal is to maximize the system’s diagnostic performance, the intelligent techniques are able to reduce the size of the evidence database to 37% of the original database by eliminating superfluous and/or detrimental examples while at the same time significantly improving the CAD system’s performance. Furthermore, if the case-base size is a main concern, the total number of examples stored in the system can be reduced to only 2–4% of the original database without a decrease in the diagnostic performance. Comparison of the techniques shows that random mutation hill climbing provides the best balance between the diagnostic performance and computational efficiency when building the evidence database of the CB-CAD system. PMID:18854606

Selective Formation of Trimethylene Carbonate (TMC): Atmospheric Pressure Carbon Dioxide Utilization

PubMed Central

Buckley, Benjamin R; Patel, Anish P; Wijayantha, K G Upul

2015-01-01

Carbon dioxide utilisation (CDU) is currently gaining increased interest due to the abundance of CO2 and its possible application as a C1 building block. We herein report the first example of atmospheric pressure carbon dioxide incorporation into oxetane to selectively form trimethylene carbonate (TMC), which is a significant challenge as TMC is thermodynamically less favoured than its corresponding co-polymer. PMID:26213485

Selective Formation of Trimethylene Carbonate (TMC): Atmospheric Pressure Carbon Dioxide Utilization.

PubMed

Buckley, Benjamin R; Patel, Anish P; Wijayantha, K G Upul

2015-01-01

Carbon dioxide utilisation (CDU) is currently gaining increased interest due to the abundance of CO 2 and its possible application as a C 1 building block. We herein report the first example of atmospheric pressure carbon dioxide incorporation into oxetane to selectively form trimethylene carbonate (TMC), which is a significant challenge as TMC is thermodynamically less favoured than its corresponding co-polymer.

Supramolecular organization of calix[4]pyrrole with a methyl-trialkylammonium anion exchanger leads to remarkable reversal of selectivity for sulfate extraction vs. nitrate

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

Borman, Christopher J.; Custelcean, Radu; Hay, Ben P.

Here, meso-Octamethylcalix[4]pyrrole (C4P) enhances sulfate selectivity in solvent extraction by Aliquat 336N, an effect ascribed to the supramolecular preorganization and thermodynamic stability imparted by insertion of the methyl group of the Aliquat cation into the cup of C4P in its cone conformation.

Cotton QTLdb: a cotton QTL database for QTL analysis, visualization, and comparison between Gossypium hirsutum and G. hirsutum × G. barbadense populations.

PubMed

Said, Joseph I; Knapka, Joseph A; Song, Mingzhou; Zhang, Jinfa

2015-08-01

A specialized database currently containing more than 2200 QTL is established, which allows graphic presentation, visualization and submission of QTL. In cotton quantitative trait loci (QTL), studies are focused on intraspecific Gossypium hirsutum and interspecific G. hirsutum × G. barbadense populations. These two populations are commercially important for the textile industry and are evaluated for fiber quality, yield, seed quality, resistance, physiological, and morphological trait QTL. With meta-analysis data based on the vast amount of QTL studies in cotton it will be beneficial to organize the data into a functional database for the cotton community. Here we provide a tool for cotton researchers to visualize previously identified QTL and submit their own QTL to the Cotton QTLdb database. The database provides the user with the option of selecting various QTL trait types from either the G. hirsutum or G. hirsutum × G. barbadense populations. Based on the user's QTL trait selection, graphical representations of chromosomes of the population selected are displayed in publication ready images. The database also provides users with trait information on QTL, LOD scores, and explained phenotypic variances for all QTL selected. The CottonQTLdb database provides cotton geneticist and breeders with statistical data on cotton QTL previously identified and provides a visualization tool to view QTL positions on chromosomes. Currently the database (Release 1) contains 2274 QTLs, and succeeding QTL studies will be updated regularly by the curators and members of the cotton community that contribute their data to keep the database current. The database is accessible from http://www.cottonqtldb.org.

Thermodynamically optimal whole-genome tiling microarray design and validation.

PubMed

Cho, Hyejin; Chou, Hui-Hsien

2016-06-13

Microarray is an efficient apparatus to interrogate the whole transcriptome of species. Microarray can be designed according to annotated gene sets, but the resulted microarrays cannot be used to identify novel transcripts and this design method is not applicable to unannotated species. Alternatively, a whole-genome tiling microarray can be designed using only genomic sequences without gene annotations, and it can be used to detect novel RNA transcripts as well as known genes. The difficulty with tiling microarray design lies in the tradeoff between probe-specificity and coverage of the genome. Sequence comparison methods based on BLAST or similar software are commonly employed in microarray design, but they cannot precisely determine the subtle thermodynamic competition between probe targets and partially matched probe nontargets during hybridizations. Using the whole-genome thermodynamic analysis software PICKY to design tiling microarrays, we can achieve maximum whole-genome coverage allowable under the thermodynamic constraints of each target genome. The resulted tiling microarrays are thermodynamically optimal in the sense that all selected probes share the same melting temperature separation range between their targets and closest nontargets, and no additional probes can be added without violating the specificity of the microarray to the target genome. This new design method was used to create two whole-genome tiling microarrays for Escherichia coli MG1655 and Agrobacterium tumefaciens C58 and the experiment results validated the design.

Thermodynamics of ligand binding to histone deacetylase like amidohydrolase from Bordetella/Alcaligenes.

PubMed

Meyners, Christian; Baud, Matthias G J; Fuchter, Matthew J; Meyer-Almes, Franz-Josef

2014-03-01

Thermodynamic studies on ligand-protein binding have become increasingly important in the process of drug design. In combination with structural data and molecular dynamics simulations, thermodynamic studies provide relevant information about the mode of interaction between compounds and their target proteins and therefore build a sound basis for further drug optimization. Using the example of histone deacetylases (HDACs), particularly the histone deacetylase like amidohydrolase (HDAH) from Bordetella/Alcaligenes, a novel sensitive competitive fluorescence resonance energy transfer-based binding assay was developed and the thermodynamics of interaction of both fluorescent ligands and inhibitors to histone deacetylase like amidohydrolase were investigated. The assay consumes only small amounts of valuable target proteins and is suitable for fast kinetic and mechanistic studies as well as high throughput screening applications. Binding affinity increased with increasing length of aliphatic spacers (n = 4-7) between the hydroxamate moiety and the dansyl head group of ligand probes. Van't Hoff plots revealed an optimum in enthalpy contribution to the free energy of binding for the dansyl-ligand with hexyl spacer. The selectivity in the series of dansyl-ligands against human class I HDAC1 but not class II HDACs 4 and 6 increased with the ratio of ΔH(0)/ΔG(0). The data clearly emphasize the importance of thermodynamic signatures as useful general guidance for the optimization of ligands or rational drug design. Copyright © 2014 John Wiley & Sons, Ltd.

RNA Thermodynamic Structural Entropy

PubMed Central

Garcia-Martin, Juan Antonio; Clote, Peter

2015-01-01

Conformational entropy for atomic-level, three dimensional biomolecules is known experimentally to play an important role in protein-ligand discrimination, yet reliable computation of entropy remains a difficult problem. Here we describe the first two accurate and efficient algorithms to compute the conformational entropy for RNA secondary structures, with respect to the Turner energy model, where free energy parameters are determined from UV absorption experiments. An algorithm to compute the derivational entropy for RNA secondary structures had previously been introduced, using stochastic context free grammars (SCFGs). However, the numerical value of derivational entropy depends heavily on the chosen context free grammar and on the training set used to estimate rule probabilities. Using data from the Rfam database, we determine that both of our thermodynamic methods, which agree in numerical value, are substantially faster than the SCFG method. Thermodynamic structural entropy is much smaller than derivational entropy, and the correlation between length-normalized thermodynamic entropy and derivational entropy is moderately weak to poor. In applications, we plot the structural entropy as a function of temperature for known thermoswitches, such as the repression of heat shock gene expression (ROSE) element, we determine that the correlation between hammerhead ribozyme cleavage activity and total free energy is improved by including an additional free energy term arising from conformational entropy, and we plot the structural entropy of windows of the HIV-1 genome. Our software RNAentropy can compute structural entropy for any user-specified temperature, and supports both the Turner’99 and Turner’04 energy parameters. It follows that RNAentropy is state-of-the-art software to compute RNA secondary structure conformational entropy. Source code is available at https://github.com/clotelab/RNAentropy/; a full web server is available at http://bioinformatics.bc.edu/clotelab/RNAentropy, including source code and ancillary programs. PMID:26555444

The importance of mRNA structure in determining the pathogenicity of synonymous and non-synonymous mutations in haemophilia

PubMed Central

Hamasaki-Katagiri, Nobuko; Lin, Brian C.; Simon, Jonathan; Hunt, Ryan C.; Schiller, Tal; Russek-Cohen, Estelle; Komar, Anton A.; Bar, Haim; Kimchi-Sarfaty, Chava

2016-01-01

Introduction Mutational analysis is commonly used to support the diagnosis and management of haemophilia. This has allowed for the generation of large mutation databases which provide unparalleled insight into genotype-phenotype relationships. Haemophilia is associated with inversions, deletions, insertions, nonsense and missense mutations. Both synonymous and non-synonymous mutations influence the base pairing of messenger RNA (mRNA), which can alter mRNA structure, cellular half-life and ribosome processivity/elongation. However, the role of mRNA structure in determining the pathogenicity of point mutations in haemophilia has not been evaluated. Aim To evaluate mRNA thermodynamic stability and associated RNA prediction software as a means to distinguish between neutral and disease-associated mutations in haemophilia. Methods Five mRNA structure prediction software programs were used to assess the thermodynamic stability of mRNA fragments carrying neutral vs. disease-associated and synonymous vs. non-synonymous point mutations in F8, F9 and a third X-linked gene, DMD (dystrophin). Results In F8 and DMD, disease-associated mutations tend to occur in more structurally stable mRNA regions, represented by lower MFE (minimum free energy) levels. In comparing multiple software packages for mRNA structure prediction, a 101–151 nucleotide fragment length appears to be a feasible range for structuring future studies. Conclusion mRNA thermodynamic stability is one predictive characteristic, which when combined with other RNA and protein features, may offer significant insight when screening sequencing data for novel disease-associated mutations. Our results also suggest potential utility in evaluating the mRNA thermodynamic stability profile of a gene when determining the viability of interchanging codons for biological and therapeutic applications. PMID:27933712

RNA Thermodynamic Structural Entropy.

PubMed

Garcia-Martin, Juan Antonio; Clote, Peter

2015-01-01

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

Creating Your Own Database.

ERIC Educational Resources Information Center

Blair, John C., Jr.

1982-01-01

Outlines the important factors to be considered in selecting a database management system for use with a microcomputer and presents a series of guidelines for developing a database. General procedures, report generation, data manipulation, information storage, word processing, data entry, database indexes, and relational databases are among the…

Selective access and editing in a database

NASA Technical Reports Server (NTRS)

Maluf, David A. (Inventor); Gawdiak, Yuri O. (Inventor)

2010-01-01

Method and system for providing selective access to different portions of a database by different subgroups of database users. Where N users are involved, up to 2.sup.N-1 distinguishable access subgroups in a group space can be formed, where no two access subgroups have the same members. Two or more members of a given access subgroup can edit, substantially simultaneously, a document accessible to each member.

Entropy as a Driver of Selectivity for Inhibitor Binding to Histone Deacetylase 6.

PubMed

Porter, Nicholas J; Wagner, Florence F; Christianson, David W

2018-05-18

Among the metal-dependent histone deacetylases, the class IIb isozyme HDAC6 is remarkable because of its role in the regulation of microtubule dynamics in the cytosol. Selective inhibition of HDAC6 results in microtubule hyperacetylation, leading to cell cycle arrest and apoptosis, which is a validated strategy for cancer chemotherapy and the treatment of other disorders. HDAC6 inhibitors generally consist of a Zn 2+ -binding group such as a hydroxamate, a linker, and a capping group; the capping group is a critical determinant of isozyme selectivity. Surprisingly, however, even "capless" inhibitors exhibit appreciable HDAC6 selectivity. To probe the chemical basis for this selectivity, we now report high-resolution crystal structures of HDAC6 complexed with capless cycloalkyl hydroxamate inhibitors 1-4. Each inhibitor hydroxamate group coordinates to the catalytic Zn 2+ ion with canonical bidentate geometry. Additionally, the olefin moieties of compounds 2 and 4 bind in an aromatic crevice between the side chains of F583 and F643. Reasoning that similar binding could be achieved in the representative class I isozyme HDAC8, we employed isothermal titration calorimetry to study the thermodynamics of inhibitor binding. These measurements indicate that the entropy of inhibitor binding is generally positive for binding to HDAC6 and negative for binding to HDAC8, resulting in ≤313-fold selectivity for binding to HDAC6 relative to HDAC8. Thus, favorable binding entropy contributes to HDAC6 selectivity. Notably, cyclohexenyl hydroxamate 2 represents a promising lead for derivatization with capping groups that may further enhance its impressive 313-fold thermodynamic selectivity for HDAC6 inhibition.

A Free Database of Auto-detected Full-sun Coronal Hole Maps

NASA Astrophysics Data System (ADS)

Caplan, R. M.; Downs, C.; Linker, J.

2016-12-01

We present a 4-yr (06/10/2010 to 08/18/14 at 6-hr cadence) database of full-sun synchronic EUV and coronal hole (CH) maps made available on a dedicated web site (http://www.predsci.com/chd). The maps are generated using STEREO/EUVI A&B 195Å and SDO/AIA 193Å images through an automated pipeline (Caplan et al, (2016) Ap.J. 823, 53).Specifically, the original data is preprocessed with PSF-deconvolution, a nonlinear limb-brightening correction, and a nonlinear inter-instrument intensity normalization. Coronal holes are then detected in the preprocessed images using a GPU-accelerated region growing segmentation algorithm. The final results from all three instruments are then merged and projected to form full-sun sine-latitude maps. All the software used in processing the maps is provided, which can easily be adapted for use with other instruments and channels. We describe the data pipeline and show examples from the database. We also detail recent CH-detection validation experiments using synthetic EUV emission images produced from global thermodynamic MHD simulations.

Limits to Dihydrogen Incorporation into Electron Sinks Alternative to Methanogenesis in Ruminal Fermentation

PubMed Central

Ungerfeld, Emilio M.

2015-01-01

Research is being conducted with the objective of decreasing methane (CH4) production in the rumen, as methane emissions from ruminants are environmentally damaging and a loss of digestible energy to ruminants. Inhibiting ruminal methanogenesis generally results in accumulation of dihydrogen (H2), which is energetically inefficient and can inhibit fermentation. It would be nutritionally beneficial to incorporate accumulated H2 into propionate or butyrate production, or reductive acetogenesis. The objective of this analysis was to examine three possible physicochemical limitations to the incorporation of accumulated H2 into propionate and butyrate production, and reductive acetogenesis, in methanogenesis-inhibited ruminal batch and continuous cultures: (i) Thermodynamics; (ii) Enzyme kinetics; (iii) Substrate kinetics. Batch (N = 109) and continuous (N = 43) culture databases of experiments with at least 50% inhibition in CH4 production were used in this meta-analysis. Incorporation of accumulated H2 into propionate production and reductive acetogenesis seemed to be thermodynamically feasible but quite close to equilibrium, whereas this was less clear for butyrate. With regard to enzyme kinetics, it was speculated that hydrogenases of ruminal microorganisms may have evolved toward high-affinity and low maximal velocity to compete for traces of H2, rather than for high pressure accumulated H2. Responses so far obtained to the addition of propionate production intermediates do not allow distinguishing between thermodynamic and substrate kinetics control. PMID:26635743

Thermodynamic properties of gaseous ruthenium species.

PubMed

Miradji, Faoulat; Souvi, Sidi; Cantrel, Laurent; Louis, Florent; Vallet, Valérie

2015-05-21

The review of thermodynamic data of ruthenium oxides reveals large uncertainties in some of the standard enthalpies of formation, motivating the use of high-level relativistic correlated quantum chemical methods to reduce the level of discrepancies. The reaction energies leading to the formation of ruthenium oxides RuO, RuO2, RuO3, and RuO4 have been calculated for a series of reactions. The combination of different quantum chemical methods has been investigated [DFT, CASSCF, MRCI, CASPT2, CCSD(T)] in order to predict the geometrical parameters, the energetics including electronic correlation and spin-orbit coupling. The most suitable method for ruthenium compounds is the use of TPSSh-5%HF for geometry optimization, followed by CCSD(T) with complete basis set (CBS) extrapolations for the calculation of the total electronic energies. SO-CASSCF seems to be accurate enough to estimate spin-orbit coupling contributions to the ground-state electronic energies. This methodology yields very accurate standard enthalpies of formations of all species, which are either in excellent agreement with the most reliable experimental data or provide an improved estimate for the others. These new data will be implemented in the thermodynamical databases that are used by the ASTEC code (accident source term evaluation code) to build models of ruthenium chemistry behavior in severe nuclear accident conditions. The paper also discusses the nature of the chemical bonds both from molecular orbital and topological view points.

CRUNCH_PARALLEL

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

Shumaker, Dana E.; Steefel, Carl I.

The code CRUNCH_PARALLEL is a parallel version of the CRUNCH code. CRUNCH code version 2.0 was previously released by LLNL, (UCRL-CODE-200063). Crunch is a general purpose reactive transport code developed by Carl Steefel and Yabusake (Steefel Yabsaki 1996). The code handles non-isothermal transport and reaction in one, two, and three dimensions. The reaction algorithm is generic in form, handling an arbitrary number of aqueous and surface complexation as well as mineral dissolution/precipitation. A standardized database is used containing thermodynamic and kinetic data. The code includes advective, dispersive, and diffusive transport.

Entropy–enthalpy transduction caused by conformational shifts can obscure the forces driving protein–ligand binding

PubMed Central

Fenley, Andrew T.; Muddana, Hari S.; Gilson, Michael K.

2012-01-01

Molecular dynamics simulations of unprecedented duration now can provide new insights into biomolecular mechanisms. Analysis of a 1-ms molecular dynamics simulation of the small protein bovine pancreatic trypsin inhibitor reveals that its main conformations have different thermodynamic profiles and that perturbation of a single geometric variable, such as a torsion angle or interresidue distance, can select for occupancy of one or another conformational state. These results establish the basis for a mechanism that we term entropy–enthalpy transduction (EET), in which the thermodynamic character of a local perturbation, such as enthalpic binding of a small molecule, is camouflaged by the thermodynamics of a global conformational change induced by the perturbation, such as a switch into a high-entropy conformational state. It is noted that EET could occur in many systems, making measured entropies and enthalpies of folding and binding unreliable indicators of actual thermodynamic driving forces. The same mechanism might also account for the high experimental variance of measured enthalpies and entropies relative to free energies in some calorimetric studies. Finally, EET may be the physical mechanism underlying many cases of entropy–enthalpy compensation. PMID:23150595

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

USGS Publications Warehouse

Hemingway, B.S.

1982-01-01

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

Applying Thermodynamics to Fossil Fuels: Heats of Combustion from Elemental Compositions.

ERIC Educational Resources Information Center

Lloyd, William G.; Davenport, Derek A.

1980-01-01

Discussed are the calculations of heats of combustions of some selected fossil fuel compounds such as some foreign shale oils and United States coals. Heating values for coal- and petroleum-derived fuel oils are also presented. (HM)

Effect of inter-species selective interactions on the thermodynamics and nucleation free-energy barriers of a tessellating polyhedral compound

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

Escobedo, Fernando A., E-mail: fe13@cornell.edu

The phase behavior and the homogeneous nucleation of an equimolar mixture of octahedra and cuboctahedra are studied using thermodynamic integration, Gibbs-Duhem integration, and umbrella sampling simulations. The components of this mixture are modeled as polybead objects of equal edge lengths so that they can assemble into a space-filling compound with the CsCl crystal structure. Taking as reference the hard-core system where the compound crystal does not spontaneously nucleate, we quantified the effect of inter-species selective interactions on facilitating the disorder-to-order transition. Facet selective and facet non-selective inter-species attractions were considered, and while the former was expectedly more favorable toward themore » target tessellating structure, the latter was found to be similarly effective in nucleating the crystal compound. Ranges for the strength of attractions and degree of supersaturation were identified where the nucleation free-energy barrier was small enough to foretell a fast process but large enough to prevent spinodal fluctuations that can trap the system in dense metastable states lacking long-range order. At those favorable conditions, the tendency toward the local orientational order favored by packing entropy is amplified and found to play a key role seeding nuclei with the CsCl structure.« less

Superconductivity in BiPbCaSrCuO thin films

NASA Astrophysics Data System (ADS)

Fu, S. M.; Yang, H. C.; Chen, F. C.; Horng, H. E.; Jao, J. C.

1989-12-01

Thin films of BiPbCaSrCuO sample were prepared by RF sputtering from sintered ceramic targets. Single crystal of MgO(100) was selected as substrate. The sputtering was held at room temperature. Different annealing conditions were carried out to obtain optimum conditions. High temperature resistivity was measured in air to study the thermodynamic reaction of the sintered films. An resistivity anomaly was found in the first heating cycle which suggests a thermodynamic reaction. A temperature dependence of I c was measured to study the coupling of grains in the granular films in different temperature ranges and the results will be discussed.

Properties of the two-dimensional heterogeneous Lennard-Jones dimers: An integral equation study

PubMed Central

Urbic, Tomaz

2016-01-01

Structural and thermodynamic properties of a planar heterogeneous soft dumbbell fluid are examined using Monte Carlo simulations and integral equation theory. Lennard-Jones particles of different sizes are the building blocks of the dimers. The site-site integral equation theory in two dimensions is used to calculate the site-site radial distribution functions and the thermodynamic properties. Obtained results are compared to Monte Carlo simulation data. The critical parameters for selected types of dimers were also estimated and the influence of the Lennard-Jones parameters was studied. We have also tested the correctness of the site-site integral equation theory using different closures. PMID:27875894

Search for promising compositions for developing new multiphase casting alloys based on Al-Cu-Mg matrix using thermodynamic calculations and mathematic simulation

NASA Astrophysics Data System (ADS)

Zolotorevskii, V. S.; Pozdnyakov, A. V.; Churyumov, A. Yu.

2012-11-01

A calculation-experimental study is carried out to improve the concept of searching for new alloying systems in order to develop new casting alloys using mathematical simulation methods in combination with thermodynamic calculations. The results show the high effectiveness of the applied methods. The real possibility of selecting the promising compositions with the required set of casting and mechanical properties is exemplified by alloys with thermally hardened Al-Cu and Al-Cu-Mg matrices, as well as poorly soluble additives that form eutectic components using mainly the calculation study methods and the minimum number of experiments.

Object-Oriented Approach to Integrating Database Semantics. Volume 4.

DTIC Science & Technology

1987-12-01

schemata for; 1. Object Classification Shema -- Entities 2. Object Structure and Relationship Schema -- Relations 3. Operation Classification and... relationships are represented in a database is non- intuitive for naive users. *It is difficult to access and combine information in multiple databases. In this...from the CURRENT-.CLASSES table. Choosing a selected item do-selects it. Choose 0 to exit. 1. STUDENTS 2. CUR~RENT-..CLASSES 3. MANAGMNT -.CLASS

Prototype Food and Nutrient Database for Dietary Studies: Branded Food Products Database for Public Health Proof of Concept

USDA-ARS?s Scientific Manuscript database

The Prototype Food and Nutrient Database for Dietary Studies (Prototype FNDDS) Branded Food Products Database for Public Health is a proof of concept database. The database contains a small selection of food products which is being used to exhibit the approach for incorporation of the Branded Food ...

Document creation, linking, and maintenance system

DOEpatents

Claghorn, Ronald [Pasco, WA

2011-02-15

A document creation and citation system designed to maintain a database of reference documents. The content of a selected document may be automatically scanned and indexed by the system. The selected documents may also be manually indexed by a user prior to the upload. The indexed documents may be uploaded and stored within a database for later use. The system allows a user to generate new documents by selecting content within the reference documents stored within the database and inserting the selected content into a new document. The system allows the user to customize and augment the content of the new document. The system also generates citations to the selected content retrieved from the reference documents. The citations may be inserted into the new document in the appropriate location and format, as directed by the user. The new document may be uploaded into the database and included with the other reference documents. The system also maintains the database of reference documents so that when changes are made to a reference document, the author of a document referencing the changed document will be alerted to make appropriate changes to his document. The system also allows visual comparison of documents so that the user may see differences in the text of the documents.

bpRNA: large-scale automated annotation and analysis of RNA secondary structure.

PubMed

Danaee, Padideh; Rouches, Mason; Wiley, Michelle; Deng, Dezhong; Huang, Liang; Hendrix, David

2018-05-09

While RNA secondary structure prediction from sequence data has made remarkable progress, there is a need for improved strategies for annotating the features of RNA secondary structures. Here, we present bpRNA, a novel annotation tool capable of parsing RNA structures, including complex pseudoknot-containing RNAs, to yield an objective, precise, compact, unambiguous, easily-interpretable description of all loops, stems, and pseudoknots, along with the positions, sequence, and flanking base pairs of each such structural feature. We also introduce several new informative representations of RNA structure types to improve structure visualization and interpretation. We have further used bpRNA to generate a web-accessible meta-database, 'bpRNA-1m', of over 100 000 single-molecule, known secondary structures; this is both more fully and accurately annotated and over 20-times larger than existing databases. We use a subset of the database with highly similar (≥90% identical) sequences filtered out to report on statistical trends in sequence, flanking base pairs, and length. Both the bpRNA method and the bpRNA-1m database will be valuable resources both for specific analysis of individual RNA molecules and large-scale analyses such as are useful for updating RNA energy parameters for computational thermodynamic predictions, improving machine learning models for structure prediction, and for benchmarking structure-prediction algorithms.

URS DataBase: universe of RNA structures and their motifs.

PubMed

Baulin, Eugene; Yacovlev, Victor; Khachko, Denis; Spirin, Sergei; Roytberg, Mikhail

2016-01-01

The Universe of RNA Structures DataBase (URSDB) stores information obtained from all RNA-containing PDB entries (2935 entries in October 2015). The content of the database is updated regularly. The database consists of 51 tables containing indexed data on various elements of the RNA structures. The database provides a web interface allowing user to select a subset of structures with desired features and to obtain various statistical data for a selected subset of structures or for all structures. In particular, one can easily obtain statistics on geometric parameters of base pairs, on structural motifs (stems, loops, etc.) or on different types of pseudoknots. The user can also view and get information on an individual structure or its selected parts, e.g. RNA-protein hydrogen bonds. URSDB employs a new original definition of loops in RNA structures. That definition fits both pseudoknot-free and pseudoknotted secondary structures and coincides with the classical definition in case of pseudoknot-free structures. To our knowledge, URSDB is the first database supporting searches based on topological classification of pseudoknots and on extended loop classification.Database URL: http://server3.lpm.org.ru/urs/. © The Author(s) 2016. Published by Oxford University Press.

URS DataBase: universe of RNA structures and their motifs

PubMed Central

Baulin, Eugene; Yacovlev, Victor; Khachko, Denis; Spirin, Sergei; Roytberg, Mikhail

2016-01-01

The Universe of RNA Structures DataBase (URSDB) stores information obtained from all RNA-containing PDB entries (2935 entries in October 2015). The content of the database is updated regularly. The database consists of 51 tables containing indexed data on various elements of the RNA structures. The database provides a web interface allowing user to select a subset of structures with desired features and to obtain various statistical data for a selected subset of structures or for all structures. In particular, one can easily obtain statistics on geometric parameters of base pairs, on structural motifs (stems, loops, etc.) or on different types of pseudoknots. The user can also view and get information on an individual structure or its selected parts, e.g. RNA–protein hydrogen bonds. URSDB employs a new original definition of loops in RNA structures. That definition fits both pseudoknot-free and pseudoknotted secondary structures and coincides with the classical definition in case of pseudoknot-free structures. To our knowledge, URSDB is the first database supporting searches based on topological classification of pseudoknots and on extended loop classification. Database URL: http://server3.lpm.org.ru/urs/ PMID:27242032

Deciphering the selectivity of Bombyx mori pheromone binding protein for bombykol over bombykal: a theoretical approach.

PubMed

Charlier, Landry; Antonczak, Serge; Jacquin-Joly, Emmanuelle; Cabrol-Bass, Daniel; Golebiowski, Jérôme

2008-12-22

In this article we report calculations dedicated to estimate the selectivity of the Bombyx mori pheromone binding protein towards the two closely related pheromonal components Bombykol and Bombykal. The selectivity is quantified by the binding free-energy difference, obtained either by the thermodynamic integration or by the MM-GBSA approach. In the latter, the selectivity is decomposed on a per-residue basis, which identifies the residues considered crucial for the selectivity of the protein for Bombykol over Bombykal. A discussion on the role of Bombyx mori pheromone binding protein is provided on the basis of these results.

Kentucky geotechnical database.

DOT National Transportation Integrated Search

2005-03-01

Development of a comprehensive dynamic, geotechnical database is described. Computer software selected to program the client/server application in windows environment, components and structure of the geotechnical database, and primary factors cons...

MTDATA and the Prediction of Phase Equilibria in Oxide Systems: 30 Years of Industrial Collaboration

NASA Astrophysics Data System (ADS)

Gisby, John; Taskinen, Pekka; Pihlasalo, Jouni; Li, Zushu; Tyrer, Mark; Pearce, Jonathan; Avarmaa, Katri; Björklund, Peter; Davies, Hugh; Korpi, Mikko; Martin, Susan; Pesonen, Lauri; Robinson, Jim

2017-02-01

This paper gives an introduction to MTDATA, Phase Equilibrium Software from the National Physical Laboratory (NPL), and describes the latest advances in the development of a comprehensive database of thermodynamic parameters to underpin calculations of phase equilibria in large oxide, sulfide, and fluoride systems of industrial interest. The database, MTOX, has been developed over a period of thirty years based upon modeling work at NPL and funded by industrial partners in a project co-ordinated by Mineral Industry Research Organisation. Applications drawn from the fields of modern copper scrap smelting, high-temperature behavior of basic oxygen steelmaking slags, flash smelting of nickel, electric furnace smelting of ilmenite, and production of pure TiO2 via a low-temperature molten salt route are discussed along with calculations to assess the impact of impurities on the uncertainty of fixed points used to realize the SI unit of temperature, the kelvin.

Mixing characterization of highly underexpanded fluid jets with real gas expansion

NASA Astrophysics Data System (ADS)

Förster, Felix J.; Baab, Steffen; Steinhausen, Christoph; Lamanna, Grazia; Ewart, Paul; Weigand, Bernhard

2018-03-01

We report a comprehensive speed of sound database for multi-component mixing of underexpanded fuel jets with real gas expansion. The paper presents several reference test cases with well-defined experimental conditions providing quantitative data for validation of computational simulations. Two injectant fluids, fundamentally different with respect to their critical properties, are brought to supercritical state and discharged into cold nitrogen at different pressures. The database features a wide range of nozzle pressure ratios covering the regimes that are generally classified as highly and extremely highly underexpanded jets. Further variation is introduced by investigating different injection temperatures. Measurements are obtained along the centerline at different axial positions. In addition, an adiabatic mixing model based on non-ideal thermodynamic mixture properties is used to extract mixture compositions from the experimental speed of sound data. The concentration data obtained are complemented by existing experimental data and represented by an empirical fit.

The effect of fenoterol stereochemistry on the β2 adrenergic receptor system: ligand directed chiral recognition

PubMed Central

Jozwiak, Krzysztof; Plazinska, Anita; Toll, Lawrence; Jimenez, Lucita; Woo, Anthony Yiu-Ho; Xiao, Rui-Ping; Wainer, Irving W.

2011-01-01

The β2 adrenergic receptor (β2-AR) is a model system for studying the ligand recognition process in G-protein coupled receptors. Fenoterol (FEN) is a β2-AR selective agonist that has two centers of chirality and exists as four stereoisomers. Radioligand binding studies determined that stereochemistry greatly influences the binding affinity. Subsequent Van’t Hoff analysis shows very different thermodynamics of binding depending on the stereoconfiguration of the molecule. The binding of (S,x’)-isomers is almost entirely enthalpy controlled whereas binding of (R,x’)-isomers is purely entropy driven. Stereochemistry of FEN molecule also affects the coupling of the receptor to different G proteins. In a rat cardiomyocyte contractility model, (R,R’)-FEN was shown to selectively activate Gs protein signaling while the (S,R’)- isomer activated both Gi and Gs protein. The overall data demonstrate that the chirality at the two chiral centers of the FEN molecule influences the magnitude of binding affinity, thermodynamics of local interactions within the binding site and the global mechanism of β2-AR activation. Differences in thermodynamic parameters and non-uniform G-protein coupling suggest a mechanism of chiral recognition in which observed enantioselectivities arise from the interaction of the (R,x’)-FEN stereoisomers with a different receptor conformation than the one with which the (S,x’)-isomer interacts. PMID:21618615

Effect of fenoterol stereochemistry on the β2 adrenergic receptor system: ligand-directed chiral recognition.

PubMed

Jozwiak, Krzysztof; Plazinska, Anita; Toll, Lawrence; Jimenez, Lucita; Woo, Anthony Yiu-Ho; Xiao, Rui-Ping; Wainer, Irving W

2011-01-01

The β(2) adrenergic receptor (β(2)-AR) is a model system for studying the ligand recognition process in G protein-coupled receptors. Fenoterol (FEN) is a β(2)-AR selective agonist that has two centers of chirality and exists as four stereoisomers. Radioligand binding studies determined that stereochemistry greatly influences the binding affinity. Subsequent Van't Hoff analysis shows very different thermodynamics of binding depending on the stereoconfiguration of the molecule. The binding of (S,x')-isomers is almost entirely enthalpy controlled whereas binding of (R,x')-isomers is purely entropy driven. Stereochemistry of FEN molecule also affects the coupling of the receptor to different G proteins. In a rat cardiomyocyte contractility model, (R,R')-FEN was shown to selectively activate G(s) protein signaling while the (S,R')-isomer activated both G(i) and G(s) protein. The overall data demonstrate that the chirality at the two chiral centers of the FEN molecule influences the magnitude of binding affinity, thermodynamics of local interactions within the binding site, and the global mechanism of β(2)-AR activation. Differences in thermodynamic parameters and nonuniform G-protein coupling suggest a mechanism of chiral recognition in which observed enantioselectivities arise from the interaction of the (R,x')-FEN stereoisomers with a different receptor conformation than the one with which the (S,x')-isomer interacts. Copyright © 2011 Wiley-Liss, Inc.

Effects of food processing on the thermodynamic and nutritive value of foods: literature and database survey.

PubMed

Prochaska, L J; Nguyen, X T; Donat, N; Piekutowski, W V

2000-02-01

One of the goals of our society is to provide adequate nourishment for the general population of humans. In the strictness sense, the foodstuffs which we ingest are bundles of thermodynamic energy. In our post-industrial society, food producers provide society with the bioenergetic content of foods, while stabilizing the food in a non-perishable form that enables the consumer to access foods that are convenient and nutritious. As our modern society developed, the processing of foodstuffs increased to allow consumers flexibility in their choice in which foods to eat (based on nutritional content and amount of post-harvest processing). The thermodynamic energy content of foodstuffs is well documented in the literature by the use of bomb calorimetry measurements. Here, we determine the effects of processing (in most cases by the application of heat) on the thermodynamic energy content of foods in order to investigate the role of processing in daily nutritional needs. We also examine which processing procedures affect the nutritive quality (vitamin and mineral content) and critically assess the rational, advantages and disadvantages of additives to food. Finally, we discuss the role of endogenous enzymes in foods not only on the nutritive quality of the food but also on the freshness and flavor of the food. Our results show that a significant decrease in thermodynamic energy content occurs in fruits, vegetables, and meat products upon processing that is independent of water content. No significant change in energy content was observed in cereals, sugars, grains, fats and oils, and nuts. The vitamin content of most foods was most dramatically decreased by canning while smaller effects were observed upon blanching and freezing. We found that most food additives had very little effect on thermodynamic energy content due to their presence in minute quantities and that most were added to preserve the foodstuff or supplement its vitamin content. The endogenous food enzymes while aiding in digestibility of some foods (yogurt or grains) also helped some foods have a more palatable taste. Our conclusions are there is some scientific merit to the idea that enzymes in food can act synergistically with those in the human body to facilitate maximum nutritive value of foods. Copyright 2000 Harcourt Publishers Ltd.

Designing Ionic Liquids for CO2 Capture: What’s the role for computation?

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

Brennecke, Joan F.

Presentation on the computational aspects of ionic liquid selection for carbon dioxide capture to the conference attendees at the New Vistas in Molecular Thermodynamics: Experimentation, Molecular Modeling, and Inverse Design, Berkeley, CA, January 7 through 9, 2018

Combining Chemistry and Music to Engage Student Interest: Using Songs to Accompany Selected Chemical Topics

ERIC Educational Resources Information Center

Last, Arthur M.

2009-01-01

The use of recorded music to add interest to a variety of lecture topics is described. Topics include the periodic table, the formation of ionic compounds, thermodynamics, carbohydrates, nuclear chemistry, and qualitative analysis. (Contains 1 note.)

Thermodynamic modeling of Cl(-), NO3(-) and SO4(2-) removal by an anion exchange resin and comparison with Dubinin-Astakhov isotherms.

PubMed

Dron, Julien; Dodi, Alain

2011-03-15

The removal of chloride, nitrate, and sulfate ions from wastewaters by a macroporous ion-exchange resin is studied through the experimental results obtained for six ion exchange systems, OH(-)/Cl(-), OH(-)/NO3(-), OH(-)/SO4(2-), and HCO3(-)/Cl(-), Cl(-)/NO3(-), Cl(-)/SO4(2-). The results are described through thermodynamic modeling, considering either an ideal or a nonideal behavior of the ionic species in the liquid and solid phases. The nonidealities are determined by the Davies equation and Wilson equations in the liquid and solid phases, respectively. The results show that the resin has a strong affinity for all the target ions, and the order of affinity obtained is OH(-) < HCO3(-) < Cl(-) < NO3(-) < SO4(2-). The calculation of the changes in standard Gibbs free energies (ΔG(0)) shows that even though HCO3(-) has a lower affinity to the resin, it may affect the removal of Cl(-), and in the same way that Cl(-) may affect the removal of NO3(-) and SO4(2-). The application of nonidealities in the thermodynamic model leads to an improved fit of the model to the experimental data with average relative deviations below 1.5% except for the OH(-)/SO4(2-) system. On the other hand, considering ideal or nonideal behaviors has no significant impact on the determination of the selectivity coefficients. The thermodynamic modeling is also compared with the Dubinin-Astakhov adsorption isotherms obtained for the same ion exchange systems. Surprisingly, the latter performs significantly better than the ideal thermodynamic model and nearly as well as the nonideal thermodynamic model.

The ATLAS TAGS database distribution and management - Operational challenges of a multi-terabyte distributed database

NASA Astrophysics Data System (ADS)

Viegas, F.; Malon, D.; Cranshaw, J.; Dimitrov, G.; Nowak, M.; Nairz, A.; Goossens, L.; Gallas, E.; Gamboa, C.; Wong, A.; Vinek, E.

2010-04-01

The TAG files store summary event quantities that allow a quick selection of interesting events. This data will be produced at a nominal rate of 200 Hz, and is uploaded into a relational database for access from websites and other tools. The estimated database volume is 6TB per year, making it the largest application running on the ATLAS relational databases, at CERN and at other voluntary sites. The sheer volume and high rate of production makes this application a challenge to data and resource management, in many aspects. This paper will focus on the operational challenges of this system. These include: uploading the data from files to the CERN's and remote sites' databases; distributing the TAG metadata that is essential to guide the user through event selection; controlling resource usage of the database, from the user query load to the strategy of cleaning and archiving of old TAG data.

Study of the thermodynamic phase of hydrometeors in convective clouds in the Amazon Basin

NASA Astrophysics Data System (ADS)

Ferreira, W. C.; Correia, A. L.; Martins, J.

2012-12-01

Aerosol-cloud interactions are responsible for large uncertainties in climatic models. One key fator when studying clouds perturbed by aerosols is determining the thermodynamic phase of hydrometeors as a function of temperature or height in the cloud. Conventional remote sensing can provide information on the thermodynamic phase of clouds over large areas, but it lacks the precision needed to understand how a single, real cloud evolves. Here we present mappings of the thermodynamic phase of droplets and ice particles in individual convective clouds in the Amazon Basin, by analyzing the emerging infrared radiance on cloud sides (Martins et al., 2011). In flights over the Amazon Basin with a research aircraft Martins et al. (2011) used imaging radiometers with spectral filters to record the emerging radiance on cloud sides at the wavelengths of 2.10 and 2.25 μm. Due to differential absorption and scattering of these wavelengths by hydrometeors in liquid or solid phases, the intensity ratio between images recorded at the two wavelengths can be used as proxy to the thermodynamic phase of these hydrometeors. In order to analyze the acquired dataset we used the MATLAB tools package, developing scripts to handle data files and derive the thermodynamic phase. In some cases parallax effects due to aircraft movement required additional data processing before calculating ratios. Only well illuminated scenes were considered, i.e. images acquired as close as possible to the backscatter vector from the incident solar radiation. It's important to notice that the intensity ratio values corresponding to a given thermodynamic phase can vary from cloud to cloud (Martins et al., 2011), however inside the same cloud the distinction between ice, water and mixed-phase is clear. Analyzing histograms of reflectance ratios 2.10/2.25 μm in selected cases, we found averages typically between 0.3 and 0.4 for ice phase hydrometeors, and between 0.5 and 0.7 for water phase droplets, consistent with the findings in Martins et al., (2011). Figure 1 shows an example of thermodynamic phase classification obtained with this technique. These experimental results can potentially be used in fast derivations of thermodynamic phase mappings in deep convective clouds, providing useful information for studies regarding aerosol-cloud interactions. Image of the ratio of reflectances at 2.10/2.25μm

E-Selective Semi-Hydrogenation of Alkynes by Heterobimetallic Catalysis.

PubMed

Karunananda, Malkanthi K; Mankad, Neal P

2015-11-25

A unique cooperative H2 activation reaction by heterobimetallic (NHC)M'-MCp(CO)2 complexes (NHC = N-heterocyclic carbene, M' = Cu or Ag, M = Fe or Ru) has been leveraged to develop a catalytic alkyne semi-hydrogenation transformation. The optimal Ag-Ru catalyst gives high selectivity for converting alkynes to E-alkenes, a rare selectivity mode for reduction reactions with H2. The transformation is tolerant of many reducible functional groups. Computational analysis of H2 activation thermodynamics guided rational catalyst development. Bimetallic alkyne hydrogenation and alkene isomerization mechanisms are proposed.

75 FR 78995 - Agency Forms Undergoing Paperwork Reduction Act Review

Federal Register 2010, 2011, 2012, 2013, 2014

2010-12-17

... fellowship applicants and alumni in one integrated database. FMS provides an efficient and effective way for processing application data, selecting qualified candidates, maintaining a current alumni database...; submission of academic transcripts and letters of recommendation; a review by selected programmatic staff and...

Online Reference Service--How to Begin: A Selected Bibliography.

ERIC Educational Resources Information Center

Shroder, Emelie J., Ed.

1982-01-01

Materials in this bibliography were selected and recommended by members of the Use of Machine-Assisted Reference in Public Libraries Committee, Reference and Adult Services Division, American Library Association. Topics include: financial aspects, equipment and communications considerations, comparing databases and database systems, advertising…

Retentivity, selectivity and thermodynamic behavior of polycyclic aromatic hydrocarbons on charge-transfer and hypercrosslinked stationary phases under conditions of normal phase high performance liquid chromatography.

PubMed

Jiang, Ping; Lucy, Charles A

2016-03-11

Charge-transfer and hypercrosslinked polystyrene phases offer retention and separation for polycyclic aromatic hydrocarbons (PAHs) and thus have potential for petroleum analysis. The size, shape and planarity selectivity for PAH standards on charge-transfer (DNAP column) and hypercrosslinked polystyrene (HC-Tol and 5HGN columns) phases are different under normal phase liquid chromatography (NPLC). The HC-Tol column behaves like a conventional NPLC column with low retention of PAHs. Retention of PAHs on the DNAP and 5HGN are strong and increases with the number of aromatic rings. The main retention mechanism is through π-π interactions and dipole-induced dipole interaction. Thermodynamics indicates that the retention mechanism of PAHs remains unchanged over the temperature range 20-60°C. In addition, on either DNAP or 5HGN column, both linear and bent PAHs are retained through the same mechanism. But DNAP possesses smaller π-π interaction and higher planarity selectivity than 5HGN for PAHs. This is suggestive that DNAP interacts with PAHs through a disordered phase arrangement, while 5HGN behaves as an ordered adsorption phase. Copyright © 2016 Elsevier B.V. All rights reserved.

A graphite-lined regeneratively cooled thrust chamber

NASA Technical Reports Server (NTRS)

Stubbs, V. R.

1972-01-01

Design concepts, based on use of graphite as a thermal barrier for regeneratively cooled FLOX-methane thrust chambers, have been screened and concepts selected for detailed thermodynamic, stress, and fabrication analyses. A single design employing AGCarb-101, a fibrous graphite composite material, for a thermal barrier liner and an electroformed nickel structure with integral coolant passages was selected for fabrication and testing. The fabrication processes and the test results are described and illustrated.

Equilibrium Noise in Ion Selective Field Effect Transistors.

DTIC Science & Technology

1982-07-21

face. These parameters have been evaluated for several ion-selective membranes. DD I JAN ") 1473 EDITION or I Mov 09SIS OSSOLETE ONi 0102-LF-0146601...the "integrated circuit" noise on the processing parameters which were different for the two laboratories. This variability in the "integrated circuit...systems and is useful in the identification of the parameters limiting the performance of -11- these systems. In thermodynamic equilibrium, every

The thermodynamic parameters of sorption and enantioselectivity of the chiral smectic liquid crystal 2-methylbutyl ester of 4-(4-decyloxybenzylideneamino)-cinnamic acid

NASA Astrophysics Data System (ADS)

Onuchak, L. A.; Stepanova, R. F.; Akopova, O. B.; Glebova, O. V.; Chernova, O. M.

2008-06-01

The thermodynamic characteristics of sorption of n-alkanes, arenes, aldehydes, monoatomic alcohols, and optical isomers of camphene and butanediol-2,3 by a chiral smectic liquid crystal, 2-methylbutyl ester of 4-(4-decyloxybenzylideneamino)-cinnamic acid, from the gas phase were studied over the temperature range including the S*C and S*A mesophases and isotropic phase. The standard and excess thermodynamic functions of sorption were determined for 26 sorbates of the classes of substances specified. The S*C and S*A mesophases exhibited selectivity with respect to the separation of para and meta xylenes (α p/m = 1.06 1.07, 90 108°C) and pronounced enantioselectivity (αR/S = 1.05 1.09, 87 108°C). The helically twisted structure of the smectic liquid crystal was shown to play an important role in the mechanism of the chiral recognition of optical isomers of polar and low-polarity compounds under gas-liquid chromatography conditions.

Photocatalysis versus photosynthesis: A sensitivity analysis of devices for solar energy conversion and chemical transformations

DOE PAGES

Osterloh, Frank E.

2017-01-18

Here, the chemical literature often does not differentiate between photocatalytic (PC) and photosynthetic (PS) processes (including artificial photosynthesis) even though these reactions differ in their thermodynamics. Photocatalytic processes are thermodynamically downhill (ΔG < 0) and are merely accelerated by the catalyst, whereas photosynthetic processes are thermodynamically unfavorable (ΔG > 0) and require photochemical energy input to occur. Here we apply this differentiation to analyze the basic functions of PC and PS devices and to formulate design criteria for improved performance. As will be shown, the corresponding devices exhibit distinctly different sensitivities to their functional parameters. For example, under conditions ofmore » optimal light absorption, carrier lifetimes, and electrochemical rates, the performance of PCs is limited only by their surface area, while type 1 PS devices are limited by their carrier mobility and mass transport, and type 2 PS devices are limited by electrochemical charge-transfer selectivity. Strategies for the optimization of type 1 and 2 photosynthetic devices and photocatalysts are also discussed.« less

Photocatalysis versus photosynthesis: A sensitivity analysis of devices for solar energy conversion and chemical transformations

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

Osterloh, Frank E.

Here, the chemical literature often does not differentiate between photocatalytic (PC) and photosynthetic (PS) processes (including artificial photosynthesis) even though these reactions differ in their thermodynamics. Photocatalytic processes are thermodynamically downhill (ΔG < 0) and are merely accelerated by the catalyst, whereas photosynthetic processes are thermodynamically unfavorable (ΔG > 0) and require photochemical energy input to occur. Here we apply this differentiation to analyze the basic functions of PC and PS devices and to formulate design criteria for improved performance. As will be shown, the corresponding devices exhibit distinctly different sensitivities to their functional parameters. For example, under conditions ofmore » optimal light absorption, carrier lifetimes, and electrochemical rates, the performance of PCs is limited only by their surface area, while type 1 PS devices are limited by their carrier mobility and mass transport, and type 2 PS devices are limited by electrochemical charge-transfer selectivity. Strategies for the optimization of type 1 and 2 photosynthetic devices and photocatalysts are also discussed.« less

Thermodynamic evidence for Ca2+-mediated self-aggregation of Lewis X gold glyconanoparticles. A model for cell adhesion via carbohydrate-carbohydrate interaction.

PubMed

de la Fuente, Jesús M; Eaton, Peter; Barrientos, Africa G; Menéndez, Margarita; Penadés, Soledad

2005-05-04

Thermodynamic evidence for the selective Ca(2+)-mediated self-aggregation via carbohydrate-carbohydrate interactions of gold glyconanoparticles functionalized with the disaccharides lactose (lacto-Au) and maltose (malto-Au), or the biologically relevant trisaccharide Lewis X (Le(X)-Au), was obtained by isothermal titration calorimetry. The aggregation process was also directly visualized by atomic force microscopy. It was shown in the case of the trisaccharide Lewis X that the Ca(2+)-mediated aggregation is a slow process that takes place with a decrease in enthalpy of 160 +/- 30 kcal mol(-)(1), while the heat evolved in the case of lactose and maltose glyconanoparticles was very low and thermal equilibrium was quickly achieved. Measurements in the presence of Mg(2+) and Na(+) cations confirm the selectivity for Ca(2+) of Le(X)-Au glyconanoparticles. The relevance of this result to cell-cell adhesion process mediated by carbohydrate-carbohydrate interactions is discussed.

The EUVE Proposal Database

NASA Astrophysics Data System (ADS)

Christian, C. A.; Olson, E. C.

1993-01-01

The proposal database and scheduling system for the Extreme Ultraviolet Explorer is described. The proposal database has been implemented to take input for approved observations selected by the EUVE Peer Review Panel and output target information suitable for the scheduling system to digest. The scheduling system is a hybrid of the SPIKE program and EUVE software which checks spacecraft constraints, produces a proposed schedule and selects spacecraft orientations with optimal configurations for acquiring star trackers, etc. This system is used to schedule the In Orbit Calibration activities that took place this summer, following the EUVE launch in early June 1992. The strategy we have implemented has implications for the selection of approved targets, which have impacted the Peer Review process. In addition, we will discuss how the proposal database, founded on Sybase, controls the processing of EUVE Guest Observer data.

Development of a database system for operational use in the selection of titanium alloys

NASA Astrophysics Data System (ADS)

Han, Yuan-Fei; Zeng, Wei-Dong; Sun, Yu; Zhao, Yong-Qing

2011-08-01

The selection of titanium alloys has become a complex decision-making task due to the growing number of creation and utilization for titanium alloys, with each having its own characteristics, advantages, and limitations. In choosing the most appropriate titanium alloys, it is very essential to offer a reasonable and intelligent service for technical engineers. One possible solution of this problem is to develop a database system (DS) to help retrieve rational proposals from different databases and information sources and analyze them to provide useful and explicit information. For this purpose, a design strategy of the fuzzy set theory is proposed, and a distributed database system is developed. Through ranking of the candidate titanium alloys, the most suitable material is determined. It is found that the selection results are in good agreement with the practical situation.

National Rehabilitation Information Center

MedlinePlus

... search the NARIC website or one of our databases Select a database or search for a webpage A NARIC webpage ... Projects conducting research and/or development (NIDILRR Program Database). Organizations, agencies, and online resources that support people ...

Formation of nanoscale networks: selectively swelling amphiphilic block copolymers with CO2-expanded liquids

NASA Astrophysics Data System (ADS)

Gong, Jianliang; Zhang, Aijuan; Bai, Hua; Zhang, Qingkun; Du, Can; Li, Lei; Hong, Yanzhen; Li, Jun

2013-01-01

Polymeric films with nanoscale networks were prepared by selectively swelling an amphiphilic diblock copolymer, polystyrene-block-poly(4-vinylpyridine) (PS-b-P4VP), with the CO2-expanded liquid (CXL), CO2-methanol. The phase behavior of the CO2-methanol system was investigated by both theoretical calculation and experiments, revealing that methanol can be expanded by CO2, forming homogeneous CXL under the experimental conditions. When treated with the CO2-methanol system, the spin cast compact PS-b-P4VP film was transformed into a network with interconnected pores, in a pressure range of 12-20 MPa and a temperature range of 45-60 °C. The formation mechanism of the network, involving plasticization of PS and selective swelling of P4VP, was proposed. Because the diblock copolymer diffusion process is controlled by the activated hopping of individual block copolymer chains with the thermodynamic barrier for moving PVP segments from one to another, the formation of the network structures is achieved in a short time scale and shows ``thermodynamically restricted'' character. Furthermore, the resulting polymer networks were employed as templates, for the preparation of polypyrrole networks, by an electrochemical polymerization process. The prepared porous polypyrrole film was used to fabricate a chemoresistor-type gas sensor which showed high sensitivity towards ammonia.Polymeric films with nanoscale networks were prepared by selectively swelling an amphiphilic diblock copolymer, polystyrene-block-poly(4-vinylpyridine) (PS-b-P4VP), with the CO2-expanded liquid (CXL), CO2-methanol. The phase behavior of the CO2-methanol system was investigated by both theoretical calculation and experiments, revealing that methanol can be expanded by CO2, forming homogeneous CXL under the experimental conditions. When treated with the CO2-methanol system, the spin cast compact PS-b-P4VP film was transformed into a network with interconnected pores, in a pressure range of 12-20 MPa and a temperature range of 45-60 °C. The formation mechanism of the network, involving plasticization of PS and selective swelling of P4VP, was proposed. Because the diblock copolymer diffusion process is controlled by the activated hopping of individual block copolymer chains with the thermodynamic barrier for moving PVP segments from one to another, the formation of the network structures is achieved in a short time scale and shows ``thermodynamically restricted'' character. Furthermore, the resulting polymer networks were employed as templates, for the preparation of polypyrrole networks, by an electrochemical polymerization process. The prepared porous polypyrrole film was used to fabricate a chemoresistor-type gas sensor which showed high sensitivity towards ammonia. Electronic supplementary information (ESI) available. See DOI: 10.1039/c2nr33188h

Drug-binding energetics of human α-1-acid glycoprotein assessed by isothermal titration calorimetry and molecular docking simulations

PubMed Central

Huang, Johnny X.; Cooper, Matthew A.; Baker, Mark A.; Azad, Mohammad A.K.; Nation, Roger L.; Li, Jian; Velkov, Tony

2012-01-01

This study utilizes sensitive, modern isothermal titration calorimetric (ITC) methods to characterize the microscopic thermodynamic parameters that drive the binding of basic drugs to α-1-acid glycoprotein (AGP) and thereby rationalize the thermodynamic data in relation to docking models and crystallographic structures of the drug-AGP complexes. The binding of basic compounds from the tricyclic antidepressant series, together with miaserine, chlorpromazine, disopyramide and cimetidine all displayed an exothermically driven binding interaction with AGP. The impact of protonation/deprotonation events, ionic strength, temperature and the individual selectivity of the A and F1*S AGP variants on drug-binding thermodynamics were characterized. A correlation plot of the thermodynamic parameters for all of the test compounds revealed enthalpy-entropy compensation is in effect. The exothermic binding energetics of the test compounds were driven by a combination of favorable (negative) enthalpic (ΔH°) and favorable (positive) entropic (ΔS°) contributions to the Gibbs free energy (ΔG°). Collectively, the data imply that the free energies that drive drug binding to AGP and its relationship to drug-serum residency evolve from the complex interplay of enthalpic and entropic forces from interactions with explicit combinations of hydrophobic and polar side-chain sub-domains within the multi-lobed AGP ligand binding cavity. PMID:23192962

Analysis of energetically biased transcripts of viruses and transposable elements

PubMed Central

Secolin, Rodrigo; Pascoal, Vinícius D’Ávila Bitencourt; Lopes-Cendes, Iscia; Pereira, Tiago Campos

2012-01-01

RNA interference (RNAi) is a natural endogenous process by which double-stranded RNA molecules trigger potent and specific gene silencing in eukaryotic cells and is characterized by target RNA cleavage. In mammals, small interfering RNAs (siRNAs) are the trigger molecules of choice and constitute a new class of RNA-based antiviral agents. In an efficient RNAi response, the antisense strand of siRNAs must enter the RNA-induced silencing complex (RISC) in a process mediated by thermodynamic features. In this report, we hypothesize that silent mutations capable of inverting thermodynamic properties can promote resistance to siRNAs. Extensive computational analyses were used to assess whether continuous selective pressure that promotes such mutations could lead to the emergence of viral strains completely resistant to RNAi (i.e., prone to transfer only the sense strands to RISC). Based on our findings, we propose that, although synonymous mutations may produce functional resistance, this strategy cannot be systematically adopted by viruses since the longest RNAi-refractory sequence is only 10 nt long. This finding also suggests that all mRNAs display fluctuating thermodynamic landscapes and that, in terms of thermodynamic features, RNAi is a very efficient antiviral system since there will always be sites susceptible to siRNAs. PMID:23271949

Practical thermodynamic quantities for aqueous vanadium- and iron-based flow batteries

DOE PAGES

Hudak, Nicholas S.

2013-12-31

A simple method for experimentally determining thermodynamic quantities for flow battery cell reactions is presented. Equilibrium cell potentials, temperature derivatives of cell potential (d E/d T), Gibbs free energies, and entropies are reported here for all-vanadium, iron–vanadium, and iron–chromium flow cells with state-of-the-art solution compositions. Proof is given that formal potentials and formal temperature coefficients can be used with modified forms of the Nernst Equation to quantify the thermodynamics of flow cell reactions as a function of state-of-charge. Such empirical quantities can be used in thermo-electrochemical models of flow batteries at the cell or system level. In most cases, themore » thermodynamic quantities measured here are significantly different from standard values reported and used previously in the literature. The data reported here are also useful in the selection of operating temperatures for flow battery systems. Because higher temperatures correspond to lower equilibrium cell potentials for the battery chemistries studied here, it can be beneficial to charge a cell at higher temperature and discharge at lower temperature. As a result, proof-of-concept of improved voltage efficiency with the use of such non-isothermal cycling is given for the all-vanadium redox flow battery, and the effect is shown to be more pronounced at lower current densities.« less

Origin of fatty acid synthesis - Thermodynamics and kinetics of reaction pathways

NASA Technical Reports Server (NTRS)

Weber, Arthur L.

1991-01-01

The primitiveness of contemporary fatty acid biosynthesis was evaluated by using the thermodynamics and kinetics of its component reactions to estimate the extent of its dependence on powerful and selective catalysis by enzymes. Since this analysis indicated that the modern pathway is not primitive because it requires sophisticated enzymatic catalysis, an alternative pathway of primitive fatty acid synthesis is proposed that uses glycolaldehyde as a substrate. In contrast to the modern pathway, this primitive pathway is not dependent on an exogenous source of phosphoanhydride energy. Furthermore, the chemical spontaneity of its reactions suggests that it could have been readily catalyzed by the rudimentary biocatalysts available at an early stage in the origin of life.

Thermodynamic Properties of Low-Density {}^{132}Xe Gas in the Temperature Range 165-275 K

NASA Astrophysics Data System (ADS)

Akour, Abdulrahman

2018-01-01

The method of static fluctuation approximation was used to calculate selected thermodynamic properties (internal energy, entropy, energy capacity, and pressure) for xenon in a particularly low-temperature range (165-270 K) under different conditions. This integrated microscopic study started from an initial basic assumption as the main input. The basic assumption in this method was to replace the local field operator with its mean value, then numerically solve a closed set of nonlinear equations using an iterative method, considering the Hartree-Fock B2-type dispersion potential as the most appropriate potential for xenon. The results are in very good agreement with those of an ideal gas.

Two Student Self-Management Techniques Applied to Data-Based Program Modification.

ERIC Educational Resources Information Center

Wesson, Caren

Two student self-management techniques, student charting and student selection of instructional activities, were applied to ongoing data-based program modification. Forty-two elementary school resource room students were assigned randomly (within teacher) to one of three treatment conditions: Teacher Chart-Teacher Select Instructional Activities…

Severe Weather Environments in Atmospheric Reanalyses

NASA Astrophysics Data System (ADS)

King, A. T.; Kennedy, A. D.

2017-12-01

Atmospheric reanalyses combine historical observation data using a fixed assimilation scheme to achieve a dynamically coherent representation of the atmosphere. How well these reanalyses represent severe weather environments via proxies is poorly defined. To quantify the performance of reanalyses, a database of proximity soundings near severe storms from the Rapid Update Cycle 2 (RUC-2) model will be compared to a suite of reanalyses including: North American Reanalysis (NARR), European Interim Reanalysis (ERA-Interim), 2nd Modern-Era Retrospective Reanalysis for Research and Applications (MERRA-2), Japanese 55-year Reanalysis (JRA-55), 20th Century Reanalysis (20CR), and Climate Forecast System Reanalysis (CFSR). A variety of severe weather parameters will be calculated from these soundings including: convective available potential energy (CAPE), storm relative helicity (SRH), supercell composite parameter (SCP), and significant tornado parameter (STP). These soundings will be generated using the SHARPpy python module, which is an open source tool used to calculate severe weather parameters. Preliminary results indicate that the NARR and JRA55 are significantly more skilled at producing accurate severe weather environments than the other reanalyses. The primary difference between these two reanalyses and the remaining reanalyses is a significant negative bias for thermodynamic parameters. To facilitate climatological studies, the scope of work will be expanded to compute these parameters for the entire domain and duration of select renalyses. Preliminary results from this effort will be presented and compared to observations at select locations. This dataset will be made pubically available to the larger scientific community, and details of this product will be provided.

Development of microwave rainfall retrieval algorithm for climate applications

NASA Astrophysics Data System (ADS)

KIM, J. H.; Shin, D. B.

2014-12-01

With the accumulated satellite datasets for decades, it is possible that satellite-based data could contribute to sustained climate applications. Level-3 products from microwave sensors for climate applications can be obtained from several algorithms. For examples, the Microwave Emission brightness Temperature Histogram (METH) algorithm produces level-3 rainfalls directly, whereas the Goddard profiling (GPROF) algorithm first generates instantaneous rainfalls and then temporal and spatial averaging process leads to level-3 products. The rainfall algorithm developed in this study follows a similar approach to averaging instantaneous rainfalls. However, the algorithm is designed to produce instantaneous rainfalls at an optimal resolution showing reduced non-linearity in brightness temperature (TB)-rain rate(R) relations. It is found that the resolution tends to effectively utilize emission channels whose footprints are relatively larger than those of scattering channels. This algorithm is mainly composed of a-priori databases (DBs) and a Bayesian inversion module. The DB contains massive pairs of simulated microwave TBs and rain rates, obtained by WRF (version 3.4) and RTTOV (version 11.1) simulations. To improve the accuracy and efficiency of retrieval process, data mining technique is additionally considered. The entire DB is classified into eight types based on Köppen climate classification criteria using reanalysis data. Among these sub-DBs, only one sub-DB which presents the most similar physical characteristics is selected by considering the thermodynamics of input data. When the Bayesian inversion is applied to the selected DB, instantaneous rain rate with 6 hours interval is retrieved. The retrieved monthly mean rainfalls are statistically compared with CMAP and GPCP, respectively.

S2RSLDB: a comprehensive manually curated, internet-accessible database of the sigma-2 receptor selective ligands.

PubMed

Nastasi, Giovanni; Miceli, Carla; Pittalà, Valeria; Modica, Maria N; Prezzavento, Orazio; Romeo, Giuseppe; Rescifina, Antonio; Marrazzo, Agostino; Amata, Emanuele

2017-01-01

Sigma (σ) receptors are accepted as a particular receptor class consisting of two subtypes: sigma-1 (σ 1 ) and sigma-2 (σ 2 ). The two receptor subtypes have specific drug actions, pharmacological profiles and molecular characteristics. The σ 2 receptor is overexpressed in several tumor cell lines, and its ligands are currently under investigation for their role in tumor diagnosis and treatment. The σ 2 receptor structure has not been disclosed, and researchers rely on σ 2 receptor radioligand binding assay to understand the receptor's pharmacological behavior and design new lead compounds. Here we present the sigma-2 Receptor Selective Ligands Database (S2RSLDB) a manually curated database of the σ 2 receptor selective ligands containing more than 650 compounds. The database is built with chemical structure information, radioligand binding affinity data, computed physicochemical properties, and experimental radioligand binding procedures. The S2RSLDB is freely available online without account login and having a powerful search engine the user may build complex queries, sort tabulated results, generate color coded 2D and 3D graphs and download the data for additional screening. The collection here reported is extremely useful for the development of new ligands endowed of σ 2 receptor affinity, selectivity, and appropriate physicochemical properties. The database will be updated yearly and in the near future, an online submission form will be available to help with keeping the database widely spread in the research community and continually updated. The database is available at http://www.researchdsf.unict.it/S2RSLDB.

Development and Operation of a Database Machine for Online Access and Update of a Large Database.

ERIC Educational Resources Information Center

Rush, James E.

1980-01-01

Reviews the development of a fault tolerant database processor system which replaced OCLC's conventional file system. A general introduction to database management systems and the operating environment is followed by a description of the hardware selection, software processes, and system characteristics. (SW)

A Comparison of Selected Bibliographic Database Subject Overlap for Agricultural Information

ERIC Educational Resources Information Center

Ritchie, Stephanie M.; Young, Lauren M.; Sigman, Jessica

2018-01-01

Agricultural researchers and science librarians must understand which research literature databases provide the most comprehensive coverage of agricultural subjects to support their inquiries. Once the domain of a few specialized databases, agricultural research literature is now covered by broad, multidisciplinary databases. The purpose of this…

Thermodynamic evaluation of the solidification phase of molten core-concrete under estimated Fukushima Daiichi nuclear power plant accident conditions

NASA Astrophysics Data System (ADS)

Kitagaki, Toru; Yano, Kimihiko; Ogino, Hideki; Washiya, Tadahiro

2017-04-01

The solidification phases of molten core-concrete under the estimated molten core-concrete interaction (MCCI) conditions in the Fukushima Daiichi Nuclear Power Plant Unit 1 were predicted using the thermodynamic equilibrium calculation tool, FactSage 6.2, and the NUCLEA database in order to contribute toward the 1F decommissioning work and to understand the accident progression via the analytical results for the 1F MCCI products. We showed that most of the U and Zr in the molten core-concrete forms (U,Zr)O2 and (Zr,U)SiO4, and the formation of other phases with these elements is limited. However, the formation of (Zr,U)SiO4 requires a relatively long time because it involves a change in the crystal structure from fcc-(U,Zr)O2 to tet-(U,Zr)O2, followed by the formation of (Zr,U)SiO4 by reaction with SiO2. Therefore, the formation of (Zr,U)SiO4 is limited under quenching conditions. Other common phases are the oxide phases, CaAl2Si2O8, SiO2, and CaSiO3, and the metallic phases of the Fe-Si and Fe-Ni alloys. The solidification phenomenon of the crust under quenching conditions and that of the molten pool under thermodynamic equilibrium conditions in the 1F MCCI progression are discussed.

Calculation of the relative metastabilities of proteins using the CHNOSZ software package

PubMed Central

Dick, Jeffrey M

2008-01-01

Background Proteins of various compositions are required by organisms inhabiting different environments. The energetic demands for protein formation are a function of the compositions of proteins as well as geochemical variables including temperature, pressure, oxygen fugacity and pH. The purpose of this study was to explore the dependence of metastable equilibrium states of protein systems on changes in the geochemical variables. Results A software package called CHNOSZ implementing the revised Helgeson-Kirkham-Flowers (HKF) equations of state and group additivity for ionized unfolded aqueous proteins was developed. The program can be used to calculate standard molal Gibbs energies and other thermodynamic properties of reactions and to make chemical speciation and predominance diagrams that represent the metastable equilibrium distributions of proteins. The approach takes account of the chemical affinities of reactions in open systems characterized by the chemical potentials of basis species. The thermodynamic database included with the package permits application of the software to mineral and other inorganic systems as well as systems of proteins or other biomolecules. Conclusion Metastable equilibrium activity diagrams were generated for model cell-surface proteins from archaea and bacteria adapted to growth in environments that differ in temperature and chemical conditions. The predicted metastable equilibrium distributions of the proteins can be compared with the optimal growth temperatures of the organisms and with geochemical variables. The results suggest that a thermodynamic assessment of protein metastability may be useful for integrating bio- and geochemical observations. PMID:18834534

The use of database management systems and artificial intelligence in automating the planning of optical navigation pictures

NASA Technical Reports Server (NTRS)

Davis, Robert P.; Underwood, Ian M.

1987-01-01

The use of database management systems (DBMS) and AI to minimize human involvement in the planning of optical navigation pictures for interplanetary space probes is discussed, with application to the Galileo mission. Parameters characterizing the desirability of candidate pictures, and the program generating them, are described. How these parameters automatically build picture records in a database, and the definition of the database structure, are then discussed. The various rules, priorities, and constraints used in selecting pictures are also described. An example is provided of an expert system, written in Prolog, for automatically performing the selection process.

Pharmaceutical Cocrystals: Regulatory and Strategic Aspects, Design and Development

PubMed Central

Gadade, Dipak Dilip; Pekamwar, Sanjay Sudhakar

2016-01-01

Cocrystal is a concept of the supramolecular chemistry which is gaining the extensive interest of researchers from pharmaceutical and chemical sciences and of drug regulatory agencies. The prominent reason of which is its ability to modify physicochemical properties of active pharmaceutical ingredients. During the development of the pharmaceutical product, formulators have to optimize the physicochemical properties of active pharmaceutical ingredients. Pharmaceutical cocrystals can be employed to improve vital physicochemical characteristics of a drug, including solubility, dissolution, bioavailability and stability of pharmaceutical compounds while maintaining its therapeutic activity. It is advantageous being a green synthesis approach for production of pharmaceutical compounds. The formation polymorphic forms, solvates, hydrates and salts of cocrystals during the synthesis reported in the literature which can be a potential issue in the development of pharmaceutical cocrystals. The approaches like hydrogen bonding rules, solubility parameters, screening through the CSD database or thermodynamic characteristics can be utilized for the rational design of cocrystals and selection of coformers for synthesis multi-component cocrystals. Considering the significance of pharmaceutical cocrystals pharmaceutical regulatory authorities in the United States and Europe issued guidance documents which may be helpful for pharmaceutical product registration in these regions. In this article, we deal with the design, synthesis, strategic aspects and characteristics of cocrystals along perspectives on its regulatory and intellectual property considerations. PMID:28101455

Weathering Patterns of Ignitable Liquids with the Advanced Distillation Curve Method

PubMed Central

Bruno, Thomas J; Allen, Samuel

2013-01-01

One can take advantage of the striking similarity of ignitable liquid vaporization (or weathering) patterns and the separation observed during distillation to predict the composition of residual compounds in fire debris. This is done with the advanced distillation curve (ADC) metrology, which separates a complex fluid by distillation into fractions that are sampled, and for which thermodynamically consistent temperatures are measured at atmospheric pressure. The collected sample fractions can be analyzed by any method that is appropriate. Analytical methods we have applied include gas chromatography (with flame ionization, mass spectrometric and sulfur chemiluminescence detection), thin layer chromatography, FTIR, Karl Fischer coulombic titrimetry, refractometry, corrosivity analysis, neutron activation analysis and cold neutron prompt gamma activation analysis. We have applied this method on product streams such as finished fuels (gasoline, diesel fuels, aviation fuels, rocket propellants), crude oils (including a crude oil made from swine manure) and waste oils streams (used automotive and transformer oils). In this paper, we present results on a variety of ignitable liquids that are not commodity fuels, chosen from the Ignitable Liquids Reference Collection (ILRC). These measurements are assembled into a preliminary database. From this selection, we discuss the significance and forensic application of the temperature data grid and the composition explicit data channel of the ADC. PMID:26401423

New support vector machine-based method for microRNA target prediction.

PubMed

Li, L; Gao, Q; Mao, X; Cao, Y

2014-06-09

MicroRNA (miRNA) plays important roles in cell differentiation, proliferation, growth, mobility, and apoptosis. An accurate list of precise target genes is necessary in order to fully understand the importance of miRNAs in animal development and disease. Several computational methods have been proposed for miRNA target-gene identification. However, these methods still have limitations with respect to their sensitivity and accuracy. Thus, we developed a new miRNA target-prediction method based on the support vector machine (SVM) model. The model supplies information of two binding sites (primary and secondary) for a radial basis function kernel as a similarity measure for SVM features. The information is categorized based on structural, thermodynamic, and sequence conservation. Using high-confidence datasets selected from public miRNA target databases, we obtained a human miRNA target SVM classifier model with high performance and provided an efficient tool for human miRNA target gene identification. Experiments have shown that our method is a reliable tool for miRNA target-gene prediction, and a successful application of an SVM classifier. Compared with other methods, the method proposed here improves the sensitivity and accuracy of miRNA prediction. Its performance can be further improved by providing more training examples.

Weathering Patterns of Ignitable Liquids with the Advanced Distillation Curve Method.

PubMed

Bruno, Thomas J; Allen, Samuel

2013-01-01

One can take advantage of the striking similarity of ignitable liquid vaporization (or weathering) patterns and the separation observed during distillation to predict the composition of residual compounds in fire debris. This is done with the advanced distillation curve (ADC) metrology, which separates a complex fluid by distillation into fractions that are sampled, and for which thermodynamically consistent temperatures are measured at atmospheric pressure. The collected sample fractions can be analyzed by any method that is appropriate. Analytical methods we have applied include gas chromatography (with flame ionization, mass spectrometric and sulfur chemiluminescence detection), thin layer chromatography, FTIR, Karl Fischer coulombic titrimetry, refractometry, corrosivity analysis, neutron activation analysis and cold neutron prompt gamma activation analysis. We have applied this method on product streams such as finished fuels (gasoline, diesel fuels, aviation fuels, rocket propellants), crude oils (including a crude oil made from swine manure) and waste oils streams (used automotive and transformer oils). In this paper, we present results on a variety of ignitable liquids that are not commodity fuels, chosen from the Ignitable Liquids Reference Collection (ILRC). These measurements are assembled into a preliminary database. From this selection, we discuss the significance and forensic application of the temperature data grid and the composition explicit data channel of the ADC.

Pharmaceutical Cocrystals: Regulatory and Strategic Aspects, Design and Development.

PubMed

Gadade, Dipak Dilip; Pekamwar, Sanjay Sudhakar

2016-12-01

Cocrystal is a concept of the supramolecular chemistry which is gaining the extensive interest of researchers from pharmaceutical and chemical sciences and of drug regulatory agencies. The prominent reason of which is its ability to modify physicochemical properties of active pharmaceutical ingredients. During the development of the pharmaceutical product, formulators have to optimize the physicochemical properties of active pharmaceutical ingredients. Pharmaceutical cocrystals can be employed to improve vital physicochemical characteristics of a drug, including solubility, dissolution, bioavailability and stability of pharmaceutical compounds while maintaining its therapeutic activity. It is advantageous being a green synthesis approach for production of pharmaceutical compounds. The formation polymorphic forms, solvates, hydrates and salts of cocrystals during the synthesis reported in the literature which can be a potential issue in the development of pharmaceutical cocrystals. The approaches like hydrogen bonding rules, solubility parameters, screening through the CSD database or thermodynamic characteristics can be utilized for the rational design of cocrystals and selection of coformers for synthesis multi-component cocrystals. Considering the significance of pharmaceutical cocrystals pharmaceutical regulatory authorities in the United States and Europe issued guidance documents which may be helpful for pharmaceutical product registration in these regions. In this article, we deal with the design, synthesis, strategic aspects and characteristics of cocrystals along perspectives on its regulatory and intellectual property considerations.

Microstructure Modeling of 3rd Generation Disk Alloys

NASA Technical Reports Server (NTRS)

Jou, Herng-Jeng

2010-01-01

The objective of this program is to model, validate, and predict the precipitation microstructure evolution, using PrecipiCalc (QuesTek Innovations LLC) software, for 3rd generation Ni-based gas turbine disc superalloys during processing and service, with a set of logical and consistent experiments and characterizations. Furthermore, within this program, the originally research-oriented microstructure simulation tool will be further improved and implemented to be a useful and user-friendly engineering tool. In this report, the key accomplishment achieved during the second year (2008) of the program is summarized. The activities of this year include final selection of multicomponent thermodynamics and mobility databases, precipitate surface energy determination from nucleation experiment, multiscale comparison of predicted versus measured intragrain precipitation microstructure in quench samples showing good agreement, isothermal coarsening experiment and interaction of grain boundary and intergrain precipitates, primary microstructure of subsolvus treatment, and finally the software implementation plan for the third year of the project. In the following year, the calibrated models and simulation tools will be validated against an independently developed experimental data set, with actual disc heat treatment process conditions. Furthermore, software integration and implementation will be developed to provide material engineers valuable information in order to optimize the processing of the 3rd generation gas turbine disc alloys.

Thermodynamic analysis of the selective chlorination of electric arc furnace dust.

PubMed

Pickles, C A

2009-07-30

The remelting of automobile scrap in an electric arc furnace (EAF) results in the production of a dust, which contains high concentrations of the oxides of zinc, iron, calcium and other metals. Typically, the lead and zinc are of commercial value, while the other metals are not worth recovering. At the present time, EAF dusts are treated in high temperature Waelz rotary kiln-type processes, where the lead and zinc oxides are selectively reduced and simultaneously reoxidized and a crude zinc oxide is produced. Another alternative processing route is selective chlorination, in which the non-ferrous metals are preferentially chlorinated to their gaseous chlorides and in this manner separated from the iron. In the present research, a detailed thermodynamic analysis of this chlorination process has been performed and the following factors were investigated; temperature, amount of chlorine, lime content, silica content, presence of an inert gas and the oxygen potential. High lead and zinc recoveries as gaseous chlorides could be achieved but some of the iron oxide was also chlorinated. Additionally, the calcium oxide in the dust consumes chlorine, but this can be minimized by adding silica, which results in the formation of stable calcium silicates. The optimum conditions were determined for a typical dust composition. The selectivities achieved with chlorination were lower than those for reduction, as reported in the literature, but there are other advantages such as the potential recovery of copper.

Reassessment of Atomic Mobilities in fcc Cu-Ag-Sn System Aiming at Establishment of an Atomic Mobility Database in Sn-Ag-Cu-In-Sb-Bi-Pb Solder Alloys

NASA Astrophysics Data System (ADS)

Xu, Huixia; Zhang, Lijun; Cheng, Kaiming; Chen, Weimin; Du, Yong

2017-04-01

To establish an accurate atomic mobility database in solder alloys, a reassessment of atomic mobilities in the fcc (face centered cubic) Cu-Ag-Sn system was performed as reported in the present work. The work entailed initial preparation of three fcc Cu-Sn diffusion couples, which were used to determine the composition-dependent interdiffusivities at 873 K, 923 K, and 973 K, to validate the literature data and provide new experimental data at low temperatures. Then, atomic mobilities in three boundary binaries, fcc Cu-Sn, fcc Ag-Sn, and fcc Cu-Ag, were updated based on the data for various experimental diffusivities obtained from the literature and the present work, together with the available thermodynamic database for solder alloys. Finally, based on the large number of interdiffusivities recently measured from the present authors, atomic mobilities in the fcc Cu-Ag-Sn ternary system were carefully evaluated. A comprehensive comparison between various calculated/model-predicted diffusion properties and the experimental data was used to validate the reliability of the obtained atomic mobilities in ternary fcc Cu-Ag-Sn alloys.

Cohesive properties of (Cu,Ni)-(In,Sn) intermetallics: Database, electron-density correlations and interpretation of bonding trends

NASA Astrophysics Data System (ADS)

Ramos, S. B.; González Lemus, N. V.; Cabeza, G. F.; Fernández Guillermet, A.

2016-06-01

This paper presents a systematic and comparative study of the composition and volume dependence of the cohesive properties for a large group of Me-X intermetallic phases (IPs) with Me=Cu,Ni and X=In,Sn, which are of interest in relation with the design of lead-free soldering (LFS) alloys. The work relies upon a database with total-energy versus volume information developed by using projected augmented waves (PAW) calculations. In previous papers by the current authors it was shown that these results account satisfactorily for the direct and indirect experimental data available. In the present work, the database is further expanded to investigate the composition dependence of the volume (V0), and the composition and volume dependence of the bulk modulus (B0) and cohesive energy (Ecoh). On these bases, an analysis is performed of the systematic effects of replacing Cu by Ni in several Me-X phases (Me=Cu,Ni and X=In,Sn) reported as stable and metastable, as well as various hypothetical compounds involved in the thermodynamic modeling of IPs using the Compound-Energy Formalism. Moreover, it is shown that the cohesion-related quantities (B0/V0)½ and (Ecoh½/V0) can be correlated with a parameter expressing the number of valence electrons per unit volume. These findings are compared in detail with related relations involving the Miedema empirical electron density at the boundary of the Wigner-Seitz cell. In view of the co-variation of the cohesive properties, Ecoh is selected as a key property and its composition and structure dependence is examined in terms of a theoretical view of the bonding which involves the hybridization of the d-states of Cu or Ni with the s and p-states of In or Sn, for this class of compounds. In particular, a comparative analysis is performed of the DOS of various representative, iso-structural Me-X compounds. Various effects of relevance to understand the consequences of replacing Cu by Ni in LFS alloys are highlighted and explained microscopically for the first time.

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

PubMed Central

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

2014-01-01

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

Thermodynamic method for generating random stress distributions on an earthquake fault

USGS Publications Warehouse

Barall, Michael; Harris, Ruth A.

2012-01-01

This report presents a new method for generating random stress distributions on an earthquake fault, suitable for use as initial conditions in a dynamic rupture simulation. The method employs concepts from thermodynamics and statistical mechanics. A pattern of fault slip is considered to be analogous to a micro-state of a thermodynamic system. The energy of the micro-state is taken to be the elastic energy stored in the surrounding medium. Then, the Boltzmann distribution gives the probability of a given pattern of fault slip and stress. We show how to decompose the system into independent degrees of freedom, which makes it computationally feasible to select a random state. However, due to the equipartition theorem, straightforward application of the Boltzmann distribution leads to a divergence which predicts infinite stress. To avoid equipartition, we show that the finite strength of the fault acts to restrict the possible states of the system. By analyzing a set of earthquake scaling relations, we derive a new formula for the expected power spectral density of the stress distribution, which allows us to construct a computer algorithm free of infinities. We then present a new technique for controlling the extent of the rupture by generating a random stress distribution thousands of times larger than the fault surface, and selecting a portion which, by chance, has a positive stress perturbation of the desired size. Finally, we present a new two-stage nucleation method that combines a small zone of forced rupture with a larger zone of reduced fracture energy.

Suitability of polymer materials for production of pulmonary microparticles using a PGSS supercritical fluid technique: thermodynamic behaviour of fatty acids, PEGs and PEG-fatty acids.

PubMed

Vijayaraghavan, Meera; Stolnik, Snjezana; Howdle, Steven M; Illum, Lisbeth

2012-11-15

The thermodynamic behaviour of selected polymeric components for preparation of controlled release microparticles using supercritical carbon dioxide (scCO(2)) processing was investigated. The polymeric materials selected were egg lecithin (a model for the lung surfactant phospholipid), poly(ethyleneglycol) (PEG) of different molecular weights, fatty acids (C18, C16, and C14), and physical blends of PEGs and fatty acids. In addition a range of PEG-stearates was also assessed. Analysis of thermodynamic behaviour was performed by differential scanning calorimetry (DSC) and by assessment of their interaction with scCO(2) in a high-pressure variable volume view cell. The key criterion was to demonstrate a strong interaction with scCO(2) and to show liquefaction of the polymeric material at acceptable processing temperatures and pressures. Positive results should then indicate the suitability of these materials for processing by the Particle from Gas Saturated Solutions (PGSS) technique using scCO(2) to create microparticles for pulmonary administration. It was found that the materials tested interacted with scCO(2) and showed a sufficient lowering of their melting temperature (T(m)) to make them suitable for use in the PGSS microparticle production rig. Fatty acids of low T(m) were shown to act as a plasticising agent and to lower the T(m) of PEG further during interaction with scCO(2). Copyright © 2012 Elsevier B.V. All rights reserved.

Using population mixtures to optimize the utility of genomic databases: linkage disequilibrium and association study design in India.

PubMed

Pemberton, T J; Jakobsson, M; Conrad, D F; Coop, G; Wall, J D; Pritchard, J K; Patel, P I; Rosenberg, N A

2008-07-01

When performing association studies in populations that have not been the focus of large-scale investigations of haplotype variation, it is often helpful to rely on genomic databases in other populations for study design and analysis - such as in the selection of tag SNPs and in the imputation of missing genotypes. One way of improving the use of these databases is to rely on a mixture of database samples that is similar to the population of interest, rather than using the single most similar database sample. We demonstrate the effectiveness of the mixture approach in the application of African, European, and East Asian HapMap samples for tag SNP selection in populations from India, a genetically intermediate region underrepresented in genomic studies of haplotype variation.

The thermodynamic properties of benzothiazole and benzoxazole

NASA Astrophysics Data System (ADS)

Steele, W. V.; Chirico, R. D.; Knipmeyer, S. E.; Nguyen, A.

1991-08-01

This research program, funded by the Department of Energy, Office of Fossil Energy, Advanced Extraction and Process Technology, provides accurate experimental thermochemical and thermophysical properties for key organic diheteroatom-containing compounds present in heavy petroleum feedstocks, and applies the experimental information to thermodynamic analyses of key hydrodesulfurization, hydrodenitrogenation, and hydrodeoxygenation reaction networks. Thermodynamic analyses, based on accurate information, provide insights for the design of cost-effective methods of heteroatom removal. The results reported here, and in a companion report to be completed, will point the way to the development of new methods of heteroatom removal from heavy petroleum. Measurements leading to the calculation of the ideal-gas thermodynamic properties are reported for benzothiazole and benzoxazole. Experimental methods included combustion calorimetry, adiabatic heat-capacity calorimetry, comparative ebulliometry, inclinded-piston gauge manometry, and differential-scanning calorimetry (d.s.c). Critical property estimates are made for both compounds. Entropies, enthalpies, and Gibbs energies of formation were derived for the ideal gas for both compounds for selected temperatures between 280 K and near 650 K. The Gibbs energies of formation will be used in a subsequent report in thermodynamic calculations to study the reaction pathways for the removal of the heteratoms by hydrogenolysis. The results obtained in this research are compared with values present in the literature. The failure of a previous adiabatic heat capacity study to see the phase transition in benzothiazole is noted. Literature vibrational frequency assignments were used to calculate ideal gas entropies in the temperature range reported here for both compounds. Resulting large deviations show the need for a revision of those assignments.

Expanding the use of administrative claims databases in conducting clinical real-world evidence studies in multiple sclerosis.

PubMed

Capkun, Gorana; Lahoz, Raquel; Verdun, Elisabetta; Song, Xue; Chen, Weston; Korn, Jonathan R; Dahlke, Frank; Freitas, Rita; Fraeman, Kathy; Simeone, Jason; Johnson, Barbara H; Nordstrom, Beth

2015-05-01

Administrative claims databases provide a wealth of data for assessing the effect of treatments in clinical practice. Our aim was to propose methodology for real-world studies in multiple sclerosis (MS) using these databases. In three large US administrative claims databases: MarketScan, PharMetrics Plus and Department of Defense (DoD), patients with MS were selected using an algorithm identified in the published literature and refined for accuracy. Algorithms for detecting newly diagnosed ('incident') MS cases were also refined and tested. Methodology based on resource and treatment use was developed to differentiate between relapses with and without hospitalization. When various patient selection criteria were applied to the MarketScan database, an algorithm requiring two MS diagnoses at least 30 days apart was identified as the preferred method of selecting patient cohorts. Attempts to detect incident MS cases were confounded by the limited continuous enrollment of patients in these databases. Relapse detection algorithms identified similar proportions of patients in the MarketScan and PharMetrics Plus databases experiencing relapses with (2% in both databases) and without (15-20%) hospitalization in the 1 year follow-up period, providing findings in the range of those in the published literature. Additional validation of the algorithms proposed here would increase their credibility. The methods suggested in this study offer a good foundation for performing real-world research in MS using administrative claims databases, potentially allowing evidence from different studies to be compared and combined more systematically than in current research practice.

Astrophysical fluid simulations of thermally ideal gases with non-constant adiabatic index: numerical implementation

NASA Astrophysics Data System (ADS)

Vaidya, B.; Mignone, A.; Bodo, G.; Massaglia, S.

2015-08-01

Context. An equation of state (EoS) is a relation between thermodynamic state variables and it is essential for closing the set of equations describing a fluid system. Although an ideal EoS with a constant adiabatic index Γ is the preferred choice owing to its simplistic implementation, many astrophysical fluid simulations may benefit from a more sophisticated treatment that can account for diverse chemical processes. Aims: In the present work we first review the basic thermodynamic principles of a gas mixture in terms of its thermal and caloric EoS by including effects like ionization, dissociation, and temperature dependent degrees of freedom such as molecular vibrations and rotations. The formulation is revisited in the context of plasmas that are either in equilibrium conditions (local thermodynamic- or collisional excitation-equilibria) or described by non-equilibrium chemistry coupled to optically thin radiative cooling. We then present a numerical implementation of thermally ideal gases obeying a more general caloric EoS with non-constant adiabatic index in Godunov-type numerical schemes. Methods: We discuss the necessary modifications to the Riemann solver and to the conversion between total energy and pressure (or vice versa) routinely invoked in Godunov-type schemes. We then present two different approaches for computing the EoS. The first employs root-finder methods and it is best suited for EoS in analytical form. The second is based on lookup tables and interpolation and results in a more computationally efficient approach, although care must be taken to ensure thermodynamic consistency. Results: A number of selected benchmarks demonstrate that the employment of a non-ideal EoS can lead to important differences in the solution when the temperature range is 500-104 K where dissociation and ionization occur. The implementation of selected EoS introduces additional computational costs although the employment of lookup table methods (when possible) can significantly reduce the overhead by a factor of ~ 3-4.

Anti-proliferative and apoptosis induction activities of extracts from Thai medicinal plant recipes selected from MANOSROI II database.

PubMed

Manosroi, Jiradej; Sainakham, Mathukorn; Manosroi, Worapaka; Manosroi, Aranya

2012-05-07

ETHONOPHARMACOLOGICAL RELEVANCES: Traditional medicines have long been used by the Thai people. Several medicinal recipes prepared from a mixture of plants are often used by traditional medicinal practitioners for the treatment of many diseases including cancer. The recipes collected from the Thai medicinal text books were recorded in MANOSROI II database. Anticancer recipes were searched and selected by a computer program using the recipe indication keywords including Ma-reng and San which means cancer in Thai, from the database for anticancer activity investigation. To investigate anti-cancer activities of the Thai medicinal plant recipes selected from the "MANOSROI II" database. Anti-proliferative and apoptotic activities of extracts from 121 recipes selected from 56,137 recipes in the Thai medicinal plant recipe "MANOSROI II" database were investigated in two cancer cell lines including human mouth epidermal carcinoma (KB) and human colon adenocarcinoma (HT-29) cell lines using sulforhodamine B (SRB) assay and acridine orange (AO) and ethidium bromide (EB) staining technique, respectively. In the SRB assay, recipes NE028 and, S003 gave the highest anti-proliferation activity on KB and HT29 with the IC(50) values of 2.48±0.24 and 6.92±0.49μg/ml, respectively. In the AO/EB staining assay, recipes S016 and NE028 exhibited the highest apoptotic induction in KB and HT-29 cell lines, respectively. This study has demonstrated that the three Thai medicinal plant recipes selected from "MANOSROI II" database (NE028, S003 and S016) gave active anti-cancer activities according to the NCI classification which can be further developed for anti-cancer treatment. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

Collection Fusion Using Bayesian Estimation of a Linear Regression Model in Image Databases on the Web.

ERIC Educational Resources Information Center

Kim, Deok-Hwan; Chung, Chin-Wan

2003-01-01

Discusses the collection fusion problem of image databases, concerned with retrieving relevant images by content based retrieval from image databases distributed on the Web. Focuses on a metaserver which selects image databases supporting similarity measures and proposes a new algorithm which exploits a probabilistic technique using Bayesian…

National Online Meeting Proceedings (15th, New York, New York, May 10-12, 1994).

ERIC Educational Resources Information Center

1994

This proceedings contains 58 papers that were reviewed and selected for presentation at the 1994 National Online Meeting. The introduction, "Highlights of the Online/CD-ROM Database Industry: Implications of the Internet for Database Producers" by Martha E. Williams, provides statistics regarding databases, database records, database…

A User's Applications of Imaging Techniques: The University of Maryland Historic Textile Database.

ERIC Educational Resources Information Center

Anderson, Clarita S.

1991-01-01

Describes the incorporation of textile images into the University of Maryland Historic Textile Database by a computer user rather than a computer expert. Selection of a database management system is discussed, and PICTUREPOWER, a system that integrates photographic quality images with text and numeric information in databases, is described. (three…

An Examination of Selected Software Testing Tools: 1992

DTIC Science & Technology

1992-12-01

Report ....................................................... 27-19 Figure 27-17. Metrics Manager Database Full Report...historical test database , the test management and problem reporting tools were examined using the sample test database provided by each supplier. 4-4...track the impact of new methods, organi- zational structures, and technologies. Metrics Manager is supported by an industry database that allows

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

Jung, Haeryong; Lee, Eunyong; Jeong, YiYeong

Korea Radioactive-waste Management Corporation (KRMC) established in 2009 has started a new project to collect information on long-term stability of deep geological environments on the Korean Peninsula. The information has been built up in the integrated natural barrier database system available on web (www.deepgeodisposal.kr). The database system also includes socially and economically important information, such as land use, mining area, natural conservation area, population density, and industrial complex, because some of this information is used as exclusionary criteria during the site selection process for a deep geological repository for safe and secure containment and isolation of spent nuclear fuel andmore » other long-lived radioactive waste in Korea. Although the official site selection process has not been started yet in Korea, current integrated natural barrier database system and socio-economic database is believed that the database system will be effectively utilized to narrow down the number of sites where future investigation is most promising in the site selection process for a deep geological repository and to enhance public acceptance by providing readily-available relevant scientific information on deep geological environments in Korea. (authors)« less

Maize databases

USDA-ARS?s Scientific Manuscript database

This chapter is a succinct overview of maize data held in the species-specific database MaizeGDB (the Maize Genomics and Genetics Database), and selected multi-species data repositories, such as Gramene/Ensembl Plants, Phytozome, UniProt and the National Center for Biotechnology Information (NCBI), ...

Self Organizing Map-Based Classification of Cathepsin k and S Inhibitors with Different Selectivity Profiles Using Different Structural Molecular Fingerprints: Design and Application for Discovery of Novel Hits.

PubMed

Ihmaid, Saleh K; Ahmed, Hany E A; Zayed, Mohamed F; Abadleh, Mohammed M

2016-01-30

The main step in a successful drug discovery pipeline is the identification of small potent compounds that selectively bind to the target of interest with high affinity. However, there is still a shortage of efficient and accurate computational methods with powerful capability to study and hence predict compound selectivity properties. In this work, we propose an affordable machine learning method to perform compound selectivity classification and prediction. For this purpose, we have collected compounds with reported activity and built a selectivity database formed of 153 cathepsin K and S inhibitors that are considered of medicinal interest. This database has three compound sets, two K/S and S/K selective ones and one non-selective KS one. We have subjected this database to the selectivity classification tool 'Emergent Self-Organizing Maps' for exploring its capability to differentiate selective cathepsin inhibitors for one target over the other. The method exhibited good clustering performance for selective ligands with high accuracy (up to 100 %). Among the possibilites, BAPs and MACCS molecular structural fingerprints were used for such a classification. The results exhibited the ability of the method for structure-selectivity relationship interpretation and selectivity markers were identified for the design of further novel inhibitors with high activity and target selectivity.

Selective Solvent-Induced Stabilization of Polar Oxide Surfaces in an Electrochemical Environment

NASA Astrophysics Data System (ADS)

Yoo, Su-Hyun; Todorova, Mira; Neugebauer, Jörg

2018-02-01

The impact of an electrochemical environment on the thermodynamic stability of polar oxide surfaces is investigated for the example of ZnO(0001) surfaces immersed in water using density functional theory calculations. We show that solvation effects are highly selective: They have little effect on surfaces showing a metallic character, but largely stabilize semiconducting structures, particularly those that have a high electrostatic penalty in vacuum. The high selectivity is shown to have direct consequences for the surface phase diagram and explains, e.g., why certain surface structures could be observed only in an electrochemical environment.

Thermodynamic properties and atomic structure of Ca-based liquid alloys

NASA Astrophysics Data System (ADS)

Poizeau, Sophie

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

Information Retrieval in Telemedicine: a Comparative Study on Bibliographic Databases

PubMed Central

Ahmadi, Maryam; Sarabi, Roghayeh Ershad; Orak, Roohangiz Jamshidi; Bahaadinbeigy, Kambiz

2015-01-01

Background and Aims: The first step in each systematic review is selection of the most valid database that can provide the highest number of relevant references. This study was carried out to determine the most suitable database for information retrieval in telemedicine field. Methods: Cinhal, PubMed, Web of Science and Scopus databases were searched for telemedicine matched with Education, cost benefit and patient satisfaction. After analysis of the obtained results, the accuracy coefficient, sensitivity, uniqueness and overlap of databases were calculated. Results: The studied databases differed in the number of retrieved articles. PubMed was identified as the most suitable database for retrieving information on the selected topics with the accuracy and sensitivity ratios of 50.7% and 61.4% respectively. The uniqueness percent of retrieved articles ranged from 38% for Pubmed to 3.0% for Cinhal. The highest overlap rate (18.6%) was found between PubMed and Web of Science. Less than 1% of articles have been indexed in all searched databases. Conclusion: PubMed is suggested as the most suitable database for starting search in telemedicine and after PubMed, Scopus and Web of Science can retrieve about 90% of the relevant articles. PMID:26236086

Information Retrieval in Telemedicine: a Comparative Study on Bibliographic Databases.

PubMed

Ahmadi, Maryam; Sarabi, Roghayeh Ershad; Orak, Roohangiz Jamshidi; Bahaadinbeigy, Kambiz

2015-06-01

The first step in each systematic review is selection of the most valid database that can provide the highest number of relevant references. This study was carried out to determine the most suitable database for information retrieval in telemedicine field. Cinhal, PubMed, Web of Science and Scopus databases were searched for telemedicine matched with Education, cost benefit and patient satisfaction. After analysis of the obtained results, the accuracy coefficient, sensitivity, uniqueness and overlap of databases were calculated. The studied databases differed in the number of retrieved articles. PubMed was identified as the most suitable database for retrieving information on the selected topics with the accuracy and sensitivity ratios of 50.7% and 61.4% respectively. The uniqueness percent of retrieved articles ranged from 38% for Pubmed to 3.0% for Cinhal. The highest overlap rate (18.6%) was found between PubMed and Web of Science. Less than 1% of articles have been indexed in all searched databases. PubMed is suggested as the most suitable database for starting search in telemedicine and after PubMed, Scopus and Web of Science can retrieve about 90% of the relevant articles.

Predicting the thermodynamic stability of double-perovskite halides from density functional theory

DOE PAGES

Han, Dan; Zhang, Tao; Huang, Menglin; ...

2018-05-24

Recently, a series of double-perovskite halide compounds such as Cs 2AgBiCl 6 and Cs 2AgBiBr 6 have attracted intensive interest as promising alternatives to the solar absorber material CH 3NH 3PbI 3 because they are Pb-free and may exhibit enhanced stability. The thermodynamic stability of a number of double-perovskite halides has been predicted based on density functional theory (DFT) calculations of compound formation energies. In this paper, we found that the stability prediction can be dependent on the approximations used for the exchange-correlation functionals, e.g., the DFT calculations using the widely used Perdew, Burke, Ernzerhof (PBE) functional predict that Csmore » 2AgBiBr 6 is thermodynamically unstable against phase-separation into the competing phases such as AgBr, Cs 2AgBr 3, Cs 3Bi 2Br 9, etc., obviously inconsistent with the good stability observed experimentally. The incorrect prediction by the PBE calculation results from its failure to predict the correct ground-state structures of AgBr, AgCl, and CsCl. By contrast, the DFT calculations based on local density approximation, optB86b-vdW, and optB88-vdW functionals predict the ground-state structures of these binary halides correctly. Furthermore, the optB88-vdW functional is found to give the most accurate description of the lattice constants of the double-perovskite halides and their competing phases. Given these two aspects, we suggest that the optB88-vdW functional should be used for predicting thermodynamic stability in the future high-throughput computational material design or the construction of the Materials Genome database for new double-perovskite halides. As a result, using different exchange-correlation functionals has little influence on the dispersion of the conduction and the valence bands near the electronic bandgap; however, the calculated bandgap can be affected indirectly by the optimized lattice constant, which varies for different functionals.« less

Predicting the thermodynamic stability of double-perovskite halides from density functional theory

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

Han, Dan; Zhang, Tao; Huang, Menglin

Recently, a series of double-perovskite halide compounds such as Cs 2AgBiCl 6 and Cs 2AgBiBr 6 have attracted intensive interest as promising alternatives to the solar absorber material CH 3NH 3PbI 3 because they are Pb-free and may exhibit enhanced stability. The thermodynamic stability of a number of double-perovskite halides has been predicted based on density functional theory (DFT) calculations of compound formation energies. In this paper, we found that the stability prediction can be dependent on the approximations used for the exchange-correlation functionals, e.g., the DFT calculations using the widely used Perdew, Burke, Ernzerhof (PBE) functional predict that Csmore » 2AgBiBr 6 is thermodynamically unstable against phase-separation into the competing phases such as AgBr, Cs 2AgBr 3, Cs 3Bi 2Br 9, etc., obviously inconsistent with the good stability observed experimentally. The incorrect prediction by the PBE calculation results from its failure to predict the correct ground-state structures of AgBr, AgCl, and CsCl. By contrast, the DFT calculations based on local density approximation, optB86b-vdW, and optB88-vdW functionals predict the ground-state structures of these binary halides correctly. Furthermore, the optB88-vdW functional is found to give the most accurate description of the lattice constants of the double-perovskite halides and their competing phases. Given these two aspects, we suggest that the optB88-vdW functional should be used for predicting thermodynamic stability in the future high-throughput computational material design or the construction of the Materials Genome database for new double-perovskite halides. As a result, using different exchange-correlation functionals has little influence on the dispersion of the conduction and the valence bands near the electronic bandgap; however, the calculated bandgap can be affected indirectly by the optimized lattice constant, which varies for different functionals.« less

Concave Reagents. 20. Sterically Shielded m-Terphenyls as Selective Agents in General Protonations(1).

PubMed

Lüning, U.; Baumgartner, H.; Manthey, C.; Meynhardt, B.

1996-11-01

New m-terphenyls with acidic substituents in the 2'-position have been used in general protonations leading to reagent-controlled selectivity enhancements: up to 96:4 for the gamma/alpha-protonation of unsymmetrically substituted allyl anions, up to 97:3 for the protonation of cyclohexyl anions generating preferentially the thermodynamically less stable cis-products. In order to allow a general, reagent-controlled protonation the acidity of the protonating agent should be as low as possible.

Computational screening of functional groups for capture of toxic industrial chemicals in porous materials.

PubMed

Kim, Ki Chul; Fairen-Jimenez, David; Snurr, Randall Q

2017-12-06

A thermodynamic analysis using quantum chemical methods was carried out to identify optimal functional group candidates that can be included in metal-organic frameworks and activated carbons for the selective capture of toxic industrial chemicals (TICs) in humid air. We calculated the binding energies of 14 critical TICs plus water with a series of 10 functional groups attached to a naphthalene ring model. Using vibrational calculations, the free energies of adsorption were calculated in addition to the binding energies. Our results show that, in these systems, the binding energies and free energies follow similar trends. We identified copper(i) carboxylate as the optimal functional group (among those studied) for the selective binding of the majority of the TICs in humid air, and this functional group exhibits especially strong binding for sulfuric acid. Further thermodynamic analysis shows that the presence of water weakens the binding strength of sulfuric acid with the copper carboxylate group. Our calculations predict that functionalization of aromatic rings would be detrimental to selective capture of COCl 2 , CO 2 , and Cl 2 under humid conditions. Finally, we found that forming an ionic complex, H 3 O + HSO 4 - , between H 2 SO 4 and H 2 O via proton transfer is not favorable on copper carboxylate.

Transdermal delivery of diclofenac using water-in-oil microemulsion: formulation and mechanistic approach of drug skin permeation.

PubMed

Thakkar, Priyanka J; Madan, Parshotam; Lin, Senshang

2014-05-01

The objective of the present investigation was to enhance skin permeation of diclofenac using water-in-oil microemulsion and to elucidate its skin permeation mechanism. The w/o microemulsion formulations were selected based on constructed pseudoternary phase diagrams depending on water solubilization capacity and thermodynamic stability. These formulations were also subjected to physical characterization based on droplet size, viscosity, pH and conductivity. Permeation of diclofenac across rat skin using side-by-side permeation cells from selected w/o microemulsion formulations were evaluated and compared with control formulations. The selected w/o microemulsion formulations were thermodynamically stable, and incorporation of diclofenac sodium into microemulsion did not affect the phase behavior of system. All microemulsion formulations had very low viscosity (11-17 cps) and droplet size range of 30-160 nm. Microemulsion formulations exhibited statistically significant increase in diclofenac permeation compared to oily solution, aqueous solution and oil-Smix solution. Higher skin permeation of diclofenac was observed with low Smix concentration and smaller droplet size. Increase in diclofenac loading in aqueous phase decreased the partition of diclofenac. Diclofenac from the oil phase of microemulsion could directly partition into skin, while diclofenac from the aqueous droplets was carried through skin by carrier effect.

Energetic basis for selective recognition of T*G mismatched base pairs in DNA by imidazole-rich polyamides.

PubMed

Lacy, Eilyn R; Nguyen, Binh; Le, Minh; Cox, Kari K; OHare, Caroline; Hartley, John A; Lee, Moses; Wilson, W David

2004-01-01

To complement available structure and binding results and to develop a detailed understanding of the basis for selective molecular recognition of T.G mismatches in DNA by imidazole containing polyamides, a full thermodynamic profile for formation of the T.G-polyamide complex has been determined. The amide-linked heterocycles f-ImImIm and f-PyImIm (where f is formamido group, Im is imidazole and Py is pyrrole) were studied by using biosensor-surface plasmon resonance (SPR) and isothermal titration calorimetry (ITC) with a T.G mismatch containing DNA hairpin duplex and a similar DNA with only Watson-Crick base pairs. Large negative binding enthalpies for all of the polyamide-DNA complexes indicate that the interactions are enthalpically driven. SPR results show slower complex formation and stronger binding of f-ImImIm to the T.G than to the match site. The thermodynamic analysis indicates that the enhanced binding to the T.G site is the result of better entropic contributions. Negative heat capacity changes for the complex are correlated with calculated solvent accessible surface area changes and indicate hydrophobic contributions to complex formation. DNase I footprinting analysis in a long DNA sequence provided supporting evidence that f-ImImIm binds selectively to T.G mismatch sites.

Energetic basis for selective recognition of T·G mismatched base pairs in DNA by imidazole-rich polyamides

PubMed Central

Lacy, Eilyn R.; Nguyen, Binh; Le, Minh; Cox, Kari K.; O'Hare, Caroline; Hartley, John A.; Lee, Moses; Wilson, W. David

2004-01-01

To complement available structure and binding results and to develop a detailed understanding of the basis for selective molecular recognition of T·G mismatches in DNA by imidazole containing polyamides, a full thermodynamic profile for formation of the T·G–polyamide complex has been determined. The amide-linked heterocycles f-ImImIm and f-PyImIm (where f is formamido group, Im is imidazole and Py is pyrrole) were studied by using biosensor-surface plasmon resonance (SPR) and isothermal titration calorimetry (ITC) with a T·G mismatch containing DNA hairpin duplex and a similar DNA with only Watson–Crick base pairs. Large negative binding enthalpies for all of the polyamide–DNA complexes indicate that the interactions are enthalpically driven. SPR results show slower complex formation and stronger binding of f-ImImIm to the T·G than to the match site. The thermodynamic analysis indicates that the enhanced binding to the T·G site is the result of better entropic contributions. Negative heat capacity changes for the complex are correlated with calculated solvent accessible surface area changes and indicate hydrophobic contributions to complex formation. DNase I footprinting analysis in a long DNA sequence provided supporting evidence that f-ImImIm binds selectively to T·G mismatch sites. PMID:15064359

Synthesis of plutonium trifluoride by hydro-fluorination and novel thermodynamic data for the PuF3-LiF system

NASA Astrophysics Data System (ADS)

Tosolin, A.; Souček, P.; Beneš, O.; Vigier, J.-F.; Luzzi, L.; Konings, R. J. M.

2018-05-01

PuF3 was synthetized by hydro-fluorination of PuO2 and subsequent reduction of the product by hydrogenation. The obtained PuF3 was analysed by X-Ray Diffraction (XRD) and found phase-pure. High purity was also confirmed by the melting point analysis using Differential Scanning Calorimetry (DSC). PuF3 was then used for thermodynamic assessment of the PuF3-LiF system. Phase equilibrium points and enthalpy of fusion of the eutectic composition were measured by DSC. XRD analyses of selected samples after DSC measurement confirm that after solidification from the liquid, the system returns to a mixture of LiF and PuF3.

Atmospheric environment for Space Shuttle (STS-41D) launch

NASA Technical Reports Server (NTRS)

Johnson, D. L.; Hill, C. K.; Jasper, G.; Batts, G. W.

1984-01-01

Selected atmospheric conditions observed near Space Shuttle STS-41D launch time on August 30, 1984, at Kennedy Space Center, Florida are summarized. Values of ambient pressure, temperature, moisture, ground winds, visual observations (cloud), and winds aloft are included. The sequence of prelaunch Jimsphere measured vertical wind profiles is given as well as wind and thermodynamic parameters representative of surface and aloft conditions in the SRB descent/impact ocean area. Final atmospheric tapes, which consist of wind and thermodynamic parameters versus altitude, for STS-41D vehicle ascent and SRB descent/impact were constructed. The STS-41D ascent meteorological data tape was constructed by Marshall Space Flight Center's Atmospheric Science Division to provide an internally consistent data set for use in post flight performance assessments.

New Dimensions for the Online Catalog: The Dartmouth College Library Experience [and] TOC/DOC at Caltech: Evolution of Citation Access Online [and] Locally Loaded Databases in Arizona State University's Online Catalog Using the CARL System.

ERIC Educational Resources Information Center

Klemperer, Katharina; And Others

1989-01-01

Each of three articles describes an academic library's online catalog that includes locally created databases. Topics covered include database and software selection; systems design and development; database producer negotiations; problems encountered during implementation; database loading; training and documentation; and future plans. (CLB)

Electron Effective-Attenuation-Length Database

National Institute of Standards and Technology Data Gateway

SRD 82 NIST Electron Effective-Attenuation-Length Database (PC database, no charge)   This database provides values of electron effective attenuation lengths (EALs) in solid elements and compounds at selected electron energies between 50 eV and 2,000 eV. The database was designed mainly to provide EALs (to account for effects of elastic-eletron scattering) for applications in surface analysis by Auger-electron spectroscopy (AES) and X-ray photoelectron spectroscopy (XPS).

[A systematic review of the effectiveness of workplace safety interventions].

PubMed

Baldasseroni, A; Olimpi, Nadia; Bonaccorsi, G

2009-01-01

The authors carried out a systematic review of the effectiveness of workplace safety interventions, as a part of a wider project funded by CCM, Centre for Disease Control. Several electronic bibliographic databases were checked, using a standardized string selection. The string contained the following four items: the intervention; job features; type of injury; efficacy/effectiveness. Of the various databases consulted, Web of Science was the most efficient. Overall 5531 articles were selected. After reading the title and abstract, 4695 were excluded and eventually 35 systematic reviews were selected, which synthesized 769 original articles. The main topics of the selected systematic reviews were: certain sectors (building industry, agriculture, health care); personal protective equipment; work organization and prevention management at plant level; evaluation of prevention policies by national and regional authorities. A clear need for multiple bibliographical data-base search emerged at the end of this study.

Feasibility of including green tea products for an analytically verified dietary supplement database

USDA-ARS?s Scientific Manuscript database

The Dietary Supplement Ingredient Database (DSID) is a federally-funded, publically-accessible dietary supplement database that currently contains analytically derived information on micronutrients in selected adult and children’s multivitamin and mineral (MVM) supplements. Other constituents in di...

Online Database Coverage of Pharmaceutical Journals.

ERIC Educational Resources Information Center

Snow, Bonnie

1984-01-01

Describes compilation of data concerning pharmaceutical journal coverage in online databases which aid information providers in collection development and database selection. Methodology, results (a core collection, overlap, timeliness, geographic scope), and implications are discussed. Eight references and a list of 337 journals indexed online in…

Selecting Data-Base Management Software for Microcomputers in Libraries and Information Units.

ERIC Educational Resources Information Center

Pieska, K. A. O.

1986-01-01

Presents a model for the evaluation of database management systems software from the viewpoint of librarians and information specialists. The properties of data management systems, database management systems, and text retrieval systems are outlined and compared. (10 references) (CLB)

Thermodynamic stability of biomolecules and evolution.

PubMed

Chakravarty, Ashim K

2017-08-01

The thermodynamic stability of biomolecules in the perspective of evolution is a complex issue and needs discussion. Intra molecular bonds maintain the structure and the state of internal energy (E) of a biomolecule at "local minima". In this communication, possibility of loss in internal energy level of a biomolecule through the changes in the bonds has been discussed, that might earn more thermodynamic stability for the molecule. In the process variations in structure and functions of the molecule could occur. Thus, E of a biomolecule is likely to have energy stature for minimization. Such change in energy status is an intrinsic factor for evolving biomolecules buying more stability and generating variations in the structure and function of DNA molecules undergoing natural selection. Thus, the variations might very well contribute towards the process of evolution. A brief discussion on conserved sequence in the light of proposition in this communication has been made at the end. Extension of the idea may resolve certain standing problems in evolution, such as maintenance of conserved sequences in genome of diverse species, pre- versus post adaptive mutations, 'orthogenesis', etc. Copyright © 2017 Elsevier Ltd. All rights reserved.

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

PubMed

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

2015-12-11

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

A Modified Benedict-Webb-Rubin Equation of State for the Thermodynamic Properties of R152a (1,1-difluoroethane)

NASA Astrophysics Data System (ADS)

Outcalt, Stephanie L.; McLinden, Mark O.

1996-03-01

A modified Benedict-Webb-Rubin (MBWR) equation of state has been developed for R152a (1,1-difluoroethane). The correlation is based on a selection of available experimental thermodynamic property data. Single-phase pressure-volume-temperature (PVT), heat capacity, and sound speed data, as well as second virial coefficient, vapor pressure, and saturated liquid and saturated vapor density data, were used with multi-property linear least-squares fitting to determine the 32 adjustable coefficients of the MBWR equation. Ancillary equations representing the vapor pressure, saturated liquid and saturated vapor densities, and the ideal gas heat capacity were determined. Coefficients for the equation of state and the ancillary equations are given. Experimental data used in this work covered temperatures from 162 K to 453 K and pressures to 35 MPa. The MBWR equation established in this work may be used to predict thermodynamic properties of R152a from the triple-point temperature of 154.56 K to 500 K and for pressures up to 60 MPa except in the immediate vicinity of the critical point.

Absorption Refrigeration Cycles with Ammonia-Ionic Liquid Working Pairs Studied by Molecular Simulation.

PubMed

Becker, Tim M; Wang, Meng; Kabra, Abhishek; Jamali, Seyed Hossein; Ramdin, Mahinder; Dubbeldam, David; Infante Ferreira, Carlos A; Vlugt, Thijs J H

2018-04-18

For absorption refrigeration, it has been shown that ionic liquids have the potential to replace conventional working pairs. Due to the huge number of possibilities, conducting lab experiments to find the optimal ionic liquid is infeasible. Here, we provide a proof-of-principle study of an alternative computational approach. The required thermodynamic properties, i.e., solubility, heat capacity, and heat of absorption, are determined via molecular simulations. These properties are used in a model of the absorption refrigeration cycle to estimate the circulation ratio and the coefficient of performance. We selected two ionic liquids as absorbents: [emim][Tf 2 N], and [emim][SCN]. As refrigerant NH 3 was chosen due to its favorable operating range. The results are compared to the traditional approach in which parameters of a thermodynamic model are fitted to reproduce experimental data. The work shows that simulations can be used to predict the required thermodynamic properties to estimate the performance of absorption refrigeration cycles. However, high-quality force fields are required to accurately predict the cycle performance.

Absorption Refrigeration Cycles with Ammonia–Ionic Liquid Working Pairs Studied by Molecular Simulation

PubMed Central

2018-01-01

For absorption refrigeration, it has been shown that ionic liquids have the potential to replace conventional working pairs. Due to the huge number of possibilities, conducting lab experiments to find the optimal ionic liquid is infeasible. Here, we provide a proof-of-principle study of an alternative computational approach. The required thermodynamic properties, i.e., solubility, heat capacity, and heat of absorption, are determined via molecular simulations. These properties are used in a model of the absorption refrigeration cycle to estimate the circulation ratio and the coefficient of performance. We selected two ionic liquids as absorbents: [emim][Tf2N], and [emim][SCN]. As refrigerant NH3 was chosen due to its favorable operating range. The results are compared to the traditional approach in which parameters of a thermodynamic model are fitted to reproduce experimental data. The work shows that simulations can be used to predict the required thermodynamic properties to estimate the performance of absorption refrigeration cycles. However, high-quality force fields are required to accurately predict the cycle performance. PMID:29749996

Design Optimization of Microalloyed Steels Using Thermodynamics Principles and Neural-Network-Based Modeling

NASA Astrophysics Data System (ADS)

Mohanty, Itishree; Chintha, Appa Rao; Kundu, Saurabh

2018-06-01

The optimization of process parameters and composition is essential to achieve the desired properties with minimal additions of alloying elements in microalloyed steels. In some cases, it may be possible to substitute such steels for those which are more richly alloyed. However, process control involves a larger number of parameters, making the relationship between structure and properties difficult to assess. In this work, neural network models have been developed to estimate the mechanical properties of steels containing Nb + V or Nb + Ti. The outcomes have been validated by thermodynamic calculations and plant data. It has been shown that subtle thermodynamic trends can be captured by the neural network model. Some experimental rolling data have also been used to support the model, which in addition has been applied to calculate the costs of optimizing microalloyed steel. The generated pareto fronts identify many combinations of strength and elongation, making it possible to select composition and process parameters for a range of applications. The ANN model and the optimization model are being used for prediction of properties in a running plant and for development of new alloys, respectively.

Determination of goslarite-bianchite equilibria by the humidity-buffer technique at 0.1 MPa

USGS Publications Warehouse

Chou, I.-Ming; Seal, R.R.

2005-01-01

Goslarite-bianchite equilibria were determined along four humidity-buffer curves at 0.1 MPa and between 27 and 36 ??C. Results, based on tight reversals along each humidity buffer, can be represented by ln K (??0.005)=19.643-7015.38/T, where K is the equilibrium constant and T is temperature in K. Our data are in excellent agreement with several previous vapor-pressure measurements and are consistent with the solubility data reported in the literature. Thermodynamic analysis of these data yields 9.634 (??0.056) kJ mol-1 for the standard Gibbs free energy of reaction, which is in good agreement with the value of 9.658 kJ mol-1 calculated from the thermodynamic data compiled and evaluated by Wagman et al. [Wagman, D.D., Evans, W.H., Parker, V.B., Schumm, R.H., Halow. I., Bailey, S.M., Churney, K.L., Nuttal, R.L., 1982. The NBS tables of chemical thermodynamic properties. Selected values for inorganic and C1 and C2 organic substances in SI units. J. Phys. Chem. Ref. Data 11, Suppl. 2].

Measurements of thermodynamic and optical properties of selected aqueous organic and organic-inorganic mixtures of atmospheric relevance.

PubMed

Lienhard, Daniel M; Bones, David L; Zuend, Andreas; Krieger, Ulrich K; Reid, Jonathan P; Peter, Thomas

2012-10-11

Atmospheric aerosol particles can exhibit liquid solution concentrations supersaturated with respect to the dissolved organic and inorganic species and supercooled with respect to ice. In this study, thermodynamic and optical properties of sub- and supersaturated aqueous solutions of atmospheric interest are presented. The density, refractive index, water activity, ice melting temperatures, and homogeneous ice freezing temperatures of binary aqueous solutions containing L(+)-tartaric acid, tannic acid, and levoglucosan and ternary aqueous solutions containing levoglucosan and one of the salts NH(4)HSO(4), (NH(4))(2)SO(4), and NH(4)NO(3) have been measured in the supersaturated concentration range for the first time. In addition, the density and refractive index of binary aqueous citric acid and raffinose solutions and the glass transition temperatures of binary aqueous L(+)-tartaric acid and levoglucosan solutions have been measured. The data presented here are derived from experiments on single levitated microdroplets and bulk solutions and should find application in thermodynamic and atmospheric aerosol models as well as in food science applications.

Drastic stabilization of parallel DNA hybridizations by a polylysine comb-type copolymer with hydrophilic graft chain.

PubMed

Miyoshi, Daisuke; Ueda, Yu-Mi; Shimada, Naohiko; Nakano, Shu-Ichi; Sugimoto, Naoki; Maruyama, Atsushi

2014-09-01

Electrostatic interactions play a major role in protein-DNA interactions. As a model system of a cationic protein, herein we focused on a comb-type copolymer of a polycation backbone and dextran side chains, poly(L-lysine)-graft-dextran (PLL-g-Dex), which has been reported to form soluble interpolyelectrolyte complexes with DNA strands. We investigated the effects of PLL-g-Dex on the conformation and thermodynamics of DNA oligonucleotides forming various secondary structures. Thermodynamic analysis of the DNA structures showed that the parallel conformations involved in both DNA duplexes and triplexes were significantly and specifically stabilized by PLL-g-Dex. On the basis of thermodynamic parameters, it was further possible to design DNA switches that undergo structural transition responding to PLL-g-Dex from an antiparallel duplex to a parallel triplex even with mismatches in the third strand hybridization. These results suggest that polycationic molecules are able to induce structural polymorphism of DNA oligonucleotides, because of the conformation-selective stabilization effects. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

dSED: A database tool for modeling sediment early diagenesis

NASA Astrophysics Data System (ADS)

Katsev, S.; Rancourt, D. G.; L'Heureux, I.

2003-04-01

Sediment early diagenesis reaction transport models (RTMs) are becoming powerful tools in providing kinetic descriptions of the metal and nutrient diagenetic cycling in marine, lacustrine, estuarine, and other aquatic sediments, as well as of exchanges with the water column. Whereas there exist several good database/program combinations for thermodynamic equilibrium calculations in aqueous systems, at present there exist no database tools for classification and analysis of the kinetic data essential to RTM development. We present a database tool that is intended to serve as an online resource for information about chemical reactions, solid phase and solute reactants, sorption reactions, transport mechanisms, and kinetic and equilibrium parameters that are relevant to sediment diagenesis processes. The list of reactive substances includes but is not limited to organic matter, Fe and Mn oxides and oxyhydroxides, sulfides and sulfates, calcium, iron, and manganese carbonates, phosphorus-bearing minerals, and silicates. Aqueous phases include dissolved carbon dioxide, oxygen, methane, hydrogen sulfide, sulfate, nitrate, phosphate, some organic compounds, and dissolved metal species. A number of filters allow extracting information according to user-specified criteria, e.g., about a class of substances contributing to the cycling of iron. The database also includes bibliographic information about published diagenetic models and the reactions and processes that they consider. At the time of preparing this abstract, dSED contained 128 reactions and 12 pre-defined filters. dSED is maintained by the Lake Sediment Structure and Evolution (LSSE) group at the University of Ottawa (www.science.uottawa.ca/LSSE/dSED) and we invite input from the geochemical community.

Radiative interactions in molecular gases under local and nonlocal thermodynamic equilibrium conditions

NASA Technical Reports Server (NTRS)

Tiwari, S. N.; Jha, M. K.

1993-01-01

Basic formulations, analyses, and numerical procedures are presented to investigate radiative heat interactions in diatomic and polyatomic gases under local and nonlocal thermodynamic equilibrium conditions. Essential governing equations are presented for both gray and nongray gases. Information is provided on absorption models, relaxation times, and transfer equations. Radiative flux equations are developed which are applicable under local and nonlocal thermodynamic equilibrium conditions. The problem is solved for fully developed laminar incompressible flows between two parallel plates under the boundary condition of a uniform surface heat flux. For specific applications, three diatomic and three polyatomic gases are considered. The results are obtained numerically by employing the method of variation of parameters. The results are compared under local and nonlocal thermodynamic equilibrium conditions at different temperature and pressure conditions. Both gray and nongray studies are conducted extensively for all molecular gases considered. The particular gases selected for this investigation are CO, NO, OH, CO2, H2O, and CH4. The temperature and pressure range considered are 300-2000 K and 0.1-10 atmosphere, respectively. In general, results demonstrate that the gray gas approximation overestimates the effect of radiative interaction for all conditions. The conditions of NLTE, however, result in underestimation of radiative interactions. The method developed for this study can be extended to solve complex problems of radiative heat transfer involving nonequilibrium phenomena.

Structure-Thermodynamics-Antioxidant Activity Relationships of Selected Natural Phenolic Acids and Derivatives: An Experimental and Theoretical Evaluation

PubMed Central

Zheng, Jie; Liang, Guizhao

2015-01-01

Phenolic acids and derivatives have potential biological functions, however, little is known about the structure-activity relationships and the underlying action mechanisms of these phenolic acids to date. Herein we investigate the structure-thermodynamics-antioxidant relationships of 20 natural phenolic acids and derivatives using DPPH• scavenging assay, density functional theory calculations at the B3LYP/6-311++G(d,p) levels of theory, and quantitative structure-activity relationship (QSAR) modeling. Three main working mechanisms (HAT, SETPT and SPLET) are explored in four micro-environments (gas-phase, benzene, water and ethanol). Computed thermodynamics parameters (BDE, IP, PDE, PA and ETE) are compared with the experimental radical scavenging activities against DPPH•. Available theoretical and experimental investigations have demonstrated that the extended delocalization and intra-molecular hydrogen bonds are the two main contributions to the stability of the radicals. The C = O or C = C in COOH, COOR, C = CCOOH and C = CCOOR groups, and orthodiphenolic functionalities are shown to favorably stabilize the specific radical species to enhance the radical scavenging activities, while the presence of the single OH in the ortho position of the COOH group disfavors the activities. HAT is the thermodynamically preferred mechanism in the gas phase and benzene, whereas SPLET in water and ethanol. Furthermore, our QSAR models robustly represent the structure-activity relationships of these explored compounds in polar media. PMID:25803685

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

PubMed

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

2015-01-01

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

Prediction of heat capacity of amine solutions using artificial neural network and thermodynamic models for CO2 capture processes

NASA Astrophysics Data System (ADS)

Afkhamipour, Morteza; Mofarahi, Masoud; Borhani, Tohid Nejad Ghaffar; Zanganeh, Masoud

2018-03-01

In this study, artificial neural network (ANN) and thermodynamic models were developed for prediction of the heat capacity ( C P ) of amine-based solvents. For ANN model, independent variables such as concentration, temperature, molecular weight and CO2 loading of amine were selected as the inputs of the model. The significance of the input variables of the ANN model on the C P values was investigated statistically by analyzing of correlation matrix. A thermodynamic model based on the Redlich-Kister equation was used to correlate the excess molar heat capacity ({C}_P^E) data as function of temperature. In addition, the effects of temperature and CO2 loading at different concentrations of conventional amines on the C P values were investigated. Both models were validated against experimental data and very good results were obtained between two mentioned models and experimental data of C P collected from various literatures. The AARD between ANN model results and experimental data of C P for 47 systems of amine-based solvents studied was 4.3%. For conventional amines, the AARD for ANN model and thermodynamic model in comparison with experimental data were 0.59% and 0.57%, respectively. The results showed that both ANN and Redlich-Kister models can be used as a practical tool for simulation and designing of CO2 removal processes by using amine solutions.

Geochemical modeling of leaching of Ca, Mg, Al, and Pb from cementitious waste forms

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

Martens, E., E-mail: evelien.martens@csiro.a; Jacques, D.; Van Gerven, T.

2010-08-15

Results from extraction tests on cement-waste samples were simulated with a thermodynamic equilibrium model using a consistent database, to which lead data were added. Subsequent diffusion tests were modeled by means of a 3D diffusive transport model combined with the geochemical model derived from the extraction tests. Modeling results of the leached major element concentrations for both uncarbonated and (partially) carbonated samples agreed well with the extraction test using the set of pure minerals and solid solutions present in the database. The observed decrease in Ca leaching with increasing carbonation level was qualitatively predicted. Simulations also revealed that Pb leachingmore » is not controlled by dissolution/precipitation only. The addition of the calcite-cerrusite solid solution and adsorption reactions on amorphous Fe- and Al-oxides improved the predictions and are considered to control the Pb leaching during the extractions tests. The dynamic diffusive leaching tests were appropriately modeled for Na, K, Ca and Pb.« less

SpectraPlot.com: Integrated spectroscopic modeling of atomic and molecular gases

NASA Astrophysics Data System (ADS)

Goldenstein, Christopher S.; Miller, Victor A.; Mitchell Spearrin, R.; Strand, Christopher L.

2017-10-01

SpectraPlot is a web-based application for simulating spectra of atomic and molecular gases. At the time this manuscript was written, SpectraPlot consisted of four primary tools for calculating: (1) atomic and molecular absorption spectra, (2) atomic and molecular emission spectra, (3) transition linestrengths, and (4) blackbody emission spectra. These tools currently employ the NIST ASD, HITRAN2012, and HITEMP2010 databases to perform line-by-line simulations of spectra. SpectraPlot employs a modular, integrated architecture, enabling multiple simulations across multiple databases and/or thermodynamic conditions to be visualized in an interactive plot window. The primary objective of this paper is to describe the architecture and spectroscopic models employed by SpectraPlot in order to provide its users with the knowledge required to understand the capabilities and limitations of simulations performed using SpectraPlot. Further, this manuscript discusses the accuracy of several underlying approximations used to decrease computational time, in particular, the use of far-wing cutoff criteria.

Selective divalent cobalt ions detection using Ag2O3-ZnO nanocones by ICP-OES method for environmental remediation.

PubMed

Rahman, Mohammed M; Khan, Sher Bahadar; Marwani, Hadi M; Asiri, Abdullah M

2014-01-01

Here, we have synthesized Ag2O3-ZnO nanocones (NCs) by a wet-chemical route using reducing agents at low temperature. The structural, optical and morphological properties of Ag2O3-ZnO NCs were investigated by several conventional techniques such as powder XRD, XPS, FESEM, XEDS, FTIR and UV/vis. spectroscopy. The analytical parameters of prepared NCs were also calculated for a selective detection of divalent cobalt [Co(II)] prior to its determination by inductively coupled plasma-optical emission spectrometry (ICP-OES). The selectivity of NCs toward various metal ions, including Cd(II), Co(II), Cr(III), Cu(II), Fe(III), Ni(II), and Zn(II) was studied. Results of the selectivity study demonstrated that Ag2O3-ZnO NC phase was the most selective towards Co(II) ion. The uptake capacity for Co(II) ion was experimentally calculated to be ∼76.69 mgg-1. Moreover, adsorption isotherm data provided that the adsorption process was mainly monolayer on homogeneous adsorbent surfaces of Ag2O3-ZnO NCs. Kinetic study revealed that the adsorption of Co(II) on Ag2O3-ZnO NCs phase followed the pseudo-second-order kinetic model. In addition, thermodynamic results provided that the adsorption mechanism of Co(II) ions on Ag2O3-ZnO NCs was a spontaneous process and thermodynamically favorable. Finally, the proposed method was validated by applying it to real environmental water samples with reasonable results.

Selective Divalent Cobalt Ions Detection Using Ag2O3-ZnO Nanocones by ICP-OES Method for Environmental Remediation

PubMed Central

Rahman, Mohammed M.; Khan, Sher Bahadar; Marwani, Hadi M.; Asiri, Abdullah M.

2014-01-01

Here, we have synthesized Ag2O3-ZnO nanocones (NCs) by a wet-chemical route using reducing agents at low temperature. The structural, optical and morphological properties of Ag2O3-ZnO NCs were investigated by several conventional techniques such as powder XRD, XPS, FESEM, XEDS, FTIR and UV/vis. spectroscopy. The analytical parameters of prepared NCs were also calculated for a selective detection of divalent cobalt [Co(II)] prior to its determination by inductively coupled plasma-optical emission spectrometry (ICP-OES). The selectivity of NCs toward various metal ions, including Cd(II), Co(II), Cr(III), Cu(II), Fe(III), Ni(II), and Zn(II) was studied. Results of the selectivity study demonstrated that Ag2O3-ZnO NC phase was the most selective towards Co(II) ion. The uptake capacity for Co(II) ion was experimentally calculated to be ∼76.69 mgg−1. Moreover, adsorption isotherm data provided that the adsorption process was mainly monolayer on homogeneous adsorbent surfaces of Ag2O3-ZnO NCs. Kinetic study revealed that the adsorption of Co(II) on Ag2O3-ZnO NCs phase followed the pseudo-second-order kinetic model. In addition, thermodynamic results provided that the adsorption mechanism of Co(II) ions on Ag2O3-ZnO NCs was a spontaneous process and thermodynamically favorable. Finally, the proposed method was validated by applying it to real environmental water samples with reasonable results. PMID:25464507

Progress in the development and optimization of polyoxometalate delignification systems

Treesearch

R.H. Atalla; I.A. Weinstock; J.S. Bond; R.S. Reiner; E.L. Springer; C.G. Hill; Yu. Geletii; V.A. Grigoriev; A.J. Bailey; L. Delannoy; C.L. Hill

2002-01-01

We have reported the use of polyoxometalates (POMs) as selective, regenerable delignification agents that are inherently thermodynamically stable, and self-buffering. The re-activation with oxygen is under conditions that mineralize the organic byproducts of the delignification process. Thus, the POMs provide the basis for a closed bleach plant wherein the consumable...

Progress in the development and optimization of polyoxometalate delignification systems

Treesearch

R.H. Atalla; I.A. Weinstock; R.S. Reiner; E.L. Springer; C.G. Hill

2003-01-01

We have reported the use of polyoxometalates (POMs) as selective, regenerable delignification agents that are inherently thermodynamically stable, and self-buffering. The re-activation with oxygen is under conditions that mineralize the organic byproducts of the delignification process. Thus, the POMs provide the basis for a closed bleach plant wherein the consumable...

Development of Silica Fibers and Microstructures with Large and Thermodynamically Stable Second Order Nonlinearity

DTIC Science & Technology

2011-06-22

high degree of symmetry directly leads to a symmetry-enforced selection rule that can produce quantum entanglement [21, 22]. This report is organized...page.) Then, using a Matlab program, we converted the microscope image to a binary bitmap, from which we extract fiber radius at any given location

O-Pu-U (Oxygen-Plutonium-Uranium)

NASA Astrophysics Data System (ADS)

Materials Science International Team MSIT

This document is part of Subvolume C4 'Non-Ferrous Metal Systems. Part 4: Selected Nuclear Materials and Engineering Systems' of Volume 11 'Ternary Alloy Systems - Phase Diagrams, Crystallographic and Thermodynamic Data critically evaluated by MSIT®' of Landolt-Börnstein - Group IV 'Physical Chemistry'. It provides data of the ternary system Oxygen-Plutonium-Uranium.

Generalized Poisson-Kac Processes: Basic Properties and Implications in Extended Thermodynamics and Transport

NASA Astrophysics Data System (ADS)

Giona, Massimiliano; Brasiello, Antonio; Crescitelli, Silvestro

2016-04-01

We introduce a new class of stochastic processes in Rn,{{{mathbb R}}^n}, referred to as generalized Poisson-Kac (GPK) processes, that generalizes the Poisson-Kac telegrapher's random motion in higher dimensions. These stochastic processes possess finite propagation velocity, almost everywhere smooth trajectories, and converge in the Kac limit to Brownian motion. GPK processes are defined by coupling the selection of a bounded velocity vector from a family of N distinct ones with a Markovian dynamics controlling probabilistically this selection. This model can be used as a probabilistic tool for a stochastically consistent formulation of extended thermodynamic theories far from equilibrium.

Theoretical Insights into Direct Methane to Methanol Conversion over Supported Dicopper Oxo Nanoclusters

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

Doan, Hieu A.; Li, Zhanyong; Farha, Omar K.

In this study, the prospect of using copper oxide nanoclusters grown by atomic layer deposition on a porphyrin support for selective oxidation of methane to methanol was examined by means of density functional theory (DFT) calculations. Ab initio thermodynamic analysis indicates that an active site in the form of Cu(μ-O)Cu can be stabilized by activation in O2 at 465K. Furthermore, a moderate methane activation energy barrier (Ea=54kJ/mol) is predicted, and the hydrogen abstraction activity of the active site could be attributed to the radical character of the bridging oxygen. Methanol extraction in this system is limited by a thermodynamic barriermore » to desorption of ΔG=57kJ/mol at 473K; however, desorption can be facilitated by the addition of water in a “stepped conversion” process. Overall, our results indicate similar activity between porphyrin-supported copper oxide nanoclusters and existing Cu-exchanged zeolites and provide a computational proof-of-concept for utilizing functionalized organic linkers in metal-organic frameworks (MOFs) for selective oxidation of methane to methanol.« less

Theoretical Insights into Direct Methane to Methanol Conversion over Supported Dicopper Oxo Nanoclusters

DOE PAGES

Doan, Hieu A.; Li, Zhanyong; Farha, Omar K.; ...

2018-04-08

In this study, the prospect of using copper oxide nanoclusters grown by atomic layer deposition on a porphyrin support for selective oxidation of methane to methanol was examined by means of density functional theory (DFT) calculations. Ab initio thermodynamic analysis indicates that an active site in the form of Cu(μ-O)Cu can be stabilized by activation in O2 at 465K. Furthermore, a moderate methane activation energy barrier (Ea=54kJ/mol) is predicted, and the hydrogen abstraction activity of the active site could be attributed to the radical character of the bridging oxygen. Methanol extraction in this system is limited by a thermodynamic barriermore » to desorption of ΔG=57kJ/mol at 473K; however, desorption can be facilitated by the addition of water in a “stepped conversion” process. Overall, our results indicate similar activity between porphyrin-supported copper oxide nanoclusters and existing Cu-exchanged zeolites and provide a computational proof-of-concept for utilizing functionalized organic linkers in metal-organic frameworks (MOFs) for selective oxidation of methane to methanol.« less

Thermo-optical Modelling of Laser Matter Interactions in Selective Laser Melting Processes.

NASA Astrophysics Data System (ADS)

Vinnakota, Raj; Genov, Dentcho

Selective laser melting (SLM) is one of the promising advanced manufacturing techniques, which is providing an ideal platform to manufacture components with zero geometric constraints. Coupling the electromagnetic and thermodynamic processes involved in the SLM, and developing the comprehensive theoretical model of the same is of great importance since it can provide significant improvements in the printing processes by revealing the optimal parametric space related to applied laser power, scan velocity, powder material, layer thickness and porosity. Here, we present a self-consistent Thermo-optical model which simultaneously solves the Maxwell's and the heat transfer equations and provides an insight into the electromagnetic energy released in the powder-beds and the concurrent thermodynamics of the particles temperature rise and onset of melting. The numerical calculations are compared with developed analytical model of the SLM process providing insight into the dynamics between laser facilitated Joule heating and radiation mitigated rise in temperature. These results provide guidelines toward improved energy efficiency and optimization of the SLM process scan rates. The current work is funded by the NSF EPSCoR CIMM project under award #OIA-1541079.

A procedure to select ground-motion time histories for deterministic seismic hazard analysis from the Next Generation Attenuation (NGA) database

NASA Astrophysics Data System (ADS)

Huang, Duruo; Du, Wenqi; Zhu, Hong

2017-10-01

In performance-based seismic design, ground-motion time histories are needed for analyzing dynamic responses of nonlinear structural systems. However, the number of ground-motion data at design level is often limited. In order to analyze seismic performance of structures, ground-motion time histories need to be either selected from recorded strong-motion database or numerically simulated using stochastic approaches. In this paper, a detailed procedure to select proper acceleration time histories from the Next Generation Attenuation (NGA) database for several cities in Taiwan is presented. Target response spectra are initially determined based on a local ground-motion prediction equation under representative deterministic seismic hazard analyses. Then several suites of ground motions are selected for these cities using the Design Ground Motion Library (DGML), a recently proposed interactive ground-motion selection tool. The selected time histories are representatives of the regional seismic hazard and should be beneficial to earthquake studies when comprehensive seismic hazard assessments and site investigations are unavailable. Note that this method is also applicable to site-specific motion selections with the target spectra near the ground surface considering the site effect.

A Web-based Tool for SDSS and 2MASS Database Searches

NASA Astrophysics Data System (ADS)

Hendrickson, M. A.; Uomoto, A.; Golimowski, D. A.

We have developed a web site using HTML, Php, Python, and MySQL that extracts, processes, and displays data from the Sloan Digital Sky Survey (SDSS) and the Two-Micron All-Sky Survey (2MASS). The goal is to locate brown dwarf candidates in the SDSS database by looking at color cuts; however, this site could also be useful for targeted searches of other databases as well. MySQL databases are created from broad searches of SDSS and 2MASS data. Broad queries on the SDSS and 2MASS database servers are run weekly so that observers have the most up-to-date information from which to select candidates for observation. Observers can look at detailed information about specific objects including finding charts, images, and available spectra. In addition, updates from previous observations can be added by any collaborators; this format makes observational collaboration simple. Observers can also restrict the database search, just before or during an observing run, to select objects of special interest.

New Resources for Computer-Aided Legal Research: An Assessment of the Usefulness of the DIALOG System in Securities Regulation Studies.

ERIC Educational Resources Information Center

Gruner, Richard; Heron, Carol E.

1984-01-01

Examines usefulness of DIALOG as legal research tool through use of DIALOG's DIALINDEX database to identify those databases among almost 200 available that contain large numbers of records related to federal securities regulation. Eight databases selected for further study are detailed. Twenty-six footnotes, database statistics, and samples are…

Thermodynamic assessment of the rhodium-ruthenium-oxygen (Rh-Ru-O) system

NASA Astrophysics Data System (ADS)

Gossé, S.; Bordier, S.; Guéneau, C.; Brackx, E.; Domenger, R.; Rogez, J.

2018-03-01

Ruthenium (Ru) and rhodium (Rh) are abundant platinum-group metals formed during burn-up of nuclear fuels. Under normal operating conditions, Rh and Ru accumulate and predominantly form metallic precipitates with other fission products like Mo, Pd and Tc. In the framework of vitrification of high-level nuclear waste, these fission products are poorly soluble in molten glasses. They precipitate as metallic particles and oxide phases. Moreover, these Ru and Rh rich phases strongly depend on temperature and the oxygen fugacity of the glass melt. In case of severe accidental conditions with air ingress, oxidation of the Ru and Rh is possible. At low temperatures (T < 1422 K for rhodium sesquioxide and T < 1815 K for ruthenium dioxide), the formed oxides are relatively stable. On the other hand, at high temperatures (T > 1422 K for rhodium sesquioxide and T > 1815 K for ruthenium dioxide), they may decompose into (Rh)-FCC or (Ru)-HCP metallic phases and radiotoxic volatile gaseous species. A thermodynamic assessment of the Rh-Ru-O system will enable the prediction of: (1) the metallic and oxide phases that form during the vitrification of high-level nuclear wastes and (2) the release of volatile gaseous species during a severe accident. The Calphad method developed herein employs a thermodynamic approach in the investigation of the thermochemistry of rhodium and ruthenium at high temperatures. Current literature on the thermodynamic properties and phase diagram data enables preliminary thermodynamic assessments of the Rh-O and Ru-O systems. Additionally, select compositions in the ternary Rh-Ru-O system underwent experimental tests to complement data found in literature and to establish the phase equilibria in the ternary system.

Nanostructured Fe-Cr Alloys for Advanced Nuclear Energy Applications

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

Scattergood, Ronald O.

2016-04-26

We have completed research on the grain-size stabilization of model nanostructured Fe14Cr base alloys at high temperatures by the addition of non-equilibrium solutes. Fe14Cr base alloys are representative for nuclear reactor applications. The neutron flux in a nuclear reactor will generate He atoms that coalesce to form He bubbles. These can lead to premature failure of the reactor components, limiting their lifetime and increasing the cost and capacity for power generation. In order to mitigate such failures, Fe14Cr base alloys have been processed to contain very small nano-size oxide particles (less than 10 nm in size) that trap He atomsmore » and reduce bubble formation. Theoretical and experimental results indicate that the grain boundaries can also be very effective traps for He atoms and bubble formation. An optimum grain size will be less than 100 nm, ie., nanocrystalline alloys must be used. Powder metallurgy methods based on high-energy ball milling can produce Fe-Cr base nanocrystalline alloys that are suitable for nuclear energy applications. The problem with nanocrystalline alloys is that excess grain-boundary energy will cause grains to grow at higher temperatures and their propensity for He trapping will be lost. The nano-size oxide particles in current generation nuclear alloys provide some grain size stabilization by reducing grain-boundary mobility (Zener pinning – a kinetic effect). However the current mitigation strategy minimizing bubble formation is based primarily on He trapping by nano-size oxide particles. An alternate approach to nanoscale grain size stabilization has been proposed. This is based on the addition of small amounts of atoms that are large compared to the base alloy. At higher temperatures these will diffuse to the grain boundaries and will produce an equilibrium state for the grain size at higher temperatures (thermodynamic stabilization – an equilibrium effect). This would be preferred compared to a kinetic effect, which is not based on an equilibrium state. The PI and coworkers have developed thermodynamic-based models that can be used to select appropriate solute additions to Fe14Cr base alloys to achieve a contribution to grain-size stabilization and He bubble mitigation by the thermodynamic effect. All such models require approximations and the proposed research was aimed at alloy selection, processing and detailed atomic-level microstructure evaluations to establish the efficacy of the thermodynamic effect. The outcome of this research shows that appropriate alloy additions can produce a contribution from the thermodynamic stabilization effect. Furthermore, due to the oxygen typically present in nominally high purity elemental powders used for powder metallurgy processing, the optimum results obtained appeared as a synergistic combination of nano-size oxide particle pinning kinetic effect and the grain-boundary segregation thermodynamic effect.« less

Federated Search Tools in Fusion Centers: Bridging Databases in the Information Sharing Environment

DTIC Science & Technology

2012-09-01

considerable variation in how fusion centers plan for, gather requirements, select and acquire federated search tools to bridge disparate databases...centers, when considering integrating federated search tools; by evaluating the importance of the planning, requirements gathering, selection and...acquisition processes for integrating federated search tools; by acknowledging the challenges faced by some fusion centers during these integration processes

Thermodynamic and kinetic modeling of Mn-Ni-Si precipitates in low-Cu reactor pressure vessel steels

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

Ke, Huibin; Wells, Peter; Edmondson, Philip D.

Formation of large volume fractions of Mn-Ni-Si precipitates (MNSPs) causes excess irradiation embrittlement of reactor pressure vessel (RPV) steels at high, extended-life fluences. Thus, a new and unique, semi-empirical cluster dynamics model was developed to study the evolution of MNSPs in low-Cu RPV steels. The model is based on CALPHAD thermodynamics and radiation enhanced diffusion kinetics. The thermodynamics dictates the compositional and temperature dependence of the free energy reductions that drive precipitation. The model treats both homogeneous and heterogeneous nucleation, where the latter occurs on cascade damage, like dislocation loops. The model has only four adjustable parameters that were fitmore » to an atom probe tomography (APT) database. The model predictions are in semi-quantitative agreement with systematic Mn, Ni and Si composition variations in alloys characterized by APT, including a sensitivity to local tip-to-tip variations even in the same steel. The model predicts that heterogeneous nucleation plays a critical role in MNSP formation in lower alloy Ni contents. Single variable assessments of compositional effects show that Ni plays a dominant role, while even small variations in irradiation temperature can have a large effect on the MNSP evolution. Within typical RPV steel ranges, Mn and Si have smaller effects. Furthermore, the delayed but then rapid growth of MNSPs to large volume fractions at high fluence is well predicted by the model. For purposes of illustration, the effect of MNSPs on transition temperature shifts are presented based on well-established microstructure-property and property-property models.« less

Recommendations for terminology and databases for biochemical thermodynamics.

PubMed

Alberty, Robert A; Cornish-Bowden, Athel; Goldberg, Robert N; Hammes, Gordon G; Tipton, Keith; Westerhoff, Hans V

2011-05-01

Chemical equations are normally written in terms of specific ionic and elemental species and balance atoms of elements and electric charge. However, in a biochemical context it is usually better to write them with ionic reactants expressed as totals of species in equilibrium with each other. This implies that atoms of elements assumed to be at fixed concentrations, such as hydrogen at a specified pH, should not be balanced in a biochemical equation used for thermodynamic analysis. However, both kinds of equations are needed in biochemistry. The apparent equilibrium constant K' for a biochemical reaction is written in terms of such sums of species and can be used to calculate standard transformed Gibbs energies of reaction Δ(r)G'°. This property for a biochemical reaction can be calculated from the standard transformed Gibbs energies of formation Δ(f)G(i)'° of reactants, which can be calculated from the standard Gibbs energies of formation of species Δ(f)G(j)° and measured apparent equilibrium constants of enzyme-catalyzed reactions. Tables of Δ(r)G'° of reactions and Δ(f)G(i)'° of reactants as functions of pH and temperature are available on the web, as are functions for calculating these properties. Biochemical thermodynamics is also important in enzyme kinetics because apparent equilibrium constant K' can be calculated from experimentally determined kinetic parameters when initial velocities have been determined for both forward and reverse reactions. Specific recommendations are made for reporting experimental results in the literature. Copyright © 2011 Elsevier B.V. All rights reserved.

Thermodynamic and kinetic modeling of Mn-Ni-Si precipitates in low-Cu reactor pressure vessel steels

DOE PAGES

Ke, Huibin; Wells, Peter; Edmondson, Philip D.; ...

2017-07-12

Formation of large volume fractions of Mn-Ni-Si precipitates (MNSPs) causes excess irradiation embrittlement of reactor pressure vessel (RPV) steels at high, extended-life fluences. Thus, a new and unique, semi-empirical cluster dynamics model was developed to study the evolution of MNSPs in low-Cu RPV steels. The model is based on CALPHAD thermodynamics and radiation enhanced diffusion kinetics. The thermodynamics dictates the compositional and temperature dependence of the free energy reductions that drive precipitation. The model treats both homogeneous and heterogeneous nucleation, where the latter occurs on cascade damage, like dislocation loops. The model has only four adjustable parameters that were fitmore » to an atom probe tomography (APT) database. The model predictions are in semi-quantitative agreement with systematic Mn, Ni and Si composition variations in alloys characterized by APT, including a sensitivity to local tip-to-tip variations even in the same steel. The model predicts that heterogeneous nucleation plays a critical role in MNSP formation in lower alloy Ni contents. Single variable assessments of compositional effects show that Ni plays a dominant role, while even small variations in irradiation temperature can have a large effect on the MNSP evolution. Within typical RPV steel ranges, Mn and Si have smaller effects. Furthermore, the delayed but then rapid growth of MNSPs to large volume fractions at high fluence is well predicted by the model. For purposes of illustration, the effect of MNSPs on transition temperature shifts are presented based on well-established microstructure-property and property-property models.« less

Cryogenic Propellant Feed System Analytical Tool Development

NASA Technical Reports Server (NTRS)

Lusby, Brian S.; Miranda, Bruno M.; Collins, Jacob A.

2011-01-01

The Propulsion Systems Branch at NASA s Lyndon B. Johnson Space Center (JSC) has developed a parametric analytical tool to address the need to rapidly predict heat leak into propellant distribution lines based on insulation type, installation technique, line supports, penetrations, and instrumentation. The Propellant Feed System Analytical Tool (PFSAT) will also determine the optimum orifice diameter for an optional thermodynamic vent system (TVS) to counteract heat leak into the feed line and ensure temperature constraints at the end of the feed line are met. PFSAT was developed primarily using Fortran 90 code because of its number crunching power and the capability to directly access real fluid property subroutines in the Reference Fluid Thermodynamic and Transport Properties (REFPROP) Database developed by NIST. A Microsoft Excel front end user interface was implemented to provide convenient portability of PFSAT among a wide variety of potential users and its ability to utilize a user-friendly graphical user interface (GUI) developed in Visual Basic for Applications (VBA). The focus of PFSAT is on-orbit reaction control systems and orbital maneuvering systems, but it may be used to predict heat leak into ground-based transfer lines as well. PFSAT is expected to be used for rapid initial design of cryogenic propellant distribution lines and thermodynamic vent systems. Once validated, PFSAT will support concept trades for a variety of cryogenic fluid transfer systems on spacecraft, including planetary landers, transfer vehicles, and propellant depots, as well as surface-based transfer systems. The details of the development of PFSAT, its user interface, and the program structure will be presented.

Equilibrium high entropy alloy phase stability from experiments and thermodynamic modeling

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

Saal, James E.; Berglund, Ida S.; Sebastian, Jason T.

Long-term stability of high entropy alloys (HEAs) is a critical consideration for the design and practical application of HEAs. It has long been assumed that many HEAs are a kinetically-stabilized metastable structure, and recent experiments have confirmed this hypothesis by observing HEA ecomposition after long-termequilibration. In the presentwork,we demonstrate the use of the CALculation of PHAse Diagrams (CALPHAD) approach to predict HEA stability and processing parameters, comparing experimental long-term annealing observations to CALPHAD phase diagrams from a commercially-available HEA database. As a result, we find good agreement between single- and multi-phase predictions and experiments.

Equilibrium high entropy alloy phase stability from experiments and thermodynamic modeling

DOE PAGES

Saal, James E.; Berglund, Ida S.; Sebastian, Jason T.; ...

2017-10-29

Long-term stability of high entropy alloys (HEAs) is a critical consideration for the design and practical application of HEAs. It has long been assumed that many HEAs are a kinetically-stabilized metastable structure, and recent experiments have confirmed this hypothesis by observing HEA ecomposition after long-termequilibration. In the presentwork,we demonstrate the use of the CALculation of PHAse Diagrams (CALPHAD) approach to predict HEA stability and processing parameters, comparing experimental long-term annealing observations to CALPHAD phase diagrams from a commercially-available HEA database. As a result, we find good agreement between single- and multi-phase predictions and experiments.

Precipitation Model Validation in 3rd Generation Aeroturbine Disc Alloys

NASA Technical Reports Server (NTRS)

Olson, G. B.; Jou, H.-J.; Jung, J.; Sebastian, J. T.; Misra, A.; Locci, I.; Hull, D.

2008-01-01

In support of application of the DARPA-AIM methodology to the accelerated hybrid thermal process optimization of 3rd generation aeroturbine disc alloys with quantified uncertainty, equilibrium and diffusion couple experiments have identified available fundamental thermodynamic and mobility databases of sufficient accuracy. Using coherent interfacial energies quantified by Single-Sensor DTA nucleation undercooling measurements, PrecipiCalc(TM) simulations of nonisothermal precipitation in both supersolvus and subsolvus treated samples show good agreement with measured gamma particle sizes and compositions. Observed longterm isothermal coarsening behavior defines requirements for further refinement of elastic misfit energy and treatment of the parallel evolution of incoherent precipitation at grain boundaries.

Selective Improvement of NO2 Gas Sensing Behavior in SnO2 Nanowires by Ion-Beam Irradiation.

PubMed

Kwon, Yong Jung; Kang, Sung Yong; Wu, Ping; Peng, Yuan; Kim, Sang Sub; Kim, Hyoun Woo

2016-06-01

We irradiated SnO2 nanowires with He ions (45 MeV) with different ion fluences. Structure and morphology of the SnO2 nanowires did not undergo noticeable changes upon ion-beam irradiation. Chemical equilibrium in SnO2/gas systems was calculated from thermodynamic principles, which were used to study the sensing selectivity of the tested gases, demonstrating the selective sensitivity of the SnO2 surface to NO2 gas. Being different from other gases, including H2, ethanol, acetone, SO2, and NH3, the sensor response to NO2 gas significantly increases as the ion fluence increases, showing a maximum under an ion fluence of 1 × 10(16) ions/cm(2). Photoluminescence analysis shows that the relative intensity of the peak at 2.1 eV to the peak at 2.5 eV increases upon ion-beam irradiation, suggesting that structural defects and/or tin interstitials have been generated. X-ray photoelectron spectroscopy indicated that the ionic ratio of Sn(2+/)Sn(4+) increases by the ion-beam irradiation, supporting the formation of surface Sn interstitials. Using thermodynamic calculations, we explained the observed selective sensing behavior. A molecular level model was also established for the adsorption of NO2 on ion-irradiated SnO2 (110) surfaces. We propose that the adsorption of NO2-related species is considerably enhanced by the generation of surface defects that are comprised of Sn interstitials.

Experimental Database with Baseline CFD Solutions: 2-D and Axisymmetric Hypersonic Shock-Wave/Turbulent-Boundary-Layer Interactions

NASA Technical Reports Server (NTRS)

Marvin, Joseph G.; Brown, James L.; Gnoffo, Peter A.

2013-01-01

A database compilation of hypersonic shock-wave/turbulent boundary layer experiments is provided. The experiments selected for the database are either 2D or axisymmetric, and include both compression corner and impinging type SWTBL interactions. The strength of the interactions range from attached to incipient separation to fully separated flows. The experiments were chosen based on criterion to ensure quality of the datasets, to be relevant to NASA's missions and to be useful for validation and uncertainty assessment of CFD Navier-Stokes predictive methods, both now and in the future. An emphasis on datasets selected was on surface pressures and surface heating throughout the interaction, but include some wall shear stress distributions and flowfield profiles. Included, for selected cases, are example CFD grids and setup information, along with surface pressure and wall heating results from simulations using current NASA real-gas Navier-Stokes codes by which future CFD investigators can compare and evaluate physics modeling improvements and validation and uncertainty assessments of future CFD code developments. The experimental database is presented tabulated in the Appendices describing each experiment. The database is also provided in computer-readable ASCII files located on a companion DVD.

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

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

Arnold, John

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

Thermodynamic determination of the metal/semiconductor separation of carbon nanotubes using hydrogels.

PubMed

Hirano, Atsushi; Tanaka, Takeshi; Kataura, Hiromichi

2012-11-27

The metal/semiconductor separation of single-wall carbon nanotubes (SWCNTs) using hydrogels, such as agarose gel and Sephacryl, together with sodium dodecyl sulfate is one of the most successful techniques necessary for industrial applications. Despite recent improvements in the technique, little is known about the separation mechanism. Here, we show that SWCNTs are reversibly adsorbed onto hydrogels in the presence of sodium dodecyl sulfate. The results enabled us to examine the thermodynamics of the adsorption reaction and thereby elucidate the separation mechanism. The adsorbability of SWCNTs onto the hydrogels was described by the standard Gibbs free energy for the adsorption, as well as the area of the hydrogels allowing the adsorption. We demonstrated, for the first time, that the free energy of adsorption for semiconducting SWCNTs was 0-12 kJ/mol lower than that for metallic SWCNTs in the temperature range of 290-320 K (e.g., ca. -4 kJ/mol for the agarose gel and ca. -9 kJ/mol for Sephacryl at 300 K), which permits metal/semiconductor separation. Importantly, the difference in the free energy was attributed to the difference in the enthalpy of adsorption: the enthalpy of adsorption of metallic SWCNTs was ca. 70 kJ/mol higher than that of semiconducting SWCNTs. Thus, the enthalpy of adsorption was found to be an important parameter in the metal/semiconductor separation of SWCNTs using hydrogels. In addition, the thermodynamic parameters depended on the hydrogel type and the surfactant concentration, which is most likely why under certain conditions hydrogels and surfactants produce different separations, e.g., chirality-selective or diameter-selective separation.

The CIS Database: Occupational Health and Safety Information Online.

ERIC Educational Resources Information Center

Siegel, Herbert; Scurr, Erica

1985-01-01

Describes document acquisition, selection, indexing, and abstracting and discusses online searching of the CIS database, an online system produced by the International Occupational Safety and Health Information Centre. This database comprehensively covers information in the field of occupational health and safety. Sample searches and search…

Feasibility of Including Green Tea Products for an Analytically Verified Dietary Supplement Database

PubMed Central

Saldanha, Leila; Dwyer, Johanna; Andrews, Karen; Betz, Joseph; Harnely, James; Pehrsson, Pamela; Rimmer, Catherine; Savarala, Sushma

2015-01-01

The Dietary Supplement Ingredient Database (DSID) is a federally funded, publicly accessible dietary supplement database that currently contains analytically-derived information on micronutrients in selected adult and children’s multivitamin and mineral (MVM) supplements. Other constituents in dietary supplement products such as botanicals are also of interest and thus are being considered for inclusion in the DSID. Thirty-eight constituents, mainly botanicals were identified and prioritized by a federal interagency committee. Green tea was selected from this list as the botanical for expansion of the DSID. This paper describes the process for prioritizing dietary ingredients in the DSID. It also discusses the criteria for inclusion of these ingredients, and the approach for selecting and testing products for the green tea pilot study. PMID:25817236

Thermodynamic properties of the Group 1A elements

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

Alcock, C.B.; Itkin, V.P.; Chase, M.W.

1994-05-01

This review describes thermodynamic properties of condensed phases of the alkali metals, excluding francium for which the amount of information is too limited. The properties considered are: heat capacities from 0 to 1600 K, temperatures and enthalpies of fusion and martensitic transformation in Li and Na; discussion of the Debye temperature and electronic heat capacity coefficient at absolute zero temperature is also included. The paper is the second part of a series. Similar to previous assessment of the IIA group [93ALC/CHA], this paper considers original studies, especially with respect to factors which influence the accuracy and reliability of results. Recommendationsmore » derived from such analyses are compared with most advanced previous reviews made at the Institute for High Temperatures (Moscow) [70SHP/YAK], [82GUR] and the National Institute of Standards and Technology (Washington) [85JAN]. The properties of individual elements of the group are compared and suggestions are made for experimental studies which should improve poorly measured quantities. The review is supplemented by an IBM PC database which contains references, assessed data, brief description of studies and has facilities for fitting and plotting of data and for adding new information.« less

Phase diagrams for understanding gold-seeded growth of GaAs and InAs nanowires

NASA Astrophysics Data System (ADS)

Ghasemi, Masoomeh; Johansson, Jonas

2017-04-01

Phase diagrams are useful tools to study the phase equilibria of nanowire materials systems because the growth of nanowires is accompanied by phase formation and phase transition. We have modeled the phase equilibria of the As-Au-Ga ternary system by means of the CALPHAD method. This method is a well-established semi-empirical technique for thermodynamic modeling in which Gibbs energy functions with free parameters are defined for all phases in a system followed by adjusting these parameters to the experimental data. Using the resulting As-Au-Ga thermodynamic database, four vertical cuts of this ternary system are calculated and all show good agreement with experiments. This ternary system is particularly useful for predicting the state of the Au seed alloys when growing GaAs nanowires and we discuss such predictions. Similar calculations are performed for Au-seeded InAs nanowires. We show that the vapor-liquid-solid (VLS) growth fails for InAs nanowires, while GaAs nanowires can grow from a liquid particle. Our calculations are in agreement with experimental data on the growth of Au-seeded GaAs and InAs nanowires.

SIMPLE estimate of the free energy change due to aliphatic mutations: superior predictions based on first principles.

PubMed

Bueno, Marta; Camacho, Carlos J; Sancho, Javier

2007-09-01

The bioinformatics revolution of the last decade has been instrumental in the development of empirical potentials to quantitatively estimate protein interactions for modeling and design. Although computationally efficient, these potentials hide most of the relevant thermodynamics in 5-to-40 parameters that are fitted against a large experimental database. Here, we revisit this longstanding problem and show that a careful consideration of the change in hydrophobicity, electrostatics, and configurational entropy between the folded and unfolded state of aliphatic point mutations predicts 20-30% less false positives and yields more accurate predictions than any published empirical energy function. This significant improvement is achieved with essentially no free parameters, validating past theoretical and experimental efforts to understand the thermodynamics of protein folding. Our first principle analysis strongly suggests that both the solute-solute van der Waals interactions in the folded state and the electrostatics free energy change of exposed aliphatic mutations are almost completely compensated by similar interactions operating in the unfolded ensemble. Not surprisingly, the problem of properly accounting for the solvent contribution to the free energy of polar and charged group mutations, as well as of mutations that disrupt the protein backbone remains open. 2007 Wiley-Liss, Inc.

Experimental Phase Equilibria Studies of the Pb-Fe-O System in Air, in Equilibrium with Metallic Lead and at Intermediate Oxygen Potentials

NASA Astrophysics Data System (ADS)

Shevchenko, M.; Jak, E.

2017-12-01

The phase equilibria information on the Pb-Fe-O system is of practical importance for the improvement of the existing thermodynamic database of lead-containing slag systems (Pb-Zn-Fe-Cu-Si-Ca-Al-Mg-O). Phase equilibria of the Pb-Fe-O system have been investigated: (a) in air at temperatures between 1053 K and 1373 K (780 °C and 1100 °C); (b) in equilibrium with metallic lead at temperatures between 1053 K and 1373 K (780 °C and 1100 °C); and (c) at intermediate oxidation conditions for the liquid slag in equilibrium with two solids (spinel + magnetoplumbite), at temperatures between 1093 K and 1373 K (820 °C and 1100 °C). The high-temperature equilibration/quenching/electron probe X-ray microanalysis technique has been used to accurately determine the compositions of the phases in equilibrium in the system. The Pb and Fe concentrations in the phases were determined directly; preliminary thermodynamic modeling with FactSage was used to estimate the ferrous-to-ferric ratios and to present the results in the ternary diagram.

Wind turbine reliability database update.

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

Peters, Valerie A.; Hill, Roger Ray; Stinebaugh, Jennifer A.

2009-03-01

This report documents the status of the Sandia National Laboratories' Wind Plant Reliability Database. Included in this report are updates on the form and contents of the Database, which stems from a fivestep process of data partnerships, data definition and transfer, data formatting and normalization, analysis, and reporting. Selected observations are also reported.

An Introduction to Database Management Systems.

ERIC Educational Resources Information Center

Warden, William H., III; Warden, Bette M.

1984-01-01

Description of database management systems for microcomputers highlights system features and factors to consider in microcomputer system selection. A method for ranking database management systems is explained and applied to a defined need, i.e., software support for indexing a weekly newspaper. A glossary of terms and 32-item bibliography are…

Academic Journal Embargoes and Full Text Databases.

ERIC Educational Resources Information Center

Brooks, Sam

2003-01-01

Documents the reasons for embargoes of academic journals in full text databases (i.e., publisher-imposed delays on the availability of full text content) and provides insight regarding common misconceptions. Tables present data on selected journals covering a cross-section of subjects and publishers and comparing two full text business databases.…

Computation of thermodynamic equilibrium in systems under stress

NASA Astrophysics Data System (ADS)

Vrijmoed, Johannes C.; Podladchikov, Yuri Y.

2016-04-01

Metamorphic reactions may be partly controlled by the local stress distribution as suggested by observations of phase assemblages around garnet inclusions related to an amphibolite shear zone in granulite of the Bergen Arcs in Norway. A particular example presented in fig. 14 of Mukai et al. [1] is discussed here. A garnet crystal embedded in a plagioclase matrix is replaced on the left side by a high pressure intergrowth of kyanite and quartz and on the right side by chlorite-amphibole. This texture apparently represents disequilibrium. In this case, the minerals adapt to the low pressure ambient conditions only where fluids were present. Alternatively, here we compute that this particular low pressure and high pressure assemblage around a stressed rigid inclusion such as garnet can coexist in equilibrium. To do the computations we developed the Thermolab software package. The core of the software package consists of Matlab functions that generate Gibbs energy of minerals and melts from the Holland and Powell database [2] and aqueous species from the SUPCRT92 database [3]. Most up to date solid solutions are included in a general formulation. The user provides a Matlab script to do the desired calculations using the core functions. Gibbs energy of all minerals, solutions and species are benchmarked versus THERMOCALC, PerpleX [4] and SUPCRT92 and are reproduced within round off computer error. Multi-component phase diagrams have been calculated using Gibbs minimization to benchmark with THERMOCALC and Perple_X. The Matlab script to compute equilibrium in a stressed system needs only two modifications of the standard phase diagram script. Firstly, Gibbs energy of phases considered in the calculation is generated for multiple values of thermodynamic pressure. Secondly, for the Gibbs minimization the proportion of the system at each particular thermodynamic pressure needs to be constrained. The user decides which part of the stress tensor is input as thermodynamic pressure. To compute a case of high and low pressure around a stressed inclusion we first did a Finite Element Method calculation of a rigid inclusion in a viscous matrix under simple shear. From the computed stress distribution we took the local pressure (mean stress) in each grid point of the FEM calculation. This was used as input thermodynamic pressure in the Gibbs minimization and the result showed it is possible to have an equilibrium situation in which chlorite-amphibole is stable in the low pressure domain and kyanite in the high pressure domain of the stress field around the inclusion. Interestingly, the calculation predicts the redistribution of fluid from an average content of fluid in the system. The fluid in equilibrium tends to accumulate in the low pressure areas whereas it leaves the high pressure areas dry. Transport of fluid components occurs not necessarily by fluid flow, but may happen for example by diffusion. We conclude that an apparent disequilibrium texture may be explained by equilibrium under pressure variations, and apparent fluid addition by redistribution of fluid controlled by the local stress distribution. [1] Mukai et al. (2014), Journal of Petrology, 55 (8), p. 1457-1477. [2] Holland and Powell (1998), Journal of Metamorphic Geology, 16, p. 309-343 [3] Johnson et al. (1992), Computers & Geosciences, 18 (7), p. 899-947 [4] Connolly (2005), Earth and Planetary Science Letters, 236, p. 524-541

Sodium Content of Foods Contributing to Sodium Intake: Comparison between Selected Foods from the CDC Packaged Food Database and the USDA National Nutrient Database for Standard Reference

PubMed Central

Maalouf, Joyce; Cogswell, Mary E.; Yuan, Keming; Martin, Carrie; Gillespie, Cathleen; Ahuja, Jaspreet KC; Pehrsson, Pamela; Merritt, Robert

2015-01-01

The sodium concentration (mg/100g) for 23 of 125 Sentinel Foods (e.g. white bread) were identified in the 2009 CDC Packaged Food Database (PFD) and compared with data in the USDA’s 2013 National Nutrient Database for Standard Reference(SR 26). Sentinel Foods are foods identified by USDA to be monitored as primary indicators to assess the changes in the sodium content of commercially processed foods from stores and restaurants. Overall, 937 products were evaluated in the CDC PFD, and between 3 (one brand of ready-to-eat cereal) and 126 products (white bread) were evaluated per selected food. The mean sodium concentrations of 17 of the 23 (74%) selected foods in the CDC PFD were 90%–110% of the mean sodium concentrations in SR 26 and differences in sodium concentration were statistically significant for 6 Sentinel Foods. The sodium concentration of most of the Sentinel Foods, as selected in the PFD, appeared to represent the sodium concentrations of the corresponding food category. The results of our study help improve the understanding of how nutrition information compares between national analytic values and the label and whether the selected Sentinel Foods represent their corresponding food category as indicators for assessment of change of the sodium content in the food supply. PMID:26484010

An evolving effective stress approach to anisotropic distortional hardening

DOE PAGES

Lester, B. T.; Scherzinger, W. M.

2018-03-11

A new yield surface with an evolving effective stress definition is proposed for consistently and efficiently describing anisotropic distortional hardening. Specifically, a new internal state variable is introduced to capture the thermodynamic evolution between different effective stress definitions. The corresponding yield surface and evolution equations of the internal variables are derived from thermodynamic considerations enabling satisfaction of the second law. A closest point projection return mapping algorithm for the proposed model is formulated and implemented for use in finite element analyses. Finally, select constitutive and larger scale boundary value problems are solved to explore the capabilities of the model andmore » examine the impact of distortional hardening on constitutive and structural responses. Importantly, these simulations demonstrate the tractability of the proposed formulation in investigating large-scale problems of interest.« less

An evolving effective stress approach to anisotropic distortional hardening

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

Lester, B. T.; Scherzinger, W. M.

A new yield surface with an evolving effective stress definition is proposed for consistently and efficiently describing anisotropic distortional hardening. Specifically, a new internal state variable is introduced to capture the thermodynamic evolution between different effective stress definitions. The corresponding yield surface and evolution equations of the internal variables are derived from thermodynamic considerations enabling satisfaction of the second law. A closest point projection return mapping algorithm for the proposed model is formulated and implemented for use in finite element analyses. Finally, select constitutive and larger scale boundary value problems are solved to explore the capabilities of the model andmore » examine the impact of distortional hardening on constitutive and structural responses. Importantly, these simulations demonstrate the tractability of the proposed formulation in investigating large-scale problems of interest.« less

Nitrogen expander cycles for large capacity liquefaction of natural gas

NASA Astrophysics Data System (ADS)

Chang, Ho-Myung; Park, Jae Hoon; Gwak, Kyung Hyun; Choe, Kun Hyung

2014-01-01

Thermodynamic study is performed on nitrogen expander cycles for large capacity liquefaction of natural gas. In order to substantially increase the capacity, a Brayton refrigeration cycle with nitrogen expander was recently added to the cold end of the reputable propane pre-cooled mixed-refrigerant (C3-MR) process. Similar modifications with a nitrogen expander cycle are extensively investigated on a variety of cycle configurations. The existing and modified cycles are simulated with commercial process software (Aspen HYSYS) based on selected specifications. The results are compared in terms of thermodynamic efficiency, liquefaction capacity, and estimated size of heat exchangers. The combination of C3-MR with partial regeneration and pre-cooling of nitrogen expander cycle is recommended to have a great potential for high efficiency and large capacity.

Atmospheric environment for Space Shuttle (STS-5) launch

NASA Technical Reports Server (NTRS)

Johnson, D. L.; Hill, C. K.; Batts, G. W.

1983-01-01

This report presents a summary of selected atmospheric conditions observed near Space Shuttle STS-5 launch time on November 11, 1982, at Kennedy Space Center, Florida. Values of ambient pressure, temperature, moisture, ground winds, visual observations (cloud), and winds aloft are included. The sequence of prelaunch Jimsphere measured vertical wind profiles is given in this report. Also presented are the wind and thermodynamic parameters measured at the surface and aloft in he SRB descent/impact ocean area. Final meteorological tapes, which consist of wind and thermodynamic parameters versus altitude, for STS-5 vehicle ascent and SRB descent have been constructed. The STS-5 ascent meteorological data tape has been constructed by Marshall Space Flight Center in response to Shuttle task agreement No. 936-53-22-368 with Johnson Space Center.

Reaction path of energetic materials using THOR code

NASA Astrophysics Data System (ADS)

Durães, L.; Campos, J.; Portugal, A.

1998-07-01

The method of predicting reaction path, using THOR code, allows for isobar and isochor adiabatic combustion and CJ detonation regimes, the calculation of the composition and thermodynamic properties of reaction products of energetic materials. THOR code assumes the thermodynamic equilibria of all possible products, for the minimum Gibbs free energy, using HL EoS. The code allows the possibility of estimating various sets of reaction products, obtained successively by the decomposition of the original reacting compound, as a function of the released energy. Two case studies of thermal decomposition procedure were selected, calculated and discussed—pure Ammonium Nitrate and its based explosive ANFO, and Nitromethane—because their equivalence ratio is respectively lower, near and greater than the stoicheiometry. Predictions of reaction path are in good correlation with experimental values, proving the validity of proposed method.

A method for the selection of a functional form for a thermodynamic equation of state using weighted linear least squares stepwise regression

NASA Technical Reports Server (NTRS)

Jacobsen, R. T.; Stewart, R. B.; Crain, R. W., Jr.; Rose, G. L.; Myers, A. F.

1976-01-01

A method was developed for establishing a rational choice of the terms to be included in an equation of state with a large number of adjustable coefficients. The methods presented were developed for use in the determination of an equation of state for oxygen and nitrogen. However, a general application of the methods is possible in studies involving the determination of an optimum polynomial equation for fitting a large number of data points. The data considered in the least squares problem are experimental thermodynamic pressure-density-temperature data. Attention is given to a description of stepwise multiple regression and the use of stepwise regression in the determination of an equation of state for oxygen and nitrogen.

Thermodynamically Leveraged Tandem Catalysis for Ester RC(O)O–R' Bond Hydrogenolysis. Scope and Mechanism

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

Lohr, Tracy L.; Li, Zhi; Assary, Rajeev S.

2015-05-18

Rapid and selective formal hydrogenolysis of aliphatic ester RC(O)O–R' linkages is achieved by a tandem homogeneous metal triflate + supported palladium catalytic system. The triflate catalyzes the mildly exothermic, turnover-limiting O–R' cleavage process, whereas the exothermic hydrogenation of the intermediate alkene further drives the overall reaction to completion.

Thermodynamically leveraged Tandem catalysis for ester RC(O)O-R' bond hydrogenolysis. scope and mechanism.

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

Lohr, Tracy L.; Li, Zhi; Assary, Rajeev S.

2015-06-01

Rapid and selective formal hydrogenolysis of aliphatic ester RC(O)O-R' linkages is achieved by a tandem homogeneous metal triflate + supported palladium catalytic system. The triflate catalyzes the mildly exothermic, turnover-limiting O-R' cleavage process, whereas the exothermic hydrogenation of the intermediate alkene further drives the overall reaction to completion.

A ratiometric fluorescent molecular probe for visualization of mitochondrial temperature in living cells.

PubMed

Homma, Mitsumasa; Takei, Yoshiaki; Murata, Atsushi; Inoue, Takafumi; Takeoka, Shinji

2015-04-11

Mitochondrial thermodynamics is the key to understand cellular activities related to homeostasis and energy balance. Here, we report the first ratiometric fluorescent molecular probe (Mito-RTP) that is selectively localized in the mitochondria and visualize the temperature. We confirmed that Mito-RTP could work as a ratiometric thermometer in a cuvette and living cells.

PA01.34. Catagorical interpretation in Microsoft excel of jangam dravya database from Bruhat-Trayi & Laghu-Trayi

PubMed Central

Saraf, Abhijeet

2012-01-01

Purpose: Not a single drug in Ayurveda has been termed as non-medicinal. This means every Dravya has medicinal value in this world. Jangam dravya is an animal sourced medicine. In samhita Jangam Dravya are described first. So as per Krama Varnan Vichar, Jangam Dravyas are significant in this type. In Ayurvedic literature there is more literature on Audbhid & Parthiva Dravyas. I Total available nighantu: more than 25. Total available Rasa Grantha: about 145. There is no one Grantha on Jangam Dravya which describes their whole information. Jangam Dravyas are described in Ayurvedic literature in different views and in different branches. Gross description is available in Samhitas. But they aren’t in format. They are not compiled according to their Guna Karma, Upayogitwa, Vyadhiharatwa, and Kalpa etc. Their use in Chikitsa is minimal as their ready references are not available, though very much effective. So due to sheer need of compilation of these references this topic was selected for study. The basic need for study of Jangam Dravya is to prepare its whole DATABASE. So through this study Database of Jangam Dravya can be available like Jangam Dravya. Method: Selection of topic this is a fundamental & literary study, Selection of material, Selection of Database software & font, Collection of data & preparation of Master Chart, Preparation of Database, Interpretation & summarization of data. Result: So in this paper, we are going to focus on literature availability of jangam dravya with the help of modern technique like Microsoft Excel. And also how we can prepare and use the categorical interpretation of jangam dravya with help of database Conclusion: Jangam Dravyas are described in Ayurvedic literature in different views and in different branches. Importances of these dravyas are the main key point of this study.

Rapid production of optimal-quality reduced-resolution representations of very large databases

DOEpatents

Sigeti, David E.; Duchaineau, Mark; Miller, Mark C.; Wolinsky, Murray; Aldrich, Charles; Mineev-Weinstein, Mark B.

2001-01-01

View space representation data is produced in real time from a world space database representing terrain features. The world space database is first preprocessed. A database is formed having one element for each spatial region corresponding to a finest selected level of detail. A multiresolution database is then formed by merging elements and a strict error metric is computed for each element at each level of detail that is independent of parameters defining the view space. The multiresolution database and associated strict error metrics are then processed in real time for real time frame representations. View parameters for a view volume comprising a view location and field of view are selected. The error metric with the view parameters is converted to a view-dependent error metric. Elements with the coarsest resolution are chosen for an initial representation. Data set first elements from the initial representation data set are selected that are at least partially within the view volume. The first elements are placed in a split queue ordered by the value of the view-dependent error metric. If the number of first elements in the queue meets or exceeds a predetermined number of elements or whether the largest error metric is less than or equal to a selected upper error metric bound, the element at the head of the queue is force split and the resulting elements are inserted into the queue. Force splitting is continued until the determination is positive to form a first multiresolution set of elements. The first multiresolution set of elements is then outputted as reduced resolution view space data representing the terrain features.

Aptamer Database

PubMed Central

Lee, Jennifer F.; Hesselberth, Jay R.; Meyers, Lauren Ancel; Ellington, Andrew D.

2004-01-01

The aptamer database is designed to contain comprehensive sequence information on aptamers and unnatural ribozymes that have been generated by in vitro selection methods. Such data are not normally collected in ‘natural’ sequence databases, such as GenBank. Besides serving as a storehouse of sequences that may have diagnostic or therapeutic utility, the database serves as a valuable resource for theoretical biologists who describe and explore fitness landscapes. The database is updated monthly and is publicly available at http://aptamer.icmb.utexas.edu/. PMID:14681367

Salt bridges: geometrically specific, designable interactions.

PubMed

Donald, Jason E; Kulp, Daniel W; DeGrado, William F

2011-03-01

Salt bridges occur frequently in proteins, providing conformational specificity and contributing to molecular recognition and catalysis. We present a comprehensive analysis of these interactions in protein structures by surveying a large database of protein structures. Salt bridges between Asp or Glu and His, Arg, or Lys display extremely well-defined geometric preferences. Several previously observed preferences are confirmed, and others that were previously unrecognized are discovered. Salt bridges are explored for their preferences for different separations in sequence and in space, geometric preferences within proteins and at protein-protein interfaces, co-operativity in networked salt bridges, inclusion within metal-binding sites, preference for acidic electrons, apparent conformational side chain entropy reduction on formation, and degree of burial. Salt bridges occur far more frequently between residues at close than distant sequence separations, but, at close distances, there remain strong preferences for salt bridges at specific separations. Specific types of complex salt bridges, involving three or more members, are also discovered. As we observe a strong relationship between the propensity to form a salt bridge and the placement of salt-bridging residues in protein sequences, we discuss the role that salt bridges might play in kinetically influencing protein folding and thermodynamically stabilizing the native conformation. We also develop a quantitative method to select appropriate crystal structure resolution and B-factor cutoffs. Detailed knowledge of these geometric and sequence dependences should aid de novo design and prediction algorithms. Copyright © 2010 Wiley-Liss, Inc.

HotSpot Wizard 3.0: web server for automated design of mutations and smart libraries based on sequence input information.

PubMed

Sumbalova, Lenka; Stourac, Jan; Martinek, Tomas; Bednar, David; Damborsky, Jiri

2018-05-23

HotSpot Wizard is a web server used for the automated identification of hotspots in semi-rational protein design to give improved protein stability, catalytic activity, substrate specificity and enantioselectivity. Since there are three orders of magnitude fewer protein structures than sequences in bioinformatic databases, the major limitation to the usability of previous versions was the requirement for the protein structure to be a compulsory input for the calculation. HotSpot Wizard 3.0 now accepts the protein sequence as input data. The protein structure for the query sequence is obtained either from eight repositories of homology models or is modeled using Modeller and I-Tasser. The quality of the models is then evaluated using three quality assessment tools-WHAT_CHECK, PROCHECK and MolProbity. During follow-up analyses, the system automatically warns the users whenever they attempt to redesign poorly predicted parts of their homology models. The second main limitation of HotSpot Wizard's predictions is that it identifies suitable positions for mutagenesis, but does not provide any reliable advice on particular substitutions. A new module for the estimation of thermodynamic stabilities using the Rosetta and FoldX suites has been introduced which prevents destabilizing mutations among pre-selected variants entering experimental testing. HotSpot Wizard is freely available at http://loschmidt.chemi.muni.cz/hotspotwizard.

Theoretical studies of aluminum and aluminide alloys using CALPHAD and first-principles approach

NASA Astrophysics Data System (ADS)

Jiang, Chao

Heat-treatable aluminum alloys have been widely used in the automobile and aerospace industries as structural materials due to their light weight and high strength. To study the age-hardening process in heat-treatable aluminum alloys, the Gibbs energies of the strengthening metastable phases, e.g. theta ' and theta″, are critical. However, those data are not included in the existing thermodynamic databases for aluminum alloys due to the semi-empirical nature of the CALPHAD approach. In the present study, the thermodynamics of the Al-Cu system, the pivotal age-hardening system, is remodeled using a combined CALPHAD and first-principles approach. The formation enthalpies and vibrational formation entropies of the stable and metastable phases in the Al-Cu system are provided by first-principles calculations. Special Quasirandom Structures (SQS's) are applied to model the substitutionally random fee and bee alloys. SQS's for binary bee alloys are developed and tested in the present study. Finally, a self-consistent thermodynamic description of the Al-Cu system including the two metastable theta″ and theta' phases is obtained. During welding of heat-treatable aluminum alloys, a detrimental phenomenon called constitutional liquation, i.e. the local eutectic melting of second-phase particles in a matrix at temperatures above the eutectic temperature but below the solidus of the alloy, may occur in the heat-affected zone (HAZ). In the present study, diffusion code DICTRA coupled with realistic thermodynamic and kinetic databases is used to simulate the constitutional liquation in the model Al-Cu system. The simulated results are in quantitative agreement with experiments. The critical heating rate to avoid constitutional liquation is also determined through computer simulations. Besides the heat-treatable aluminum alloys, intermetallic compounds based on transition metal aluminides, e.g. NiAl and FeAl, are also promising candidates for the next-generation of high-temperature structural materials for aerospace applications due to their high melting temperature and good oxidation resistance. Many important properties of B2 aluminides are governed by the existences of point defects. In the present study, Special Quasirandom Structures (SQS's) are developed to model non-stoichiometric B2 compounds containing large concentrations of constitutional point defects. The SQS's are then applied to study B2 NiAl. The first-principles SQS results provide formation enthalpies, equilibrium lattice parameters and elastic constants of B2 NiAl which agree satisfactorily with the existing experimental data in the literature. It is unambiguously shown that, at T = 0K and zero pressure, Ni vacancies and antisite Ni atoms are the energetically favorable point defects in Al-rich and Ni-rich B2 NiAl, respectively. Remarkably, it is predicted that high defect concentrations can lead to structural instability of B2 NiAl, which explains well the martensitic transformation observed in this compound at high Ni concentrations.

Searching fee and non-fee toxicology information resources: an overview of selected databases.

PubMed

Wright, L L

2001-01-12

Toxicology profiles organize information by broad subjects, the first of which affirms identity of the agent studied. Studies here show two non-fee databases (ChemFinder and ChemIDplus) verify the identity of compounds with high efficiency (63% and 73% respectively) with the fee-based Chemical Abstracts Registry file serving well to fill data gaps (100%). Continued searching proceeds using knowledge of structure, scope and content to select databases. Valuable sources for information are factual databases that collect data and facts in special subject areas organized in formats available for analysis or use. Some sources representative of factual files are RTECS, CCRIS, HSDB, GENE-TOX and IRIS. Numerous factual databases offer a wealth of reliable information; however, exhaustive searches probe information published in journal articles and/or technical reports with records residing in bibliographic databases such as BIOSIS, EMBASE, MEDLINE, TOXLINE and Web of Science. Listed with descriptions are numerous factual and bibliographic databases supplied by 11 producers. Given the multitude of options and resources, it is often necessary to seek service desk assistance. Questions were posed by telephone and e-mail to service desks at DIALOG, ISI, MEDLARS, Micromedex and STN International. Results of the survey are reported.

Modeling the Non-Equilibrium Process of the Chemical Adsorption of Ammonia on GaN(0001) Reconstructed Surfaces Based on Steepest-Entropy-Ascent Quantum Thermodynamics.

PubMed

Kusaba, Akira; Li, Guanchen; von Spakovsky, Michael R; Kangawa, Yoshihiro; Kakimoto, Koichi

2017-08-15

Clearly understanding elementary growth processes that depend on surface reconstruction is essential to controlling vapor-phase epitaxy more precisely. In this study, ammonia chemical adsorption on GaN(0001) reconstructed surfaces under metalorganic vapor phase epitaxy (MOVPE) conditions (3Ga-H and N ad -H + Ga-H on a 2 × 2 unit cell) is investigated using steepest-entropy-ascent quantum thermodynamics (SEAQT). SEAQT is a thermodynamic-ensemble based, first-principles framework that can predict the behavior of non-equilibrium processes, even those far from equilibrium where the state evolution is a combination of reversible and irreversible dynamics. SEAQT is an ideal choice to handle this problem on a first-principles basis since the chemical adsorption process starts from a highly non-equilibrium state. A result of the analysis shows that the probability of adsorption on 3Ga-H is significantly higher than that on N ad -H + Ga-H. Additionally, the growth temperature dependence of these adsorption probabilities and the temperature increase due to the heat of reaction is determined. The non-equilibrium thermodynamic modeling applied can lead to better control of the MOVPE process through the selection of preferable reconstructed surfaces. The modeling also demonstrates the efficacy of DFT-SEAQT coupling for determining detailed non-equilibrium process characteristics with a much smaller computational burden than would be entailed with mechanics-based, microscopic-mesoscopic approaches.

Modeling the Non-Equilibrium Process of the Chemical Adsorption of Ammonia on GaN(0001) Reconstructed Surfaces Based on Steepest-Entropy-Ascent Quantum Thermodynamics

PubMed Central

Kusaba, Akira; von Spakovsky, Michael R.; Kangawa, Yoshihiro; Kakimoto, Koichi

2017-01-01

Clearly understanding elementary growth processes that depend on surface reconstruction is essential to controlling vapor-phase epitaxy more precisely. In this study, ammonia chemical adsorption on GaN(0001) reconstructed surfaces under metalorganic vapor phase epitaxy (MOVPE) conditions (3Ga-H and Nad-H + Ga-H on a 2 × 2 unit cell) is investigated using steepest-entropy-ascent quantum thermodynamics (SEAQT). SEAQT is a thermodynamic-ensemble based, first-principles framework that can predict the behavior of non-equilibrium processes, even those far from equilibrium where the state evolution is a combination of reversible and irreversible dynamics. SEAQT is an ideal choice to handle this problem on a first-principles basis since the chemical adsorption process starts from a highly non-equilibrium state. A result of the analysis shows that the probability of adsorption on 3Ga-H is significantly higher than that on Nad-H + Ga-H. Additionally, the growth temperature dependence of these adsorption probabilities and the temperature increase due to the heat of reaction is determined. The non-equilibrium thermodynamic modeling applied can lead to better control of the MOVPE process through the selection of preferable reconstructed surfaces. The modeling also demonstrates the efficacy of DFT-SEAQT coupling for determining detailed non-equilibrium process characteristics with a much smaller computational burden than would be entailed with mechanics-based, microscopic-mesoscopic approaches. PMID:28809816

THE ROLE OF METASTABLE STATES IN POLYMER PHASE TRANSITIONS: Concepts, Principles, and Experimental Observations

NASA Astrophysics Data System (ADS)

Cheng, Stephen Z. D.; Keller, Andrew

1998-08-01

Polymer phases can be described in the same way as phases in other condensed matter using a number density operator and its correlation functions. This description requires the understanding of symmetry operations and order at different atomic and molecular levels. Statistical mechanics provides a link between the microscopic description of the structure and motion and the macroscopic thermodynamic properties. Within the limits of the laws of thermodynamics, polymers exhibit a rich variety of phase transition behaviors. By definition, a first-order phase transition describes a transformation that involves a sudden change of thermodynamic properties at its transition temperature, whereas higher-order phase transitions are classified as critical phenomena. Of special interest is the role of metastability in phase and phase transition behaviors. Although a metastable state possesses a local free energy minimum, it is not at the global equilibrium. Furthermore, metastable states can also be associated with phase sizes. Metastable behavior is also observed in phase transformations that are impeded by kinetic limitations along the pathway to thermodynamic equilibrium. This is illustrated in structural and morphological investigations of crystallization and mesophase transitions, liquid-liquid phase separation, vitrification, and gel formation, as well as combinations of transformation processes. In these cases, the metastable state often becomes the dominant state for the entire system and is observed over a range of time and size scales. This review describes the general principles of metastability in polymer phases and phase transitions and provides illustrations from current experimental works in selected areas.

Self-microemulsifying smaller molecular volume oil (Capmul MCM) using non-ionic surfactants: a delivery system for poorly water-soluble drug.

PubMed

Bandivadeka, Mithun Mohanraor; Pancholi, Shyam Sundar; Kaul-Ghanekar, Ruchika; Choudhari, Amit; Koppikar, Soumya

2012-07-01

The main purpose of this work is to formulate self-microemulsifying drug delivery system (SMEDDS) using smaller molecular oil with Atorvastatin calcium as a model drug. Solubility of the selected drug was accessed in oils and surfactants. Percent transmittance (%T) test study was performed to identify the efficient self-microemulsifying formulations. Those formulations which showed higher value for %T were evaluated for droplet size, polydispersity index, ζ potential, refractive index and cloud point measurement. Effect of drug loading on droplet size, increasing dilution in different media, thermodynamic stability and in vitro dissolution was performed to observe the performance of the selected formulation. Further cytotoxicity and permeation enhancement studies were carried out on Caco2 cell lines. Of all the oils accessed for drug solubility, Capmul MCM showed higher solubility capacity for Atorvastatin calcium. Capmul MCM was better microemulsified using combination of Tween 20 and Labrasol surfactant. Droplet size was as low as 86.93 nm with polydispersity index and ζ potential at 0.195 ± 0.011 and -7.27 ± 3.11 mV respectively. The selected undiluted formulation showed refractive index values ranging from 1.40 to 1.47 indicating the isotropicity of the formulation. The selected formulation was robust to dilution in different media and thermodynamically stable. Dissolution profile was enhanced for the selected drug as compared to marketed formulation with t85% and DE values at 10 min and 80.15 respectively. Also cytotoxicity measurement showed minimum effect with good permeation enhancing capacity. Thus our study demonstrates the use of smaller molecular oil (Capmul MCM) for developing self-microemulsifying drug delivery system for better in vitro and in vivo performance.

Prediction of Phase Behavior of Spray-Dried Amorphous Solid Dispersions: Assessment of Thermodynamic Models, Standard Screening Methods and a Novel Atomization Screening Device with Regard to Prediction Accuracy

PubMed Central

Chavez, Pierre-François; Meeus, Joke; Robin, Florent; Schubert, Martin Alexander; Somville, Pascal

2018-01-01

The evaluation of drug–polymer miscibility in the early phase of drug development is essential to ensure successful amorphous solid dispersion (ASD) manufacturing. This work investigates the comparison of thermodynamic models, conventional experimental screening methods (solvent casting, quench cooling), and a novel atomization screening device based on their ability to predict drug–polymer miscibility, solid state properties (Tg value and width), and adequate polymer selection during the development of spray-dried amorphous solid dispersions (SDASDs). Binary ASDs of four drugs and seven polymers were produced at 20:80, 40:60, 60:40, and 80:20 (w/w). Samples were systematically analyzed using modulated differential scanning calorimetry (mDSC) and X-ray powder diffraction (XRPD). Principal component analysis (PCA) was used to qualitatively assess the predictability of screening methods with regards to SDASD development. Poor correlation was found between theoretical models and experimentally-obtained results. Additionally, the limited ability of usual screening methods to predict the miscibility of SDASDs did not guarantee the appropriate selection of lead excipient for the manufacturing of robust SDASDs. Contrary to standard approaches, our novel screening device allowed the selection of optimal polymer and drug loading and established insight into the final properties and performance of SDASDs at an early stage, therefore enabling the optimization of the scaled-up late-stage development. PMID:29518936

Detecting Selection on Protein Stability through Statistical Mechanical Models of Folding and Evolution

PubMed Central

Bastolla, Ugo

2014-01-01

The properties of biomolecules depend both on physics and on the evolutionary process that formed them. These two points of view produce a powerful synergism. Physics sets the stage and the constraints that molecular evolution has to obey, and evolutionary theory helps in rationalizing the physical properties of biomolecules, including protein folding thermodynamics. To complete the parallelism, protein thermodynamics is founded on the statistical mechanics in the space of protein structures, and molecular evolution can be viewed as statistical mechanics in the space of protein sequences. In this review, we will integrate both points of view, applying them to detecting selection on the stability of the folded state of proteins. We will start discussing positive design, which strengthens the stability of the folded against the unfolded state of proteins. Positive design justifies why statistical potentials for protein folding can be obtained from the frequencies of structural motifs. Stability against unfolding is easier to achieve for longer proteins. On the contrary, negative design, which consists in destabilizing frequently formed misfolded conformations, is more difficult to achieve for longer proteins. The folding rate can be enhanced by strengthening short-range native interactions, but this requirement contrasts with negative design, and evolution has to trade-off between them. Finally, selection can accelerate functional movements by favoring low frequency normal modes of the dynamics of the native state that strongly correlate with the functional conformation change. PMID:24970217

47 CFR 15.703 - Definitions.

Code of Federal Regulations, 2010 CFR

2010-10-01

... database or spectrum sensing. (b) Client device. A TVBD operating in client mode. (c) Client mode. An... TVBD is able to select a channel itself based on a list provided by the database and initiate a network... does not require use of a geo-location capability or access to the TV bands database and requires...

An Evaluation of Online Business Databases.

ERIC Educational Resources Information Center

van der Heyde, Angela J.

The purpose of this study was to evaluate the credibility and timeliness of online business databases. The areas of evaluation were the currency, reliability, and extent of financial information in the databases. These were measured by performing an online search for financial information on five U.S. companies. The method of selection for the…

Defining Electron Bifurcation in the Electron-Transferring Flavoprotein Family.

PubMed

Garcia Costas, Amaya M; Poudel, Saroj; Miller, Anne-Frances; Schut, Gerrit J; Ledbetter, Rhesa N; Fixen, Kathryn R; Seefeldt, Lance C; Adams, Michael W W; Harwood, Caroline S; Boyd, Eric S; Peters, John W

2017-11-01

Electron bifurcation is the coupling of exergonic and endergonic redox reactions to simultaneously generate (or utilize) low- and high-potential electrons. It is the third recognized form of energy conservation in biology and was recently described for select electron-transferring flavoproteins (Etfs). Etfs are flavin-containing heterodimers best known for donating electrons derived from fatty acid and amino acid oxidation to an electron transfer respiratory chain via Etf-quinone oxidoreductase. Canonical examples contain a flavin adenine dinucleotide (FAD) that is involved in electron transfer, as well as a non-redox-active AMP. However, Etfs demonstrated to bifurcate electrons contain a second FAD in place of the AMP. To expand our understanding of the functional variety and metabolic significance of Etfs and to identify amino acid sequence motifs that potentially enable electron bifurcation, we compiled 1,314 Etf protein sequences from genome sequence databases and subjected them to informatic and structural analyses. Etfs were identified in diverse archaea and bacteria, and they clustered into five distinct well-supported groups, based on their amino acid sequences. Gene neighborhood analyses indicated that these Etf group designations largely correspond to putative differences in functionality. Etfs with the demonstrated ability to bifurcate were found to form one group, suggesting that distinct conserved amino acid sequence motifs enable this capability. Indeed, structural modeling and sequence alignments revealed that identifying residues occur in the NADH- and FAD-binding regions of bifurcating Etfs. Collectively, a new classification scheme for Etf proteins that delineates putative bifurcating versus nonbifurcating members is presented and suggests that Etf-mediated bifurcation is associated with surprisingly diverse enzymes. IMPORTANCE Electron bifurcation has recently been recognized as an electron transfer mechanism used by microorganisms to maximize energy conservation. Bifurcating enzymes couple thermodynamically unfavorable reactions with thermodynamically favorable reactions in an overall spontaneous process. Here we show that the electron-transferring flavoprotein (Etf) enzyme family exhibits far greater diversity than previously recognized, and we provide a phylogenetic analysis that clearly delineates bifurcating versus nonbifurcating members of this family. Structural modeling of proteins within these groups reveals key differences between the bifurcating and nonbifurcating Etfs. Copyright © 2017 American Society for Microbiology.

Defining Electron Bifurcation in the Electron-Transferring Flavoprotein Family

PubMed Central

Garcia Costas, Amaya M.; Poudel, Saroj; Miller, Anne-Frances; Schut, Gerrit J.; Ledbetter, Rhesa N.; Seefeldt, Lance C.; Adams, Michael W. W.

2017-01-01

ABSTRACT Electron bifurcation is the coupling of exergonic and endergonic redox reactions to simultaneously generate (or utilize) low- and high-potential electrons. It is the third recognized form of energy conservation in biology and was recently described for select electron-transferring flavoproteins (Etfs). Etfs are flavin-containing heterodimers best known for donating electrons derived from fatty acid and amino acid oxidation to an electron transfer respiratory chain via Etf-quinone oxidoreductase. Canonical examples contain a flavin adenine dinucleotide (FAD) that is involved in electron transfer, as well as a non-redox-active AMP. However, Etfs demonstrated to bifurcate electrons contain a second FAD in place of the AMP. To expand our understanding of the functional variety and metabolic significance of Etfs and to identify amino acid sequence motifs that potentially enable electron bifurcation, we compiled 1,314 Etf protein sequences from genome sequence databases and subjected them to informatic and structural analyses. Etfs were identified in diverse archaea and bacteria, and they clustered into five distinct well-supported groups, based on their amino acid sequences. Gene neighborhood analyses indicated that these Etf group designations largely correspond to putative differences in functionality. Etfs with the demonstrated ability to bifurcate were found to form one group, suggesting that distinct conserved amino acid sequence motifs enable this capability. Indeed, structural modeling and sequence alignments revealed that identifying residues occur in the NADH- and FAD-binding regions of bifurcating Etfs. Collectively, a new classification scheme for Etf proteins that delineates putative bifurcating versus nonbifurcating members is presented and suggests that Etf-mediated bifurcation is associated with surprisingly diverse enzymes. IMPORTANCE Electron bifurcation has recently been recognized as an electron transfer mechanism used by microorganisms to maximize energy conservation. Bifurcating enzymes couple thermodynamically unfavorable reactions with thermodynamically favorable reactions in an overall spontaneous process. Here we show that the electron-transferring flavoprotein (Etf) enzyme family exhibits far greater diversity than previously recognized, and we provide a phylogenetic analysis that clearly delineates bifurcating versus nonbifurcating members of this family. Structural modeling of proteins within these groups reveals key differences between the bifurcating and nonbifurcating Etfs. PMID:28808132

A cluster-based approach to selecting representative stimuli from the International Affective Picture System (IAPS) database.

PubMed

Constantinescu, Alexandra C; Wolters, Maria; Moore, Adam; MacPherson, Sarah E

2017-06-01

The International Affective Picture System (IAPS; Lang, Bradley, & Cuthbert, 2008) is a stimulus database that is frequently used to investigate various aspects of emotional processing. Despite its extensive use, selecting IAPS stimuli for a research project is not usually done according to an established strategy, but rather is tailored to individual studies. Here we propose a standard, replicable method for stimulus selection based on cluster analysis, which re-creates the group structure that is most likely to have produced the valence arousal, and dominance norms associated with the IAPS images. Our method includes screening the database for outliers, identifying a suitable clustering solution, and then extracting the desired number of stimuli on the basis of their level of certainty of belonging to the cluster they were assigned to. Our method preserves statistical power in studies by maximizing the likelihood that the stimuli belong to the cluster structure fitted to them, and by filtering stimuli according to their certainty of cluster membership. In addition, although our cluster-based method is illustrated using the IAPS, it can be extended to other stimulus databases.

International Data on Radiological Sources

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

Martha Finck; Margaret Goldberg

2010-07-01

ABSTRACT The mission of radiological dispersal device (RDD) nuclear forensics is to identify the provenance of nuclear and radiological materials used in RDDs and to aid law enforcement in tracking nuclear materials and routes. The application of databases to radiological forensics is to match RDD source material to a source model in the database, provide guidance regarding a possible second device, and aid the FBI by providing a short list of manufacturers and distributors, and ultimately to the last legal owner of the source. The Argonne/Idaho National Laboratory RDD attribution database is a powerful technical tool in radiological forensics. Themore » database (1267 unique vendors) includes all sealed sources and a device registered in the U.S., is complemented by data from the IAEA Catalogue, and is supported by rigorous in-lab characterization of selected sealed sources regarding physical form, radiochemical composition, and age-dating profiles. Close working relationships with global partners in the commercial sealed sources industry provide invaluable technical information and expertise in the development of signature profiles. These profiles are critical to the down-selection of potential candidates in either pre- or post- event RDD attribution. The down-selection process includes a match between an interdicted (or detonated) source and a model in the database linked to one or more manufacturers and distributors.« less

LactMed: Drugs and Lactation Database

MedlinePlus

... App LactMed Record Format Database Creation & Peer Review Process Help Fact Sheet Sample Record TOXNET FAQ Glossary Selected References About Dietary Supplements Breastfeeding Links Get LactMed Widget Contact Us Email: tehip@ ...

Development of a personalized training system using the Lung Image Database Consortium and Image Database resource Initiative Database.

PubMed

Lin, Hongli; Wang, Weisheng; Luo, Jiawei; Yang, Xuedong

2014-12-01

The aim of this study was to develop a personalized training system using the Lung Image Database Consortium (LIDC) and Image Database resource Initiative (IDRI) Database, because collecting, annotating, and marking a large number of appropriate computed tomography (CT) scans, and providing the capability of dynamically selecting suitable training cases based on the performance levels of trainees and the characteristics of cases are critical for developing a efficient training system. A novel approach is proposed to develop a personalized radiology training system for the interpretation of lung nodules in CT scans using the Lung Image Database Consortium (LIDC) and Image Database Resource Initiative (IDRI) database, which provides a Content-Boosted Collaborative Filtering (CBCF) algorithm for predicting the difficulty level of each case of each trainee when selecting suitable cases to meet individual needs, and a diagnostic simulation tool to enable trainees to analyze and diagnose lung nodules with the help of an image processing tool and a nodule retrieval tool. Preliminary evaluation of the system shows that developing a personalized training system for interpretation of lung nodules is needed and useful to enhance the professional skills of trainees. The approach of developing personalized training systems using the LIDC/IDRL database is a feasible solution to the challenges of constructing specific training program in terms of cost and training efficiency. Copyright © 2014 AUR. Published by Elsevier Inc. All rights reserved.

Effective concentration as a tool for quantitatively addressing preorganization in multicomponent assemblies: application to the selective complexation of lanthanide cations.

PubMed

Canard, Gabriel; Koeller, Sylvain; Bernardinelli, Gérald; Piguet, Claude

2008-01-23

The beneficial entropic effect, which may be expected from the connection of three tridentate binding units to a strain-free covalent tripod for complexing nine-coordinate cations (Mz+ = Ca2+, La3+, Eu3+, Lu3+), is quantitatively analyzed by using a simple thermodynamic additive model. The switch from pure intermolecular binding processes, characterizing the formation of the triple-helical complexes [M(L2)3]z+, to a combination of inter- and intramolecular complexation events in [M(L8)]z+ shows that the ideal structural fit observed in [M(L8)]z+ indeed masks large energetic constraints. This limitation is evidenced by the faint effective concentrations, ceff, which control the intramolecular ring-closing reactions operating in [M(L8)]z+. This predominence of the thermodynamic approach over the usual structural analysis agrees with the hierarchical relationships linking energetics and structures. Its simple estimation by using a single microscopic parameter, ceff, opens novel perspectives for the molecular tuning of specific receptors for the recognition of large cations, a crucial point for the programming of heterometallic f-f complexes under thermodynamic control.

Thermodynamics of Small Alkali Metal Halide Cluster Ions: Comparison of Classical Molecular Simulations with Experiment and Quantum Chemistry

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

Vlcek, Lukas; Uhlik, Filip; Moucka, Filip

We evaluate the ability of selected classical molecular models to describe the thermodynamic and structural aspects of gas-phase hydration of alkali halide ions and the formation of small water clusters. To understand the effect of many-body interactions (polarization) and charge penetration effects on the accuracy of a force field, we perform Monte Carlo simulations with three rigid water models using different functional forms to account for these effects: (i) point charge non-polarizable SPC/E, (ii) Drude point charge polarizable SWM4- DP, and (iii) Drude Gaussian charge polarizable BK3. Model predictions are compared with experimental Gibbs free energies and enthalpies of ionmore » hydration, and with microscopic structural properties obtained from quantum DFT calculations. We find that all three models provide comparable predictions for pure water clusters and cation hydration, but differ significantly in their description of anion hydration. None of the investigated classical force fields can consistently and quantitatively reproduce the experimental gas phase hydration thermodynamics. The outcome of this study highlights the relation between the functional form that describes the effective intermolecular interactions and the accuracy of the resulting ion hydration properties.« less

Thermodynamic Analysis of TEG-TEC Device Including Influence of Thomson Effect

NASA Astrophysics Data System (ADS)

Feng, Yuanli; Chen, Lingen; Meng, Fankai; Sun, Fengrui

2018-01-01

A thermodynamic model of a thermoelectric cooler driven by thermoelectric generator (TEG-TEC) device is established considering Thomson effect. The performance is analyzed and optimized using numerical calculation based on non-equilibrium thermodynamic theory. The influence characteristics of Thomson effect on the optimal performance and variable selection are investigated by comparing the condition with and without Thomson effect. The results show that Thomson effect degrades the performance of TEG-TEC device, it decreases the cooling capacity by 27 %, decreases the coefficient of performance (COP) by 19 %, decreases the maximum cooling temperature difference by 11 % when the ratio of thermoelectric elements number is 0.6, the cold junction temperature of thermoelectric cooler (TEC) is 285 K and the hot junction temperature of thermoelectric generator (TEG) is 450 K. Thomson effect degrades the optimal performance of TEG-TEC device, it decreases the maximum cooling capacity by 28 % and decreases the maximum COP by 28 % under the same junction temperatures. Thomson effect narrows the optimal variable range and optimal working range. In the design of the devices, limited-number thermoelectric elements should be more allocated appropriately to TEG when consider Thomson effect. The results may provide some guidelines for the design of TEG-TEC devices.

Performance comparison of different thermodynamic cycles for an innovative central receiver solar power plant

NASA Astrophysics Data System (ADS)

Reyes-Belmonte, Miguel A.; Sebastián, Andrés; González-Aguilar, José; Romero, Manuel

2017-06-01

The potential of using different thermodynamic cycles coupled to a solar tower central receiver that uses a novel heat transfer fluid is analyzed. The new fluid, named as DPS, is a dense suspension of solid particles aerated through a tubular receiver used to convert concentrated solar energy into thermal power. This novel fluid allows reaching high temperatures at the solar receiver what opens a wide range of possibilities for power cycle selection. This work has been focused into the assessment of power plant performance using conventional, but optimized cycles but also novel thermodynamic concepts. Cases studied are ranging from subcritical steam Rankine cycle; open regenerative Brayton air configurations at medium and high temperature; combined cycle; closed regenerative Brayton helium scheme and closed recompression supercritical carbon dioxide Brayton cycle. Power cycle diagrams and working conditions for design point are compared amongst the studied cases for a common reference thermal power of 57 MWth reaching the central cavity receiver. It has been found that Brayton air cycle working at high temperature or using supercritical carbon dioxide are the most promising solutions in terms of efficiency conversion for the power block of future generation by means of concentrated solar power plants.

Linking the thermodynamic temperature to an optical frequency: recent advances in Doppler broadening thermometry

PubMed Central

2016-01-01

Laser spectroscopy in the linear regime of radiation–matter interaction is a powerful tool for measuring thermodynamic quantities in a gas at thermodynamic equilibrium. In particular, the Doppler effect can be considered a gift of nature, linking the thermal energy to an optical frequency, namely the line centre frequency of an atomic or molecular spectral line. This is the basis of a relatively new method of primary gas thermometry, known as Doppler broadening thermometry (DBT). This paper reports on the efforts that have been carried out, in the last decade, worldwide, to the end of making DBT competitive with more consolidated and accurate methodologies, such as acoustic gas thermometry and dielectric constant gas thermometry. The main requirements for low-uncertainty DBT, of both theoretical and technical nature, will be discussed, with a special focus on those related to the line shape model and to the frequency scale. A deep comparison among the different molecules that have been selected in successful DBT implementations is also reported. Finally, for the first time, to the best of my knowledge, the influence of refractive index effects is discussed. PMID:26903093

Towards a definition of life.

PubMed

Macklem, Peter T; Seely, Andrew

2010-01-01

This article offers a new definition of life as a "self-contained, self-regulating, self-organizing, self-reproducing, interconnected, open thermodynamic network of component parts which performs work, existing in a complex regime which combines stability and adaptability in the phase transition between order and chaos, as a plant, animal, fungus, or microbe." Open thermodynamic networks, which create and maintain order and are used by all organisms to perform work, import energy from and export entropy into the environment. Intra- and extracellular interconnected networks also confer order. Although life obeys the laws of physics and chemistry, the design of living organisms is not determined by these laws, but by Darwinian selection of the fittest designs. Over a short range of normalized energy consumption, open thermodynamic systems change from deeply ordered to chaotic, and life is found in this phase transition, where a dynamic balance between stability and adaptability allows for homeokinesis. Organisms and cells move within the phase transition with changes in metabolic rate. Seeds, spores and cryo-preserved tissue are well within the ordered regime, while health probably cannot be maintained with displacements into the chaotic regime. Understanding life in these terms may provide new insights into what constitutes health and lead to new theories of disease.

Thermodynamic Modeling of Gas Transport in Glassy Polymeric Membranes.

PubMed

Minelli, Matteo; Sarti, Giulio Cesare

2017-08-19

Solubility and permeability of gases in glassy polymers have been considered with the aim of illustrating the applicability of thermodynamically-based models for their description and prediction. The solubility isotherms are described by using the nonequilibrium lattice fluid (NELF) (model, already known to be appropriate for nonequilibrium glassy polymers, while the permeability isotherms are described through a general transport model in which diffusivity is the product of a purely kinetic factor, the mobility coefficient, and a thermodynamic factor. The latter is calculated from the NELF model and mobility is considered concentration-dependent through an exponential relationship containing two parameters only. The models are tested explicitly considering solubility and permeability data of various penetrants in three glassy polymers, PSf, PPh and 6FDA-6FpDA, selected as the reference for different behaviors. It is shown that the models are able to calculate the different behaviors observed, and in particular the permeability dependence on upstream pressure, both when it is decreasing as well as when it is increasing, with no need to invoke the onset of additional plasticization phenomena. The correlations found between polymer and penetrant properties with the two parameters of the mobility coefficient also lead to the predictive ability of the transport model.

Thermodynamic Modeling of Gas Transport in Glassy Polymeric Membranes

PubMed Central

Minelli, Matteo; Sarti, Giulio Cesare

2017-01-01

Solubility and permeability of gases in glassy polymers have been considered with the aim of illustrating the applicability of thermodynamically-based models for their description and prediction. The solubility isotherms are described by using the nonequilibrium lattice fluid (NELF) (model, already known to be appropriate for nonequilibrium glassy polymers, while the permeability isotherms are described through a general transport model in which diffusivity is the product of a purely kinetic factor, the mobility coefficient, and a thermodynamic factor. The latter is calculated from the NELF model and mobility is considered concentration-dependent through an exponential relationship containing two parameters only. The models are tested explicitly considering solubility and permeability data of various penetrants in three glassy polymers, PSf, PPh and 6FDA-6FpDA, selected as the reference for different behaviors. It is shown that the models are able to calculate the different behaviors observed, and in particular the permeability dependence on upstream pressure, both when it is decreasing as well as when it is increasing, with no need to invoke the onset of additional plasticization phenomena. The correlations found between polymer and penetrant properties with the two parameters of the mobility coefficient also lead to the predictive ability of the transport model. PMID:28825619

Interfacial engineering of solution-processed Ni nanochain-SiO x (x< 2) cermets towards thermodynamically stable, anti-oxidation solar selective absorbers

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

Yu, Xiaobai; Wang, Xiaoxin; Zhang, Qinglin

Here, cermet solar thermal selective absorber coatings are an important component of high-efficiency concentrated solar power (CSP) receivers. The oxidation of the metal nanoparticles in cermet solar absorbers is a great challenge for vacuum-free operation. Recently, we have demonstrated that oxidation is kinetically retarded in solution processed, high-optical-performance Ni nanochain-SiO x cermet system compared to conventional Ni-Al 2O 3 system when annealed in air at 450–600 °C for several hours. However, for long-term, high-temperature applications in CSP systems, thermodynamically stable antioxidation behavior is highly desirable, which requires new mechanisms beyond kinetically reducing the oxidation rate. Towards this goal, in thismore » paper, we demonstrate that pre-operation annealing of Ni nanochain-SiO x cermets at 900 °C in N 2 forms the thermodynamically stable orthorhombic phase of NiSi at the Ni/SiO x interfaces, leading to self-terminated oxidation at 550 °C in air due to this interfacial engineering. In contrast, pre-operation annealing at a lower temperature of 750 °C in N 2 (as conducted in our previous work) cannot achieve interfacial NiSi formation directly, and further annealing in air at 450–600 °C for >4 h only leads to the formation of the less stable (metastable) hexagonal phase of NiSi. Therefore, the high-temperature pre-operation annealing is critical to form the desirable orthorhombic phase of NiSi at Ni/SiO x interfaces towards thermodynamically stable antioxidation behavior. Remarkably, with this improved interfacial engineering, the oxidation of 80-nm-diameter Ni nanochain-SiO x saturates after annealing at 550 °C in air for 12 h. Additional annealing at 550 °C in air for as long as 20 h (i.e., 32 h air annealing at >550 °C in total) has almost no further impact on the structural or optical properties of the coatings, the latter being very sensitive to any interfacial changes due to the localized surface plasmon resonances of the metal nanostructures. This phenomenon holds true for Ni nanoparticle diameter down to 40 nm in Ni-SiO x system, where the optical response remains stable for 53 h at 550 °C in air. The oxidation vs. time curve also shows saturation behavior deviating from the kinetic Deal-Grove oxidation model. These results strongly suggest a promising approach to thermodynamically stable, anti-oxidation Ni/SiO x cermet absorbers via interfacial engineering.« less

Interfacial engineering of solution-processed Ni nanochain-SiO x (x< 2) cermets towards thermodynamically stable, anti-oxidation solar selective absorbers

DOE PAGES

Yu, Xiaobai; Wang, Xiaoxin; Zhang, Qinglin; ...

2016-04-01

Here, cermet solar thermal selective absorber coatings are an important component of high-efficiency concentrated solar power (CSP) receivers. The oxidation of the metal nanoparticles in cermet solar absorbers is a great challenge for vacuum-free operation. Recently, we have demonstrated that oxidation is kinetically retarded in solution processed, high-optical-performance Ni nanochain-SiO x cermet system compared to conventional Ni-Al 2O 3 system when annealed in air at 450–600 °C for several hours. However, for long-term, high-temperature applications in CSP systems, thermodynamically stable antioxidation behavior is highly desirable, which requires new mechanisms beyond kinetically reducing the oxidation rate. Towards this goal, in thismore » paper, we demonstrate that pre-operation annealing of Ni nanochain-SiO x cermets at 900 °C in N 2 forms the thermodynamically stable orthorhombic phase of NiSi at the Ni/SiO x interfaces, leading to self-terminated oxidation at 550 °C in air due to this interfacial engineering. In contrast, pre-operation annealing at a lower temperature of 750 °C in N 2 (as conducted in our previous work) cannot achieve interfacial NiSi formation directly, and further annealing in air at 450–600 °C for >4 h only leads to the formation of the less stable (metastable) hexagonal phase of NiSi. Therefore, the high-temperature pre-operation annealing is critical to form the desirable orthorhombic phase of NiSi at Ni/SiO x interfaces towards thermodynamically stable antioxidation behavior. Remarkably, with this improved interfacial engineering, the oxidation of 80-nm-diameter Ni nanochain-SiO x saturates after annealing at 550 °C in air for 12 h. Additional annealing at 550 °C in air for as long as 20 h (i.e., 32 h air annealing at >550 °C in total) has almost no further impact on the structural or optical properties of the coatings, the latter being very sensitive to any interfacial changes due to the localized surface plasmon resonances of the metal nanostructures. This phenomenon holds true for Ni nanoparticle diameter down to 40 nm in Ni-SiO x system, where the optical response remains stable for 53 h at 550 °C in air. The oxidation vs. time curve also shows saturation behavior deviating from the kinetic Deal-Grove oxidation model. These results strongly suggest a promising approach to thermodynamically stable, anti-oxidation Ni/SiO x cermet absorbers via interfacial engineering.« less

REPDOSE: A database on repeated dose toxicity studies of commercial chemicals--A multifunctional tool.

PubMed

Bitsch, A; Jacobi, S; Melber, C; Wahnschaffe, U; Simetska, N; Mangelsdorf, I

2006-12-01

A database for repeated dose toxicity data has been developed. Studies were selected by data quality. Review documents or risk assessments were used to get a pre-screened selection of available valid data. The structure of the chemicals should be rather simple for well defined chemical categories. The database consists of three core data sets for each chemical: (1) structural features and physico-chemical data, (2) data on study design, (3) study results. To allow consistent queries, a high degree of standardization categories and glossaries were developed for relevant parameters. At present, the database consists of 364 chemicals investigated in 1018 studies which resulted in a total of 6002 specific effects. Standard queries have been developed, which allow analyzing the influence of structural features or PC data on LOELs, target organs and effects. Furthermore, it can be used as an expert system. First queries have shown that the database is a very valuable tool.

Cost considerations in database selection - A comparison of DIALOG and ESA/IRS

NASA Technical Reports Server (NTRS)

Jack, R. F.

1984-01-01

It is pointed out that there are many factors which affect the decision-making process in determining which databases should be selected for conducting the online search on a given topic. In many cases, however, the major consideration will be related to cost. The present investigation is concerned with a comparison of the costs involved in making use of DIALOG and the European Space Agency's Information Retrieval Service (ESA/IRS). The two services are very comparable in many respects. Attention is given to pricing structure, telecommunications, the number of databases, prints, time requirements, a table listing online costs for DIALOG and ESA/IRS, and differences in mounting databases. It is found that ESA/IRS is competitively priced when compared to DIALOG, and, despite occasionally higher telecommunications costs, may be even more economical to use in some cases.

Sodium content of foods contributing to sodium intake: A comparison between selected foods from the CDC Packaged Food Database and the USDA National Nutrient Database for Standard Reference

USDA-ARS?s Scientific Manuscript database

The sodium concentration (mg/100g) for 23 of 125 Sentinel Foods were identified in the 2009 CDC Packaged Food Database (PFD) and compared with data in the USDA’s 2013 Standard Reference 26 (SR 26) database. Sentinel Foods are foods and beverages identified by USDA to be monitored as primary indicat...

Ion Selectivity in the KcsA Potassium Channel from the Perspective of the Ion Binding Site

PubMed Central

Dixit, Purushottam D.; Merchant, Safir; Asthagiri, D.

2009-01-01

To understand the thermodynamic exclusion of Na+ relative to K+ from the S2 site of the selectivity filter, the distribution PX(ɛ) (X = K+ or Na+) of the binding energy (ɛ) of the ion with the channel is analyzed using the potential distribution theorem. By expressing the excess chemical potential of the ion as a sum of mean-field 〈ɛ〉 and fluctuation μexflux,X contributions, we find that selectivity arises from a higher value of μflux,Na+ex relative to μflux,K+ex. To understand the role of site-site interactions on μexflux,X, we decompose PX(ɛ) into n-dependent distributions, where n is the number of ion-coordinating ligands within a distance λ from the ion. For λ comparable to typical ion-oxygen bond distances, investigations building on this multistate model reveal an inverse correlation between favorable ion-site and site-site interactions: the ion-coordination states that most influence the thermodynamics of the ion are also those for which the binding site is energetically less strained and vice versa. This correlation motivates understanding entropic effects in ion binding to the site and leads to the finding that μexflux,X is directly proportional to the average site-site interaction energy, a quantity that is sensitive to the chemical type of the ligand coordinating the ion. Increasing the coordination number around Na+ only partially accounts for the observed magnitude of selectivity; acknowledging the chemical type of the ion-coordinating ligand is essential. PMID:19289040

A Chemically Defined Medium for Rabbit Embryo Cryopreservation

PubMed Central

Bruyère, Pierre; Baudot, Anne; Joly, Thierry; Commin, Loris; Pillet, Elodie; Guérin, Pierre; Louis, Gérard; Josson-Schramme, Anne; Buff, Samuel

2013-01-01

This study evaluates a new synthetic substitute (CRYO3, Ref. 5617, Stem Alpha, France) for animal-based products in rabbit embryo cryopreservation solutions. This evaluation was performed using two approaches: a thermodynamic approach using differential scanning calorimetry and a biological approach using rabbit embryo slow-freezing. During the experiment, foetal calf serum (FCS) was used as a reference. Because FCS varies widely by supplier, three different FCS were selected for the thermodynamic approach. The rabbit embryo slow-freezing solutions were made from Dulbecco's phosphate buffer saline containing 1.5 M Dimethyl Sulfoxide and 18% (v.v−1) of CRYO3 or 18% (v.v−1) of FCS. These solutions were evaluated using four characteristics: the end of melting temperature, the enthalpy of crystallisation (thermodynamic approach) and the embryo survival rates after culture and embryo transfer (biological approach). In the thermodynamic approach, the solutions containing one of the three different FCS had similar mean thermodynamic characteristics but had different variabilities in the overall data with aberrant values. The solution containing CRYO3 had similar thermodynamic properties when compared to those containing FCS. Moreover, no aberrant value was measured in the solution containing CRYO3. This solution appears to be more stable than the solutions containing a FCS. In the biological approach, the in vitro embryo survival rates obtained with the solution containing CRYO3 (73.7% and 81.3%) and with the solution containing a FCS (77.6% and 71.9%) were similar (p = 0.7). Nevertheless, during the in vivo evaluation, the implantation rate (21.8%) and the live-foetuses rate (18.8%) of the CRYO3 group were significantly higher than the implantation rate (7.1%, p = 0.0002) and the live-foetuses rate (5.3%, p = 0.0002) of the FCS group. The pregnancy rate was also higher in the CRYO3 group compared to the FCS group (81.3% and 43.8%, respectively, p = 0.066). We conclude that CRYO3 can be used as a chemically defined substitute for animal-based products in rabbit embryo cryopreservation solutions. PMID:23977074

Revolutionary Materials for Hypersonic Flight

DTIC Science & Technology

2011-10-01

Transactions A (in preparation ). 16. M.D. Novak, CG. Levi, " Silicide Coatings on Niobium Substrates II: Thermodynamic Analysis and Mechanism of...These conditions impose significant challenges to material selection. While metallic materials are favored for their durability to thermal distortion...those of even the most highly-conducting engineering materials. While metallic systems are desirable for use in hypersonic vehicles for durability and

YouTube Fridays: Engaging the Net Generation in 5 Minutes a Week

ERIC Educational Resources Information Center

Liberatore, Matthew W.

2010-01-01

YouTube Fridays is a teaching tool that devotes the first five minutes of class each Friday to a YouTube video related to the course. Students select the videos, which expand the class's educational content in courses such as thermodynamics and material and energy balances. From assessments of two pilot studies using YouTube Fridays in Chemical…

On the upper bound of the thermodynamic stability of fullerenes from small to giant

NASA Astrophysics Data System (ADS)

Pankratyev, Evgeniy Yu; Khatymov, Rustem V.; Sabirov, Denis Sh; Yuldashev, Arthur V.

2018-07-01

From the large variety of C20sbnd C720 fullerenes, the energetically most stable isomers were chosen and studied within the PBE/3ζ quantum-chemical approximation. A phenomenological model of the dependence of the standard enthalpy of formation and entropy of the selected isomers on the number of the carbon atoms is developed. From the analysis of the constants of the phenomenological model, it follows that the C60, C70, C180, and C1500 molecules hold a prominent position among the hypothetical and/or experimentally discovered fullerenes. For the selected energy-stable isomers, the values of the singlet-triplet splitting were calculated. The ground state of the C260sbnd C3, C320sbnd D3d and C500sbnd D3d molecules were found to be of triplet multiplicity that may indicate their low kinetic stability and/or possibility of existence in the derivatized forms. In view of the lack of relevant experimental thermodynamic data on fullerenes, the obtained in this work approximation dependences, expressed in a simple analytical form, may provide useful tool for fast assessing the energetic characteristics of fullerenes, as well as for prediction of those undiscovered yet.

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

PubMed

Meysman, Filip J R; Bruers, Stijn

2010-05-12

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

Adsorption of bacteriophages on clay minerals

USGS Publications Warehouse

Chattopadhyay, Sandip; Puls, Robert W.

1999-01-01

The ability to predict the fate of microorganisms in soil is dependent on an understanding of the process of their sorption on soil and subsurface materials. Presently, we have focused on studying the thermodynamics of sorption of bacteriophages (T-2, MS-2, and φX-174) on clays (hectorite, saponite, kaolinite, and clay fraction of samples collected from a landfill site). The thermodynamic study not only determines the feasibility of the process but also provides information on the relative magnitudes of the different forces under a particular set of conditions. The total free energy of interaction during sorption of bacteriophages on clays (ΔG) has been assumed to be the summation of ΔGH (ΔG due to hydrophobic interactions) and ΔGEL (ΔG due to electrostatic interactions). The magnitude of ΔGH was determined from the different interfacial tensions (γ) present in the system, while ΔGEL was calculated from ζ-potentials of the colloidal particles. Calculated results show that surface hydrophobicities of the selected sorbents and sorbates dictate sorption. Among the selected bacteriophages, maximum sorption was observed with T-2, while hectorite has the maximum sorption capacity. Experimental results obtained from the batch adsorption studies also corroborated those obtained from the theoretical study.

Exploring the site-selective binding of jatrorrhizine to human serum albumin: spectroscopic and molecular modeling approaches.

PubMed

Mi, Ran; Hu, Yan-Jun; Fan, Xiao-Yang; Ouyang, Yu; Bai, Ai-Min

2014-01-03

This paper exploring the site-selective binding of jatrorrhizine to human serum albumin (HSA) under physiological conditions (pH=7.4). The investigation was carried out using fluorescence spectroscopy, UV-vis spectroscopy, and molecular modeling. The results of fluorescence quenching and UV-vis absorption spectra experiments indicated the formation of the complex of HSA-jatrorrhizine. Binding parameters calculating from Stern-Volmer method and Scatchard method were calculated at 298, 304 and 310 K, with the corresponding thermodynamic parameters ΔG, ΔH and ΔS as well. Binding parameters calculating from Stern-Volmer method and Scatchard method showed that jatrorrhizine bind to HSA with the binding affinities of the order 10(4) L mol(-1). The thermodynamic parameters studies revealed that the binding was characterized by negative enthalpy and positive entropy changes and the electrostatic interactions play a major role for jatrorrhizine-HSA association. Site marker competitive displacement experiments and molecular modeling calculation demonstrating that jatrorrhizine is mainly located within the hydrophobic pocket of the subdomain IIIA of HSA. Furthermore, the synchronous fluorescence spectra suggested that the association between jatrorrhizine and HSA changed molecular conformation of HSA. Copyright © 2013. Published by Elsevier B.V.

Efficient sampling over rough energy landscapes with high barriers: A combination of metadynamics with integrated tempering sampling.

PubMed

Yang, Y Isaac; Zhang, Jun; Che, Xing; Yang, Lijiang; Gao, Yi Qin

2016-03-07

In order to efficiently overcome high free energy barriers embedded in a complex energy landscape and calculate overall thermodynamics properties using molecular dynamics simulations, we developed and implemented a sampling strategy by combining the metadynamics with (selective) integrated tempering sampling (ITS/SITS) method. The dominant local minima on the potential energy surface (PES) are partially exalted by accumulating history-dependent potentials as in metadynamics, and the sampling over the entire PES is further enhanced by ITS/SITS. With this hybrid method, the simulated system can be rapidly driven across the dominant barrier along selected collective coordinates. Then, ITS/SITS ensures a fast convergence of the sampling over the entire PES and an efficient calculation of the overall thermodynamic properties of the simulation system. To test the accuracy and efficiency of this method, we first benchmarked this method in the calculation of ϕ - ψ distribution of alanine dipeptide in explicit solvent. We further applied it to examine the design of template molecules for aromatic meta-C-H activation in solutions and investigate solution conformations of the nonapeptide Bradykinin involving slow cis-trans isomerizations of three proline residues.