The building loads analysis system thermodynamics (BLAST) program, Version 2. 0: input booklet. Final report

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

Sowell, E.

1979-06-01

The Building Loads Analysis and System Thermodynamics (BLAST) program is a comprehensive set of subprograms for predicting energy consumption in buildings. There are three major subprograms: (1) the space load predicting subprogram, which computes hourly space loads in a building or zone based on user input and hourly weather data; (2) the air distribution system simulation subprogram, which uses the computed space load and user inputs describing the building air-handling system to calculate hot water or steam, chilled water, and electric energy demands; and (3) the central plant simulation program, which simulates boilers, chillers, onsite power generating equipment and solarmore » energy systems and computes monthly and annual fuel and electrical power consumption and plant life cycle cost.« less

Computer programs for thermodynamic and transport properties of hydrogen (tabcode-II)

NASA Technical Reports Server (NTRS)

Roder, H. M.; Mccarty, R. D.; Hall, W. J.

1972-01-01

The thermodynamic and transport properties of para and equilibrium hydrogen have been programmed into a series of computer routines. Input variables are the pair's pressure-temperature and pressure-enthalpy. The programs cover the range from 1 to 5000 psia with temperatures from the triple point to 6000 R or enthalpies from minus 130 BTU/lb to 25,000 BTU/lb. Output variables are enthalpy or temperature, density, entropy, thermal conductivity, viscosity, at constant volume, the heat capacity ratio, and a heat transfer parameter. Property values on the liquid and vapor boundaries are conveniently obtained through two small routines. The programs achieve high speed by using linear interpolation in a grid of precomputed points which define the surface of the property returned.

Computer Series, 13: Bits and Pieces, 11.

ERIC Educational Resources Information Center

Moore, John W., Ed.

1982-01-01

Describes computer programs (with ordering information) on various topics including, among others, modeling of thermodynamics and economics of solar energy, radioactive decay simulation, stoichiometry drill/tutorial (in Spanish), computer-generated safety quiz, medical chemistry computer game, medical biochemistry question bank, generation of…

Computer program for obtaining thermodynamic and transport properties of air and products of combustion of ASTM-A-1 fuel and air

NASA Technical Reports Server (NTRS)

Hippensteele, S. A.; Colladay, R. S.

1978-01-01

A computer program for determining desired thermodynamic and transport property values by means of a three-dimensional (pressure, fuel-air ratio, and either enthalpy or temperature) interpolation routine was developed. The program calculates temperature (or enthalpy), molecular weight, viscosity, specific heat at constant pressure, thermal conductivity, isentropic exponent (equal to the specific heat ratio at conditions where gases do not react), Prandtl number, and entropy for air and a combustion gas mixture of ASTM-A-1 fuel and air over fuel-air ratios from zero to stoichiometric, pressures from 1 to 40 atm, and temperatures from 250 to 2800 K.

Computer program for determining the thermodynamic properties of Freon refrigerants

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

Riemer, D.H.; Jacobs, H.R.; Boehm, R.F.

1977-12-01

This program was written to be used as a subroutine. The program determines the thermodynamics of Freon refrigerants. The following refrigerants can be analyzed F-11, F-12, F-13, F-14, F-21, F-22, F-23, F-113, and F-114. The subroutine can evaluate a thermodynamic state for these refrigerants given any of the following pairs of state quantities: pressure and quality, pressure and entropy, pressure and enthalpy, temperature and quality, temperature and specific volume, and temperature and pressure. These six pairs of knowns allow the user to analyze any thermodynamic cycle utilizing a refrigerant as the working fluid. The Downing form of the Martin equationmore » of state was used. This report contains a brief description, flow chart and listing of all subroutines required.« less

Computer program for determining the thermodynamic properties of freon refrigerants

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

Riemer, D.H.; Jacobs, H.R.; Boehm, R.F.

1976-07-01

This program was written to be used as a subroutine. The program determines the thermodynamics of Freon refrigerants. The following refrigerants can be analyzed F-11, F-12, F-13, F-14, F-21, F-22, F-23, F-113, and F-114. The subroutine can evaluate a thermodynamic state for these refrigerants given any of the following pairs of state quantities: pressure and quality, pressure and entropy, pressure and enthalpy, temperature and quality, temperature and specific volume and temperature and pressure. These six pairs of knowns allow the user to analyze any thermodynamic cycle utilizing a refrigerant as the working fluid. The Downing form of the Martin equationmore » of state was used. A brief description, flow chart, and listing of all subroutines required are presented.« less

Computer program determines chemical composition of physical system at equilibrium

NASA Technical Reports Server (NTRS)

Kwong, S. S.

1966-01-01

FORTRAN 4 digital computer program calculates equilibrium composition of complex, multiphase chemical systems. This is a free energy minimization method with solution of the problem reduced to mathematical operations, without concern for the chemistry involved. Also certain thermodynamic properties are determined as byproducts of the main calculations.

Thermodynamic Data to 20,000 K For Monatomic Gases

NASA Technical Reports Server (NTRS)

Gordon, Sanford; McBride, Bonnie J.

1999-01-01

This report contains standard-state thermodynamic functions for 50 gaseous atomic elements plus deuterium and electron gas, 51 singly ionized positive ions, and 36 singly ionized negative ions. The data were generated by the NASA Lewis computer program PAC97, a modified version of PAC91 reported in McBride and Gordon. This report is being published primarily to document part of the data currently being used in several NASA Lewis computer programs. The data are presented in tabular and graphical format and are also represented in the form of least-squares coefficients. The tables give the following data as functions of temperature : heat capacity, enthalpy, entropy Gibbs energy, enthalpy of formation, and equilibrium constant. A brief discussion and a comparison of calculated results are given for several models for calculating ideal thermodynamic data for monatomic gases.

BLAKE - A Thermodynamics Code Based on TIGER: Users’ Guide to the Revised Program

DTIC Science & Technology

1998-07-01

thermodynamics program derived from an older version of TIGER.-*-2 Although it is applicable to a wide range of chemical equilibrium calculations...BLAKE is specifically intended for computing the properties of gun propellants at chamber conditions. Its principal difference from other chemical ...for Use with Electrothermal- Chemical (ETC) Systems," ARL-TR-488 (July 1994). The rationale for excluding charged species is presented here. 2

CET89 - CHEMICAL EQUILIBRIUM WITH TRANSPORT PROPERTIES, 1989

NASA Technical Reports Server (NTRS)

Mcbride, B.

1994-01-01

Scientists and engineers need chemical equilibrium composition data to calculate the theoretical thermodynamic properties of a chemical system. This information is essential in the design and analysis of equipment such as compressors, turbines, nozzles, engines, shock tubes, heat exchangers, and chemical processing equipment. The substantial amount of numerical computation required to obtain equilibrium compositions and transport properties for complex chemical systems led scientists at NASA's Lewis Research Center to develop CET89, a program designed to calculate the thermodynamic and transport properties of these systems. CET89 is a general program which will calculate chemical equilibrium compositions and mixture properties for any chemical system with available thermodynamic data. Generally, mixtures may include condensed and gaseous products. CET89 performs the following operations: it 1) obtains chemical equilibrium compositions for assigned thermodynamic states, 2) calculates dilute-gas transport properties of complex chemical mixtures, 3) obtains Chapman-Jouguet detonation properties for gaseous species, 4) calculates incident and reflected shock properties in terms of assigned velocities, and 5) calculates theoretical rocket performance for both equilibrium and frozen compositions during expansion. The rocket performance function allows the option of assuming either a finite area or an infinite area combustor. CET89 accommodates problems involving up to 24 reactants, 20 elements, and 600 products (400 of which may be condensed). The program includes a library of thermodynamic and transport properties in the form of least squares coefficients for possible reaction products. It includes thermodynamic data for over 1300 gaseous and condensed species and transport data for 151 gases. The subroutines UTHERM and UTRAN convert thermodynamic and transport data to unformatted form for faster processing. The program conforms to the FORTRAN 77 standard, except for some input in NAMELIST format. It requires about 423 KB memory, and is designed to be used on mainframe, workstation, and mini computers. Due to its memory requirements, this program does not readily lend itself to implementation on MS-DOS based machines.

Operational procedure for computer program for design point characteristics of a gas generator or a turbojet lift engine for V/STOL applications

NASA Technical Reports Server (NTRS)

Krebs, R. P.

1972-01-01

The computer program described calculates the design-point characteristics of a gas generator or a turbojet lift engine for V/STOL applications. The program computes the dimensions and mass, as well as the thermodynamic performance of the model engine and its components. The program was written in FORTRAN 4 language. Provision has been made so that the program accepts input values in either SI Units or U.S. Customary Units. Each engine design-point calculation requires less than 0.5 second of 7094 computer time.

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.

Program Gives Data On Physical Properties Of Hydrogen

NASA Technical Reports Server (NTRS)

Roder, H. M.; Mccarty, R. D.; Hall, W. J.

1994-01-01

TAB II computer program provides values of thermodynamic and transport properties of hydrogen in useful format. Also, provides values for equilibrium hydrogen and para-hydrogen. Program fast, moderately accurate, and operates over wide ranges of input variables. Written in FORTRAN 77.

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

NASA Technical Reports Server (NTRS)

Nguyen, Han

1994-01-01

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

Thermodynamics of Irreversible Processes. Physical Processes in Terrestrial and Aquatic Ecosystems, Transport Processes.

ERIC Educational Resources Information Center

Levin, Michael; Gallucci, V. F.

These materials were designed to be used by life science students for instruction in the application of physical theory to ecosystem operation. Most modules contain computer programs which are built around a particular application of a physical process. This module describes the application of irreversible thermodynamics to biology. It begins with…

Computing Properties Of Chemical Mixtures At Equilibrium

NASA Technical Reports Server (NTRS)

Mcbride, B. J.; Gordon, S.

1995-01-01

Scientists and engineers need data on chemical equilibrium compositions to calculate theoretical thermodynamic properties of chemical systems. Information essential in design and analysis of such equipment as compressors, turbines, nozzles, engines, shock tubes, heat exchangers, and chemical-processing equipment. CET93 is general program that calculates chemical equilibrium compositions and properties of mixtures for any chemical system for which thermodynamic data are available. Includes thermodynamic data for more than 1,300 gaseous and condensed species and thermal-transport data for 151 gases. Written in FORTRAN 77.

Computer Program for Calculation of Complex Chemical Equilibrium Compositions, Rocket Performance, Incident and Reflected Shocks, and Chapman-Jouguet Detonations. Interim Revision, March 1976

NASA Technical Reports Server (NTRS)

Gordon, S.; Mcbride, B. J.

1976-01-01

A detailed description of the equations and computer program for computations involving chemical equilibria in complex systems is given. A free-energy minimization technique is used. The program permits calculations such as (1) chemical equilibrium for assigned thermodynamic states (T,P), (H,P), (S,P), (T,V), (U,V), or (S,V), (2) theoretical rocket performance for both equilibrium and frozen compositions during expansion, (3) incident and reflected shock properties, and (4) Chapman-Jouguet detonation properties. The program considers condensed species as well as gaseous species.

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.

LARC: computer codes for Lagrangian analysis of stress-gauge data to obtain decomposition rates through correlation to thermodynamic variables

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

Anderson, A.B.; Wackerle, J.

1983-07-01

This report describes a package of five computer codes for analyzing stress-gauge data from shock-wave experiments on reactive materials. The aim of the analysis is to obtain rate laws from experiment. A Lagrangian analysis of the stress records, performed by program LANAL, provides flow histories of particle velocity, density, and energy. Three postprocessing programs, LOOKIT, LOOK1, and LOOK2, are included in the package of codes for producing graphical output of the results of LANAL. Program RATE uses the flow histories in conjunction with an equation of state to calculate reaction-rate histories. RATE can be programmed to examine correlations between themore » rate histories and thermodynamic variables. Observed correlations can be incorporated into an appropriately parameterized rate law. Program RATE determines the values of these parameters that best reproduce the observed rate histories. The procedure is illustrated with a sample problem.« less

Optimization of thermal protection systems for the space shuttle vehicle. Volume 1: Final report

NASA Technical Reports Server (NTRS)

1972-01-01

A study performed to continue development of computational techniques for the Space Shuttle Thermal Protection System is reported. The resulting computer code was used to perform some additional optimization studies on several TPS configurations. The program was developed in Fortran 4 for the CDC 6400, and it was converted to Fortran 5 to be used for the Univac 1108. The computational methodology is developed in modular fashion to facilitate changes and updating of the techniques and to allow overlaying the computer code to fit into approximately 131,000 octal words of core storage. The program logic involves subroutines which handle input and output of information between computer and user, thermodynamic stress, dynamic, and weight/estimate analyses of a variety of panel configurations. These include metallic, ablative, RSI (with and without an underlying phase change material), and a thermodynamic analysis only of carbon-carbon systems applied to the leading edge and flat cover panels. Two different thermodynamic analyses are used. The first is a two-dimensional, explicit precedure with variable time steps which is used to describe the behavior of metallic and carbon-carbon leading edges. The second is a one-dimensional implicity technique used to predict temperature in the charring ablator and the noncharring RSI. The latter analysis is performed simply by suppressing the chemical reactions and pyrolysis of the TPS material.

The Use of the ’BLAKE’ Computer Program to Calculate Thermodynamic Properties of Australian-Made Gun Propellants.

DTIC Science & Technology

1982-04-01

data for gun propellants manufactured in Australia, and several which are candidates for local production, are tabulated for reference. A summary of the theoretical framework of the program is included. (Author)

The A [plus] B [double arrow] C of Chemical Thermodynamics.

ERIC Educational Resources Information Center

Gerhartl, F. J.

1994-01-01

Basic chemical thermodynamics usually treats non-p,T reactions in a stepmotherly fashion. This paper covers the main aspects of the theoretical principles of reactions (p,T; V,T; p,H; and V,U) and offers results from the ABC computer program, which was designed to show the validity of the equilibrium theory to all types of reaction modes. (PVD)

Computer program for natural gas flow through nozzles

NASA Technical Reports Server (NTRS)

Johnson, R. C.

1972-01-01

Subroutines, FORTRAN 4 type, were developed for calculating isentropic natural gas mass flow rate through nozzle. Thermodynamic functions covering compressibility, entropy, enthalpy, and specific heat are included.

A 4-cylinder Stirling engine computer program with dynamic energy equations

NASA Technical Reports Server (NTRS)

Daniele, C. J.; Lorenzo, C. F.

1983-01-01

A computer program for simulating the steady state and transient performance of a four cylinder Stirling engine is presented. The thermodynamic model includes both continuity and energy equations and linear momentum terms (flow resistance). Each working space between the pistons is broken into seven control volumes. Drive dynamics and vehicle load effects are included. The model contains 70 state variables. Also included in the model are piston rod seal leakage effects. The computer program includes a model of a hydrogen supply system, from which hydrogen may be added to the system to accelerate the engine. Flow charts are provided.

Computer program for calculation of complex chemical equilibrium compositions and applications. Part 1: Analysis

NASA Technical Reports Server (NTRS)

Gordon, Sanford; Mcbride, Bonnie J.

1994-01-01

This report presents the latest in a number of versions of chemical equilibrium and applications programs developed at the NASA Lewis Research Center over more than 40 years. These programs have changed over the years to include additional features and improved calculation techniques and to take advantage of constantly improving computer capabilities. The minimization-of-free-energy approach to chemical equilibrium calculations has been used in all versions of the program since 1967. The two principal purposes of this report are presented in two parts. The first purpose, which is accomplished here in part 1, is to present in detail a number of topics of general interest in complex equilibrium calculations. These topics include mathematical analyses and techniques for obtaining chemical equilibrium; formulas for obtaining thermodynamic and transport mixture properties and thermodynamic derivatives; criteria for inclusion of condensed phases; calculations at a triple point; inclusion of ionized species; and various applications, such as constant-pressure or constant-volume combustion, rocket performance based on either a finite- or infinite-chamber-area model, shock wave calculations, and Chapman-Jouguet detonations. The second purpose of this report, to facilitate the use of the computer code, is accomplished in part 2, entitled 'Users Manual and Program Description'. Various aspects of the computer code are discussed, and a number of examples are given to illustrate its versatility.

Implementation of a Thermodynamic Solver within a Computer Program for Calculating Fission-Product Release Fractions

NASA Astrophysics Data System (ADS)

Barber, Duncan Henry

During some postulated accidents at nuclear power stations, fuel cooling may be impaired. In such cases, the fuel heats up and the subsequent increased fission-gas release from the fuel to the gap may result in fuel sheath failure. After fuel sheath failure, the barrier between the coolant and the fuel pellets is lost or impaired, gases and vapours from the fuel-to-sheath gap and other open voids in the fuel pellets can be vented. Gases and steam from the coolant can enter the broken fuel sheath and interact with the fuel pellet surfaces and the fission-product inclusion on the fuel surface (including material at the surface of the fuel matrix). The chemistry of this interaction is an important mechanism to model in order to assess fission-product releases from fuel. Starting in 1995, the computer program SOURCE 2.0 was developed by the Canadian nuclear industry to model fission-product release from fuel during such accidents. SOURCE 2.0 has employed an early thermochemical model of irradiated uranium dioxide fuel developed at the Royal Military College of Canada. To overcome the limitations of computers of that time, the implementation of the RMC model employed lookup tables to pre-calculated equilibrium conditions. In the intervening years, the RMC model has been improved, the power of computers has increased significantly, and thermodynamic subroutine libraries have become available. This thesis is the result of extensive work based on these three factors. A prototype computer program (referred to as SC11) has been developed that uses a thermodynamic subroutine library to calculate thermodynamic equilibria using Gibbs energy minimization. The Gibbs energy minimization requires the system temperature (T) and pressure (P), and the inventory of chemical elements (n) in the system. In order to calculate the inventory of chemical elements in the fuel, the list of nuclides and nuclear isomers modelled in SC11 had to be expanded from the list used by SOURCE 2.0. A benchmark calculation demonstrates the improvement in agreement of the total inventory of those chemical elements included in the RMC fuel model to an ORIGEN-S calculation. ORIGEN-S is the Oak Ridge isotope generation and depletion computer program. The Gibbs energy minimizer requires a chemical database containing coefficients from which the Gibbs energy of pure compounds, gas and liquid mixtures, and solid solutions can be calculated. The RMC model of irradiated uranium dioxide fuel has been converted into the required format. The Gibbs energy minimizer has been incorporated into a new model of fission-product vaporization from the fuel surface. Calculated release fractions using the new code have been compared to results calculated with SOURCE IST 2.0P11 and to results of tests used in the validation of SOURCE 2.0. The new code shows improvements in agreement with experimental releases for a number of nuclides. Of particular significance is the better agreement between experimental and calculated release fractions for 140La. The improved agreement reflects the inclusion in the RMC model of the solubility of lanthanum (III) oxide (La2O3) in the fuel matrix. Calculated lanthanide release fractions from earlier computer programs were a challenge to environmental qualification analysis of equipment for some accident scenarios. The new prototype computer program would alleviate this concern. Keywords: Nuclear Engineering; Material Science; Thermodynamics; Radioactive Material, Gibbs Energy Minimization, Actinide Generation and Depletion, FissionProduct Generation and Depletion.

Computer program for Stirling engine performance calculations

NASA Technical Reports Server (NTRS)

Tew, R. C., Jr.

1983-01-01

The thermodynamic characteristics of the Stirling engine were analyzed and modeled on a computer to support its development as a possible alternative to the automobile spark ignition engine. The computer model is documented. The documentation includes a user's manual, symbols list, a test case, comparison of model predictions with test results, and a description of the analytical equations used in the model.

Coefficients for calculating thermodynamic and transport properties of individual species

NASA Technical Reports Server (NTRS)

Mcbride, Bonnie J.; Gordon, Sanford; Reno, Martin A.

1993-01-01

Libraries of thermodynamic data and transport properties are given for individual species in the form of least-squares coefficients. Values of C(sup 0)(sub p)(T), H(sup 0)(T), and S(sup 0)(T) are available for 1130 solid, liquid, and gaseous species. Viscosity and thermal conductivity data are given for 155 gases. The original C(sup 0)(sub p)(T) values were fit to a fourth-order polynomial with integration constants for H(sup 0)(T) and S(sup 0)(T). For each species the integration constant for H(sup 0)(T) includes the heat of formation. Transport properties have a different functional form. The temperature range for most of the data is 300 to 5000 K, although some of the newer thermodynamic data have a range of 200 to 6000 K. Because the species are mainly possible products of reaction, the data are useful for chemical equilibrium and kinetics computer codes. Much of the data has been distributed for several years with the NASA Lewis equilibrium program CET89. The thermodynamic properties of the reference elements were updated along with about 175 species that involve the elements carbon, hydrogen, oxygen, and nitrogen. These sets of data will be distributed with the NASA Lewis personal computer program for calculating chemical equilibria, CETPC.

Nonequilibrium air radiation (Nequair) program: User's manual

NASA Technical Reports Server (NTRS)

Park, C.

1985-01-01

A supplement to the data relating to the calculation of nonequilibrium radiation in flight regimes of aeroassisted orbital transfer vehicles contains the listings of the computer code NEQAIR (Nonequilibrium Air Radiation), its primary input data, and explanation of the user-supplied input variables. The user-supplied input variables are the thermodynamic variables of air at a given point, i.e., number densities of various chemical species, translational temperatures of heavy particles and electrons, and vibrational temperature. These thermodynamic variables do not necessarily have to be in thermodynamic equilibrium. The code calculates emission and absorption characteristics of air under these given conditions.

Computing the Thermodynamic State of a Cryogenic Fluid

NASA Technical Reports Server (NTRS)

Willen, G. Scott; Hanna, Gregory J.; Anderson, Kevin R.

2005-01-01

The Cryogenic Tank Analysis Program (CTAP) predicts the time-varying thermodynamic state of a cryogenic fluid in a tank or a Dewar flask. CTAP is designed to be compatible with EASY5x, which is a commercial software package that can be used to simulate a variety of processes and equipment systems. The mathematical model implemented in CTAP is a first-order differential equation for the pressure as a function of time.

Generalized Fluid System Simulation Program (GFSSP) - Version 6

NASA Technical Reports Server (NTRS)

Majumdar, Alok; LeClair, Andre; Moore, Ric; Schallhorn, Paul

2015-01-01

The Generalized Fluid System Simulation Program (GFSSP) is a finite-volume based general-purpose computer program for analyzing steady state and time-dependent flow rates, pressures, temperatures, and concentrations in a complex flow network. The program is capable of modeling real fluids with phase changes, compressibility, mixture thermodynamics, conjugate heat transfer between solid and fluid, fluid transients, pumps, compressors, flow control valves and external body forces such as gravity and centrifugal. The thermo-fluid system to be analyzed is discretized into nodes, branches, and conductors. The scalar properties such as pressure, temperature, and concentrations are calculated at nodes. Mass flow rates and heat transfer rates are computed in branches and conductors. The graphical user interface allows users to build their models using the 'point, drag, and click' method; the users can also run their models and post-process the results in the same environment. The integrated fluid library supplies thermodynamic and thermo-physical properties of 36 fluids, and 24 different resistance/source options are provided for modeling momentum sources or sinks in the branches. Users can introduce new physics, non-linear and time-dependent boundary conditions through user-subroutine.

Generalized Fluid System Simulation Program, Version 6.0

NASA Technical Reports Server (NTRS)

Majumdar, A. K.; LeClair, A. C.; Moore, A.; Schallhorn, P. A.

2013-01-01

The Generalized Fluid System Simulation Program (GFSSP) is a finite-volume based general-purpose computer program for analyzing steady state and time-dependant flow rates, pressures, temperatures, and concentrations in a complex flow network. The program is capable of modeling real fluids with phase changes, compressibility, mixture thermodynamics, conjugate heat transfer between solid and fluid, fluid transients, pumps, compressors and external body forces such as gravity and centrifugal. The thermo-fluid system to be analyzed is discretized into nodes, branches, and conductors. The scalar properties such as pressure, temperature, and concentrations are calculated at nodes. Mass flow rates and heat transfer rates are computed in branches and conductors. The graphical user interface allows users to build their models using the 'point, drag, and click' method; the users can also run their models and post-process the results in the same environment. The integrated fluid library supplies thermodynamic and thermo-physical properties of 36 fluids, and 24 different resistance/source options are provided for modeling momentum sources or sinks in the branches. This Technical Memorandum illustrates the application and verification of the code through 25 demonstrated example problems.

Generalized Fluid System Simulation Program, Version 5.0-Educational

NASA Technical Reports Server (NTRS)

Majumdar, A. K.

2011-01-01

The Generalized Fluid System Simulation Program (GFSSP) is a finite-volume based general-purpose computer program for analyzing steady state and time-dependent flow rates, pressures, temperatures, and concentrations in a complex flow network. The program is capable of modeling real fluids with phase changes, compressibility, mixture thermodynamics, conjugate heat transfer between solid and fluid, fluid transients, pumps, compressors and external body forces such as gravity and centrifugal. The thermofluid system to be analyzed is discretized into nodes, branches, and conductors. The scalar properties such as pressure, temperature, and concentrations are calculated at nodes. Mass flow rates and heat transfer rates are computed in branches and conductors. The graphical user interface allows users to build their models using the point, drag and click method; the users can also run their models and post-process the results in the same environment. The integrated fluid library supplies thermodynamic and thermo-physical properties of 36 fluids and 21 different resistance/source options are provided for modeling momentum sources or sinks in the branches. This Technical Memorandum illustrates the application and verification of the code through 12 demonstrated example problems.

WETAIR: A computer code for calculating thermodynamic and transport properties of air-water mixtures

NASA Technical Reports Server (NTRS)

Fessler, T. E.

1979-01-01

A computer program subroutine, WETAIR, was developed to calculate the thermodynamic and transport properties of air water mixtures. It determines the thermodynamic state from assigned values of temperature and density, pressure and density, temperature and pressure, pressure and entropy, or pressure and enthalpy. The WETAIR calculates the properties of dry air and water (steam) by interpolating to obtain values from property tables. Then it uses simple mixing laws to calculate the properties of air water mixtures. Properties of mixtures with water contents below 40 percent (by mass) can be calculated at temperatures from 273.2 to 1497 K and pressures to 450 MN/sq m. Dry air properties can be calculated at temperatures as low as 150 K. Water properties can be calculated at temperatures to 1747 K and pressures to 100 MN/sq m. The WETAIR is available in both SFTRAN and FORTRAN.

A Network Thermodynamic Approach to Compartmental Analysis

PubMed Central

Mikulecky, D. C.; Huf, E. G.; Thomas, S. R.

1979-01-01

We introduce a general network thermodynamic method for compartmental analysis which uses a compartmental model of sodium flows through frog skin as an illustrative example (Huf and Howell, 1974a). We use network thermodynamics (Mikulecky et al., 1977b) to formulate the problem, and a circuit simulation program (ASTEC 2, SPICE2, or PCAP) for computation. In this way, the compartment concentrations and net fluxes between compartments are readily obtained for a set of experimental conditions involving a square-wave pulse of labeled sodium at the outer surface of the skin. Qualitative features of the influx at the outer surface correlate very well with those observed for the short circuit current under another similar set of conditions by Morel and LeBlanc (1975). In related work, the compartmental model is used as a basis for simulation of the short circuit current and sodium flows simultaneously using a two-port network (Mikulecky et al., 1977a, and Mikulecky et al., A network thermodynamic model for short circuit current transients in frog skin. Manuscript in preparation; Gary-Bobo et al., 1978). The network approach lends itself to computation of classic compartmental problems in a simple manner using circuit simulation programs (Chua and Lin, 1975), and it further extends the compartmental models to more complicated situations involving coupled flows and non-linearities such as concentration dependencies, chemical reaction kinetics, etc. PMID:262387

Network thermodynamic approach compartmental analysis. Na+ transients in frog skin.

PubMed

Mikulecky, D C; Huf, E G; Thomas, S R

1979-01-01

We introduce a general network thermodynamic method for compartmental analysis which uses a compartmental model of sodium flows through frog skin as an illustrative example (Huf and Howell, 1974a). We use network thermodynamics (Mikulecky et al., 1977b) to formulate the problem, and a circuit simulation program (ASTEC 2, SPICE2, or PCAP) for computation. In this way, the compartment concentrations and net fluxes between compartments are readily obtained for a set of experimental conditions involving a square-wave pulse of labeled sodium at the outer surface of the skin. Qualitative features of the influx at the outer surface correlate very well with those observed for the short circuit current under another similar set of conditions by Morel and LeBlanc (1975). In related work, the compartmental model is used as a basis for simulation of the short circuit current and sodium flows simultaneously using a two-port network (Mikulecky et al., 1977a, and Mikulecky et al., A network thermodynamic model for short circuit current transients in frog skin. Manuscript in preparation; Gary-Bobo et al., 1978). The network approach lends itself to computation of classic compartmental problems in a simple manner using circuit simulation programs (Chua and Lin, 1975), and it further extends the compartmental models to more complicated situations involving coupled flows and non-linearities such as concentration dependencies, chemical reaction kinetics, etc.

A stirling engine computer model for performance calculations

NASA Technical Reports Server (NTRS)

Tew, R.; Jefferies, K.; Miao, D.

1978-01-01

To support the development of the Stirling engine as a possible alternative to the automobile spark-ignition engine, the thermodynamic characteristics of the Stirling engine were analyzed and modeled on a computer. The modeling techniques used are presented. The performance of an existing rhombic-drive Stirling engine was simulated by use of this computer program, and some typical results are presented. Engine tests are planned in order to evaluate this model.

Computer program for thermodynamic analysis of open cycle multishaft power system with multiple reheat and intercool

NASA Technical Reports Server (NTRS)

Glassman, A. J.

1974-01-01

A computer program to analyze power systems having any number of shafts up to a maximum of five is presented. On each shaft there can be as many as five compressors and five turbines, along with any specified number of intervening intercoolers and reheaters. A recuperator can be included. Turbine coolant flow can be accounted for. Any fuel consisting entirely of hydrogen and/or carbon can be used. The program is valid for maximum temperatures up to about 2000 K (3600 R). The system description, the analysis method, a detailed explanation of program input and output including an illustrative example, a dictionary of program variables, and the program listing are explained.

A General Method for Automatic Computation of Equilibrium Compositions and Theoretical Rocket Performance of Propellants

NASA Technical Reports Server (NTRS)

Gordon, Sanford; Zeleznik, Frank J.; Huff, Vearl N.

1959-01-01

A general computer program for chemical equilibrium and rocket performance calculations was written for the IBM 650 computer with 2000 words of drum storage, 60 words of high-speed core storage, indexing registers, and floating point attachments. The program is capable of carrying out combustion and isentropic expansion calculations on a chemical system that may include as many as 10 different chemical elements, 30 reaction products, and 25 pressure ratios. In addition to the equilibrium composition, temperature, and pressure, the program calculates specific impulse, specific impulse in vacuum, characteristic velocity, thrust coefficient, area ratio, molecular weight, Mach number, specific heat, isentropic exponent, enthalpy, entropy, and several thermodynamic first derivatives.

Skylab program CSM verification analysis report

NASA Technical Reports Server (NTRS)

Schaefer, J. L.; Vanderpol, G. A.

1970-01-01

The application of the SINDA computer program for the transient thermodynamic simulation of the Apollo fuel cell/radiator system for the limit condition of the proposed Skylab mission is described. Results are included for the thermal constraints imposed upon the Pratt and Whitney fuel cell power capability by the Block 2 EPS radiator system operating under the Skylab fixed attitude orbits.

Solid State Cooling with Advanced Oxide Materials

DTIC Science & Technology

2014-06-03

Department of Materials Science and Engineering , Department of Mechanical Science and Engineering , and Department of Electrical and Computer... Engineering University of Illinois, Urbana-Champaign Program Overview The focus of this program was to probe electro-(magneto-)caloric materials for... engineering systems by developing theoretical and experimental approaches to study thermodynamic properties and effects in thin film systems. Despite

Lost in folding space? Comparing four variants of the thermodynamic model for RNA secondary structure prediction.

PubMed

Janssen, Stefan; Schudoma, Christian; Steger, Gerhard; Giegerich, Robert

2011-11-03

Many bioinformatics tools for RNA secondary structure analysis are based on a thermodynamic model of RNA folding. They predict a single, "optimal" structure by free energy minimization, they enumerate near-optimal structures, they compute base pair probabilities and dot plots, representative structures of different abstract shapes, or Boltzmann probabilities of structures and shapes. Although all programs refer to the same physical model, they implement it with considerable variation for different tasks, and little is known about the effects of heuristic assumptions and model simplifications used by the programs on the outcome of the analysis. We extract four different models of the thermodynamic folding space which underlie the programs RNAFOLD, RNASHAPES, and RNASUBOPT. Their differences lie within the details of the energy model and the granularity of the folding space. We implement probabilistic shape analysis for all models, and introduce the shape probability shift as a robust measure of model similarity. Using four data sets derived from experimentally solved structures, we provide a quantitative evaluation of the model differences. We find that search space granularity affects the computed shape probabilities less than the over- or underapproximation of free energy by a simplified energy model. Still, the approximations perform similar enough to implementations of the full model to justify their continued use in settings where computational constraints call for simpler algorithms. On the side, we observe that the rarely used level 2 shapes, which predict the complete arrangement of helices, multiloops, internal loops and bulges, include the "true" shape in a rather small number of predicted high probability shapes. This calls for an investigation of new strategies to extract high probability members from the (very large) level 2 shape space of an RNA sequence. We provide implementations of all four models, written in a declarative style that makes them easy to be modified. Based on our study, future work on thermodynamic RNA folding may make a choice of model based on our empirical data. It can take our implementations as a starting point for further program development.

On introduction of artificial intelligence elements to heat power engineering

NASA Astrophysics Data System (ADS)

Dregalin, A. F.; Nazyrova, R. R.

1993-10-01

The basic problems of 'the thermodynamic intelligence' of personal computers have been outlined. The thermodynamic intellect of personal computers as a concept has been introduced to heat processes occurring in engines of flying vehicles. In particular, the thermodynamic intellect of computers is determined by the possibility of deriving formal relationships between thermodynamic functions. In chemical thermodynamics, a concept of a characteristic function has been introduced.

Generalized Fluid System Simulation Program, Version 5.0-Educational. Supplemental Information for NASA/TM-2011-216470. Supplement

NASA Technical Reports Server (NTRS)

Majumdar, A. K.

2011-01-01

The Generalized Fluid System Simulation Program (GFSSP) is a finite-volume based general-purpose computer program for analyzing steady state and time-dependent flow rates, pressures, temperatures, and concentrations in a complex flow network. The program is capable of modeling real fluids with phase changes, compressibility, mixture thermodynamics, conjugate heat transfer between solid and fluid, fluid transients, pumps, compressors and external body forces such as gravity and centrifugal. The thermofluid system to be analyzed is discretized into nodes, branches, and conductors. The scalar properties such as pressure, temperature, and concentrations are calculated at nodes. Mass flow rates and heat transfer rates are computed in branches and conductors. The graphical user interface allows users to build their models using the point, drag and click method; the users can also run their models and post-process the results in the same environment. The integrated fluid library supplies thermodynamic and thermo-physical properties of 36 fluids and 21 different resistance/source options are provided for modeling momentum sources or sinks in the branches. This Technical Memorandum illustrates the application and verification of the code through 12 demonstrated example problems. This supplement gives the input and output data files for the examples.

Thermodynamics Study of Removal of Heavy Metal by TiN-Nanotubes

NASA Astrophysics Data System (ADS)

Mahdavian, Leila

2015-12-01

The ability of TiN-nanotube to remove lead (Pb(II)) and arsenic (As(III)) ions from aqueous solutions is investigated. The thermodynamics properties of Pb(II) and As(III) ions passing through TiN-nanotubes (TiN-NTs) is calculated in basis set (B3LYP/6-31G**) DFT-IR method by Gaussian program package. The results showed, Pb(II) and As(III) passing through had low potential in middle nanotubes, and are trapped in this place. The thermodynamic properties showed; the passing through are spontaneous and favorable because ΔGele (MJ/mol) is negative for them. The goal of this study is the detection of surface species of TiN-NTs for metal ions removal by using computer calculations. The structural and thermodynamic properties studied ions absorption on TiN-NTs at room temperature.

Polynomial approximations of thermodynamic properties of arbitrary gas mixtures over wide pressure and density ranges

NASA Technical Reports Server (NTRS)

Allison, D. O.

1972-01-01

Computer programs for flow fields around planetary entry vehicles require real-gas equilibrium thermodynamic properties in a simple form which can be evaluated quickly. To fill this need, polynomial approximations were found for thermodynamic properties of air and model planetary atmospheres. A coefficient-averaging technique was used for curve fitting in lieu of the usual least-squares method. The polynomials consist of terms up to the ninth degree in each of two variables (essentially pressure and density) including all cross terms. Four of these polynomials can be joined to cover, for example, a range of about 1000 to 11000 K and 0.00001 to 1 atmosphere (1 atm = 1.0133 x 100,000 N/m sq) for a given thermodynamic property. Relative errors of less than 1 percent are found over most of the applicable range.

Modeling the complete Otto cycle: Preliminary version. [computer programming

NASA Technical Reports Server (NTRS)

Zeleznik, F. J.; Mcbride, B. J.

1977-01-01

A description is given of the equations and the computer program being developed to model the complete Otto cycle. The program incorporates such important features as: (1) heat transfer, (2) finite combustion rates, (3) complete chemical kinetics in the burned gas, (4) exhaust gas recirculation, and (5) manifold vacuum or supercharging. Changes in thermodynamic, kinetic and transport data as well as model parameters can be made without reprogramming. Preliminary calculations indicate that: (1) chemistry and heat transfer significantly affect composition and performance, (2) there seems to be a strong interaction among model parameters, and (3) a number of cycles must be calculated in order to obtain steady-state conditions.

GASP - THERMODYNAMIC AND TRANSPORT PROPERTIES OF HELIUM, METHANE, NEON, NITROGEN, CARBON MONOXIDE, CARBON DIOXIDE, OXYGEN, AND ARGON

NASA Technical Reports Server (NTRS)

Hendricks, R. C.

1994-01-01

A computer program, GASP, has been written to calculate the thermodynamic and transport properties of argon, carbon dioxide, carbon monoxide, fluorine, methane, neon, nitrogen, and oxygen. GASP accepts any two of pressure, temperature, or density as input. In addition, entropy and enthalpy are possible inputs. Outputs are temperature, density, pressure, entropy, enthalpy, specific heats, expansion coefficient, sonic velocity, viscosity, thermal conductivity, and surface tension. A special technique is provided to estimate the thermal conductivity near the thermodynamic critical point. GASP is a group of FORTRAN subroutines. The user typically would write a main program that invoked GASP to provide only the described outputs. Subroutines are structured so that the user may call only those subroutines needed for his particular calculations. Allowable pressures range from 0.l atmosphere to 100 to l,000 atmospheres, depending on the fluid. Similarly, allowable pressures range from the triple point of each substance to 300 degrees K to 2000 degrees K, depending on the substance. The GASP package was developed to be used with heat transfer and fluid flow applications. It is particularly useful in applications of cryogenic fluids. Some problems associated with the liquefication, storage, and gasification of liquefied natural gas and liquefied petroleum gas can also be studied using GASP. This program is written in FORTRAN IV for batch execution and is available for implementation on IBM 7000 series computers. GASP was developed in 1971.

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

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.

Computing Equilibrium Chemical Compositions

NASA Technical Reports Server (NTRS)

Mcbride, Bonnie J.; Gordon, Sanford

1995-01-01

Chemical Equilibrium With Transport Properties, 1993 (CET93) computer program provides data on chemical-equilibrium compositions. Aids calculation of thermodynamic properties of chemical systems. Information essential in design and analysis of such equipment as compressors, turbines, nozzles, engines, shock tubes, heat exchangers, and chemical-processing equipment. CET93/PC is version of CET93 specifically designed to run within 640K memory limit of MS-DOS operating system. CET93/PC written in FORTRAN.

Space Life Support Engineering Program

NASA Technical Reports Server (NTRS)

Seagrave, Richard C.

1993-01-01

This report covers the second year of research relating to the development of closed-loop long-term life support systems. Emphasis was directed toward concentrating on the development of dynamic simulation techniques and software and on performing a thermodynamic systems analysis in an effort to begin optimizing the system needed for water purification. Four appendices are attached. The first covers the ASPEN modeling of the closed loop Environmental Control Life Support System (ECLSS) and its thermodynamic analysis. The second is a report on the dynamic model development for water regulation in humans. The third regards the development of an interactive computer-based model for determining exercise limitations. The fourth attachment is an estimate of the second law thermodynamic efficiency of the various units comprising an ECLSS.

Integrating Computational Chemistry into a Course in Classical Thermodynamics

ERIC Educational Resources Information Center

Martini, Sheridan R.; Hartzell, Cynthia J.

2015-01-01

Computational chemistry is commonly addressed in the quantum mechanics course of undergraduate physical chemistry curricula. Since quantum mechanics traditionally follows the thermodynamics course, there is a lack of curricula relating computational chemistry to thermodynamics. A method integrating molecular modeling software into a semester long…

ms2: A molecular simulation tool for thermodynamic properties

NASA Astrophysics Data System (ADS)

Deublein, Stephan; Eckl, Bernhard; Stoll, Jürgen; Lishchuk, Sergey V.; Guevara-Carrion, Gabriela; Glass, Colin W.; Merker, Thorsten; Bernreuther, Martin; Hasse, Hans; Vrabec, Jadran

2011-11-01

This work presents the molecular simulation program ms2 that is designed for the calculation of thermodynamic properties of bulk fluids in equilibrium consisting of small electro-neutral molecules. ms2 features the two main molecular simulation techniques, molecular dynamics (MD) and Monte-Carlo. It supports the calculation of vapor-liquid equilibria of pure fluids and multi-component mixtures described by rigid molecular models on the basis of the grand equilibrium method. Furthermore, it is capable of sampling various classical ensembles and yields numerous thermodynamic properties. To evaluate the chemical potential, Widom's test molecule method and gradual insertion are implemented. Transport properties are determined by equilibrium MD simulations following the Green-Kubo formalism. ms2 is designed to meet the requirements of academia and industry, particularly achieving short response times and straightforward handling. It is written in Fortran90 and optimized for a fast execution on a broad range of computer architectures, spanning from single processor PCs over PC-clusters and vector computers to high-end parallel machines. The standard Message Passing Interface (MPI) is used for parallelization and ms2 is therefore easily portable to different computing platforms. Feature tools facilitate the interaction with the code and the interpretation of input and output files. The accuracy and reliability of ms2 has been shown for a large variety of fluids in preceding work. Program summaryProgram title:ms2 Catalogue identifier: AEJF_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEJF_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Special Licence supplied by the authors No. of lines in distributed program, including test data, etc.: 82 794 No. of bytes in distributed program, including test data, etc.: 793 705 Distribution format: tar.gz Programming language: Fortran90 Computer: The simulation tool ms2 is usable on a wide variety of platforms, from single processor machines over PC-clusters and vector computers to vector-parallel architectures. (Tested with Fortran compilers: gfortran, Intel, PathScale, Portland Group and Sun Studio.) Operating system: Unix/Linux, Windows Has the code been vectorized or parallelized?: Yes. Message Passing Interface (MPI) protocol Scalability. Excellent scalability up to 16 processors for molecular dynamics and >512 processors for Monte-Carlo simulations. RAM:ms2 runs on single processors with 512 MB RAM. The memory demand rises with increasing number of processors used per node and increasing number of molecules. Classification: 7.7, 7.9, 12 External routines: Message Passing Interface (MPI) Nature of problem: Calculation of application oriented thermodynamic properties for rigid electro-neutral molecules: vapor-liquid equilibria, thermal and caloric data as well as transport properties of pure fluids and multi-component mixtures. Solution method: Molecular dynamics, Monte-Carlo, various classical ensembles, grand equilibrium method, Green-Kubo formalism. Restrictions: No. The system size is user-defined. Typical problems addressed by ms2 can be solved by simulating systems containing typically 2000 molecules or less. Unusual features: Feature tools are available for creating input files, analyzing simulation results and visualizing molecular trajectories. Additional comments: Sample makefiles for multiple operation platforms are provided. Documentation is provided with the installation package and is available at http://www.ms-2.de. Running time: The running time of ms2 depends on the problem set, the system size and the number of processes used in the simulation. Running four processes on a "Nehalem" processor, simulations calculating VLE data take between two and twelve hours, calculating transport properties between six and 24 hours.

EQ3NR, a computer program for geochemical aqueous speciation-solubility calculations: Theoretical manual, user`s guide, and related documentation (Version 7.0); Part 3

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

Wolery, T.J.

1992-09-14

EQ3NR is an aqueous solution speciation-solubility modeling code. It is part of the EQ3/6 software package for geochemical modeling. It computes the thermodynamic state of an aqueous solution by determining the distribution of chemical species, including simple ions, ion pairs, and complexes, using standard state thermodynamic data and various equations which describe the thermodynamic activity coefficients of these species. The input to the code describes the aqueous solution in terms of analytical data, including total (analytical) concentrations of dissolved components and such other parameters as the pH, pHCl, Eh, pe, and oxygen fugacity. The input may also include a desiredmore » electrical balancing adjustment and various constraints which impose equilibrium with special pure minerals, solid solution end-member components (of specified mole fractions), and gases (of specified fugacities). The code evaluates the degree of disequilibrium in terms of the saturation index (SI = 1og Q/K) and the thermodynamic affinity (A = {minus}2.303 RT log Q/K) for various reactions, such as mineral dissolution or oxidation-reduction in the aqueous solution itself. Individual values of Eh, pe, oxygen fugacity, and Ah (redox affinity) are computed for aqueous redox couples. Equilibrium fugacities are computed for gas species. The code is highly flexible in dealing with various parameters as either model inputs or outputs. The user can specify modification or substitution of equilibrium constants at run time by using options on the input file.« less

NIST Libraries of Peptide Fragmentation Mass Spectra Databass

National Institute of Standards and Technology Data Gateway

SRD 4 NIST Libraries of Peptide Fragmentation Mass Spectra Databass (PC database for purchase)   Interactive computer program for predicting thermodynamic and transport properties of pure fluids and fluid mixtures containing up to 20 components. The components are selected from a database of 196 components, mostly hydrocarbons.

USAF Summer Research Program - 1993 Summer Research Extension Program Final Reports, Volume 1B, Armstrong Laboratory

DTIC Science & Technology

1994-11-01

For example, the Collimating scotopic components of the ERG flash response are significantly attenuated by retinitis pigmentosa [7]. It is possible... RETINAL DAMAGE Bernard S. Gerstman Associate Professor Department of Physics Florida International University University Park Miami, FL 33199 Final...and Florida International University April 1994 6-1 A COMPUTATIONAL THERMAL MODEL AND THEORETICAL THERMODYNAMIC MODEL OF LASER INDUCED RETINAL DAMAGE

Interactive Educational Tool for Turbofan and Afterburning Turbojet Engines

NASA Technical Reports Server (NTRS)

Benson, Thomas J.

1997-01-01

A workstation-based, interactive educational computer program has been developed at the NASA Lewis Research Center to aid in the teaching and understanding of turbine engine design and analysis. This tool has recently been extended to model the performance of two-spool turbofans and afterburning turbojets. The program solves for the flow conditions through the engine by using classical one-dimensional thermodynamic analysis found in various propulsion textbooks. Either an approximately thermally perfect or calorically perfect gas can be used in the thermodynamic analysis. Students can vary the design conditions through a graphical user interface; engine performance is calculated immediately. A variety of graphical formats are used to present results, including numerical results, moving bar charts, and student-generated temperature versus entropy (Ts), pressure versus specific volume (pv), and engine performance plots. The package includes user-controlled printed output, restart capability, online help screens, and a browser that displays teacher-prepared lessons in turbomachinery. The program runs on a variety of workstations or a personal computer using the UNIX operating system and X-based graphics. It is being tested at several universities in the midwestern United States; the source and executables are available free from the author.

WATEQF; a FORTRAN IV version of WATEQ : a computer program for calculating chemical equilibrium of natural waters

USGS Publications Warehouse

Plummer, Niel; Jones, Blair F.; Truesdell, Alfred Hemingway

1976-01-01

WATEQF is a FORTRAN IV computer program that models the thermodynamic speciation of inorganic ions and complex species in solution for a given water analysis. The original version (WATEQ) was written in 1973 by A. H. Truesdell and B. F. Jones in Programming Language/one (PL/1.) With but a few exceptions, the thermochemical data, speciation, coefficients, and general calculation procedure of WATEQF is identical to the PL/1 version. This report notes the differences between WATEQF and WATEQ, demonstrates how to set up the input data to execute WATEQF, provides a test case for comparison, and makes available a listing of WATEQF. (Woodard-USGS)

Thermodynamic and transport properties of gaseous tetrafluoromethane in chemical equilibrium

NASA Technical Reports Server (NTRS)

Hunt, J. L.; Boney, L. R.

1973-01-01

Equations and in computer code are presented for the thermodynamic and transport properties of gaseous, undissociated tetrafluoromethane (CF4) in chemical equilibrium. The computer code calculates the thermodynamic and transport properties of CF4 when given any two of five thermodynamic variables (entropy, temperature, volume, pressure, and enthalpy). Equilibrium thermodynamic and transport property data are tabulated and pressure-enthalpy diagrams are presented.

Computer program to solve two-dimensional shock-wave interference problems with an equilibrium chemically reacting air model

NASA Technical Reports Server (NTRS)

Glass, Christopher E.

1990-01-01

The computer program EASI, an acronym for Equilibrium Air Shock Interference, was developed to calculate the inviscid flowfield, the maximum surface pressure, and the maximum heat flux produced by six shock wave interference patterns on a 2-D, cylindrical configuration. Thermodynamic properties of the inviscid flowfield are determined using either an 11-specie, 7-reaction equilibrium chemically reacting air model or a calorically perfect air model. The inviscid flowfield is solved using the integral form of the conservation equations. Surface heating calculations at the impingement point for the equilibrium chemically reacting air model use variable transport properties and specific heat. However, for the calorically perfect air model, heating rate calculations use a constant Prandtl number. Sample calculations of the six shock wave interference patterns, a listing of the computer program, and flowcharts of the programming logic are included.

Computer program to solve two-dimensional shock-wave interference problems with an equilibrium chemically reacting air model

NASA Astrophysics Data System (ADS)

Glass, Christopher E.

1990-08-01

The computer program EASI, an acronym for Equilibrium Air Shock Interference, was developed to calculate the inviscid flowfield, the maximum surface pressure, and the maximum heat flux produced by six shock wave interference patterns on a 2-D, cylindrical configuration. Thermodynamic properties of the inviscid flowfield are determined using either an 11-specie, 7-reaction equilibrium chemically reacting air model or a calorically perfect air model. The inviscid flowfield is solved using the integral form of the conservation equations. Surface heating calculations at the impingement point for the equilibrium chemically reacting air model use variable transport properties and specific heat. However, for the calorically perfect air model, heating rate calculations use a constant Prandtl number. Sample calculations of the six shock wave interference patterns, a listing of the computer program, and flowcharts of the programming logic are included.

Information thermodynamics of near-equilibrium computation

NASA Astrophysics Data System (ADS)

Prokopenko, Mikhail; Einav, Itai

2015-06-01

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

Thermodynamic cost of computation, algorithmic complexity and the information metric

NASA Technical Reports Server (NTRS)

Zurek, W. H.

1989-01-01

Algorithmic complexity is discussed as a computational counterpart to the second law of thermodynamics. It is shown that algorithmic complexity, which is a measure of randomness, sets limits on the thermodynamic cost of computations and casts a new light on the limitations of Maxwell's demon. Algorithmic complexity can also be used to define distance between binary strings.

Nonequilibrium radiation and chemistry models for aerocapture vehicle flowfields, volume 3

NASA Technical Reports Server (NTRS)

Carlson, Leland A.

1991-01-01

The computer programs developed to calculate the shock wave precursor and the method of using them are described. This method calculated the precursor flow field in a nitrogen gas including the effects of emission and absorption of radiation on the energy and composition of gas. The radiative transfer is calculated including the effects of absorption and emission through the line as well as the continuum process in the shock layer and through the continuum processes only in the precursor. The effects of local thermodynamic nonequilibrium in the shock layer and precursor regions are also included in the radiative transfer calculations. Three computer programs utilized by this computational scheme to calculate the precursor flow field solution for a given shock layer flow field are discussed.

A computer program for two-dimensional and axisymmetric nonreacting perfect gas and equilibrium chemically reacting laminar, transitional and-or turbulent boundary layer flows

NASA Technical Reports Server (NTRS)

Miner, E. W.; Anderson, E. C.; Lewis, C. H.

1971-01-01

A computer program is described in detail for laminar, transitional, and/or turbulent boundary-layer flows of non-reacting (perfect gas) and reacting gas mixtures in chemical equilibrium. An implicit finite difference scheme was developed for both two dimensional and axisymmetric flows over bodies, and in rocket nozzles and hypervelocity wind tunnel nozzles. The program, program subroutines, variables, and input and output data are described. Also included is the output from a sample calculation of fully developed turbulent, perfect gas flow over a flat plate. Input data coding forms and a FORTRAN source listing of the program are included. A method is discussed for obtaining thermodynamic and transport property data which are required to perform boundary-layer calculations for reacting gases in chemical equilibrium.

A computer program for the calculation of laminar and turbulent boundary layer flows

NASA Technical Reports Server (NTRS)

Dwyer, H. A.; Doss, E. D.; Goldman, A. L.

1972-01-01

The results are presented of a study to produce a computer program to calculate laminar and turbulent boundary layer flows. The program is capable of calculating the following types of flow: (1) incompressible or compressible, (2) two dimensional or axisymmetric, and (3) flows with significant transverse curvature. Also, the program can handle a large variety of boundary conditions, such as blowing or suction, arbitrary temperature distributions and arbitrary wall heat fluxes. The program has been specialized to the calculation of equilibrium air flows and all of the thermodynamic and transport properties used are for air. For the turbulent transport properties, the eddy viscosity approach has been used. Although the eddy viscosity models are semi-empirical, the model employed in the program has corrections for pressure gradients, suction and blowing and compressibility. The basic method of approach is to put the equations of motion into a finite difference form and then solve them by use of a digital computer. The program is written in FORTRAN 4 and requires small amounts of computer time on most scientific machines. For example, most laminar flows can be calculated in less than one minute of machine time, while turbulent flows usually require three or four minutes.

Computer Program for Analysis, Design and Optimization of Propulsion, Dynamics, and Kinematics of Multistage Rockets

NASA Astrophysics Data System (ADS)

Lali, Mehdi

2009-03-01

A comprehensive computer program is designed in MATLAB to analyze, design and optimize the propulsion, dynamics, thermodynamics, and kinematics of any serial multi-staging rocket for a set of given data. The program is quite user-friendly. It comprises two main sections: "analysis and design" and "optimization." Each section has a GUI (Graphical User Interface) in which the rocket's data are entered by the user and by which the program is run. The first section analyzes the performance of the rocket that is previously devised by the user. Numerous plots and subplots are provided to display the performance of the rocket. The second section of the program finds the "optimum trajectory" via billions of iterations and computations which are done through sophisticated algorithms using numerical methods and incremental integrations. Innovative techniques are applied to calculate the optimal parameters for the engine and designing the "optimal pitch program." This computer program is stand-alone in such a way that it calculates almost every design parameter in regards to rocket propulsion and dynamics. It is meant to be used for actual launch operations as well as educational and research purposes.

Thermodynamics of RNA structures by Wang–Landau sampling

PubMed Central

Lou, Feng; Clote, Peter

2010-01-01

Motivation: Thermodynamics-based dynamic programming RNA secondary structure algorithms have been of immense importance in molecular biology, where applications range from the detection of novel selenoproteins using expressed sequence tag (EST) data, to the determination of microRNA genes and their targets. Dynamic programming algorithms have been developed to compute the minimum free energy secondary structure and partition function of a given RNA sequence, the minimum free-energy and partition function for the hybridization of two RNA molecules, etc. However, the applicability of dynamic programming methods depends on disallowing certain types of interactions (pseudoknots, zig-zags, etc.), as their inclusion renders structure prediction an nondeterministic polynomial time (NP)-complete problem. Nevertheless, such interactions have been observed in X-ray structures. Results: A non-Boltzmannian Monte Carlo algorithm was designed by Wang and Landau to estimate the density of states for complex systems, such as the Ising model, that exhibit a phase transition. In this article, we apply the Wang-Landau (WL) method to compute the density of states for secondary structures of a given RNA sequence, and for hybridizations of two RNA sequences. Our method is shown to be much faster than existent software, such as RNAsubopt. From density of states, we compute the partition function over all secondary structures and over all pseudoknot-free hybridizations. The advantage of the WL method is that by adding a function to evaluate the free energy of arbitary pseudoknotted structures and of arbitrary hybridizations, we can estimate thermodynamic parameters for situations known to be NP-complete. This extension to pseudoknots will be made in the sequel to this article; in contrast, the current article describes the WL algorithm applied to pseudoknot-free secondary structures and hybridizations. Availability: The WL RNA hybridization web server is under construction at http://bioinformatics.bc.edu/clotelab/. Contact: clote@bc.edu PMID:20529917

Thermodynamic characterization of networks using graph polynomials

NASA Astrophysics Data System (ADS)

Ye, Cheng; Comin, César H.; Peron, Thomas K. DM.; Silva, Filipi N.; Rodrigues, Francisco A.; Costa, Luciano da F.; Torsello, Andrea; Hancock, Edwin R.

2015-09-01

In this paper, we present a method for characterizing the evolution of time-varying complex networks by adopting a thermodynamic representation of network structure computed from a polynomial (or algebraic) characterization of graph structure. Commencing from a representation of graph structure based on a characteristic polynomial computed from the normalized Laplacian matrix, we show how the polynomial is linked to the Boltzmann partition function of a network. This allows us to compute a number of thermodynamic quantities for the network, including the average energy and entropy. Assuming that the system does not change volume, we can also compute the temperature, defined as the rate of change of entropy with energy. All three thermodynamic variables can be approximated using low-order Taylor series that can be computed using the traces of powers of the Laplacian matrix, avoiding explicit computation of the normalized Laplacian spectrum. These polynomial approximations allow a smoothed representation of the evolution of networks to be constructed in the thermodynamic space spanned by entropy, energy, and temperature. We show how these thermodynamic variables can be computed in terms of simple network characteristics, e.g., the total number of nodes and node degree statistics for nodes connected by edges. We apply the resulting thermodynamic characterization to real-world time-varying networks representing complex systems in the financial and biological domains. The study demonstrates that the method provides an efficient tool for detecting abrupt changes and characterizing different stages in network evolution.

Propeller performance and weight predictions appended to the Navy/NASA engine program

NASA Technical Reports Server (NTRS)

Plencner, R. M.; Senty, P.; Wickenheiser, T. J.

1983-01-01

The Navy/NASA Engine Performance (NNEP) is a general purpose computer program currently employed by government, industry and university personnel to simulate the thermodynamic cycles of turbine engines. NNEP is a modular program which has the ability to evaluate the performance of an arbitrary engine configuration defined by the user. In 1979, a program to calculate engine weight (WATE-2) was developed by Boeing's Military Division under NASA contract. This program uses a preliminary design approach to determine engine weights and dimensions. Because the thermodynamic and configuration information required by the weight code was available in NNEP, the weight code was appended to NNEP. Due to increased emphasis on fuel economy, a renewed interest has developed in propellers. This report describes the modifications developed by NASA to both NNEP and WATE-2 to determine the performance, weight and dimensions of propellers and the corresponding gearbox. The propeller performance model has three options, two of which are based on propeller map interpolation. Propeller and gearbox weights are obtained from empirical equations which may easily be modified by the user.

Applications of the First Law to Ecological Systems. Physical Processes in Terrestrial and Aquatic Ecosystems, Thermodynamics.

ERIC Educational Resources Information Center

Stevenson, R. D.

These materials were designed to be used by life science students for instruction in the application of physical theory to ecosystem operation. Most modules contain computer programs which are built around a particular application of a physical process. This report describes concepts presented in another module called "The First Law of…

Generalized Fluid System Simulation Program, Version 6.0

NASA Technical Reports Server (NTRS)

Majumdar, A. K.; LeClair, A. C.; Moore, R.; Schallhorn, P. A.

2016-01-01

The Generalized Fluid System Simulation Program (GFSSP) is a general purpose computer program for analyzing steady state and time-dependent flow rates, pressures, temperatures, and concentrations in a complex flow network. The program is capable of modeling real fluids with phase changes, compressibility, mixture thermodynamics, conjugate heat transfer between solid and fluid, fluid transients, pumps, compressors, and external body forces such as gravity and centrifugal. The thermofluid system to be analyzed is discretized into nodes, branches, and conductors. The scalar properties such as pressure, temperature, and concentrations are calculated at nodes. Mass flow rates and heat transfer rates are computed in branches and conductors. The graphical user interface allows users to build their models using the 'point, drag, and click' method; the users can also run their models and post-process the results in the same environment. Two thermodynamic property programs (GASP/WASP and GASPAK) provide required thermodynamic and thermophysical properties for 36 fluids: helium, methane, neon, nitrogen, carbon monoxide, oxygen, argon, carbon dioxide, fluorine, hydrogen, parahydrogen, water, kerosene (RP-1), isobutene, butane, deuterium, ethane, ethylene, hydrogen sulfide, krypton, propane, xenon, R-11, R-12, R-22, R-32, R-123, R-124, R-125, R-134A, R-152A, nitrogen trifluoride, ammonia, hydrogen peroxide, and air. The program also provides the options of using any incompressible fluid with constant density and viscosity or ideal gas. The users can also supply property tables for fluids that are not in the library. Twenty-four different resistance/source options are provided for modeling momentum sources or sinks in the branches. These options include pipe flow, flow through a restriction, noncircular duct, pipe flow with entrance and/or exit losses, thin sharp orifice, thick orifice, square edge reduction, square edge expansion, rotating annular duct, rotating radial duct, labyrinth seal, parallel plates, common fittings and valves, pump characteristics, pump power, valve with a given loss coefficient, Joule-Thompson device, control valve, heat exchanger core, parallel tube, and compressible orifice. The program has the provision of including additional resistance options through User Subroutines. GFSSP employs a finite volume formulation of mass, momentum, and energy conservation equations in conjunction with the thermodynamic equations of state for real fluids as well as energy conservation equations for the solid. The system of equations describing the fluid network is solved by a hybrid numerical method that is a combination of the Newton-Raphson and successive substitution methods. The application and verification of the code has been demonstrated through 30 example problems.

A rapid method for the computation of equilibrium chemical composition of air to 15000 K

NASA Technical Reports Server (NTRS)

Prabhu, Ramadas K.; Erickson, Wayne D.

1988-01-01

A rapid computational method has been developed to determine the chemical composition of equilibrium air to 15000 K. Eleven chemically reacting species, i.e., O2, N2, O, NO, N, NO+, e-, N+, O+, Ar, and Ar+ are included. The method involves combining algebraically seven nonlinear equilibrium equations and four linear elemental mass balance and charge neutrality equations. Computational speeds for determining the equilibrium chemical composition are significantly faster than the often used free energy minimization procedure. Data are also included from which the thermodynamic properties of air can be computed. A listing of the computer program together with a set of sample results are included.

Analytical exploration of the thermodynamic potentials by using symbolic computation software

NASA Astrophysics Data System (ADS)

Hantsaridou, Anastasia P.; Polatoglou, Hariton M.

2005-09-01

Thermodynamics is a very general theory, based on fundamental symmetries. It generalizes classical mechanics and incorporates theoretical concepts such as field and field equations. Although all these ingredients are of the highest importance for a scientist, they are not given the attention they perhaps deserve in most undergraduate courses. Nowadays, powerful computers in conjunction with equally powerful software can ease the exploration of the crucial ideas of thermodynamics. The purpose of the present work is to show how the utilization of symbolic computation software can lead to a complementary understanding of thermodynamics. The method was applied to first and second year physics students in the Aristotle University of Thessaloniki (Greece) during the 2002-2003 academic year. The results indicate that symbolic computation software is appropriate not only for enhancing the teaching of the fundamental principles in thermodynamics and their applications, but also for increasing students' motivation for learning.

Thermodynamics of Computational Copying in Biochemical Systems

NASA Astrophysics Data System (ADS)

Ouldridge, Thomas E.; Govern, Christopher C.; ten Wolde, Pieter Rein

2017-04-01

Living cells use readout molecules to record the state of receptor proteins, similar to measurements or copies in typical computational devices. But is this analogy rigorous? Can cells be optimally efficient, and if not, why? We show that, as in computation, a canonical biochemical readout network generates correlations; extracting no work from these correlations sets a lower bound on dissipation. For general input, the biochemical network cannot reach this bound, even with arbitrarily slow reactions or weak thermodynamic driving. It faces an accuracy-dissipation trade-off that is qualitatively distinct from and worse than implied by the bound, and more complex steady-state copy processes cannot perform better. Nonetheless, the cost remains close to the thermodynamic bound unless accuracy is extremely high. Additionally, we show that biomolecular reactions could be used in thermodynamically optimal devices under exogenous manipulation of chemical fuels, suggesting an experimental system for testing computational thermodynamics.

Thermodynamic equilibrium-air correlations for flowfield applications

NASA Technical Reports Server (NTRS)

Zoby, E. V.; Moss, J. N.

1981-01-01

Equilibrium-air thermodynamic correlations have been developed for flowfield calculation procedures. A comparison between the postshock results computed by the correlation equations and detailed chemistry calculations is very good. The thermodynamic correlations are incorporated in an approximate inviscid flowfield code with a convective heating capability for the purpose of defining the thermodynamic environment through the shock layer. Comparisons of heating rates computed by the approximate code and a viscous-shock-layer method are good. In addition to presenting the thermodynamic correlations, the impact of several viscosity models on the convective heat transfer is demonstrated.

A Novel Approach for Modeling Chemical Reaction in Generalized Fluid System Simulation Program

NASA Technical Reports Server (NTRS)

Sozen, Mehmet; Majumdar, Alok

2002-01-01

The Generalized Fluid System Simulation Program (GFSSP) is a computer code developed at NASA Marshall Space Flight Center for analyzing steady state and transient flow rates, pressures, temperatures, and concentrations in a complex flow network. The code, which performs system level simulation, can handle compressible and incompressible flows as well as phase change and mixture thermodynamics. Thermodynamic and thermophysical property programs, GASP, WASP and GASPAK provide the necessary data for fluids such as helium, methane, neon, nitrogen, carbon monoxide, oxygen, argon, carbon dioxide, fluorine, hydrogen, water, a hydrogen, isobutane, butane, deuterium, ethane, ethylene, hydrogen sulfide, krypton, propane, xenon, several refrigerants, nitrogen trifluoride and ammonia. The program which was developed out of need for an easy to use system level simulation tool for complex flow networks, has been used for the following purposes to name a few: Space Shuttle Main Engine (SSME) High Pressure Oxidizer Turbopump Secondary Flow Circuits, Axial Thrust Balance of the Fastrac Engine Turbopump, Pressurized Propellant Feed System for the Propulsion Test Article at Stennis Space Center, X-34 Main Propulsion System, X-33 Reaction Control System and Thermal Protection System, and International Space Station Environmental Control and Life Support System design. There has been an increasing demand for implementing a combustion simulation capability into GFSSP in order to increase its system level simulation capability of a liquid rocket propulsion system starting from the propellant tanks up to the thruster nozzle for spacecraft as well as launch vehicles. The present work was undertaken for addressing this need. The chemical equilibrium equations derived from the second law of thermodynamics and the energy conservation equation derived from the first law of thermodynamics are solved simultaneously by a Newton-Raphson method. The numerical scheme was implemented as a User Subroutine in GFSSP.

Interfacing Computer-Assisted Drafting and Design with the Building Loads Analysis and System Thermodynamics (BLAST) Program

DTIC Science & Technology

1992-10-01

Manual CI APPENDIX D: Drawing Navigator Field Test D1 DISTRIBUTION Accesion For NTIS CRA&I OTIC TAB Unannouncea JustiteCdtOn By Distribution I "".i•I...methods replace manual methods, the automation will handle the data for the designer, thus reducing error and increasing throughput. However, the two...actively move data from one automation tool (CADD) to the other (the analysis program). This intervention involves a manual rekeying of data already in

Tables and charts of equilibrium thermodynamic properties of ammonia for temperatures from 500 to 50,000 K.

NASA Technical Reports Server (NTRS)

Simmonds, A. L.; Miller, C. G., III; Nealy, J. E.

1976-01-01

Equilibrium thermodynamic properties for pure ammonia were generated for a range of temperature from 500 to 50,000 K and pressure from 0.01 to 40 MN/sq m and are presented in tabulated and graphical form. Properties include pressure, temperature, density, enthalpy, speed of sound, entropy, molecular-weight ratio, specific heat at constant pressure, specific heat at constant volume, isentropic exponent, and species mole fractions. These properties were calculated by the method which is based on minimization of the Gibbs free energy. The data presented herein are for an 18-species ammonia model. Heats of formation and spectroscopic constants used as input data are presented. Comparison of several thermodynamic properties calculated with the present program and a second computer code is performed for a range of pressure and for temperatures up to 30,000 K.

SPECIES - EVALUATING THERMODYNAMIC PROPERTIES, TRANSPORT PROPERTIES & EQUILIBRIUM CONSTANTS OF AN 11-SPECIES AIR MODEL

NASA Technical Reports Server (NTRS)

Thompson, R. A.

1994-01-01

Accurate numerical prediction of high-temperature, chemically reacting flowfields requires a knowledge of the physical properties and reaction kinetics for the species involved in the reacting gas mixture. Assuming an 11-species air model at temperatures below 30,000 degrees Kelvin, SPECIES (Computer Codes for the Evaluation of Thermodynamic Properties, Transport Properties, and Equilibrium Constants of an 11-Species Air Model) computes values for the species thermodynamic and transport properties, diffusion coefficients and collision cross sections for any combination of the eleven species, and reaction rates for the twenty reactions normally occurring. The species represented in the model are diatomic nitrogen, diatomic oxygen, atomic nitrogen, atomic oxygen, nitric oxide, ionized nitric oxide, the free electron, ionized atomic nitrogen, ionized atomic oxygen, ionized diatomic nitrogen, and ionized diatomic oxygen. Sixteen subroutines compute the following properties for both a single species, interaction pair, or reaction, and an array of all species, pairs, or reactions: species specific heat and static enthalpy, species viscosity, species frozen thermal conductivity, diffusion coefficient, collision cross section (OMEGA 1,1), collision cross section (OMEGA 2,2), collision cross section ratio, and equilibrium constant. The program uses least squares polynomial curve-fits of the most accurate data believed available to provide the requested values more quickly than is possible with table look-up methods. The subroutines for computing transport coefficients and collision cross sections use additional code to correct for any electron pressure when working with ionic species. SPECIES was developed on a SUN 3/280 computer running the SunOS 3.5 operating system. It is written in standard FORTRAN 77 for use on any machine, and requires roughly 92K memory. The standard distribution medium for SPECIES is a 5.25 inch 360K MS-DOS format diskette. The contents of the diskettes are compressed using the PKWARE archiving tools. The utility to unarchive the files, PKUNZIP.EXE, is included. This program was last updated in 1991. SUN and SunOS are registered trademarks of Sun Microsystems, Inc.

Digital computer program for nuclear reactor design water properties (LWBR Development Program)

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

Lynn, L.L.

1967-07-01

An edit program MO899 for the tabulation of thermodynamic and transport properties of liquid and vapor water, frequently used in design calculations for pressurized water nuclear reactors, is described. The data tabulated are obtained from a FORTRAN IV subroutine named HOH. Values of enthalpy, specific volume, viscosity, and thermal conductivity are given for the following ranges: pressure from one bar (14.5 psia) to 175 bars (2538 psia) and temperature from as much as 320 deg C (608 deg F) below saturation up to 500 deg C (932 deg F) above saturation. (NSA 21: 38472)

KONFIG and REKONFIG: Two interactive preprocessing to the Navy/NASA Engine Program (NNEP)

NASA Technical Reports Server (NTRS)

Fishbach, L. H.

1981-01-01

The NNEP is a computer program that is currently being used to simulate the thermodynamic cycle performance of almost all types of turbine engines by many government, industry, and university personnel. The NNEP uses arrays of input data to set up the engine simulation and component matching method as well as to describe the characteristics of the components. A preprocessing program (KONFIG) is described in which the user at a terminal on a time shared computer can interactively prepare the arrays of data required. It is intended to make it easier for the occasional or new user to operate NNEP. Another preprocessing program (REKONFIG) in which the user can modify the component specifications of a previously configured NNEP dataset is also described. It is intended to aid in preparing data for parametric studies and/or studies of similar engines such a mixed flow turbofans, turboshafts, etc.

A Tractable Disequilbrium Framework for Integrating Computational Thermodynamics and Geodynamics

NASA Astrophysics Data System (ADS)

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

2017-12-01

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

New t-gap insertion-deletion-like metrics for DNA hybridization thermodynamic modeling.

PubMed

D'yachkov, Arkadii G; Macula, Anthony J; Pogozelski, Wendy K; Renz, Thomas E; Rykov, Vyacheslav V; Torney, David C

2006-05-01

We discuss the concept of t-gap block isomorphic subsequences and use it to describe new abstract string metrics that are similar to the Levenshtein insertion-deletion metric. Some of the metrics that we define can be used to model a thermodynamic distance function on single-stranded DNA sequences. Our model captures a key aspect of the nearest neighbor thermodynamic model for hybridized DNA duplexes. One version of our metric gives the maximum number of stacked pairs of hydrogen bonded nucleotide base pairs that can be present in any secondary structure in a hybridized DNA duplex without pseudoknots. Thermodynamic distance functions are important components in the construction of DNA codes, and DNA codes are important components in biomolecular computing, nanotechnology, and other biotechnical applications that employ DNA hybridization assays. We show how our new distances can be calculated by using a dynamic programming method, and we derive a Varshamov-Gilbert-like lower bound on the size of some of codes using these distance functions as constraints. We also discuss software implementation of our DNA code design methods.

Computer code for single-point thermodynamic analysis of hydrogen/oxygen expander-cycle rocket engines

NASA Technical Reports Server (NTRS)

Glassman, Arthur J.; Jones, Scott M.

1991-01-01

This analysis and this computer code apply to full, split, and dual expander cycles. Heat regeneration from the turbine exhaust to the pump exhaust is allowed. The combustion process is modeled as one of chemical equilibrium in an infinite-area or a finite-area combustor. Gas composition in the nozzle may be either equilibrium or frozen during expansion. This report, which serves as a users guide for the computer code, describes the system, the analysis methodology, and the program input and output. Sample calculations are included to show effects of key variables such as nozzle area ratio and oxidizer-to-fuel mass ratio.

A study of the optimization method used in the NAVY/NASA gas turbine engine computer code

NASA Technical Reports Server (NTRS)

Horsewood, J. L.; Pines, S.

1977-01-01

Sources of numerical noise affecting the convergence properties of the Powell's Principal Axis Method of Optimization in the NAVY/NASA gas turbine engine computer code were investigated. The principal noise source discovered resulted from loose input tolerances used in terminating iterations performed in subroutine CALCFX to satisfy specified control functions. A minor source of noise was found to be introduced by an insufficient number of digits in stored coefficients used by subroutine THERM in polynomial expressions of thermodynamic properties. Tabular results of several computer runs are presented to show the effects on program performance of selective corrective actions taken to reduce noise.

The Personal Computer in Mechanical Engineering Thermodynamics Courses.

ERIC Educational Resources Information Center

Romer, I. C., Jr.; Balmer, R. T.

1986-01-01

Describes experiences over several semesters with microcomputers in a mechanical engineering applied thermodynamics course. Includes course objectives, computer assignment structure, typical assignments, prewritten versus student-written software, and other topic areas. (JN)

The Climate Space Concept: Analysis of the Steady State Heat Energy Budget of Animals. Physical Processes in Terrestrial and Aquatic Ecosystems, Transport Processes.

ERIC Educational Resources Information Center

Stevenson, R. D.

These materials were designed to be used by life science students for instruction in the application of physical theory to ecosystem operation. Most modules contain computer programs which are built around a particular application of a physical process. Several modules in the thermodynamic series considered the application of the First Law to…

Thermodynamics of computation and information distance

NASA Astrophysics Data System (ADS)

Bennett, Charles H.; Gacs, Peter; Li, Ming; Vitanyi, Paul M. R. B.; Zurek, Wojciech H.

1993-06-01

Intuitively, the minimal information distance between x and y is the length of the shortest program for a universal computer to transform x into y and y into x. This measure is shown to be, up to a logarithmic additive term, equal to the maximum of the conditional Kolmogorov complexities E(sub 1)(x,y) = max(K(y/x), K(x/y)). Any reasonable distance to measure similarity of pictures should be an effectively approximable, symmetric, positive function of x and y satisfying a reasonable normalization condition and obeying the triangle inequality. It turns out that E(sub 1) is minimal up to an additive constant among all such distances. Hence it is a universal 'picture distance', which accounts for any effective similarity between pictures. A third information distance, based on the ideal that the aim should be for dissipationless computations, and hence for reversible ones, is given by the length E(sub 2)(x,y) = KR(y/x) = KR(x/y) of the shortest reversible program that transforms x into y and y into x on a universal reversible computer. It is shown that also E(sub 2) = E(sub 1), up to a logarithmic additive term. It is remarkable that three so differently motivated definitions turn out to define one and the same notion. Another information distance, E(sub 3), is obtained by minimizing the total amount of information flowing in and out during a reversible computation in which the program is not retained, in other words the number of extra bits (apart from x) that must be irreversibly supplied at the beginning, plus the number of garbage bits (apart from y) that must be irreversibly erased at the end of the computation to obtain a 'clean' y. This distance is within a logarithmic additive term of the sum of the conditional complexities, E(sub 3)(x, y) = K(y/x) + K(x/y). Using the physical theory of reversible computation, the simple difference K(x) - K(y) is shown to be an appropriate (universal, antisymmetric, and transitive) measure of the amount of thermodynamic work required to transform string x into string y by the most efficient process.

Computer program for calculation of real gas turbulent boundary layers with variable edge entropy

NASA Technical Reports Server (NTRS)

Boney, L. R.

1974-01-01

A user's manual for a computer program which calculates real gas turbulent boundary layers with variable edge entropy on a blunt cone or flat plate at zero angle of attack is presented. An integral method is used. The method includes the effect of real gas in thermodynamic equilibrium and variable edge entropy. A modified Crocco enthalpy velocity relationship is used for the enthalpy profiles and an empirical correlation of the N-power law profile is used for the velocity profile. The skin-friction-coefficient expressions of Spalding and Chi and Van Driest are used in the solution of the momentum equation and in the heat-transfer predictions that use several modified forms of Reynolds analogy.

A Generalized Fluid System Simulation Program to Model Flow Distribution in Fluid Networks

NASA Technical Reports Server (NTRS)

Majumdar, Alok; Bailey, John W.; Schallhorn, Paul; Steadman, Todd

1998-01-01

This paper describes a general purpose computer program for analyzing steady state and transient flow in a complex network. The program is capable of modeling phase changes, compressibility, mixture thermodynamics and external body forces such as gravity and centrifugal. The program's preprocessor allows the user to interactively develop a fluid network simulation consisting of nodes and branches. Mass, energy and specie conservation equations are solved at the nodes; the momentum conservation equations are solved in the branches. The program contains subroutines for computing "real fluid" thermodynamic and thermophysical properties for 33 fluids. The fluids are: helium, methane, neon, nitrogen, carbon monoxide, oxygen, argon, carbon dioxide, fluorine, hydrogen, parahydrogen, water, kerosene (RP-1), isobutane, butane, deuterium, ethane, ethylene, hydrogen sulfide, krypton, propane, xenon, R-11, R-12, R-22, R-32, R-123, R-124, R-125, R-134A, R-152A, nitrogen trifluoride and ammonia. The program also provides the options of using any incompressible fluid with constant density and viscosity or ideal gas. Seventeen different resistance/source options are provided for modeling momentum sources or sinks in the branches. These options include: pipe flow, flow through a restriction, non-circular duct, pipe flow with entrance and/or exit losses, thin sharp orifice, thick orifice, square edge reduction, square edge expansion, rotating annular duct, rotating radial duct, labyrinth seal, parallel plates, common fittings and valves, pump characteristics, pump power, valve with a given loss coefficient, and a Joule-Thompson device. The system of equations describing the fluid network is solved by a hybrid numerical method that is a combination of the Newton-Raphson and successive substitution methods. This paper also illustrates the application and verification of the code by comparison with Hardy Cross method for steady state flow and analytical solution for unsteady flow.

Computational Design and Discovery of Ni-Based Alloys and Coatings: Thermodynamic Approaches Validated by Experiments

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

Liu, Zi-Kui; Gleeson, Brian; Shang, Shunli

This project developed computational tools that can complement and support experimental efforts in order to enable discovery and more efficient development of Ni-base structural materials and coatings. The project goal was reached through an integrated computation-predictive and experimental-validation approach, including first-principles calculations, thermodynamic CALPHAD (CALculation of PHAse Diagram), and experimental investigations on compositions relevant to Ni-base superalloys and coatings in terms of oxide layer growth and microstructure stabilities. The developed description included composition ranges typical for coating alloys and, hence, allow for prediction of thermodynamic properties for these material systems. The calculation of phase compositions, phase fraction, and phase stabilities,more » which are directly related to properties such as ductility and strength, was a valuable contribution, along with the collection of computational tools that are required to meet the increasing demands for strong, ductile and environmentally-protective coatings. Specifically, a suitable thermodynamic description for the Ni-Al-Cr-Co-Si-Hf-Y system was developed for bulk alloy and coating compositions. Experiments were performed to validate and refine the thermodynamics from the CALPHAD modeling approach. Additionally, alloys produced using predictions from the current computational models were studied in terms of their oxidation performance. Finally, results obtained from experiments aided in the development of a thermodynamic modeling automation tool called ESPEI/pycalphad - for more rapid discovery and development of new materials.« less

Application of computational thermodynamics in the study of magnsium alloys and bulk metallic glasses

NASA Astrophysics Data System (ADS)

Cao, Hongbo

In this thesis, the application of the computational thermodynamics has been explored on two subjects, the study of magnesium alloys (Chapter 1-5) and bulk metallic glasses (BMGs) (Chapter 6-9). For the former case, a strategy of experiments coupled with the CALPHAD approach was employed to establish a thermodynamic description of the quaternary system Mg-Al-Ca-Sr focusing on the Mg-rich phase equilibria. Multicomponent Mg-rich alloys based on the MgAl-Ca-Sr system are one of the most promising candidates for the high temperature applications in the transportation industry. The Mg-Al-Ca-Sr quaternary consists of four ternaries and six binaries. Thermodynamic descriptions of all constituent binaries are available in the literature. Thermodynamic descriptions of the two key ternaries, Mg-Al-Sr and Mg-Al-Ca, were obtained by an efficient and reliable methodology, combining computational thermodynamics with key experiments. The obtained thermodynamic descriptions were validated by performing extensive comparisons between the calculations and experimental information. Thermodynamic descriptions of the other two ternaries, MgCa-Sr and Al-Ca-Sr, were obtained by extrapolation. For the later case, a computational thermodynamic strategy was formulated to obtain a minor but optimum amount of additional element into a base alloy to improve its glass forming ability (GFA). This was done through thermodynamically calculating the maximum liquidus depressions caused by various alloying addition (or replacement) schemes. The success of this approach has been examined in two multicomponent systems, Zr-based Zr-Cu-Ni-Al-Ti and Cu-rich Cu-Zr-Ti-Y. For both cases, experimental results showed conclusively that the GFA increases more than 100% from the base alloy to the one with minor but optimal elemental addition. Furthermore, a thermodynamic computational approach was employed to identify the compositions of Zr-Ti-Ni-Cu-Al alloys exhibiting low-lying liquidus surfaces, which tend to favor the BMG formation. Guided by these calculations, several series of new Zr-based alloys with excellent GFA were synthesized. The approach using the thermodynamically calculated liquidus temperatures was proved to be robust in locating BMGs and can be considered as a universal method to predict novel BMGs not only of scientific interest but also potential technological applications.

Calculation of kinetic rate constants from thermodynamic data

NASA Technical Reports Server (NTRS)

Marek, C. John

1995-01-01

A new scheme for relating the absolute value for the kinetic rate constant k to the thermodynamic constant Kp is developed for gases. In this report the forward and reverse rate constants are individually related to the thermodynamic data. The kinetic rate constants computed from thermodynamics compare well with the current kinetic rate constants. This method is self consistent and does not have extensive rules. It is first demonstrated and calibrated by computing the HBr reaction from H2 and Br2. This method then is used on other reactions.

Does a Computer Have an Arrow of Time?

NASA Astrophysics Data System (ADS)

Maroney, Owen J. E.

2010-02-01

Schulman (Entropy 7(4):221-233, 2005) has argued that Boltzmann’s intuition, that the psychological arrow of time is necessarily aligned with the thermodynamic arrow, is correct. Schulman gives an explicit physical mechanism for this connection, based on the brain being representable as a computer, together with certain thermodynamic properties of computational processes. Hawking (Physical Origins of Time Asymmetry, Cambridge University Press, Cambridge, 1994) presents similar, if briefer, arguments. The purpose of this paper is to critically examine the support for the link between thermodynamics and an arrow of time for computers. The principal arguments put forward by Schulman and Hawking will be shown to fail. It will be shown that any computational process that can take place in an entropy increasing universe, can equally take place in an entropy decreasing universe. This conclusion does not automatically imply a psychological arrow can run counter to the thermodynamic arrow. Some alternative possible explanations for the alignment of the two arrows will be briefly discussed.

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.

Theoretical study of thermodynamic properties and reaction rates of importance in the high-speed research program

NASA Technical Reports Server (NTRS)

Langhoff, Stephen; Bauschlicher, Charles; Jaffe, Richard

1992-01-01

One of the primary goals of NASA's high-speed research program is to determine the feasibility of designing an environmentally safe commercial supersonic transport airplane. The largest environmental concern is focused on the amount of ozone destroying nitrogen oxides (NO(x)) that would be injected into the lower stratosphere during the cruise portion of the flight. The limitations placed on NO(x) emission require more than an order of magnitude reduction over current engine designs. To develop strategies to meet this goal requires first gaining a fundamental understanding of the combustion chemistry. To accurately model the combustor requires a computational fluid dynamics approach that includes both turbulence and chemistry. Since many of the important chemical processes in this regime involve highly reactive radicals, an experimental determination of the required thermodynamic data and rate constants is often very difficult. Unlike experimental approaches, theoretical methods are as applicable to highly reactive species as stable ones. Also our approximation of treating the dynamics classically becomes more accurate with increasing temperature. In this article we review recent progress in generating thermodynamic properties and rate constants that are required to understand NO(x) formation in the combustion process. We also describe our one-dimensional modeling efforts to validate an NH3 combustion reaction mechanism. We have been working in collaboration with researchers at LeRC, to ensure that our theoretical work is focused on the most important thermodynamic quantities and rate constants required in the chemical data base.

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

Wolverton, Christopher; Ozolins, Vidvuds; Kung, Harold H.

The objective of the proposed program is to discover novel mixed hydrides for hydrogen storage, which enable the DOE 2010 system-level goals. Our goal is to find a material that desorbs 8.5 wt.% H 2 or more at temperatures below 85°C. The research program will combine first-principles calculations of reaction thermodynamics and kinetics with material and catalyst synthesis, testing, and characterization. We will combine materials from distinct categories (e.g., chemical and complex hydrides) to form novel multicomponent reactions. Systems to be studied include mixtures of complex hydrides and chemical hydrides [e.g. LiNH 2+NH 3BH 3] and nitrogen-hydrogen based borohydrides [e.g.more » Al(BH 4) 3(NH 3) 3]. The 2010 and 2015 FreedomCAR/DOE targets for hydrogen storage systems are very challenging, and cannot be met with existing materials. The vast majority of the work to date has delineated materials into various classes, e.g., complex and metal hydrides, chemical hydrides, and sorbents. However, very recent studies indicate that mixtures of storage materials, particularly mixtures between various classes, hold promise to achieve technological attributes that materials within an individual class cannot reach. Our project involves a systematic, rational approach to designing novel multicomponent mixtures of materials with fast hydrogenation/dehydrogenation kinetics and favorable thermodynamics using a combination of state-of-the-art scientific computing and experimentation. We will use the accurate predictive power of first-principles modeling to understand the thermodynamic and microscopic kinetic processes involved in hydrogen release and uptake and to design new material/catalyst systems with improved properties. Detailed characterization and atomic-scale catalysis experiments will elucidate the effect of dopants and nanoscale catalysts in achieving fast kinetics and reversibility. And, state-of-the-art storage experiments will give key storage attributes of the investigated reactions, validate computational predictions, and help guide and improve computational methods. In sum, our approach involves a powerful blend of: 1) H2 Storage measurements and characterization, 2) State-of-the-art computational modeling, 3) Detailed catalysis experiments, 4) In-depth automotive perspective.« less

Automated symbolic calculations in nonequilibrium thermodynamics

NASA Astrophysics Data System (ADS)

Kröger, Martin; Hütter, Markus

2010-12-01

We cast the Jacobi identity for continuous fields into a local form which eliminates the need to perform any partial integration to the expense of performing variational derivatives. This allows us to test the Jacobi identity definitely and efficiently and to provide equations between different components defining a potential Poisson bracket. We provide a simple Mathematica TM notebook which allows to perform this task conveniently, and which offers some additional functionalities of use within the framework of nonequilibrium thermodynamics: reversible equations of change for fields, and the conservation of entropy during the reversible dynamics. Program summaryProgram title: Poissonbracket.nb Catalogue identifier: AEGW_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEGW_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 227 952 No. of bytes in distributed program, including test data, etc.: 268 918 Distribution format: tar.gz Programming language: Mathematica TM 7.0 Computer: Any computer running Mathematica TM 6.0 and later versions Operating system: Linux, MacOS, Windows RAM: 100 Mb Classification: 4.2, 5, 23 Nature of problem: Testing the Jacobi identity can be a very complex task depending on the structure of the Poisson bracket. The Mathematica TM notebook provided here solves this problem using a novel symbolic approach based on inherent properties of the variational derivative, highly suitable for the present tasks. As a by product, calculations performed with the Poisson bracket assume a compact form. Solution method: The problem is first cast into a form which eliminates the need to perform partial integration for arbitrary functionals at the expense of performing variational derivatives. The corresponding equations are conveniently obtained using the symbolic programming environment Mathematica TM. Running time: For the test cases and most typical cases in the literature, the running time is of the order of seconds or minutes, respectively.

Computational techniques for design optimization of thermal protection systems for the space shuttle vehicle. Volume 1: Final report

NASA Technical Reports Server (NTRS)

1971-01-01

Computational techniques were developed and assimilated for the design optimization. The resulting computer program was then used to perform initial optimization and sensitivity studies on a typical thermal protection system (TPS) to demonstrate its application to the space shuttle TPS design. The program was developed in Fortran IV for the CDC 6400 but was subsequently converted to the Fortran V language to be used on the Univac 1108. The program allows for improvement and update of the performance prediction techniques. The program logic involves subroutines which handle the following basic functions: (1) a driver which calls for input, output, and communication between program and user and between the subroutines themselves; (2) thermodynamic analysis; (3) thermal stress analysis; (4) acoustic fatigue analysis; and (5) weights/cost analysis. In addition, a system total cost is predicted based on system weight and historical cost data of similar systems. Two basic types of input are provided, both of which are based on trajectory data. These are vehicle attitude (altitude, velocity, and angles of attack and sideslip), for external heat and pressure loads calculation, and heating rates and pressure loads as a function of time.

Thermodynamic modeling using BINGO-ANTIDOTE: A new strategy to investigate metamorphic rocks

NASA Astrophysics Data System (ADS)

Lanari, Pierre; Duesterhoeft, Erik

2016-04-01

BINGO-ANTIDOTE is a new program, combing the achievements of the two petrological software packages XMAPTOOLS[1] and THERIAK-DOMINO[2]. XMAPTOOLS affords information about compositional zoning in mineral and local bulk composition of domains at the thin sections scale. THERIAK-DOMINO calculates equilibrium phase assemblages from given bulk rock composition, temperature T and pressure P. Primarily BINGO-ANTIDOTE can be described as an inverse THERIAK-DOMINO, because it uses the information provided by XMAPTOOLS to calculate the probable P-T equilibrium conditions of metamorphic rocks. Consequently, the introduced program combines the strengths of forward Gibbs free energy minimization models with the intuitive output of inverse thermobarometry models. In order to get "best" P-T equilibrium conditions of a metamorphic rock sample and thus estimating the degree of agreement between the observed and calculated mineral assemblage, it is critical to define a reliable scoring strategy. BINGO uses the THERIAKD ADD-ON[3] (Duesterhoeft and de Capitani, 2013) and is a flexible model scorer with 3+1 evaluation criteria. These criteria are the statistical agreement between the observed and calculated mineral-assemblage, -proportions (vol%) and -composition (mol). Additionally, a total likelihood, consisting of the first three criteria, allows the user an evaluation of the most probable equilibrium P-T condition. ANTIDOTE is an interactive user interface, displaying the 3+1 evaluation criteria as probability P-T-maps. It can be used with and without XMAPTOOLS. As a stand-alone program, the user is able to give the program macroscopic observations (i.e., mineral names and proportions), which ANTIDOTE converts to a readable BINGO input. In this manner, the use of BINGO-ANTIDOTE opens up thermodynamics to students and people with only a basic knowledge of phase diagrams and thermodynamic modeling techniques. This presentation introduces BINGO-ANTIDOTE and includes typical examples of its functionality, such as the determination of P-T conditions of high-grade rocks. BINGO-ANTIDOTE is still under development and will soon be freely available online. References: [1] Lanari P., Vidal O., De Andrade V., Dubacq B., Lewin E., Grosch E. G. and Schwartz S. (2013) XMapTools: a MATLAB©-based program for electron microprobe X-ray image processing and geothermobarometry. Comput. Geosci. 62, 227-240. [2] de Capitani C. and Petrakakis K. (2010) The computation of equilibrium assemblage diagrams with Theriak/Domino software. Am. Mineral. 95, 1006-1016. [3] Duesterhoeft E. and de Capitani C. (2013) Theriak_D: An add-on to implement equilibrium computations in geodynamic models. Geochem. Geophys. Geosyst. 14, 4962-4967.

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.

Thermodynamic properties of UF sub 6 measured with a ballistic piston compressor

NASA Technical Reports Server (NTRS)

Sterritt, D. E.; Lalos, G. T.; Schneider, R. T.

1973-01-01

From experiments performed with a ballistic piston compressor, certain thermodynamic properties of uranium hexafluoride were investigated. Difficulties presented by the nonideal processes encountered in ballistic compressors are discussed and a computer code BCCC (Ballistic Compressor Computer Code) is developed to analyze the experimental data. The BCCC unfolds the thermodynamic properties of uranium hexafluoride from the helium-uranium hexafluoride mixture used as the test gas in the ballistic compressor. The thermodynamic properties deduced include the specific heat at constant volume, the ratio of specific heats for UF6, and the viscous coupling constant of helium-uranium hexafluoride mixtures.

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

PubMed

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

2018-01-09

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

FLUID: A numerical interpolation procedure for obtaining thermodynamic and transport properties of fluids

NASA Technical Reports Server (NTRS)

Fessler, T. E.

1977-01-01

A computer program subroutine, FLUID, was developed to calculate thermodynamic and transport properties of pure fluid substances. It provides for determining the thermodynamic state from assigned values for temperature-density, pressure-density, temperature-pressure, pressure-entropy, or pressure-enthalpy. Liquid or two-phase (liquid-gas) conditions are considered as well as the gas phase. A van der Waals model is used to obtain approximate state values; these values are then corrected for real gas effects by model-correction factors obtained from tables based on experimental data. Saturation conditions, specific heat, entropy, and enthalpy data are included in the tables for each gas. Since these tables are external to the FLUID subroutine itself, FLUID can implement any gas for which a set of tables has been generated. (A setup phase is used to establish pointers dynamically to the tables for a specific gas.) Data-table preparation is described. FLUID is available in both SFTRAN and FORTRAN

GUI for Computational Simulation of a Propellant Mixer

NASA Technical Reports Server (NTRS)

Figueroa, Fernando; Richter, Hanz; Barbieri, Enrique; Granger, Jamie

2005-01-01

Control Panel is a computer program that generates a graphical user interface (GUI) for computational simulation of a rocket-test-stand propellant mixer in which gaseous hydrogen (GH2) is injected into flowing liquid hydrogen (LH2) to obtain a combined flow having desired thermodynamic properties. The GUI is used in conjunction with software that models the mixer as a system having three inputs (the positions of the GH2 and LH2 inlet valves and an outlet valve) and three outputs (the pressure inside the mixer and the outlet flow temperature and flow rate). The user can specify valve characteristics and thermodynamic properties of the input fluids via userfriendly dialog boxes. The user can enter temporally varying input values or temporally varying desired output values. The GUI provides (1) a set-point calculator function for determining fixed valve positions that yield desired output values and (2) simulation functions that predict the response of the mixer to variations in the properties of the LH2 and GH2 and manual- or feedback-control variations in valve positions. The GUI enables scheduling of a sequence of operations that includes switching from manual to feedback control when a certain event occurs.

The Mechanics of Atmospheric Systems Derived Through Vertical and Horizontal Analysis of Parametric Data

NASA Technical Reports Server (NTRS)

Turner, R. E.

1977-01-01

For 36 hours during April 1975, an atmospheric variability experiment was conducted. This research effort supported an observational program in which rawinsonde data, radar data, and satellite data were collected from a network of 42 stations east of the Rocky Mountains at intervals of 3 hours. This program presents data with a high degree of time resolution over a spatially and temporally extensive network. Reduction of the experiment data is intended primarily as a documentation of the checking and processing of the data and should be useful to prospective users. Various flow diagrams of the data processing procedures are described, and a complete summary of the formulas used in the data processing is provided. A wind computation scheme designed to extract as much detailed wind information as possible from the unique experiment data set is discussed. The accuracy of the thermodynamic and wind data were estimated. Errors in the thermodynamic and wind data are given.

An integrated computational tool for precipitation simulation

NASA Astrophysics Data System (ADS)

Cao, W.; Zhang, F.; Chen, S.-L.; Zhang, C.; Chang, Y. A.

2011-07-01

Computer aided materials design is of increasing interest because the conventional approach solely relying on experimentation is no longer viable within the constraint of available resources. Modeling of microstructure and mechanical properties during precipitation plays a critical role in understanding the behavior of materials and thus accelerating the development of materials. Nevertheless, an integrated computational tool coupling reliable thermodynamic calculation, kinetic simulation, and property prediction of multi-component systems for industrial applications is rarely available. In this regard, we are developing a software package, PanPrecipitation, under the framework of integrated computational materials engineering to simulate precipitation kinetics. It is seamlessly integrated with the thermodynamic calculation engine, PanEngine, to obtain accurate thermodynamic properties and atomic mobility data necessary for precipitation simulation.

Path Integral Computation of Quantum Free Energy Differences Due to Alchemical Transformations Involving Mass and Potential.

PubMed

Pérez, Alejandro; von Lilienfeld, O Anatole

2011-08-09

Thermodynamic integration, perturbation theory, and λ-dynamics methods were applied to path integral molecular dynamics calculations to investigate free energy differences due to "alchemical" transformations. Several estimators were formulated to compute free energy differences in solvable model systems undergoing changes in mass and/or potential. Linear and nonlinear alchemical interpolations were used for the thermodynamic integration. We find improved convergence for the virial estimators, as well as for the thermodynamic integration over nonlinear interpolation paths. Numerical results for the perturbative treatment of changes in mass and electric field strength in model systems are presented. We used thermodynamic integration in ab initio path integral molecular dynamics to compute the quantum free energy difference of the isotope transformation in the Zundel cation. The performance of different free energy methods is discussed.

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.

Integrated modeling of advanced optical systems

NASA Astrophysics Data System (ADS)

Briggs, Hugh C.; Needels, Laura; Levine, B. Martin

1993-02-01

This poster session paper describes an integrated modeling and analysis capability being developed at JPL under funding provided by the JPL Director's Discretionary Fund and the JPL Control/Structure Interaction Program (CSI). The posters briefly summarize the program capabilities and illustrate them with an example problem. The computer programs developed under this effort will provide an unprecedented capability for integrated modeling and design of high performance optical spacecraft. The engineering disciplines supported include structural dynamics, controls, optics and thermodynamics. Such tools are needed in order to evaluate the end-to-end system performance of spacecraft such as OSI, POINTS, and SMMM. This paper illustrates the proof-of-concept tools that have been developed to establish the technology requirements and demonstrate the new features of integrated modeling and design. The current program also includes implementation of a prototype tool based upon the CAESY environment being developed under the NASA Guidance and Control Research and Technology Computational Controls Program. This prototype will be available late in FY-92. The development plan proposes a major software production effort to fabricate, deliver, support and maintain a national-class tool from FY-93 through FY-95.

The minimal work cost of information processing

NASA Astrophysics Data System (ADS)

Faist, Philippe; Dupuis, Frédéric; Oppenheim, Jonathan; Renner, Renato

2015-07-01

Irreversible information processing cannot be carried out without some inevitable thermodynamical work cost. This fundamental restriction, known as Landauer's principle, is increasingly relevant today, as the energy dissipation of computing devices impedes the development of their performance. Here we determine the minimal work required to carry out any logical process, for instance a computation. It is given by the entropy of the discarded information conditional to the output of the computation. Our formula takes precisely into account the statistically fluctuating work requirement of the logical process. It enables the explicit calculation of practical scenarios, such as computational circuits or quantum measurements. On the conceptual level, our result gives a precise and operational connection between thermodynamic and information entropy, and explains the emergence of the entropy state function in macroscopic thermodynamics.

Computer modeling of batteries from nonlinear circuit elements

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

Waaben, S.; Dyer, C.K.; Federico, J.

1985-06-01

Circuit analogs for a single battery cell have previously been composed of resistors, capacitors, and inductors. This work introduces a nonlinear circuit model for cell behavior. The circuit is configured around the PIN junction diode, whose charge-storage behavior has features similar to those of electrochemical cells. A user-friendly integrated circuit simulation computer program has reproduced a variety of complex cell responses including electrica isolation effects causing capacity loss, as well as potentiodynamic peaks and discharge phenomena hitherto thought to be thermodynamic in origin. However, in this work, they are shown to be simply due to spatial distribution of stored chargemore » within a practical electrode.« less

Computer program for analysis of split-Stirling-cycle cryogenic coolers

NASA Technical Reports Server (NTRS)

Brown, M. T.; Russo, S. C.

1983-01-01

A computer program for predicting the detailed thermodynamic performance of split-Stirling-cycle refrigerators has been developed. The mathematical model includes the refrigerator cold head, free-displacer/regenerator, gas transfer line, and provision for modeling a mechanical or thermal compressor. To allow for dynamic processes (such as aerodynamic friction and heat transfer) temperature, pressure, and mass flow rate are varied by sub-dividing the refrigerator into an appropriate number of fluid and structural control volumes. Of special importance to modeling of cryogenic coolers is the inclusion of real gas properties, and allowance for variation of thermo-physical properties such as thermal conductivities, specific heats and viscosities, with temperature and/or pressure. The resulting model, therefore, comprehensively simulates the split-cycle cooler both spatially and temporally by reflecting the effects of dynamic processes and real material properties.

Designing overall stoichiometric conversions and intervening metabolic reactions

DOE PAGES

Chowdhury, Anupam; Maranas, Costas D.

2015-11-04

Existing computational tools for de novo metabolic pathway assembly, either based on mixed integer linear programming techniques or graph-search applications, generally only find linear pathways connecting the source to the target metabolite. The overall stoichiometry of conversion along with alternate co-reactant (or co-product) combinations is not part of the pathway design. Therefore, global carbon and energy efficiency is in essence fixed with no opportunities to identify more efficient routes for recycling carbon flux closer to the thermodynamic limit. Here, we introduce a two-stage computational procedure that both identifies the optimum overall stoichiometry (i.e., optStoic) and selects for (non-)native reactions (i.e.,more » minRxn/minFlux) that maximize carbon, energy or price efficiency while satisfying thermodynamic feasibility requirements. Implementation for recent pathway design studies identified non-intuitive designs with improved efficiencies. Specifically, multiple alternatives for non-oxidative glycolysis are generated and non-intuitive ways of co-utilizing carbon dioxide with methanol are revealed for the production of C 2+ metabolites with higher carbon efficiency.« less

Computational models for the viscous/inviscid analysis of jet aircraft exhaust plumes

NASA Astrophysics Data System (ADS)

Dash, S. M.; Pergament, H. S.; Thorpe, R. D.

1980-05-01

Computational models which analyze viscous/inviscid flow processes in jet aircraft exhaust plumes are discussed. These models are component parts of an NASA-LaRC method for the prediction of nozzle afterbody drag. Inviscid/shock processes are analyzed by the SCIPAC code which is a compact version of a generalized shock capturing, inviscid plume code (SCIPPY). The SCIPAC code analyzes underexpanded jet exhaust gas mixtures with a self-contained thermodynamic package for hydrocarbon exhaust products and air. A detailed and automated treatment of the embedded subsonic zones behind Mach discs is provided in this analysis. Mixing processes along the plume interface are analyzed by two upgraded versions of an overlaid, turbulent mixing code (BOAT) developed previously for calculating nearfield jet entrainment. The BOATAC program is a frozen chemistry version of BOAT containing the aircraft thermodynamic package as SCIPAC; BOATAB is an afterburning version with a self-contained aircraft (hydrocarbon/air) finite-rate chemistry package. The coupling of viscous and inviscid flow processes is achieved by an overlaid procedure with interactive effects accounted for by a displacement thickness type correction to the inviscid plume interface.

Computational models for the viscous/inviscid analysis of jet aircraft exhaust plumes. [predicting afterbody drag

NASA Technical Reports Server (NTRS)

Dash, S. M.; Pergament, H. S.; Thorpe, R. D.

1980-01-01

Computational models which analyze viscous/inviscid flow processes in jet aircraft exhaust plumes are discussed. These models are component parts of an NASA-LaRC method for the prediction of nozzle afterbody drag. Inviscid/shock processes are analyzed by the SCIPAC code which is a compact version of a generalized shock capturing, inviscid plume code (SCIPPY). The SCIPAC code analyzes underexpanded jet exhaust gas mixtures with a self-contained thermodynamic package for hydrocarbon exhaust products and air. A detailed and automated treatment of the embedded subsonic zones behind Mach discs is provided in this analysis. Mixing processes along the plume interface are analyzed by two upgraded versions of an overlaid, turbulent mixing code (BOAT) developed previously for calculating nearfield jet entrainment. The BOATAC program is a frozen chemistry version of BOAT containing the aircraft thermodynamic package as SCIPAC; BOATAB is an afterburning version with a self-contained aircraft (hydrocarbon/air) finite-rate chemistry package. The coupling of viscous and inviscid flow processes is achieved by an overlaid procedure with interactive effects accounted for by a displacement thickness type correction to the inviscid plume interface.

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.

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

Open-cycle systems performance analysis programming guide

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

Olson, D.A.

1981-12-01

The Open-Cycle OTEC Systems Performance Analysis Program is an algorithm programmed on SERI's CDC Cyber 170/720 computer to predict the performance of a Claude-cycle, open-cycle OTEC plant. The algorithm models the Claude-cycle system as consisting of an evaporator, a turbine, a condenser, deaerators, a condenser gas exhaust, a cold water pipe and cold and warm seawater pumps. Each component is a separate subroutine in the main program. A description is given of how to write Fortran subroutines to fit into the main program for the components of the OTEC plant. An explanation is provided of how to use the algorithm.more » The main program and existing component subroutines are described. Appropriate common blocks and input and output variables are listed. Preprogrammed thermodynamic property functions for steam, fresh water, and seawater are described.« 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.

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

NASA Technical Reports Server (NTRS)

Marek, C. John

1996-01-01

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

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.

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

PubMed

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

2016-06-01

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

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

Treesearch

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

2014-01-01

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

Thermodynamics of statistical inference by cells.

PubMed

Lang, Alex H; Fisher, Charles K; Mora, Thierry; Mehta, Pankaj

2014-10-03

The deep connection between thermodynamics, computation, and information is now well established both theoretically and experimentally. Here, we extend these ideas to show that thermodynamics also places fundamental constraints on statistical estimation and learning. To do so, we investigate the constraints placed by (nonequilibrium) thermodynamics on the ability of biochemical signaling networks to estimate the concentration of an external signal. We show that accuracy is limited by energy consumption, suggesting that there are fundamental thermodynamic constraints on statistical inference.

Design of nucleic acid sequences for DNA computing based on a thermodynamic approach

PubMed Central

Tanaka, Fumiaki; Kameda, Atsushi; Yamamoto, Masahito; Ohuchi, Azuma

2005-01-01

We have developed an algorithm for designing multiple sequences of nucleic acids that have a uniform melting temperature between the sequence and its complement and that do not hybridize non-specifically with each other based on the minimum free energy (ΔGmin). Sequences that satisfy these constraints can be utilized in computations, various engineering applications such as microarrays, and nano-fabrications. Our algorithm is a random generate-and-test algorithm: it generates a candidate sequence randomly and tests whether the sequence satisfies the constraints. The novelty of our algorithm is that the filtering method uses a greedy search to calculate ΔGmin. This effectively excludes inappropriate sequences before ΔGmin is calculated, thereby reducing computation time drastically when compared with an algorithm without the filtering. Experimental results in silico showed the superiority of the greedy search over the traditional approach based on the hamming distance. In addition, experimental results in vitro demonstrated that the experimental free energy (ΔGexp) of 126 sequences correlated well with ΔGmin (|R| = 0.90) than with the hamming distance (|R| = 0.80). These results validate the rationality of a thermodynamic approach. We implemented our algorithm in a graphic user interface-based program written in Java. PMID:15701762

Sodium sulfate: Vaporization thermodynamics and role in corrosive flames

NASA Technical Reports Server (NTRS)

Kohl, F. J.

1975-01-01

Gaseous species over liquid Na2SO4 were identified by the technique of molecular beam mass spectrometry. The heat and entropy of vaporization of the Na2SO4 molecule were measured directly. Comparisons of the experimental entropy with values calculated using various molecular parameters were used to estimate the molecular structure and vibrational frequencies. The thermodynamic properties of gaseous and condensed phase Na2SO4, along with additional pertinent species, were used in a computer program to calculate equilibrium flame compositions and temperatures for representative turbine engine and burner rig flames. Compositions were calculated at various fuel-to-oxidant ratios with additions of sulfur to the fuel and the components of sea salt to the intake air. Temperatures for condensation of Na2SO4 were obtained as a function of sulfur and sea salt concentrations.

Free Energy Perturbation Hamiltonian Replica-Exchange Molecular Dynamics (FEP/H-REMD) for Absolute Ligand Binding Free Energy Calculations.

PubMed

Jiang, Wei; Roux, Benoît

2010-07-01

Free Energy Perturbation with Replica Exchange Molecular Dynamics (FEP/REMD) offers a powerful strategy to improve the convergence of free energy computations. In particular, it has been shown previously that a FEP/REMD scheme allowing random moves within an extended replica ensemble of thermodynamic coupling parameters "lambda" can improve the statistical convergence in calculations of absolute binding free energy of ligands to proteins [J. Chem. Theory Comput. 2009, 5, 2583]. In the present study, FEP/REMD is extended and combined with an accelerated MD simulations method based on Hamiltonian replica-exchange MD (H-REMD) to overcome the additional problems arising from the existence of kinetically trapped conformations within the protein receptor. In the combined strategy, each system with a given thermodynamic coupling factor lambda in the extended ensemble is further coupled with a set of replicas evolving on a biased energy surface with boosting potentials used to accelerate the inter-conversion among different rotameric states of the side chains in the neighborhood of the binding site. Exchanges are allowed to occur alternatively along the axes corresponding to the thermodynamic coupling parameter lambda and the boosting potential, in an extended dual array of coupled lambda- and H-REMD simulations. The method is implemented on the basis of new extensions to the REPDSTR module of the biomolecular simulation program CHARMM. As an illustrative example, the absolute binding free energy of p-xylene to the nonpolar cavity of the L99A mutant of T4 lysozyme was calculated. The tests demonstrate that the dual lambda-REMD and H-REMD simulation scheme greatly accelerates the configurational sampling of the rotameric states of the side chains around the binding pocket, thereby improving the convergence of the FEP computations.

Systematic assignment of thermodynamic constraints in metabolic network models

PubMed Central

Kümmel, Anne; Panke, Sven; Heinemann, Matthias

2006-01-01

Background The availability of genome sequences for many organisms enabled the reconstruction of several genome-scale metabolic network models. Currently, significant efforts are put into the automated reconstruction of such models. For this, several computational tools have been developed that particularly assist in identifying and compiling the organism-specific lists of metabolic reactions. In contrast, the last step of the model reconstruction process, which is the definition of the thermodynamic constraints in terms of reaction directionalities, still needs to be done manually. No computational method exists that allows for an automated and systematic assignment of reaction directions in genome-scale models. Results We present an algorithm that – based on thermodynamics, network topology and heuristic rules – automatically assigns reaction directions in metabolic models such that the reaction network is thermodynamically feasible with respect to the production of energy equivalents. It first exploits all available experimentally derived Gibbs energies of formation to identify irreversible reactions. As these thermodynamic data are not available for all metabolites, in a next step, further reaction directions are assigned on the basis of network topology considerations and thermodynamics-based heuristic rules. Briefly, the algorithm identifies reaction subsets from the metabolic network that are able to convert low-energy co-substrates into their high-energy counterparts and thus net produce energy. Our algorithm aims at disabling such thermodynamically infeasible cyclic operation of reaction subnetworks by assigning reaction directions based on a set of thermodynamics-derived heuristic rules. We demonstrate our algorithm on a genome-scale metabolic model of E. coli. The introduced systematic direction assignment yielded 130 irreversible reactions (out of 920 total reactions), which corresponds to about 70% of all irreversible reactions that are required to disable thermodynamically infeasible energy production. Conclusion Although not being fully comprehensive, our algorithm for systematic reaction direction assignment could define a significant number of irreversible reactions automatically with low computational effort. We envision that the presented algorithm is a valuable part of a computational framework that assists the automated reconstruction of genome-scale metabolic models. PMID:17123434

Experimental verification of the thermodynamic properties for a jet-A fuel

NASA Technical Reports Server (NTRS)

Graciasalcedo, Carmen M.; Brabbs, Theodore A.; Mcbride, Bonnie J.

1988-01-01

Thermodynamic properties for a Jet-A fuel were determined by Shell Development Company in 1970 under a contract for NASA Lewis Research Center. The polynomial fit necessary to include Jet-A fuel (liquid and gaseous phases) in the library of thermodynamic properties of the NASA Lewis Chemical Equilibrium Program is calculated. To verify the thermodynamic data, the temperatures of mixtures of liquid Jet-A injected into a hot nitrogen stream were experimentally measured and compared to those calculated by the program. Iso-octane, a fuel for which the thermodynamic properties are well known, was used as a standard to calibrate the apparatus. The measured temperatures for the iso-octane/nitrogen mixtures reproduced the calculated temperatures except for a small loss due to the non-adiabatic behavior of the apparatus. The measurements for Jet-A were corrected for this heat loss and showed excellent agreement with the calculated temperatures. These experiments show that this process can be adequately described by the thermodynamic properties fitted for the Chemical Equilibrium Program.

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

Ceder, Gerbrand

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

An investigation of the energy balance of solar active regions using the ACRIM irradiance data

NASA Technical Reports Server (NTRS)

Petro, L. D.

1986-01-01

The detection of a significant correlation between the solar irradiance, corrected for flux deficit due to sunspots, and both the 205 nm flux and a photometric facular index were examined. A detailed analysis supports facular emission as the more likely source of correlation with the corrected radiance, rather then the error in sunspot correction. A computer program which simulates two dimensional convection in a compressible, stratified medium was investigated. Subroutines to calculate ionization and other thermodynamic variables were also completed.

Component-specific modeling

NASA Technical Reports Server (NTRS)

Mcknight, R. L.

1985-01-01

Accomplishments are described for the second year effort of a 3-year program to develop methodology for component specific modeling of aircraft engine hot section components (turbine blades, turbine vanes, and burner liners). These accomplishments include: (1) engine thermodynamic and mission models; (2) geometry model generators; (3) remeshing; (4) specialty 3-D inelastic stuctural analysis; (5) computationally efficient solvers, (6) adaptive solution strategies; (7) engine performance parameters/component response variables decomposition and synthesis; (8) integrated software architecture and development, and (9) validation cases for software developed.

Component-specific modeling. [jet engine hot section components

NASA Technical Reports Server (NTRS)

Mcknight, R. L.; Maffeo, R. J.; Tipton, M. T.; Weber, G.

1992-01-01

Accomplishments are described for a 3 year program to develop methodology for component-specific modeling of aircraft hot section components (turbine blades, turbine vanes, and burner liners). These accomplishments include: (1) engine thermodynamic and mission models, (2) geometry model generators, (3) remeshing, (4) specialty three-dimensional inelastic structural analysis, (5) computationally efficient solvers, (6) adaptive solution strategies, (7) engine performance parameters/component response variables decomposition and synthesis, (8) integrated software architecture and development, and (9) validation cases for software developed.

Horizontal steam generator thermal-hydraulics

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

Ubra, O.; Doubek, M.

1995-09-01

Horizontal steam generators are typical components of nuclear power plants with pressure water reactor type VVER. Thermal-hydraulic behavior of horizontal steam generators is very different from the vertical U-tube steam generator, which has been extensively studied for several years. To contribute to the understanding of the horizontal steam generator thermal-hydraulics a computer program for 3-D steady state analysis of the PGV-1000 steam generator has been developed. By means of this computer program, a detailed thermal-hydraulic and thermodynamic study of the horizontal steam generator PGV-1000 has been carried out and a set of important steam generator characteristics has been obtained. Themore » 3-D distribution of the void fraction and 3-D level profile as functions of load and secondary side pressure have been investigated and secondary side volumes and masses as functions of load and pressure have been evaluated. Some of the interesting results of calculations are presented in the paper.« less

The thermodynamic efficiency of computations made in cells across the range of life

NASA Astrophysics Data System (ADS)

Kempes, Christopher P.; Wolpert, David; Cohen, Zachary; Pérez-Mercader, Juan

2017-11-01

Biological organisms must perform computation as they grow, reproduce and evolve. Moreover, ever since Landauer's bound was proposed, it has been known that all computation has some thermodynamic cost-and that the same computation can be achieved with greater or smaller thermodynamic cost depending on how it is implemented. Accordingly an important issue concerning the evolution of life is assessing the thermodynamic efficiency of the computations performed by organisms. This issue is interesting both from the perspective of how close life has come to maximally efficient computation (presumably under the pressure of natural selection), and from the practical perspective of what efficiencies we might hope that engineered biological computers might achieve, especially in comparison with current computational systems. Here we show that the computational efficiency of translation, defined as free energy expended per amino acid operation, outperforms the best supercomputers by several orders of magnitude, and is only about an order of magnitude worse than the Landauer bound. However, this efficiency depends strongly on the size and architecture of the cell in question. In particular, we show that the useful efficiency of an amino acid operation, defined as the bulk energy per amino acid polymerization, decreases for increasing bacterial size and converges to the polymerization cost of the ribosome. This cost of the largest bacteria does not change in cells as we progress through the major evolutionary shifts to both single- and multicellular eukaryotes. However, the rates of total computation per unit mass are non-monotonic in bacteria with increasing cell size, and also change across different biological architectures, including the shift from unicellular to multicellular eukaryotes. This article is part of the themed issue 'Reconceptualizing the origins of life'.

Irreversible thermodynamics of Poisson processes with reaction.

PubMed

Méndez, V; Fort, J

1999-11-01

A kinetic model is derived to study the successive movements of particles, described by a Poisson process, as well as their generation. The irreversible thermodynamics of this system is also studied from the kinetic model. This makes it possible to evaluate the differences between thermodynamical quantities computed exactly and up to second-order. Such differences determine the range of validity of the second-order approximation to extended irreversible thermodynamics.

Constant curvature black holes in Einstein AdS gravity: Euclidean action and thermodynamics

NASA Astrophysics Data System (ADS)

Guilleminot, Pablo; Olea, Rodrigo; Petrov, Alexander N.

2018-03-01

We compute the Euclidean action for constant curvature black holes (CCBHs), as an attempt to associate thermodynamic quantities to these solutions of Einstein anti-de Sitter (AdS) gravity. CCBHs are gravitational configurations obtained by identifications along isometries of a D -dimensional globally AdS space, such that the Riemann tensor remains constant. Here, these solutions are interpreted as extended objects, which contain a (D -2 )-dimensional de-Sitter brane as a subspace. Nevertheless, the computation of the free energy for these solutions shows that they do not obey standard thermodynamic relations.

Vapor-liquid equilibrium thermodynamics of N2 + CH4 - Model and Titan applications

NASA Technical Reports Server (NTRS)

Thompson, W. R.; Zollweg, John A.; Gabis, David H.

1992-01-01

A thermodynamic model is presented for vapor-liquid equilibrium in the N2 + CH4 system, which is implicated in calculations of the Titan tropospheric clouds' vapor-liquid equilibrium thermodynamics. This model imposes constraints on the consistency of experimental equilibrium data, and embodies temperature effects by encompassing enthalpy data; it readily calculates the saturation criteria, condensate composition, and latent heat for a given pressure-temperature profile of the Titan atmosphere. The N2 content of condensate is about half of that computed from Raoult's law, and about 30 percent greater than that computed from Henry's law.

Computerized systems analysis and optimization of aircraft engine performance, weight, and life cycle costs

NASA Technical Reports Server (NTRS)

Fishbach, L. H.

1979-01-01

The computational techniques utilized to determine the optimum propulsion systems for future aircraft applications and to identify system tradeoffs and technology requirements are described. The characteristics and use of the following computer codes are discussed: (1) NNEP - a very general cycle analysis code that can assemble an arbitrary matrix fans, turbines, ducts, shafts, etc., into a complete gas turbine engine and compute on- and off-design thermodynamic performance; (2) WATE - a preliminary design procedure for calculating engine weight using the component characteristics determined by NNEP; (3) POD DRG - a table look-up program to calculate wave and friction drag of nacelles; (4) LIFCYC - a computer code developed to calculate life cycle costs of engines based on the output from WATE; and (5) INSTAL - a computer code developed to calculate installation effects, inlet performance and inlet weight. Examples are given to illustrate how these computer techniques can be applied to analyze and optimize propulsion system fuel consumption, weight, and cost for representative types of aircraft and missions.

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

Thermodynamic model for the regeneration of sulfur-poisoned nickel catalyst. 1. Using thermodynamic properties of bulk nickel compounds only

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

Chughtai, A.R.; Riter, J.R. Jr.

1979-10-18

By the use of the modified computer programs of Gordon and McBride for the determination of heterogeneous phase and chemical equilibria at preassigned temperatures (300-1100 K) and atmospheric pressure (101 325 N m/sup -2/), the oxidation with O/sub 2/ of sulfur-poisoned Raney nickel catalyst and subsequent reduction with H/sub 2/ have been modeled thermodynamically by using the properties of bulk nickel compounds. An alternate process, the direct reduction with H/sub 2/ of the sulfidized nickel, has also been modeled and arguments are advanced for the further investigation of this thermodynamically favored second process. In both processes the mole ratios ofmore » reactants, H/sub 2//NiSO/sub 4/ and H/sub 2//Ni/sub 3/S/sub 2/, respectively, for complete disappearance of the last product to be reduced, Ni/sub 3/S/sub 2/, increase markedly as the desired temperature for complete thermodynamic reduction decreases. These ratios and the equilibrium activity quotient P/sub H/sub 2///P/sub H/sub 2/S/ have been determined as quantitative functions of this critical reduction temperature. A complete thermodynamic hierarchy of oxidation processes for the reaction of O/sub 2/ with mixtures of Ni and Ni/sub 3/S/sub 2/ is developed. From the equilibrium calculations it is brought out that Ni/sub 3/S/sub 2/ is relatively more stable both to oxidation with O/sub 2/ than is Ni and to reduction with H/sub 2/ than is NiO. One point of modest connection with experiment is presented for the reduction processes. 1 figure, 1 table.« less

Thermodynamic and economic analysis of heat pumps for energy recovery in industrial processes

NASA Astrophysics Data System (ADS)

Urdaneta-B, A. H.; Schmidt, P. S.

1980-09-01

A computer code has been developed for analyzing the thermodynamic performance, cost and economic return for heat pump applications in industrial heat recovery. Starting with basic defining characteristics of the waste heat stream and the desired heat sink, the algorithm first evaluates the potential for conventional heat recovery with heat exchangers, and if applicable, sizes the exchanger. A heat pump system is then designed to process the residual heating and cooling requirements of the streams. In configuring the heat pump, the program searches a number of parameters, including condenser temperature, evaporator temperature, and condenser and evaporator approaches. All system components are sized for each set of parameters, and economic return is estimated and compared with system economics for conventional processing of the heated and cooled streams (i.e., with process heaters and coolers). Two case studies are evaluated, one in a food processing application and the other in an oil refinery unit.

Polynomial complexity despite the fermionic sign

NASA Astrophysics Data System (ADS)

Rossi, R.; Prokof'ev, N.; Svistunov, B.; Van Houcke, K.; Werner, F.

2017-04-01

It is commonly believed that in unbiased quantum Monte Carlo approaches to fermionic many-body problems, the infamous sign problem generically implies prohibitively large computational times for obtaining thermodynamic-limit quantities. We point out that for convergent Feynman diagrammatic series evaluated with a recently introduced Monte Carlo algorithm (see Rossi R., arXiv:1612.05184), the computational time increases only polynomially with the inverse error on thermodynamic-limit quantities.

COED Transactions, Vol. 8, No. 10, October 1976. The Computer Generation of Thermodynamic Phase Diagrams.

ERIC Educational Resources Information Center

Jolls, Kenneth R.; And Others

A technique is described for the generation of perspective views of three-dimensional models using computer graphics. The technique is applied to models of familiar thermodynamic phase diagrams and the results are presented for the ideal gas and van der Waals equations of state as well as the properties of liquid water and steam from the Steam…

Computational Thermodynamic Modeling of Hot Corrosion of Alloys Haynes 242 and Hastelloy TM N for Molten Salt Service in Advanced High Temperature Reactors

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

V. Glazoff, Michael; Charit, Indrajt; Sabharwall, Piyush

An evaluation of thermodynamic aspects of hot corrosion of the superalloys Haynes 242 and HastelloyTM N in the eutectic mixtures of KF and ZrF4 is carried out for development of Advanced High Temperature Reactor (AHTR). This work models the behavior of several superalloys, potential candidates for the AHTR, using computational thermodynamics tool (ThermoCalc), leading to the development of thermodynamic description of the molten salt eutectic mixtures, and on that basis, mechanistic prediction of hot corrosion. The results from these studies indicated that the principal mechanism of hot corrosion was associated with chromium leaching for all of the superalloys described above.more » However, HastelloyTM N displayed the best hot corrosion performance. This was not surprising given it was developed originally to withstand the harsh conditions of molten salt environment. However, the results obtained in this study provided confidence in the employed methods of computational thermodynamics and could be further used for future alloy design efforts. Finally, several potential solutions to mitigate hot corrosion were proposed for further exploration, including coating development and controlled scaling of intermediate compounds in the KF-ZrF4 system.« less

Thermodynamics properties of lanthanide series near melting point-A pseudopotential approach

NASA Astrophysics Data System (ADS)

Suthar, P. H.; Gajjar, P. N.

2018-04-01

The present paper deals with computational study of thermodynamics properties for fifteen elements of lanthanide series. The Helmholtz free energy (F), Internal energy (E) and Entropy (S)have been computed using variational method based on the Gibbs-Bogoliubov (GB) along with Percus-Yevick hard sphere reference system and Gajjar's model potential. The local field correction function proposed by Taylor is applied to introduce the exchange and correlation effects in the study of thermodynamics of these metals. The present results in comparison with available theoretical and experimental are found to be in good agreement and confirm the ability of the model potential.

Rotary engine performance computer program (RCEMAP and RCEMAPPC): User's guide

NASA Technical Reports Server (NTRS)

Bartrand, Timothy A.; Willis, Edward A.

1993-01-01

This report is a user's guide for a computer code that simulates the performance of several rotary combustion engine configurations. It is intended to assist prospective users in getting started with RCEMAP and/or RCEMAPPC. RCEMAP (Rotary Combustion Engine performance MAP generating code) is the mainframe version, while RCEMAPPC is a simplified subset designed for the personal computer, or PC, environment. Both versions are based on an open, zero-dimensional combustion system model for the prediction of instantaneous pressures, temperature, chemical composition and other in-chamber thermodynamic properties. Both versions predict overall engine performance and thermal characteristics, including bmep, bsfc, exhaust gas temperature, average material temperatures, and turbocharger operating conditions. Required inputs include engine geometry, materials, constants for use in the combustion heat release model, and turbomachinery maps. Illustrative examples and sample input files for both versions are included.

Thermodynamic properties of gaseous fluorocarbons and isentropic equilibrium expansions of two binary mixtures of fluorocarbons and argon

NASA Technical Reports Server (NTRS)

Talcott, N. A., Jr.

1977-01-01

Equations and computer code are given for the thermodynamic properties of gaseous fluorocarbons in chemical equilibrium. In addition, isentropic equilibrium expansions of two binary mixtures of fluorocarbons and argon are included. The computer code calculates the equilibrium thermodynamic properties and, in some cases, the transport properties for the following fluorocarbons: CCl2F, CCl2F2, CBrF3, CF4, CHCl2F, CHF3, CCL2F-CCl2F, CCLF2-CClF2, CF3-CF3, and C4F8. Equilibrium thermodynamic properties are tabulated for six of the fluorocarbons(CCl3F, CCL2F2, CBrF3, CF4, CF3-CF3, and C4F8) and pressure-enthalpy diagrams are presented for CBrF3.

Mass-independent area (or entropy) and thermodynamic volume products in conformal gravity

NASA Astrophysics Data System (ADS)

Pradhan, Parthapratim

2017-06-01

In this work, we investigate the thermodynamic properties of conformal gravity in four dimensions. We compute the area (or entropy) functional relation for this black hole (BH). We consider both de Sitter (dS) and anti-de Sitter (AdS) cases. We derive the Cosmic-Censorship-Inequality which is an important relation in general relativity that relates the total mass of a spacetime to the area of all the BH horizons. Local thermodynamic stability is studied by computing the specific heat. The second-order phase transition occurs at a certain condition. Various types of second-order phase structure have been given for various values of a and the cosmological constant Λ in the Appendix. When a = 0, one obtains the result of Schwarzschild-dS and Schwarzschild-AdS cases. In the limit aM ≪ 1, one obtains the result of Grumiller spacetime, where a is nontrivial Rindler parameter or Rindler acceleration and M is the mass parameter. The thermodynamic volume functional relation is derived in the extended phase space, where the cosmological constant is treated as a thermodynamic pressure and its conjugate variable as a thermodynamic volume. The mass-independent area (or entropy) functional relation and thermodynamic volume functional relation that we have derived could turn out to be a universal quantity.

A thermodynamic study of Abeta(16-21) dissociation from a fibril using computer simulations

NASA Astrophysics Data System (ADS)

Dias, Cristiano; Mahmoudinobar, Farbod; Su, Zhaoqian

Here, I will discuss recent all-atom molecular dynamics simulations with explicit water in which we studied the thermodynamic properties of Abeta(16-21) dissociation from an amyloid fibril. Changes in thermodynamics quantities, e.g., entropy, enthalpy, and volume, are computed from the temperature dependence of the free-energy computed using the umbrella sampling method. We find similarities and differences between the thermodynamics of peptide dissociation and protein unfolding. Similarly to protein unfolding, Abeta(16-21) dissociation is characterized by an unfavorable change in enthalpy, a favorable change in the entropic energy, and an increase in the heat capacity. A main difference is that peptide dissociation is characterized by a weak enthalpy-entropy compensation. We characterize dock and lock states of the peptide based on the solvent accessible surface area. The Lennard-Jones energy of the system is observed to increase continuously in lock and dock states as the peptide dissociates. The electrostatic energy increases in the lock state and it decreases in the dock state as the peptide dissociates. These results will be discussed as well as their implication for fibril growth.

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.

Thermodynamics of reformulated automotive fuels

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

Zudkevitch, D.; Murthy, A.K.S.; Gmehling, J.

1995-06-01

Two methods for predicting Reid vapor pressure (Rvp) and initial vapor emissions of reformulated gasoline blends that contain one or more oxygenated compounds show excellent agreement with experimental data. In the first method, method A, D-86 distillation data for gasoline blends are used for predicting Rvp from a simulation of the mini dry vapor pressure equivalent (Dvpe) experiment. The other method, method B, relies on analytical information (PIANO analyses) of the base gasoline and uses classical thermodynamics for simulating the same Rvp equivalent (Rvpe) mini experiment. Method B also predicts composition and other properties for the fuel`s initial vapor emission.more » Method B, although complex, is more useful in that is can predict properties of blends without a D-86 distillation. An important aspect of method B is its capability to predict composition of initial vapor emissions from gasoline blends. Thus, it offers a powerful tool to planners of gasoline blending. Method B uses theoretically sound formulas, rigorous thermodynamic routines and uses data and correlations of physical properties that are in the public domain. Results indicate that predictions made with both methods agree very well with experimental values of Dvpe. Computer simulation methods were programmed and tested.« less

Detailed thermodynamic analyses of high-speed compressible turbulence

NASA Astrophysics Data System (ADS)

Towery, Colin; Darragh, Ryan; Poludnenko, Alexei; Hamlington, Peter

2016-11-01

Interactions between high-speed turbulence and flames (or chemical reactions) are important in the dynamics and description of many different combustion phenomena, including autoignition and deflagration-to-detonation transition. The probability of these phenomena to occur depends on the magnitude and spectral content of turbulence fluctuations, which can impact a wide range of science and engineering problems, from the hypersonic scramjet engine to the onset of Type Ia supernovae. In this talk, we present results from new direct numerical simulations (DNS) of homogeneous isotropic turbulence with turbulence Mach numbers ranging from 0 . 05 to 1 . 0 and Taylor-scale Reynolds numbers as high as 700. A set of detailed analyses are described in both Eulerian and Lagrangian reference frames in order to assess coherent (structural) and incoherent (stochastic) thermodynamic flow features. These analyses provide direct insights into the thermodynamics of strongly compressible turbulence. Furthermore, presented results provide a non-reacting baseline for future studies of turbulence-chemistry interactions in DNS with complex chemistry mechanisms. This work was supported by the Air Force Office of Scientific Research (AFOSR) under Award No. FA9550-14-1-0273, and the Department of Defense (DoD) High Performance Computing Modernization Program (HPCMP) under a Frontier project award.

Infinitely dilute partial molar properties of proteins from computer simulation.

PubMed

Ploetz, Elizabeth A; Smith, Paul E

2014-11-13

A detailed understanding of temperature and pressure effects on an infinitely dilute protein's conformational equilibrium requires knowledge of the corresponding infinitely dilute partial molar properties. Established molecular dynamics methodologies generally have not provided a way to calculate these properties without either a loss of thermodynamic rigor, the introduction of nonunique parameters, or a loss of information about which solute conformations specifically contributed to the output values. Here we implement a simple method that is thermodynamically rigorous and possesses none of the above disadvantages, and we report on the method's feasibility and computational demands. We calculate infinitely dilute partial molar properties for two proteins and attempt to distinguish the thermodynamic differences between a native and a denatured conformation of a designed miniprotein. We conclude that simple ensemble average properties can be calculated with very reasonable amounts of computational power. In contrast, properties corresponding to fluctuating quantities are computationally demanding to calculate precisely, although they can be obtained more easily by following the temperature and/or pressure dependence of the corresponding ensemble averages.

Thermodynamics of quasideterministic digital computers

NASA Astrophysics Data System (ADS)

Chu, Dominique

2018-02-01

A central result of stochastic thermodynamics is that irreversible state transitions of Markovian systems entail a cost in terms of an infinite entropy production. A corollary of this is that strictly deterministic computation is not possible. Using a thermodynamically consistent model, we show that quasideterministic computation can be achieved at finite, and indeed modest cost with accuracies that are indistinguishable from deterministic behavior for all practical purposes. Concretely, we consider the entropy production of stochastic (Markovian) systems that behave like and and a not gates. Combinations of these gates can implement any logical function. We require that these gates return the correct result with a probability that is very close to 1, and additionally, that they do so within finite time. The central component of the model is a machine that can read and write binary tapes. We find that the error probability of the computation of these gates falls with the power of the system size, whereas the cost only increases linearly with the system size.

Correlations for determining thermodynamic properties of hydrogen-helium gas mixtures at temperatures from 7,000 to 35,000 K

NASA Technical Reports Server (NTRS)

Zoby, E. V.; Gnoffo, P. A.; Graves, R. A., Jr.

1976-01-01

Simple relations for determining the enthalpy and temperature of hydrogen-helium gas mixtures were developed for hydrogen volumetric compositions from 1.0 to 0.7. These relations are expressed as a function of pressure and density and are valid for a range of temperatures from 7,000 to 35,000 K and pressures from 0.10 to 3.14 MPa. The proportionality constant and exponents in the correlation equations were determined for each gas composition by applying a linear least squares curve fit to a large number of thermodynamic calculations obtained from a detailed computer code. Although these simple relations yielded thermodynamic properties suitable for many engineering applications, their accuracy was improved significantly by evaluating the proportionality constants at postshock conditions and correlating these values as a function of the gas composition and the product of freestream velocity and shock angle. The resulting equations for the proportionality constants in terms of velocity and gas composition and the corresponding simple realtions for enthalpy and temperature were incorporated into a flow field computational scheme. Comparison was good between the thermodynamic properties determined from these relations and those obtained by using a detailed computer code to determine the properties. Thus, an appreciable savings in computer time was realized with no significant loss in accuracy.

METAGUI. A VMD interface for analyzing metadynamics and molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Biarnés, Xevi; Pietrucci, Fabio; Marinelli, Fabrizio; Laio, Alessandro

2012-01-01

We present a new computational tool, METAGUI, which extends the VMD program with a graphical user interface that allows constructing a thermodynamic and kinetic model of a given process simulated by large-scale molecular dynamics. The tool is specially designed for analyzing metadynamics based simulations. The huge amount of diverse structures generated during such a simulation is partitioned into a set of microstates (i.e. structures with similar values of the collective variables). Their relative free energies are then computed by a weighted-histogram procedure and the most relevant free energy wells are identified by diagonalization of the rate matrix followed by a commitor analysis. All this procedure leads to a convenient representation of the metastable states and long-time kinetics of the system which can be compared with experimental data. The tool allows to seamlessly switch between a collective variables space representation of microstates and their atomic structure representation, which greatly facilitates the set-up and analysis of molecular dynamics simulations. METAGUI is based on the output format of the PLUMED plugin, making it compatible with a number of different molecular dynamics packages like AMBER, NAMD, GROMACS and several others. The METAGUI source files can be downloaded from the PLUMED web site ( http://www.plumed-code.org). Program summaryProgram title: METAGUI Catalogue identifier: AEKH_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEKH_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU General Public License version 3 No. of lines in distributed program, including test data, etc.: 117 545 No. of bytes in distributed program, including test data, etc.: 8 516 203 Distribution format: tar.gz Programming language: TK/TCL, Fortran Computer: Any computer with a VMD installation and capable of running an executable produced by a gfortran compiler Operating system: Linux, Unix OS-es RAM: 1 073 741 824 bytes Classification: 23 External routines: A VMD installation ( http://www.ks.uiuc.edu/Research/vmd/) Nature of problem: Extract thermodynamic data and build a kinetic model of a given process simulated by metadynamics or molecular dynamics simulations, and provide this information on a dual representation that allows navigating and exploring the molecular structures corresponding to each point along the multi-dimensional free energy hypersurface. Solution method: Graphical-user interface linked to VMD that clusterizes the simulation trajectories in the space of a set of collective variables and assigns each frame to a given microstate, determines the free energy of each microstate by a weighted histogram analysis method, and identifies the most relevant free energy wells (kinetic basins) by diagonalization of the rate matrix followed by a commitor analysis. Restrictions: Input format files compatible with PLUMED and all the MD engines supported by PLUMED and VMD. Running time: A few minutes.

Thermodynamics and combustion modeling

NASA Technical Reports Server (NTRS)

Zeleznik, Frank J.

1986-01-01

Modeling fluid phase phenomena blends the conservation equations of continuum mechanics with the property equations of thermodynamics. The thermodynamic contribution becomes especially important when the phenomena involve chemical reactions as they do in combustion systems. The successful study of combustion processes requires (1) the availability of accurate thermodynamic properties for both the reactants and the products of reaction and (2) the computational capabilities to use the properties. A discussion is given of some aspects of the problem of estimating accurate thermodynamic properties both for reactants and products of reaction. Also, some examples of the use of thermodynamic properties for modeling chemically reacting systems are presented. These examples include one-dimensional flow systems and the internal combustion engine.

Parametric Analysis of Energy Consumption in Army Buildings by the Building Loads Analysis and System Thermodynamics (BLAST) Computer Program.

DTIC Science & Technology

1980-08-01

orientation, and HVAC systems have on three Army buildings in five different climatic regions. f Optimization of EnerV Usage in Military Facilities...The clinic’s environment is maintained by a multizone air-handling unit served by its own boiler and chiller . The building was modeled with 30... setpoints for the space temperature. This type of throttling range allows the heating system to control around a throttling range of 67 to 69oF (19 to 200

The Effects of the Uncertainty of Thermodynamic and Kinetic Properties on Nucleation and Evolution Kinetics of Cr-Rich Phase in Fe-Cr Alloys

DTIC Science & Technology

2012-12-01

M. A.; Horstemeyer, M. F.; Gao, F.; Sun, X.: Khaleel, M. Scripta Materialia. 2011, 64, 908. 80. Plimpton , S . Journal of Computational Physics...99 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR( S ) Mark Tschopp,* Fei Gao,** and Xin Sun** 5d. PROJECT NUMBER 5e. TASK NUMBER...5f. WORK UNIT NUMBER 7. PERFORMING ORGANIZATION NAME( S ) AND ADDRESS(ES) U.S. Army Research Laboratory ATTN: RDRL-WMM-F Aberdeen Proving Ground

The Navy/NASA Engine Program (NNEP89): A user's manual

NASA Technical Reports Server (NTRS)

Plencner, Robert M.; Snyder, Christopher A.

1991-01-01

An engine simulation computer code called NNEP89 was written to perform 1-D steady state thermodynamic analysis of turbine engine cycles. By using a very flexible method of input, a set of standard components are connected at execution time to simulate almost any turbine engine configuration that the user could imagine. The code was used to simulate a wide range of engine cycles from turboshafts and turboprops to air turborockets and supersonic cruise variable cycle engines. Off design performance is calculated through the use of component performance maps. A chemical equilibrium model is incorporated to adequately predict chemical dissociation as well as model virtually any fuel. NNEP89 is written in standard FORTRAN77 with clear structured programming and extensive internal documentation. The standard FORTRAN77 programming allows it to be installed onto most mainframe computers and workstations without modification. The NNEP89 code was derived from the Navy/NASA Engine program (NNEP). NNEP89 provides many improvements and enhancements to the original NNEP code and incorporates features which make it easier to use for the novice user. This is a comprehensive user's guide for the NNEP89 code.

Computational studies of physical properties of Nb-Si based alloys

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

Ouyang, Lizhi

2015-04-16

The overall goal is to provide physical properties data supplementing experiments for thermodynamic modeling and other simulations such as phase filed simulation for microstructure and continuum simulations for mechanical properties. These predictive computational modeling and simulations may yield insights that can be used to guide materials design, processing, and manufacture. Ultimately, they may lead to usable Nb-Si based alloy which could play an important role in current plight towards greener energy. The main objectives of the proposed projects are: (1) developing a first principles method based supercell approach for calculating thermodynamic and mechanic properties of ordered crystals and disordered latticesmore » including solid solution; (2) application of the supercell approach to Nb-Si base alloy to compute physical properties data that can be used for thermodynamic modeling and other simulations to guide the optimal design of Nb-Si based alloy.« less

Thermodynamic model effects on the design and optimization of natural gas plants

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

Diaz, S.; Zabaloy, M.; Brignole, E.A.

1999-07-01

The design and optimization of natural gas plants is carried out on the basis of process simulators. The physical property package is generally based on cubic equations of state. By rigorous thermodynamics phase equilibrium conditions, thermodynamic functions, equilibrium phase separations, work and heat are computed. The aim of this work is to analyze the NGL turboexpansion process and identify possible process computations that are more sensitive to model predictions accuracy. Three equations of state, PR, SRK and Peneloux modification, are used to study the effect of property predictions on process calculations and plant optimization. It is shown that turboexpander plantsmore » have moderate sensitivity with respect to phase equilibrium computations, but higher accuracy is required for the prediction of enthalpy and turboexpansion work. The effect of modeling CO{sub 2} solubility is also critical in mixtures with high CO{sub 2} content in the feed.« less

Thermodynamic and transport properties of nitrogen fluid: Molecular theory and computer simulations

NASA Astrophysics Data System (ADS)

Eskandari Nasrabad, A.; Laghaei, R.

2018-04-01

Computer simulations and various theories are applied to compute the thermodynamic and transport properties of nitrogen fluid. To model the nitrogen interaction, an existing potential in the literature is modified to obtain a close agreement between the simulation results and experimental data for the orthobaric densities. We use the Generic van der Waals theory to calculate the mean free volume and apply the results within the modified Cohen-Turnbull relation to obtain the self-diffusion coefficient. Compared to experimental data, excellent results are obtained via computer simulations for the orthobaric densities, the vapor pressure, the equation of state, and the shear viscosity. We analyze the results of the theory and computer simulations for the various thermophysical properties.

Theoretical Studies of Small-System Thermodynamics in Energetic Materials

DTIC Science & Technology

2016-01-06

SECURITY CLASSIFICATION OF: This is a comprehensive theoretical research program to investigate the fundamental principles of small-system thermodynamics ...a.k.a. nanothermodynamics). The proposed work is motivated by our desire to better understand the fundamental dynamics and thermodynamics of...for Public Release; Distribution Unlimited Final Report: Theoretical Studies of Small-System Thermodynamics in Energetic Materials The views, opinions

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.

The OpenCalphad thermodynamic software interface.

PubMed

Sundman, Bo; Kattner, Ursula R; Sigli, Christophe; Stratmann, Matthias; Le Tellier, Romain; Palumbo, Mauro; Fries, Suzana G

2016-12-01

Thermodynamic data are needed for all kinds of simulations of materials processes. Thermodynamics determines the set of stable phases and also provides chemical potentials, compositions and driving forces for nucleation of new phases and phase transformations. Software to simulate materials properties needs accurate and consistent thermodynamic data to predict metastable states that occur during phase transformations. Due to long calculation times thermodynamic data are frequently pre-calculated into "lookup tables" to speed up calculations. This creates additional uncertainties as data must be interpolated or extrapolated and conditions may differ from those assumed for creating the lookup table. Speed and accuracy requires that thermodynamic software is fully parallelized and the Open-Calphad (OC) software is the first thermodynamic software supporting this feature. This paper gives a brief introduction to computational thermodynamics and introduces the basic features of the OC software and presents four different application examples to demonstrate its versatility.

The OpenCalphad thermodynamic software interface

PubMed Central

Sundman, Bo; Kattner, Ursula R; Sigli, Christophe; Stratmann, Matthias; Le Tellier, Romain; Palumbo, Mauro; Fries, Suzana G

2017-01-01

Thermodynamic data are needed for all kinds of simulations of materials processes. Thermodynamics determines the set of stable phases and also provides chemical potentials, compositions and driving forces for nucleation of new phases and phase transformations. Software to simulate materials properties needs accurate and consistent thermodynamic data to predict metastable states that occur during phase transformations. Due to long calculation times thermodynamic data are frequently pre-calculated into “lookup tables” to speed up calculations. This creates additional uncertainties as data must be interpolated or extrapolated and conditions may differ from those assumed for creating the lookup table. Speed and accuracy requires that thermodynamic software is fully parallelized and the Open-Calphad (OC) software is the first thermodynamic software supporting this feature. This paper gives a brief introduction to computational thermodynamics and introduces the basic features of the OC software and presents four different application examples to demonstrate its versatility. PMID:28260838

Quantum vertex model for reversible classical computing.

PubMed

Chamon, C; Mucciolo, E R; Ruckenstein, A E; Yang, Z-C

2017-05-12

Mappings of classical computation onto statistical mechanics models have led to remarkable successes in addressing some complex computational problems. However, such mappings display thermodynamic phase transitions that may prevent reaching solution even for easy problems known to be solvable in polynomial time. Here we map universal reversible classical computations onto a planar vertex model that exhibits no bulk classical thermodynamic phase transition, independent of the computational circuit. Within our approach the solution of the computation is encoded in the ground state of the vertex model and its complexity is reflected in the dynamics of the relaxation of the system to its ground state. We use thermal annealing with and without 'learning' to explore typical computational problems. We also construct a mapping of the vertex model into the Chimera architecture of the D-Wave machine, initiating an approach to reversible classical computation based on state-of-the-art implementations of quantum annealing.

Quantum vertex model for reversible classical computing

NASA Astrophysics Data System (ADS)

Chamon, C.; Mucciolo, E. R.; Ruckenstein, A. E.; Yang, Z.-C.

2017-05-01

Mappings of classical computation onto statistical mechanics models have led to remarkable successes in addressing some complex computational problems. However, such mappings display thermodynamic phase transitions that may prevent reaching solution even for easy problems known to be solvable in polynomial time. Here we map universal reversible classical computations onto a planar vertex model that exhibits no bulk classical thermodynamic phase transition, independent of the computational circuit. Within our approach the solution of the computation is encoded in the ground state of the vertex model and its complexity is reflected in the dynamics of the relaxation of the system to its ground state. We use thermal annealing with and without `learning' to explore typical computational problems. We also construct a mapping of the vertex model into the Chimera architecture of the D-Wave machine, initiating an approach to reversible classical computation based on state-of-the-art implementations of quantum annealing.

Reproducing Quantum Probability Distributions at the Speed of Classical Dynamics: A New Approach for Developing Force-Field Functors.

PubMed

Sundar, Vikram; Gelbwaser-Klimovsky, David; Aspuru-Guzik, Alán

2018-04-05

Modeling nuclear quantum effects is required for accurate molecular dynamics (MD) simulations of molecules. The community has paid special attention to water and other biomolecules that show hydrogen bonding. Standard methods of modeling nuclear quantum effects like Ring Polymer Molecular Dynamics (RPMD) are computationally costlier than running classical trajectories. A force-field functor (FFF) is an alternative method that computes an effective force field that replicates quantum properties of the original force field. In this work, we propose an efficient method of computing FFF using the Wigner-Kirkwood expansion. As a test case, we calculate a range of thermodynamic properties of Neon, obtaining the same level of accuracy as RPMD, but with the shorter runtime of classical simulations. By modifying existing MD programs, the proposed method could be used in the future to increase the efficiency and accuracy of MD simulations involving water and proteins.

Reaction Mechanism Generator: Automatic construction of chemical kinetic mechanisms

NASA Astrophysics Data System (ADS)

Gao, Connie W.; Allen, Joshua W.; Green, William H.; West, Richard H.

2016-06-01

Reaction Mechanism Generator (RMG) constructs kinetic models composed of elementary chemical reaction steps using a general understanding of how molecules react. Species thermochemistry is estimated through Benson group additivity and reaction rate coefficients are estimated using a database of known rate rules and reaction templates. At its core, RMG relies on two fundamental data structures: graphs and trees. Graphs are used to represent chemical structures, and trees are used to represent thermodynamic and kinetic data. Models are generated using a rate-based algorithm which excludes species from the model based on reaction fluxes. RMG can generate reaction mechanisms for species involving carbon, hydrogen, oxygen, sulfur, and nitrogen. It also has capabilities for estimating transport and solvation properties, and it automatically computes pressure-dependent rate coefficients and identifies chemically-activated reaction paths. RMG is an object-oriented program written in Python, which provides a stable, robust programming architecture for developing an extensible and modular code base with a large suite of unit tests. Computationally intensive functions are cythonized for speed improvements.

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.

Computation of Thermodynamic Equilibria Pertinent to Nuclear Materials in Multi-Physics Codes

NASA Astrophysics Data System (ADS)

Piro, Markus Hans Alexander

Nuclear energy plays a vital role in supporting electrical needs and fulfilling commitments to reduce greenhouse gas emissions. Research is a continuing necessity to improve the predictive capabilities of fuel behaviour in order to reduce costs and to meet increasingly stringent safety requirements by the regulator. Moreover, a renewed interest in nuclear energy has given rise to a "nuclear renaissance" and the necessity to design the next generation of reactors. In support of this goal, significant research efforts have been dedicated to the advancement of numerical modelling and computational tools in simulating various physical and chemical phenomena associated with nuclear fuel behaviour. This undertaking in effect is collecting the experience and observations of a past generation of nuclear engineers and scientists in a meaningful way for future design purposes. There is an increasing desire to integrate thermodynamic computations directly into multi-physics nuclear fuel performance and safety codes. A new equilibrium thermodynamic solver is being developed with this matter as a primary objective. This solver is intended to provide thermodynamic material properties and boundary conditions for continuum transport calculations. There are several concerns with the use of existing commercial thermodynamic codes: computational performance; limited capabilities in handling large multi-component systems of interest to the nuclear industry; convenient incorporation into other codes with quality assurance considerations; and, licensing entanglements associated with code distribution. The development of this software in this research is aimed at addressing all of these concerns. The approach taken in this work exploits fundamental principles of equilibrium thermodynamics to simplify the numerical optimization equations. In brief, the chemical potentials of all species and phases in the system are constrained by estimates of the chemical potentials of the system components at each iterative step, and the objective is to minimize the residuals of the mass balance equations. Several numerical advantages are achieved through this simplification. In particular, computational expense is reduced and the rate of convergence is enhanced. Furthermore, the software has demonstrated the ability to solve systems involving as many as 118 component elements. An early version of the code has already been integrated into the Advanced Multi-Physics (AMP) code under development by the Oak Ridge National Laboratory, Los Alamos National Laboratory, Idaho National Laboratory and Argonne National Laboratory. Keywords: Engineering, Nuclear -- 0552, Engineering, Material Science -- 0794, Chemistry, Mathematics -- 0405, Computer Science -- 0984

Partial compilation and revision of basic data in the WATEQ programs

USGS Publications Warehouse

Nordstrom, D. Kirk; Valentine, S.D.; Ball, J.W.; Plummer, Niel; Jones, B.F.

1984-01-01

Several portions of the basic data in the WATEQ series of computer programs (WATEQ, WATEQF, WATEQ2, WATEQ3, and PHREEQE) are compiled. The density and dielectric constant of water and their temperature dependence are evaluated for the purpose of updating the Debye-Huckel solvent parameters in the activity coefficient equations. The standard state thermodynamic properties of the Fe2+ and Fe3+ aqueous ions are refined. The main portion of this report is a comprehensive listing of aluminum hydrolysis constants, aluminum fluoride, aluminum sulfate, calcium chloride, magnesium chloride, potassium sulfate and sodium sulfate stability constants, solubility product constants for gibbsite and amorphous aluminum hydroxide, and the standard electrode potentials for Fe (s)/Fe2+(aq) and Fe2 +(aq)/Fe3+(aq). (USGS)

Comparison of Themodynamic and Transport Property Models for Computing Equilibrium High Enthalpy Flows

NASA Astrophysics Data System (ADS)

Ramasahayam, Veda Krishna Vyas; Diwakar, Anant; Bodi, Kowsik

2017-11-01

To study the flow of high temperature air in vibrational and chemical equilibrium, accurate models for thermodynamic state and transport phenomena are required. In the present work, the performance of a state equation model and two mixing rules for determining equilibrium air thermodynamic and transport properties are compared with that of curve fits. The thermodynamic state model considers 11 species which computes flow chemistry by an iterative process and the mixing rules considered for viscosity are Wilke and Armaly-Sutton. The curve fits of Srinivasan, which are based on Grabau type transition functions, are chosen for comparison. A two-dimensional Navier-Stokes solver is developed to simulate high enthalpy flows with numerical fluxes computed by AUSM+-up. The accuracy of state equation model and curve fits for thermodynamic properties is determined using hypersonic inviscid flow over a circular cylinder. The performance of mixing rules and curve fits for viscosity are compared using hypersonic laminar boundary layer prediction on a flat plate. It is observed that steady state solutions from state equation model and curve fits match with each other. Though curve fits are significantly faster the state equation model is more general and can be adapted to any flow composition.

Quantum information processing by a continuous Maxwell demon

NASA Astrophysics Data System (ADS)

Stevens, Josey; Deffner, Sebastian

Quantum computing is believed to be fundamentally superior to classical computing; however quantifying the specific thermodynamic advantage has been elusive. Experimentally motivated, we generalize previous minimal models of discrete demons to continuous state space. Analyzing our model allows one to quantify the thermodynamic resources necessary to process quantum information. By further invoking the semi-classical limit we compare the quantum demon with its classical analogue. Finally, this model also serves as a starting point to study open quantum systems.

The Molybdenum titanium Phase Diagram Evaluated from Ab initio Calculations

DTIC Science & Technology

2016-10-07

thermodynamic properties of this binary system are not well known and two conflicting descriptions of the β-phase stability have been presented in the...computational thermodynamics CALPHAD approach [13] and the Thermo-Calc software [14]. These studies led to two conflicting descriptions of the stability of...energy calculations, with an energy cutoff separating core and valence states of -6 Ry. 2.2. Thermodynamic modeling The formation enthalpy of a

Computational Thermodynamics and Kinetics-Based ICME Framework for High-Temperature Shape Memory Alloys

NASA Astrophysics Data System (ADS)

Arróyave, Raymundo; Talapatra, Anjana; Johnson, Luke; Singh, Navdeep; Ma, Ji; Karaman, Ibrahim

2015-11-01

Over the last decade, considerable interest in the development of High-Temperature Shape Memory Alloys (HTSMAs) for solid-state actuation has increased dramatically as key applications in the aerospace and automotive industry demand actuation temperatures well above those of conventional SMAs. Most of the research to date has focused on establishing the (forward) connections between chemistry, processing, (micro)structure, properties, and performance. Much less work has been dedicated to the development of frameworks capable of addressing the inverse problem of establishing necessary chemistry and processing schedules to achieve specific performance goals. Integrated Computational Materials Engineering (ICME) has emerged as a powerful framework to address this problem, although it has yet to be applied to the development of HTSMAs. In this paper, the contributions of computational thermodynamics and kinetics to ICME of HTSMAs are described. Some representative examples of the use of computational thermodynamics and kinetics to understand the phase stability and microstructural evolution in HTSMAs are discussed. Some very recent efforts at combining both to assist in the design of HTSMAs and limitations to the full implementation of ICME frameworks for HTSMA development are presented.

Infinitely Dilute Partial Molar Properties of Proteins from Computer Simulation

PubMed Central

2015-01-01

A detailed understanding of temperature and pressure effects on an infinitely dilute protein’s conformational equilibrium requires knowledge of the corresponding infinitely dilute partial molar properties. Established molecular dynamics methodologies generally have not provided a way to calculate these properties without either a loss of thermodynamic rigor, the introduction of nonunique parameters, or a loss of information about which solute conformations specifically contributed to the output values. Here we implement a simple method that is thermodynamically rigorous and possesses none of the above disadvantages, and we report on the method’s feasibility and computational demands. We calculate infinitely dilute partial molar properties for two proteins and attempt to distinguish the thermodynamic differences between a native and a denatured conformation of a designed miniprotein. We conclude that simple ensemble average properties can be calculated with very reasonable amounts of computational power. In contrast, properties corresponding to fluctuating quantities are computationally demanding to calculate precisely, although they can be obtained more easily by following the temperature and/or pressure dependence of the corresponding ensemble averages. PMID:25325571

Vibrational and electronic investigations, thermodynamic parameters, HOMO and LUMO analysis on Lornoxicam by density functional theory

NASA Astrophysics Data System (ADS)

Suhasini, M.; Sailatha, E.; Gunasekaran, S.; Ramkumaar, G. R.

2015-11-01

The Fourier transform infrared (FT-IR) and FT-Raman spectra of Lornoxicam were recorded in the region 4000-450 cm-1 and 4000-50 cm-1 respectively. Density functional theory (DFT) has been used to calculate the optimized geometrical parameters, atomic charges, and vibrational wavenumbers and intensity of the vibrational bands. The computed vibrational wave numbers were compared with the FT-IR and FT-Raman experimental data. The computational calculations at DFT/B3LYP level with 6-31G(d,p) and 6-31++G(d,p) basis sets. The complete vibrational assignments were performed on the basis of the potential energy distribution (PED) of the Vibrational modes calculated using Vibrational Energy Distribution Analysis (VEDA 4) program. The oscillator's strength calculated by TD-DFT and Lornoxicam is approach complement with the experimental findings. The NMR chemical shifts 13C and 1H were recorded and calculated using the gauge independent atomic orbital (GIAO) method. The Natural charges and intermolecular contacts have been interpreted using Natural Bond orbital (NBO) analysis and the HOMO-LUMO energy gap has been calculated. The thermodynamic properties like Entropy, Enthalpy, Specific heat capacity and zero vibrational energy have been calculated. Besides, molecular electrostatic potential (MEP) was investigated using theoretical calculations.

Students' explanations in complex learning of disciplinary programming

NASA Astrophysics Data System (ADS)

Vieira, Camilo

Computational Science and Engineering (CSE) has been denominated as the third pillar of science and as a set of important skills to solve the problems of a global society. Along with the theoretical and the experimental approaches, computation offers a third alternative to solve complex problems that require processing large amounts of data, or representing complex phenomena that are not easy to experiment with. Despite the relevance of CSE, current professionals and scientists are not well prepared to take advantage of this set of tools and methods. Computation is usually taught in an isolated way from engineering disciplines, and therefore, engineers do not know how to exploit CSE affordances. This dissertation intends to introduce computational tools and methods contextualized within the Materials Science and Engineering curriculum. Considering that learning how to program is a complex task, the dissertation explores effective pedagogical practices that can support student disciplinary and computational learning. Two case studies will be evaluated to identify the characteristics of effective worked examples in the context of CSE. Specifically, this dissertation explores students explanations of these worked examples in two engineering courses with different levels of transparency: a programming course in materials science and engineering glass box and a thermodynamics course involving computational representations black box. Results from this study suggest that students benefit in different ways from writing in-code comments. These benefits include but are not limited to: connecting xv individual lines of code to the overall problem, getting familiar with the syntax, learning effective algorithm design strategies, and connecting computation with their discipline. Students in the glass box context generate higher quality explanations than students in the black box context. These explanations are related to students prior experiences. Specifically, students with low ability to do programming engage in a more thorough explanation process than students with high ability. This dissertation concludes proposing an adaptation to the instructional principles of worked-examples for the context of CSE education.

Automated Guidance for Thermodynamics Essays: Critiquing versus Revisiting

ERIC Educational Resources Information Center

Donnelly, Dermot F.; Vitale, Jonathan M.; Linn, Marcia C.

2015-01-01

Middle school students struggle to explain thermodynamics concepts. In this study, to help students succeed, we use a natural language processing program to analyze their essays explaining the aspects of thermodynamics and provide guidance based on the automated score. The 346 sixth-grade students were assigned to either the critique condition…

A Program for Simulated Thermodynamic Experiments.

ERIC Educational Resources Information Center

Olds, Dan W.

A time-sharing FORTRAN program is described. It was created to allow a student to design and perform classical thermodynamic experiments on three models of a working substance. One goal was to develop a simulation which gave the student maximum freedom and responsibility in the design of the experiment and provided only the primary experimental…

Integrated Experimental and Modelling Research for Non-Ferrous Smelting and Recycling Systems

NASA Astrophysics Data System (ADS)

Jak, Evgueni; Hidayat, Taufiq; Shishin, Denis; Mehrjardi, Ata Fallah; Chen, Jiang; Decterov, Sergei; Hayes, Peter

The chemistries of industrial pyrometallurgical non-ferrous smelting and recycling processes are becoming increasingly complex. Optimisation of process conditions, charge composition, temperature, oxygen partial pressure, and partitioning of minor elements between phases and different process streams require accurate description of phase equilibria and thermodynamics which are the focus of the present research. The experiments involve high temperature equilibration in controlled gas atmospheres, rapid quenching and direct measurement of equilibrium phase compositions with quantitative microanalytical techniques including electron probe X-ray microanalysis and Laser Ablation ICP-MS. The thermodynamic modelling is undertaken using computer package FactSage with the quasi-chemical model for the liquid slag phase and other advanced models. Experimental and modelling studies are combined into an integrated research program focused on the major elements Cu-Pb-Fe-O-Si-S system, slagging Al, Ca, Mg and other minor elements. The ongoing development of the research methodologies has resulted in significant advances in research capabilities. Examples of applications are given.

Improved thermodynamic modeling of the no-vent fill process and correlation with experimental data

NASA Technical Reports Server (NTRS)

Taylor, William J.; Chato, David J.

1991-01-01

The United States' plans to establish a permanent manned presence in space and to explore the Solar System created the need to efficiently handle large quantities of subcritical cryogenic fluids, particularly propellants such as liquid hydrogen and liquid oxygen, in low- to zero-gravity environments. One of the key technologies to be developed for fluid handling is the ability to transfer the cryogens between storage and spacecraft tanks. The no-vent fill method was identified as one way to perform this transfer. In order to understand how to apply this method, a model of the no-vent fill process is being developed and correlated with experimental data. The verified models then can be used to design and analyze configurations for tankage and subcritical fluid depots. The development of an improved macroscopic thermodynamic model is discussed of the no-vent fill process and the analytical results from the computer program implementation of the model are correlated with experimental results for two different test tanks.

Spatial Analysis and Quantification of the Thermodynamic Driving Forces in Protein-Ligand Binding: Binding Site Variability

PubMed Central

Raman, E. Prabhu; MacKerell, Alexander D.

2015-01-01

The thermodynamic driving forces behind small molecule-protein binding are still not well understood, including the variability of those forces associated with different types of ligands in different binding pockets. To better understand these phenomena we calculate spatially resolved thermodynamic contributions of the different molecular degrees of freedom for the binding of propane and methanol to multiple pockets on the proteins Factor Xa and p38 MAP kinase. Binding thermodynamics are computed using a statistical thermodynamics based end-point method applied on a canonical ensemble comprising the protein-ligand complexes and the corresponding free states in an explicit solvent environment. Energetic and entropic contributions of water and ligand degrees of freedom computed from the configurational ensemble provides an unprecedented level of detail into the mechanisms of binding. Direct protein-ligand interaction energies play a significant role in both non-polar and polar binding, which is comparable to water reorganization energy. Loss of interactions with water upon binding strongly compensates these contributions leading to relatively small binding enthalpies. For both solutes, the entropy of water reorganization is found to favor binding in agreement with the classical view of the “hydrophobic effect”. Depending on the specifics of the binding pocket, both energy-entropy compensation and reinforcement mechanisms are observed. Notable is the ability to visualize the spatial distribution of the thermodynamic contributions to binding at atomic resolution showing significant differences in the thermodynamic contributions of water to the binding of propane versus methanol. PMID:25625202

Find_tfSBP: find thermodynamics-feasible and smallest balanced pathways with high yield from large-scale metabolic networks.

PubMed

Xu, Zixiang; Sun, Jibin; Wu, Qiaqing; Zhu, Dunming

2017-12-11

Biologically meaningful metabolic pathways are important references in the design of industrial bacterium. At present, constraint-based method is the only way to model and simulate a genome-scale metabolic network under steady-state criteria. Due to the inadequate assumption of the relationship in gene-enzyme-reaction as one-to-one unique association, computational difficulty or ignoring the yield from substrate to product, previous pathway finding approaches can't be effectively applied to find out the high yield pathways that are mass balanced in stoichiometry. In addition, the shortest pathways may not be the pathways with high yield. At the same time, a pathway, which exists in stoichiometry, may not be feasible in thermodynamics. By using mixed integer programming strategy, we put forward an algorithm to identify all the smallest balanced pathways which convert the source compound to the target compound in large-scale metabolic networks. The resulting pathways by our method can finely satisfy the stoichiometric constraints and non-decomposability condition. Especially, the functions of high yield and thermodynamics feasibility have been considered in our approach. This tool is tailored to direct the metabolic engineering practice to enlarge the metabolic potentials of industrial strains by integrating the extensive metabolic network information built from systems biology dataset.

A survey of spacecraft thermal design solutions

NASA Technical Reports Server (NTRS)

Humphries, R.; Wegrich, R.; Pierce, E.; Patterson, W.

1991-01-01

A review of activities at the NASA/Marshall Space Flight Center in the heat transfer and thermodynamics disciplines as well as attendant fluid mechanics, transport phenomena, and computer science applications is presented. Attention is focused on recent activities including the Hubble Space Telescope, and large space instruments, particularly telescope thermal control systems such as those flown aboard Spacelab 2 and the Astro missions. Emphasis is placed on defining the thermal control features, unique design schemes, and performance of selected programs. Results obtained both by ground testing and analytical means, as well as flight and postflight data are presented.

THEORETICAL Computations of Equilibrium Compositions, Thermodynamic Properties, and Performance Characteristics of Propellant Systems

DTIC Science & Technology

1979-04-01

U5 7 450o NITRATE 5h 3,4 -V -932 457 NITRIC ACID WuAS) lh IN 30 -509 .00lu 45t 43 NWC TP 6037 N,’TRO AM INI.GUA iiI u It, E1 51 h S5N 20 45 .COOO...and performance characteristics of propellant systems, and it will handle a maximum of 12 chemical elements and 200 combustion products . Some of the...used in the program, which will handle a maximum of 12 chemical elements and 200 combustion products . Flame temperature, chemical composition, enthalpy

Understanding Solubility through Excel Spreadsheets

NASA Astrophysics Data System (ADS)

Brown, Pamela

2001-02-01

This article describes assignments related to the solubility of inorganic salts that can be given in an introductory general chemistry course. Le Châtelier's principle, solubility, unit conversion, and thermodynamics are tied together to calculate heats of solution by two methods: heats of formation and an application of the van't Hoff equation. These assignments address the need for math, graphing, and computer skills in the chemical technology program by developing skill in the use of Microsoft Excel to prepare spreadsheets and graphs and to perform linear and nonlinear curve-fitting. Background information on the value of understanding and predicting solubility is provided.

Analysis of a combined refrigerator-generator space power system

NASA Technical Reports Server (NTRS)

Klann, J. L.

1973-01-01

Description of a single-shaft and a two-shaft rotating machinery arrangements using neon for application in a combined refrigerator-generator power system for space missions. The arrangements consist of combined assemblies of a power turbine, alternator, compressor, and cry-turbine with a single-stage radial-flow design. A computer program was prepared to study the thermodynamics of the dual system in the evaluation of its cryocooling/electric capacity and appropriate weight. A preliminary analysis showed that a two-shaft arrangement of the power- and refrigeration-loop rotating machinery provided better output capacities than a single-shaft arrangement, without prohibitive operating compromises.

Holographic free energy and thermodynamic geometry

NASA Astrophysics Data System (ADS)

Ghorai, Debabrata; Gangopadhyay, Sunandan

2016-12-01

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

Numerical Modeling of Nonlinear Thermodynamics in SMA Wires

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

Reynolds, D R; Kloucek, P

We present a mathematical model describing the thermodynamic behavior of shape memory alloy wires, as well as a computational technique to solve the resulting system of partial differential equations. The model consists of conservation equations based on a new Helmholtz free energy potential. The computational technique introduces a viscosity-based continuation method, which allows the model to handle dynamic applications where the temporally local behavior of solutions is desired. Computational experiments document that this combination of modeling and solution techniques appropriately predicts the thermally- and stress-induced martensitic phase transitions, as well as the hysteretic behavior and production of latent heat associatedmore » with such materials.« less

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

PubMed

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

2013-07-14

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

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

NASA Astrophysics Data System (ADS)

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

2013-07-01

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

Mean-field potential approach for thermodynamic properties of lanthanide: Europium as a prototype

NASA Astrophysics Data System (ADS)

Kumar, Priyank; Bhatt, N. K.; Vyas, P. R.; Gohel, V. B.

2018-03-01

In the present paper, a simple conjunction scheme [mean-field potential (MFP) + local pseudopotential] is used to study the thermodynamic properties of divalent lanthanide europium (Eu) at extreme environment. Present study has been carried out due to the fact that divalent nature of Eu arises because of stable half-filled 4f-shell at ambient condition, which has great influence on the thermodynamic properties at extreme environment. Due to such electronic structure, it is different from remaining lanthanides having incomplete 4f-shell. The presently computed results of thermodynamic properties of Eu are in good agreement with the experimental results. Looking to such success, it seems that the concept of MFP approach is successful to account contribution due to nuclear motion to the total Helmholtz free energy at finite temperatures and pressure-induced inter-band transfer of electrons for condensed state of matter. The local pseudopotential is used to evaluate cold energy and hence MFP accounts the s-p-d-f hybridization properly. Looking to the reliability and transferability along with its computational and conceptual simplicity, we would like to extend the present scheme for the study of thermodynamic properties of remaining lanthanides and actinides at extreme environment.

Thermodynamics in High Rhythms and Rhymes: Creative Ways of Knowing in Engineering

ERIC Educational Resources Information Center

Bairaktarova, Diana; Eodice, Michele

2017-01-01

Thermodynamics is a foundational course in nearly every engineering program. In a traditional classroom, instructors focus on the analysis of thermodynamic energy systems and their application to real world contexts. Because these complex systems can be difficult to understand, some instructors encourage students to tap into their creative side…

Toward more environmentally resistant gas turbines: Progress in NASA-Lewis programs

NASA Technical Reports Server (NTRS)

Lowell, C. E.; Grisaffe, S. J.; Levine, S. R.

1976-01-01

A wide range of programs are being conducted for improving the environmental resistance to oxidation and hot corrosion of gas turbine and power system materials. They range from fundamental efforts to delineate attack mechanisms, allow attack modeling and permit life prediction, to more applied efforts to develop potentially more resistant alloys and coatings. Oxidation life prediction efforts have resulted in a computer program which provides an initial method for predicting long time metal loss using short time oxidation data by means of a paralinear attack model. Efforts in alloy development have centered on oxide-dispersion strengthened alloys based on the Ni-Cr-Al system. Compositions have been identified which are compromises between oxidation and thermal fatigue resistance. Fundamental studies of hot corrosion mechanisms include thermodynamic studies of sodium sulfate formation during turbine combustion. Information concerning species formed during the vaporization of Na2SO4 has been developed using high temperature mass spectrometry.

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!

Statistical Mechanical Derivation of Jarzynski's Identity for Thermostated Non-Hamiltonian Dynamics

NASA Astrophysics Data System (ADS)

Cuendet, Michel A.

2006-03-01

The recent Jarzynski identity (JI) relates thermodynamic free energy differences to nonequilibrium work averages. Several proofs of the JI have been provided on the thermodynamic level. They rely on assumptions such as equivalence of ensembles in the thermodynamic limit or weakly coupled infinite heat baths. However, the JI is widely applied to NVT computer simulations involving finite numbers of particles, whose equations of motion are strongly coupled to a few extra degrees of freedom modeling a thermostat. In this case, the above assumptions are no longer valid. We propose a statistical mechanical approach to the JI solely based on the specific equations of motion, without any further assumption. We provide a detailed derivation for the non-Hamiltonian Nosé-Hoover dynamics, which is routinely used in computer simulations to produce canonical sampling.

An anisotropic thermomechanical damage model for concrete at transient elevated temperatures.

PubMed

Baker, Graham; de Borst, René

2005-11-15

The behaviour of concrete at elevated temperatures is important for an assessment of integrity (strength and durability) of structures exposed to a high-temperature environment, in applications such as fire exposure, smelting plants and nuclear installations. In modelling terms, a coupled thermomechanical analysis represents a generalization of the computational mechanics of fracture and damage. Here, we develop a fully coupled anisotropic thermomechanical damage model for concrete under high stress and transient temperature, with emphasis on the adherence of the model to the laws of thermodynamics. Specific analytical results are given, deduced from thermodynamics, of a novel interpretation on specific heat, evolution of entropy and the identification of the complete anisotropic, thermomechanical damage surface. The model is also shown to be stable in a computational sense, and to satisfy the laws of thermodynamics.

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.

Thermodynamic and Transport Properties of Real Air Plasma in Wide Range of Temperature and Pressure

NASA Astrophysics Data System (ADS)

Wang, Chunlin; Wu, Yi; Chen, Zhexin; Yang, Fei; Feng, Ying; Rong, Mingzhe; Zhang, Hantian

2016-07-01

Air plasma has been widely applied in industrial manufacture. In this paper, both dry and humid air plasmas' thermodynamic and transport properties are calculated in temperature 300-100000 K and pressure 0.1-100 atm. To build a more precise model of real air plasma, over 70 species are considered for composition. Two different methods, the Gibbs free energy minimization method and the mass action law method, are used to determinate the composition of the air plasma in a different temperature range. For the transport coefficients, the simplified Chapman-Enskog method developed by Devoto has been applied using the most recent collision integrals. It is found that the presence of CO2 has almost no effect on the properties of air plasma. The influence of H2O can be ignored except in low pressure air plasma, in which the saturated vapor pressure is relatively high. The results will serve as credible inputs for computational simulation of air plasma. supported by the National Key Basic Research Program of China (973 Program)(No. 2015CB251002), National Natural Science Foundation of China (Nos. 51521065, 51577145), the Science and Technology Project Funds of the Grid State Corporation (SGTYHT/13-JS-177), the Fundamental Research Funds for the Central Universities, and State Grid Corporation Project (GY71-14-004)

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.

Rapid determination of thermodynamic parameters from one-dimensional programmed-temperature gas chromatography for use in retention time prediction in comprehensive multidimensional chromatography.

PubMed

McGinitie, Teague M; Ebrahimi-Najafabadi, Heshmatollah; Harynuk, James J

2014-01-17

A new method for estimating the thermodynamic parameters of ΔH(T0), ΔS(T0), and ΔCP for use in thermodynamic modeling of GC×GC separations has been developed. The method is an alternative to the traditional isothermal separations required to fit a three-parameter thermodynamic model to retention data. Herein, a non-linear optimization technique is used to estimate the parameters from a series of temperature-programmed separations using the Nelder-Mead simplex algorithm. With this method, the time required to obtain estimates of thermodynamic parameters a series of analytes is significantly reduced. This new method allows for precise predictions of retention time with the average error being only 0.2s for 1D separations. Predictions for GC×GC separations were also in agreement with experimental measurements; having an average relative error of 0.37% for (1)tr and 2.1% for (2)tr. Copyright © 2013 Elsevier B.V. All rights reserved.

Evaluating marginal likelihood with thermodynamic integration method and comparison with several other numerical methods

DOE PAGES

Liu, Peigui; Elshall, Ahmed S.; Ye, Ming; ...

2016-02-05

Evaluating marginal likelihood is the most critical and computationally expensive task, when conducting Bayesian model averaging to quantify parametric and model uncertainties. The evaluation is commonly done by using Laplace approximations to evaluate semianalytical expressions of the marginal likelihood or by using Monte Carlo (MC) methods to evaluate arithmetic or harmonic mean of a joint likelihood function. This study introduces a new MC method, i.e., thermodynamic integration, which has not been attempted in environmental modeling. Instead of using samples only from prior parameter space (as in arithmetic mean evaluation) or posterior parameter space (as in harmonic mean evaluation), the thermodynamicmore » integration method uses samples generated gradually from the prior to posterior parameter space. This is done through a path sampling that conducts Markov chain Monte Carlo simulation with different power coefficient values applied to the joint likelihood function. The thermodynamic integration method is evaluated using three analytical functions by comparing the method with two variants of the Laplace approximation method and three MC methods, including the nested sampling method that is recently introduced into environmental modeling. The thermodynamic integration method outperforms the other methods in terms of their accuracy, convergence, and consistency. The thermodynamic integration method is also applied to a synthetic case of groundwater modeling with four alternative models. The application shows that model probabilities obtained using the thermodynamic integration method improves predictive performance of Bayesian model averaging. As a result, the thermodynamic integration method is mathematically rigorous, and its MC implementation is computationally general for a wide range of environmental problems.« less

Microgravity sciences application visiting scientist program

NASA Technical Reports Server (NTRS)

1994-01-01

Contract NAS8-38785, Microgravity Experimental and Theoretical Research, is a project involving a large number of individual research programs related to: determination of the structure of human serum albumin and other biomedically important proteins; analysis of thermodynamic properties of various proteins and models of protein nucleation; development of experimental techniques for the growth of protein crystals in space; study of the physics of electrical double layers in the mechanics of liquid interfaces; computational analysis of vapor crystal growth processes in microgravity; analysis of the influence of magnetic fields in damping residual flows in directional solidification processes; crystal growth and characterization of II-VI semiconductor alloys; and production of thin films for nonlinear optics. It is not intended that the programs will be necessarily limited to this set at any one time. The visiting scientists accomplishing these programs shall serve on-site at MSFC to take advantage of existing laboratory facilities and the daily opportunities for technical communications with various senior scientists.

The NATA code; theory and analysis. Volume 2: User's manual

NASA Technical Reports Server (NTRS)

Bade, W. L.; Yos, J. M.

1975-01-01

The NATA code is a computer program for calculating quasi-one-dimensional gas flow in axisymmetric nozzles and rectangular channels, primarily to describe conditions in electric archeated wind tunnels. The program provides solutions based on frozen chemistry, chemical equilibrium, and nonequilibrium flow with finite reaction rates. The shear and heat flux on the nozzle wall are calculated and boundary layer displacement effects on the inviscid flow are taken into account. The program contains compiled-in thermochemical, chemical kinetic and transport cross section data for high-temperature air, CO2-N2-Ar mixtures, helium, and argon. It calculates stagnation conditions on axisymmetric or two-dimensional models and conditions on the flat surface of a blunt wedge. Included in the report are: definitions of the inputs and outputs; precoded data on gas models, reactions, thermodynamic and transport properties of species, and nozzle geometries; explanations of diagnostic outputs and code abort conditions; test problems; and a user's manual for an auxiliary program (NOZFIT) used to set up analytical curvefits to nozzle profiles.

Discrete Thermodynamics

DOE PAGES

Margolin, L. G.; Hunter, A.

2017-10-18

Here, we consider the dependence of velocity probability distribution functions on the finite size of a thermodynamic system. We are motivated by applications to computational fluid dynamics, hence discrete thermodynamics. We then begin by describing a coarsening process that represents geometric renormalization. Then, based only on the requirements of conservation, we demonstrate that the pervasive assumption of local thermodynamic equilibrium is not form invariant. We develop a perturbative correction that restores form invariance to second-order in a small parameter associated with macroscopic gradients. Finally, we interpret the corrections in terms of unresolved kinetic energy and discuss the implications of ourmore » results both in theory and as applied to numerical simulation.« less

Discrete Thermodynamics

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

Margolin, L. G.; Hunter, A.

Here, we consider the dependence of velocity probability distribution functions on the finite size of a thermodynamic system. We are motivated by applications to computational fluid dynamics, hence discrete thermodynamics. We then begin by describing a coarsening process that represents geometric renormalization. Then, based only on the requirements of conservation, we demonstrate that the pervasive assumption of local thermodynamic equilibrium is not form invariant. We develop a perturbative correction that restores form invariance to second-order in a small parameter associated with macroscopic gradients. Finally, we interpret the corrections in terms of unresolved kinetic energy and discuss the implications of ourmore » results both in theory and as applied to numerical simulation.« less

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

PubMed Central

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

2013-01-01

The thermodynamic perturbation theory was tested against newly obtained Monte Carlo computer simulations to describe the major features of the hydrophobic effect in a simple 3D-Mercedes-Benz water model: the temperature and hydrophobe size dependence on entropy, enthalpy, and free energy of transfer of a simple hydrophobic solute into water. An excellent agreement was obtained between the theoretical and simulation results. Further, the thermodynamic perturbation theory qualitatively correctly (with respect to the experimental data) describes the solvation thermodynamics under conditions where the simulation results are difficult to obtain with good enough accuracy, e.g., at high pressures. PMID:23862923

Optimization of binary thermodynamic and phase diagram data

NASA Astrophysics Data System (ADS)

Bale, Christopher W.; Pelton, A. D.

1983-03-01

An optimization technique based upon least squares regression is presented to permit the simultaneous analysis of diverse experimental binary thermodynamic and phase diagram data. Coefficients of polynomial expansions for the enthalpy and excess entropy of binary solutions are obtained which can subsequently be used to calculate the thermodynamic properties or the phase diagram. In an interactive computer-assisted analysis employing this technique, one can critically analyze a large number of diverse data in a binary system rapidly, in a manner which is fully self-consistent thermodynamically. Examples of applications to the Bi-Zn, Cd-Pb, PbCl2-KCl, LiCl-FeCl2, and Au-Ni binary systems are given.

Radioactivity and Environmental Security in the Oceans: New Research and Policy Priorities in the Arctic and North Atlantic

DTIC Science & Technology

1993-06-09

within the framework of an update for the computer database "DiaNIK" which has been developed at the Vernadsky Institute of Geochemistry and Analytical...chemical thermodynamic data for minerals and mineral-forming substances. The structure of thermodynamic database "DiaNIK" is based on the principles...in the database . A substantial portion of the thermodynamic values recommended by "DiaNIK" experts for the substances in User Version 3.1 resulted from

Computational Thermodynamics of Materials Zi-Kui Liu and Yi Wang

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

Devanathan, Ram

This authoritative volume introduces the reader to computational thermodynamics and the use of this approach to the design of material properties by tailoring the chemical composition. The text covers applications of this approach, introduces the relevant computational codes, and offers exercises at the end of each chapter. The book has nine chapters and two appendices that provide background material on computer codes. Chapter 1 covers the first and second laws of thermodynamics, introduces the spinodal as the limit of stability, and presents the Gibbs-Duhem equation. Chapter 2 focuses on the Gibbs energy function. Starting with a homogeneous system with amore » single phase, the authors proceed to phases with variable compositions, and polymer blends. The discussion includes the contributions of external electric and magnetic fields to the Gibbs energy. Chapter 3 deals with phase equilibria in heterogeneous systems, the Gibbs phase rule, and phase diagrams. Chapter 4 briefly covers experimental measurements of thermodynamic properties used as input for thermodynamic modeling by Calculation of Phase Diagrams (CALPHAD). Chapter 5 discusses the use of density functional theory to obtain thermochemical data and fill gaps where experimental data is missing. The reader is introduced to the Vienna Ab Initio Simulation Package (VASP) for density functional theory and the YPHON code for phonon calculations. Chapter 6 introduces the modeling of Gibbs energy of phases with the CALPHAD method. Chapter 7 deals with chemical reactions and the Ellingham diagram for metal-oxide systems and presents the calculation of the maximum reaction rate from equilibrium thermodynamics. Chapter 8 is devoted to electrochemical reactions and Pourbaix diagrams with application examples. Chapter 9 concludes this volume with the application of a model of multiple microstates to Ce and Fe3Pt. CALPHAD modeling is briefly discussed in the context of genomics of materials. The book introduces basic thermodynamic concepts clearly and directs readers to appropriate references for advanced concepts and details of software implementation. The list of references is quite comprehensive. The authors make liberal use of diagrams to illustrate key concepts. The two Appendices at the end discuss software requirements and the file structure, and present templates for special quasi-random structures. There is also a link to download pre-compiled binary files of the YPHON code for Linux or Microsoft Windows systems. The exercises at the end of the chapters assume that the reader has access to VASP, which is not freeware. Readers without access to this code can work on a limited number of exercises. However, results from other first principles codes can be organized in the YPHON format as explained in the Appendix. This book will serve as an excellent reference on computational thermodynamics and the exercises provided at the end of each chapter make it valuable as a graduate level textbook. Reviewer: Ram Devanathan is Acting Director of Earth Systems Science Division, Pacific Northwest National Laboratory, USA.« less

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.

Thermodynamic studies of different black holes with modifications of entropy

NASA Astrophysics Data System (ADS)

Haldar, Amritendu; Biswas, Ritabrata

2018-02-01

In recent years, the thermodynamic properties of black holes are topics of interests. We investigate the thermodynamic properties like surface gravity and Hawking temperature on event horizon of regular black holes viz. Hayward Class and asymptotically AdS (Anti-de Sitter) black holes. We also analyze the thermodynamic volume and naive geometric volume of asymptotically AdS black holes and show that the entropy of these black holes is simply the ratio of the naive geometric volume to thermodynamic volume. We plot the different graphs and interpret them physically. We derive the `cosmic-Censorship-Inequality' for both type of black holes. Moreover, we calculate the thermal heat capacity of aforesaid black holes and study their stabilities in different regimes. Finally, we compute the logarithmic correction to the entropy for both the black holes considering the quantum fluctuations around the thermal equilibrium and study the corresponding thermodynamics.

Thermodynamic efficiency of learning a rule in neural networks

NASA Astrophysics Data System (ADS)

Goldt, Sebastian; Seifert, Udo

2017-11-01

Biological systems have to build models from their sensory input data that allow them to efficiently process previously unseen inputs. Here, we study a neural network learning a binary classification rule for these inputs from examples provided by a teacher. We analyse the ability of the network to apply the rule to new inputs, that is to generalise from past experience. Using stochastic thermodynamics, we show that the thermodynamic costs of the learning process provide an upper bound on the amount of information that the network is able to learn from its teacher for both batch and online learning. This allows us to introduce a thermodynamic efficiency of learning. We analytically compute the dynamics and the efficiency of a noisy neural network performing online learning in the thermodynamic limit. In particular, we analyse three popular learning algorithms, namely Hebbian, Perceptron and AdaTron learning. Our work extends the methods of stochastic thermodynamics to a new type of learning problem and might form a suitable basis for investigating the thermodynamics of decision-making.

Thermodynamic and classical instability of AdS black holes in fourth-order gravity

NASA Astrophysics Data System (ADS)

Myung, Yun Soo; Moon, Taeyoon

2014-04-01

We study thermodynamic and classical instability of AdS black holes in fourth-order gravity. These include the BTZ black hole in new massive gravity, Schwarzschild-AdS black hole, and higher-dimensional AdS black holes in fourth-order gravity. All thermo-dynamic quantities which are computed using the Abbot-Deser-Tekin method are used to study thermodynamic instability of AdS black holes. On the other hand, we investigate the s-mode Gregory-Laflamme instability of the massive graviton propagating around the AdS black holes. We establish the connection between the thermodynamic instability and the GL instability of AdS black holes in fourth-order gravity. This shows that the Gubser-Mitra conjecture holds for AdS black holes found from fourth-order gravity.

Reaction Mechanism Generator: Automatic construction of chemical kinetic mechanisms

DOE PAGES

Gao, Connie W.; Allen, Joshua W.; Green, William H.; ...

2016-02-24

Reaction Mechanism Generator (RMG) constructs kinetic models composed of elementary chemical reaction steps using a general understanding of how molecules react. Species thermochemistry is estimated through Benson group additivity and reaction rate coefficients are estimated using a database of known rate rules and reaction templates. At its core, RMG relies on two fundamental data structures: graphs and trees. Graphs are used to represent chemical structures, and trees are used to represent thermodynamic and kinetic data. Models are generated using a rate-based algorithm which excludes species from the model based on reaction fluxes. RMG can generate reaction mechanisms for species involvingmore » carbon, hydrogen, oxygen, sulfur, and nitrogen. It also has capabilities for estimating transport and solvation properties, and it automatically computes pressure-dependent rate coefficients and identifies chemically-activated reaction paths. RMG is an object-oriented program written in Python, which provides a stable, robust programming architecture for developing an extensible and modular code base with a large suite of unit tests. Computationally intensive functions are cythonized for speed improvements.« less

From in silica to in silico: retention thermodynamics at solid-liquid interfaces.

PubMed

El Hage, Krystel; Bemish, Raymond J; Meuwly, Markus

2018-06-28

The dynamics of solvated molecules at the solid/liquid interface is essential for a molecular-level understanding for the solution thermodynamics in reversed phase liquid chromatography (RPLC). The heterogeneous nature of the systems and the competing intermolecular interactions makes solute retention in RPLC a surprisingly challenging problem which benefits greatly from modelling at atomistic resolution. However, the quality of the underlying computational model needs to be sufficiently accurate to provide a realistic description of the energetics and dynamics of systems, especially for solution-phase simulations. Here, the retention thermodynamics and the retention mechanism of a range of benzene-derivatives in C18 stationary-phase chains in contact with water/methanol mixtures is studied using point charge (PC) and multipole (MTP) electrostatic models. The results demonstrate that free energy simulations with a faithful MTP representation of the computational model provide quantitative and molecular level insight into the thermodynamics of adsorption/desorption in chromatographic systems while a conventional PC representation fails in doing so. This provides a rational basis to develop more quantitative and validated models for the optimization of separation systems.

A thermodynamic approach to obtain materials properties for engineering applications

NASA Technical Reports Server (NTRS)

Chang, Y. Austin

1993-01-01

With the ever increases in the capabilities of computers for numerical computations, we are on the verge of using these tools to model manufacturing processes for improving the efficiency of these processes as well as the quality of the products. One such process is casting for the production of metals. However, in order to model metal casting processes in a meaningful way it is essential to have the basic properties of these materials in their molten state, solid state as well as in the mixed state of solid and liquid. Some of the properties needed may be considered as intrinsic such as the density, heat capacity or enthalpy of freezing of a pure metal, while others are not. For instance, the enthalpy of solidification of an alloy is not a defined thermodynamic quantity. Its value depends on the micro-segregation of the phases during the course of solidification. The objective of the present study is to present a thermodynamic approach to obtain some of the intrinsic properties and combining thermodynamics with kinetic models to estimate such quantities as the enthalpy of solidification of an alloy.

Thermodynamic properties of Kehagias-Sfetsos black hole and KS/CFT correspondence

NASA Astrophysics Data System (ADS)

Pradhan, Parthapratim

2017-11-01

We speculate on various thermodynamic features of the inner horizon ({\\mathcal H}-) and outer horizons ({\\mathcal H}+) of Kehagias-Sfetsos (KS) black hole (BH) in the background of the Hořava-Lifshitz gravity. We compute particularly the area product, area sum, area minus and area division of the BH horizons. We find that they all are not showing universal behavior whereas the product is a universal quantity (PRADHAN P., Phys. Lett. B, 747 (2015) 64). Based on these relations, we derive the area bound of all horizons. From the area bound we derive the entropy bound and irreducible mass bound for all the horizons ({\\mathcal H}+/-) . We also observe that the first law of BH thermodynamics and Smarr-Gibbs-Duhem relations do not hold for this BH. The underlying reason behind this failure is due to the scale invariance of the coupling constant. Moreover, we compute the Cosmic-Censorship-Inequality for this BH which gives the lower bound for the total mass of the spacetime and it is supported by the cosmic cencorship conjecture. Finally, we discuss the KS/CFT correspondence via a thermodynamic procedure.

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.

Modeling the internal combustion engine

NASA Technical Reports Server (NTRS)

Zeleznik, F. J.; Mcbride, B. J.

1985-01-01

A flexible and computationally economical model of the internal combustion engine was developed for use on large digital computer systems. It is based on a system of ordinary differential equations for cylinder-averaged properties. The computer program is capable of multicycle calculations, with some parameters varying from cycle to cycle, and has restart capabilities. It can accommodate a broad spectrum of reactants, permits changes in physical properties, and offers a wide selection of alternative modeling functions without any reprogramming. It readily adapts to the amount of information available in a particular case because the model is in fact a hierarchy of five models. The models range from a simple model requiring only thermodynamic properties to a complex model demanding full combustion kinetics, transport properties, and poppet valve flow characteristics. Among its many features the model includes heat transfer, valve timing, supercharging, motoring, finite burning rates, cycle-to-cycle variations in air-fuel ratio, humid air, residual and recirculated exhaust gas, and full combustion kinetics.

Rapid Computation of Thermodynamic Properties over Multidimensional Nonbonded Parameter Spaces Using Adaptive Multistate Reweighting.

PubMed

Naden, Levi N; Shirts, Michael R

2016-04-12

We show how thermodynamic properties of molecular models can be computed over a large, multidimensional parameter space by combining multistate reweighting analysis with a linear basis function approach. This approach reduces the computational cost to estimate thermodynamic properties from molecular simulations for over 130,000 tested parameter combinations from over 1000 CPU years to tens of CPU days. This speed increase is achieved primarily by computing the potential energy as a linear combination of basis functions, computed from either modified simulation code or as the difference of energy between two reference states, which can be done without any simulation code modification. The thermodynamic properties are then estimated with the Multistate Bennett Acceptance Ratio (MBAR) as a function of multiple model parameters without the need to define a priori how the states are connected by a pathway. Instead, we adaptively sample a set of points in parameter space to create mutual configuration space overlap. The existence of regions of poor configuration space overlap are detected by analyzing the eigenvalues of the sampled states' overlap matrix. The configuration space overlap to sampled states is monitored alongside the mean and maximum uncertainty to determine convergence, as neither the uncertainty or the configuration space overlap alone is a sufficient metric of convergence. This adaptive sampling scheme is demonstrated by estimating with high precision the solvation free energies of charged particles of Lennard-Jones plus Coulomb functional form with charges between -2 and +2 and generally physical values of σij and ϵij in TIP3P water. We also compute entropy, enthalpy, and radial distribution functions of arbitrary unsampled parameter combinations using only the data from these sampled states and use the estimates of free energies over the entire space to examine the deviation of atomistic simulations from the Born approximation to the solvation free energy.

Numerical Prediction of the Influence of Process Parameters on Large Area Diamond Deposition by DC Arcjet with ARC Roots Rotating and Operating at Gas Recycling Mode

NASA Astrophysics Data System (ADS)

Lu, F. X.; Huang, T. B.; Tang, W. Z.; Song, J. H.; Tong, Y. M.

A computer model have been set up for simulation of the flow and temperature field, and the radial distribution of atomic hydrogen and active carbonaceous species over a large area substrate surface for a new type dc arc plasma torch with rotating arc roots and operating at gas recycling mode A gas recycling radio of 90% was assumed. In numerical calculation of plasma chemistry, the Thermal-Calc program and a powerful thermodynamic database were employed. Numerical calculations to the computer model were performed using boundary conditions close to the experimental setup for large area diamond films deposition. The results showed that the flow and temperature field over substrate surface of Φ60-100mm were smooth and uniform. Calculations were also made with plasma of the same geometry but no arc roots rotation. It was clearly demonstrated that the design of rotating arc roots was advantageous for high quality uniform deposition of large area diamond films. Theoretical predictions on growth rate and film quality as well as their radial uniformity, and the influence of process parameters on large area diamond deposition were discussed in detail based on the spatial distribution of atomic hydrogen and the carbonaceous species in the plasma over the substrate surface obtained from thermodynamic calculations of plasma chemistry, and were compared with experimental observations.

lncRNATargets: A platform for lncRNA target prediction based on nucleic acid thermodynamics.

PubMed

Hu, Ruifeng; Sun, Xiaobo

2016-08-01

Many studies have supported that long noncoding RNAs (lncRNAs) perform various functions in various critical biological processes. Advanced experimental and computational technologies allow access to more information on lncRNAs. Determining the functions and action mechanisms of these RNAs on a large scale is urgently needed. We provided lncRNATargets, which is a web-based platform for lncRNA target prediction based on nucleic acid thermodynamics. The nearest-neighbor (NN) model was used to calculate binging-free energy. The main principle of NN model for nucleic acid assumes that identity and orientation of neighbor base pairs determine stability of a given base pair. lncRNATargets features the following options: setting of a specific temperature that allow use not only for human but also for other animals or plants; processing all lncRNAs in high throughput without RNA size limitation that is superior to any other existing tool; and web-based, user-friendly interface, and colored result displays that allow easy access for nonskilled computer operators and provide better understanding of results. This technique could provide accurate calculation on the binding-free energy of lncRNA-target dimers to predict if these structures are well targeted together. lncRNATargets provides high accuracy calculations, and this user-friendly program is available for free at http://www.herbbol.org:8001/lrt/ .

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.

Toward optimized potential functions for protein-protein interactions in aqueous solutions: osmotic second virial coefficient calculations using the MARTINI coarse-grained force field

PubMed Central

Stark, Austin C.; Andrews, Casey T.

2013-01-01

Coarse-grained (CG) simulation methods are now widely used to model the structure and dynamics of large biomolecular systems. One important issue for using such methods – especially with regard to using them to model, for example, intracellular environments – is to demonstrate that they can reproduce experimental data on the thermodynamics of protein-protein interactions in aqueous solutions. To examine this issue, we describe here simulations performed using the popular coarse-grained MARTINI force field, aimed at computing the thermodynamics of lysozyme and chymotrypsinogen self-interactions in aqueous solution. Using molecular dynamics simulations to compute potentials of mean force between a pair of protein molecules, we show that the original parameterization of the MARTINI force field is likely to significantly overestimate the strength of protein-protein interactions to the extent that the computed osmotic second virial coefficients are orders of magnitude more negative than experimental estimates. We then show that a simple down-scaling of the van der Waals parameters that describe the interactions between protein pseudo-atoms can bring the simulated thermodynamics into much closer agreement with experiment. Overall, the work shows that it is feasible to test explicit-solvent CG force fields directly against thermodynamic data for proteins in aqueous solutions, and highlights the potential usefulness of osmotic second virial coefficient measurements for fully parameterizing such force fields. PMID:24223529

Toward optimized potential functions for protein-protein interactions in aqueous solutions: osmotic second virial coefficient calculations using the MARTINI coarse-grained force field.

PubMed

Stark, Austin C; Andrews, Casey T; Elcock, Adrian H

2013-09-10

Coarse-grained (CG) simulation methods are now widely used to model the structure and dynamics of large biomolecular systems. One important issue for using such methods - especially with regard to using them to model, for example, intracellular environments - is to demonstrate that they can reproduce experimental data on the thermodynamics of protein-protein interactions in aqueous solutions. To examine this issue, we describe here simulations performed using the popular coarse-grained MARTINI force field, aimed at computing the thermodynamics of lysozyme and chymotrypsinogen self-interactions in aqueous solution. Using molecular dynamics simulations to compute potentials of mean force between a pair of protein molecules, we show that the original parameterization of the MARTINI force field is likely to significantly overestimate the strength of protein-protein interactions to the extent that the computed osmotic second virial coefficients are orders of magnitude more negative than experimental estimates. We then show that a simple down-scaling of the van der Waals parameters that describe the interactions between protein pseudo-atoms can bring the simulated thermodynamics into much closer agreement with experiment. Overall, the work shows that it is feasible to test explicit-solvent CG force fields directly against thermodynamic data for proteins in aqueous solutions, and highlights the potential usefulness of osmotic second virial coefficient measurements for fully parameterizing such force fields.

Two-state thermodynamics and the possibility of a liquid-liquid phase transition in supercooled TIP4P/2005 water

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

Singh, Rakesh S.; Debenedetti, Pablo G.; Biddle, John W.

Water shows intriguing thermodynamic and dynamic anomalies in the supercooled liquid state. One possible explanation of the origin of these anomalies lies in the existence of a metastable liquid-liquid phase transition (LLPT) between two (high and low density) forms of water. While the anomalies are observed in experiments on bulk and confined water and by computer simulation studies of different water-like models, the existence of a LLPT in water is still debated. Unambiguous experimental proof of the existence of a LLPT in bulk supercooled water is hampered by fast ice nucleation which is a precursor of the hypothesized LLPT. Moreover,more » the hypothesized LLPT, being metastable, in principle cannot exist in the thermodynamic limit (infinite size, infinite time). Therefore, computer simulations of water models are crucial for exploring the possibility of the metastable LLPT and the nature of the anomalies. In this work, we present new simulation results in the NVT ensemble for one of the most accurate classical molecular models of water, TIP4P/2005. To describe the computed properties and explore the possibility of a LLPT, we have applied two-structure thermodynamics, viewing water as a non-ideal mixture of two interconvertible local structures (“states”). The results suggest the presence of a liquid-liquid critical point and are consistent with the existence of a LLPT in this model for the simulated length and time scales. We have compared the behavior of TIP4P/2005 with other popular water-like models, namely, mW and ST2, and with real water, all of which are well described by two-state thermodynamics. In view of the current debate involving different studies of TIP4P/2005, we discuss consequences of metastability and finite size in observing the liquid-liquid separation. We also address the relationship between the phenomenological order parameter of two-structure thermodynamics and the microscopic nature of the low-density structure.« less

Quantum chemical approach to estimating the thermodynamics of metabolic reactions.

PubMed

Jinich, Adrian; Rappoport, Dmitrij; Dunn, Ian; Sanchez-Lengeling, Benjamin; Olivares-Amaya, Roberto; Noor, Elad; Even, Arren Bar; Aspuru-Guzik, Alán

2014-11-12

Thermodynamics plays an increasingly important role in modeling and engineering metabolism. We present the first nonempirical computational method for estimating standard Gibbs reaction energies of metabolic reactions based on quantum chemistry, which can help fill in the gaps in the existing thermodynamic data. When applied to a test set of reactions from core metabolism, the quantum chemical approach is comparable in accuracy to group contribution methods for isomerization and group transfer reactions and for reactions not including multiply charged anions. The errors in standard Gibbs reaction energy estimates are correlated with the charges of the participating molecules. The quantum chemical approach is amenable to systematic improvements and holds potential for providing thermodynamic data for all of metabolism.

On the thermodynamic properties of thermal plasma in the flame kernel of hydrocarbon/air premixed gases

NASA Astrophysics Data System (ADS)

Askari, Omid; Beretta, Gian Paolo; Eisazadeh-Far, Kian; Metghalchi, Hameed

2016-07-01

Thermodynamic properties of hydrocarbon/air plasma mixtures at ultra-high temperatures must be precisely calculated due to important influence on the flame kernel formation and propagation in combusting flows and spark discharge applications. A new algorithm based on the complete chemical equilibrium assumption is developed to calculate the ultra-high temperature plasma composition and thermodynamic properties, including enthalpy, entropy, Gibbs free energy, specific heat at constant pressure, specific heat ratio, speed of sound, mean molar mass, and degree of ionization. The method is applied to compute the thermodynamic properties of H2/air and CH4/air plasma mixtures for different temperatures (1000-100 000 K), different pressures (10-6-100 atm), and different fuel/air equivalence ratios within flammability limit. In calculating the individual thermodynamic properties of the atomic species needed to compute the complete equilibrium composition, the Debye-Huckel cutoff criterion has been used for terminating the series expression of the electronic partition function so as to capture the reduction of the ionization potential due to pressure and the intense connection between the electronic partition function and the thermodynamic properties of the atomic species and the number of energy levels taken into account. Partition functions have been calculated using tabulated data for available atomic energy levels. The Rydberg and Ritz extrapolation and interpolation laws have been used for energy levels which are not observed. The calculated plasma properties are then presented as functions of temperature, pressure and equivalence ratio, in terms of a new set of thermodynamically self-consistent correlations that are shown to provide very accurate fits suitable for efficient use in CFD simulations. Comparisons with existing data for air plasma show excellent agreement.

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

NASA Technical Reports Server (NTRS)

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

1991-01-01

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

Thermodynamic analysis of journal bearings operating under steady state loading in laminar regime. Ph.D. Thesis

NASA Technical Reports Server (NTRS)

Khonsari, M. M.

1983-01-01

Thermohydrodynamic effects in journal bearings operating under steady load in laminar regime are investigated. An analytical model for the finite and infinitely long journal bearings is formulated. The model includes correction factors for the cavitation effects in the unloaded region of the bearing and the mixing of the recirculating oil and supply oil at the oil inlet. A finite difference computer program is developed to numerically solve the governing equations of the continuity, Reynolds, energy, Laplace heat conduction, and a viscosity-temperature relation simultaneously. The program includes a numerical technique for obtaining an isothermal shaft temperature. The numerical results of temperature distribution and the heat effects on the bearing load carrying capacity agree closely with those of experimental findings. Several different sets of simpler boundary conditions for the energy equation are studied.

Computer Simulations of Intrinsically Disordered Proteins

NASA Astrophysics Data System (ADS)

Chong, Song-Ho; Chatterjee, Prathit; Ham, Sihyun

2017-05-01

The investigation of intrinsically disordered proteins (IDPs) is a new frontier in structural and molecular biology that requires a new paradigm to connect structural disorder to function. Molecular dynamics simulations and statistical thermodynamics potentially offer ideal tools for atomic-level characterizations and thermodynamic descriptions of this fascinating class of proteins that will complement experimental studies. However, IDPs display sensitivity to inaccuracies in the underlying molecular mechanics force fields. Thus, achieving an accurate structural characterization of IDPs via simulations is a challenge. It is also daunting to perform a configuration-space integration over heterogeneous structural ensembles sampled by IDPs to extract, in particular, protein configurational entropy. In this review, we summarize recent efforts devoted to the development of force fields and the critical evaluations of their performance when applied to IDPs. We also survey recent advances in computational methods for protein configurational entropy that aim to provide a thermodynamic link between structural disorder and protein activity.

Study of thermodynamic properties of liquid binary alloys by a pseudopotential method

NASA Astrophysics Data System (ADS)

Vora, Aditya M.

2010-11-01

On the basis of the Percus-Yevick hard-sphere model as a reference system and the Gibbs-Bogoliubov inequality, a thermodynamic perturbation method is applied with the use of the well-known model potential. By applying a variational method, the hard-core diameters are found which correspond to a minimum free energy. With this procedure, the thermodynamic properties such as the internal energy, entropy, Helmholtz free energy, entropy of mixing, and heat of mixing are computed for liquid NaK binary systems. The influence of the local-field correction functions of Hartree, Taylor, Ichimaru-Utsumi, Farid-Heine-Engel-Robertson, and Sarkar-Sen-Haldar-Roy is also investigated. The computed excess entropy is in agreement with available experimental data in the case of liquid alloys, whereas the agreement for the heat of mixing is poor. This may be due to the sensitivity of the latter to the potential parameters and dielectric function.

Progress of Stirling cycle analysis and loss mechanism characterization

NASA Technical Reports Server (NTRS)

Tew, R. C., Jr.

1986-01-01

An assessment of Stirling engine thermodynamic modeling and design codes shows a general deficiency; this deficiency is due to poor understanding of the fluid flow and heat transfer phenomena that occur in the oscillating flow and pressure level environment within the engines. Stirling engine thermodynamic loss mechanisms are listed. Several experimental and computational research efforts now underway to characterize various loss mechanisms are reviewed. The need for additional experimental rigs and rig upgrades is discussed. Recent developments and current efforts in Stirling engine thermodynamic modeling are also reviewed.

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.

Integrating Statistical Mechanics with Experimental Data from the Rotational-Vibrational Spectrum of HCl into the Physical Chemistry Laboratory

ERIC Educational Resources Information Center

Findley, Bret R.; Mylon, Steven E.

2008-01-01

We introduce a computer exercise that bridges spectroscopy and thermodynamics using statistical mechanics and the experimental data taken from the commonly used laboratory exercise involving the rotational-vibrational spectrum of HCl. Based on the results from the analysis of their HCl spectrum, students calculate bulk thermodynamic properties…

An Interactive Computer Lab of the Galvanic Cell for Students in Biochemistry

ERIC Educational Resources Information Center

Ahlstrand, Emma; Buetti-Dinh, Antoine; Friedman, Ran

2018-01-01

We describe an interactive module that can be used to teach basic concepts in electrochemistry and thermodynamics to first year natural science students. The module is used together with an experimental laboratory and improves the students' understanding of thermodynamic quantities such as ?rG, ?rH, and ?rS that are calculated but not directly…

Using the Metropolis Algorithm to Calculate Thermodynamic Quantities: An Undergraduate Computational Experiment

ERIC Educational Resources Information Center

Beddard, Godfrey S.

2011-01-01

Thermodynamic quantities such as the average energy, heat capacity, and entropy are calculated using a Monte Carlo method based on the Metropolis algorithm. This method is illustrated with reference to the harmonic oscillator but is particularly useful when the partition function cannot be evaluated; an example using a one-dimensional spin system…

Prototype of a computer method for designing and analyzing heating, ventilating and air conditioning proportional, electronic control systems

NASA Astrophysics Data System (ADS)

Barlow, Steven J.

1986-09-01

The Air Force needs a better method of designing new and retrofit heating, ventilating and air conditioning (HVAC) control systems. Air Force engineers currently use manual design/predict/verify procedures taught at the Air Force Institute of Technology, School of Civil Engineering, HVAC Control Systems course. These existing manual procedures are iterative and time-consuming. The objectives of this research were to: (1) Locate and, if necessary, modify an existing computer-based method for designing and analyzing HVAC control systems that is compatible with the HVAC Control Systems manual procedures, or (2) Develop a new computer-based method of designing and analyzing HVAC control systems that is compatible with the existing manual procedures. Five existing computer packages were investigated in accordance with the first objective: MODSIM (for modular simulation), HVACSIM (for HVAC simulation), TRNSYS (for transient system simulation), BLAST (for building load and system thermodynamics) and Elite Building Energy Analysis Program. None were found to be compatible or adaptable to the existing manual procedures, and consequently, a prototype of a new computer method was developed in accordance with the second research objective.

Solution influence on biomolecular equilibria - Nucleic acid base associations

NASA Technical Reports Server (NTRS)

Pohorille, A.; Pratt, L. R.; Burt, S. K.; Macelroy, R. D.

1984-01-01

Various attempts to construct an understanding of the influence of solution environment on biomolecular equilibria at the molecular level using computer simulation are discussed. First, the application of the formal statistical thermodynamic program for investigating biomolecular equilibria in solution is presented, addressing modeling and conceptual simplications such as perturbative methods, long-range interaction approximations, surface thermodynamics, and hydration shell. Then, Monte Carlo calculations on the associations of nucleic acid bases in both polar and nonpolar solvents such as water and carbon tetrachloride are carried out. The solvent contribution to the enthalpy of base association is positive (destabilizing) in both polar and nonpolar solvents while negative enthalpies for stacked complexes are obtained only when the solute-solute in vacuo energy is added to the total energy. The release upon association of solvent molecules from the first hydration layer around a solute to the bulk is accompanied by an increase in solute-solvent energy and decrease in solvent-solvent energy. The techniques presented are expectd to displace less molecular and more heuristic modeling of biomolecular equilibria in solution.

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.

Simulation of the Reflected Blast Wave froma C-4 Charge

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

Howard, W M; Kuhl, A L; Tringe, J W

2011-08-01

The reflection of a blast wave from a C4 charge detonated above a planar surface is simulated with our ALE3D code. We used a finely-resolved, fixed Eulerian 2-D mesh (167 {micro}m per cell) to capture the detonation of the charge, the blast wave propagation in nitrogen, and its reflection from the surface. The thermodynamic properties of the detonation products and nitrogen were specified by the Cheetah code. A programmed-burn model was used to detonate the charge at a rate based on measured detonation velocities. Computed pressure histories are compared with pressures measured by Kistler 603B piezoelectric gauges at 8 rangesmore » (GR = 0, 2, 4, 8, 10, and 12 inches) along the reflecting surface. Computed and measured waveforms and positive-phase impulses were similar, except at close-in ranges (GR < 2 inches), which were dominated by jetting effects.« less

Simulation of the reflected blast wave from a C-4 charge

NASA Astrophysics Data System (ADS)

Howard, W. Michael; Kuhl, Allen L.; Tringe, Joseph

2012-03-01

The reflection of a blast wave from a C4 charge detonated above a planar surface is simulated with our ALE3D code. We used a finely-resolved, fixed Eulerian 2-D mesh (167 μm per cell) to capture the detonation of the charge, the blast wave propagation in nitrogen, and its reflection from the surface. The thermodynamic properties of the detonation products and nitrogen were specified by the Cheetah code. A programmed-burn model was used to detonate the charge at a rate based on measured detonation velocities. Computed pressure histories are compared with pressures measured by Kistler 603B piezoelectric gauges at 7 ranges (GR = 0, 5.08, 10.16, 15.24, 20.32, 25.4, and 30.48 cm) along the reflecting surface. Computed and measured waveforms and positive-phase impulses were similar, except at close-in ranges (GR < 5 cm), which were dominated by jetting effects.

Stochastic thermodynamics

NASA Astrophysics Data System (ADS)

Eichhorn, Ralf; Aurell, Erik

2014-04-01

'Stochastic thermodynamics as a conceptual framework combines the stochastic energetics approach introduced a decade ago by Sekimoto [1] with the idea that entropy can consistently be assigned to a single fluctuating trajectory [2]'. This quote, taken from Udo Seifert's [3] 2008 review, nicely summarizes the basic ideas behind stochastic thermodynamics: for small systems, driven by external forces and in contact with a heat bath at a well-defined temperature, stochastic energetics [4] defines the exchanged work and heat along a single fluctuating trajectory and connects them to changes in the internal (system) energy by an energy balance analogous to the first law of thermodynamics. Additionally, providing a consistent definition of trajectory-wise entropy production gives rise to second-law-like relations and forms the basis for a 'stochastic thermodynamics' along individual fluctuating trajectories. In order to construct meaningful concepts of work, heat and entropy production for single trajectories, their definitions are based on the stochastic equations of motion modeling the physical system of interest. Because of this, they are valid even for systems that are prevented from equilibrating with the thermal environment by external driving forces (or other sources of non-equilibrium). In that way, the central notions of equilibrium thermodynamics, such as heat, work and entropy, are consistently extended to the non-equilibrium realm. In the (non-equilibrium) ensemble, the trajectory-wise quantities acquire distributions. General statements derived within stochastic thermodynamics typically refer to properties of these distributions, and are valid in the non-equilibrium regime even beyond the linear response. The extension of statistical mechanics and of exact thermodynamic statements to the non-equilibrium realm has been discussed from the early days of statistical mechanics more than 100 years ago. This debate culminated in the development of linear response theory for small deviations from equilibrium, in which a general framework is constructed from the analysis of non-equilibrium states close to equilibrium. In a next step, Prigogine and others developed linear irreversible thermodynamics, which establishes relations between transport coefficients and entropy production on a phenomenological level in terms of thermodynamic forces and fluxes. However, beyond the realm of linear response no general theoretical results were available for quite a long time. This situation has changed drastically over the last 20 years with the development of stochastic thermodynamics, revealing that the range of validity of thermodynamic statements can indeed be extended deep into the non-equilibrium regime. Early developments in that direction trace back to the observations of symmetry relations between the probabilities for entropy production and entropy annihilation in non-equilibrium steady states [5-8] (nowadays categorized in the class of so-called detailed fluctuation theorems), and the derivations of the Bochkov-Kuzovlev [9, 10] and Jarzynski relations [11] (which are now classified as so-called integral fluctuation theorems). Apart from its fundamental theoretical interest, the developments in stochastic thermodynamics have experienced an additional boost from the recent experimental progress in fabricating, manipulating, controlling and observing systems on the micro- and nano-scale. These advances are not only of formidable use for probing and monitoring biological processes on the cellular, sub-cellular and molecular level, but even include the realization of a microscopic thermodynamic heat engine [12] or the experimental verification of Landauer's principle in a colloidal system [13]. The scientific program Stochastic Thermodynamics held between 4 and 15 March 2013, and hosted by The Nordic Institute for Theoretical Physics (Nordita), was attended by more than 50 scientists from the Nordic countries and elsewhere, amongst them many leading experts in the field. During the program, the most recent developments, open questions and new ideas in stochastic thermodynamics were presented and discussed. From the talks and debates, the notion of information in stochastic thermodynamics, the fundamental properties of entropy production (rate) in non-equilibrium, the efficiency of small thermodynamic machines and the characteristics of optimal protocols for the applied (cyclic) forces were crystallizing as main themes. Surprisingly, the long-studied adiabatic piston, its peculiarities and its relation to stochastic thermodynamics were also the subject of intense discussions. The comment on the Nordita program Stochastic Thermodynamics published in this issue of Physica Scripta exploits the Jarzynski relation for determining free energy differences in the adiabatic piston. This scientific program and the contribution presented here were made possible by the financial and administrative support of The Nordic Institute for Theoretical Physics.

Thermodynamic properties of water solvating biomolecular surfaces

NASA Astrophysics Data System (ADS)

Heyden, Matthias

Changes in the potential energy and entropy of water molecules hydrating biomolecular interfaces play a significant role for biomolecular solubility and association. Free energy perturbation and thermodynamic integration methods allow calculations of free energy differences between two states from simulations. However, these methods are computationally demanding and do not provide insights into individual thermodynamic contributions, i.e. changes in the solvent energy or entropy. Here, we employ methods to spatially resolve distributions of hydration water thermodynamic properties in the vicinity of biomolecular surfaces. This allows direct insights into thermodynamic signatures of the hydration of hydrophobic and hydrophilic solvent accessible sites of proteins and small molecules and comparisons to ideal model surfaces. We correlate dynamic properties of hydration water molecules, i.e. translational and rotational mobility, to their thermodynamics. The latter can be used as a guide to extract thermodynamic information from experimental measurements of site-resolved water dynamics. Further, we study energy-entropy compensations of water at different hydration sites of biomolecular surfaces. This work is supported by the Cluster of Excellence RESOLV (EXC 1069) funded by the Deutsche Forschungsgemeinschaft.

Integrating Computational Science Tools into a Thermodynamics Course

ERIC Educational Resources Information Center

Vieira, Camilo; Magana, Alejandra J.; García, R. Edwin; Jana, Aniruddha; Krafcik, Matthew

2018-01-01

Computational tools and methods have permeated multiple science and engineering disciplines, because they enable scientists and engineers to process large amounts of data, represent abstract phenomena, and to model and simulate complex concepts. In order to prepare future engineers with the ability to use computational tools in the context of…

Thermodynamics of Inozemtsev's elliptic spin chain

NASA Astrophysics Data System (ADS)

Klabbers, Rob

2016-06-01

We study the thermodynamic behaviour of Inozemtsev's long-range elliptic spin chain using the Bethe ansatz equations describing the spectrum of the model in the infinite-length limit. We classify all solutions of these equations in that limit and argue which of these solutions determine the spectrum in the thermodynamic limit. Interestingly, some of the solutions are not selfconjugate, which puts the model in sharp contrast to one of the model's limiting cases, the Heisenberg XXX spin chain. Invoking the string hypothesis we derive the thermodynamic Bethe ansatz equations (TBA-equations) from which we determine the Helmholtz free energy in thermodynamic equilibrium and derive the associated Y-system. We corroborate our results by comparing numerical solutions of the TBA-equations to a direct computation of the free energy for the finite-length hamiltonian. In addition we confirm numerically the interesting conjecture put forward by Finkel and González-López that the original and supersymmetric versions of Inozemtsev's elliptic spin chain are equivalent in the thermodynamic limit.

Computational methods in preformulation study for pharmaceutical solid dosage forms of therapeutic proteins

NASA Astrophysics Data System (ADS)

Majee, Sutapa Biswas; Biswas, Gopa Roy

2017-06-01

Design and delivery of protein-based biopharmaceuticals needs detailed planning and strict monitoring of intermediate processing steps, storage conditions and container-closure system to ensure a stable, elegant and biopharmaceutically acceptable dosage form. Selection of manufacturing process variables and conditions along with packaging specifications can be achieved through properly designed preformulation study protocol for the formulation. Thermodynamic stability and biological activity of therapeutic proteins depend on folding-unfolding and three-dimensional packing dynamics of amino acid network in the protein molecule. Lack of favourable environment may cause protein aggregation with loss in activity and even fatal immunological reaction. Although lyophilization can enhance the stability of protein-based formulations in the solid state, it can induce protein unfolding leading to thermodynamic instability. Formulation stabilizers such as preservatives can also result in aggregation of therapeutic proteins. Modern instrumental techniques in conjunction with computational tools enable rapid and accurate prediction of amino acid sequence, thermodynamic parameters associated with protein folding and detection of aggregation "hot-spots." Globular proteins pose a challenge during investigations on their aggregation propensity. Biobetter therapeutic monoclonal antibodies with enhanced stability, solubility and reduced immunogenic potential can be designed through mutation of aggregation-prone zones. The objective of the present review article is to focus on the various analytical methods and computational approaches used in the study of thermodynamic stability and aggregation tendency of therapeutic proteins, with an aim to develop optimal and marketable formulation. Knowledge of protein dynamics through application of computational tools will provide the essential inputs and relevant information for successful and meaningful completion of preformulation studies on solid dosage forms of therapeutic proteins.

Atomistic calculations of interface elastic properties in noncoherent metallic bilayers

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

Mi Changwen; Jun, Sukky; Kouris, Demitris A.

2008-02-15

The paper describes theoretical and computational studies associated with the interface elastic properties of noncoherent metallic bicrystals. Analytical forms of interface energy, interface stresses, and interface elastic constants are derived in terms of interatomic potential functions. Embedded-atom method potentials are then incorporated into the model to compute these excess thermodynamics variables, using energy minimization in a parallel computing environment. The proposed model is validated by calculating surface thermodynamic variables and comparing them with preexisting data. Next, the interface elastic properties of several fcc-fcc bicrystals are computed. The excess energies and stresses of interfaces are smaller than those on free surfacesmore » of the same crystal orientations. In addition, no negative values of interface stresses are observed. Current results can be applied to various heterogeneous materials where interfaces assume a prominent role in the systems' mechanical behavior.« less

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

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

Yang, Ying

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

CO2 packing polymorphism under pressure: Mechanism and thermodynamics of the I-III polymorphic transition

NASA Astrophysics Data System (ADS)

Gimondi, Ilaria; Salvalaglio, Matteo

2017-09-01

In this work, we describe the thermodynamics and mechanism of CO2 polymorphic transitions under pressure from form I to form III combining standard molecular dynamics, well-tempered metadynamics, and committor analysis. We find that the phase transformation takes place through a concerted rearrangement of CO2 molecules, which unfolds via an anisotropic expansion of the CO2 supercell. Furthermore, at high pressures, we find that defected form I configurations are thermodynamically more stable with respect to form I without structural defects. Our computational approach shows the capability of simultaneously providing an extensive sampling of the configurational space, estimates of the thermodynamic stability, and a suitable description of a complex, collective polymorphic transition mechanism.

CO2 packing polymorphism under pressure: Mechanism and thermodynamics of the I-III polymorphic transition.

PubMed

Gimondi, Ilaria; Salvalaglio, Matteo

2017-09-21

In this work, we describe the thermodynamics and mechanism of CO 2 polymorphic transitions under pressure from form I to form III combining standard molecular dynamics, well-tempered metadynamics, and committor analysis. We find that the phase transformation takes place through a concerted rearrangement of CO 2 molecules, which unfolds via an anisotropic expansion of the CO 2 supercell. Furthermore, at high pressures, we find that defected form I configurations are thermodynamically more stable with respect to form I without structural defects. Our computational approach shows the capability of simultaneously providing an extensive sampling of the configurational space, estimates of the thermodynamic stability, and a suitable description of a complex, collective polymorphic transition mechanism.

Quantum Chemical Approach to Estimating the Thermodynamics of Metabolic Reactions

PubMed Central

Jinich, Adrian; Rappoport, Dmitrij; Dunn, Ian; Sanchez-Lengeling, Benjamin; Olivares-Amaya, Roberto; Noor, Elad; Even, Arren Bar; Aspuru-Guzik, Alán

2014-01-01

Thermodynamics plays an increasingly important role in modeling and engineering metabolism. We present the first nonempirical computational method for estimating standard Gibbs reaction energies of metabolic reactions based on quantum chemistry, which can help fill in the gaps in the existing thermodynamic data. When applied to a test set of reactions from core metabolism, the quantum chemical approach is comparable in accuracy to group contribution methods for isomerization and group transfer reactions and for reactions not including multiply charged anions. The errors in standard Gibbs reaction energy estimates are correlated with the charges of the participating molecules. The quantum chemical approach is amenable to systematic improvements and holds potential for providing thermodynamic data for all of metabolism. PMID:25387603

Calculating phase diagrams using PANDAT and panengine

NASA Astrophysics Data System (ADS)

Chen, S.-L.; Zhang, F.; Xie, F.-Y.; Daniel, S.; Yan, X.-Y.; Chang, Y. A.; Schmid-Fetzer, R.; Oates, W. A.

2003-12-01

Knowledge of phase equilibria or phase diagrams and thermodynamic properties is important in alloy design and materials-processing simulation. In principle, stable phase equilibrium is uniquely determined by the thermodynamic properties of the system, such as the Gibbs energy functions of the phases. PANDAT, a new computer software package for multicomponent phase-diagram calculation, was developed under the guidance of this principle.

Computational study of frontier orbitals, moments, chemical reactivity and thermodynamic parameters of sildenafil

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

Sachdeva, Ritika, E-mail: ritika.sachdeva21@gmail.com; Kaur, Prabhjot; Singh, V. P.

2016-05-06

Analysis of frontier orbitals of sildenafil has been carried using Density Functional Theory. On the basis of HOMO-LUMO energy, values of global chemical reactivity descriptors such as electronegativity, chemical hardness, softness, chemical potential, electrophilicity index have been calculated. Calculated values of dipole moment, polarizability, hyperpolarizability have also been reported for sildenafil along with its thermodynamic parameters.

Fast and Reliable Thermodynamic Approach for Determining the Protonation State of the Asp Dyad.

PubMed

Huang, Jinfeng; Sun, Bin; Yao, Yuan; Liu, Junjun

2017-09-25

The protonation state of the asp dyad is significantly important in revealing enzymatic mechanisms and developing drugs. However, it is hard to determine by calculating free energy changes between possible protonation states, because the free energy changes due to protein conformational flexibility are usually much larger than those originating from different locations of protons. Sophisticated and computationally expensive methods such as free energy perturbation, thermodynamic integration (TI), and quantum mechanics/molecular mechanics are therefore usually used for this purpose. In the present study, we have developed a simple thermodynamic approach to effectively eliminating the free energy changes arising from protein conformational flexibility and estimating the free energy changes only originated from the locations of protons, which provides a fast and reliable method for determining the protonation state of asp dyads. The test of this approach on a total of 15 asp dyad systems, including BACE-1 and HIV-1 protease, shows that the predictions from this approach are all consistent with experiments or with the computationally expensive TI calculations. It is clear that our thermodynamic approach could be used to rapidly and reliably determine the protonation state of the asp dyad.

Thermodynamic Routes to Novel Metastable Nitrogen-Rich Nitrides

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

Sun, Wenhao; Holder, Aaron; Orvañanos, Bernardo

Compared to oxides, the nitrides are relatively unexplored, making them a promising chemical space for novel materials discovery. Of particular interest are nitrogen-rich nitrides, which often possess useful semiconducting properties for electronic and optoelectronic applications. However, such nitrogen-rich compounds are generally metastable, and the lack of a guiding theory for their synthesis has limited their exploration. Here, we review the remarkable metastability of observed nitrides, and examine the thermodynamics of how reactive nitrogen precursors can stabilize metastable nitrogen-rich compositions during materials synthesis. We map these thermodynamic strategies onto a predictive computational search, training a data-mined ionic substitution algorithm specifically formore » nitride discovery, which we combine with grand-canonical DFT-SCAN phase stability calculations to compute stabilizing nitrogen chemical potentials. We identify several new nitrogen-rich binary nitrides for experimental investigation, notably the transition metal nitrides Mn3N4, Cr3N4, V3N4, and Nb3N5, the main group nitride SbN, and the pernitrides FeN2, CrN2, and Cu2N2. By formulating rational thermodynamic routes to metastable compounds, we expand the search space for functional technological materials beyond equilibrium phases and compositions.« less

Thermodynamic Routes to Novel Metastable Nitrogen-Rich Nitrides

DOE PAGES

Sun, Wenhao; Holder, Aaron; Orvañanos, Bernardo; ...

2017-07-17

Compared to oxides, the nitrides are relatively unexplored, making them a promising chemical space for novel materials discovery. Of particular interest are nitrogen-rich nitrides, which often possess useful semiconducting properties for electronic and optoelectronic applications. However, such nitrogen-rich compounds are generally metastable, and the lack of a guiding theory for their synthesis has limited their exploration. Here, we review the remarkable metastability of observed nitrides, and examine the thermodynamics of how reactive nitrogen precursors can stabilize metastable nitrogen-rich compositions during materials synthesis. We map these thermodynamic strategies onto a predictive computational search, training a data-mined ionic substitution algorithm specifically formore » nitride discovery, which we combine with grand-canonical DFT-SCAN phase stability calculations to compute stabilizing nitrogen chemical potentials. We identify several new nitrogen-rich binary nitrides for experimental investigation, notably the transition metal nitrides Mn3N4, Cr3N4, V3N4, and Nb3N5, the main group nitride SbN, and the pernitrides FeN2, CrN2, and Cu2N2. By formulating rational thermodynamic routes to metastable compounds, we expand the search space for functional technological materials beyond equilibrium phases and compositions.« less

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

Symmetry-conserving purification of quantum states within the density matrix renormalization group

DOE PAGES

Nocera, Alberto; Alvarez, Gonzalo

2016-01-28

The density matrix renormalization group (DMRG) algorithm was originally designed to efficiently compute the zero-temperature or ground-state properties of one-dimensional strongly correlated quantum systems. The development of the algorithm at finite temperature has been a topic of much interest, because of the usefulness of thermodynamics quantities in understanding the physics of condensed matter systems, and because of the increased complexity associated with efficiently computing temperature-dependent properties. The ancilla method is a DMRG technique that enables the computation of these thermodynamic quantities. In this paper, we review the ancilla method, and improve its performance by working on reduced Hilbert spaces andmore » using canonical approaches. Furthermore we explore its applicability beyond spins systems to t-J and Hubbard models.« less

Independent-Trajectory Thermodynamic Integration: a practical guide to protein-drug binding free energy calculations using distributed computing.

PubMed

Lawrenz, Morgan; Baron, Riccardo; Wang, Yi; McCammon, J Andrew

2012-01-01

The Independent-Trajectory Thermodynamic Integration (IT-TI) approach for free energy calculation with distributed computing is described. IT-TI utilizes diverse conformational sampling obtained from multiple, independent simulations to obtain more reliable free energy estimates compared to single TI predictions. The latter may significantly under- or over-estimate the binding free energy due to finite sampling. We exemplify the advantages of the IT-TI approach using two distinct cases of protein-ligand binding. In both cases, IT-TI yields distributions of absolute binding free energy estimates that are remarkably centered on the target experimental values. Alternative protocols for the practical and general application of IT-TI calculations are investigated. We highlight a protocol that maximizes predictive power and computational efficiency.

The development of flux-split algorithms for flows with non-equilibrium thermodynamics and chemical reactions

NASA Technical Reports Server (NTRS)

Grossman, B.; Cinella, P.

1988-01-01

A finite-volume method for the numerical computation of flows with nonequilibrium thermodynamics and chemistry is presented. A thermodynamic model is described which simplifies the coupling between the chemistry and thermodynamics and also results in the retention of the homogeneity property of the Euler equations (including all the species continuity and vibrational energy conservation equations). Flux-splitting procedures are developed for the fully coupled equations involving fluid dynamics, chemical production and thermodynamic relaxation processes. New forms of flux-vector split and flux-difference split algorithms are embodied in a fully coupled, implicit, large-block structure, including all the species conservation and energy production equations. Several numerical examples are presented, including high-temperature shock tube and nozzle flows. The methodology is compared to other existing techniques, including spectral and central-differenced procedures, and favorable comparisons are shown regarding accuracy, shock-capturing and convergence rates.

Viscoelastic Waves Simulation in a Blocky Medium with Fluid-Saturated Interlayers Using High-Performance Computing

NASA Astrophysics Data System (ADS)

Sadovskii, Vladimir; Sadovskaya, Oxana

2017-04-01

A thermodynamically consistent approach to the description of linear and nonlinear wave processes in a blocky medium, which consists of a large number of elastic blocks interacting with each other via pliant interlayers, is proposed. The mechanical properties of interlayers are defined by means of the rheological schemes of different levels of complexity. Elastic interaction between the blocks is considered in the framework of the linear elasticity theory [1]. The effects of viscoelastic shear in the interblock interlayers are taken into consideration using the Pointing-Thomson rheological scheme. The model of an elastic porous material is used in the interlayers, where the pores collapse if an abrupt compressive stress is applied. On the basis of the Biot equations for a fluid-saturated porous medium, a new mathematical model of a blocky medium is worked out, in which the interlayers provide a convective fluid motion due to the external perturbations. The collapse of pores is modeled within the generalized rheological approach, wherein the mechanical properties of a material are simulated using four rheological elements. Three of them are the traditional elastic, viscous and plastic elements, the fourth element is the so-called rigid contact [2], which is used to describe the behavior of materials with different resistance to tension and compression. Thermodynamic consistency of the equations in interlayers with the equations in blocks guarantees fulfillment of the energy conservation law for a blocky medium in a whole, i.e. kinetic and potential energy of the system is the sum of kinetic and potential energies of the blocks and interlayers. As a result of discretization of the equations of the model, robust computational algorithm is constructed, that is stable because of the thermodynamic consistency of the finite difference equations at a discrete level. The splitting method by the spatial variables and the Godunov gap decay scheme are used in the blocks, the dissipationless finite difference Ivanov scheme is applied in the interlayers. The parallel program is designed, using the MPI technology. By means of this software, nonlinear wave processes in the case of initial rotation of the central block in a rock mass as well as in the case of concentrated couple stress load, applied at the boundary of a rock mass, are analyzed. Results of computations on the multiprocessor computer systems demonstrate the strong anisotropy of a blocky medium. This work was supported by the Complex Fundamental Research Program no. II.2P "Integration and Development" of Siberian Branch of the Russian Academy of Sciences. References 1. Sadovskii V.M., Sadovskaya O.V. Modeling of Elastic Waves in a Blocky Medium Based on Equations of the Cosserat Continuum // Wave Motion. 2015. V. 52. P. 138-150. 2. Sadovskaya O., Sadovskii V. Mathematical Modeling in Mechanics of Granular Materials. Ser.: Advanced Structured Materials, V. 21. Heidelberg - New York - Dordrecht - London, Springer, 2012. 390 p.

Microscopic approaches to liquid nitromethane detonation properties.

PubMed

Hervouët, Anaïs; Desbiens, Nicolas; Bourasseau, Emeric; Maillet, Jean-Bernard

2008-04-24

In this paper, thermodynamic and chemical properties of nitromethane are investigated using microscopic simulations. The Hugoniot curve of the inert explosive is computed using Monte Carlo simulations with a modified version of the adaptative Erpenbeck equation of state and a recently developed intermolecular potential. Molecular dynamic simulations of nitromethane decomposition have been performed using a reactive potential, allowing the calculation of kinetic rate constants and activation energies. Finally, the Crussard curve of detonation products as well as thermodynamic properties at the Chapman-Jouguet (CJ) point are computed using reactive ensemble Monte Carlo simulations. Results are in good agreement with both thermochemical calculations and experimental measurements.

Calculating binding free energies for protein-carbohydrate complexes.

PubMed

Hadden, Jodi A; Tessier, Matthew B; Fadda, Elisa; Woods, Robert J

2015-01-01

A variety of computational techniques may be applied to compute theoretical binding free energies for protein-carbohydrate complexes. Elucidation of the intermolecular interactions, as well as the thermodynamic effects, that contribute to the relative strength of receptor binding can shed light on biomolecular recognition, and the resulting initiation or inhibition of a biological process. Three types of free energy methods are discussed here, including MM-PB/GBSA, thermodynamic integration, and a non-equilibrium alternative utilizing SMD. Throughout this chapter, the well-known concanavalin A lectin is employed as a model system to demonstrate the application of these methods to the special case of carbohydrate binding.

Synthesis, crystal structure investigation, spectroscopic characterizations and DFT computations on a novel 1-(2-chloro-4-phenylquinolin-3-yl)ethanone

NASA Astrophysics Data System (ADS)

Murugavel, S.; Stephen, C. S. Jacob Prasanna; Subashini, R.; Reddy, H. Raveendranatha; AnanthaKrishnan, Dhanabalan

2016-10-01

The title compound 1-(2-chloro-4-phenylquinolin-3-yl)ethanone (CPQE) was synthesised effectively by chlorination of 3-acetyl-4-phenylquinolin-2(1H)-one (APQ) using POCl3 reagent. Structural and vibrational spectroscopic studies were performed by utilizing single crystal X-ray diffraction, FTIR and NMR spectral analysis along with DFT method utilizing GAUSSIAN‧ 03 software. Veda program has been employed to perform a detailed interpretation of vibrational spectra. Mulliken population analyses on atomic charges, MEP, HOMO-LUMO, NBO, Global chemical reactivity descriptors and thermodynamic properties have been examined by (DFT/B3LYP) method with the 6-311G(d,p) basis set level.

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

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).

A FORTRAN program for calculating three dimensional, inviscid and rotational flows with shock waves in axial compressor blade rows: User's manual

NASA Technical Reports Server (NTRS)

Thompkins, W. T., Jr.

1982-01-01

A FORTRAN-IV computer program was developed for the calculation of the inviscid transonic/supersonic flow field in a fully three dimensional blade passage of an axial compressor rotor or stator. Rotors may have dampers (part span shrouds). MacCormack's explicit time marching method is used to solve the unsteady Euler equations on a finite difference mesh. This technique captures shocks and smears them over several grid points. Input quantities are blade row geometry, operating conditions and thermodynamic quanities. Output quantities are three velocity components, density and internal energy at each mesh point. Other flow quanities are calculated from these variables. A short graphics package is included with the code, and may be used to display the finite difference grid, blade geometry and static pressure contour plots on blade to blade calculation surfaces or blade suction and pressure surfaces. The flow in a low aspect ratio transonic compressor was analyzed and compared with high response total pressure probe measurements and gas fluorescence static density measurements made in the MIT blowdown wind tunnel. These comparisons show that the computed flow fields accurately model the measured shock wave locations and overall aerodynamic performance.

On a partial differential equation method for determining the free energies and coexisting phase compositions of ternary mixtures from light scattering data.

PubMed

Ross, David S; Thurston, George M; Lutzer, Carl V

2008-08-14

In this paper we present a method for determining the free energies of ternary mixtures from light scattering data. We use an approximation that is appropriate for liquid mixtures, which we formulate as a second-order nonlinear partial differential equation. This partial differential equation (PDE) relates the Hessian of the intensive free energy to the efficiency of light scattering in the forward direction. This basic equation applies in regions of the phase diagram in which the mixtures are thermodynamically stable. In regions in which the mixtures are unstable or metastable, the appropriate PDE is the nonlinear equation for the convex hull. We formulate this equation along with continuity conditions for the transition between the two equations at cloud point loci. We show how to discretize this problem to obtain a finite-difference approximation to it, and we present an iterative method for solving the discretized problem. We present the results of calculations that were done with a computer program that implements our method. These calculations show that our method is capable of reconstructing test free energy functions from simulated light scattering data. If the cloud point loci are known, the method also finds the tie lines and tie triangles that describe thermodynamic equilibrium between two or among three liquid phases. A robust method for solving this PDE problem, such as the one presented here, can be a basis for optical, noninvasive means of characterizing the thermodynamics of multicomponent mixtures.

Computer Program for Calculation of Complex Chemical Equilibrium Compositions and Applications II. Users Manual and Program Description. 2; Users Manual and Program Description

NASA Technical Reports Server (NTRS)

McBride, Bonnie J.; Gordon, Sanford

1996-01-01

This users manual is the second part of a two-part report describing the NASA Lewis CEA (Chemical Equilibrium with Applications) program. The program obtains chemical equilibrium compositions of complex mixtures with applications to several types of problems. The topics presented in this manual are: (1) details for preparing input data sets; (2) a description of output tables for various types of problems; (3) the overall modular organization of the program with information on how to make modifications; (4) a description of the function of each subroutine; (5) error messages and their significance; and (6) a number of examples that illustrate various types of problems handled by CEA and that cover many of the options available in both input and output. Seven appendixes give information on the thermodynamic and thermal transport data used in CEA; some information on common variables used in or generated by the equilibrium module; and output tables for 14 example problems. The CEA program was written in ANSI standard FORTRAN 77. CEA should work on any system with sufficient storage. There are about 6300 lines in the source code, which uses about 225 kilobytes of memory. The compiled program takes about 975 kilobytes.

Chemical and biochemical thermodynamics: Is it time for a reunification?

PubMed

Iotti, Stefano; Raff, Lionel; Sabatini, Antonio

2017-02-01

The thermodynamics of chemical reactions in which all species are explicitly considered with atoms and charge balanced is compared with the transformed thermodynamics generally used to treat biochemical reactions where atoms and charges are not balanced. The transformed thermodynamic quantities suggested by Alberty are obtained by execution of Legendre transformation of the usual thermodynamic potentials. The present analysis demonstrates that the transformed values for Δ r G' 0 and Δ r H' 0 can be obtained directly without performing Legendre transformations by simply writing the chemical reactions with all the pseudoisomers explicitly included and charges balanced. The appropriate procedures for computing the stoichiometric coefficients for the pseudoisomers are fully explained by means of an example calculation for the biochemical ATP hydrolysis reaction. It is concluded that the analysis has reunited the "two separate worlds" of conventional thermodynamics and transformed thermodynamics. In addition, it is also shown that the value of the conditional Gibbs energy of reaction, Δ r G', for a biochemical reaction is the same of the value of Δ r G for any chemical reaction involving pseudoisomers of the biochemical reagents. Copyright © 2016 Elsevier B.V. All rights reserved.

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.

Computing the absolute Gibbs free energy in atomistic simulations: Applications to defects in solids

NASA Astrophysics Data System (ADS)

Cheng, Bingqing; Ceriotti, Michele

2018-02-01

The Gibbs free energy is the fundamental thermodynamic potential underlying the relative stability of different states of matter under constant-pressure conditions. However, computing this quantity from atomic-scale simulations is far from trivial, so the potential energy of a system is often used as a proxy. In this paper, we use a combination of thermodynamic integration methods to accurately evaluate the Gibbs free energies associated with defects in crystals, including the vacancy formation energy in bcc iron, and the stacking fault energy in fcc nickel, iron, and cobalt. We quantify the importance of entropic and anharmonic effects in determining the free energies of defects at high temperatures, and show that the potential energy approximation as well as the harmonic approximation may produce inaccurate or even qualitatively wrong results. Our calculations manifest the necessity to employ accurate free energy methods such as thermodynamic integration to estimate the stability of crystallographic defects at high temperatures.

Study of Thermodynamics of Liquid Noble-Metals Alloys Through a Pseudopotential Theory

NASA Astrophysics Data System (ADS)

Vora, Aditya M.

2010-09-01

The Gibbs-Bogoliubov (GB) inequality is applied to investigate the thermodynamic properties of some equiatomic noble metal alloys in liquid phase such as Au-Cu, Ag-Cu, and Ag-Au using well recognized pseudopotential formalism. For description of the structure, well known Percus-Yevick (PY) hard sphere model is used as a reference system. By applying a variation method the best hard core diameters have been found which correspond to minimum free energy. With this procedure the thermodynamic properties such as entropy and heat of mixing have been computed. The influence of local field correction function viz; Hartree (H), Taylor (T), Ichimaru-Utsumi (IU), Farid et al. (F), and Sarkar et al. (S) is also investigated. The computed results of the excess entropy compares favourably in the case of liquid alloys while the agreement with experiment is poor in the case of heats of mixing. This may be due to the sensitivity of the heats of mixing with the potential parameters and the dielectric function.

Thermodynamics and computation during collective motion near criticality

NASA Astrophysics Data System (ADS)

Crosato, Emanuele; Spinney, Richard E.; Nigmatullin, Ramil; Lizier, Joseph T.; Prokopenko, Mikhail

2018-01-01

We study self-organization of collective motion as a thermodynamic phenomenon in the context of the first law of thermodynamics. It is expected that the coherent ordered motion typically self-organises in the presence of changes in the (generalized) internal energy and of (generalized) work done on, or extracted from, the system. We aim to explicitly quantify changes in these two quantities in a system of simulated self-propelled particles and contrast them with changes in the system's configuration entropy. In doing so, we adapt a thermodynamic formulation of the curvatures of the internal energy and the work, with respect to two parameters that control the particles' alignment. This allows us to systematically investigate the behavior of the system by varying the two control parameters to drive the system across a kinetic phase transition. Our results identify critical regimes and show that during the phase transition, where the configuration entropy of the system decreases, the rates of change of the work and of the internal energy also decrease, while their curvatures diverge. Importantly, the reduction of entropy achieved through expenditure of work is shown to peak at criticality. We relate this both to a thermodynamic efficiency and the significance of the increased order with respect to a computational path. Additionally, this study provides an information-geometric interpretation of the curvature of the internal energy as the difference between two curvatures: the curvature of the free entropy, captured by the Fisher information, and the curvature of the configuration entropy.

Thermodynamic consistency test procedure using orthogonal collocation and the Peng-Robinson equation of state

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

Hamm, L.L.; Van Brunt, V.

The Christiansen and Fredenslund programs for calculating vapor-liquid equilibria have been modified by replacing the Soave-Redlich-Kwong equation of state with the newly developed Peng-Robinson equation of state. This modification was shown to be a decided improvement for high pressure systems, especially in the critical and upper retrograde regions. Thermodynamic consistency tests were developed and used to evaluate and compare calculated values from both the modified and unmodified programs with reported experimental data for several vapor-liquid systems.

Structural study, NCA, FT-IR, FT-Raman spectral investigations, NBO analysis, thermodynamic functions of N-acetyl-l-phenylalanine.

PubMed

Raja, B; Balachandran, V; Revathi, B

2015-03-05

The FT-IR and FT-Raman spectra of N-acetyl-l-phenylalanine were recorded and analyzed. Natural bond orbital analysis has been carried out for various intramolecular interactions that are responsible for the stabilization of the molecule. HOMO-LUMO energy gap has been computed with the help of density functional theory. The statistical thermodynamic functions (heat capacity, entropy, vibrational partition function and Gibbs energy) were obtained for the range of temperature 100-1000K. The polarizability, first hyperpolarizability, anisotropy polarizability invariant has been computed using quantum chemical calculations. The infrared and Raman spectra were also predicted from the calculated intensities. Comparison of the experimental and theoretical spectra values provides important information about the ability of the computational method to describe the vibrational modes. Copyright © 2014 Elsevier B.V. All rights reserved.

Microcomputer Calculation of Thermodynamic Properties from Molecular Parameters of Gases.

ERIC Educational Resources Information Center

Venugopalan, Mundiyath

1990-01-01

Described in this article is a problem-solving activity which integrates the application of microcomputers with the learning of physical chemistry. Students use the program with spectroscopic data to calculate the thermodynamic properties and compare them with the values from the thermochemical tables. (Author/KR)

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

A Simple Explanation of Complexation

ERIC Educational Resources Information Center

Elliott, J. Richard

2010-01-01

The topics of solution thermodynamics, activity coefficients, and complex formation are introduced through computational exercises and sample applications. The presentation is designed to be accessible to freshmen in a chemical engineering computations course. The MOSCED model is simplified to explain complex formation in terms of hydrogen…

Integrating Thermodynamic Models in Geodynamic Simulations: The Example of the Community Software ASPECT

NASA Astrophysics Data System (ADS)

Dannberg, J.; Heister, T.; Grove, R. R.; Gassmoeller, R.; Spiegelman, M. W.; Bangerth, W.

2017-12-01

Earth's surface shows many features whose genesis can only be understood through the interplay of geodynamic and thermodynamic models. This is particularly important in the context of melt generation and transport: Mantle convection determines the distribution of temperature and chemical composition, the melting process itself is then controlled by the thermodynamic relations and in turn influences the properties and the transport of melt. Here, we present our extension of the community geodynamics code ASPECT, which solves the equations of coupled magma/mantle dynamics, and allows to integrate different parametrizations of reactions and phase transitions: They may alternatively be implemented as simple analytical expressions, look-up tables, or computed by a thermodynamics software. As ASPECT uses a variety of numerical methods and solvers, this also gives us the opportunity to compare different approaches of modelling the melting process. In particular, we will elaborate on the spatial and temporal resolution that is required to accurately model phase transitions, and show the potential of adaptive mesh refinement when applied to melt generation and transport. We will assess the advantages and disadvantages of iterating between fluid dynamics and chemical reactions derived from thermodynamic models within each time step, or decoupling them, allowing for different time step sizes. Beyond that, we will expand on the functionality required for an interface between computational thermodynamics and fluid dynamics models from the geodynamics side. Finally, using a simple example of melting of a two-phase, two-component system, we compare different time-stepping and solver schemes in terms of accuracy and efficiency, in dependence of the time scales of fluid flow and chemical reactions relative to each other. Our software provides a framework to integrate thermodynamic models in high resolution, 3d simulations of coupled magma/mantle dynamics, and can be used as a tool to study links between physical processes and geochemical signals in the Earth.

Proates a computer modelling system for power plant: Its description and application to heatrate improvement within PowerGen

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

Green, C.H.; Ready, A.B.; Rea, J.

1995-06-01

Versions of the computer program PROATES (PROcess Analysis for Thermal Energy Systems) have been used since 1979 to analyse plant performance improvement proposals relating to existing plant and also to evaluate new plant designs. Several plant modifications have been made to improve performance based on the model predictions and the predicted performance has been realised in practice. The program was born out of a need to model the overall steady state performance of complex plant to enable proposals to change plant component items or operating strategy to be evaluated. To do this with confidence it is necessary to model themore » multiple thermodynamic interactions between the plant components. The modelling system is modular in concept allowing the configuration of individual plant components to represent any particular power plant design. A library exists of physics based modules which have been extensively validated and which provide representations of a wide range of boiler, turbine and CW system components. Changes to model data and construction is achieved via a user friendly graphical model editing/analysis front-end with results being presented via the computer screen or hard copy. The paper describes briefly the modelling system but concentrates mainly on the application of the modelling system to assess design re-optimisation, firing with different fuels and the re-powering of an existing plant.« less

Global optimization algorithms to compute thermodynamic equilibria in large complex systems with performance considerations

DOE PAGES

Piro, M. H. A.; Simunovic, S.

2016-03-17

Several global optimization methods are reviewed that attempt to ensure that the integral Gibbs energy of a closed isothermal isobaric system is a global minimum to satisfy the necessary and sufficient conditions for thermodynamic equilibrium. In particular, the integral Gibbs energy function of a multicomponent system containing non-ideal phases may be highly non-linear and non-convex, which makes finding a global minimum a challenge. Consequently, a poor numerical approach may lead one to the false belief of equilibrium. Furthermore, confirming that one reaches a global minimum and that this is achieved with satisfactory computational performance becomes increasingly more challenging in systemsmore » containing many chemical elements and a correspondingly large number of species and phases. Several numerical methods that have been used for this specific purpose are reviewed with a benchmark study of three of the more promising methods using five case studies of varying complexity. A modification of the conventional Branch and Bound method is presented that is well suited to a wide array of thermodynamic applications, including complex phases with many constituents and sublattices, and ionic phases that must adhere to charge neutrality constraints. Also, a novel method is presented that efficiently solves the system of linear equations that exploits the unique structure of the Hessian matrix, which reduces the calculation from a O(N 3) operation to a O(N) operation. As a result, this combined approach demonstrates efficiency, reliability and capabilities that are favorable for integration of thermodynamic computations into multi-physics codes with inherent performance considerations.« less

Global optimization algorithms to compute thermodynamic equilibria in large complex systems with performance considerations

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

Piro, M. H. A.; Simunovic, S.

Several global optimization methods are reviewed that attempt to ensure that the integral Gibbs energy of a closed isothermal isobaric system is a global minimum to satisfy the necessary and sufficient conditions for thermodynamic equilibrium. In particular, the integral Gibbs energy function of a multicomponent system containing non-ideal phases may be highly non-linear and non-convex, which makes finding a global minimum a challenge. Consequently, a poor numerical approach may lead one to the false belief of equilibrium. Furthermore, confirming that one reaches a global minimum and that this is achieved with satisfactory computational performance becomes increasingly more challenging in systemsmore » containing many chemical elements and a correspondingly large number of species and phases. Several numerical methods that have been used for this specific purpose are reviewed with a benchmark study of three of the more promising methods using five case studies of varying complexity. A modification of the conventional Branch and Bound method is presented that is well suited to a wide array of thermodynamic applications, including complex phases with many constituents and sublattices, and ionic phases that must adhere to charge neutrality constraints. Also, a novel method is presented that efficiently solves the system of linear equations that exploits the unique structure of the Hessian matrix, which reduces the calculation from a O(N 3) operation to a O(N) operation. As a result, this combined approach demonstrates efficiency, reliability and capabilities that are favorable for integration of thermodynamic computations into multi-physics codes with inherent performance considerations.« less

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.

pK(A) in proteins solving the Poisson-Boltzmann equation with finite elements.

PubMed

Sakalli, Ilkay; Knapp, Ernst-Walter

2015-11-05

Knowledge on pK(A) values is an eminent factor to understand the function of proteins in living systems. We present a novel approach demonstrating that the finite element (FE) method of solving the linearized Poisson-Boltzmann equation (lPBE) can successfully be used to compute pK(A) values in proteins with high accuracy as a possible replacement to finite difference (FD) method. For this purpose, we implemented the software molecular Finite Element Solver (mFES) in the framework of the Karlsberg+ program to compute pK(A) values. This work focuses on a comparison between pK(A) computations obtained with the well-established FD method and with the new developed FE method mFES, solving the lPBE using protein crystal structures without conformational changes. Accurate and coarse model systems are set up with mFES using a similar number of unknowns compared with the FD method. Our FE method delivers results for computations of pK(A) values and interaction energies of titratable groups, which are comparable in accuracy. We introduce different thermodynamic cycles to evaluate pK(A) values and we show for the FE method how different parameters influence the accuracy of computed pK(A) values. © 2015 Wiley Periodicals, Inc.

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.

Qualitative and quantitative reasoning about thermodynamics

NASA Technical Reports Server (NTRS)

Skorstad, Gordon; Forbus, Ken

1989-01-01

One goal of qualitative physics is to capture the tacit knowledge of engineers and scientists. It is shown how Qualitative Process theory can be used to express concepts of engineering thermodynamics. In particular, it is shown how to integrate qualitative and quantitative knowledge to solve textbook problems involving thermodynamic cycles, such as gas turbine plants and steam power plants. These ideas were implemented in a program called SCHISM. Its analysis of a sample textbook problem is described and plans for future work are discussed.

A sub-grid, mixture-fraction-based thermodynamic equilibrium model for gas phase combustion in FIRETEC: development and results

Treesearch

M. M. Clark; T. H. Fletcher; R. R. Linn

2010-01-01

The chemical processes of gas phase combustion in wildland fires are complex and occur at length-scales that are not resolved in computational fluid dynamics (CFD) models of landscape-scale wildland fire. A new approach for modelling fire chemistry in HIGRAD/FIRETEC (a landscape-scale CFD wildfire model) applies a mixture– fraction model relying on thermodynamic...

Miscibility and Thermodynamics of Mixing of Different Models of Formamide and Water in Computer Simulation.

PubMed

Kiss, Bálint; Fábián, Balázs; Idrissi, Abdenacer; Szőri, Milán; Jedlovszky, Pál

2017-07-27

The thermodynamic changes that occur upon mixing five models of formamide and three models of water, including the miscibility of these model combinations itself, is studied by performing Monte Carlo computer simulations using an appropriately chosen thermodynamic cycle and the method of thermodynamic integration. The results show that the mixing of these two components is close to the ideal mixing, as both the energy and entropy of mixing turn out to be rather close to the ideal term in the entire composition range. Concerning the energy of mixing, the OPLS/AA_mod model of formamide behaves in a qualitatively different way than the other models considered. Thus, this model results in negative, while the other ones in positive energy of mixing values in combination with all three water models considered. Experimental data supports this latter behavior. Although the Helmholtz free energy of mixing always turns out to be negative in the entire composition range, the majority of the model combinations tested either show limited miscibility, or, at least, approach the miscibility limit very closely in certain compositions. Concerning both the miscibility and the energy of mixing of these model combinations, we recommend the use of the combination of the CHARMM formamide and TIP4P water models in simulations of water-formamide mixtures.

Entanglement entropy of dispersive media from thermodynamic entropy in one higher dimension.

PubMed

Maghrebi, M F; Reid, M T H

2015-04-17

A dispersive medium becomes entangled with zero-point fluctuations in the vacuum. We consider an arbitrary array of material bodies weakly interacting with a quantum field and compute the quantum mutual information between them. It is shown that the mutual information in D dimensions can be mapped to classical thermodynamic entropy in D+1 dimensions. As a specific example, we compute the mutual information both analytically and numerically for a range of separation distances between two bodies in D=2 dimensions and find a logarithmic correction to the area law at short separations. A key advantage of our method is that it allows the strong subadditivity property to be easily verified.

Solving traveling salesman problems with DNA molecules encoding numerical values.

PubMed

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

2004-12-01

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

An interactive computer lab of the galvanic cell for students in biochemistry.

PubMed

Ahlstrand, Emma; Buetti-Dinh, Antoine; Friedman, Ran

2018-01-01

We describe an interactive module that can be used to teach basic concepts in electrochemistry and thermodynamics to first year natural science students. The module is used together with an experimental laboratory and improves the students' understanding of thermodynamic quantities such as Δ r G, Δ r H, and Δ r S that are calculated but not directly measured in the lab. We also discuss how new technologies can substitute some parts of experimental chemistry courses, and improve accessibility to course material. Cloud computing platforms such as CoCalc facilitate the distribution of computer codes and allow students to access and apply interactive course tools beyond the course's scope. Despite some limitations imposed by cloud computing, the students appreciated the approach and the enhanced opportunities to discuss study questions with their classmates and instructor as facilitated by the interactive tools. © 2017 by The International Union of Biochemistry and Molecular Biology, 46(1):58-65, 2018. © 2017 The International Union of Biochemistry and Molecular Biology.

Thermodynamic and transport properties of spiro-(1,1')-bipyrrolidinium tetrafluoroborate and acetonitrile mixtures: A molecular dynamics study

NASA Astrophysics Data System (ADS)

Qing-Yin, Zhang; Peng, Xie; Xin, Wang; Xue-Wen, Yu; Zhi-Qiang, Shi; Shi-Huai, Zhao

2016-06-01

Organic salts such as spiro-(1,1')-bipyrrolidinium tetrafluoroborate ([SBP][BF4]) dissolved in liquid acetonitrile (ACN) are a new kind of organic salt solution, which is expected to be used as an electrolyte in electrical double layer capacitors (EDLCs). To explore the physicochemical properties of the solution, an all-atom force field is established on the basis of AMBER parameter values and quantum mechanical calculations. Molecular dynamics (MD) simulations are carried out to explore the liquid structure and physicochemical properties of [SBP][BF4] electrolyte at room temperature. The computed thermodynamic and transport properties match the available experimental results very well. The microscopic structures of [SBP][BF4] salt solution are also discussed in detail. The method used in this work provides an efficient way of predicting the properties of organic salt solvent as an electrolyte in EDLCs. Project supported by the National Natural Science Foundation of China (Grant Nos. 21476172 and 51172160), the National High Technology Research and Development Program of China (Grant No. 2013AA050905), and the Natural Science Foundation of Tianjin, China (Grant Nos. 12JCZDJC28400, 14RCHZGX00859, 14JCTPJC00484, and 14JCQNJC07200).

Black hole thermodynamics in Lovelock gravity's rainbow with (A)dS asymptote

NASA Astrophysics Data System (ADS)

Hendi, Seyed Hossein; Dehghani, Ali; Faizal, Mir

2017-01-01

In this paper, we combine Lovelock gravity with gravity's rainbow to construct Lovelock gravity's rainbow. Considering the Lovelock gravity's rainbow coupled to linear and also nonlinear electromagnetic gauge fields, we present two new classes of topological black hole solutions. We compute conserved and thermodynamic quantities of these black holes (such as temperature, entropy, electric potential, charge and mass) and show that these quantities satisfy the first law of thermodynamics. In order to study the thermal stability in canonical ensemble, we calculate the heat capacity and determinant of the Hessian matrix and show in what regions there are thermally stable phases for black holes. Also, we discuss the dependence of thermodynamic behavior and thermal stability of black holes on rainbow functions. Finally, we investigate the critical behavior of black holes in the extended phase space and study their interesting properties.

Finite-Size Effects of Binary Mutual Diffusion Coefficients from Molecular Dynamics

PubMed Central

2018-01-01

Molecular dynamics simulations were performed for the prediction of the finite-size effects of Maxwell-Stefan diffusion coefficients of molecular mixtures and a wide variety of binary Lennard–Jones systems. A strong dependency of computed diffusivities on the system size was observed. Computed diffusivities were found to increase with the number of molecules. We propose a correction for the extrapolation of Maxwell–Stefan diffusion coefficients to the thermodynamic limit, based on the study by Yeh and Hummer (J. Phys. Chem. B, 2004, 108, 15873−15879). The proposed correction is a function of the viscosity of the system, the size of the simulation box, and the thermodynamic factor, which is a measure for the nonideality of the mixture. Verification is carried out for more than 200 distinct binary Lennard–Jones systems, as well as 9 binary systems of methanol, water, ethanol, acetone, methylamine, and carbon tetrachloride. Significant deviations between finite-size Maxwell–Stefan diffusivities and the corresponding diffusivities at the thermodynamic limit were found for mixtures close to demixing. In these cases, the finite-size correction can be even larger than the simulated (finite-size) Maxwell–Stefan diffusivity. Our results show that considering these finite-size effects is crucial and that the suggested correction allows for reliable computations. PMID:29664633

Adsorption Behavior, Thermodynamics, and Kinetics of the Methanol Decomposition Reaction on defective graphene-supported Pt13

NASA Astrophysics Data System (ADS)

Gasper, Raymond; Ramasubramaniam, Ashwin

Defective graphene has been shown experimentally to be an excellent support for transition-metal electrocatalysts in direct methanol fuel cells. Prior computational modeling has shown that the improved catalytic activity of graphene-supported metal clusters is in part due to increased resistance to catalyst sintering and CO poisoning, but the increased reaction rate for the methanol decomposition reaction (MDR) is not yet fully explained. Using DFT, we investigate the adsorption of MDR intermediates and reaction thermodynamics on defective graphene-supported Pt13 nanoclusters with realistic, low-symmetry morphologies. We find that the support-induced shifts in Pt13 electronic structure correlate well with a rigid shift in adsorption of MDR intermediates, and that adsorption energy scaling relationships perform well on the low-symmetry surface. We investigate the reaction kinetics and thermodynamics, including testing the effectiveness of scaling relationships for predicting reaction barriers on the nanoclusters. Using these fundamental data, we perform microkinetic modeling to quantify the effect of the support on the MDR, and to understand how the support influences surface coverages, CO poisoning, and the relationships between reaction pathways. Funded by U.S. Department of Energy under Award Number DE-SC0010610. Computational resources were provided by National Energy Research Scientific Computing Center.

Joint density-functional theory for energetics and spectroscopy in complex aqueous and nonaqueous solvents

NASA Astrophysics Data System (ADS)

Gunceler, Deniz

Solvents are of great importance in many technological applications, but are difficult to study using standard, off-the-shelf ab initio electronic structure methods. This is because a single configuration of molecular positions in the solvent (a "snapshot" of the fluid) is not necessarily representative of the thermodynamic average. To obtain any thermodynamic averages (e.g. free energies), the phase space of the solvent must be sampled, typically using molecular dynamics. This greatly increases the computational cost involved in studying solvated systems. Joint density-functional theory has made its mark by being a computationally efficient yet rigorous theory by which to study solvation. It replaces the need for thermodynamic sampling with an effective continuum description of the solvent environment that is in-principle exact, computationally efficient and intuitive (easier to interpret). It has been very successful in aqueous systems, with potential applications in (among others) energy materials discovery, catalysis and surface science. In this dissertation, we develop accurate and fast joint density functional theories for complex, non-aqueous solvent enviroments, including organic solvents and room temperature ionic liquids, as well as new methods for calculating electron excitation spectra in such systems. These theories are then applied to a range of physical problems, from dendrite formation in lithium-metal batteries to the optical spectra of solvated ions.

Computing Relative Free Energies of Solvation using Single Reference Thermodynamic Integration Augmented with Hamiltonian Replica Exchange.

PubMed

Khavrutskii, Ilja V; Wallqvist, Anders

2010-11-09

This paper introduces an efficient single-topology variant of Thermodynamic Integration (TI) for computing relative transformation free energies in a series of molecules with respect to a single reference state. The presented TI variant that we refer to as Single-Reference TI (SR-TI) combines well-established molecular simulation methodologies into a practical computational tool. Augmented with Hamiltonian Replica Exchange (HREX), the SR-TI variant can deliver enhanced sampling in select degrees of freedom. The utility of the SR-TI variant is demonstrated in calculations of relative solvation free energies for a series of benzene derivatives with increasing complexity. Noteworthy, the SR-TI variant with the HREX option provides converged results in a challenging case of an amide molecule with a high (13-15 kcal/mol) barrier for internal cis/trans interconversion using simulation times of only 1 to 4 ns.

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

Pradhan, P., E-mail: pppradhan77@gmail.com

We derive various important thermodynamic relations of the inner and outer horizons in the background of the Taub–NUT (Newman–Unti–Tamburino) black hole in four-dimensional Lorentzian geometry. We compare these properties with the properties of the Reissner–Nordström black hole. We compute the area product, area sum, area subtraction, and area division of black hole horizons. We show that they all are not universal quantities. Based on these relations, we compute the area bound of all horizons. From the area bound, we derive an entropy bound and an irreducible mass bound for both horizons. We further study the stability of such black holesmore » by computing the specific heat for both horizons. It is shown that due to the negative specific heat, the black hole is thermodynamically unstable. All these calculations might be helpful in understanding the nature of the black hole entropy (both interior and exterior) at the microscopic level.« less

Simulations of thermodynamics and kinetics on rough energy landscapes with milestoning.

PubMed

Bello-Rivas, Juan M; Elber, Ron

2016-03-05

We investigated by computational means the kinetics and stationary behavior of stochastic dynamics on an ensemble of rough two-dimensional energy landscapes. There are no obvious separations of temporal scales in these systems, which constitute a simple model for the behavior of glasses and some biomaterials. Even though there are significant computational challenges present in these systems due to the large number of metastable states, the Milestoning method is able to compute their kinetic and thermodynamic properties exactly. We observe two clearly distinguished regimes in the overall kinetics: one in which diffusive behavior dominates and another that follows an Arrhenius law (despite the absence of a dominant barrier). We compare our results with those obtained with an exactly-solvable one-dimensional model, and with the results from the rough one-dimensional energy model introduced by Zwanzig. © 2015 Wiley Periodicals, Inc. © 2015 Wiley Periodicals, Inc.

User's guide to PHREEQC, a computer program for speciation, reaction-path, advective-transport, and inverse geochemical calculations

USGS Publications Warehouse

Parkhurst, D.L.

1995-01-01

PHREEQC is a computer program written in the C pwgranuning language that is designed to perform a wide variety of aqueous geochemical calculations. PHREEQC is based on an ion-association aqueous model and has capabilities for (1) speciation and saturation-index calculations, (2) reaction-path and advective-transport calculations involving specified irreversible reactions, mixing of solutions, mineral and gas equilibria surface-complex-ation reactions, and ion-exchange reactions, and (3) inverse modeling, which finds sets of mineral and gas mole transfers that account for composition differences between waters, within specified compositional uncertainties. PHREEQC is derived from the Fortran program PHREEQE, but it has been completely rewritten in C with the addition many new capabilities. New features include the capabilities to use redox couples to distribute redox elements among their valence states in speciation calculations; to model ion-exchange and surface-compiexation reactions; to model reactions with a fixed-pressure, multicomponent gas phase (that is, a gas bubble); to calculate the mass of water in the aqueous phase during reaction and transport calculations; to keep track of the moles of minerals present in the solid phases and determine antomaticaHy the thermodynamically stable phase assemblage; to simulate advective transport in combination with PHREEQC's reaction-modeling capability; and to make inverse modeling calculations that allow for uncertainties in the analytical data. The user interface is improved through the use of a simplified approach to redox reactions, which includes explicit mole-balance equations for hydrogen and oxygen; the use of a revised input that is modular and completely free format; and the use of mineral names and standard chemical symbolism rather than index numbers. The use of (2 eliminates nearly all limitations on army sizes, including numbers of elements, aqueous species, solutions, phases, and lengths of character strings. A new equation solver that optimizes a set of equalities subject to both equality and inequality constraints is used to determine the thermodynamically stable set of phases in equilibrium with a solution. A more complete Newton-Raphson formulation, master-species switching, and scaling of the algebraic equations reduce the number of failures of the nunmrical method in PHREEQC relative to PHREEQE. This report presents the equations that are the basis for chemical equilibrium and inverse-modeling calculations in PHREEQC, describes the input for the program, and presents twelve examples that demonstrate most of the program's capabilities.

Preparation and Extension of the Thermodynamics Program BLAKE and Its Library to 10,000 K for Use with Electrothermal-Chemical (ETC) Systems

DTIC Science & Technology

1994-07-01

AD-A283 642 0 ARMY RESEARCH LABORATORY • Preparation and Extension of the Thermodynamics Program BLAKE and Its Library to 10,000 K for Use With...unless so designated by other authorized documents. The use of trade names or manufacturers’ names in this report does not oonstitut indorsement of any...Offic. of Man4gemet and Budget. Papuork Iteductnion Progect (070404IM). Wmhwgton. DC 20503. 1. AGENCY USE ONLY (Leeve bink) 2. PORT DATE . 3. REPORT

ONEGUN: an interior ballistics code for closed breech guns

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

Reis, G.E.

1982-07-01

This program computes the gun and projectile motion and the gas thermodynamic properties (the internal ballistics) of a closed breech gun. Heat losses and friction losses are taken into account. A dual grain charge can be used. The inputs required are the usual propellant characteristics (density, impetus, gamma, burn rate coefficient and exponent, grain geometry, covolume and isochoric flame temperature). The gun characteristics (chamber volume and length, rifle twist rate, bore diameter, gun weight and start pressure) and the projectile characteristics (projectile weight, radius of gyration and start pressure). The output consists of the motion (displacement, velocity, and acceleration) ofmore » both the projectile and the recoiling gun and the gas pressures and temperature, all as a function of time.« less

Homogeneous processes of atmospheric interest

NASA Technical Reports Server (NTRS)

Rossi, M. J.; Barker, J. R.; Golden, D. M.

1983-01-01

Upper atmospheric research programs in the department of chemical kinetics are reported. Topics discussed include: (1) third-order rate constants of atmospheric importance; (2) a computational study of the HO2 + HO2 and DO2 + DO2 reactions; (3) measurement and estimation of rate constants for modeling reactive systems; (4) kinetics and thermodynamics of ion-molecule association reactions; (5) entropy barriers in ion-molecule reactions; (6) reaction rate constant for OH + HOONO2 yields products over the temperature range 246 to 324 K; (7) very low-pressure photolysis of tert-bytyl nitrite at 248 nm; (8) summary of preliminary data for the photolysis of C1ONO2 and N2O5 at 285 nm; and (9) heterogeneous reaction of N2O5 and H2O.

Analysis of opposed jet hydrogen-air counter flow diffusion flame

NASA Technical Reports Server (NTRS)

Ho, Y. H.; Isaac, K. M.

1989-01-01

A computational simulation of the opposed-jet diffusion flame is performed to study its structure and extinction limits. The present analysis concentrates on the nitrogen-diluted hydrogen-air diffusion flame, which provides the basic information for many vehicle designs such as the aerospace plane for which hydrogen is a candidate as the fuel. The computer program uses the time-marching technique to solve the energy and species equations coupled with the momentum equation solved by the collocation method. The procedure is implemented in two stages. In the first stage, a one-step forward overal chemical reaction is chosen with the gas phase chemical reaction rate determined by comparison with experimental data. In the second stage, a complete chemical reaction mechanism is introduced with detailed thermodynamic and transport property calculations. Comparison between experimental extinction data and theoretical predictions is discussed. The effects of thermal diffusion as well as Lewis number and Prandtl number variations on the diffusion flame are also presented.

Cascade Optimization Strategy with Neural Network and Regression Approximations Demonstrated on a Preliminary Aircraft Engine Design

NASA Technical Reports Server (NTRS)

Hopkins, Dale A.; Patnaik, Surya N.

2000-01-01

A preliminary aircraft engine design methodology is being developed that utilizes a cascade optimization strategy together with neural network and regression approximation methods. The cascade strategy employs different optimization algorithms in a specified sequence. The neural network and regression methods are used to approximate solutions obtained from the NASA Engine Performance Program (NEPP), which implements engine thermodynamic cycle and performance analysis models. The new methodology is proving to be more robust and computationally efficient than the conventional optimization approach of using a single optimization algorithm with direct reanalysis. The methodology has been demonstrated on a preliminary design problem for a novel subsonic turbofan engine concept that incorporates a wave rotor as a cycle-topping device. Computations of maximum thrust were obtained for a specific design point in the engine mission profile. The results (depicted in the figure) show a significant improvement in the maximum thrust obtained using the new methodology in comparison to benchmark solutions obtained using NEPP in a manual design mode.

Dephosphorization of complexly alloyed nickel melts under vacuum induction melting conditions: I. Thermodynamics of dephosphorization

NASA Astrophysics Data System (ADS)

Burtsev, V. T.; Anuchkin, S. N.; Sidorov, V. V.; Rigin, V. E.

2013-01-01

A thermodynamic computer simulation of the oxidation potential of a gas-melt-ceramic (80 wt% MgO, 20 wt % Al2O3) system under vacuum induction furnace conditions is used to find that the major contribution to this potential at temperatures ranging from 1673 to 2273 K is made by a nickel melt with additives of nickel protoxide. This provides the possibility of oxidative dephosphorization of the metallic melt. The computation of the saturated vapor pressure of phosphorus compounds with the IIA group elements shows that the data obtained for magnesium, calcium, and barium metaphosphates and europium orthophosphate at 1873 K indicate the principal possibility of melt dephosphorization by the evaporation of these compounds under oxidative conditions.

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.

Phases and stability of non-uniform black strings

NASA Astrophysics Data System (ADS)

Emparan, Roberto; Luna, Raimon; Martínez, Marina; Suzuki, Ryotaku; Tanabe, Kentaro

2018-05-01

We construct solutions of non-uniform black strings in dimensions from D ≈ 9 all the way up to D = ∞, and investigate their thermodynamics and dynamical stability. Our approach employs the large- D perturbative expansion beyond the leading order, including corrections up to 1 /D 4. Combining both analytical techniques and relatively simple numerical solution of ODEs, we map out the ranges of parameters in which non-uniform black strings exist in each dimension and compute their thermodynamics and quasinormal modes with accuracy. We establish with very good precision the existence of Sorkin's critical dimension and we prove that not only the thermodynamic stability, but also the dynamic stability of the solutions changes at it.

Scalar charges and the first law of black hole thermodynamics

NASA Astrophysics Data System (ADS)

Astefanesei, Dumitru; Ballesteros, Romina; Choque, David; Rojas, Raúl

2018-07-01

We present a variational formulation of Einstein-Maxwell-dilaton theory in flat spacetime, when the asymptotic value of the scalar field is not fixed. We obtain the boundary terms that make the variational principle well posed and then compute the finite gravitational action and corresponding Brown-York stress tensor. We show that the total energy has a new contribution that depends on the asymptotic value of the scalar field and discuss the role of scalar charges for the first law of thermodynamics. We also extend our analysis to hairy black holes in Anti-de Sitter spacetime and investigate the thermodynamics of an exact solution that breaks the conformal symmetry of the boundary.

Finite-size polyelectrolyte bundles at thermodynamic equilibrium

NASA Astrophysics Data System (ADS)

Sayar, M.; Holm, C.

2007-01-01

We present the results of extensive computer simulations performed on solutions of monodisperse charged rod-like polyelectrolytes in the presence of trivalent counterions. To overcome energy barriers we used a combination of parallel tempering and hybrid Monte Carlo techniques. Our results show that for small values of the electrostatic interaction the solution mostly consists of dispersed single rods. The potential of mean force between the polyelectrolyte monomers yields an attractive interaction at short distances. For a range of larger values of the Bjerrum length, we find finite-size polyelectrolyte bundles at thermodynamic equilibrium. Further increase of the Bjerrum length eventually leads to phase separation and precipitation. We discuss the origin of the observed thermodynamic stability of the finite-size aggregates.

Solubility prediction, solvate and cocrystal screening as tools for rational crystal engineering.

PubMed

Loschen, Christoph; Klamt, Andreas

2015-06-01

The fact that novel drug candidates are becoming increasingly insoluble is a major problem of current drug development. Computational tools may address this issue by screening for suitable solvents or by identifying potential novel cocrystal formers that increase bioavailability. In contrast to other more specialized methods, the fluid phase thermodynamics approach COSMO-RS (conductor-like screening model for real solvents) allows for a comprehensive treatment of drug solubility, solvate and cocrystal formation and many other thermodynamics properties in liquids. This article gives an overview of recent COSMO-RS developments that are of interest for drug development and contains several new application examples for solubility prediction and solvate/cocrystal screening. For all property predictions COSMO-RS has been used. The basic concept of COSMO-RS consists of using the screening charge density as computed from first principles calculations in combination with fast statistical thermodynamics to compute the chemical potential of a compound in solution. The fast and accurate assessment of drug solubility and the identification of suitable solvents, solvate or cocrystal formers is nowadays possible and may be used to complement modern drug development. Efficiency is increased by avoiding costly quantum-chemical computations using a database of previously computed molecular fragments. COSMO-RS theory can be applied to a range of physico-chemical properties, which are of interest in rational crystal engineering. Most notably, in combination with experimental reference data, accurate quantitative solubility predictions in any solvent or solvent mixture are possible. Additionally, COSMO-RS can be extended to the prediction of cocrystal formation, which results in considerable predictive accuracy concerning coformer screening. In a recent variant costly quantum chemical calculations are avoided resulting in a significant speed-up and ease-of-use. © 2015 Royal Pharmaceutical Society.

Predicting RNA pseudoknot folding thermodynamics

PubMed Central

Cao, Song; Chen, Shi-Jie

2006-01-01

Based on the experimentally determined atomic coordinates for RNA helices and the self-avoiding walks of the P (phosphate) and C4 (carbon) atoms in the diamond lattice for the polynucleotide loop conformations, we derive a set of conformational entropy parameters for RNA pseudoknots. Based on the entropy parameters, we develop a folding thermodynamics model that enables us to compute the sequence-specific RNA pseudoknot folding free energy landscape and thermodynamics. The model is validated through extensive experimental tests both for the native structures and for the folding thermodynamics. The model predicts strong sequence-dependent helix-loop competitions in the pseudoknot stability and the resultant conformational switches between different hairpin and pseudoknot structures. For instance, for the pseudoknot domain of human telomerase RNA, a native-like and a misfolded hairpin intermediates are found to coexist on the (equilibrium) folding pathways, and the interplay between the stabilities of these intermediates causes the conformational switch that may underlie a human telomerase disease. PMID:16709732

Comparing contribution of flexural and planar modes to thermodynamic properties

NASA Astrophysics Data System (ADS)

Mann, Sarita; Rani, Pooja; Jindal, V. K.

2017-05-01

Graphene, the most studied and explored 2D structure has unusual thermal properties such as negative thermal expansion, high thermal conductivity etc. We have already studied the thermal expansion behavior and various thermodynamic properties of pure graphene like heat capacity, entropy and free energy. The results of thermal expansion and various thermodynamic properties match well with available theoretical studies. For a deeper understanding of these properties, we analyzed the contribution of each phonon branch towards the total value of the individual property. To compute these properties, the dynamical matrix was calculated using VASP code where the density functional perturbation theory (DFPT) is employed under quasi-harmonic approximation in interface with phonopy code. It is noticed that transverse mode has major contribution to negative thermal expansion and all branches have almost same contribution towards the various thermodynamic properties with the contribution of ZA mode being the highest.

Thermodynamics of Liquid Alkali Metals and Their Binary Alloys

NASA Astrophysics Data System (ADS)

Thakor, P. B.; Patel, Minal H.; Gajjar, P. N.; Jani, A. R.

2009-07-01

The theoretical investigation of thermodynamic properties like internal energy, entropy, Helmholtz free energy, heat of mixing (ΔE) and entropy of mixing (ΔS) of liquid alkali metals and their binary alloys are reported in the present paper. The effect of concentration on the thermodynamic properties of Ac1Bc2 alloy of the alkali-alkali elements is investigated and reported for the first time using our well established local pseudopotential. To investigate influence of exchange and correlation effects, we have used five different local field correction functions viz; Hartree(H), Taylor(T), Ichimaru and Utsumi(IU), Farid et al. (F) and Sarkar et al. (S). The increase of concentration C2, increases the internal energy and Helmholtz free energy of liquid alloy Ac1Bc2. The behavior of present computation is not showing any abnormality in the outcome and hence confirms the applicability of our model potential in explaining the thermodynamics of liquid binary alloys.

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

PubMed

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

2011-08-01

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

Thermodynamics of charged black holes with a nonlinear electrodynamics source

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

Gonzalez, Hernan A.; Hassaiene, Mokhtar; Martinez, Cristian

2009-11-15

We study the thermodynamical properties of electrically charged black hole solutions of a nonlinear electrodynamics theory defined by a power p of the Maxwell invariant, which is coupled to Einstein gravity in four and higher spacetime dimensions. Depending on the range of the parameter p, these solutions present different asymptotic behaviors. We compute the Euclidean action with the appropriate boundary term in the grand canonical ensemble. The thermodynamical quantities are identified and, in particular, the mass and the charge are shown to be finite for all classes of solutions. Interestingly, a generalized Smarr formula is derived and it is shownmore » that this latter encodes perfectly the different asymptotic behaviors of the black hole solutions. The local stability is analyzed by computing the heat capacity and the electrical permittivity and we find that a set of small black holes is locally stable. In contrast to the standard Reissner-Nordstroem solution, there is a first-order phase transition between a class of these nonlinear charged black holes and the Minkowski spacetime.« less

Long-ranged contributions to solvation free energies from theory and short-ranged models

PubMed Central

Remsing, Richard C.; Liu, Shule; Weeks, John D.

2016-01-01

Long-standing problems associated with long-ranged electrostatic interactions have plagued theory and simulation alike. Traditional lattice sum (Ewald-like) treatments of Coulomb interactions add significant overhead to computer simulations and can produce artifacts from spurious interactions between simulation cell images. These subtle issues become particularly apparent when estimating thermodynamic quantities, such as free energies of solvation in charged and polar systems, to which long-ranged Coulomb interactions typically make a large contribution. In this paper, we develop a framework for determining very accurate solvation free energies of systems with long-ranged interactions from models that interact with purely short-ranged potentials. Our approach is generally applicable and can be combined with existing computational and theoretical techniques for estimating solvation thermodynamics. We demonstrate the utility of our approach by examining the hydration thermodynamics of hydrophobic and ionic solutes and the solvation of a large, highly charged colloid that exhibits overcharging, a complex nonlinear electrostatic phenomenon whereby counterions from the solvent effectively overscreen and locally invert the integrated charge of the solvated object. PMID:26929375

USSR and Eastern Europe Scientific Abstracts, Engineering and Equipment, Number 31

DTIC Science & Technology

1977-04-18

average coefficient of air absorption is computed by the method of approximate replacement of the real spectrum by the graduated one. The entire range...end of transition area with an accuracy of 15%. Figures 5; References 7. USSR UDC 541.24:532.5 PARAMETRIC METHOD OF CALCULATION OF THERMODYNAMIC...12, 1976 Abstract No 12B723 by V. A. Polyanskiy] GLEBOV, G. A., and KOSHKIN, V. K. [Text] A method is presented for calculation of thermodynamic

Physico-chemical properties of aqueous drug solutions: From the basic thermodynamics to the advanced experimental and simulation results.

PubMed

Bellich, Barbara; Gamini, Amelia; Brady, John W; Cesàro, Attilio

2018-04-05

The physical chemical properties of aqueous solutions of model compounds are illustrated in relation to hydration and solubility issues by using three perspectives: thermodynamic, spectroscopic and molecular dynamics simulations. The thermodynamic survey of the fundamental backgrounds of concentration dependence and experimental solubility results show some peculiar behavior of aqueous solutions with several types of similar solutes. Secondly, the use of a variety of experimental spectroscopic devices, operating under different experimental conditions of dimension and frequency, has produced a large amount of structural and dynamic data on aqueous solutions showing the richness of the information produced, depending on where and how the experiment is carried out. Finally, the use of molecular dynamics computational work is presented to highlight how the different types of solute functional groups and surface topologies organize adjacent water molecules differently. The highly valuable contribution of computer simulation studies in providing molecular explanations for experimental deductions, either of a thermodynamic or spectroscopic nature, is shown to have changed the current knowledge of many aqueous solution processes. While this paper is intended to provide a collective view on the latest literature results, still the presentation aims at a tutorial explanation of the potentials of the three methodologies in the field of aqueous solutions of pharmaceutical molecules. Copyright © 2018. Published by Elsevier B.V.

Cantera and Cantera Electrolyte Thermodynamics Objects

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

John Hewson, Harry Moffat

Cantera is a suite of object-oriented software tools for problems involving chemical kinetics, thermodynamics, and/or transport processes. It is a multi-organizational effort to create and formulate high quality 0D and 1D constitutive modeling tools for reactive transport codes.Institutions involved with the effort include Sandia, MIT, Colorado School of Mines, U. Texas, NASA, and Oak Ridge National Labs. Specific to Sandia's contributions, the Cantera Electrolyte Thermo Objects (CETO) packages is comprised of add-on routines for Cantera that handle electrolyte thermochemistry and reactions within the overall Cantera package. Cantera is a C++ Cal Tech code that handles gas phase species transport, reaction,more » and thermodynamics. With this addition, Cantera can be extended to handle problems involving liquid phase reactions and transport in electrolyte systems, and phase equilibrium problemsinvolving concentrated electrolytes and gas/solid phases. A full treatment of molten salt thermodynamics and transport has also been implemented in CETO. The routines themselves consist of .cpp and .h files containing C++ objects that are derived from parent Cantera objects representing thermodynamic functions. They are linked unto the main Cantera libraries when requested by the user. As an addendum to the main thermodynamics objects, several utility applications are provided. The first is multiphase Gibbs free energy minimizer based on the vcs algorithm, called vcs_cantera. This code allows for the calculation of thermodynamic equilibrium in multiple phases at constant temperature and pressure. Note, a similar code capability exists already in Cantera. This version follows the same algorithm, but gas a different code-base starting point, and is used as a research tool for algorithm development. The second program, cttables, prints out tables of thermodynamic and kinetic information for thermodynamic and kinetic objects within Cantera. This program serves as a "Get the numbers out" utility for Cantera, and as such it is very useful as a verification tool. These add-on utilities are encapsulated into a directory structure named cantera_apps, whose installation uses autoconf and also utilizes Cantera's application environment (i.e., they utilize Cantera as a library).« less

Thermodynamic properties and transport coefficients of air thermal plasmas mixed with ablated vapors of Cu and polytetrafluoroethylene

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

Zhang, JunMin, E-mail: jmzhang@buaa.edu.cn, E-mail: guanyg@tsinghua.edu.cn; Lu, ChunRong; Guan, YongGang, E-mail: jmzhang@buaa.edu.cn, E-mail: guanyg@tsinghua.edu.cn

2015-10-15

Because the fault arc in aircraft electrical system often causes a fire, it is particularly important to analyze its energy and transfer for aircraft safety. The calculation of arc energy requires the basic parameters of the arc. This paper is mainly devoted to the calculations of equilibrium composition, thermodynamic properties (density, molar weight, enthalpy, and specific heat at constant pressure) and transport coefficients (thermal conductivity, electrical conductivity, and viscosity) of plasmas produced by a mixture of air, Cu, and polytetrafluoroethylene under the condition of local thermodynamic equilibrium. The equilibrium composition is determined by solving a system of equations around themore » number densities of each species. The thermodynamic properties are obtained according to the standard thermodynamic relationships. The transport coefficients are calculated using the Chapman-Enskog approximations. Results are presented in the temperature range from 3000 to 30 000 K for pressures of 0.08 and 0.1 MPa, respectively. The results are more accurate and are reliable reference data for theoretical analysis and computational simulation of the behavior of fault arc.« less

Using Articulate Virtual Laboratories in Teaching Energy Conversion at the U.S. Naval Academy.

ERIC Educational Resources Information Center

Wu, C.

1998-01-01

The Mechanical Engineering Department at the U.S. Naval Academy is currently evaluating a new teaching method which uses computer software. Utilizing the thermodynamic-based software CyclePad, Intelligent Computer Aided Instruction is incorporated in an advanced energy conversion course for Mechanical Engineering students. The CyclePad software…

Thermodynamic Constraints Improve Metabolic Networks.

PubMed

Krumholz, Elias W; Libourel, Igor G L

2017-08-08

In pursuit of establishing a realistic metabolic phenotypic space, the reversibility of reactions is thermodynamically constrained in modern metabolic networks. The reversibility constraints follow from heuristic thermodynamic poise approximations that take anticipated cellular metabolite concentration ranges into account. Because constraints reduce the feasible space, draft metabolic network reconstructions may need more extensive reconciliation, and a larger number of genes may become essential. Notwithstanding ubiquitous application, the effect of reversibility constraints on the predictive capabilities of metabolic networks has not been investigated in detail. Instead, work has focused on the implementation and validation of the thermodynamic poise calculation itself. With the advance of fast linear programming-based network reconciliation, the effects of reversibility constraints on network reconciliation and gene essentiality predictions have become feasible and are the subject of this study. Networks with thermodynamically informed reversibility constraints outperformed gene essentiality predictions compared to networks that were constrained with randomly shuffled constraints. Unconstrained networks predicted gene essentiality as accurately as thermodynamically constrained networks, but predicted substantially fewer essential genes. Networks that were reconciled with sequence similarity data and strongly enforced reversibility constraints outperformed all other networks. We conclude that metabolic network analysis confirmed the validity of the thermodynamic constraints, and that thermodynamic poise information is actionable during network reconciliation. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

An interactive graphics program to retrieve, display, compare, manipulate, curve fit, difference and cross plot wind tunnel data

NASA Technical Reports Server (NTRS)

Elliott, R. D.; Werner, N. M.; Baker, W. M.

1975-01-01

The Aerodynamic Data Analysis and Integration System (ADAIS), developed as a highly interactive computer graphics program capable of manipulating large quantities of data such that addressable elements of a data base can be called up for graphic display, compared, curve fit, stored, retrieved, differenced, etc., was described. The general nature of the system is evidenced by the fact that limited usage has already occurred with data bases consisting of thermodynamic, basic loads, and flight dynamics data. Productivity using ADAIS of five times that for conventional manual methods of wind tunnel data analysis is routinely achieved. In wind tunnel data analysis, data from one or more runs of a particular test may be called up and displayed along with data from one or more runs of a different test. Curves may be faired through the data points by any of four methods, including cubic spline and least squares polynomial fit up to seventh order.

Finite temperature effects on the X-ray absorption spectra of energy related materials

NASA Astrophysics Data System (ADS)

Pascal, Tod; Prendergast, David

2014-03-01

We elucidate the role of room-temperature-induced instantaneous structural distortions in the Li K-edge X-ray absorption spectra (XAS) of crystalline LiF, Li2SO4, Li2O, Li3N and Li2CO3 using high resolution X-ray Raman spectroscopy (XRS) measurements and first-principles density functional theory calculations within the eXcited electron and Core Hole (XCH) approach. Based on thermodynamic sampling via ab-initio molecular dynamics (MD) simulations, we find calculated XAS in much better agreement with experiment than those computed using the rigid crystal structure alone. We show that local instantaneous distortion of the atomic lattice perturbs the symmetry of the Li 1 s core-excited-state electronic structure, broadening spectral line-shapes and, in some cases, producing additional spectral features. This work was conducted within the Batteries for Advanced Transportation Technologies (BATT) Program, supported by the U.S. Department of Energy Vehicle Technologies Program under Contract No. DE-AC02-05CH11231.

TARGET/CRYOCHIL - THERMODYNAMIC ANALYSIS AND SUBSCALE MODELING OF SPACE-BASED ORBIT TRANSFER VEHICLE CRYOGENIC PROPELLANT RESUPPLY

NASA Technical Reports Server (NTRS)

Defelice, D. M.

1994-01-01

The resupply of the cryogenic propellants is an enabling technology for space-based transfer vehicles. As part of NASA Lewis's ongoing efforts in micro-gravity fluid management, thermodynamic analysis and subscale modeling techniques have been developed to support an on-orbit test bed for cryogenic fluid management technologies. These efforts have been incorporated into two FORTRAN programs, TARGET and CRYOCHIL. The TARGET code is used to determine the maximum temperature at which the filling of a given tank can be initiated and subsequently filled to a specified pressure and fill level without venting. The main process is the transfer of the energy stored in the thermal mass of the tank walls into the inflowing liquid. This process is modeled by examining the end state of the no-vent fill process. This state is assumed to be at thermal equilibrium between the tank and the fluid which is well mixed and saturated at the tank pressure. No specific assumptions are made as to the processes or the intermediate thermodynamic states during the filling. It is only assumed that the maximum tank pressure occurs at the final state. This assumption implies that, during the initial phases of the filling, the injected liquid must pass through the bulk vapor in such a way that it absorbs a sufficient amount of its superheat so that moderate tank pressures can be maintained. It is believed that this is an achievable design goal for liquid injection systems. TARGET can be run with any fluid for which the user has a properties data base. Currently it will only run for hydrogen, oxygen, and nitrogen since pressure-enthalpy data sets have been included for these fluids only. CRYOCHIL's primary function is to predict the optimum liquid charge to be injected for each of a series of charge-hold-vent chilldown cycles. This information can then be used with specified mass flow rates and valve response times to control a liquid injection system for tank chilldown operations. This will insure that the operations proceed quickly and efficiently. These programs are written in FORTRAN for batch execution on IBM 370 class mainframe computers. It requires 360K of RAM for execution. The standard distribution medium for this program is a 1600 BPI 9track magnetic tape in EBCDIC format. TARGET/CRYOCHIL was developed in 1988.

Density functional theory in the solid state

PubMed Central

Hasnip, Philip J.; Refson, Keith; Probert, Matt I. J.; Yates, Jonathan R.; Clark, Stewart J.; Pickard, Chris J.

2014-01-01

Density functional theory (DFT) has been used in many fields of the physical sciences, but none so successfully as in the solid state. From its origins in condensed matter physics, it has expanded into materials science, high-pressure physics and mineralogy, solid-state chemistry and more, powering entire computational subdisciplines. Modern DFT simulation codes can calculate a vast range of structural, chemical, optical, spectroscopic, elastic, vibrational and thermodynamic phenomena. The ability to predict structure–property relationships has revolutionized experimental fields, such as vibrational and solid-state NMR spectroscopy, where it is the primary method to analyse and interpret experimental spectra. In semiconductor physics, great progress has been made in the electronic structure of bulk and defect states despite the severe challenges presented by the description of excited states. Studies are no longer restricted to known crystallographic structures. DFT is increasingly used as an exploratory tool for materials discovery and computational experiments, culminating in ex nihilo crystal structure prediction, which addresses the long-standing difficult problem of how to predict crystal structure polymorphs from nothing but a specified chemical composition. We present an overview of the capabilities of solid-state DFT simulations in all of these topics, illustrated with recent examples using the CASTEP computer program. PMID:24516184

Calculating the Bending Modulus for Multicomponent Lipid Membranes in Different Thermodynamic Phases

PubMed Central

2013-01-01

We establish a computational approach to extract the bending modulus, KC, for lipid membranes from relatively small-scale molecular simulations. Fluctuations in the splay of individual pairs of lipids faithfully inform on KC in multicomponent membranes over a large range of rigidities in different thermodynamic phases. Predictions are validated by experiments even where the standard spectral analysis-based methods fail. The local nature of this method potentially allows its extension to calculations of KC in protein-laden membranes. PMID:24039553

A review of reaction rates and thermodynamic and transport properties for the 11-species air model for chemical and thermal nonequilibrium calculations to 30000 K

NASA Technical Reports Server (NTRS)

Gupta, Roop N.; Yos, Jerrold M.; Thompson, Richard A.

1989-01-01

Reaction rate coefficients and thermodynamic and transport properties are provided for the 11-species air model which can be used for analyzing flows in chemical and thermal nonequilibrium. Such flows will likely occur around currently planned and future hypersonic vehicles. Guidelines for determining the state of the surrounding environment are provided. Approximate and more exact formulas are provided for computing the properties of partially ionized air mixtures in such environments.

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.

Temperature dependence of strain energy and thermodynamic properties of V2 O5 -based single-walled nanotubes: Zone-folding approach.

PubMed

Porsev, Vitaly V; Bandura, Andrei V; Evarestov, Robert A

2016-06-15

A zone-folding approach is applied to estimate the thermodynamic properties of V2 O5 -based nanotubes. The results obtained are compared with those from the direct calculations. It is shown that the zone-folding approximation allows an accurate estimation of nanotube thermodynamic properties and gives a gain in computation time compared to their direct calculations. Both approaches show that temperature effects do not change the relative stability of V2 O5 free layers and nanotubes derived from the α- and γ-phase. The internal energy thermal contributions into the strain energy of nanotubes are small and can be ignored. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Applying the Coupled-Cluster Ansatz to Solids and Surfaces in the Thermodynamic Limit

NASA Astrophysics Data System (ADS)

Gruber, Thomas; Liao, Ke; Tsatsoulis, Theodoros; Hummel, Felix; Grüneis, Andreas

2018-04-01

Modern electronic structure theories can predict and simulate a wealth of phenomena in surface science and solid-state physics. In order to allow for a direct comparison with experiment, such ab initio predictions have to be made in the thermodynamic limit, substantially increasing the computational cost of many-electron wave-function theories. Here, we present a method that achieves thermodynamic limit results for solids and surfaces using the "gold standard" coupled cluster ansatz of quantum chemistry with unprecedented efficiency. We study the energy difference between carbon diamond and graphite crystals, adsorption energies of water on h -BN, as well as the cohesive energy of the Ne solid, demonstrating the increased efficiency and accuracy of coupled cluster theory for solids and surfaces.

Thermodynamic and related properties of parahydrogen from the triple point to 300 K at pressures to 1000 bar

NASA Technical Reports Server (NTRS)

Weber, L. A.

1975-01-01

Compressibility measurements and thermodynamic properties data for parahydrogen were extended to higher temperatures and pressures. Results of an experimental program are presented in the form of new pressure, volume and temperature data in the temperature range 23 to 300 K at pressures up to 800 bar. Also given are tables of thermodynamic properties on isobars to 1000 bar including density, internal energy, enthalpy, entropy, specific heats at constant volume and constant pressure, velocity of sound, and surface derivatives. The accuracy of the data is discussed and comparisons are made with previous data.

STATEQ: a nonlinear least-squares code for obtaining Martin thermodynamic representations of fluids in the gaseous and dense gaseous regions

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

Milora, S. L.

1976-02-01

The use of the code NLIN (IBM Share Program No. 1428) to obtain empirical thermodynamic pressure-volume-temperature (P-V-T) relationships for substances in the gaseous and dense gaseous states is described. When sufficient experimental data exist, the code STATEQ will provide least-squares estimates for the 21 parameters of the Martin model. Another code, APPROX, is described which also obtains parameter estimates for the model by making use of the approximate generalized behavior of fluids. Use of the codes is illustrated in obtaining thermodynamic representations for isobutane. (auth)

A subsequent closed-form description of propagated signaling phenomena in the membrane of an axon

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

Melendy, Robert F., E-mail: rfmelendy@liberty.edu

2016-05-15

I recently introduced a closed-form description of propagated signaling phenomena in the membrane of an axon [R.F. Melendy, Journal of Applied Physics 118, 244701 (2015)]. Those results demonstrate how intracellular conductance, the thermodynamics of magnetization, and current modulation, function together in generating an action potential in a unified, closed-form description. At present, I report on a subsequent closed-form model that unifies intracellular conductance and the thermodynamics of magnetization, with the membrane electric field, E{sub m}. It’s anticipated this work will compel researchers in biophysics, physical biology, and the computational neurosciences, to probe deeper into the classical and quantum features ofmore » membrane magnetization and signaling, informed by the computational features of this subsequent model.« less

Single-ion hydration thermodynamics from clusters to bulk solutions: Recent insights from molecular modeling

DOE PAGES

Vlcek, Lukas; Chialvo, Ariel A.

2016-01-03

The importance of single-ion hydration thermodynamic properties for understanding the driving forces of aqueous electrolyte processes, along with the impossibility of their direct experimental measurement, have prompted a large number of experimental, theoretical, and computational studies aimed at separating the cation and anion contributions. Here we provide an overview of historical approaches based on extrathermodynamic assumptions and more recent computational studies of single-ion hydration in order to evaluate the approximations involved in these methods, quantify their accuracy, reliability, and limitations in the light of the latest developments. Finally, we also offer new insights into the factors that influence the accuracymore » of ion–water interaction models and our views on possible ways to fill this substantial knowledge gap in aqueous physical chemistry.« less

The use of analytical sedimentation velocity to extract thermodynamic linkage.

PubMed

Cole, James L; Correia, John J; Stafford, Walter F

2011-11-01

For 25 years, the Gibbs Conference on Biothermodynamics has focused on the use of thermodynamics to extract information about the mechanism and regulation of biological processes. This includes the determination of equilibrium constants for macromolecular interactions by high precision physical measurements. These approaches further reveal thermodynamic linkages to ligand binding events. Analytical ultracentrifugation has been a fundamental technique in the determination of macromolecular reaction stoichiometry and energetics for 85 years. This approach is highly amenable to the extraction of thermodynamic couplings to small molecule binding in the overall reaction pathway. In the 1980s this approach was extended to the use of sedimentation velocity techniques, primarily by the analysis of tubulin-drug interactions by Na and Timasheff. This transport method necessarily incorporates the complexity of both hydrodynamic and thermodynamic nonideality. The advent of modern computational methods in the last 20 years has subsequently made the analysis of sedimentation velocity data for interacting systems more robust and rigorous. Here we review three examples where sedimentation velocity has been useful at extracting thermodynamic information about reaction stoichiometry and energetics. Approaches to extract linkage to small molecule binding and the influence of hydrodynamic nonideality are emphasized. These methods are shown to also apply to the collection of fluorescence data with the new Aviv FDS. Copyright © 2011 Elsevier B.V. All rights reserved.

The use of analytical sedimentation velocity to extract thermodynamic linkage

PubMed Central

Cole, James L.; Correia, John J.; Stafford, Walter F.

2011-01-01

For 25 years, the Gibbs Conference on Biothermodynamics has focused on the use of thermodynamics to extract information about the mechanism and regulation of biological processes. This includes the determination of equilibrium constants for macromolecular interactions by high precision physical measurements. These approaches further reveal thermodynamic linkages to ligand binding events. Analytical ultracentrifugation has been a fundamental technique in the determination of macromolecular reaction stoichiometry and energetics for 85 years. This approach is highly amenable to the extraction of thermodynamic couplings to small molecule binding in the overall reaction pathway. In the 1980’s this approach was extended to the use of sedimentation velocity techniques, primarily by the analysis of tubulin-drug interactions by Na and Timasheff. This transport method necessarily incorporates the complexity of both hydrodynamic and thermodynamic nonideality. The advent of modern computational methods in the last 20 years has subsequently made the analysis of sedimentation velocity data for interacting systems more robust and rigorous. Here we review three examples where sedimentation velocity has been useful at extracting thermodynamic information about reaction stoichiometry and energetics. Approaches to extract linkage to small molecule binding and the influence of hydrodynamic nonideality are emphasized. These methods are shown to also apply to the collection of fluorescence data with the new Aviv FDS. PMID:21703752

Quantitative Assessment of Thermodynamic Constraints on the Solution Space of Genome-Scale Metabolic Models

PubMed Central

Hamilton, Joshua J.; Dwivedi, Vivek; Reed, Jennifer L.

2013-01-01

Constraint-based methods provide powerful computational techniques to allow understanding and prediction of cellular behavior. These methods rely on physiochemical constraints to eliminate infeasible behaviors from the space of available behaviors. One such constraint is thermodynamic feasibility, the requirement that intracellular flux distributions obey the laws of thermodynamics. The past decade has seen several constraint-based methods that interpret this constraint in different ways, including those that are limited to small networks, rely on predefined reaction directions, and/or neglect the relationship between reaction free energies and metabolite concentrations. In this work, we utilize one such approach, thermodynamics-based metabolic flux analysis (TMFA), to make genome-scale, quantitative predictions about metabolite concentrations and reaction free energies in the absence of prior knowledge of reaction directions, while accounting for uncertainties in thermodynamic estimates. We applied TMFA to a genome-scale network reconstruction of Escherichia coli and examined the effect of thermodynamic constraints on the flux space. We also assessed the predictive performance of TMFA against gene essentiality and quantitative metabolomics data, under both aerobic and anaerobic, and optimal and suboptimal growth conditions. Based on these results, we propose that TMFA is a useful tool for validating phenotypes and generating hypotheses, and that additional types of data and constraints can improve predictions of metabolite concentrations. PMID:23870272

EASI - EQUILIBRIUM AIR SHOCK INTERFERENCE

NASA Technical Reports Server (NTRS)

Glass, C. E.

1994-01-01

New research on hypersonic vehicles, such as the National Aero-Space Plane (NASP), has raised concerns about the effects of shock-wave interference on various structural components of the craft. State-of-the-art aerothermal analysis software is inadequate to predict local flow and heat flux in areas of extremely high heat transfer, such as the surface impingement of an Edney-type supersonic jet. EASI revives and updates older computational methods for calculating inviscid flow field and maximum heating from shock wave interference. The program expands these methods to solve problems involving the six shock-wave interference patterns on a two-dimensional cylindrical leading edge with an equilibrium chemically reacting gas mixture (representing, for example, the scramjet cowl of the NASP). The inclusion of gas chemistry allows for a more accurate prediction of the maximum pressure and heating loads by accounting for the effects of high temperature on the air mixture. Caloric imperfections and specie dissociation of high-temperature air cause shock-wave angles, flow deflection angles, and thermodynamic properties to differ from those calculated by a calorically perfect gas model. EASI contains pressure- and temperature-dependent thermodynamic and transport properties to determine heating rates, and uses either a calorically perfect air model or an 11-specie, 7-reaction reacting air model at equilibrium with temperatures up to 15,000 K for the inviscid flowfield calculations. EASI solves the flow field and the associated maximum surface pressure and heat flux for the six common types of shock wave interference. Depending on the type of interference, the program solves for shock-wave/boundary-layer interaction, expansion-fan/boundary-layer interaction, attaching shear layer or supersonic jet impingement. Heat flux predictions require a knowledge (from experimental data or relevant calculations) of a pertinent length scale of the interaction. Output files contain flow-field information for the various shock-wave interference patterns and their associated maximum surface pressure and heat flux predictions. EASI is written in FORTRAN 77 for a DEC VAX 8500 series computer using the VAX/VMS operating system, and requires 75K of memory. The program is available on a 9-track 1600 BPI magnetic tape in DEC VAX BACKUP format. EASI was developed in 1989. DEC, VAX, and VMS are registered trademarks of the Digital Equipment Corporation.

Thermodynamics of Hydrophobic Amino Acids in Solution: A Combined Experimental–Computational Study

DOE PAGES

Song, Lingshuang; Yang, Lin; Meng, Jie; ...

2016-12-29

Here, we present a joint experimental-computational study to quantitatively describe the thermodynamics of hydrophobic leucine amino acids in aqueous solution. X-ray scattering data were acquired at a series of solute and salt concentrations to effectively measure inter-leucine interactions, indicating that a major scattering peak is observed consistently at q = 0.83 Å -1. Atomistic molecular dynamics simulations were then performed and compared with the scattering data, achieving high consistency at both small and wider scattering angles (q = 0$-$1.5 Å -1). This experimental-computational consistence enables a first glimpse of the leucineleucine interacting landscape, where two leucine molecules are aligned mostlymore » in a parallel fashion, as opposed to anti-parallel, but also allows us to derive effective leucine-leucine interactions in solution. Collectively, this combined approach of employing experimental scattering and molecular simulation enables a quantitative characterization on effective inter-molecular interactions of hydrophobic amino acids, critical for protein function and dynamics such as protein folding.« less

Thermodynamics of Hydrophobic Amino Acids in Solution: A Combined Experimental–Computational Study

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

Song, Lingshuang; Yang, Lin; Meng, Jie

Here, we present a joint experimental-computational study to quantitatively describe the thermodynamics of hydrophobic leucine amino acids in aqueous solution. X-ray scattering data were acquired at a series of solute and salt concentrations to effectively measure inter-leucine interactions, indicating that a major scattering peak is observed consistently at q = 0.83 Å -1. Atomistic molecular dynamics simulations were then performed and compared with the scattering data, achieving high consistency at both small and wider scattering angles (q = 0$-$1.5 Å -1). This experimental-computational consistence enables a first glimpse of the leucineleucine interacting landscape, where two leucine molecules are aligned mostlymore » in a parallel fashion, as opposed to anti-parallel, but also allows us to derive effective leucine-leucine interactions in solution. Collectively, this combined approach of employing experimental scattering and molecular simulation enables a quantitative characterization on effective inter-molecular interactions of hydrophobic amino acids, critical for protein function and dynamics such as protein folding.« less

Marcus canonical integral for non-Gaussian processes and its computation: pathwise simulation and tau-leaping algorithm.

PubMed

Li, Tiejun; Min, Bin; Wang, Zhiming

2013-03-14

The stochastic integral ensuring the Newton-Leibnitz chain rule is essential in stochastic energetics. Marcus canonical integral has this property and can be understood as the Wong-Zakai type smoothing limit when the driving process is non-Gaussian. However, this important concept seems not well-known for physicists. In this paper, we discuss Marcus integral for non-Gaussian processes and its computation in the context of stochastic energetics. We give a comprehensive introduction to Marcus integral and compare three equivalent definitions in the literature. We introduce the exact pathwise simulation algorithm and give the error analysis. We show how to compute the thermodynamic quantities based on the pathwise simulation algorithm. We highlight the information hidden in the Marcus mapping, which plays the key role in determining thermodynamic quantities. We further propose the tau-leaping algorithm, which advance the process with deterministic time steps when tau-leaping condition is satisfied. The numerical experiments and its efficiency analysis show that it is very promising.

Thermodynamics of organisms in the context of dynamic energy budget theory.

PubMed

Sousa, Tânia; Mota, Rui; Domingos, Tiago; Kooijman, S A L M

2006-11-01

We carry out a thermodynamic analysis to an organism. It is applicable to any type of organism because (1) it is based on a thermodynamic formalism applicable to all open thermodynamic systems and (2) uses a general model to describe the internal structure of the organism--the dynamic energy budget (DEB) model. Our results on the thermodynamics of DEB organisms are the following. (1) Thermodynamic constraints for the following types of organisms: (a) aerobic and exothermic, (b) anaerobic and exothermic, and (c) anaerobic and endothermic; showing that anaerobic organisms have a higher thermodynamic flexibility. (2) A way to compute the changes in the enthalpy and in the entropy of living biomass that accompany changes in growth rate solving the problem of evaluating the thermodynamic properties of biomass as a function of the amount of reserves. (3) Two expressions for Thornton's coefficient that explain its experimental variability and theoretically underpin its use in metabolic studies. (4) A mechanism that organisms in non-steady-state use to rid themselves of internal entropy production: "dilution of entropy production by growth." To demonstrate the practical applicability of DEB theory to quantify thermodynamic changes in organisms we use published data on Klebsiella aerogenes growing aerobically in a continuous culture. We obtain different values for molar entropies of the reserve and the structure of Klebsiella aerogenes proving that the reserve density concept of DEB theory is essential in discussions concerning (a) the relationship between organization and entropy and (b) the mechanism of storing entropy in new biomass. Additionally, our results suggest that the entropy of dead biomass is significantly different from the entropy of living biomass.

Coding considerations for standalone molecular dynamics simulations of atomistic structures

NASA Astrophysics Data System (ADS)

Ocaya, R. O.; Terblans, J. J.

2017-10-01

The laws of Newtonian mechanics allow ab-initio molecular dynamics to model and simulate particle trajectories in material science by defining a differentiable potential function. This paper discusses some considerations for the coding of ab-initio programs for simulation on a standalone computer and illustrates the approach by C language codes in the context of embedded metallic atoms in the face-centred cubic structure. The algorithms use velocity-time integration to determine particle parameter evolution for up to several thousands of particles in a thermodynamical ensemble. Such functions are reusable and can be placed in a redistributable header library file. While there are both commercial and free packages available, their heuristic nature prevents dissection. In addition, developing own codes has the obvious advantage of teaching techniques applicable to new problems.

RNA nanotechnology for computer design and in vivo computation

PubMed Central

Qiu, Meikang; Khisamutdinov, Emil; Zhao, Zhengyi; Pan, Cheryl; Choi, Jeong-Woo; Leontis, Neocles B.; Guo, Peixuan

2013-01-01

Molecular-scale computing has been explored since 1989 owing to the foreseeable limitation of Moore's law for silicon-based computation devices. With the potential of massive parallelism, low energy consumption and capability of working in vivo, molecular-scale computing promises a new computational paradigm. Inspired by the concepts from the electronic computer, DNA computing has realized basic Boolean functions and has progressed into multi-layered circuits. Recently, RNA nanotechnology has emerged as an alternative approach. Owing to the newly discovered thermodynamic stability of a special RNA motif (Shu et al. 2011 Nat. Nanotechnol. 6, 658–667 (doi:10.1038/nnano.2011.105)), RNA nanoparticles are emerging as another promising medium for nanodevice and nanomedicine as well as molecular-scale computing. Like DNA, RNA sequences can be designed to form desired secondary structures in a straightforward manner, but RNA is structurally more versatile and more thermodynamically stable owing to its non-canonical base-pairing, tertiary interactions and base-stacking property. A 90-nucleotide RNA can exhibit 490 nanostructures, and its loops and tertiary architecture can serve as a mounting dovetail that eliminates the need for external linking dowels. Its enzymatic and fluorogenic activity creates diversity in computational design. Varieties of small RNA can work cooperatively, synergistically or antagonistically to carry out computational logic circuits. The riboswitch and enzymatic ribozyme activities and its special in vivo attributes offer a great potential for in vivo computation. Unique features in transcription, termination, self-assembly, self-processing and acid resistance enable in vivo production of RNA nanoparticles that harbour various regulators for intracellular manipulation. With all these advantages, RNA computation is promising, but it is still in its infancy. Many challenges still exist. Collaborations between RNA nanotechnologists and computer scientists are necessary to advance this nascent technology. PMID:24000362

RNA nanotechnology for computer design and in vivo computation.

PubMed

Qiu, Meikang; Khisamutdinov, Emil; Zhao, Zhengyi; Pan, Cheryl; Choi, Jeong-Woo; Leontis, Neocles B; Guo, Peixuan

2013-10-13

Molecular-scale computing has been explored since 1989 owing to the foreseeable limitation of Moore's law for silicon-based computation devices. With the potential of massive parallelism, low energy consumption and capability of working in vivo, molecular-scale computing promises a new computational paradigm. Inspired by the concepts from the electronic computer, DNA computing has realized basic Boolean functions and has progressed into multi-layered circuits. Recently, RNA nanotechnology has emerged as an alternative approach. Owing to the newly discovered thermodynamic stability of a special RNA motif (Shu et al. 2011 Nat. Nanotechnol. 6, 658-667 (doi:10.1038/nnano.2011.105)), RNA nanoparticles are emerging as another promising medium for nanodevice and nanomedicine as well as molecular-scale computing. Like DNA, RNA sequences can be designed to form desired secondary structures in a straightforward manner, but RNA is structurally more versatile and more thermodynamically stable owing to its non-canonical base-pairing, tertiary interactions and base-stacking property. A 90-nucleotide RNA can exhibit 4⁹⁰ nanostructures, and its loops and tertiary architecture can serve as a mounting dovetail that eliminates the need for external linking dowels. Its enzymatic and fluorogenic activity creates diversity in computational design. Varieties of small RNA can work cooperatively, synergistically or antagonistically to carry out computational logic circuits. The riboswitch and enzymatic ribozyme activities and its special in vivo attributes offer a great potential for in vivo computation. Unique features in transcription, termination, self-assembly, self-processing and acid resistance enable in vivo production of RNA nanoparticles that harbour various regulators for intracellular manipulation. With all these advantages, RNA computation is promising, but it is still in its infancy. Many challenges still exist. Collaborations between RNA nanotechnologists and computer scientists are necessary to advance this nascent technology.

Characterization of real gas properties for space shuttle main engine fuel turbine and performance calculations

NASA Technical Reports Server (NTRS)

Harloff, G. J.

1986-01-01

Real thermodynamic and transport properties of hydrogen, steam, the SSME mixture, and air are developed. The SSME mixture properties are needed for the analysis of the space shuttle main engine fuel turbine. The mixture conditions for the gases, except air, are presented graphically over a temperature range from 800 to 1200 K, and a pressure range from 1 to 500 atm. Air properties are given over a temperature range of 320 to 500 K, which are within the bounds of the thermodynamics programs used, in order to provide mixture data which is more easily checked (than H2/H2O). The real gas property variation of the SSME mixture is quantified. Polynomial expressions, needed for future computer analysis, for viscosity, Prandtl number, and thermal conductivity are given for the H2/H2O SSME fuel turbine mixture at a pressure of 305 atm over a range of temperatures from 950 to 1140 K. These conditions are representative of the SSME turbine operation. Performance calculations are presented for the space shuttle main engine (SSME) fuel turbine. The calculations use the air equivalent concept. Progress towards obtaining the capability to evaluate the performance of the SSME fuel turbine, with the H2/H2O mixture, is described.

Structural and Thermodynamic Properties of the Argon Dimer: A Computational Chemistry Exercise in Quantum and Statistical Mechanics

ERIC Educational Resources Information Center

Halpern, Arthur M.

2010-01-01

Using readily available computational applications and resources, students can construct a high-level ab initio potential energy surface (PES) for the argon dimer. From this information, they can obtain detailed molecular constants of the dimer, including its dissociation energy, which compare well with experimental determinations. Using both…

Characterization of High Explosives and Other Energetic Compounds by Computational Chemistry and Molecular Modeling: Experiments for Undergraduate Curriculum

ERIC Educational Resources Information Center

Bumpus, John A.; Lewis, Anne; Stotts, Corey; Cramer, Christopher J.

2007-01-01

Experiments suited for the undergraduate instructional laboratory in which the heats of formation of several aliphatic and aromatic compounds are calculated, are described. The experiments could be used to introduce students to commercially available computational chemistry and its thermodynamics, while assess and compare the energy content of…

Including metabolite concentrations into flux balance analysis: thermodynamic realizability as a constraint on flux distributions in metabolic networks

PubMed Central

Hoppe, Andreas; Hoffmann, Sabrina; Holzhütter, Hermann-Georg

2007-01-01

Background In recent years, constrained optimization – usually referred to as flux balance analysis (FBA) – has become a widely applied method for the computation of stationary fluxes in large-scale metabolic networks. The striking advantage of FBA as compared to kinetic modeling is that it basically requires only knowledge of the stoichiometry of the network. On the other hand, results of FBA are to a large degree hypothetical because the method relies on plausible but hardly provable optimality principles that are thought to govern metabolic flux distributions. Results To augment the reliability of FBA-based flux calculations we propose an additional side constraint which assures thermodynamic realizability, i.e. that the flux directions are consistent with the corresponding changes of Gibb's free energies. The latter depend on metabolite levels for which plausible ranges can be inferred from experimental data. Computationally, our method results in the solution of a mixed integer linear optimization problem with quadratic scoring function. An optimal flux distribution together with a metabolite profile is determined which assures thermodynamic realizability with minimal deviations of metabolite levels from their expected values. We applied our novel approach to two exemplary metabolic networks of different complexity, the metabolic core network of erythrocytes (30 reactions) and the metabolic network iJR904 of Escherichia coli (931 reactions). Our calculations show that increasing network complexity entails increasing sensitivity of predicted flux distributions to variations of standard Gibb's free energy changes and metabolite concentration ranges. We demonstrate the usefulness of our method for assessing critical concentrations of external metabolites preventing attainment of a metabolic steady state. Conclusion Our method incorporates the thermodynamic link between flux directions and metabolite concentrations into a practical computational algorithm. The weakness of conventional FBA to rely on intuitive assumptions about the reversibility of biochemical reactions is overcome. This enables the computation of reliable flux distributions even under extreme conditions of the network (e.g. enzyme inhibition, depletion of substrates or accumulation of end products) where metabolite concentrations may be drastically altered. PMID:17543097

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

Molecular dynamics simulation studies of tailored nanostructured polymers

NASA Astrophysics Data System (ADS)

Liu, Lixin

With recent advancements in the synthesis and characterization of polymeric materials, scientists are able to create multi-scale novel polymers with various cases of chemical functionalities, diversified topologies, as well as cross-linking networks. Due to those remarkable achievements, there are a broad range of possible applications of smart polymers in catalysis, in environmental remediation, and especially in drug-delivery. Because of rising interest in developing therapeutic drug binding to specific treating target, polymer chemists are in particular interests in design and engineering the drug delivery materials to be not only bio-compatible, but also to be capable of self-assembly at various in-vivo physiological stimulus. Both experimental and theoretical work indicate that the thermodynamic properties relating to the hydrophobic effect play an important role in determining self-assembly process. At the same time, computational simulation and modeling are powerful instruments to contribute to microscopic thermodynamics' understanding toward self-assembly phenomenon. Along with statistical approaches, constructing empirical model based on simulation results would also help predict for further development of tailored nano-structured materials. My Research mainly focused on investigating physical and chemical characteristics of polymer materials through molecular dynamics simulation and probing the fundamental thermodynamic driving force of self-assembly behavior. We tried to surmount technological obstacles in computational chemistry and build an efficient scheme to identify the physical and chemical Feature of molecules, to reproduce underlying properties, to understand the origin of thermodynamic signatures, and to speed up current trial and error process in screening new materials.

A complete thermodynamic analysis of enzyme turnover links the free energy landscape to enzyme catalysis.

PubMed

Jones, Hannah B L; Wells, Stephen A; Prentice, Erica J; Kwok, Anthony; Liang, Liyin L; Arcus, Vickery L; Pudney, Christopher R

2017-09-01

Our understanding of how enzymes work is coloured by static structure depictions where the enzyme scaffold is presented as either immobile, or in equilibrium between well-defined static conformations. Proteins, however, exhibit a large degree of motion over a broad range of timescales and magnitudes and this is defined thermodynamically by the enzyme free energy landscape (FEL). The role and importance of enzyme motion is extremely contentious. Much of the challenge is in the experimental detection of so called 'conformational sampling' involved in enzyme turnover. Herein we apply combined pressure and temperature kinetics studies to elucidate the full suite of thermodynamic parameters defining an enzyme FEL as it relates to enzyme turnover. We find that the key thermodynamic parameters governing vibrational modes related to enzyme turnover are the isobaric expansivity term and the change in heat capacity for enzyme catalysis. Variation in the enzyme FEL affects these terms. Our analysis is supported by a range of biophysical and computational approaches that specifically capture information on protein vibrational modes and the FEL (all atom flexibility calculations, red edge excitation shift spectroscopy and viscosity studies) that provide independent evidence for our findings. Our data suggest that restricting the enzyme FEL may be a powerful strategy when attempting to rationally engineer enzymes, particularly to alter thermal activity. Moreover, we demonstrate how rational predictions can be made with a rapid computational approach. © 2017 Federation of European Biochemical Societies.

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.

Predicting structural properties of fluids by thermodynamic extrapolation

NASA Astrophysics Data System (ADS)

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

2018-05-01

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

Temperature of maximum density and excess thermodynamics of aqueous mixtures of methanol

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

González-Salgado, D.; Zemánková, K.; Noya, E. G.

In this work, we present a study of representative excess thermodynamic properties of aqueous mixtures of methanol over the complete concentration range, based on extensive computer simulation calculations. In addition to test various existing united atom model potentials, we have developed a new force-field which accurately reproduces the excess thermodynamics of this system. Moreover, we have paid particular attention to the behavior of the temperature of maximum density (TMD) in dilute methanol mixtures. The presence of a temperature of maximum density is one of the essential anomalies exhibited by water. This anomalous behavior is modified in a non-monotonous fashion bymore » the presence of fully miscible solutes that partly disrupt the hydrogen bond network of water, such as methanol (and other short chain alcohols). In order to obtain a better insight into the phenomenology of the changes in the TMD of water induced by small amounts of methanol, we have performed a new series of experimental measurements and computer simulations using various force fields. We observe that none of the force-fields tested capture the non-monotonous concentration dependence of the TMD for highly diluted methanol solutions.« less

Effects of N/C Ratio on Solidification Behaviors of Novel Nb-Bearing Austenitic Heat-Resistant Cast Steels for Exhaust Components of Gasoline Engines

NASA Astrophysics Data System (ADS)

Zhang, Yinhui; Li, Mei; Godlewski, Larry A.; Zindel, Jacob W.; Feng, Qiang

2017-03-01

In order to comply with more stringent environmental and fuel consumption regulations, novel Nb-bearing austenitic heat-resistant cast steels that withstand exhaust temperatures as high as 1,323 K (1,050 °C) is urgently demanded from automotive industries. In the current research, the solidification behavior of these alloys with variations of N/C ratio is investigated. Directional solidification methods were carried out to examine the microstructural development in mushy zones. Computational thermodynamic calculations under partial equilibrium conditions were performed to predict the solidification sequence of different phases. Microstructural characterization of the mushy zones indicates that N/C ratio significantly influenced the stability of γ-austenite and the precipitation temperature of NbC/Nb(C,N), thereby altering the solidification path, as well as the morphology and distribution of NbC/Nb(C,N) and γ-ferrite. The solidification sequence of different phases predicted by thermodynamic software agreed well with the experimental results, except the specific precipitation temperatures. The generated data and fundamental understanding will be helpful for the application of computational thermodynamic methods to predict the as-cast microstructure of Nb-bearing austenitic heat-resistant steels.

Predicting low-temperature free energy landscapes with flat-histogram Monte Carlo methods

NASA Astrophysics Data System (ADS)

Mahynski, Nathan A.; Blanco, Marco A.; Errington, Jeffrey R.; Shen, Vincent K.

2017-02-01

We present a method for predicting the free energy landscape of fluids at low temperatures from flat-histogram grand canonical Monte Carlo simulations performed at higher ones. We illustrate our approach for both pure and multicomponent systems using two different sampling methods as a demonstration. This allows us to predict the thermodynamic behavior of systems which undergo both first order and continuous phase transitions upon cooling using simulations performed only at higher temperatures. After surveying a variety of different systems, we identify a range of temperature differences over which the extrapolation of high temperature simulations tends to quantitatively predict the thermodynamic properties of fluids at lower ones. Beyond this range, extrapolation still provides a reasonably well-informed estimate of the free energy landscape; this prediction then requires less computational effort to refine with an additional simulation at the desired temperature than reconstruction of the surface without any initial estimate. In either case, this method significantly increases the computational efficiency of these flat-histogram methods when investigating thermodynamic properties of fluids over a wide range of temperatures. For example, we demonstrate how a binary fluid phase diagram may be quantitatively predicted for many temperatures using only information obtained from a single supercritical state.

Multiple Ion Binding Equilibria, Reaction Kinetics, and Thermodynamics in Dynamic Models of Biochemical Pathways

PubMed Central

Vinnakota, Kalyan C.; Wu, Fan; Kushmerick, Martin J.; Beard, Daniel A.

2009-01-01

The operation of biochemical systems in vivo and in vitro is strongly influenced by complex interactions between biochemical reactants and ions such as H+, Mg2+, K+, and Ca2+. These are important second messengers in metabolic and signaling pathways that directly influence the kinetics and thermodynamics of biochemical systems. Herein we describe the biophysical theory and computational methods to account for multiple ion binding to biochemical reactants and demonstrate the crucial effects of ion binding on biochemical reaction kinetics and thermodynamics. In simulations of realistic systems, the concentrations of these ions change with time due to dynamic buffering and competitive binding. In turn, the effective thermodynamic properties vary as functions of cation concentrations and important environmental variables such as temperature and overall ionic strength. Physically realistic simulations of biochemical systems require incorporating all of these phenomena into a coherent mathematical description. Several applications to physiological systems are demonstrated based on this coherent simulation framework. PMID:19216922

The importance of hydration thermodynamics in fragment-to-lead optimization.

PubMed

Ichihara, Osamu; Shimada, Yuzo; Yoshidome, Daisuke

2014-12-01

Using a computational approach to assess changes in solvation thermodynamics upon ligand binding, we investigated the effects of water molecules on the binding energetics of over 20 fragment hits and their corresponding optimized lead compounds. Binding activity and X-ray crystallographic data of published fragment-to-lead optimization studies from various therapeutically relevant targets were studied. The analysis reveals a distinct difference between the thermodynamic profile of water molecules displaced by fragment hits and those displaced by the corresponding optimized lead compounds. Specifically, fragment hits tend to displace water molecules with notably unfavorable excess entropies-configurationally constrained water molecules-relative to those displaced by the newly added moieties of the lead compound during the course of fragment-to-lead optimization. Herein we describe the details of this analysis with the goal of providing practical guidelines for exploiting thermodynamic signatures of binding site water molecules in the context of fragment-to-lead optimization. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Compositional Effects on Nickel-Base Superalloy Single Crystal Microstructures

NASA Technical Reports Server (NTRS)

MacKay, Rebecca A.; Gabb, Timothy P.; Garg,Anita; Rogers, Richard B.; Nathal, Michael V.

2012-01-01

Fourteen nickel-base superalloy single crystals containing 0 to 5 wt% chromium (Cr), 0 to 11 wt% cobalt (Co), 6 to 12 wt% molybdenum (Mo), 0 to 4 wt% rhenium (Re), and fixed amounts of aluminum (Al) and tantalum (Ta) were examined to determine the effect of bulk composition on basic microstructural parameters, including gamma' solvus, gamma' volume fraction, volume fraction of topologically close-packed (TCP) phases, phase chemistries, and gamma - gamma'. lattice mismatch. Regression models were developed to describe the influence of bulk alloy composition on the microstructural parameters and were compared to predictions by a commercially available software tool that used computational thermodynamics. Co produced the largest change in gamma' solvus over the wide compositional range used in this study, and Mo produced the largest effect on the gamma lattice parameter and the gamma - gamma' lattice mismatch over its compositional range, although Re had a very potent influence on all microstructural parameters investigated. Changing the Cr, Co, Mo, and Re contents in the bulk alloy had a significant impact on their concentrations in the gamma matrix and, to a smaller extent, in the gamma' phase. The gamma phase chemistries exhibited strong temperature dependencies that were influenced by the gamma and gamma' volume fractions. A computational thermodynamic modeling tool significantly underpredicted gamma' solvus temperatures and grossly overpredicted the amount of TCP phase at 982 C. Furthermore, the predictions by the software tool for the gamma - gamma' lattice mismatch were typically of the wrong sign and magnitude, but predictions could be improved if TCP formation was suspended within the software program. However, the statistical regression models provided excellent estimations of the microstructural parameters based on bulk alloy composition, thereby demonstrating their usefulness.

Water Hammer Simulations of MMH Propellant - New Capability Demonstration of the Generalized Fluid Flow Simulation Program

NASA Technical Reports Server (NTRS)

Burkhardt, Z.; Ramachandran, N.; Majumdar, A.

2017-01-01

Fluid Transient analysis is important for the design of spacecraft propulsion system to ensure structural stability of the system in the event of sudden closing or opening of the valve. Generalized Fluid System Simulation Program (GFSSP), a general purpose flow network code developed at NASA/MSFC is capable of simulating pressure surge due to sudden opening or closing of valve when thermodynamic properties of real fluid are available for the entire range of simulation. Specifically GFSSP needs an accurate representation of pressure-density relationship in order to predict pressure surge during a fluid transient. Unfortunately, the available thermodynamic property programs such as REFPROP, GASP or GASPAK does not provide the thermodynamic properties of Monomethylhydrazine (MMH). This paper will illustrate the process used for building a customized table of properties of state variables from available properties and speed of sound that is required by GFSSP for simulation. Good agreement was found between the simulations and measured data. This method can be adopted for modeling flow networks and systems with other fluids whose properties are not known in detail in order to obtain general technical insight. Rigorous code validation of this approach will be done and reported at a future date.

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

PubMed

Latella, Ivan; Pérez-Madrid, Agustín

2013-10-01

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

Thermodynamic aspects of reformulation of automotive fuels

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

Zudkevitch, D.; Murthy, A.K.S.; Gmehling, J.

1995-09-01

A study of procedures for measuring and predicting the RVP and the initial vapor emissions of reformulated gasoline blends which contain one or more oxygenated compounds, viz., Ethanol, MTBE, ETBE, and TAME is discussed. Two computer simulation methods were programmed and tested. In one method, Method A, the D-86 distillation data on the blend are used for predicting the blend`s RVP from a simulation of the Mini RVPE (RVP Equivalent) experiment. The other method, Method B, relies on analytical information (PIANO analyzes) on the nature of the base gasoline and utilizes classical thermodynamics for simulating the same RVPE, Mini experiment.more » Method B, also, predicts the composition and other properties of the initial vapor emission from the fuel. The results indicate that predictions made with both methods agree very well with experimental values. The predictions with Method B illustrate that the admixture of an oxygenate to a gasoline blend changes the volatility of the blend and, also, the composition of the vapor emission. From the example simulations, a blend with 10 vol % ethanol increases the RVP by about 0.8 psi. The accompanying vapor emission will contain about 15% ethanol. Similarly, the vapor emission of a fuel blend with 11 vol % MTBE was calculated to contain about 11 vol % MTBE. Predictions of the behavior of blends with ETBE and ETBE+Ethanol are also presented and discussed. Recognizing that quite some efforts have been invested in developing empirical correlations for predicting RVP, the writers consider the purpose of this paper to be pointing out that the methods of classical thermodynamics are adequate and that there is a need for additional work in developing certain fundamental data that are still lacking.« less

SteamTablesGrid: An ActiveX control for thermodynamic properties of pure water

NASA Astrophysics Data System (ADS)

Verma, Mahendra P.

2011-04-01

An ActiveX control, steam tables grid ( StmTblGrd) to speed up the calculation of the thermodynamic properties of pure water is developed. First, it creates a grid (matrix) for a specified range of temperature (e.g. 400-600 K with 40 segments) and pressure (e.g. 100,000-20,000,000 Pa with 40 segments). Using the ActiveX component SteamTables, the values of selected properties of water for each element (nodal point) of the 41×41 matrix are calculated. The created grid can be saved in a file for its reuse. A linear interpolation within an individual phase, vapor or liquid is implemented to calculate the properties at a given value of temperature and pressure. A demonstration program to illustrate the functionality of StmTblGrd is written in Visual Basic 6.0. Similarly, a methodology is presented to explain the use of StmTblGrd in MS-Excel 2007. In an Excel worksheet, the enthalpy of 1000 random datasets for temperature and pressure is calculated using StmTblGrd and SteamTables. The uncertainty in the enthalpy calculated with StmTblGrd is within ±0.03%. The calculations were performed on a personal computer that has a "Pentium(R) 4 CPU 3.2 GHz, RAM 1.0 GB" processor and Windows XP. The total execution time for the calculation with StmTblGrd was 0.3 s, while it was 60.0 s for SteamTables. Thus, the ActiveX control approach is reliable, accurate and efficient for the numerical simulation of complex systems that demand the thermodynamic properties of water at several values of temperature and pressure like steam flow in a geothermal pipeline network.

Connecting Free Energy Surfaces in Implicit and Explicit Solvent: an Efficient Method to Compute Conformational and Solvation Free Energies

PubMed Central

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

2015-01-01

The ability to accurately model solvent effects on free energy surfaces is important for understanding many biophysical processes including protein folding and misfolding, allosteric transitions and protein-ligand binding. Although all-atom simulations in explicit solvent can provide an accurate model for biomolecules in solution, explicit solvent simulations are hampered by the slow equilibration on rugged landscapes containing multiple basins separated by barriers. In many cases, implicit solvent models can be used to significantly speed up the conformational sampling; however, implicit solvent simulations do not fully capture the effects of a molecular solvent, and this can lead to loss of accuracy in the estimated free energies. Here we introduce a new approach to compute free energy changes in which the molecular details of explicit solvent simulations are retained while also taking advantage of the speed of the implicit solvent simulations. In this approach, the slow equilibration in explicit solvent, due to the long waiting times before barrier crossing, is avoided by using a thermodynamic cycle which connects the free energy basins in implicit solvent and explicit solvent using a localized decoupling scheme. We test this method by computing conformational free energy differences and solvation free energies of the model system alanine dipeptide in water. The free energy changes between basins in explicit solvent calculated using fully explicit solvent paths agree with the corresponding free energy differences obtained using the implicit/explicit thermodynamic cycle to within 0.3 kcal/mol out of ~3 kcal/mol at only ~8 % of the computational cost. We note that WHAM methods can be used to further improve the efficiency and accuracy of the explicit/implicit thermodynamic cycle. PMID:26236174

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

PubMed

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

2015-06-09

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

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.

Thermodynamic forces in coarse-grained simulations

NASA Astrophysics Data System (ADS)

Noid, William

Atomically detailed molecular dynamics simulations have profoundly advanced our understanding of the structure and interactions in soft condensed phases. Nevertheless, despite dramatic advances in the methodology and resources for simulating atomically detailed models, low-resolution coarse-grained (CG) models play a central and rapidly growing role in science. CG models not only empower researchers to investigate phenomena beyond the scope of atomically detailed simulations, but also to precisely tailor models for specific phenomena. However, in contrast to atomically detailed simulations, which evolve on a potential energy surface, CG simulations should evolve on a free energy surface. Therefore, the forces in CG models should reflect the thermodynamic information that has been eliminated from the CG configuration space. As a consequence of these thermodynamic forces, CG models often demonstrate limited transferability and, moreover, rarely provide an accurate description of both structural and thermodynamic properties. In this talk, I will present a framework that clarifies the origin and impact of these thermodynamic forces. Additionally, I will present computational methods for quantifying these forces and incorporating their effects into CG MD simulations. As time allows, I will demonstrate applications of this framework for liquids, polymers, and interfaces. We gratefully acknowledge the support of the National Science Foundation via CHE 1565631.

Equation of State of Detonation Products for TNT by Aquarium Technique

NASA Astrophysics Data System (ADS)

Han, Yong

2017-06-01

During explosive detonation, the detonation pressure (P) and temperature (T) will decay quickly with the expansion of detonation products, and the damage effect is determined by the thermodynamic state of detonation products under high pressure. The traditional and important method for calibrating the parameters of thermodynamic state is cylinder test, but the results showed that when the cylinder expanded to a certain distance, the cylinder wall would break up and the detonation products would jet out, which would affect the accuracy of the calibration parameters of thermodynamic state. In this paper, the aquarium technique was used to study the detonation product thermodynamic state of TNT explosive, obtaining the shock wave track under the water and the trace of the interface between water and detonation products in the specific position with the high speed rotating mirror camera. By thermodynamic calculation program BKW and VHL, the parameters of equation of state were obtained. Using the parameters and the dynamic software LS-DYNA, the underwater explosion of TNT was simulated. Comparison with experimental results shows that the thermodynamic state parameters which is calculated by VHL is more accurate than that of BKW. It is concluded that the aquarium test is a more effective method to calibrate the thermodynamic state than cylinder test.

Assessing exchange-correlation functionals for elasticity and thermodynamics of α -ZrW2O8 : A density functional perturbation theory study

NASA Astrophysics Data System (ADS)

Weck, Philippe F.; Kim, Eunja; Greathouse, Jeffery A.; Gordon, Margaret E.; Bryan, Charles R.

2018-04-01

Elastic and thermodynamic properties of negative thermal expansion (NTE) α -ZrW2O8 have been calculated using PBEsol and PBE exchange-correlation functionals within the framework of density functional perturbation theory (DFPT). Measured elastic constants are reproduced within ∼ 2 % with PBEsol and ∼ 6 % with PBE. The thermal evolution of the Grüneisen parameter computed within the quasi-harmonic approximation exhibits negative values below the Debye temperature, consistent with observation. The standard molar heat capacity is predicted to be CP0 = 192.2 and 193.8 J mol-1K-1 with PBEsol and PBE, respectively. These results suggest superior accuracy of DFPT/PBEsol for studying the lattice dynamics, elasticity and thermodynamics of NTE materials.

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

NASA Astrophysics Data System (ADS)

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

2018-06-01

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

Experimental determination of thermodynamic equilibrium in biocatalytic transamination.

PubMed

Tufvesson, Pär; Jensen, Jacob S; Kroutil, Wolfgang; Woodley, John M

2012-08-01

The equilibrium constant is a critical parameter for making rational design choices in biocatalytic transamination for the synthesis of chiral amines. However, very few reports are available in the scientific literature determining the equilibrium constant (K) for the transamination of ketones. Various methods for determining (or estimating) equilibrium have previously been suggested, both experimental as well as computational (based on group contribution methods). However, none of these were found suitable for determining the equilibrium constant for the transamination of ketones. Therefore, in this communication we suggest a simple experimental methodology which we hope will stimulate more accurate determination of thermodynamic equilibria when reporting the results of transaminase-catalyzed reactions in order to increase understanding of the relationship between substrate and product molecular structure on reaction thermodynamics. Copyright © 2012 Wiley Periodicals, Inc.

Probabilistic Analysis of Gas Turbine Field Performance

NASA Technical Reports Server (NTRS)

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

2002-01-01

A gas turbine thermodynamic cycle was computationally simulated and probabilistically evaluated in view of the several uncertainties in the performance parameters, which are indices of gas turbine health. Cumulative distribution functions and sensitivity factors were computed for the overall thermal efficiency and net specific power output due to the thermodynamic random variables. These results can be used to quickly identify the most critical design variables in order to optimize the design, enhance performance, increase system availability and make it cost effective. The analysis leads to the selection of the appropriate measurements to be used in the gas turbine health determination and to the identification of both the most critical measurements and parameters. Probabilistic analysis aims at unifying and improving the control and health monitoring of gas turbine aero-engines by increasing the quality and quantity of information available about the engine's health and performance.

Hot, cold, and annual reference atmospheres for Edwards Air Force Base, California (1975 version)

NASA Technical Reports Server (NTRS)

Johnson, D. L.

1975-01-01

Reference atmospheres pertaining to summer (hot), winter (cold), and mean annual conditions for Edwards Air Force Base, California, are presented from surface to 90 km altitude (700 km for the annual model). Computed values of pressure, kinetic temperature, virtual temperature, and density and relative differences percentage departure from the Edwards reference atmospheres, 1975 (ERA-75) of the atmospheric parameters versus altitude are tabulated in 250 m increments. Hydrostatic and gas law equations were used in conjunction with radiosonde and rocketsonde thermodynamic data in determining the vertical structure of these atmospheric models. The thermodynamic parameters were all subjected to a fifth degree least-squares curve-fit procedure, and the resulting coefficients were incorporated into Univac 1108 computer subroutines so that any quantity may be recomputed at any desired altitude using these subroutines.

Simple calculation of ab initio melting curves: Application to aluminum.

PubMed

Robert, Grégory; Legrand, Philippe; Arnault, Philippe; Desbiens, Nicolas; Clérouin, Jean

2015-03-01

We present a simple, fast, and promising method to compute the melting curves of materials with ab initio molecular dynamics. It is based on the two-phase thermodynamic model of Lin et al [J. Chem. Phys. 119, 11792 (2003)] and its improved version given by Desjarlais [Phys. Rev. E 88, 062145 (2013)]. In this model, the velocity autocorrelation function is utilized to calculate the contribution of the nuclei motion to the entropy of the solid and liquid phases. It is then possible to find the thermodynamic conditions of equal Gibbs free energy between these phases, defining the melting curve. The first benchmark on the face-centered cubic melting curve of aluminum from 0 to 300 GPa demonstrates how to obtain an accuracy of 5%-10%, comparable to the most sophisticated methods, for a much lower computational cost.

Ab-intio study of phonon and thermodynamic properties of Znic-blende ZnSe

NASA Astrophysics Data System (ADS)

Khatta, Swati; Kaur, Veerpal; Tripathi, S. K.; Prakash, Satya

2018-04-01

The Phonon and thermodynamic properties of ZnSe are investigated using density functional perturbation theory (DFPT) and quasi-harmonic approximation (QHA) implemented in Quantum espresso code. The phonon dispersion curve and phonon density of states of ZnSe are obtained. It is shown that high symmetries D→X and D→L directions, there are four branches of dispersion curves which split into six branches along the X→W, W→X and X→D directions. The LO-TO splitting frequencies (in cm-1) at the zone center (D point) are LO=255 and TO=215. The total and partial phonon density of states is used to compute the entropy and specific heat capacity of ZnSe. The computed values are in reasonable agreement with experimental data and other with available theoretical calculations.

On the mass and thermodynamics of the Higgs boson

NASA Astrophysics Data System (ADS)

Fokas, A. S.; Vayenas, C. G.; Grigoriou, D. P.

2018-02-01

In two recent works we have shown that the masses of the W± and Zo bosons can be computed from first principles by modeling these bosons as bound relativistic gravitationally confined rotational states consisting of e±-νe pairs in the case of W± bosons and of a e+-νe-e- triplet in the case of the Zo boson. Here, we present similar calculations for the Higgs boson which we model as a bound rotational state consisting of a positron, an electron, a neutrino and an antineutrino. The model contains no adjustable parameters and the computed boson mass of 125.7 GeV/c2, is in very good agreement with the experimental value of 125.1 ± 1 GeV/c2. The thermodynamics and potential connection of this particle with the Higgs field are also briefly addressed.

Computational Thermodynamics Analysis of Vaporizing Fuel Droplets in the Human Upper Airways

NASA Astrophysics Data System (ADS)

Zhang, Zhe; Kleinstreuer, Clement

The detailed knowledge of air flow structures as well as particle transport and deposition in the human lung for typical inhalation flow rates is an important precursor for dosimetry-and-health-effect studies of toxic particles as well as for targeted drug delivery of therapeutic aerosols. Focusing on highly toxic JP-8 fuel aerosols, 3-D airflow and fluid-particle thermodynamics in a human upper airway model starting from mouth to Generation G3 (G0 is the trachea) are simulated using a user-enhanced and experimentally validated finite-volume code. The temperature distributions and their effects on airflow structures, fuel vapor deposition and droplet motion/evaporation are discussed. The computational results show that the thermal effect on vapor deposition is minor, but it may greatly affect droplet deposition in human airways.

Solution for a bipartite Euclidean traveling-salesman problem in one dimension

NASA Astrophysics Data System (ADS)

Caracciolo, Sergio; Di Gioacchino, Andrea; Gherardi, Marco; Malatesta, Enrico M.

2018-05-01

The traveling-salesman problem is one of the most studied combinatorial optimization problems, because of the simplicity in its statement and the difficulty in its solution. We characterize the optimal cycle for every convex and increasing cost function when the points are thrown independently and with an identical probability distribution in a compact interval. We compute the average optimal cost for every number of points when the distance function is the square of the Euclidean distance. We also show that the average optimal cost is not a self-averaging quantity by explicitly computing the variance of its distribution in the thermodynamic limit. Moreover, we prove that the cost of the optimal cycle is not smaller than twice the cost of the optimal assignment of the same set of points. Interestingly, this bound is saturated in the thermodynamic limit.

Solution for a bipartite Euclidean traveling-salesman problem in one dimension.

PubMed

Caracciolo, Sergio; Di Gioacchino, Andrea; Gherardi, Marco; Malatesta, Enrico M

2018-05-01

The traveling-salesman problem is one of the most studied combinatorial optimization problems, because of the simplicity in its statement and the difficulty in its solution. We characterize the optimal cycle for every convex and increasing cost function when the points are thrown independently and with an identical probability distribution in a compact interval. We compute the average optimal cost for every number of points when the distance function is the square of the Euclidean distance. We also show that the average optimal cost is not a self-averaging quantity by explicitly computing the variance of its distribution in the thermodynamic limit. Moreover, we prove that the cost of the optimal cycle is not smaller than twice the cost of the optimal assignment of the same set of points. Interestingly, this bound is saturated in the thermodynamic limit.

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.

First-Principles Thermodynamics Study of Spinel MgAl 2 O 4 Surface Stability

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

Cai, Qiuxia; Wang, Jian-guo; Wang, Yong

The surface stability of all possible terminations for three low-index (111, 110, 100) structures of the spinel MgAl2O4 has been studied using first-principles based thermodynamic approach. The surface Gibbs free energy results indicate that the 100_AlO2 termination is the most stable surface structure under ultra-high vacuum at T=1100 K regardless of Al-poor or Al-rich environment. With increasing oxygen pressure, the 111_O2(Al) termination becomes the most stable surface in the Al-rich environment. The oxygen vacancy formation is thermodynamically favorable over the 100_AlO2, 111_O2(Al) and the (111) structure with Mg/O connected terminations. On the basis of surface Gibbs free energies for bothmore » perfect and defective surface terminations, the 100_AlO2 and 111_O2(Al) are the most dominant surfaces in Al-rich environment under atmospheric condition. This is also consistent with our previously reported experimental observation. This work was supported by a Laboratory Directed Research and Development (LDRD) project of the Pacific Northwest National Laboratory (PNNL). The computing time was granted by the National Energy Research Scientific Computing Center (NERSC). Part of computing time was also granted by a scientific theme user proposal in the William R. Wiley Environmental Molecular Sciences Laboratory (EMSL), which is a U.S. Department of Energy national scientific user facility located at PNNL in Richland, Washington.« less

Determination of partial molar volumes from free energy perturbation theory†

PubMed Central

Vilseck, Jonah Z.; Tirado-Rives, Julian

2016-01-01

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

Determination of partial molar volumes from free energy perturbation theory.

PubMed

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

2015-04-07

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

Consistent data-driven computational mechanics

NASA Astrophysics Data System (ADS)

González, D.; Chinesta, F.; Cueto, E.

2018-05-01

We present a novel method, within the realm of data-driven computational mechanics, to obtain reliable and thermodynamically sound simulation from experimental data. We thus avoid the need to fit any phenomenological model in the construction of the simulation model. This kind of techniques opens unprecedented possibilities in the framework of data-driven application systems and, particularly, in the paradigm of industry 4.0.

Computing Critical Properties with Yang-Yang Anomalies

NASA Astrophysics Data System (ADS)

Orkoulas, Gerassimos; Cerdeirina, Claudio; Fisher, Michael

2017-01-01

Computation of the thermodynamics of fluids in the critical region is a challenging task owing to divergence of the correlation length and lack of particle-hole symmetries found in Ising or lattice-gas models. In addition, analysis of experiments and simulations reveals a Yang-Yang (YY) anomaly which entails sharing of the specific heat singularity between the pressure and the chemical potential. The size of the YY anomaly is measured by the YY ratio Rμ =C μ /CV of the amplitudes of C μ = - T d2 μ /dT2 and of the total specific heat CV. A ``complete scaling'' theory, in which the pressure mixes into the scaling fields, accounts for the YY anomaly. In Phys. Rev. Lett. 116, 040601 (2016), compressible cell gas (CCG) models which exhibit YY and singular diameter anomalies, have been advanced for near-critical fluids. In such models, the individual cell volumes are allowed to fluctuate. The thermodynamics of CCGs can be computed through mapping onto the Ising model via the seldom-used great grand canonical ensemble. The computations indicate that local free volume fluctuations are the origins of the YY effects. Furthermore, local energy-volume coupling (to model water) is another crucial factor underlying the phenomena.

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.

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.

Interrelated structure of high altitude atmospheric profiles

NASA Technical Reports Server (NTRS)

Engler, N. A.; Goldschmidt, M. A.

1972-01-01

A preliminary development of a mathematical model to compute probabilities of thermodynamic profiles is presented. The model assumes an exponential expression for pressure and utilizes the hydrostatic law and equation of state in the determination of density and temperature. It is shown that each thermodynamic variable can be factored into the produce of steady state and perturbation functions. The steady state functions have profiles similar to those of the 1962 standard atmosphere while the perturbation functions oscillate about 1. Limitations of the model and recommendations for future work are presented.

Temperature specification in atomistic molecular dynamics and its impact on simulation efficacy

NASA Astrophysics Data System (ADS)

Ocaya, R. O.; Terblans, J. J.

2017-10-01

Temperature is a vital thermodynamical function for physical systems. Knowledge of system temperature permits assessment of system ergodicity, entropy, system state and stability. Rapid theoretical and computational developments in the fields of condensed matter physics, chemistry, material science, molecular biology, nanotechnology and others necessitate clarity in the temperature specification. Temperature-based materials simulations, both standalone and distributed computing, are projected to grow in prominence over diverse research fields. In this article we discuss the apparent variability of temperature modeling formalisms used currently in atomistic molecular dynamics simulations, with respect to system energetics,dynamics and structural evolution. Commercial simulation programs, which by nature are heuristic, do not openly discuss this fundamental question. We address temperature specification in the context of atomistic molecular dynamics. We define a thermostat at 400K relative to a heat bath at 300K firstly using a modified ab-initio Newtonian method, and secondly using a Monte-Carlo method. The thermostatic vacancy formation and cohesion energies, equilibrium lattice constant for FCC copper is then calculated. Finally we compare and contrast the results.

Experimental and Computational Interrogation of Fast SCR Mechanism and Active Sites on H-Form SSZ-13

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

Li, Sichi; Zheng, Yang; Gao, Feng

Experiment and density functional theory (DFT) models are combined to develop a unified, quantitative model of the mechanism and kinetics of fast selective catalytic reduction (SCR) of NO/NO2 mixtures over H-SSZ-13 zeolite. Rates, rate orders, and apparent activation energies collected under differential conditions reveal two distinct kinetic regimes. First-principles thermodynamics simulations are used to determine the relative coverages of free Brønsted sites, chemisorbed NH4+ and physisorbed NH3 as a function of reaction conditions. First-principles metadynamics calculations show that all three sites can contribute to the rate-limiting N-N bond forming step in fast SCR. The results are used to parameterize amore » kinetic model that encompasses the full range of reaction conditions and recovers observed rate orders and apparent activation energies. Observed kinetic regimes are related to changes in most-abundant surface intermediates. Financial support was provided by the National Science Foundation GAOLI program under award number 1258690-CBET. We thank the Center for Research Computing at Notre« less

GVIPS Models and Software

NASA Technical Reports Server (NTRS)

Arnold, Steven M.; Gendy, Atef; Saleeb, Atef F.; Mark, John; Wilt, Thomas E.

2007-01-01

Two reports discuss, respectively, (1) the generalized viscoplasticity with potential structure (GVIPS) class of mathematical models and (2) the Constitutive Material Parameter Estimator (COMPARE) computer program. GVIPS models are constructed within a thermodynamics- and potential-based theoretical framework, wherein one uses internal state variables and derives constitutive equations for both the reversible (elastic) and the irreversible (viscoplastic) behaviors of materials. Because of the underlying potential structure, GVIPS models not only capture a variety of material behaviors but also are very computationally efficient. COMPARE comprises (1) an analysis core and (2) a C++-language subprogram that implements a Windows-based graphical user interface (GUI) for controlling the core. The GUI relieves the user of the sometimes tedious task of preparing data for the analysis core, freeing the user to concentrate on the task of fitting experimental data and ultimately obtaining a set of material parameters. The analysis core consists of three modules: one for GVIPS material models, an analysis module containing a specialized finite-element solution algorithm, and an optimization module. COMPARE solves the problem of finding GVIPS material parameters in the manner of a design-optimization problem in which the parameters are the design variables.

Fist Principles Approach to the Magneto Caloric Effect: Application to Ni2MnGa

NASA Astrophysics Data System (ADS)

Odbadrakh, Khorgolkhuu; Nicholson, Don; Rusanu, Aurelian; Eisenbach, Markus; Brown, Gregory; Evans, Boyd, III

2011-03-01

The magneto-caloric effect (MCE) has potential application in heating and cooling technologies. In this work, we present calculated magnetic structure of a candidate MCE material, Ni 2 MnGa. The magnetic configurations of a 144 atom supercell is first explored using first-principle, the results are then used to fit exchange parameters of a Heisenberg Hamiltonian. The Wang-Landau method is used to calculate the magnetic density of states of the Heisenberg Hamiltonian. Based on this classical estimate, the magnetic density of states is calculated using the Wang Landau method with energies obtained from the first principles method. The Currie temperature and other thermodynamic properties are calculated using the density of states. The relationships between the density of magnetic states and the field induced adiabatic temperature change and isothermal entropy change are discussed. This work was sponsored by the Laboratory Directed Research and Development Program (ORNL), by the Mathematical, Information, and Computational Sciences Division; Office of Advanced Scientific Computing Research (US DOE), and by the Materials Sciences and Engineering Division; Office of Basic Energy Sciences (US DOE).

ABSIM. Simulation of Absorption Systems in Flexible and Modular Form

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

Grossman, G.

1994-06-01

The computer code has been developed for simulation of absorption systems at steady-state in a flexible and modular form, making it possible to investigate various cycle configurations with different working fluids. The code is based on unit subroutines containing the governing equations for the system`s components. When all the equations have been established, a mathematical solver routine is employed to solve them simultaneously. Property subroutines contained in a separate data base serve to provide thermodynamic properties of the working fluids. The code is user-oriented and requires a relatively simple input containing the given operating conditions and the working fluid atmore » each state point. the user conveys to the computer an image of the cycle by specifying the different components and their interconnections. Based on this information, the program calculates the temperature, flowrate, concentration, pressure and vapor fraction at each state point in the system and the heat duty at each unit, from which the coefficient of performance may be determined. A graphical user-interface is provided to facilitate interactive input and study of the output.« less

ABSIM. Simulation of Absorption Systems in Flexible and Modular Form

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

Grossman, G.

1994-06-01

The computer code has been developed for simulation of absorption systems at steady-state in a flexible and modular form, making it possible to investigate various cycle configurations with different working fluids. The code is based on unit subroutines containing the governing equations for the system's components. When all the equations have been established, a mathematical solver routine is employed to solve them simultaneously. Property subroutines contained in a separate data base serve to provide thermodynamic properties of the working fluids. The code is user-oriented and requires a relatively simple input containing the given operating conditions and the working fluid atmore » each state point. the user conveys to the computer an imagev of the cycle by specifying the different components and their interconnections. Based on this information, the program calculates the temperature, flowrate, concentration, pressure and vapor fraction at each state point in the system and the heat duty at each unit, from which the coefficient of performance may be determined. A graphical user-interface is provided to fcilitate interactive input and study of the output.« less

Fast-SNP: a fast matrix pre-processing algorithm for efficient loopless flux optimization of metabolic models

PubMed Central

Saa, Pedro A.; Nielsen, Lars K.

2016-01-01

Motivation: Computation of steady-state flux solutions in large metabolic models is routinely performed using flux balance analysis based on a simple LP (Linear Programming) formulation. A minimal requirement for thermodynamic feasibility of the flux solution is the absence of internal loops, which are enforced using ‘loopless constraints’. The resulting loopless flux problem is a substantially harder MILP (Mixed Integer Linear Programming) problem, which is computationally expensive for large metabolic models. Results: We developed a pre-processing algorithm that significantly reduces the size of the original loopless problem into an easier and equivalent MILP problem. The pre-processing step employs a fast matrix sparsification algorithm—Fast- sparse null-space pursuit (SNP)—inspired by recent results on SNP. By finding a reduced feasible ‘loop-law’ matrix subject to known directionalities, Fast-SNP considerably improves the computational efficiency in several metabolic models running different loopless optimization problems. Furthermore, analysis of the topology encoded in the reduced loop matrix enabled identification of key directional constraints for the potential permanent elimination of infeasible loops in the underlying model. Overall, Fast-SNP is an effective and simple algorithm for efficient formulation of loop-law constraints, making loopless flux optimization feasible and numerically tractable at large scale. Availability and Implementation: Source code for MATLAB including examples is freely available for download at http://www.aibn.uq.edu.au/cssb-resources under Software. Optimization uses Gurobi, CPLEX or GLPK (the latter is included with the algorithm). Contact: lars.nielsen@uq.edu.au Supplementary information: Supplementary data are available at Bioinformatics online. PMID:27559155

Quantitative assessment of thermodynamic constraints on the solution space of genome-scale metabolic models.

PubMed

Hamilton, Joshua J; Dwivedi, Vivek; Reed, Jennifer L

2013-07-16

Constraint-based methods provide powerful computational techniques to allow understanding and prediction of cellular behavior. These methods rely on physiochemical constraints to eliminate infeasible behaviors from the space of available behaviors. One such constraint is thermodynamic feasibility, the requirement that intracellular flux distributions obey the laws of thermodynamics. The past decade has seen several constraint-based methods that interpret this constraint in different ways, including those that are limited to small networks, rely on predefined reaction directions, and/or neglect the relationship between reaction free energies and metabolite concentrations. In this work, we utilize one such approach, thermodynamics-based metabolic flux analysis (TMFA), to make genome-scale, quantitative predictions about metabolite concentrations and reaction free energies in the absence of prior knowledge of reaction directions, while accounting for uncertainties in thermodynamic estimates. We applied TMFA to a genome-scale network reconstruction of Escherichia coli and examined the effect of thermodynamic constraints on the flux space. We also assessed the predictive performance of TMFA against gene essentiality and quantitative metabolomics data, under both aerobic and anaerobic, and optimal and suboptimal growth conditions. Based on these results, we propose that TMFA is a useful tool for validating phenotypes and generating hypotheses, and that additional types of data and constraints can improve predictions of metabolite concentrations. Copyright © 2013 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Thermodynamic Modeling and Analysis of Human Stress Response

NASA Technical Reports Server (NTRS)

Boregowda, S. C.; Tiwari, S. N.

1999-01-01

A novel approach based on the second law of thermodynamics is developed to investigate the psychophysiology and quantify human stress level. Two types of stresses (thermal and mental) are examined. A Unified Stress Response Theory (USRT) is developed under the new proposed field of study called Engineering Psychophysiology. The USRT is used to investigate both thermal and mental stresses from a holistic (human body as a whole) and thermodynamic viewpoint. The original concepts and definitions are established as postulates which form the basis for thermodynamic approach to quantify human stress level. An Objective Thermal Stress Index (OTSI) is developed by applying the second law of thermodynamics to the human thermal system to quantify thermal stress or dis- comfort in the human body. The human thermal model based on finite element method is implemented. It is utilized as a "Computational Environmental Chamber" to conduct series of simulations to examine the human thermal stress responses under different environmental conditions. An innovative hybrid technique is developed to analyze human thermal behavior based on series of human-environment interaction simulations. Continuous monitoring of thermal stress is demonstrated with the help of OTSI. It is well established that the human thermal system obeys the second law of thermodynamics. Further, the OTSI is validated against the experimental data. Regarding mental stress, an Objective Mental Stress Index (OMSI) is developed by applying the Maxwell relations of thermodynamics to the combined thermal and cardiovascular system in the human body. The OMSI is utilized to demonstrate the technique of monitoring mental stress continuously and is validated with the help of series of experimental studies. Although the OMSI indicates the level of mental stress, it provides a strong thermodynamic and mathematical relationship between activities of thermal and cardiovascular systems of the human body.

Thermodynamics of de Sitter Black Holes in Massive Gravity

NASA Astrophysics Data System (ADS)

Ma, Yu-Bo; Zhang, Si-Xuan; Wu, Yan; Ma, Li; Cao, Shuo

2018-05-01

In this paper, by taking de Sitter space-time as a thermodynamic system, we study the effective thermodynamic quantities of de Sitter black holes in massive gravity, and furthermore obtain the effective thermodynamic quantities of the space-time. Our results show that the entropy of this type of space-time takes the same form as that in Reissner-Nordström-de Sitter space-time, which lays a solid foundation for deeply understanding the universal thermodynamic characteristics of de Sitter space-time in the future. Moreover, our analysis indicates that the effective thermodynamic quantities and relevant parameters play a very important role in the investigation of the stability and evolution of de Sitter space-time. Supported by the Young Scientists Fund of the National Natural Science Foundation of China under Grant Nos. 11605107 and 11503001, the National Natural Science Foundation of China under Grant No. 11475108, Program for the Innovative Talents of Higher Learning Institutions of Shanxi, the Natural Science Foundation of Shanxi Province under Grant No. 201601D102004, the Natural Science Foundation for Young Scientists of Shanxi Province under Grant No. 201601D021022, and the Natural Science Foundation of Datong City under Grant No. 20150110

Steam tables for pure water as an ActiveX component in Visual Basic 6.0

NASA Astrophysics Data System (ADS)

Verma, Mahendra P.

2003-11-01

The IAPWS-95 formulation for the thermodynamic properties of pure water was implemented as an ActiveX component ( SteamTables) in Visual Basic 6.0. For input parameters as temperature ( T=190-2000 K) and pressure ( P=3.23×10 -8-10,000 MPa) the program SteamTables calculates the following properties: volume ( V), density ( D), compressibility factor ( Z0), internal energy ( U), enthalpy ( H), Gibbs free energy ( G), Helmholtz free energy ( A), entropy ( S), heat capacity at constant pressure ( Cp), heat capacity at constant volume ( Cv), coefficient of thermal expansion ( CTE), isothermal compressibility ( Ziso), velocity of sound ( VelS), partial derivative of P with T at constant V (d Pd T), partial derivative of T with V at constant P (d Td V), partial derivative of V with P at constant T (d Vd P), Joule-Thomson coefficient ( JTC), isothermal throttling coefficient ( IJTC), viscosity ( Vis), thermal conductivity ( ThrmCond), surface tension ( SurfTen), Prandtl number ( PrdNum) and dielectric constant ( DielCons) for the liquid and vapor phases of pure water. It also calculates T as a function of P (or P as a function of T) along the sublimation, saturation and critical isochor curves, depending on the values of P (or T). The SteamTables can be incorporated in a program in any computer language, which supports object link embedding (OLE) in the Windows environment. An application of SteamTables is illustrated in a program in Visual Basic 6.0 to tabulate the values of the thermodynamic properties of water and vapor. Similarly, four functions, Temperature(Press), Pressure(Temp), State(Temp, Press) and WtrStmTbls(Temp, Press, Nphs, Nprop), where Temp, Press, Nphs and Nprop are temperature, pressure, phase number and property number, respectively, are written in Visual Basic for Applications (VBA) to use the SteamTables in a workbook in MS-Excel.

A computational investigation of the thermodynamics and structure in colloid and polymer mixtures

NASA Astrophysics Data System (ADS)

Mahynski, Nathan Alexander

In this dissertation I use computational tools to study the structure and thermodynamics of colloid-polymer mixtures. I show that fluid-fluid phase separation in mixtures of colloids and linear polymers cannot be universally reduced using polymer-based scaling principles since these assume the binodals exist in a single scaling regime, whereas accurate simulations clearly demonstrate otherwise. I show that rethinking these solutions in terms of multiple length scales is necessary to properly explain the thermodynamic stability and structure of these fluid phases, and produce phase diagrams in nearly quantitative agreement with experimental results. I then extend this work to encompass more geometrically complex "star" polymers revealing how the phase behavior for many of these binary mixtures may be mapped onto that of mixtures containing only linear polymers. I further consider the depletion-driven crystallization of athermal colloidal hard spheres induced by polymers. I demonstrate how the partitioning of a finite amount of polymer into the colloidal crystal phase implies that the polymer's architecture can be tailored to interact with the internal void structure of different crystal polymorphs uniquely, thus providing a direct route to thermodynamically stabilizing one arbitrarily chosen structure over another, e.g., the hexagonal close-packed crystal over the face-centered cubic. I then begin to generalize this result by considering the consequences of thermal interactions and complex polymer architectures. These principles lay the groundwork for intelligently engineering co-solute additives in crystallizing colloidal suspensions that can be used to thermodynamically isolate single crystal morphologies. Finally, I examine the competition between self-assembly and phase separation in polymer-grafted nanoparticle systems by comparing and contrasting the validity of two different models for grafted nanoparticles: "nanoparticle amphiphiles" versus "patchy particles." The latter suggests these systems have some utility in forming novel "equilibrium gel" phases, however, I find that considering grafted nanoparticles as amphiphiles provides a qualitatively accurate description of their thermodynamics revealing either first-order phase separation into two isotropic phases or continuous self-assembly. I find no signs of empty liquid formation, suggesting that these nanoparticles do not provide a route to such phases.

Atmospheric aerosols: Their Optical Properties and Effects

NASA Technical Reports Server (NTRS)

1976-01-01

Measured properties of atmospheric aerosol particles are presented. These include aerosol size frequency distribution and complex retractive index. The optical properties of aerosols are computed based on the presuppositions of thermodynamic equilibrium and of Mie-theory.

A computer aided thermodynamic approach for predicting the formation of Z-DNA in naturally occurring sequences

NASA Technical Reports Server (NTRS)

Ho, P. S.; Ellison, M. J.; Quigley, G. J.; Rich, A.

1986-01-01

The ease with which a particular DNA segment adopts the left-handed Z-conformation depends largely on the sequence and on the degree of negative supercoiling to which it is subjected. We describe a computer program (Z-hunt) that is designed to search long sequences of naturally occurring DNA and retrieve those nucleotide combinations of up to 24 bp in length which show a strong propensity for Z-DNA formation. Incorporated into Z-hunt is a statistical mechanical model based on empirically determined energetic parameters for the B to Z transition accumulated to date. The Z-forming potential of a sequence is assessed by ranking its behavior as a function of negative superhelicity relative to the behavior of similar sized randomly generated nucleotide sequences assembled from over 80,000 combinations. The program makes it possible to compare directly the Z-forming potential of sequences with different base compositions and different sequence lengths. Using Z-hunt, we have analyzed the DNA sequences of the bacteriophage phi X174, plasmid pBR322, the animal virus SV40 and the replicative form of the eukaryotic adenovirus-2. The results are compared with those previously obtained by others from experiments designed to locate Z-DNA forming regions in these sequences using probes which show specificity for the left-handed DNA conformation.

Evaluating Thermodynamic Integration Performance of the New Amber Molecular Dynamics Package and Assess Potential Halogen Bonds of Enoyl-ACP Reductase (FabI) Benzimidazole Inhibitors

PubMed Central

Su, Pin-Chih; Johnson, Michael E.

2015-01-01

Thermodynamic integration (TI) can provide accurate binding free energy insights in a lead optimization program, but its high computational expense has limited its usage. In the effort of developing an efficient and accurate TI protocol for FabI inhibitors lead optimization program, we carefully compared TI with different Amber molecular dynamics (MD) engines (sander and pmemd), MD simulation lengths, the number of intermediate states and transformation steps, and the Lennard-Jones and Coulomb Softcore potentials parameters in the one-step TI, using eleven benzimidazole inhibitors in complex with Francisella tularensis enoyl acyl reductase (FtFabI). To our knowledge, this is the first study to extensively test the new AMBER MD engine, pmemd, on TI and compare the parameters of the Softcore potentials in the one-step TI in a protein-ligand binding system. The best performing model, the one-step pmemd TI, using 6 intermediate states and 1 ns MD simulations, provides better agreement with experimental results (RMSD = 0.52 kcal/mol) than the best performing implicit solvent method, QM/MM-GBSA from our previous study (RMSD = 3.00 kcal/mol), while maintaining similar efficiency. Briefly, we show the optimized TI protocol to be highly accurate and affordable for the FtFabI system. This approach can be implemented in a larger scale benzimidazole scaffold lead optimization against FtFabI. Lastly, the TI results here also provide structure-activity relationship insights, and suggest the para-halogen in benzimidazole compounds might form a weak halogen bond with FabI, which is a well-known halogen bond favoring enzyme. PMID:26666582

Evaluating thermodynamic integration performance of the new amber molecular dynamics package and assess potential halogen bonds of enoyl-ACP reductase (FabI) benzimidazole inhibitors.

PubMed

Su, Pin-Chih; Johnson, Michael E

2016-04-05

Thermodynamic integration (TI) can provide accurate binding free energy insights in a lead optimization program, but its high computational expense has limited its usage. In the effort of developing an efficient and accurate TI protocol for FabI inhibitors lead optimization program, we carefully compared TI with different Amber molecular dynamics (MD) engines (sander and pmemd), MD simulation lengths, the number of intermediate states and transformation steps, and the Lennard-Jones and Coulomb Softcore potentials parameters in the one-step TI, using eleven benzimidazole inhibitors in complex with Francisella tularensis enoyl acyl reductase (FtFabI). To our knowledge, this is the first study to extensively test the new AMBER MD engine, pmemd, on TI and compare the parameters of the Softcore potentials in the one-step TI in a protein-ligand binding system. The best performing model, the one-step pmemd TI, using 6 intermediate states and 1 ns MD simulations, provides better agreement with experimental results (RMSD = 0.52 kcal/mol) than the best performing implicit solvent method, QM/MM-GBSA from our previous study (RMSD = 3.00 kcal/mol), while maintaining similar efficiency. Briefly, we show the optimized TI protocol to be highly accurate and affordable for the FtFabI system. This approach can be implemented in a larger scale benzimidazole scaffold lead optimization against FtFabI. Lastly, the TI results here also provide structure-activity relationship insights, and suggest the parahalogen in benzimidazole compounds might form a weak halogen bond with FabI, which is a well-known halogen bond favoring enzyme. © 2015 Wiley Periodicals, Inc.

Simulation of existing gas-fuelled conventional steam power plant using Cycle Tempo

NASA Astrophysics Data System (ADS)

Jamel, M. S.; Abd Rahman, A.; Shamsuddin, A. H.

2013-06-01

Simulation of a 200 MW gas-fuelled conventional steam power plant located in Basra, Iraq was carried out. The thermodynamic performance of the considered power plant is estimated by a system simulation. A flow-sheet computer program, "Cycle-Tempo" is used for the study. The plant components and piping systems were considered and described in detail. The simulation results were verified against data gathered from the log sheet obtained from the station during its operation hours and good results were obtained. Operational factors like the stack exhaust temperature and excess air percentage were studied and discussed, as were environmental factors, such as ambient air temperature and water inlet temperature. In addition, detailed exergy losses were illustrated and describe the temperature profiles for the main plant components. The results prompted many suggestions for improvement of the plant performance.

Finite-rate chemistry effects upon convective and radiative heating of an atmospheric entry vehicle. [reentry aerothermochemistry

NASA Technical Reports Server (NTRS)

Guillermo, P.

1975-01-01

A mathematical model of the aerothermochemical environment along the stagnation line of a planetary return spacecraft using an ablative thermal protection system was developed and solved for conditions typical of atmospheric entry from planetary missions. The model, implemented as a FORTRAN 4 computer program, was designed to predict viscous, reactive and radiative coupled shock layer structure and the resulting body heating rates. The analysis includes flow field coupling with the ablator surface, binary diffusion, coupled line and continuum radiative and equilibrium or finite rate chemistry effects. The gas model used includes thermodynamic, transport, kinetic and radiative properties of air and ablation product species, including 19 chemical species and 16 chemical reactions. Specifically, the impact of nonequilibrium chemistry effects upon stagnation line shock layer structure and body heating rates was investigated.

Nitric Acid and Water Extraction by T2EHDGA in n -Dodecane

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

Campbell, Emily L.; Holfeltz, Vanessa E.; Hall, Gabriel B.

Liquid-liquid distribution behavior of nitric acid (HNO3) and water by a diglycolamide ligand, N,N,N',N'-tetra-2-ethylhexyldiglycolamide (T2EHDGA) into n-dodecane diluent was investigated. Spectroscopic FTIR and NMR characterization of the organic extraction solutions indicate T2EHDGA carbonyl coordinates HNO3 and progressively aggregates at high acid conditions. Water extraction increases in the presence of HNO3. The experimentally observed distribution of HNO3 was modeled using the computer program, SXLSQI. The results indicated that the formation of two organic phase species—HNO3·T2EHDGA and (HNO3)2·T2EHDGA—satisfactory describes the acid transport behavior. Temperature dependent solvent extraction studies allowed for determination of thermodynamic extraction constants and ΔH and ΔS parameters for themore » corresponding extractive processes.« less

Computation of Phase Equilibria, State Diagrams and Gas/Particle Partitioning of Mixed Organic-Inorganic Aerosols

NASA Astrophysics Data System (ADS)

Zuend, A.; Marcolli, C.; Peter, T.

2009-04-01

The chemical composition of organic-inorganic aerosols is linked to several processes and specific topics in the field of atmospheric aerosol science. Photochemical oxidation of organics in the gas phase lowers the volatility of semi-volatile compounds and contributes to the particulate matter by gas/particle partitioning. Heterogeneous chemistry and changes in the ambient relative humidity influence the aerosol composition as well. Molecular interactions between condensed phase species show typically non-ideal thermodynamic behavior. Liquid-liquid phase separations into a mainly polar, aqueous and a less polar, organic phase may considerably influence the gas/particle partitioning of semi-volatile organics and inorganics (Erdakos and Pankow, 2004; Chang and Pankow, 2006). Moreover, the phases present in the aerosol particles feed back on the heterogeneous, multi-phase chemistry, influence the scattering and absorption of radiation and affect the CCN ability of the particles. Non-ideal thermodynamic behavior in mixtures is usually described by an expression for the excess Gibbs energy, enabling the calculation of activity coefficients. We use the group-contribution model AIOMFAC (Zuend et al., 2008) to calculate activity coefficients, chemical potentials and the total Gibbs energy of mixed organic-inorganic systems. This thermodynamic model was combined with a robust global optimization module to compute potential liquid-liquid (LLE) and vapor-liquid-liquid equilibria (VLLE) as a function of particle composition at room temperature. And related to that, the gas/particle partitioning of semi-volatile components. Furthermore, we compute the thermodynamic stability (spinodal limits) of single-phase solutions, which provides information on the process type and kinetics of a phase separation. References Chang, E. I. and Pankow, J. F.: Prediction of activity coefficients in liquid aerosol particles containing organic compounds, dissolved inorganic salts, and water - Part 2: Consideration of phase separation effects by an XUNIFAC model, Atmos. Environ., 40, 6422-6436, 2006. Erdakos, G. B. and Pankow, J. F.: Gas/particle partitioning of neutral and ionizing compounds to single- and multi-phase aerosol particles. 2. Phase separation in liquid particulate matter containing both polar and low-polarity organic compounds, Atmos. Environ., 38, 1005-1013, 2004. Zuend, A., Marcolli, C., Luo, B. P., and Peter, T.: A thermodynamic model of mixed organic-inorganic aerosols to predict activity coefficients, Atmos. Chem. Phys., 8, 4559-4593, 2008.

Internal Flow Thermal/Fluid Modeling of STS-107 Port Wing in Support of the Columbia Accident Investigation Board

NASA Technical Reports Server (NTRS)

Sharp, John R.; Kittredge, Ken; Schunk, Richard G.

2003-01-01

As part of the aero-thermodynamics team supporting the Columbia Accident Investigation Board (CAB), the Marshall Space Flight Center was asked to perform engineering analyses of internal flows in the port wing. The aero-thermodynamics team was split into internal flow and external flow teams with the support being divided between shorter timeframe engineering methods and more complex computational fluid dynamics. In order to gain a rough order of magnitude type of knowledge of the internal flow in the port wing for various breach locations and sizes (as theorized by the CAB to have caused the Columbia re-entry failure), a bulk venting model was required to input boundary flow rates and pressures to the computational fluid dynamics (CFD) analyses. This paper summarizes the modeling that was done by MSFC in Thermal Desktop. A venting model of the entire Orbiter was constructed in FloCAD based on Rockwell International s flight substantiation analyses and the STS-107 reentry trajectory. Chemical equilibrium air thermodynamic properties were generated for SINDA/FLUINT s fluid property routines from a code provided by Langley Research Center. In parallel, a simplified thermal mathematical model of the port wing, including the Thermal Protection System (TPS), was based on more detailed Shuttle re-entry modeling previously done by the Dryden Flight Research Center. Once the venting model was coupled with the thermal model of the wing structure with chemical equilibrium air properties, various breach scenarios were assessed in support of the aero-thermodynamics team. The construction of the coupled model and results are presented herein.

Electronic structure, mechanical and thermodynamic properties of BaPaO3 under pressure.

PubMed

Khandy, Shakeel Ahmad; Islam, Ishtihadah; Gupta, Dinesh C; Laref, Amel

2018-05-07

Density functional theory (DFT)-based investigations have been put forward on the elastic, mechanical, and thermo-dynamical properties of BaPaO 3 . The pressure dependence of electronic band structure and other physical properties has been carefully analyzed. The increase in Bulk modulus and decrease in lattice constant is seen on going from 0 to 30 GPa. The predicted lattice constants describe this material as anisotropic and ductile in nature at ambient conditions. Post-DFT calculations using quasi-harmonic Debye model are employed to envisage the pressure-dependent thermodynamic properties like Debye temperature, specific heat capacity, Grüneisen parameter, thermal expansion, etc. Also, the computed Debye temperature and melting temperature of BaPaO 3 at 0 K are 523 K and 1764.75 K, respectively.

Communication: Non-Hadwiger terms in morphological thermodynamics of fluids

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

Hansen-Goos, Hendrik, E-mail: hendrik.hansen-goos@uni-tuebingen.de

We demonstrate that the Hadwiger form of the free energy of a fluid in contact with a wall is insufficient to describe the low-density behavior of a hard-sphere fluid. This implies that morphological thermodynamics of the hard-sphere fluid is an approximate theory if only four geometric measures are included. In order to quantify deviations from the Hadwiger form we extend standard fundamental measure theory of the bulk fluid by introducing additional scaled-particle variables which allow for the description of non-Hadwiger coefficients. The theory is in excellent agreement with recent computer simulations. The fact that the leading non-Hadwiger coefficient is onemore » order of magnitude smaller than the smallest Hadwiger coefficient lends confidence to the numerous results that have been previously obtained within standard morphological thermodynamics.« less

Integral equation and thermodynamic perturbation theory for a two-dimensional model of dimerising fluid

PubMed Central

Urbic, Tomaz

2016-01-01

In this paper we applied an analytical theory for the two dimensional dimerising fluid. We applied Wertheims thermodynamic perturbation theory (TPT) and integral equation theory (IET) for associative liquids to the dimerising model with arbitrary position of dimerising points from center of the particles. The theory was used to study thermodynamical and structural properties. To check the accuracy of the theories we compared theoretical results with corresponding results obtained by Monte Carlo computer simulations. The theories are accurate for the different positions of patches of the model at all values of the temperature and density studied. IET correctly predicts the pair correlation function of the model. Both TPT and IET are in good agreement with the Monte Carlo values of the energy, pressure, chemical potential, compressibility and ratios of free and bonded particles. PMID:28529396

Thermodynamics and Hawking radiation of five-dimensional rotating charged Goedel black holes

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

Wu Shuangqing; Peng Junjin; College of Science, Wuhan Textile University, Wuhan, Hubei 430074

2011-02-15

We study the thermodynamics of Goedel-type rotating charged black holes in five-dimensional minimal supergravity. These black holes exhibit some peculiar features such as the presence of closed timelike curves and the absence of a globally spatial-like Cauchy surface. We explicitly compute their energies, angular momenta, and electric charges that are consistent with the first law of thermodynamics. Besides, we extend the covariant anomaly cancellation method, as well as the approach of the effective action, to derive their Hawking fluxes. Both the methods of the anomaly cancellation and the effective action give the same Hawking fluxes as those from the Planckmore » distribution for blackbody radiation in the background of the charged rotating Goedel black holes. Our results further support that Hawking radiation is a quantum phenomenon arising at the event horizon.« less

Assessing exchange-correlation functionals for elasticity and thermodynamics of α - ZrW 2 O 8 : A density functional perturbation theory study

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

Weck, Philippe F.; Kim, Eunja; Greathouse, Jeffery A.

Elastic and thermodynamic properties of negative thermal expansion (NTE) αα-ZrW2O8 have been calculated using PBEsol and PBE exchange-correlation functionals within the framework of density functional perturbation theory (DFPT). Measured elastic constants are reproduced within ~2% with PBEsol and 6% with PBE. The thermal evolution of the Grüneisen parameter computed within the quasi-harmonic approximation exhibits negative values below the Debye temperature, consistent with observation. The standard molar heat capacity is predicted to be Cmore » $$O\\atop{P}$$=192.2 and 193.8 J mol -1K -1 with PBEsol and PBE, respectively. These results suggest superior accuracy of DFPT/PBEsol for studying the lattice dynamics, elasticity and thermodynamics of NTE materials.« less

Assessing exchange-correlation functionals for elasticity and thermodynamics of α - ZrW 2 O 8 : A density functional perturbation theory study

DOE PAGES

Weck, Philippe F.; Kim, Eunja; Greathouse, Jeffery A.; ...

2018-03-15

Elastic and thermodynamic properties of negative thermal expansion (NTE) αα-ZrW2O8 have been calculated using PBEsol and PBE exchange-correlation functionals within the framework of density functional perturbation theory (DFPT). Measured elastic constants are reproduced within ~2% with PBEsol and 6% with PBE. The thermal evolution of the Grüneisen parameter computed within the quasi-harmonic approximation exhibits negative values below the Debye temperature, consistent with observation. The standard molar heat capacity is predicted to be Cmore » $$O\\atop{P}$$=192.2 and 193.8 J mol -1K -1 with PBEsol and PBE, respectively. These results suggest superior accuracy of DFPT/PBEsol for studying the lattice dynamics, elasticity and thermodynamics of NTE materials.« less

A Low Mach Number Model for Moist Atmospheric Flows

DOE PAGES

Duarte, Max; Almgren, Ann S.; Bell, John B.

2015-04-01

A low Mach number model for moist atmospheric flows is introduced that accurately incorporates reversible moist processes in flows whose features of interest occur on advective rather than acoustic time scales. Total water is used as a prognostic variable, so that water vapor and liquid water are diagnostically recovered as needed from an exact Clausius–Clapeyron formula for moist thermodynamics. Low Mach number models can be computationally more efficient than a fully compressible model, but the low Mach number formulation introduces additional mathematical and computational complexity because of the divergence constraint imposed on the velocity field. Here in this paper, latentmore » heat release is accounted for in the source term of the constraint by estimating the rate of phase change based on the time variation of saturated water vapor subject to the thermodynamic equilibrium constraint. Finally, the authors numerically assess the validity of the low Mach number approximation for moist atmospheric flows by contrasting the low Mach number solution to reference solutions computed with a fully compressible formulation for a variety of test problems.« less

Extent of hydrogen coverage of Si(001) under chemical vapor deposition conditions from ab initio approaches

NASA Astrophysics Data System (ADS)

Rosenow, Phil; Tonner, Ralf

2016-05-01

The extent of hydrogen coverage of the Si(001) c(4 × 2) surface in the presence of hydrogen gas has been studied with dispersion corrected density functional theory. Electronic energy contributions are well described using a hybrid functional. The temperature dependence of the coverage in thermodynamic equilibrium was studied computing the phonon spectrum in a supercell approach. As an approximation to these demanding computations, an interpolated phonon approach was found to give comparable accuracy. The simpler ab initio thermodynamic approach is not accurate enough for the system studied, even if corrections by the Einstein model for surface vibrations are considered. The on-set of H2 desorption from the fully hydrogenated surface is predicted to occur at temperatures around 750 K. Strong changes in hydrogen coverage are found between 1000 and 1200 K in good agreement with previous reflectance anisotropy spectroscopy experiments. These findings allow a rational choice for the surface state in the computational treatment of chemical reactions under typical metal organic vapor phase epitaxy conditions on Si(001).

A Low Mach Number Model for Moist Atmospheric Flows

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

Duarte, Max; Almgren, Ann S.; Bell, John B.

A low Mach number model for moist atmospheric flows is introduced that accurately incorporates reversible moist processes in flows whose features of interest occur on advective rather than acoustic time scales. Total water is used as a prognostic variable, so that water vapor and liquid water are diagnostically recovered as needed from an exact Clausius–Clapeyron formula for moist thermodynamics. Low Mach number models can be computationally more efficient than a fully compressible model, but the low Mach number formulation introduces additional mathematical and computational complexity because of the divergence constraint imposed on the velocity field. Here in this paper, latentmore » heat release is accounted for in the source term of the constraint by estimating the rate of phase change based on the time variation of saturated water vapor subject to the thermodynamic equilibrium constraint. Finally, the authors numerically assess the validity of the low Mach number approximation for moist atmospheric flows by contrasting the low Mach number solution to reference solutions computed with a fully compressible formulation for a variety of test problems.« less

Extent of hydrogen coverage of Si(001) under chemical vapor deposition conditions from ab initio approaches

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

Rosenow, Phil; Tonner, Ralf, E-mail: tonner@chemie.uni-marburg.de

2016-05-28

The extent of hydrogen coverage of the Si(001) c(4 × 2) surface in the presence of hydrogen gas has been studied with dispersion corrected density functional theory. Electronic energy contributions are well described using a hybrid functional. The temperature dependence of the coverage in thermodynamic equilibrium was studied computing the phonon spectrum in a supercell approach. As an approximation to these demanding computations, an interpolated phonon approach was found to give comparable accuracy. The simpler ab initio thermodynamic approach is not accurate enough for the system studied, even if corrections by the Einstein model for surface vibrations are considered. Themore » on-set of H{sub 2} desorption from the fully hydrogenated surface is predicted to occur at temperatures around 750 K. Strong changes in hydrogen coverage are found between 1000 and 1200 K in good agreement with previous reflectance anisotropy spectroscopy experiments. These findings allow a rational choice for the surface state in the computational treatment of chemical reactions under typical metal organic vapor phase epitaxy conditions on Si(001).« less

CICE, The Los Alamos Sea Ice Model

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

Hunke, Elizabeth; Lipscomb, William; Jones, Philip

The Los Alamos sea ice model (CICE) is the result of an effort to develop a computationally efficient sea ice component for a fully coupled atmosphere–land–ocean–ice global climate model. It was originally designed to be compatible with the Parallel Ocean Program (POP), an ocean circulation model developed at Los Alamos National Laboratory for use on massively parallel computers. CICE has several interacting components: a vertical thermodynamic model that computes local growth rates of snow and ice due to vertical conductive, radiative and turbulent fluxes, along with snowfall; an elastic-viscous-plastic model of ice dynamics, which predicts the velocity field of themore » ice pack based on a model of the material strength of the ice; an incremental remapping transport model that describes horizontal advection of the areal concentration, ice and snow volume and other state variables; and a ridging parameterization that transfers ice among thickness categories based on energetic balances and rates of strain. It also includes a biogeochemical model that describes evolution of the ice ecosystem. The CICE sea ice model is used for climate research as one component of complex global earth system models that include atmosphere, land, ocean and biogeochemistry components. It is also used for operational sea ice forecasting in the polar regions and in numerical weather prediction models.« less

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

Simunovic, Srdjan; Piro, Markus H.A.

Thermochimica is a software library that determines a unique combination of phases and their compositions at thermochemical equilibrium. Thermochimica can be used for stand-alone calculations or it can be directly coupled to other codes. This release of the software does not have a graphical user interface (GUI) and it can be executed from the command line or from an Application Programming Interface (API). Also, it is not intended for thermodynamic model development or for constructing phase diagrams. The main purpose of the software is to be directly coupled with a multi-physics code to provide material properties and boundary conditions formore » various physical phenomena. Significant research efforts have been dedicated to enhance computational performance through advanced algorithm development, such as improved estimation techniques and non-linear solvers. Various useful parameters can be provided as output from Thermochimica, such as: determination of which phases are stable at equilibrium, the mass of solution species and phases at equilibrium, mole fractions of solution phase constituents, thermochemical activities (which are related to partial pressures for gaseous species), chemical potentials of solution species and phases, and integral Gibbs energy (referenced relative to standard state). The overall goal is to provide an open source computational tool to enhance the predictive capability of multi-physics codes without significantly impeding computational performance.« less

Thermodynamic evaluation of transonic compressor rotors using the finite volume approach

NASA Technical Reports Server (NTRS)

Moore, John; Nicholson, Stephen; Moore, Joan G.

1986-01-01

The development of a computational capability to handle viscous flow with an explicit time-marching method based on the finite volume approach is summarized. Emphasis is placed on the extensions to the computational procedure which allow the handling of shock induced separation and large regions of strong backflow. Appendices contain abstracts of papers and whole reports generated during the contract period.

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

Thermodynamic Properties of Actinides and Actinide Compounds

NASA Astrophysics Data System (ADS)

Konings, Rudy J. M.; Morss, Lester R.; Fuger, Jean

The necessity of obtaining accurate thermodynamic quantities for the actinide elements and their compounds was recognized at the outset of the Manhattan Project, when a dedicated team of scientists and engineers initiated the program to exploit nuclear energy for military purposes. Since the end of World War II, both fundamental and applied objectives have motivated a great deal of further study of actinide thermodynamics. This chapter brings together many research papers and critical reviews on this subject. It also seeks to assess, to systematize, and to predict important properties of the actinide elements, ions, and compounds, especially for species in which there is significant interest and for which there is an experimental basis for the prediction.

A new helium gas bearing turboexpander

NASA Astrophysics Data System (ADS)

Xiong, L. Y.; Chen, C. Z.; Liu, L. Q.; Hou, Y.; Wang, J.; Lin, M. F.

2002-05-01

A new helium gas bearing turboexpander of a helium refrigeration system used for space environment simulation experiments is described in this paper. The main design parameters and construction type of some key parts are presented. An improved calculation of thermodynamic efficiency and instability speed of this turboexpander has been obtained by a multiple objects optimization program. Experiments of examining mechanical and thermodynamic performance have been repeatedly conducted in the laboratory by using air at ambient and liquid nitrogen temperature, respectively. In order to predict the helium turboexpander performance, a similarity principles study has been developed. According to the laboratory and on-the-spot experiments, the mechanical and thermodynamic performances of this helium turboexpander are excellent.

General method and thermodynamic tables for computation of equilibrium composition and temperature of chemical reactions

NASA Technical Reports Server (NTRS)

Huff, Vearl N; Gordon, Sanford; Morrell, Virginia E

1951-01-01

A rapidly convergent successive approximation process is described that simultaneously determines both composition and temperature resulting from a chemical reaction. This method is suitable for use with any set of reactants over the complete range of mixture ratios as long as the products of reaction are ideal gases. An approximate treatment of limited amounts of liquids and solids is also included. This method is particularly suited to problems having a large number of products of reaction and to problems that require determination of such properties as specific heat or velocity of sound of a dissociating mixture. The method presented is applicable to a wide variety of problems that include (1) combustion at constant pressure or volume; and (2) isentropic expansion to an assigned pressure, temperature, or Mach number. Tables of thermodynamic functions needed with this method are included for 42 substances for convenience in numerical computations.

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

Kim, Sun Ung, E-mail: sunung@umich.edu; Monroe, Charles W., E-mail: cwmonroe@umich.edu

The inverse problem of parameterizing intermolecular potentials given macroscopic transport and thermodynamic data is addressed. Procedures are developed to create arbitrary-precision algorithms for transport collision integrals, using the Lennard-Jones (12–6) potential as an example. Interpolation formulas are produced that compute these collision integrals to four-digit accuracy over the reduced-temperature range 0.3≤T{sup ⁎}≤400, allowing very fast computation. Lennard-Jones parameters for neon, argon, and krypton are determined by simultaneously fitting the observed temperature dependences of their viscosities and second virial coefficients—one of the first times that a thermodynamic and a dynamic property have been used simultaneously for Lennard-Jones parameterization. In addition tomore » matching viscosities and second virial coefficients within the bounds of experimental error, the determined Lennard-Jones parameters are also found to predict the thermal conductivity and self-diffusion coefficient accurately, supporting the value of the Lennard-Jones (12–6) potential for noble-gas transport-property correlation.« less

A survey of upwind methods for flows with equilibrium and non-equilibrium chemistry and thermodynamics

NASA Technical Reports Server (NTRS)

Grossman, B.; Garrett, J.; Cinnella, P.

1989-01-01

Several versions of flux-vector split and flux-difference split algorithms were compared with regard to general applicability and complexity. Test computations were performed using curve-fit equilibrium air chemistry for an M = 5 high-temperature inviscid flow over a wedge, and an M = 24.5 inviscid flow over a blunt cylinder for test computations; for these cases, little difference in accuracy was found among the versions of the same flux-split algorithm. For flows with nonequilibrium chemistry, the effects of the thermodynamic model on the development of flux-vector split and flux-difference split algorithms were investigated using an equilibrium model, a general nonequilibrium model, and a simplified model based on vibrational relaxation. Several numerical examples are presented, including nonequilibrium air chemistry in a high-temperature shock tube and nonequilibrium hydrogen-air chemistry in a supersonic diffuser.

Chemical reaction mechanisms in solution from brute force computational Arrhenius plots.

PubMed

Kazemi, Masoud; Åqvist, Johan

2015-06-01

Decomposition of activation free energies of chemical reactions, into enthalpic and entropic components, can provide invaluable signatures of mechanistic pathways both in solution and in enzymes. Owing to the large number of degrees of freedom involved in such condensed-phase reactions, the extensive configurational sampling needed for reliable entropy estimates is still beyond the scope of quantum chemical calculations. Here we show, for the hydrolytic deamination of cytidine and dihydrocytidine in water, how direct computer simulations of the temperature dependence of free energy profiles can be used to extract very accurate thermodynamic activation parameters. The simulations are based on empirical valence bond models, and we demonstrate that the energetics obtained is insensitive to whether these are calibrated by quantum mechanical calculations or experimental data. The thermodynamic activation parameters are in remarkable agreement with experiment results and allow discrimination among alternative mechanisms, as well as rationalization of their different activation enthalpies and entropies.

Chemical reaction mechanisms in solution from brute force computational Arrhenius plots

PubMed Central

Kazemi, Masoud; Åqvist, Johan

2015-01-01

Decomposition of activation free energies of chemical reactions, into enthalpic and entropic components, can provide invaluable signatures of mechanistic pathways both in solution and in enzymes. Owing to the large number of degrees of freedom involved in such condensed-phase reactions, the extensive configurational sampling needed for reliable entropy estimates is still beyond the scope of quantum chemical calculations. Here we show, for the hydrolytic deamination of cytidine and dihydrocytidine in water, how direct computer simulations of the temperature dependence of free energy profiles can be used to extract very accurate thermodynamic activation parameters. The simulations are based on empirical valence bond models, and we demonstrate that the energetics obtained is insensitive to whether these are calibrated by quantum mechanical calculations or experimental data. The thermodynamic activation parameters are in remarkable agreement with experiment results and allow discrimination among alternative mechanisms, as well as rationalization of their different activation enthalpies and entropies. PMID:26028237

BurnMan: Towards a multidisciplinary toolkit for reproducible deep Earth science

NASA Astrophysics Data System (ADS)

Myhill, R.; Cottaar, S.; Heister, T.; Rose, I.; Unterborn, C. T.; Dannberg, J.; Martin-Short, R.

2016-12-01

BurnMan (www.burnman.org) is an open-source toolbox to compute thermodynamic and thermoelastic properties as a function of pressure and temperature using published mineral physical parameters and equations-of-state. The framework is user-friendly, written in Python, and modular, allowing the user to implement their own equations of state, endmember and solution model libraries, geotherms, and averaging schemes. Here we introduce various new modules, which can be used to: Fit thermodynamic variables to data from high pressure static and shock wave experiments, Calculate equilibrium assemblages given a bulk composition, pressure and temperature, Calculate chemical potentials and oxygen fugacities for given assemblages Compute 3D synthetic seismic models using output from geodynamic models and compare these results with global seismic tomographic models, Create input files for synthetic seismogram codes. Users can contribute scripts that reproduce the results from peer-reviewed articles and practical demonstrations (e.g. Cottaar et al., 2014).

Viabilty of atomistic potentials for thermodynamic properties of carbon dioxide at low temperatures.

PubMed

Kuznetsova, Tatyana; Kvamme, Bjørn

2001-11-30

Investigation into volumetric and energetic properties of several atomistic models mimicking carbon dioxide geometry and quadrupole momentum covered the liquid-vapor coexistence curve. Thermodynamic integration over a polynomial and an exponential-polynomial path was used to calculate free energy. Computational results showed that model using GROMOS Lennard-Jones parameters was unsuitable for bulk CO(2) simulations. On the other hand, model with potential fitted to reproduce only correct density-pressure relationship in the supercritical region proved to yield correct enthalpy of vaporization and free energy of liquid CO(2) in the low-temperature region. Except for molar volume at the upper part of the vapor-liquid equilibrium line, the bulk properties of exp-6-1 parametrization of ab initio CO(2) potential were in a close agreement with the experimental results. Copyright 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1772-1781, 2001

Calculation of open and closed system elastic coefficients for multicomponent solids

NASA Astrophysics Data System (ADS)

Mishin, Y.

2015-06-01

Thermodynamic equilibrium in multicomponent solids subject to mechanical stresses is a complex nonlinear problem whose exact solution requires extensive computations. A few decades ago, Larché and Cahn proposed a linearized solution of the mechanochemical equilibrium problem by introducing the concept of open system elastic coefficients [Acta Metall. 21, 1051 (1973), 10.1016/0001-6160(73)90021-7]. Using the Ni-Al solid solution as a model system, we demonstrate that open system elastic coefficients can be readily computed by semigrand canonical Monte Carlo simulations in conjunction with the shape fluctuation approach. Such coefficients can be derived from a single simulation run, together with other thermodynamic properties needed for prediction of compositional fields in solid solutions containing defects. The proposed calculation approach enables streamlined solutions of mechanochemical equilibrium problems in complex alloys. Second order corrections to the linear theory are extended to multicomponent systems.

Influence of system size on the properties of a fluid adsorbed in a nanopore: Physical manifestations and methodological consequences

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

Puibasset, Joël, E-mail: puibasset@cnrs-orleans.fr; Kierlik, Edouard, E-mail: edouard.kierlik@upmc.fr; Tarjus, Gilles, E-mail: tarjus@lptl.jussieu.fr

Hysteresis and discontinuities in the isotherms of a fluid adsorbed in a nanopore in general hamper the determination of equilibrium thermodynamic properties, even in computer simulations. A way around this has been to consider both a reservoir of small size and a pore of small extent in order to restrict the fluctuations of density and approach a classical van der Waals loop. We assess this suggestion by thoroughly studying through Monte Carlo simulations and density functional theory the influence of system size on the equilibrium configurations of the adsorbed fluid and on the resulting isotherms. We stress the importance ofmore » pore-symmetry-breaking states that even for modest pore sizes lead to discontinuous isotherms and we discuss the physical relevance of these states and the methodological consequences for computing thermodynamic quantities.« less

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

NASA Astrophysics Data System (ADS)

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

2018-02-01

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

A review of reaction rates and thermodynamic and transport properties for an 11-species air model for chemical and thermal nonequilibrium calculations to 30000 K

NASA Technical Reports Server (NTRS)

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

1990-01-01

Reaction rate coefficients and thermodynamic and transport properties are reviewed and supplemented for the 11-species air model which can be used for analyzing flows in chemical and thermal nonequilibrium up to temperatures of 3000 K. Such flows will likely occur around currently planned and future hypersonic vehicles. Guidelines for determining the state of the surrounding environment are provided. Curve fits are given for the various species properties for their efficient computation in flowfield codes. Approximate and more exact formulas are provided for computing the properties of partially ionized air mixtures in a high energy environment. Limitations of the approximate mixing laws are discussed for a mixture of ionized species. An electron number-density correction for the transport properties of the charged species is obtained. This correction has been generally ignored in the literature.

Black-hole entropy and thermodynamics from symmetries

NASA Astrophysics Data System (ADS)

Silva, Sebastián

2002-08-01

Given a boundary of spacetime preserved by a Diff(S1) sub-algebra, we propose a systematic method to compute the zero mode and the central extension of the associated Virasoro algebra of charges. Using these values in the Cardy formula, we may derive an associated statistical entropy to be compared with the Bekenstein-Hawking result. To illustrate our method, we study in detail the BTZ and the rotating Kerr-adS4 black holes (at spatial infinity and on the horizon). In both cases, we are able to reproduce the area law with the correct factor of 1/4 for the entropy. We also recover within our framework the first law of black-hole thermodynamics. We compare our results with the analogous derivations proposed by Carlip and others. Although similar, our method differs in the computation of the zero mode. In particular, the normalization of the ground state is automatically fixed by our construction.

Finite-size anomalies of the Drude weight: Role of symmetries and ensembles

NASA Astrophysics Data System (ADS)

Sánchez, R. J.; Varma, V. K.

2017-12-01

We revisit the numerical problem of computing the high temperature spin stiffness, or Drude weight, D of the spin-1 /2 X X Z chain using exact diagonalization to systematically analyze its dependence on system symmetries and ensemble. Within the canonical ensemble and for states with zero total magnetization, we find D vanishes exactly due to spin-inversion symmetry for all but the anisotropies Δ˜M N=cos(π M /N ) with N ,M ∈Z+ coprimes and N >M , provided system sizes L ≥2 N , for which states with different spin-inversion signature become degenerate due to the underlying s l2 loop algebra symmetry. All these loop-algebra degenerate states carry finite currents which we conjecture [based on data from the system sizes and anisotropies Δ˜M N (with N

Microstructural characterization, petrophysics and upscaling - from porous media to fractural media

NASA Astrophysics Data System (ADS)

Liu, J.; Liu, K.; Regenauer-Lieb, K.

2017-12-01

We present an integrated study for the characterization of complex geometry, fluid transport features and mechanical deformation at micro-scale and the upscaling of properties using microtomographic data: We show how to integrate microstructural characterization by the volume fraction, specific surface area, connectivity (percolation), shape and orientation of microstructures with identification of individual fractures from a 3D fractural network. In a first step we use stochastic analyses of microstructures to determine the geometric RVE (representative volume element) of samples. We proceed by determining the size of a thermodynamic RVE by computing upper/lower bounds of entropy production through Finite Element (FE) analyses on a series of models with increasing sizes. The minimum size for thermodynamic RVE's is identified on the basis of the convergence criteria of the FE simulations. Petrophysical properties (permeability and mechanical parameters, including plastic strength) are then computed numerically if thermodynamic convergence criteria are fulfilled. Upscaling of properties is performed by means of percolation theory. The percolation threshold is detected by using a shrinking/expanding algorithm on static micro-CT images of rocks. Parameters of the scaling laws can be extracted from quantitative analyses and/or numerical simulations on a series of models with similar structures but different porosities close to the percolation threshold. Different rock samples are analyzed. Characterizing parameters of porous/fractural rocks are obtained. Synthetic derivative models of the microstructure are used to estimate the relationships between porosity and mechanical properties. Results obtained from synthetic sandstones show that yield stress, cohesion and the angle of friction are linearly proportional to porosity. Our integrated study shows that digital rock technology can provide meaningful parameters for effective upscaling if thermodynamic volume averaging satisfies the convergence criteria. For strongly heterogeneous rocks, however, thermodynamic convergence criteria may not meet; a continuum approach cannot be justified in this case.

Network design and analysis for multi-enzyme biocatalysis.

PubMed

Blaß, Lisa Katharina; Weyler, Christian; Heinzle, Elmar

2017-08-10

As more and more biological reaction data become available, the full exploration of the enzymatic potential for the synthesis of valuable products opens up exciting new opportunities but is becoming increasingly complex. The manual design of multi-step biosynthesis routes involving enzymes from different organisms is very challenging. To harness the full enzymatic potential, we developed a computational tool for the directed design of biosynthetic production pathways for multi-step catalysis with in vitro enzyme cascades, cell hydrolysates and permeabilized cells. We present a method which encompasses the reconstruction of a genome-scale pan-organism metabolic network, path-finding and the ranking of the resulting pathway candidates for proposing suitable synthesis pathways. The network is based on reaction and reaction pair data from the Kyoto Encyclopedia of Genes and Genomes (KEGG) and the thermodynamics calculator eQuilibrator. The pan-organism network is especially useful for finding the most suitable pathway to a target metabolite from a thermodynamic or economic standpoint. However, our method can be used with any network reconstruction, e.g. for a specific organism. We implemented a path-finding algorithm based on a mixed-integer linear program (MILP) which takes into account both topology and stoichiometry of the underlying network. Unlike other methods we do not specify a single starting metabolite, but our algorithm searches for pathways starting from arbitrary start metabolites to a target product of interest. Using a set of biochemical ranking criteria including pathway length, thermodynamics and other biological characteristics such as number of heterologous enzymes or cofactor requirement, it is possible to obtain well-designed meaningful pathway alternatives. In addition, a thermodynamic profile, the overall reactant balance and potential side reactions as well as an SBML file for visualization are generated for each pathway alternative. We present an in silico tool for the design of multi-enzyme biosynthetic production pathways starting from a pan-organism network. The method is highly customizable and each module can be adapted to the focus of the project at hand. This method is directly applicable for (i) in vitro enzyme cascades, (ii) cell hydrolysates and (iii) permeabilized cells.

ZMOTTO- MODELING THE INTERNAL COMBUSTION ENGINE

NASA Technical Reports Server (NTRS)

Zeleznik, F. J.

1994-01-01

The ZMOTTO program was developed to model mathematically a spark-ignited internal combustion engine. ZMOTTO is a large, general purpose program whose calculations can be established at five levels of sophistication. These five models range from an ideal cycle requiring only thermodynamic properties, to a very complex representation demanding full combustion kinetics, transport properties, and poppet valve flow characteristics. ZMOTTO is a flexible and computationally economical program based on a system of ordinary differential equations for cylinder-averaged properties. The calculations assume that heat transfer is expressed in terms of a heat transfer coefficient and that the cylinder average of kinetic plus potential energies remains constant. During combustion, the pressures of burned and unburned gases are assumed equal and their heat transfer areas are assumed proportional to their respective mass fractions. Even the simplest ZMOTTO model provides for residual gas effects, spark advance, exhaust gas recirculation, supercharging, and throttling. In the more complex models, 1) finite rate chemistry replaces equilibrium chemistry in descriptions of both the flame and the burned gases, 2) poppet valve formulas represent fluid flow instead of a zero pressure drop flow, and 3) flame propagation is modeled by mass burning equations instead of as an instantaneous process. Input to ZMOTTO is determined by the model chosen. Thermodynamic data is required for all models. Transport properties and chemical kinetics data are required only as the model complexity grows. Other input includes engine geometry, working fluid composition, operating characteristics, and intake/exhaust data. ZMOTTO accommodates a broad spectrum of reactants. The program will calculate many Otto cycle performance parameters for a number of consecutive cycles (a cycle being an interval of 720 crankangle degrees). A typical case will have a number of initial ideal cycles and progress through levels of nonideal cycles. ZMOTTO has restart capabilities and permits multicycle calculations with parameters varying from cycle to cycle. ZMOTTO is written in FORTRAN IV (IBM Level H) but has also been compiled with IBM VSFORTRAN (1977 standard). It was developed on an IBM 3033 under the TSS operating system and has also been implemented under MVS. Approximately 412K of 8 bit bytes of central memory are required in a nonpaging environment. ZMOTTO was developed in 1985.

Chemical Equilibrium And Transport (CET)

NASA Technical Reports Server (NTRS)

Mcbride, B. J.

1991-01-01

Powerful, machine-independent program calculates theoretical thermodynamic properties of chemical systems. Aids in design of compressors, turbines, engines, heat exchangers, and chemical processing equipment.

Critical evaluation and thermodynamic optimization of the Iron-Rare-Earth systems

NASA Astrophysics Data System (ADS)

Konar, Bikram

Rare-Earth elements by virtue of its typical magnetic, electronic and chemical properties are gaining importance in power, electronics, telecommunications and sustainable green technology related industries. The Magnets from RE-alloys are more powerful than conventional magnets which have more longevity and high temperature workability. The dis-equilibrium in the Rare-Earth element supply and demand has increased the importance of recycling and extraction of REE's from used permanent Magnets. However, lack of the thermodynamic data on RE alloys has made it difficult to design an effective extraction and recycling process. In this regard, Computational Thermodynamic calculations can serve as a cost effective and less time consuming tool to design a waste magnet recycling process. The most common RE permanent magnet is Nd magnet (Nd 2Fe14B). Various elements such as Dy, Tb, Pr, Cu, Co, Ni, etc. are also added to increase its magnetic and mechanical properties. In order to perform reliable thermodynamic calculations for the RE recycling process, accurate thermodynamic database for RE and related alloys are required. The thermodynamic database can be developed using the so-called CALPHAD method. The database development based on the CALPHAD method is essentially the critical evaluation and optimization of all available thermodynamic and phase diagram data. As a results, one set of self-consistent thermodynamic functions for all phases in the given system can be obtained, which can reproduce all reliable thermodynamic and phase diagram data. The database containing the optimized Gibbs energy functions can be used to calculate complex chemical reactions for any high temperature processes. Typically a Gibbs energy minimization routine, such as in FactSage software, can be used to obtain the accurate thermodynamic equilibrium in multicomponent systems. As part of a large thermodynamic database development for permanent magnet recycling and Mg alloy design, all thermodynamic and phase diagram data in the literature for the fourteen Fe-RE binary systems: Fe-La, Fe-Ce, Fe-Pr, Fe-Nd, Fe-Sm, Fe-Gd, Fe-Tb, Fe-Dy, Fe-Ho, Fe-Er, Fe-Tm, Fe-Lu, Fe-Sc and Fe-Y are critically evaluated and optimized to obtain thermodynamic model parameters. The model parameters can be used to calculate phase diagrams and Gibbs energies of all phases as functions of temperature and composition. This database can be incorporated with the present thermodynamic database in FactSage software to perform complex chemical reactions and phase diagram calculations for RE magnet recycling process.

Thermodynamic properties by equation of state and from Ab initio molecular dynamics of liquid potassium under pressure

NASA Astrophysics Data System (ADS)

Li, Huaming; Tian, Yanting; Sun, Yongli; Li, Mo; Nonequilibrium materials; physics Team; Computational materials science Team

In this work, we apply a general equation of state of liquid and Ab initio molecular-dynamics method to study thermodynamic properties in liquid potassium under high pressure. Isothermal bulk modulus and molar volume of molten sodium are calculated within good precision as compared with the experimental data. The calculated internal energy data and the calculated values of isobaric heat capacity of molten potassium show the minimum along the isothermal lines as the previous result obtained in liquid sodium. The expressions for acoustical parameter and nonlinearity parameter are obtained based on thermodynamic relations from the equation of state. Both parameters for liquid potassium are calculated under high pressure along the isothermal lines by using the available thermodynamic data and numeric derivations. Furthermore, Ab initio molecular-dynamics simulations are used to calculate some thermodynamic properties of liquid potassium along the isothermal lines. Scientific Research Starting Foundation from Taiyuan university of Technology, Shanxi Provincial government (``100-talents program''), China Scholarship Council and National Natural Science Foundation of China (NSFC) under Grant No. 51602213.

First-Principles Modeling of Hydrogen Storage in Metal Hydride Systems

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

J. Karl Johnson

The objective of this project is to complement experimental efforts of MHoCE partners by using state-of-the-art theory and modeling to study the structure, thermodynamics, and kinetics of hydrogen storage materials. Specific goals include prediction of the heats of formation and other thermodynamic properties of alloys from first principles methods, identification of new alloys that can be tested experimentally, calculation of surface and energetic properties of nanoparticles, and calculation of kinetics involved with hydrogenation and dehydrogenation processes. Discovery of new metal hydrides with enhanced properties compared with existing materials is a critical need for the Metal Hydride Center of Excellence. Newmore » materials discovery can be aided by the use of first principles (ab initio) computational modeling in two ways: (1) The properties, including mechanisms, of existing materials can be better elucidated through a combined modeling/experimental approach. (2) The thermodynamic properties of novel materials that have not been made can, in many cases, be quickly screened with ab initio methods. We have used state-of-the-art computational techniques to explore millions of possible reaction conditions consisting of different element spaces, compositions, and temperatures. We have identified potentially promising single- and multi-step reactions that can be explored experimentally.« less

Analysis of energy conservation alternatives for standard Army building. Final report

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

Hittle, D.C.; O'Brien, R.E.; Percivall, G.S.

1983-03-01

This report describes energy conservation alternatives for five standard Army building designs. By surveying maps of major Army installations and using the Integrated Facilities System, the most popular designs were determined to be a two-company, rolling-pin-shaped barracks for enlisted personnel; a Type 64 barracks; a motor repair shop; a battalion headquarters and classroom building; and an enlisted personnel mess hall. The Building Loads Analysis and System Thermodynamics (BLAST) energy-analysis computer program was used to develop baseline energy consumption for each design based on the building descriptions and calibrated by comparison with the measured energy usage of similar buildings. Once themore » baseline was established, the BLAST program was used to study energy conservation alternatives (ECAs) which could be retrofit to the existing buildings. The ECAs included closing off air-handling units, adding storm windows, adding 2 in. (0.051 m) of exterior insulation to the walls, partially blocking the windows, adding roof insulation, putting up south overhangs, installing programmable thermostats, recovering heat from exhaust fans, installing temperature economizers, replacing lights, and installing partitions between areas of differing temperature.« less

Numerical simulation of hypersonic inlet flows with equilibrium or finite rate chemistry

NASA Technical Reports Server (NTRS)

Yu, Sheng-Tao; Hsieh, Kwang-Chung; Shuen, Jian-Shun; Mcbride, Bonnie J.

1988-01-01

An efficient numerical program incorporated with comprehensive high temperature gas property models has been developed to simulate hypersonic inlet flows. The computer program employs an implicit lower-upper time marching scheme to solve the two-dimensional Navier-Stokes equations with variable thermodynamic and transport properties. Both finite-rate and local-equilibrium approaches are adopted in the chemical reaction model for dissociation and ionization of the inlet air. In the finite rate approach, eleven species equations coupled with fluid dynamic equations are solved simultaneously. In the local-equilibrium approach, instead of solving species equations, an efficient chemical equilibrium package has been developed and incorporated into the flow code to obtain chemical compositions directly. Gas properties for the reaction products species are calculated by methods of statistical mechanics and fit to a polynomial form for C(p). In the present study, since the chemical reaction time is comparable to the flow residence time, the local-equilibrium model underpredicts the temperature in the shock layer. Significant differences of predicted chemical compositions in shock layer between finite rate and local-equilibrium approaches have been observed.

Computing the melting point and thermodynamic stability of the orthorhombic and monoclinic crystalline polymorphs of the ionic liquid 1-n-butyl-3-methylimidazolium chloride

NASA Astrophysics Data System (ADS)

Jayaraman, Saivenkataraman; Maginn, Edward J.

2007-12-01

The melting point, enthalpy of fusion, and thermodynamic stability of two crystal polymorphs of the ionic liquid 1-n-butyl-3-methylimidazolium chloride are calculated using a thermodynamic integration-based atomistic simulation method. The computed melting point of the orthorhombic phase ranges from 365 to 369 K, depending on the classical force field used. This compares reasonably well with the experimental values, which range from 337 to 339 K. The computed enthalpy of fusion ranges from 19 to 29 kJ/mol, compared to the experimental values of 18.5-21.5 kJ/mol. Only one of the two force fields evaluated in this work yielded a stable monoclinic phase, despite the fact that both give accurate liquid state densities. The computed melting point of the monoclinic polymorph was found to be 373 K, which is somewhat higher than the experimental range of 318-340 K. The computed enthalpy of fusion was 23 kJ/mol, which is also higher than the experimental value of 9.3-14.5 kJ/mol. The simulations predict that the monoclinic form is more stable than the orthorhombic form at low temperature, in agreement with one set of experiments but in conflict with another. The difference in free energy between the two polymorphs is very small, due to the fact that a single trans-gauche conformational difference in an alkyl sidechain distinguishes the two structures. As a result, it is very difficult to construct simple classical force fields that are accurate enough to definitively predict which polymorph is most stable. A liquid phase analysis of the probability distribution of the dihedral angles in the alkyl chain indicates that less than half of the dihedral angles are in the gauche-trans configuration that is adopted in the orthorhombic crystal. The low melting point and glass forming tendency of this ionic liquid is likely due to the energy barrier for conversion of the remaining dihedral angles into the gauche-trans state. The simulation procedure used to perform the melting point calculations is an extension of the so-called pseudosupercritical path sampling procedure. This study demonstrates that the method can be effectively applied to quite complex systems such as ionic liquids and that the appropriate choice of tethering potentials for a key step in the thermodynamic path can enable first order phase transitions to be avoided.

Estimating the uncertainty in thermochemical calculations for oxygen-hydrogen combustors

NASA Astrophysics Data System (ADS)

Sims, Joseph David

The thermochemistry program CEA2 was combined with the statistical thermodynamics program PAC99 in a Monte Carlo simulation to determine the uncertainty in several CEA2 output variables due to uncertainty in thermodynamic reference values for the reactant and combustion species. In all, six typical performance parameters were examined, along with the required intermediate calculations (five gas properties and eight stoichiometric coefficients), for three hydrogen-oxygen combustors: a main combustor, an oxidizer preburner and a fuel preburner. The three combustors were analyzed in two different modes: design mode, where, for the first time, the uncertainty in thermodynamic reference values---taken from the literature---was considered (inputs to CEA2 were specified and so had no uncertainty); and data reduction mode, where inputs to CEA2 did have uncertainty. The inputs to CEA2 were contrived experimental measurements that were intended to represent the typical combustor testing facility. In design mode, uncertainties in the performance parameters were on the order of 0.1% for the main combustor, on the order of 0.05% for the oxidizer preburner and on the order of 0.01% for the fuel preburner. Thermodynamic reference values for H2O were the dominant sources of uncertainty, as was the assigned enthalpy for liquid oxygen. In data reduction mode, uncertainties in performance parameters increased significantly as a result of the uncertainties in experimental measurements compared to uncertainties in thermodynamic reference values. Main combustor and fuel preburner theoretical performance values had uncertainties of about 0.5%, while the oxidizer preburner had nearly 2%. Associated experimentally-determined performance values for all three combustors were 3% to 4%. The dominant sources of uncertainty in this mode were the propellant flowrates. These results only apply to hydrogen-oxygen combustors and should not be generalized to every propellant combination. Species for a hydrogen-oxygen system are relatively simple, thereby resulting in low thermodynamic reference value uncertainties. Hydrocarbon combustors, solid rocket motors and hybrid rocket motors have combustion gases containing complex molecules that will likely have thermodynamic reference values with large uncertainties. Thus, every chemical system should be analyzed in a similar manner as that shown in this work.

Thermodynamic properties of diamond and wurtzite model fluids from computer simulation and thermodynamic perturbation theory

NASA Astrophysics Data System (ADS)

Zhou, S.; Solana, J. R.

2018-03-01

Monte Carlo NVT simulations have been performed to obtain the thermodynamic and structural properties and perturbation coefficients up to third order in the inverse temperature expansion of the Helmholtz free energy of fluids with potential models proposed in the literature for diamond and wurtzite lattices. These data are used to analyze performance of a coupling parameter series expansion (CPSE). The main findings are summarized as follows, (1) The CPSE provides accurate predictions of the first three coefficient in the inverse temperature expansion of Helmholtz free energy for the potential models considered and the thermodynamic properties of these fluids are predicted more accurately when the CPSE is truncated at second or third order. (2) The Barker-Henderson (BH) recipe is appropriate for determining the effective hard sphere diameter for strongly repulsive potential cores, but its performance worsens with increasing the softness of the potential core. (3) For some thermodynamic properties the first-order CPSE works better for the diamond potential, whose tail is dominated by repulsive interactions, than for the potential, whose tail is dominated by attractive interactions. However, the first-order CPSE provides unsatisfactory results for the excess internal energy and constant-volume excess heat capacity for the two potential models.

Quantitative thermodynamic predication of interactions between nucleic acid and non-nucleic acid species using Microsoft excel.

PubMed

Zou, Jiaqi; Li, Na

2013-09-01

Proper design of nucleic acid sequences is crucial for many applications. We have previously established a thermodynamics-based quantitative model to help design aptamer-based nucleic acid probes by predicting equilibrium concentrations of all interacting species. To facilitate customization of this thermodynamic model for different applications, here we present a generic and easy-to-use platform to implement the algorithm of the model with Microsoft(®) Excel formulas and VBA (Visual Basic for Applications) macros. Two Excel spreadsheets have been developed: one for the applications involving only nucleic acid species, the other for the applications involving both nucleic acid and non-nucleic acid species. The spreadsheets take the nucleic acid sequences and the initial concentrations of all species as input, guide the user to retrieve the necessary thermodynamic constants, and finally calculate equilibrium concentrations for all species in various bound and unbound conformations. The validity of both spreadsheets has been verified by comparing the modeling results with the experimental results on nucleic acid sequences reported in the literature. This Excel-based platform described here will allow biomedical researchers to rationalize the sequence design of nucleic acid probes using the thermodynamics-based modeling even without relevant theoretical and computational skills. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

Thermodynamic Calculations for Molecules with Asymmetric Internal Rotors. II. Application to the 1,2-Dihaloethanes

PubMed Central

Wong, Bryan M.; Fadri, Maria M.; Raman, Sumathy

2012-01-01

The thermodynamic properties of three halocarbon molecules relevant in atmospheric and public health applications are presented from ab initio calculations. Our technique makes use of a reaction path-like Hamiltonian to couple all the vibrational modes to a large-amplitude torsion for 1,2-difluoroethane, 1,2-dichloroethane, and 1,2-dibromoethane, each of which possesses a heavy asymmetric rotor. Optimized ab initio energies and Hessians were calculated at the CCSD(T) and MP2 levels of theory, respectively. In addition, to investigate the contribution of electronically excited states to thermodynamic properties, several excited singlet and triplet states for each of the halocarbons were computed at the CASSCF/MRCI level. Using the resulting potentials and projected frequencies, the couplings of all the vibrational modes to the large-amplitude torsion are calculated using the new STAR-P 2.4.0 software platform that automatically parallelizes our codes with distributed memory via a familiar MATLAB interface. Utilizing the efficient parallelization scheme of STAR-P, we obtain thermodynamic properties for each of the halocarbons, with temperatures ranging from 298.15 to 1000 K. We propose that the free energies, entropies, and heat capacities obtained from our methods be used to supplement theoretical and experimental values found in current thermodynamic tables. PMID:17663439

Thermodynamic calculations for molecules with asymmetric internal rotors. II. Application to the 1,2-dihaloethanes.

PubMed

Wong, Bryan M; Fadri, Maria M; Raman, Sumathy

2008-02-01

The thermodynamic properties of three halocarbon molecules relevant in atmospheric and public health applications are presented from ab initio calculations. Our technique makes use of a reaction path-like Hamiltonian to couple all the vibrational modes to a large-amplitude torsion for 1,2-difluoroethane, 1,2-dichloroethane, and 1,2-dibromoethane, each of which possesses a heavy asymmetric rotor. Optimized ab initio energies and Hessians were calculated at the CCSD(T) and MP2 levels of theory, respectively. In addition, to investigate the contribution of electronically excited states to thermodynamic properties, several excited singlet and triplet states for each of the halocarbons were computed at the CASSCF/MRCI level. Using the resulting potentials and projected frequencies, the couplings of all the vibrational modes to the large-amplitude torsion are calculated using the new STAR-P 2.4.0 software platform that automatically parallelizes our codes with distributed memory via a familiar MATLAB interface. Utilizing the efficient parallelization scheme of STAR-P, we obtain thermodynamic properties for each of the halocarbons, with temperatures ranging from 298.15 to 1000 K. We propose that the free energies, entropies, and heat capacities obtained from our methods be used to supplement theoretical and experimental values found in current thermodynamic tables. (c) 2007 Wiley Periodicals, Inc.

Ab initio interatomic potentials and the thermodynamic properties of fluids

NASA Astrophysics Data System (ADS)

Vlasiuk, Maryna; Sadus, Richard J.

2017-07-01

Monte Carlo simulations with accurate ab initio interatomic potentials are used to investigate the key thermodynamic properties of argon and krypton in both vapor and liquid phases. Data are reported for the isochoric and isobaric heat capacities, the Joule-Thomson coefficient, and the speed of sound calculated using various two-body interatomic potentials and different combinations of two-body plus three-body terms. The results are compared to either experimental or reference data at state points between the triple and critical points. Using accurate two-body ab initio potentials, combined with three-body interaction terms such as the Axilrod-Teller-Muto and Marcelli-Wang-Sadus potentials, yields systematic improvements to the accuracy of thermodynamic predictions. The effect of three-body interactions is to lower the isochoric and isobaric heat capacities and increase both the Joule-Thomson coefficient and speed of sound. The Marcelli-Wang-Sadus potential is a computationally inexpensive way to utilize accurate two-body ab initio potentials for the prediction of thermodynamic properties. In particular, it provides a very effective way of extending two-body ab initio potentials to liquid phase properties.

First-principles calculations, experimental study, and thermodynamic modeling of the Al-Co-Cr system.

PubMed

Liu, Xuan L; Gheno, Thomas; Lindahl, Bonnie B; Lindwall, Greta; Gleeson, Brian; Liu, Zi-Kui

2015-01-01

The phase relations and thermodynamic properties of the condensed Al-Co-Cr ternary alloy system are investigated using first-principles calculations based on density functional theory (DFT) and phase-equilibria experiments that led to X-ray diffraction (XRD) and electron probe micro-analysis (EPMA) measurements. A thermodynamic description is developed by means of the calculations of phase diagrams (CALPHAD) method using experimental and computational data from the present work and the literature. Emphasis is placed on modeling the bcc-A2, B2, fcc-γ, and tetragonal-σ phases in the temperature range of 1173 to 1623 K. Liquid, bcc-A2 and fcc-γ phases are modeled using substitutional solution descriptions. First-principles special quasirandom structures (SQS) calculations predict a large bcc-A2 (disordered)/B2 (ordered) miscibility gap, in agreement with experiments. A partitioning model is then used for the A2/B2 phase to effectively describe the order-disorder transitions. The critically assessed thermodynamic description describes all phase equilibria data well. A2/B2 transitions are also shown to agree well with previous experimental findings.

Standard Model thermodynamics across the electroweak crossover

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

Laine, M.; Meyer, M., E-mail: laine@itp.unibe.ch, E-mail: meyer@itp.unibe.ch

Even though the Standard Model with a Higgs mass m{sub H} = 125GeV possesses no bulk phase transition, its thermodynamics still experiences a 'soft point' at temperatures around T = 160GeV, with a deviation from ideal gas thermodynamics. Such a deviation may have an effect on precision computations of weakly interacting dark matter relic abundances if their mass is in the few TeV range, or on leptogenesis scenarios operating in this temperature range. By making use of results from lattice simulations based on a dimensionally reduced effective field theory, we estimate the relevant thermodynamic functions across the crossover. The resultsmore » are tabulated in a numerical form permitting for their insertion as a background equation of state into cosmological particle production/decoupling codes. We find that Higgs dynamics induces a non-trivial 'structure' visible e.g. in the heat capacity, but that in general the largest radiative corrections originate from QCD effects, reducing the energy density by a couple of percent from the free value even at T > 160GeV.« less

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.

Standard Model thermodynamics across the electroweak crossover

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

Laine, M.; Meyer, M.

Even though the Standard Model with a Higgs mass m{sub \\tiny H}=125 GeV possesses no bulk phase transition, its thermodynamics still experiences a “soft point” at temperatures around T=160 GeV, with a deviation from ideal gas thermodynamics. Such a deviation may have an effect on precision computations of weakly interacting dark matter relic abundances if their mass is in the few TeV range, or on leptogenesis scenarios operating in this temperature range. By making use of results from lattice simulations based on a dimensionally reduced effective field theory, we estimate the relevant thermodynamic functions across the crossover. The results are tabulatedmore » in a numerical form permitting for their insertion as a background equation of state into cosmological particle production/decoupling codes. We find that Higgs dynamics induces a non-trivial “structure” visible e.g. in the heat capacity, but that in general the largest radiative corrections originate from QCD effects, reducing the energy density by a couple of percent from the free value even at T>160 GeV.« less

The thermodynamics of pyrochemical processes for liquid metal reactor fuel cycles

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

Johnson, I.

1987-01-01

The thermodynamic basis for pyrochemical processes for the recovery and purification of fuel for the liquid metal reactor fuel cycle is described. These processes involve the transport of the uranium and plutonium from one liquid alloy to another through a molten salt. The processes discussed use liquid alloys of cadmium, zinc, and magnesium and molten chloride salts. The oxidation-reduction steps are done either chemically by the use of an auxiliary redox couple or electrochemically by the use of an external electrical supply. The same basic thermodynamics apply to both the salt transport and the electrotransport processes. Large deviations from idealmore » solution behavior of the actinides and lanthanides in the liquid alloys have a major influence on the solubilities and the performance of both the salt transport and electrotransport processes. Separation of plutonium and uranium from each other and decontamination from the more noble fission product elements can be achieved using both transport processes. The thermodynamic analysis is used to make process design computations for different process conditions.« less

Probing the extensive nature of entropy

NASA Astrophysics Data System (ADS)

Salagaram, T.; Chetty, N.

2013-08-01

We have devised a general numerical scheme applied to a system of independent, distinguishable, non-interacting particles, to demonstrate in a direct manner the extensive nature of statistical entropy. Working within the microcanonical ensemble, our methods enable one to directly monitor the approach to the thermodynamic limit (N → ∞) in a manner that has not been known before. We show that (sN - s∞) → N-α where sN is the entropy per particle for N particles and S∞ is the entropy per particle in the thermodynamic limit. We demonstrate universal behaviour by considering a number of different systems each defined by its unique single-particle spectrum. Various thermodynamic quantities as a function of N may be computed using our methods; in this paper, we focus on the entropy, the chemical potential and the temperature. Our results are applicable to systems of finite size, e.g. nano-particle systems. Furthermore, we demonstrate a new phenomenon, referred to as entropic interference, which manifests as a cancellation of terms in the thermodynamic limit and which results in the additive nature of entropy.

Ab initio interatomic potentials and the thermodynamic properties of fluids.

PubMed

Vlasiuk, Maryna; Sadus, Richard J

2017-07-14

Monte Carlo simulations with accurate ab initio interatomic potentials are used to investigate the key thermodynamic properties of argon and krypton in both vapor and liquid phases. Data are reported for the isochoric and isobaric heat capacities, the Joule-Thomson coefficient, and the speed of sound calculated using various two-body interatomic potentials and different combinations of two-body plus three-body terms. The results are compared to either experimental or reference data at state points between the triple and critical points. Using accurate two-body ab initio potentials, combined with three-body interaction terms such as the Axilrod-Teller-Muto and Marcelli-Wang-Sadus potentials, yields systematic improvements to the accuracy of thermodynamic predictions. The effect of three-body interactions is to lower the isochoric and isobaric heat capacities and increase both the Joule-Thomson coefficient and speed of sound. The Marcelli-Wang-Sadus potential is a computationally inexpensive way to utilize accurate two-body ab initio potentials for the prediction of thermodynamic properties. In particular, it provides a very effective way of extending two-body ab initio potentials to liquid phase properties.

Thermodynamic criteria for estimating the kinetic parameters of catalytic reactions

NASA Astrophysics Data System (ADS)

Mitrichev, I. I.; Zhensa, A. V.; Kol'tsova, E. M.

2017-01-01

Kinetic parameters are estimated using two criteria in addition to the traditional criterion that considers the consistency between experimental and modeled conversion data: thermodynamic consistency and the consistency with entropy production (i.e., the absolute rate of the change in entropy due to exchange with the environment is consistent with the rate of entropy production in the steady state). A special procedure is developed and executed on a computer to achieve the thermodynamic consistency of a set of kinetic parameters with respect to both the standard entropy of a reaction and the standard enthalpy of a reaction. A problem of multi-criterion optimization, reduced to a single-criterion problem by summing weighted values of the three criteria listed above, is solved. Using the reaction of NO reduction with CO on a platinum catalyst as an example, it is shown that the set of parameters proposed by D.B. Mantri and P. Aghalayam gives much worse agreement with experimental values than the set obtained on the basis of three criteria: the sum of the squares of deviations for conversion, the thermodynamic consistency, and the consistency with entropy production.

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.

Determination of thermodynamic and transport parameters of naphthenic acids and organic process chemicals in oil sand tailings pond water.

PubMed

Wang, Xiaomeng; Robinson, Lisa; Wen, Qing; Kasperski, Kim L

2013-07-01

Oil sand tailings pond water contains naphthenic acids and process chemicals (e.g., alkyl sulphates, quaternary ammonium compounds, and alkylphenol ethoxylates). These chemicals are toxic and can seep through the foundation of the tailings pond to the subsurface, potentially affecting the quality of groundwater. As a result, it is important to measure the thermodynamic and transport parameters of these chemicals in order to study the transport behavior of contaminants through the foundation as well as underground. In this study, batch adsorption studies and column experiments were performed. It was found that the transport parameters of these chemicals are related to their molecular structures and other properties. The computer program (CXTFIT) was used to further evaluate the transport process in the column experiments. The results from this study show that the transport of naphthenic acids in a glass column is an equilibrium process while the transport of process chemicals seems to be a non-equilibrium process. At the end of this paper we present a real-world case study in which the transport of the contaminants through the foundation of an external tailings pond is calculated using the lab-measured data. The results show that long-term groundwater monitoring of contaminant transport at the oil sand mining site may be necessary to avoid chemicals from reaching any nearby receptors.

Thermodynamics of technetium: Reconciling theory and experiment using density functional perturbation analysis

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

Weck, Philippe F.; Kim, Eunja

The structure, lattice dynamics and thermodynamic properties of bulk technetium were investigated within the framework of density functional theory. The phonon density of states spectrum computed with density functional perturbation theory closely matches inelastic coherent neutron scattering measurements. The thermal properties of technetium were derived from phonon frequencies calculated within the quasi-harmonic approximation (QHA), which introduces a volume dependence of phonon frequencies as a part of the anharmonic effect. As a result, the predicted thermal expansion and isobaric heat capacity of technetium are in excellent agreement with available experimental data for temperatures up to ~1600 K.