Sample records for accurate computed enthalpies

  1. Bulk Enthalpy Calculations in the Arc Jet Facility at NASA ARC

    NASA Technical Reports Server (NTRS)

    Thompson, Corinna S.; Prabhu, Dinesh; Terrazas-Salinas, Imelda; Mach, Jeffrey J.

    2011-01-01

    The Arc Jet Facilities at NASA Ames Research Center generate test streams with enthalpies ranging from 5 MJ/kg to 25 MJ/kg. The present work describes a rigorous method, based on equilibrium thermodynamics, for calculating the bulk enthalpy of the flow produced in two of these facilities. The motivation for this work is to determine a dimensionally-correct formula for calculating the bulk enthalpy that is at least as accurate as the conventional formulas that are currently used. Unlike previous methods, the new method accounts for the amount of argon that is present in the flow. Comparisons are made with bulk enthalpies computed from an energy balance method. An analysis of primary facility operating parameters and their associated uncertainties is presented in order to further validate the enthalpy calculations reported herein.

  2. The CPA Equation of State and an Activity Coefficient Model for Accurate Molar Enthalpy Calculations of Mixtures with Carbon Dioxide and Water/Brine

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

    Myint, P. C.; Hao, Y.; Firoozabadi, A.

    2015-03-27

    Thermodynamic property calculations of mixtures containing carbon dioxide (CO 2) and water, including brines, are essential in theoretical models of many natural and industrial processes. The properties of greatest practical interest are density, solubility, and enthalpy. Many models for density and solubility calculations have been presented in the literature, but there exists only one study, by Spycher and Pruess, that has compared theoretical molar enthalpy predictions with experimental data [1]. In this report, we recommend two different models for enthalpy calculations: the CPA equation of state by Li and Firoozabadi [2], and the CO 2 activity coefficient model by Duanmore » and Sun [3]. We show that the CPA equation of state, which has been demonstrated to provide good agreement with density and solubility data, also accurately calculates molar enthalpies of pure CO 2, pure water, and both CO 2-rich and aqueous (H 2O-rich) mixtures of the two species. It is applicable to a wider range of conditions than the Spycher and Pruess model. In aqueous sodium chloride (NaCl) mixtures, we show that Duan and Sun’s model yields accurate results for the partial molar enthalpy of CO 2. It can be combined with another model for the brine enthalpy to calculate the molar enthalpy of H 2O-CO 2-NaCl mixtures. We conclude by explaining how the CPA equation of state may be modified to further improve agreement with experiments. This generalized CPA is the basis of our future work on this topic.« less

  3. 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.

  4. High Enthalpy Effects on Two Boundary Layer Disturbances in Supersonic and Hypersonic Flow

    NASA Astrophysics Data System (ADS)

    Wagnild, Ross Martin

    The fluid flow phenomenon of boundary layer transition is a complicated and difficult process to model and predict. The importance of the state of the boundary layer with regard to vehicle design cannot be understated. The high enthalpy environment in which high speed vehicles operate in further complicates the transition process by adding several more degrees of freedom. In this environment, the internal properties of the gas can stabilize or destabilize the boundary layer as well as modify the disturbances that cause transition. In the current work, the interaction of two types of disturbances with the high enthalpy flow environment are analyzed. The first is known as a second mode disturbance, which is acoustic in nature. The second type is known as a transient growth disturbance and is associated with flows behind roughness elements. Theoretical analyses, linear stability analyses, and computation fluid dynamics (CFD) are used to determine the ways in which these disturbances interact with the high enthalpy environment as well as the consequences of these interactions. First, acoustic wave are directly studied in order to gain a basic understanding of the response of second mode disturbances in the high enthalpy boundary layer. Next, this understanding is used in interpreting the results of several computations attempting to simulate the flow through a high enthalpy flow facility as well as experiments attempting to take advantage of the acoustic interaction with the high enthalpy environment. Because of the difficulty in modeling these experiments, direct simulations of acoustic waves in a hypersonic flow of a gas with molecular vibration are performed. Lastly, compressible transient growth disturbances are simulated using a linear optimal disturbance solver as well as a CFD solver. The effect of an internal molecular process on this type of disturbance is tested through the use of a vibrational mode. It is the goal of the current work to reinforce the

  5. Determination of molar enthalpy of sublimation in case of orotic acid as obtained from experimental and computational data

    NASA Astrophysics Data System (ADS)

    Marochkin, Ilya I.; Altova, Ekaterina P.; Chilingarov, Norbert S.; Vilkova, Anna L.; Shishkov, Igor F.

    2018-03-01

    Saturated vapor pressure, ln(p/Pa) = (-21316 ± 511)/(T/K)+(41.64 ± 0.11), and enthalpy of sublimation of orotic acid, Δsub Hm0 (Tm) = 177 ± 4 kJ/mol, were determined by means of Knudsen effusion mass spectrometry in the temperature range of 423÷493 K. The computational approaches supported the experimental results reported. The theoretical estimation of the gas-phase enthalpy of formation for orotic acid was done with different working reactions used.

  6. Enthalpy of Mixing in Al–Tb Liquid

    DOE PAGES

    Zhou, Shihuai; Tackes, Carl; Napolitano, Ralph

    2017-06-21

    The liquid-phase enthalpy of mixing for Al$-$Tb alloys is measured for 3, 5, 8, 10, and 20 at% Tb at selected temperatures in the range from 1364 to 1439 K. Methods include isothermal solution calorimetry and isoperibolic electromagnetic levitation drop calorimetry. Mixing enthalpy is determined relative to the unmixed pure (Al and Tb) components. The required formation enthalpy for the Al3Tb phase is computed from first-principles calculations. Finally, based on our measurements, three different semi-empirical solution models are offered for the excess free energy of the liquid, including regular, subregular, and associate model formulations. These models are also compared withmore » the Miedema model prediction of mixing enthalpy.« less

  7. Enthalpies of Formation of Hydrazine and Its Derivatives.

    PubMed

    Dorofeeva, Olga V; Ryzhova, Oxana N; Suchkova, Taisiya A

    2017-07-20

    Enthalpies of formation, Δ f H 298 ° , in both the gas and condensed phase, and enthalpies of sublimation or vaporization have been estimated for hydrazine, NH 2 NH 2 , and its 36 various derivatives using quantum chemical calculations. The composite G4 method has been used along with isodesmic reaction schemes to derive a set of self-consistent high-accuracy gas-phase enthalpies of formation. To estimate the enthalpies of sublimation and vaporization with reasonable accuracy (5-20 kJ/mol), the method of molecular electrostatic potential (MEP) has been used. The value of Δ f H 298 ° (NH 2 NH 2 ,g) = 97.0 ± 3.0 kJ/mol was determined from 75 isogyric reactions involving about 50 reference species; for most of these species, the accurate Δ f H 298 ° (g) values are available in Active Thermochemical Tables (ATcT). The calculated value is in excellent agreement with the reported results of the most accurate models based on coupled cluster theory (97.3 kJ/mol, the average of six calculations). Thus, the difference between the values predicted by high-level theoretical calculations and the experimental value of Δ f H 298 ° (NH 2 NH 2 ,g) = 95.55 ± 0.19 kJ/mol recommended in the ATcT and other comprehensive reference sources is sufficiently large and requires further investigation. Different hydrazine derivatives have been also considered in this work. For some of them, both the enthalpy of formation in the condensed phase and the enthalpy of sublimation or vaporization are available; for other compounds, experimental data for only one of these properties exist. Evidence of accuracy of experimental data for the first group of compounds was provided by the agreement with theoretical Δ f H 298 ° (g) value. The unknown property for the second group of compounds was predicted using the MEP model. This paper presents a systematic comparison of experimentally determined enthalpies of formation and enthalpies of sublimation or vaporization with the results of

  8. Calculating the enthalpy of vaporization for ionic liquid clusters.

    PubMed

    Kelkar, Manish S; Maginn, Edward J

    2007-08-16

    Classical atomistic simulations are used to compute the enthalpy of vaporization of a series of ionic liquids composed of 1-alkyl-3-methylimidazolium cations paired with the bis(trifluoromethylsulfonyl)imide anion. The calculations show that the enthalpy of vaporization is lowest for neutral ion pairs. The enthalpy of vaporization increases by about 40 kJ/mol with the addition of each ion pair to the vaporizing cluster. Non-neutral clusters have much higher vaporization enthalpies than their neutral counterparts and thus are not expected to make up a significant fraction of volatile species. The enthalpy of vaporization increases slightly as the cation alkyl chain length increases and as temperature decreases. The calculated vaporization enthalpies are consistent with two sets of recent experimental measurements as well as with previous atomistic simulations.

  9. Proton affinity and enthalpy of formation of formaldehyde

    NASA Astrophysics Data System (ADS)

    Czakó, Gábor; Nagy, Balázs; Tasi, Gyula; Somogyi, Árpád; Šimunek, Ján; Noga, Jozef; Braams, Bastiaan J.; Bowman, Joel M.; Császár; , Attila G.

    The proton affinity and the enthalpy of formation of the prototypical carbonyl, formaldehyde, have been determined by the first-principles composite focal-point analysis (FPA) approach. The electronic structure computations employed the all-electron coupled-cluster method with up to single, double, triple, quadruple, and even pentuple excitations. In these computations the aug-cc-p(C)VXZ [X = 2(D), 3(T), 4(Q), 5, and 6] correlation-consistent Gaussian basis sets for C and O were used in conjunction with the corresponding aug-cc-pVXZ (X = 2-6) sets for H. The basis set limit values have been confirmed via explicitly correlated computations. Our FPA study supersedes previous computational work for the proton affinity and to some extent the enthalpy of formation of formaldehyde by accounting for (a) electron correlation beyond the "gold standard" CCSD(T) level; (b) the non-additivity of core electron correlation effects; (c) scalar relativity; (d) diagonal Born-Oppenheimer corrections computed at a correlated level; (e) anharmonicity of zero-point vibrational energies, based on global potential energy surfaces and variational vibrational computations; and (f) thermal corrections to enthalpies by direct summation over rovibrational energy levels. Our final proton affinities at 298.15 (0.0) K are ΔpaHo (H2CO) = 711.02 (704.98) ± 0.39 kJ mol-1. Our final enthalpies of formation at 298.15 (0.0) K are ΔfHo (H2CO) = -109.23 (-105.42) ± 0.33 kJ mol-1. The latter values are based on the enthalpy of the H2 + CO → H2CO reaction but supported by two further reaction schemes, H2O + C → H2CO and 2H + C + O → H2CO. These values, especially ΔpaHo (H2CO), have better accuracy and considerably lower uncertainty than the best previous recommendations and thus should be employed in future studies.

  10. Partial molar enthalpies and reaction enthalpies from equilibrium molecular dynamics simulation

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

    Schnell, Sondre K.; Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720; Department of Chemistry, Faculty of Natural Science and Technology, Norwegian University of Science and Technology, 4791 Trondheim

    2014-10-14

    We present a new molecular simulation technique for determining partial molar enthalpies in mixtures of gases and liquids from single simulations, without relying on particle insertions, deletions, or identity changes. The method can also be applied to systems with chemical reactions. We demonstrate our method for binary mixtures of Weeks-Chandler-Anderson particles by comparing with conventional simulation techniques, as well as for a simple model that mimics a chemical reaction. The method considers small subsystems inside a large reservoir (i.e., the simulation box), and uses the construction of Hill to compute properties in the thermodynamic limit from small-scale fluctuations. Results obtainedmore » with the new method are in excellent agreement with those from previous methods. Especially for modeling chemical reactions, our method can be a valuable tool for determining reaction enthalpies directly from a single MD simulation.« less

  11. Enthalpy effects on hypervelocity boundary layers

    NASA Astrophysics Data System (ADS)

    Adam, Philippe H.

    Shots with air and carbon dioxide were carried out in the T5 shock tunnel at GALCIT to study enthalpy effects on hypervelocity boundary layers. The model tested was a 1-meter long, 5-deg half-angle cone. It was instrumented with 51 chromel-constantan coaxial thermocouples and the surface heat transfer rate was computed to deduce the state of the boundary layer. Transitional boundary layers obtained confirm the stabilizing effect of enthalpy. As the reservoir enthalpy is increased, the transition Reynolds number evaluated at the reference conditions increases. This stabilizing effect is more rapid in gases with lower dissociation energy and it seems to level off when no further dissociation can be achieved. Normalizing the reservoir enthalpy with the edge enthalpy appears to collapse the data for all gases onto a single curve. A similar collapse is obtained when normalizing both the transition location and the reservoir enthalpy with the maximum temperature conditions obtained with BLIMPK, a nonequilibrium boundary layer code. The observation that reference conditions are more appropriate to normalize high enthalpy transition data was taken a step further by comparing the tunnel data with results from a reentry experiment. When the edge conditions are used, the tunnel and flight data are around an order of magnitude apart. This is commonly attributed to high disturbance levels in tunnels that cause the boundary layer to transition early. However, when the reference conditions are used instead, the tunnel and flight data come within striking distance of one another although the trends with enthalpy are reversed. This difference could be due to the cone bending and nose blunting. Experimental laminar heat transfer levels were compared to numerical results obtained with BLIMPK. Results for air indicate that the reactions are probably in nonequilibrium and that the wall is catalytic. The catalycity is seen to yield higher surface heat transfer rates than the

  12. Pauling's electronegativity equation and a new corollary accurately predict bond dissociation enthalpies and enhance current understanding of the nature of the chemical bond.

    PubMed

    Matsunaga, Nikita; Rogers, Donald W; Zavitsas, Andreas A

    2003-04-18

    Contrary to other recent reports, Pauling's original electronegativity equation, applied as Pauling specified, describes quite accurately homolytic bond dissociation enthalpies of common covalent bonds, including highly polar ones, with an average deviation of +/-1.5 kcal mol(-1) from literature values for 117 such bonds. Dissociation enthalpies are presented for more than 250 bonds, including 79 for which experimental values are not available. Some previous evaluations of accuracy gave misleadingly poor results by applying the equation to cases for which it was not derived and for which it should not reproduce experimental values. Properly interpreted, the results of the equation provide new and quantitative insights into many facets of chemistry such as radical stabilities, factors influencing reactivity in electrophilic aromatic substitutions, the magnitude of steric effects, conjugative stabilization in unsaturated systems, rotational barriers, molecular and electronic structure, and aspects of autoxidation. A new corollary of the original equation expands its applicability and provides a rationale for previously observed empirical correlations. The equation raises doubts about a new bonding theory. Hydrogen is unique in that its electronegativity is not constant.

  13. Formation enthalpies for transition metal alloys using machine learning

    NASA Astrophysics Data System (ADS)

    Ubaru, Shashanka; Miedlar, Agnieszka; Saad, Yousef; Chelikowsky, James R.

    2017-06-01

    The enthalpy of formation is an important thermodynamic property. Developing fast and accurate methods for its prediction is of practical interest in a variety of applications. Material informatics techniques based on machine learning have recently been introduced in the literature as an inexpensive means of exploiting materials data, and can be used to examine a variety of thermodynamics properties. We investigate the use of such machine learning tools for predicting the formation enthalpies of binary intermetallic compounds that contain at least one transition metal. We consider certain easily available properties of the constituting elements complemented by some basic properties of the compounds, to predict the formation enthalpies. We show how choosing these properties (input features) based on a literature study (using prior physics knowledge) seems to outperform machine learning based feature selection methods such as sensitivity analysis and LASSO (least absolute shrinkage and selection operator) based methods. A nonlinear kernel based support vector regression method is employed to perform the predictions. The predictive ability of our model is illustrated via several experiments on a dataset containing 648 binary alloys. We train and validate the model using the formation enthalpies calculated using a model by Miedema, which is a popular semiempirical model used for the prediction of formation enthalpies of metal alloys.

  14. Prediction of solvation enthalpy of gaseous organic compounds in propanol

    NASA Astrophysics Data System (ADS)

    Golmohammadi, Hassan; Dashtbozorgi, Zahra

    2016-09-01

    The purpose of this paper is to present a novel way for developing quantitative structure-property relationship (QSPR) models to predict the gas-to-propanol solvation enthalpy (Δ H solv) of 95 organic compounds. Different kinds of descriptors were calculated for each compound using the Dragon software package. The variable selection technique of replacement method (RM) was employed to select the optimal subset of solute descriptors. Our investigation reveals that the dependence of physical chemistry properties of solution on solvation enthalpy is nonlinear and that the RM method is unable to model the solvation enthalpy accurately. The results established that the calculated Δ H solv values by SVM were in good agreement with the experimental ones, and the performances of the SVM models were superior to those obtained by RM model.

  15. Monte Carlo method for computing density of states and quench probability of potential energy and enthalpy landscapes.

    PubMed

    Mauro, John C; Loucks, Roger J; Balakrishnan, Jitendra; Raghavan, Srikanth

    2007-05-21

    The thermodynamics and kinetics of a many-body system can be described in terms of a potential energy landscape in multidimensional configuration space. The partition function of such a landscape can be written in terms of a density of states, which can be computed using a variety of Monte Carlo techniques. In this paper, a new self-consistent Monte Carlo method for computing density of states is described that uses importance sampling and a multiplicative update factor to achieve rapid convergence. The technique is then applied to compute the equilibrium quench probability of the various inherent structures (minima) in the landscape. The quench probability depends on both the potential energy of the inherent structure and the volume of its corresponding basin in configuration space. Finally, the methodology is extended to the isothermal-isobaric ensemble in order to compute inherent structure quench probabilities in an enthalpy landscape.

  16. Evaluation of Enthalpy Diagrams for NH3-H2O Absorption Refrigerator

    NASA Astrophysics Data System (ADS)

    Takei, Toshitaka; Saito, Kiyoshi; Kawai, Sunao

    The protection of environment is becoming a grave problem nowadays and an absorption refrigerator, which does not use fleon as a refrigerant, is acquiring a close attention. Among the absorption refrigerators, a number of ammonia-water absorption refrigerators are being used in realm such as refrigeration and ice accumulation, since this type of refrigerator can produce below zero degree products. It is essential to conduct an investigation on the characteristics of ammonia-water absorption refrigerator in detail by means of computer simulation in order to realize low cost, highly efficient operation. Unfortunately, there have been number of problems in order to conduct computer simulations. Firstly, Merkel's achievements of enthalpy diagram does not give the relational equations. And secondly, although relational equation are being proposed by Ziegler, simpler equations that can be applied to computer simulation are yet to be proposed. In this research, simper equations based on Ziegler's equations have been derived to make computer simulation concerning the performance of ammonia-water absorption refrigerator possible-Both results of computer simulations using simple equations and Merkel's enthalpy diagram respectively, have been compared with the actual experimental data of one staged ammonia-water absorption refrigerator. Consequently, it is clarified that the results from Ziegler's equations agree with experimental data better than those from Merkel's enthalpy diagram.

  17. Undergraduate Students' Conceptions of Enthalpy, Enthalpy Change and Related Concepts

    ERIC Educational Resources Information Center

    Nilsson, Tor; Niedderer, Hans

    2014-01-01

    Research shows that students have problems understanding thermodynamic concepts and that a gap exists at the tertiary level related to more specific chemistry concepts such as enthalpy. Therefore, the aim of this study is to construct undergraduate students' conceptions of enthalpy, its change and related concepts. Three explorative small-scale…

  18. A flow calorimeter for determining combustion efficiency from residual enthalpy of exhaust gases

    NASA Technical Reports Server (NTRS)

    Evans, Albert; Hibbard, Robert R

    1954-01-01

    A flow calorimeter for determining the combustion efficiency of turbojet and ram-jet combustors from measurement of the residual enthalpy of combustion of the exhaust gas is described. Briefly, the calorimeter catalytically oxidizes the combustible constituents of exhaust-gas samples, and the resultant temperature rise is measured. This temperature rise is related to the residual enthalpy of combustion of the sample by previous calibration of the calorimeter. Combustion efficiency can be calculated from a knowledge of the residual enthalpy of the exhaust gas and the combustor input enthalpy. An accuracy of +-0.2 Btu per cubic foot was obtained with prepared fuel-air mixtures, and the combustion efficiencies of single turbojet combustors measured by both the flow-calorimeter and heat-balance methods compared within 3 percentage units. Flow calorimetry appears to be a suitable method for determining combustion efficiencies at high combustor temperatures where ordinary thermocouples cannot be used. The method is fundamentally more accurate than heat-balance methods at high combustion efficiencies and can be used to verify near-100-percent efficiency data.

  19. Behavior of the Enthalpy of Adsorption in Nanoporous Materials Close to Saturation Conditions

    PubMed Central

    2017-01-01

    Many important industrial separation processes based on adsorption operate close to saturation. In this regime, the underlying adsorption processes are mostly driven by entropic forces. At equilibrium, the entropy of adsorption is closely related to the enthalpy of adsorption. Thus, studying the behavior of the enthalpy of adsorption as a function of loading is fundamental to understanding separation processes. Unfortunately, close to saturation, the enthalpy of adsorption is hard to measure experimentally and hard to compute in simulations. In simulations, the enthalpy of adsorption is usually obtained from energy/particle fluctuations in the grand-canonical ensemble, but this methodology is hampered by vanishing insertions/deletions at high loading. To investigate the fundamental behavior of the enthalpy and entropy of adsorption at high loading, we develop a simplistic model of adsorption in a channel and show that at saturation the enthalpy of adsorption diverges to large positive values due to repulsive intermolecular interactions. However, there are many systems that can avoid repulsive intermolecular interactions and hence do not show this drastic increase in enthalpy of adsorption close to saturation. We find that the conventional grand-canonical Monte Carlo method is incapable of determining the enthalpy of adsorption from energy/particle fluctuations at high loading. Here, we show that by using the continuous fractional component Monte Carlo, the enthalpy of adsorption close to saturation conditions can be reliably obtained from the energy/particle fluctuations in the grand-canonical ensemble. The best method to study properties at saturation is the NVT energy (local-) slope methodology. PMID:28521093

  20. Numerical simulation of mushrooms during freezing using the FEM and an enthalpy: Kirchhoff formulation

    NASA Astrophysics Data System (ADS)

    Santos, M. V.; Lespinard, A. R.

    2011-12-01

    The shelf life of mushrooms is very limited since they are susceptible to physical and microbial attack; therefore they are usually blanched and immediately frozen for commercial purposes. The aim of this work was to develop a numerical model using the finite element technique to predict freezing times of mushrooms considering the actual shape of the product. The original heat transfer equation was reformulated using a combined enthalpy-Kirchhoff formulation, therefore an own computational program using Matlab 6.5 (MathWorks, Natick, Massachusetts) was developed, considering the difficulties encountered when simulating this non-linear problem in commercial softwares. Digital images were used to generate the irregular contour and the domain discretization. The numerical predictions agreed with the experimental time-temperature curves during freezing of mushrooms (maximum absolute error <3.2°C) obtaining accurate results and minimum computer processing times. The codes were then applied to determine required processing times for different operating conditions (external fluid temperatures and surface heat transfer coefficients).

  1. Facing the challenge of predicting the standard formation enthalpies of n-butyl-phosphate species with ab initio methods

    NASA Astrophysics Data System (ADS)

    Saab, Mohamad; Réal, Florent; Šulka, Martin; Cantrel, Laurent; Virot, François; Vallet, Valérie

    2017-06-01

    Tributyl-phosphate (TBP), a ligand used in the PUREX liquid-liquid separation process of spent nuclear fuel, can form an explosive mixture in contact with nitric acid that might lead to a violent explosive thermal runaway. In the context of safety of a nuclear reprocessing plant facility, it is crucial to predict the stability of TBP at elevated temperatures. So far, only the enthalpies of formation of TBP are available in the literature with rather large uncertainties, while those of its degradation products, di-(HDBP) and mono-(H2MBP), are unknown. In this goal, we have used state-of-the art quantum chemical methods to compute the formation enthalpies and entropies of TBP and its degradation products di-(HDBP) and mono-(H2MBP) in gas and liquid phases. Comparisons of levels of quantum chemical theory revealed that there are significant effects of correlation on their electronic structures, pushing for the need of not only high level of electronic correlation treatment, namely, local coupled cluster with single and double excitation operators and perturbative treatment of triple excitations, but also extrapolations to the complete basis to produce reliable and accurate thermodynamics data. Solvation enthalpies were computed with the conductor-like screening model for real solvents [COSMO-RS], for which we observe errors not exceeding 22 kJ mol-1. We thus propose with final uncertainty of about 20 kJ mol-1 standard enthalpies of formation of TBP, HDBP, and H2MBP which amounts to -1281.7 ± 24.4, -1229.4 ± 19.6, and -1176.7 ± 14.8 kJ mol-1, respectively, in the gas phase. In the liquid phase, the predicted values are -1367.3 ± 24.4, -1348.7 ± 19.6, and -1323.8± 14.8 kJ mol-1, to which we may add about -22 kJ mol-1 error from the COSMO-RS solvent model. From these data, the complete hydrolysis of TBP is predicted as an exothermic phenomena but showing a slightly endergonic process.

  2. Computational investigation of enthalpy-entropy compensation in complexation of glycoconjugated bile salts with β-cyclodextrin and analogs.

    PubMed

    Tidemand, Kasper D; Schönbeck, Christian; Holm, René; Westh, Peter; Peters, Günther H

    2014-09-18

    The inclusion complexes of glycoconjugated bile salts with β-cyclodextrin (β-CD) and 2-hydroxypropyl-β-cyclodextrins (HP-β-CD) in aqueous solution were investigated by molecular dynamics simulations to provide a molecular explanation of the experimentally observed destabilizing effect of the HP substituents. Good agreement with experimental data was found with respect to penetration depths of CDs. An increased degree of HP substitution (DS) resulted in an increased probability of blocking the cavity opening, thereby hindering the bile salt from entering CD. Further, the residence time of water molecules in the cavity increased with the DS. Release of water from the cavity resulted in a positive enthalpy change, which correlates qualitatively with the experimentally determined increase in complexation enthalpy and contributes to the enthalpy-entropy compensation. The positive change in complexation entropy with DS was not able to compensate for this unfavorable change in enthalpy induced by the HP substituents, resulting in a destabilizing effect. This was found to originate from fixation of the HP substituents and decreased free rotation of the bile salts within the CD cavities.

  3. Skin-friction measurements in high-enthalpy hypersonic boundary layers

    NASA Astrophysics Data System (ADS)

    Goyne, C. P.; Stalker, R. J.; Paull, A.

    2003-06-01

    Skin-friction measurements are reported for high-enthalpy and high-Mach-number laminar, transitional and turbulent boundary layers. The measurements were performed in a free-piston shock tunnel with air-flow Mach number, stagnation enthalpy and Reynolds numbers in the ranges of 4.4 6.7, 3 13 MJ kg(-1) and 0.16× 10(6) 21× 10(6) , respectively. Wall temperatures were near 300 K and this resulted in ratios of wall enthalpy to flow-stagnation enthalpy in the range of 0.1 0.02. The experiments were performed using rectangular ducts. The measurements were accomplished using a new skin-friction gauge that was developed for impulse facility testing. The gauge was an acceleration compensated piezoelectric transducer and had a lowest natural frequency near 40 kHz. Turbulent skin-friction levels were measured to within a typical uncertainty of ± 7%. The systematic uncertainty in measured skin-friction coefficient was high for the tested laminar conditions; however, to within experimental uncertainty, the skin-friction and heat-transfer measurements were in agreement with the laminar theory of van Driest (1952). For predicting turbulent skin-friction coefficient, it was established that, for the range of Mach numbers and Reynolds numbers of the experiments, with cold walls and boundary layers approaching the turbulent equilibrium state, the Spalding & Chi (1964) method was the most suitable of the theories tested. It was also established that if the heat transfer rate to the wall is to be predicted, then the Spalding & Chi (1964) method should be used in conjunction with a Reynolds analogy factor near unity. If more accurate results are required, then an experimentally observed relationship between the Reynolds analogy factor and the skin-friction coefficient may be applied.

  4. Accurate atom-mapping computation for biochemical reactions.

    PubMed

    Latendresse, Mario; Malerich, Jeremiah P; Travers, Mike; Karp, Peter D

    2012-11-26

    The complete atom mapping of a chemical reaction is a bijection of the reactant atoms to the product atoms that specifies the terminus of each reactant atom. Atom mapping of biochemical reactions is useful for many applications of systems biology, in particular for metabolic engineering where synthesizing new biochemical pathways has to take into account for the number of carbon atoms from a source compound that are conserved in the synthesis of a target compound. Rapid, accurate computation of the atom mapping(s) of a biochemical reaction remains elusive despite significant work on this topic. In particular, past researchers did not validate the accuracy of mapping algorithms. We introduce a new method for computing atom mappings called the minimum weighted edit-distance (MWED) metric. The metric is based on bond propensity to react and computes biochemically valid atom mappings for a large percentage of biochemical reactions. MWED models can be formulated efficiently as Mixed-Integer Linear Programs (MILPs). We have demonstrated this approach on 7501 reactions of the MetaCyc database for which 87% of the models could be solved in less than 10 s. For 2.1% of the reactions, we found multiple optimal atom mappings. We show that the error rate is 0.9% (22 reactions) by comparing these atom mappings to 2446 atom mappings of the manually curated Kyoto Encyclopedia of Genes and Genomes (KEGG) RPAIR database. To our knowledge, our computational atom-mapping approach is the most accurate and among the fastest published to date. The atom-mapping data will be available in the MetaCyc database later in 2012; the atom-mapping software will be available within the Pathway Tools software later in 2012.

  5. Substituent and ring effects on enthalpies of formation: 2-methyl- and 2-ethylbenzimidazoles versus benzene- and imidazole-derivatives

    NASA Astrophysics Data System (ADS)

    Jiménez, Pilar; Roux, María Victoria; Dávalos, Juan Z.; Temprado, Manuel; Ribeiro da Silva, Manuel A. V.; Ribeiro da Silva, Maria Das Dores M. C.; Amaral, Luísa M. P. F.; Cabildo, Pilar; Claramunt, Rosa M.; Mó, Otilia; Yáñez, Manuel; Elguero, José

    The enthalpies of combustion, heat capacities, enthalpies of sublimation and enthalpies of formation of 2-methylbenzimidazole (2MeBIM) and 2-ethylbenzimidazole (2EtBIM) are reported and the results compared with those of benzimidazole itself (BIM). Theoretical estimates of the enthalpies of formation were obtained through the use of atom equivalent schemes. The necessary energies were obtained in single-point calculations at the B3LYP/6-311+G(d,p) on B3LYP/6-31G* optimized geometries. The comparison of experimental and calculated values of benzenes, imidazoles and benzimidazoles bearing H (unsubstituted), methyl and ethyl groups shows remarkable homogeneity. The energetic group contribution transferability is not followed, but either using it or adding an empirical interaction term, it is possible to generate an enormous collection of reasonably accurate data for different substituted heterocycles (pyrazole-derivatives, pyridine-derivatives, etc.) from the large amount of values available for substituted benzenes and those of the parent (pyrazole, pyridine) heterocycles.

  6. Enthalpies of a binary alloy during solidification

    NASA Technical Reports Server (NTRS)

    Poirier, D. R.; Nandapurkar, P.

    1988-01-01

    The purpose of the paper is to present a method of calculating the enthalpy of a dendritic alloy during solidification. The enthalpies of the dendritic solid and interdendritic liquid of alloys of the Pb-Sn system are evaluated, but the method could be applied to other binaries, as well. The enthalpies are consistent with a recent evaluation of the thermodynamics of Pb-Sn alloys and with the redistribution of solute in the same during dendritic solidification. Because of the heat of mixing in Pb-Sn alloys, the interdendritic liquid of hypoeutectic alloys (Pb-rich) of less than 50 wt pct Sn has enthalpies that increase as temperature decreases during solidification.

  7. On the Use of Enveloping Distribution Sampling (EDS) to Compute Free Enthalpy Differences between Different Conformational States of Molecules: Application to 310-, α-, and π-Helices.

    PubMed

    Lin, Zhixiong; Liu, Haiyan; Riniker, Sereina; van Gunsteren, Wilfred F

    2011-12-13

    Enveloping distribution sampling (EDS) is a powerful method to compute relative free energies from simulation. So far, the EDS method has only been applied to alchemical free energy differences, i.e., between different Hamiltonians defining different systems, and not yet to obtain free energy differences between different conformations or conformational states of a system. In this article, we extend the EDS formalism such that it can be applied to compute free energy differences of different conformations and apply it to compute the relative free enthalpy ΔG of 310-, α-, and π-helices of an alanine deca-peptide in explicit water solvent. The resulting ΔG values are compared to those obtained by standard thermodynamic integration (TI) and from so-called end-state simulations. A TI simulation requires the definition of a λ-dependent pathway which in the present case is based on hydrogen bonds of the different helical conformations. The values of ⟨(∂VTI)/(∂λ)⟩λ show a sharp change for a particular range of λ values, which is indicative of an energy barrier along the pathway, which lowers the accuracy of the resulting ΔG value. In contrast, in a two-state EDS simulation, an unphysical reference-state Hamiltonian which connects the parts of conformational space that are relevant to the different end states is constructed automatically; that is, no pathway needs to be defined. In the simulation using this reference state, both helices were sampled, and many transitions between them occurred, thus ensuring the accuracy of the resulting free enthalpy difference. According to the EDS simulations, the free enthalpy differences of the π-helix and the 310-helix versus the α-helix are 5 kJ mol(-1) and 47 kJ mol(-1), respectively, for an alanine deca-peptide in explicit SPC water solvent using the GROMOS 53A6 force field. The EDS method, which is a particular form of umbrella sampling, is thus applicable to compute free energy differences between

  8. Determination of Air Enthalpy Based on Meteorological Data as an Indicator for Heat Stress Assessment in Occupational Outdoor Environments, a Field Study in IRAN.

    PubMed

    Heidari, Hamidreza; Golbabaei, Farideh; Shamsipour, Aliakbar; Rahimi Forushani, Abbas; Gaeini, Abbasali

    2016-01-01

    Heat stress evaluation and timely notification, especially using meteorological data is an important issue attracted attention in recent years. Therefore, this study aimed at answering the following research questions: 1) can enthalpy as a common environmental parameter reported by meteorological agencies be applied accurately for evaluation of thermal condition of outdoor settings, and 2) if so, what is it's the best criterion to detect areas in stress or stress-free situations, separately. Nine climatic regions were selected throughout Iran covering a wide variety of climatic conditions like those, which exist around the world. Three types of parameters including measured (ta, RH, Pa and WBGT), estimated (metabolic rate and cloth thermal insulation), and calculated parameters (enthalpy and effective WBGT) were recorded for 1452 different situations. Enthalpy as a new indicator in this research was compared to WBGT in selected regions. Altogether, a good consistency was obtained between enthalpy and WBGT in selected regions (Kappa value: 0.815). Based on the good ROC curve obtained using MedCal software, the criterion of the values more than 74.24 for the new index was determined to explain heat stress situation for outdoor environments. Because of simplicity in measurement, applicability of the indicator for weather agencies, the consistency observed between enthalpy and a valid as well as accurate index (WBGT), sensor requirements which take only a few seconds to reach equilibrium and so on, enthalpy indicator can be introduced and applied as a good substitute for WBGT for outdoor settings.

  9. Enthalpy of phase transitions of lactams

    NASA Astrophysics Data System (ADS)

    Emel'yanenko, V. N.; Verevkin, S. P.; Ralys, R. V.; Turovtsev, V. V.; Orlov, V. Yu.

    2012-10-01

    The transpiration method is used to measure the temperature dependences of the vapors pressures of azacyclobutan-2-one (I, CAS 930-21-2) azacyclohexan-2-one (II, CAS 675-20-7); azacyclooctan-2-one (III, CAS 673-66-5); azacyclononan-2-one (IV, CAS 935-30-8) and azacyclotridecan-2-one (V, CAS 947-04-6). Enthalpies of sublimation and vaporisation are determined. The temperatures and enthalpies of fusion of compounds (I, III-V) are found by means of differential scanning calorimetry. The dependences of the enthalpies of vaporisation of lactones, lactams, cycloalkanes, cycloalkanones on the size of a cycle are analyzed.

  10. A DFT study on the enthalpies of thermite reactions and enthalpies of formation of metal composite oxide

    NASA Astrophysics Data System (ADS)

    Zhang, Yu-ying; Wang, Meng-jie; Chang, Chun-ran; Xu, Kang-zhen; Ma, Hai-xia; Zhao, Feng-qi

    2018-05-01

    The standard thermite reaction enthalpies (ΔrHmθ) for seven metal oxides were theoretically analyzed using density functional theory (DFT) under five different functional levels, and the results were compared with experimental values. Through the comparison of the linear fitting constants, mean error and root mean square error, the Perdew-Wang functional within the framework of local density approximation (LDA-PWC) and Perdew-Burke-Ernzerhof exchange-correlation functional within the framework of generalized gradient approximation (GGA-PBE) were selected to further calculate the thermite reaction enthalpies for metal composite oxides (MCOs). According to the Kirchhoff formula, the standard molar reaction enthalpies for these MCOs were obtained and their standard molar enthalpies of formation (ΔfHmθ) were finally calculated. The results indicated that GGA-PBE is the most suitable one out of the total five methods to calculate these oxides. Tungstate crystals present the maximum deviation of the enthalpies of thermite reactions for MCOs and these of their physical metal oxide mixtures, but ferrite crystals are the minimum. The correlation coefficients are all above 0.95, meaning linear fitting results are very precise. And the molar enthalpies of formation for NiMoO4, CuMoO4, PbZrO3 (Pm/3m), PbZrO3 (PBA2), PbZrO3 (PBam), MgZrO3, CdZrO3, MnZrO3, CuWO4 and Fe2WO6 were first obtained as -1078.75, -1058.45, -1343.87, -1266.54, -1342.29, -1333.03, -1210.43, -1388.05, -1131.07 and - 1860.11 kJ·mol-1, respectively.

  11. Automated Development of Accurate Algorithms and Efficient Codes for Computational Aeroacoustics

    NASA Technical Reports Server (NTRS)

    Goodrich, John W.; Dyson, Rodger W.

    1999-01-01

    The simulation of sound generation and propagation in three space dimensions with realistic aircraft components is a very large time dependent computation with fine details. Simulations in open domains with embedded objects require accurate and robust algorithms for propagation, for artificial inflow and outflow boundaries, and for the definition of geometrically complex objects. The development, implementation, and validation of methods for solving these demanding problems is being done to support the NASA pillar goals for reducing aircraft noise levels. Our goal is to provide algorithms which are sufficiently accurate and efficient to produce usable results rapidly enough to allow design engineers to study the effects on sound levels of design changes in propulsion systems, and in the integration of propulsion systems with airframes. There is a lack of design tools for these purposes at this time. Our technical approach to this problem combines the development of new, algorithms with the use of Mathematica and Unix utilities to automate the algorithm development, code implementation, and validation. We use explicit methods to ensure effective implementation by domain decomposition for SPMD parallel computing. There are several orders of magnitude difference in the computational efficiencies of the algorithms which we have considered. We currently have new artificial inflow and outflow boundary conditions that are stable, accurate, and unobtrusive, with implementations that match the accuracy and efficiency of the propagation methods. The artificial numerical boundary treatments have been proven to have solutions which converge to the full open domain problems, so that the error from the boundary treatments can be driven as low as is required. The purpose of this paper is to briefly present a method for developing highly accurate algorithms for computational aeroacoustics, the use of computer automation in this process, and a brief survey of the algorithms that

  12. Enthalpy Distributions of Arc Jet Flow Based on Measured Laser Induced Fluorescence, Heat Flux and Stagnation Pressure Distributions

    NASA Technical Reports Server (NTRS)

    Suess, Leonard E.; Milhoan, James D.; Oelke, Lance; Godfrey, Dennis; Larin, Maksim Y.; Scott, Carl D.; Grinstead, Jay H.; DelPapa, Steven

    2011-01-01

    The centerline total enthalpy of arc jet flow is determined using laser induced fluorescence of oxygen and nitrogen atoms. Each component of the energy, kinetic, thermal, and chemical can be determined from LIF measurements. Additionally, enthalpy distributions are inferred from heat flux and pressure probe distribution measurements using an engineering formula. Average enthalpies are determined by integration over the radius of the jet flow, assuming constant mass flux and a mass flux distribution estimated from computational fluid dynamics calculations at similar arc jet conditions. The trends show favorable agreement, but there is an uncertainty that relates to the multiple individual measurements and assumptions inherent in LIF measurements.

  13. Computer-based personality judgments are more accurate than those made by humans.

    PubMed

    Youyou, Wu; Kosinski, Michal; Stillwell, David

    2015-01-27

    Judging others' personalities is an essential skill in successful social living, as personality is a key driver behind people's interactions, behaviors, and emotions. Although accurate personality judgments stem from social-cognitive skills, developments in machine learning show that computer models can also make valid judgments. This study compares the accuracy of human and computer-based personality judgments, using a sample of 86,220 volunteers who completed a 100-item personality questionnaire. We show that (i) computer predictions based on a generic digital footprint (Facebook Likes) are more accurate (r = 0.56) than those made by the participants' Facebook friends using a personality questionnaire (r = 0.49); (ii) computer models show higher interjudge agreement; and (iii) computer personality judgments have higher external validity when predicting life outcomes such as substance use, political attitudes, and physical health; for some outcomes, they even outperform the self-rated personality scores. Computers outpacing humans in personality judgment presents significant opportunities and challenges in the areas of psychological assessment, marketing, and privacy.

  14. Enthalpy-entropy compensation: the role of solvation.

    PubMed

    Dragan, Anatoliy I; Read, Christopher M; Crane-Robinson, Colyn

    2017-05-01

    Structural modifications to interacting systems frequently lead to changes in both the enthalpy (heat) and entropy of the process that compensate each other, so that the Gibbs free energy is little changed: a major barrier to the development of lead compounds in drug discovery. The conventional explanation for such enthalpy-entropy compensation (EEC) is that tighter contacts lead to a more negative enthalpy but increased molecular constraints, i.e., a compensating conformational entropy reduction. Changes in solvation can also contribute to EEC but this contribution is infrequently discussed. We review long-established and recent cases of EEC and conclude that the large fluctuations in enthalpy and entropy observed are too great to be a result of only conformational changes and must result, to a considerable degree, from variations in the amounts of water immobilized or released on forming complexes. Two systems exhibiting EEC show a correlation between calorimetric entropies and local mobilities, interpreted to mean conformational control of the binding entropy/free energy. However, a substantial contribution from solvation gives the same effect, as a consequence of a structural link between the amount of bound water and the protein flexibility. Only by assuming substantial changes in solvation-an intrinsically compensatory process-can a more complete understanding of EEC be obtained. Faced with such large, and compensating, changes in the enthalpies and entropies of binding, the best approach to engineering elevated affinities must be through the addition of ionic links, as they generate increased entropy without affecting the enthalpy.

  15. Enthalpy of mixing of liquid Co–Sn alloys

    PubMed Central

    Yakymovych, A.; Fürtauer, S.; Elmahfoudi, A.; Ipser, H.; Flandorfer, H.

    2014-01-01

    A literature overview of enthalpy of mixing data for liquid Co–Sn alloys shows large scattering but no clear temperature dependence. Therefore drop calorimetry was performed in the Co–Sn system at twelve different temperatures in 100 K steps in the temperature range (673 to 1773) K. The integral enthalpy of mixing was determined starting from 1173 K and fitted to a standard Redlich–Kister polynomial. In addition, the limiting partial molar enthalpy of Co in Sn was investigated by small additions of Co to liquid Sn at temperatures (673 to 1773) K. The integral and partial molar enthalpies of the Co–Sn system generally show an exothermic mixing behavior. Significant temperature dependence was detected for the enthalpies of mixing. The minimum integral enthalpy values vary with rising temperature from approx. −7820 J/mol at T = 1173 K to −1350 J/mol at T = 1773 K; the position of the minimum is between (59 and 61) at.% Co. The results are discussed and compared with literature data available for this system. X-ray studies and scanning electron microscopy of selected alloys obtained from the calorimetric measurements were carried out in order to check the completeness of the solution process. PMID:24994940

  16. Enthalpy generation from mixing in hohlraum-driven targets

    NASA Astrophysics Data System (ADS)

    Amendt, Peter; Milovich, Jose

    2016-10-01

    The increase in enthalpy from the physical mixing of two initially separated materials is analytically estimated and applied to ICF implosions and gas-filled hohlraums. Pressure and temperature gradients across a classical interface are shown to be the origin of enthalpy generation from mixing. The amount of enthalpy generation is estimated to be on the order of 100 Joules for a 10 micron-scale annular mixing layer between the solid deuterium-tritium fuel and the undoped high-density carbon ablator of a NIF-scale implosion. A potential resonance is found between the mixing layer thickness and gravitational (Cs2/ g) and temperature-gradient scale lengths, leading to elevated enthalpy generation. These results suggest that if mixing occurs in current capsule designs for the National Ignition Facility, the ignition margin may be appreciably eroded by the associated enthalpy of mixing. The degree of enthalpy generation from mixing of high- Z hohlraum wall material and low- Z gas fills is estimated to be on the order of 100 kJ or more for recent NIF-scale hohlraum experiments, which is consistent with the inferred missing energy based on observed delays in capsule implosion times. Work performed under the auspices of Lawrence Livermore National Security, LLC (LLNS) under Contract No. DE-AC52-07NA27344.

  17. An accurate computational method for the diffusion regime verification

    NASA Astrophysics Data System (ADS)

    Zhokh, Alexey A.; Strizhak, Peter E.

    2018-04-01

    The diffusion regime (sub-diffusive, standard, or super-diffusive) is defined by the order of the derivative in the corresponding transport equation. We develop an accurate computational method for the direct estimation of the diffusion regime. The method is based on the derivative order estimation using the asymptotic analytic solutions of the diffusion equation with the integer order and the time-fractional derivatives. The robustness and the computational cheapness of the proposed method are verified using the experimental methane and methyl alcohol transport kinetics through the catalyst pellet.

  18. Computer-based personality judgments are more accurate than those made by humans

    PubMed Central

    Youyou, Wu; Kosinski, Michal; Stillwell, David

    2015-01-01

    Judging others’ personalities is an essential skill in successful social living, as personality is a key driver behind people’s interactions, behaviors, and emotions. Although accurate personality judgments stem from social-cognitive skills, developments in machine learning show that computer models can also make valid judgments. This study compares the accuracy of human and computer-based personality judgments, using a sample of 86,220 volunteers who completed a 100-item personality questionnaire. We show that (i) computer predictions based on a generic digital footprint (Facebook Likes) are more accurate (r = 0.56) than those made by the participants’ Facebook friends using a personality questionnaire (r = 0.49); (ii) computer models show higher interjudge agreement; and (iii) computer personality judgments have higher external validity when predicting life outcomes such as substance use, political attitudes, and physical health; for some outcomes, they even outperform the self-rated personality scores. Computers outpacing humans in personality judgment presents significant opportunities and challenges in the areas of psychological assessment, marketing, and privacy. PMID:25583507

  19. Enthalpy of formation of anisole: implications for the controversy on the O-H bond dissociation enthalpy in phenol.

    PubMed

    Simões, Ricardo G; Agapito, Filipe; Diogo, Hermínio P; da Piedade, Manuel E Minas

    2014-11-20

    Significant discrepancies in the literature data for the enthalpy of formation of gaseous anisole, ΔfHmo(PhOCH3, g), have fueled an ongoing controversy regarding the most reliable enthalpy of formation of the phenoxy radical and of the gas phase O-H bond dissociation enthalpy, DHo(PhO-H), in phenol. In the present work ΔfHmo(PhOCH3, g) was reassessed using a combination of calorimetric determinations and high-level (W2-F12) ab initio calculations. Static-bomb combustion calorimetry led to the standard molar enthalpy of formation of liquid anisole at 298.15 K, ΔfHmo(PhOCH3, l) = −(117.1 ± 1.4) kJ·mol(-1). The corresponding enthalpy of vaporization was obtained as, ΔvapHmo(PhOCH3) = 46.41 ± 0.26 kJ·mol(-1), by Calvet-drop microcalorimetry. These results give ΔfHmo(PhOCH3, g) = −(70.7 ± 1.4) kJ·mol(-1), in excellent agreement with ΔfHmo(PhOCH3, g) = −(70.8 ± 3.2) kJ·mol(-1), obtained from the W2-F12 calculations. The ΔfHmo(PhOCH3, g) here recommended leads to ΔfHmo(PhO•, g) = 55.5 ± 2.4 kJ·mol(-)1 and DH°(PhO-H) = 368.1 ± 2.6 kJ·mol(-1).

  20. Fast and accurate computation of projected two-point functions

    NASA Astrophysics Data System (ADS)

    Grasshorn Gebhardt, Henry S.; Jeong, Donghui

    2018-01-01

    We present the two-point function from the fast and accurate spherical Bessel transformation (2-FAST) algorithmOur code is available at https://github.com/hsgg/twoFAST. for a fast and accurate computation of integrals involving one or two spherical Bessel functions. These types of integrals occur when projecting the galaxy power spectrum P (k ) onto the configuration space, ξℓν(r ), or spherical harmonic space, Cℓ(χ ,χ'). First, we employ the FFTLog transformation of the power spectrum to divide the calculation into P (k )-dependent coefficients and P (k )-independent integrations of basis functions multiplied by spherical Bessel functions. We find analytical expressions for the latter integrals in terms of special functions, for which recursion provides a fast and accurate evaluation. The algorithm, therefore, circumvents direct integration of highly oscillating spherical Bessel functions.

  1. The thermochemistry of 2,4-pentanedione revisited: observance of a nonzero enthalpy of mixing between tautomers and its effects on enthalpies of formation.

    PubMed

    Temprado, Manuel; Roux, Maria Victoria; Umnahanant, Patamaporn; Zhao, Hui; Chickos, James S

    2005-06-30

    The enthalpies of formation of pure liquid and gas-phase (Z)-4-hydroxy-3-penten-2-one and 2,4-pentanedione are examined in the light of some more recent NMR studies on the enthalpy differences between gas-phase enthalpies of the two tautomers. Correlation gas chromatography experiments are used to evaluate the vaporization enthalpies of the pure tautomers. Values of (51.2 +/- 2.2) and (50.8 +/- 0.6) kJ.mol(-1) are measured for pure 2,4-pentanedione and (Z)-4-hydroxy-3-penten-2-one, respectively. The value of (50.8 +/- 0.6) kJ.mol(-1) can be contrasted to a value of (43.2 +/- 0.2) kJ.mol(-1) calculated for pure (Z)-4-hydroxy-3-penten-2-one when the vaporization enthalpy is measured in a mixture of tautomers. The difference is attributed to an endothermic enthalpy of mixing that destabilizes the mixture relative to the pure components. Calculation of new enthalpies of formation for (Z)-4-hydroxy-3-penten-2-one and 2,4-pentanedione in both the gas, Delta(f)H degrees (m)(g) = (-378.2 +/- 1.2) and (-358.9 +/- 2.5) kJ.mol(-1), respectively, and liquid phases, Delta(f)H degrees (m)(l) = (-429.0 +/- 1.0) and (-410.1 +/- 1.2) kJ.mol(-1), respectively, results in enthalpy differences between the two tautomers both in the liquid and gas phases that are identical within experimental error, and in excellent agreement with recent gas-phase NMR studies.

  2. Petascale self-consistent electromagnetic computations using scalable and accurate algorithms for complex structures

    NASA Astrophysics Data System (ADS)

    Cary, John R.; Abell, D.; Amundson, J.; Bruhwiler, D. L.; Busby, R.; Carlsson, J. A.; Dimitrov, D. A.; Kashdan, E.; Messmer, P.; Nieter, C.; Smithe, D. N.; Spentzouris, P.; Stoltz, P.; Trines, R. M.; Wang, H.; Werner, G. R.

    2006-09-01

    As the size and cost of particle accelerators escalate, high-performance computing plays an increasingly important role; optimization through accurate, detailed computermodeling increases performance and reduces costs. But consequently, computer simulations face enormous challenges. Early approximation methods, such as expansions in distance from the design orbit, were unable to supply detailed accurate results, such as in the computation of wake fields in complex cavities. Since the advent of message-passing supercomputers with thousands of processors, earlier approximations are no longer necessary, and it is now possible to compute wake fields, the effects of dampers, and self-consistent dynamics in cavities accurately. In this environment, the focus has shifted towards the development and implementation of algorithms that scale to large numbers of processors. So-called charge-conserving algorithms evolve the electromagnetic fields without the need for any global solves (which are difficult to scale up to many processors). Using cut-cell (or embedded) boundaries, these algorithms can simulate the fields in complex accelerator cavities with curved walls. New implicit algorithms, which are stable for any time-step, conserve charge as well, allowing faster simulation of structures with details small compared to the characteristic wavelength. These algorithmic and computational advances have been implemented in the VORPAL7 Framework, a flexible, object-oriented, massively parallel computational application that allows run-time assembly of algorithms and objects, thus composing an application on the fly.

  3. Enthalpy of sublimation as measured using a silicon oscillator

    NASA Astrophysics Data System (ADS)

    Shakeel, Hamza; Pomeroy, J. M.

    In this study, we report the enthalpy of sublimation of common gases (nitrogen, oxygen, argon, carbon dioxide, neon, krypton, xenon, and water vapor) using a large area silicon oscillator with a sub-ng (~0.027 ng/cm2) mass sensitivity. The double paddle oscillator design enables high frequency stability (17 ppb) at cryogenic temperatures and provides a consistent technique for enthalpy measurements. The enthalpies of sublimation are derived from the rate of mass loss during programmed thermal desorption and are detected as a change in the resonance frequency of the self-tracking oscillator. These measured enthalpy values show excellent agreement with the accepted literature values.

  4. Increase of stagnation pressure and enthalpy in shock tunnels

    NASA Technical Reports Server (NTRS)

    Bogdanoff, David W.; Cambier, Jean-Luc

    1992-01-01

    High stagnation pressures and enthalpies are required for the testing of aerospace vehicles such as aerospace planes, aeroassist vehicles, and reentry vehicles. Among the most useful ground test facilities for performing such tests are shock tunnels. With a given driver gas condition, the enthalpy and pressure in the driven tube nozzle reservoir condition can be varied by changing the driven tube geometry and initial gas fill pressure. Reducing the driven tube diameter yields only very modest increases in reservoir pressure and enthalpy. Reducing the driven tube initial gas fill pressure can increase the reservoir enthalpy significantly, but at the cost of reduced reservoir pressure and useful test time. A new technique, the insertion of a converging section in the driven tube is found to produce substantial increases in both reservoir pressure and enthalpy. Using a one-dimensional inviscid full kinetics code, a number of different locations and shapes for the converging driven tube section were studied and the best cases found. For these best cases, for driven tube diameter reductions of factors of 2 and 3, the reservoir pressure can be increased by factors of 2.1 and 3.2, respectively and the enthalpy can be increased by factors of 1.5 and 2.1, respectively.

  5. Experimental formation enthalpies for intermetallic phases and other inorganic compounds

    PubMed Central

    Kim, George; Meschel, S. V.; Nash, Philip; Chen, Wei

    2017-01-01

    The standard enthalpy of formation of a compound is the energy associated with the reaction to form the compound from its component elements. The standard enthalpy of formation is a fundamental thermodynamic property that determines its phase stability, which can be coupled with other thermodynamic data to calculate phase diagrams. Calorimetry provides the only direct method by which the standard enthalpy of formation is experimentally measured. However, the measurement is often a time and energy intensive process. We present a dataset of enthalpies of formation measured by high-temperature calorimetry. The phases measured in this dataset include intermetallic compounds with transition metal and rare-earth elements, metal borides, metal carbides, and metallic silicides. These measurements were collected from over 50 years of calorimetric experiments. The dataset contains 1,276 entries on experimental enthalpy of formation values and structural information. Most of the entries are for binary compounds but ternary and quaternary compounds are being added as they become available. The dataset also contains predictions of enthalpy of formation from first-principles calculations for comparison. PMID:29064466

  6. Calibration of Axisymmetric and Quasi-1D Solvers for High Enthalpy Nozzles

    NASA Technical Reports Server (NTRS)

    Papadopoulos, P. E.; Gochberg, L. A.; Tokarcik-Polsky, S.; Venkatapathy, E.; Deiwert, G. S.; Edwards, Thomas A. (Technical Monitor)

    1994-01-01

    The proposed paper will present a numerical investigation of the flow characteristics and boundary layer development in the nozzles of high enthalpy shock tunnel facilities used for hypersonic propulsion testing. The computed flow will be validated against existing experimental data. Pitot pressure data obtained at the entrance of the test cabin will be used to validate the numerical simulations. It is necessary to accurately model the facility nozzles in order to characterize the test article flow conditions. Initially the axisymmetric nozzle flow will be computed using a Navier Stokes solver for a range of reservoir conditions. The calculated solutions will be compared and calibrated against available experimental data from the DLR HEG piston-driven shock tunnel and the 16-inch shock tunnel at NASA Ames Research Center. The Reynolds number is assumed to be high enough at the throat that the boundary layer flow is assumed turbulent at this point downstream. The real gas affects will be examined. In high Mach number facilities the boundary layer is thick. Attempts will be made to correlate the boundary layer displacement thickness. The displacement thickness correlation will be used to calibrate the quasi-1D codes NENZF and LSENS in order to provide fast and efficient tools of characterizing the facility nozzles. The calibrated quasi-1D codes will be implemented to study the effects of chemistry and the flow condition variations at the test section due to small variations in the driver gas conditions.

  7. Accounting for apparent deviations between calorimetric and van't Hoff enthalpies.

    PubMed

    Kantonen, Samuel A; Henriksen, Niel M; Gilson, Michael K

    2018-03-01

    In theory, binding enthalpies directly obtained from calorimetry (such as ITC) and the temperature dependence of the binding free energy (van't Hoff method) should agree. However, previous studies have often found them to be discrepant. Experimental binding enthalpies (both calorimetric and van't Hoff) are obtained for two host-guest pairs using ITC, and the discrepancy between the two enthalpies is examined. Modeling of artificial ITC data is also used to examine how different sources of error propagate to both types of binding enthalpies. For the host-guest pairs examined here, good agreement, to within about 0.4kcal/mol, is obtained between the two enthalpies. Additionally, using artificial data, we find that different sources of error propagate to either enthalpy uniquely, with concentration error and heat error propagating primarily to calorimetric and van't Hoff enthalpies, respectively. With modern calorimeters, good agreement between van't Hoff and calorimetric enthalpies should be achievable, barring issues due to non-ideality or unanticipated measurement pathologies. Indeed, disagreement between the two can serve as a flag for error-prone datasets. A review of the underlying theory supports the expectation that these two quantities should be in agreement. We address and arguably resolve long-standing questions regarding the relationship between calorimetric and van't Hoff enthalpies. In addition, we show that comparison of these two quantities can be used as an internal consistency check of a calorimetry study. Copyright © 2017 Elsevier B.V. All rights reserved.

  8. A new approach to compute accurate velocity of meteors

    NASA Astrophysics Data System (ADS)

    Egal, Auriane; Gural, Peter; Vaubaillon, Jeremie; Colas, Francois; Thuillot, William

    2016-10-01

    The CABERNET project was designed to push the limits of meteoroid orbit measurements by improving the determination of the meteors' velocities. Indeed, despite of the development of the cameras networks dedicated to the observation of meteors, there is still an important discrepancy between the measured orbits of meteoroids computed and the theoretical results. The gap between the observed and theoretic semi-major axis of the orbits is especially significant; an accurate determination of the orbits of meteoroids therefore largely depends on the computation of the pre-atmospheric velocities. It is then imperative to dig out how to increase the precision of the measurements of the velocity.In this work, we perform an analysis of different methods currently used to compute the velocities and trajectories of the meteors. They are based on the intersecting planes method developed by Ceplecha (1987), the least squares method of Borovicka (1990), and the multi-parameter fitting (MPF) method published by Gural (2012).In order to objectively compare the performances of these techniques, we have simulated realistic meteors ('fakeors') reproducing the different error measurements of many cameras networks. Some fakeors are built following the propagation models studied by Gural (2012), and others created by numerical integrations using the Borovicka et al. 2007 model. Different optimization techniques have also been investigated in order to pick the most suitable one to solve the MPF, and the influence of the geometry of the trajectory on the result is also presented.We will present here the results of an improved implementation of the multi-parameter fitting that allow an accurate orbit computation of meteors with CABERNET. The comparison of different velocities computation seems to show that if the MPF is by far the best method to solve the trajectory and the velocity of a meteor, the ill-conditioning of the costs functions used can lead to large estimate errors for noisy

  9. Boundary Layer Transition and Trip Effectiveness on an Apollo Capsule in the JAXA High Enthalpy Shock Tunnel (HIEST) Facility

    NASA Technical Reports Server (NTRS)

    Kirk, Lindsay C.; Lillard, Randolph P.; Olejniczak, Joseph; Tanno, Hideyuki

    2015-01-01

    Computational assessments were performed to size boundary layer trips for a scaled Apollo capsule model in the High Enthalpy Shock Tunnel (HIEST) facility at the JAXA Kakuda Space Center in Japan. For stagnation conditions between 2 MJ/kg and 20 MJ/kg and between 10 MPa and 60 MPa, the appropriate trips were determined to be between 0.2 mm and 1.3 mm high, which provided kappa/delta values on the heatshield from 0.15 to 2.25. The tripped configuration consisted of an insert with a series of diamond shaped trips along the heatshield downstream of the stagnation point. Surface heat flux measurements were obtained on a capsule with a 250 mm diameter, 6.4% scale model, and pressure measurements were taken at axial stations along the nozzle walls. At low enthalpy conditions, the computational predictions agree favorably to the test data along the heatshield centerline. However, agreement becomes less favorable as the enthalpy increases conditions. The measured surface heat flux on the heatshield from the HIEST facility was under-predicted by the computations in these cases. Both smooth and tripped configurations were tested for comparison, and a post-test computational analysis showed that kappa/delta values based on the as-measured stagnation conditions ranged between 0.5 and 1.2. Tripped configurations for both 0.6 mm and 0.8 mm trip heights were able to effectively trip the flow to fully turbulent for a range of freestream conditions.

  10. Creation of Anatomically Accurate Computer-Aided Design (CAD) Solid Models from Medical Images

    NASA Technical Reports Server (NTRS)

    Stewart, John E.; Graham, R. Scott; Samareh, Jamshid A.; Oberlander, Eric J.; Broaddus, William C.

    1999-01-01

    Most surgical instrumentation and implants used in the world today are designed with sophisticated Computer-Aided Design (CAD)/Computer-Aided Manufacturing (CAM) software. This software automates the mechanical development of a product from its conceptual design through manufacturing. CAD software also provides a means of manipulating solid models prior to Finite Element Modeling (FEM). Few surgical products are designed in conjunction with accurate CAD models of human anatomy because of the difficulty with which these models are created. We have developed a novel technique that creates anatomically accurate, patient specific CAD solids from medical images in a matter of minutes.

  11. Free enthalpies of replacing water molecules in protein binding pockets.

    PubMed

    Riniker, Sereina; Barandun, Luzi J; Diederich, François; Krämer, Oliver; Steffen, Andreas; van Gunsteren, Wilfred F

    2012-12-01

    Water molecules in the binding pocket of a protein and their role in ligand binding have increasingly raised interest in recent years. Displacement of such water molecules by ligand atoms can be either favourable or unfavourable for ligand binding depending on the change in free enthalpy. In this study, we investigate the displacement of water molecules by an apolar probe in the binding pocket of two proteins, cyclin-dependent kinase 2 and tRNA-guanine transglycosylase, using the method of enveloping distribution sampling (EDS) to obtain free enthalpy differences. In both cases, a ligand core is placed inside the respective pocket and the remaining water molecules are converted to apolar probes, both individually and in pairs. The free enthalpy difference between a water molecule and a CH(3) group at the same location in the pocket in comparison to their presence in bulk solution calculated from EDS molecular dynamics simulations corresponds to the binding free enthalpy of CH(3) at this location. From the free enthalpy difference and the enthalpy difference, the entropic contribution of the displacement can be obtained too. The overlay of the resulting occupancy volumes of the water molecules with crystal structures of analogous ligands shows qualitative correlation between experimentally measured inhibition constants and the calculated free enthalpy differences. Thus, such an EDS analysis of the water molecules in the binding pocket may give valuable insight for potency optimization in drug design.

  12. Free enthalpies of replacing water molecules in protein binding pockets

    NASA Astrophysics Data System (ADS)

    Riniker, Sereina; Barandun, Luzi J.; Diederich, François; Krämer, Oliver; Steffen, Andreas; van Gunsteren, Wilfred F.

    2012-12-01

    Water molecules in the binding pocket of a protein and their role in ligand binding have increasingly raised interest in recent years. Displacement of such water molecules by ligand atoms can be either favourable or unfavourable for ligand binding depending on the change in free enthalpy. In this study, we investigate the displacement of water molecules by an apolar probe in the binding pocket of two proteins, cyclin-dependent kinase 2 and tRNA-guanine transglycosylase, using the method of enveloping distribution sampling (EDS) to obtain free enthalpy differences. In both cases, a ligand core is placed inside the respective pocket and the remaining water molecules are converted to apolar probes, both individually and in pairs. The free enthalpy difference between a water molecule and a CH3 group at the same location in the pocket in comparison to their presence in bulk solution calculated from EDS molecular dynamics simulations corresponds to the binding free enthalpy of CH3 at this location. From the free enthalpy difference and the enthalpy difference, the entropic contribution of the displacement can be obtained too. The overlay of the resulting occupancy volumes of the water molecules with crystal structures of analogous ligands shows qualitative correlation between experimentally measured inhibition constants and the calculated free enthalpy differences. Thus, such an EDS analysis of the water molecules in the binding pocket may give valuable insight for potency optimization in drug design.

  13. Phase Transition Enthalpy Measurements of Organic and Organometallic Compounds. Sublimation, Vaporization and Fusion Enthalpies From 1880 to 2015. Part 1. C1 - C10

    NASA Astrophysics Data System (ADS)

    Acree, William; Chickos, James S.

    2016-09-01

    A compendium of phase change enthalpies published in 2010 is updated to include the period 1880-2015. Phase change enthalpies including fusion, vaporization, and sublimation enthalpies are included for organic, organometallic, and a few inorganic compounds. Part 1 of this compendium includes organic compounds from C1 to C10. Part 2 of this compendium, to be published separately, will include organic and organometallic compounds from C11 to C192. Sufficient data are presently available to permit thermodynamic cycles to be constructed as an independent means of evaluating the reliability of the data. Temperature adjustments of phase change enthalpies from the temperature of measurement to the standard reference temperature, T = 298.15 K, and a protocol for doing so are briefly discussed.

  14. Kinetic Evidence of an Apparent Negative Activation Enthalpy in an Organocatalytic Process

    PubMed Central

    Han, Xiao; Lee, Richmond; Chen, Tao; Luo, Jie; Lu, Yixin; Huang, Kuo-Wei

    2013-01-01

    A combined kinetic and computational study on our tryptophan-based bifunctional thiourea catalyzed asymmetric Mannich reactions reveals an apparent negative activation enthalpy. The formation of the pre-transition state complex has been unambiguously confirmed and these observations provide an experimental support for the formation of multiple hydrogen bonding network between the substrates and the catalyst. Such interactions allow the creation of a binding cavity, a key factor to install high enantioselectivity. PMID:23990028

  15. Improved patient size estimates for accurate dose calculations in abdomen computed tomography

    NASA Astrophysics Data System (ADS)

    Lee, Chang-Lae

    2017-07-01

    The radiation dose of CT (computed tomography) is generally represented by the CTDI (CT dose index). CTDI, however, does not accurately predict the actual patient doses for different human body sizes because it relies on a cylinder-shaped head (diameter : 16 cm) and body (diameter : 32 cm) phantom. The purpose of this study was to eliminate the drawbacks of the conventional CTDI and to provide more accurate radiation dose information. Projection radiographs were obtained from water cylinder phantoms of various sizes, and the sizes of the water cylinder phantoms were calculated and verified using attenuation profiles. The effective diameter was also calculated using the attenuation of the abdominal projection radiographs of 10 patients. When the results of the attenuation-based method and the geometry-based method shown were compared with the results of the reconstructed-axial-CT-image-based method, the effective diameter of the attenuation-based method was found to be similar to the effective diameter of the reconstructed-axial-CT-image-based method, with a difference of less than 3.8%, but the geometry-based method showed a difference of less than 11.4%. This paper proposes a new method of accurately computing the radiation dose of CT based on the patient sizes. This method computes and provides the exact patient dose before the CT scan, and can therefore be effectively used for imaging and dose control.

  16. Enthalpy measurement of coal-derived liquids. Final report, April 1981-September 1983. [517 to 10342 kPa; 340 to 664 K

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

    Kidnay, A.J.; Yesavage, V.F.

    This report summarizes the results of experimental measurements of enthalpies for quinoline using a freon boil-off flow calorimeter, and an investigation of the applicability of cubic equations of state to correlating the enthalpy of coal-liquids. In Part A the compound quinoline is discussed. Process flow in the flow calorimeter, operational problems, and equipment modifications are described. Procedural modifications, including a new sample purification procedure, are described. Part B discusses the correlational effort. This includes a discussion of past correlational work and the difficulties associated with a general correlation for coal liquid enthalpy. In addition experimental data and computer generated predictionsmore » are presented. Three equations of state were used to predict vapor pressures and enthalpies for ten pure component systems previously studied in the lab. In general, the results were encouraging. All three equations were found to be effective in predicting both enthalpies and vapor pressures. In addition, the equations worked well when fit to mixture enthalpies. The Modified SRK equation was found to be superior to the other equations and modeled all properties for both associating and nonassociating systems well. The Modified SRK equation did have a drawback in that it was not readily generalized since it required two parameters which must be fit to data for best results. In sum, it was shown that a four parameter equation of state could be used successfully to correlate the enthalpy of coal-liquid model compounds.« less

  17. Accurate computation of survival statistics in genome-wide studies.

    PubMed

    Vandin, Fabio; Papoutsaki, Alexandra; Raphael, Benjamin J; Upfal, Eli

    2015-05-01

    A key challenge in genomics is to identify genetic variants that distinguish patients with different survival time following diagnosis or treatment. While the log-rank test is widely used for this purpose, nearly all implementations of the log-rank test rely on an asymptotic approximation that is not appropriate in many genomics applications. This is because: the two populations determined by a genetic variant may have very different sizes; and the evaluation of many possible variants demands highly accurate computation of very small p-values. We demonstrate this problem for cancer genomics data where the standard log-rank test leads to many false positive associations between somatic mutations and survival time. We develop and analyze a novel algorithm, Exact Log-rank Test (ExaLT), that accurately computes the p-value of the log-rank statistic under an exact distribution that is appropriate for any size populations. We demonstrate the advantages of ExaLT on data from published cancer genomics studies, finding significant differences from the reported p-values. We analyze somatic mutations in six cancer types from The Cancer Genome Atlas (TCGA), finding mutations with known association to survival as well as several novel associations. In contrast, standard implementations of the log-rank test report dozens-hundreds of likely false positive associations as more significant than these known associations.

  18. Accurate Computation of Survival Statistics in Genome-Wide Studies

    PubMed Central

    Vandin, Fabio; Papoutsaki, Alexandra; Raphael, Benjamin J.; Upfal, Eli

    2015-01-01

    A key challenge in genomics is to identify genetic variants that distinguish patients with different survival time following diagnosis or treatment. While the log-rank test is widely used for this purpose, nearly all implementations of the log-rank test rely on an asymptotic approximation that is not appropriate in many genomics applications. This is because: the two populations determined by a genetic variant may have very different sizes; and the evaluation of many possible variants demands highly accurate computation of very small p-values. We demonstrate this problem for cancer genomics data where the standard log-rank test leads to many false positive associations between somatic mutations and survival time. We develop and analyze a novel algorithm, Exact Log-rank Test (ExaLT), that accurately computes the p-value of the log-rank statistic under an exact distribution that is appropriate for any size populations. We demonstrate the advantages of ExaLT on data from published cancer genomics studies, finding significant differences from the reported p-values. We analyze somatic mutations in six cancer types from The Cancer Genome Atlas (TCGA), finding mutations with known association to survival as well as several novel associations. In contrast, standard implementations of the log-rank test report dozens-hundreds of likely false positive associations as more significant than these known associations. PMID:25950620

  19. High enthalpy hypersonic boundary layer flow

    NASA Technical Reports Server (NTRS)

    Yanow, G.

    1972-01-01

    A theoretical and experimental study of an ionizing laminar boundary layer formed by a very high enthalpy flow (in excess of 12 eV per atom or 7000 cal/gm) with allowance for the presence of helium driver gas is described. The theoretical investigation has shown that the use of variable transport properties and their respective derivatives is very important in the solution of equilibrium boundary layer equations of high enthalpy flow. The effect of low level helium contamination on the surface heat transfer rate is minimal. The variation of ionization is much smaller in a chemically frozen boundary layer solution than in an equilibrium boundary layer calculation and consequently, the variation of the transport properties in the case of the former was not essential in the integration. The experiments have been conducted in a free piston shock tunnel, and a detailed study of its nozzle operation, including the effects of low levels of helium driver gas contamination has been made. Neither the extreme solutions of an equilibrium nor of a frozen boundary layer will adequately predict surface heat transfer rate in very high enthalpy flows.

  20. Enthalpies of solvation for dopamine hydrochloride in water-ethanol solutions

    NASA Astrophysics Data System (ADS)

    Vandyshev, V. N.; Ledenkov, S. F.; Molchanov, A. S.

    2012-10-01

    The enthalpies of dissolution of dopamine hydrochloride (H2Dop · HCl) in water-ethanol solvents containing from 0 to 0.8 mole fraction of ethanol are measured by calorimetry at 298.15 K. Standard enthalpies of transfer (Δtr H ∘) for the molecular (H2Dop) and cationic (H3Dop+) forms of dopamine from water into binary solvents are calculated from the obtained data. The enthalpies of transfer of H3Dop+ cation are determined from the enthalpies of dissolution of H2Dop · HCl using the familiar method of separating the molar quantities into ionic contributions (Ph4P+ = BPh{4/-}), and by an original alternative procedure. The effect of the composition of the binary solvent on the solvation of dopamine is considered.

  1. Determination of vaporization enthalpies of polychlorinated biphenyls by correlation gas chromatography.

    PubMed

    Puri, S; Chickos, J S; Welsh, W J

    2001-04-01

    The vaporization enthalpies of 16 polychlorinated biphenyls have been determined by correlation gas chromatography. This study was prompted by the realization that the vaporization enthalpy of the standard compounds used in previous studies, octadecane and eicosane, were values measured at 340 and 362 K, respectively, rather than at 298 K. Adjustment to 298 K amounts to a 7-8 kJ/mol increment in the values. With the inclusion of this adjustment, vaporization enthalpies evaluated by correlation gas chromatography are in good agreement with the values determined previously in the literature. The present results are based on the vaporization enthalpies of several standards whose values are well established in the literature. The standards include a variety of n-alkanes and various chlorinated hydrocarbons. The vaporization enthalpies of PCBs increased with the number of chlorine atoms and were found to be larger for meta- and para-substituted polychlorinated biphenyls.

  2. An Accurate and Dynamic Computer Graphics Muscle Model

    NASA Technical Reports Server (NTRS)

    Levine, David Asher

    1997-01-01

    A computer based musculo-skeletal model was developed at the University in the departments of Mechanical and Biomedical Engineering. This model accurately represents human shoulder kinematics. The result of this model is the graphical display of bones moving through an appropriate range of motion based on inputs of EMGs and external forces. The need existed to incorporate a geometric muscle model in the larger musculo-skeletal model. Previous muscle models did not accurately represent muscle geometries, nor did they account for the kinematics of tendons. This thesis covers the creation of a new muscle model for use in the above musculo-skeletal model. This muscle model was based on anatomical data from the Visible Human Project (VHP) cadaver study. Two-dimensional digital images from the VHP were analyzed and reconstructed to recreate the three-dimensional muscle geometries. The recreated geometries were smoothed, reduced, and sliced to form data files defining the surfaces of each muscle. The muscle modeling function opened these files during run-time and recreated the muscle surface. The modeling function applied constant volume limitations to the muscle and constant geometry limitations to the tendons.

  3. Protonation enthalpies of metal oxides from high temperature electrophoresis

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

    Rodriguez-Santiago, V; Fedkin, Mark V.; Lvov, Serguei N.

    2012-01-01

    Surface protonation reactions play an important role in the behavior of mineral and colloidal systems, specifically in hydrothermal aqueous environments. However, studies addressing the reactions at the solid/liquid interface at temperatures above 100 C are scarce. In this study, newly and previously obtained high temperature electrophoresis data (up to 260 C) zeta potentials and isoelectric points for metal oxides, including SiO2, SnO2, ZrO2, TiO2, and Fe3O4, were used in thermodynamic analysis to derive the standard enthalpies of their surface protonation. Two different approaches were used for calculating the protonation enthalpy: one is based on thermodynamic description of the 1-pKa modelmore » for surface protonation, and another one on a combination of crystal chemistry and solvation theories which link the relative permittivity of the solid phase and the ratio of the Pauling bond strength and bond length to standard protonation enthalpy. From this analysis, two expressions relating the protonation enthalpy to the relative permittivity of the solid phase were obtained.« less

  4. Protonation enthalpies of metal oxides from high temperature electrophoresis.

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

    Rodriguez-Santiago, V; Fedkin, Mark V; Lvov, Serguei N.

    2012-01-01

    Surface protonation reactions play an important role in the behavior of mineral and colloidal systems, specifically in hydrothermal aqueous environments. However, studies addressing the reactions at the solid/liquid interface at temperatures above 100 C are scarce. In this study, newly and previously obtained high temperature electrophoresis data (up to 260 C) - zeta potentials and isoelectric points - for metal oxides, including SiO{sub 2}, SnO{sub 2}, ZrO{sub 2}, TiO{sub 2}, and Fe{sub 3}O{sub 4}, were used in thermodynamic analysis to derive the standard enthalpies of their surface protonation. Two different approaches were used for calculating the protonation enthalpy: one ismore » based on thermodynamic description of the 1-pKa model for surface protonation, and another one - on a combination of crystal chemistry and solvation theories which link the relative permittivity of the solid phase and the ratio of the Pauling bond strength and bond length to standard protonation enthalpy. From this analysis, two expressions relating the protonation enthalpy to the relative permittivity of the solid phase were obtained.« less

  5. A Unified Methodology for Computing Accurate Quaternion Color Moments and Moment Invariants.

    PubMed

    Karakasis, Evangelos G; Papakostas, George A; Koulouriotis, Dimitrios E; Tourassis, Vassilios D

    2014-02-01

    In this paper, a general framework for computing accurate quaternion color moments and their corresponding invariants is proposed. The proposed unified scheme arose by studying the characteristics of different orthogonal polynomials. These polynomials are used as kernels in order to form moments, the invariants of which can easily be derived. The resulted scheme permits the usage of any polynomial-like kernel in a unified and consistent way. The resulted moments and moment invariants demonstrate robustness to noisy conditions and high discriminative power. Additionally, in the case of continuous moments, accurate computations take place to avoid approximation errors. Based on this general methodology, the quaternion Tchebichef, Krawtchouk, Dual Hahn, Legendre, orthogonal Fourier-Mellin, pseudo Zernike and Zernike color moments, and their corresponding invariants are introduced. A selected paradigm presents the reconstruction capability of each moment family, whereas proper classification scenarios evaluate the performance of color moment invariants.

  6. Calculation of Five Thermodynamic Molecular Descriptors by Means of a General Computer Algorithm Based on the Group-Additivity Method: Standard Enthalpies of Vaporization, Sublimation and Solvation, and Entropy of Fusion of Ordinary Organic Molecules and Total Phase-Change Entropy of Liquid Crystals.

    PubMed

    Naef, Rudolf; Acree, William E

    2017-06-25

    The calculation of the standard enthalpies of vaporization, sublimation and solvation of organic molecules is presented using a common computer algorithm on the basis of a group-additivity method. The same algorithm is also shown to enable the calculation of their entropy of fusion as well as the total phase-change entropy of liquid crystals. The present method is based on the complete breakdown of the molecules into their constituting atoms and their immediate neighbourhood; the respective calculations of the contribution of the atomic groups by means of the Gauss-Seidel fitting method is based on experimental data collected from literature. The feasibility of the calculations for each of the mentioned descriptors was verified by means of a 10-fold cross-validation procedure proving the good to high quality of the predicted values for the three mentioned enthalpies and for the entropy of fusion, whereas the predictive quality for the total phase-change entropy of liquid crystals was poor. The goodness of fit ( Q ²) and the standard deviation (σ) of the cross-validation calculations for the five descriptors was as follows: 0.9641 and 4.56 kJ/mol ( N = 3386 test molecules) for the enthalpy of vaporization, 0.8657 and 11.39 kJ/mol ( N = 1791) for the enthalpy of sublimation, 0.9546 and 4.34 kJ/mol ( N = 373) for the enthalpy of solvation, 0.8727 and 17.93 J/mol/K ( N = 2637) for the entropy of fusion and 0.5804 and 32.79 J/mol/K ( N = 2643) for the total phase-change entropy of liquid crystals. The large discrepancy between the results of the two closely related entropies is discussed in detail. Molecules for which both the standard enthalpies of vaporization and sublimation were calculable, enabled the estimation of their standard enthalpy of fusion by simple subtraction of the former from the latter enthalpy. For 990 of them the experimental enthalpy-of-fusion values are also known, allowing their comparison with predictions, yielding a correlation coefficient R

  7. Methods for Efficiently and Accurately Computing Quantum Mechanical Free Energies for Enzyme Catalysis.

    PubMed

    Kearns, F L; Hudson, P S; Boresch, S; Woodcock, H L

    2016-01-01

    Enzyme activity is inherently linked to free energies of transition states, ligand binding, protonation/deprotonation, etc.; these free energies, and thus enzyme function, can be affected by residue mutations, allosterically induced conformational changes, and much more. Therefore, being able to predict free energies associated with enzymatic processes is critical to understanding and predicting their function. Free energy simulation (FES) has historically been a computational challenge as it requires both the accurate description of inter- and intramolecular interactions and adequate sampling of all relevant conformational degrees of freedom. The hybrid quantum mechanical molecular mechanical (QM/MM) framework is the current tool of choice when accurate computations of macromolecular systems are essential. Unfortunately, robust and efficient approaches that employ the high levels of computational theory needed to accurately describe many reactive processes (ie, ab initio, DFT), while also including explicit solvation effects and accounting for extensive conformational sampling are essentially nonexistent. In this chapter, we will give a brief overview of two recently developed methods that mitigate several major challenges associated with QM/MM FES: the QM non-Boltzmann Bennett's acceptance ratio method and the QM nonequilibrium work method. We will also describe usage of these methods to calculate free energies associated with (1) relative properties and (2) along reaction paths, using simple test cases with relevance to enzymes examples. © 2016 Elsevier Inc. All rights reserved.

  8. Accurate computation of gravitational field of a tesseroid

    NASA Astrophysics Data System (ADS)

    Fukushima, Toshio

    2018-02-01

    We developed an accurate method to compute the gravitational field of a tesseroid. The method numerically integrates a surface integral representation of the gravitational potential of the tesseroid by conditionally splitting its line integration intervals and by using the double exponential quadrature rule. Then, it evaluates the gravitational acceleration vector and the gravity gradient tensor by numerically differentiating the numerically integrated potential. The numerical differentiation is conducted by appropriately switching the central and the single-sided second-order difference formulas with a suitable choice of the test argument displacement. If necessary, the new method is extended to the case of a general tesseroid with the variable density profile, the variable surface height functions, and/or the variable intervals in longitude or in latitude. The new method is capable of computing the gravitational field of the tesseroid independently on the location of the evaluation point, namely whether outside, near the surface of, on the surface of, or inside the tesseroid. The achievable precision is 14-15 digits for the potential, 9-11 digits for the acceleration vector, and 6-8 digits for the gradient tensor in the double precision environment. The correct digits are roughly doubled if employing the quadruple precision computation. The new method provides a reliable procedure to compute the topographic gravitational field, especially that near, on, and below the surface. Also, it could potentially serve as a sure reference to complement and elaborate the existing approaches using the Gauss-Legendre quadrature or other standard methods of numerical integration.

  9. Enthalpy of Formation of N 2 H 4 (Hydrazine) Revisited

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

    Feller, David; Bross, David H.; Ruscic, Branko

    2017-08-02

    In order to address the accuracy of the long-standing experimental enthalpy of formation of gas-phase hydrazine, fully confirmed in earlier versions of Active Thermochemical Tables (ATcT), the provenance of that value is re-examined in light of new high-end calculations of the Feller-Peterson-Dixon (FPD) variety. An overly optimistic determination of the vaporization enthalpy of hydrazine, which created an unrealistically strong connection between the gas phase thermochemistry and the calorimetric results defining the thermochemistry of liquid hydrazine was identified as the probable culprit. The new enthalpy of formation of gas-phase hydrazine, based on balancing all available knowledge, was determined to be 111.57more » ± 0.47 kJ/mol at 0 K (97.41 kJ/mol at 298.15 K). Close agreement was found between the ATcT (even excluding the latest theoretical result) and FPD enthalpies.« less

  10. Enthalpy of Formation of N2H4 (Hydrazine) Revisited.

    PubMed

    Feller, David; Bross, David H; Ruscic, Branko

    2017-08-17

    In order to address the accuracy of the long-standing experimental enthalpy of formation of gas-phase hydrazine, fully confirmed in earlier versions of Active Thermochemical Tables (ATcT), the provenance of that value is re-examined in light of new high-end calculations of the Feller-Peterson-Dixon (FPD) variety. An overly optimistic determination of the vaporization enthalpy of hydrazine, which created an unrealistically strong connection between the gas phase thermochemistry and the calorimetric results defining the thermochemistry of liquid hydrazine, was identified as the probable culprit. The new enthalpy of formation of gas-phase hydrazine, based on balancing all available knowledge, was determined to be 111.57 ± 0.47 kJ/mol at 0 K (97.42 ± 0.47 kJ/mol at 298.15 K). Close agreement was found between the ATcT (even excluding the latest theoretical result) and the FPD enthalpy.

  11. Predicting the enthalpies of melting and vaporization for pure components

    NASA Astrophysics Data System (ADS)

    Esina, Z. N.; Korchuganova, M. R.

    2014-12-01

    A mathematical model of the melting and vaporization enthalpies of organic components based on the theory of thermodynamic similarity is proposed. In this empirical model, the phase transition enthalpy for the homological series of n-alkanes, carboxylic acids, n-alcohols, glycols, and glycol ethers is presented as a function of the molecular mass, the number of carbon atoms in a molecule, and the normal transition temperature. The model also uses a critical or triple point temperature. It is shown that the results from predicting the melting and vaporization enthalpies enable the calculation of binary phase diagrams.

  12. Mixing Enthalpies of TbBr3-MBr Liquid Mixtures

    NASA Astrophysics Data System (ADS)

    Rycerz, L.; Gaune-Escard, M.

    2001-12-01

    The molar enthalpies of mixing, Δmix Hm in the binary liquid systems TbBr3-MBr (M = Li, Na, K, Rb, Cs) have been m easured with a Calvet-type high-tem perature microcalorimeter over the entire composition range with an accuracy of about 6 %. Mixing of the two liquid components was achieved by using the "break-off am poule" technique. All the investigated systems show negative enthalpies of mixing with a minim um value of approxim ately -1.25, - 8 .3 , -17.0, - 2 0 . 0 and -22.5 kJ mol -1, for M = Li, Na, K, Rb and Cs, respectively. The mixing enthalpy in the TbBr3- LiBr system is positive in the TbBr3-rich region. For all the systems, the enthalpy minimum occurs at mole fraction xTbBr3 ≈ 0.3 - 0.4. The molar enthalpies of form ation Δ formHm (3MBr, TbBr3, 1) for M = Li, Na, K, Rb and Cs at 1113 K (arising from the reaction 3M Br(1) +TbBr3(1) = (3MBr, TbBr3) (1)) are found to be -4 .8 , -31.3, -63.3, -70.3 and -8 1 .2 kJ mol-1 , respectively. The leastsquares coefficients A, B, C, D and E in the equation λ (kJ mol-1) = A + B x + C x2 + Dx3 + Ex4, where A is an interaction param eter and x = xTbBr , are also reported.

  13. Numerical Investigation of Double-Cone Flows with High Enthalpy Effects

    NASA Astrophysics Data System (ADS)

    Nompelis, I.; Candler, G. V.

    2009-01-01

    A numerical study of shock/shock and shock/boundary layer interactions generated by a double-cone model that is placed in a hypersonic free-stream is presented. Computational results are compared with the experimental measurements made at the CUBRC LENS facility for nitrogen flows at high enthalpy conditions. The CFD predictions agree well with surface pressure and heat-flux measurements for all but one of the double-cone cases that have been studied by the authors. Unsteadiness is observed in computations of one of the LENS cases, however for this case the experimental measurements show that the flowfield is steady. To understand this discrepancy, several double-cone experiments performed in two different facilities with both air and nitrogen as the working gas are examined in the present study. Computational results agree well with measurements made in both the AEDC tunnel 9 and the CUBRC LENS facility for double-cone flows at low free-stream Reynolds numbers where the flow is steady. It is shown that at higher free- stream pressures the double-cone simulations develop instabilities that result in an unsteady separation.

  14. Phase Transition Enthalpy Measurements of Organic and Organometallic Compounds. Sublimation, Vaporization and Fusion Enthalpies From 1880 to 2015. Part 1. C{sub 1} − C{sub 10}

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

    Acree, William; Chickos, James S.

    2016-09-15

    A compendium of phase change enthalpies published in 2010 is updated to include the period 1880–2015. Phase change enthalpies including fusion, vaporization, and sublimation enthalpies are included for organic, organometallic, and a few inorganic compounds. Part 1 of this compendium includes organic compounds from C{sub 1} to C{sub 10}. Part 2 of this compendium, to be published separately, will include organic and organometallic compounds from C{sub 11} to C{sub 192}. Sufficient data are presently available to permit thermodynamic cycles to be constructed as an independent means of evaluating the reliability of the data. Temperature adjustments of phase change enthalpies frommore » the temperature of measurement to the standard reference temperature, T = 298.15 K, and a protocol for doing so are briefly discussed.« less

  15. Enthalpy-based multiple-relaxation-time lattice Boltzmann method for solid-liquid phase-change heat transfer in metal foams.

    PubMed

    Liu, Qing; He, Ya-Ling; Li, Qing

    2017-08-01

    In this paper, an enthalpy-based multiple-relaxation-time (MRT) lattice Boltzmann (LB) method is developed for solid-liquid phase-change heat transfer in metal foams under the local thermal nonequilibrium (LTNE) condition. The enthalpy-based MRT-LB method consists of three different MRT-LB models: one for flow field based on the generalized non-Darcy model, and the other two for phase-change material (PCM) and metal-foam temperature fields described by the LTNE model. The moving solid-liquid phase interface is implicitly tracked through the liquid fraction, which is simultaneously obtained when the energy equations of PCM and metal foam are solved. The present method has several distinctive features. First, as compared with previous studies, the present method avoids the iteration procedure; thus it retains the inherent merits of the standard LB method and is superior to the iteration method in terms of accuracy and computational efficiency. Second, a volumetric LB scheme instead of the bounce-back scheme is employed to realize the no-slip velocity condition in the interface and solid phase regions, which is consistent with the actual situation. Last but not least, the MRT collision model is employed, and with additional degrees of freedom, it has the ability to reduce the numerical diffusion across the phase interface induced by solid-liquid phase change. Numerical tests demonstrate that the present method can serve as an accurate and efficient numerical tool for studying metal-foam enhanced solid-liquid phase-change heat transfer in latent heat storage. Finally, comparisons and discussions are made to offer useful information for practical applications of the present method.

  16. Enthalpy-based multiple-relaxation-time lattice Boltzmann method for solid-liquid phase-change heat transfer in metal foams

    NASA Astrophysics Data System (ADS)

    Liu, Qing; He, Ya-Ling; Li, Qing

    2017-08-01

    In this paper, an enthalpy-based multiple-relaxation-time (MRT) lattice Boltzmann (LB) method is developed for solid-liquid phase-change heat transfer in metal foams under the local thermal nonequilibrium (LTNE) condition. The enthalpy-based MRT-LB method consists of three different MRT-LB models: one for flow field based on the generalized non-Darcy model, and the other two for phase-change material (PCM) and metal-foam temperature fields described by the LTNE model. The moving solid-liquid phase interface is implicitly tracked through the liquid fraction, which is simultaneously obtained when the energy equations of PCM and metal foam are solved. The present method has several distinctive features. First, as compared with previous studies, the present method avoids the iteration procedure; thus it retains the inherent merits of the standard LB method and is superior to the iteration method in terms of accuracy and computational efficiency. Second, a volumetric LB scheme instead of the bounce-back scheme is employed to realize the no-slip velocity condition in the interface and solid phase regions, which is consistent with the actual situation. Last but not least, the MRT collision model is employed, and with additional degrees of freedom, it has the ability to reduce the numerical diffusion across the phase interface induced by solid-liquid phase change. Numerical tests demonstrate that the present method can serve as an accurate and efficient numerical tool for studying metal-foam enhanced solid-liquid phase-change heat transfer in latent heat storage. Finally, comparisons and discussions are made to offer useful information for practical applications of the present method.

  17. Theoretical calculation of enthalpy of formation of multiconformational molecules: 1,2-ethanediol, propanediols, and glycerol

    NASA Astrophysics Data System (ADS)

    Dorofeeva, Olga V.; Suchkova, Taisiya A.

    2018-04-01

    The gas-phase enthalpies of formation of four molecules with high flexibility, which leads to the existence of a large number of low-energy conformers, were calculated with the G4 method to see whether the lowest energy conformer is sufficient to achieve high accuracy in the computed values. The calculated values were in good agreement with the experiment, whereas adding the correction for conformer distribution makes the agreement worse. The reason for this effect is a large anharmonicity of low-frequency torsional motions, which is ignored in the calculation of ZPVE and thermal enthalpy. It was shown that the approximate correction for anharmonicity estimated using a free rotor model is of very similar magnitude compared with the conformer correction but has the opposite sign, and thus almost fully compensates for it. Therefore, the common practice of adding only the conformer correction is not without problems.

  18. Machine Learning of Parameters for Accurate Semiempirical Quantum Chemical Calculations

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

    Dral, Pavlo O.; von Lilienfeld, O. Anatole; Thiel, Walter

    2015-05-12

    We investigate possible improvements in the accuracy of semiempirical quantum chemistry (SQC) methods through the use of machine learning (ML) models for the parameters. For a given class of compounds, ML techniques require sufficiently large training sets to develop ML models that can be used for adapting SQC parameters to reflect changes in molecular composition and geometry. The ML-SQC approach allows the automatic tuning of SQC parameters for individual molecules, thereby improving the accuracy without deteriorating transferability to molecules with molecular descriptors very different from those in the training set. The performance of this approach is demonstrated for the semiempiricalmore » OM2 method using a set of 6095 constitutional isomers C7H10O2, for which accurate ab initio atomization enthalpies are available. The ML-OM2 results show improved average accuracy and a much reduced error range compared with those of standard OM2 results, with mean absolute errors in atomization enthalpies dropping from 6.3 to 1.7 kcal/mol. They are also found to be superior to the results from specific OM2 reparameterizations (rOM2) for the same set of isomers. The ML-SQC approach thus holds promise for fast and reasonably accurate high-throughput screening of materials and molecules.« less

  19. Machine learning of parameters for accurate semiempirical quantum chemical calculations

    DOE PAGES

    Dral, Pavlo O.; von Lilienfeld, O. Anatole; Thiel, Walter

    2015-04-14

    We investigate possible improvements in the accuracy of semiempirical quantum chemistry (SQC) methods through the use of machine learning (ML) models for the parameters. For a given class of compounds, ML techniques require sufficiently large training sets to develop ML models that can be used for adapting SQC parameters to reflect changes in molecular composition and geometry. The ML-SQC approach allows the automatic tuning of SQC parameters for individual molecules, thereby improving the accuracy without deteriorating transferability to molecules with molecular descriptors very different from those in the training set. The performance of this approach is demonstrated for the semiempiricalmore » OM2 method using a set of 6095 constitutional isomers C 7H 10O 2, for which accurate ab initio atomization enthalpies are available. The ML-OM2 results show improved average accuracy and a much reduced error range compared with those of standard OM2 results, with mean absolute errors in atomization enthalpies dropping from 6.3 to 1.7 kcal/mol. They are also found to be superior to the results from specific OM2 reparameterizations (rOM2) for the same set of isomers. The ML-SQC approach thus holds promise for fast and reasonably accurate high-throughput screening of materials and molecules.« less

  20. An Accurate and Computationally Efficient Model for Membrane-Type Circular-Symmetric Micro-Hotplates

    PubMed Central

    Khan, Usman; Falconi, Christian

    2014-01-01

    Ideally, the design of high-performance micro-hotplates would require a large number of simulations because of the existence of many important design parameters as well as the possibly crucial effects of both spread and drift. However, the computational cost of FEM simulations, which are the only available tool for accurately predicting the temperature in micro-hotplates, is very high. As a result, micro-hotplate designers generally have no effective simulation-tools for the optimization. In order to circumvent these issues, here, we propose a model for practical circular-symmetric micro-hot-plates which takes advantage of modified Bessel functions, computationally efficient matrix-approach for considering the relevant boundary conditions, Taylor linearization for modeling the Joule heating and radiation losses, and external-region-segmentation strategy in order to accurately take into account radiation losses in the entire micro-hotplate. The proposed model is almost as accurate as FEM simulations and two to three orders of magnitude more computationally efficient (e.g., 45 s versus more than 8 h). The residual errors, which are mainly associated to the undesired heating in the electrical contacts, are small (e.g., few degrees Celsius for an 800 °C operating temperature) and, for important analyses, almost constant. Therefore, we also introduce a computationally-easy single-FEM-compensation strategy in order to reduce the residual errors to about 1 °C. As illustrative examples of the power of our approach, we report the systematic investigation of a spread in the membrane thermal conductivity and of combined variations of both ambient and bulk temperatures. Our model enables a much faster characterization of micro-hotplates and, thus, a much more effective optimization prior to fabrication. PMID:24763214

  1. Active Thermochemical Tables: Sequential Bond Dissociation Enthalpies of Methane, Ethane, and Methanol and the Related Thermochemistry

    DOE PAGES

    Ruscic, Branko

    2015-03-31

    Active Thermochemical Tables (ATcT) thermochemistry for the sequential bond dissociations of methane, ethane, and methanol systems were obtained by analyzing and solving a very large thermochemical network (TN). Values for all possible C–H, C–C, C–O, and O–H bond dissociation enthalpies at 298.15 K (BDE 298) and bond dissociation energies at 0 K (D 0) are presented. The corresponding ATcT standard gas-phase enthalpies of formation of the resulting CH n, n = 4–0 species (methane, methyl, methylene, methylidyne, and carbon atom), C 2H n, n = 6–0 species (ethane, ethyl, ethylene, ethylidene, vinyl, ethylidyne, acetylene, vinylidene, ethynyl, and ethynylene), and COHmore » n, n = 4–0 species (methanol, hydroxymethyl, methoxy, formaldehyde, hydroxymethylene, formyl, isoformyl, and carbon monoxide) are also presented. The ATcT thermochemistry of carbon dioxide, water, hydroxyl, and carbon, oxygen, and hydrogen atoms is also included, together with the sequential BDEs of CO 2 and H 2O. The provenances of the ATcT enthalpies of formation, which are quite distributed and involve a large number of relevant determinations, are analyzed by variance decomposition and discussed in terms of principal contributions. The underlying reasons for periodic appearances of remarkably low and/or unusually high BDEs, alternating along the dissociation sequences, are analyzed and quantitatively rationalized. The present ATcT results are the most accurate thermochemical values currently available for these species.« less

  2. Enthalpy of Vaporization by Gas Chromatography: A Physical Chemistry Experiment

    ERIC Educational Resources Information Center

    Ellison, Herbert R.

    2005-01-01

    An experiment is conducted to measure the enthalpy of vaporization of volatile compounds like methylene chloride, carbon tetrachloride, and others by using gas chromatography. This physical property was measured using a very tiny quantity of sample revealing that it is possible to measure the enthalpies of two or more compounds at the same time.

  3. Aerosol volatility and enthalpy of sublimation of carboxylic acids.

    PubMed

    Salo, Kent; Jonsson, Asa M; Andersson, Patrik U; Hallquist, Mattias

    2010-04-08

    The enthalpy of sublimation has been determined for nine carboxylic acids, two cyclic (pinonic and pinic acid) and seven straight-chain dicarboxylic acids (C(4) to C(10)). The enthalpy of sublimation was determined from volatility measurements of nano aerosol particles using a volatility tandem differential mobility analyzer (VTDMA) set-up. Compared to the previous use of a VTDMA, this novel method gives enthalpy of sublimation determined over an extended temperature range (DeltaT approximately 40 K). The determined enthalpy of sublimation for the straight-chain dicarboxylic acids ranged from 96 to 161 kJ mol(-1), and the calculated vapor pressures at 298 K are in the range of 10(-6)-10(-3) Pa. These values indicate that dicarboxylic acids can take part in gas-to-particle partitioning at ambient conditions and may contribute to atmospheric nucleation, even though homogeneous nucleation is unlikely. To obtain consistent results, some experimental complications in producing nanosized crystalline aerosol particles were addressed. It was demonstrated that pinonic acid "used as received" needed a further purification step before being suspended as a nanoparticle aerosol. Furthermore, it was noted from distinct differences in thermal properties that aerosols generated from pimelic acid solutions gave two types of particles. These two types were attributed to crystalline and amorphous configurations, and based on measured thermal properties, the enthalpy of vaporization was 127 kJ mol(-1) and that of sublimation was 161 kJ mol(-1). This paper describes a new method that is complementary to other similar methods and provides an extension of existing experimental data on physical properties of atmospherically relevant compounds.

  4. Air-Sea Momentum and Enthalpy Exchange in Coupled Atmosphere-Wave-Ocean Modeling of Tropical Cyclones

    NASA Astrophysics Data System (ADS)

    Curcic, M.; Chen, S. S.

    2016-02-01

    The atmosphere and ocean are coupled through momentum, enthalpy, and mass fluxes. Accurate representation of these fluxes in a wide range of weather and climate conditions is one of major challenges in prediction models. Their current parameterizations are based on sparse observations in low-to-moderate winds and are not suited for high wind conditions such as tropical cyclones (TCs) and winter storms. In this study, we use the Unified Wave INterface - Coupled Model (UWIN-CM), a high resolution, fully-coupled atmosphere-wave-ocean model, to better understand the role of ocean surface waves in mediating air-sea momentum and enthalpy exchange in TCs. In particular, we focus on the explicit treatment of wave growth and dissipation for calculating atmospheric and oceanic stress, and its role in upper ocean mixing and surface cooling in the wake of the storm. Wind-wave misalignment and local wave disequilibrium result in difference between atmospheric and oceanic stress being largest on the left side of the storm. We find that explicit wave calculation in the coupled model reduces momentum transfer into the ocean by more than 10% on average, resulting in reduced cooling in TC's wake and subsequent weakening of the storm. We also investigate the impacts of sea surface temperature and upper ocean parameterization on air-sea enthalpy fluxes in the fully coupled model. High-resolution UWIN-CM simulations of TCs with various intensities and structure are conducted in this study to better understand the complex TC-ocean interaction and improve the representation of air-sea coupling processes in coupled prediction models.

  5. Multislice Computed Tomography Accurately Detects Stenosis in Coronary Artery Bypass Conduits

    PubMed Central

    Duran, Cihan; Sagbas, Ertan; Caynak, Baris; Sanisoglu, Ilhan; Akpinar, Belhhan; Gulbaran, Murat

    2007-01-01

    The aim of this study was to evaluate the accuracy of multislice computed tomography in detecting graft stenosis or occlusion after coronary artery bypass grafting, using coronary angiography as the standard. From January 2005 through May 2006, 25 patients (19 men and 6 women; mean age, 54 ± 11.3 years) underwent diagnostic investigation of their bypass grafts by multislice computed tomography within 1 month of coronary angiography. The mean time elapsed after coronary artery bypass grafting was 6.2 years. In these 25 patients, we examined 65 bypass conduits (24 arterial and 41 venous) and 171 graft segments (the shaft, proximal anastomosis, and distal anastomosis). Compared with coronary angiography, the segment-based sensitivity, specificity, and positive and negative predictive values of multislice computed tomography in the evaluation of stenosis were 89%, 100%, 100%, and 99%, respectively. The patency rate for multislice compu-ted tomography was 85% (55/65: 3 arterial and 7 venous grafts were occluded), with 100% sensitivity and specificity. From these data, we conclude that multislice computed tomography can accurately evaluate the patency and stenosis of bypass grafts during outpatient follow-up. PMID:17948078

  6. Ionic liquids: differential scanning calorimetry as a new indirect method for determination of vaporization enthalpies.

    PubMed

    Verevkin, Sergey P; Emel'yanenko, Vladimir N; Zaitsau, Dzmitry H; Ralys, Ricardas V; Schick, Christoph

    2012-04-12

    Differential scanning calorimetry (DSC) has been used to measure enthalpies of synthesis reactions of the 1-alkyl-3-methylimidazolium bromide [C(n)mim][Br] ionic liquids from 1-methylimidazole and n-alkyl bromides (with n = 4, 5, 6, 7, and 8). The optimal experimental conditions have been elaborated. Enthalpies of formation of these ionic liquids in the liquid state have been determined using the DSC results according to the Hess Law. The ideal-gas enthalpies of formation of [C(n)mim][Br] were calculated using the methods of quantum chemistry. They were used together with the DSC results to derive indirectly the enthalpies of vaporization of the ionic liquids under study. In order to validate the indirect determination, the experimental vaporization enthalpy of [C(4)mim][Br] was measured by using a quartz crystal microbalance (QCM). The combination of reaction enthalpy measurements by DSC with modern high-level first-principles calculations opens valuable indirect thermochemical options to obtain values of vaporization enthalpies of ionic liquids.

  7. Phase Transition Enthalpy Measurements of Organic and Organometallic Compounds and Ionic Liquids. Sublimation, Vaporization, and Fusion Enthalpies from 1880 to 2015. Part 2. C11-C192

    NASA Astrophysics Data System (ADS)

    Acree, William; Chickos, James S.

    2017-03-01

    The second part of this compendium concludes with a collection of phase change enthalpies of organic molecules inclusive of C11-C192 reported over the period 1880-2015. Also included are phase change enthalpies including fusion, vaporization, and sublimation enthalpies for organometallic, ionic liquids, and a few inorganic compounds. Paper I of this compendium, published separately, includes organic compounds from C1 to C10 and describes a group additivity method for evaluating solid, liquid, and gas phase heat capacities as well as temperature adjustments of phase changes. Paper II of this compendium also includes an updated version of a group additivity method for evaluating total phase change entropies which together with the fusion temperature can be useful in estimating total phase change enthalpies. Other uses include application in identifying potential substances that either form liquid or plastic crystals or exhibit additional phase changes such as undetected solid-solid transitions or behave anisotropically in the liquid state.

  8. Enthalpy Landscape Dictates the Irradiation-Induced Disordering of Quartz

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

    Krishnan, N. M. Anoop; Wang, Bu; Yu, Yingtian

    Here, under irradiation, minerals tend to experience an accumulation of structural defects, ultimately leading to a disordered atomic network. Despite the critical importance of understanding and predicting irradiation-induced damage, the physical origin of the initiation and saturation of defects remains poorly understood. Here, based on molecular dynamics simulations of α-quartz, we show that the topography of the enthalpy landscape governs irradiation-induced disordering. Specifically, we show that such disordering differs from that observed upon vitrification in that, prior to saturation, irradiated quartz accesses forbidden regions of the enthalpy landscape, i.e., those that are inaccessible by simply heating and cooling. Furthermore, wemore » demonstrate that damage saturates when the system accesses a local region of the enthalpy landscape corresponding to the configuration of an allowable liquid. At this stage, a sudden decrease in the heights of the energy barriers enhances relaxation, thereby preventing any further accumulation of defects and resulting in a defect-saturated disordered state.« less

  9. Enthalpy Landscape Dictates the Irradiation-Induced Disordering of Quartz

    DOE PAGES

    Krishnan, N. M. Anoop; Wang, Bu; Yu, Yingtian; ...

    2017-07-28

    Here, under irradiation, minerals tend to experience an accumulation of structural defects, ultimately leading to a disordered atomic network. Despite the critical importance of understanding and predicting irradiation-induced damage, the physical origin of the initiation and saturation of defects remains poorly understood. Here, based on molecular dynamics simulations of α-quartz, we show that the topography of the enthalpy landscape governs irradiation-induced disordering. Specifically, we show that such disordering differs from that observed upon vitrification in that, prior to saturation, irradiated quartz accesses forbidden regions of the enthalpy landscape, i.e., those that are inaccessible by simply heating and cooling. Furthermore, wemore » demonstrate that damage saturates when the system accesses a local region of the enthalpy landscape corresponding to the configuration of an allowable liquid. At this stage, a sudden decrease in the heights of the energy barriers enhances relaxation, thereby preventing any further accumulation of defects and resulting in a defect-saturated disordered state.« less

  10. A correct enthalpy relationship as thermal comfort index for livestock.

    PubMed

    Rodrigues, Valéria Cristina; da Silva, Iran José Oliveira; Vieira, Frederico Márcio Corrêa; Nascimento, Sheila Tavares

    2011-05-01

    Researchers working with thermal comfort have been using enthalpy to measure thermal energy inside rural facilities, establishing indicator values for many situations of thermal comfort and heat stress. This variable turned out to be helpful in analyzing thermal exchange in livestock systems. The animals are exposed to an environment which is decisive for the thermoregulatory process, and, consequently, the reactions reflect states of thermal comfort or heat stress, the last being responsable for problems of sanity, behavior and productivity. There are researchers using enthalpy as a qualitative indicator of thermal environment of livestock such as poultry, cattle and hogs in tropical regions. This preliminary work intends to check different enthalpy equations using information from classical thermodynamics, and proposes a direct equation as thermal comfort index for livestock systems.

  11. Time accurate application of the MacCormack 2-4 scheme on massively parallel computers

    NASA Technical Reports Server (NTRS)

    Hudson, Dale A.; Long, Lyle N.

    1995-01-01

    Many recent computational efforts in turbulence and acoustics research have used higher order numerical algorithms. One popular method has been the explicit MacCormack 2-4 scheme. The MacCormack 2-4 scheme is second order accurate in time and fourth order accurate in space, and is stable for CFL's below 2/3. Current research has shown that the method can give accurate results but does exhibit significant Gibbs phenomena at sharp discontinuities. The impact of adding Jameson type second, third, and fourth order artificial viscosity was examined here. Category 2 problems, the nonlinear traveling wave and the Riemann problem, were computed using a CFL number of 0.25. This research has found that dispersion errors can be significantly reduced or nearly eliminated by using a combination of second and third order terms in the damping. Use of second and fourth order terms reduced the magnitude of dispersion errors but not as effectively as the second and third order combination. The program was coded using Thinking Machine's CM Fortran, a variant of Fortran 90/High Performance Fortran, and was executed on a 2K CM-200. Simple extrapolation boundary conditions were used for both problems.

  12. Experimental and Computational Aerothermodynamics of a Mars Entry Vehicle

    NASA Technical Reports Server (NTRS)

    Hollis, Brian R.

    1996-01-01

    An aerothermodynamic database has been generated through both experimental testing and computational fluid dynamics simulations for a 70 deg sphere-cone configuration based on the NASA Mars Pathfinder entry vehicle. The aerothermodynamics of several related parametric configurations were also investigated. Experimental heat-transfer data were obtained at hypersonic test conditions in both a perfect gas air wind tunnel and in a hypervelocity, high-enthalpy expansion tube in which both air and carbon dioxide were employed as test gases. In these facilities, measurements were made with thin-film temperature-resistance gages on both the entry vehicle models and on the support stings of the models. Computational results for freestream conditions equivalent to those of the test facilities were generated using an axisymmetric/2D laminar Navier-Stokes solver with both perfect-gas and nonequilibrium thermochemical models. Forebody computational and experimental heating distributions agreed to within the experimental uncertainty for both the perfect-gas and high-enthalpy test conditions. In the wake, quantitative differences between experimental and computational heating distributions for the perfect-gas conditions indicated transition of the free shear layer near the reattachment point on the sting. For the high enthalpy cases, agreement to within, or slightly greater than, the experimental uncertainty was achieved in the wake except within the recirculation region, where further grid resolution appeared to be required. Comparisons between the perfect-gas and high-enthalpy results indicated that the wake remained laminar at the high-enthalpy test conditions, for which the Reynolds number was significantly lower than that of the perfect-gas conditions.

  13. A general structure-property relationship to predict the enthalpy of vaporisation at ambient temperatures.

    PubMed

    Oberg, T

    2007-01-01

    The vapour pressure is the most important property of an anthropogenic organic compound in determining its partitioning between the atmosphere and the other environmental media. The enthalpy of vaporisation quantifies the temperature dependence of the vapour pressure and its value around 298 K is needed for environmental modelling. The enthalpy of vaporisation can be determined by different experimental methods, but estimation methods are needed to extend the current database and several approaches are available from the literature. However, these methods have limitations, such as a need for other experimental results as input data, a limited applicability domain, a lack of domain definition, and a lack of predictive validation. Here we have attempted to develop a quantitative structure-property relationship (QSPR) that has general applicability and is thoroughly validated. Enthalpies of vaporisation at 298 K were collected from the literature for 1835 pure compounds. The three-dimensional (3D) structures were optimised and each compound was described by a set of computationally derived descriptors. The compounds were randomly assigned into a calibration set and a prediction set. Partial least squares regression (PLSR) was used to estimate a low-dimensional QSPR model with 12 latent variables. The predictive performance of this model, within the domain of application, was estimated at n=560, q2Ext=0.968 and s=0.028 (log transformed values). The QSPR model was subsequently applied to a database of 100,000+ structures, after a similar 3D optimisation and descriptor generation. Reliable predictions can be reported for compounds within the previously defined applicability domain.

  14. Enthalpy versus entropy: What drives hard-particle ordering in condensed phases?

    DOE PAGES

    Anthamatten, Mitchell; Ou, Jane J.; Weinfeld, Jeffrey A.; ...

    2016-07-27

    In support of mesoscopic-scale materials processing, spontaneous hard-particle ordering has been actively pursued for over a half-century. The generally accepted view that entropy alone can drive hard particle ordering is evaluated. Furthermore, a thermodynamic analysis of hard particle ordering was conducted and shown to agree with existing computations and experiments. Conclusions are that (i) hard particle ordering transitions between states in equilibrium are forbidden at constant volume but are allowed at constant pressure; (ii) spontaneous ordering transitions at constant pressure are driven by enthalpy, and (iii) ordering under constant volume necessarily involves a non-equilibrium initial state which has yet tomore » be rigorously defined.« less

  15. Split-step eigenvector-following technique for exploring enthalpy landscapes at absolute zero.

    PubMed

    Mauro, John C; Loucks, Roger J; Balakrishnan, Jitendra

    2006-03-16

    The mapping of enthalpy landscapes is complicated by the coupling of particle position and volume coordinates. To address this issue, we have developed a new split-step eigenvector-following technique for locating minima and transition points in an enthalpy landscape at absolute zero. Each iteration is split into two steps in order to independently vary system volume and relative atomic coordinates. A separate Lagrange multiplier is used for each eigendirection in order to provide maximum flexibility in determining step sizes. This technique will be useful for mapping the enthalpy landscapes of bulk systems such as supercooled liquids and glasses.

  16. Hypersonic aerothermodynamic and scramjet research using high enthalpy shock tunnel

    NASA Astrophysics Data System (ADS)

    Itoh, K.; Ueda, S.; Tanno, H.; Komuro, T.; Sato, K.

    A high enthalpy shock tunnel is a potential facility for gaining knowledge to develop modern aerothermodynamic and propulsion technologies. The largest high enthalpy shock tunnel HIEST was built at NAL Kakuda in 1997, aiming for aerothermodynamic tests of Japan's space vehicle HOPE and scramjet propulsion systems. Selected topics from the experimental studies carried out using HIEST so far, such as the nonequilibrium aerodynamics of HOPE, the surface catalytic effect on aerodynamic heating and scramjet performance are described.

  17. Insights on activation enthalpy for non-Schmid slip in body-centered cubic metals

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

    Hale, Lucas M.; Lim, Hojun; Zimmerman, Jonathan A.

    2014-12-18

    We use insights gained from atomistic simulation to develop an activation enthalpy model for dislocation slip in body-centered cubic iron. Furthermore, using a classical potential that predicts dislocation core stabilities consistent with ab initio predictions, we quantify the non-Schmid stress-dependent effects of slip. The kink-pair activation enthalpy is evaluated and a model is identified as a function of the general stress state. Thus, our model enlarges the applicability of the classic Kocks activation enthalpy model to materials with non-Schmid behavior.

  18. Higher-order accurate space-time schemes for computational astrophysics—Part I: finite volume methods

    NASA Astrophysics Data System (ADS)

    Balsara, Dinshaw S.

    2017-12-01

    As computational astrophysics comes under pressure to become a precision science, there is an increasing need to move to high accuracy schemes for computational astrophysics. The algorithmic needs of computational astrophysics are indeed very special. The methods need to be robust and preserve the positivity of density and pressure. Relativistic flows should remain sub-luminal. These requirements place additional pressures on a computational astrophysics code, which are usually not felt by a traditional fluid dynamics code. Hence the need for a specialized review. The focus here is on weighted essentially non-oscillatory (WENO) schemes, discontinuous Galerkin (DG) schemes and PNPM schemes. WENO schemes are higher order extensions of traditional second order finite volume schemes. At third order, they are most similar to piecewise parabolic method schemes, which are also included. DG schemes evolve all the moments of the solution, with the result that they are more accurate than WENO schemes. PNPM schemes occupy a compromise position between WENO and DG schemes. They evolve an Nth order spatial polynomial, while reconstructing higher order terms up to Mth order. As a result, the timestep can be larger. Time-dependent astrophysical codes need to be accurate in space and time with the result that the spatial and temporal accuracies must be matched. This is realized with the help of strong stability preserving Runge-Kutta schemes and ADER (Arbitrary DERivative in space and time) schemes, both of which are also described. The emphasis of this review is on computer-implementable ideas, not necessarily on the underlying theory.

  19. Accurate optimization of amino acid form factors for computing small-angle X-ray scattering intensity of atomistic protein structures

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

    Tong, Dudu; Yang, Sichun; Lu, Lanyuan

    2016-06-20

    Structure modellingviasmall-angle X-ray scattering (SAXS) data generally requires intensive computations of scattering intensity from any given biomolecular structure, where the accurate evaluation of SAXS profiles using coarse-grained (CG) methods is vital to improve computational efficiency. To date, most CG SAXS computing methods have been based on a single-bead-per-residue approximation but have neglected structural correlations between amino acids. To improve the accuracy of scattering calculations, accurate CG form factors of amino acids are now derived using a rigorous optimization strategy, termed electron-density matching (EDM), to best fit electron-density distributions of protein structures. This EDM method is compared with and tested againstmore » other CG SAXS computing methods, and the resulting CG SAXS profiles from EDM agree better with all-atom theoretical SAXS data. By including the protein hydration shell represented by explicit CG water molecules and the correction of protein excluded volume, the developed CG form factors also reproduce the selected experimental SAXS profiles with very small deviations. Taken together, these EDM-derived CG form factors present an accurate and efficient computational approach for SAXS computing, especially when higher molecular details (represented by theqrange of the SAXS data) become necessary for effective structure modelling.« less

  20. Fast and accurate computation of system matrix for area integral model-based algebraic reconstruction technique

    NASA Astrophysics Data System (ADS)

    Zhang, Shunli; Zhang, Dinghua; Gong, Hao; Ghasemalizadeh, Omid; Wang, Ge; Cao, Guohua

    2014-11-01

    Iterative algorithms, such as the algebraic reconstruction technique (ART), are popular for image reconstruction. For iterative reconstruction, the area integral model (AIM) is more accurate for better reconstruction quality than the line integral model (LIM). However, the computation of the system matrix for AIM is more complex and time-consuming than that for LIM. Here, we propose a fast and accurate method to compute the system matrix for AIM. First, we calculate the intersection of each boundary line of a narrow fan-beam with pixels in a recursive and efficient manner. Then, by grouping the beam-pixel intersection area into six types according to the slopes of the two boundary lines, we analytically compute the intersection area of the narrow fan-beam with the pixels in a simple algebraic fashion. Overall, experimental results show that our method is about three times faster than the Siddon algorithm and about two times faster than the distance-driven model (DDM) in computation of the system matrix. The reconstruction speed of our AIM-based ART is also faster than the LIM-based ART that uses the Siddon algorithm and DDM-based ART, for one iteration. The fast reconstruction speed of our method was accomplished without compromising the image quality.

  1. G3//BMK and Its Application to Calculation of Bond Dissociation Enthalpies.

    PubMed

    Zheng, Wen-Rui; Fu, Yao; Guo, Qing-Xiang

    2008-08-01

    On the basis of systematic examinations it was found that the BMK functional significantly outperformed the other popular density functional theory methods including B3LYP, B3P86, KMLYP, MPW1P86, O3LYP, and X3LYP for the calculation of bond dissociation enthalpies (BDEs). However, it was also found that even the BMK functional might dramatically fail in predicting the BDEs of some chemical bonds. To solve this problem, a new composite ab initio method named G3//BMK was developed by combining the strengths of both the G3 theory and BMK. G3//BMK was found to outperform the G3 and G3//B3LYP methods. It could accurately predict the BDEs of diverse types of chemical bonds in various organic molecules within a precision of ca. 1.2 kcal/mol.

  2. Characterization of Adsorption Enthalpy of Novel Water-Stable Zeolites and Metal-Organic Frameworks

    NASA Astrophysics Data System (ADS)

    Kim, Hyunho; Cho, H. Jeremy; Narayanan, Shankar; Yang, Sungwoo; Furukawa, Hiroyasu; Schiffres, Scott; Li, Xiansen; Zhang, Yue-Biao; Jiang, Juncong; Yaghi, Omar M.; Wang, Evelyn N.

    2016-01-01

    Water adsorption is becoming increasingly important for many applications including thermal energy storage, desalination, and water harvesting. To develop such applications, it is essential to understand both adsorbent-adsorbate and adsorbate-adsorbate interactions, and also the energy required for adsorption/desorption processes of porous material-adsorbate systems, such as zeolites and metal-organic frameworks (MOFs). In this study, we present a technique to characterize the enthalpy of adsorption/desorption of zeolites and MOF-801 with water as an adsorbate by conducting desorption experiments with conventional differential scanning calorimetry (DSC) and thermogravimetric analyzer (TGA). With this method, the enthalpies of adsorption of previously uncharacterized adsorbents were estimated as a function of both uptake and temperature. Our characterizations indicate that the adsorption enthalpies of type I zeolites can increase to greater than twice the latent heat whereas adsorption enthalpies of MOF-801 are nearly constant for a wide range of vapor uptakes.

  3. Enthalpy relaxation studies of two structurally related amorphous drugs and their binary dispersions.

    PubMed

    Bansal, Shyam Sunder; Kaushal, Aditya Mohan; Bansal, Arvind Kumar

    2010-11-01

    The purpose of the current study was to evaluate the enthalpy relaxation behavior of valdecoxib (VLB) and etoricoxib (ETB) and their binary dispersions to derive relaxation constants and to understand their molecular mobilities. Solid dispersions of VLB and ETB were prepared with 1%, 2%, 5%, 10%, 15%, and 20% (w/w) concentrations of polyvinylpyrrolidone (PVP) in situ using differential scanning calorimetry (DSC). Enthalpy relaxation studies were carried out with isothermal storage periods of 1, 2, 4, 6, 16, and 24 hours at 40°C and 0% relative humidity (RH). PVP increased the glass transition temperature (T(g)) and decreased the enthalpy relaxation. Significant differences between two drugs were observed with respect to their relaxation behavior which may be due to differences in intermolecular interactions as predicted by Couchman-Karasz equation and molecular mobility. Kohlrausch-Williams-Watts equation was found to be inadequate in describing complex molecular relaxations in binary dispersions. The enthalpy relaxation behavior of VLB and ETB was found to be significantly different. PVP stabilized VLB significantly; however, its effect on ETB was negligible. The extent of enthalpy relaxation was found to correlate with hydrogen bonding tendency of the drug molecules. The outcome can help in rational designing of amorphous systems with optimal performance.

  4. A simplified approach to characterizing a kilovoltage source spectrum for accurate dose computation.

    PubMed

    Poirier, Yannick; Kouznetsov, Alexei; Tambasco, Mauro

    2012-06-01

    %. The HVL and kVp are sufficient for characterizing a kV x-ray source spectrum for accurate dose computation. As these parameters can be easily and accurately measured, they provide for a clinically feasible approach to characterizing a kV energy spectrum to be used for patient specific x-ray dose computations. Furthermore, these results provide experimental validation of our novel hybrid dose computation algorithm. © 2012 American Association of Physicists in Medicine.

  5. Characterization of Adsorption Enthalpy of Novel Water-Stable Zeolites and Metal-Organic Frameworks

    PubMed Central

    Kim, Hyunho; Cho, H. Jeremy; Narayanan, Shankar; Yang, Sungwoo; Furukawa, Hiroyasu; Schiffres, Scott; Li, Xiansen; Zhang, Yue-Biao; Jiang, Juncong; Yaghi, Omar M.; Wang, Evelyn N.

    2016-01-01

    Water adsorption is becoming increasingly important for many applications including thermal energy storage, desalination, and water harvesting. To develop such applications, it is essential to understand both adsorbent-adsorbate and adsorbate-adsorbate interactions, and also the energy required for adsorption/desorption processes of porous material-adsorbate systems, such as zeolites and metal-organic frameworks (MOFs). In this study, we present a technique to characterize the enthalpy of adsorption/desorption of zeolites and MOF-801 with water as an adsorbate by conducting desorption experiments with conventional differential scanning calorimetry (DSC) and thermogravimetric analyzer (TGA). With this method, the enthalpies of adsorption of previously uncharacterized adsorbents were estimated as a function of both uptake and temperature. Our characterizations indicate that the adsorption enthalpies of type I zeolites can increase to greater than twice the latent heat whereas adsorption enthalpies of MOF-801 are nearly constant for a wide range of vapor uptakes. PMID:26796523

  6. Preliminary Results from Electric Arc Furnace Off-Gas Enthalpy Modeling

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

    Nimbalkar, Sachin U; Thekdi, Arvind; Keiser, James R

    2015-01-01

    This article describes electric arc furnace (EAF) off-gas enthalpy models developed at Oak Ridge National Laboratory (ORNL) to calculate overall heat availability (sensible and chemical enthalpy) and recoverable heat values (steam or power generation potential) for existing EAF operations and to test ORNL s new EAF waste heat recovery (WHR) concepts. ORNL s new EAF WHR concepts are: Regenerative Drop-out Box System and Fluidized Bed System. The two EAF off-gas enthalpy models described in this paper are: 1.Overall Waste Heat Recovery Model that calculates total heat availability in off-gases of existing EAF operations 2.Regenerative Drop-out Box System Model in whichmore » hot EAF off-gases alternately pass through one of two refractory heat sinks that store heat and then transfer it to another gaseous medium These models calculate the sensible and chemical enthalpy of EAF off-gases based on the off-gas chemical composition, temperature, and mass flow rate during tap to tap time, and variations in those parameters in terms of actual values over time. The models provide heat transfer analysis for the aforementioned concepts to confirm the overall system and major component sizing (preliminary) to assess the practicality of the systems. Real-time EAF off-gas composition (e.g., CO, CO2, H2, and H2O), volume flow, and temperature data from one EAF operation was used to test the validity and accuracy of the modeling work. The EAF off-gas data was used to calculate the sensible and chemical enthalpy of the EAF off-gases to generate steam and power. The article provides detailed results from the modeling work that are important to the success of ORNL s EAF WHR project. The EAF WHR project aims to develop and test new concepts and materials that allow cost-effective recovery of sensible and chemical heat from high-temperature gases discharged from EAFs.« less

  7. The Intramolecular Hydrogen Bond N-H···S in 2,2'-Diaminodiphenyl Disulfide: Experimental and Computational Thermochemistry.

    PubMed

    Ramos, Fernando; Flores, Henoc; Hernández-Pérez, Julio M; Sandoval-Lira, Jacinto; Camarillo, E Adriana

    2018-01-11

    The intramolecular hydrogen bond of the N-H···S type has been investigated sparingly by thermochemical and computational methods. In order to study this interaction, the standard molar enthalpies of formation in gaseous phase of diphenyl disulfide, 2,2'-diaminodiphenyl disulfide and 4,4'-diaminodiphenyl disulfide at T = 298.15 K were determined by experimental thermochemical methods and computational calculations. The experimental enthalpies of formation in gas-phase were obtained from enthalpies of formation in crystalline phase and enthalpies of sublimation. Enthalpies of formation in crystalline phase were obtained using rotatory bomb combustion calorimetry. By thermogravimetry, enthalpies of vaporization were obtained, and by combining them with enthalpies of fusion, the enthalpies of sublimation were calculated. The Gaussian-4 procedure and the atomization method were applied to obtain enthalpies of formation in gas-phase of the compounds under study. Theoretical and experimental values are in good agreement. Through natural bond orbital (NBO) analysis and a topological analysis of the electronic density, the intramolecular hydrogen bridge (N-H···S) in the 2,2'-diaminodiphenyl disulfide was confirmed. Finally, an enthalpic difference of 11.8 kJ·mol -1 between the 2,2'-diaminodiphenyl disulfide and 4,4'-diaminodiphenyl disulfide was found, which is attributed to the intramolecular N-H···S interaction.

  8. Determination of ideal-gas enthalpies of formation for key compounds:

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

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

    1991-10-01

    The results of a study aimed at improvement of group-contribution methodology for estimation of thermodynamic properties of organic and organosilicon substances are reported. Specific weaknesses where particular group-contribution terms were unknown, or estimated because of lack of experimental data, are addressed by experimental studies of enthalpies of combustion in the condensed phase, vapor-pressure measurements, and differential scanning calorimetric (d.s.c.) heat-capacity measurements. Ideal-gas enthalpies of formation of ({plus minus})-butan-2-ol, tetradecan-1-ol, hexan-1,6-diol, methacrylamide, benzoyl formic acid, naphthalene-2,6-dicarboxylic acid dimethyl ester, and tetraethylsilane are reported. A crystalline-phase enthalpy of formation at 298.15 K was determined for naphthalene-2,6-dicarboxylic acid, which decomposed at 695 Kmore » before melting. The combustion calorimetry of tetraethylsilane used the proven fluorine-additivity methodology. Critical temperature and critical density were determined for tetraethylsilane with differential scanning calorimeter and the critical pressure was derived. Group-additivity parameters useful in the application of group- contribution correlations are derived. 112 refs., 13 figs., 19 tabs.« less

  9. Measuring the enthalpies of interaction between glycine, L-cysteine, glycylglycine, and sodium dodecyl sulfate in aqueous solutions

    NASA Astrophysics Data System (ADS)

    Badelin, V. G.; Mezhevoi, I. N.; Tyunina, E. Yu.

    2017-03-01

    Calorimetric measurements of enthalpies of solution Δsol H m for glycine, L-cysteine, and glycylglycine in aqueous solutions of sodium dodecyl sulfate (SDS) with concentrations of up to 0.05 mol kg-1 are made. Standard enthalpy of solution Δsol H 0 and enthalpy of transfer Δtr H 0 of the dipeptide from water into mixed solvent are calculated. The calculated enthalpy coefficients of paired interactions of amino acids and dipeptide with SDS prove to be positive. Hydrophobic interactions between the biomolecules and SDS are found to have a major impact on the enthalpies of interaction in the three-component systems under study, within the indicated range of concentrations.

  10. Development and application of computational aerothermodynamics flowfield computer codes

    NASA Technical Reports Server (NTRS)

    Venkatapathy, Ethiraj

    1994-01-01

    Research was performed in the area of computational modeling and application of hypersonic, high-enthalpy, thermo-chemical nonequilibrium flow (Aerothermodynamics) problems. A number of computational fluid dynamic (CFD) codes were developed and applied to simulate high altitude rocket-plume, the Aeroassist Flight Experiment (AFE), hypersonic base flow for planetary probes, the single expansion ramp model (SERN) connected with the National Aerospace Plane, hypersonic drag devices, hypersonic ramp flows, ballistic range models, shock tunnel facility nozzles, transient and steady flows in the shock tunnel facility, arc-jet flows, thermochemical nonequilibrium flows around simple and complex bodies, axisymmetric ionized flows of interest to re-entry, unsteady shock induced combustion phenomena, high enthalpy pulsed facility simulations, and unsteady shock boundary layer interactions in shock tunnels. Computational modeling involved developing appropriate numerical schemes for the flows on interest and developing, applying, and validating appropriate thermochemical processes. As part of improving the accuracy of the numerical predictions, adaptive grid algorithms were explored, and a user-friendly, self-adaptive code (SAGE) was developed. Aerothermodynamic flows of interest included energy transfer due to strong radiation, and a significant level of effort was spent in developing computational codes for calculating radiation and radiation modeling. In addition, computational tools were developed and applied to predict the radiative heat flux and spectra that reach the model surface.

  11. Molecular simulation of excess isotherm and excess enthalpy change in gas-phase adsorption.

    PubMed

    Do, D D; Do, H D; Nicholson, D

    2009-01-29

    We present a new approach to calculating excess isotherm and differential enthalpy of adsorption on surfaces or in confined spaces by the Monte Carlo molecular simulation method. The approach is very general and, most importantly, is unambiguous in its application to any configuration of solid structure (crystalline, graphite layer or disordered porous glass), to any type of fluid (simple or complex molecule), and to any operating conditions (subcritical or supercritical). The behavior of the adsorbed phase is studied using the partial molar energy of the simulation box. However, to characterize adsorption for comparison with experimental data, the isotherm is best described by the excess amount, and the enthalpy of adsorption is defined as the change in the total enthalpy of the simulation box with the change in the excess amount, keeping the total number (gas + adsorbed phases) constant. The excess quantities (capacity and energy) require a choice of a reference gaseous phase, which is defined as the adsorptive gas phase occupying the accessible volume and having a density equal to the bulk gas density. The accessible volume is defined as the mean volume space accessible to the center of mass of the adsorbate under consideration. With this choice, the excess isotherm passes through a maximum but always remains positive. This is in stark contrast to the literature where helium void volume is used (which is always greater than the accessible volume) and the resulting excess can be negative. Our definition of enthalpy change is equivalent to the difference between the partial molar enthalpy of the gas phase and the partial molar enthalpy of the adsorbed phase. There is no need to assume ideal gas or negligible molar volume of the adsorbed phase as is traditionally done in the literature. We illustrate this new approach with adsorption of argon, nitrogen, and carbon dioxide under subcritical and supercritical conditions.

  12. On the Enthalpy and Entropy of Point Defect Formation in Crystals

    NASA Astrophysics Data System (ADS)

    Kobelev, N. P.; Khonik, V. A.

    2018-03-01

    A standard way to determine the formation enthalpy H and entropy S of point defect formation in crystals consists in the application of the Arrhenius equation for the defect concentration. In this work, we show that a formal use of this method actually gives the effective (apparent) values of these quantities, which appear to be significantly overestimated. The underlying physical reason lies in temperature-dependent formation enthalpy of the defects, which is controlled by temperature dependence of the elastic moduli. We present an evaluation of the "true" H- and S-values for aluminum, which are derived on the basis of experimental data by taking into account temperature dependence of the formation enthalpy related to temperature dependence of the elastic moduli. The knowledge of the "true" activation parameters is needed for a correct calculation of the defect concentration constituting thus an issue of major importance for different fundamental and application issues of condensed matter physics and chemistry.

  13. Study of Shallow Low-Enthalpy Geothermal Resources Using Integrated Geophysical Methods

    NASA Astrophysics Data System (ADS)

    De Giorgi, Lara; Leucci, Giovanni

    2015-02-01

    The paper is focused on low enthalpy geothermal exploration performed in south Italy and provides an integrated presentation of geological, hydrogeological, and geophysical surveys carried out in the area of municipality of Lecce. Geological and hydrogeological models were performed using the stratigraphical data from 51 wells. A ground-water flow (direction and velocity) model was obtained. Using the same wells data, the ground-water annual temperature was modeled. Furthermore, the ground surface temperature records from ten meteorological stations were studied. This allowed us to obtain a model related to the variations of the temperature at different depths in the subsoil. Integrated geophysical surveys were carried out in order to explore the low-enthalpy geothermal fluids and to evaluate the results of the model. Electrical resistivity tomography (ERT) and self-potential (SP) methods were used. The results obtained upon integrating the geophysical data with the models show a low-enthalpy geothermal resource constituted by a shallow ground-water system.

  14. Ionic liquids. Combination of combustion calorimetry with high-level quantum chemical calculations for deriving vaporization enthalpies.

    PubMed

    Emel'yanenko, Vladimir N; Verevkin, Sergey P; Heintz, Andreas; Schick, Christoph

    2008-07-10

    In this work, the molar enthalpies of formation of the ionic liquids [C2MIM][NO3] and [C4MIM][NO3] were measured by means of combustion calorimetry. The molar enthalpy of fusion of [C2MIM][NO3] was measured using differential scanning calorimetry. Ab initio calculations of the enthalpy of formation in the gaseous phase have been performed for the ionic species using the G3MP2 theory. We have used a combination of traditional combustion calorimetry with modern high-level ab initio calculations in order to obtain the molar enthalpies of vaporization of a series of the ionic liquids under study.

  15. Borate-polyol complexes in aqueous solution: determination of enthalpies by thermometric titrimetry.

    PubMed

    Aruga, R

    1985-06-01

    Enthalpies for the reaction of borate with 1,2-ethanediol, 1,2-propanediol, 1,2,3-propanetriol and d-mannitol have been determined by thermometric titrimetry. From these enthalpies and equilibrium constants taken from the literature, corresponding entropies have been calculated. The data refer to aqueous solutions at 25 degrees and I = 1.0M (NaNO(3)). The results indicate reasons for the differences in the stabilities of the complexes.

  16. Hydration of dimethyldodecylamine-N-oxide: enthalpy and entropy driven processes.

    PubMed

    Kocherbitov, Vitaly; Söderman, Olle

    2006-07-13

    Dimethyldodecylamine-N-oxide (DDAO) has only one polar atom that is able to interact with water. Still, this surfactant shows very hydrophilic properties: in mixtures with water, it forms normal liquid crystalline phases and micelles. Moreover, there is data in the literature indicating that the hydration of this surfactant is driven by enthalpy while other studies show that hydration of surfactants and lipids typically is driven by entropy. Sorption calorimetry allows resolving enthalpic and entropic contributions to the free energy of hydration at constant temperature and thus directly determines the driving forces of hydration. The results of the present sorption calorimetric study show that the hydration of liquid crystalline phases of DDAO is driven by entropy, except for the hydration of the liquid crystalline lamellar phase which is co-driven by enthalpy. The exothermic heat effect of the hydration of the lamellar phase arises from formation of strong hydrogen bonds between DDAO and water. Another issue is the driving forces of the phase transitions caused by the hydration. The sorption calorimetric results show that the transitions from the lamellar to cubic and from the cubic to the hexagonal phase are driven by enthalpy. Transitions from solid phases to the liquid crystalline lamellar phase are entropically driven, while the formation of the monohydrate from the dry surfactant is driven by enthalpy. The driving forces of the transition from the hexagonal phase to the isotropic solution are close to zero. These sorption calorimetric results are in good agreement with the analysis of the binary phase diagram based on the van der Waals differential equation. The phase diagram of the DDAO-water system determined using DSC and sorption calorimetry is presented.

  17. Validation of the enthalpy method by means of analytical solution

    NASA Astrophysics Data System (ADS)

    Kleiner, Thomas; Rückamp, Martin; Bondzio, Johannes; Humbert, Angelika

    2014-05-01

    Numerical simulations moved in the recent year(s) from describing the cold-temperate transition surface (CTS) towards an enthalpy description, which allows avoiding incorporating a singular surface inside the model (Aschwanden et al., 2012). In Enthalpy methods the CTS is represented as a level set of the enthalpy state variable. This method has several numerical and practical advantages (e.g. representation of the full energy by one scalar field, no restriction to topology and shape of the CTS). The proposed method is rather new in glaciology and to our knowledge not verified and validated against analytical solutions. Unfortunately we are still lacking analytical solutions for sufficiently complex thermo-mechanically coupled polythermal ice flow. However, we present two experiments to test the implementation of the enthalpy equation and corresponding boundary conditions. The first experiment tests particularly the functionality of the boundary condition scheme and the corresponding basal melt rate calculation. Dependent on the different thermal situations that occur at the base, the numerical code may have to switch to another boundary type (from Neuman to Dirichlet or vice versa). The main idea of this set-up is to test the reversibility during transients. A former cold ice body that run through a warmer period with an associated built up of a liquid water layer at the base must be able to return to its initial steady state. Since we impose several assumptions on the experiment design analytical solutions can be formulated for different quantities during distinct stages of the simulation. The second experiment tests the positioning of the internal CTS in a parallel-sided polythermal slab. We compare our simulation results to the analytical solution proposed by Greve and Blatter (2009). Results from three different ice flow-models (COMIce, ISSM, TIMFD3) are presented.

  18. Experimental and computational study on the molecular energetics of indoline and indole.

    PubMed

    da Silva, Manuel A V Ribeiro; Cabral, Joana I T A; Gomes, José R B

    2008-11-27

    Static bomb calorimetry, Calvet microcalorimetry and the Knudsen effusion technique were used to determine the standard molar enthalpy of formation in the gas phase, at T = 298.15 K, of the indole and indoline heterocyclic compounds. The values obtained were 164.3 +/- 1.3 kJ x mol(-1) and 120.0 +/- 2.9 kJ x mol(-1), respectively. Several different computational approaches and different working reactions were used to estimate the gas-phase enthalpies of formation for indole and indoline. The computational approaches support the experimental results reported. The calculations were further extended to the determination of other properties such as bond dissociation enthalpies, gas-phase acidities, proton and electron affinities and ionization energies. The agreement between theoretical and experimental data for indole is very good supporting the data calculated for indoline.

  19. Dominant Alcohol-Protein Interaction via Hydration-Enabled Enthalpy-Driven Binding Mechanism

    PubMed Central

    Chong, Yuan; Kleinhammes, Alfred; Tang, Pei; Xu, Yan; Wu, Yue

    2015-01-01

    Water plays an important role in weak associations of small drug molecules with proteins. Intense focus has been on binding-induced structural changes in the water network surrounding protein binding sites, especially their contributions to binding thermodynamics. However, water is also tightly coupled to protein conformations and dynamics, and so far little is known about the influence of water-protein interactions on ligand binding. Alcohols are a type of low-affinity drugs, and it remains unclear how water affects alcohol-protein interactions. Here, we present alcohol adsorption isotherms under controlled protein hydration using in-situ NMR detection. As functions of hydration level, Gibbs free energy, enthalpy, and entropy of binding were determined from the temperature dependence of isotherms. Two types of alcohol binding were found. The dominant type is low-affinity nonspecific binding, which is strongly dependent on temperature and the level of hydration. At low hydration levels, this nonspecific binding only occurs above a threshold of alcohol vapor pressure. An increased hydration level reduces this threshold, with it finally disappearing at a hydration level of h~0.2 (g water/g protein), gradually shifting alcohol binding from an entropy-driven to an enthalpy-driven process. Water at charged and polar groups on the protein surface was found to be particularly important in enabling this binding. Although further increase in hydration has smaller effects on the changes of binding enthalpy and entropy, it results in significant negative change in Gibbs free energy due to unmatched enthalpy-entropy compensation. These results show the crucial role of water-protein interplay in alcohol binding. PMID:25856773

  20. Numerical algorithm comparison for the accurate and efficient computation of high-incidence vortical flow

    NASA Technical Reports Server (NTRS)

    Chaderjian, Neal M.

    1991-01-01

    Computations from two Navier-Stokes codes, NSS and F3D, are presented for a tangent-ogive-cylinder body at high angle of attack. Features of this steady flow include a pair of primary vortices on the leeward side of the body as well as secondary vortices. The topological and physical plausibility of this vortical structure is discussed. The accuracy of these codes are assessed by comparison of the numerical solutions with experimental data. The effects of turbulence model, numerical dissipation, and grid refinement are presented. The overall efficiency of these codes are also assessed by examining their convergence rates, computational time per time step, and maximum allowable time step for time-accurate computations. Overall, the numerical results from both codes compared equally well with experimental data, however, the NSS code was found to be significantly more efficient than the F3D code.

  1. Effects of partitioned enthalpy of mixing on glass-forming ability

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

    Song, Wen-Xiong; Zhao, Shi-Jin, E-mail: shijin.zhao@shu.edu.cn

    2015-04-14

    We explore the inherent reason at atomic level for the glass-forming ability of alloys by molecular simulation, in which the effect of partitioned enthalpy of mixing is studied. Based on Morse potential, we divide the enthalpy of mixing into three parts: the chemical part (Δ E{sub nn}), strain part (Δ E{sub strain}), and non-bond part (Δ E{sub nnn}). We find that a large negative Δ E{sub nn} value represents strong AB chemical bonding in AB alloy and is the driving force to form a local ordered structure, meanwhile the transformed local ordered structure needs to satisfy the condition (Δ E{submore » nn}/2 + Δ E{sub strain}) < 0 to be stabilized. Understanding the chemical and strain parts of enthalpy of mixing is helpful to design a new metallic glass with a good glass forming ability. Moreover, two types of metallic glasses (i.e., “strain dominant” and “chemical dominant”) are classified according to the relative importance between chemical effect and strain effect, which enriches our knowledge of the forming mechanism of metallic glass. Finally, a soft sphere model is established, different from the common hard sphere model.« less

  2. Enthalpy-based equation of state for highly porous materials employing modified soft sphere fluid model

    NASA Astrophysics Data System (ADS)

    Nayak, Bishnupriya; Menon, S. V. G.

    2018-01-01

    Enthalpy-based equation of state based on a modified soft sphere model for the fluid phase, which includes vaporization and ionization effects, is formulated for highly porous materials. Earlier developments and applications of enthalpy-based approach had not accounted for the fact that shocked states of materials with high porosity (e.g., porosity more than two for Cu) are in the expanded fluid region. We supplement the well known soft sphere model with a generalized Lennard-Jones formula for the zero temperature isotherm, with parameters determined from cohesive energy, specific volume and bulk modulus of the solid at normal condition. Specific heats at constant pressure, ionic and electronic enthalpy parameters and thermal excitation effects are calculated using the modified approach and used in the enthalpy-based equation of state. We also incorporate energy loss from the shock due to expansion of shocked material in calculating porous Hugoniot. Results obtained for Cu, even up to initial porosities ten, show good agreement with experimental data.

  3. Enthalpy characteristics of L-proline dissolution in certain water-organic mixtures at 298.15 K

    NASA Astrophysics Data System (ADS)

    Badelin, V. G.; Smirnov, V. I.

    2017-01-01

    A thermochemical study of the processes of L-proline dissolution in aqueous solutions of acetonitrile, 1,4-dioxane, acetone, dimethyl sulfoxide, nitromethane and tetrahydrofuran at T = 298.15 K in the range of organic solvent concentrations x2 = 0-0.25 mole fractions is performed. Standard values of the enthalpies of solution and transfer of L-proline from water to mixed solvent, and the enthalpy coefficients of pairwise interactions between L-proline and molecules of organic solvents, are calculated. The effect the composition of a water-organic mixture and the structure of organic solvents have on the enthalpy characteristics of L-proline dissolution and transfer is examined. The effect the energy properties of intermolecular interactions between components of a mixed solvent has on the intermolecular interactions between L-proline and molecules of cosolvent is estimated. The correlation between the enthalpy characteristics of L-proline dissolution and electron-donor properties of organic cosolvent in aqueous solutions is determined.

  4. Binding the Mammalian High Mobility Group Protein AT-hook 2 to AT-Rich Deoxyoligonucleotides: Enthalpy-Entropy Compensation

    PubMed Central

    Joynt, Suzanne; Morillo, Victor; Leng, Fenfei

    2009-01-01

    HMGA2 is a DNA minor-groove binding protein. We previously demonstrated that HMGA2 binds to AT-rich DNA with very high binding affinity where the binding of HMGA2 to poly(dA-dT)2 is enthalpy-driven and to poly(dA)poly(dT) is entropy-driven. This is a typical example of enthalpy-entropy compensation. To further study enthalpy-entropy compensation of HMGA2, we used isothermal-titration-calorimetry to examine the interactions of HMGA2 with two AT-rich DNA hairpins: 5′-CCAAAAAAAAAAAAAAAGCCCCCGCTTTTTTTTTTTTTTTGG-3′ (FL-AT-1) and 5′-CCATATATATATATATAGCCCCCGCTATATATATATATATGG-3′ (FL-AT-2). Surprisingly, we observed an atypical isothermal-titration-calorimetry-binding curve at low-salt aqueous solutions whereby the apparent binding-enthalpy decreased dramatically as the titration approached the end. This unusual behavior can be attributed to the DNA-annealing coupled to the ligand DNA-binding and is eliminated by increasing the salt concentration to ∼200 mM. At this condition, HMGA2 binding to FL-AT-1 is entropy-driven and to FL-AT-2 is enthalpy-driven. Interestingly, the DNA-binding free energies for HMGA2 binding to both hairpins are almost temperature independent; however, the enthalpy-entropy changes are dependent on temperature, which is another aspect of enthalpy-entropy compensation. The heat capacity change for HMGA2 binding to FL-AT-1 and FL-AT-2 are almost identical, indicating that the solvent displacement and charge-charge interaction in the coupled folding/binding processes for both binding reactions are similar. PMID:19450485

  5. Determination of some pure compound ideal-gas enthalpies of formation

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

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

    1989-06-01

    The results of a study aimed at improvement of group-additivity methodology for estimation of thermodynamic properties of organic substances are reported. Specific weaknesses where ring corrections were unknown or next-nearest-neighbor interactions were only estimated because of lack of experimental data are addressed by experimental studies of enthalpies of combustion in the condensed- phase and vapor pressure measurements. Ideal-gas enthalpies of formation are reported for acrylamide, succinimide, ..gamma..-butyrolactone, 2-pyrrolidone, 2,3-dihydrofuran, 3,4-dihydro-2H-pyran, 1,3-cyclohexadiene, 1,4-cyclohexadiene, and 1-methyl-1-phenylhydrazine. Ring corrections, group terms, and next-nearest-neighbor interaction terms useful in the application of group additivity correlations are derived. 44 refs., 2 figs., 59 tabs.

  6. Estimating the melting point, entropy of fusion, and enthalpy of fusion of organic compounds via SPARC.

    PubMed

    Whiteside, T S; Hilal, S H; Brenner, A; Carreira, L A

    2016-08-01

    The entropy of fusion, enthalpy of fusion, and melting point of organic compounds can be estimated through three models developed using the SPARC (SPARC Performs Automated Reasoning in Chemistry) platform. The entropy of fusion is modelled through a combination of interaction terms and physical descriptors. The enthalpy of fusion is modelled as a function of the entropy of fusion, boiling point, and flexibility of the molecule. The melting point model is the enthalpy of fusion divided by the entropy of fusion. These models were developed in part to improve SPARC's vapour pressure and solubility models. These models have been tested on 904 unique compounds. The entropy model has a RMS of 12.5 J mol(-1) K(-1). The enthalpy model has a RMS of 4.87 kJ mol(-1). The melting point model has a RMS of 54.4°C.

  7. Experimental and computational investigation of the thermochemistry of the six isomers of dichloroaniline.

    PubMed

    Ribeiro da Silva, Manuel A V; Amaral, Luísa M P F; Gomes, José R B

    2006-07-27

    The standard (p(o) = 0.1 MPa) molar enthalpies of formation of 2,3-, 2,4-, 2,5-, 2,6-, 3,4- and 3,5-dichloroanilines were derived from the standard molar energies of combustion, in oxygen, to yield CO(2)(g), N(2)(g) and HCl.600H(2)O(l), at T = 298.15 K, measured by rotating bomb combustion calorimetry. The Calvet high-temperature vacuum sublimation technique was used to measure the enthalpies of sublimation of the six isomers. These two thermodynamic parameters yielded the standard molar enthalpies of formation of the six isomers of dichloroaniline, in the gaseous phase, at T = 298.15 K. The gas-phase enthalpies of formation were also estimated by G3MP2B3 calculations, which were further extended to the computation of gas-phase acidities, proton affinities, and ionization enthalpies.

  8. An accurate, compact and computationally efficient representation of orbitals for quantum Monte Carlo calculations

    NASA Astrophysics Data System (ADS)

    Luo, Ye; Esler, Kenneth; Kent, Paul; Shulenburger, Luke

    Quantum Monte Carlo (QMC) calculations of giant molecules, surface and defect properties of solids have been feasible recently due to drastically expanding computational resources. However, with the most computationally efficient basis set, B-splines, these calculations are severely restricted by the memory capacity of compute nodes. The B-spline coefficients are shared on a node but not distributed among nodes, to ensure fast evaluation. A hybrid representation which incorporates atomic orbitals near the ions and B-spline ones in the interstitial regions offers a more accurate and less memory demanding description of the orbitals because they are naturally more atomic like near ions and much smoother in between, thus allowing coarser B-spline grids. We will demonstrate the advantage of hybrid representation over pure B-spline and Gaussian basis sets and also show significant speed-up like computing the non-local pseudopotentials with our new scheme. Moreover, we discuss a new algorithm for atomic orbital initialization which used to require an extra workflow step taking a few days. With this work, the highly efficient hybrid representation paves the way to simulate large size even in-homogeneous systems using QMC. This work was supported by the U.S. Department of Energy, Office of Science, Basic Energy Sciences, Computational Materials Sciences Program.

  9. An efficient reliable method to estimate the vaporization enthalpy of pure substances according to the normal boiling temperature and critical properties.

    PubMed

    Mehmandoust, Babak; Sanjari, Ehsan; Vatani, Mostafa

    2014-03-01

    The heat of vaporization of a pure substance at its normal boiling temperature is a very important property in many chemical processes. In this work, a new empirical method was developed to predict vaporization enthalpy of pure substances. This equation is a function of normal boiling temperature, critical temperature, and critical pressure. The presented model is simple to use and provides an improvement over the existing equations for 452 pure substances in wide boiling range. The results showed that the proposed correlation is more accurate than the literature methods for pure substances in a wide boiling range (20.3-722 K).

  10. Spatial adaption procedures on unstructured meshes for accurate unsteady aerodynamic flow computation

    NASA Technical Reports Server (NTRS)

    Rausch, Russ D.; Batina, John T.; Yang, Henry T. Y.

    1991-01-01

    Spatial adaption procedures for the accurate and efficient solution of steady and unsteady inviscid flow problems are described. The adaption procedures were developed and implemented within a two-dimensional unstructured-grid upwind-type Euler code. These procedures involve mesh enrichment and mesh coarsening to either add points in a high gradient region or the flow or remove points where they are not needed, respectively, to produce solutions of high spatial accuracy at minimal computational costs. A detailed description is given of the enrichment and coarsening procedures and comparisons with alternative results and experimental data are presented to provide an assessment of the accuracy and efficiency of the capability. Steady and unsteady transonic results, obtained using spatial adaption for the NACA 0012 airfoil, are shown to be of high spatial accuracy, primarily in that the shock waves are very sharply captured. The results were obtained with a computational savings of a factor of approximately fifty-three for a steady case and as much as twenty-five for the unsteady cases.

  11. Spatial adaption procedures on unstructured meshes for accurate unsteady aerodynamic flow computation

    NASA Technical Reports Server (NTRS)

    Rausch, Russ D.; Yang, Henry T. Y.; Batina, John T.

    1991-01-01

    Spatial adaption procedures for the accurate and efficient solution of steady and unsteady inviscid flow problems are described. The adaption procedures were developed and implemented within a two-dimensional unstructured-grid upwind-type Euler code. These procedures involve mesh enrichment and mesh coarsening to either add points in high gradient regions of the flow or remove points where they are not needed, respectively, to produce solutions of high spatial accuracy at minimal computational cost. The paper gives a detailed description of the enrichment and coarsening procedures and presents comparisons with alternative results and experimental data to provide an assessment of the accuracy and efficiency of the capability. Steady and unsteady transonic results, obtained using spatial adaption for the NACA 0012 airfoil, are shown to be of high spatial accuracy, primarily in that the shock waves are very sharply captured. The results were obtained with a computational savings of a factor of approximately fifty-three for a steady case and as much as twenty-five for the unsteady cases.

  12. Numerically accurate computational techniques for optimal estimator analyses of multi-parameter models

    NASA Astrophysics Data System (ADS)

    Berger, Lukas; Kleinheinz, Konstantin; Attili, Antonio; Bisetti, Fabrizio; Pitsch, Heinz; Mueller, Michael E.

    2018-05-01

    Modelling unclosed terms in partial differential equations typically involves two steps: First, a set of known quantities needs to be specified as input parameters for a model, and second, a specific functional form needs to be defined to model the unclosed terms by the input parameters. Both steps involve a certain modelling error, with the former known as the irreducible error and the latter referred to as the functional error. Typically, only the total modelling error, which is the sum of functional and irreducible error, is assessed, but the concept of the optimal estimator enables the separate analysis of the total and the irreducible errors, yielding a systematic modelling error decomposition. In this work, attention is paid to the techniques themselves required for the practical computation of irreducible errors. Typically, histograms are used for optimal estimator analyses, but this technique is found to add a non-negligible spurious contribution to the irreducible error if models with multiple input parameters are assessed. Thus, the error decomposition of an optimal estimator analysis becomes inaccurate, and misleading conclusions concerning modelling errors may be drawn. In this work, numerically accurate techniques for optimal estimator analyses are identified and a suitable evaluation of irreducible errors is presented. Four different computational techniques are considered: a histogram technique, artificial neural networks, multivariate adaptive regression splines, and an additive model based on a kernel method. For multiple input parameter models, only artificial neural networks and multivariate adaptive regression splines are found to yield satisfactorily accurate results. Beyond a certain number of input parameters, the assessment of models in an optimal estimator analysis even becomes practically infeasible if histograms are used. The optimal estimator analysis in this paper is applied to modelling the filtered soot intermittency in large eddy

  13. A new method for the determination of vaporization enthalpies of ionic liquids at low temperatures.

    PubMed

    Verevkin, Sergey P; Zaitsau, Dzmitry H; Emelyanenko, Vladimir N; Heintz, Andreas

    2011-11-10

    A new method for the determination of vaporization enthalpies of extremely low volatile ILs has been developed using a newly constructed quartz crystal microbalance (QCM) vacuum setup. Because of the very high sensitivity of the QCM it has been possible to reduce the average temperature of the vaporization studies by approximately 100 K in comparison to other conventional techniques. The physical basis of the evaluation procedure has been developed and test measurements have been performed with the common ionic liquid 1-ethyl-3-methylimidazolium bis(trifluoromethanesulfonyl)imide [C(2)mim][NTf(2)] extending the range of measuring vaporization enthalpies down to 363 K. The results obtained for [C(2)mim][NTf(2)] have been tested for thermodynamic consistency by comparison with data already available at higher temperatures. Comparison of the temperature-dependent vaporization enthalpy data taken from the literature show only acceptable agreement with the heat capacity difference of -40 J K(-1) mol(-1). The method developed in this work opens also a new way to obtain reliable values of vaporization enthalpies of thermally unstable ionic liquids.

  14. Enthalpy - Improved Dielectric Insulation for Superconducting Wires.

    DTIC Science & Technology

    1982-05-01

    these materials are also bein, studickd as regenerator matrix materials for Stirling cycle cryocoolers (7), yet, 1’~l incredibly enough, their...1A0.Az 4. TI T LE (iind SThti tfe) 5 TYPE OF REPORT & PERIOD COVERFID Enthalpy - Improved Dielectric Insulation for Final JUN 80 - MAR 82...resistance, and suggestions are made for improving these conductivities. The SC-2 and SC-3 type materials have near-metallic thermal conductivities near

  15. Measurement of the aerothermodynamic state in a high enthalpy plasma wind-tunnel flow

    NASA Astrophysics Data System (ADS)

    Hermann, Tobias; Löhle, Stefan; Zander, Fabian; Fasoulas, Stefanos

    2017-11-01

    This paper presents spatially resolved measurements of absolute particle densities of N2, N2+, N, O, N+ , O+ , e- and excitation temperatures of electronic, rotational and vibrational modes of an air plasma free stream. All results are based on optical emission spectroscopy data. The measured parameters are combined to determine the local mass-specific enthalpy of the free stream. The analysis of the radiative transport, relative and absolute intensities, and spectral shape is used to determine various thermochemical parameters. The model uncertainty of each analysis method is assessed. The plasma flow is shown to be close to equilibrium. The strongest deviations from equilibrium occur for N, N+ and N2+ number densities in the free stream. Additional measurements of the local mass-specific enthalpy are conducted using a mass injection probe as well as a heat flux and total pressure probe. The agreement between all methods of enthalpy determination is good.

  16. The CC/DFT Route towards Accurate Structures and Spectroscopic Features for Observed and Elusive Conformers of Flexible Molecules: Pyruvic Acid as Case Study

    PubMed Central

    Barone, Vincenzo; Biczysko, Malgorzata; Bloino, Julien; Cimino, Paola; Penocchio, Emanuele; Puzzarini, Cristina

    2018-01-01

    The structures, relative stabilities as well as the rotational and vibrational spectra of the three low-energy conformers of Pyruvic acid (PA) have been characterized using a state-of-the-art quantum-mechanical approach designed for flexible molecules. By making use of the available experimental rotational constants for several isotopologues of the most stable PA conformer, Tc-PA, the semi-experimental equilibrium structure has been derived. The latter provides a reference for the pure theoretical determination of the equilibrium geometries for all conformers, thus confirming for these structures an accuracy of 0.001 Å and 0.1 deg. for bond lengths and angles, respectively. Highly accurate relative energies of all conformers (Tc-, Tt- and Ct-PA) and of the transition states connecting them are provided along with the thermodynamic properties at low and high temperatures, thus leading to conformational enthalpies accurate to 1 kJ mol−1. Concerning microwave spectroscopy, rotational constants accurate to about 20 MHz are provided for the Tt- and Ct-PA conformers, together with the computed centrifugal-distortion constants and dipole moments required to simulate their rotational spectra. For Ct-PA, vibrational frequencies in the mid-infrared region accurate to 10 cm−1 are reported along with theoretical estimates for the transitions in the near-infrared range, and the corresponding infrared spectrum including fundamental transitions, overtones and combination bands has been simulated. In addition to the new data described above, theoretical results for the Tc- and Tt-PA conformers are compared with all available experimental data to further confirm the accuracy of the hybrid coupled-cluster/density functional theory (CC/DFT) protocol applied in the present study. Finally, we discuss in detail the accuracy of computational models fully based on double-hybrid DFT functionals (mainly at the B2PLYP/aug-cc-pVTZ level) that avoid the use of very expensive CC

  17. Isothermogravimetric determination of the enthalpies of vaporization of 1-alkyl-3-methylimidazolium ionic liquids.

    PubMed

    Luo, Huimin; Baker, Gary A; Dai, Sheng

    2008-08-21

    Vaporization enthalpies for two series of ionic liquids (ILs) composed of 1- n-alkyl-3-methylimidazolium cations, [Imm1+] (m=2, 3, 4, 6, 8, or 10), paired with either the bis(trifluoromethanesulfonyl)amide, [Tf2N-], or the bis(perfluoroethylsulfonyl)amide anion, [beti-], were determined using a simple, convenient, and highly reproducible thermogravimetric approach, and from these values, Hildebrand solubility parameters were estimated. Our results reveal two interesting and unanticipated outcomes: (i) methylation at the C2 position of [Imm1+] affords a significantly higher vaporization enthalpy; (ii) in all cases, the [beti-] anion served to lower the enthalpy of vaporization relative to [Tf2N-]. The widespread availability of the apparatus required for these measurements coupled with the ease of automation suggests the broad potential of this methodology for determining this critical parameter in a multitude of ILs.

  18. 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

  19. Estimation of Enthalpy of Formation of Liquid Transition Metal Alloys: A Modified Prescription Based on Macroscopic Atom Model of Cohesion

    NASA Astrophysics Data System (ADS)

    Raju, Subramanian; Saibaba, Saroja

    2016-09-01

    The enthalpy of formation Δo H f is an important thermodynamic quantity, which sheds significant light on fundamental cohesive and structural characteristics of an alloy. However, being a difficult one to determine accurately through experiments, simple estimation procedures are often desirable. In the present study, a modified prescription for estimating Δo H f L of liquid transition metal alloys is outlined, based on the Macroscopic Atom Model of cohesion. This prescription relies on self-consistent estimation of liquid-specific model parameters, namely electronegativity ( ϕ L) and bonding electron density ( n b L ). Such unique identification is made through the use of well-established relationships connecting surface tension, compressibility, and molar volume of a metallic liquid with bonding charge density. The electronegativity is obtained through a consistent linear scaling procedure. The preliminary set of values for ϕ L and n b L , together with other auxiliary model parameters, is subsequently optimized to obtain a good numerical agreement between calculated and experimental values of Δo H f L for sixty liquid transition metal alloys. It is found that, with few exceptions, the use of liquid-specific model parameters in Macroscopic Atom Model yields a physically consistent methodology for reliable estimation of mixing enthalpies of liquid alloys.

  20. The Molecular Origin of Enthalpy/Entropy Compensation in Biomolecular Recognition.

    PubMed

    Fox, Jerome M; Zhao, Mengxia; Fink, Michael J; Kang, Kyungtae; Whitesides, George M

    2018-05-20

    Biomolecular recognition can be stubborn; changes in the structures of associating molecules, or the environments in which they associate, often yield compensating changes in enthalpies and entropies of binding and no net change in affinities. This phenomenon-termed enthalpy/entropy (H/S) compensation-hinders efforts in biomolecular design, and its incidence-often a surprise to experimentalists-makes interactions between biomolecules difficult to predict. Although characterizing H/S compensation requires experimental care, it is unquestionably a real phenomenon that has, from an engineering perspective, useful physical origins. Studying H/S compensation can help illuminate the still-murky roles of water and dynamics in biomolecular recognition and self-assembly. This review summarizes known sources of H/ S compensation (real and perceived) and lays out a conceptual framework for understanding and dissecting-and, perhaps, avoiding or exploiting-this phenomenon in biophysical systems.

  1. Enthalpy Costs of Making and Breaking Bonds: A Game of Generating Molecules with Proper Lewis Structures

    ERIC Educational Resources Information Center

    Bell, Peter T.; Adkins, Alyssa D.; Gamble, Rex J.; Schultz, Linda D.

    2009-01-01

    "Enthalpy Costs" is a simple card game created to assist students in developing proper Lewis structure drawing skills. Score keeping is accomplished by tracking the enthalpy changes associated with bond-making and bond-breaking processes during formation of molecules represented by proper Lewis structures. Playing the game requires the student to…

  2. Enthalpy measurement of coal-derived liquids. Combined quarterly technical progress reports, April-June 1979 and July-September 1979. [Effect of association

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

    Kidnay, A.J.; Yesavage, V.F.

    1979-01-01

    Enthalpy measurements on a coal-derived naphtha and middle distillate, both produced by the SRC-II process, were made using flow calorimetry. The accuracy of the measurements, as reported by Omid, was within +- 1% of the measured enthalpy differences, ..delta..H. Experimental data for the naphtha were obtained over a pressure range of 100-300 psia and temperatures from 148/sup 0/ to 456/sup 0/F. The middle distillate enthalpy measurements were made in the pressure and temperature ranges of 130 to 1000 psia, and 157/sup 0/ to 675/sup 0/F, respectively. The methods of prediction of enthalpy developed for petroleum fractions were unsatisfactory when appliedmore » to the above data. A negative bias was observed in the predicted enthalpy values for several of the coal-liquids. Based on these results, it was theorized that the high experimental enthalpy values for coal-liquids were due to an energy of association attributed, primarily, to hydrogen-bonding effects. The petroleum-fraction enthalpy correlations were then tested on the experimental data for pure compounds, both associating and non-associating. The predicted values compared very well with the experimental results for non-associating model compounds. However, for associating model compounds the predicted enthalpy values were considerably lower than their experimental data. This served to confirm the basic premise that the high experimental enthalpy values, for model compounds and coal liquids, were a direct consequence of an energy of association attributed, primarily, to hydrogen-bonding effects.« less

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

    PubMed Central

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

    2012-01-01

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

  4. Temperature dependences of saturated vapor pressure and the enthalpy of vaporization of n-pentyl esters of dicarboxylic acids

    NASA Astrophysics Data System (ADS)

    Portnova, S. V.; Krasnykh, E. L.; Levanova, S. V.

    2016-05-01

    The saturated vapor pressures and enthalpies of vaporization of n-pentyl esters of linear C2-C6 dicarboxylic acids are determined by the transpiration method in the temperature range of 309.2-361.2 K. The dependences of enthalpies of vaporization on the number of carbon atoms in the molecule and on the retention indices have been determined. The predictive capabilities of the existing calculation schemes for estimation of enthalpy of vaporization of the studied compounds have been analyzed.

  5. An efficient reliable method to estimate the vaporization enthalpy of pure substances according to the normal boiling temperature and critical properties

    PubMed Central

    Mehmandoust, Babak; Sanjari, Ehsan; Vatani, Mostafa

    2013-01-01

    The heat of vaporization of a pure substance at its normal boiling temperature is a very important property in many chemical processes. In this work, a new empirical method was developed to predict vaporization enthalpy of pure substances. This equation is a function of normal boiling temperature, critical temperature, and critical pressure. The presented model is simple to use and provides an improvement over the existing equations for 452 pure substances in wide boiling range. The results showed that the proposed correlation is more accurate than the literature methods for pure substances in a wide boiling range (20.3–722 K). PMID:25685493

  6. Group vector space method for estimating enthalpy of vaporization of organic compounds at the normal boiling point.

    PubMed

    Wenying, Wei; Jinyu, Han; Wen, Xu

    2004-01-01

    The specific position of a group in the molecule has been considered, and a group vector space method for estimating enthalpy of vaporization at the normal boiling point of organic compounds has been developed. Expression for enthalpy of vaporization Delta(vap)H(T(b)) has been established and numerical values of relative group parameters obtained. The average percent deviation of estimation of Delta(vap)H(T(b)) is 1.16, which show that the present method demonstrates significant improvement in applicability to predict the enthalpy of vaporization at the normal boiling point, compared the conventional group methods.

  7. Molar volume, excess enthalpy, and Prigogine-Defay ratio of some silicate glasses with different (P,T) histories.

    PubMed

    Wondraczek, Lothar; Behrens, Harald

    2007-10-21

    Structural relaxation in silicate glasses with different (p,T) histories was experimentally examined by differential scanning calorimetry and measurements of molar volume under ambient pressure. Temperature and pressure-dependent rates of changes in molar volume and generation of excess enthalpy were determined for sodium trisilicate, soda lime silicate, and sodium borosilicate (NBS) compositions. From the derived data, Prigogine-Defay ratios are calculated and discussed. Changes of excess enthalpy are governed mainly by changes in short-range structure, as is shown for NBS where boron coordination is highly sensitive to pressure. For all three glasses, it is shown how the relaxation functions that underlie volume, enthalpy, and structural relaxation decouple for changes in cooling rates and pressure of freezing, respectively. The magnitude of the divergence between enthalpy and volume may be related to differences in structural sensitivity to changes in the (p,V,T,t) space on different length scales. The findings suggest that the Prigogine-Defay ratio is related to the magnitude of the discussed decoupling effect.

  8. Blunt-Body Aerothermodynamic Database from High-Enthalpy CO2 Testing in an Expansion Tunnel

    NASA Technical Reports Server (NTRS)

    Hollis, Brian R.; Prabhu, Dinesh K.; Maclean, Matthew; Dufrene, Aaron

    2016-01-01

    An extensive database of heating, pressure, and flow field measurements on a 70-deg sphere-cone blunt body geometry in high-enthalpy, CO2 flow has been generated through testing in an expansion tunnel. This database is intended to support development and validation of computational tools and methods to be employed in the design of future Mars missions. The test was conducted in an expansion tunnel in order to avoid uncertainties in the definition of free stream conditions noted in previous studies performed in reflected shock tunnels. Data were obtained across a wide range of test velocity/density conditions that produced various physical phenomena of interest, including laminar and transitional/turbulent boundary layers, non-reacting to completely dissociated post-shock gas composition and shock-layer radiation. Flow field computations were performed at the test conditions and comparisons were made with the experimental data. Based on these comparisons, it is recommended that computational uncertainties on surface heating and pressure, for laminar, reacting-gas environments can be reduced to +/-10% and +/-5%, respectively. However, for flows with turbulence and shock-layer radiation, there were not sufficient validation-quality data obtained in this study to make any conclusions with respect to uncertainties, which highlights the need for further research in these areas.

  9. Bond dissociation enthalpies of a pinoresinol lignin model compound

    Treesearch

    Thomas Elder

    2014-01-01

    ABSTRACT: The pinoresinol unit is one of the principal interunit linkages in lignin. As such, its chemistry and properties are of major importance in understanding the behavior or the polymer. This work examines the homolytic cleavage of the pinoresinol system, representing the initial step in thermal degradation. The bond dissociation enthalpy of this reaction has...

  10. Enthalpy of Vaporization and Vapor Pressures: An Inexpensive Apparatus

    ERIC Educational Resources Information Center

    Battino, Rubin; Dolson, David A.; Hall, Michael A.; Letcher, Trevor M.

    2007-01-01

    A simple and inexpensive method to determine the enthalpy of vaporization of liquids by measuring vapor pressure as a function of temperature is described. The vapor pressures measured with the stopcock cell were higher than the literature values and those measured with the sidearm rubber septum cell were both higher and lower than literature…

  11. Design of a Mach-15 Total-Enthalpy Nozzle With Non-uniform Inflow Using Rotational MOC

    NASA Technical Reports Server (NTRS)

    Gaffney, Richard L., Jr.

    2004-01-01

    A new computer program to design nozzles with non-uniform inflow has been developed using the rotational method of characteristics (MOC). This program has been used to design a nozzle for the NASA's HYPULSE shock-expansion tunnel for use in scramjet engine tests at a Mach-15 flight-enthalpy condition. The nozzle has an area ratio of 9.5:1 that expands the inflow from Mach 6 along the centerline to Mach 8.7. Although the density and Mach number vary radially at the exit due to the non-uniformities of the inflow, the MOC procedure produces exit flow that is parallel and has uniform static pressure. The design has been verified with CFD which compares favorably with the MOC solution.

  12. Problem-Based Learning in Teaching Chemistry: Enthalpy Changes in Systems

    ERIC Educational Resources Information Center

    Ayyildiz, Yildizay; Tarhan, Leman

    2018-01-01

    Background: Problem-based learning (PBL) as a teaching strategy has recently become quite widespread in especially chemistry classes. Research has found that students, from elementary through college, have many alternative conceptions regarding "enthalpy changes in systems." Although there are several studies focused on identifying…

  13. A combined experimental and computational thermodynamic study of difluoronitrobenzene isomers.

    PubMed

    Ribeiro da Silva, Manuel A V; Monte, Manuel J S; Lobo Ferreira, Ana I M C; Oliveira, Juliana A S A; Cimas, Álvaro

    2010-10-14

    This work reports the experimental and computational thermochemical study performed on three difluorinated nitrobenzene isomers: 2,4-difluoronitrobenzene (2,4-DFNB), 2,5-difluoronitrobenzene (2,5-DFNB), and 3,4-difluoronitrobenzene (3,4-DFNB). The standard (p° = 0.1 MPa) molar enthalpies of formation in the liquid phase of these compounds were derived from the standard molar energies of combustion, in oxygen, at T = 298.15 K, measured by rotating bomb combustion calorimetry. A static method was used to perform the vapor pressure study of the referred compounds allowing the construction of the phase diagrams and determination of the respective triple point coordinates, as well as the standard molar enthalpies of vaporization, sublimation, and fusion for two of the isomers (2,4-DFNB and 3,4-DFNB). For 2,5-difluoronitrobenzene, only liquid vapor pressures were measured enabling the determination of the standard molar enthalpies of vaporization. Combining the thermodynamic parameters of the compounds studied, the following standard (p° = 0.1 MPa) molar enthalpies of formation in the gaseous phase, at T = 298.15 K, were derived: Δ(f)H(m)° (2,4-DFNB, g) = -(296.3 ± 1.8) kJ · mol⁻¹, Δ(f)H(m)° (2,5-DFNB, g) = -(288.2 ± 2.1) kJ · mol⁻¹, and Δ(f)H(m)° (3,4-DFNB, g) = -(302.4 ± 2.1) kJ · mol⁻¹. Using the empirical scheme developed by Cox, several approaches were evaluated in order to identify the best method for estimating the standard molar gas phase enthalpies of formation of these compounds. The estimated values were compared to the ones obtained experimentally, and the approach providing the best comparison with experiment was used to estimate the thermodynamic behavior of the other difluorinated nitrobenzene isomers not included in this study. Additionally, the enthalpies of formation of these compounds along with the enthalpies of formation of the other isomers not studied experimentally, i.e., 2,3-DFNB, 2,6-DFNB, and 3,5-DFNB, were estimated

  14. Isothermal enthalpy relaxation of glassy 1,2,6-hexanetriol

    NASA Astrophysics Data System (ADS)

    Fransson, Å.; Bäckström, G.

    The isothermal enthalpy relaxation of glassy 1,2,6-hexanetriol has been measured at six temperatures. The relaxation time and the distribution parameters extracted from fits of the Williams-Watts relaxation function are compared with parameters obtained by other techniques and on other substances. A detailed comparison of the Williams-Watts and the Davidson-Cole relaxation functions is presented.

  15. Computational assessment of several hydrogen-free high energy compounds.

    PubMed

    Tan, Bisheng; Huang, Ming; Long, Xinping; Li, Jinshan; Fan, Guijuan

    2016-01-01

    Tetrazino-tetrazine-tetraoxide (TTTO) is an attractive high energy compound, but unfortunately, it is not yet experimentally synthesized so far. Isomerization of TTTO leads to its five isomers, bond-separation energies were empolyed to compare the global stability of six compounds, it is found that isomer 1 has the highest bond-separation energy (1204.6kJ/mol), compared with TTTO (1151.2kJ/mol); thermodynamic properties of six compounds were theoretically calculated, including standard formation enthalpies (solid and gaseous), standard fusion enthalpies, standard vaporation enthalpies, standard sublimation enthalpies, lattice energies and normal melting points, normal boiling points; their detonation performances were also computed, including detonation heat (Q, cal/g), detonation velocity (D, km/s), detonation pressure (P, GPa) and impact sensitivity (h50, cm), compared with TTTO (Q=1311.01J/g, D=9.228km/s, P=40.556GPa, h50=12.7cm), isomer 5 exhibites better detonation performances (Q=1523.74J/g, D=9.389km/s, P=41.329GPa, h50= 28.4cm). Copyright © 2015 Elsevier Inc. All rights reserved.

  16. The effects of finite rate chemical processes on high enthalpy nozzle performance - A comparison between SPARK and SEAGULL

    NASA Technical Reports Server (NTRS)

    Carpenter, M. H.

    1988-01-01

    The generalized chemistry version of the computer code SPARK is extended to include two higher-order numerical schemes, yielding fourth-order spatial accuracy for the inviscid terms. The new and old formulations are used to study the influences of finite rate chemical processes on nozzle performance. A determination is made of the computationally optimum reaction scheme for use in high-enthalpy nozzles. Finite rate calculations are compared with the frozen and equilibrium limits to assess the validity of each formulation. In addition, the finite rate SPARK results are compared with the constant ratio of specific heats (gamma) SEAGULL code, to determine its accuracy in variable gamma flow situations. Finally, the higher-order SPARK code is used to calculate nozzle flows having species stratification. Flame quenching occurs at low nozzle pressures, while for high pressures, significant burning continues in the nozzle.

  17. Free Enthalpy Differences between α-, π-, and 310-Helices of an Atomic Level Fine-Grained Alanine Deca-Peptide Solvated in Supramolecular Coarse-Grained Water.

    PubMed

    Lin, Zhixiong; Riniker, Sereina; van Gunsteren, Wilfred F

    2013-03-12

    Atomistic molecular dynamics simulations of peptides or proteins in aqueous solution are still limited to the multi-nanosecond time scale and multi-nanometer range by computational cost. Combining atomic solutes with a supramolecular solvent model in hybrid fine-grained/coarse-grained (FG/CG) simulations allows atomic detail in the region of interest while being computationally more efficient. We used enveloping distribution sampling (EDS) to calculate the free enthalpy differences between different helical conformations, i.e., α-, π-, and 310-helices, of an atomic level FG alanine deca-peptide solvated in a supramolecular CG water solvent. The free enthalpy differences obtained show that by replacing the FG solvent by the CG solvent, the π-helix is destabilized with respect to the α-helix by about 2.5 kJ mol(-1), and the 310-helix is stabilized with respect to the α-helix by about 9 kJ mol(-1). In addition, the dynamics of the peptide becomes faster. By introducing a FG water layer of 0.8 nm around the peptide, both thermodynamic and dynamic properties are recovered, while the hybrid FG/CG simulations are still four times more efficient than the atomistic simulations, even when the cutoff radius for the nonbonded interactions is increased from 1.4 to 2.0 nm. Hence, the hybrid FG/CG model, which yields an appropriate balance between reduced accuracy and enhanced computational speed, is very suitable for molecular dynamics simulation investigations of biomolecules.

  18. Accurate Arabic Script Language/Dialect Classification

    DTIC Science & Technology

    2014-01-01

    Army Research Laboratory Accurate Arabic Script Language/Dialect Classification by Stephen C. Tratz ARL-TR-6761 January 2014 Approved for public...1197 ARL-TR-6761 January 2014 Accurate Arabic Script Language/Dialect Classification Stephen C. Tratz Computational and Information Sciences...Include area code) Standard Form 298 (Rev. 8/98) Prescribed by ANSI Std. Z39.18 January 2014 Final Accurate Arabic Script Language/Dialect Classification

  19. Estimating the melting point, entropy of fusion, and enthalpy of ...

    EPA Pesticide Factsheets

    The entropies of fusion, enthalies of fusion, and melting points of organic compounds can be estimated through three models developed using the SPARC (SPARC Performs Automated Reasoning in Chemistry) platform. The entropy of fusion is modeled through a combination of interaction terms and physical descriptors. The enthalpy of fusion is modeled as a function of the entropy of fusion, boiling point, and fexibility of the molecule. The melting point model is the enthlapy of fusion divided by the entropy of fusion. These models were developed in part to improve SPARC's vapor pressure and solubility models. These models have been tested on 904 unique compounds. The entropy model has a RMS of 12.5 J mol-1K-1. The enthalpy model has a RMS of 4.87 kJ mol-1. The melting point model has a RMS of 54.4°C. Published in the journal, SAR and QSAR in Environmental Research

  20. Coupling geophysical investigation with hydrothermal modeling to constrain the enthalpy classification of a potential geothermal resource.

    USGS Publications Warehouse

    White, Jeremy T.; Karakhanian, Arkadi; Connor, Chuck; Connor, Laura; Hughes, Joseph D.; Malservisi, Rocco; Wetmore, Paul

    2015-01-01

    An appreciable challenge in volcanology and geothermal resource development is to understand the relationships between volcanic systems and low-enthalpy geothermal resources. The enthalpy of an undeveloped geothermal resource in the Karckar region of Armenia is investigated by coupling geophysical and hydrothermal modeling. The results of 3-dimensional inversion of gravity data provide key inputs into a hydrothermal circulation model of the system and associated hot springs, which is used to evaluate possible geothermal system configurations. Hydraulic and thermal properties are specified using maximum a priori estimates. Limited constraints provided by temperature data collected from an existing down-gradient borehole indicate that the geothermal system can most likely be classified as low-enthalpy and liquid dominated. We find the heat source for the system is likely cooling quartz monzonite intrusions in the shallow subsurface and that meteoric recharge in the pull-apart basin circulates to depth, rises along basin-bounding faults and discharges at the hot springs. While other combinations of subsurface properties and geothermal system configurations may fit the temperature distribution equally well, we demonstrate that the low-enthalpy system is reasonably explained based largely on interpretation of surface geophysical data and relatively simple models.

  1. 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.

  2. Enabling high grayscale resolution displays and accurate response time measurements on conventional computers.

    PubMed

    Li, Xiangrui; Lu, Zhong-Lin

    2012-02-29

    Display systems based on conventional computer graphics cards are capable of generating images with 8-bit gray level resolution. However, most experiments in vision research require displays with more than 12 bits of luminance resolution. Several solutions are available. Bit++ (1) and DataPixx (2) use the Digital Visual Interface (DVI) output from graphics cards and high resolution (14 or 16-bit) digital-to-analog converters to drive analog display devices. The VideoSwitcher (3) described here combines analog video signals from the red and blue channels of graphics cards with different weights using a passive resister network (4) and an active circuit to deliver identical video signals to the three channels of color monitors. The method provides an inexpensive way to enable high-resolution monochromatic displays using conventional graphics cards and analog monitors. It can also provide trigger signals that can be used to mark stimulus onsets, making it easy to synchronize visual displays with physiological recordings or response time measurements. Although computer keyboards and mice are frequently used in measuring response times (RT), the accuracy of these measurements is quite low. The RTbox is a specialized hardware and software solution for accurate RT measurements. Connected to the host computer through a USB connection, the driver of the RTbox is compatible with all conventional operating systems. It uses a microprocessor and high-resolution clock to record the identities and timing of button events, which are buffered until the host computer retrieves them. The recorded button events are not affected by potential timing uncertainties or biases associated with data transmission and processing in the host computer. The asynchronous storage greatly simplifies the design of user programs. Several methods are available to synchronize the clocks of the RTbox and the host computer. The RTbox can also receive external triggers and be used to measure RT with respect

  3. A study of the vaporization enthalpies of some 1-substituted imidazoles and pyrazoles by correlation-gas chromatography.

    PubMed

    Lipkind, Dmitry; Plienrasri, Chatchawat; Chickos, James S

    2010-12-23

    The vaporization enthalpies of 1-methyl-, 1-ethyl-, 1-phenyl-, and 1-benzylimidazole, 1-methyl- and 1-phenylpyrazole, and trans-azobenzene are evaluated by correlation-gas chromatography (C-GC) using a variety of azines and diazines as standards. The vaporization enthalpies obtained by C-GC when compared to literature values are approximately 14 kJ·mol(-1) smaller for the imidazoles and 6 kJ·mol(-1) smaller for the pyrazoles. The literature vaporization enthalpies of 1-methylpyrrole and 1-methylindole, two closely related compounds with one less nitrogen, are reproduced by C-GC. These results suggest that the magnitude of the intermolecular interactions present in 1-substituted imidazoles and pyrazoles are significantly larger than the those present in the reference compounds and greater than or equal in magnitude to the enhanced intermolecular interactions observed previously in aromatic 1,2-diazines. The vaporization enthalpy and vapor pressure of a trans-1,2-diazine, trans-azobenzene, measured by C-GC using similar standards reproduced the literature values within experimental error.

  4. Enthalpy measurement of coal-derived liquids. Technical progress report, November 1982-January 1983

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

    Kidnay, A.J.; Yesavage, V.F.

    The objective of this research is to measure the enthalpy for representative coal-derived liquids and model compounds over the pressure and temperature regions most likely to be encountered in both liquefaction and processing systems, and to prepare from the data an enthalpy correlation suitable for process design calculations. The correlational effort this past quarter on the enthalpy of coal-derived syncrudes and model compounds has emphasized the experimental determination of a correlating factor for association in coal liquids. As in previous work, the degree of association is to be related to cryoscopic molecular weight determinations on the coal liquids. To thismore » end, work on and an evaluationof a cryoscopic molecular weight apparatus was completed this quarter. Molecular weights of coal liquids determined by the standard Beckman freezing point depression apparatus were consistently low (5 to 10%). After modifications of the apparatus, it was tested with the following compounds: hexane, dodecane, m-xylene and naphthalene. Benzene was the solvent used. However, the molecular weight measurements were again consistently lower than the true values, and in many cases the experimental error was greater than that of the Beckman apparatus.« less

  5. The Relation between Vaporization Enthalpies and Viscosities: Eyring's Theory Applied to Selected Ionic Liquids.

    PubMed

    Bonsa, Anne-Marie; Paschek, Dietmar; Zaitsau, Dzmitry H; Emel'yanenko, Vladimir N; Verevkin, Sergey P; Ludwig, Ralf

    2017-05-19

    Key properties for the use of ionic liquids as electrolytes in batteries are low viscosities, low vapor pressure and high vaporization enthalpies. Whereas the measurement of transport properties is well established, the determination of vaporization enthalpies of these extremely low volatile compounds is still a challenge. At a first glance both properties seem to describe different thermophysical phenomena. However, eighty years ago Eyring suggested a theory which related viscosities and vaporization enthalpies to each other. The model is based on Eyring's theory of absolute reaction rates. Recent attempts to apply Eyring's theory to ionic liquids failed. The motivation of our study is to show that Eyring's theory works, if the assumptions specific for ionic liquids are fulfilled. For that purpose we measured the viscosities of three well selected protic ionic liquids (PILs) at different temperatures. The temperature dependences of viscosities were approximated by the Vogel-Fulcher-Tamann (VFT) relation and extrapolated to the high-temperature regime up to 600 K. Then the VFT-data could be fitted to the Eyring-model. The values of vaporization enthalpies for the three selected PILs predicted by the Eyring model have been very close to the experimental values measured by well-established techniques. We conclude that the Eyring theory can be successfully applied to the chosen set of PILs, if the assumption that ionic pairs of the viscous flow in the liquid and the ionic pairs in the gas phase are similar is fulfilled. It was also noticed that proper transfer of energies can be only derived if the viscosities and the vaporization energies are known for temperatures close to the liquid-gas transition temperature. The idea to correlate easy measurable viscosities of ionic liquids with their vaporization enthalpies opens a new way for a reliable assessment of these thermodynamic properties for a broad range of ionic liquids. © 2017 Wiley-VCH Verlag GmbH & Co. KGa

  6. Heat Effect of the Protonation of Glycine and the Enthalpies of Resolvation of Participating Chemical Species in Water-Dimethylsulfoxide Solvent Mixtures

    NASA Astrophysics Data System (ADS)

    Isaeva, V. A.; Sharnin, V. A.

    2018-02-01

    Enthalpies of the protonation of glycine in water‒dimethylsulfoxide (DMSO) mixed solvents are determined calorimetrically in the range of DMSO mole fractions of 0.0 to 0.9, at T = 298.15 K and an ionic strength μ = 0.3 (NaClO4). It is established that the protonation of glycine becomes more exothermic with an increasing mole fraction of DMSO, and the enthalpies of resolvation of glycine and glycinium ions in water‒DMSO solvent mixtures are calculated. It is shown that the small changes in the enthalpy of protonation observed at low mole fractions of DMSO are caused by the contributions from the solvation of proton and protonated glycine cancelling each other out. The enthalpy term of the Gibbs energy of the reaction leading to the formation of glycinium ion is estimated along with the enthalpy of resolvation of the reacting species in the water‒DMSO mixed solvent.

  7. Enthalpy of Formation for Cu–Zn–Sn–S (CZTS) Calculated from Surface Binding Energies Experimentally Measured by Ion Sputtering

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

    Baryshev, Sergey V.; Thimsen, Elijah

    2015-04-14

    Herein, we report an analytical procedure to calculate the enthalpy of formation for thin film multinary compounds from sputtering rates measured during ion bombardment. The method is based on Sigmunds sputtering theory and the BornHaber cycle. Using this procedure, an enthalpy of formation for a CZTS film of the composition Cu1.9Zn1.5Sn0.8S4 was measured as -930 +/- 98 kJ mol1. This value is much more negative than the sum of the enthalpies of formation for the constituent binary compounds, meaning the multinary formation reaction is predicted to be exothermic. The measured enthalpy of formation was used to estimate the temperature dependencemore » of the Gibbs free energy of reaction, which appears consistent with many experimental reports in the CZTS processing literature.« less

  8. A proposal to investigate higher enthalpy geothermal systems in the USA

    NASA Astrophysics Data System (ADS)

    Elders, W. A.

    2013-12-01

    After more than 50 years of development only ~3,400 MWe of electric power is currently being produced from geothermal resources in the USA. That is only about 0.33% of the country's total installed electrical capacity. In spite of the large demonstrated potential of geothermal resources, only ~2,500 MWe of new geothermal electrical capacity are under development, and the growth rate of this environmentally benign energy resource is overshadowed by the rapid increase in the installed capacity of wind and solar energy. Most of the new geothermal developments in the USA involve relatively small, moderate-temperature, geothermal systems. In contrast, development of higher enthalpy geothermal systems for power production has obvious advantages; specifically higher temperatures yield higher power outputs per well so that fewer wells are needed, leading to smaller environmental footprints for a given size of power plant. Disadvantages include that the fact that locations of suitable geothermal systems are restricted to young volcanic terrains, production of very high enthalpy fluids usually requires drilling deeper wells and may require enhanced geothermal (EGS) technology, and drilling deep into hot hostile environments is technologically challenging. However the potential for very favorable economic returns suggests that the USA should begin developing such a program. One approach to mitigating the cost issue is to form a consortium of industry, government and academia to share the costs and broaden the scope an investigation. An excellent example of such a collaboration is the Iceland Deep Drilling Project (IDDP) which is investigating the economic feasibility of producing electricity from supercritical geothermal reservoirs. This industry-government consortium planned to drill a deep well in the volcanic caldera of Krafla in NE Iceland. However drilling had to be terminated at 2.1 km depth when 900°C rhyolite magma flowed into the well. The resultant well was highly

  9. Enthalpies of formation of U-, Th-, Ce-brannerite: implications for plutonium immobilization

    NASA Astrophysics Data System (ADS)

    Helean, K. B.; Navrotsky, A.; Lumpkin, G. R.; Colella, M.; Lian, J.; Ewing, R. C.; Ebbinghaus, B.; Catalano, J. G.

    2003-08-01

    Brannerite, ideally MTi 2O 6, (M=actinides, lanthanides and Ca) occurs in titanate-based ceramics proposed for the immobilization of plutonium. Standard enthalpies of formation, Δ H0f at 298 K, for three brannerite compositions (kJ/mol): CeTi 2O 6 (-2948.8 ± 4.3), U 0.97Ti 2.03O 6 (-2977.9 ± 3.5) and ThTi 2O 6 (-3096.5 ± 4.3) were determined by high temperature oxide melt drop solution calorimetry at 975 K using 3Na 2O · 4MoO 3 solvent. The enthalpies of formation were also calculated from an oxide phase assemblage (Δ H0f-ox at 298 K): MO 2 + 2TiO 2=MTi 2O 6. Only UTi 2O 6 is energetically stable with respect to an oxide assemblage: U 0.97Ti 2.03O 6 (Δ H0f-ox=-7.7±2.8 kJ/mol). Both CeTi 2O 6 and ThTi 2O 6 are higher in enthalpy with respect to their oxide assemblages with (Δ H0f-ox=+29.4±3.6 kJ/mol) and (Δ H0f-ox=+19.4±1.6 kJ/mol) respectively. Thus, Ce- and Th-brannerite are entropy stabilized and are thermodynamically stable only at high temperature.

  10. Prediction of enthalpy and standard Gibbs energy of vaporization of haloaromatics from atomic properties.

    PubMed

    Monte, M J S; Almeida, A R R P; Liebman, J F

    2015-11-01

    Halogenated benzenes form a class of pollutants with a huge number of members - 1504 distinct benzene compounds, where one or more hydrogen atoms are replaced by halogens, may exist theoretically. This study presents a user friendly method for accurate prediction of vapor pressures and enthalpies of vaporization, at 298.15 K, of any mono or poly halobenzene compound. The derived equations for the prediction of those vaporization properties depend just on the number of each constituent halogen atom. This is a consequence of the absence of intramolecular interactions between the halogen atoms, revealed after examining vaporization results of ca. 40 halogenated benzenes. In order to rationalize the estimation equations, the contribution of the halogen atoms for the referred to above properties of vaporization was decomposed into two atomic properties - the volume and electron affinity. Extension of the applicability of the estimation method to substituted benzenes containing other substituent groups beyond halogen atoms as well as to some polycyclic aromatic species was tested with success. Copyright © 2015 Elsevier Ltd. All rights reserved.

  11. Big Data Meets Quantum Chemistry Approximations: The Δ-Machine Learning Approach.

    PubMed

    Ramakrishnan, Raghunathan; Dral, Pavlo O; Rupp, Matthias; von Lilienfeld, O Anatole

    2015-05-12

    Chemically accurate and comprehensive studies of the virtual space of all possible molecules are severely limited by the computational cost of quantum chemistry. We introduce a composite strategy that adds machine learning corrections to computationally inexpensive approximate legacy quantum methods. After training, highly accurate predictions of enthalpies, free energies, entropies, and electron correlation energies are possible, for significantly larger molecular sets than used for training. For thermochemical properties of up to 16k isomers of C7H10O2 we present numerical evidence that chemical accuracy can be reached. We also predict electron correlation energy in post Hartree-Fock methods, at the computational cost of Hartree-Fock, and we establish a qualitative relationship between molecular entropy and electron correlation. The transferability of our approach is demonstrated, using semiempirical quantum chemistry and machine learning models trained on 1 and 10% of 134k organic molecules, to reproduce enthalpies of all remaining molecules at density functional theory level of accuracy.

  12. Solid-State Characterization and Relative Formation Enthalpies To Evaluate Stability of Cocrystals of an Antidiabetic Drug.

    PubMed

    Duggirala, Naga Kiran; Frericks Schmidt, Heather L; Lei, Zhaohui; Zaworotko, Michael J; Krzyzaniak, Joseph F; Arora, Kapildev K

    2018-05-07

    The current study integrates formation enthalpy and traditional slurry experiments to quickly assess the physical stability of cocrystal drug substance candidates for their potential to support drug development. Cocrystals of an antidiabetic drug (GKA) with nicotinamide (NMA), vanillic acid (VLA), and ethyl vanillin (EVL) were prepared and characterized by powder X-ray diffractometry (PXRD), spectroscopic, and thermal techniques. The formation enthalpies of the cocrystals, and their physical mixtures (GKA + coformer) were measured by the differential scanning calorimetry (DSC) method reported by Zhang et al. [ Cryst. Growth Des. 2012 , 12 ( 8 ), 4090 - 4097 ]. The experimentally measured differences in the relative formation enthalpies obtained by integrating the heat flow of each cocrystal against the respective physical mixture were correlated to the physical stability of the cocrystals in the solid state. The relative formation enthalpies of all of the cocrystals studied suggest that the cocrystals are not physically stable at room temperature versus their physical mixtures. To further address relative stability, the cocrystals were slurried in 30% v/v aqueous ethanol, and it was observed that all of the cocrystals revert to GKA within 48 h at room temperature. The slurry experiments are consistent with the relative instability of the cocrystals with respect to their physical mixtures suggested by the DSC results.

  13. Impact of Flight Enthalpy, Fuel Simulant, and Chemical Reactions on the Mixing Characteristics of Several Injectors at Hypervelocity Flow Conditions

    NASA Technical Reports Server (NTRS)

    Drozda, Tomasz G.; Baurle, Robert A.; Drummond, J. Philip

    2016-01-01

    conditions. The mixing parameters of interest, such as mixing efficiency and total pressure recovery, are then computed and compared to the values obtained from RAS under the true enthalpy conditions and using helium and hydrogen. Finally, the impact of combustion on mixing, often deemed small enough to neglect at hypervelocity conditions, is assessed by comparing the results obtained from the hydrogen-fueled reacting and non-reacting RAS. For reacting flows, in addition to mixing efficiency and total pressure recovery, the combustion efficiency and thrust potential are also considered. In all of the simulations, the incoming air Mach number and the fuel-to-air ratio are the same, while the total pressure, total enthalpy, and the fuel simulant vary depending on the case considered. It is found that under some conditions the "cold" flow experiments are a good approximation of the flight.

  14. Free Energy, Enthalpy and Entropy from Implicit Solvent End-Point Simulations.

    PubMed

    Fogolari, Federico; Corazza, Alessandra; Esposito, Gennaro

    2018-01-01

    Free energy is the key quantity to describe the thermodynamics of biological systems. In this perspective we consider the calculation of free energy, enthalpy and entropy from end-point molecular dynamics simulations. Since the enthalpy may be calculated as the ensemble average over equilibrated simulation snapshots the difficulties related to free energy calculation are ultimately related to the calculation of the entropy of the system and in particular of the solvent entropy. In the last two decades implicit solvent models have been used to circumvent the problem and to take into account solvent entropy implicitly in the solvation terms. More recently outstanding advancement in both implicit solvent models and in entropy calculations are making the goal of free energy estimation from end-point simulations more feasible than ever before. We review briefly the basic theory and discuss the advancements in light of practical applications.

  15. Enthalpy characteristics of the dissolution of L-valine in water/formamide mixtures at 298.15 K

    NASA Astrophysics Data System (ADS)

    Smirnov, V. I.; Badelin, V. G.

    2016-11-01

    The thermochemical dissolution of L-valine in solvent mixtures H2O + (formamide, N-methylformamide, and N, N-dimethylformamide) is studied at an organic component concentration of x 2 = 0-0.35 molar fractions and a temperature of 298.15 K. The experimental data are used to calculate standard enthalpies of dissolution, the transferring of L-valine from water to a mixed solvent, and the enthalpy coefficients of pairwise interactions ( h xy ) with organic solvent molecules. The correlation between the enthalpy characteristics of the dissolution of L-valine with the composition of aqueous organic mixtures and the nature of the organic solvent (its physicochemical properties) is determined. A comparative analysis of the values of h xy of a number of aliphatic L-amino acids in similar solvent mixtures with the hydrophobicity parameters of their side chains is performed.

  16. Free-flight measurement technique in the free-piston high-enthalpy shock tunnel.

    PubMed

    Tanno, H; Komuro, T; Sato, K; Fujita, K; Laurence, S J

    2014-04-01

    A novel multi-component force-measurement technique has been developed and implemented at the impulse facility JAXA-HIEST, in which the test model is completely unrestrained during the test and thus experiences free-flight conditions for a period on the order of milliseconds. Advantages over conventional free-flight techniques include the complete absence of aerodynamic interference from a model support system and less variation in model position and attitude during the test itself. A miniature on-board data recorder, which was a key technology for this technique, was also developed in order to acquire and store the measured data. The technique was demonstrated in a HIEST wind-tunnel test campaign in which three-component aerodynamic force measurement was performed on a blunted cone of length 316 mm, total mass 19.75 kg, and moment of inertia 0.152 kgm(2). During the test campaign, axial force, normal forces, and pitching moment coefficients were obtained at angles of attack from 14° to 32° under two conditions: H0 = 4 MJ/kg, P0 = 14 MPa; and H0 = 16 MJ/kg, P0 = 16 MPa. For the first, low-enthalpy condition, the test flow was considered a perfect gas; measurements were thus directly compared with those obtained in a conventional blow-down wind tunnel (JAXA-HWT2) to evaluate the accuracy of the technique. The second test condition was a high-enthalpy condition in which 85% of the oxygen molecules were expected to be dissociated; high-temperature real-gas effects were therefore evaluated by comparison with results obtained in perfect-gas conditions. The precision of the present measurements was evaluated through an uncertainty analysis, which showed the aerodynamic coefficients in the HIEST low enthalpy test agreeing well with those of JAXA-HWT2. The pitching-moment coefficient, however, showed significant differences between low- and high-enthalpy tests. These differences are thought to result from high-temperature real-gas effects.

  17. Free-flight measurement technique in the free-piston high-enthalpy shock tunnel

    NASA Astrophysics Data System (ADS)

    Tanno, H.; Komuro, T.; Sato, K.; Fujita, K.; Laurence, S. J.

    2014-04-01

    A novel multi-component force-measurement technique has been developed and implemented at the impulse facility JAXA-HIEST, in which the test model is completely unrestrained during the test and thus experiences free-flight conditions for a period on the order of milliseconds. Advantages over conventional free-flight techniques include the complete absence of aerodynamic interference from a model support system and less variation in model position and attitude during the test itself. A miniature on-board data recorder, which was a key technology for this technique, was also developed in order to acquire and store the measured data. The technique was demonstrated in a HIEST wind-tunnel test campaign in which three-component aerodynamic force measurement was performed on a blunted cone of length 316 mm, total mass 19.75 kg, and moment of inertia 0.152 kgm2. During the test campaign, axial force, normal forces, and pitching moment coefficients were obtained at angles of attack from 14° to 32° under two conditions: H0 = 4 MJ/kg, P0 = 14 MPa; and H0 = 16 MJ/kg, P0 = 16 MPa. For the first, low-enthalpy condition, the test flow was considered a perfect gas; measurements were thus directly compared with those obtained in a conventional blow-down wind tunnel (JAXA-HWT2) to evaluate the accuracy of the technique. The second test condition was a high-enthalpy condition in which 85% of the oxygen molecules were expected to be dissociated; high-temperature real-gas effects were therefore evaluated by comparison with results obtained in perfect-gas conditions. The precision of the present measurements was evaluated through an uncertainty analysis, which showed the aerodynamic coefficients in the HIEST low enthalpy test agreeing well with those of JAXA-HWT2. The pitching-moment coefficient, however, showed significant differences between low- and high-enthalpy tests. These differences are thought to result from high-temperature real-gas effects.

  18. Investigating ultra high-enthalpy geothermal systems: a collaborative initiative to promote scientific opportunities

    NASA Astrophysics Data System (ADS)

    Elders, W. A.; Nielson, D.; Schiffman, P.; Schriener, A., Jr.

    2014-12-01

    Scientists, engineers, and policy makers gathered at a workshop in the San Bernardino Mountains of southern California in October 2013 to discuss the science and technology involved in developing high-enthalpy geothermal fields. A typical high-enthalpy geothermal well between 2000 and 3000 m deep produces a mixture of hot water and steam at 200-300 °C that can be used to generate about 5-10 MWe of electric power. The theme of the workshop was to explore the feasibility and economic potential of increasing the power output of geothermal wells by an order of magnitude by drilling deeper to reach much higher pressures and temperatures. Development of higher enthalpy geothermal systems for power production has obvious advantages; specifically higher temperatures yield higher power outputs per well so that fewer wells are needed, leading to smaller environmental footprints for a given size of power plant. Plans for resource assessment and drilling in such higher enthalpy areas are already underway in Iceland, New Zealand, and Japan. There is considerable potential for similar developments in other countries that already have a large production of electricity from geothermal steam, such as Mexico, the Philippines, Indonesia, Italy, and the USA. However drilling deeper involves technical and economic challenges. One approach to mitigating the cost issue is to form a consortium of industry, government and academia to share the costs and broaden the scope of investigation. An excellent example of such collaboration is the Iceland Deep Drilling Project (IDDP), which is investigating the economic feasibility of producing electricity from supercritical geothermal reservoirs, and this approach could serve as model for future developments elsewhere. A planning committee was formed to explore creating a similar initiative in the USA.

  19. Computer Series, 101: Accurate Equations of State in Computational Chemistry Projects.

    ERIC Educational Resources Information Center

    Albee, David; Jones, Edward

    1989-01-01

    Discusses the use of computers in chemistry courses at the United States Military Academy. Provides two examples of computer projects: (1) equations of state, and (2) solving for molar volume. Presents BASIC and PASCAL listings for the second project. Lists 10 applications for physical chemistry. (MVL)

  20. Geophysical techniques for low enthalpy geothermal exploration in New Zealand

    NASA Astrophysics Data System (ADS)

    Soengkono, Supri; Bromley, Chris; Reeves, Robert; Bennie, Stewart; Graham, Duncan

    2013-05-01

    Shallow warm water resources associated with low enthalpy geothermal systems are often difficult to explore using geophysical techniques, mainly because the warm water creates an insufficient physical change from the host rocks to be easily detectable. In addition, often the system also has a limited or narrow size. However, appropriate use of geophysical techniques can still help the exploration and further investigation of low enthalpy geothermal resources. We present case studies on the use of geophysical techniques for shallow warm water explorations over a variety of settings in New Zealand (mostly in the North Island) with variable degrees of success. A simple and direct method for the exploration of warm water systems is shallow temperature measurements. In some New Zealand examples, measurements of near surface temperatures helped to trace the extent of deeper thermal water. The gravity method was utilised as a structural technique for the exploration of some warm water systems in New Zealand. Our case studies show the technique can be useful in identifying basement depths and tracing fault systems associated with the occurrence of hot springs. Direct current (DC) ground resistivity measurements using a variety of electrode arrays have been the most common method for the exploration of low enthalpy geothermal resources in New Zealand. The technique can be used to detect the extent of shallow warm waters that are more electrically conductive than the surrounding cold groundwater. Ground resistivity investigations using the electromagnetic (EM) techniques of audio magnetotellurics (AMT or shallow MT), controlled source audio magnetotellurics (CSAMT) and transient electromagnetic (TEM) methods have also been used. Highly conductive clays of thermal or sedimentary origin often limit the penetration depth of the resistivity techniques and can create some interpretation difficulties. Interpretation of resistivity anomalies needs to be treated in a site specific

  1. Accurate Time-Dependent Traveling-Wave Tube Model Developed for Computational Bit-Error-Rate Testing

    NASA Technical Reports Server (NTRS)

    Kory, Carol L.

    2001-01-01

    The phenomenal growth of the satellite communications industry has created a large demand for traveling-wave tubes (TWT's) operating with unprecedented specifications requiring the design and production of many novel devices in record time. To achieve this, the TWT industry heavily relies on computational modeling. However, the TWT industry's computational modeling capabilities need to be improved because there are often discrepancies between measured TWT data and that predicted by conventional two-dimensional helical TWT interaction codes. This limits the analysis and design of novel devices or TWT's with parameters differing from what is conventionally manufactured. In addition, the inaccuracy of current computational tools limits achievable TWT performance because optimized designs require highly accurate models. To address these concerns, a fully three-dimensional, time-dependent, helical TWT interaction model was developed using the electromagnetic particle-in-cell code MAFIA (Solution of MAxwell's equations by the Finite-Integration-Algorithm). The model includes a short section of helical slow-wave circuit with excitation fed by radiofrequency input/output couplers, and an electron beam contained by periodic permanent magnet focusing. A cutaway view of several turns of the three-dimensional helical slow-wave circuit with input/output couplers is shown. This has been shown to be more accurate than conventionally used two-dimensional models. The growth of the communications industry has also imposed a demand for increased data rates for the transmission of large volumes of data. To achieve increased data rates, complex modulation and multiple access techniques are employed requiring minimum distortion of the signal as it is passed through the TWT. Thus, intersymbol interference (ISI) becomes a major consideration, as well as suspected causes such as reflections within the TWT. To experimentally investigate effects of the physical TWT on ISI would be

  2. Investigation of wood combustion in the high-enthalpy oxidizer flow

    NASA Astrophysics Data System (ADS)

    Reshetnikov, S. M.; Zyryanov, I. A.; Budin, A. G.; Pozolotin, A. P.

    2017-01-01

    The experimental data of wood combustion in the high-enthalpy oxidizer flowresearch is presented. Combustion laws of two wood species (pine and birch) in a hybrid rocket engine (HRE) are obtained. Heat flows from the flame to the condensed phase surface are defined. The prospects of the wood use in the HRE (based on thrust characteristics) are shown.

  3. Muver, a computational framework for accurately calling accumulated mutations.

    PubMed

    Burkholder, Adam B; Lujan, Scott A; Lavender, Christopher A; Grimm, Sara A; Kunkel, Thomas A; Fargo, David C

    2018-05-09

    Identification of mutations from next-generation sequencing data typically requires a balance between sensitivity and accuracy. This is particularly true of DNA insertions and deletions (indels), that can impart significant phenotypic consequences on cells but are harder to call than substitution mutations from whole genome mutation accumulation experiments. To overcome these difficulties, we present muver, a computational framework that integrates established bioinformatics tools with novel analytical methods to generate mutation calls with the extremely low false positive rates and high sensitivity required for accurate mutation rate determination and comparison. Muver uses statistical comparison of ancestral and descendant allelic frequencies to identify variant loci and assigns genotypes with models that include per-sample assessments of sequencing errors by mutation type and repeat context. Muver identifies maximally parsimonious mutation pathways that connect these genotypes, differentiating potential allelic conversion events and delineating ambiguities in mutation location, type, and size. Benchmarking with a human gold standard father-son pair demonstrates muver's sensitivity and low false positive rates. In DNA mismatch repair (MMR) deficient Saccharomyces cerevisiae, muver detects multi-base deletions in homopolymers longer than the replicative polymerase footprint at rates greater than predicted for sequential single-base deletions, implying a novel multi-repeat-unit slippage mechanism. Benchmarking results demonstrate the high accuracy and sensitivity achieved with muver, particularly for indels, relative to available tools. Applied to an MMR-deficient Saccharomyces cerevisiae system, muver mutation calls facilitate mechanistic insights into DNA replication fidelity.

  4. Development and Validation of a Fast, Accurate and Cost-Effective Aeroservoelastic Method on Advanced Parallel Computing Systems

    NASA Technical Reports Server (NTRS)

    Goodwin, Sabine A.; Raj, P.

    1999-01-01

    Progress to date towards the development and validation of a fast, accurate and cost-effective aeroelastic method for advanced parallel computing platforms such as the IBM SP2 and the SGI Origin 2000 is presented in this paper. The ENSAERO code, developed at the NASA-Ames Research Center has been selected for this effort. The code allows for the computation of aeroelastic responses by simultaneously integrating the Euler or Navier-Stokes equations and the modal structural equations of motion. To assess the computational performance and accuracy of the ENSAERO code, this paper reports the results of the Navier-Stokes simulations of the transonic flow over a flexible aeroelastic wing body configuration. In addition, a forced harmonic oscillation analysis in the frequency domain and an analysis in the time domain are done on a wing undergoing a rigid pitch and plunge motion. Finally, to demonstrate the ENSAERO flutter-analysis capability, aeroelastic Euler and Navier-Stokes computations on an L-1011 wind tunnel model including pylon, nacelle and empennage are underway. All computational solutions are compared with experimental data to assess the level of accuracy of ENSAERO. As the computations described above are performed, a meticulous log of computational performance in terms of wall clock time, execution speed, memory and disk storage is kept. Code scalability is also demonstrated by studying the impact of varying the number of processors on computational performance on the IBM SP2 and the Origin 2000 systems.

  5. Molecular energetics of cytosine revisited: a joint computational and experimental study.

    PubMed

    Gomes, José R B; Ribeiro da Silva, Maria D M C; Freitas, Vera L S; Ribeiro da Silva, Manuel A V

    2007-08-02

    A static bomb calorimeter has been used to measure the standard molar energy of combustion, in oxygen, at T = 298.15 K, of a commercial sample of cytosine. From this energy, the standard (p degrees = 0.1 MPa) molar enthalpy of formation in the crystalline state was derived as -(221.9 +/- 1.7) kJ.mol(-1). This value confirms one experimental value already published in the literature but differs from another literature value by 13.5 kJ.mol(-1). Using the present standard molar enthalpy of formation in the condensed phase and the enthalpy of sublimation due to Burkinshaw and Mortimer [J. Chem. Soc., Dalton Trans. 1984, 75], (155.0 +/- 3.0) kJ.mol(-1), results in a value for the gas-phase standard molar enthalpy of formation for cytosine of -66.9 kJ.mol(-1). A similar value, -65.1 kJ.mol(-1), has been estimated after G3MP2B3 calculations combined with the reaction of atomization on three different tautomers of cytosine. In agreement with experimental evidence, the hydroxy-amino tautomer is the most stable form of cytosine in the gas phase. The enthalpies of formation of the other two tautomers were also estimated as -60.7 kJ.mol(-1) and -57.2 kJ.mol(-1) for the oxo-amino and oxo-imino tautomers, respectively. The same composite approach was also used to compute other thermochemical data, which is difficult to be measured experimentally, such as C-H, N-H, and O-H bond dissociation enthalpies, gas-phase acidities, and ionization enthalpies.

  6. Influence of Countercation Hydration Enthalpies on the Formation of Molecular Complexes: A Thorium–Nitrate Example

    DOE PAGES

    Jin, Geng Bang; Lin, Jian; Estes, Shanna L.; ...

    2017-11-17

    Here, the influence of countercations (A n+) in directing the composition of monomeric metal–ligand (ML) complexes that precipitate from solution are often overlooked despite the wide usage of A n+ in materials synthesis. Herein, we describe a correlation between the composition of ML complexes and A + hydration enthalpies found for two related series of thorium (Th)–nitrate molecular compounds obtained by evaporating acidic aqueous Th–nitrate solutions in the presence of A + counterions. Analyses of their chemical composition and solid-state structures demonstrate that A + not only affects the overall solid-state packing of the Th–nitrato complexes but also influences themore » composition of the Th–nitrato monomeric anions themselves. Trends in composition and structure are found to correlate with A + hydration enthalpies, such that the A + with smaller hydration enthalpies associate with less hydrated and more anionic Th–nitrato complexes. This perspective, broader than the general assumption of size and charge as the dominant influence of A n+, opens a new avenue for the design and synthesis of targeted metal–ligand complexes.« less

  7. Influence of Countercation Hydration Enthalpies on the Formation of Molecular Complexes: A Thorium–Nitrate Example

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

    Jin, Geng Bang; Lin, Jian; Estes, Shanna L.

    Here, the influence of countercations (A n+) in directing the composition of monomeric metal–ligand (ML) complexes that precipitate from solution are often overlooked despite the wide usage of A n+ in materials synthesis. Herein, we describe a correlation between the composition of ML complexes and A + hydration enthalpies found for two related series of thorium (Th)–nitrate molecular compounds obtained by evaporating acidic aqueous Th–nitrate solutions in the presence of A + counterions. Analyses of their chemical composition and solid-state structures demonstrate that A + not only affects the overall solid-state packing of the Th–nitrato complexes but also influences themore » composition of the Th–nitrato monomeric anions themselves. Trends in composition and structure are found to correlate with A + hydration enthalpies, such that the A + with smaller hydration enthalpies associate with less hydrated and more anionic Th–nitrato complexes. This perspective, broader than the general assumption of size and charge as the dominant influence of A n+, opens a new avenue for the design and synthesis of targeted metal–ligand complexes.« less

  8. Problem-based learning in teaching chemistry: enthalpy changes in systems

    NASA Astrophysics Data System (ADS)

    Ayyildiz, Yildizay; Tarhan, Leman

    2018-01-01

    Problem-based learning (PBL) as a teaching strategy has recently become quite widespread in especially chemistry classes. Research has found that students, from elementary through college, have many alternative conceptions regarding enthalpy changes in systems. Although there are several studies focused on identifying student alternative conceptions and misunderstandings of this subject, studies on preventing the formation of these alternative conceptions are limited.

  9. 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.

  10. Reference States and Relative Values of Internal Energy, Enthalpy, and Entropy.

    ERIC Educational Resources Information Center

    Fredrickson, A. G.

    1983-01-01

    Discusses two reference states (pure chemical compounds and pure elements at specified condition of temperature and pressure) and the relation between these reference states for internal energy and enthalpy. Problem 5.11 from Modell and Reid's "Thermodynamics and its Applications" (p. 141) is used to apply the ideas discussed. (JN)

  11. Effect of N-Methyl Substitution in the Glycine Molecule on the Enthalpy of Dissolution in Mixed Water-Alcohol Solvents at 298.15 K

    NASA Astrophysics Data System (ADS)

    Badelin, V. G.; Smirnov, V. I.

    2018-07-01

    The enthalpies of dissolution of N-methylglycine in water + ethanol, water + (1-propanol) and water + (2-propanol) are determined via calorimetry at an alcohol concentration of x 2 = 0-0.25 mole fraction. The standard values of enthalpies of dissolution (Δ_{sol}H°) and transfer (Δ_{tr}H°) of N-methylglycine from water to solution are calculated. The effect the structure and properties of N-methylglycine and the composition of a water-alcohol mixture have on N-methylglycine's enthalpy characteristics is examined. The enthalpy coefficients of pair interactions ( h xy ) between N-methylglycine and alcohol molecules are calculated. They have positive values and grow in the series ethanol (EtOH) < 1-propanol (1-PrOH), < 2-propanol (2-PrOH). A comparative analysis is performed of the enthalpy characteristics of dissolution and transfer of N-methylglycine and the analogous characteristics of glycine and DL-α-alanine in similar mixtures.

  12. Calorimetric determination of the enthalpy of 1-butyl-3-methylimidazolium bromide synthesis: a key quantity in thermodynamics of ionic liquids.

    PubMed

    Paulechka, Yauheni U; Kabo, Andrey G; Blokhin, Andrey V

    2009-11-05

    The enthalpy of the 1-butyl-3-methylimidazolium bromide [C(4)mim]Br ionic liquid synthesis reaction 1-methylimidazole (liq) + 1-bromobutane (liq) --> [C(4)mim]Br (liq) was determined in a homemade small-volume isoperibol calorimeter to be Delta(r)H degrees (298) = -87.7 +/- 1.6 kJ x mol(-1). The activation energy for this reaction in a homogeneous system E(A) = 73 +/- 4 kJ x mol(-1) was found from the results of calorimetric measurements. The formation enthalpies for the crystalline and liquid [C(4)mim]Br were determined from the calorimetric data: Delta(f)H degrees (298)(cr) = -178 +/- 5 kJ x mol(-1) and Delta(f)H degrees (298)(liq) = -158 +/- 5 kJ x mol(-1). The ideal-gas formation enthalpy of this compound Delta(f)H degrees (298)(g) = 16 +/- 7 kJ x mol(-1) was calculated using the methods of quantum chemistry and statistical thermodynamics. The vaporization enthalpy of [C(4)mim]Br, Delta(vap)H degrees (298) = 174 +/- 9 kJ x mol(-1), was estimated from the experimental and calculated formation enthalpies. It was demonstrated that vapor pressure of this ionic liquid cannot be experimentally determined.

  13. Beyond mean-field approximations for accurate and computationally efficient models of on-lattice chemical kinetics

    NASA Astrophysics Data System (ADS)

    Pineda, M.; Stamatakis, M.

    2017-07-01

    Modeling the kinetics of surface catalyzed reactions is essential for the design of reactors and chemical processes. The majority of microkinetic models employ mean-field approximations, which lead to an approximate description of catalytic kinetics by assuming spatially uncorrelated adsorbates. On the other hand, kinetic Monte Carlo (KMC) methods provide a discrete-space continuous-time stochastic formulation that enables an accurate treatment of spatial correlations in the adlayer, but at a significant computation cost. In this work, we use the so-called cluster mean-field approach to develop higher order approximations that systematically increase the accuracy of kinetic models by treating spatial correlations at a progressively higher level of detail. We further demonstrate our approach on a reduced model for NO oxidation incorporating first nearest-neighbor lateral interactions and construct a sequence of approximations of increasingly higher accuracy, which we compare with KMC and mean-field. The latter is found to perform rather poorly, overestimating the turnover frequency by several orders of magnitude for this system. On the other hand, our approximations, while more computationally intense than the traditional mean-field treatment, still achieve tremendous computational savings compared to KMC simulations, thereby opening the way for employing them in multiscale modeling frameworks.

  14. 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.

  15. 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

  16. Thermochemical properties for isooctane and carbon radicals: computational study.

    PubMed

    Snitsiriwat, Suarwee; Bozzelli, Joseph W

    2013-01-17

    Thermochemical properties for isooctane, its internal rotation conformers, and radicals with corresponding bond energies are determined by use of computational chemistry. Enthalpies of formation are determined using isodesmic reactions with B3LYP density function theory and composite CBS-QB3 methods. Application of group additivity with comparison to calculated values is illustrated. Entropy and heat capacities are determined using geometric parameters, internal rotor potentials, and frequencies from B3LYP/6-31G(d,p) calculations for the lowest energy conformer. Internal rotor potentials are determined for the isooctane parent and for the primary, secondary, and tertiary radicals in order to identify isomer energies. Intramolecular interactions are shown to have a significant effect on the enthalpy of formation of the isooctane parent and its radicals. The computed standard enthalpy of formation for the lowest energy conformers of isooctane from this study is -54.40 ± 1.60 kcal mol(-1), which is 0.8 kcal mol(-1) lower than the evaluated experimental value -53.54 ± 0.36 kcal mol(-1). The standard enthalpy of formation for the primary radical for a methyl on the quaternary carbon is -5.00 ± 1.69 kcal mol(-1), for the primary radical on the tertiary carbon is -5.18 ± 1.69 kcal mol(-1), for the secondary isooctane radical is -9.03 ± 1.84 kcal mol(-1), and for the tertiary isooctane radical is -12.30 ± 2.02 kcal mol(-1). Bond energy values for the isooctane radicals are 100.64 ± 1.73, 100.46 ± 1.73, 96.41 ± 1.88 and 93.14 ± 2.05 kcal mol(-1) for C3•CCCC2, C3CCCC2•, C3CC•CC2, and C3CCC•C2, respectively. Entropy and heat capacity values are reported for the lowest energy homologues.

  17. An accurate and computationally efficient algorithm for ground peak identification in large footprint waveform LiDAR data

    NASA Astrophysics Data System (ADS)

    Zhuang, Wei; Mountrakis, Giorgos

    2014-09-01

    Large footprint waveform LiDAR sensors have been widely used for numerous airborne studies. Ground peak identification in a large footprint waveform is a significant bottleneck in exploring full usage of the waveform datasets. In the current study, an accurate and computationally efficient algorithm was developed for ground peak identification, called Filtering and Clustering Algorithm (FICA). The method was evaluated on Land, Vegetation, and Ice Sensor (LVIS) waveform datasets acquired over Central NY. FICA incorporates a set of multi-scale second derivative filters and a k-means clustering algorithm in order to avoid detecting false ground peaks. FICA was tested in five different land cover types (deciduous trees, coniferous trees, shrub, grass and developed area) and showed more accurate results when compared to existing algorithms. More specifically, compared with Gaussian decomposition, the RMSE ground peak identification by FICA was 2.82 m (5.29 m for GD) in deciduous plots, 3.25 m (4.57 m for GD) in coniferous plots, 2.63 m (2.83 m for GD) in shrub plots, 0.82 m (0.93 m for GD) in grass plots, and 0.70 m (0.51 m for GD) in plots of developed areas. FICA performance was also relatively consistent under various slope and canopy coverage (CC) conditions. In addition, FICA showed better computational efficiency compared to existing methods. FICA's major computational and accuracy advantage is a result of the adopted multi-scale signal processing procedures that concentrate on local portions of the signal as opposed to the Gaussian decomposition that uses a curve-fitting strategy applied in the entire signal. The FICA algorithm is a good candidate for large-scale implementation on future space-borne waveform LiDAR sensors.

  18. Development of highly accurate approximate scheme for computing the charge transfer integral

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

    Pershin, Anton; Szalay, Péter G.

    The charge transfer integral is a key parameter required by various theoretical models to describe charge transport properties, e.g., in organic semiconductors. The accuracy of this important property depends on several factors, which include the level of electronic structure theory and internal simplifications of the applied formalism. The goal of this paper is to identify the performance of various approximate approaches of the latter category, while using the high level equation-of-motion coupled cluster theory for the electronic structure. The calculations have been performed on the ethylene dimer as one of the simplest model systems. By studying different spatial perturbations, itmore » was shown that while both energy split in dimer and fragment charge difference methods are equivalent with the exact formulation for symmetrical displacements, they are less efficient when describing transfer integral along the asymmetric alteration coordinate. Since the “exact” scheme was found computationally expensive, we examine the possibility to obtain the asymmetric fluctuation of the transfer integral by a Taylor expansion along the coordinate space. By exploring the efficiency of this novel approach, we show that the Taylor expansion scheme represents an attractive alternative to the “exact” calculations due to a substantial reduction of computational costs, when a considerably large region of the potential energy surface is of interest. Moreover, we show that the Taylor expansion scheme, irrespective of the dimer symmetry, is very accurate for the entire range of geometry fluctuations that cover the space the molecule accesses at room temperature.« less

  19. Extreme Entropy-Enthalpy Compensation in a Drug Resistant Variant of HIV-1 Protease

    PubMed Central

    King, Nancy M.; Prabu-Jeyabalan, Moses; Bandaranayake, Rajintha M.; Nalam, Madhavi N. L.; Nalivaika, Ellen A.; Özen, Ayşegül; Haliloglu, Türkan; Yılmaz, Neşe Kurt; Schiffer, Celia A.

    2012-01-01

    The development of HIV-1 protease inhibitors has been the historic paradigm of rational structure-based drug design, where structural and thermodynamic analyses have assisted in the discovery of novel inhibitors. While the total enthalpy and entropy change upon binding determine the affinity, often the thermodynamics are considered in terms of inhibitor properties only. In the current study, profound changes are observed in the binding thermodynamics of a drug resistant variant compared to wild-type HIV-1 protease, irrespective of the inhibitor bound. This variant (Flap+) has a combination of flap and active site mutations and exhibits extremely large entropy-enthalpy compensation compared to wild-type protease, 5–15 kcal/mol, while losing only 1–3 kcal/mol in total binding free energy for any of six FDA approved inhibitors. Although entropy-enthalpy compensation has been previously observed for a variety of systems, never have changes of this magnitude been reported. The co-crystal structures of Flap+ protease with four of the inhibitors were determined and compared with complexes of both the wildtype protease and another drug resistant variant that does not exhibit this energetic compensation. Structural changes conserved across the Flap+ complexes, which are more pronounced for the flaps covering the active site, likely contribute to the thermodynamic compensation. The finding that drug resistant mutations can profoundly modulate the relative thermodynamic properties of a therapeutic target independent of the inhibitor presents a new challenge for rational drug design. PMID:22712830

  20. Binding of volatile anesthetics to serum albumin: measurements of enthalpy and solvent contributions.

    PubMed

    Sawas, Abdul H; Pentyala, Srinivas N; Rebecchi, Mario J

    2004-10-05

    This study directly examines the enthalpic contributions to binding in aqueous solution of closely related anesthetic haloethers (desflurane, isoflurane, enflurane, and sevoflurane), a haloalkane (halothane), and an intravenous anesthetic (propofol) to bovine and human serum albumin (BSA and HSA) using isothermal titration calorimetry. Binding to serum albumin is exothermic, yielding enthalpies (DeltaH(obs)) of -3 to -6 kcal/mol for BSA with a rank order of apparent equilibrium association constants (K(a) values): desflurane > isoflurane approximately enflurane > halothane >or= sevoflurane, with the differences being largely ascribed to entropic contributions. Competition experiments indicate that volatile anesthetics, at low concentrations, share the same sites in albumin previously identified in crystallographic and photo-cross-linking studies. The magnitude of the observed DeltaH increased linearly with increased reaction temperature, reflecting negative changes in heat capacities (DeltaC(p)). These -DeltaC(p) values significantly exceed those calculated for burial of each anesthetic in a hydrophobic pocket. The enhanced stabilities of the albumin/anesthetic complexes and -DeltaC(p) are consistent with favorable solvent rearrangements that promote binding. This idea is supported by substitution of D(2)O for H(2)O that significantly reduces the favorable binding enthalpy observed for desflurane and isoflurane, with an opposing increase of DeltaS(obs). From these results, we infer that solvent restructuring, resulting from release of water weakly bound to anesthetic and anesthetic-binding sites, is a dominant and favorable contributor to the enthalpy and entropy of binding to proteins.

  1. Enthalpies of melting of LnSF compounds (Ln = La, Ce, Pr, Nd, Sm)

    NASA Astrophysics Data System (ADS)

    Andreev, P. O.; Mikhalkina, O. G.; Andreev, O. V.; Elyshev, A. V.

    2015-05-01

    The melting temperatures and enthalpies of such congruently melting compounds as LaSF ( T m = 1713 ± 7 K, Δ H = 45.7 ± 4.6 kJ/mol), CeSF ( T m = 1683 ± 7 K, Δ H = 40.7 ± 4.1 kJ/mol), PrSF ( T m = 1661 ± 7 K, Δ H = 39.7 ± 4.0 kJ/mol), NdSF ( T m = 1654 ± 7 K, Δ H = 40.2 ± 4.0 kJ/mol), and SmSF ( T m = 1587 ± 7 K, Δ H = 36.1 ± 3.6 kJ/mol) are determined via synchronous thermal analysis. The tetrad effect is evident in the change of the melting temperatures and enthalpies of LnSF compounds (Ln = La, Ce, Pr, Nd, Sm) depending on r(Ln3+).

  2. The Role of Structural Enthalpy in Spherical Nucleic Acid Hybridization.

    PubMed

    Fong, Lam-Kiu; Wang, Ziwei; Schatz, George C; Luijten, Erik; Mirkin, Chad A

    2018-05-23

    DNA hybridization onto DNA-functionalized nanoparticle surfaces (e.g., in the form of a spherical nucleic acid (SNA)) is known to be enhanced relative to hybridization free in solution. Surprisingly, via isothermal titration calorimetry, we reveal that this enhancement is enthalpically, as opposed to entropically, dominated by ∼20 kcal/mol. Coarse-grained molecular dynamics simulations suggest that the observed enthalpic enhancement results from structurally confining the DNA on the nanoparticle surface and preventing it from adopting enthalpically unfavorable conformations like those observed in the solution case. The idea that structural confinement leads to the formation of energetically more stable duplexes is evaluated by decreasing the degree of confinement a duplex experiences on the nanoparticle surface. Both experiment and simulation confirm that when the surface-bound duplex is less confined, i.e., at lower DNA surface density or at greater distance from the nanoparticle surface, its enthalpy of formation approaches the less favorable enthalpy of duplex formation for the linear strand in solution. This work provides insight into one of the most important and enabling properties of SNAs and will inform the design of materials that rely on the thermodynamics of hybridization onto DNA-functionalized surfaces, including diagnostic probes and therapeutic agents.

  3. A Simple Experiment for Determining Vapor Pressure and Enthalpy of Vaporization of Water.

    ERIC Educational Resources Information Center

    Levinson, Gerald S.

    1982-01-01

    Laboratory procedures, calculations, and sample results are described for a freshman chemistry experiment in which the Clausius-Clapeyron equation is introduced as a means of describing the variation of vapor pressure with temperature and for determining enthalpy of vaporization. (Author/SK)

  4. Enthalpy-entropy compensation for the solubility of drugs in solvent mixtures: paracetamol, acetanilide, and nalidixic acid in dioxane-water.

    PubMed

    Bustamante, P; Romero, S; Pena, A; Escalera, B; Reillo, A

    1998-12-01

    In earlier work, a nonlinear enthalpy-entropy compensation was observed for the solubility of phenacetin in dioxane-water mixtures. This effect had not been earlier reported for the solubility of drugs in solvent mixtures. To gain insight into the compensation effect, the behavior of the apparent thermodynamic magnitudes for the solubility of paracetamol, acetanilide, and nalidixic acid is studied in this work. The solubility of these drugs was measured at several temperatures in dioxane-water mixtures. DSC analysis was performed on the original powders and on the solid phases after equilibration with the solvent mixture. The thermal properties of the solid phases did not show significant changes. The three drugs display a solubility maximum against the cosolvent ratio. The solubility peaks of acetanilide and nalidixic acid shift to a more polar region at the higher temperatures. Nonlinear van't Hoff plots were observed for nalidixic acid whereas acetanilide and paracetamol show linear behavior at the temperature range studied. The apparent enthalpies of solution are endothermic going through a maximum at 50% dioxane. Two different mechanisms, entropy and enthalpy, are suggested to be the driving forces that increase the solubility of the three drugs. Solubility is entropy controlled at the water-rich region (0-50% dioxane) and enthalpy controlled at the dioxane-rich region (50-100% dioxane). The enthalpy-entropy compensation analysis also suggests that two different mechanisms, dependent on cosolvent ratio, are involved in the solubility enhancement of the three drugs. The plots of deltaH versus deltaG are nonlinear, and the slope changes from positive to negative above 50% dioxane. The compensation effect for the thermodynamic magnitudes of transfer from water to the aqueous mixtures can be described by a common empirical nonlinear relationship, with the exception of paracetamol, which follows a separate linear relationship at dioxane ratios above 50%. The

  5. A hybrid solution using computational prediction and measured data to accurately determine process corrections with reduced overlay sampling

    NASA Astrophysics Data System (ADS)

    Noyes, Ben F.; Mokaberi, Babak; Mandoy, Ram; Pate, Alex; Huijgen, Ralph; McBurney, Mike; Chen, Owen

    2017-03-01

    Reducing overlay error via an accurate APC feedback system is one of the main challenges in high volume production of the current and future nodes in the semiconductor industry. The overlay feedback system directly affects the number of dies meeting overlay specification and the number of layers requiring dedicated exposure tools through the fabrication flow. Increasing the former number and reducing the latter number is beneficial for the overall efficiency and yield of the fabrication process. An overlay feedback system requires accurate determination of the overlay error, or fingerprint, on exposed wafers in order to determine corrections to be automatically and dynamically applied to the exposure of future wafers. Since current and future nodes require correction per exposure (CPE), the resolution of the overlay fingerprint must be high enough to accommodate CPE in the overlay feedback system, or overlay control module (OCM). Determining a high resolution fingerprint from measured data requires extremely dense overlay sampling that takes a significant amount of measurement time. For static corrections this is acceptable, but in an automated dynamic correction system this method creates extreme bottlenecks for the throughput of said system as new lots have to wait until the previous lot is measured. One solution is using a less dense overlay sampling scheme and employing computationally up-sampled data to a dense fingerprint. That method uses a global fingerprint model over the entire wafer; measured localized overlay errors are therefore not always represented in its up-sampled output. This paper will discuss a hybrid system shown in Fig. 1 that combines a computationally up-sampled fingerprint with the measured data to more accurately capture the actual fingerprint, including local overlay errors. Such a hybrid system is shown to result in reduced modelled residuals while determining the fingerprint, and better on-product overlay performance.

  6. Entropy-enthalpy compensation at the single protein level: pH sensing in the bacterial channel OmpF.

    PubMed

    Alcaraz, Antonio; Queralt-Martín, María; Verdiá-Báguena, Carmina; Aguilella, Vicente M; Mafé, Salvador

    2014-12-21

    The pH sensing mechanism of the OmpF channel operates via ligand modification: increasing acidity induces the replacement of cations with protons in critical binding sites decreasing the channel conductance. Aside from the change in enthalpy associated with the binding, there is also a change in the microscopic arrangements of ligands, receptors and the surrounding solvent. We show that the pH-modulation of the single channel conduction involves small free energy changes because large enthalpic and entropic contributions change in opposite ways, demonstrating an approximate enthalpy-entropy compensation for different salts and concentrations.

  7. Enthalpies of Dissolution of Crystalline Naproxen Sodium in Water and Potassium Hydroxide Aqueous Solutions at 298 K

    NASA Astrophysics Data System (ADS)

    Lytkin, A. I.; Chernikov, V. V.; Krutova, O. N.; Bychkova, S. A.; Volkov, A. V.; Skvortsov, I. A.

    2018-03-01

    The enthalpies of dissolution of crystalline naproxen sodium in water and aqueous solutions of KOH at 298.15 K are measured by direct calorimetric means in a wide range of concentrations. The acid-base properties of naproxen sodium at ionic strength I 0 and I = 0.1 (KNO3) and a temperature of 298.15 K are studied by spectrophotometric means. The concentration and thermodynamic dissociation constants are determined. The standard enthalpies of the formation of naproxen sodium and the products of its dissociation in aqueous solution are calculated.

  8. Determination of the origin and magnitude of Al/Si ordering enthalpy in framework aluminosilicates from ab initio calculations

    NASA Astrophysics Data System (ADS)

    McConnell, J. D. C.; De Vita, A.; Kenny, S. D.; Heine, V.

    Ab initio total energy calculations based on a new optimised oxygen pseudopotential has been used to determine the enthalpy of disorder for the exchange of Al and Si in tetrahedral coordination in simple derivative aluminosilicate structures based on the high temperature tridymite structure. The problem has been studied as a function of defect interaction, and defect concentration, and the results indicate that the energy for Al/Al neighbouring tetrahedra can be assigned primarily to two effects, the first, a coulombic effect, associated with the disturbed charge distribution, and the second associated with the strain related to misfit due to the very different dimensions of the Si and Al containing tetrahedra. In practice each of these effects contributes approximately 0.2 eV per Al-Al neighbour to the overal disorder enthalpy. These simple results were obtained after a careful study of possible chemical interaction between adjacent Al/Si containing tetrahedra which showed that chemical interaction was effectively absent. Since individual Al/Si tetrahedra proved to be discrete entities that are individually heavily screened by the shared oxygens it follows that coulombic and strain effects in disorder effectively account for the whole of the disorder enthalpy. The complete set of results have been used to establish new criteria for the structure and disorder enthalpies of the feldspar group of minerals and their long period derivatives.

  9. Relation Between the Adsorbed Quantity and the Immersion Enthalpy in Catechol Aqueous Solutions on Activated Carbons

    PubMed Central

    Moreno-Piraján, Juan Carlos; Blanco, Diego; Giraldo, Liliana

    2012-01-01

    An activated carbon, CarbochemTM—PS230, was modified by chemical and thermal treatment in flow of H2, in order to evaluate the influence of the activated carbon chemical characteristics in the adsorption of the catechol. The catechol adsorption in aqueous solution was studied along with the effect of the pH solution in the adsorption process of modified activated carbons and the variation of immersion enthalpy of activated carbons in the aqueous solutions of catechol. The interaction solid-solution is characterized by adsorption isotherms analysis, at 298 K and pH 7, 9 and 11 in order to evaluate the adsorption value above and below that of the catechol pKa. The adsorption capacity of carbons increases when the solution pH decreases. The retained amount increases slightly in the reduced carbon to maximum adsorption pH and diminishes in the oxidized carbon. Similar conclusions are obtained from the immersion enthalpies, whose values increase with the solute quantity retained. In granular activated carbon (CAG), the immersion enthalpies obtained are between 21.5 and 45.7 J·g−1 for catechol aqueous solutions in a range of 20 at 1500 mg·L−1. PMID:22312237

  10. Relation between the adsorbed quantity and the immersion enthalpy in catechol aqueous solutions on activated carbons.

    PubMed

    Moreno-Piraján, Juan Carlos; Blanco, Diego; Giraldo, Liliana

    2012-01-01

    An activated carbon, Carbochem(TM)-PS230, was modified by chemical and thermal treatment in flow of H(2), in order to evaluate the influence of the activated carbon chemical characteristics in the adsorption of the catechol. The catechol adsorption in aqueous solution was studied along with the effect of the pH solution in the adsorption process of modified activated carbons and the variation of immersion enthalpy of activated carbons in the aqueous solutions of catechol. The interaction solid-solution is characterized by adsorption isotherms analysis, at 298 K and pH 7, 9 and 11 in order to evaluate the adsorption value above and below that of the catechol pK(a). The adsorption capacity of carbons increases when the solution pH decreases. The retained amount increases slightly in the reduced carbon to maximum adsorption pH and diminishes in the oxidized carbon. Similar conclusions are obtained from the immersion enthalpies, whose values increase with the solute quantity retained. In granular activated carbon (CAG), the immersion enthalpies obtained are between 21.5 and 45.7 J·g(-1) for catechol aqueous solutions in a range of 20 at 1500 mg·L(-1).

  11. Parallel Higher-order Finite Element Method for Accurate Field Computations in Wakefield and PIC Simulations

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

    Candel, A.; Kabel, A.; Lee, L.

    Over the past years, SLAC's Advanced Computations Department (ACD), under SciDAC sponsorship, has developed a suite of 3D (2D) parallel higher-order finite element (FE) codes, T3P (T2P) and Pic3P (Pic2P), aimed at accurate, large-scale simulation of wakefields and particle-field interactions in radio-frequency (RF) cavities of complex shape. The codes are built on the FE infrastructure that supports SLAC's frequency domain codes, Omega3P and S3P, to utilize conformal tetrahedral (triangular)meshes, higher-order basis functions and quadratic geometry approximation. For time integration, they adopt an unconditionally stable implicit scheme. Pic3P (Pic2P) extends T3P (T2P) to treat charged-particle dynamics self-consistently using the PIC (particle-in-cell)more » approach, the first such implementation on a conformal, unstructured grid using Whitney basis functions. Examples from applications to the International Linear Collider (ILC), Positron Electron Project-II (PEP-II), Linac Coherent Light Source (LCLS) and other accelerators will be presented to compare the accuracy and computational efficiency of these codes versus their counterparts using structured grids.« less

  12. A transient kinetic study of enthalpy changes during the reaction of myosin subfragment 1 with ATP.

    PubMed Central

    Millar, N C; Howarth, J V; Gutfreund, H

    1987-01-01

    1. The enthalpy changes during individual reaction steps of the myosin subfragment 1 ATPase were studied with the use of a new stopped-flow calorimeter [Howarth, Millar & Gutfreund (1987) Biochem. J. 248, 677-682]. 2. At 5 degrees C and pH 7.0, the endothermic on-enzyme ATP-cleavage step was observed directly (delta H = +64 kJ.mol-1). 3. ADP binding is accompanied by a biphasic enthalpy change. 4. The release and uptake of protons was investigated by the use of two buffers with widely different heats of ionization. 5. Protons are involved in all four principal steps of the myosin subfragment 1 ATPase. PMID:2829836

  13. Prediction of the vapor pressure and vaporization enthalpy of 1-n-alkyl-3-methylimidazolium-bis-(trifluoromethanesulfonyl) amide ionic liquids.

    PubMed

    Diedenhofen, Michael; Klamt, Andreas; Marsh, Kenneth; Schäfer, Ansgar

    2007-09-07

    The vapor pressures and vaporization enthalpies of a series of 1-n-alkyl-3-methylimidazolium-bis-(trifluoromethanesulfonyl) amide ionic liquids have been predicted with two different approaches using the COSMO-RS method and quantum chemical gas phase calculations. While the calculated enthalpies are in good agreement with the experimental data, COSMO-RS seems to underestimate the vapor pressures by roughly 0.5-4 log units dependent on the IL and approach used.

  14. A method to simultaneously determine sorption isotherms and sorption enthalpies with a double twin microcalorimeter

    NASA Astrophysics Data System (ADS)

    Wadso, Lars; Markova, Natalia

    2002-07-01

    Sorption of vapors of water, ethanol, and other liquids on solids like pharmaceuticals, textiles and food stuffs are of both practical and theoretical importance. In this article we present a technique to simultaneously measure sorption isotherms and sorption enthalpies. The sample is contained in one end of a sorption vessel. In the other end a vaporizable liquid is introduced to start the measurement. Mass transfer from the liquid to the sample is by vapor diffusion and the rate of mass transfer is calculated from the measured thermal power of vaporization. Simultaneously, the thermal power of sorption is measured and from this one may calculate the differential enthalpy of sorption. The thermal power measurements are made by inserting the sorption vessel in an isothermal double twin microcalorimeter.

  15. Constant Enthalpy Change Value during Pyrophosphate Hydrolysis within the Physiological Limits of NaCl*

    PubMed Central

    Wakai, Satoshi; Kidokoro, Shun-ichi; Masaki, Kazuo; Nakasone, Kaoru; Sambongi, Yoshihiro

    2013-01-01

    A decrease in water activity was thought to result in smaller enthalpy change values during PPi hydrolysis, indicating the importance of solvation for the reaction. However, the physiological significance of this phenomenon is unknown. Here, we combined biochemistry and calorimetry to solve this problem using NaCl, a physiologically occurring water activity-reducing reagent. The pyrophosphatase activities of extremely halophilic Haloarcula japonica, which can grow at ∼4 m NaCl, and non-halophilic Escherichia coli and Saccharomyces cerevisiae were maximal at 2.0 and 0.1 m NaCl, respectively. Thus, halophilic and non-halophilic pyrophosphatases exhibit distinct maximal activities at different NaCl concentration ranges. Upon calorimetry, the same exothermic enthalpy change of −35 kJ/mol was obtained for the halophile and non-halophiles at 1.5–4.0 and 0.1–2.0 m NaCl, respectively. These results show that solvation changes caused by up to 4.0 m NaCl (water activity of ∼0.84) do not affect the enthalpy change in PPi hydrolysis. It has been postulated that PPi is an ATP analog, having a so-called high energy phosphate bond, and that the hydrolysis of both compounds is enthalpically driven. Therefore, our results indicate that the hydrolysis of high energy phosphate compounds, which are responsible for biological energy conversion, is enthalpically driven within the physiological limits of NaCl. PMID:23965994

  16. Enthalpies of mixing of liquid systems for lead free soldering: Co–Sb–Sn

    PubMed Central

    Elmahfoudi, A.; Sabbar, A.; Flandorfer, H.

    2012-01-01

    The partial and integral enthalpy of mixing of molten ternary Co–Sb–Sn alloys was determined performing high temperature drop calorimetry in a large compositional range at 1273 K. Measurements have been done along five sections, xSb/xSn ≈ 1:1, xSb/xSn ≈ 1:3, xSb/xSn ≈ 3:1, xCo/xSn ≈ 1:4, and xCo/xSb ≈ 1:5. Additionally, binary alloys of the constituent systems Co–Sb and Co–Sn were investigated at the same temperature. All the binary data were evaluated by means of a standard Redlich–Kister polynomial fit whereas ternary data were fitted on the basis of an extended Redlich–Kister–Muggianu model for substitutional solutions. An iso-enthalpy plot of the ternary system was constructed. In addition, the extrapolation Model of Toop was applied and compared to our data. PMID:27087752

  17. Enthalpies of mixing of liquid systems for lead free soldering: Co-Sb-Sn.

    PubMed

    Elmahfoudi, A; Sabbar, A; Flandorfer, H

    2012-04-01

    The partial and integral enthalpy of mixing of molten ternary Co-Sb-Sn alloys was determined performing high temperature drop calorimetry in a large compositional range at 1273 K. Measurements have been done along five sections, x Sb / x Sn  ≈ 1:1, x Sb / x Sn  ≈ 1:3, x Sb / x Sn  ≈ 3:1, x Co / x Sn  ≈ 1:4, and x Co / x Sb  ≈ 1:5. Additionally, binary alloys of the constituent systems Co-Sb and Co-Sn were investigated at the same temperature. All the binary data were evaluated by means of a standard Redlich-Kister polynomial fit whereas ternary data were fitted on the basis of an extended Redlich-Kister-Muggianu model for substitutional solutions. An iso-enthalpy plot of the ternary system was constructed. In addition, the extrapolation Model of Toop was applied and compared to our data.

  18. Computer Code For Turbocompounded Adiabatic Diesel Engine

    NASA Technical Reports Server (NTRS)

    Assanis, D. N.; Heywood, J. B.

    1988-01-01

    Computer simulation developed to study advantages of increased exhaust enthalpy in adiabatic turbocompounded diesel engine. Subsytems of conceptual engine include compressor, reciprocator, turbocharger turbine, compounded turbine, ducting, and heat exchangers. Focus of simulation of total system is to define transfers of mass and energy, including release and transfer of heat and transfer of work in each subsystem, and relationship among subsystems. Written in FORTRAN IV.

  19. Experimental and computational thermochemical study and solid-phase structure of 5,5-dimethylbarbituric acid.

    PubMed

    Roux, María Victoria; Notario, Rafael; Foces-Foces, Concepción; Temprado, Manuel; Ros, Francisco; Emel'yanenko, Vladimir N; Verevkin, Sergey P

    2010-03-18

    This paper reports an experimental and computational thermochemical study on 5,5-dimethylbarbituric acid and the solid-phase structure of the compound. The value of the standard (p(o) = 0.1 MPa) molar enthalpy of formation in the gas phase at T = 298.15 K has been determined. The energy of combustion was measured by static bomb combustion calorimetry, and from the result obtained, the standard molar enthalpy of formation in the crystalline state at T = 298.15 K was calculated as -(706.4 +/- 2.2) kJ x mol(-1). The enthalpy of sublimation was determined using a transference (transpiration) method in a saturated NB(2) stream, and a value of the enthalpy of sublimation at T = 298.15 K was derived as (115.8 +/- 0.5) kJ x mol(-1). From these results a value of -(590.6 +/- 2.3) kJ x mol(-1) for the gas-phase enthalpy of formation at T = 298.15 K was determined. Theoretical calculations at the G3 level were performed, and a study on molecular and electronic structure of the compound has been carried out. Calculated enthalpies of formation are in reasonable agreement with the experimental value. 5,5-Dimethylbarbituric acid was characterized by single crystal X-ray diffraction analysis. In the crystal structure, N-H...O=C hydrogen bonds lead to the formation of ribbons connected further by weak C-H...O=C hydrogen bonds into a three-dimensional network. The molecular and supramolecular structures observed in the solid state were also investigated in the gas phase by DFT calculations.

  20. The gaseous enthalpy of formation of the ionic liquid 1-butyl-3-methylimidazolium dicyanamide from combustion calorimetry, vapor pressure measurements, and ab initio calculations.

    PubMed

    Emel'yanenko, Vladimir N; Verevkin, Sergey P; Heintz, Andreas

    2007-04-04

    Ionic liquids are attracting growing interest as alternatives to conventional molecular solvents. Experimental values of vapor pressure, enthalpy of vaporization, and enthalpy of formation of ionic liquids are the key thermodynamic quantities, which are required for the validation and development of the molecular modeling and ab initio methods toward this new class of solvents. In this work, the molar enthalpy of formation of the liquid 1-butyl-3-methylimidazolium dicyanamide, 206.2 +/- 2.5 kJ.mol-1, was measured by means of combustion calorimetry. The molar enthalpy of vaporization of 1-butyl-3-methylimidazolium dicyanamide, 157.2 +/- 1.1 kJ.mol-1, was obtained from the temperature dependence of the vapor pressure measured using the transpiration method. The latter method has been checked with measurements of 1-butyl-3-methylimidazolium bis(trifluoromethylsulfonyl) imide, where data are available from the effusion technique. The first experimental determination of the gaseous enthalpy of formation of the ionic liquid 1-butyl-3-methylimidazolium dicyanamide, 363.4 +/- 2.7 kJ.mol-1, from thermochemical measurements (combustion and transpiration) is presented. Ab initio calculations of the enthalpy of formation in the gaseous phase have been performed for 1-butyl-3-methylimidazolium dicyanamide using the G3MP2 theory. Excellent agreement with experimental results has been observed. The method developed opens a new way to obtain thermodynamic properties of ionic liquids which have not been available so far.

  1. Making sense of enthalpy of vaporization trends for ionic liquids: new experimental and simulation data show a simple linear relationship and help reconcile previous data.

    PubMed

    Verevkin, Sergey P; Zaitsau, Dzmitry H; Emel'yanenko, Vladimir N; Yermalayeu, Andrei V; Schick, Christoph; Liu, Hongjun; Maginn, Edward J; Bulut, Safak; Krossing, Ingo; Kalb, Roland

    2013-05-30

    Vaporization enthalpy of an ionic liquid (IL) is a key physical property for applications of ILs as thermofluids and also is useful in developing liquid state theories and validating intermolecular potential functions used in molecular modeling of these liquids. Compilation of the data for a homologous series of 1-alkyl-3-methylimidazolium bis(trifluoromethane-sulfonyl)imide ([C(n)mim][NTf2]) ILs has revealed an embarrassing disarray of literature results. New experimental data, based on the concurring results from quartz crystal microbalance, thermogravimetric analyses, and molecular dynamics simulation have revealed a clear linear dependence of IL vaporization enthalpies on the chain length of the alkyl group on the cation. Ambiguity of the procedure for extrapolation of vaporization enthalpies to the reference temperature 298 K was found to be a major source of the discrepancies among previous data sets. Two simple methods for temperature adjustment of vaporization enthalpies have been suggested. Resulting vaporization enthalpies obey group additivity, although the values of the additivity parameters for ILs are different from those for molecular compounds.

  2. G3X-K theory: A composite theoretical method for thermochemical kinetics

    NASA Astrophysics Data System (ADS)

    da Silva, Gabriel

    2013-02-01

    A composite theoretical method for accurate thermochemical kinetics, G3X-K, is described. This method is accurate to around 0.5 kcal mol-1 for barrier heights and 0.8 kcal mol-1 for enthalpies of formation. G3X-K is a modification of G3SX theory using the M06-2X density functional for structures and zero-point energies and parameterized for a test set of 223 heats of formation and 23 barrier heights. A reduced perturbation-order variant, G3X(MP3)-K, is also developed, providing around 0.7 kcal mol-1 accuracy for barrier heights and 0.9 kcal mol-1 accuracy for enthalpies, at reduced computational cost. Some opportunities to further improve Gn composite methods are identified and briefly discussed.

  3. Enthalpy of formation of Fe 3Al 2Si 3O 12 (almandine) by high temperature alkali borate solution calorimetry

    NASA Astrophysics Data System (ADS)

    Chatillon-Colinet, C.; Kleppa, O. J.; Newton, R. C.; Perkins, D., III

    1983-03-01

    A high-temperature solution calorimetric method suitable for thermochemical studies of anhydrous minerals containing Fe 2+ ions has been developed. The method is based on an oxide melt solvent with 52 wt% LiBO 2 and 48 wt% NaBO 2 maintained at a temperature of 750°C. In a first application of this method the enthalpies of solution of synthetic almandine, fayalite, a mixture of fayalite plus quartz on FeSiO 3 composition, and natural quartz were measured. For the reaction: ? the enthalpy change at 1023 K is -3.82 ± 0.87 kcal, based on fayalite, quartz, corundum and almandine, and -5.96 ± 0.90 kcal based on the fayalite plus quartz mixture, corundum, and almandine. These values lead to standard molar enthalpies of formation of almandine from the oxides at 1023 K of -14.10 ± 1.22 kcal and -16.24 ± 1.74 kcal, respectively. The measured enthalpy of formation of almandine is less negative by several kilocalories than values derived from analysis of the phase equilibrium work of HSU (1968), but in closer agreement with the phase equilibrium study of O'NEILL and WOOD (1979) and similar to the phase equilibrium deduction of FROESE (1973). The agreement of the present almandine enthalpy of formation with O'NEILL and WOOD (1979) and FROESE (1973) suggests that almandine entropies at 298 K to be obtained from their studies, in the range 79-81 cal/K, are more nearly correct than the several estimates based on oxide sum and volume-entropy systematics, most of which are much lower.

  4. Computational Fluid Dynamics (CFD) simulations of a Heisenberg Vortex Tube

    NASA Astrophysics Data System (ADS)

    Bunge, Carl; Sitaraman, Hariswaran; Leachman, Jake

    2017-11-01

    A 3D Computational Fluid Dynamics (CFD) simulation of a Heisenberg Vortex Tube (HVT) is performed to estimate cooling potential with cryogenic hydrogen. The main mechanism driving operation of the vortex tube is the use of fluid power for enthalpy streaming in a highly turbulent swirl in a dual-outlet tube. This enthalpy streaming creates a temperature separation between the outer and inner regions of the flow. Use of a catalyst on the peripheral wall of the centrifuge enables endothermic conversion of para-ortho hydrogen to aid primary cooling. A κ- ɛ turbulence model is used with a cryogenic, non-ideal equation of state, and para-orthohydrogen species evolution. The simulations are validated with experiments and strategies for parametric optimization of this device are presented.

  5. Device and method for measuring the energy content of hot and humid air streams

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

    Rosen, H. N.; Girod, G. F.; Kent, A. C.

    1985-12-24

    a portable device and method for measuring enthalpy and humidity of humid air from a space or flow channel at temperatures from 80/sup 0/ to 400/sup 0/ F. is described. the device consists of a psychrometer for measuring wet-bulb temperature, a vacuum pump for inducing sample air flow through the unit, a water-heating system for accurate psychrometer readings, an electronic computer system for evaluation of enthalpy and humidity from corrected and averaged values of wet- and dry- bulb temperatures, and a monitor for displaying the values. The device is programmable by the user to modify evaluation methods as necessary.

  6. Computer simulation of the heavy-duty turbo-compounded diesel cycle for studies of engine efficiency and performance

    NASA Technical Reports Server (NTRS)

    Assanis, D. N.; Ekchian, J. A.; Heywood, J. B.; Replogle, K. K.

    1984-01-01

    Reductions in heat loss at appropriate points in the diesel engine which result in substantially increased exhaust enthalpy were shown. The concepts for this increased enthalpy are the turbocharged, turbocompounded diesel engine cycle. A computer simulation of the heavy duty turbocharged turbo-compounded diesel engine system was undertaken. This allows the definition of the tradeoffs which are associated with the introduction of ceramic materials in various parts of the total engine system, and the study of system optimization. The basic assumptions and the mathematical relationships used in the simulation of the model engine are described.

  7. A streamline splitting pore-network approach for computationally inexpensive and accurate simulation of transport in porous media

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

    Mehmani, Yashar; Oostrom, Martinus; Balhoff, Matthew

    2014-03-20

    Several approaches have been developed in the literature for solving flow and transport at the pore-scale. Some authors use a direct modeling approach where the fundamental flow and transport equations are solved on the actual pore-space geometry. Such direct modeling, while very accurate, comes at a great computational cost. Network models are computationally more efficient because the pore-space morphology is approximated. Typically, a mixed cell method (MCM) is employed for solving the flow and transport system which assumes pore-level perfect mixing. This assumption is invalid at moderate to high Peclet regimes. In this work, a novel Eulerian perspective on modelingmore » flow and transport at the pore-scale is developed. The new streamline splitting method (SSM) allows for circumventing the pore-level perfect mixing assumption, while maintaining the computational efficiency of pore-network models. SSM was verified with direct simulations and excellent matches were obtained against micromodel experiments across a wide range of pore-structure and fluid-flow parameters. The increase in the computational cost from MCM to SSM is shown to be minimal, while the accuracy of SSM is much higher than that of MCM and comparable to direct modeling approaches. Therefore, SSM can be regarded as an appropriate balance between incorporating detailed physics and controlling computational cost. The truly predictive capability of the model allows for the study of pore-level interactions of fluid flow and transport in different porous materials. In this paper, we apply SSM and MCM to study the effects of pore-level mixing on transverse dispersion in 3D disordered granular media.« less

  8. A sparse matrix-vector multiplication based algorithm for accurate density matrix computations on systems of millions of atoms

    NASA Astrophysics Data System (ADS)

    Ghale, Purnima; Johnson, Harley T.

    2018-06-01

    We present an efficient sparse matrix-vector (SpMV) based method to compute the density matrix P from a given Hamiltonian in electronic structure computations. Our method is a hybrid approach based on Chebyshev-Jackson approximation theory and matrix purification methods like the second order spectral projection purification (SP2). Recent methods to compute the density matrix scale as O(N) in the number of floating point operations but are accompanied by large memory and communication overhead, and they are based on iterative use of the sparse matrix-matrix multiplication kernel (SpGEMM), which is known to be computationally irregular. In addition to irregularity in the sparse Hamiltonian H, the nonzero structure of intermediate estimates of P depends on products of H and evolves over the course of computation. On the other hand, an expansion of the density matrix P in terms of Chebyshev polynomials is straightforward and SpMV based; however, the resulting density matrix may not satisfy the required constraints exactly. In this paper, we analyze the strengths and weaknesses of the Chebyshev-Jackson polynomials and the second order spectral projection purification (SP2) method, and propose to combine them so that the accurate density matrix can be computed using the SpMV computational kernel only, and without having to store the density matrix P. Our method accomplishes these objectives by using the Chebyshev polynomial estimate as the initial guess for SP2, which is followed by using sparse matrix-vector multiplications (SpMVs) to replicate the behavior of the SP2 algorithm for purification. We demonstrate the method on a tight-binding model system of an oxide material containing more than 3 million atoms. In addition, we also present the predicted behavior of our method when applied to near-metallic Hamiltonians with a wide energy spectrum.

  9. A More Accurate and Efficient Technique Developed for Using Computational Methods to Obtain Helical Traveling-Wave Tube Interaction Impedance

    NASA Technical Reports Server (NTRS)

    Kory, Carol L.

    1999-01-01

    The phenomenal growth of commercial communications has created a great demand for traveling-wave tube (TWT) amplifiers. Although the helix slow-wave circuit remains the mainstay of the TWT industry because of its exceptionally wide bandwidth, until recently it has been impossible to accurately analyze a helical TWT using its exact dimensions because of the complexity of its geometrical structure. For the first time, an accurate three-dimensional helical model was developed that allows accurate prediction of TWT cold-test characteristics including operating frequency, interaction impedance, and attenuation. This computational model, which was developed at the NASA Lewis Research Center, allows TWT designers to obtain a more accurate value of interaction impedance than is possible using experimental methods. Obtaining helical slow-wave circuit interaction impedance is an important part of the design process for a TWT because it is related to the gain and efficiency of the tube. This impedance cannot be measured directly; thus, conventional methods involve perturbing a helical circuit with a cylindrical dielectric rod placed on the central axis of the circuit and obtaining the difference in resonant frequency between the perturbed and unperturbed circuits. A mathematical relationship has been derived between this frequency difference and the interaction impedance (ref. 1). However, because of the complex configuration of the helical circuit, deriving this relationship involves several approximations. In addition, this experimental procedure is time-consuming and expensive, but until recently it was widely accepted as the most accurate means of determining interaction impedance. The advent of an accurate three-dimensional helical circuit model (ref. 2) made it possible for Lewis researchers to fully investigate standard approximations made in deriving the relationship between measured perturbation data and interaction impedance. The most prominent approximations made

  10. On numerically accurate finite element

    NASA Technical Reports Server (NTRS)

    Nagtegaal, J. C.; Parks, D. M.; Rice, J. R.

    1974-01-01

    A general criterion for testing a mesh with topologically similar repeat units is given, and the analysis shows that only a few conventional element types and arrangements are, or can be made suitable for computations in the fully plastic range. Further, a new variational principle, which can easily and simply be incorporated into an existing finite element program, is presented. This allows accurate computations to be made even for element designs that would not normally be suitable. Numerical results are given for three plane strain problems, namely pure bending of a beam, a thick-walled tube under pressure, and a deep double edge cracked tensile specimen. The effects of various element designs and of the new variational procedure are illustrated. Elastic-plastic computation at finite strain are discussed.

  11. Fast and accurate mock catalogue generation for low-mass galaxies

    NASA Astrophysics Data System (ADS)

    Koda, Jun; Blake, Chris; Beutler, Florian; Kazin, Eyal; Marin, Felipe

    2016-06-01

    We present an accurate and fast framework for generating mock catalogues including low-mass haloes, based on an implementation of the COmoving Lagrangian Acceleration (COLA) technique. Multiple realisations of mock catalogues are crucial for analyses of large-scale structure, but conventional N-body simulations are too computationally expensive for the production of thousands of realizations. We show that COLA simulations can produce accurate mock catalogues with a moderate computation resource for low- to intermediate-mass galaxies in 1012 M⊙ haloes, both in real and redshift space. COLA simulations have accurate peculiar velocities, without systematic errors in the velocity power spectra for k ≤ 0.15 h Mpc-1, and with only 3-per cent error for k ≤ 0.2 h Mpc-1. We use COLA with 10 time steps and a Halo Occupation Distribution to produce 600 mock galaxy catalogues of the WiggleZ Dark Energy Survey. Our parallelized code for efficient generation of accurate halo catalogues is publicly available at github.com/junkoda/cola_halo.

  12. Enthalpy-Based Thermal Evolution of Loops: II. Improvements to the Model

    NASA Technical Reports Server (NTRS)

    Cargill, P. J.; Bradshaw, S. J.; Klimchuk, J. A.

    2011-01-01

    This paper further develops the zero-dimensional (0D) hydrodynamic coronal loop model "Enthalpy-based Thermal Evolution of Loops" (EBTEL) originally proposed by Klimchuk et al (2008), which studies the plasma response to evolving coronal heating. It has typically been applied to impulsive heating events. The basis of EBTEL is the modelling of mass exchange between the corona and transition region and chromosphere in response to heating variations, with the key parameter being the ratio of transition region to coronal radiation. We develop new models for this parameter that now include gravitational stratification and a physically motivated approach to radiative cooling. A number of examples are presented, including nanoflares in short and long loops, and a small flare. It is found that while the evolution of the loop temperature is rather insensitive to the details of the model, accurate tracking of the density requires the inclusion of our new features. In particular, we are able to now obtain highly over-dense loops in the late cooling phase and decreases to the coronal density arising due to stratification. The 0D results are compared to a 1D hydro code (Hydrad). The agreement is acceptable, with the exception of the flare case where some versions of Hydrad can give significantly lower densities. This is attributed to the method used to model the chromosphere in a flare. EBTEL is suitable for general use as a tool for (a) quick-look results of loop evolution in response to a given heating function and (b) situations where the modelling of hundreds or thousands of elemental loops is needed. A single run takes a few seconds on a contemporary laptop.

  13. ACCURATE CHEMICAL MASTER EQUATION SOLUTION USING MULTI-FINITE BUFFERS

    PubMed Central

    Cao, Youfang; Terebus, Anna; Liang, Jie

    2016-01-01

    The discrete chemical master equation (dCME) provides a fundamental framework for studying stochasticity in mesoscopic networks. Because of the multi-scale nature of many networks where reaction rates have large disparity, directly solving dCMEs is intractable due to the exploding size of the state space. It is important to truncate the state space effectively with quantified errors, so accurate solutions can be computed. It is also important to know if all major probabilistic peaks have been computed. Here we introduce the Accurate CME (ACME) algorithm for obtaining direct solutions to dCMEs. With multi-finite buffers for reducing the state space by O(n!), exact steady-state and time-evolving network probability landscapes can be computed. We further describe a theoretical framework of aggregating microstates into a smaller number of macrostates by decomposing a network into independent aggregated birth and death processes, and give an a priori method for rapidly determining steady-state truncation errors. The maximal sizes of the finite buffers for a given error tolerance can also be pre-computed without costly trial solutions of dCMEs. We show exactly computed probability landscapes of three multi-scale networks, namely, a 6-node toggle switch, 11-node phage-lambda epigenetic circuit, and 16-node MAPK cascade network, the latter two with no known solutions. We also show how probabilities of rare events can be computed from first-passage times, another class of unsolved problems challenging for simulation-based techniques due to large separations in time scales. Overall, the ACME method enables accurate and efficient solutions of the dCME for a large class of networks. PMID:27761104

  14. An accurate model for the computation of the dose of protons in water.

    PubMed

    Embriaco, A; Bellinzona, V E; Fontana, A; Rotondi, A

    2017-06-01

    The accurate and fast calculation of the dose in proton radiation therapy is an essential ingredient for successful treatments. We propose a novel approach with a minimal number of parameters. The approach is based on the exact calculation of the electromagnetic part of the interaction, namely the Molière theory of the multiple Coulomb scattering for the transversal 1D projection and the Bethe-Bloch formula for the longitudinal stopping power profile, including a gaussian energy straggling. To this e.m. contribution the nuclear proton-nucleus interaction is added with a simple two-parameter model. Then, the non gaussian lateral profile is used to calculate the radial dose distribution with a method that assumes the cylindrical symmetry of the distribution. The results, obtained with a fast C++ based computational code called MONET (MOdel of ioN dosE for Therapy), are in very good agreement with the FLUKA MC code, within a few percent in the worst case. This study provides a new tool for fast dose calculation or verification, possibly for clinical use. Copyright © 2017 Associazione Italiana di Fisica Medica. Published by Elsevier Ltd. All rights reserved.

  15. Glass transition memorized by the enthalpy-entropy compensation in the shear thinning of supercooled metallic liquids.

    PubMed

    Zhang, Meng; Liu, Lin

    2018-05-03

    To unravel the true nature of glass transition, broader insights into glass forming have been gained by examining the stress-driven glassy systems, where strong shear thinning, i.e., a reduced viscosity under increasing shear rate, is encountered. It is argued that arbitrarily small stress-driven shear rates would "melt" the glass and erase any memory of its thermal history. In this work, we report a glass transition memorized by the enthalpy-entropy compensation in strongly shear-thinned supercooled metallic liquids, which coincides with the thermal glass transition in both the transition temperature and the activation Gibbs free energy. Our findings provide distinctive insights into both glass forming and shear thinning, and enrich current knowledge on the ubiquitous enthalpy-entropy compensation empirical law in condensed matter physics. © 2018 IOP Publishing Ltd.

  16. Glass transition memorized by the enthalpy-entropy compensation in the shear thinning of supercooled metallic liquids

    NASA Astrophysics Data System (ADS)

    Zhang, Meng; Liu, Lin

    2018-06-01

    To unravel the true nature of glass transition, broader insights into glass forming have been gained by examining the stress-driven glassy systems, where strong shear thinning, i.e. a reduced viscosity under increasing shear rate, is encountered. It is argued that arbitrarily small stress-driven shear rates would ‘melt’ the glass and erase any memory of its thermal history. In this work, we report a glass transition memorized by the enthalpy-entropy compensation in strongly shear-thinned supercooled metallic liquids, which coincides with the thermal glass transition in both the transition temperature and the activation Gibbs free energy. Our findings provide distinctive insights into both glass forming and shear thinning, and enrich current knowledge on the ubiquitous enthalpy-entropy compensation empirical law in condensed matter physics.

  17. The Evaluation of Empirical Resonance Energies as Reaction Enthalpies with Particular Reference to Benzene.

    ERIC Educational Resources Information Center

    George, Philip; And Others

    1984-01-01

    Discusses the nature of experimental resonance energy, explaining how its magnitude depends upon choice of reference molecules from which bond energies are derived. Also explains how it can be evaluated more simply, without recourse to bond energies, as enthalpy change for a reaction predetermined by choice of reference molecules. (JN)

  18. Memory conformity affects inaccurate memories more than accurate memories.

    PubMed

    Wright, Daniel B; Villalba, Daniella K

    2012-01-01

    After controlling for initial confidence, inaccurate memories were shown to be more easily distorted than accurate memories. In two experiments groups of participants viewed 50 stimuli and were then presented with these stimuli plus 50 fillers. During this test phase participants reported their confidence that each stimulus was originally shown. This was followed by computer-generated responses from a bogus participant. After being exposed to this response participants again rated the confidence of their memory. The computer-generated responses systematically distorted participants' responses. Memory distortion depended on initial memory confidence, with uncertain memories being more malleable than confident memories. This effect was moderated by whether the participant's memory was initially accurate or inaccurate. Inaccurate memories were more malleable than accurate memories. The data were consistent with a model describing two types of memory (i.e., recollective and non-recollective memories), which differ in how susceptible these memories are to memory distortion.

  19. The preliminary exploration of 64-slice volume computed tomography in the accurate measurement of pleural effusion.

    PubMed

    Guo, Zhi-Jun; Lin, Qiang; Liu, Hai-Tao; Lu, Jun-Ying; Zeng, Yan-Hong; Meng, Fan-Jie; Cao, Bin; Zi, Xue-Rong; Han, Shu-Ming; Zhang, Yu-Huan

    2013-09-01

    Using computed tomography (CT) to rapidly and accurately quantify pleural effusion volume benefits medical and scientific research. However, the precise volume of pleural effusions still involves many challenges and currently does not have a recognized accurate measuring. To explore the feasibility of using 64-slice CT volume-rendering technology to accurately measure pleural fluid volume and to then analyze the correlation between the volume of the free pleural effusion and the different diameters of the pleural effusion. The 64-slice CT volume-rendering technique was used to measure and analyze three parts. First, the fluid volume of a self-made thoracic model was measured and compared with the actual injected volume. Second, the pleural effusion volume was measured before and after pleural fluid drainage in 25 patients, and the volume reduction was compared with the actual volume of the liquid extract. Finally, the free pleural effusion volume was measured in 26 patients to analyze the correlation between it and the diameter of the effusion, which was then used to calculate the regression equation. After using the 64-slice CT volume-rendering technique to measure the fluid volume of the self-made thoracic model, the results were compared with the actual injection volume. No significant differences were found, P = 0.836. For the 25 patients with drained pleural effusions, the comparison of the reduction volume with the actual volume of the liquid extract revealed no significant differences, P = 0.989. The following linear regression equation was used to compare the pleural effusion volume (V) (measured by the CT volume-rendering technique) with the pleural effusion greatest depth (d): V = 158.16 × d - 116.01 (r = 0.91, P = 0.000). The following linear regression was used to compare the volume with the product of the pleural effusion diameters (l × h × d): V = 0.56 × (l × h × d) + 39.44 (r = 0.92, P = 0.000). The 64-slice CT volume-rendering technique can

  20. Enthalpy and phase behavior of coal derived liquid mixtures. Technical progress report, April-June 1986

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

    Yesavage, V.F.; Kidnay, A.J.

    Enthalpy measurements for the m-cresol/tetralin binary system, and the quinoline/tertralin binary system have been completed and are included. A calibration check on the calorimeter was performed and is presented in Appendix C. Vapor liquid equilibria measurements for the quinoline/tetralin system have been completed for four isotherms; 250, 275, 300, and 325/sup 0/C. These results and a summary of progress to date for the VLE apparatus are in the appendix at the end of this report. Also, preliminary work has begun on the quinoline/m-cresol/tetralin ternary system. Correlational work has consisted of the development of mathematical expressions for fugacity and enthalpy usingmore » various combinations of mixing rules and equations of state discussed in earlier reports. Also maximum likelihood routines has been written to determine the necessary parameters for binary data obtained in this investigation.« less

  1. An efficient and accurate 3D displacements tracking strategy for digital volume correlation

    NASA Astrophysics Data System (ADS)

    Pan, Bing; Wang, Bo; Wu, Dafang; Lubineau, Gilles

    2014-07-01

    Owing to its inherent computational complexity, practical implementation of digital volume correlation (DVC) for internal displacement and strain mapping faces important challenges in improving its computational efficiency. In this work, an efficient and accurate 3D displacement tracking strategy is proposed for fast DVC calculation. The efficiency advantage is achieved by using three improvements. First, to eliminate the need of updating Hessian matrix in each iteration, an efficient 3D inverse compositional Gauss-Newton (3D IC-GN) algorithm is introduced to replace existing forward additive algorithms for accurate sub-voxel displacement registration. Second, to ensure the 3D IC-GN algorithm that converges accurately and rapidly and avoid time-consuming integer-voxel displacement searching, a generalized reliability-guided displacement tracking strategy is designed to transfer accurate and complete initial guess of deformation for each calculation point from its computed neighbors. Third, to avoid the repeated computation of sub-voxel intensity interpolation coefficients, an interpolation coefficient lookup table is established for tricubic interpolation. The computational complexity of the proposed fast DVC and the existing typical DVC algorithms are first analyzed quantitatively according to necessary arithmetic operations. Then, numerical tests are performed to verify the performance of the fast DVC algorithm in terms of measurement accuracy and computational efficiency. The experimental results indicate that, compared with the existing DVC algorithm, the presented fast DVC algorithm produces similar precision and slightly higher accuracy at a substantially reduced computational cost.

  2. Enthalpy Changes during Photosynthetic Water Oxidation Tracked by Time-Resolved Calorimetry Using a Photothermal Beam Deflection Technique☆☆☆

    PubMed Central

    Krivanek, Roland; Dau, Holger; Haumann, Michael

    2008-01-01

    The energetics of the individual reaction steps in the catalytic cycle of photosynthetic water oxidation at the Mn4Ca complex of photosystem II (PSII) are of prime interest. We studied the electron transfer reactions in oxygen-evolving PSII membrane particles from spinach by a photothermal beam deflection technique, allowing for time-resolved calorimetry in the micro- to millisecond domain. For an ideal quantum yield of 100%, the enthalpy change, ΔH, coupled to the formation of the radical pair YZ⋅+QA− (where YZ is Tyr-161 of the D1 subunit of PSII) is estimated as −820 ± 250 meV. For a lower quantum yield of 70%, the enthalpy change is estimated to be −400 ± 250 meV. The observed nonthermal signal possibly is due to a contraction of the PSII protein volume (apparent ΔV of about −13 Å3). For the first time, the enthalpy change of the O2-evolving transition of the S-state cycle was monitored directly. Surprisingly, the reaction is only slightly exergonic. A value of ΔH(S3 ⇒ S0) of −210 meV is estimated, but also an enthalpy change of zero is within the error range. A prominent nonthermal photothermal beam deflection signal (apparent ΔV of about +42 Å3) may reflect O2 and proton release from the manganese complex, but also reorganization of the protein matrix. PMID:17993488

  3. Enthalpy measurement of coal-derived liquids. Technical progress report, August-October 1982

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

    Kidnay, A.J.; Yesavage, V.F.

    The correlational effort on the coal syncrudes and model compounds has been proceeding along two fronts. The first involves experimental work on a correlating factor for association in the liquids and the second involves an investigation of the modeling capabilities of cubic equations of state. The first area of investigation is the experimental measurement of a correlating factor for assocition in coal liquids. The procedure involves molecular weight measurement by freezing point depression. To facilitate these measurements, a simple Beckman freezing point depression apparatus is being currently modified to increase the accuracy, speed, and ease of measurement. The second areamore » of effort has involved establishing a set of cubic equations of state which can adequately model the enthalpy departures of quinoline and m-cresol. To this effort, a number of standard and association specific equations of state have been tested against a data base of previously measured enthalpy departures of m-cresol and quinoline. It has been found that these equations do quantitatively a poor job on m-cresol and quinoline. These problems are probably due to the highly polar nature of m-cresol and to a lesser extent quinoline, and to the poor quality of critical parameters for quinoline.« less

  4. Accurate Finite Difference Algorithms

    NASA Technical Reports Server (NTRS)

    Goodrich, John W.

    1996-01-01

    Two families of finite difference algorithms for computational aeroacoustics are presented and compared. All of the algorithms are single step explicit methods, they have the same order of accuracy in both space and time, with examples up to eleventh order, and they have multidimensional extensions. One of the algorithm families has spectral like high resolution. Propagation with high order and high resolution algorithms can produce accurate results after O(10(exp 6)) periods of propagation with eight grid points per wavelength.

  5. 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.

  6. A computational investigation of fuel mixing in a hypersonic scramjet

    NASA Technical Reports Server (NTRS)

    Fathauer, Brett W.; Rogers, R. C.

    1993-01-01

    A parabolized, Navier-Stokes code, SHIP3D, is used to numerically investigate the mixing between air injection and hydrogen injection from a swept ramp injector configuration into either a mainstream low-enthalpy flow or a hypervelocity test flow. The mixing comparisons between air and hydrogen injection reveal the importance of matching injectant-to-mainstream mass flow ratios. In flows with the same injectant-to-mainstream dynamic pressure ratio, the mixing definition was altered for the air injection cases. Comparisons of the computed results indicate that the air injection cases overestimate the mixing performance associated with hydrogen injection simulation. A lifting length parameter, to account for the time a fluid particle transverses through the mixing region, is defined and used to establish a connection of injectant mixing in hypervelocity flows, based on nonreactive, low-enthalpy flows.

  7. In pursuit of an accurate spatial and temporal model of biomolecules at the atomistic level: a perspective on computer simulation.

    PubMed

    Gray, Alan; Harlen, Oliver G; Harris, Sarah A; Khalid, Syma; Leung, Yuk Ming; Lonsdale, Richard; Mulholland, Adrian J; Pearson, Arwen R; Read, Daniel J; Richardson, Robin A

    2015-01-01

    Despite huge advances in the computational techniques available for simulating biomolecules at the quantum-mechanical, atomistic and coarse-grained levels, there is still a widespread perception amongst the experimental community that these calculations are highly specialist and are not generally applicable by researchers outside the theoretical community. In this article, the successes and limitations of biomolecular simulation and the further developments that are likely in the near future are discussed. A brief overview is also provided of the experimental biophysical methods that are commonly used to probe biomolecular structure and dynamics, and the accuracy of the information that can be obtained from each is compared with that from modelling. It is concluded that progress towards an accurate spatial and temporal model of biomacromolecules requires a combination of all of these biophysical techniques, both experimental and computational.

  8. Using Enthalpy as a Prognostic Variable in Atmospheric Modelling with Variable Composition

    DTIC Science & Technology

    2016-04-14

    the first place. It then becomes clear that specific enthalpy provides a viable alternative to account for the effects of composi- tional changes on...forces. It is also assumed that external forces acting on a molecule are proportional to its mass, mi , as is the case with the gravity or Coriolis ...relative humidity and is introduced into Equation (11) to account for the effects of water vapour on the gas constant R and, consequently, on the

  9. Accurate chemical master equation solution using multi-finite buffers

    DOE PAGES

    Cao, Youfang; Terebus, Anna; Liang, Jie

    2016-06-29

    Here, the discrete chemical master equation (dCME) provides a fundamental framework for studying stochasticity in mesoscopic networks. Because of the multiscale nature of many networks where reaction rates have a large disparity, directly solving dCMEs is intractable due to the exploding size of the state space. It is important to truncate the state space effectively with quantified errors, so accurate solutions can be computed. It is also important to know if all major probabilistic peaks have been computed. Here we introduce the accurate CME (ACME) algorithm for obtaining direct solutions to dCMEs. With multifinite buffers for reducing the state spacemore » by $O(n!)$, exact steady-state and time-evolving network probability landscapes can be computed. We further describe a theoretical framework of aggregating microstates into a smaller number of macrostates by decomposing a network into independent aggregated birth and death processes and give an a priori method for rapidly determining steady-state truncation errors. The maximal sizes of the finite buffers for a given error tolerance can also be precomputed without costly trial solutions of dCMEs. We show exactly computed probability landscapes of three multiscale networks, namely, a 6-node toggle switch, 11-node phage-lambda epigenetic circuit, and 16-node MAPK cascade network, the latter two with no known solutions. We also show how probabilities of rare events can be computed from first-passage times, another class of unsolved problems challenging for simulation-based techniques due to large separations in time scales. Overall, the ACME method enables accurate and efficient solutions of the dCME for a large class of networks.« less

  10. Accurate chemical master equation solution using multi-finite buffers

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

    Cao, Youfang; Terebus, Anna; Liang, Jie

    Here, the discrete chemical master equation (dCME) provides a fundamental framework for studying stochasticity in mesoscopic networks. Because of the multiscale nature of many networks where reaction rates have a large disparity, directly solving dCMEs is intractable due to the exploding size of the state space. It is important to truncate the state space effectively with quantified errors, so accurate solutions can be computed. It is also important to know if all major probabilistic peaks have been computed. Here we introduce the accurate CME (ACME) algorithm for obtaining direct solutions to dCMEs. With multifinite buffers for reducing the state spacemore » by $O(n!)$, exact steady-state and time-evolving network probability landscapes can be computed. We further describe a theoretical framework of aggregating microstates into a smaller number of macrostates by decomposing a network into independent aggregated birth and death processes and give an a priori method for rapidly determining steady-state truncation errors. The maximal sizes of the finite buffers for a given error tolerance can also be precomputed without costly trial solutions of dCMEs. We show exactly computed probability landscapes of three multiscale networks, namely, a 6-node toggle switch, 11-node phage-lambda epigenetic circuit, and 16-node MAPK cascade network, the latter two with no known solutions. We also show how probabilities of rare events can be computed from first-passage times, another class of unsolved problems challenging for simulation-based techniques due to large separations in time scales. Overall, the ACME method enables accurate and efficient solutions of the dCME for a large class of networks.« less

  11. A molecular dynamics study of ambient and high pressure phases of silica: structure and enthalpy variation with molar volume.

    PubMed

    Rajappa, Chitra; Sringeri, S Bhuvaneshwari; Subramanian, Yashonath; Gopalakrishnan, J

    2014-06-28

    Extensive molecular dynamics studies of 13 different silica polymorphs are reported in the isothermal-isobaric ensemble with the Parrinello-Rahman variable shape simulation cell. The van Beest-Kramer-van Santen (BKS) potential is shown to predict lattice parameters for most phases within 2%-3% accuracy, as well as the relative stabilities of different polymorphs in agreement with experiment. Enthalpies of high-density polymorphs - CaCl2-type, α-PbO2-type, and pyrite-type - for which no experimental data are available as yet, are predicted here. Further, the calculated enthalpies exhibit two distinct regimes as a function of molar volume-for low and medium-density polymorphs, it is almost independent of volume, while for high-pressure phases a steep dependence is seen. A detailed analysis indicates that the increased short-range contributions to enthalpy in the high-density phases arise not only from an increased coordination number of silicon but also shorter Si-O bond lengths. Our results indicate that amorphous phases of silica exhibit better optimization of short-range interactions than crystalline phases at the same density while the magnitude of Coulombic contributions is lower in the amorphous phase.

  12. The Relationship between Lattice Enthalpy and Melting Point in Magnesium and Aluminium Oxides. Science Notes

    ERIC Educational Resources Information Center

    Talbot, Christopher; Yap, Lydia

    2013-01-01

    This "Science Note" presents a study by Christopher Talbot and Lydia Yap, who teach IB Chemistry at Anglo-Chinese School (Independent), Republic of Singapore, to pre-university students. Pre-university students may postulate the correlation between the magnitude of the lattice enthalpy compound and its melting point, since both…

  13. Toward accurate tooth segmentation from computed tomography images using a hybrid level set model

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

    Gan, Yangzhou; Zhao, Qunfei; Xia, Zeyang, E-mail: zy.xia@siat.ac.cn, E-mail: jing.xiong@siat.ac.cn

    Purpose: A three-dimensional (3D) model of the teeth provides important information for orthodontic diagnosis and treatment planning. Tooth segmentation is an essential step in generating the 3D digital model from computed tomography (CT) images. The aim of this study is to develop an accurate and efficient tooth segmentation method from CT images. Methods: The 3D dental CT volumetric images are segmented slice by slice in a two-dimensional (2D) transverse plane. The 2D segmentation is composed of a manual initialization step and an automatic slice by slice segmentation step. In the manual initialization step, the user manually picks a starting slicemore » and selects a seed point for each tooth in this slice. In the automatic slice segmentation step, a developed hybrid level set model is applied to segment tooth contours from each slice. Tooth contour propagation strategy is employed to initialize the level set function automatically. Cone beam CT (CBCT) images of two subjects were used to tune the parameters. Images of 16 additional subjects were used to validate the performance of the method. Volume overlap metrics and surface distance metrics were adopted to assess the segmentation accuracy quantitatively. The volume overlap metrics were volume difference (VD, mm{sup 3}) and Dice similarity coefficient (DSC, %). The surface distance metrics were average symmetric surface distance (ASSD, mm), RMS (root mean square) symmetric surface distance (RMSSSD, mm), and maximum symmetric surface distance (MSSD, mm). Computation time was recorded to assess the efficiency. The performance of the proposed method has been compared with two state-of-the-art methods. Results: For the tested CBCT images, the VD, DSC, ASSD, RMSSSD, and MSSD for the incisor were 38.16 ± 12.94 mm{sup 3}, 88.82 ± 2.14%, 0.29 ± 0.03 mm, 0.32 ± 0.08 mm, and 1.25 ± 0.58 mm, respectively; the VD, DSC, ASSD, RMSSSD, and MSSD for the canine were 49.12 ± 9.33 mm{sup 3}, 91.57 ± 0.82%, 0.27 ± 0

  14. Computational and Experimental Study of Thermodynamics of the Reaction of Titania and Water at High Temperatures.

    PubMed

    Nguyen, Q N; Bauschlicher, C W; Myers, D L; Jacobson, N S; Opila, E J

    2017-12-14

    Gaseous titanium hydroxide and oxyhydroxide species were studied with quantum chemical methods. The results are used in conjunction with an experimental transpiration study of titanium dioxide (TiO 2 ) in water vapor-containing environments at elevated temperatures to provide a thermodynamic description of the Ti(OH) 4 (g) and TiO(OH) 2 (g) species. The geometry and harmonic vibrational frequencies of these species were computed using the coupled-cluster singles and doubles method with a perturbative correction for connected triple substitutions [CCSD(T)]. For the OH bending and rotation, the B3LYP density functional theory was used to compute corrections to the harmonic approximations. These results were combined to determine the enthalpy of formation. Experimentally, the transpiration method was used with water contents from 0 to 76 mol % in oxygen or argon carrier gases for 20-250 h exposure times at 1473-1673 K. Results indicate that oxygen is not a key contributor to volatilization, and the primary reaction for volatilization in this temperature range is TiO 2 (s) + H 2 O(g) = TiO(OH) 2 (g). Data were analyzed with both the second and third law methods using the thermal functions derived from the theoretical calculations. The third law enthalpy of formation at 298.15 K for TiO(OH) 2 (g) at 298 K was -838.9 ± 6.5 kJ/mol, which compares favorably to the theoretical calculation of -838.7 ± 25 kJ/mol. We recommend the experimentally derived third law enthalpy of formation at 298.15 K for TiO(OH) 2 , the computed entropy of 320.67 J/mol·K, and the computed heat capacity [149.192 + (-0.02539)T + (8.28697 × 10 -6 )T 2 + (-15614.05)/T + (-5.2182 × 10 -11 )/T 2 ] J/mol-K, where T is the temperature in K.

  15. Determination of saturation pressure and enthalpy of vaporization of semi-volatile aerosols: the integrated volume mentod

    EPA Science Inventory

    This study presents the integrated volume method for estimating saturation pressure and enthalpy of vaporization of a whole aerosol distribution. We measure the change of total volume of an aerosol distribution between a reference state and several heated states, with the heating...

  16. GASP: A computer code for calculating the thermodynamic and transport properties for ten fluids: Parahydrogen, helium, neon, methane, nitrogen, carbon monoxide, oxygen, fluorine, argon, and carbon dioxide. [enthalpy, entropy, thermal conductivity, and specific heat

    NASA Technical Reports Server (NTRS)

    Hendricks, R. C.; Baron, A. K.; Peller, I. C.

    1975-01-01

    A FORTRAN IV subprogram called GASP is discussed which calculates the thermodynamic and transport properties for 10 pure fluids: parahydrogen, helium, neon, methane, nitrogen, carbon monoxide, oxygen, fluorine, argon, and carbon dioxide. The pressure range is generally from 0.1 to 400 atmospheres (to 100 atm for helium and to 1000 atm for hydrogen). The temperature ranges are from the triple point to 300 K for neon; to 500 K for carbon monoxide, oxygen, and fluorine; to 600 K for methane and nitrogen; to 1000 K for argon and carbon dioxide; to 2000 K for hydrogen; and from 6 to 500 K for helium. GASP accepts any two of pressure, temperature and density as input conditions along with pressure, and either entropy or enthalpy. The properties available in any combination as output include temperature, density, pressure, entropy, enthalpy, specific heats, sonic velocity, viscosity, thermal conductivity, and surface tension. The subprogram design is modular so that the user can choose only those subroutines necessary to the calculations.

  17. The Correlation of Standard Entropy with Enthalpy Supplied from 0 to 298.15 K

    ERIC Educational Resources Information Center

    Lambert, Frank L.; Leff, Harvey S.

    2009-01-01

    As a substance is heated at constant pressure from near 0 K to 298 K, each incremental enthalpy increase, dH, alters entropy by dH/T, bringing it from approximately zero to its standard molar entropy S degrees. Using heat capacity data for 32 solids and CODATA results for another 45, we found a roughly linear relationship between S degrees and…

  18. Heat capacty, relative enthalpy, and calorimetric entropy of silicate minerals: an empirical method of prediction.

    USGS Publications Warehouse

    Robinson, G.R.; Haas, J.L.

    1983-01-01

    Through the evaluation of experimental calorimetric data and estimates of the molar isobaric heat capacities, relative enthalpies and entropies of constituent oxides, a procedure for predicting the thermodynamic properties of silicates is developed. Estimates of the accuracy and precision of the technique and examples of its application are also presented. -J.A.Z.

  19. Three-dimensional quantitative structure-property relationship (3D-QSPR) models for prediction of thermodynamic properties of polychlorinated biphenyls (PCBs): enthalpy of vaporization.

    PubMed

    Puri, Swati; Chickos, James S; Welsh, William J

    2002-01-01

    Three-dimensional Quantitative Structure-Property Relationship (QSPR) models have been derived using Comparative Molecular Field Analysis (CoMFA) to correlate the vaporization enthalpies of a representative set of polychlorinated biphenyls (PCBs) at 298.15 K with their CoMFA-calculated physicochemical properties. Various alignment schemes, such as inertial, as is, and atom fit, were employed in this study. The CoMFA models were also developed using different partial charge formalisms, namely, electrostatic potential (ESP) charges and Gasteiger-Marsili (GM) charges. The most predictive model for vaporization enthalpy (Delta(vap)H(m)(298.15 K)), with atom fit alignment and Gasteiger-Marsili charges, yielded r2 values 0.852 (cross-validated) and 0.996 (conventional). The vaporization enthalpies of PCBs increased with the number of chlorine atoms and were found to be larger for the meta- and para-substituted isomers. This model was used to predict Delta(vap)H(m)(298.15 K) of the entire set of 209 PCB congeners.

  20. Enthalpy of mixing of liquid systems for lead free soldering: Ni-Sb-Sn system.

    PubMed

    Elmahfoudi, A; Fürtauer, S; Sabbar, A; Flandorfer, H

    2012-04-20

    The partial and integral enthalpies of mixing of liquid ternary Ni-Sb-Sn alloys were determined along five sections x Sb / x Sn  = 3:1, x Sb / x Sn  = 1:1, x Sb / x Sn  = 1:3, x Ni / x Sn  = 1:4, and x Ni / x Sb  = 1:4 at 1000 °C in a large compositional range using drop calorimetry techniques. The mixing enthalpy of Ni-Sb alloys was determined at the same temperature and described by a Redlich-Kister polynomial. The other binary data were carefully evaluated from literature values. Our measured ternary data were fitted on the basis of an extended Redlich-Kister-Muggianu model for substitutional solutions. Additionally, a comparison of these results to the extrapolation model of Toop is given. The entire ternary system shows exothermic values of Δ mix H ranging from approx. -1300 J/mol, the minimum in the Sb-Sn binary system down to approx. -24,500 J/mol towards Ni-Sb. No significant ternary interaction could be deduced from our data.

  1. Sequential water molecule binding enthalpies for aqueous nanodrops containing a mono-, di- or trivalent ion and between 20 and 500 water molecules† †Electronic supplementary information (ESI) available: Detailed description of the experimental and computational modeling methods. Isolation, BIRD and UVPD sequence for [Ru(NH3)6]3+·(H2O)169–171, nanoESI spectra for 2+ and 3+ ions. Detailed description of the isotope distribution simulation program. Comparison between experimental and simulated 1+, 2+ and 3+ ion isotope distributions. Wavelength dependence of the deduced sequential binding enthalpies. Comparison of experimental UVPD binding enthalpies to the liquid drop model at different temperatures. Complete list of binding enthalpies and average number of water molecules lost upon UVPD. See DOI: 10.1039/c6sc04957e Click here for additional data file.

    PubMed Central

    Heiles, Sven; Cooper, Richard J.; DiTucci, Matthew J.

    2017-01-01

    Sequential water molecule binding enthalpies, ΔH n,n–1, are important for a detailed understanding of competitive interactions between ions, water and solute molecules, and how these interactions affect physical properties of ion-containing nanodrops that are important in aerosol chemistry. Water molecule binding enthalpies have been measured for small clusters of many different ions, but these values for ion-containing nanodrops containing more than 20 water molecules are scarce. Here, ΔH n,n–1 values are deduced from high-precision ultraviolet photodissociation (UVPD) measurements as a function of ion identity, charge state and cluster size between 20–500 water molecules and for ions with +1, +2 and +3 charges. The ΔH n,n–1 values are obtained from the number of water molecules lost upon photoexcitation at a known wavelength, and modeling of the release of energy into the translational, rotational and vibrational motions of the products. The ΔH n,n–1 values range from 36.82 to 50.21 kJ mol–1. For clusters containing more than ∼250 water molecules, the binding enthalpies are between the bulk heat of vaporization (44.8 kJ mol–1) and the sublimation enthalpy of bulk ice (51.0 kJ mol–1). These values depend on ion charge state for clusters with fewer than 150 water molecules, but there is a negligible dependence at larger size. There is a minimum in the ΔH n,n–1 values that depends on the cluster size and ion charge state, which can be attributed to the competing effects of ion solvation and surface energy. The experimental ΔH n,n–1 values can be fit to the Thomson liquid drop model (TLDM) using bulk ice parameters. By optimizing the surface tension and temperature change of the logarithmic partial pressure for the TLDM, the experimental sequential water molecule binding enthalpies can be fit with an accuracy of ±3.3 kJ mol–1 over the entire range of cluster sizes. PMID:28451364

  2. Highly Accurate Calculations of the Phase Diagram of Cold Lithium

    NASA Astrophysics Data System (ADS)

    Shulenburger, Luke; Baczewski, Andrew

    The phase diagram of lithium is particularly complicated, exhibiting many different solid phases under the modest application of pressure. Experimental efforts to identify these phases using diamond anvil cells have been complemented by ab initio theory, primarily using density functional theory (DFT). Due to the multiplicity of crystal structures whose enthalpy is nearly degenerate and the uncertainty introduced by density functional approximations, we apply the highly accurate many-body diffusion Monte Carlo (DMC) method to the study of the solid phases at low temperature. These calculations span many different phases, including several with low symmetry, demonstrating the viability of DMC as a method for calculating phase diagrams for complex solids. Our results can be used as a benchmark to test the accuracy of various density functionals. This can strengthen confidence in DFT based predictions of more complex phenomena such as the anomalous melting behavior predicted for lithium at high pressures. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. DOE's National Nuclear Security Administration under contract DE-AC04-94AL85000.

  3. Comparison of Experimental and Computational Aerothermodynamics of a 70-deg Sphere-Cone

    NASA Technical Reports Server (NTRS)

    Hollis, Brian R.; Perkins, John N.

    1996-01-01

    Numerical solutions for hypersonic flows of carbon-dioxide and air around a 70-deg sphere-cone have been computed using an axisymmetric non-equilibrium Navier-Stokes solver. Freestream flow conditions for these computations were equivalent to those obtained in an experimental blunt-body heat-transfer study conducted in a high-enthalpy, hypervelocity expansion tube. Comparisons have been made between the computed and measured surface heat-transfer rates on the forebody and afterbody of the sphere-cone and on the sting which supported the test model. Computed forebody heating rates were within the estimated experimental uncertainties of 10% on the forebody and 15% in the wake except for within the recirculating flow region of the wake.

  4. Melting temperature and enthalpy variations of phase change materials (PCMs): a differential scanning calorimetry (DSC) analysis

    NASA Astrophysics Data System (ADS)

    Sun, Xiaoqin; Lee, Kyoung Ok; Medina, Mario A.; Chu, Youhong; Li, Chuanchang

    2018-06-01

    Differential scanning calorimetry (DSC) analysis is a standard thermal analysis technique used to determine the phase transition temperature, enthalpy, heat of fusion, specific heat and activation energy of phase change materials (PCMs). To determine the appropriate heating rate and sample mass, various DSC measurements were carried out using two kinds of PCMs, namely N-octadecane paraffin and calcium chloride hexahydrate. The variations in phase transition temperature, enthalpy, heat of fusion, specific heat and activation energy were observed within applicable heating rates and sample masses. It was found that the phase transition temperature range increased with increasing heating rate and sample mass; while the heat of fusion varied without any established pattern. The specific heat decreased with the increase of heating rate and sample mass. For accuracy purpose, it is recommended that for PCMs with high thermal conductivity (e.g. hydrated salt) the focus will be on heating rate rather than sample mass.

  5. Planar laser-induced fluorescence measurements of high-enthalpy free jet flow with nitric oxide

    NASA Technical Reports Server (NTRS)

    Palmer, Jennifer L.; Mcmillin, Brian K.; Hanson, Ronald K.

    1992-01-01

    Planar laser-induced fluorescence (PLIF) measurements of property fields in a high-enthalpy, supersonic, underexpanded free jet generated in a reflection-type shock tunnel are reported. PLIF images showing velocity and temperature sensitivity are presented. The inferred radial velocity and relative rotational temperature fields are found to be in agreement with those predicted by a numerical simulation of the flowfield using the method of characteristics.

  6. Calorimetric and computational study of indanones.

    PubMed

    Matos, M Agostinha R; Miranda, Margarida S; Monte, Manuel J S; Santos, Luís M N B F; Morais, Victor M F; Chickos, James S; Umnahanant, Patamaporn; Liebman, Joel F

    2007-11-01

    Condensed phase standard (p degrees = 0.1 MPa) molar enthalpies of formation for 1-indanone, 2-indanone, and 1,3-indandione were derived from the standard molar enthalpies of combustion, in oxygen, at T = 298.15 K, measured by static bomb combustion calorimetry. The standard molar enthalpies of sublimation for 1-indanone and 2-indanone, at T = 298.15 K, were measured both by correlation-gas chromatography and by Calvet microcalorimetry leading to a mean value for each compound. For 1,3-indandione, the standard molar enthalpy of sublimation was derived from the vapor pressure dependence on temperature. The following enthalpies of formation in gas phase, at T = 298.15 K, were then derived: 1-indanone, -64.0 +/- 3.8 kJ mol(-1); 2-indanone, -56.6 +/- 4.8 kJ mol(-1); 1,3-indandione, -165.0 +/- 2.6 kJ mol(-1). The vaporization and fusion enthalpies of the indanones studied are also reported. In addition, theoretical calculations using the density functional theory with the B3LYP and MPW1B95 energy functionals and the 6-311G** and cc-pVTZ basis sets have been performed for these molecules and the corresponding one-ring species to obtain the most stable geometries and to access their energetic stabilities.

  7. Computational Calorimetry: High-Precision Calculation of Host–Guest Binding Thermodynamics

    PubMed Central

    2015-01-01

    We present a strategy for carrying out high-precision calculations of binding free energy and binding enthalpy values from molecular dynamics simulations with explicit solvent. The approach is used to calculate the thermodynamic profiles for binding of nine small molecule guests to either the cucurbit[7]uril (CB7) or β-cyclodextrin (βCD) host. For these systems, calculations using commodity hardware can yield binding free energy and binding enthalpy values with a precision of ∼0.5 kcal/mol (95% CI) in a matter of days. Crucially, the self-consistency of the approach is established by calculating the binding enthalpy directly, via end point potential energy calculations, and indirectly, via the temperature dependence of the binding free energy, i.e., by the van’t Hoff equation. Excellent agreement between the direct and van’t Hoff methods is demonstrated for both host–guest systems and an ion-pair model system for which particularly well-converged results are attainable. Additionally, we find that hydrogen mass repartitioning allows marked acceleration of the calculations with no discernible cost in precision or accuracy. Finally, we provide guidance for accurately assessing numerical uncertainty of the results in settings where complex correlations in the time series can pose challenges to statistical analysis. The routine nature and high precision of these binding calculations opens the possibility of including measured binding thermodynamics as target data in force field optimization so that simulations may be used to reliably interpret experimental data and guide molecular design. PMID:26523125

  8. Force Field Benchmark of Organic Liquids: Density, Enthalpy of Vaporization, Heat Capacities, Surface Tension, Isothermal Compressibility, Volumetric Expansion Coefficient, and Dielectric Constant.

    PubMed

    Caleman, Carl; van Maaren, Paul J; Hong, Minyan; Hub, Jochen S; Costa, Luciano T; van der Spoel, David

    2012-01-10

    The chemical composition of small organic molecules is often very similar to amino acid side chains or the bases in nucleic acids, and hence there is no a priori reason why a molecular mechanics force field could not describe both organic liquids and biomolecules with a single parameter set. Here, we devise a benchmark for force fields in order to test the ability of existing force fields to reproduce some key properties of organic liquids, namely, the density, enthalpy of vaporization, the surface tension, the heat capacity at constant volume and pressure, the isothermal compressibility, the volumetric expansion coefficient, and the static dielectric constant. Well over 1200 experimental measurements were used for comparison to the simulations of 146 organic liquids. Novel polynomial interpolations of the dielectric constant (32 molecules), heat capacity at constant pressure (three molecules), and the isothermal compressibility (53 molecules) as a function of the temperature have been made, based on experimental data, in order to be able to compare simulation results to them. To compute the heat capacities, we applied the two phase thermodynamics method (Lin et al. J. Chem. Phys.2003, 119, 11792), which allows one to compute thermodynamic properties on the basis of the density of states as derived from the velocity autocorrelation function. The method is implemented in a new utility within the GROMACS molecular simulation package, named g_dos, and a detailed exposé of the underlying equations is presented. The purpose of this work is to establish the state of the art of two popular force fields, OPLS/AA (all-atom optimized potential for liquid simulation) and GAFF (generalized Amber force field), to find common bottlenecks, i.e., particularly difficult molecules, and to serve as a reference point for future force field development. To make for a fair playing field, all molecules were evaluated with the same parameter settings, such as thermostats and barostats

  9. Force Field Benchmark of Organic Liquids: Density, Enthalpy of Vaporization, Heat Capacities, Surface Tension, Isothermal Compressibility, Volumetric Expansion Coefficient, and Dielectric Constant

    PubMed Central

    2011-01-01

    The chemical composition of small organic molecules is often very similar to amino acid side chains or the bases in nucleic acids, and hence there is no a priori reason why a molecular mechanics force field could not describe both organic liquids and biomolecules with a single parameter set. Here, we devise a benchmark for force fields in order to test the ability of existing force fields to reproduce some key properties of organic liquids, namely, the density, enthalpy of vaporization, the surface tension, the heat capacity at constant volume and pressure, the isothermal compressibility, the volumetric expansion coefficient, and the static dielectric constant. Well over 1200 experimental measurements were used for comparison to the simulations of 146 organic liquids. Novel polynomial interpolations of the dielectric constant (32 molecules), heat capacity at constant pressure (three molecules), and the isothermal compressibility (53 molecules) as a function of the temperature have been made, based on experimental data, in order to be able to compare simulation results to them. To compute the heat capacities, we applied the two phase thermodynamics method (Lin et al. J. Chem. Phys.2003, 119, 11792), which allows one to compute thermodynamic properties on the basis of the density of states as derived from the velocity autocorrelation function. The method is implemented in a new utility within the GROMACS molecular simulation package, named g_dos, and a detailed exposé of the underlying equations is presented. The purpose of this work is to establish the state of the art of two popular force fields, OPLS/AA (all-atom optimized potential for liquid simulation) and GAFF (generalized Amber force field), to find common bottlenecks, i.e., particularly difficult molecules, and to serve as a reference point for future force field development. To make for a fair playing field, all molecules were evaluated with the same parameter settings, such as thermostats and barostats

  10. Accurate quantum chemical calculations

    NASA Technical Reports Server (NTRS)

    Bauschlicher, Charles W., Jr.; Langhoff, Stephen R.; Taylor, Peter R.

    1989-01-01

    An important goal of quantum chemical calculations is to provide an understanding of chemical bonding and molecular electronic structure. A second goal, the prediction of energy differences to chemical accuracy, has been much harder to attain. First, the computational resources required to achieve such accuracy are very large, and second, it is not straightforward to demonstrate that an apparently accurate result, in terms of agreement with experiment, does not result from a cancellation of errors. Recent advances in electronic structure methodology, coupled with the power of vector supercomputers, have made it possible to solve a number of electronic structure problems exactly using the full configuration interaction (FCI) method within a subspace of the complete Hilbert space. These exact results can be used to benchmark approximate techniques that are applicable to a wider range of chemical and physical problems. The methodology of many-electron quantum chemistry is reviewed. Methods are considered in detail for performing FCI calculations. The application of FCI methods to several three-electron problems in molecular physics are discussed. A number of benchmark applications of FCI wave functions are described. Atomic basis sets and the development of improved methods for handling very large basis sets are discussed: these are then applied to a number of chemical and spectroscopic problems; to transition metals; and to problems involving potential energy surfaces. Although the experiences described give considerable grounds for optimism about the general ability to perform accurate calculations, there are several problems that have proved less tractable, at least with current computer resources, and these and possible solutions are discussed.

  11. 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.

  12. Large-scale high-throughput computer-aided discovery of advanced materials using cloud computing

    NASA Astrophysics Data System (ADS)

    Bazhirov, Timur; Mohammadi, Mohammad; Ding, Kevin; Barabash, Sergey

    Recent advances in cloud computing made it possible to access large-scale computational resources completely on-demand in a rapid and efficient manner. When combined with high fidelity simulations, they serve as an alternative pathway to enable computational discovery and design of new materials through large-scale high-throughput screening. Here, we present a case study for a cloud platform implemented at Exabyte Inc. We perform calculations to screen lightweight ternary alloys for thermodynamic stability. Due to the lack of experimental data for most such systems, we rely on theoretical approaches based on first-principle pseudopotential density functional theory. We calculate the formation energies for a set of ternary compounds approximated by special quasirandom structures. During an example run we were able to scale to 10,656 CPUs within 7 minutes from the start, and obtain results for 296 compounds within 38 hours. The results indicate that the ultimate formation enthalpy of ternary systems can be negative for some of lightweight alloys, including Li and Mg compounds. We conclude that compared to traditional capital-intensive approach that requires in on-premises hardware resources, cloud computing is agile and cost-effective, yet scalable and delivers similar performance.

  13. Computer simulation of the carbon activity in austenite

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

    Murch, G.E.; Thorn, R.J.

    1979-02-01

    Carbon activity in austenite is described in terms of an Ising-like f.c.c. lattice gas model in which carbon interstitials repel only at the distance of nearest neighbors. A Monte Carlo simulation method in the petit canonical ensemble is employed to calculate directly the carbon activity as a function of composition and temperature. The computed activities are in satisfactory agreement with the experimental data, similarly for the decompostion of the activity to the partial molar enthalpy and entropy.

  14. Fast and Accurate Circuit Design Automation through Hierarchical Model Switching.

    PubMed

    Huynh, Linh; Tagkopoulos, Ilias

    2015-08-21

    In computer-aided biological design, the trifecta of characterized part libraries, accurate models and optimal design parameters is crucial for producing reliable designs. As the number of parts and model complexity increase, however, it becomes exponentially more difficult for any optimization method to search the solution space, hence creating a trade-off that hampers efficient design. To address this issue, we present a hierarchical computer-aided design architecture that uses a two-step approach for biological design. First, a simple model of low computational complexity is used to predict circuit behavior and assess candidate circuit branches through branch-and-bound methods. Then, a complex, nonlinear circuit model is used for a fine-grained search of the reduced solution space, thus achieving more accurate results. Evaluation with a benchmark of 11 circuits and a library of 102 experimental designs with known characterization parameters demonstrates a speed-up of 3 orders of magnitude when compared to other design methods that provide optimality guarantees.

  15. Extracting Time-Accurate Acceleration Vectors From Nontrivial Accelerometer Arrangements.

    PubMed

    Franck, Jennifer A; Blume, Janet; Crisco, Joseph J; Franck, Christian

    2015-09-01

    Sports-related concussions are of significant concern in many impact sports, and their detection relies on accurate measurements of the head kinematics during impact. Among the most prevalent recording technologies are videography, and more recently, the use of single-axis accelerometers mounted in a helmet, such as the HIT system. Successful extraction of the linear and angular impact accelerations depends on an accurate analysis methodology governed by the equations of motion. Current algorithms are able to estimate the magnitude of acceleration and hit location, but make assumptions about the hit orientation and are often limited in the position and/or orientation of the accelerometers. The newly formulated algorithm presented in this manuscript accurately extracts the full linear and rotational acceleration vectors from a broad arrangement of six single-axis accelerometers directly from the governing set of kinematic equations. The new formulation linearizes the nonlinear centripetal acceleration term with a finite-difference approximation and provides a fast and accurate solution for all six components of acceleration over long time periods (>250 ms). The approximation of the nonlinear centripetal acceleration term provides an accurate computation of the rotational velocity as a function of time and allows for reconstruction of a multiple-impact signal. Furthermore, the algorithm determines the impact location and orientation and can distinguish between glancing, high rotational velocity impacts, or direct impacts through the center of mass. Results are shown for ten simulated impact locations on a headform geometry computed with three different accelerometer configurations in varying degrees of signal noise. Since the algorithm does not require simplifications of the actual impacted geometry, the impact vector, or a specific arrangement of accelerometer orientations, it can be easily applied to many impact investigations in which accurate kinematics need

  16. A flexible and accurate digital volume correlation method applicable to high-resolution volumetric images

    NASA Astrophysics Data System (ADS)

    Pan, Bing; Wang, Bo

    2017-10-01

    Digital volume correlation (DVC) is a powerful technique for quantifying interior deformation within solid opaque materials and biological tissues. In the last two decades, great efforts have been made to improve the accuracy and efficiency of the DVC algorithm. However, there is still a lack of a flexible, robust and accurate version that can be efficiently implemented in personal computers with limited RAM. This paper proposes an advanced DVC method that can realize accurate full-field internal deformation measurement applicable to high-resolution volume images with up to billions of voxels. Specifically, a novel layer-wise reliability-guided displacement tracking strategy combined with dynamic data management is presented to guide the DVC computation from slice to slice. The displacements at specified calculation points in each layer are computed using the advanced 3D inverse-compositional Gauss-Newton algorithm with the complete initial guess of the deformation vector accurately predicted from the computed calculation points. Since only limited slices of interest in the reference and deformed volume images rather than the whole volume images are required, the DVC calculation can thus be efficiently implemented on personal computers. The flexibility, accuracy and efficiency of the presented DVC approach are demonstrated by analyzing computer-simulated and experimentally obtained high-resolution volume images.

  17. Modelling the complete operation of a free-piston shock tunnel for a low enthalpy condition

    NASA Astrophysics Data System (ADS)

    McGilvray, M.; Dann, A. G.; Jacobs, P. A.

    2013-07-01

    Only a limited number of free-stream flow properties can be measured in hypersonic impulse facilities at the nozzle exit. This poses challenges for experimenters when subsequently analysing experimental data obtained from these facilities. Typically in a reflected shock tunnel, a simple analysis that requires small amounts of computational resources is used to calculate quasi-steady gas properties. This simple analysis requires initial fill conditions and experimental measurements in analytical calculations of each major flow process, using forward coupling with minor corrections to include processes that are not directly modeled. However, this simplistic approach leads to an unknown level of discrepancy to the true flow properties. To explore the simple modelling techniques accuracy, this paper details the use of transient one and two-dimensional numerical simulations of a complete facility to obtain more refined free-stream flow properties from a free-piston reflected shock tunnel operating at low-enthalpy conditions. These calculations were verified by comparison to experimental data obtained from the facility. For the condition and facility investigated, the test conditions at nozzle exit produced with the simple modelling technique agree with the time and space averaged results from the complete facility calculations to within the accuracy of the experimental measurements.

  18. Transformation of topologically close-packed β-W to body-centered cubic α-W: Comparison of experiments and computations.

    PubMed

    Barmak, Katayun; Liu, Jiaxing; Harlan, Liam; Xiao, Penghao; Duncan, Juliana; Henkelman, Graeme

    2017-10-21

    The enthalpy and activation energy for the transformation of the metastable form of tungsten, β-W, which has the topologically close-packed A15 structure (space group Pm3¯n), to equilibrium α-W, which is body-centered cubic (A2, space group Im3¯m), was measured using differential scanning calorimetry. The β-W films were 1 μm-thick and were prepared by sputter deposition in argon with a small amount of nitrogen. The transformation enthalpy was measured as -8.3 ± 0.4 kJ/mol (-86 ± 4 meV/atom) and the transformation activation energy as 2.2 ± 0.1 eV. The measured enthalpy was found to agree well with the difference in energies of α and β tungsten computed using density functional theory, which gave a value of -82 meV/atom for the transformation enthalpy. A calculated concerted transformation mechanism with a barrier of 0.4 eV/atom, in which all the atoms in an A15 unit cell transform into A2, was found to be inconsistent with the experimentally measured activation energy for any critical nucleus larger than two A2 unit cells. Larger calculations of eight A15 unit cells spontaneously relax to a mechanism in which part of the supercell first transforms from A15 to A2, creating a phase boundary, before the remaining A15 transforms into the A2 phase. Both calculations indicate that a nucleation and growth mechanism is favored over a concerted transformation. More consistent with the experimental activation energy was that of a calculated local transformation mechanism at the A15-A2 phase boundary, computed as 1.7 eV using molecular dynamics simulations. This calculated phase transformation mechanism involves collective rearrangements of W atoms in the disordered interface separating the A15 and A2 phases.

  19. Enthalpies of mixing of liquid systems for lead free soldering: Al-Cu-Sn system.

    PubMed

    Flandorfer, Hans; Rechchach, Meryem; Elmahfoudi, A; Bencze, László; Popovič, Arkadij; Ipser, Herbert

    2011-11-01

    The present work refers to high-temperature drop calorimetric measurements on liquid Al-Cu, Al-Sn, and Al-Cu-Sn alloys. The binary systems have been investigated at 973 K, up to 40 at.% Cu in case of Al-Cu, and over the entire concentrational range in case of Al-Sn. Measurements in the ternary Al-Cu-Sn system were performed along the following cross-sections: x(Al)/x(Cu) = 1:1, x(Al)/x(Sn) = 1:1, x(Cu)/x(Sn) = 7:3, x(Cu)/x(Sn) = 1:1, and x(Cu)/x(Sn) = 3:7 at 1273 K. Experimental data were used to find ternary interaction parameters by applying the Redlich-Kister-Muggianu model for substitutional solutions, and a full set of parameters describing the concentration dependence of the enthalpy of mixing was derived. From these, the isoenthalpy curves were constructed for 1273 K. The ternary system shows an exothermic enthalpy minimum of approx. -18,000 J/mol in the Al-Cu binary and a maximum of approx. 4000 J/mol in the Al-Sn binary system. The Al-Cu-Sn system is characterized by considerable repulsive ternary interactions as shown by the positive ternary interaction parameters.

  20. Sentinel nodes identified by computed tomography-lymphography accurately stage the axilla in patients with breast cancer

    PubMed Central

    2013-01-01

    Background Sentinel node biopsy often results in the identification and removal of multiple nodes as sentinel nodes, although most of these nodes could be non-sentinel nodes. This study investigated whether computed tomography-lymphography (CT-LG) can distinguish sentinel nodes from non-sentinel nodes and whether sentinel nodes identified by CT-LG can accurately stage the axilla in patients with breast cancer. Methods This study included 184 patients with breast cancer and clinically negative nodes. Contrast agent was injected interstitially. The location of sentinel nodes was marked on the skin surface using a CT laser light navigator system. Lymph nodes located just under the marks were first removed as sentinel nodes. Then, all dyed nodes or all hot nodes were removed. Results The mean number of sentinel nodes identified by CT-LG was significantly lower than that of dyed and/or hot nodes removed (1.1 vs 1.8, p <0.0001). Twenty-three (12.5%) patients had ≥2 sentinel nodes identified by CT-LG removed, whereas 94 (51.1%) of patients had ≥2 dyed and/or hot nodes removed (p <0.0001). Pathological evaluation demonstrated that 47 (25.5%) of 184 patients had metastasis to at least one node. All 47 patients demonstrated metastases to at least one of the sentinel nodes identified by CT-LG. Conclusions CT-LG can distinguish sentinel nodes from non-sentinel nodes, and sentinel nodes identified by CT-LG can accurately stage the axilla in patients with breast cancer. Successful identification of sentinel nodes using CT-LG may facilitate image-based diagnosis of metastasis, possibly leading to the omission of sentinel node biopsy. PMID:24321242

  1. Time-Accurate Computations of Isolated Circular Synthetic Jets in Crossflow

    NASA Technical Reports Server (NTRS)

    Rumsey, C. L.; Schaeffler, N. W.; Milanovic, I. M.; Zaman, K. B. M. Q.

    2007-01-01

    Results from unsteady Reynolds-averaged Navier-Stokes computations are described for two different synthetic jet flows issuing into a turbulent boundary layer crossflow through a circular orifice. In one case the jet effect is mostly contained within the boundary layer, while in the other case the jet effect extends beyond the boundary layer edge. Both cases have momentum flux ratios less than 2. Several numerical parameters are investigated, and some lessons learned regarding the CFD methods for computing these types of flow fields are summarized. Results in both cases are compared to experiment.

  2. Accurate Evaluation Method of Molecular Binding Affinity from Fluctuation Frequency

    NASA Astrophysics Data System (ADS)

    Hoshino, Tyuji; Iwamoto, Koji; Ode, Hirotaka; Ohdomari, Iwao

    2008-05-01

    Exact estimation of the molecular binding affinity is significantly important for drug discovery. The energy calculation is a direct method to compute the strength of the interaction between two molecules. This energetic approach is, however, not accurate enough to evaluate a slight difference in binding affinity when distinguishing a prospective substance from dozens of candidates for medicine. Hence more accurate estimation of drug efficacy in a computer is currently demanded. Previously we proposed a concept of estimating molecular binding affinity, focusing on the fluctuation at an interface between two molecules. The aim of this paper is to demonstrate the compatibility between the proposed computational technique and experimental measurements, through several examples for computer simulations of an association of human immunodeficiency virus type-1 (HIV-1) protease and its inhibitor (an example for a drug-enzyme binding), a complexation of an antigen and its antibody (an example for a protein-protein binding), and a combination of estrogen receptor and its ligand chemicals (an example for a ligand-receptor binding). The proposed affinity estimation has proven to be a promising technique in the advanced stage of the discovery and the design of drugs.

  3. High accurate time system of the Low Latitude Meridian Circle.

    NASA Astrophysics Data System (ADS)

    Yang, Jing; Wang, Feng; Li, Zhiming

    In order to obtain the high accurate time signal for the Low Latitude Meridian Circle (LLMC), a new GPS accurate time system is developed which include GPS, 1 MC frequency source and self-made clock system. The second signal of GPS is synchronously used in the clock system and information can be collected by a computer automatically. The difficulty of the cancellation of the time keeper can be overcomed by using this system.

  4. Program Helps To Determine Chemical-Reaction Mechanisms

    NASA Technical Reports Server (NTRS)

    Bittker, D. A.; Radhakrishnan, K.

    1995-01-01

    General Chemical Kinetics and Sensitivity Analysis (LSENS) computer code developed for use in solving complex, homogeneous, gas-phase, chemical-kinetics problems. Provides for efficient and accurate chemical-kinetics computations and provides for sensitivity analysis for variety of problems, including problems involving honisothermal conditions. Incorporates mathematical models for static system, steady one-dimensional inviscid flow, reaction behind incident shock wave (with boundary-layer correction), and perfectly stirred reactor. Computations of equilibrium properties performed for following assigned states: enthalpy and pressure, temperature and pressure, internal energy and volume, and temperature and volume. Written in FORTRAN 77 with exception of NAMELIST extensions used for input.

  5. Capacitive Detection of Low-Enthalpy, Higher-Order Phase Transitions in Synthetic and Natural Composition Lipid Membranes

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

    Taylor, Graham J.; Heberle, Frederick A.; Seinfeld, Jason S.

    In-plane lipid organization and phase separation in natural membranes play key roles in regulating many cellular processes. Highly cooperative, first-order phase transitions in model membranes consisting of few lipid components are well understood and readily detectable via calorimetry, densitometry, and fluorescence. However, far less is known about natural membranes containing numerous lipid species and high concentrations of cholesterol, for which thermotropic transitions are undetectable by the above-mentioned techniques. We demonstrate that membrane capacitance is highly sensitive to low-enthalpy thermotropic transitions taking place in complex lipid membranes. Specifically, we measured the electrical capacitance as a function of temperature for droplet interfacemore » bilayer model membranes of increasing compositional complexity, namely, (a) a single lipid species, (b) domain-forming ternary mixtures, and (c) natural brain total lipid extract (bTLE). We observed that, for single-species lipid bilayers and some ternary compositions, capacitance exhibited an abrupt, temperature-dependent change that coincided with the transition detected by other techniques. In addition, capacitance measurements revealed transitions in mixed-lipid membranes that were not detected by the other techniques. Most notably, capacitance measurements of bTLE bilayers indicated a transition at ~38 °C not seen with any other method. Likewise, capacitance measurements detected transitions in some well-studied ternary mixtures that, while known to yield coexisting lipid phases, are not detected with calorimetry or densitometry. These results indicate that capacitance is exquisitely sensitive to low-enthalpy membrane transitions because of its sensitivity to changes in bilayer thickness that occur when lipids and excess solvent undergo subtle rearrangements near a phase transition. Our findings also suggest that heterogeneity confers stability to natural membranes that function near

  6. Capacitive Detection of Low-Enthalpy, Higher-Order Phase Transitions in Synthetic and Natural Composition Lipid Membranes

    DOE PAGES

    Taylor, Graham J.; Heberle, Frederick A.; Seinfeld, Jason S.; ...

    2017-08-15

    In-plane lipid organization and phase separation in natural membranes play key roles in regulating many cellular processes. Highly cooperative, first-order phase transitions in model membranes consisting of few lipid components are well understood and readily detectable via calorimetry, densitometry, and fluorescence. However, far less is known about natural membranes containing numerous lipid species and high concentrations of cholesterol, for which thermotropic transitions are undetectable by the above-mentioned techniques. We demonstrate that membrane capacitance is highly sensitive to low-enthalpy thermotropic transitions taking place in complex lipid membranes. Specifically, we measured the electrical capacitance as a function of temperature for droplet interfacemore » bilayer model membranes of increasing compositional complexity, namely, (a) a single lipid species, (b) domain-forming ternary mixtures, and (c) natural brain total lipid extract (bTLE). We observed that, for single-species lipid bilayers and some ternary compositions, capacitance exhibited an abrupt, temperature-dependent change that coincided with the transition detected by other techniques. In addition, capacitance measurements revealed transitions in mixed-lipid membranes that were not detected by the other techniques. Most notably, capacitance measurements of bTLE bilayers indicated a transition at ~38 °C not seen with any other method. Likewise, capacitance measurements detected transitions in some well-studied ternary mixtures that, while known to yield coexisting lipid phases, are not detected with calorimetry or densitometry. These results indicate that capacitance is exquisitely sensitive to low-enthalpy membrane transitions because of its sensitivity to changes in bilayer thickness that occur when lipids and excess solvent undergo subtle rearrangements near a phase transition. Our findings also suggest that heterogeneity confers stability to natural membranes that function near

  7. Mo-Si-B Alloys and Diboride Systems for High Enthalpy Environments: Design and Evaluation

    DTIC Science & Technology

    2016-01-15

    candidate material species production over a range of test gas enthalpies and pressures for UWM and ISU samples. Year 3: 3.1 Begin FTIR...emission measurements on CO2-laser heated samples at SRI. 3.2 Continue experiments to optimize Si-, B-, and C-species LIF detection schemes in hot gas ...material tests to identify data that can be used to benchmark development of physics-based models of gas -surface interactions. • Employ the

  8. Accurate coupled cluster reaction enthalpies and activation energies for X+H2 --> XH+H (X=F, OH, NH2, and CH3)

    NASA Astrophysics Data System (ADS)

    Kraka, Elfi; Gauss, Jürgen; Cremer, Dieter

    1993-10-01

    Coupled cluster calculations at the CCSD(T)/[5s4p3d/4s3p] and CCSD(T)/[5s4p3d2 f1g/4s3p2d] level of theory are reported for reactions X+H2→XH+H [X=F (1a), OH (1b), NH2 (1c), and CH3 (1d)] utilizing analytical energy gradients for geometry, frequency, charge distribution, and dipole moment calculations of reactants, transition states, and products. A careful analysis of vibrational corrections leads to reaction enthalpies at 300 K, which are within 0.04, 0.15, 0.62, and 0.89 kcal/mol of experimental values. For reaction (1a) a bent transition state and for reactions (1b) and (1c) transition states with a cis arrangement of the reactants are calculated. The cis forms of transition states (1b) and (1c) are energetically favored because of electrostatic interactions, in particular dipole-dipole attraction as is revealed by calculated charge distributions. For reactions (1a)-(1d), the CCSD(T)/[5s4p3d2 f1g/4s3p2d] activation energies at 300 K are 1.1, 5.4, 10.8, and 12.7 kcal/mol which differ by just 0.1, 1.4, 2.3, and 1.8 kcal/mol, respectively, from the corresponding experimental values of 1±0.1, 4±0.5, 8.5±0.5, and 10.9±0.5 kcal/mol. For reactions (1), this is the best agreement between experiment and theory that has been obtained from ab initio calculations not including any empirically based corrections. Agreement is achieved after considering basis set effects, basis set superposition errors, spin contamination, tunneling effect and, in particular, zero-point energies as well as temperature corrections. Net corrections for the four activation energies are -1.05, -0.2, 1.25, and 0.89 kcal/mol, which shows that for high accuracy calculations a direct comparison of classical barriers and activation energies is misleading.

  9. Sulfide scaling in low enthalpy geothermal environments; A survey

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

    Criaud, A.; Fouillac, C.

    1989-01-01

    A review of the sulfide scaling phenomena in low-temperature environments is presented. While high-temperature fluids tend to deposit metal sulfides because of their high concentrations of dissolved metals and variations of temperature, pressure and fluid chemistry, low temperature media are characterized by very low metal content but much higher dissolved sulfide. In the case of the goethermal wells of the Paris Basin, detailed studies demonstrate that the relatively large concentrations of chloride and dissolved sulfide are responsible for corrosion and consequent formation of iron sulfide scale composed of mackinawite, pyrite and pyrrhotite. The effects of the exploitation schemes are farmore » less important than the corrosion of the casings. The low-enthalpy fluids that do not originate from sedimentary aquifers (such as in Iceland and Bulgaria), have a limited corrosion potential, and the thin sulfide film that appears may prevent the progress of corrosion.« less

  10. An interactive computer code for calculation of gas-phase chemical equilibrium (EQLBRM)

    NASA Technical Reports Server (NTRS)

    Pratt, B. S.; Pratt, D. T.

    1984-01-01

    A user friendly, menu driven, interactive computer program known as EQLBRM which calculates the adiabatic equilibrium temperature and product composition resulting from the combustion of hydrocarbon fuels with air, at specified constant pressure and enthalpy is discussed. The program is developed primarily as an instructional tool to be run on small computers to allow the user to economically and efficiency explore the effects of varying fuel type, air/fuel ratio, inlet air and/or fuel temperature, and operating pressure on the performance of continuous combustion devices such as gas turbine combustors, Stirling engine burners, and power generation furnaces.

  11. Ab initio molecular orbital calculations on HBr - 2 Geometry, frequencies, and enthalpy changes

    NASA Astrophysics Data System (ADS)

    Ikuta, Shigeru; Saitoh, Toshikazu; Nomura, Okio

    1990-08-01

    HBr-2 has D∞h symmetry at both the second-order (MP2) and third-order (MP3) Møller-Plesset perturbation levels of theory with the extended basis sets, whereas the Hartree-Fock level of theory predicts that it has C∞v symmetry. A potential energy map is calculated with the MP2 method as a function of two parameters, i.e., the distance of two Br atoms and the displacement of H from the center of them. Two-dimensional vibration analysis is performed by using this potential energy map. The calculated ν1 is 200 cm-1 and the ν3 is 837 cm-1 in HBr-2, and those in DBr-2 are 199 and 569 cm-1, respectively. Thus the ratio of the asymmetric vibration (ν3)H/(ν3)D is 1.47, being somewhat greater than the value of √2 expected for a harmonic oscillator. The enthalpy changes (ΔH°) in the reaction of Br- with an HBr molecule are determined by both the MP3 total energy changes and the thermal energy changes between the reactants and the product. The calculated enthalpy change of -21.2 kcal/mol is in good agreement with the experimental one (-21 kcal/mol) recently observed by Caldwell and Kebarle. These calculated data on HBr-2, which will provide us with a useful guide for future measurements of gas-phase vibrational spectra, are compared with those on HCl-2 and HF-2.

  12. Second-order accurate nonoscillatory schemes for scalar conservation laws

    NASA Technical Reports Server (NTRS)

    Huynh, Hung T.

    1989-01-01

    Explicit finite difference schemes for the computation of weak solutions of nonlinear scalar conservation laws is presented and analyzed. These schemes are uniformly second-order accurate and nonoscillatory in the sense that the number of extrema of the discrete solution is not increasing in time.

  13. A general strategy for the experimental study of the thermochemistry of protic ionic liquids: enthalpy of formation and vaporisation of 1-methylimidazolium ethanoate.

    PubMed

    Vitorino, Joana; Bernardes, Carlos E S; Minas da Piedade, Manuel E

    2012-04-07

    A general strategy to determine enthalpies of formation of protic ionic liquids, based solely on enthalpy of solution measurements, was conceived and tested for 1-methylimidazolium ethanoate, leading to Δ(f)H°(m){[Hmim][O(2)CCH(3)], 1} = -(425.7 ± 1.2) kJ mol(-1). This result in conjunction with the enthalpy of formation of gaseous 1-methylimidazole (mim) proposed in this work, Δ(f)H°(m)(mim, g) = 126.5 ± 1.1 kJ mol(-1), and Δ(f)H°(m)(CH(3)COOH, g) taken from the literature, allowed the calculation of the enthalpy of the vaporisation process [Hmim][O(2)CCH(3)](l) → mim(g) + CH(3)COOH(g) as Δ(vap)H°(m){[Hmim][O(2)CCH(3)]} = 119.4 ± 3.0 kJ mol(-1). The agreement between this value and Δ(vap)H°(m){[Hmim][O(2)CCH(3)]} = 117.3 ± 0.5 kJ mol(-1), obtained for the direct vaporisation of [Hmim][O(2)CCH(3)], by Calvet-drop microcalorimetry, gives a good indication that, as previously suggested by Fourier transform ion cyclotron resonance mass spectrometry, Raman spectroscopy, and GC-MS experiments, the vaporisation of [Hmim][O(2)CCH(3)] essentially involves a proton transfer mechanism with formation of the two volatile neutral precursor molecules (mim and CH(3)COOH). Although being a low ionicity protic ionic liquid, [Hmim][O(2)CCH(3)] was chosen to validate the methodology proposed here, since its vaporisation mechanism has been unequivocally demonstrated by different methods and for different pressure ranges.

  14. Accurate computational design of multipass transmembrane proteins.

    PubMed

    Lu, Peilong; Min, Duyoung; DiMaio, Frank; Wei, Kathy Y; Vahey, Michael D; Boyken, Scott E; Chen, Zibo; Fallas, Jorge A; Ueda, George; Sheffler, William; Mulligan, Vikram Khipple; Xu, Wenqing; Bowie, James U; Baker, David

    2018-03-02

    The computational design of transmembrane proteins with more than one membrane-spanning region remains a major challenge. We report the design of transmembrane monomers, homodimers, trimers, and tetramers with 76 to 215 residue subunits containing two to four membrane-spanning regions and up to 860 total residues that adopt the target oligomerization state in detergent solution. The designed proteins localize to the plasma membrane in bacteria and in mammalian cells, and magnetic tweezer unfolding experiments in the membrane indicate that they are very stable. Crystal structures of the designed dimer and tetramer-a rocket-shaped structure with a wide cytoplasmic base that funnels into eight transmembrane helices-are very close to the design models. Our results pave the way for the design of multispan membrane proteins with new functions. Copyright © 2018 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.

  15. Funnel metadynamics as accurate binding free-energy method

    PubMed Central

    Limongelli, Vittorio; Bonomi, Massimiliano; Parrinello, Michele

    2013-01-01

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

  16. High Enthalpy Effects on Two Boundary Layer Disturbances in Supersonic and Hypersonic Flow

    DTIC Science & Technology

    2012-05-01

    Reshotko[37], and Reda[ 73 ]. These reviews discuss how a number of different flow features and geometry can affect the transition location including the...MODELS 35 The species enthalpy is defined as hs = cvsT + Ps ρs + evs + h◦s = cpsT + evs + h ◦ s, where cps is the specific heat at constant pressure of...derived from the Lewis number, which is Le = κ ρcpD , where cp and κ are based on the gas mixture. The mixture value of cp is determined using a mass

  17. Thermochemical Properties Enthalpy, Entropy, and Heat Capacity of C1-C4 Fluorinated Hydrocarbons: Fluorocarbon Group Additivity.

    PubMed

    Wang, Heng; Castillo, Álvaro; Bozzelli, Joseph W

    2015-07-23

    Enthalpies of formation for 14 C2–C4 fluorinated hydrocarbons were calculated with nine popular ab initio and density functional theory methods: B3LYP, CBS-QB3, CBS-APNO, M06, M06-2X, ωB97X, G4, G4(MP2)-6X, and W1U via several series of isodesmic reactions. The recommended ideal gas phase ΔHf298° (kcal mol(–1)) values calculated in this study are the following: −65.4 for CH3CH2F; −70.2 for CH3CH2CH2F; −75.3 for CH3CHFCH3; −75.2 for CH3CH2CH2CH2F; −80.3 for CH3CHFCH2CH3; −108.1 for CH2F2; −120.9 for CH3CHF2; −125.8 for CH3CH2CHF2; −133.3 for CH3CF2CH3; −166.7 for CHF3; −180.5 for CH3CF3; −185.5 for CH3CH2CF3; −223.2 for CF4; and −85.8 for (CH3)3CF. Entropies (S298° in cal mol(–1) K(–1)) were estimated using B3LYP/6-31+G(d,p) computed frequencies and geometries. Rotational barriers were determined and hindered internal rotational contributions for S298°, and Cp(T) were calculated using the rigid rotor harmonic oscillator approximation, with direct integration over energy levels of the intramolecular rotation potential energy curve. Thermochemical properties for the fluorinated carbon groups C/C/F/H2, C/C2/F/H, C/C/F2/H, C/C2/F2, and C/C/F3 were derived from the above target fluorocarbons. Previously published enthalpies and groups for 1,2-difluoroethane, 1,1,2-trifluoroethane, 1,1,2,2-tetrafluoroethane, 1,1,1,2-tetrafluoroethane, 1,1,1,2,2-pentafluoroethane, 2-fluoro-2-methylpropane that were previously determined via work reaction schemes are revised using updated reference species values. Standard deviations are compared for the calculation methods.

  18. Demystifying Introductory Chemistry. Part 4: An Approach to Reaction Thermodynamics through Enthalpies, Entropies, and Free Energies of Atomization.

    ERIC Educational Resources Information Center

    Spencer, James N.; And Others

    1996-01-01

    Presents an alternative approach to teaching reaction thermodynamics in introductory chemistry courses using calculations of enthalpies, entropies, and free energies of atomization. Uses a consistent concept, that of decomposition of a compound to its gaseous atoms, to discuss not only thermodynamic parameters but also equilibrium and…

  19. An implicit higher-order spatially accurate scheme for solving time dependent flows on unstructured meshes

    NASA Astrophysics Data System (ADS)

    Tomaro, Robert F.

    1998-07-01

    The present research is aimed at developing a higher-order, spatially accurate scheme for both steady and unsteady flow simulations using unstructured meshes. The resulting scheme must work on a variety of general problems to ensure the creation of a flexible, reliable and accurate aerodynamic analysis tool. To calculate the flow around complex configurations, unstructured grids and the associated flow solvers have been developed. Efficient simulations require the minimum use of computer memory and computational times. Unstructured flow solvers typically require more computer memory than a structured flow solver due to the indirect addressing of the cells. The approach taken in the present research was to modify an existing three-dimensional unstructured flow solver to first decrease the computational time required for a solution and then to increase the spatial accuracy. The terms required to simulate flow involving non-stationary grids were also implemented. First, an implicit solution algorithm was implemented to replace the existing explicit procedure. Several test cases, including internal and external, inviscid and viscous, two-dimensional, three-dimensional and axi-symmetric problems, were simulated for comparison between the explicit and implicit solution procedures. The increased efficiency and robustness of modified code due to the implicit algorithm was demonstrated. Two unsteady test cases, a plunging airfoil and a wing undergoing bending and torsion, were simulated using the implicit algorithm modified to include the terms required for a moving and/or deforming grid. Secondly, a higher than second-order spatially accurate scheme was developed and implemented into the baseline code. Third- and fourth-order spatially accurate schemes were implemented and tested. The original dissipation was modified to include higher-order terms and modified near shock waves to limit pre- and post-shock oscillations. The unsteady cases were repeated using the higher

  20. Enthalpy-Driven RNA Folding: Single-Molecule Thermodynamics of Tetraloop–Receptor Tertiary Interaction†

    PubMed Central

    Fiore, Julie L.; Kraemer, Benedikt; Koberling, Felix; Edmann, Rainer; Nesbitt, David J.

    2010-01-01

    RNA folding thermodynamics are crucial for structure prediction, which requires characterization of both enthalpic and entropic contributions of tertiary motifs to conformational stability. We explore the temperature dependence of RNA folding due to the ubiquitous GAAA tetraloop–receptor docking interaction, exploiting immobilized and freely diffusing single-molecule fluorescence resonance energy transfer (smFRET) methods. The equilibrium constant for intramolecular docking is obtained as a function of temperature (T = 21–47 °C), from which a van’t Hoff analysis yields the enthalpy (ΔH°) and entropy (ΔS°) of docking. Tetraloop–receptor docking is significantly exothermic and entropically unfavorable in 1 mM MgCl2 and 100 mM NaCl, with excellent agreement between immobilized (ΔH° = −17.4 ± 1.6 kcal/mol, and ΔS° = −56.2 ± 5.4 cal mol−1 K−1) and freely diffusing (ΔH° = −17.2 ± 1.6 kcal/mol, and ΔS° = −55.9 ± 5.2 cal mol−1 K−1) species. Kinetic heterogeneity in the tetraloop–receptor construct is unaffected over the temperature range investigated, indicating a large energy barrier for interconversion between the actively docking and nondocking subpopulations. Formation of the tetraloop–receptor interaction can account for ~60% of the ΔH° and ΔS° of P4–P6 domain folding in the Tetrahymena ribozyme, suggesting that it may act as a thermodynamic clamp for the domain. Comparison of the isolated tetraloop–receptor and other tertiary folding thermodynamics supports a theme that enthalpy- versus entropy-driven folding is determined by the number of hydrogen bonding and base stacking interactions. PMID:19186984

  1. Bayer Digester Optimization Studies using Computer Techniques

    NASA Astrophysics Data System (ADS)

    Kotte, Jan J.; Schleider, Victor H.

    Theoretically required heat transfer performance by the multistaged flash heat reclaim system of a high pressure Bayer digester unit is determined for various conditions of discharge temperature, excess flash vapor and indirect steam addition. Solution of simultaneous heat balances around the digester vessels and the heat reclaim system yields the magnitude of available heat for representation of each case on a temperature-enthalpy diagram, where graphical fit of the number of flash stages fixes the heater requirements. Both the heat balances and the trial-and-error graphical solution are adapted to solution by digital computer techniques.

  2. COTHERM: Geophysical Modeling of High Enthalpy Geothermal Systems

    NASA Astrophysics Data System (ADS)

    Grab, Melchior; Maurer, Hansruedi; Greenhalgh, Stewart

    2014-05-01

    In recent years geothermal heating and electricity generation have become an attractive alternative energy resource, especially natural high enthalpy geothermal systems such as in Iceland. However, the financial risk of installing and operating geothermal power plants is still high and more needs to be known about the geothermal processes and state of the reservoir in the subsurface. A powerful tool for probing the underground system structure is provided by geophysical techniques, which are able to detect flow paths and fracture systems without drilling. It has been amply demonstrated that small-scale features can be well imaged at shallow depths, but only gross structures can be delineated for depths of several kilometers, where most high enthalpy systems are located. Therefore a major goal of our study is to improve geophysical mapping strategies by multi-method geophysical simulations and synthetic data inversions, to better resolve structures at greater depth, characterize the reservoir and monitor any changes within it. The investigation forms part of project COTHERM - COmbined hydrological, geochemical and geophysical modeling of geoTHERMal systems - in which a holistic and synergistic approach is being adopted to achieve multidisciplinary cooperation and mutual benefit. The geophysical simulations are being performed in combination with hydrothermal fluid flow modeling and chemical fluid rock interaction modeling, to provide realistic constraints on lithology, pressure, temperature and fluid conditions of the subsurface. Two sites in Iceland have been selected for the study, Krafla and Reykjanes. As a starting point for the geophysical modeling, we seek to establish petrophysical relations, connecting rock properties and reservoir conditions with geophysical parameters such as seismic wave speed, attenuation, electrical conductivity and magnetic susceptibility with a main focus on seismic properties. Therefore, we follow a comprehensive approach involving

  3. Assessment of Aerothermal Heating Augmentation Attributed to Surface Catalysis in High Enthalpy Shock Tunnel Flows

    NASA Astrophysics Data System (ADS)

    MacLean, M.; Holden, M.

    2009-01-01

    The effect of gas/surface interaction in making CFD predictions of convective heating has been considered with application to ground tests performed in high enthalpy shock tunnels where additional heating augmentation attributable to surface recombination has been observed for nitrogen, air and carbon dioxide flows. For test articles constructed of stainless steel and aluminum, measurements have been made with several types of heat transfer instrumentation including thin- film, calorimeter, and coaxial thermocouple sensors. These experiments have been modeled by computations made with the high quality, chemically reacting, Navier- Stokes solver, DPLR and the heating results compared. Some typical cases considered include results on an axisymmetric sphere-cone, axisymmetric spherical capsule, spherical capsule at angle of attack, and two- dimensional cylinder. In nitrogen flows, cases considered show a recombination probability on the order of 10-3, which agrees with published data. In many cases in air and CO2, measurements exceeding the predicted level of convective heating have been observed which are consistent with approximately complete recombination (to O2/N2 or CO2) on the surface of the model (sometimes called a super-catalytic wall). It has been recognized that the conclusion that this behavior is tied to an excessively high degree of catalytic efficiency is dependent on the current understanding of the freestream and shock-layer state of the gas.

  4. A fourth order accurate finite difference scheme for the computation of elastic waves

    NASA Technical Reports Server (NTRS)

    Bayliss, A.; Jordan, K. E.; Lemesurier, B. J.; Turkel, E.

    1986-01-01

    A finite difference for elastic waves is introduced. The model is based on the first order system of equations for the velocities and stresses. The differencing is fourth order accurate on the spatial derivatives and second order accurate in time. The model is tested on a series of examples including the Lamb problem, scattering from plane interf aces and scattering from a fluid-elastic interface. The scheme is shown to be effective for these problems. The accuracy and stability is insensitive to the Poisson ratio. For the class of problems considered here it is found that the fourth order scheme requires for two-thirds to one-half the resolution of a typical second order scheme to give comparable accuracy.

  5. Computational Aerothermodynamic Assessment of Space Shuttle Orbiter Tile Damage: Open Cavities

    NASA Technical Reports Server (NTRS)

    Pulsonetti, Maria; Wood, William

    2005-01-01

    Computational aerothermodynamic simulations of Orbiter windside tile damage in flight were performed in support of the Space Shuttle Return-to-Flight effort. The simulations were performed for both hypervelocity flight and low-enthalpy wind tunnel conditions and contributed to the Return-to-Flight program by providing information to support a variety of damage scenario analyses. Computations at flight conditions were performed at or very near the peak heating trajectory point for multiple damage scenarios involving damage windside acreage reaction cured glass (RCG) coated silica tile(s). The cavities formed by the missing tile examined in this study were relatively short leading to flow features which indicated open cavity behavior. Results of the computations indicated elevated heating bump factor levels predicted for flight over the predictions for wind tunnel conditions. The peak heating bump factors, defined as the local heating to a reference value upstream of the cavity, on the cavity floor for flight simulation were 67% larger than the peak wind tunnel simulation value. On the downstream face of the cavity the flight simulation values were 60% larger than the wind tunnel simulation values. On the outer mold line (OML) downstream of the cavity, the flight values are about 20% larger than the wind tunnel simulation values. The higher heating bump factors observed in the flight simulations were due to the larger driving potential in terms of energy entering the cavity for the flight simulations. This is evidenced by the larger rate of increase in the total enthalpy through the boundary layer prior to the cavity for the flight simulation.

  6. Energy and enthalpy distribution functions for a few physical systems.

    PubMed

    Wu, K L; Wei, J H; Lai, S K; Okabe, Y

    2007-08-02

    The present work is devoted to extracting the energy or enthalpy distribution function of a physical system from the moments of the distribution using the maximum entropy method. This distribution theory has the salient traits that it utilizes only the experimental thermodynamic data. The calculated distribution functions provide invaluable insight into the state or phase behavior of the physical systems under study. As concrete evidence, we demonstrate the elegance of the distribution theory by studying first a test case of a two-dimensional six-state Potts model for which simulation results are available for comparison, then the biphasic behavior of the binary alloy Na-K whose excess heat capacity, experimentally observed to fall in a narrow temperature range, has yet to be clarified theoretically, and finally, the thermally induced state behavior of a collection of 16 proteins.

  7. Time-Accurate Solutions of Incompressible Navier-Stokes Equations for Potential Turbopump Applications

    NASA Technical Reports Server (NTRS)

    Kiris, Cetin; Kwak, Dochan

    2001-01-01

    Two numerical procedures, one based on artificial compressibility method and the other pressure projection method, are outlined for obtaining time-accurate solutions of the incompressible Navier-Stokes equations. The performance of the two method are compared by obtaining unsteady solutions for the evolution of twin vortices behind a at plate. Calculated results are compared with experimental and other numerical results. For an un- steady ow which requires small physical time step, pressure projection method was found to be computationally efficient since it does not require any subiterations procedure. It was observed that the artificial compressibility method requires a fast convergence scheme at each physical time step in order to satisfy incompressibility condition. This was obtained by using a GMRES-ILU(0) solver in our computations. When a line-relaxation scheme was used, the time accuracy was degraded and time-accurate computations became very expensive.

  8. Determining the Enthalpy of Vaporization of Salt Solutions Using the Cooling Effect of a Bubble Column Evaporator

    ERIC Educational Resources Information Center

    Fan, Chao; Pashley, Richard M.

    2016-01-01

    The enthalpy of vaporization (?H[subscript vap]) of salt solutions is not easily measured, as a certain quantity of pure water has to be evaporated from a solution, at constant composition, and at a fixed temperature and pressure; then the corresponding heat input has to be measured. However, a simple bubble column evaporator (BCE) was used as a…

  9. Enthalpies of formation of CaAl4O7 and CaAl12O19 (hibonite) by high temperature, alkali borate solution calorimetry

    NASA Technical Reports Server (NTRS)

    Geiger, C. A.; Kleppa, O. J.; Grossman, L.; Mysen, B. O.; Lattimer, J. M.

    1988-01-01

    Enthalpies of formation were determined for two calcium aluminate phases, CaAl4O7 and CaAl12O19, using high-temperature alkali borate solution calorimetry. The aluminates were synthesized by multiple-cycle heating and grinding stoichiometric mixtures of CaCO3 and Al2O3, and the products were characteized by X-ray diffraction and SEM microbeam analysis. The data on impurities (CaAl4O7 was found to be about 89.00 percent pure by weight and the CaAl12O19 samples about 91.48 percent pure) were used to correct the heat of solution values of the synthetic products. The enthalpies of formation, at 1063 K, from oxides, were found to be equal to -(25.6 + or - 4.7) kJ/g.f.w. for CaAl4O7 and -(33.0 + or - 9.7) kJ/g.f.w. for CaAl12O19; the respective standard enthalpies of formation from elements, at 298 K, were estimated to be -4007 + or - 5.2 kJ/g.f.w. and -10,722 + or - 12 kJ/g.f.w.

  10. Transpiration and film cooling boundary layer computer program. Volume 2: Computer program and user's manual

    NASA Technical Reports Server (NTRS)

    Gloss, R. J.

    1971-01-01

    A finite difference turbulent boundary layer computer program which allows for mass transfer wall cooling and equilibrium chemistry effects is presented. The program is capable of calculating laminar or turbulent boundary layer solutions for an arbitrary ideal gas or an equilibrium hydrogen oxygen system. Either two dimensional or axisymmetric geometric configurations may be considered. The equations are solved, in nondimension-alized physical coordinates, using the implicit Crank-Nicolson technique. The finite difference forms of the conservation of mass, momentum, total enthalpy and elements equations are linearized and uncoupled, thereby generating easily solvable tridiagonal sets of algebraic equations. A detailed description of the computer program, as well as a program user's manual is provided. Detailed descriptions of all boundary layer subroutines are included, as well as a section defining all program symbols of principal importance. Instructions are then given for preparing card input to the program and for interpreting the printed output. Finally, two sample cases are included to illustrate the use of the program.

  11. Accurate Bit Error Rate Calculation for Asynchronous Chaos-Based DS-CDMA over Multipath Channel

    NASA Astrophysics Data System (ADS)

    Kaddoum, Georges; Roviras, Daniel; Chargé, Pascal; Fournier-Prunaret, Daniele

    2009-12-01

    An accurate approach to compute the bit error rate expression for multiuser chaosbased DS-CDMA system is presented in this paper. For more realistic communication system a slow fading multipath channel is considered. A simple RAKE receiver structure is considered. Based on the bit energy distribution, this approach compared to others computation methods existing in literature gives accurate results with low computation charge. Perfect estimation of the channel coefficients with the associated delays and chaos synchronization is assumed. The bit error rate is derived in terms of the bit energy distribution, the number of paths, the noise variance, and the number of users. Results are illustrated by theoretical calculations and numerical simulations which point out the accuracy of our approach.

  12. Heat flux and shock shape measurements on an Aeroassist Flight Experiment model in a high enthalpy free piston shock tunnel

    NASA Technical Reports Server (NTRS)

    Gai, S. L.; Mudford, N. R.; Hackett, C.

    1992-01-01

    This paper describes measurements of heat flux and shock shapes made on a 2.08 percent scale model of the proposed Aeroassist Flight Experiment model in a high enthalpy free piston shock tunnel T3 at the Australian National University in Canberra, Australia. The enthalpy and Reynolds number range covered were 7.5 MJ/kg to 20 MJ/kg and 150,000 to 270,000 per meter respectively. The test Mach number varied between 7.5 and 8. Two test gases, air and nitrogen, were used and the model angle of attack varied from -10 deg to +10 deg to the free stream. The results are discussed and compared to the Mach 10 cold hypersonic air data as obtained in the Langley 31 inch Mach 10 Facility as well as the perfect gas CFD calculations of NASA LaRC.

  13. Enthalpy-Entropy Compensation in the Binding of Modulators at Ionotropic Glutamate Receptor GluA2.

    PubMed

    Krintel, Christian; Francotte, Pierre; Pickering, Darryl S; Juknaitė, Lina; Pøhlsgaard, Jacob; Olsen, Lars; Frydenvang, Karla; Goffin, Eric; Pirotte, Bernard; Kastrup, Jette S

    2016-06-07

    The 1,2,4-benzothiadiazine 1,1-dioxide type of positive allosteric modulators of the ionotropic glutamate receptor A2 (GluA2) are promising lead compounds for the treatment of cognitive disorders, e.g., Alzheimer's disease. The modulators bind in a cleft formed by the interface of two neighboring ligand binding domains and act by stabilizing the agonist-bound open-channel conformation. The driving forces behind the binding of these modulators can be significantly altered with only minor substitutions to the parent molecules. In this study, we show that changing the 7-fluorine substituent of modulators BPAM97 (2) and BPAM344 (3) into a hydroxyl group (BPAM557 (4) and BPAM521 (5), respectively), leads to a more favorable binding enthalpy (ΔH, kcal/mol) from -4.9 (2) and -7.5 (3) to -6.2 (4) and -14.5 (5), but also a less favorable binding entropy (-TΔS, kcal/mol) from -2.3 (2) and -1.3 (3) to -0.5 (4) and 4.8 (5). Thus, the dissociation constants (Kd, μM) of 4 (11.2) and 5 (0.16) are similar to those of 2 (5.6) and 3 (0.35). Functionally, 4 and 5 potentiated responses of 10 μM L-glutamate at homomeric rat GluA2(Q)i receptors with EC50 values of 67.3 and 2.45 μM, respectively. The binding mode of 5 was examined with x-ray crystallography, showing that the only change compared to that of earlier compounds was the orientation of Ser-497 pointing toward the hydroxyl group of 5. The favorable enthalpy can be explained by the formation of a hydrogen bond from the side-chain hydroxyl group of Ser-497 to the hydroxyl group of 5, whereas the unfavorable entropy might be due to desolvation effects combined with a conformational restriction of Ser-497 and 5. In summary, this study shows a remarkable example of enthalpy-entropy compensation in drug development accompanied with a likely explanation of the underlying structural mechanism. Copyright © 2016 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  14. Computational Chemistry-Based Enthalpy-of-Formation, Enthalpy-of-Vaporization, and Enthalpy-of-Sublimation Predictions for Azide-Functionalized Compounds

    DTIC Science & Technology

    2006-04-01

    93.0g 92.8 102.8 Benzene+HN3 → Azidobenzene+H2 Azidomethylbenzene 99.5f 93.0 102.0 Methylbenzene+HN3 → Azidomethylbenzene+H2 2 -Azido- 2 - phenylpropane ...87.4d 73.5 86.4 2 - Phenylpropane +HN3 → 2 -Azido- 2 - phenylpropane +H2 Azidocyclopentane 52.8h 58.4 67.0 Cyclopentane+HN3 → Azidocyclopentane+H2...experimentally derived results for “higher homologous azides” (1-azidoadamantane, 3-azido-3-ethylpentane and 2 -azido- 2 - phenylpropane ) (Wayne et al., 1993

  15. Measuring Enthalpy of Sublimation of Volatiles by Means of Piezoelectric Crystal Microbalances

    NASA Astrophysics Data System (ADS)

    Dirri, Fabrizio; Palomba, Ernesto; Longobardo, Andrea; Zampetti, Emiliano

    2017-12-01

    Piezoelectric Crystal Microbalances (PCM's) are widely used to study the chemical processes involving volatile compounds in any environment, such as condensation process. Since PCM's are miniaturized sensor, they are very suitable for planetary in situ missions, where can be used to detect and to measure the mass amount of astrobiologically significant compounds, such as water and organics. This work focuses on the realization and testing of a new experimental setup, able to characterize volatiles which can be found in a planetary environment. In particular the enthalpy of sublimation of some dicarboxylic acids has been measured. The importance of dicarboxylic acids in planetology and astrobiology is due to the fact that they have been detected in carbonaceous chondritic material (e.g. Murchinson), among the most pristine material present in our Solar System. In this work, a sample of acid was heated in an effusion cell up to its sublimation. For a set of temperatures (from 30 °C to 75 °C), the deposition rate on the PCM surface has been measured. From these measurements, it has been possible to infer the enthalpy of sublimation of Adipic acid, i.e. ΔH = 141.6 ± 0.8 kJ/mol and Succinic acid, i.e. ΔH = 113.3 ± 1.3 kJ/mol. This technique has so demonstrated to be a good choice to recognise a single compound or a mixture (with an analysis upstream) even if some improvements concerning the thermal stabilization of the system will be implemented in order to enhance the results' accuracy. The experiment has been performed in support of the VISTA (Volatile In Situ Thermogravimetry Analyzer) project, which is included in the scientific payload of the ESA MarcoPolo-R mission study.

  16. A combined calorimetric and computational study of the energetics of rare earth substituted UO 2 systems

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

    Zhang, Lei; Solomon, Jonathan M.; Asta, Mark

    2015-09-01

    The energetics of rare earth substituted UO2 solid solutions (U1-xLnxO2-0.5x+y, where Ln = La, Y, and Nd) are investigated employing a combination of calorimetric measurements and density functional theory based computations. Calculated and measured formation enthalpies agree within 10 kJ/mol for stoichiometric oxygen/metal compositions. To better understand the factors governing the stability and defect binding in rare earth substituted urania solid solutions, systematic trends in the energetics are investigated based on the present results and previous computational and experimental thermochemical studies of rare earth substituted fluorite oxides (A1-xLnxO2-0.5x, where A = Hf, Zr, Ce, and Th). A consistent trend towardsmore » increased energetic stability with larger size mismatch between the smaller host tetravalent cation and the larger rare earth trivalent cation is found for both actinide and non-actinide fluorite oxide systems where aliovalent substitution of Ln cations is compensated by oxygen vacancies. However, the large exothermic oxidation enthalpy in the UO2 based systems favors oxygen rich compositions where charge compensation occurs through the formation of uranium cations with higher oxidation states.« less

  17. Application of enthalpy model for floating zone silicon crystal growth

    NASA Astrophysics Data System (ADS)

    Krauze, A.; Bergfelds, K.; Virbulis, J.

    2017-09-01

    A 2D simplified crystal growth model based on the enthalpy method and coupled with a low-frequency harmonic electromagnetic model is developed to simulate the silicon crystal growth near the external triple point (ETP) and crystal melting on the open melting front of a polycrystalline feed rod in FZ crystal growth systems. Simulations of the crystal growth near the ETP show significant influence of the inhomogeneities of the EM power distribution on the crystal growth rate for a 4 in floating zone (FZ) system. The generated growth rate fluctuations are shown to be larger in the system with higher crystal pull rate. Simulations of crystal melting on the open melting front of the polycrystalline rod show the development of melt-filled grooves at the open melting front surface. The distance between the grooves is shown to grow with the increase of the skin-layer depth in the solid material.

  18. Oxygen migration enthalpy likely limits oxide precipitate dissolution during tabula rasa

    NASA Astrophysics Data System (ADS)

    Looney, E. E.; Laine, H. S.; Youssef, A.; Jensen, M. A.; LaSalvia, V.; Stradins, P.; Buonassisi, T.

    2017-09-01

    In industrial silicon solar cells, oxygen-related defects lower device efficiencies by up to 20% (rel.). In order to mitigate these defects, a high-temperature homogenization anneal called tabula rasa (TR) that has been used in the electronics industry is now proposed for use in solar-grade wafers. This work addresses the kinetics of tabula rasa by elucidating the activation energy governing oxide precipitate dissolution, which is found to be 2.6 ± 0.5 eV. This value is consistent within uncertainty to the migration enthalpy of oxygen interstitials in silicon, implying TR to be kinetically limited by oxygen point-defect diffusion. This large activation energy is observed to limit oxygen precipitate dissolution during standard TR conditions, suggesting that more aggressive annealing conditions than conventionally used are required for complete bulk microdefect mitigation.

  19. Creation of an idealized nasopharynx geometry for accurate computational fluid dynamics simulations of nasal airflow in patient-specific models lacking the nasopharynx anatomy

    PubMed Central

    Borojeni, Azadeh A.T.; Frank-Ito, Dennis O.; Kimbell, Julia S.; Rhee, John S.; Garcia, Guilherme J. M.

    2016-01-01

    Virtual surgery planning based on computational fluid dynamics (CFD) simulations has the potential to improve surgical outcomes for nasal airway obstruction (NAO) patients, but the benefits of virtual surgery planning must outweigh the risks of radiation exposure. Cone beam computed tomography (CBCT) scans represent an attractive imaging modality for virtual surgery planning due to lower costs and lower radiation exposures compared with conventional CT scans. However, to minimize the radiation exposure, the CBCT sinusitis protocol sometimes images only the nasal cavity, excluding the nasopharynx. The goal of this study was to develop an idealized nasopharynx geometry for accurate representation of outlet boundary conditions when the nasopharynx geometry is unavailable. Anatomically-accurate models of the nasopharynx created from thirty CT scans were intersected with planes rotated at different angles to obtain an average geometry. Cross sections of the idealized nasopharynx were approximated as ellipses with cross-sectional areas and aspect ratios equal to the average in the actual patient-specific models. CFD simulations were performed to investigate whether nasal airflow patterns were affected when the CT-based nasopharynx was replaced by the idealized nasopharynx in 10 NAO patients. Despite the simple form of the idealized geometry, all biophysical variables (nasal resistance, airflow rate, and heat fluxes) were very similar in the idealized vs. patient-specific models. The results confirmed the expectation that the nasopharynx geometry has a minimal effect in the nasal airflow patterns during inspiration. The idealized nasopharynx geometry will be useful in future CFD studies of nasal airflow based on medical images that exclude the nasopharynx. PMID:27525807

  20. Application of an enthalpy balance model of the relation between growth and respiration to temperature acclimation of Eucalyptus globulus seedlings.

    PubMed Central

    Macfarlane, Craig; Adams, Mark A; Hansen, Lee D

    2002-01-01

    The enthalpy balance model of growth uses measurements of the rates of heat and CO(2) production to quantify rates of decarboxylation, oxidative phosphorylation and net anabolism. Enthalpy conversion efficiency (eta(H)) and the net rate of conservation of enthalpy in reduced biosynthetic products (R(SG)DeltaH(B)) can be calculated from metabolic heat rate (q) and CO(2) rate (R(CO2)). eta(H) is closely related to carbon conversion efficiency and the efficiency of conservation of available electrons in biosynthetic products. R(SG)DeltaH(B) and eta(H) can be used, together with biomass composition, to describe the rate and efficiency of growth of plant tissues. q is directly related to the rate of O(2) consumption and the ratio q:R(CO2) is inversely related to the respiratory quotient. We grew seedlings of Eucalyptus globulus at 16 and 28 degrees C for four to six weeks, then measured q and R(CO2) using isothermal calorimetry. Respiratory rate at a given temperature was increased by a lower growth temperature but eta(H) was unaffected. Enthalpy conversion efficiency - and, therefore, carbon conversion efficiency - decreased with increasing temperature from 15 to 35 degrees C. The ratio of oxidative phosphorylation to oxygen consumption (P/O ratio) was inferred in vivo from eta(H) and by assuming a constant ratio of growth to maintenance respiration with changing temperature. The P/O ratio decreased from 2.1 at 10-15 degrees C to less than 0.3 at 35 degrees C, suggesting that decreased efficiency was not only due to activity of the alternative oxidase pathway. In agreement with predictions from non-equilibrium thermodynamics, growth rate was maximal near 25 degrees C, where the calculated P/O ratio was about half maximum. We propose that less efficient pathways, such as the alternative oxidase pathway, are necessary to satisfy the condition of conductance matching whilst maintaining a near constant phosphorylation potential. These conditions minimize entropy production

  1. FASTSIM2: a second-order accurate frictional rolling contact algorithm

    NASA Astrophysics Data System (ADS)

    Vollebregt, E. A. H.; Wilders, P.

    2011-01-01

    In this paper we consider the frictional (tangential) steady rolling contact problem. We confine ourselves to the simplified theory, instead of using full elastostatic theory, in order to be able to compute results fast, as needed for on-line application in vehicle system dynamics simulation packages. The FASTSIM algorithm is the leading technology in this field and is employed in all dominant railway vehicle system dynamics packages (VSD) in the world. The main contribution of this paper is a new version "FASTSIM2" of the FASTSIM algorithm, which is second-order accurate. This is relevant for VSD, because with the new algorithm 16 times less grid points are required for sufficiently accurate computations of the contact forces. The approach is based on new insights in the characteristics of the rolling contact problem when using the simplified theory, and on taking precise care of the contact conditions in the numerical integration scheme employed.

  2. Accurate evaluation of exchange fields in finite element micromagnetic solvers

    NASA Astrophysics Data System (ADS)

    Chang, R.; Escobar, M. A.; Li, S.; Lubarda, M. V.; Lomakin, V.

    2012-04-01

    Quadratic basis functions (QBFs) are implemented for solving the Landau-Lifshitz-Gilbert equation via the finite element method. This involves the introduction of a set of special testing functions compatible with the QBFs for evaluating the Laplacian operator. The results by using QBFs are significantly more accurate than those via linear basis functions. QBF approach leads to significantly more accurate results than conventionally used approaches based on linear basis functions. Importantly QBFs allow reducing the error of computing the exchange field by increasing the mesh density for structured and unstructured meshes. Numerical examples demonstrate the feasibility of the method.

  3. Automated particle correspondence and accurate tilt-axis detection in tilted-image pairs

    DOE PAGES

    Shatsky, Maxim; Arbelaez, Pablo; Han, Bong-Gyoon; ...

    2014-07-01

    Tilted electron microscope images are routinely collected for an ab initio structure reconstruction as a part of the Random Conical Tilt (RCT) or Orthogonal Tilt Reconstruction (OTR) methods, as well as for various applications using the "free-hand" procedure. These procedures all require identification of particle pairs in two corresponding images as well as accurate estimation of the tilt-axis used to rotate the electron microscope (EM) grid. Here we present a computational approach, PCT (particle correspondence from tilted pairs), based on tilt-invariant context and projection matching that addresses both problems. The method benefits from treating the two problems as a singlemore » optimization task. It automatically finds corresponding particle pairs and accurately computes tilt-axis direction even in the cases when EM grid is not perfectly planar.« less

  4. A convenient and accurate parallel Input/Output USB device for E-Prime.

    PubMed

    Canto, Rosario; Bufalari, Ilaria; D'Ausilio, Alessandro

    2011-03-01

    Psychological and neurophysiological experiments require the accurate control of timing and synchrony for Input/Output signals. For instance, a typical Event-Related Potential (ERP) study requires an extremely accurate synchronization of stimulus delivery with recordings. This is typically done via computer software such as E-Prime, and fast communications are typically assured by the Parallel Port (PP). However, the PP is an old and disappearing technology that, for example, is no longer available on portable computers. Here we propose a convenient USB device enabling parallel I/O capabilities. We tested this device against the PP on both a desktop and a laptop machine in different stress tests. Our data demonstrate the accuracy of our system, which suggests that it may be a good substitute for the PP with E-Prime.

  5. The ground states of iron(III) porphines: role of entropy-enthalpy compensation, Fermi correlation, dispersion, and zero-point energies.

    PubMed

    Kepp, Kasper P

    2011-10-01

    Porphyrins are much studied due to their biochemical relevance and many applications. The density functional TPSSh has previously accurately described the energy of close-lying electronic states of transition metal systems such as porphyrins. However, a recent study questioned this conclusion based on calculations of five iron(III) porphines. Here, we compute the geometries of 80 different electronic configurations and the free energies of the most stable configurations with the functionals TPSSh, TPSS, and B3LYP. Zero-point energies and entropy favor high-spin by ~4kJ/mol and 0-10kJ/mol, respectively. When these effects are included, and all electronic configurations are evaluated, TPSSh correctly predicts the spin of all the four difficult phenylporphine cases and is within the lower bound of uncertainty of any known theoretical method for the fifth, iron(III) chloroporphine. Dispersion computed with DFT-D3 favors low-spin by 3-53kJ/mol (TPSSh) or 4-15kJ/mol (B3LYP) due to the attractive r(-6) term and the shorter distances in low-spin. The very large and diverse corrections from TPSS and TPSSh seem less consistent with the similarity of the systems than when calculated from B3LYP. If the functional-specific corrections are used, B3LYP and TPSSh are of equal accuracy, and TPSS is much worse, whereas if the physically reasonable B3LYP-computed dispersion effect is used for all functionals, TPSSh is accurate for all systems. B3LYP is significantly more accurate when dispersion is added, confirming previous results. Copyright © 2011 Elsevier Inc. All rights reserved.

  6. Third-order accurate conservative method on unstructured meshes for gasdynamic simulations

    NASA Astrophysics Data System (ADS)

    Shirobokov, D. A.

    2017-04-01

    A third-order accurate finite-volume method on unstructured meshes is proposed for solving viscous gasdynamic problems. The method is described as applied to the advection equation. The accuracy of the method is verified by computing the evolution of a vortex on meshes of various degrees of detail with variously shaped cells. Additionally, unsteady flows around a cylinder and a symmetric airfoil are computed. The numerical results are presented in the form of plots and tables.

  7. Effect of the composition of a solution on the enthalpies of solvation of piperidine in methanol-acetonitrile and dimethylsulfoxide-acetonitrile mixed solvents

    NASA Astrophysics Data System (ADS)

    Kuz'mina, I. A.; Volkova, M. A.; Sitnikova, K. A.; Sharnin, V. A.

    2014-01-01

    Heat effects of dissolution of piperidine (ppd) are measured by calorimetry at 298.15 K over the range of composition of acetonitrile-methanol (AN-MeOH) mixed solvents. Based on the Δsol H ○(ppd)AN-MeOH values obtained using the literature data on Δsol H ○ (ppd) in acetonitrile-dimethylsulfoxide (AN-DMSO) mixed solvents and the vaporization enthalpy of ppd, the enthalpies of solvation of amine in AN-MeOH and AN-DMSO binary mixtures are calculated. A rise in the exothermicity of solvation of piperidine is observed upon the transition from AN to DMSO and MeOH, due mainly to the enhanced solvation of the amino group of ppd as a result of changes in the acid-base properties of the mixed solvent.

  8. An elegant access to formation and vaporization enthalpies of ionic liquids by indirect DSC experiment and "in silico" calculations.

    PubMed

    Verevkin, Sergey P; Zaitsau, Dzmitry H; Emel'yanenko, Vladimir N; Schick, Christoph; Jayaraman, Saivenkataraman; Maginn, Edward J

    2012-07-14

    We used DSC for determination of the reaction enthalpy of the synthesis of the ionic liquid [C(4)mim][Cl]. A combination of DSC and quantum chemical calculations presents a new, indirect way to study thermodynamics of ionic liquids. The new procedure was validated with two direct experimental measurements and MD simulations.

  9. Enhancing Entropy and Enthalpy Fluctuations to Drive Crystallization in Atomistic Simulations.

    PubMed

    Piaggi, Pablo M; Valsson, Omar; Parrinello, Michele

    2017-07-07

    Crystallization is a process of great practical relevance in which rare but crucial fluctuations lead to the formation of a solid phase starting from the liquid. As in all first order first transitions, there is an interplay between enthalpy and entropy. Based on this idea, in order to drive crystallization in molecular simulations, we introduce two collective variables, one enthalpic and the other entropic. Defined in this way, these collective variables do not prejudge the structure into which the system is going to crystallize. We show the usefulness of this approach by studying the cases of sodium and aluminum that crystallize in the bcc and fcc crystalline structures, respectively. Using these two generic collective variables, we perform variationally enhanced sampling and well tempered metadynamics simulations and find that the systems transform spontaneously and reversibly between the liquid and the solid phases.

  10. Oxygen migration enthalpy likely limits oxide precipitate dissolution during tabula rasa

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

    Looney, E. E.; Laine, H. S.; Youssef, A.

    In industrial silicon solar cells, oxygen-related defects lower device efficiencies by up to 20% (rel.). In order to mitigate these defects, a high-temperature homogenization anneal called tabula rasa (TR) that has been used in the electronics industry is now proposed for use in solar-grade wafers. This work addresses the kinetics of tabula rasa by elucidating the activation energy governing oxide precipitate dissolution, which is found to be 2.6 +/- 0.5 eV. This value is consistent within uncertainty to the migration enthalpy of oxygen interstitials in silicon, implying TR to be kinetically limited by oxygen point-defect diffusion. This large activation energymore » is observed to limit oxygen precipitate dissolution during standard TR conditions, suggesting that more aggressive annealing conditions than conventionally used are required for complete bulk microdefect mitigation.« less

  11. A unified momentum equation approach for computing thermal residual stresses during melting and solidification

    NASA Astrophysics Data System (ADS)

    Yeo, Haram; Ki, Hyungson

    2018-03-01

    In this article, we present a novel numerical method for computing thermal residual stresses from a viewpoint of fluid-structure interaction (FSI). In a thermal processing of a material, residual stresses are developed as the material undergoes melting and solidification, and liquid, solid, and a mixture of liquid and solid (or mushy state) coexist and interact with each other during the process. In order to accurately account for the stress development during phase changes, we derived a unified momentum equation from the momentum equations of incompressible fluids and elastoplastic solids. In this approach, the whole fluid-structure system is treated as a single continuum, and the interaction between fluid and solid phases across the mushy zone is naturally taken into account in a monolithic way. For thermal analysis, an enthalpy-based method was employed. As a numerical example, a two-dimensional laser heating problem was considered, where a carbon steel sheet was heated by a Gaussian laser beam. Momentum and energy equations were discretized on a uniform Cartesian grid in a finite volume framework, and temperature-dependent material properties were used. The austenite-martensite phase transformation of carbon steel was also considered. In this study, the effects of solid strains, fluid flow, mushy zone size, and laser heating time on residual stress formation were investigated.

  12. Time-Accurate, Unstructured-Mesh Navier-Stokes Computations with the Space-Time CESE Method

    NASA Technical Reports Server (NTRS)

    Chang, Chau-Lyan

    2006-01-01

    Application of the newly emerged space-time conservation element solution element (CESE) method to compressible Navier-Stokes equations is studied. In contrast to Euler equations solvers, several issues such as boundary conditions, numerical dissipation, and grid stiffness warrant systematic investigations and validations. Non-reflecting boundary conditions applied at the truncated boundary are also investigated from the stand point of acoustic wave propagation. Validations of the numerical solutions are performed by comparing with exact solutions for steady-state as well as time-accurate viscous flow problems. The test cases cover a broad speed regime for problems ranging from acoustic wave propagation to 3D hypersonic configurations. Model problems pertinent to hypersonic configurations demonstrate the effectiveness of the CESE method in treating flows with shocks, unsteady waves, and separations. Good agreement with exact solutions suggests that the space-time CESE method provides a viable alternative for time-accurate Navier-Stokes calculations of a broad range of problems.

  13. Fractional labelmaps for computing accurate dose volume histograms

    NASA Astrophysics Data System (ADS)

    Sunderland, Kyle; Pinter, Csaba; Lasso, Andras; Fichtinger, Gabor

    2017-03-01

    PURPOSE: In radiation therapy treatment planning systems, structures are represented as parallel 2D contours. For treatment planning algorithms, structures must be converted into labelmap (i.e. 3D image denoting structure inside/outside) representations. This is often done by triangulated a surface from contours, which is converted into a binary labelmap. This surface to binary labelmap conversion can cause large errors in small structures. Binary labelmaps are often represented using one byte per voxel, meaning a large amount of memory is unused. Our goal is to develop a fractional labelmap representation containing non-binary values, allowing more information to be stored in the same amount of memory. METHODS: We implemented an algorithm in 3D Slicer, which converts surfaces to fractional labelmaps by creating 216 binary labelmaps, changing the labelmap origin on each iteration. The binary labelmap values are summed to create the fractional labelmap. In addition, an algorithm is implemented in the SlicerRT toolkit that calculates dose volume histograms (DVH) using fractional labelmaps. RESULTS: We found that with manually segmented RANDO head and neck structures, fractional labelmaps represented structure volume up to 19.07% (average 6.81%) more accurately than binary labelmaps, while occupying the same amount of memory. When compared to baseline DVH from treatment planning software, DVH from fractional labelmaps had agreement acceptance percent (1% ΔD, 1% ΔV) up to 57.46% higher (average 4.33%) than DVH from binary labelmaps. CONCLUSION: Fractional labelmaps promise to be an effective method for structure representation, allowing considerably more information to be stored in the same amount of memory.

  14. How to compute isomerization energies of organic molecules with quantum chemical methods.

    PubMed

    Grimme, Stefan; Steinmetz, Marc; Korth, Martin

    2007-03-16

    The reaction energies for 34 typical organic isomerizations including oxygen and nitrogen heteroatoms are investigated with modern quantum chemical methods that have the perspective of also being applicable to large systems. The experimental reaction enthalpies are corrected for vibrational and thermal effects, and the thus derived "experimental" reaction energies are compared to corresponding theoretical data. A series of standard AO basis sets in combination with second-order perturbation theory (MP2, SCS-MP2), conventional density functionals (e.g., PBE, TPSS, B3-LYP, MPW1K, BMK), and new perturbative functionals (B2-PLYP, mPW2-PLYP) are tested. In three cases, obvious errors of the experimental values could be detected, and accurate coupled-cluster [CCSD(T)] reference values have been used instead. It is found that only triple-zeta quality AO basis sets provide results close enough to the basis set limit and that sets like the popular 6-31G(d) should be avoided in accurate work. Augmentation of small basis sets with diffuse functions has a notable effect in B3-LYP calculations that is attributed to intramolecular basis set superposition error and covers basic deficiencies of the functional. The new methods based on perturbation theory (SCS-MP2, X2-PLYP) are found to be clearly superior to many other approaches; that is, they provide mean absolute deviations of less than 1.2 kcal mol-1 and only a few (<10%) outliers. The best performance in the group of conventional functionals is found for the highly parametrized BMK hybrid meta-GGA. Contrary to accepted opinion, hybrid density functionals offer no real advantage over simple GGAs. For reasonably large AO basis sets, results of poor quality are obtained with the popular B3-LYP functional that cannot be recommended for thermochemical applications in organic chemistry. The results of this study are complementary to often used benchmarks based on atomization energies and should guide chemists in their search for

  15. Possible Computer Vision Systems and Automated or Computer-Aided Edging and Trimming

    Treesearch

    Philip A. Araman

    1990-01-01

    This paper discusses research which is underway to help our industry reduce costs, increase product volume and value recovery, and market more accurately graded and described products. The research is part of a team effort to help the hardwood sawmill industry automate with computer vision systems, and computer-aided or computer controlled processing. This paper...

  16. Vapour pressure and standard enthalpy of sublimation of KBF 4 by a TG based transpiration technique

    NASA Astrophysics Data System (ADS)

    Pankajavalli, R.; Ananthasivan, K.; Anthonysamy, S.; Vasudeva Rao, P. R.

    2005-10-01

    A horizontal thermobalance was adapted as a transpiration apparatus for the measurement of the vapour pressure of KBF4 (s). Attainment of equilibrium was ascertained by the invariance of the measured values of the vapour pressures over a range of flows under isothermal conditions. Measured values of the vapour pressures could be represented by the least-squares expressions: log (p/Pa) = 8.16(±0.01) - 4892(±248)/T(K)(538-560 K), log (p/Pa) = 6.85(±0.06) - 4158(±240)/T(K) (576-660 K), which correspond to the equilibria of orthorhombic and cubic KBF4 vapours, respectively. From these expressions the temperature of transformation of the orthorhombic to the cubic phase was identified to be 561 K. From the slopes of the above equations, the enthalpies of sublimation of the orthorhombic and cubic phases were found to be (93.7 ± 4.7) and (79.6 ± 4.6) kJ mol-1, respectively. These values differ by 14.1 kJ mol-1 which could be ascribed to the enthalpy of the orthorhombic to cubic phase transition of KBF4. Third-law analysis of the vapour pressure data yielded a value of (104.6 ± 1.0) kJ mol-1 for Δ Hsubo of KBF4 (s) at 298.15 K.

  17. On the accurate estimation of gap fraction during daytime with digital cover photography

    NASA Astrophysics Data System (ADS)

    Hwang, Y. R.; Ryu, Y.; Kimm, H.; Macfarlane, C.; Lang, M.; Sonnentag, O.

    2015-12-01

    Digital cover photography (DCP) has emerged as an indirect method to obtain gap fraction accurately. Thus far, however, the intervention of subjectivity, such as determining the camera relative exposure value (REV) and threshold in the histogram, hindered computing accurate gap fraction. Here we propose a novel method that enables us to measure gap fraction accurately during daytime under various sky conditions by DCP. The novel method computes gap fraction using a single DCP unsaturated raw image which is corrected for scattering effects by canopies and a reconstructed sky image from the raw format image. To test the sensitivity of the novel method derived gap fraction to diverse REVs, solar zenith angles and canopy structures, we took photos in one hour interval between sunrise to midday under dense and sparse canopies with REV 0 to -5. The novel method showed little variation of gap fraction across different REVs in both dense and spares canopies across diverse range of solar zenith angles. The perforated panel experiment, which was used to test the accuracy of the estimated gap fraction, confirmed that the novel method resulted in the accurate and consistent gap fractions across different hole sizes, gap fractions and solar zenith angles. These findings highlight that the novel method opens new opportunities to estimate gap fraction accurately during daytime from sparse to dense canopies, which will be useful in monitoring LAI precisely and validating satellite remote sensing LAI products efficiently.

  18. Determination of enthalpies of formation of energetic molecules with composite quantum chemical methods

    DOE PAGES

    Manaa, M. Riad; Fried, Laurence E.; Kuo, I-Feng W.

    2016-02-01

    We report gas-phase enthalpies of formation for the set of energetic molecules NTO, DADE, LLM-105, TNT, RDX, TATB, HMX, and PETN using the G2, G3, G4, and ccCA-PS3 quantum composite methods. Calculations for HMX and PETN hitherto represent the largest molecules attempted with these methods. G3 and G4 calculations are typically close to one another, with a larger difference found between these methods and ccCA-PS3. Furthermore there is significant uncertainty in experimental values, the mean absolute deviation between the average experimental value and calculations are 12, 6, 7, and 3 kcal/mol for G2, G3, G4, and ccCA-PS3, respectively.

  19. Accurate complex scaling of three dimensional numerical potentials

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

    Cerioni, Alessandro; Genovese, Luigi; Duchemin, Ivan

    2013-05-28

    The complex scaling method, which consists in continuing spatial coordinates into the complex plane, is a well-established method that allows to compute resonant eigenfunctions of the time-independent Schroedinger operator. Whenever it is desirable to apply the complex scaling to investigate resonances in physical systems defined on numerical discrete grids, the most direct approach relies on the application of a similarity transformation to the original, unscaled Hamiltonian. We show that such an approach can be conveniently implemented in the Daubechies wavelet basis set, featuring a very promising level of generality, high accuracy, and no need for artificial convergence parameters. Complex scalingmore » of three dimensional numerical potentials can be efficiently and accurately performed. By carrying out an illustrative resonant state computation in the case of a one-dimensional model potential, we then show that our wavelet-based approach may disclose new exciting opportunities in the field of computational non-Hermitian quantum mechanics.« less

  20. 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.

  1. FAMBE-pH: A Fast and Accurate Method to Compute the Total Solvation Free Energies of Proteins

    PubMed Central

    Vorobjev, Yury N.; Vila, Jorge A.

    2009-01-01

    A fast and accurate method to compute the total solvation free energies of proteins as a function of pH is presented. The method makes use of a combination of approaches, some of which have already appeared in the literature; (i) the Poisson equation is solved with an optimized fast adaptive multigrid boundary element (FAMBE) method; (ii) the electrostatic free energies of the ionizable sites are calculated for their neutral and charged states by using a detailed model of atomic charges; (iii) a set of optimal atomic radii is used to define a precise dielectric surface interface; (iv) a multilevel adaptive tessellation of this dielectric surface interface is achieved by using multisized boundary elements; and (v) 1:1 salt effects are included. The equilibrium proton binding/release is calculated with the Tanford–Schellman integral if the proteins contain more than ∼20–25 ionizable groups; for a smaller number of ionizable groups, the ionization partition function is calculated directly. The FAMBE method is tested as a function of pH (FAMBE-pH) with three proteins, namely, bovine pancreatic trypsin inhibitor (BPTI), hen egg white lysozyme (HEWL), and bovine pancreatic ribonuclease A (RNaseA). The results are (a) the FAMBE-pH method reproduces the observed pKa's of the ionizable groups of these proteins within an average absolute value of 0.4 pK units and a maximum error of 1.2 pK units and (b) comparison of the calculated total pH-dependent solvation free energy for BPTI, between the exact calculation of the ionization partition function and the Tanford–Schellman integral method, shows agreement within 1.2 kcal/mol. These results indicate that calculation of total solvation free energies with the FAMBE-pH method can provide an accurate prediction of protein conformational stability at a given fixed pH and, if coupled with molecular mechanics or molecular dynamics methods, can also be used for more realistic studies of protein folding, unfolding, and dynamics

  2. Altered Enthalpy-Entropy Compensation in Picomolar Transition State Analogues of Human Purine Nucleoside Phosphorylase†

    PubMed Central

    Edwards, Achelle A.; Mason, Jennifer M.; Clinch, Keith; Tyler, Peter C.; Evans, Gary B.; Schramm, Vern L.

    2009-01-01

    Human purine nucleoside phosphorylase (PNP) belongs to the trimeric class of PNPs and is essential for catabolism of deoxyguanosine. Genetic deficiency of PNP in humans causes a specific T-cell immune deficiency and transition state analogue inhibitors of PNP are in development for treatment of T-cell cancers and autoimmune disorders. Four generations of Immucillins have been developed, each of which contains inhibitors binding with picomolar affinity to human PNP. Full inhibition of PNP occurs upon binding to the first of three subunits and binding to subsequent sites occurs with negative cooperativity. In contrast, substrate analogue and product bind without cooperativity. Titrations of human PNP using isothermal calorimetery indicate that binding of a structurally rigid first-generation Immucillin (K d = 56 pM) is driven by large negative enthalpy values (ΔH = −21.2 kcal/mol) with a substantial entropic (-TΔS) penalty. The tightest-binding inhibitors (K d = 5 to 9 pM) have increased conformational flexibility. Despite their conformational freedom in solution, flexible inhibitors bind with high affinity because of reduced entropic penalties. Entropic penalties are proposed to arise from conformational freezing of the PNP·inhibitor complex with the entropy term dominated by protein dynamics. The conformationally flexible Immucillins reduce the system entropic penalty. Disrupting the ribosyl 5’-hydroxyl interaction of transition state analogues with PNP causes favorable entropy of binding. Tight binding of the seventeen Immucillins is characterized by large enthalpic contributions, emphasizing their similarity to the transition state. By introducing flexibility into the inhibitor structure, the enthalpy-entropy compensation pattern is altered to permit tighter binding. PMID:19425594

  3. ACCURATE SOLUTION AND GRADIENT COMPUTATION FOR ELLIPTIC INTERFACE PROBLEMS WITH VARIABLE COEFFICIENTS

    PubMed Central

    LI, ZHILIN; JI, HAIFENG; CHEN, XIAOHONG

    2016-01-01

    A new augmented method is proposed for elliptic interface problems with a piecewise variable coefficient that has a finite jump across a smooth interface. The main motivation is not only to get a second order accurate solution but also a second order accurate gradient from each side of the interface. The key of the new method is to introduce the jump in the normal derivative of the solution as an augmented variable and re-write the interface problem as a new PDE that consists of a leading Laplacian operator plus lower order derivative terms near the interface. In this way, the leading second order derivatives jump relations are independent of the jump in the coefficient that appears only in the lower order terms after the scaling. An upwind type discretization is used for the finite difference discretization at the irregular grid points near or on the interface so that the resulting coefficient matrix is an M-matrix. A multi-grid solver is used to solve the linear system of equations and the GMRES iterative method is used to solve the augmented variable. Second order convergence for the solution and the gradient from each side of the interface has also been proved in this paper. Numerical examples for general elliptic interface problems have confirmed the theoretical analysis and efficiency of the new method. PMID:28983130

  4. Including crystal structure attributes in machine learning models of formation energies via Voronoi tessellations

    NASA Astrophysics Data System (ADS)

    Ward, Logan; Liu, Ruoqian; Krishna, Amar; Hegde, Vinay I.; Agrawal, Ankit; Choudhary, Alok; Wolverton, Chris

    2017-07-01

    While high-throughput density functional theory (DFT) has become a prevalent tool for materials discovery, it is limited by the relatively large computational cost. In this paper, we explore using DFT data from high-throughput calculations to create faster, surrogate models with machine learning (ML) that can be used to guide new searches. Our method works by using decision tree models to map DFT-calculated formation enthalpies to a set of attributes consisting of two distinct types: (i) composition-dependent attributes of elemental properties (as have been used in previous ML models of DFT formation energies), combined with (ii) attributes derived from the Voronoi tessellation of the compound's crystal structure. The ML models created using this method have half the cross-validation error and similar training and evaluation speeds to models created with the Coulomb matrix and partial radial distribution function methods. For a dataset of 435 000 formation energies taken from the Open Quantum Materials Database (OQMD), our model achieves a mean absolute error of 80 meV/atom in cross validation, which is lower than the approximate error between DFT-computed and experimentally measured formation enthalpies and below 15% of the mean absolute deviation of the training set. We also demonstrate that our method can accurately estimate the formation energy of materials outside of the training set and be used to identify materials with especially large formation enthalpies. We propose that our models can be used to accelerate the discovery of new materials by identifying the most promising materials to study with DFT at little additional computational cost.

  5. Progress in fast, accurate multi-scale climate simulations

    DOE PAGES

    Collins, W. D.; Johansen, H.; Evans, K. J.; ...

    2015-06-01

    We present a survey of physical and computational techniques that have the potential to contribute to the next generation of high-fidelity, multi-scale climate simulations. Examples of the climate science problems that can be investigated with more depth with these computational improvements include the capture of remote forcings of localized hydrological extreme events, an accurate representation of cloud features over a range of spatial and temporal scales, and parallel, large ensembles of simulations to more effectively explore model sensitivities and uncertainties. Numerical techniques, such as adaptive mesh refinement, implicit time integration, and separate treatment of fast physical time scales are enablingmore » improved accuracy and fidelity in simulation of dynamics and allowing more complete representations of climate features at the global scale. At the same time, partnerships with computer science teams have focused on taking advantage of evolving computer architectures such as many-core processors and GPUs. As a result, approaches which were previously considered prohibitively costly have become both more efficient and scalable. In combination, progress in these three critical areas is poised to transform climate modeling in the coming decades.« less

  6. Probabilistic techniques for obtaining accurate patient counts in Clinical Data Warehouses

    PubMed Central

    Myers, Risa B.; Herskovic, Jorge R.

    2011-01-01

    Proposal and execution of clinical trials, computation of quality measures and discovery of correlation between medical phenomena are all applications where an accurate count of patients is needed. However, existing sources of this type of patient information, including Clinical Data Warehouses (CDW) may be incomplete or inaccurate. This research explores applying probabilistic techniques, supported by the MayBMS probabilistic database, to obtain accurate patient counts from a clinical data warehouse containing synthetic patient data. We present a synthetic clinical data warehouse (CDW), and populate it with simulated data using a custom patient data generation engine. We then implement, evaluate and compare different techniques for obtaining patients counts. We model billing as a test for the presence of a condition. We compute billing’s sensitivity and specificity both by conducting a “Simulated Expert Review” where a representative sample of records are reviewed and labeled by experts, and by obtaining the ground truth for every record. We compute the posterior probability of a patient having a condition through a “Bayesian Chain”, using Bayes’ Theorem to calculate the probability of a patient having a condition after each visit. The second method is a “one-shot” approach that computes the probability of a patient having a condition based on whether the patient is ever billed for the condition Our results demonstrate the utility of probabilistic approaches, which improve on the accuracy of raw counts. In particular, the simulated review paired with a single application of Bayes’ Theorem produces the best results, with an average error rate of 2.1% compared to 43.7% for the straightforward billing counts. Overall, this research demonstrates that Bayesian probabilistic approaches improve patient counts on simulated patient populations. We believe that total patient counts based on billing data are one of the many possible applications of our

  7. Time Accurate Unsteady Pressure Loads Simulated for the Space Launch System at a Wind Tunnel Condition

    NASA Technical Reports Server (NTRS)

    Alter, Stephen J.; Brauckmann, Gregory J.; Kleb, Bil; Streett, Craig L; Glass, Christopher E.; Schuster, David M.

    2015-01-01

    Using the Fully Unstructured Three-Dimensional (FUN3D) computational fluid dynamics code, an unsteady, time-accurate flow field about a Space Launch System configuration was simulated at a transonic wind tunnel condition (Mach = 0.9). Delayed detached eddy simulation combined with Reynolds Averaged Naiver-Stokes and a Spallart-Almaras turbulence model were employed for the simulation. Second order accurate time evolution scheme was used to simulate the flow field, with a minimum of 0.2 seconds of simulated time to as much as 1.4 seconds. Data was collected at 480 pressure taps at locations, 139 of which matched a 3% wind tunnel model, tested in the Transonic Dynamic Tunnel (TDT) facility at NASA Langley Research Center. Comparisons between computation and experiment showed agreement within 5% in terms of location for peak RMS levels, and 20% for frequency and magnitude of power spectral densities. Grid resolution and time step sensitivity studies were performed to identify methods for improved accuracy comparisons to wind tunnel data. With limited computational resources, accurate trends for reduced vibratory loads on the vehicle were observed. Exploratory methods such as determining minimized computed errors based on CFL number and sub-iterations, as well as evaluating frequency content of the unsteady pressures and evaluation of oscillatory shock structures were used in this study to enhance computational efficiency and solution accuracy. These techniques enabled development of a set of best practices, for the evaluation of future flight vehicle designs in terms of vibratory loads.

  8. Moderate point: Balanced entropy and enthalpy contributions in soft matter

    NASA Astrophysics Data System (ADS)

    He, Baoji; Wang, Yanting

    2017-03-01

    Various soft materials share some common features, such as significant entropic effect, large fluctuations, sensitivity to thermodynamic conditions, and mesoscopic characteristic spatial and temporal scales. However, no quantitative definitions have yet been provided for soft matter, and the intrinsic mechanisms leading to their common features are unclear. In this work, from the viewpoint of statistical mechanics, we show that soft matter works in the vicinity of a specific thermodynamic state named moderate point, at which entropy and enthalpy contributions among substates along a certain order parameter are well balanced or have a minimal difference. Around the moderate point, the order parameter fluctuation, the associated response function, and the spatial correlation length maximize, which explains the large fluctuation, the sensitivity to thermodynamic conditions, and mesoscopic spatial and temporal scales of soft matter, respectively. Possible applications to switching chemical bonds or allosteric biomachines determining their best working temperatures are also briefly discussed. Project supported by the National Basic Research Program of China (Grant No. 2013CB932804) and the National Natural Science Foundation of China (Grant Nos. 11274319 and 11421063).

  9. Identification of fidgety movements and prediction of CP by the use of computer-based video analysis is more accurate when based on two video recordings.

    PubMed

    Adde, Lars; Helbostad, Jorunn; Jensenius, Alexander R; Langaas, Mette; Støen, Ragnhild

    2013-08-01

    This study evaluates the role of postterm age at assessment and the use of one or two video recordings for the detection of fidgety movements (FMs) and prediction of cerebral palsy (CP) using computer vision software. Recordings between 9 and 17 weeks postterm age from 52 preterm and term infants (24 boys, 28 girls; 26 born preterm) were used. Recordings were analyzed using computer vision software. Movement variables, derived from differences between subsequent video frames, were used for quantitative analysis. Sensitivities, specificities, and area under curve were estimated for the first and second recording, or a mean of both. FMs were classified based on the Prechtl approach of general movement assessment. CP status was reported at 2 years. Nine children developed CP of whom all recordings had absent FMs. The mean variability of the centroid of motion (CSD) from two recordings was more accurate than using only one recording, and identified all children who were diagnosed with CP at 2 years. Age at assessment did not influence the detection of FMs or prediction of CP. The accuracy of computer vision techniques in identifying FMs and predicting CP based on two recordings should be confirmed in future studies.

  10. Piezoelectric crystal microbalance measurements of enthalpy of sublimation of C2-C9 dicarboxylic acids

    NASA Astrophysics Data System (ADS)

    Dirri, F.; Palomba, E.; Longobardo, A.; Zampetti, E.

    2016-02-01

    We present here a novel experimental set-up that is able to measure the enthalpy of sublimation of a given compound by means of piezoelectric crystal microbalances (PCMs). The PCM sensors have already been used for space measurements, such as for the detection of organic and non-organic volatile species and refractory materials in planetary environments. In Earth atmospherics applications, PCMs can be also used to obtain some physical-chemical processes concerning the volatile organic compounds (VOCs) present in atmospheric environments. The experimental set-up has been developed and tested on dicarboxylic acids. In this work, a temperature-controlled effusion cell was used to sublimate VOC, creating a molecular flux that was collimated onto a cold PCM. The VOC recondensed onto the PCM quartz crystal, allowing the determination of the deposition rate. From the measurements of deposition rates, it has been possible to infer the enthalpy of sublimation of adipic acid, i.e. ΔHsub : 141.6 ± 0.8 kJ mol-1, succinic acid, i.e. 113.3 ± 1.3 kJ mol-1, oxalic acid, i.e. 62.5 ± 3.1 kJ mol-1, and azelaic acid, i.e. 124.2 ± 1.2 kJ mol-1. The results obtained show an accuracy of 1 % for succinic, adipic, and azelaic acid and within 5 % for oxalic acid and are in very good agreement with previous works (within 6 % for adipic, succinic, and oxalic acid and within 11 % or larger for azelaic acid).

  11. Accurate transport properties for H–CO and H–CO{sub 2}

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

    Dagdigian, Paul J., E-mail: pjdagdigian@jhu.edu

    2015-08-07

    Transport properties for collisions of hydrogen atoms with CO and CO{sub 2} have been computed by means of quantum scattering calculations. The carbon oxides are important species in hydrocarbon combustion. The following potential energy surfaces (PES’s) for the interaction of the molecule fixed in its equilibrium geometry were employed: for H–CO, the PES was taken from the work of Song et al. [J. Phys. Chem. A 117, 7571 (2013)], while the PES for H–CO{sub 2} was computed in this study by a restricted coupled cluster method that included single, double, and (perturbatively) triple excitations. The computed transport properties were foundmore » to be significantly different from those computed by the conventional approach that employs isotropic Lennard-Jones (12-6) potentials. The effect of using the presently computed accurate transport properties in 1-dimensional combustion simulations of methane-air flames was investigated.« less

  12. Matrix-vector multiplication using digital partitioning for more accurate optical computing

    NASA Technical Reports Server (NTRS)

    Gary, C. K.

    1992-01-01

    Digital partitioning offers a flexible means of increasing the accuracy of an optical matrix-vector processor. This algorithm can be implemented with the same architecture required for a purely analog processor, which gives optical matrix-vector processors the ability to perform high-accuracy calculations at speeds comparable with or greater than electronic computers as well as the ability to perform analog operations at a much greater speed. Digital partitioning is compared with digital multiplication by analog convolution, residue number systems, and redundant number representation in terms of the size and the speed required for an equivalent throughput as well as in terms of the hardware requirements. Digital partitioning and digital multiplication by analog convolution are found to be the most efficient alogrithms if coding time and hardware are considered, and the architecture for digital partitioning permits the use of analog computations to provide the greatest throughput for a single processor.

  13. Treatment of refractory powders by a novel, high enthalpy dc plasma

    NASA Astrophysics Data System (ADS)

    Pershin, L.; Mitrasinovic, A.; Mostaghimi, J.

    2013-06-01

    Thermophysical properties of CO2-CH4 mixtures at high temperatures are very attractive for materials processing. In comparison with argon, at the same temperature, such a mixture possesses much higher enthalpy and higher thermal conductivity. At high temperatures, CO2-CH4 mixture has a complex composition with strong presence of CO which, in the case of powder treatment, could reduce oxidation. In this work, a dc plasma torch with graphite cathode was used to study the effect of plasma gas composition on spheroidization of tungsten carbide and alumina powders. Two different gas compositions were used to generate the plasma while the torch current was kept at 300 A. Various techniques were employed to assess the average concentration of carbides and oxides and the final shape of the treated powders. Process parameters such as input power and plasma gas composition allow controlling the degree of powder oxidation and spheroidization of high melting point ceramic powders.

  14. Accurate and efficient calculation of response times for groundwater flow

    NASA Astrophysics Data System (ADS)

    Carr, Elliot J.; Simpson, Matthew J.

    2018-03-01

    We study measures of the amount of time required for transient flow in heterogeneous porous media to effectively reach steady state, also known as the response time. Here, we develop a new approach that extends the concept of mean action time. Previous applications of the theory of mean action time to estimate the response time use the first two central moments of the probability density function associated with the transition from the initial condition, at t = 0, to the steady state condition that arises in the long time limit, as t → ∞ . This previous approach leads to a computationally convenient estimation of the response time, but the accuracy can be poor. Here, we outline a powerful extension using the first k raw moments, showing how to produce an extremely accurate estimate by making use of asymptotic properties of the cumulative distribution function. Results are validated using an existing laboratory-scale data set describing flow in a homogeneous porous medium. In addition, we demonstrate how the results also apply to flow in heterogeneous porous media. Overall, the new method is: (i) extremely accurate; and (ii) computationally inexpensive. In fact, the computational cost of the new method is orders of magnitude less than the computational effort required to study the response time by solving the transient flow equation. Furthermore, the approach provides a rigorous mathematical connection with the heuristic argument that the response time for flow in a homogeneous porous medium is proportional to L2 / D , where L is a relevant length scale, and D is the aquifer diffusivity. Here, we extend such heuristic arguments by providing a clear mathematical definition of the proportionality constant.

  15. Ca(AlH4)2, CaAlH5, and CaH2+6LiBH4: Calculated dehydrogenation enthalpy, including zero point energy, and the structure of the phonon spectra.

    PubMed

    Marashdeh, Ali; Frankcombe, Terry J

    2008-06-21

    The dehydrogenation enthalpies of Ca(AlH(4))(2), CaAlH(5), and CaH(2)+6LiBH(4) have been calculated using density functional theory calculations at the generalized gradient approximation level. Harmonic phonon zero point energy (ZPE) corrections have been included using Parlinski's direct method. The dehydrogenation of Ca(AlH(4))(2) is exothermic, indicating a metastable hydride. Calculations for CaAlH(5) including ZPE effects indicate that it is not stable enough for a hydrogen storage system operating near ambient conditions. The destabilized combination of LiBH(4) with CaH(2) is a promising system after ZPE-corrected enthalpy calculations. The calculations confirm that including ZPE effects in the harmonic approximation for the dehydrogenation of Ca(AlH(4))(2), CaAlH(5), and CaH(2)+6LiBH(4) has a significant effect on the calculated reaction enthalpy. The contribution of ZPE to the dehydrogenation enthalpies of Ca(AlH(4))(2) and CaAlH(5) calculated by the direct method phonon analysis was compared to that calculated by the frozen-phonon method. The crystal structure of CaAlH(5) is presented in the more useful standard setting of P2(1)c symmetry and the phonon density of states of CaAlH(5), significantly different to other common complex metal hydrides, is rationalized.

  16. Ca(AlH4)2, CaAlH5, and CaH2+6LiBH4: Calculated dehydrogenation enthalpy, including zero point energy, and the structure of the phonon spectra

    NASA Astrophysics Data System (ADS)

    Marashdeh, Ali; Frankcombe, Terry J.

    2008-06-01

    The dehydrogenation enthalpies of Ca(AlH4)2, CaAlH5, and CaH2+6LiBH4 have been calculated using density functional theory calculations at the generalized gradient approximation level. Harmonic phonon zero point energy (ZPE) corrections have been included using Parlinski's direct method. The dehydrogenation of Ca(AlH4)2 is exothermic, indicating a metastable hydride. Calculations for CaAlH5 including ZPE effects indicate that it is not stable enough for a hydrogen storage system operating near ambient conditions. The destabilized combination of LiBH4 with CaH2 is a promising system after ZPE-corrected enthalpy calculations. The calculations confirm that including ZPE effects in the harmonic approximation for the dehydrogenation of Ca(AlH4)2, CaAlH5, and CaH2+6LiBH4 has a significant effect on the calculated reaction enthalpy. The contribution of ZPE to the dehydrogenation enthalpies of Ca(AlH4)2 and CaAlH5 calculated by the direct method phonon analysis was compared to that calculated by the frozen-phonon method. The crystal structure of CaAlH5 is presented in the more useful standard setting of P21/c symmetry and the phonon density of states of CaAlH5, significantly different to other common complex metal hydrides, is rationalized.

  17. Computer program for calculating and fitting thermodynamic functions

    NASA Technical Reports Server (NTRS)

    Mcbride, Bonnie J.; Gordon, Sanford

    1992-01-01

    A computer program is described which (1) calculates thermodynamic functions (heat capacity, enthalpy, entropy, and free energy) for several optional forms of the partition function, (2) fits these functions to empirical equations by means of a least-squares fit, and (3) calculates, as a function of temperture, heats of formation and equilibrium constants. The program provides several methods for calculating ideal gas properties. For monatomic gases, three methods are given which differ in the technique used for truncating the partition function. For diatomic and polyatomic molecules, five methods are given which differ in the corrections to the rigid-rotator harmonic-oscillator approximation. A method for estimating thermodynamic functions for some species is also given.

  18. Computer-assisted adjuncts for aneurysmal morphologic assessment: toward more precise and accurate approaches

    NASA Astrophysics Data System (ADS)

    Rajabzadeh-Oghaz, Hamidreza; Varble, Nicole; Davies, Jason M.; Mowla, Ashkan; Shakir, Hakeem J.; Sonig, Ashish; Shallwani, Hussain; Snyder, Kenneth V.; Levy, Elad I.; Siddiqui, Adnan H.; Meng, Hui

    2017-03-01

    Neurosurgeons currently base most of their treatment decisions for intracranial aneurysms (IAs) on morphological measurements made manually from 2D angiographic images. These measurements tend to be inaccurate because 2D measurements cannot capture the complex geometry of IAs and because manual measurements are variable depending on the clinician's experience and opinion. Incorrect morphological measurements may lead to inappropriate treatment strategies. In order to improve the accuracy and consistency of morphological analysis of IAs, we have developed an image-based computational tool, AView. In this study, we quantified the accuracy of computer-assisted adjuncts of AView for aneurysmal morphologic assessment by performing measurement on spheres of known size and anatomical IA models. AView has an average morphological error of 0.56% in size and 2.1% in volume measurement. We also investigate the clinical utility of this tool on a retrospective clinical dataset and compare size and neck diameter measurement between 2D manual and 3D computer-assisted measurement. The average error was 22% and 30% in the manual measurement of size and aneurysm neck diameter, respectively. Inaccuracies due to manual measurements could therefore lead to wrong treatment decisions in 44% and inappropriate treatment strategies in 33% of the IAs. Furthermore, computer-assisted analysis of IAs improves the consistency in measurement among clinicians by 62% in size and 82% in neck diameter measurement. We conclude that AView dramatically improves accuracy for morphological analysis. These results illustrate the necessity of a computer-assisted approach for the morphological analysis of IAs.

  19. Accurate Cold-Test Model of Helical TWT Slow-Wave Circuits

    NASA Technical Reports Server (NTRS)

    Kory, Carol L.; Dayton, James A., Jr.

    1997-01-01

    Recently, a method has been established to accurately calculate cold-test data for helical slow-wave structures using the three-dimensional electromagnetic computer code, MAFIA. Cold-test parameters have been calculated for several helical traveling-wave tube (TWT) slow-wave circuits possessing various support rod configurations, and results are presented here showing excellent agreement with experiment. The helical models include tape thickness, dielectric support shapes and material properties consistent with the actual circuits. The cold-test data from this helical model can be used as input into large-signal helical TWT interaction codes making it possible, for the first time, to design a complete TWT via computer simulation.

  20. Optimized structure and thermochemical properties of flavonoids determined by the CHIH(medium) DFT model chemistry versus experimental techniques

    NASA Astrophysics Data System (ADS)

    Mendoza-Wilson, Ana María.; Lardizabal-Gutiérrez, Daniel; Torres-Moye, Enrique; Fuentes-Cobas, Luis; Balandrán-Quintana, René R.; Camacho-Dávila, Alejandro; Quintero-Ramos, Armando; Glossman-Mitnik, Daniel

    2007-12-01

    The purpose of this work was to evaluate the accuracy of the CHIH(medium)-DFT model chemistry (PBEg/CBSB2 ∗∗//PBEg/CBSB4) in the determination of the optimized structure and thermochemical properties of heterocyclic systems of medium size such as flavonoids, wherefore were selected three of the most abundant flavonoids in vegetable tissues, and which posses the higher antioxidant activity: quercetin, (+)-catechin and cyanidin. As reference systems were employed three cyclic compounds: phenol, catechol and resorcinol. The thermochemical properties evaluated were enthalpy of formation, bond dissociation enthalpy (BDE) and ionization potential (IP), following the scheme of isodesmic reactions. The theoretical results were compared with experimental data generated by X-ray diffraction and calorimetric techniques realized in part by us, whereas other data were taken from the literature. The results obtained in this work reveal that the CHIH(medium)-DFT model chemistry represents an accurate computational tool to calculate structural and thermochemical properties in the studied flavonoid and reference compounds. The average absolute deviation of enthalpy of formation for reference compounds was 3.0 kcal/mol, 2.64 kcal/mol for BDE, and 2.97 kcal/mol for IP.

  1. LCC-Demons: a robust and accurate symmetric diffeomorphic registration algorithm.

    PubMed

    Lorenzi, M; Ayache, N; Frisoni, G B; Pennec, X

    2013-11-01

    Non-linear registration is a key instrument for computational anatomy to study the morphology of organs and tissues. However, in order to be an effective instrument for the clinical practice, registration algorithms must be computationally efficient, accurate and most importantly robust to the multiple biases affecting medical images. In this work we propose a fast and robust registration framework based on the log-Demons diffeomorphic registration algorithm. The transformation is parameterized by stationary velocity fields (SVFs), and the similarity metric implements a symmetric local correlation coefficient (LCC). Moreover, we show how the SVF setting provides a stable and consistent numerical scheme for the computation of the Jacobian determinant and the flux of the deformation across the boundaries of a given region. Thus, it provides a robust evaluation of spatial changes. We tested the LCC-Demons in the inter-subject registration setting, by comparing with state-of-the-art registration algorithms on public available datasets, and in the intra-subject longitudinal registration problem, for the statistically powered measurements of the longitudinal atrophy in Alzheimer's disease. Experimental results show that LCC-Demons is a generic, flexible, efficient and robust algorithm for the accurate non-linear registration of images, which can find several applications in the field of medical imaging. Without any additional optimization, it solves equally well intra & inter-subject registration problems, and compares favorably to state-of-the-art methods. Copyright © 2013 Elsevier Inc. All rights reserved.

  2. Highly accurate potential energy surface for the He-H2 dimer

    NASA Astrophysics Data System (ADS)

    Bakr, Brandon W.; Smith, Daniel G. A.; Patkowski, Konrad

    2013-10-01

    A new highly accurate interaction potential is constructed for the He-H2 van der Waals complex. This potential is fitted to 1900 ab initio energies computed at the very large-basis coupled-cluster level and augmented by corrections for higher-order excitations (up to full configuration interaction level) and the diagonal Born-Oppenheimer correction. At the vibrationally averaged H-H bond length of 1.448736 bohrs, the well depth of our potential, 15.870 ± 0.065 K, is nearly 1 K larger than the most accurate previous studies have indicated. In addition to constructing our own three-dimensional potential in the van der Waals region, we present a reparameterization of the Boothroyd-Martin-Peterson potential surface [A. I. Boothroyd, P. G. Martin, and M. R. Peterson, J. Chem. Phys. 119, 3187 (2003)] that is suitable for all configurations of the triatomic system. Finally, we use the newly developed potentials to compute the properties of the lone bound states of 4He-H2 and 3He-H2 and the interaction second virial coefficient of the hydrogen-helium mixture.

  3. Nasal computed tomography.

    PubMed

    Kuehn, Ned F

    2006-05-01

    Chronic nasal disease is often a challenge to diagnose. Computed tomography greatly enhances the ability to diagnose chronic nasal disease in dogs and cats. Nasal computed tomography provides detailed information regarding the extent of disease, accurate discrimination of neoplastic versus nonneoplastic diseases, and identification of areas of the nose to examine rhinoscopically and suspicious regions to target for biopsy.

  4. Covariance approximation for fast and accurate computation of channelized Hotelling observer statistics

    NASA Astrophysics Data System (ADS)

    Bonetto, P.; Qi, Jinyi; Leahy, R. M.

    2000-08-01

    Describes a method for computing linear observer statistics for maximum a posteriori (MAP) reconstructions of PET images. The method is based on a theoretical approximation for the mean and covariance of MAP reconstructions. In particular, the authors derive here a closed form for the channelized Hotelling observer (CHO) statistic applied to 2D MAP images. The theoretical analysis models both the Poission statistics of PET data and the inhomogeneity of tracer uptake. The authors show reasonably good correspondence between these theoretical results and Monte Carlo studies. The accuracy and low computational cost of the approximation allow the authors to analyze the observer performance over a wide range of operating conditions and parameter settings for the MAP reconstruction algorithm.

  5. Lattice potential energy and standard molar enthalpy in the formation of 1—dodecylamine hydrobromide (1-C12H25NH3·Br)(s)

    NASA Astrophysics Data System (ADS)

    Liu, Yu-Pu; Di, You-Ying; Dan, Wen-Yan; He, Dong-Hua; Kong, Yu-Xia; Yang, Wei-Wei

    2011-02-01

    This paper reports that 1-dodecylamine hydrobromide (1-C12H25NH3·Br)(s) has been synthesized using the liquid phase reaction method. The lattice potential energy of the compound 1-C12H25NH3·Br and the ionic volume and radius of the 1-C12H25NH3+ cation are obtained from the crystallographic data and other auxiliary thermodynamic data. The constant-volume energy of combustion of 1-C12H25NH3·Br(s) is measured to be ΔcUmo(1-C12H25NH3·Br, s) = -(7369.03±3.28) kJ·mol-1 by means of an RBC-II precision rotating-bomb combustion calorimeter at T = (298.15±0.001) K. The standard molar enthalpy of combustion of the compound is derived to be ΔcHmo(1-C12H25NH3·Br, s) = -(7384.52±3.28) kJ·mol-1 from the constant-volume energy of combustion. The standard molar enthalpy of formation of the compound is calculated to be ΔfHmo(1-C12H25NH3·Br, s)=-(1317.86±3.67) kJ·mol-1 from the standard molar enthalpy of combustion of the title compound and other auxiliary thermodynamic quantities through a thermochemical cycle.

  6. Mass dependence of the activation enthalpy and entropy of unentangled linear alkane chains

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

    Jeong, Cheol; Douglas, Jack F.

    2015-10-14

    The mass scaling of the self-diffusion coefficient D of polymers in the liquid state, D ∼ M{sup β}, is one of the most basic characteristics of these complex fluids. Although traditional theories such as the Rouse and reptation models of unentangled and entangled polymer melts, respectively, predict that β is constant, this exponent for alkanes has been estimated experimentally to vary from −1.8 to −2.7 upon cooling. Significantly, β changes with temperature T under conditions where the chains are not entangled and at temperatures far above the glass transition temperature T{sub g} where dynamic heterogeneity does not complicate the descriptionmore » of the liquid dynamics. Based on atomistic molecular dynamics simulations on unentangled linear alkanes in the melt, we find that the variation of β with T can be directly attributed to the dependence of the enthalpy ΔH{sub a} and entropy ΔS{sub a} of activation on the number of alkane backbone carbon atoms, n. In addition, we find a sharp change in the melt dynamics near a “critical” chain length, n ≈ 17. A close examination of this phenomenon indicates that a “buckling transition” from rod-like to coiled chain configurations occurs at this characteristic chain length and distinct entropy-enthalpy compensation relations, ΔS{sub a} ∝ ΔH{sub a}, hold on either side of this polymer conformational transition. We conclude that the activation free energy parameters exert a significant influence on the dynamics of polymer melts that is not anticipated by either the Rouse and reptation models. In addition to changes of ΔH{sub a} and ΔS{sub a} with M, we expect changes in these free energy parameters to be crucial for understanding the dynamics of polymer blends, nanocomposites, and confined polymers because of changes of the fluid free energy by interfacial interactions and geometrical confinement.« less

  7. Accurate Phylogenetic Tree Reconstruction from Quartets: A Heuristic Approach

    PubMed Central

    Reaz, Rezwana; Bayzid, Md. Shamsuzzoha; Rahman, M. Sohel

    2014-01-01

    Supertree methods construct trees on a set of taxa (species) combining many smaller trees on the overlapping subsets of the entire set of taxa. A ‘quartet’ is an unrooted tree over taxa, hence the quartet-based supertree methods combine many -taxon unrooted trees into a single and coherent tree over the complete set of taxa. Quartet-based phylogeny reconstruction methods have been receiving considerable attentions in the recent years. An accurate and efficient quartet-based method might be competitive with the current best phylogenetic tree reconstruction methods (such as maximum likelihood or Bayesian MCMC analyses), without being as computationally intensive. In this paper, we present a novel and highly accurate quartet-based phylogenetic tree reconstruction method. We performed an extensive experimental study to evaluate the accuracy and scalability of our approach on both simulated and biological datasets. PMID:25117474

  8. Light Field Imaging Based Accurate Image Specular Highlight Removal

    PubMed Central

    Wang, Haoqian; Xu, Chenxue; Wang, Xingzheng; Zhang, Yongbing; Peng, Bo

    2016-01-01

    Specular reflection removal is indispensable to many computer vision tasks. However, most existing methods fail or degrade in complex real scenarios for their individual drawbacks. Benefiting from the light field imaging technology, this paper proposes a novel and accurate approach to remove specularity and improve image quality. We first capture images with specularity by the light field camera (Lytro ILLUM). After accurately estimating the image depth, a simple and concise threshold strategy is adopted to cluster the specular pixels into “unsaturated” and “saturated” category. Finally, a color variance analysis of multiple views and a local color refinement are individually conducted on the two categories to recover diffuse color information. Experimental evaluation by comparison with existed methods based on our light field dataset together with Stanford light field archive verifies the effectiveness of our proposed algorithm. PMID:27253083

  9. Piezoelectric crystal microbalance measurements of enthalpy of sublimation of C2-C9 dicarboxylic acids

    NASA Astrophysics Data System (ADS)

    Dirri, F.; Palomba, E.; Longobardo, A.; Zampetti, E.

    2015-07-01

    We present here a novel experimental setup able to measure the enthalpy of sublimation of a given compound by means of Piezoelectric Crystal Microbalances (PCM). This experiment was performed in the TG-Lab facility in IAPS-INAF, dedicated to the development of TGA sensors for space measurements, such as detection of organic and non-organic volatile species and refractory materials in planetary environments. In order to study physical-chemical processes concerning the Volatile Organic Compounds (VOC) present in atmospheric environments, the setup has been tested on Dicarboxylic acids. Acids with low molecular weight are among the components of organic fraction of particulate matter in the atmosphere, coming from different sources (biogenic and anthropogenic). Considering their relative abundance, it is useful to consider Dicarboxylic acid as "markers" to define the biogenic or anthropogenic origin of the aerosol, thus obtaining some information of the emission sources. In this work, a temperature controlled effusion cell was used to sublimate VOC, creating a molecular flux that was collimated onto a cold PCM. The VOC re-condensed onto the PCM quartz crystal allowing the determination of the deposition rate. From the measurements of deposition rates, it was possible to infer the enthalpy of sublimation of Adipic acid, i.e. Δ Hsub: 141.6 ± 0.8 kJ mol-1, Succinic acid, i.e. 113.3 ± 1.3 kJ mol-1, Oxalic acid, i.e. 62.5 ± 3.1 kJ mol-1 and Azelaic acid, i.e. 124.2 ± 1.2 kJ mol-1 (weight average values). The results obtained are in very good agreement with literature within 10 % for the Adipic, Succinic and Oxalic acid.

  10. The new insight into dynamic crossover in glass forming liquids from the apparent enthalpy analysis

    NASA Astrophysics Data System (ADS)

    Martinez-Garcia, Julio Cesar; Martinez-Garcia, Jorge; Rzoska, Sylwester J.; Hulliger, Jürg

    2012-08-01

    One of the most intriguing phenomena in glass forming systems is the dynamic crossover (TB), occurring well above the glass temperature (Tg). So far, it was estimated mainly from the linearized derivative analysis of the primary relaxation time τ(T) or viscosity η(T) experimental data, originally proposed by Stickel et al. [J. Chem. Phys. 104, 2043 (1996), 10.1063/1.470961; Stickel et al. J. Chem. Phys. 107, 1086 (1997)], 10.1063/1.474456. However, this formal procedure is based on the general validity of the Vogel-Fulcher-Tammann equation, which has been strongly questioned recently [T. Hecksher et al. Nature Phys. 4, 737 (2008), 10.1038/nphys1033; P. Lunkenheimer et al. Phys. Rev. E 81, 051504 (2010), 10.1103/PhysRevE.81.051504; J. C. Martinez-Garcia et al. J. Chem. Phys. 134, 024512 (2011)], 10.1063/1.3514589. We present a qualitatively new way to identify the dynamic crossover based on the apparent enthalpy space (H_a^' = {{dln τ }/{d({1/T})}}) analysis via a new plot ln H_a^' vs. 1/T supported by the Savitzky-Golay filtering procedure for getting an insight into the noise-distorted high order derivatives. It is shown that depending on the ratio between the "virtual" fragility in the high temperature dynamic domain (mhigh) and the "real" fragility at Tg (the low temperature dynamic domain, m = mlow) glass formers can be splitted into two groups related to f < 1 and f > 1, (f = mhigh/mlow). The link of this phenomenon to the ratio between the apparent enthalpy and activation energy as well as the behavior of the configurational entropy is indicated.

  11. Accurate first-principles structures and energies of diversely bonded systems from an efficient density functional

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

    Sun, Jianwei; Remsing, Richard C.; Zhang, Yubo

    2016-06-13

    One atom or molecule binds to another through various types of bond, the strengths of which range from several meV to several eV. Although some computational methods can provide accurate descriptions of all bond types, those methods are not efficient enough for many studies (for example, large systems, ab initio molecular dynamics and high-throughput searches for functional materials). Here, we show that the recently developed non-empirical strongly constrained and appropriately normed (SCAN) meta-generalized gradient approximation (meta-GGA) within the density functional theory framework predicts accurate geometries and energies of diversely bonded molecules and materials (including covalent, metallic, ionic, hydrogen and vanmore » der Waals bonds). This represents a significant improvement at comparable efficiency over its predecessors, the GGAs that currently dominate materials computation. Often, SCAN matches or improves on the accuracy of a computationally expensive hybrid functional, at almost-GGA cost. SCAN is therefore expected to have a broad impact on chemistry and materials science.« less

  12. Accurate first-principles structures and energies of diversely bonded systems from an efficient density functional.

    PubMed

    Sun, Jianwei; Remsing, Richard C; Zhang, Yubo; Sun, Zhaoru; Ruzsinszky, Adrienn; Peng, Haowei; Yang, Zenghui; Paul, Arpita; Waghmare, Umesh; Wu, Xifan; Klein, Michael L; Perdew, John P

    2016-09-01

    One atom or molecule binds to another through various types of bond, the strengths of which range from several meV to several eV. Although some computational methods can provide accurate descriptions of all bond types, those methods are not efficient enough for many studies (for example, large systems, ab initio molecular dynamics and high-throughput searches for functional materials). Here, we show that the recently developed non-empirical strongly constrained and appropriately normed (SCAN) meta-generalized gradient approximation (meta-GGA) within the density functional theory framework predicts accurate geometries and energies of diversely bonded molecules and materials (including covalent, metallic, ionic, hydrogen and van der Waals bonds). This represents a significant improvement at comparable efficiency over its predecessors, the GGAs that currently dominate materials computation. Often, SCAN matches or improves on the accuracy of a computationally expensive hybrid functional, at almost-GGA cost. SCAN is therefore expected to have a broad impact on chemistry and materials science.

  13. Accuracy and speed in computing the Chebyshev collocation derivative

    NASA Technical Reports Server (NTRS)

    Don, Wai-Sun; Solomonoff, Alex

    1991-01-01

    We studied several algorithms for computing the Chebyshev spectral derivative and compare their roundoff error. For a large number of collocation points, the elements of the Chebyshev differentiation matrix, if constructed in the usual way, are not computed accurately. A subtle cause is is found to account for the poor accuracy when computing the derivative by the matrix-vector multiplication method. Methods for accurately computing the elements of the matrix are presented, and we find that if the entities of the matrix are computed accurately, the roundoff error of the matrix-vector multiplication is as small as that of the transform-recursion algorithm. Results of CPU time usage are shown for several different algorithms for computing the derivative by the Chebyshev collocation method for a wide variety of two-dimensional grid sizes on both an IBM and a Cray 2 computer. We found that which algorithm is fastest on a particular machine depends not only on the grid size, but also on small details of the computer hardware as well. For most practical grid sizes used in computation, the even-odd decomposition algorithm is found to be faster than the transform-recursion method.

  14. High enthalpy arc-heated plasma flow diagnostics by tunable diode laser absorption spectroscopy

    NASA Astrophysics Data System (ADS)

    Lin, Xin; Chen, Lianzhong; Zeng, Hui; Ou, Dongbin; Dong, Yonghui

    2017-05-01

    This paper reports the laser absorption measurements of atomic oxygen in the FD04 arc-heater at China Academy of Aerospace Aerodynamics (CAAA). An atomic oxygen absorption line at 777.19 nm is utilizied for detecting the population of electronically excited oxygen atom in an air plasma flow. A scanned-wavelength direct absorption mode is used in this study. The laser is scanned in wavelength across the absorption feature at a rate of 200 Hz. Under the assumption of thermal equilibrium, time-resolved temperature measurements are obtained on one line-of-sight in the arc-heater. The good agreement of the temperature inferred from the sonic throat method suggests the equilibrium assumption is valid. These results illustrate the feasibility of the diode laser sensors for flow parameters in high enthalpy arc-heated facilities.

  15. Solvation molar enthalpies and heat capacities of n-alkanes and n-alkylbenzenes on stationary phases of wide-ranging polarity.

    PubMed

    Lebrón-Aguilar, Rosa; Quintanilla-López, Jesús Eduardo; Santiuste, José María

    2010-12-03

    A comparison of the most usual gas chromatographic methods for the calculation of partial molar enthalpies of solvation (Δ(sol)H(o)) has been carried out. Those methods based on the fitting of lnV(g) or ln(k/T) vs. 1/T and ln(k/T) vs. (1/T and the temperature arrangement, T(a)) are the most adequate ones for obtaining Δ(sol)H(o) values. However, the latter is the only reliable option for Δ(sol)H(o) estimation when commercial WCOT capillary columns are used, since in this case the estimation of some variables involved in the V(g) determination is less accurate or even impossible. Consequently, in this paper, Δ(sol)H(o) obtained from ln(k/T) vs. (1/T+T(a)) fitting at 373.15 and 298.15K for n-alkanes and n-alkylbenzenes on 12 commercial capillary columns coated with stationary phases covering the 203-3608 McReynolds polarity range are reported. Moreover, molar heat capacities of solvation at constant pressure (Δ(sol)C(p)(o)) have also been calculated using this method. A clear influence on Δ(sol)H(o) of the type and content of the substitution group in the stationary phase was observed. In addition, a linear relationship of Δ(sol)C(p)(o) with the van der Waals volume of the n-alkanes and the temperature gradient of density of the stationary phase was found. The effect of the size of the hydrocarbon on both thermodynamic variables was also investigated. Copyright © 2010 Elsevier B.V. All rights reserved.

  16. Multi-Physics Computational Grains (MPCGs): Newly-Developed Accurate and Efficient Numerical Methods for Micromechanical Modeling of Multifunctional Materials and Composites

    NASA Astrophysics Data System (ADS)

    Bishay, Peter L.

    This study presents a new family of highly accurate and efficient computational methods for modeling the multi-physics of multifunctional materials and composites in the micro-scale named "Multi-Physics Computational Grains" (MPCGs). Each "mathematical grain" has a random polygonal/polyhedral geometrical shape that resembles the natural shapes of the material grains in the micro-scale where each grain is surrounded by an arbitrary number of neighboring grains. The physics that are incorporated in this study include: Linear Elasticity, Electrostatics, Magnetostatics, Piezoelectricity, Piezomagnetism and Ferroelectricity. However, the methods proposed here can be extended to include more physics (thermo-elasticity, pyroelectricity, electric conduction, heat conduction, etc.) in their formulation, different analysis types (dynamics, fracture, fatigue, etc.), nonlinearities, different defect shapes, and some of the 2D methods can also be extended to 3D formulation. We present "Multi-Region Trefftz Collocation Grains" (MTCGs) as a simple and efficient method for direct and inverse problems, "Trefftz-Lekhnitskii Computational Gains" (TLCGs) for modeling porous and composite smart materials, "Hybrid Displacement Computational Grains" (HDCGs) as a general method for modeling multifunctional materials and composites, and finally "Radial-Basis-Functions Computational Grains" (RBFCGs) for modeling functionally-graded materials, magneto-electro-elastic (MEE) materials and the switching phenomena in ferroelectric materials. The first three proposed methods are suitable for direct numerical simulation (DNS) of the micromechanics of smart composite/porous materials with non-symmetrical arrangement of voids/inclusions, and provide minimal effort in meshing and minimal time in computations, since each grain can represent the matrix of a composite and can include a pore or an inclusion. The last three methods provide stiffness matrix in their formulation and hence can be readily

  17. Development of a computer code for calculating the steady super/hypersonic inviscid flow around real configurations. Volume 1: Computational technique

    NASA Technical Reports Server (NTRS)

    Marconi, F.; Salas, M.; Yaeger, L.

    1976-01-01

    A numerical procedure has been developed to compute the inviscid super/hypersonic flow field about complex vehicle geometries accurately and efficiently. A second order accurate finite difference scheme is used to integrate the three dimensional Euler equations in regions of continuous flow, while all shock waves are computed as discontinuities via the Rankine Hugoniot jump conditions. Conformal mappings are used to develop a computational grid. The effects of blunt nose entropy layers are computed in detail. Real gas effects for equilibrium air are included using curve fits of Mollier charts. Typical calculated results for shuttle orbiter, hypersonic transport, and supersonic aircraft configurations are included to demonstrate the usefulness of this tool.

  18. Robust and accurate vectorization of line drawings.

    PubMed

    Hilaire, Xavier; Tombre, Karl

    2006-06-01

    This paper presents a method for vectorizing the graphical parts of paper-based line drawings. The method consists of separating the input binary image into layers of homogeneous thickness, skeletonizing each layer, segmenting the skeleton by a method based on random sampling, and simplifying the result. The segmentation method is robust with a best bound of 50 percent noise reached for indefinitely long primitives. Accurate estimation of the recognized vector's parameters is enabled by explicitly computing their feasibility domains. Theoretical performance analysis and expression of the complexity of the segmentation method are derived. Experimental results and comparisons with other vectorization systems are also provided.

  19. Application of CT-PSF-based computer-simulated lung nodules for evaluating the accuracy of computer-aided volumetry.

    PubMed

    Funaki, Ayumu; Ohkubo, Masaki; Wada, Shinichi; Murao, Kohei; Matsumoto, Toru; Niizuma, Shinji

    2012-07-01

    With the wide dissemination of computed tomography (CT) screening for lung cancer, measuring the nodule volume accurately with computer-aided volumetry software is increasingly important. Many studies for determining the accuracy of volumetry software have been performed using a phantom with artificial nodules. These phantom studies are limited, however, in their ability to reproduce the nodules both accurately and in the variety of sizes and densities required. Therefore, we propose a new approach of using computer-simulated nodules based on the point spread function measured in a CT system. The validity of the proposed method was confirmed by the excellent agreement obtained between computer-simulated nodules and phantom nodules regarding the volume measurements. A practical clinical evaluation of the accuracy of volumetry software was achieved by adding simulated nodules onto clinical lung images, including noise and artifacts. The tested volumetry software was revealed to be accurate within an error of 20 % for nodules >5 mm and with the difference between nodule density and background (lung) (CT value) being 400-600 HU. Such a detailed analysis can provide clinically useful information on the use of volumetry software in CT screening for lung cancer. We concluded that the proposed method is effective for evaluating the performance of computer-aided volumetry software.

  20. Accurate traveltime computation in complex anisotropic media with discontinuous Galerkin method

    NASA Astrophysics Data System (ADS)

    Le Bouteiller, P.; Benjemaa, M.; Métivier, L.; Virieux, J.

    2017-12-01

    Travel time computation is of major interest for a large range of geophysical applications, among which source localization and characterization, phase identification, data windowing and tomography, from decametric scale up to global Earth scale.Ray-tracing tools, being essentially 1D Lagrangian integration along a path, have been used for their efficiency but present some drawbacks, such as a rather difficult control of the medium sampling. Moreover, they do not provide answers in shadow zones. Eikonal solvers, based on an Eulerian approach, have attracted attention in seismology with the pioneering work of Vidale (1988), while such approach has been proposed earlier by Riznichenko (1946). They have been used now for first-arrival travel-time tomography at various scales (Podvin & Lecomte (1991). The framework for solving this non-linear partial differential equation is now well understood and various finite-difference approaches have been proposed, essentially for smooth media. We propose a novel finite element approach which builds a precise solution for strongly heterogeneous anisotropic medium (still in the limit of Eikonal validity). The discontinuous Galerkin method we have developed allows local refinement of the mesh and local high orders of interpolation inside elements. High precision of the travel times and its spatial derivatives is obtained through this formulation. This finite element method also honors boundary conditions, such as complex topographies and absorbing boundaries for mimicking an infinite medium. Applications from travel-time tomography, slope tomography are expected, but also for migration and take-off angles estimation, thanks to the accuracy obtained when computing first-arrival times.References:Podvin, P. and Lecomte, I., 1991. Finite difference computation of traveltimes in very contrasted velocity model: a massively parallel approach and its associated tools, Geophys. J. Int., 105, 271-284.Riznichenko, Y., 1946. Geometrical

  1. An accurate method for computer-generating tungsten anode x-ray spectra from 30 to 140 kV.

    PubMed

    Boone, J M; Seibert, J A

    1997-11-01

    A tungsten anode spectral model using interpolating polynomials (TASMIP) was used to compute x-ray spectra at 1 keV intervals over the range from 30 kV to 140 kV. The TASMIP is not semi-empirical and uses no physical assumptions regarding x-ray production, but rather interpolates measured constant potential x-ray spectra published by Fewell et al. [Handbook of Computed Tomography X-ray Spectra (U.S. Government Printing Office, Washington, D.C., 1981)]. X-ray output measurements (mR/mAs measured at 1 m) were made on a calibrated constant potential generator in our laboratory from 50 kV to 124 kV, and with 0-5 mm added aluminum filtration. The Fewell spectra were slightly modified (numerically hardened) and normalized based on the attenuation and output characteristics of a constant potential generator and metal-insert x-ray tube in our laboratory. Then, using the modified Fewell spectra of different kVs, the photon fluence phi at each 1 keV energy bin (E) over energies from 10 keV to 140 keV was characterized using polynomial functions of the form phi (E) = a0[E] + a1[E] kV + a2[E] kV2 + ... + a(n)[E] kVn. A total of 131 polynomial functions were used to calculate accurate x-ray spectra, each function requiring between two and four terms. The resulting TASMIP algorithm produced x-ray spectra that match both the quality and quantity characteristics of the x-ray system in our laboratory. For photon fluences above 10% of the peak fluence in the spectrum, the average percent difference (and standard deviation) between the modified Fewell spectra and the TASMIP photon fluence was -1.43% (3.8%) for the 50 kV spectrum, -0.89% (1.37%) for the 70 kV spectrum, and for the 80, 90, 100, 110, 120, 130 and 140 kV spectra, the mean differences between spectra were all less than 0.20% and the standard deviations were less than approximately 1.1%. The model was also extended to include the effects of generator-induced kV ripple. Finally, the x-ray photon fluence in the units of

  2. Stable and Spectrally Accurate Schemes for the Navier-Stokes Equations

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

    Jia, Jun; Liu, Jie

    2011-01-01

    In this paper, we present an accurate, efficient and stable numerical method for the incompressible Navier-Stokes equations (NSEs). The method is based on (1) an equivalent pressure Poisson equation formulation of the NSE with proper pressure boundary conditions, which facilitates the design of high-order and stable numerical methods, and (2) the Krylov deferred correction (KDC) accelerated method of lines transpose (mbox MoL{sup T}), which is very stable, efficient, and of arbitrary order in time. Numerical tests with known exact solutions in three dimensions show that the new method is spectrally accurate in time, and a numerical order of convergence 9more » was observed. Two-dimensional computational results of flow past a cylinder and flow in a bifurcated tube are also reported.« less

  3. 3ARM: A Fast, Accurate Radiative Transfer Model for Use in Climate Models

    NASA Technical Reports Server (NTRS)

    Bergstrom, R. W.; Kinne, S.; Sokolik, I. N.; Toon, O. B.; Mlawer, E. J.; Clough, S. A.; Ackerman, T. P.; Mather, J.

    1996-01-01

    A new radiative transfer model combining the efforts of three groups of researchers is discussed. The model accurately computes radiative transfer in a inhomogeneous absorbing, scattering and emitting atmospheres. As an illustration of the model, results are shown for the effects of dust on the thermal radiation.

  4. 3ARM: A Fast, Accurate Radiative Transfer Model for use in Climate Models

    NASA Technical Reports Server (NTRS)

    Bergstrom, R. W.; Kinne, S.; Sokolik, I. N.; Toon, O. B.; Mlawer, E. J.; Clough, S. A.; Ackerman, T. P.; Mather, J.

    1996-01-01

    A new radiative transfer model combining the efforts of three groups of researchers is discussed. The model accurately computes radiative transfer in a inhomogeneous absorbing, scattering and emitting atmospheres. As an illustration of the model, results are shown for the effects of dust on the thermal radiation.

  5. 3ARM: A Fast, Accurate Radiative Transfer Model For Use in Climate Models

    NASA Technical Reports Server (NTRS)

    Bergstrom, R. W.; Kinne, S.; Sokolik, I. N.; Toon, O. B.; Mlawer, E. J.; Clough, S. A.; Ackerman, T. P.; Mather, J.

    1996-01-01

    A new radiative transfer model combining the efforts of three groups of researchers is discussed. The model accurately computes radiative transfer in a inhomogeneous absorbing, scattering and emitting atmospheres. As an illustration of the model, results are shown for the effects of dust on the thermal radiation.

  6. Fast and accurate reference-free alignment of subtomograms.

    PubMed

    Chen, Yuxiang; Pfeffer, Stefan; Hrabe, Thomas; Schuller, Jan Michael; Förster, Friedrich

    2013-06-01

    In cryoelectron tomography alignment and averaging of subtomograms, each dnepicting the same macromolecule, improves the resolution compared to the individual subtomogram. Major challenges of subtomogram alignment are noise enhancement due to overfitting, the bias of an initial reference in the iterative alignment process, and the computational cost of processing increasingly large amounts of data. Here, we propose an efficient and accurate alignment algorithm via a generalized convolution theorem, which allows computation of a constrained correlation function using spherical harmonics. This formulation increases computational speed of rotational matching dramatically compared to rotation search in Cartesian space without sacrificing accuracy in contrast to other spherical harmonic based approaches. Using this sampling method, a reference-free alignment procedure is proposed to tackle reference bias and overfitting, which also includes contrast transfer function correction by Wiener filtering. Application of the method to simulated data allowed us to obtain resolutions near the ground truth. For two experimental datasets, ribosomes from yeast lysate and purified 20S proteasomes, we achieved reconstructions of approximately 20Å and 16Å, respectively. The software is ready-to-use and made public to the community. Copyright © 2013 Elsevier Inc. All rights reserved.

  7. Discussion of enthalpy, entropy and free energy of formation of GaN

    NASA Astrophysics Data System (ADS)

    Jacob, K. T.; Rajitha, G.

    2009-07-01

    Presented in this letter is a critical discussion of a recent paper on experimental investigation of the enthalpy, entropy and free energy of formation of gallium nitride (GaN) published in this journal [T.J. Peshek, J.C. Angus, K. Kash, J. Cryst. Growth 311 (2008) 185-189]. It is shown that the experimental technique employed detects neither the equilibrium partial pressure of N 2 corresponding to the equilibrium between Ga and GaN at fixed temperatures nor the equilibrium temperature at constant pressure of N 2. The results of Peshek et al. are discussed in the light of other information on the Gibbs energy of formation available in the literature. Entropy of GaN is derived from heat-capacity measurements. Based on a critical analysis of all thermodynamic information now available, a set of optimized parameters is identified and a table of thermodynamic data for GaN developed from 298.15 to 1400 K.

  8. Enthalpy-Based Thermal Evolution of Loops: III. Comparison of Zero-Dimensional Models

    NASA Technical Reports Server (NTRS)

    Cargill, P. J.; Bradshaw, Stephen J.; Klimchuk, James A.

    2012-01-01

    Zero dimensional (0D) hydrodynamic models, provide a simple and quick way to study the thermal evolution of coronal loops subjected to time-dependent heating. This paper presents a comparison of a number of 0D models that have been published in the past and is intended to provide a guide for those interested in either using the old models or developing new ones. The principal difference between the models is the way the exchange of mass and energy between corona, transition region and chromosphere is treated, as plasma cycles into and out of a loop during a heating-cooling cycle. It is shown that models based on the principles of mass and energy conservation can give satisfactory results at some, or, in the case of the Enthalpy Based Thermal Evolution of Loops (EBTEL) model, all stages of the loop evolution. Empirical models can lead to low coronal densities, spurious delays between the peak density and temperature, and, for short heating pulses, overly short loop lifetimes.

  9. Time-Accurate Simulations and Acoustic Analysis of Slat Free-Shear Layer

    NASA Technical Reports Server (NTRS)

    Khorrami, Mehdi R.; Singer, Bart A.; Berkman, Mert E.

    2001-01-01

    A detailed computational aeroacoustic analysis of a high-lift flow field is performed. Time-accurate Reynolds Averaged Navier-Stokes (RANS) computations simulate the free shear layer that originates from the slat cusp. Both unforced and forced cases are studied. Preliminary results show that the shear layer is a good amplifier of disturbances in the low to mid-frequency range. The Ffowcs-Williams and Hawkings equation is solved to determine the acoustic field using the unsteady flow data from the RANS calculations. The noise radiated from the excited shear layer has a spectral shape qualitatively similar to that obtained from measurements in a corresponding experimental study of the high-lift system.

  10. Computational Study of Nonequilibrium Chemistry in High Temperature Flows

    NASA Astrophysics Data System (ADS)

    Doraiswamy, Sriram

    Recent experimental measurements in the reflected shock tunnel CUBRC LENS-I facility raise questions about our ability to correctly model the recombination processes in high enthalpy flows. In the carbon dioxide flow, the computed shock standoff distance over the Mars Science Laboratory (MSL) shape was less than half of the experimental result. For the oxygen flows, both pressure and heat transfer data on the double cone geometry were not correctly predicted. The objective of this work is to investigate possible reasons for these discrepancies. This process involves systematically addressing different factors that could possibly explain the differences. These factors include vibrational modeling, role of electronic states and chemistry-vibrational coupling in high enthalpy flows. A state-specific vibrational model for CO2, CO, O2 and O system is devised by taking into account the first few vibrational states of each species. All vibrational states with energies at or below 1 eV are included in the present work. Of the three modes of vibration in CO2 , the antisymmetric mode is considered separately from the symmetric stretching mode and the doubly degenerate bending modes. The symmetric and the bending modes are grouped together since the energy transfer rates between the two modes are very large due to Fermi resonance. The symmetric and bending modes are assumed to be in equilibrium with the translational and rotational modes. The kinetic rates for the vibrational-translation energy exchange reactions, and the intermolecular and intramolecular vibrational-vibrational energy exchange reactions are based on experimental data to the maximum extent possible. Extrapolation methods are employed when necessary. This vibrational model is then coupled with an axisymmetric computational fluid dynamics code to study the expansion of CO2 in a nozzle. The potential role of low lying electronic states is also investigated. Carbon dioxide has a single excited state just below

  11. Effect of the pH in the adsorption and in the immersion enthalpy of monohydroxylated phenols from aqueous solutions on activated carbons.

    PubMed

    Blanco-Martínez, D A; Giraldo, L; Moreno-Piraján, J C

    2009-09-30

    An activated carbon Carbochem--PS230 was modified by chemical and thermal treatment in flow of H(2) in order to evaluate the influence of the activated carbon chemical surface in the adsorption of the monohydroxylated phenols. The solid-solution interaction was determined by analyzing the adsorption isotherms at 298 K at pH 7, 9 and 11 during 48 h. The adsorption capacity of activated carbons increases when the pH solution decreases. The amount adsorbed increases in the reduced carbon at the maximum adsorption pH and decreases in the oxidized carbon. In the sample of granulated activated carbon, CAG, the monohydroxylated phenols adsorption capacity diminishes in the following order catechol >hydroquinone >resorcinol, at the three pH values. The experimental data are evaluated with Freundlich's and Langmuir's models. The immersion enthalpies are determined and increase with the retained amount, ranging between 21.5 and 45.7 J g(-1). In addition, the immersion enthalpies show more interaction with the reduced activated carbon that has lower total acidity contents.

  12. Accurate pressure gradient calculations in hydrostatic atmospheric models

    NASA Technical Reports Server (NTRS)

    Carroll, John J.; Mendez-Nunez, Luis R.; Tanrikulu, Saffet

    1987-01-01

    A method for the accurate calculation of the horizontal pressure gradient acceleration in hydrostatic atmospheric models is presented which is especially useful in situations where the isothermal surfaces are not parallel to the vertical coordinate surfaces. The present method is shown to be exact if the potential temperature lapse rate is constant between the vertical pressure integration limits. The technique is applied to both the integration of the hydrostatic equation and the computation of the slope correction term in the horizontal pressure gradient. A fixed vertical grid and a dynamic grid defined by the significant levels in the vertical temperature distribution are employed.

  13. Can a numerically stable subgrid-scale model for turbulent flow computation be ideally accurate?: a preliminary theoretical study for the Gaussian filtered Navier-Stokes equations.

    PubMed

    Ida, Masato; Taniguchi, Nobuyuki

    2003-09-01

    This paper introduces a candidate for the origin of the numerical instabilities in large eddy simulation repeatedly observed in academic and practical industrial flow computations. Without resorting to any subgrid-scale modeling, but based on a simple assumption regarding the streamwise component of flow velocity, it is shown theoretically that in a channel-flow computation, the application of the Gaussian filtering to the incompressible Navier-Stokes equations yields a numerically unstable term, a cross-derivative term, which is similar to one appearing in the Gaussian filtered Vlasov equation derived by Klimas [J. Comput. Phys. 68, 202 (1987)] and also to one derived recently by Kobayashi and Shimomura [Phys. Fluids 15, L29 (2003)] from the tensor-diffusivity subgrid-scale term in a dynamic mixed model. The present result predicts that not only the numerical methods and the subgrid-scale models employed but also only the applied filtering process can be a seed of this numerical instability. An investigation concerning the relationship between the turbulent energy scattering and the unstable term shows that the instability of the term does not necessarily represent the backscatter of kinetic energy which has been considered a possible origin of numerical instabilities in large eddy simulation. The present findings raise the question whether a numerically stable subgrid-scale model can be ideally accurate.

  14. A dental vision system for accurate 3D tooth modeling.

    PubMed

    Zhang, Li; Alemzadeh, K

    2006-01-01

    This paper describes an active vision system based reverse engineering approach to extract the three-dimensional (3D) geometric information from dental teeth and transfer this information into Computer-Aided Design/Computer-Aided Manufacture (CAD/CAM) systems to improve the accuracy of 3D teeth models and at the same time improve the quality of the construction units to help patient care. The vision system involves the development of a dental vision rig, edge detection, boundary tracing and fast & accurate 3D modeling from a sequence of sliced silhouettes of physical models. The rig is designed using engineering design methods such as a concept selection matrix and weighted objectives evaluation chart. Reconstruction results and accuracy evaluation are presented on digitizing different teeth models.

  15. Production, pathways and budgets of melts in mid-ocean ridges: An enthalpy based thermo-mechanical model

    NASA Astrophysics Data System (ADS)

    Mandal, Nibir; Sarkar, Shamik; Baruah, Amiya; Dutta, Urmi

    2018-04-01

    Using an enthalpy based thermo-mechanical model we provide a theoretical evaluation of melt production beneath mid-ocean ridges (MORs), and demonstrate how the melts subsequently develop their pathways to sustain the major ridge processes. Our model employs a Darcy idealization of the two-phase (solid-melt) system, accounting enthalpy (ΔH) as a function of temperature dependent liquid fraction (ϕ). Random thermal perturbations imposed in this model set in local convection that drive melts to flow through porosity controlled pathways with a typical mushroom-like 3D structure. We present across- and along-MOR axis model profiles to show the mode of occurrence of melt-rich zones within mushy regions, connected to deeper sources by single or multiple feeders. The upwelling of melts experiences two synchronous processes: 1) solidification-accretion, and 2) eruption, retaining a large melt fraction in the framework of mantle dynamics. Using a bifurcation analysis we determine the threshold condition for melt eruption, and estimate the potential volumes of eruptible melts (∼3.7 × 106 m3/yr) and sub-crustal solidified masses (∼1-8.8 × 106 m3/yr) on an axis length of 500 km. The solidification process far dominates over the eruption process in the initial phase, but declines rapidly on a time scale (t) of 1 Myr. Consequently, the eruption rate takes over the solidification rate, but attains nearly a steady value as t > 1.5 Myr. We finally present a melt budget, where a maximum of ∼5% of the total upwelling melt volume is available for eruption, whereas ∼19% for deeper level solidification; the rest continue to participate in the sub-crustal processes.

  16. Dissociation constants, neutralization enthalpies and reactions of 3-styryl-2-mercaptopropenoic and 3-(1-naphthyl)-2-mercaptopropenoic acids.

    PubMed

    Izquierdo, A; Bosch, E; Beltran, J L

    1984-06-01

    Dissociation constants (pK(a1) and pK(a2) in water-ethanol medium for 3-styryl-2-mercaptopropenoic and 3-(1-naphthyl)-2-mercaptopropenoic acid have been determined potentiometrically, and pK(a2) for both in aqueous medium, spectrophotometrically. Neutralization enthalpies in water-ethanol medium have been determined by thermometric titration. The reactions with metal ions have been studied, and the main reactions are described. The most sensitive reactions are with titanium(IV) (pD = 7.00) and nickel(II) (pD = 6.50).

  17. Low-Temperature Heat Capacities and Standard Molar Enthalpy of Formation of Potassium Benzoate C7H5O2K(s)

    NASA Astrophysics Data System (ADS)

    Yang, Wei-Wei; di, You-Ying; Yin, Zhen-Fen; Kong, Yu-Xia; Tan, Zhi-Cheng

    2009-04-01

    Potassium benzoate C7H5O2K (CAS Registry No. 582-25-2) was synthesized by the method of liquid phase reaction. Chemical and elemental analyses, FTIR, and X-ray powder diffraction (XRD) techniques were applied to characterize the composition and structure of the compound. Low-temperature heat capacities of the compound were measured by a precision automated adiabatic calorimeter over the temperature range from 78 K to 398 K. A polynomial equation of the heat capacities as a function of temperature was fitted by the least-squares method. Smoothed heat capacities and thermodynamic functions of the compound were calculated based on the fitted polynomial. In accordance with Hess’s law, a reasonable thermochemical cycle was designed, and 100 mL of 1 mol · dm-3 NaOH solution was chosen as the calorimetric solvent. The standard molar enthalpies of dissolution for the reactants and products of the supposed reaction in the selected solvent were measured by an isoperibol solution-reaction calorimeter. Finally, the standard molar enthalpy of formation of the title compound C7H5O2K (s) was derived to be -(610.94 ± 0.77) kJ · mol-1.

  18. Accurate computation and continuation of homoclinic and heteroclinic orbits for singular perturbation problems

    NASA Technical Reports Server (NTRS)

    Vaughan, William W.; Friedman, Mark J.; Monteiro, Anand C.

    1993-01-01

    In earlier papers, Doedel and the authors have developed a numerical method and derived error estimates for the computation of branches of heteroclinic orbits for a system of autonomous ordinary differential equations in R(exp n). The idea of the method is to reduce a boundary value problem on the real line to a boundary value problem on a finite interval by using a local (linear or higher order) approximation of the stable and unstable manifolds. A practical limitation for the computation of homoclinic and heteroclinic orbits has been the difficulty in obtaining starting orbits. Typically these were obtained from a closed form solution or via a homotopy from a known solution. Here we consider extensions of our algorithm which allow us to obtain starting orbits on the continuation branch in a more systematic way as well as make the continuation algorithm more flexible. In applications, we use the continuation software package AUTO in combination with some initial value software. The examples considered include computation of homoclinic orbits in a singular perturbation problem and in a turbulent fluid boundary layer in the wall region problem.

  19. Accurate van der Waals coefficients from density functional theory

    PubMed Central

    Tao, Jianmin; Perdew, John P.; Ruzsinszky, Adrienn

    2012-01-01

    The van der Waals interaction is a weak, long-range correlation, arising from quantum electronic charge fluctuations. This interaction affects many properties of materials. A simple and yet accurate estimate of this effect will facilitate computer simulation of complex molecular materials and drug design. Here we develop a fast approach for accurate evaluation of dynamic multipole polarizabilities and van der Waals (vdW) coefficients of all orders from the electron density and static multipole polarizabilities of each atom or other spherical object, without empirical fitting. Our dynamic polarizabilities (dipole, quadrupole, octupole, etc.) are exact in the zero- and high-frequency limits, and exact at all frequencies for a metallic sphere of uniform density. Our theory predicts dynamic multipole polarizabilities in excellent agreement with more expensive many-body methods, and yields therefrom vdW coefficients C6, C8, C10 for atom pairs with a mean absolute relative error of only 3%. PMID:22205765

  20. Discrete breathers dynamic in a model for DNA chain with a finite stacking enthalpy

    NASA Astrophysics Data System (ADS)

    Gninzanlong, Carlos Lawrence; Ndjomatchoua, Frank Thomas; Tchawoua, Clément

    2018-04-01

    The nonlinear dynamics of a homogeneous DNA chain based on site-dependent finite stacking and pairing enthalpies is studied. A new variant of extended discrete nonlinear Schrödinger equation describing the dynamics of modulated wave is derived. The regions of discrete modulational instability of plane carrier waves are studied, and it appears that these zones depend strongly on the phonon frequency of Fourier's mode. The staggered/unstaggered discrete breather (SDB/USDB) is obtained straightforwardly without the staggering transformation, and it is demonstrated that SDBs are less unstable than USDB. The instability of discrete multi-humped SDB/USDB solution does not depend on the number of peaks of the discrete breather (DB). By using the concept of Peierls-Nabarro energy barrier, it appears that the low-frequency DBs are more mobile.

  1. Efficiency and Accuracy of Time-Accurate Turbulent Navier-Stokes Computations

    NASA Technical Reports Server (NTRS)

    Rumsey, Christopher L.; Sanetrik, Mark D.; Biedron, Robert T.; Melson, N. Duane; Parlette, Edward B.

    1995-01-01

    The accuracy and efficiency of two types of subiterations in both explicit and implicit Navier-Stokes codes are explored for unsteady laminar circular-cylinder flow and unsteady turbulent flow over an 18-percent-thick circular-arc (biconvex) airfoil. Grid and time-step studies are used to assess the numerical accuracy of the methods. Nonsubiterative time-stepping schemes and schemes with physical time subiterations are subject to time-step limitations in practice that are removed by pseudo time sub-iterations. Computations for the circular-arc airfoil indicate that a one-equation turbulence model predicts the unsteady separated flow better than an algebraic turbulence model; also, the hysteresis with Mach number of the self-excited unsteadiness due to shock and boundary-layer separation is well predicted.

  2. Exploiting Locality in Quantum Computation for Quantum Chemistry.

    PubMed

    McClean, Jarrod R; Babbush, Ryan; Love, Peter J; Aspuru-Guzik, Alán

    2014-12-18

    Accurate prediction of chemical and material properties from first-principles quantum chemistry is a challenging task on traditional computers. Recent developments in quantum computation offer a route toward highly accurate solutions with polynomial cost; however, this solution still carries a large overhead. In this Perspective, we aim to bring together known results about the locality of physical interactions from quantum chemistry with ideas from quantum computation. We show that the utilization of spatial locality combined with the Bravyi-Kitaev transformation offers an improvement in the scaling of known quantum algorithms for quantum chemistry and provides numerical examples to help illustrate this point. We combine these developments to improve the outlook for the future of quantum chemistry on quantum computers.

  3. A Time-Accurate Upwind Unstructured Finite Volume Method for Compressible Flow with Cure of Pathological Behaviors

    NASA Technical Reports Server (NTRS)

    Loh, Ching Y.; Jorgenson, Philip C. E.

    2007-01-01

    A time-accurate, upwind, finite volume method for computing compressible flows on unstructured grids is presented. The method is second order accurate in space and time and yields high resolution in the presence of discontinuities. For efficiency, the Roe approximate Riemann solver with an entropy correction is employed. In the basic Euler/Navier-Stokes scheme, many concepts of high order upwind schemes are adopted: the surface flux integrals are carefully treated, a Cauchy-Kowalewski time-stepping scheme is used in the time-marching stage, and a multidimensional limiter is applied in the reconstruction stage. However even with these up-to-date improvements, the basic upwind scheme is still plagued by the so-called "pathological behaviors," e.g., the carbuncle phenomenon, the expansion shock, etc. A solution to these limitations is presented which uses a very simple dissipation model while still preserving second order accuracy. This scheme is referred to as the enhanced time-accurate upwind (ETAU) scheme in this paper. The unstructured grid capability renders flexibility for use in complex geometry; and the present ETAU Euler/Navier-Stokes scheme is capable of handling a broad spectrum of flow regimes from high supersonic to subsonic at very low Mach number, appropriate for both CFD (computational fluid dynamics) and CAA (computational aeroacoustics). Numerous examples are included to demonstrate the robustness of the methods.

  4. 40 CFR 194.23 - Models and computer codes.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 40 Protection of Environment 26 2013-07-01 2013-07-01 false Models and computer codes. 194.23... General Requirements § 194.23 Models and computer codes. (a) Any compliance application shall include: (1... obtain stable solutions; (iv) Computer models accurately implement the numerical models; i.e., computer...

  5. 40 CFR 194.23 - Models and computer codes.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 40 Protection of Environment 26 2012-07-01 2011-07-01 true Models and computer codes. 194.23... General Requirements § 194.23 Models and computer codes. (a) Any compliance application shall include: (1... obtain stable solutions; (iv) Computer models accurately implement the numerical models; i.e., computer...

  6. 40 CFR 194.23 - Models and computer codes.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 40 Protection of Environment 25 2014-07-01 2014-07-01 false Models and computer codes. 194.23... General Requirements § 194.23 Models and computer codes. (a) Any compliance application shall include: (1... obtain stable solutions; (iv) Computer models accurately implement the numerical models; i.e., computer...

  7. 40 CFR 194.23 - Models and computer codes.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 40 Protection of Environment 24 2010-07-01 2010-07-01 false Models and computer codes. 194.23... General Requirements § 194.23 Models and computer codes. (a) Any compliance application shall include: (1... obtain stable solutions; (iv) Computer models accurately implement the numerical models; i.e., computer...

  8. 40 CFR 194.23 - Models and computer codes.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 40 Protection of Environment 25 2011-07-01 2011-07-01 false Models and computer codes. 194.23... General Requirements § 194.23 Models and computer codes. (a) Any compliance application shall include: (1... obtain stable solutions; (iv) Computer models accurately implement the numerical models; i.e., computer...

  9. Tau-independent Phase Analysis: A Novel Method for Accurately Determining Phase Shifts.

    PubMed

    Tackenberg, Michael C; Jones, Jeff R; Page, Terry L; Hughey, Jacob J

    2018-06-01

    Estimations of period and phase are essential in circadian biology. While many techniques exist for estimating period, comparatively few methods are available for estimating phase. Current approaches to analyzing phase often vary between studies and are sensitive to coincident changes in period and the stage of the circadian cycle at which the stimulus occurs. Here we propose a new technique, tau-independent phase analysis (TIPA), for quantifying phase shifts in multiple types of circadian time-course data. Through comprehensive simulations, we show that TIPA is both more accurate and more precise than the standard actogram approach. TIPA is computationally simple and therefore will enable accurate and reproducible quantification of phase shifts across multiple subfields of chronobiology.

  10. FILMPAR: A parallel algorithm designed for the efficient and accurate computation of thin film flow on functional surfaces containing micro-structure

    NASA Astrophysics Data System (ADS)

    Lee, Y. C.; Thompson, H. M.; Gaskell, P. H.

    2009-12-01

    , industrial and physical applications. However, despite recent modelling advances, the accurate numerical solution of the equations governing such problems is still at a relatively early stage. Indeed, recent studies employing a simplifying long-wave approximation have shown that highly efficient numerical methods are necessary to solve the resulting lubrication equations in order to achieve the level of grid resolution required to accurately capture the effects of micro- and nano-scale topographical features. Solution method: A portable parallel multigrid algorithm has been developed for the above purpose, for the particular case of flow over submerged topographical features. Within the multigrid framework adopted, a W-cycle is used to accelerate convergence in respect of the time dependent nature of the problem, with relaxation sweeps performed using a fixed number of pre- and post-Red-Black Gauss-Seidel Newton iterations. In addition, the algorithm incorporates automatic adaptive time-stepping to avoid the computational expense associated with repeated time-step failure. Running time: 1.31 minutes using 128 processors on BlueGene/P with a problem size of over 16.7 million mesh points.

  11. Computational Fluid Dynamics of Whole-Body Aircraft

    NASA Astrophysics Data System (ADS)

    Agarwal, Ramesh

    1999-01-01

    The current state of the art in computational aerodynamics for whole-body aircraft flowfield simulations is described. Recent advances in geometry modeling, surface and volume grid generation, and flow simulation algorithms have led to accurate flowfield predictions for increasingly complex and realistic configurations. As a result, computational aerodynamics has emerged as a crucial enabling technology for the design and development of flight vehicles. Examples illustrating the current capability for the prediction of transport and fighter aircraft flowfields are presented. Unfortunately, accurate modeling of turbulence remains a major difficulty in the analysis of viscosity-dominated flows. In the future, inverse design methods, multidisciplinary design optimization methods, artificial intelligence technology, and massively parallel computer technology will be incorporated into computational aerodynamics, opening up greater opportunities for improved product design at substantially reduced costs.

  12. On canonical cylinder sections for accurate determination of contact angle in microgravity

    NASA Technical Reports Server (NTRS)

    Concus, Paul; Finn, Robert; Zabihi, Farhad

    1992-01-01

    Large shifts of liquid arising from small changes in certain container shapes in zero gravity can be used as a basis for accurately determining contact angle. Canonical geometries for this purpose, recently developed mathematically, are investigated here computationally. It is found that the desired nearly-discontinuous behavior can be obtained and that the shifts of liquid have sufficient volume to be readily observed.

  13. A computer-based physics laboratory apparatus: Signal generator software

    NASA Astrophysics Data System (ADS)

    Thanakittiviroon, Tharest; Liangrocapart, Sompong

    2005-09-01

    This paper describes a computer-based physics laboratory apparatus to replace expensive instruments such as high-precision signal generators. This apparatus uses a sound card in a common personal computer to give sinusoidal signals with an accurate frequency that can be programmed to give different frequency signals repeatedly. An experiment on standing waves on an oscillating string uses this apparatus. In conjunction with interactive lab manuals, which have been developed using personal computers in our university, we achieve a complete set of low-cost, accurate, and easy-to-use equipment for teaching a physics laboratory.

  14. DNA Nanostructures as Models for Evaluating the Role of Enthalpy and Entropy in Polyvalent Binding

    PubMed Central

    Nangreave, Jeanette; Yan, Hao; Liu, Yan

    2011-01-01

    DNA nanotechnology allows the design and construction of nano-scale objects that have finely tuned dimensions, orientation, and structure with remarkable ease and convenience. Synthetic DNA nanostructures can be precisely engineered to model a variety of molecules and systems, providing the opportunity to probe very subtle biophysical phenomena. In this study, several such synthetic DNA nanostructures were designed to serve as models to study the binding behavior of polyvalent molecules and gain insight into how small changes to the ligand/receptor scaffolds, intended to vary their conformational flexibility, will affect their association equilibrium. This approach has yielded a quantitative identification of the roles of enthalpy and entropy in the affinity of polyvalent DNA nanostructure interactions, which exhibit an intriguing compensating effect. PMID:21381740

  15. Thermodynamic limitations on the temperature sensitivity of cell-membrane ion channels: Trouble with enthalpy uncertainty

    NASA Astrophysics Data System (ADS)

    Zheltikov, A. M.

    2018-06-01

    Energy exchange between a thermodynamic ensemble of heat- and cold-activated cell-membrane ion channels and the surrounding heat reservoir is shown to impose fundamental limitations on the performance of such channels as temperature-controlled gates for thermal cell activation. Analysis of unavoidable thermodynamic internal-energy fluctuations caused by energy exchange between the ion channels and the heat bath suggests that the resulting enthalpy uncertainty is too high for a robust ion-current gating by a single ion channel, implying that large ensembles of ion channels are needed for thermal cell activation. We argue, based on this thermodynamic analysis, that, had thermosensitive cell-membrane ion channels operated individually, rather than as large ensembles, robust thermal cell activation would have been impossible because of thermodynamic fluctuations.

  16. Thermal Conductivities in Solids from First Principles: Accurate Computations and Rapid Estimates

    NASA Astrophysics Data System (ADS)

    Carbogno, Christian; Scheffler, Matthias

    In spite of significant research efforts, a first-principles determination of the thermal conductivity κ at high temperatures has remained elusive. Boltzmann transport techniques that account for anharmonicity perturbatively become inaccurate under such conditions. Ab initio molecular dynamics (MD) techniques using the Green-Kubo (GK) formalism capture the full anharmonicity, but can become prohibitively costly to converge in time and size. We developed a formalism that accelerates such GK simulations by several orders of magnitude and that thus enables its application within the limited time and length scales accessible in ab initio MD. For this purpose, we determine the effective harmonic potential occurring during the MD, the associated temperature-dependent phonon properties and lifetimes. Interpolation in reciprocal and frequency space then allows to extrapolate to the macroscopic scale. For both force-field and ab initio MD, we validate this approach by computing κ for Si and ZrO2, two materials known for their particularly harmonic and anharmonic character. Eventually, we demonstrate how these techniques facilitate reasonable estimates of κ from existing MD calculations at virtually no additional computational cost.

  17. Laser absorption of nitric oxide for thermometry in high-enthalpy air

    NASA Astrophysics Data System (ADS)

    Spearrin, R. M.; Schultz, I. A.; Jeffries, J. B.; Hanson, R. K.

    2014-12-01

    The design and demonstration of a laser absorption sensor for thermometry in high-enthalpy air is presented. The sensor exploits the highly temperature-sensitive and largely pressure-independent concentration of nitric oxide in air at chemical equilibrium. Temperature is thus inferred from an in situ measurement of nascent nitric oxide. The strategy is developed by utilizing a quantum cascade laser source for access to the strong fundamental absorption band in the mid-infrared spectrum of nitric oxide. Room temperature measurements in a high-pressure static cell validate the suitability of the Voigt lineshape model to the nitric oxide spectra at high gas densities. Shock-tube experiments enable calibration of a collision-broadening model for temperatures between 1200-3000 K. Finally, sensor performance is demonstrated in a high-pressure shock tube by measuring temperature behind reflected shock waves for both fixed-chemistry experiments where nitric oxide is seeded, and for experiments involving nitric oxide formation in shock-heated mixtures of N2 and O2. Results show excellent performance of the sensor across a wide range of operating conditions from 1100-2950 K and at pressures up to 140 atm.

  18. Computational Simulations of the NASA Langley HyMETS Arc-Jet Facility

    NASA Technical Reports Server (NTRS)

    Brune, A. J.; Bruce, W. E., III; Glass, D. E.; Splinter, S. C.

    2017-01-01

    The Hypersonic Materials Environmental Test System (HyMETS) arc-jet facility located at the NASA Langley Research Center in Hampton, Virginia, is primarily used for the research, development, and evaluation of high-temperature thermal protection systems for hypersonic vehicles and reentry systems. In order to improve testing capabilities and knowledge of the test article environment, an effort is underway to computationally simulate the flow-field using computational fluid dynamics (CFD). A detailed three-dimensional model of the arc-jet nozzle and free-jet portion of the flow-field has been developed and compared to calibration probe Pitot pressure and stagnation-point heat flux for three test conditions at low, medium, and high enthalpy. The CFD model takes into account uniform pressure and non-uniform enthalpy profiles at the nozzle inlet as well as catalytic recombination efficiency effects at the probe surface. Comparing the CFD results and test data indicates an effectively fully-catalytic copper surface on the heat flux probe of about 10% efficiency and a 2-3 kpa pressure drop from the arc heater bore, where the pressure is measured, to the plenum section, prior to the nozzle. With these assumptions, the CFD results are well within the uncertainty of the stagnation pressure and heat flux measurements. The conditions at the nozzle exit were also compared with radial and axial velocimetry. This simulation capability will be used to evaluate various three-dimensional models that are tested in the HyMETS facility. An end-to-end aerothermal and thermal simulation of HyMETS test articles will follow this work to provide a better understanding of the test environment, test results, and to aid in test planning. Additional flow-field diagnostic measurements will also be considered to improve the modeling capability.

  19. A fast and accurate dihedral interpolation loop subdivision scheme

    NASA Astrophysics Data System (ADS)

    Shi, Zhuo; An, Yalei; Wang, Zhongshuai; Yu, Ke; Zhong, Si; Lan, Rushi; Luo, Xiaonan

    2018-04-01

    In this paper, we propose a fast and accurate dihedral interpolation Loop subdivision scheme for subdivision surfaces based on triangular meshes. In order to solve the problem of surface shrinkage, we keep the limit condition unchanged, which is important. Extraordinary vertices are handled using modified Butterfly rules. Subdivision schemes are computationally costly as the number of faces grows exponentially at higher levels of subdivision. To address this problem, our approach is to use local surface information to adaptively refine the model. This is achieved simply by changing the threshold value of the dihedral angle parameter, i.e., the angle between the normals of a triangular face and its adjacent faces. We then demonstrate the effectiveness of the proposed method for various 3D graphic triangular meshes, and extensive experimental results show that it can match or exceed the expected results at lower computational cost.

  20. Enabling fast, stable and accurate peridynamic computations using multi-time-step integration

    DOE PAGES

    Lindsay, P.; Parks, M. L.; Prakash, A.

    2016-04-13

    Peridynamics is a nonlocal extension of classical continuum mechanics that is well-suited for solving problems with discontinuities such as cracks. This paper extends the peridynamic formulation to decompose a problem domain into a number of smaller overlapping subdomains and to enable the use of different time steps in different subdomains. This approach allows regions of interest to be isolated and solved at a small time step for increased accuracy while the rest of the problem domain can be solved at a larger time step for greater computational efficiency. Lastly, performance of the proposed method in terms of stability, accuracy, andmore » computational cost is examined and several numerical examples are presented to corroborate the findings.« less

  1. Toward Accurate and Quantitative Comparative Metagenomics

    PubMed Central

    Nayfach, Stephen; Pollard, Katherine S.

    2016-01-01

    Shotgun metagenomics and computational analysis are used to compare the taxonomic and functional profiles of microbial communities. Leveraging this approach to understand roles of microbes in human biology and other environments requires quantitative data summaries whose values are comparable across samples and studies. Comparability is currently hampered by the use of abundance statistics that do not estimate a meaningful parameter of the microbial community and biases introduced by experimental protocols and data-cleaning approaches. Addressing these challenges, along with improving study design, data access, metadata standardization, and analysis tools, will enable accurate comparative metagenomics. We envision a future in which microbiome studies are replicable and new metagenomes are easily and rapidly integrated with existing data. Only then can the potential of metagenomics for predictive ecological modeling, well-powered association studies, and effective microbiome medicine be fully realized. PMID:27565341

  2. Absolute Hounsfield unit measurement on noncontrast computed tomography cannot accurately predict struvite stone composition.

    PubMed

    Marchini, Giovanni Scala; Gebreselassie, Surafel; Liu, Xiaobo; Pynadath, Cindy; Snyder, Grace; Monga, Manoj

    2013-02-01

    The purpose of our study was to determine, in vivo, whether single-energy noncontrast computed tomography (NCCT) can accurately predict the presence/percentage of struvite stone composition. We retrospectively searched for all patients with struvite components on stone composition analysis between January 2008 and March 2012. Inclusion criteria were NCCT prior to stone analysis and stone size ≥4 mm. A single urologist, blinded to stone composition, reviewed all NCCT to acquire stone location, dimensions, and Hounsfield unit (HU). HU density (HUD) was calculated by dividing mean HU by the stone's largest transverse diameter. Stone analysis was performed via Fourier transform infrared spectrometry. Independent sample Student's t-test and analysis of variance (ANOVA) were used to compare HU/HUD among groups. Spearman's correlation test was used to determine the correlation between HU and stone size and also HU/HUD to % of each component within the stone. Significance was considered if p<0.05. Fourty-four patients met the inclusion criteria. Struvite was the most prevalent component with mean percentage of 50.1%±17.7%. Mean HU and HUD were 820.2±357.9 and 67.5±54.9, respectively. Struvite component analysis revealed a nonsignificant positive correlation with HU (R=0.017; p=0.912) and negative with HUD (R=-0.20; p=0.898). Overall, 3 (6.8%) had <20% of struvite component; 11 (25%), 25 (56.8%), and 5 (11.4%) had 21% to 40%, 41% to 60%, and 61% to 80% of struvite, respectively. ANOVA revealed no difference among groups regarding HU (p=0.68) and HUD (p=0.37), with important overlaps. When comparing pure struvite stones (n=5) with other miscellaneous stones (n=39), no difference was found for HU (p=0.09) but HUD was significantly lower for pure stones (27.9±23.6 v 72.5±55.9, respectively; p=0.006). Again, significant overlaps were seen. Pure struvite stones have significantly lower HUD than mixed struvite stones, but overlap exists. A low HUD may increase the

  3. Accurate quantum Z rotations with less magic

    NASA Astrophysics Data System (ADS)

    Landahl, Andrew; Cesare, Chris

    2013-03-01

    We present quantum protocols for executing arbitrarily accurate π /2k rotations of a qubit about its Z axis. Unlike reduced instruction set computing (RISC) protocols which use a two-step process of synthesizing high-fidelity ``magic'' states from which T = Z (π / 4) gates can be teleported and then compiling a sequence of adaptive stabilizer operations and T gates to approximate Z (π /2k) , our complex instruction set computing (CISC) protocol distills magic states for the Z (π /2k) gates directly. Replacing this two-step process with a single step results in substantial reductions in the number of gates needed. The key to our construction is a family of shortened quantum Reed-Muller codes of length 2 k + 2 - 1 , whose distillation threshold shrinks with k but is greater than 0.85% for k <= 6 . AJL and CC were supported in part by the Laboratory Directed Research and Development program at Sandia National Laboratories. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000.

  4. Accurate spectroscopic characterization of oxirane: A valuable route to its identification in Titan's atmosphere and the assignment of unidentified infrared bands

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

    Puzzarini, Cristina; Biczysko, Malgorzata; Bloino, Julien

    2014-04-20

    In an effort to provide an accurate spectroscopic characterization of oxirane, state-of-the-art computational methods and approaches have been employed to determine highly accurate fundamental vibrational frequencies and rotational parameters. Available experimental data were used to assess the reliability of our computations, and an accuracy on average of 10 cm{sup –1} for fundamental transitions as well as overtones and combination bands has been pointed out. Moving to rotational spectroscopy, relative discrepancies of 0.1%, 2%-3%, and 3%-4% were observed for rotational, quartic, and sextic centrifugal-distortion constants, respectively. We are therefore confident that the highly accurate spectroscopic data provided herein can be usefulmore » for identification of oxirane in Titan's atmosphere and the assignment of unidentified infrared bands. Since oxirane was already observed in the interstellar medium and some astronomical objects are characterized by very high D/H ratios, we also considered the accurate determination of the spectroscopic parameters for the mono-deuterated species, oxirane-d1. For the latter, an empirical scaling procedure allowed us to improve our computed data and to provide predictions for rotational transitions with a relative accuracy of about 0.02% (i.e., an uncertainty of about 40 MHz for a transition lying at 200 GHz).« less

  5. Accurate and computationally efficient prediction of thermochemical properties of biomolecules using the generalized connectivity-based hierarchy.

    PubMed

    Sengupta, Arkajyoti; Ramabhadran, Raghunath O; Raghavachari, Krishnan

    2014-08-14

    In this study we have used the connectivity-based hierarchy (CBH) method to derive accurate heats of formation of a range of biomolecules, 18 amino acids and 10 barbituric acid/uracil derivatives. The hierarchy is based on the connectivity of the different atoms in a large molecule. It results in error-cancellation reaction schemes that are automated, general, and can be readily used for a broad range of organic molecules and biomolecules. Herein, we first locate stable conformational and tautomeric forms of these biomolecules using an accurate level of theory (viz. CCSD(T)/6-311++G(3df,2p)). Subsequently, the heats of formation of the amino acids are evaluated using the CBH-1 and CBH-2 schemes and routinely employed density functionals or wave function-based methods. The calculated heats of formation obtained herein using modest levels of theory and are in very good agreement with those obtained using more expensive W1-F12 and W2-F12 methods on amino acids and G3 results on barbituric acid derivatives. Overall, the present study (a) highlights the small effect of including multiple conformers in determining the heats of formation of biomolecules and (b) in concurrence with previous CBH studies, proves that use of the more effective error-cancelling isoatomic scheme (CBH-2) results in more accurate heats of formation with modestly sized basis sets along with common density functionals or wave function-based methods.

  6. Thermodynamic studies of aqueous solutions of 2,2,2-cryptand at 298.15 K: enthalpy-entropy compensation, partial entropies, and complexation with K+ ions.

    PubMed

    Shaikh, Vasim R; Terdale, Santosh S; Ahamad, Abdul; Gupta, Gaurav R; Dagade, Dilip H; Hundiwale, Dilip G; Patil, Kesharsingh J

    2013-12-19

    The osmotic coefficient measurements for binary aqueous solutions of 2,2,2-cryptand (4,7,13,16,21,24-hexaoxa-1,10-diazabicyclo[8.8.8] hexacosane) in the concentration range of ~0.009 to ~0.24 mol·kg(-1) and in ternary aqueous solutions containing a fixed concentration of 2,2,2-cryptand of ~0.1 mol·kg(-1) with varying concentration of KBr (~0.06 to ~0.16 mol·kg(-1)) have been reported at 298.15 K. The diamine gets hydrolyzed in aqueous solutions and needs proper approach to obtain meaningful thermodynamic properties. The measured osmotic coefficient values are corrected for hydrolysis and are used to determine the solvent activity and mean ionic activity coefficients of solute as a function of concentration. Strong ion-pair formation is observed, and the ion-pair dissociation constant for the species [CrptH](+)[OH(-)] is reported. The excess and mixing thermodynamic properties (Gibbs free energy, enthalpy, and entropy changes) have been obtained using the activity data from this study and the heat data reported in the literature. Further, the data are utilized to compute the partial molal entropies of solvent and solute at finite as well as infinite dilution of 2,2,2-cryptand in water. The concentration dependent non-linear enthalpy-entropy compensation effect has been observed for the studied system, and the compensation temperature along with entropic parameter are reported. Using solute activity coefficient data in ternary solutions, the transfer Gibbs free energies for transfer of the cryptand from water to aqueous KBr as well as transfer of KBr from water to aqueous cryptand were obtained and utilized to obtain the salting constant (ks) and thermodynamic equilibrium constant (log K) values for the complex (2,2,2-cryptand:K(+)) at 298.15 K. The value of log K = 5.8 ± 0.1 obtained in this work is found to be in good agreement with that reported by Lehn and Sauvage. The standard molar entropy for complexation is also estimated for the 2,2,2-cryptand

  7. Time-Accurate Numerical Prediction of Free Flight Aerodynamics of a Finned Projectile

    DTIC Science & Technology

    2005-09-01

    develop (with fewer dollars) more lethal and effective munitions. The munitions must stay abreast of the latest technology available to our...consuming. Computer simulations can and have provided an effective means of determining the unsteady aerodynamics and flight mechanics of guided projectile...Recently, the time-accurate technique was used to obtain improved results for Magnus moment and roll damping moment of a spinning projectile at transonic

  8. Magnetic gaps in organic tri-radicals: From a simple model to accurate estimates.

    PubMed

    Barone, Vincenzo; Cacelli, Ivo; Ferretti, Alessandro; Prampolini, Giacomo

    2017-03-14

    The calculation of the energy gap between the magnetic states of organic poly-radicals still represents a challenging playground for quantum chemistry, and high-level techniques are required to obtain accurate estimates. On these grounds, the aim of the present study is twofold. From the one side, it shows that, thanks to recent algorithmic and technical improvements, we are able to compute reliable quantum mechanical results for the systems of current fundamental and technological interest. From the other side, proper parameterization of a simple Hubbard Hamiltonian allows for a sound rationalization of magnetic gaps in terms of basic physical effects, unraveling the role played by electron delocalization, Coulomb repulsion, and effective exchange in tuning the magnetic character of the ground state. As case studies, we have chosen three prototypical organic tri-radicals, namely, 1,3,5-trimethylenebenzene, 1,3,5-tridehydrobenzene, and 1,2,3-tridehydrobenzene, which differ either for geometric or electronic structure. After discussing the differences among the three species and their consequences on the magnetic properties in terms of the simple model mentioned above, accurate and reliable values for the energy gap between the lowest quartet and doublet states are computed by means of the so-called difference dedicated configuration interaction (DDCI) technique, and the final results are discussed and compared to both available experimental and computational estimates.

  9. Experimental and computational thermochemical study of α-alanine (DL) and β-alanine.

    PubMed

    da Silva, Manuel A V Ribeiro; da Silva, Maria das Dores M C Ribeiro; Santos, Ana Filipa L O M; Roux, Maria Victoria; Foces-Foces, Concepción; Notario, Rafael; Guzmán-Mejía, Ramón; Juaristi, Eusebio

    2010-12-16

    This paper reports an experimental and theoretical study of the gas phase standard (p° = 0.1 MPa) molar enthalpies of formation, at T = 298.15 K, of α-alanine (DL) and β-alanine. The standard (p° = 0.1 MPa) molar enthalpies of formation of crystalline α-alanine (DL) and β-alanine were calculated from the standard molar energies of combustion, in oxygen, to yield CO2(g), N2(g), and H2O(l), measured by static-bomb combustion calorimetry at T = 298.15 K. The vapor pressures of both amino acids were measured as function of temperature by the Knudsen effusion mass-loss technique. The standard molar enthalpies of sublimation at T = 298.15 K was derived from the Clausius−Clapeyron equation. The experimental values were used to calculate the standard (p° = 0.1 MPa) enthalpy of formation of α-alanine (DL) and β-alanine in the gaseous phase, Δ(f)H(m)°(g), as −426.3 ± 2.9 and −421.2 ± 1.9 kJ·mol(−1), respectively. Standard ab initio molecular orbital calculations at the G3 level were performed. Enthalpies of formation, using atomization reactions, were calculated and compared with experimental data. Detailed inspections of the molecular and electronic structures of the compounds studied were carried out.

  10. Two distinct DNA sequences recognized by transcription factors represent enthalpy and entropy optima

    PubMed Central

    Yin, Yimeng; Das, Pratyush K; Jolma, Arttu; Zhu, Fangjie; Popov, Alexander; Xu, You; Nilsson, Lennart

    2018-01-01

    Most transcription factors (TFs) can bind to a population of sequences closely related to a single optimal site. However, some TFs can bind to two distinct sequences that represent two local optima in the Gibbs free energy of binding (ΔG). To determine the molecular mechanism behind this effect, we solved the structures of human HOXB13 and CDX2 bound to their two optimal DNA sequences, CAATAAA and TCGTAAA. Thermodynamic analyses by isothermal titration calorimetry revealed that both sites were bound with similar ΔG. However, the interaction with the CAA sequence was driven by change in enthalpy (ΔH), whereas the TCG site was bound with similar affinity due to smaller loss of entropy (ΔS). This thermodynamic mechanism that leads to at least two local optima likely affects many macromolecular interactions, as ΔG depends on two partially independent variables ΔH and ΔS according to the central equation of thermodynamics, ΔG = ΔH - TΔS. PMID:29638214

  11. Compression-based distance (CBD): a simple, rapid, and accurate method for microbiota composition comparison

    PubMed Central

    2013-01-01

    Background Perturbations in intestinal microbiota composition have been associated with a variety of gastrointestinal tract-related diseases. The alleviation of symptoms has been achieved using treatments that alter the gastrointestinal tract microbiota toward that of healthy individuals. Identifying differences in microbiota composition through the use of 16S rRNA gene hypervariable tag sequencing has profound health implications. Current computational methods for comparing microbial communities are usually based on multiple alignments and phylogenetic inference, making them time consuming and requiring exceptional expertise and computational resources. As sequencing data rapidly grows in size, simpler analysis methods are needed to meet the growing computational burdens of microbiota comparisons. Thus, we have developed a simple, rapid, and accurate method, independent of multiple alignments and phylogenetic inference, to support microbiota comparisons. Results We create a metric, called compression-based distance (CBD) for quantifying the degree of similarity between microbial communities. CBD uses the repetitive nature of hypervariable tag datasets and well-established compression algorithms to approximate the total information shared between two datasets. Three published microbiota datasets were used as test cases for CBD as an applicable tool. Our study revealed that CBD recaptured 100% of the statistically significant conclusions reported in the previous studies, while achieving a decrease in computational time required when compared to similar tools without expert user intervention. Conclusion CBD provides a simple, rapid, and accurate method for assessing distances between gastrointestinal tract microbiota 16S hypervariable tag datasets. PMID:23617892

  12. Compression-based distance (CBD): a simple, rapid, and accurate method for microbiota composition comparison.

    PubMed

    Yang, Fang; Chia, Nicholas; White, Bryan A; Schook, Lawrence B

    2013-04-23

    Perturbations in intestinal microbiota composition have been associated with a variety of gastrointestinal tract-related diseases. The alleviation of symptoms has been achieved using treatments that alter the gastrointestinal tract microbiota toward that of healthy individuals. Identifying differences in microbiota composition through the use of 16S rRNA gene hypervariable tag sequencing has profound health implications. Current computational methods for comparing microbial communities are usually based on multiple alignments and phylogenetic inference, making them time consuming and requiring exceptional expertise and computational resources. As sequencing data rapidly grows in size, simpler analysis methods are needed to meet the growing computational burdens of microbiota comparisons. Thus, we have developed a simple, rapid, and accurate method, independent of multiple alignments and phylogenetic inference, to support microbiota comparisons. We create a metric, called compression-based distance (CBD) for quantifying the degree of similarity between microbial communities. CBD uses the repetitive nature of hypervariable tag datasets and well-established compression algorithms to approximate the total information shared between two datasets. Three published microbiota datasets were used as test cases for CBD as an applicable tool. Our study revealed that CBD recaptured 100% of the statistically significant conclusions reported in the previous studies, while achieving a decrease in computational time required when compared to similar tools without expert user intervention. CBD provides a simple, rapid, and accurate method for assessing distances between gastrointestinal tract microbiota 16S hypervariable tag datasets.

  13. Computer Simulation of Microwave Devices

    NASA Technical Reports Server (NTRS)

    Kory, Carol L.

    1997-01-01

    The accurate simulation of cold-test results including dispersion, on-axis beam interaction impedance, and attenuation of a helix traveling-wave tube (TWT) slow-wave circuit using the three-dimensional code MAFIA (Maxwell's Equations Solved by the Finite Integration Algorithm) was demonstrated for the first time. Obtaining these results is a critical step in the design of TWT's. A well-established procedure to acquire these parameters is to actually build and test a model or a scale model of the circuit. However, this procedure is time-consuming and expensive, and it limits freedom to examine new variations to the basic circuit. These limitations make the need for computational methods crucial since they can lower costs, reduce tube development time, and lessen limitations on novel designs. Computer simulation has been used to accurately obtain cold-test parameters for several slow-wave circuits. Although the helix slow-wave circuit remains the mainstay of the TWT industry because of its exceptionally wide bandwidth, until recently it has been impossible to accurately analyze a helical TWT using its exact dimensions because of the complexity of its geometrical structure. A new computer modeling technique developed at the NASA Lewis Research Center overcomes these difficulties. The MAFIA three-dimensional mesh for a C-band helix slow-wave circuit is shown.

  14. Demystifying the GMAT: Computer-Based Testing Terms

    ERIC Educational Resources Information Center

    Rudner, Lawrence M.

    2012-01-01

    Computer-based testing can be a powerful means to make all aspects of test administration not only faster and more efficient, but also more accurate and more secure. While the Graduate Management Admission Test (GMAT) exam is a computer adaptive test, there are other approaches. This installment presents a primer of computer-based testing terms.

  15. Fiber optic sensors based on hybrid phenyl-silica xerogel films to detect n-hexane: determination of the isosteric enthalpy of adsorption.

    PubMed

    Echeverría, Jesús C; Calleja, Ignacio; Moriones, Paula; Garrido, Julián J

    2017-01-01

    We investigated the response of three fiber optic sensing elements prepared at pH 10 from phenyltriethoxysilane (PhTEOS) and tetraethylsilane (TEOS) mixtures with 30, 40, and 50% PhTEOS in the silicon precursor mixture. The sensing elements are referred to as Ph30, Ph40 and Ph50, respectively. The films were synthesized by the sol-gel method and affixed to the end of optical fibers by the dip-coating technique. Fourier transform infrared spectroscopy, N 2 adsorption-desorption at 77 K and X-ray diffraction analysis were used to characterize the xerogels. At a given pressure of n -hexane, the response of each sensing element decreased with temperature, indicating an exothermic process that confirmed the role of adsorption in the overall performance of the sensing elements. The isosteric adsorption enthalpies were obtained from the calibration curves at different temperatures. The magnitude of the isosteric enthalpy of n -hexane increased with the relative response and reached a plateau that stabilized at approximately -31 kJ mol -1 for Ph40 and Ph50 and at approximately -37 kJ mol -1 for Ph30. This indicates that the adsorbate-adsorbent interaction was dominant at lower relative pressure and condensation of the adsorbate on the mesopores was dominant at higher relative pressure.

  16. Estimating enthalpy of vaporization from vapor pressure using Trouton's rule.

    PubMed

    MacLeod, Matthew; Scheringer, Martin; Hungerbühler, Konrad

    2007-04-15

    The enthalpy of vaporization of liquids and subcooled liquids at 298 K (delta H(VAP)) is an important parameter in environmental fate assessments that consider spatial and temporal variability in environmental conditions. It has been shown that delta H(VAP)P for non-hydrogen-bonding substances can be estimated from vapor pressure at 298 K (P(L)) using an empirically derived linear relationship. Here, we demonstrate that the relationship between delta H(VAP)and PL is consistent with Trouton's rule and the ClausiusClapeyron equation under the assumption that delta H(VAP) is linearly dependent on temperature between 298 K and the boiling point temperature. Our interpretation based on Trouton's rule substantiates the empirical relationship between delta H(VAP) degree and P(L) degrees for non-hydrogen-bonding chemicals with subcooled liquid vapor pressures ranging over 15 orders of magnitude. We apply the relationship between delta H(VAP) degrees and P(L) degrees to evaluate data reported in literature reviews for several important classes of semivolatile environmental contaminants, including polycyclic aromatic hydrocarbons, chlorobenzenes, polychlorinated biphenyls and polychlorinated dibenzo-dioxins and -furans and illustrate the temperature dependence of results from a multimedia model presented as a partitioning map. The uncertainty associated with estimating delta H(VAP)degrees from P(L) degrees using this relationship is acceptable for most environmental fate modeling of non-hydrogen-bonding semivolatile organic chemicals.

  17. Allele-sharing models: LOD scores and accurate linkage tests.

    PubMed

    Kong, A; Cox, N J

    1997-11-01

    Starting with a test statistic for linkage analysis based on allele sharing, we propose an associated one-parameter model. Under general missing-data patterns, this model allows exact calculation of likelihood ratios and LOD scores and has been implemented by a simple modification of existing software. Most important, accurate linkage tests can be performed. Using an example, we show that some previously suggested approaches to handling less than perfectly informative data can be unacceptably conservative. Situations in which this model may not perform well are discussed, and an alternative model that requires additional computations is suggested.

  18. Allele-sharing models: LOD scores and accurate linkage tests.

    PubMed Central

    Kong, A; Cox, N J

    1997-01-01

    Starting with a test statistic for linkage analysis based on allele sharing, we propose an associated one-parameter model. Under general missing-data patterns, this model allows exact calculation of likelihood ratios and LOD scores and has been implemented by a simple modification of existing software. Most important, accurate linkage tests can be performed. Using an example, we show that some previously suggested approaches to handling less than perfectly informative data can be unacceptably conservative. Situations in which this model may not perform well are discussed, and an alternative model that requires additional computations is suggested. PMID:9345087

  19. Method and apparatus for accurately manipulating an object during microelectrophoresis

    DOEpatents

    Parvin, Bahram A.; Maestre, Marcos F.; Fish, Richard H.; Johnston, William E.

    1997-01-01

    An apparatus using electrophoresis provides accurate manipulation of an object on a microscope stage for further manipulations add reactions. The present invention also provides an inexpensive and easily accessible means to move an object without damage to the object. A plurality of electrodes are coupled to the stage in an array whereby the electrode array allows for distinct manipulations of the electric field for accurate manipulations of the object. There is an electrode array control coupled to the plurality of electrodes for manipulating the electric field. In an alternative embodiment, a chamber is provided on the stage to hold the object. The plurality of electrodes are positioned in the chamber, and the chamber is filled with fluid. The system can be automated using visual servoing, which manipulates the control parameters, i.e., x, y stage, applying the field, etc., after extracting the significant features directly from image data. Visual servoing includes an imaging device and computer system to determine the location of the object. A second stage having a plurality of tubes positioned on top of the second stage, can be accurately positioned by visual servoing so that one end of one of the plurality of tubes surrounds at least part of the object on the first stage.

  20. Method and apparatus for accurately manipulating an object during microelectrophoresis

    DOEpatents

    Parvin, B.A.; Maestre, M.F.; Fish, R.H.; Johnston, W.E.

    1997-09-23

    An apparatus using electrophoresis provides accurate manipulation of an object on a microscope stage for further manipulations and reactions. The present invention also provides an inexpensive and easily accessible means to move an object without damage to the object. A plurality of electrodes are coupled to the stage in an array whereby the electrode array allows for distinct manipulations of the electric field for accurate manipulations of the object. There is an electrode array control coupled to the plurality of electrodes for manipulating the electric field. In an alternative embodiment, a chamber is provided on the stage to hold the object. The plurality of electrodes are positioned in the chamber, and the chamber is filled with fluid. The system can be automated using visual servoing, which manipulates the control parameters, i.e., x, y stage, applying the field, etc., after extracting the significant features directly from image data. Visual servoing includes an imaging device and computer system to determine the location of the object. A second stage having a plurality of tubes positioned on top of the second stage, can be accurately positioned by visual servoing so that one end of one of the plurality of tubes surrounds at least part of the object on the first stage. 11 figs.

  1. Structures and standard molar enthalpies of formation of a series of Ln(III)–Cu(II) heteronuclear compounds with pyrazine-2,3-dicarboxylic acid

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

    Yang, Qi; Xie, Gang; Wei, Qing

    2014-07-01

    Fifteen lanthanide–copper heteronuclear compounds, formulated as [CuLn{sub 2}(pzdc){sub 4}(H{sub 2}O){sub 6}]·xH{sub 2}O (1–6(x=2), 8(x=3), 9–10(x=4)); [CuLn{sub 2}(pzdc){sub 4}(H{sub 2}O){sub 4}]·xH{sub 2}O (7, 12–13, 15(x=4), 14(x=5), 11(x=8)) (Ln(III)=La(1); Ce(2); Pr(3); Nd(4); Sm(5); Eu(6); Gd(7); Tb(8); Dy(9); Ho(10); Er(11); Tm(12); Yb(13); Lu(14); Y(15); H{sub 2}pzdc (C{sub 6}H{sub 4}N{sub 2}O{sub 4})=pyrazine-2,3-dicarboxylic acid) have been hydrothermally synthesized. All compounds were characterized by element analysis, IR spectroscopy, single-crystal X-ray diffraction and thermal analysis. X-ray diffraction analyses confirm that all compounds are isostructural and feature a 3D brick-like framework structure with (4.6{sup 2}){sub 2}(4{sup 2}.6{sup 2}.8{sup 2})(6{sup 3}){sup 2}(6{sup 5}.8){sub 2} topology. Using 1 mol cm{supmore » −3} HCl(aq) as calorimetric solvent, with an isoperibol solution–reaction calorimeter, the standard molar enthalpies of formation of all compounds were determined by a designed thermochemical cycle. In addition, solid state luminescence properties of compounds 5, 6, 8 and 9 were studied in the solid state. - Graphical abstract: According to Hess' rule, the standard molar enthalpies of formation of Ln–Cu heterometallic coordination compounds were determined by a designed thermochemical cycle. - Highlights: • Fifteen lanthanide–copper heteronuclear isostructural compounds. • Structurally characterization by IR, X-ray diffraction and thermal analysis. • The standard molar enthalpy of formation. • Isoperibol solution–reaction calorimetry.« less

  2. Toward Improved Force-Field Accuracy through Sensitivity Analysis of Host-Guest Binding Thermodynamics

    PubMed Central

    Yin, Jian; Fenley, Andrew T.; Henriksen, Niel M.; Gilson, Michael K.

    2015-01-01

    Improving the capability of atomistic computer models to predict the thermodynamics of noncovalent binding is critical for successful structure-based drug design, and the accuracy of such calculations remains limited by non-optimal force field parameters. Ideally, one would incorporate protein-ligand affinity data into force field parametrization, but this would be inefficient and costly. We now demonstrate that sensitivity analysis can be used to efficiently tune Lennard-Jones parameters of aqueous host-guest systems for increasingly accurate calculations of binding enthalpy. These results highlight the promise of a comprehensive use of calorimetric host-guest binding data, along with existing validation data sets, to improve force field parameters for the simulation of noncovalent binding, with the ultimate goal of making protein-ligand modeling more accurate and hence speeding drug discovery. PMID:26181208

  3. Development and application of computational aerothermodynamics flowfield computer codes

    NASA Technical Reports Server (NTRS)

    Venkatapathy, Ethiraj

    1992-01-01

    Presented is a collection of papers on research activities carried out during the funding period of October 1991 to March 1992. Topics covered include: blunt body flows in thermochemical equilibrium; thermochemical relaxation in high enthalpy nozzle flow; single expansion ramp nozzle simulations; lunar return aerobraking; line boundary problem for three dimensional grids; and unsteady shock induced combustion.

  4. Accurate upwind methods for the Euler equations

    NASA Technical Reports Server (NTRS)

    Huynh, Hung T.

    1993-01-01

    A new class of piecewise linear methods for the numerical solution of the one-dimensional Euler equations of gas dynamics is presented. These methods are uniformly second-order accurate, and can be considered as extensions of Godunov's scheme. With an appropriate definition of monotonicity preservation for the case of linear convection, it can be shown that they preserve monotonicity. Similar to Van Leer's MUSCL scheme, they consist of two key steps: a reconstruction step followed by an upwind step. For the reconstruction step, a monotonicity constraint that preserves uniform second-order accuracy is introduced. Computational efficiency is enhanced by devising a criterion that detects the 'smooth' part of the data where the constraint is redundant. The concept and coding of the constraint are simplified by the use of the median function. A slope steepening technique, which has no effect at smooth regions and can resolve a contact discontinuity in four cells, is described. As for the upwind step, existing and new methods are applied in a manner slightly different from those in the literature. These methods are derived by approximating the Euler equations via linearization and diagonalization. At a 'smooth' interface, Harten, Lax, and Van Leer's one intermediate state model is employed. A modification for this model that can resolve contact discontinuities is presented. Near a discontinuity, either this modified model or a more accurate one, namely, Roe's flux-difference splitting. is used. The current presentation of Roe's method, via the conceptually simple flux-vector splitting, not only establishes a connection between the two splittings, but also leads to an admissibility correction with no conditional statement, and an efficient approximation to Osher's approximate Riemann solver. These reconstruction and upwind steps result in schemes that are uniformly second-order accurate and economical at smooth regions, and yield high resolution at discontinuities.

  5. Large-scale extraction of accurate drug-disease treatment pairs from biomedical literature for drug repurposing

    PubMed Central

    2013-01-01

    Background A large-scale, highly accurate, machine-understandable drug-disease treatment relationship knowledge base is important for computational approaches to drug repurposing. The large body of published biomedical research articles and clinical case reports available on MEDLINE is a rich source of FDA-approved drug-disease indication as well as drug-repurposing knowledge that is crucial for applying FDA-approved drugs for new diseases. However, much of this information is buried in free text and not captured in any existing databases. The goal of this study is to extract a large number of accurate drug-disease treatment pairs from published literature. Results In this study, we developed a simple but highly accurate pattern-learning approach to extract treatment-specific drug-disease pairs from 20 million biomedical abstracts available on MEDLINE. We extracted a total of 34,305 unique drug-disease treatment pairs, the majority of which are not included in existing structured databases. Our algorithm achieved a precision of 0.904 and a recall of 0.131 in extracting all pairs, and a precision of 0.904 and a recall of 0.842 in extracting frequent pairs. In addition, we have shown that the extracted pairs strongly correlate with both drug target genes and therapeutic classes, therefore may have high potential in drug discovery. Conclusions We demonstrated that our simple pattern-learning relationship extraction algorithm is able to accurately extract many drug-disease pairs from the free text of biomedical literature that are not captured in structured databases. The large-scale, accurate, machine-understandable drug-disease treatment knowledge base that is resultant of our study, in combination with pairs from structured databases, will have high potential in computational drug repurposing tasks. PMID:23742147

  6. High Order Schemes in Bats-R-US for Faster and More Accurate Predictions

    NASA Astrophysics Data System (ADS)

    Chen, Y.; Toth, G.; Gombosi, T. I.

    2014-12-01

    BATS-R-US is a widely used global magnetohydrodynamics model that originally employed second order accurate TVD schemes combined with block based Adaptive Mesh Refinement (AMR) to achieve high resolution in the regions of interest. In the last years we have implemented fifth order accurate finite difference schemes CWENO5 and MP5 for uniform Cartesian grids. Now the high order schemes have been extended to generalized coordinates, including spherical grids and also to the non-uniform AMR grids including dynamic regridding. We present numerical tests that verify the preservation of free-stream solution and high-order accuracy as well as robust oscillation-free behavior near discontinuities. We apply the new high order accurate schemes to both heliospheric and magnetospheric simulations and show that it is robust and can achieve the same accuracy as the second order scheme with much less computational resources. This is especially important for space weather prediction that requires faster than real time code execution.

  7. Toward Accurate and Quantitative Comparative Metagenomics.

    PubMed

    Nayfach, Stephen; Pollard, Katherine S

    2016-08-25

    Shotgun metagenomics and computational analysis are used to compare the taxonomic and functional profiles of microbial communities. Leveraging this approach to understand roles of microbes in human biology and other environments requires quantitative data summaries whose values are comparable across samples and studies. Comparability is currently hampered by the use of abundance statistics that do not estimate a meaningful parameter of the microbial community and biases introduced by experimental protocols and data-cleaning approaches. Addressing these challenges, along with improving study design, data access, metadata standardization, and analysis tools, will enable accurate comparative metagenomics. We envision a future in which microbiome studies are replicable and new metagenomes are easily and rapidly integrated with existing data. Only then can the potential of metagenomics for predictive ecological modeling, well-powered association studies, and effective microbiome medicine be fully realized. Copyright © 2016 Elsevier Inc. All rights reserved.

  8. Automatic temperature computation for realistic IR simulation

    NASA Astrophysics Data System (ADS)

    Le Goff, Alain; Kersaudy, Philippe; Latger, Jean; Cathala, Thierry; Stolte, Nilo; Barillot, Philippe

    2000-07-01

    Polygon temperature computation in 3D virtual scenes is fundamental for IR image simulation. This article describes in detail the temperature calculation software and its current extensions, briefly presented in [1]. This software, called MURET, is used by the simulation workshop CHORALE of the French DGA. MURET is a one-dimensional thermal software, which accurately takes into account the material thermal attributes of three-dimensional scene and the variation of the environment characteristics (atmosphere) as a function of the time. Concerning the environment, absorbed incident fluxes are computed wavelength by wavelength, for each half an hour, druing 24 hours before the time of the simulation. For each polygon, incident fluxes are compsed of: direct solar fluxes, sky illumination (including diffuse solar fluxes). Concerning the materials, classical thermal attributes are associated to several layers, such as conductivity, absorption, spectral emissivity, density, specific heat, thickness and convection coefficients are taken into account. In the future, MURET will be able to simulate permeable natural materials (water influence) and vegetation natural materials (woods). This model of thermal attributes induces a very accurate polygon temperature computation for the complex 3D databases often found in CHORALE simulations. The kernel of MUET consists of an efficient ray tracer allowing to compute the history (over 24 hours) of the shadowed parts of the 3D scene and a library, responsible for the thermal computations. The great originality concerns the way the heating fluxes are computed. Using ray tracing, the flux received in each 3D point of the scene accurately takes into account the masking (hidden surfaces) between objects. By the way, this library supplies other thermal modules such as a thermal shows computation tool.

  9. 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.

  10. 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.

  11. RICO: A NEW APPROACH FOR FAST AND ACCURATE REPRESENTATION OF THE COSMOLOGICAL RECOMBINATION HISTORY

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

    Fendt, W. A.; Wandelt, B. D.; Chluba, J.

    2009-04-15

    We present RICO, a code designed to compute the ionization fraction of the universe during the epoch of hydrogen and helium recombination with an unprecedented combination of speed and accuracy. This is accomplished by training the machine learning code PICO on the calculations of a multilevel cosmological recombination code which self-consistently includes several physical processes that were neglected previously. After training, RICO is used to fit the free electron fraction as a function of the cosmological parameters. While, for example, at low redshifts (z {approx}< 900), much of the net change in the ionization fraction can be captured by loweringmore » the hydrogen fudge factor in RECFAST by about 3%, RICO provides a means of effectively using the accurate ionization history of the full recombination code in the standard cosmological parameter estimation framework without the need to add new or refined fudge factors or functions to a simple recombination model. Within the new approach presented here, it is easy to update RICO whenever a more accurate full recombination code becomes available. Once trained, RICO computes the cosmological ionization history with negligible fitting error in {approx}10 ms, a speedup of at least 10{sup 6} over the full recombination code that was used here. Also RICO is able to reproduce the ionization history of the full code to a level well below 0.1%, thereby ensuring that the theoretical power spectra of cosmic microwave background (CMB) fluctuations can be computed to sufficient accuracy and speed for analysis from upcoming CMB experiments like Planck. Furthermore, it will enable cross-checking different recombination codes across cosmological parameter space, a comparison that will be very important in order to assure the accurate interpretation of future CMB data.« less

  12. Fast and Accurate Approximation to Significance Tests in Genome-Wide Association Studies

    PubMed Central

    Zhang, Yu; Liu, Jun S.

    2011-01-01

    Genome-wide association studies commonly involve simultaneous tests of millions of single nucleotide polymorphisms (SNP) for disease association. The SNPs in nearby genomic regions, however, are often highly correlated due to linkage disequilibrium (LD, a genetic term for correlation). Simple Bonferonni correction for multiple comparisons is therefore too conservative. Permutation tests, which are often employed in practice, are both computationally expensive for genome-wide studies and limited in their scopes. We present an accurate and computationally efficient method, based on Poisson de-clumping heuristics, for approximating genome-wide significance of SNP associations. Compared with permutation tests and other multiple comparison adjustment approaches, our method computes the most accurate and robust p-value adjustments for millions of correlated comparisons within seconds. We demonstrate analytically that the accuracy and the efficiency of our method are nearly independent of the sample size, the number of SNPs, and the scale of p-values to be adjusted. In addition, our method can be easily adopted to estimate false discovery rate. When applied to genome-wide SNP datasets, we observed highly variable p-value adjustment results evaluated from different genomic regions. The variation in adjustments along the genome, however, are well conserved between the European and the African populations. The p-value adjustments are significantly correlated with LD among SNPs, recombination rates, and SNP densities. Given the large variability of sequence features in the genome, we further discuss a novel approach of using SNP-specific (local) thresholds to detect genome-wide significant associations. This article has supplementary material online. PMID:22140288

  13. Ratio of entropy to enthalpy in thermal transitions in biological tissues.

    PubMed

    Jacques, Steven L

    2006-01-01

    Thermal transitions in biological tissues that have been reported in the literature are summarized in terms of the apparent molar entropy (DeltaS) and molar enthalpy (DeltaH) involved in the transition. A plot of DeltaS versus DeltaH for all the data yields a straight line, consistent with the definition of free energy, DeltaG=DeltaH+TDeltaS. Various bonds may be involved in cooperative bond breakage during thermal transitions; however, for the sake of description, the equivalent number of cooperative hydrogen bonds can be cited. Most of the tissue data behave as if 10 to 20 hydrogen bonds are cooperatively broken during coagulation, with one transition, the expression of heat shock protein, involving 90 cooperative hydrogen bonds. The data are consistent with DeltaS=a+bDeltaH, where a=-327.5 J(mol K) and b=31.47 x 10(-4) K(-1). If each additional hydrogen bond adds 19 x 10(3) Jmol to DeltaH, then each additional bond adds 59.8 J(mol K) to DeltaS. Hence, the dynamics of irreversible thermal transitions can be described in terms of one free parameter, the apparent number of cooperative hydrogen bonds broken during the transition.

  14. Accurate structural and spectroscopic characterization of prebiotic molecules: The neutral and cationic acetyl cyanide and their related species.

    PubMed

    Bellili, A; Linguerri, R; Hochlaf, M; Puzzarini, C

    2015-11-14

    In an effort to provide an accurate structural and spectroscopic characterization of acetyl cyanide, its two enolic isomers and the corresponding cationic species, state-of-the-art computational methods, and approaches have been employed. The coupled-cluster theory including single and double excitations together with a perturbative treatment of triples has been used as starting point in composite schemes accounting for extrapolation to the complete basis-set limit as well as core-valence correlation effects to determine highly accurate molecular structures, fundamental vibrational frequencies, and rotational parameters. The available experimental data for acetyl cyanide allowed us to assess the reliability of our computations: structural, energetic, and spectroscopic properties have been obtained with an overall accuracy of about, or better than, 0.001 Å, 2 kcal/mol, 1-10 MHz, and 11 cm(-1) for bond distances, adiabatic ionization potentials, rotational constants, and fundamental vibrational frequencies, respectively. We are therefore confident that the highly accurate spectroscopic data provided herein can be useful for guiding future experimental investigations and/or astronomical observations.

  15. Time-Accurate Simulations and Acoustic Analysis of Slat Free-Shear-Layer. Part 2

    NASA Technical Reports Server (NTRS)

    Khorrami, Mehdi R.; Singer, Bart A.; Lockard, David P.

    2002-01-01

    Unsteady computational simulations of a multi-element, high-lift configuration are performed. Emphasis is placed on accurate spatiotemporal resolution of the free shear layer in the slat-cove region. The excessive dissipative effects of the turbulence model, so prevalent in previous simulations, are circumvented by switching off the turbulence-production term in the slat cove region. The justifications and physical arguments for taking such a step are explained in detail. The removal of this excess damping allows the shear layer to amplify large-scale structures, to achieve a proper non-linear saturation state, and to permit vortex merging. The large-scale disturbances are self-excited, and unlike our prior fully turbulent simulations, no external forcing of the shear layer is required. To obtain the farfield acoustics, the Ffowcs Williams and Hawkings equation is evaluated numerically using the simulated time-accurate flow data. The present comparison between the computed and measured farfield acoustic spectra shows much better agreement for the amplitude and frequency content than past calculations. The effect of the angle-of-attack on the slat's flow features radiated acoustic field are also simulated presented.

  16. Computer Model Inversion and Uncertainty Quantification in the Geosciences

    NASA Astrophysics Data System (ADS)

    White, Jeremy T.

    The subject of this dissertation is use of computer models as data analysis tools in several different geoscience settings, including integrated surface water/groundwater modeling, tephra fallout modeling, geophysical inversion, and hydrothermal groundwater modeling. The dissertation is organized into three chapters, which correspond to three individual publication manuscripts. In the first chapter, a linear framework is developed to identify and estimate the potential predictive consequences of using a simple computer model as a data analysis tool. The framework is applied to a complex integrated surface-water/groundwater numerical model with thousands of parameters. Several types of predictions are evaluated, including particle travel time and surface-water/groundwater exchange volume. The analysis suggests that model simplifications have the potential to corrupt many types of predictions. The implementation of the inversion, including how the objective function is formulated, what minimum of the objective function value is acceptable, and how expert knowledge is enforced on parameters, can greatly influence the manifestation of model simplification. Depending on the prediction, failure to specifically address each of these important issues during inversion is shown to degrade the reliability of some predictions. In some instances, inversion is shown to increase, rather than decrease, the uncertainty of a prediction, which defeats the purpose of using a model as a data analysis tool. In the second chapter, an efficient inversion and uncertainty quantification approach is applied to a computer model of volcanic tephra transport and deposition. The computer model simulates many physical processes related to tephra transport and fallout. The utility of the approach is demonstrated for two eruption events. In both cases, the importance of uncertainty quantification is highlighted by exposing the variability in the conditioning provided by the observations used for

  17. Computer simulation of rapid crystal growth under microgravity

    NASA Astrophysics Data System (ADS)

    Hisada, Yasuhiro; Saito, Osami; Mitachi, Koshi; Nishinaga, Tatau

    We are planning to grow a Ge single crystal under microgravity by the TR-IA rocket in 1992. The furnace temperature should be controlled so as to finish the crystal growth in a quite short time interval (about 6 min). This study deals with the computer simulation of rapid crystal growth in space to find the proper conditions for the experiment. The crystal growth process is influenced by various physical phenomena such as heat conduction, natural and Marangoni convections, phase change, and radiation from the furnace. In this study, a 2D simulation with axial symmetry is carried out, taking into account the radiation field with a specific temperature distribution of the furnace wall. The simulation program consists of four modules. The first module is applied for the calculation of the parabolic partial differential equation by using the control volume method. The second one evaluates implicitly the phase change by the enthalpy method. The third one is for computing the heat flux from surface by radiation. The last one is for calculating with the Monte Carlo method the view factors which are necessary to obtain the heat flux.

  18. Self-monitoring of dietary intake by young women: online food records completed on computer or smartphone are as accurate as paper-based food records but more acceptable.

    PubMed

    Hutchesson, Melinda J; Rollo, Megan E; Callister, Robin; Collins, Clare E

    2015-01-01

    Adherence and accuracy of self-monitoring of dietary intake influences success in weight management interventions. Information technologies such as computers and smartphones have the potential to improve adherence and accuracy by reducing the burden associated with monitoring dietary intake using traditional paper-based food records. We evaluated the acceptability and accuracy of three different 7-day food record methods (online accessed via computer, online accessed via smartphone, and paper-based). Young women (N=18; aged 23.4±2.9 years; body mass index 24.0±2.2) completed the three 7-day food records in random order with 7-day washout periods between each method. Total energy expenditure (TEE) was derived from resting energy expenditure (REE) measured by indirect calorimetry and physical activity level (PAL) derived from accelerometers (TEE=REE×PAL). Accuracy of the three methods was assessed by calculating absolute (energy intake [EI]-TEE) and percentage difference (EI/TEE×100) between self-reported EI and TEE. Acceptability was assessed via questionnaire. Mean±standard deviation TEE was 2,185±302 kcal/day and EI was 1,729±249 kcal/day, 1,675±287kcal/day, and 1,682±352 kcal/day for computer, smartphone, and paper records, respectively. There were no significant differences between absolute and percentage differences between EI and TEE for the three methods: computer, -510±389 kcal/day (78%); smartphone, -456±372 kcal/day (80%); and paper, -503±513 kcal/day (79%). Half of participants (n=9) preferred computer recording, 44.4% preferred smartphone, and 5.6% preferred paper-based records. Most participants (89%) least preferred the paper-based record. Because online food records completed on either computer or smartphone were as accurate as paper-based records but more acceptable to young women, they should be considered when self-monitoring of intake is recommended to young women. Copyright © 2015 Academy of Nutrition and Dietetics. Published by

  19. Transonic Blunt Body Aerodynamic Coefficients Computation

    NASA Astrophysics Data System (ADS)

    Sancho, Jorge; Vargas, M.; Gonzalez, Ezequiel; Rodriguez, Manuel

    2011-05-01

    In the framework of EXPERT (European Experimental Re-entry Test-bed) accurate transonic aerodynamic coefficients are of paramount importance for the correct trajectory assessment and parachute deployment. A combined CFD (Computational Fluid Dynamics) modelling and experimental campaign strategy was selected to obtain accurate coefficients. A preliminary set of coefficients were obtained by CFD Euler inviscid computation. Then experimental campaign was performed at DNW facilities at NLR. A profound review of the CFD modelling was done lighten up by WTT results, aimed to obtain reliable values of the coefficients in the future (specially the pitching moment). Study includes different turbulence modelling and mesh sensitivity analysis. Comparison with the WTT results is explored, and lessons learnt are collected.

  20. Cars Thermometry in a Supersonic Combustor for CFD Code Validation

    NASA Technical Reports Server (NTRS)

    Cutler, A. D.; Danehy, P. M.; Springer, R. R.; DeLoach, R.; Capriotti, D. P.

    2002-01-01

    An experiment has been conducted to acquire data for the validation of computational fluid dynamics (CFD) codes used in the design of supersonic combustors. The primary measurement technique is coherent anti-Stokes Raman spectroscopy (CARS), although surface pressures and temperatures have also been acquired. Modern- design- of-experiment techniques have been used to maximize the quality of the data set (for the given level of effort) and minimize systematic errors. The combustor consists of a diverging duct with single downstream- angled wall injector. Nominal entrance Mach number is 2 and enthalpy nominally corresponds to Mach 7 flight. Temperature maps are obtained at several planes in the flow for two cases: in one case the combustor is piloted by injecting fuel upstream of the main injector, the second is not. Boundary conditions and uncertainties are adequately characterized. Accurate CFD calculation of the flow will ultimately require accurate modeling of the chemical kinetics and turbulence-chemistry interactions as well as accurate modeling of the turbulent mixing

  1. Measurements of Enthalpy of Sublimation of Ne, N2, O2, Ar, CO2, Kr, Xe, and H2O using a Double Paddle Oscillator.

    PubMed

    Shakeel, Hamza; Wei, Haoyan; Pomeroy, Joshua M

    2018-03-01

    We report precise experimental values of the enthalpy of sublimation (Δ H s ) of quenched condensed films of neon (Ne), nitrogen (N 2 ), oxygen (O 2 ), argon (Ar), carbon dioxide (CO 2 ), krypton (Kr), xenon (Xe), and water (H 2 O) vapor using a single consistent measurement platform. The experiments are performed well below the triple point temperature of each gas and fall in the temperature range where existing experimental data is very limited. A 6 cm 2 and 400 µm thick double paddle oscillator (DPO) with high quality factor (Q ≈ 4 × 10 5 at 298K) and high frequency stability (33 parts per billion) is utilized for the measurements. The enthalpies of sublimation are derived by measuring the rate of mass loss during temperature programmed desorption. The mass change is detected due to change in the resonance frequency of the self-tracking oscillator. Our measurements typically remain within 10% of the available literature, theory, and National Institute of Standards and Technology (NIST) Web Thermo Tables ( WTT ) values, but are performed using an internally consistent method across different gases.

  2. Fiber optic sensors based on hybrid phenyl-silica xerogel films to detect n-hexane: determination of the isosteric enthalpy of adsorption

    PubMed Central

    Calleja, Ignacio; Moriones, Paula; Garrido, Julián J

    2017-01-01

    We investigated the response of three fiber optic sensing elements prepared at pH 10 from phenyltriethoxysilane (PhTEOS) and tetraethylsilane (TEOS) mixtures with 30, 40, and 50% PhTEOS in the silicon precursor mixture. The sensing elements are referred to as Ph30, Ph40 and Ph50, respectively. The films were synthesized by the sol–gel method and affixed to the end of optical fibers by the dip-coating technique. Fourier transform infrared spectroscopy, N2 adsorption–desorption at 77 K and X-ray diffraction analysis were used to characterize the xerogels. At a given pressure of n-hexane, the response of each sensing element decreased with temperature, indicating an exothermic process that confirmed the role of adsorption in the overall performance of the sensing elements. The isosteric adsorption enthalpies were obtained from the calibration curves at different temperatures. The magnitude of the isosteric enthalpy of n-hexane increased with the relative response and reached a plateau that stabilized at approximately −31 kJ mol−1 for Ph40 and Ph50 and at approximately −37 kJ mol−1 for Ph30. This indicates that the adsorbate–adsorbent interaction was dominant at lower relative pressure and condensation of the adsorbate on the mesopores was dominant at higher relative pressure. PMID:28326238

  3. Guggenheim's rule and the enthalpy of vaporization of simple and polar fluids, molten salts, and room temperature ionic liquids.

    PubMed

    Weiss, Volker C

    2010-07-22

    One of Guggenheim's many corresponding-states rules for simple fluids implies that the molar enthalpy of vaporization (determined at the temperature at which the pressure reaches 1/50th of its critical value, which approximately coincides with the normal boiling point) divided by the critical temperature has a value of roughly 5.2R, where R is the universal gas constant. For more complex fluids, such as strongly polar and ionic fluids, one must expect deviations from Guggenheim's rule. Such a deviation has far-reaching consequences for other empirical rules related to the vaporization of fluids, namely Guldberg's rule and Trouton's rule. We evaluate these characteristic quantities for simple fluids, polar fluids, hydrogen-bonding fluids, simple inorganic molten salts, and room temperature ionic liquids (RTILs). For the ionic fluids, the critical parameters are not accessible to direct experimental observation; therefore, suitable extrapolation schemes have to be applied. For the RTILs [1-n-alkyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imides, where the alkyl chain is ethyl, butyl, hexyl, or octyl], the critical temperature is estimated by extrapolating the surface tension to zero using Guggenheim's and Eotvos' rules; the critical density is obtained using the linear-diameter rule. It is shown that the RTILs adhere to Guggenheim's master curve for the reduced surface tension of simple and moderately polar fluids, but that they deviate significantly from his rule for the reduced enthalpy of vaporization of simple fluids. Consequences for evaluating the Trouton constant of RTILs, the value of which has been discussed controversially in the literature, are indicated.

  4. Structure-energy relationship in barbituric acid: a calorimetric, computational, and crystallographic study.

    PubMed

    Roux, María Victoria; Temprado, Manuel; Notario, Rafael; Foces-Foces, Concepción; Emel'yanenko, Vladimir N; Verevkin, Sergey P

    2008-08-14

    This paper reports the value of the standard (p(o) = 0.1 MPa) molar enthalpy of formation in the gas phase at T = 298.15 K for barbituric acid. The enthalpies of combustion and sublimation were measured by static bomb combustion calorimetry and transference (transpiration) method in a saturated N2 stream and a gas-phase enthalpy of formation value of -(534.3 +/- 1.7) kJ x mol(-1) was determined at T = 298.15 K. G3-calculated enthalpies of formation are in very good agreement with the experimental value. The behavior of the sample as a function of the temperature was studied by differential scanning calorimetry, and a new polymorph of barbituric acid at high temperature was found. In the solid state, two anhydrous forms are known displaying two out of the six hydrogen-bonding patterns observed in the alkyl/alkenyl derivatives retrieved from the Cambridge Crystallographic Database. The stability of these motifs has been analyzed by theoretical calculations. X-ray powder diffraction technique was used to establish to which polymorphic form corresponds to the commercial sample used in this study and to characterize the new form at high temperature.

  5. Accurate, efficient, and (iso)geometrically flexible collocation methods for phase-field models

    NASA Astrophysics Data System (ADS)

    Gomez, Hector; Reali, Alessandro; Sangalli, Giancarlo

    2014-04-01

    We propose new collocation methods for phase-field models. Our algorithms are based on isogeometric analysis, a new technology that makes use of functions from computational geometry, such as, for example, Non-Uniform Rational B-Splines (NURBS). NURBS exhibit excellent approximability and controllable global smoothness, and can represent exactly most geometries encapsulated in Computer Aided Design (CAD) models. These attributes permitted us to derive accurate, efficient, and geometrically flexible collocation methods for phase-field models. The performance of our method is demonstrated by several numerical examples of phase separation modeled by the Cahn-Hilliard equation. We feel that our method successfully combines the geometrical flexibility of finite elements with the accuracy and simplicity of pseudo-spectral collocation methods, and is a viable alternative to classical collocation methods.

  6. PconsD: ultra rapid, accurate model quality assessment for protein structure prediction.

    PubMed

    Skwark, Marcin J; Elofsson, Arne

    2013-07-15

    Clustering methods are often needed for accurately assessing the quality of modeled protein structures. Recent blind evaluation of quality assessment methods in CASP10 showed that there is little difference between many different methods as far as ranking models and selecting best model are concerned. When comparing many models, the computational cost of the model comparison can become significant. Here, we present PconsD, a fast, stream-computing method for distance-driven model quality assessment that runs on consumer hardware. PconsD is at least one order of magnitude faster than other methods of comparable accuracy. The source code for PconsD is freely available at http://d.pcons.net/. Supplementary benchmarking data are also available there. arne@bioinfo.se Supplementary data are available at Bioinformatics online.

  7. Accurate ab initio quartic force fields for the ions HCO(+) and HOC(+)

    NASA Technical Reports Server (NTRS)

    Martin, J. M. L.; Taylor, Peter R.; Lee, Timothy J.

    1993-01-01

    The quartic force fields of HCO(+) and HOC(+) have been computed using augmented coupled cluster methods and basis sets of spdf and spdfg quality. Calculations on HCN, CO, and N2 have been performed to assist in calibrating the computed results. Going from an spdf to an spdfg basis shortens triple bonds by about 0.004 A, and increases the corresponding harmonic frequency by 10-20/cm, leaving bond distances about 0.003 A too long and triple bond stretching frequencies about 5/cm too low. Accurate estimates for the bond distances, fundamental frequencies, and thermochemical quantities are given. HOC(+) lies 37.8 +/- 0.5 kcal/mol (0 K) above HCO(+); the classical barrier height for proton exchange is 76.7 +/- 1.0 kcal/mol.

  8. Enthalpy and high temperature relaxation kinetics of stable vapor-deposited glasses of toluene

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

    Bhattacharya, Deepanjan; Sadtchenko, Vlad, E-mail: vlad@gwu.edu

    Stable non-crystalline toluene films of micrometer and nanometer thicknesses were grown by vapor deposition at distinct rates and probed by fast scanning calorimetry. Fast scanning calorimetry is shown to be extremely sensitive to the structure of the vapor-deposited phase and was used to characterize simultaneously its kinetic stability and its thermodynamic properties. According to our analysis, transformation of vapor-deposited samples of toluene during heating with rates in excess 10{sup 5} K s{sup −1} follows the zero-order kinetics. The transformation rate correlates strongly with the initial enthalpy of the sample, which increases with the deposition rate according to sub-linear law. Analysismore » of the transformation kinetics of vapor-deposited toluene films of various thicknesses reveal a sudden increase in the transformation rate for films thinner than 250 nm. The change in kinetics seems to correlate with the surface roughness scale of the substrate. The implications of these findings for the formation mechanism and structure of vapor-deposited stable glasses are discussed.« less

  9. Interaction Enthalpy of Side Chain and Backbone Amides in Polyglutamine Solution Monomers and Fibrils.

    PubMed

    Punihaole, David; Jakubek, Ryan S; Workman, Riley J; Asher, Sanford A

    2018-04-19

    We determined an empirical correlation that relates the amide I vibrational band frequencies of the glutamine (Q) side chain to the strength of hydrogen bonding, van der Waals, and Lewis acid-base interactions of its primary amide carbonyl. We used this correlation to determine the Q side chain carbonyl interaction enthalpy (Δ H int ) in monomeric and amyloid-like fibril conformations of D 2 Q 10 K 2 (Q10). We independently verified these Δ H int values through molecular dynamics simulations that showed excellent agreement with experiments. We found that side chain-side chain and side chain-peptide backbone interactions in fibrils and monomers are more enthalpically favorable than are Q side chain-water interactions. Q10 fibrils also showed a more favorable Δ H int for side chain-side chain interactions compared to backbone-backbone interactions. This work experimentally demonstrates that interamide side chain interactions are important in the formation and stabilization of polyQ fibrils.

  10. Simulations of nanocrystals under pressure: combining electronic enthalpy and linear-scaling density-functional theory.

    PubMed

    Corsini, Niccolò R C; Greco, Andrea; Hine, Nicholas D M; Molteni, Carla; Haynes, Peter D

    2013-08-28

    We present an implementation in a linear-scaling density-functional theory code of an electronic enthalpy method, which has been found to be natural and efficient for the ab initio calculation of finite systems under hydrostatic pressure. Based on a definition of the system volume as that enclosed within an electronic density isosurface [M. Cococcioni, F. Mauri, G. Ceder, and N. Marzari, Phys. Rev. Lett. 94, 145501 (2005)], it supports both geometry optimizations and molecular dynamics simulations. We introduce an approach for calibrating the parameters defining the volume in the context of geometry optimizations and discuss their significance. Results in good agreement with simulations using explicit solvents are obtained, validating our approach. Size-dependent pressure-induced structural transformations and variations in the energy gap of hydrogenated silicon nanocrystals are investigated, including one comparable in size to recent experiments. A detailed analysis of the polyamorphic transformations reveals three types of amorphous structures and their persistence on depressurization is assessed.

  11. Simulations of nanocrystals under pressure: Combining electronic enthalpy and linear-scaling density-functional theory

    NASA Astrophysics Data System (ADS)

    Corsini, Niccolò R. C.; Greco, Andrea; Hine, Nicholas D. M.; Molteni, Carla; Haynes, Peter D.

    2013-08-01

    We present an implementation in a linear-scaling density-functional theory code of an electronic enthalpy method, which has been found to be natural and efficient for the ab initio calculation of finite systems under hydrostatic pressure. Based on a definition of the system volume as that enclosed within an electronic density isosurface [M. Cococcioni, F. Mauri, G. Ceder, and N. Marzari, Phys. Rev. Lett. 94, 145501 (2005)], 10.1103/PhysRevLett.94.145501, it supports both geometry optimizations and molecular dynamics simulations. We introduce an approach for calibrating the parameters defining the volume in the context of geometry optimizations and discuss their significance. Results in good agreement with simulations using explicit solvents are obtained, validating our approach. Size-dependent pressure-induced structural transformations and variations in the energy gap of hydrogenated silicon nanocrystals are investigated, including one comparable in size to recent experiments. A detailed analysis of the polyamorphic transformations reveals three types of amorphous structures and their persistence on depressurization is assessed.

  12. GASPLOT - A computer graphics program that draws a variety of thermophysical property charts

    NASA Technical Reports Server (NTRS)

    Trivisonno, R. J.; Hendricks, R. C.

    1977-01-01

    A FORTRAN V computer program, written for the UNIVAC 1100 series, is used to draw a variety of precision thermophysical property charts on the Calcomp plotter. In addition to the program (GASPLOT), which requires (15 160) sub 10 storages, a thermophysical properties routine needed to produce plots. The program is designed so that any two of the state variables, the derived variables, or the transport variables may be plotted as the ordinate - abscissa pair with as many as five parametric variables. The parameters may be temperature, pressure, density, enthalpy, and entropy. Each parameter may have as many a 49 values, and the range of the variables is limited only by the thermophysical properties routine.

  13. Phase diagram of the Y–Y{sub 2}Se{sub 3} system, enthalpies of phase transformations

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

    Andreev, O.V.; Kharitontsev, V.B.; Polkovnikov, A.A., E-mail: a.a.polkovnikov@yandex.ru

    A phase diagram for the Y–Y{sub 2}Se{sub 3} system has been constructed in which the YSe and Y{sub 2}Se{sub 3} phases melt congruently. The daltonide type YSe phase (ST Y{sub 0,75}Se, a=1.1393 nm, melting point=2380 K, H=2200 MPa) forms a double-sided solid solution from 49–50–53 at% Se. In the 50–53 at% Se range, the unit cell parameter increases to 1.1500 nm, the microhardness increases to 4100 MPa and electrical resistivity increases from 0.018 to 0.114 Ω m. These changes are caused by the dominating influx of newly formed structural cationic vacancies arising from the selenium anions that are surplus formore » the 1:1 Y:Se stoichiometry. The full-valence Y{sub 2}Se{sub 3} composition exists as a low-temperature modification of ε-Y{sub 2}Se{sub 3} (ST Sc{sub 2}S{sub 3}, a=1.145 nm, b=0.818 nm, c=2.438 nm, melting point=1780 K, ∆fusion enthalpy=4±0.4 J/g) and transforms into a modification of ξ-Y{sub 2}Se{sub 3} that does not undergo fixing by thermo-hardening. The eutectic melting point between the YSe and Y{sub 2}Se{sub 3} phases is 1625±5 K, with a eutectic composition that is assumed to be 57.5 at% Se and have an enthalpy of fusion of 43±4.3 J/g. The eutectic for the Y and YSe phases appears at a temperature of 1600 K and 5 at% Se. - Highlights: • Phase equilibria in the Y–Y{sub 2}Se{sub 3} system from 1000 K to melt were studies. • High-temperature polymorphic transition for Y{sub 2}Se{sub 3} were observed. • Singular points in solid solutions areas for YSe and Y{sub 2}Se{sub 3} were found.« less

  14. An examination of the thermodynamics of fusion, vaporization, and sublimation of several parabens by correlation gas chromatography.

    PubMed

    Umnahanant, Patamaporn; Chickos, James

    2011-05-01

    The vaporization, fusion, and sublimation enthalpies of methyl, ethyl, propyl, and butyl paraben are reported and compared with literature values. The vaporization enthalpies were measured by correlation gas chromatography and the fusion enthalpies by differential scanning calorimetry. Adjusted to T = 298.15 K, these enthalpies were combined to yield the sublimation enthalpy. The results compare favorably to some of the literature values but do not support the reversal in magnitude of both the vaporization and sublimation enthalpy previously reported for propyl and butyl paraben. The following fusion and vaporization enthalpies were measured for methyl through to butyl paraben, respectively: ΔH(fus) (T(fus) ) 26.3 ± 0.1 (398.6 K), 26.5 ± 0.1 (388.5 K), 27.3 ± 0.1 (368.8), and 25.9 ± 0.3 (340.7 K) kJ·mol(-1); ΔH(vap) (298.15 K) 79.5 ± 0.5, 84.0 ± 0.5, 89.7 ± 0.6, and 95.8 ± 0.6 kJ·mol(-1). The results are believed to be accurate to ± 4 kJ·mol(-1). Copyright © 2011 Wiley-Liss, Inc.

  15. A Highly Accurate Face Recognition System Using Filtering Correlation

    NASA Astrophysics Data System (ADS)

    Watanabe, Eriko; Ishikawa, Sayuri; Kodate, Kashiko

    2007-09-01

    The authors previously constructed a highly accurate fast face recognition optical correlator (FARCO) [E. Watanabe and K. Kodate: Opt. Rev. 12 (2005) 460], and subsequently developed an improved, super high-speed FARCO (S-FARCO), which is able to process several hundred thousand frames per second. The principal advantage of our new system is its wide applicability to any correlation scheme. Three different configurations were proposed, each depending on correlation speed. This paper describes and evaluates a software correlation filter. The face recognition function proved highly accurate, seeing that a low-resolution facial image size (64 × 64 pixels) has been successfully implemented. An operation speed of less than 10 ms was achieved using a personal computer with a central processing unit (CPU) of 3 GHz and 2 GB memory. When we applied the software correlation filter to a high-security cellular phone face recognition system, experiments on 30 female students over a period of three months yielded low error rates: 0% false acceptance rate and 2% false rejection rate. Therefore, the filtering correlation works effectively when applied to low resolution images such as web-based images or faces captured by a monitoring camera.

  16. Reverse radiance: a fast accurate method for determining luminance

    NASA Astrophysics Data System (ADS)

    Moore, Kenneth E.; Rykowski, Ronald F.; Gangadhara, Sanjay

    2012-10-01

    Reverse ray tracing from a region of interest backward to the source has long been proposed as an efficient method of determining luminous flux. The idea is to trace rays only from where the final flux needs to be known back to the source, rather than tracing in the forward direction from the source outward to see where the light goes. Once the reverse ray reaches the source, the radiance the equivalent forward ray would have represented is determined and the resulting flux computed. Although reverse ray tracing is conceptually simple, the method critically depends upon an accurate source model in both the near and far field. An overly simplified source model, such as an ideal Lambertian surface substantially detracts from the accuracy and thus benefit of the method. This paper will introduce an improved method of reverse ray tracing that we call Reverse Radiance that avoids assumptions about the source properties. The new method uses measured data from a Source Imaging Goniometer (SIG) that simultaneously measures near and far field luminous data. Incorporating this data into a fast reverse ray tracing integration method yields fast, accurate data for a wide variety of illumination problems.

  17. Accurate Projection Methods for the Incompressible Navier–Stokes Equations

    DOE PAGES

    Brown, David L.; Cortez, Ricardo; Minion, Michael L.

    2001-04-10

    This paper considers the accuracy of projection method approximations to the initial–boundary-value problem for the incompressible Navier–Stokes equations. The issue of how to correctly specify numerical boundary conditions for these methods has been outstanding since the birth of the second-order methodology a decade and a half ago. It has been observed that while the velocity can be reliably computed to second-order accuracy in time and space, the pressure is typically only first-order accurate in the L ∞-norm. Here, we identify the source of this problem in the interplay of the global pressure-update formula with the numerical boundary conditions and presentsmore » an improved projection algorithm which is fully second-order accurate, as demonstrated by a normal mode analysis and numerical experiments. In addition, a numerical method based on a gauge variable formulation of the incompressible Navier–Stokes equations, which provides another option for obtaining fully second-order convergence in both velocity and pressure, is discussed. The connection between the boundary conditions for projection methods and the gauge method is explained in detail.« less

  18. The NASA MERIT program - Developing new concepts for accurate flight planning

    NASA Technical Reports Server (NTRS)

    Steinberg, R.

    1982-01-01

    It is noted that the rising cost of aviation fuel has necessitated the development of a new approach to upper air forecasting for flight planning. It is shown that the spatial resolution of the present weather forecast models used in fully automated computer flight planning is an important accuracy-limiting factor, and it is proposed that man be put back into the system, although not in the way he has been used in the past. A new approach is proposed which uses the application of man-computer interactive display techniques to upper air forecasting to retain the fine scale features of the atmosphere inherent in the present data base in order to provide a more accurate and cost effective flight plan. It is pointed out that, as a result of NASA research, the hardware required for this approach already exists.

  19. Current Status on the use of Parallel Computing in Turbulent Reacting Flow Computations Involving Sprays, Monte Carlo PDF and Unstructured Grids. Chapter 4

    NASA Technical Reports Server (NTRS)

    Raju, M. S.

    1998-01-01

    The state of the art in multidimensional combustor modeling as evidenced by the level of sophistication employed in terms of modeling and numerical accuracy considerations, is also dictated by the available computer memory and turnaround times afforded by present-day computers. With the aim of advancing the current multi-dimensional computational tools used in the design of advanced technology combustors, a solution procedure is developed that combines the novelty of the coupled CFD/spray/scalar Monte Carlo PDF (Probability Density Function) computations on unstructured grids with the ability to run on parallel architectures. In this approach, the mean gas-phase velocity and turbulence fields are determined from a standard turbulence model, the joint composition of species and enthalpy from the solution of a modeled PDF transport equation, and a Lagrangian-based dilute spray model is used for the liquid-phase representation. The gas-turbine combustor flows are often characterized by a complex interaction between various physical processes associated with the interaction between the liquid and gas phases, droplet vaporization, turbulent mixing, heat release associated with chemical kinetics, radiative heat transfer associated with highly absorbing and radiating species, among others. The rate controlling processes often interact with each other at various disparate time 1 and length scales. In particular, turbulence plays an important role in determining the rates of mass and heat transfer, chemical reactions, and liquid phase evaporation in many practical combustion devices.

  20. ACCURATE SPECTROSCOPIC CHARACTERIZATION OF PROTONATED OXIRANE: A POTENTIAL PREBIOTIC SPECIES IN TITAN'S ATMOSPHERE.

    PubMed

    Puzzarini, Cristina; Ali, Ashraf; Biczysko, Malgorzata; Barone, Vincenzo

    2014-09-10

    An accurate spectroscopic characterization of protonated oxirane has been carried out by means of state-of-the-art computational methods and approaches. The calculated spectroscopic parameters from our recent computational investigation of oxirane together with the corresponding experimental data available were used to assess the accuracy of our predicted rotational and IR spectra of protonated oxirane. We found an accuracy of about 10 cm -1 for vibrational transitions (fundamentals as well as overtones and combination bands) and, in relative terms, of 0.1% for rotational transitions. We are therefore confident that the spectroscopic data provided herein are a valuable support for the detection of protonated oxirane not only in Titan's atmosphere but also in the interstellar medium.

  1. The accurate assessment of small-angle X-ray scattering data

    DOE PAGES

    Grant, Thomas D.; Luft, Joseph R.; Carter, Lester G.; ...

    2015-01-23

    Small-angle X-ray scattering (SAXS) has grown in popularity in recent times with the advent of bright synchrotron X-ray sources, powerful computational resources and algorithms enabling the calculation of increasingly complex models. However, the lack of standardized data-quality metrics presents difficulties for the growing user community in accurately assessing the quality of experimental SAXS data. Here, a series of metrics to quantitatively describe SAXS data in an objective manner using statistical evaluations are defined. These metrics are applied to identify the effects of radiation damage, concentration dependence and interparticle interactions on SAXS data from a set of 27 previously described targetsmore » for which high-resolution structures have been determined via X-ray crystallography or nuclear magnetic resonance (NMR) spectroscopy. Studies show that these metrics are sufficient to characterize SAXS data quality on a small sample set with statistical rigor and sensitivity similar to or better than manual analysis. The development of data-quality analysis strategies such as these initial efforts is needed to enable the accurate and unbiased assessment of SAXS data quality.« less

  2. Accurate atomistic potentials and training sets for boron-nitride nanostructures

    NASA Astrophysics Data System (ADS)

    Tamblyn, Isaac

    Boron nitride nanotubes exhibit exceptional structural, mechanical, and thermal properties. They are optically transparent and have high thermal stability, suggesting a wide range of opportunities for structural reinforcement of materials. Modeling can play an important role in determining the optimal approach to integrating nanotubes into a supporting matrix. Developing accurate, atomistic scale models of such nanoscale interfaces embedded within composites is challenging, however, due to the mismatch of length scales involved. Typical nanotube diameters range from 5-50 nm, with a length as large as a micron (i.e. a relevant length-scale for structural reinforcement). Unlike their carbon-based counterparts, well tested and transferable interatomic force fields are not common for BNNT. In light of this, we have developed an extensive training database of BN rich materials, under conditions relevant for BNNT synthesis and composites based on extensive first principles molecular dynamics simulations. Using this data, we have produced an artificial neural network potential capable of reproducing the accuracy of first principles data at significantly reduced computational cost, allowing for accurate simulation at the much larger length scales needed for composite design.

  3. BLESS 2: accurate, memory-efficient and fast error correction method.

    PubMed

    Heo, Yun; Ramachandran, Anand; Hwu, Wen-Mei; Ma, Jian; Chen, Deming

    2016-08-01

    The most important features of error correction tools for sequencing data are accuracy, memory efficiency and fast runtime. The previous version of BLESS was highly memory-efficient and accurate, but it was too slow to handle reads from large genomes. We have developed a new version of BLESS to improve runtime and accuracy while maintaining a small memory usage. The new version, called BLESS 2, has an error correction algorithm that is more accurate than BLESS, and the algorithm has been parallelized using hybrid MPI and OpenMP programming. BLESS 2 was compared with five top-performing tools, and it was found to be the fastest when it was executed on two computing nodes using MPI, with each node containing twelve cores. Also, BLESS 2 showed at least 11% higher gain while retaining the memory efficiency of the previous version for large genomes. Freely available at https://sourceforge.net/projects/bless-ec dchen@illinois.edu Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  4. Localized orbital corrections applied to thermochemical errors in density functional theory: The role of basis set and application to molecular reactions

    NASA Astrophysics Data System (ADS)

    Goldfeld, Dahlia A.; Bochevarov, Arteum D.; Friesner, Richard A.

    2008-12-01

    This paper is a logical continuation of the 22 parameter, localized orbital correction (LOC) methodology that we developed in previous papers [R. A. Friesner et al., J. Chem. Phys. 125, 124107 (2006); E. H. Knoll and R. A. Friesner, J. Phys. Chem. B 110, 18787 (2006).] This methodology allows one to redress systematic density functional theory (DFT) errors, rooted in DFT's inherent inability to accurately describe nondynamical correlation. Variants of the LOC scheme, in conjunction with B3LYP (denoted as B3LYP-LOC), were previously applied to enthalpies of formation, ionization potentials, and electron affinities and showed impressive reduction in the errors. In this paper, we demonstrate for the first time that the B3LYP-LOC scheme is robust across different basis sets [6-31G∗, 6-311++G(3df,3pd), cc-pVTZ, and aug-cc-pVTZ] and reaction types (atomization reactions and molecular reactions). For example, for a test set of 70 molecular reactions, the LOC scheme reduces their mean unsigned error from 4.7 kcal/mol [obtained with B3LYP/6-311++G(3df,3pd)] to 0.8 kcal/mol. We also verified whether the LOC methodology would be equally successful if applied to the promising M05-2X functional. We conclude that although M05-2X produces better reaction enthalpies than B3LYP, the LOC scheme does not combine nearly as successfully with M05-2X than with B3LYP. A brief analysis of another functional, M06-2X, reveals that it is more accurate than M05-2X but its combination with LOC still cannot compete in accuracy with B3LYP-LOC. Indeed, B3LYP-LOC remains the best method of computing reaction enthalpies.

  5. Real-time Accurate Surface Reconstruction Pipeline for Vision Guided Planetary Exploration Using Unmanned Ground and Aerial Vehicles

    NASA Technical Reports Server (NTRS)

    Almeida, Eduardo DeBrito

    2012-01-01

    This report discusses work completed over the summer at the Jet Propulsion Laboratory (JPL), California Institute of Technology. A system is presented to guide ground or aerial unmanned robots using computer vision. The system performs accurate camera calibration, camera pose refinement and surface extraction from images collected by a camera mounted on the vehicle. The application motivating the research is planetary exploration and the vehicles are typically rovers or unmanned aerial vehicles. The information extracted from imagery is used primarily for navigation, as robot location is the same as the camera location and the surfaces represent the terrain that rovers traverse. The processed information must be very accurate and acquired very fast in order to be useful in practice. The main challenge being addressed by this project is to achieve high estimation accuracy and high computation speed simultaneously, a difficult task due to many technical reasons.

  6. Accurate, robust and reliable calculations of Poisson-Boltzmann binding energies

    PubMed Central

    Nguyen, Duc D.; Wang, Bao

    2017-01-01

    Poisson-Boltzmann (PB) model is one of the most popular implicit solvent models in biophysical modeling and computation. The ability of providing accurate and reliable PB estimation of electrostatic solvation free energy, ΔGel, and binding free energy, ΔΔGel, is important to computational biophysics and biochemistry. In this work, we investigate the grid dependence of our PB solver (MIBPB) with SESs for estimating both electrostatic solvation free energies and electrostatic binding free energies. It is found that the relative absolute error of ΔGel obtained at the grid spacing of 1.0 Å compared to ΔGel at 0.2 Å averaged over 153 molecules is less than 0.2%. Our results indicate that the use of grid spacing 0.6 Å ensures accuracy and reliability in ΔΔGel calculation. In fact, the grid spacing of 1.1 Å appears to deliver adequate accuracy for high throughput screening. PMID:28211071

  7. 32 CFR 701.52 - Computation of fees.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... correspondence and preparation costs, these fees are not recoupable from the requester. (b) DD 2086, Record of... costs, as requesters may solicit a copy of that document to ensure accurate computation of fees. Costs... 32 National Defense 5 2010-07-01 2010-07-01 false Computation of fees. 701.52 Section 701.52...

  8. Accurate Classification of Diminutive Colorectal Polyps Using Computer-Aided Analysis.

    PubMed

    Chen, Peng-Jen; Lin, Meng-Chiung; Lai, Mei-Ju; Lin, Jung-Chun; Lu, Henry Horng-Shing; Tseng, Vincent S

    2018-02-01

    Narrow-band imaging is an image-enhanced form of endoscopy used to observed microstructures and capillaries of the mucosal epithelium which allows for real-time prediction of histologic features of colorectal polyps. However, narrow-band imaging expertise is required to differentiate hyperplastic from neoplastic polyps with high levels of accuracy. We developed and tested a system of computer-aided diagnosis with a deep neural network (DNN-CAD) to analyze narrow-band images of diminutive colorectal polyps. We collected 1476 images of neoplastic polyps and 681 images of hyperplastic polyps, obtained from the picture archiving and communications system database in a tertiary hospital in Taiwan. Histologic findings from the polyps were also collected and used as the reference standard. The images and data were used to train the DNN. A test set of images (96 hyperplastic and 188 neoplastic polyps, smaller than 5 mm), obtained from patients who underwent colonoscopies from March 2017 through August 2017, was then used to test the diagnostic ability of the DNN-CAD vs endoscopists (2 expert and 4 novice), who were asked to classify the images of the test set as neoplastic or hyperplastic. Their classifications were compared with findings from histologic analysis. The primary outcome measures were diagnostic accuracy, sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), and diagnostic time. The accuracy, sensitivity, specificity, PPV, NPV, and diagnostic time were compared among DNN-CAD, the novice endoscopists, and the expert endoscopists. The study was designed to detect a difference of 10% in accuracy by a 2-sided McNemar test. In the test set, the DNN-CAD identified neoplastic or hyperplastic polyps with 96.3% sensitivity, 78.1% specificity, a PPV of 89.6%, and a NPV of 91.5%. Fewer than half of the novice endoscopists classified polyps with a NPV of 90% (their NPVs ranged from 73.9% to 84.0%). DNN-CAD classified polyps as

  9. Accurate and efficient seismic data interpolation in the principal frequency wavenumber domain

    NASA Astrophysics Data System (ADS)

    Wang, Benfeng; Lu, Wenkai

    2017-12-01

    Seismic data irregularity caused by economic limitations, acquisition environmental constraints or bad trace elimination, can decrease the performance of the below multi-channel algorithms, such as surface-related multiple elimination (SRME), though some can overcome the irregularity defects. Therefore, accurate interpolation to provide the necessary complete data is a pre-requisite, but its wide applications are constrained because of its large computational burden for huge data volume, especially in 3D explorations. For accurate and efficient interpolation, the curvelet transform- (CT) based projection onto convex sets (POCS) method in the principal frequency wavenumber (PFK) domain is introduced. The complex-valued PF components can characterize their original signal with a high accuracy, but are at least half the size, which can help provide a reasonable efficiency improvement. The irregularity of the observed data is transformed into incoherent noise in the PFK domain, and curvelet coefficients may be sparser when CT is performed on the PFK domain data, enhancing the interpolation accuracy. The performance of the POCS-based algorithms using complex-valued CT in the time space (TX), principal frequency space, and PFK domains are compared. Numerical examples on synthetic and field data demonstrate the validity and effectiveness of the proposed method. With less computational burden, the proposed method can achieve a better interpolation result, and it can be easily extended into higher dimensions.

  10. Security Applications Of Computer Motion Detection

    NASA Astrophysics Data System (ADS)

    Bernat, Andrew P.; Nelan, Joseph; Riter, Stephen; Frankel, Harry

    1987-05-01

    An important area of application of computer vision is the detection of human motion in security systems. This paper describes the development of a computer vision system which can detect and track human movement across the international border between the United States and Mexico. Because of the wide range of environmental conditions, this application represents a stringent test of computer vision algorithms for motion detection and object identification. The desired output of this vision system is accurate, real-time locations for individual aliens and accurate statistical data as to the frequency of illegal border crossings. Because most detection and tracking routines assume rigid body motion, which is not characteristic of humans, new algorithms capable of reliable operation in our application are required. Furthermore, most current detection and tracking algorithms assume a uniform background against which motion is viewed - the urban environment along the US-Mexican border is anything but uniform. The system works in three stages: motion detection, object tracking and object identi-fication. We have implemented motion detection using simple frame differencing, maximum likelihood estimation, mean and median tests and are evaluating them for accuracy and computational efficiency. Due to the complex nature of the urban environment (background and foreground objects consisting of buildings, vegetation, vehicles, wind-blown debris, animals, etc.), motion detection alone is not sufficiently accurate. Object tracking and identification are handled by an expert system which takes shape, location and trajectory information as input and determines if the moving object is indeed representative of an illegal border crossing.

  11. Control surface hinge moment prediction using computational fluid dynamics

    NASA Astrophysics Data System (ADS)

    Simpson, Christopher David

    The following research determines the feasibility of predicting control surface hinge moments using various computational methods. A detailed analysis is conducted using a 2D GA(W)-1 airfoil with a 20% plain flap. Simple hinge moment prediction methods are tested, including empirical Datcom relations and XFOIL. Steady-state and time-accurate turbulent, viscous, Navier-Stokes solutions are computed using Fun3D. Hinge moment coefficients are computed. Mesh construction techniques are discussed. An adjoint-based mesh adaptation case is also evaluated. An NACA 0012 45-degree swept horizontal stabilizer with a 25% elevator is also evaluated using Fun3D. Results are compared with experimental wind-tunnel data obtained from references. Finally, the costs of various solution methods are estimated. Results indicate that while a steady-state Navier-Stokes solution can accurately predict control surface hinge moments for small angles of attack and deflection angles, a time-accurate solution is necessary to accurately predict hinge moments in the presence of flow separation. The ability to capture the unsteady vortex shedding behavior present in moderate to large control surface deflections is found to be critical to hinge moment prediction accuracy. Adjoint-based mesh adaptation is shown to give hinge moment predictions similar to a globally-refined mesh for a steady-state 2D simulation.

  12. Feasibility study for application of the compressed-sensing framework to interior computed tomography (ICT) for low-dose, high-accurate dental x-ray imaging

    NASA Astrophysics Data System (ADS)

    Je, U. K.; Cho, H. M.; Cho, H. S.; Park, Y. O.; Park, C. K.; Lim, H. W.; Kim, K. S.; Kim, G. A.; Park, S. Y.; Woo, T. H.; Choi, S. I.

    2016-02-01

    In this paper, we propose a new/next-generation type of CT examinations, the so-called Interior Computed Tomography (ICT), which may presumably lead to dose reduction to the patient outside the target region-of-interest (ROI), in dental x-ray imaging. Here an x-ray beam from each projection position covers only a relatively small ROI containing a target of diagnosis from the examined structure, leading to imaging benefits such as decreasing scatters and system cost as well as reducing imaging dose. We considered the compressed-sensing (CS) framework, rather than common filtered-backprojection (FBP)-based algorithms, for more accurate ICT reconstruction. We implemented a CS-based ICT algorithm and performed a systematic simulation to investigate the imaging characteristics. Simulation conditions of two ROI ratios of 0.28 and 0.14 between the target and the whole phantom sizes and four projection numbers of 360, 180, 90, and 45 were tested. We successfully reconstructed ICT images of substantially high image quality by using the CS framework even with few-view projection data, still preserving sharp edges in the images.

  13. The accurate particle tracer code

    NASA Astrophysics Data System (ADS)

    Wang, Yulei; Liu, Jian; Qin, Hong; Yu, Zhi; Yao, Yicun

    2017-11-01

    The Accurate Particle Tracer (APT) code is designed for systematic large-scale applications of geometric algorithms for particle dynamical simulations. Based on a large variety of advanced geometric algorithms, APT possesses long-term numerical accuracy and stability, which are critical for solving multi-scale and nonlinear problems. To provide a flexible and convenient I/O interface, the libraries of Lua and Hdf5 are used. Following a three-step procedure, users can efficiently extend the libraries of electromagnetic configurations, external non-electromagnetic forces, particle pushers, and initialization approaches by use of the extendible module. APT has been used in simulations of key physical problems, such as runaway electrons in tokamaks and energetic particles in Van Allen belt. As an important realization, the APT-SW version has been successfully distributed on the world's fastest computer, the Sunway TaihuLight supercomputer, by supporting master-slave architecture of Sunway many-core processors. Based on large-scale simulations of a runaway beam under parameters of the ITER tokamak, it is revealed that the magnetic ripple field can disperse the pitch-angle distribution significantly and improve the confinement of energetic runaway beam on the same time.

  14. The accurate particle tracer code

    DOE PAGES

    Wang, Yulei; Liu, Jian; Qin, Hong; ...

    2017-07-20

    The Accurate Particle Tracer (APT) code is designed for systematic large-scale applications of geometric algorithms for particle dynamical simulations. Based on a large variety of advanced geometric algorithms, APT possesses long-term numerical accuracy and stability, which are critical for solving multi-scale and nonlinear problems. To provide a flexible and convenient I/O interface, the libraries of Lua and Hdf5 are used. Following a three-step procedure, users can efficiently extend the libraries of electromagnetic configurations, external non-electromagnetic forces, particle pushers, and initialization approaches by use of the extendible module. APT has been used in simulations of key physical problems, such as runawaymore » electrons in tokamaks and energetic particles in Van Allen belt. As an important realization, the APT-SW version has been successfully distributed on the world’s fastest computer, the Sunway TaihuLight supercomputer, by supporting master–slave architecture of Sunway many-core processors. Here, based on large-scale simulations of a runaway beam under parameters of the ITER tokamak, it is revealed that the magnetic ripple field can disperse the pitch-angle distribution significantly and improve the confinement of energetic runaway beam on the same time.« less

  15. The accurate particle tracer code

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

    Wang, Yulei; Liu, Jian; Qin, Hong

    The Accurate Particle Tracer (APT) code is designed for systematic large-scale applications of geometric algorithms for particle dynamical simulations. Based on a large variety of advanced geometric algorithms, APT possesses long-term numerical accuracy and stability, which are critical for solving multi-scale and nonlinear problems. To provide a flexible and convenient I/O interface, the libraries of Lua and Hdf5 are used. Following a three-step procedure, users can efficiently extend the libraries of electromagnetic configurations, external non-electromagnetic forces, particle pushers, and initialization approaches by use of the extendible module. APT has been used in simulations of key physical problems, such as runawaymore » electrons in tokamaks and energetic particles in Van Allen belt. As an important realization, the APT-SW version has been successfully distributed on the world’s fastest computer, the Sunway TaihuLight supercomputer, by supporting master–slave architecture of Sunway many-core processors. Here, based on large-scale simulations of a runaway beam under parameters of the ITER tokamak, it is revealed that the magnetic ripple field can disperse the pitch-angle distribution significantly and improve the confinement of energetic runaway beam on the same time.« less

  16. FragBag, an accurate representation of protein structure, retrieves structural neighbors from the entire PDB quickly and accurately.

    PubMed

    Budowski-Tal, Inbal; Nov, Yuval; Kolodny, Rachel

    2010-02-23

    Fast identification of protein structures that are similar to a specified query structure in the entire Protein Data Bank (PDB) is fundamental in structure and function prediction. We present FragBag: An ultrafast and accurate method for comparing protein structures. We describe a protein structure by the collection of its overlapping short contiguous backbone segments, and discretize this set using a library of fragments. Then, we succinctly represent the protein as a "bags-of-fragments"-a vector that counts the number of occurrences of each fragment-and measure the similarity between two structures by the similarity between their vectors. Our representation has two additional benefits: (i) it can be used to construct an inverted index, for implementing a fast structural search engine of the entire PDB, and (ii) one can specify a structure as a collection of substructures, without combining them into a single structure; this is valuable for structure prediction, when there are reliable predictions only of parts of the protein. We use receiver operating characteristic curve analysis to quantify the success of FragBag in identifying neighbor candidate sets in a dataset of over 2,900 structures. The gold standard is the set of neighbors found by six state of the art structural aligners. Our best FragBag library finds more accurate candidate sets than the three other filter methods: The SGM, PRIDE, and a method by Zotenko et al. More interestingly, FragBag performs on a par with the computationally expensive, yet highly trusted structural aligners STRUCTAL and CE.

  17. Computation of records of streamflow at control structures

    USGS Publications Warehouse

    Collins, Dannie L.

    1977-01-01

    Traditional methods of computing streamflow records on large, low-gradient streams require a continuous record of water-surface slope over a natural channel reach. This slope must be of sufficient magnitude to be accuratly measured with available stage measuring devices. On highly regulated streams, this slope approaches zero during periods of low flow and accurate measurement is difficult. Methods are described to calibrate multipurpose regulating control structures to more accurately compute streamflow records on highly-regulated streams. Hydraulic theory, assuming steady, uniform flow during a computational interval, is described for five different types of flow control. The controls are: Tainter gates, hydraulic turbines, fixed spillways, navigation locks, and crest gates. Detailed calibration procedures are described for the five different controls as well as for several flow regimes for some of the controls. The instrumentation package and computer programs necessary to collect and process the field data are discussed. Two typical calibration procedures and measurement data are presented to illustrate the accuracy of the methods. (Woodard-USGS)

  18. Unconditionally stable, second-order accurate schemes for solid state phase transformations driven by mechano-chemical spinodal decomposition

    DOE PAGES

    Sagiyama, Koki; Rudraraju, Shiva; Garikipati, Krishna

    2016-09-13

    Here, we consider solid state phase transformations that are caused by free energy densities with domains of non-convexity in strain-composition space; we refer to the non-convex domains as mechano-chemical spinodals. The non-convexity with respect to composition and strain causes segregation into phases with different crystal structures. We work on an existing model that couples the classical Cahn-Hilliard model with Toupin’s theory of gradient elasticity at finite strains. Both systems are represented by fourth-order, nonlinear, partial differential equations. The goal of this work is to develop unconditionally stable, second-order accurate time-integration schemes, motivated by the need to carry out large scalemore » computations of dynamically evolving microstructures in three dimensions. We also introduce reduced formulations naturally derived from these proposed schemes for faster computations that are still second-order accurate. Although our method is developed and analyzed here for a specific class of mechano-chemical problems, one can readily apply the same method to develop unconditionally stable, second-order accurate schemes for any problems for which free energy density functions are multivariate polynomials of solution components and component gradients. Apart from an analysis and construction of methods, we present a suite of numerical results that demonstrate the schemes in action.« less

  19. Computer programs: Operational and mathematical, a compilation

    NASA Technical Reports Server (NTRS)

    1973-01-01

    Several computer programs which are available through the NASA Technology Utilization Program are outlined. Presented are: (1) Computer operational programs which can be applied to resolve procedural problems swiftly and accurately. (2) Mathematical applications for the resolution of problems encountered in numerous industries. Although the functions which these programs perform are not new and similar programs are available in many large computer center libraries, this collection may be of use to centers with limited systems libraries and for instructional purposes for new computer operators.

  20. Accurate macromolecular structures using minimal measurements from X-ray free-electron lasers

    PubMed Central

    Hattne, Johan; Echols, Nathaniel; Tran, Rosalie; Kern, Jan; Gildea, Richard J.; Brewster, Aaron S.; Alonso-Mori, Roberto; Glöckner, Carina; Hellmich, Julia; Laksmono, Hartawan; Sierra, Raymond G.; Lassalle-Kaiser, Benedikt; Lampe, Alyssa; Han, Guangye; Gul, Sheraz; DiFiore, Dörte; Milathianaki, Despina; Fry, Alan R.; Miahnahri, Alan; White, William E.; Schafer, Donald W.; Seibert, M. Marvin; Koglin, Jason E.; Sokaras, Dimosthenis; Weng, Tsu-Chien; Sellberg, Jonas; Latimer, Matthew J.; Glatzel, Pieter; Zwart, Petrus H.; Grosse-Kunstleve, Ralf W.; Bogan, Michael J.; Messerschmidt, Marc; Williams, Garth J.; Boutet, Sébastien; Messinger, Johannes; Zouni, Athina; Yano, Junko; Bergmann, Uwe; Yachandra, Vittal K.; Adams, Paul D.; Sauter, Nicholas K.

    2014-01-01

    X-ray free-electron laser (XFEL) sources enable the use of crystallography to solve three-dimensional macromolecular structures under native conditions and free from radiation damage. Results to date, however, have been limited by the challenge of deriving accurate Bragg intensities from a heterogeneous population of microcrystals, while at the same time modeling the X-ray spectrum and detector geometry. Here we present a computational approach designed to extract statistically significant high-resolution signals from fewer diffraction measurements. PMID:24633409