Bayesian Estimation of the DINA Model with Gibbs Sampling

ERIC Educational Resources Information Center

Culpepper, Steven Andrew

2015-01-01

A Bayesian model formulation of the deterministic inputs, noisy "and" gate (DINA) model is presented. Gibbs sampling is employed to simulate from the joint posterior distribution of item guessing and slipping parameters, subject attribute parameters, and latent class probabilities. The procedure extends concepts in Béguin and Glas,…

Bayesian inference based on stationary Fokker-Planck sampling.

PubMed

Berrones, Arturo

2010-06-01

A novel formalism for bayesian learning in the context of complex inference models is proposed. The method is based on the use of the stationary Fokker-Planck (SFP) approach to sample from the posterior density. Stationary Fokker-Planck sampling generalizes the Gibbs sampler algorithm for arbitrary and unknown conditional densities. By the SFP procedure, approximate analytical expressions for the conditionals and marginals of the posterior can be constructed. At each stage of SFP, the approximate conditionals are used to define a Gibbs sampling process, which is convergent to the full joint posterior. By the analytical marginals efficient learning methods in the context of artificial neural networks are outlined. Offline and incremental bayesian inference and maximum likelihood estimation from the posterior are performed in classification and regression examples. A comparison of SFP with other Monte Carlo strategies in the general problem of sampling from arbitrary densities is also presented. It is shown that SFP is able to jump large low-probability regions without the need of a careful tuning of any step-size parameter. In fact, the SFP method requires only a small set of meaningful parameters that can be selected following clear, problem-independent guidelines. The computation cost of SFP, measured in terms of loss function evaluations, grows linearly with the given model's dimension.

Time-reversal imaging for classification of submerged elastic targets via Gibbs sampling and the Relevance Vector Machine.

PubMed

Dasgupta, Nilanjan; Carin, Lawrence

2005-04-01

Time-reversal imaging (TRI) is analogous to matched-field processing, although TRI is typically very wideband and is appropriate for subsequent target classification (in addition to localization). Time-reversal techniques, as applied to acoustic target classification, are highly sensitive to channel mismatch. Hence, it is crucial to estimate the channel parameters before time-reversal imaging is performed. The channel-parameter statistics are estimated here by applying a geoacoustic inversion technique based on Gibbs sampling. The maximum a posteriori (MAP) estimate of the channel parameters are then used to perform time-reversal imaging. Time-reversal implementation requires a fast forward model, implemented here by a normal-mode framework. In addition to imaging, extraction of features from the time-reversed images is explored, with these applied to subsequent target classification. The classification of time-reversed signatures is performed by the relevance vector machine (RVM). The efficacy of the technique is analyzed on simulated in-channel data generated by a free-field finite element method (FEM) code, in conjunction with a channel propagation model, wherein the final classification performance is demonstrated to be relatively insensitive to the associated channel parameters. The underlying theory of Gibbs sampling and TRI are presented along with the feature extraction and target classification via the RVM.

Hierarchical Bayesian sparse image reconstruction with application to MRFM.

PubMed

Dobigeon, Nicolas; Hero, Alfred O; Tourneret, Jean-Yves

2009-09-01

This paper presents a hierarchical Bayesian model to reconstruct sparse images when the observations are obtained from linear transformations and corrupted by an additive white Gaussian noise. Our hierarchical Bayes model is well suited to such naturally sparse image applications as it seamlessly accounts for properties such as sparsity and positivity of the image via appropriate Bayes priors. We propose a prior that is based on a weighted mixture of a positive exponential distribution and a mass at zero. The prior has hyperparameters that are tuned automatically by marginalization over the hierarchical Bayesian model. To overcome the complexity of the posterior distribution, a Gibbs sampling strategy is proposed. The Gibbs samples can be used to estimate the image to be recovered, e.g., by maximizing the estimated posterior distribution. In our fully Bayesian approach, the posteriors of all the parameters are available. Thus, our algorithm provides more information than other previously proposed sparse reconstruction methods that only give a point estimate. The performance of the proposed hierarchical Bayesian sparse reconstruction method is illustrated on synthetic data and real data collected from a tobacco virus sample using a prototype MRFM instrument.

Quantum Enhanced Inference in Markov Logic Networks

NASA Astrophysics Data System (ADS)

Wittek, Peter; Gogolin, Christian

2017-04-01

Markov logic networks (MLNs) reconcile two opposing schools in machine learning and artificial intelligence: causal networks, which account for uncertainty extremely well, and first-order logic, which allows for formal deduction. An MLN is essentially a first-order logic template to generate Markov networks. Inference in MLNs is probabilistic and it is often performed by approximate methods such as Markov chain Monte Carlo (MCMC) Gibbs sampling. An MLN has many regular, symmetric structures that can be exploited at both first-order level and in the generated Markov network. We analyze the graph structures that are produced by various lifting methods and investigate the extent to which quantum protocols can be used to speed up Gibbs sampling with state preparation and measurement schemes. We review different such approaches, discuss their advantages, theoretical limitations, and their appeal to implementations. We find that a straightforward application of a recent result yields exponential speedup compared to classical heuristics in approximate probabilistic inference, thereby demonstrating another example where advanced quantum resources can potentially prove useful in machine learning.

Quantum Enhanced Inference in Markov Logic Networks.

PubMed

Wittek, Peter; Gogolin, Christian

2017-04-19

Markov logic networks (MLNs) reconcile two opposing schools in machine learning and artificial intelligence: causal networks, which account for uncertainty extremely well, and first-order logic, which allows for formal deduction. An MLN is essentially a first-order logic template to generate Markov networks. Inference in MLNs is probabilistic and it is often performed by approximate methods such as Markov chain Monte Carlo (MCMC) Gibbs sampling. An MLN has many regular, symmetric structures that can be exploited at both first-order level and in the generated Markov network. We analyze the graph structures that are produced by various lifting methods and investigate the extent to which quantum protocols can be used to speed up Gibbs sampling with state preparation and measurement schemes. We review different such approaches, discuss their advantages, theoretical limitations, and their appeal to implementations. We find that a straightforward application of a recent result yields exponential speedup compared to classical heuristics in approximate probabilistic inference, thereby demonstrating another example where advanced quantum resources can potentially prove useful in machine learning.

Quantum Enhanced Inference in Markov Logic Networks

PubMed Central

Wittek, Peter; Gogolin, Christian

2017-01-01

Markov logic networks (MLNs) reconcile two opposing schools in machine learning and artificial intelligence: causal networks, which account for uncertainty extremely well, and first-order logic, which allows for formal deduction. An MLN is essentially a first-order logic template to generate Markov networks. Inference in MLNs is probabilistic and it is often performed by approximate methods such as Markov chain Monte Carlo (MCMC) Gibbs sampling. An MLN has many regular, symmetric structures that can be exploited at both first-order level and in the generated Markov network. We analyze the graph structures that are produced by various lifting methods and investigate the extent to which quantum protocols can be used to speed up Gibbs sampling with state preparation and measurement schemes. We review different such approaches, discuss their advantages, theoretical limitations, and their appeal to implementations. We find that a straightforward application of a recent result yields exponential speedup compared to classical heuristics in approximate probabilistic inference, thereby demonstrating another example where advanced quantum resources can potentially prove useful in machine learning. PMID:28422093

Multivariate Bayesian analysis of Gaussian, right censored Gaussian, ordered categorical and binary traits using Gibbs sampling

PubMed Central

Korsgaard, Inge Riis; Lund, Mogens Sandø; Sorensen, Daniel; Gianola, Daniel; Madsen, Per; Jensen, Just

2003-01-01

A fully Bayesian analysis using Gibbs sampling and data augmentation in a multivariate model of Gaussian, right censored, and grouped Gaussian traits is described. The grouped Gaussian traits are either ordered categorical traits (with more than two categories) or binary traits, where the grouping is determined via thresholds on the underlying Gaussian scale, the liability scale. Allowances are made for unequal models, unknown covariance matrices and missing data. Having outlined the theory, strategies for implementation are reviewed. These include joint sampling of location parameters; efficient sampling from the fully conditional posterior distribution of augmented data, a multivariate truncated normal distribution; and sampling from the conditional inverse Wishart distribution, the fully conditional posterior distribution of the residual covariance matrix. Finally, a simulated dataset was analysed to illustrate the methodology. This paper concentrates on a model where residuals associated with liabilities of the binary traits are assumed to be independent. A Bayesian analysis using Gibbs sampling is outlined for the model where this assumption is relaxed. PMID:12633531

Quantum Gibbs ensemble Monte Carlo

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

Fantoni, Riccardo, E-mail: rfantoni@ts.infn.it; Moroni, Saverio, E-mail: moroni@democritos.it

We present a path integral Monte Carlo method which is the full quantum analogue of the Gibbs ensemble Monte Carlo method of Panagiotopoulos to study the gas-liquid coexistence line of a classical fluid. Unlike previous extensions of Gibbs ensemble Monte Carlo to include quantum effects, our scheme is viable even for systems with strong quantum delocalization in the degenerate regime of temperature. This is demonstrated by an illustrative application to the gas-superfluid transition of {sup 4}He in two dimensions.

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

ERIC Educational Resources Information Center

Vargas, Francisco M.

2014-01-01

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

Building test data from real outbreaks for evaluating detection algorithms.

PubMed

Texier, Gaetan; Jackson, Michael L; Siwe, Leonel; Meynard, Jean-Baptiste; Deparis, Xavier; Chaudet, Herve

2017-01-01

Benchmarking surveillance systems requires realistic simulations of disease outbreaks. However, obtaining these data in sufficient quantity, with a realistic shape and covering a sufficient range of agents, size and duration, is known to be very difficult. The dataset of outbreak signals generated should reflect the likely distribution of authentic situations faced by the surveillance system, including very unlikely outbreak signals. We propose and evaluate a new approach based on the use of historical outbreak data to simulate tailored outbreak signals. The method relies on a homothetic transformation of the historical distribution followed by resampling processes (Binomial, Inverse Transform Sampling Method-ITSM, Metropolis-Hasting Random Walk, Metropolis-Hasting Independent, Gibbs Sampler, Hybrid Gibbs Sampler). We carried out an analysis to identify the most important input parameters for simulation quality and to evaluate performance for each of the resampling algorithms. Our analysis confirms the influence of the type of algorithm used and simulation parameters (i.e. days, number of cases, outbreak shape, overall scale factor) on the results. We show that, regardless of the outbreaks, algorithms and metrics chosen for the evaluation, simulation quality decreased with the increase in the number of days simulated and increased with the number of cases simulated. Simulating outbreaks with fewer cases than days of duration (i.e. overall scale factor less than 1) resulted in an important loss of information during the simulation. We found that Gibbs sampling with a shrinkage procedure provides a good balance between accuracy and data dependency. If dependency is of little importance, binomial and ITSM methods are accurate. Given the constraint of keeping the simulation within a range of plausible epidemiological curves faced by the surveillance system, our study confirms that our approach can be used to generate a large spectrum of outbreak signals.

A Bayesian Nonparametric Approach to Image Super-Resolution.

PubMed

Polatkan, Gungor; Zhou, Mingyuan; Carin, Lawrence; Blei, David; Daubechies, Ingrid

2015-02-01

Super-resolution methods form high-resolution images from low-resolution images. In this paper, we develop a new Bayesian nonparametric model for super-resolution. Our method uses a beta-Bernoulli process to learn a set of recurring visual patterns, called dictionary elements, from the data. Because it is nonparametric, the number of elements found is also determined from the data. We test the results on both benchmark and natural images, comparing with several other models from the research literature. We perform large-scale human evaluation experiments to assess the visual quality of the results. In a first implementation, we use Gibbs sampling to approximate the posterior. However, this algorithm is not feasible for large-scale data. To circumvent this, we then develop an online variational Bayes (VB) algorithm. This algorithm finds high quality dictionaries in a fraction of the time needed by the Gibbs sampler.

Estimating the Gibbs energy of hydration from molecular dynamics trajectories obtained by integral equations of the theory of liquids in the RISM approximation

NASA Astrophysics Data System (ADS)

Tikhonov, D. A.; Sobolev, E. V.

2011-04-01

A method of integral equations of the theory of liquids in the reference interaction site model (RISM) approximation is used to estimate the Gibbs energy averaged over equilibrium trajectories computed by molecular mechanics. Peptide oxytocin is selected as the object of interest. The Gibbs energy is calculated using all chemical potential formulas introduced in the RISM approach for the excess chemical potential of solvation and is compared with estimates by the generalized Born model. Some formulas are shown to give the wrong sign of Gibbs energy changes when peptide passes from the gas phase into water environment; the other formulas give overestimated Gibbs energy changes with the right sign. Note that allowance for the repulsive correction in the approximate analytical expressions for the Gibbs energy derived by thermodynamic perturbation theory is not a remedy.

An Improved Estimation Using Polya-Gamma Augmentation for Bayesian Structural Equation Models with Dichotomous Variables

ERIC Educational Resources Information Center

Kim, Seohyun; Lu, Zhenqiu; Cohen, Allan S.

2018-01-01

Bayesian algorithms have been used successfully in the social and behavioral sciences to analyze dichotomous data particularly with complex structural equation models. In this study, we investigate the use of the Polya-Gamma data augmentation method with Gibbs sampling to improve estimation of structural equation models with dichotomous variables.…

Recovery of Graded Response Model Parameters: A Comparison of Marginal Maximum Likelihood and Markov Chain Monte Carlo Estimation

ERIC Educational Resources Information Center

Kieftenbeld, Vincent; Natesan, Prathiba

2012-01-01

Markov chain Monte Carlo (MCMC) methods enable a fully Bayesian approach to parameter estimation of item response models. In this simulation study, the authors compared the recovery of graded response model parameters using marginal maximum likelihood (MML) and Gibbs sampling (MCMC) under various latent trait distributions, test lengths, and…

Hierarchical Bayesian modeling of ionospheric TEC disturbances as non-stationary processes

NASA Astrophysics Data System (ADS)

Seid, Abdu Mohammed; Berhane, Tesfahun; Roininen, Lassi; Nigussie, Melessew

2018-03-01

We model regular and irregular variation of ionospheric total electron content as stationary and non-stationary processes, respectively. We apply the method developed to SCINDA GPS data set observed at Bahir Dar, Ethiopia (11.6 °N, 37.4 °E) . We use hierarchical Bayesian inversion with Gaussian Markov random process priors, and we model the prior parameters in the hyperprior. We use Matérn priors via stochastic partial differential equations, and use scaled Inv -χ2 hyperpriors for the hyperparameters. For drawing posterior estimates, we use Markov Chain Monte Carlo methods: Gibbs sampling and Metropolis-within-Gibbs for parameter and hyperparameter estimations, respectively. This allows us to quantify model parameter estimation uncertainties as well. We demonstrate the applicability of the method proposed using a synthetic test case. Finally, we apply the method to real GPS data set, which we decompose to regular and irregular variation components. The result shows that the approach can be used as an accurate ionospheric disturbance characterization technique that quantifies the total electron content variability with corresponding error uncertainties.

An Evaluation of a Markov Chain Monte Carlo Method for the Two-Parameter Logistic Model.

ERIC Educational Resources Information Center

Kim, Seock-Ho; Cohen, Allan S.

The accuracy of the Markov Chain Monte Carlo (MCMC) procedure Gibbs sampling was considered for estimation of item parameters of the two-parameter logistic model. Data for the Law School Admission Test (LSAT) Section 6 were analyzed to illustrate the MCMC procedure. In addition, simulated data sets were analyzed using the MCMC, marginal Bayesian…

Building test data from real outbreaks for evaluating detection algorithms

PubMed Central

Texier, Gaetan; Jackson, Michael L.; Siwe, Leonel; Meynard, Jean-Baptiste; Deparis, Xavier; Chaudet, Herve

2017-01-01

Benchmarking surveillance systems requires realistic simulations of disease outbreaks. However, obtaining these data in sufficient quantity, with a realistic shape and covering a sufficient range of agents, size and duration, is known to be very difficult. The dataset of outbreak signals generated should reflect the likely distribution of authentic situations faced by the surveillance system, including very unlikely outbreak signals. We propose and evaluate a new approach based on the use of historical outbreak data to simulate tailored outbreak signals. The method relies on a homothetic transformation of the historical distribution followed by resampling processes (Binomial, Inverse Transform Sampling Method—ITSM, Metropolis-Hasting Random Walk, Metropolis-Hasting Independent, Gibbs Sampler, Hybrid Gibbs Sampler). We carried out an analysis to identify the most important input parameters for simulation quality and to evaluate performance for each of the resampling algorithms. Our analysis confirms the influence of the type of algorithm used and simulation parameters (i.e. days, number of cases, outbreak shape, overall scale factor) on the results. We show that, regardless of the outbreaks, algorithms and metrics chosen for the evaluation, simulation quality decreased with the increase in the number of days simulated and increased with the number of cases simulated. Simulating outbreaks with fewer cases than days of duration (i.e. overall scale factor less than 1) resulted in an important loss of information during the simulation. We found that Gibbs sampling with a shrinkage procedure provides a good balance between accuracy and data dependency. If dependency is of little importance, binomial and ITSM methods are accurate. Given the constraint of keeping the simulation within a range of plausible epidemiological curves faced by the surveillance system, our study confirms that our approach can be used to generate a large spectrum of outbreak signals. PMID:28863159

Computational methods for reactive transport modeling: A Gibbs energy minimization approach for multiphase equilibrium calculations

NASA Astrophysics Data System (ADS)

Leal, Allan M. M.; Kulik, Dmitrii A.; Kosakowski, Georg

2016-02-01

We present a numerical method for multiphase chemical equilibrium calculations based on a Gibbs energy minimization approach. The method can accurately and efficiently determine the stable phase assemblage at equilibrium independently of the type of phases and species that constitute the chemical system. We have successfully applied our chemical equilibrium algorithm in reactive transport simulations to demonstrate its effective use in computationally intensive applications. We used FEniCS to solve the governing partial differential equations of mass transport in porous media using finite element methods in unstructured meshes. Our equilibrium calculations were benchmarked with GEMS3K, the numerical kernel of the geochemical package GEMS. This allowed us to compare our results with a well-established Gibbs energy minimization algorithm, as well as their performance on every mesh node, at every time step of the transport simulation. The benchmark shows that our novel chemical equilibrium algorithm is accurate, robust, and efficient for reactive transport applications, and it is an improvement over the Gibbs energy minimization algorithm used in GEMS3K. The proposed chemical equilibrium method has been implemented in Reaktoro, a unified framework for modeling chemically reactive systems, which is now used as an alternative numerical kernel of GEMS.

Revised values for the Gibbs free energy of formation of [Al(OH)4 aq-], diaspore, boehmite and bayerite at 298.15 K and 1 bar, the thermodynamic properties of kaolinite to 800 K and 1 bar, and the heats of solution of several gibbsite samples

USGS Publications Warehouse

Hemingway, B.S.; Robie, R.A.; Kittrick, J.A.

1978-01-01

Solution calorimetric measurements compared with solubility determinations from the literature for the same samples of gibbsite have provided a direct thermochemical cycle through which the Gibbs free energy of formation of [Al(OH)4 aq-] can be determined. The Gibbs free energy of formation of [Al(OH)4 aq-] at 298.15 K is -1305 ?? 1 kJ/mol. These heat-of-solution results show no significant difference in the thermodynamic properties of gibbsite particles in the range from 50 to 0.05 ??m. The Gibbs free energies of formation at 298.15 K and 1 bar pressure of diaspore, boehmite and bayerite are -9210 ?? 5.0, -918.4 ?? 2.1 and -1153 ?? 2 kJ/mol based upon the Gibbs free energy of [A1(OH)4 aq-] calculated in this paper and the acceptance of -1582.2 ?? 1.3 and -1154.9 ?? 1.2 kJ/mol for the Gibbs free energy of formation of corundum and gibbsite, respectively. Values for the Gibbs free energy formation of [Al(OH)2 aq+] and [AlO2 aq-] were also calculated as -914.2 ?? 2.1 and -830.9 ?? 2.1 kJ/mol, respectively. The use of [AlC2 aq-] as a chemical species is discouraged. A revised Gibbs free energy of formation for [H4SiO4aq0] was recalculated from calorimetric data yielding a value of -1307.5 ?? 1.7 kJ/mol which is in good agreement with the results obtained from several solubility studies. Smoothed values for the thermodynamic functions CP0, ( HT0 - H2980) T, ( GT0 - H2980) T, ST0 - S00, ??Hf{hook},2980 kaolinite are listed at integral temperatures between 298.15 and 800 K. The heat capacity of kaolinite at temperatures between 250 and 800 K may be calculated from the following equation: CP0 = 1430.26 - 0.78850 T + 3.0340 ?? 10-4 T2 -1.85158 ?? 10-4 T2 1 2 + 8.3341 ?? 106 T-2. The thermodynamic properties of most of the geologically important Al-bearing phases have been referenced to the same reference state for Al, namely gibbsite. ?? 1978.

Sampling schemes and parameter estimation for nonlinear Bernoulli-Gaussian sparse models

NASA Astrophysics Data System (ADS)

Boudineau, Mégane; Carfantan, Hervé; Bourguignon, Sébastien; Bazot, Michael

2016-06-01

We address the sparse approximation problem in the case where the data are approximated by the linear combination of a small number of elementary signals, each of these signals depending non-linearly on additional parameters. Sparsity is explicitly expressed through a Bernoulli-Gaussian hierarchical model in a Bayesian framework. Posterior mean estimates are computed using Markov Chain Monte-Carlo algorithms. We generalize the partially marginalized Gibbs sampler proposed in the linear case in [1], and build an hybrid Hastings-within-Gibbs algorithm in order to account for the nonlinear parameters. All model parameters are then estimated in an unsupervised procedure. The resulting method is evaluated on a sparse spectral analysis problem. It is shown to converge more efficiently than the classical joint estimation procedure, with only a slight increase of the computational cost per iteration, consequently reducing the global cost of the estimation procedure.

Representing and computing regular languages on massively parallel networks

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

Miller, M.I.; O'Sullivan, J.A.; Boysam, B.

1991-01-01

This paper proposes a general method for incorporating rule-based constraints corresponding to regular languages into stochastic inference problems, thereby allowing for a unified representation of stochastic and syntactic pattern constraints. The authors' approach first established the formal connection of rules to Chomsky grammars, and generalizes the original work of Shannon on the encoding of rule-based channel sequences to Markov chains of maximum entropy. This maximum entropy probabilistic view leads to Gibb's representations with potentials which have their number of minima growing at precisely the exponential rate that the language of deterministically constrained sequences grow. These representations are coupled to stochasticmore » diffusion algorithms, which sample the language-constrained sequences by visiting the energy minima according to the underlying Gibbs' probability law. The coupling to stochastic search methods yields the all-important practical result that fully parallel stochastic cellular automata may be derived to generate samples from the rule-based constraint sets. The production rules and neighborhood state structure of the language of sequences directly determines the necessary connection structures of the required parallel computing surface. Representations of this type have been mapped to the DAP-510 massively-parallel processor consisting of 1024 mesh-connected bit-serial processing elements for performing automated segmentation of electron-micrograph images.« less

Free energy and phase equilibria for the restricted primitive model of ionic fluids from Monte Carlo simulations

NASA Astrophysics Data System (ADS)

Orkoulas, Gerassimos; Panagiotopoulos, Athanassios Z.

1994-07-01

In this work, we investigate the liquid-vapor phase transition of the restricted primitive model of ionic fluids. We show that at the low temperatures where the phase transition occurs, the system cannot be studied by conventional molecular simulation methods because convergence to equilibrium is slow. To accelerate convergence, we propose cluster Monte Carlo moves capable of moving more than one particle at a time. We then address the issue of charged particle transfers in grand canonical and Gibbs ensemble Monte Carlo simulations, for which we propose a biased particle insertion/destruction scheme capable of sampling short interparticle distances. We compute the chemical potential for the restricted primitive model as a function of temperature and density from grand canonical Monte Carlo simulations and the phase envelope from Gibbs Monte Carlo simulations. Our calculated phase coexistence curve is in agreement with recent results of Caillol obtained on the four-dimensional hypersphere and our own earlier Gibbs ensemble simulations with single-ion transfers, with the exception of the critical temperature, which is lower in the current calculations. Our best estimates for the critical parameters are T*c=0.053, ρ*c=0.025. We conclude with possible future applications of the biased techniques developed here for phase equilibrium calculations for ionic fluids.

Consistent Estimation of Gibbs Energy Using Component Contributions

PubMed Central

Milo, Ron; Fleming, Ronan M. T.

2013-01-01

Standard Gibbs energies of reactions are increasingly being used in metabolic modeling for applying thermodynamic constraints on reaction rates, metabolite concentrations and kinetic parameters. The increasing scope and diversity of metabolic models has led scientists to look for genome-scale solutions that can estimate the standard Gibbs energy of all the reactions in metabolism. Group contribution methods greatly increase coverage, albeit at the price of decreased precision. We present here a way to combine the estimations of group contribution with the more accurate reactant contributions by decomposing each reaction into two parts and applying one of the methods on each of them. This method gives priority to the reactant contributions over group contributions while guaranteeing that all estimations will be consistent, i.e. will not violate the first law of thermodynamics. We show that there is a significant increase in the accuracy of our estimations compared to standard group contribution. Specifically, our cross-validation results show an 80% reduction in the median absolute residual for reactions that can be derived by reactant contributions only. We provide the full framework and source code for deriving estimates of standard reaction Gibbs energy, as well as confidence intervals, and believe this will facilitate the wide use of thermodynamic data for a better understanding of metabolism. PMID:23874165

A Gibbs sampler for Bayesian analysis of site-occupancy data

USGS Publications Warehouse

Dorazio, Robert M.; Rodriguez, Daniel Taylor

2012-01-01

1. A Bayesian analysis of site-occupancy data containing covariates of species occurrence and species detection probabilities is usually completed using Markov chain Monte Carlo methods in conjunction with software programs that can implement those methods for any statistical model, not just site-occupancy models. Although these software programs are quite flexible, considerable experience is often required to specify a model and to initialize the Markov chain so that summaries of the posterior distribution can be estimated efficiently and accurately. 2. As an alternative to these programs, we develop a Gibbs sampler for Bayesian analysis of site-occupancy data that include covariates of species occurrence and species detection probabilities. This Gibbs sampler is based on a class of site-occupancy models in which probabilities of species occurrence and detection are specified as probit-regression functions of site- and survey-specific covariate measurements. 3. To illustrate the Gibbs sampler, we analyse site-occupancy data of the blue hawker, Aeshna cyanea (Odonata, Aeshnidae), a common dragonfly species in Switzerland. Our analysis includes a comparison of results based on Bayesian and classical (non-Bayesian) methods of inference. We also provide code (based on the R software program) for conducting Bayesian and classical analyses of site-occupancy data.

Relativistic hydrodynamics from quantum field theory on the basis of the generalized Gibbs ensemble method

NASA Astrophysics Data System (ADS)

Hayata, Tomoya; Hidaka, Yoshimasa; Noumi, Toshifumi; Hongo, Masaru

2015-09-01

We derive relativistic hydrodynamics from quantum field theories by assuming that the density operator is given by a local Gibbs distribution at initial time. We decompose the energy-momentum tensor and particle current into nondissipative and dissipative parts, and analyze their time evolution in detail. Performing the path-integral formulation of the local Gibbs distribution, we microscopically derive the generating functional for the nondissipative hydrodynamics. We also construct a basis to study dissipative corrections. In particular, we derive the first-order dissipative hydrodynamic equations without a choice of frame such as the Landau-Lifshitz or Eckart frame.

Boosting association rule mining in large datasets via Gibbs sampling.

PubMed

Qian, Guoqi; Rao, Calyampudi Radhakrishna; Sun, Xiaoying; Wu, Yuehua

2016-05-03

Current algorithms for association rule mining from transaction data are mostly deterministic and enumerative. They can be computationally intractable even for mining a dataset containing just a few hundred transaction items, if no action is taken to constrain the search space. In this paper, we develop a Gibbs-sampling-induced stochastic search procedure to randomly sample association rules from the itemset space, and perform rule mining from the reduced transaction dataset generated by the sample. Also a general rule importance measure is proposed to direct the stochastic search so that, as a result of the randomly generated association rules constituting an ergodic Markov chain, the overall most important rules in the itemset space can be uncovered from the reduced dataset with probability 1 in the limit. In the simulation study and a real genomic data example, we show how to boost association rule mining by an integrated use of the stochastic search and the Apriori algorithm.

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

ERIC Educational Resources Information Center

Smith, Norman O.

2004-01-01

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

Gibbs Ensemble Simulations of the Solvent Swelling of Polymer Films

NASA Astrophysics Data System (ADS)

Gartner, Thomas; Epps, Thomas, III; Jayaraman, Arthi

Solvent vapor annealing (SVA) is a useful technique to tune the morphology of block polymer, polymer blend, and polymer nanocomposite films. Despite SVA's utility, standardized SVA protocols have not been established, partly due to a lack of fundamental knowledge regarding the interplay between the polymer(s), solvent, substrate, and free-surface during solvent annealing and evaporation. An understanding of how to tune polymer film properties in a controllable manner through SVA processes is needed. Herein, the thermodynamic implications of the presence of solvent in the swollen polymer film is explored through two alternative Gibbs ensemble simulation methods that we have developed and extended: Gibbs ensemble molecular dynamics (GEMD) and hybrid Monte Carlo (MC)/molecular dynamics (MD). In this poster, we will describe these simulation methods and demonstrate their application to polystyrene films swollen by toluene and n-hexane. Polymer film swelling experiments, Gibbs ensemble molecular simulations, and polymer reference interaction site model (PRISM) theory are combined to calculate an effective Flory-Huggins χ (χeff) for polymer-solvent mixtures. The effects of solvent chemistry, solvent content, polymer molecular weight, and polymer architecture on χeff are examined, providing a platform to control and understand the thermodynamics of polymer film swelling.

Thermodynamic properties of adsorption and micellization of n-oktyl-β-D-glucopiranoside.

PubMed

Mańko, Diana; Zdziennicka, Anna; Jańczuk, Bronisław

2014-02-01

Measurements of the surface tension, density and viscosity of aqueous solutions of n-oktyl-β-D-glucopiranoside (OGP) were made at 293 K. From the obtained results the Gibbs surface excess concentration of OGP at the water-air interface and its critical micelle concentration were determined. The Gibbs surface excess concentration of OGP used in the Gu and Zhu isotherm equation allowed us to determine the Gibbs standard free energy of OGP adsorption at the water-air interface. The Gibbs standard free energy of OGP adsorption was also determined on the basis of the Langmuir, Szyszkowski, Gamboa and Olea equations as well the surface tension of "hydrophobic" part of OGP and "hydrophobic" part-water interface tension. It appeared that there is an agreement between the values of Gibbs standard free energy of OGP adsorption at the water-air interface determined by using all the above mentioned methods. It also proved that standard free energy of OGP micellization determined from CMC is consistent with that obtained on the basis of the free energy of the interactions between the "hydrophobic" part of the OPG through the water phase. Copyright © 2013 Elsevier B.V. All rights reserved.

Simulating the Generalized Gibbs Ensemble (GGE): A Hilbert space Monte Carlo approach

NASA Astrophysics Data System (ADS)

Alba, Vincenzo

By combining classical Monte Carlo and Bethe ansatz techniques we devise a numerical method to construct the Truncated Generalized Gibbs Ensemble (TGGE) for the spin-1/2 isotropic Heisenberg (XXX) chain. The key idea is to sample the Hilbert space of the model with the appropriate GGE probability measure. The method can be extended to other integrable systems, such as the Lieb-Liniger model. We benchmark the approach focusing on GGE expectation values of several local observables. As finite-size effects decay exponentially with system size, moderately large chains are sufficient to extract thermodynamic quantities. The Monte Carlo results are in agreement with both the Thermodynamic Bethe Ansatz (TBA) and the Quantum Transfer Matrix approach (QTM). Remarkably, it is possible to extract in a simple way the steady-state Bethe-Gaudin-Takahashi (BGT) roots distributions, which encode complete information about the GGE expectation values in the thermodynamic limit. Finally, it is straightforward to simulate extensions of the GGE, in which, besides the local integral of motion (local charges), one includes arbitrary functions of the BGT roots. As an example, we include in the GGE the first non-trivial quasi-local integral of motion.

Bayesian Estimation of Fish Disease Prevalence from Pooled Samples Incorporating Sensitivity and Specificity

NASA Astrophysics Data System (ADS)

Williams, Christopher J.; Moffitt, Christine M.

2003-03-01

An important emerging issue in fisheries biology is the health of free-ranging populations of fish, particularly with respect to the prevalence of certain pathogens. For many years, pathologists focused on captive populations and interest was in the presence or absence of certain pathogens, so it was economically attractive to test pooled samples of fish. Recently, investigators have begun to study individual fish prevalence from pooled samples. Estimation of disease prevalence from pooled samples is straightforward when assay sensitivity and specificity are perfect, but this assumption is unrealistic. Here we illustrate the use of a Bayesian approach for estimating disease prevalence from pooled samples when sensitivity and specificity are not perfect. We also focus on diagnostic plots to monitor the convergence of the Gibbs-sampling-based Bayesian analysis. The methods are illustrated with a sample data set.

Representation of complex probabilities and complex Gibbs sampling

NASA Astrophysics Data System (ADS)

Salcedo, Lorenzo Luis

2018-03-01

Complex weights appear in Physics which are beyond a straightforward importance sampling treatment, as required in Monte Carlo calculations. This is the wellknown sign problem. The complex Langevin approach amounts to effectively construct a positive distribution on the complexified manifold reproducing the expectation values of the observables through their analytical extension. Here we discuss the direct construction of such positive distributions paying attention to their localization on the complexified manifold. Explicit localized representations are obtained for complex probabilities defined on Abelian and non Abelian groups. The viability and performance of a complex version of the heat bath method, based on such representations, is analyzed.

Revised values for the thermodynamic properties of boehmite, AlO(OH) , and related species and phases in the system Al-H-O

USGS Publications Warehouse

Hemingway, B.S.; Robie, R.A.; Apps, J.A.

1991-01-01

Heat capacity measurements are reported for a well-characterized boehmite that differ significantly from results reported earlier by Shomate and Cook (1946) for a monohydrate of alumina. It is suggested that the earlier measurements were made on a sample that was a mixture of phases and that use of that heat-capacity and derived thermodynamic data be discontinued. The entropy of boehmite derived in this study is 37.19 ?? 0.10 J/(mol.K) at 298.15 K. Based on our value for the entropy and accepting the recommended Gibbs free energy for Al(OH)-4, the Gibbs free energy and enthalpy of formation of boehmite are calculated to be -918.4 ?? 2.1 and -996.4 ?? 2.2 kJ/mol, respectively, from solubility data for boehmite. The Gibbs energy for boehmite is unchanged from that given by Hemingway et al. (1978). -from Authors

Leveraging Gibbs Ensemble Molecular Dynamics and Hybrid Monte Carlo/Molecular Dynamics for Efficient Study of Phase Equilibria.

PubMed

Gartner, Thomas E; Epps, Thomas H; Jayaraman, Arthi

2016-11-08

We describe an extension of the Gibbs ensemble molecular dynamics (GEMD) method for studying phase equilibria. Our modifications to GEMD allow for direct control over particle transfer between phases and improve the method's numerical stability. Additionally, we found that the modified GEMD approach had advantages in computational efficiency in comparison to a hybrid Monte Carlo (MC)/MD Gibbs ensemble scheme in the context of the single component Lennard-Jones fluid. We note that this increase in computational efficiency does not compromise the close agreement of phase equilibrium results between the two methods. However, numerical instabilities in the GEMD scheme hamper GEMD's use near the critical point. We propose that the computationally efficient GEMD simulations can be used to map out the majority of the phase window, with hybrid MC/MD used as a follow up for conditions under which GEMD may be unstable (e.g., near-critical behavior). In this manner, we can capitalize on the contrasting strengths of these two methods to enable the efficient study of phase equilibria for systems that present challenges for a purely stochastic GEMC method, such as dense or low temperature systems, and/or those with complex molecular topologies.

Cerebella segmentation on MR images of pediatric patients with medulloblastoma

NASA Astrophysics Data System (ADS)

Shan, Zu Y.; Ji, Qing; Glass, John; Gajjar, Amar; Reddick, Wilburn E.

2005-04-01

In this study, an automated method has been developed to identify the cerebellum from T1-weighted MR brain images of patients with medulloblastoma. A new objective function that is similar to Gibbs free energy in classic physics was defined; and the brain structure delineation was viewed as a process of minimizing Gibbs free energy. We used a rigid-body registration and an active contour (snake) method to minimize the Gibbs free energy in this study. The method was applied to 20 patient data sets to generate cerebellum images and volumetric results. The generated cerebellum images were compared with two manually drawn results. Strong correlations were found between the automatically and manually generated volumetric results, the correlation coefficients with each of manual results were 0.971 and 0.974, respectively. The average Jaccard similarities with each of two manual results were 0.89 and 0.88, respectively. The average Kappa indexes with each of two manual results were 0.94 and 0.93, respectively. These results showed this method was both robust and accurate for cerebellum segmentation. The method may be applied to various research and clinical investigation in which cerebellum segmentation and quantitative MR measurement of cerebellum are needed.

Q-Space Truncation and Sampling in Diffusion Spectrum Imaging

PubMed Central

Tian, Qiyuan; Rokem, Ariel; Folkerth, Rebecca D.; Nummenmaa, Aapo; Fan, Qiuyun; Edlow, Brian L.; McNab, Jennifer A.

2015-01-01

Purpose To characterize the q-space truncation and sampling on the spin-displacement probability density function (PDF) in diffusion spectrum imaging (DSI). Methods DSI data were acquired using the MGH-USC connectome scanner (Gmax=300mT/m) with bmax=30,000s/mm2, 17×17×17, 15×15×15 and 11×11×11 grids in ex vivo human brains and bmax=10,000s/mm2, 11×11×11 grid in vivo. An additional in vivo scan using bmax=7,000s/mm2, 11×11×11 grid was performed with a derated gradient strength of 40mT/m. PDFs and orientation distribution functions (ODFs) were reconstructed with different q-space filtering and PDF integration lengths, and from down-sampled data by factors of two and three. Results Both ex vivo and in vivo data showed Gibbs ringing in PDFs, which becomes the main source of artifact in the subsequently reconstructed ODFs. For down-sampled data, PDFs interfere with the first replicas or their ringing, leading to obscured orientations in ODFs. Conclusion The minimum required q-space sampling density corresponds to a field-of-view approximately equal to twice the mean displacement distance (MDD) of the tissue. The 11×11×11 grid is suitable for both ex vivo and in vivo DSI experiments. To minimize the effects of Gibbs ringing, ODFs should be reconstructed from unfiltered q-space data with the integration length over the PDF constrained to around the MDD. PMID:26762670

First-pass myocardial perfusion MRI with reduced subendocardial dark-rim artifact using optimized Cartesian sampling.

PubMed

Zhou, Zhengwei; Bi, Xiaoming; Wei, Janet; Yang, Hsin-Jung; Dharmakumar, Rohan; Arsanjani, Reza; Bairey Merz, C Noel; Li, Debiao; Sharif, Behzad

2017-02-01

The presence of subendocardial dark-rim artifact (DRA) remains an ongoing challenge in first-pass perfusion (FPP) cardiac magnetic resonance imaging (MRI). We propose a free-breathing FPP imaging scheme with Cartesian sampling that is optimized to minimize the DRA and readily enables near-instantaneous image reconstruction. The proposed FPP method suppresses Gibbs ringing effects-a major underlying factor for the DRA-by "shaping" the underlying point spread function through a two-step process: 1) an undersampled Cartesian sampling scheme that widens the k-space coverage compared to the conventional scheme; and 2) a modified parallel-imaging scheme that incorporates optimized apodization (k-space data filtering) to suppress Gibbs-ringing effects. Healthy volunteer studies (n = 10) were performed to compare the proposed method against the conventional Cartesian technique-both using a saturation-recovery gradient-echo sequence at 3T. Furthermore, FPP imaging studies using the proposed method were performed in infarcted canines (n = 3), and in two symptomatic patients with suspected coronary microvascular dysfunction for assessment of myocardial hypoperfusion. Width of the DRA and the number of DRA-affected myocardial segments were significantly reduced in the proposed method compared to the conventional approach (width: 1.3 vs. 2.9 mm, P < 0.001; number of segments: 2.6 vs. 8.7; P < 0.0001). The number of slices with severe DRA was markedly lower for the proposed method (by 10-fold). The reader-assigned image quality scores were similar (P = 0.2), although the quantified myocardial signal-to-noise ratio was lower for the proposed method (P < 0.05). Animal studies showed that the proposed method can detect subendocardial perfusion defects and patient results were consistent with the gold-standard invasive test. The proposed free-breathing Cartesian FPP imaging method significantly reduces the prevalence of severe DRAs compared to the conventional approach while maintaining similar resolution and image quality. 2 J. Magn. Reson. Imaging 2017;45:542-555. © 2016 International Society for Magnetic Resonance in Medicine.

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

NASA Astrophysics Data System (ADS)

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

2018-04-01

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

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

NASA Astrophysics Data System (ADS)

Cheng, Bingqing; Ceriotti, Michele

2018-02-01

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

A statistical model investigating the prevalence of tuberculosis in New York City using counting processes with two change-points

PubMed Central

ACHCAR, J. A.; MARTINEZ, E. Z.; RUFFINO-NETTO, A.; PAULINO, C. D.; SOARES, P.

2008-01-01

SUMMARY We considered a Bayesian analysis for the prevalence of tuberculosis cases in New York City from 1970 to 2000. This counting dataset presented two change-points during this period. We modelled this counting dataset considering non-homogeneous Poisson processes in the presence of the two-change points. A Bayesian analysis for the data is considered using Markov chain Monte Carlo methods. Simulated Gibbs samples for the parameters of interest were obtained using WinBugs software. PMID:18346287

Markov chain sampling of the O(n) loop models on the infinite plane

NASA Astrophysics Data System (ADS)

Herdeiro, Victor

2017-07-01

A numerical method was recently proposed in Herdeiro and Doyon [Phys. Rev. E 94, 043322 (2016), 10.1103/PhysRevE.94.043322] showing a precise sampling of the infinite plane two-dimensional critical Ising model for finite lattice subsections. The present note extends the method to a larger class of models, namely the O(n) loop gas models for n ∈(1 ,2 ] . We argue that even though the Gibbs measure is nonlocal, it is factorizable on finite subsections when sufficient information on the loops touching the boundaries is stored. Our results attempt to show that provided an efficient Markov chain mixing algorithm and an improved discrete lattice dilation procedure the planar limit of the O(n) models can be numerically studied with efficiency similar to the Ising case. This confirms that scale invariance is the only requirement for the present numerical method to work.

Calculating phase equilibrium properties of plasma pseudopotential model using hybrid Gibbs statistical ensemble Monte-Carlo technique

NASA Astrophysics Data System (ADS)

Butlitsky, M. A.; Zelener, B. B.; Zelener, B. V.

2015-11-01

Earlier a two-component pseudopotential plasma model, which we called a “shelf Coulomb” model has been developed. A Monte-Carlo study of canonical NVT ensemble with periodic boundary conditions has been undertaken to calculate equations of state, pair distribution functions, internal energies and other thermodynamics properties of the model. In present work, an attempt is made to apply so-called hybrid Gibbs statistical ensemble Monte-Carlo technique to this model. First simulation results data show qualitatively similar results for critical point region for both methods. Gibbs ensemble technique let us to estimate the melting curve position and a triple point of the model (in reduced temperature and specific volume coordinates): T* ≈ 0.0476, v* ≈ 6 × 10-4.

Quantum Gibbs Samplers: The Commuting Case

NASA Astrophysics Data System (ADS)

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

2016-06-01

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

Estimation hydrophilic-lipophilic balance number of surfactants

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

Pawignya, Harsa, E-mail: harsa-paw@yahoo.co.id; Chemical Engineering Departement University of Pembangunan Nasional Yogyakarta; Prasetyaningrum, Aji, E-mail: ajiprasetyaningrum@gmail.com

Any type of surfactant has a hydrophilic-lipophilic balance number (HLB number) of different. There are several methods for determining the HLB number, with ohysical properties of surfactant (solubility cloud point and interfacial tension), CMC methods and by thermodynamics properties (Free energy Gibbs). This paper proposes to determined HLB numbers from interfelation methods. The result of study indicated that the CMC method described by Hair and Moulik espesially for nonionic surfactant. The application of exess Gibbs free energy and by implication activity coefficient provides the ability to predict the behavior of surfactants in multi component mixtures of different concentration. Determination ofmore » HLB number by solubility and cloud point parameter is spesific for anionic and nonionic surfactant but this methods not available for cationic surfactants.« less

The use of computational thermodynamics for the determination of surface tension and Gibbs-Thomson coefficient of multicomponent alloys

NASA Astrophysics Data System (ADS)

Ferreira, D. J. S.; Bezerra, B. N.; Collyer, M. N.; Garcia, A.; Ferreira, I. L.

2018-04-01

The simulation of casting processes demands accurate information on the thermophysical properties of the alloy; however, such information is scarce in the literature for multicomponent alloys. Generally, metallic alloys applied in industry have more than three solute components. In the present study, a general solution of Butler's formulation for surface tension is presented for multicomponent alloys and is applied in quaternary Al-Cu-Si-Fe alloys, thus permitting the Gibbs-Thomson coefficient to be determined. Such coefficient is a determining factor to the reliability of predictions furnished by microstructure growth models and by numerical computations of solidification thermal parameters, which will depend on the thermophysical properties assumed in the calculations. The Gibbs-Thomson coefficient for ternary and quaternary alloys is seldom reported in the literature. A numerical model based on Powell's hybrid algorithm and a finite difference Jacobian approximation has been coupled to a Thermo-Calc TCAPI interface to assess the excess Gibbs energy of the liquid phase, permitting liquidus temperature, latent heat, alloy density, surface tension and Gibbs-Thomson coefficient for Al-Cu-Si-Fe hypoeutectic alloys to be calculated, as an example of calculation capabilities for multicomponent alloys of the proposed method. The computed results are compared with thermophysical properties of binary Al-Cu and ternary Al-Cu-Si alloys found in the literature and presented as a function of the Cu solute composition.

Ab Initio Prediction of Adsorption Isotherms for Small Molecules in Metal-Organic Frameworks.

PubMed

Kundu, Arpan; Piccini, GiovanniMaria; Sillar, Kaido; Sauer, Joachim

2016-10-26

For CO and N 2 on Mg 2+ sites of the metal-organic framework CPO-27-Mg (Mg-MOF-74), ab initio calculations of Gibbs free energies of adsorption have been performed. Combined with the Bragg-Williams/Langmuir model and taking into account the experimental site availability (76.5%), we obtained adsorption isotherms in close agreement with those in experiment. The remaining deviations in the Gibbs free energy (about 1 kJ/mol) are significantly smaller than the "chemical accuracy" limit of about 4 kJ/mol. The presented approach uses (i) a DFT dispersion method (PBE+D2) to optimize the structure and to calculate anharmonic frequencies for vibrational partition functions and (ii) a "hybrid MP2:(PBE+D2)+ΔCCSD(T)" method to determine electronic energies. With the achieved accuracy (estimated uncertainty ±1.4 kJ/mol), the ab initio energies become useful benchmarks for assessing different DFT + dispersion methods (PBE+D2, B3LYP+D*, and vdW-D2), whereas the ab initio heats, entropies, and Gibbs free energies of adsorption are used to assess the reliability of experimental values derived from fitting isotherms or from variable-temperature IR studies.

A Nonlinear Framework of Delayed Particle Smoothing Method for Vehicle Localization under Non-Gaussian Environment.

PubMed

Xiao, Zhu; Havyarimana, Vincent; Li, Tong; Wang, Dong

2016-05-13

In this paper, a novel nonlinear framework of smoothing method, non-Gaussian delayed particle smoother (nGDPS), is proposed, which enables vehicle state estimation (VSE) with high accuracy taking into account the non-Gaussianity of the measurement and process noises. Within the proposed method, the multivariate Student's t-distribution is adopted in order to compute the probability distribution function (PDF) related to the process and measurement noises, which are assumed to be non-Gaussian distributed. A computation approach based on Ensemble Kalman Filter (EnKF) is designed to cope with the mean and the covariance matrix of the proposal non-Gaussian distribution. A delayed Gibbs sampling algorithm, which incorporates smoothing of the sampled trajectories over a fixed-delay, is proposed to deal with the sample degeneracy of particles. The performance is investigated based on the real-world data, which is collected by low-cost on-board vehicle sensors. The comparison study based on the real-world experiments and the statistical analysis demonstrates that the proposed nGDPS has significant improvement on the vehicle state accuracy and outperforms the existing filtering and smoothing methods.

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

Bertholon, François; Harant, Olivier; Bourlon, Bertrand

This article introduces a joined Bayesian estimation of gas samples issued from a gas chromatography column (GC) coupled with a NEMS sensor based on Giddings Eyring microscopic molecular stochastic model. The posterior distribution is sampled using a Monte Carlo Markov Chain and Gibbs sampling. Parameters are estimated using the posterior mean. This estimation scheme is finally applied on simulated and real datasets using this molecular stochastic forward model.

Solubility and dissolution thermodynamics of tetranitroglycoluril in organic solvents at 295-318 K

NASA Astrophysics Data System (ADS)

Zheng, Zhihua; Wang, Jianlong; Hu, Zhiyan; Du, Hongbin

2017-08-01

The solubility data of tetranitroglycoluril in acetone, methanol, ethanol, ethyl acetate, nitromethane and chloroform at temperatures ranging from 295-318 K were measured by gravimetric method. The solubility data of tetranitroglycoluril were fitted with Apelblat semiempirical equation. The dissolution enthalpy, entropy and Gibbs energy of tetranitroglycoluril were calculated using the Van't Hoff and Gibbs equations. The results showed that the Apelblat semiempirical equation was significantly correlated with solubility data. The dissolving process was endothermic, entropy-driven, and nonspontaneous.

Bayesian transformation cure frailty models with multivariate failure time data.

PubMed

Yin, Guosheng

2008-12-10

We propose a class of transformation cure frailty models to accommodate a survival fraction in multivariate failure time data. Established through a general power transformation, this family of cure frailty models includes the proportional hazards and the proportional odds modeling structures as two special cases. Within the Bayesian paradigm, we obtain the joint posterior distribution and the corresponding full conditional distributions of the model parameters for the implementation of Gibbs sampling. Model selection is based on the conditional predictive ordinate statistic and deviance information criterion. As an illustration, we apply the proposed method to a real data set from dentistry.

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

NASA Astrophysics Data System (ADS)

Kadanoff, Leo P.

2014-07-01

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

Quantum chemical approach to estimating the thermodynamics of metabolic reactions.

PubMed

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

2014-11-12

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

A Gibbs sampler for motif detection in phylogenetically close sequences

NASA Astrophysics Data System (ADS)

Siddharthan, Rahul; van Nimwegen, Erik; Siggia, Eric

2004-03-01

Genes are regulated by transcription factors that bind to DNA upstream of genes and recognize short conserved ``motifs'' in a random intergenic ``background''. Motif-finders such as the Gibbs sampler compare the probability of these short sequences being represented by ``weight matrices'' to the probability of their arising from the background ``null model'', and explore this space (analogous to a free-energy landscape). But closely related species may show conservation not because of functional sites but simply because they have not had sufficient time to diverge, so conventional methods will fail. We introduce a new Gibbs sampler algorithm that accounts for common ancestry when searching for motifs, while requiring minimal ``prior'' assumptions on the number and types of motifs, assessing the significance of detected motifs by ``tracking'' clusters that stay together. We apply this scheme to motif detection in sporulation-cycle genes in the yeast S. cerevisiae, using recent sequences of other closely-related Saccharomyces species.

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

Kagan, D. N., E-mail: d.n.kagan@mtu-net.ru; Krechetova, G. A.; Shpil'rain, E. E.

A detailed procedural analysis is given and results of implementation of the new version of the effusion method for determining the Gibbs energy (thermodynamic activity) of binary and ternary systems of alkali metals Cs-Na, K-Na, Cs-K, and Cs-K-Na are presented. The activity is determined using partial pressures of the components measured according the effusion method by the intensity of their atomic beams. The pressure range used in the experiment is intermediate between the Knudsen and hydrodynamic effusion modes. A generalized version of the effusion method involves the pressure range beyond the limits of the applicability of the Hertz-Knudsen equation. Employmentmore » of this method provides the differential equation of chemical thermodynamics; solution of this equation makes it possible to construct the Gibbs energy in the range of temperatures 400 {<=} T {<=} 1200 K and concentrations 0 {<=} x{sub i} {<=} 1.« less

An Interactive Image Segmentation Method in Hand Gesture Recognition

PubMed Central

Chen, Disi; Li, Gongfa; Sun, Ying; Kong, Jianyi; Jiang, Guozhang; Tang, Heng; Ju, Zhaojie; Yu, Hui; Liu, Honghai

2017-01-01

In order to improve the recognition rate of hand gestures a new interactive image segmentation method for hand gesture recognition is presented, and popular methods, e.g., Graph cut, Random walker, Interactive image segmentation using geodesic star convexity, are studied in this article. The Gaussian Mixture Model was employed for image modelling and the iteration of Expectation Maximum algorithm learns the parameters of Gaussian Mixture Model. We apply a Gibbs random field to the image segmentation and minimize the Gibbs Energy using Min-cut theorem to find the optimal segmentation. The segmentation result of our method is tested on an image dataset and compared with other methods by estimating the region accuracy and boundary accuracy. Finally five kinds of hand gestures in different backgrounds are tested on our experimental platform, and the sparse representation algorithm is used, proving that the segmentation of hand gesture images helps to improve the recognition accuracy. PMID:28134818

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

PubMed

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

2017-06-13

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

Non-proportional odds multivariate logistic regression of ordinal family data.

PubMed

Zaloumis, Sophie G; Scurrah, Katrina J; Harrap, Stephen B; Ellis, Justine A; Gurrin, Lyle C

2015-03-01

Methods to examine whether genetic and/or environmental sources can account for the residual variation in ordinal family data usually assume proportional odds. However, standard software to fit the non-proportional odds model to ordinal family data is limited because the correlation structure of family data is more complex than for other types of clustered data. To perform these analyses we propose the non-proportional odds multivariate logistic regression model and take a simulation-based approach to model fitting using Markov chain Monte Carlo methods, such as partially collapsed Gibbs sampling and the Metropolis algorithm. We applied the proposed methodology to male pattern baldness data from the Victorian Family Heart Study. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Bayesian focalization: quantifying source localization with environmental uncertainty.

PubMed

Dosso, Stan E; Wilmut, Michael J

2007-05-01

This paper applies a Bayesian formulation to study ocean acoustic source localization as a function of uncertainty in environmental properties (water column and seabed) and of data information content [signal-to-noise ratio (SNR) and number of frequencies]. The approach follows that of the optimum uncertain field processor [A. M. Richardson and L. W. Nolte, J. Acoust. Soc. Am. 89, 2280-2284 (1991)], in that localization uncertainty is quantified by joint marginal probability distributions for source range and depth integrated over uncertain environmental properties. The integration is carried out here using Metropolis Gibbs' sampling for environmental parameters and heat-bath Gibbs' sampling for source location to provide efficient sampling over complicated parameter spaces. The approach is applied to acoustic data from a shallow-water site in the Mediterranean Sea where previous geoacoustic studies have been carried out. It is found that reliable localization requires a sufficient combination of prior (environmental) information and data information. For example, sources can be localized reliably for single-frequency data at low SNR (-3 dB) only with small environmental uncertainties, whereas successful localization with large environmental uncertainties requires higher SNR and/or multifrequency data.

Quantum Chemical Approach to Estimating the Thermodynamics of Metabolic Reactions

PubMed Central

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

2014-01-01

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

A Nonlinear Framework of Delayed Particle Smoothing Method for Vehicle Localization under Non-Gaussian Environment

PubMed Central

Xiao, Zhu; Havyarimana, Vincent; Li, Tong; Wang, Dong

2016-01-01

In this paper, a novel nonlinear framework of smoothing method, non-Gaussian delayed particle smoother (nGDPS), is proposed, which enables vehicle state estimation (VSE) with high accuracy taking into account the non-Gaussianity of the measurement and process noises. Within the proposed method, the multivariate Student’s t-distribution is adopted in order to compute the probability distribution function (PDF) related to the process and measurement noises, which are assumed to be non-Gaussian distributed. A computation approach based on Ensemble Kalman Filter (EnKF) is designed to cope with the mean and the covariance matrix of the proposal non-Gaussian distribution. A delayed Gibbs sampling algorithm, which incorporates smoothing of the sampled trajectories over a fixed-delay, is proposed to deal with the sample degeneracy of particles. The performance is investigated based on the real-world data, which is collected by low-cost on-board vehicle sensors. The comparison study based on the real-world experiments and the statistical analysis demonstrates that the proposed nGDPS has significant improvement on the vehicle state accuracy and outperforms the existing filtering and smoothing methods. PMID:27187405

Parameter estimation of multivariate multiple regression model using bayesian with non-informative Jeffreys’ prior distribution

NASA Astrophysics Data System (ADS)

Saputro, D. R. S.; Amalia, F.; Widyaningsih, P.; Affan, R. C.

2018-05-01

Bayesian method is a method that can be used to estimate the parameters of multivariate multiple regression model. Bayesian method has two distributions, there are prior and posterior distributions. Posterior distribution is influenced by the selection of prior distribution. Jeffreys’ prior distribution is a kind of Non-informative prior distribution. This prior is used when the information about parameter not available. Non-informative Jeffreys’ prior distribution is combined with the sample information resulting the posterior distribution. Posterior distribution is used to estimate the parameter. The purposes of this research is to estimate the parameters of multivariate regression model using Bayesian method with Non-informative Jeffreys’ prior distribution. Based on the results and discussion, parameter estimation of β and Σ which were obtained from expected value of random variable of marginal posterior distribution function. The marginal posterior distributions for β and Σ are multivariate normal and inverse Wishart. However, in calculation of the expected value involving integral of a function which difficult to determine the value. Therefore, approach is needed by generating of random samples according to the posterior distribution characteristics of each parameter using Markov chain Monte Carlo (MCMC) Gibbs sampling algorithm.

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

PubMed

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

2012-04-01

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

Standard Gibbs energy of metabolic reactions: II. Glucose-6-phosphatase reaction and ATP hydrolysis.

PubMed

Meurer, Florian; Do, Hoang Tam; Sadowski, Gabriele; Held, Christoph

2017-04-01

ATP (adenosine triphosphate) is a key reaction for metabolism. Tools from systems biology require standard reaction data in order to predict metabolic pathways accurately. However, literature values for standard Gibbs energy of ATP hydrolysis are highly uncertain and differ strongly from each other. Further, such data usually neglect the activity coefficients of reacting agents, and published data like this is apparent (condition-dependent) data instead of activity-based standard data. In this work a consistent value for the standard Gibbs energy of ATP hydrolysis was determined. The activity coefficients of reacting agents were modeled with electrolyte Perturbed-Chain Statistical Associating Fluid Theory (ePC-SAFT). The Gibbs energy of ATP hydrolysis was calculated by combining the standard Gibbs energies of hexokinase reaction and of glucose-6-phosphate hydrolysis. While the standard Gibbs energy of hexokinase reaction was taken from previous work, standard Gibbs energy of glucose-6-phosphate hydrolysis reaction was determined in this work. For this purpose, reaction equilibrium molalities of reacting agents were measured at pH7 and pH8 at 298.15K at varying initial reacting agent molalities. The corresponding activity coefficients at experimental equilibrium molalities were predicted with ePC-SAFT yielding the Gibbs energy of glucose-6-phosphate hydrolysis of -13.72±0.75kJ·mol -1 . Combined with the value for hexokinase, the standard Gibbs energy of ATP hydrolysis was finally found to be -31.55±1.27kJ·mol -1 . For both, ATP hydrolysis and glucose-6-phosphate hydrolysis, a good agreement with own and literature values were obtained when influences of pH, temperature, and activity coefficients were explicitly taken into account in order to calculate standard Gibbs energy at pH7, 298.15K and standard state. Copyright © 2017 Elsevier B.V. All rights reserved.

Discovery of a young asteroid cluster associated with P/2012 F5 (Gibbs)

NASA Astrophysics Data System (ADS)

Novaković, Bojan; Hsieh, Henry H.; Cellino, Alberto; Micheli, Marco; Pedani, Marco

2014-03-01

We present the results of our search for a dynamical family around the active Asteroid P/2012 F5 (Gibbs). By applying the hierarchical clustering method, we discover an extremely compact 9-body cluster associated with P/2012 F5. The statistical significance of this newly discovered Gibbs cluster is estimated to be >99.9%, strongly suggesting that its members share a common origin. The cluster is located in a dynamically cold region of the outer main-belt at a proper semi-major axis of ∼3.005 AU, and all members are found to be dynamically stable over very long timescales. Backward numerical orbital integrations show that the age of the cluster is only 1.5 ± 0.1 Myr. Taxonomic classifications are unavailable for most of the cluster members, but SDSS spectrophotometry available for two cluster members indicate that both appear to be Q-type objects. We also estimate a lower limit of the size of the parent body to be about 10 km, and find that the impact event which produced the Gibbs cluster is intermediate between a cratering and a catastrophic collision. In addition, we search for new main-belt comets in the region of the Gibbs cluster by observing seven asteroids either belonging to the cluster, or being very close in the space of orbital proper elements. However, we do not detect any convincing evidence of the presence of a tail or coma in any our targets. Finally, we obtain optical images of P/2012 F5, and find absolute R-band and V-band magnitudes of HR = 17.0 ± 0.1 mag and HV = 17.4 ± 0.1 mag, respectively, corresponding to an upper limit on the diameter of the P/2012 F5 nucleus of ∼2 km.

A class-based link prediction using Distance Dependent Chinese Restaurant Process

NASA Astrophysics Data System (ADS)

Andalib, Azam; Babamir, Seyed Morteza

2016-08-01

One of the important tasks in relational data analysis is link prediction which has been successfully applied on many applications such as bioinformatics, information retrieval, etc. The link prediction is defined as predicting the existence or absence of edges between nodes of a network. In this paper, we propose a novel method for link prediction based on Distance Dependent Chinese Restaurant Process (DDCRP) model which enables us to utilize the information of the topological structure of the network such as shortest path and connectivity of the nodes. We also propose a new Gibbs sampling algorithm for computing the posterior distribution of the hidden variables based on the training data. Experimental results on three real-world datasets show the superiority of the proposed method over other probabilistic models for link prediction problem.

A formula for the entropy of the convolution of Gibbs probabilities on the circle

NASA Astrophysics Data System (ADS)

Lopes, Artur O.

2018-07-01

Consider the transformation , such that (mod 1), and where S 1 is the unitary circle. Suppose is Hölder continuous and positive, and moreover that, for any , we have that We say that ρ is a Gibbs probability for the Hölder continuous potential , if where is the Ruelle operator for . We call J the Jacobian of ρ. Suppose is the convolution of two Gibbs probabilities and associated, respectively, to and . We show that ν is also Gibbs and its Jacobian is given by . In this case, the entropy is given by the expression For a fixed we consider differentiable variations , , of on the Banach manifold of Gibbs probabilities, where , and we estimate the derivative of the entropy at t  =  0. We also present an expression for the Jacobian of the convolution of a Gibbs probability ρ with the invariant probability with support on a periodic orbit of period two. This expression is based on the Jacobian of ρ and two Radon–Nidodym derivatives.

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

NASA Astrophysics Data System (ADS)

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

2016-12-01

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

Predicting cyclohexane/water distribution coefficients for the SAMPL5 challenge using MOSCED and the SMD solvation model.

PubMed

Diaz-Rodriguez, Sebastian; Bozada, Samantha M; Phifer, Jeremy R; Paluch, Andrew S

2016-11-01

We present blind predictions using the solubility parameter based method MOSCED submitted for the SAMPL5 challenge on calculating cyclohexane/water distribution coefficients at 298 K. Reference data to parameterize MOSCED was generated with knowledge only of chemical structure by performing solvation free energy calculations using electronic structure calculations in the SMD continuum solvent. To maintain simplicity and use only a single method, we approximate the distribution coefficient with the partition coefficient of the neutral species. Over the final SAMPL5 set of 53 compounds, we achieved an average unsigned error of [Formula: see text] log units (ranking 15 out of 62 entries), the correlation coefficient (R) was [Formula: see text] (ranking 35), and [Formula: see text] of the predictions had the correct sign (ranking 30). While used here to predict cyclohexane/water distribution coefficients at 298 K, MOSCED is broadly applicable, allowing one to predict temperature dependent infinite dilution activity coefficients in any solvent for which parameters exist, and provides a means by which an excess Gibbs free energy model may be parameterized to predict composition dependent phase-equilibrium.

Accelerating the Convergence of Replica Exchange Simulations Using Gibbs Sampling and Adaptive Temperature Sets

DOE PAGES

Vogel, Thomas; Perez, Danny

2015-08-28

We recently introduced a novel replica-exchange scheme in which an individual replica can sample from states encountered by other replicas at any previous time by way of a global configuration database, enabling the fast propagation of relevant states through the whole ensemble of replicas. This mechanism depends on the knowledge of global thermodynamic functions which are measured during the simulation and not coupled to the heat bath temperatures driving the individual simulations. Therefore, this setup also allows for a continuous adaptation of the temperature set. In this paper, we will review the new scheme and demonstrate its capability. Furthermore, themore » method is particularly useful for the fast and reliable estimation of the microcanonical temperature T(U) or, equivalently, of the density of states g(U) over a wide range of energies.« less

Monte Carlo Algorithms for a Bayesian Analysis of the Cosmic Microwave Background

NASA Technical Reports Server (NTRS)

Jewell, Jeffrey B.; Eriksen, H. K.; ODwyer, I. J.; Wandelt, B. D.; Gorski, K.; Knox, L.; Chu, M.

2006-01-01

A viewgraph presentation on the review of Bayesian approach to Cosmic Microwave Background (CMB) analysis, numerical implementation with Gibbs sampling, a summary of application to WMAP I and work in progress with generalizations to polarization, foregrounds, asymmetric beams, and 1/f noise is given.

Order-Constrained Bayes Inference for Dichotomous Models of Unidimensional Nonparametric IRT

ERIC Educational Resources Information Center

Karabatsos, George; Sheu, Ching-Fan

2004-01-01

This study introduces an order-constrained Bayes inference framework useful for analyzing data containing dichotomous scored item responses, under the assumptions of either the monotone homogeneity model or the double monotonicity model of nonparametric item response theory (NIRT). The framework involves the implementation of Gibbs sampling to…

Preferential Solvation of Silver (I) Bromate in Methanol-Dimethylsulfoxide Mixtures

NASA Astrophysics Data System (ADS)

Janardhanan, S.; Kalidas, C.

1984-06-01

The solubiltiy of silver bromate, the Gibbs transfer energy of Ag+ and BrO3- and the solvent transport number in methanol-dimethyl sulfoxide mixtures are reported. The solubility of silver bromate increases with addition of DMSO. The Gibbs energy of transfer of the silver ion (based on the ferrocene reference method) decreases, while that of the bromate ion becomes slightly negative with the addition of DMSO. The solvent transport number A passes through a maximum (⊿ = 1.0 at XDMSO = 0.65. From these results, it is concluded that the silver ion is preferentially solvated by DMSO whereas the bromate ion shows no preferential solvation.

The Gibbs Phenomenon for Series of Orthogonal Polynomials

ERIC Educational Resources Information Center

Fay, T. H.; Kloppers, P. Hendrik

2006-01-01

This note considers the four classes of orthogonal polynomials--Chebyshev, Hermite, Laguerre, Legendre--and investigates the Gibbs phenomenon at a jump discontinuity for the corresponding orthogonal polynomial series expansions. The perhaps unexpected thing is that the Gibbs constant that arises for each class of polynomials appears to be the same…

Enzyme Catalysis and the Gibbs Energy

ERIC Educational Resources Information Center

Ault, Addison

2009-01-01

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

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

PubMed

Toure, Oumar; Dussap, Claude-Gilles

2016-08-01

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

GSimp: A Gibbs sampler based left-censored missing value imputation approach for metabolomics studies

PubMed Central

Jia, Erik; Chen, Tianlu

2018-01-01

Left-censored missing values commonly exist in targeted metabolomics datasets and can be considered as missing not at random (MNAR). Improper data processing procedures for missing values will cause adverse impacts on subsequent statistical analyses. However, few imputation methods have been developed and applied to the situation of MNAR in the field of metabolomics. Thus, a practical left-censored missing value imputation method is urgently needed. We developed an iterative Gibbs sampler based left-censored missing value imputation approach (GSimp). We compared GSimp with other three imputation methods on two real-world targeted metabolomics datasets and one simulation dataset using our imputation evaluation pipeline. The results show that GSimp outperforms other imputation methods in terms of imputation accuracy, observation distribution, univariate and multivariate analyses, and statistical sensitivity. Additionally, a parallel version of GSimp was developed for dealing with large scale metabolomics datasets. The R code for GSimp, evaluation pipeline, tutorial, real-world and simulated targeted metabolomics datasets are available at: https://github.com/WandeRum/GSimp. PMID:29385130

Geostatistical methods in evaluating spatial variability of groundwater quality in Al-Kharj Region, Saudi Arabia

NASA Astrophysics Data System (ADS)

Al-Omran, Abdulrasoul M.; Aly, Anwar A.; Al-Wabel, Mohammad I.; Al-Shayaa, Mohammad S.; Sallam, Abdulazeam S.; Nadeem, Mahmoud E.

2017-11-01

The analyses of 180 groundwater samples of Al-Kharj, Saudi Arabia, recorded that most groundwaters are unsuitable for drinking uses due to high salinity; however, they can be used for irrigation with some restriction. The electric conductivity of studied groundwater ranged between 1.05 and 10.15 dS m-1 with an average of 3.0 dS m-1. Nitrate was also found in high concentration in some groundwater. Piper diagrams revealed that the majority of water samples are magnesium-calcium/sulfate-chloride water type. The Gibbs's diagram revealed that the chemical weathering of rock-forming minerals and evaporation are influencing the groundwater chemistry. A kriging method was used for predicting spatial distribution of salinity (EC dS m-1) and NO3 - (mg L-1) in Al-Kharj's groundwater using data of 180 different locations. After normalization of data, variogram was drawn, for selecting suitable model for fitness on experimental variogram, less residual sum of squares value was used. Then cross-validation and root mean square error were used to select the best method for interpolation. The kriging method was found suitable methods for groundwater interpolation and management using either GS+ or ArcGIS.

A CONTINUATION OF REMEDIATION OF BRINE SPILLS WITH HAY

EPA Science Inventory

First order rate constants for salt removal are shown in Table 1. For Gibbs 7, tilling with hay and fertilizers proved to be the best treatment for salt removal (80% confidence level, CL). For Gibbs 9, which is rockier than Gibbs 7, tilling was the best treatment for salt remo...

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

PubMed

Masuda, Yosuke; Yamaotsu, Noriyuki; Hirono, Shuichi

2017-01-01

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

Order parameter free enhanced sampling of the vapor-liquid transition using the generalized replica exchange method.

PubMed

Lu, Qing; Kim, Jaegil; Straub, John E

2013-03-14

The generalized Replica Exchange Method (gREM) is extended into the isobaric-isothermal ensemble, and applied to simulate a vapor-liquid phase transition in Lennard-Jones fluids. Merging an optimally designed generalized ensemble sampling with replica exchange, gREM is particularly well suited for the effective simulation of first-order phase transitions characterized by "backbending" in the statistical temperature. While the metastable and unstable states in the vicinity of the first-order phase transition are masked by the enthalpy gap in temperature replica exchange method simulations, they are transformed into stable states through the parameterized effective sampling weights in gREM simulations, and join vapor and liquid phases with a succession of unimodal enthalpy distributions. The enhanced sampling across metastable and unstable states is achieved without the need to identify a "good" order parameter for biased sampling. We performed gREM simulations at various pressures below and near the critical pressure to examine the change in behavior of the vapor-liquid phase transition at different pressures. We observed a crossover from the first-order phase transition at low pressure, characterized by the backbending in the statistical temperature and the "kink" in the Gibbs free energy, to a continuous second-order phase transition near the critical pressure. The controlling mechanisms of nucleation and continuous phase transition are evident and the coexistence properties and phase diagram are found in agreement with literature results.

Reflections on Gibbs: From Critical Phenomena to the Amistad

NASA Astrophysics Data System (ADS)

Kadanoff, Leo P.

2003-03-01

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

Extension of Gibbs-Duhem equation including influences of external fields

NASA Astrophysics Data System (ADS)

Guangze, Han; Jianjia, Meng

2018-03-01

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

BiodMHC: an online server for the prediction of MHC class II-peptide binding affinity.

PubMed

Wang, Lian; Pan, Danling; Hu, Xihao; Xiao, Jinyu; Gao, Yangyang; Zhang, Huifang; Zhang, Yan; Liu, Juan; Zhu, Shanfeng

2009-05-01

Effective identification of major histocompatibility complex (MHC) molecules restricted peptides is a critical step in discovering immune epitopes. Although many online servers have been built to predict class II MHC-peptide binding affinity, they have been trained on different datasets, and thus fail in providing a unified comparison of various methods. In this paper, we present our implementation of seven popular predictive methods, namely SMM-align, ARB, SVR-pairwise, Gibbs sampler, ProPred, LP-top2, and MHCPred, on a single web server named BiodMHC (http://biod.whu.edu.cn/BiodMHC/index.html, the software is available upon request). Using a standard measure of AUC (Area Under the receiver operating characteristic Curves), we compare these methods by means of not only cross validation but also prediction on independent test datasets. We find that SMM-align, ProPred, SVR-pairwise, ARB, and Gibbs sampler are the five best-performing methods. For the binding affinity prediction of class II MHC-peptide, BiodMHC provides a convenient online platform for researchers to obtain binding information simultaneously using various methods.

Computational methods for reactive transport modeling: An extended law of mass-action, xLMA, method for multiphase equilibrium calculations

NASA Astrophysics Data System (ADS)

Leal, Allan M. M.; Kulik, Dmitrii A.; Kosakowski, Georg; Saar, Martin O.

2016-10-01

We present an extended law of mass-action (xLMA) method for multiphase equilibrium calculations and apply it in the context of reactive transport modeling. This extended LMA formulation differs from its conventional counterpart in that (i) it is directly derived from the Gibbs energy minimization (GEM) problem (i.e., the fundamental problem that describes the state of equilibrium of a chemical system under constant temperature and pressure); and (ii) it extends the conventional mass-action equations with Lagrange multipliers from the Gibbs energy minimization problem, which can be interpreted as stability indices of the chemical species. Accounting for these multipliers enables the method to determine all stable phases without presuming their types (e.g., aqueous, gaseous) or their presence in the equilibrium state. Therefore, the here proposed xLMA method inherits traits of Gibbs energy minimization algorithms that allow it to naturally detect the phases present in equilibrium, which can be single-component phases (e.g., pure solids or liquids) or non-ideal multi-component phases (e.g., aqueous, melts, gaseous, solid solutions, adsorption, or ion exchange). Moreover, our xLMA method requires no technique that tentatively adds or removes reactions based on phase stability indices (e.g., saturation indices for minerals), since the extended mass-action equations are valid even when their corresponding reactions involve unstable species. We successfully apply the proposed method to a reactive transport modeling problem in which we use PHREEQC and GEMS as alternative backends for the calculation of thermodynamic properties such as equilibrium constants of reactions, standard chemical potentials of species, and activity coefficients. Our tests show that our algorithm is efficient and robust for demanding applications, such as reactive transport modeling, where it converges within 1-3 iterations in most cases. The proposed xLMA method is implemented in Reaktoro, a unified open-source framework for modeling chemically reactive systems.

A Bayesian hierarchical model with spatial variable selection: the effect of weather on insurance claims

PubMed Central

Scheel, Ida; Ferkingstad, Egil; Frigessi, Arnoldo; Haug, Ola; Hinnerichsen, Mikkel; Meze-Hausken, Elisabeth

2013-01-01

Climate change will affect the insurance industry. We develop a Bayesian hierarchical statistical approach to explain and predict insurance losses due to weather events at a local geographic scale. The number of weather-related insurance claims is modelled by combining generalized linear models with spatially smoothed variable selection. Using Gibbs sampling and reversible jump Markov chain Monte Carlo methods, this model is fitted on daily weather and insurance data from each of the 319 municipalities which constitute southern and central Norway for the period 1997–2006. Precise out-of-sample predictions validate the model. Our results show interesting regional patterns in the effect of different weather covariates. In addition to being useful for insurance pricing, our model can be used for short-term predictions based on weather forecasts and for long-term predictions based on downscaled climate models. PMID:23396890

Reformulation of the Michaelis-Menten Equation: How Enzyme-Catalyzed Reactions Depend on Gibbs Energy

ERIC Educational Resources Information Center

Bozlee, Brian J.

2007-01-01

The impact of raising Gibbs energy of the enzyme-substrate complex (G[subscript 3]) and the reformulation of the Michaelis-Menten equation are discussed. The maximum velocity of the reaction (v[subscript m]) and characteristic constant for the enzyme (K[subscript M]) will increase with increase in Gibbs energy, indicating that the rate of reaction…

Illustrating the Effect of pH on Enzyme Activity Using Gibbs Energy Profiles

ERIC Educational Resources Information Center

Bearne, Stephen L.

2014-01-01

Gibbs energy profiles provide students with a visual representation of the energy changes that occur during enzyme catalysis, making such profiles useful as teaching and learning tools. Traditional kinetic topics, such as the effect of pH on enzyme activity, are often not discussed in terms of Gibbs energy profiles. Herein, the symbolism of Gibbs…

Marangoni and Gibbs elasticity of flowing soap films

NASA Astrophysics Data System (ADS)

Kim, Ildoo; Sane, Aakash; Mandre, Shreyas

2017-11-01

A flowing soap film has two elasticities. Marangoni elasticity dynamically stabilizes the film from sudden disturbance, and Gibbs elasticity is an equilibrium property that influences the film's persistence over time. In our experimental investigation, we find that Marangoni elasticity is 22 mN/m independent of the film thickness. On the other hand, Gibbs elasticity depends both on the film thickness and the soap concentration. Interestingly, the soap film made of dilute soap solution has the greater Gibbs elasticity, which is not consistent to the existing theory. Such discrepancy is originated from the flowing nature of our soap films, in which surfactants are continuously replenished.

A label field fusion bayesian model and its penalized maximum rand estimator for image segmentation.

PubMed

Mignotte, Max

2010-06-01

This paper presents a novel segmentation approach based on a Markov random field (MRF) fusion model which aims at combining several segmentation results associated with simpler clustering models in order to achieve a more reliable and accurate segmentation result. The proposed fusion model is derived from the recently introduced probabilistic Rand measure for comparing one segmentation result to one or more manual segmentations of the same image. This non-parametric measure allows us to easily derive an appealing fusion model of label fields, easily expressed as a Gibbs distribution, or as a nonstationary MRF model defined on a complete graph. Concretely, this Gibbs energy model encodes the set of binary constraints, in terms of pairs of pixel labels, provided by each segmentation results to be fused. Combined with a prior distribution, this energy-based Gibbs model also allows for definition of an interesting penalized maximum probabilistic rand estimator with which the fusion of simple, quickly estimated, segmentation results appears as an interesting alternative to complex segmentation models existing in the literature. This fusion framework has been successfully applied on the Berkeley image database. The experiments reported in this paper demonstrate that the proposed method is efficient in terms of visual evaluation and quantitative performance measures and performs well compared to the best existing state-of-the-art segmentation methods recently proposed in the literature.

Quantification of Microbial Phenotypes

PubMed Central

Martínez, Verónica S.; Krömer, Jens O.

2016-01-01

Metabolite profiling technologies have improved to generate close to quantitative metabolomics data, which can be employed to quantitatively describe the metabolic phenotype of an organism. Here, we review the current technologies available for quantitative metabolomics, present their advantages and drawbacks, and the current challenges to generate fully quantitative metabolomics data. Metabolomics data can be integrated into metabolic networks using thermodynamic principles to constrain the directionality of reactions. Here we explain how to estimate Gibbs energy under physiological conditions, including examples of the estimations, and the different methods for thermodynamics-based network analysis. The fundamentals of the methods and how to perform the analyses are described. Finally, an example applying quantitative metabolomics to a yeast model by 13C fluxomics and thermodynamics-based network analysis is presented. The example shows that (1) these two methods are complementary to each other; and (2) there is a need to take into account Gibbs energy errors. Better estimations of metabolic phenotypes will be obtained when further constraints are included in the analysis. PMID:27941694

Removal of the Gibbs phenomenon and its application to fast-Fourier-transform-based mode solvers.

PubMed

Wangüemert-Pérez, J G; Godoy-Rubio, R; Ortega-Moñux, A; Molina-Fernández, I

2007-12-01

A simple strategy for accurately recovering discontinuous functions from their Fourier series coefficients is presented. The aim of the proposed approach, named spectrum splitting (SS), is to remove the Gibbs phenomenon by making use of signal-filtering-based concepts and some properties of the Fourier series. While the technique can be used in a vast range of situations, it is particularly suitable for being incorporated into fast-Fourier-transform-based electromagnetic mode solvers (FFT-MSs), which are known to suffer from very poor convergence rates when applied to situations where the field distributions are highly discontinuous (e.g., silicon-on-insulator photonic wires). The resultant method, SS-FFT-MS, is exhaustively tested under the assumption of a simplified one-dimensional model, clearly showing a dramatic improvement of the convergence rates with respect to the original FFT-based methods.

Thermodynamic integration based on classical atomistic simulations to determine the Gibbs energy of condensed phases: Calculation of the aluminum-zirconium system

NASA Astrophysics Data System (ADS)

Harvey, J.-P.; Gheribi, A. E.; Chartrand, P.

2012-12-01

In this work, an in silico procedure to generate a fully coherent set of thermodynamic properties obtained from classical molecular dynamics (MD) and Monte Carlo (MC) simulations is proposed. The procedure is applied to the Al-Zr system because of its importance in the development of high strength Al-Li alloys and of bulk metallic glasses. Cohesive energies of the studied condensed phases of the Al-Zr system (the liquid phase, the fcc solid solution, and various orthorhombic stoichiometric compounds) are calculated using the modified embedded atom model (MEAM) in the second-nearest-neighbor formalism (2NN). The Al-Zr MEAM-2NN potential is parameterized in this work using ab initio and experimental data found in the literature for the AlZr3-L12 structure, while its predictive ability is confirmed for several other solid structures and for the liquid phase. The thermodynamic integration (TI) method is implemented in a general MC algorithm in order to evaluate the absolute Gibbs energy of the liquid and the fcc solutions. The entropy of mixing calculated from the TI method, combined to the enthalpy of mixing and the heat capacity data generated from MD/MC simulations performed in the isobaric-isothermal/canonical (NPT/NVT) ensembles are used to parameterize the Gibbs energy function of all the condensed phases in the Al-rich side of the Al-Zr system in a CALculation of PHAse Diagrams (CALPHAD) approach. The modified quasichemical model in the pair approximation (MQMPA) and the cluster variation method (CVM) in the tetrahedron approximation are used to define the Gibbs energy of the liquid and the fcc solid solution respectively for their entire range of composition. Thermodynamic and structural data generated from our MD/MC simulations are used as input data to parameterize these thermodynamic models. A detailed analysis of the validity and transferability of the Al-Zr MEAM-2NN potential is presented throughout our work by comparing the predicted properties obtained from this formalism with available ab initio and experimental data for both liquid and solid phases.

Markov Chain Monte Carlo Inference of Parametric Dictionaries for Sparse Bayesian Approximations

PubMed Central

Chaspari, Theodora; Tsiartas, Andreas; Tsilifis, Panagiotis; Narayanan, Shrikanth

2016-01-01

Parametric dictionaries can increase the ability of sparse representations to meaningfully capture and interpret the underlying signal information, such as encountered in biomedical problems. Given a mapping function from the atom parameter space to the actual atoms, we propose a sparse Bayesian framework for learning the atom parameters, because of its ability to provide full posterior estimates, take uncertainty into account and generalize on unseen data. Inference is performed with Markov Chain Monte Carlo, that uses block sampling to generate the variables of the Bayesian problem. Since the parameterization of dictionary atoms results in posteriors that cannot be analytically computed, we use a Metropolis-Hastings-within-Gibbs framework, according to which variables with closed-form posteriors are generated with the Gibbs sampler, while the remaining ones with the Metropolis Hastings from appropriate candidate-generating densities. We further show that the corresponding Markov Chain is uniformly ergodic ensuring its convergence to a stationary distribution independently of the initial state. Results on synthetic data and real biomedical signals indicate that our approach offers advantages in terms of signal reconstruction compared to previously proposed Steepest Descent and Equiangular Tight Frame methods. This paper demonstrates the ability of Bayesian learning to generate parametric dictionaries that can reliably represent the exemplar data and provides the foundation towards inferring the entire variable set of the sparse approximation problem for signal denoising, adaptation and other applications. PMID:28649173

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

ERIC Educational Resources Information Center

Gary, Ronald K.

2004-01-01

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

Quantitative Characterization of Spurious Gibbs Waves in 45 CMIP5 Models

NASA Astrophysics Data System (ADS)

Geil, K. L.; Zeng, X.

2014-12-01

Gibbs oscillations appear in global climate models when representing fields, such as orography, that contain discontinuities or sharp gradients. It has been known for decades that the oscillations are associated with the transformation of the truncated spectral representation of a field to physical space and that the oscillations can also be present in global models that do not use spectral methods. The spurious oscillations are potentially detrimental to model simulations (e.g., over ocean) and this work provides a quantitative characterization of the Gibbs oscillations that appear across the Coupled Model Intercomparison Project Phase 5 (CMIP5) models. An ocean transect running through the South Pacific High toward the Andes is used to characterize the oscillations in ten different variables. These oscillations are found to be stationary and hence are not caused by (physical) waves in the atmosphere. We quantify the oscillation amplitude using the root mean square difference (RMSD) between the transect of a variable and its running mean (rather than the constant mean across the transect). We also compute the RMSD to interannual variability (IAV) ratio, which provides a relative measure of the oscillation amplitude. Of the variables examined, the largest RMSD values exist in the surface pressure field of spectral models, while the smallest RMSD values within the surface pressure field come from models that use finite difference (FD) techniques. Many spectral models have a surface pressure RMSD that is 2 to 15 times greater than IAV over the transect and an RMSD:IAV ratio greater than one for many other variables including surface temperature, incoming shortwave radiation at the surface, incoming longwave radiation at the surface, and total cloud fraction. In general, the FD models out-perform the spectral models, but not all the spectral models have large amplitude oscillations and there are a few FD models where the oscillations do appear. Finally, we present a brief comparison of the numerical methods of a select few models to better understand their Gibbs oscillations.

Uncovering a latent multinomial: Analysis of mark-recapture data with misidentification

USGS Publications Warehouse

Link, W.A.; Yoshizaki, J.; Bailey, L.L.; Pollock, K.H.

2010-01-01

Natural tags based on DNA fingerprints or natural features of animals are now becoming very widely used in wildlife population biology. However, classic capture-recapture models do not allow for misidentification of animals which is a potentially very serious problem with natural tags. Statistical analysis of misidentification processes is extremely difficult using traditional likelihood methods but is easily handled using Bayesian methods. We present a general framework for Bayesian analysis of categorical data arising from a latent multinomial distribution. Although our work is motivated by a specific model for misidentification in closed population capture-recapture analyses, with crucial assumptions which may not always be appropriate, the methods we develop extend naturally to a variety of other models with similar structure. Suppose that observed frequencies f are a known linear transformation f = A???x of a latent multinomial variable x with cell probability vector ?? = ??(??). Given that full conditional distributions [?? | x] can be sampled, implementation of Gibbs sampling requires only that we can sample from the full conditional distribution [x | f, ??], which is made possible by knowledge of the null space of A???. We illustrate the approach using two data sets with individual misidentification, one simulated, the other summarizing recapture data for salamanders based on natural marks. ?? 2009, The International Biometric Society.

Uncovering a Latent Multinomial: Analysis of Mark-Recapture Data with Misidentification

USGS Publications Warehouse

Link, W.A.; Yoshizaki, J.; Bailey, L.L.; Pollock, K.H.

2009-01-01

Natural tags based on DNA fingerprints or natural features of animals are now becoming very widely used in wildlife population biology. However, classic capture-recapture models do not allow for misidentification of animals which is a potentially very serious problem with natural tags. Statistical analysis of misidentification processes is extremely difficult using traditional likelihood methods but is easily handled using Bayesian methods. We present a general framework for Bayesian analysis of categorical data arising from a latent multinomial distribution. Although our work is motivated by a specific model for misidentification in closed population capture-recapture analyses, with crucial assumptions which may not always be appropriate, the methods we develop extend naturally to a variety of other models with similar structure. Suppose that observed frequencies f are a known linear transformation f=A'x of a latent multinomial variable x with cell probability vector pi= pi(theta). Given that full conditional distributions [theta | x] can be sampled, implementation of Gibbs sampling requires only that we can sample from the full conditional distribution [x | f, theta], which is made possible by knowledge of the null space of A'. We illustrate the approach using two data sets with individual misidentification, one simulated, the other summarizing recapture data for salamanders based on natural marks.

Hydrogeophysical Assessment of Aquifer Uncertainty Using Simulated Annealing driven MRF-Based Stochastic Joint Inversion

NASA Astrophysics Data System (ADS)

Oware, E. K.

2017-12-01

Geophysical quantification of hydrogeological parameters typically involve limited noisy measurements coupled with inadequate understanding of the target phenomenon. Hence, a deterministic solution is unrealistic in light of the largely uncertain inputs. Stochastic imaging (SI), in contrast, provides multiple equiprobable realizations that enable probabilistic assessment of aquifer properties in a realistic manner. Generation of geologically realistic prior models is central to SI frameworks. Higher-order statistics for representing prior geological features in SI are, however, usually borrowed from training images (TIs), which may produce undesirable outcomes if the TIs are unpresentatitve of the target structures. The Markov random field (MRF)-based SI strategy provides a data-driven alternative to TI-based SI algorithms. In the MRF-based method, the simulation of spatial features is guided by Gibbs energy (GE) minimization. Local configurations with smaller GEs have higher likelihood of occurrence and vice versa. The parameters of the Gibbs distribution for computing the GE are estimated from the hydrogeophysical data, thereby enabling the generation of site-specific structures in the absence of reliable TIs. In Metropolis-like SI methods, the variance of the transition probability controls the jump-size. The procedure is a standard Markov chain Monte Carlo (McMC) method when a constant variance is assumed, and becomes simulated annealing (SA) when the variance (cooling temperature) is allowed to decrease gradually with time. We observe that in certain problems, the large variance typically employed at the beginning to hasten burn-in may be unideal for sampling at the equilibrium state. The powerfulness of SA stems from its flexibility to adaptively scale the variance at different stages of the sampling. Degeneration of results were reported in a previous implementation of the MRF-based SI strategy based on a constant variance. Here, we present an updated version of the algorithm based on SA that appears to resolve the degeneration problem with seemingly improved results. We illustrate the performance of the SA version with a joint inversion of time-lapse concentration and electrical resistivity measurements in a hypothetical trinary hydrofacies aquifer characterization problem.

Predicting cyclohexane/water distribution coefficients for the SAMPL5 challenge using MOSCED and the SMD solvation model

NASA Astrophysics Data System (ADS)

Diaz-Rodriguez, Sebastian; Bozada, Samantha M.; Phifer, Jeremy R.; Paluch, Andrew S.

2016-11-01

We present blind predictions using the solubility parameter based method MOSCED submitted for the SAMPL5 challenge on calculating cyclohexane/water distribution coefficients at 298 K. Reference data to parameterize MOSCED was generated with knowledge only of chemical structure by performing solvation free energy calculations using electronic structure calculations in the SMD continuum solvent. To maintain simplicity and use only a single method, we approximate the distribution coefficient with the partition coefficient of the neutral species. Over the final SAMPL5 set of 53 compounds, we achieved an average unsigned error of 2.2± 0.2 log units (ranking 15 out of 62 entries), the correlation coefficient ( R) was 0.6± 0.1 (ranking 35), and 72± 6 % of the predictions had the correct sign (ranking 30). While used here to predict cyclohexane/water distribution coefficients at 298 K, MOSCED is broadly applicable, allowing one to predict temperature dependent infinite dilution activity coefficients in any solvent for which parameters exist, and provides a means by which an excess Gibbs free energy model may be parameterized to predict composition dependent phase-equilibrium.

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

PubMed

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

2013-04-16

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

A Method to Calculate the Surface Tension of a Cylindrical Droplet

ERIC Educational Resources Information Center

Wang, Xiaosong; Zhu, Ruzeng

2010-01-01

The history of Laplace's equations for spherical and cylindrical droplets and the concept of dividing surface in Gibbs' thermodynamic theory of capillary phenomena are briefly reviewed. The existing theories of surface tensions of cylindrical droplets are briefly reviewed too. For cylindrical droplets, a new method to calculate the radius and the…

Reduction of the allotropic transition temperature in nanocrystalline zirconium: Predicted by modified equation of state (MEOS) method and molecular dynamics simulation

NASA Astrophysics Data System (ADS)

Salati, Amin; Mokhtari, Esmail; Panjepour, Masoud; Aryanpour, Gholamreza

2013-04-01

The temperature at which polymorphic phase transformation occurs in nanocrystalline (NC) materials is different from that of coarse-grained specimens. This anomaly has been related to the role of grain boundary component in these materials and can be predicted by a dilated crystal model. In this study, based on this model, a modified equation of state (MEOS) method (instead of equation of state, EOS, method) is used to calculate the total Gibbs free energy of each phase (β-Zr or α-Zr) in NC Zr. Thereupon, the change in the total Gibbs free energy for β-Zr to α-Zr phase transformation (ΔGβ→α) via the grain size is calculated by this method. Similar to polymorphic transformation in other NC materials (Fe, Nb, Co, TiO2, Al2O3 and ZnS), it is found that the estimated transformation temperature in NC Zr (β→α) is reduced with decreasing grain size. Finally, a molecular dynamics (MD) simulation is employed to confirm the theoretical results.

Chemical potential, Gibbs-Duhem equation and quantum gases

NASA Astrophysics Data System (ADS)

Lee, M. Howard

2017-05-01

Thermodynamic relations like the Gibbs-Duhem are valid from the lowest to the highest temperatures. But they cannot by themselves provide any specific temperature behavior of thermodynamic functions like the chemical potential. In this work, we show that if some general conditions are attached to the Gibbs-Duhem equation, it is possible to obtain the low temperature form of the chemical potential for the ideal Fermi and Bose gases very directly.

High-temperature mass spectrometric study of the vaporization processes and thermodynamic properties of melts in the PbO-B2O3-SiO2 system.

PubMed

Stolyarova, V L; Lopatin, S I; Shilov, A L; Shugurov, S M

2013-07-15

The unique properties of the PbO-B2O3-SiO2 system, especially its extensive range of glass-forming compositions, make it valuable for various practical applications. The thermodynamic properties and vaporization of PbO-B2O3-SiO2 melts are not well established so far and the data obtained on these will be useful for optimization of technology and thermodynamic modeling of glasses. High-temperature Knudsen effusion mass spectrometry was used to study vaporization processes and to determine the partial pressures of components of the PbO-B2O3-SiO2 melts. Measurements were performed with a MS-1301 mass spectrometer. Vaporization was carried out using two quartz effusion cells containing the sample under study and pure PbO (reference substance). Ions were produced by electron ionization at an energy of 25 eV. To facilitate interpretation of the mass spectra, the appearance energies of ions were also measured. Pb, PbO and O2 were found to be the main vapor species over the samples studied at 1100 K. The PbO activities as a function of the composition of the system were derived from the measured PbO partial pressures. The B2O3 and SiO2 activities, the Gibbs energy of formation, the excess Gibbs energy of formation and mass losses in the samples studied were calculated. Partial pressures of the vapor species over PbO-B2O3-SiO2 melts were measured at 1100 K in the wide range of compositions using the Knudsen mass spectrometric method. The data enabled the PbO, B2O3, and SiO2 activities in these melts to be derived and provided evidence of their negative deviations from ideal behavior. Copyright © 2013 John Wiley & Sons, Ltd.

Pan-STARRS 1 observations of the unusual active Centaur P/2011 S1(Gibbs)

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

Lin, H. W.; Ip, W. H.; Chen, W. P.

2014-05-01

P/2011 S1 (Gibbs) is an outer solar system comet or active Centaur with a similar orbit to that of the famous 29P/Schwassmann-Wachmann 1. P/2011 S1 (Gibbs) has been observed by the Pan-STARRS 1 (PS1) sky survey from 2010 to 2012. The resulting data allow us to perform multi-color studies of the nucleus and coma of the comet. Analysis of PS1 images reveals that P/2011 S1 (Gibbs) has a small nucleus <4 km radius, with colors g {sub P1} – r {sub P1} = 0.5 ± 0.02, r {sub P1} – i {sub P1} = 0.12 ± 0.02, and i {submore » P1} – z {sub P1} = 0.46 ± 0.03. The comet remained active from 2010 to 2012, with a model-dependent mass-loss rate of ∼100 kg s{sup –1}. The mass-loss rate per unit surface area of P/2011 S1 (Gibbs) is as high as that of 29P/Schwassmann-Wachmann 1, making it one of the most active Centaurs. The mass-loss rate also varies with time from ∼40 kg s{sup –1} to 150 kg s{sup –1}. Due to its rather circular orbit, we propose that P/2011 S1 (Gibbs) has 29P/Schwassmann-Wachmann 1-like outbursts that control the outgassing rate. The results indicate that it may have a similar surface composition to that of 29P/Schwassmann-Wachmann 1. Our numerical simulations show that the future orbital evolution of P/2011 S1 (Gibbs) is more similar to that of the main population of Centaurs than to that of 29P/Schwassmann-Wachmann 1. The results also demonstrate that P/2011 S1 (Gibbs) is dynamically unstable and can only remain near its current orbit for roughly a thousand years.« less

Carbon deposition thresholds on nickel-based solid oxide fuel cell anodes II. Steam:carbon ratio and current density

NASA Astrophysics Data System (ADS)

Kuhn, J.; Kesler, O.

2015-03-01

For the second part of a two part publication, coking thresholds with respect to molar steam:carbon ratio (SC) and current density in nickel-based solid oxide fuel cells were determined. Anode-supported button cell samples were exposed to 2-component and 5-component gas mixtures with 1 ≤ SC ≤ 2 and zero fuel utilization for 10 h, followed by measurement of the resulting carbon mass. The effect of current density was explored by measuring carbon mass under conditions known to be prone to coking while increasing the current density until the cell was carbon-free. The SC coking thresholds were measured to be ∼1.04 and ∼1.18 at 600 and 700 °C, respectively. Current density experiments validated the thresholds measured with respect to fuel utilization and steam:carbon ratio. Coking thresholds at 600 °C could be predicted with thermodynamic equilibrium calculations when the Gibbs free energy of carbon was appropriately modified. Here, the Gibbs free energy of carbon on nickel-based anode support cermets was measured to be -6.91 ± 0.08 kJ mol-1. The results of this two part publication show that thermodynamic equilibrium calculations with appropriate modification to the Gibbs free energy of solid-phase carbon can be used to predict coking thresholds on nickel-based anodes at 600-700 °C.

Collaborative Research: Ground Truth of African and Eastern Mediterranean Shallow Seismicity Using SAR Interferometry and Gibbs Sampling Inversion

DTIC Science & Technology

2006-10-05

the likely existence of a small foreshock . 2. BACKGROUND 2.1. InSAR The most well-known examples of InSAR used as a geodetic tool involve...the event. We have used the seismic waveforms in the Sultan Dag event to identify a small foreshock preceding the main shock by about 3 seconds

Model-based Bayesian inference for ROC data analysis

NASA Astrophysics Data System (ADS)

Lei, Tianhu; Bae, K. Ty

2013-03-01

This paper presents a study of model-based Bayesian inference to Receiver Operating Characteristics (ROC) data. The model is a simple version of general non-linear regression model. Different from Dorfman model, it uses a probit link function with a covariate variable having zero-one two values to express binormal distributions in a single formula. Model also includes a scale parameter. Bayesian inference is implemented by Markov Chain Monte Carlo (MCMC) method carried out by Bayesian analysis Using Gibbs Sampling (BUGS). Contrast to the classical statistical theory, Bayesian approach considers model parameters as random variables characterized by prior distributions. With substantial amount of simulated samples generated by sampling algorithm, posterior distributions of parameters as well as parameters themselves can be accurately estimated. MCMC-based BUGS adopts Adaptive Rejection Sampling (ARS) protocol which requires the probability density function (pdf) which samples are drawing from be log concave with respect to the targeted parameters. Our study corrects a common misconception and proves that pdf of this regression model is log concave with respect to its scale parameter. Therefore, ARS's requirement is satisfied and a Gaussian prior which is conjugate and possesses many analytic and computational advantages is assigned to the scale parameter. A cohort of 20 simulated data sets and 20 simulations from each data set are used in our study. Output analysis and convergence diagnostics for MCMC method are assessed by CODA package. Models and methods by using continuous Gaussian prior and discrete categorical prior are compared. Intensive simulations and performance measures are given to illustrate our practice in the framework of model-based Bayesian inference using MCMC method.

Supervised Gamma Process Poisson Factorization

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

Anderson, Dylan Zachary

This thesis develops the supervised gamma process Poisson factorization (S- GPPF) framework, a novel supervised topic model for joint modeling of count matrices and document labels. S-GPPF is fully generative and nonparametric: document labels and count matrices are modeled under a uni ed probabilistic framework and the number of latent topics is controlled automatically via a gamma process prior. The framework provides for multi-class classification of documents using a generative max-margin classifier. Several recent data augmentation techniques are leveraged to provide for exact inference using a Gibbs sampling scheme. The first portion of this thesis reviews supervised topic modeling andmore » several key mathematical devices used in the formulation of S-GPPF. The thesis then introduces the S-GPPF generative model and derives the conditional posterior distributions of the latent variables for posterior inference via Gibbs sampling. The S-GPPF is shown to exhibit state-of-the-art performance for joint topic modeling and document classification on a dataset of conference abstracts, beating out competing supervised topic models. The unique properties of S-GPPF along with its competitive performance make it a novel contribution to supervised topic modeling.« less

Gibbs-Curie-Wulff Theorem in Organic Materials: A Case Study on the Relationship between Surface Energy and Crystal Growth.

PubMed

Li, Rongjin; Zhang, Xiaotao; Dong, Huanli; Li, Qikai; Shuai, Zhigang; Hu, Wenping

2016-02-24

The equilibrium crystal shape and shape evolution of organic crystals are found to follow the Gibbs-Curie-Wulff theorem. Organic crystals are grown by the physical vapor transport technique and exhibit exactly the same shape as predicted by the Gibbs-Curie-Wulff theorem under optimal conditions. This accordance provides concrete proof for the theorem. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

GLASS VISCOSITY AS A FUNCTION OF TEMPERATURE AND COMPOSITION: A MODEL BASED ON ADAM-GIBBS EQUATION

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

Hrma, Pavel R.

2008-07-01

Within the temperature range and composition region of processing and product forming, the viscosity of commercial and waste glasses spans over 12 orders of magnitude. This paper shows that a generalized Adam-Gibbs relationship reasonably approximates the real behavior of glasses with four temperature-independent parameters of which two are linear functions of the composition vector. The equation is subjected to two constraints, one requiring that the viscosity-temperature relationship approaches the Arrhenius function at high temperatures with a composition-independent pre-exponential factor and the other that the viscosity value is independent of composition at the glass-transition temperature. Several sets of constant coefficients weremore » obtained by fitting the generalized Adam-Gibbs equation to data of two glass families: float glass and Hanford waste glass. Other equations (the Vogel-Fulcher-Tammann equation, original and modified, the Avramov equation, and the Douglass-Doremus equation) were fitted to float glass data series and compared with the Adam-Gibbs equation, showing that Adam-Gibbs glass appears an excellent approximation of real glasses even as compared with other candidate constitutive relations.« less

Determination of total antioxidant capacity of humic acids using CUPRAC, Folin-Ciocalteu, noble metal nanoparticle- and solid-liquid extraction-based methods.

PubMed

Karadirek, Şeyda; Kanmaz, Nergis; Balta, Zeynep; Demirçivi, Pelin; Üzer, Ayşem; Hızal, Jülide; Apak, Reşat

2016-06-01

Total antioxidant capacity (TAC) of humic acid (HA) samples was determined using CUPRAC (CUPric Reducing Antioxidant Capacity), FC (Folin-Ciocalteu), QUENCHER-CUPRAC, QUENCHER-FC, Ag-NP (Silver nanoparticle)‒ and Au-NP (Gold nanoparticle)‒based methods. Conventional FC and modified FC (MFC) methods were applied to solid samples. Because of decreased solubility of Folin-Ciocalteu's phenol reagent in organic solvents, solvent effect on TAC measurement was investigated using QUENCHER-CUPRAC assay by using ethanol:distilled water and dimethyl sulfoxide:distilled water with varying ratios. To see the combined effect of solubilization (leaching) and TAC measurement of humic acids simultaneously, QUENCHER experiments were performed at 25°C and 50°C; QUENCHER-CUPRAC and QUENCHER-FC methods agreed well and had similar precision in F-statistics. Although the Gibbs free energy change (ΔG°) of the oxidation of HA dihydroxy phenols with the test reagents were negative, the ΔG° was positive only for the reaction of CUPRAC reagent with isolated monohydric phenols, showing CUPRAC selectivity toward polyphenolic antioxidants. This is the first work on the antioxidant capacity measurement of HA having a sparingly soluble matrix where enhanced solubilization of bound phenolics is achieved with coupled oxidation by TAC reagents. Copyright © 2016 Elsevier B.V. All rights reserved.

Phase Equilibria and Thermodynamic Descriptions of Ag-Ge and Ag-Ge-Ni Systems

NASA Astrophysics Data System (ADS)

Rajkumar, V. B.; Chen, Sinn-Wen

2018-07-01

Gibbs energy modeling of Ag-Ge and Ag-Ge-Ni systems was done using the calculation of the phase diagram method with associated data from this work and relevant literature information. In the Ag-Ge system, the solidus temperatures of Ag-rich alloys are measured using differential thermal analysis, and the energy of mixing for the FCC_A1 phase is calculated using the special quasi-random structures technique. The isothermal sections of the Ag-Ge-Ni system at 1023 K and 673 K are also experimentally determined. These data and findings in the relevant literature are used to model the Gibbs energy of the Ag-Ge and Ag-Ge- Ni systems. A reaction scheme and a liquidus projection of the Ag-Ge-Ni system are determined.

Analytic second derivatives of the energy in the fragment molecular orbital method

NASA Astrophysics Data System (ADS)

Nakata, Hiroya; Nagata, Takeshi; Fedorov, Dmitri G.; Yokojima, Satoshi; Kitaura, Kazuo; Nakamura, Shinichiro

2013-04-01

We developed the analytic second derivatives of the energy for the fragment molecular orbital (FMO) method. First we derived the analytic expressions and then introduced some approximations related to the first and second order coupled perturbed Hartree-Fock equations. We developed a parallel program for the FMO Hessian with approximations in GAMESS and used it to calculate infrared (IR) spectra and Gibbs free energies and to locate the transition states in SN2 reactions. The accuracy of the Hessian is demonstrated in comparison to ab initio results for polypeptides and a water cluster. By using the two residues per fragment division, we achieved the accuracy of 3 cm-1 in the reduced mean square deviation of vibrational frequencies from ab initio for all three polyalanine isomers, while the zero point energy had the error not exceeding 0.3 kcal/mol. The role of the secondary structure on IR spectra, zero point energies, and Gibbs free energies is discussed.

Thermochemical investigations in the system Cd–Gd

PubMed Central

Reichmann, Thomas L.; Ganesan, Rajesh; Ipser, Herbert

2014-01-01

Vapour pressure measurements were performed in terms of a non-isothermal isopiestic method to determine vapour pressures of Cd in the system Cd–Gd between 693 and 1045 K. From these results thermodynamic activities of Cd were derived as a function of temperature for the composition range 52–86 at.% Cd. By employing an adapted Gibbs–Helmholtz equation, partial molar enthalpies of mixing of Cd were obtained for the corresponding composition range, which were used to convert the activity values of Cd to a common average sample temperature of 773 K. The relatively large variation of the activity across the homogeneity ranges of the phases Cd2Gd and Cd45Gd11 indicates that they probably belong to the most stable intermetallic compounds in this system. An activity value of Gd for the two phase field Cd6Gd+L was available from literature and served as an integration constant for a Gibbs–Duhem integration. Integral Gibbs energies are presented between 51 and 100 at.% Cd at 773 K, referred to Cd(l) and α-Gd(s) as standard states. Gibbs energies of formation for the exact stoichiometric compositions of the phases Cd58Gd13, Cd45Gd11, Cd3Gd and Cd2Gd were obtained at 773 K as about −19.9, −21.1, −24.8, and −30.0 kJ g atom−1, respectively. PMID:25328283

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

PubMed

Mora Osorio, Camilo Andrés; González Barrios, Andrés Fernando

2016-12-07

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

Bayesian methods for outliers detection in GNSS time series

NASA Astrophysics Data System (ADS)

Qianqian, Zhang; Qingming, Gui

2013-07-01

This article is concerned with the problem of detecting outliers in GNSS time series based on Bayesian statistical theory. Firstly, a new model is proposed to simultaneously detect different types of outliers based on the conception of introducing different types of classification variables corresponding to the different types of outliers; the problem of outlier detection is converted into the computation of the corresponding posterior probabilities, and the algorithm for computing the posterior probabilities based on standard Gibbs sampler is designed. Secondly, we analyze the reasons of masking and swamping about detecting patches of additive outliers intensively; an unmasking Bayesian method for detecting additive outlier patches is proposed based on an adaptive Gibbs sampler. Thirdly, the correctness of the theories and methods proposed above is illustrated by simulated data and then by analyzing real GNSS observations, such as cycle slips detection in carrier phase data. Examples illustrate that the Bayesian methods for outliers detection in GNSS time series proposed by this paper are not only capable of detecting isolated outliers but also capable of detecting additive outlier patches. Furthermore, it can be successfully used to process cycle slips in phase data, which solves the problem of small cycle slips.

Thermal, structural, functional, optical and magnetic studies of pure and Ba doped CdO nanoparticles.

PubMed

Sivakumar, S; Venkatesan, A; Soundhirarajan, P; Khatiwada, Chandra Prasad

2015-12-05

In this research, a chemical precipitation method was used to synthesize undoped and doped cadmium oxide nanoparticles and studied by TG-DTA, XRD, FT-IR, SEM, with EDX and antibacterial activities, respectively. The melting points, thermal stability and the kinetic parameters like entropy (ΔS), enthalpy (ΔH), Gibb's energy (ΔG), activation energy (E), frequency factor (A) were evaluated from TG-DTA measurements. X-ray diffraction analysis (XRD) brought out the information about the synthesized products exist in spherical in shape with cubic structure. The functional groups and band area of the samples were established by Fourier transform infrared (FT-IR) spectroscopy. The direct and indirect band gap energy of pure and doped samples were determined by UV-Vis-DRS. The surface morphological, elemental compositions and particles sizes were evaluated by scanning electron microscopy (SEM) and energy dispersive X-ray spectroscopy (EDS). Finally, antibacterial activities indicated the Gram-positive and Gram-negative bacteria are more active in transporter, dehydrogenize and periplasmic enzymatic activities of pure and doped samples. Copyright © 2015 Elsevier B.V. All rights reserved.

Joint Bayesian Component Separation and CMB Power Spectrum Estimation

NASA Technical Reports Server (NTRS)

Eriksen, H. K.; Jewell, J. B.; Dickinson, C.; Banday, A. J.; Gorski, K. M.; Lawrence, C. R.

2008-01-01

We describe and implement an exact, flexible, and computationally efficient algorithm for joint component separation and CMB power spectrum estimation, building on a Gibbs sampling framework. Two essential new features are (1) conditional sampling of foreground spectral parameters and (2) joint sampling of all amplitude-type degrees of freedom (e.g., CMB, foreground pixel amplitudes, and global template amplitudes) given spectral parameters. Given a parametric model of the foreground signals, we estimate efficiently and accurately the exact joint foreground- CMB posterior distribution and, therefore, all marginal distributions such as the CMB power spectrum or foreground spectral index posteriors. The main limitation of the current implementation is the requirement of identical beam responses at all frequencies, which restricts the analysis to the lowest resolution of a given experiment. We outline a future generalization to multiresolution observations. To verify the method, we analyze simple models and compare the results to analytical predictions. We then analyze a realistic simulation with properties similar to the 3 yr WMAP data, downgraded to a common resolution of 3 deg FWHM. The results from the actual 3 yr WMAP temperature analysis are presented in a companion Letter.

Data Analysis with Graphical Models: Software Tools

NASA Technical Reports Server (NTRS)

Buntine, Wray L.

1994-01-01

Probabilistic graphical models (directed and undirected Markov fields, and combined in chain graphs) are used widely in expert systems, image processing and other areas as a framework for representing and reasoning with probabilities. They come with corresponding algorithms for performing probabilistic inference. This paper discusses an extension to these models by Spiegelhalter and Gilks, plates, used to graphically model the notion of a sample. This offers a graphical specification language for representing data analysis problems. When combined with general methods for statistical inference, this also offers a unifying framework for prototyping and/or generating data analysis algorithms from graphical specifications. This paper outlines the framework and then presents some basic tools for the task: a graphical version of the Pitman-Koopman Theorem for the exponential family, problem decomposition, and the calculation of exact Bayes factors. Other tools already developed, such as automatic differentiation, Gibbs sampling, and use of the EM algorithm, make this a broad basis for the generation of data analysis software.

Genomic analysis of cow mortality and milk production using a threshold-linear model.

PubMed

Tsuruta, S; Lourenco, D A L; Misztal, I; Lawlor, T J

2017-09-01

The objective of this study was to investigate the feasibility of genomic evaluation for cow mortality and milk production using a single-step methodology. Genomic relationships between cow mortality and milk production were also analyzed. Data included 883,887 (866,700) first-parity, 733,904 (711,211) second-parity, and 516,256 (492,026) third-parity records on cow mortality (305-d milk yields) of Holsteins from Northeast states in the United States. The pedigree consisted of up to 1,690,481 animals including 34,481 bulls genotyped with 36,951 SNP markers. Analyses were conducted with a bivariate threshold-linear model for each parity separately. Genomic information was incorporated as a genomic relationship matrix in the single-step BLUP. Traditional and genomic estimated breeding values (GEBV) were obtained with Gibbs sampling using fixed variances, whereas reliabilities were calculated from variances of GEBV samples. Genomic EBV were then converted into single nucleotide polymorphism (SNP) marker effects. Those SNP effects were categorized according to values corresponding to 1 to 4 standard deviations. Moving averages and variances of SNP effects were calculated for windows of 30 adjacent SNP, and Manhattan plots were created for SNP variances with the same window size. Using Gibbs sampling, the reliability for genotyped bulls for cow mortality was 28 to 30% in EBV and 70 to 72% in GEBV. The reliability for genotyped bulls for 305-d milk yields was 53 to 65% to 81 to 85% in GEBV. Correlations of SNP effects between mortality and 305-d milk yields within categories were the highest with the largest SNP effects and reached >0.7 at 4 standard deviations. All SNP regions explained less than 0.6% of the genetic variance for both traits, except regions close to the DGAT1 gene, which explained up to 2.5% for cow mortality and 4% for 305-d milk yields. Reliability for GEBV with a moderate number of genotyped animals can be calculated by Gibbs samples. Genomic information can greatly increase the reliability of predictions not only for milk but also for mortality. The existence of a common region on Bos taurus autosome 14 affecting both traits may indicate a major gene with a pleiotropic effect on milk and mortality. Copyright © 2017 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Ferrous sulfate based low temperature synthesis and magnetic properties of nickel ferrite nanostructures

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

Tejabhiram, Y., E-mail: tejabhiram@gmail.com; Pradeep, R.; Helen, A.T.

2014-12-15

Highlights: • Novel low temperature synthesis of nickel ferrite nanoparticles. • Comparison with two conventional synthesis techniques including hydrothermal method. • XRD results confirm the formation of crystalline nickel ferrites at 110 °C. • Superparamagnetic particles with applications in drug delivery and hyperthermia. • Magnetic properties superior to conventional methods found in new process. - Abstract: We report a simple, low temperature and surfactant free co-precipitation method for the preparation of nickel ferrite nanostructures using ferrous sulfate as the iron precursor. The products obtained from this method were compared for their physical properties with nickel ferrites produced through conventional co-precipitationmore » and hydrothermal methods which used ferric nitrate as the iron precursor. X-ray diffraction analysis confirmed the synthesis of single phase inverse spinel nanocrystalline nickel ferrites at temperature as low as 110 °C in the low temperature method. Electron microscopy analysis on the samples revealed the formation of nearly spherical nanostructures in the size range of 20–30 nm which are comparable to other conventional methods. Vibrating sample magnetometer measurements showed the formation of superparamagnetic particles with high magnetic saturation 41.3 emu/g which corresponds well with conventional synthesis methods. The spontaneous synthesis of the nickel ferrite nanoparticles by the low temperature synthesis method was attributed to the presence of 0.808 kJ mol{sup −1} of excess Gibbs free energy due to ferrous sulfate precursor.« less

Mesohysteresis model for ferromagnetic materials by minimization of the micromagnetic free energy

NASA Astrophysics Data System (ADS)

van den Berg, A.; Dupré, L.; Van de Wiele, B.; Crevecoeur, G.

2009-04-01

To study the connection between macroscopic hysteretic behavior and the microstructural properties, this paper presents and validates a new material dependent three-dimensional mesoscopic magnetic hysteresis model. In the presented mesoscopic description, the different micromagnetic energy terms are reformulated on the space scale of the magnetic domains. The sample is discretized in cubic cells, each with a local stress state, local bcc crystallographic axes, etc. The magnetization is assumed to align with one of the three crystallographic axes, in positive or negative sense, defining six volume fractions within each cell. The micromagnetic Gibbs free energy is described in terms of these volume fractions. Hysteresis loops are computed by minimizing the mesoscopic Gibbs free energy using a modified gradient search for a sequence of external applied fields. To validate the mesohysteresis model, we studied the magnetic memory properties. Numerical experiments reveal that (1) minor hysteresis loops are indeed closed and (2) the closed minor loops are erased from the memory.

Genome-wide regression and prediction with the BGLR statistical package.

PubMed

Pérez, Paulino; de los Campos, Gustavo

2014-10-01

Many modern genomic data analyses require implementing regressions where the number of parameters (p, e.g., the number of marker effects) exceeds sample size (n). Implementing these large-p-with-small-n regressions poses several statistical and computational challenges, some of which can be confronted using Bayesian methods. This approach allows integrating various parametric and nonparametric shrinkage and variable selection procedures in a unified and consistent manner. The BGLR R-package implements a large collection of Bayesian regression models, including parametric variable selection and shrinkage methods and semiparametric procedures (Bayesian reproducing kernel Hilbert spaces regressions, RKHS). The software was originally developed for genomic applications; however, the methods implemented are useful for many nongenomic applications as well. The response can be continuous (censored or not) or categorical (either binary or ordinal). The algorithm is based on a Gibbs sampler with scalar updates and the implementation takes advantage of efficient compiled C and Fortran routines. In this article we describe the methods implemented in BGLR, present examples of the use of the package, and discuss practical issues emerging in real-data analysis. Copyright © 2014 by the Genetics Society of America.

Weakly Nonergodic Dynamics in the Gross-Pitaevskii Lattice

NASA Astrophysics Data System (ADS)

Mithun, Thudiyangal; Kati, Yagmur; Danieli, Carlo; Flach, Sergej

2018-05-01

The microcanonical Gross-Pitaevskii (also known as the semiclassical Bose-Hubbard) lattice model dynamics is characterized by a pair of energy and norm densities. The grand canonical Gibbs distribution fails to describe a part of the density space, due to the boundedness of its kinetic energy spectrum. We define Poincaré equilibrium manifolds and compute the statistics of microcanonical excursion times off them. The tails of the distribution functions quantify the proximity of the many-body dynamics to a weakly nonergodic phase, which occurs when the average excursion time is infinite. We find that a crossover to weakly nonergodic dynamics takes place inside the non-Gibbs phase, being unnoticed by the largest Lyapunov exponent. In the ergodic part of the non-Gibbs phase, the Gibbs distribution should be replaced by an unknown modified one. We relate our findings to the corresponding integrable limit, close to which the actions are interacting through a short range coupling network.

Time-dependent generalized Gibbs ensembles in open quantum systems

NASA Astrophysics Data System (ADS)

Lange, Florian; Lenarčič, Zala; Rosch, Achim

2018-04-01

Generalized Gibbs ensembles have been used as powerful tools to describe the steady state of integrable many-particle quantum systems after a sudden change of the Hamiltonian. Here, we demonstrate numerically that they can be used for a much broader class of problems. We consider integrable systems in the presence of weak perturbations which break both integrability and drive the system to a state far from equilibrium. Under these conditions, we show that the steady state and the time evolution on long timescales can be accurately described by a (truncated) generalized Gibbs ensemble with time-dependent Lagrange parameters, determined from simple rate equations. We compare the numerically exact time evolutions of density matrices for small systems with a theory based on block-diagonal density matrices (diagonal ensemble) and a time-dependent generalized Gibbs ensemble containing only a small number of approximately conserved quantities, using the one-dimensional Heisenberg model with perturbations described by Lindblad operators as an example.

Gibbs Energy Modeling of Digenite and Adjacent Solid-State Phases

NASA Astrophysics Data System (ADS)

Waldner, Peter

2017-08-01

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

Thermodynamics of Bioreactions.

PubMed

Held, Christoph; Sadowski, Gabriele

2016-06-07

Thermodynamic principles have been applied to enzyme-catalyzed reactions since the beginning of the 1930s in an attempt to understand metabolic pathways. Currently, thermodynamics is also applied to the design and analysis of biotechnological processes. The key thermodynamic quantity is the Gibbs energy of reaction, which must be negative for a reaction to occur spontaneously. However, the application of thermodynamic feasibility studies sometimes yields positive Gibbs energies of reaction even for reactions that are known to occur spontaneously, such as glycolysis. This article reviews the application of thermodynamics in enzyme-catalyzed reactions. It summarizes the basic thermodynamic relationships used for describing the Gibbs energy of reaction and also refers to the nonuniform application of these relationships in the literature. The review summarizes state-of-the-art approaches that describe the influence of temperature, pH, electrolytes, solvents, and concentrations of reacting agents on the Gibbs energy of reaction and, therefore, on the feasibility and yield of biological reactions.

Gibbs measures with memory of length 2 on an arbitrary-order Cayley tree

NASA Astrophysics Data System (ADS)

Akın, Hasan

In this paper, we consider the Ising-Vanniminus model on an arbitrary-order Cayley tree. We generalize the results conjectured by Akın [Chinese J. Phys. 54(4), 635-649 (2016) and Int. J. Mod. Phys. B 31(13), 1750093 (2017)] for an arbitrary-order Cayley tree. We establish the existence and a full classification of translation-invariant Gibbs measures (TIGMs) with a memory of length 2 associated with the model on arbitrary-order Cayley tree. We construct the recurrence equations corresponding to the generalized ANNNI model. We satisfy the Kolmogorov consistency condition. We propose a rigorous measure-theoretical approach to investigate the Gibbs measures with a memory of length 2 for the model. We explain if the number of branches of the tree does not change the number of Gibbs measures. Also, we try to determine when the phase transition does occur.

Generalized thermalization for integrable system under quantum quench.

PubMed

Muralidharan, Sushruth; Lochan, Kinjalk; Shankaranarayanan, S

2018-01-01

We investigate equilibration and generalized thermalization of the quantum Harmonic chain under local quantum quench. The quench action we consider is connecting two disjoint harmonic chains of different sizes and the system jumps between two integrable settings. We verify the validity of the generalized Gibbs ensemble description for this infinite-dimensional Hilbert space system and also identify equilibration between the subsystems as in classical systems. Using Bogoliubov transformations, we show that the eigenstates of the system prior to the quench evolve toward the Gibbs Generalized Ensemble description. Eigenstates that are more delocalized (in the sense of inverse participation ratio) prior to the quench, tend to equilibrate more rapidly. Further, through the phase space properties of a generalized Gibbs ensemble and the strength of stimulated emission, we identify the necessary criterion on the initial states for such relaxation at late times and also find out the states that would potentially not be described by the generalized Gibbs ensemble description.

Development of Simulation Methods in the Gibbs Ensemble to Predict Polymer-Solvent Phase Equilibria

NASA Astrophysics Data System (ADS)

Gartner, Thomas; Epps, Thomas; Jayaraman, Arthi

Solvent vapor annealing (SVA) of polymer thin films is a promising method for post-deposition polymer film morphology control. The large number of important parameters relevant to SVA (polymer, solvent, and substrate chemistries, incoming film condition, annealing and solvent evaporation conditions) makes systematic experimental study of SVA a time-consuming endeavor, motivating the application of simulation and theory to the SVA system to provide both mechanistic insight and scans of this wide parameter space. However, to rigorously treat the phase equilibrium between polymer film and solvent vapor while still probing the dynamics of SVA, new simulation methods must be developed. In this presentation, we compare two methods to study polymer-solvent phase equilibrium-Gibbs Ensemble Molecular Dynamics (GEMD) and Hybrid Monte Carlo/Molecular Dynamics (Hybrid MC/MD). Liquid-vapor equilibrium results are presented for the Lennard Jones fluid and for coarse-grained polymer-solvent systems relevant to SVA. We found that the Hybrid MC/MD method is more stable and consistent than GEMD, but GEMD has significant advantages in computational efficiency. We propose that Hybrid MC/MD simulations be used for unfamiliar systems in certain choice conditions, followed by much faster GEMD simulations to map out the remainder of the phase window.

Unsupervised Bayesian linear unmixing of gene expression microarrays.

PubMed

Bazot, Cécile; Dobigeon, Nicolas; Tourneret, Jean-Yves; Zaas, Aimee K; Ginsburg, Geoffrey S; Hero, Alfred O

2013-03-19

This paper introduces a new constrained model and the corresponding algorithm, called unsupervised Bayesian linear unmixing (uBLU), to identify biological signatures from high dimensional assays like gene expression microarrays. The basis for uBLU is a Bayesian model for the data samples which are represented as an additive mixture of random positive gene signatures, called factors, with random positive mixing coefficients, called factor scores, that specify the relative contribution of each signature to a specific sample. The particularity of the proposed method is that uBLU constrains the factor loadings to be non-negative and the factor scores to be probability distributions over the factors. Furthermore, it also provides estimates of the number of factors. A Gibbs sampling strategy is adopted here to generate random samples according to the posterior distribution of the factors, factor scores, and number of factors. These samples are then used to estimate all the unknown parameters. Firstly, the proposed uBLU method is applied to several simulated datasets with known ground truth and compared with previous factor decomposition methods, such as principal component analysis (PCA), non negative matrix factorization (NMF), Bayesian factor regression modeling (BFRM), and the gradient-based algorithm for general matrix factorization (GB-GMF). Secondly, we illustrate the application of uBLU on a real time-evolving gene expression dataset from a recent viral challenge study in which individuals have been inoculated with influenza A/H3N2/Wisconsin. We show that the uBLU method significantly outperforms the other methods on the simulated and real data sets considered here. The results obtained on synthetic and real data illustrate the accuracy of the proposed uBLU method when compared to other factor decomposition methods from the literature (PCA, NMF, BFRM, and GB-GMF). The uBLU method identifies an inflammatory component closely associated with clinical symptom scores collected during the study. Using a constrained model allows recovery of all the inflammatory genes in a single factor.

Teaching the Concept of Gibbs Energy Minimization through Its Application to Phase-Equilibrium Calculation

ERIC Educational Resources Information Center

Privat, Romain; Jaubert, Jean-Noe¨l; Berger, Etienne; Coniglio, Lucie; Lemaitre, Ce´cile; Meimaroglou, Dimitrios; Warth, Vale´rie

2016-01-01

Robust and fast methods for chemical or multiphase equilibrium calculation are routinely needed by chemical-process engineers working on sizing or simulation aspects. Yet, while industrial applications essentially require calculation tools capable of discriminating between stable and nonstable states and converging to nontrivial solutions,…

Quantum dynamics of thermalizing systems

NASA Astrophysics Data System (ADS)

White, Christopher David; Zaletel, Michael; Mong, Roger S. K.; Refael, Gil

2018-01-01

We introduce a method "DMT" for approximating density operators of 1D systems that, when combined with a standard framework for time evolution (TEBD), makes possible simulation of the dynamics of strongly thermalizing systems to arbitrary times. We demonstrate that the method performs well for both near-equilibrium initial states (Gibbs states with spatially varying temperatures) and far-from-equilibrium initial states, including quenches across phase transitions and pure states.

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

NASA Astrophysics Data System (ADS)

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

2018-06-01

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

Estimating the dose response relationship for occupational radiation exposure measured with minimum detection level.

PubMed

Xue, Xiaonan; Shore, Roy E; Ye, Xiangyang; Kim, Mimi Y

2004-10-01

Occupational exposures are often recorded as zero when the exposure is below the minimum detection level (BMDL). This can lead to an underestimation of the doses received by individuals and can lead to biased estimates of risk in occupational epidemiologic studies. The extent of the exposure underestimation is increased with the magnitude of the minimum detection level (MDL) and the frequency of monitoring. This paper uses multiple imputation methods to impute values for the missing doses due to BMDL. A Gibbs sampling algorithm is developed to implement the method, which is applied to two distinct scenarios: when dose information is available for each measurement (but BMDL is recorded as zero or some other arbitrary value), or when the dose information available represents the summation of a series of measurements (e.g., only yearly cumulative exposure is available but based on, say, weekly measurements). Then the average of the multiple imputed exposure realizations for each individual is used to obtain an unbiased estimate of the relative risk associated with exposure. Simulation studies are used to evaluate the performance of the estimators. As an illustration, the method is applied to a sample of historical occupational radiation exposure data from the Oak Ridge National Laboratory.

Multilocus lod scores in large pedigrees: combination of exact and approximate calculations.

PubMed

Tong, Liping; Thompson, Elizabeth

2008-01-01

To detect the positions of disease loci, lod scores are calculated at multiple chromosomal positions given trait and marker data on members of pedigrees. Exact lod score calculations are often impossible when the size of the pedigree and the number of markers are both large. In this case, a Markov Chain Monte Carlo (MCMC) approach provides an approximation. However, to provide accurate results, mixing performance is always a key issue in these MCMC methods. In this paper, we propose two methods to improve MCMC sampling and hence obtain more accurate lod score estimates in shorter computation time. The first improvement generalizes the block-Gibbs meiosis (M) sampler to multiple meiosis (MM) sampler in which multiple meioses are updated jointly, across all loci. The second one divides the computations on a large pedigree into several parts by conditioning on the haplotypes of some 'key' individuals. We perform exact calculations for the descendant parts where more data are often available, and combine this information with sampling of the hidden variables in the ancestral parts. Our approaches are expected to be most useful for data on a large pedigree with a lot of missing data. (c) 2007 S. Karger AG, Basel

Multilocus Lod Scores in Large Pedigrees: Combination of Exact and Approximate Calculations

PubMed Central

Tong, Liping; Thompson, Elizabeth

2007-01-01

To detect the positions of disease loci, lod scores are calculated at multiple chromosomal positions given trait and marker data on members of pedigrees. Exact lod score calculations are often impossible when the size of the pedigree and the number of markers are both large. In this case, a Markov Chain Monte Carlo (MCMC) approach provides an approximation. However, to provide accurate results, mixing performance is always a key issue in these MCMC methods. In this paper, we propose two methods to improve MCMC sampling and hence obtain more accurate lod score estimates in shorter computation time. The first improvement generalizes the block-Gibbs meiosis (M) sampler to multiple meiosis (MM) sampler in which multiple meioses are updated jointly, across all loci. The second one divides the computations on a large pedigree into several parts by conditioning on the haplotypes of some ‘key’ individuals. We perform exact calculations for the descendant parts where more data are often available, and combine this information with sampling of the hidden variables in the ancestral parts. Our approaches are expected to be most useful for data on a large pedigree with a lot of missing data. PMID:17934317

Ergodicity of a singly-thermostated harmonic oscillator

NASA Astrophysics Data System (ADS)

Hoover, William Graham; Sprott, Julien Clinton; Hoover, Carol Griswold

2016-03-01

Although Nosé's thermostated mechanics is formally consistent with Gibbs' canonical ensemble, the thermostated Nosé-Hoover (harmonic) oscillator, with its mean kinetic temperature controlled, is far from ergodic. Much of its phase space is occupied by regular conservative tori. Oscillator ergodicity has previously been achieved by controlling two oscillator moments with two thermostat variables. Here we use computerized searches in conjunction with visualization to find singly-thermostated motion equations for the oscillator which are consistent with Gibbs' canonical distribution. Such models are the simplest able to bridge the gap between Gibbs' statistical ensembles and Newtonian single-particle dynamics.

Comparison of different interpolation operators including nonlinear subdivision schemes in the simulation of particle trajectories

NASA Astrophysics Data System (ADS)

Bensiali, Bouchra; Bodi, Kowsik; Ciraolo, Guido; Ghendrih, Philippe; Liandrat, Jacques

2013-03-01

In this work, we compare different interpolation operators in the context of particle tracking with an emphasis on situations involving velocity field with steep gradients. Since, in this case, most classical methods give rise to the Gibbs phenomenon (generation of oscillations near discontinuities), we present new methods for particle tracking based on subdivision schemes and especially on the Piecewise Parabolic Harmonic (PPH) scheme which has shown its advantage in image processing in presence of strong contrasts. First an analytic univariate case with a discontinuous velocity field is considered in order to highlight the effect of the Gibbs phenomenon on trajectory calculation. Theoretical results are provided. Then, we show, regardless of the interpolation method, the need to use a conservative approach when integrating a conservative problem with a velocity field deriving from a potential. Finally, the PPH scheme is applied in a more realistic case of a time-dependent potential encountered in the edge turbulence of magnetically confined plasmas, to compare the propagation of density structures (turbulence bursts) with the dynamics of test particles. This study highlights the difference between particle transport and density transport in turbulent fields.

Application of polyurethane foam as a sorbent for trace metal pre-concentration — A review

NASA Astrophysics Data System (ADS)

Lemos, V. A.; Santos, M. S.; Santos, E. S.; Santos, M. J. S.; dos Santos, W. N. L.; Souza, A. S.; de Jesus, D. S.; das Virgens, C. F.; Carvalho, M. S.; Oleszczuk, N.; Vale, M. G. R.; Welz, B.; Ferreira, S. L. C.

2007-01-01

The first publication on the use of polyurethane foam (PUF) for sorption processes dates back to 1970, and soon after the material was applied for separation processes. The application of PUF as a sorbent for solid phase extraction of inorganic analytes for separation and pre-concentration purposes is reviewed. The physical and chemical characteristics of PUF (polyether and polyester type) are discussed and an introduction to the characterization of these sorption processes using different types of isotherms is given. Separation and pre-concentration methods using unloaded and loaded PUF in batch and on-line procedures with continuous flow and flow injection systems are presented. Methods for the direct solid sampling analysis of the PUF after pre-concentration are discussed as well as approaches for speciation analysis. Thermodynamic proprieties of some extraction processes are evaluated and the interpretation of determined parameters, such as enthalpy, entropy and Gibbs free energy in light of the physico-chemical processes is explained.

Aggression Replacement Training and Childhood Trauma

ERIC Educational Resources Information Center

Amendola, A. Mark; Oliver, Robert W.

2013-01-01

Aggression Replacement Training (ART) was developed by the late Arnold Goldstein of Syracuse University to teach positive alternatives to children and youth with emotional and behavioral problems (Glick & Gibbs, 2011; Goldstein, Glick, & Gibbs, 1998). ART provides cognitive, affective, and behavioral interventions to build competence in…

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

PubMed

Feng, Dong-xia; Nguyen, Anh V

2016-03-01

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

A Unified Graphical Representation of Chemical Thermodynamics and Equilibrium

ERIC Educational Resources Information Center

Hanson, Robert M.

2012-01-01

During the years 1873-1879, J. Willard Gibbs published his now-famous set of articles that form the basis of the current perspective on chemical thermodynamics. The second article of this series, "A Method of Geometrical Representation of the Thermodynamic Properties of Substances by Means of Surfaces," published in 1873, is particularly notable…

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

ERIC Educational Resources Information Center

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

2008-01-01

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

Combinatorial Statistics on Trees and Networks

DTIC Science & Technology

2010-09-29

interaction graph is drawn from the Erdos- Renyi , G(n,p), where each edge is present independently with probability p. For this model we establish a double...special interest is the behavior of Gibbs sampling on the Erdos- Renyi random graph G{n, d/n), where each edge is chosen independently with...which have no counterparts in the coloring setting. Our proof presented here exploits in novel ways the local treelike structure of Erdos- Renyi

Finite-temperature H behaviors in tungsten and molybdenum: first-principles total energy and vibration spectrum calculations

NASA Astrophysics Data System (ADS)

Liu, Yue-Lin; Ding, Fang; Luo, G.-N.; Chen, Chang-An

2017-12-01

We have carried out systematic first-principles total energy and vibration spectrum calculations to investigate the finite-temperature H dissolution behaviors in tungsten and molybdenum, which are considered promising candidates for the first wall in nuclear fusion reactors. The temperature effect is considered by the lattice expansion and phonon vibration. We demonstrate that the H Gibbs energy of formation in both tetrahedral and octahedral interstitial positions depends strongly on the temperature. The H Gibbs energy of formation under one atmosphere of pressure increases significantly with increasing temperature. The phonon vibration contribution plays a decisive role in the H Gibbs energy of formation with the increasing temperature. Using the predicted H Gibbs energy of formation, our calculated H concentrations in both metals are about one or two orders of magnitude lower than the experimental data at temperature range from 900 to 2400 K. Such a discrepancy can be reasonably explained by the defect-capturing effect.

Tightness of the Ising-Kac Model on the Two-Dimensional Torus

NASA Astrophysics Data System (ADS)

Hairer, Martin; Iberti, Massimo

2018-05-01

We consider the sequence of Gibbs measures of Ising models with Kac interaction defined on a periodic two-dimensional discrete torus near criticality. Using the convergence of the Glauber dynamic proven by Mourrat and Weber (Commun Pure Appl Math 70:717-812, 2017) and a method by Tsatsoulis and Weber employed in (arXiv:1609.08447 2016), we show tightness for the sequence of Gibbs measures of the Ising-Kac model near criticality and characterise the law of the limit as the Φ ^4_2 measure on the torus. Our result is very similar to the one obtained by Cassandro et al. (J Stat Phys 78(3):1131-1138, 1995) on Z^2, but our strategy takes advantage of the dynamic, instead of correlation inequalities. In particular, our result covers the whole critical regime and does not require the large temperature/large mass/small coupling assumption present in earlier results.

Measuring effective temperatures in a generalized Gibbs ensemble

NASA Astrophysics Data System (ADS)

Foini, Laura; Gambassi, Andrea; Konik, Robert; Cugliandolo, Leticia F.

2017-05-01

The local physical properties of an isolated quantum statistical system in the stationary state reached long after a quench are generically described by the Gibbs ensemble, which involves only its Hamiltonian and the temperature as a parameter. If the system is instead integrable, additional quantities conserved by the dynamics intervene in the description of the stationary state. The resulting generalized Gibbs ensemble involves a number of temperature-like parameters, the determination of which is practically difficult. Here we argue that in a number of simple models these parameters can be effectively determined by using fluctuation-dissipation relationships between response and correlation functions of natural observables, quantities which are accessible in experiments.

Four competing interactions for models with an uncountable set of spin values on a Cayley tree

NASA Astrophysics Data System (ADS)

Rozikov, U. A.; Haydarov, F. H.

2017-06-01

We consider models with four competing interactions ( external field, nearest neighbor, second neighbor, and three neighbors) and an uncountable set [0, 1] of spin values on the Cayley tree of order two. We reduce the problem of describing the splitting Gibbs measures of the model to the problem of analyzing solutions of a nonlinear integral equation and study some particular cases for Ising and Potts models. We also show that periodic Gibbs measures for the given models either are translation invariant or have the period two. We present examples where periodic Gibbs measures with the period two are not unique.

Swimbladder Allometry of Selected Midwater Fish Species

DTIC Science & Technology

1976-01-05

Gibbs, R. II., Jr., 1971. "Notes on Fishes of the Genus Eustomias ( Stomiatoidei , Melanstomiatidae) in Bermuda Waters, With the Description of...N00140-70-C-0307, Smithsonian Institution. Goodyear, R. H. and R. H. Gibbs, Jr., 1970. "Systematics and Zoogeography of Stomiatoid Fishes of the

How reliable are thermodynamic feasibility statements of biochemical pathways?

PubMed

Maskow, Thomas; von Stockar, Urs

2005-10-20

The driving force for organo- or lithotrophic growth as well as for each step in the metabolic network is the Gibbs reaction energy. For each enzymatic step it must be negative. Thermodynamics contributes therefore to the in-silico description of living systems. It may be used for assessing the feasibility of a given pathway because it provides a further constraint for those pathways which are feasible from the point of view of mass balance calculations (metabolic flux analysis) and the genetic potential of an organism. However, when this constraint was applied to lactic acid fermentation according to a method proposed by Mavrovouniotis (1993a, ISMB 93:273-283) it turned out that an unrealistically wide metabolite concentration range had to be assumed to make this well-known glycolytic pathway thermodynamically feasible. During a search for the reasons of this surprising result the insufficient consideration of the activity coefficients was identified as main cause. However, it is shown in the present contribution that the influence of the activity coefficients on Gibbs reaction energy can be easily taken into account based on the intracellular ionic strength. The uncertainty of the tabulated equilibrium constants and of the apparent standard Gibbs energies derived from them was found to be the second most important reason for the erroneous result of the feasibility analysis. Deviations of intracellular pH from the standard value and bad estimations of currency metabolites, e.g., NAD(+) and NADH, were found to be of lesser importance but not negligible. The pH dependency of Gibbs reaction enthalpy was proved to be easily taken into account. Therefore, the application of thermodynamics for a better in-silico prediction of the behavior of living cell factories calls predominantly for better equilibrium data determined under well defined conditions and also for a more detailed knowledge about the intracellular ionic strength and pH value. Copyright 2005 Wiley Periodicals, Inc.

Are electrostatic potentials between regions of different chemical composition measurable? The Gibbs-Guggenheim Principle reconsidered, extended and its consequences revisited.

PubMed

Pethica, Brian A

2007-12-21

As indicated by Gibbs and made explicit by Guggenheim, the electrical potential difference between two regions of different chemical composition cannot be measured. The Gibbs-Guggenheim Principle restricts the use of classical electrostatics in electrochemical theories as thermodynamically unsound with some few approximate exceptions, notably for dilute electrolyte solutions and concomitant low potentials where the linear limit for the exponential of the relevant Boltzmann distribution applies. The Principle invalidates the widespread use of forms of the Poisson-Boltzmann equation which do not include the non-electrostatic components of the chemical potentials of the ions. From a thermodynamic analysis of the parallel plate electrical condenser, employing only measurable electrical quantities and taking into account the chemical potentials of the components of the dielectric and their adsorption at the surfaces of the condenser plates, an experimental procedure to provide exceptions to the Principle has been proposed. This procedure is now reconsidered and rejected. No other related experimental procedures circumvent the Principle. Widely-used theoretical descriptions of electrolyte solutions, charged surfaces and colloid dispersions which neglect the Principle are briefly discussed. MD methods avoid the limitations of the Poisson-Bolzmann equation. Theoretical models which include the non-electrostatic components of the inter-ion and ion-surface interactions in solutions and colloid systems assume the additivity of dispersion and electrostatic forces. An experimental procedure to test this assumption is identified from the thermodynamics of condensers at microscopic plate separations. The available experimental data from Kelvin probe studies are preliminary, but tend against additivity. A corollary to the Gibbs-Guggenheim Principle is enunciated, and the Principle is restated that for any charged species, neither the difference in electrostatic potential nor the sum of the differences in the non-electrostatic components of the thermodynamic potential difference between regions of different chemical compositions can be measured.

The convolutional differentiator method for numerical modelling of acoustic and elastic wavefields

NASA Astrophysics Data System (ADS)

Zhang, Zhong-Jie; Teng, Ji-Wen; Yang, Ding-Hui

1996-02-01

Based on the techniques of forward and inverse Fourier transformation, the authors discussed the design scheme of ordinary differentiator used and applied in the simulation of acoustic and elastic wavefields in isotropic media respectively. To compress Gibbs effects by truncation effectively, Hanning window is introduced in. The model computation shows that, the convolutional differentiator method has the advantages of rapidity, low requirements of computer’s inner storage and high precision, which is a potential method of numerical simulation.

Development of uncertainty-based work injury model using Bayesian structural equation modelling.

PubMed

Chatterjee, Snehamoy

2014-01-01

This paper proposed a Bayesian method-based structural equation model (SEM) of miners' work injury for an underground coal mine in India. The environmental and behavioural variables for work injury were identified and causal relationships were developed. For Bayesian modelling, prior distributions of SEM parameters are necessary to develop the model. In this paper, two approaches were adopted to obtain prior distribution for factor loading parameters and structural parameters of SEM. In the first approach, the prior distributions were considered as a fixed distribution function with specific parameter values, whereas, in the second approach, prior distributions of the parameters were generated from experts' opinions. The posterior distributions of these parameters were obtained by applying Bayesian rule. The Markov Chain Monte Carlo sampling in the form Gibbs sampling was applied for sampling from the posterior distribution. The results revealed that all coefficients of structural and measurement model parameters are statistically significant in experts' opinion-based priors, whereas, two coefficients are not statistically significant when fixed prior-based distributions are applied. The error statistics reveals that Bayesian structural model provides reasonably good fit of work injury with high coefficient of determination (0.91) and less mean squared error as compared to traditional SEM.

Illustrating Enzyme Inhibition Using Gibbs Energy Profiles

ERIC Educational Resources Information Center

Bearne, Stephen L.

2012-01-01

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

SPERTI Electric Control Building (PER608). Plan, elevations, and details. Gibbs ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

SPERT-I Electric Control Building (PER-608). Plan, elevations, and details. Gibbs and Hill, Inc. 1087-PER-608-S5. Date: August 1956. INEEL index no. 760-0608-00-312-108328 - Idaho National Engineering Laboratory, SPERT-I & Power Burst Facility Area, Scoville, Butte County, ID

The ecosystem of the Mid-Atlantic Ridge at the sub-polar front and Charlie-Gibbs Fracture Zone; ECO-MAR project strategy and description of the sampling programme 2007-2010

NASA Astrophysics Data System (ADS)

Priede, Imants G.; Billett, David S. M.; Brierley, Andrew S.; Hoelzel, A. Rus; Inall, Mark; Miller, Peter I.; Cousins, Nicola J.; Shields, Mark A.; Fujii, Toyonobu

2013-12-01

The ECOMAR project investigated photosynthetically-supported life on the North Mid-Atlantic Ridge (MAR) between the Azores and Iceland focussing on the Charlie-Gibbs Fracture Zone area in the vicinity of the sub-polar front where the North Atlantic Current crosses the MAR. Repeat visits were made to four stations at 2500 m depth on the flanks of the MAR in the years 2007-2010; a pair of northern stations at 54°N in cold water north of the sub-polar front and southern stations at 49°N in warmer water influenced by eddies from the North Atlantic Current. At each station an instrumented mooring was deployed with current meters and sediment traps (100 and 1000 m above the sea floor) to sample downward flux of particulate matter. The patterns of water flow, fronts, primary production and export flux in the region were studied by a combination of remote sensing and in situ measurements. Sonar, tow nets and profilers sampled pelagic fauna over the MAR. Swath bathymetry surveys across the ridge revealed sediment-covered flat terraces parallel to the axis of the MAR with intervening steep rocky slopes. Otter trawls, megacores, baited traps and a suite of tools carried by the R.O.V. Isis including push cores, grabs and a suction device collected benthic fauna. Video and photo surveys were also conducted using the SHRIMP towed vehicle and the R.O.V. Isis. Additional surveying and sampling by landers and R.O.V. focussed on the summit of a seamount (48°44‧N, 28°10‧W) on the western crest of the MAR between the two southern stations.

Thermodynamic properties and crystallization kinetics at high liquid undercooling

NASA Technical Reports Server (NTRS)

Fecht, Hans J.

1990-01-01

The heat capacities of liquid and crystalline Au-Pb-Sb alloys in the glass-forming composition range were measured with droplet emulsion and bulk samples. Based on the measured C(sub p) data, the entropy, enthalpy, and Gibbs free energy functions of the eutectic, solid mixture, and undercooled liquid were determined as a function of undercooling and compared with theoretical predictions. The results indicate an isentropic temperature at 313 + or - 5 K, which agrees well with experimental data for the glass transition. A kinetics analysis of the nucleation undercooling response suggests that the proper choice for the Gibbs free energy change during crystallization is most important in analyzing the nucleation kinetics. By classical nucleation theory, the prefactors obtained, based on a variety of theoretical predictions for the driving force, can differ by six orders of magnitude. If the nucleation rates are extrapolated to high undercooling, the extrapolations based on measured heat capacity data show agreement, whereas the predicted nucleation rates are inconsistent with results from drop tower experiments. The implications for microg experiments are discussed.

Gibbs motif sampling: detection of bacterial outer membrane protein repeats.

PubMed Central

Neuwald, A. F.; Liu, J. S.; Lawrence, C. E.

1995-01-01

The detection and alignment of locally conserved regions (motifs) in multiple sequences can provide insight into protein structure, function, and evolution. A new Gibbs sampling algorithm is described that detects motif-encoding regions in sequences and optimally partitions them into distinct motif models; this is illustrated using a set of immunoglobulin fold proteins. When applied to sequences sharing a single motif, the sampler can be used to classify motif regions into related submodels, as is illustrated using helix-turn-helix DNA-binding proteins. Other statistically based procedures are described for searching a database for sequences matching motifs found by the sampler. When applied to a set of 32 very distantly related bacterial integral outer membrane proteins, the sampler revealed that they share a subtle, repetitive motif. Although BLAST (Altschul SF et al., 1990, J Mol Biol 215:403-410) fails to detect significant pairwise similarity between any of the sequences, the repeats present in these outer membrane proteins, taken as a whole, are highly significant (based on a generally applicable statistical test for motifs described here). Analysis of bacterial porins with known trimeric beta-barrel structure and related proteins reveals a similar repetitive motif corresponding to alternating membrane-spanning beta-strands. These beta-strands occur on the membrane interface (as opposed to the trimeric interface) of the beta-barrel. The broad conservation and structural location of these repeats suggests that they play important functional roles. PMID:8520488

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

NASA Astrophysics Data System (ADS)

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

2012-11-01

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

An inverse problem for Gibbs fields with hard core potential

NASA Astrophysics Data System (ADS)

Koralov, Leonid

2007-05-01

It is well known that for a regular stable potential of pair interaction and a small value of activity one can define the corresponding Gibbs field (a measure on the space of configurations of points in Rd). In this paper we consider a converse problem. Namely, we show that for a sufficiently small constant ρ¯1 and a sufficiently small function ρ¯2(x), x ∈Rd, that is equal to zero in a neighborhood of the origin, there exist a hard core pair potential and a value of activity such that ρ¯1 is the density and ρ¯2 is the pair correlation function of the corresponding Gibbs field.

Measuring effective temperatures in a generalized Gibbs ensemble

DOE PAGES

Foini, Laura; Gambassi, Andrea; Konik, Robert; ...

2017-05-11

The local physical properties of an isolated quantum statistical system in the stationary state reached long after a quench are generically described by the Gibbs ensemble, which involves only its Hamiltonian and the temperature as a parameter. Additional quantities conserved by the dynamics intervene in the description of the stationary state, if the system is instead integrable. The resulting generalized Gibbs ensemble involves a number of temperature-like parameters, the determination of which is practically difficult. We argue that in a number of simple models these parameters can be effectively determined by using fluctuation-dissipation relationships between response and correlation functions ofmore » natural observables, quantities which are accessible in experiments.« less

Near-monodisperse sodium polymethacrylates: characterization by linear salt gradient anion-exchange chromatography

PubMed

Freydank; Krasia; Tiddy; Patrickios

2000-05-01

A family of six near-monodisperse homopolymers of sodium methacrylate (Mn = 1100, 3200, 5500, 7200, 14100, and 21000) is characterized by linear salt gradient anion-exchange chromatography. Although the retention times depend on the initial and final salt concentrations of the gradient, they are almost independent of the molecular weight of poly(sodium methacrylate). This suggests that anion-exchange chromatography is incapable of resolving mixtures of a given polyelectrolyte to their components of various molecular weights, and it is therefore impossible to identify the polydispersity of such a sample using this method. The independence of the retention times from molecular weight is also predicted by a theory based on stoichiometric mass-action ion-exchange. Using this theory and our experimental retention times, the equilibrium anion-exchange constant and the corresponding Gibbs free energy of anion-exchange of the monomer repeat unit are calculated to be around 2.1 and -1.8 kJ/mol, respectively.

Of bugs and birds: Markov Chain Monte Carlo for hierarchical modeling in wildlife research

USGS Publications Warehouse

Link, W.A.; Cam, E.; Nichols, J.D.; Cooch, E.G.

2002-01-01

Markov chain Monte Carlo (MCMC) is a statistical innovation that allows researchers to fit far more complex models to data than is feasible using conventional methods. Despite its widespread use in a variety of scientific fields, MCMC appears to be underutilized in wildlife applications. This may be due to a misconception that MCMC requires the adoption of a subjective Bayesian analysis, or perhaps simply to its lack of familiarity among wildlife researchers. We introduce the basic ideas of MCMC and software BUGS (Bayesian inference using Gibbs sampling), stressing that a simple and satisfactory intuition for MCMC does not require extraordinary mathematical sophistication. We illustrate the use of MCMC with an analysis of the association between latent factors governing individual heterogeneity in breeding and survival rates of kittiwakes (Rissa tridactyla). We conclude with a discussion of the importance of individual heterogeneity for understanding population dynamics and designing management plans.

Constructing Topic Models of Internet of Things for Information Processing

PubMed Central

Xin, Jie; Cui, Zhiming; Zhang, Shukui; He, Tianxu; Li, Chunhua; Huang, Haojing

2014-01-01

Internet of Things (IoT) is regarded as a remarkable development of the modern information technology. There is abundant digital products data on the IoT, linking with multiple types of objects/entities. Those associated entities carry rich information and usually in the form of query records. Therefore, constructing high quality topic hierarchies that can capture the term distribution of each product record enables us to better understand users' search intent and benefits tasks such as taxonomy construction, recommendation systems, and other communications solutions for the future IoT. In this paper, we propose a novel record entity topic model (RETM) for IoT environment that is associated with a set of entities and records and a Gibbs sampling-based algorithm is proposed to learn the model. We conduct extensive experiments on real-world datasets and compare our approach with existing methods to demonstrate the advantage of our approach. PMID:25110737

Probabilistic graphlet transfer for photo cropping.

PubMed

Zhang, Luming; Song, Mingli; Zhao, Qi; Liu, Xiao; Bu, Jiajun; Chen, Chun

2013-02-01

As one of the most basic photo manipulation processes, photo cropping is widely used in the printing, graphic design, and photography industries. In this paper, we introduce graphlets (i.e., small connected subgraphs) to represent a photo's aesthetic features, and propose a probabilistic model to transfer aesthetic features from the training photo onto the cropped photo. In particular, by segmenting each photo into a set of regions, we construct a region adjacency graph (RAG) to represent the global aesthetic feature of each photo. Graphlets are then extracted from the RAGs, and these graphlets capture the local aesthetic features of the photos. Finally, we cast photo cropping as a candidate-searching procedure on the basis of a probabilistic model, and infer the parameters of the cropped photos using Gibbs sampling. The proposed method is fully automatic. Subjective evaluations have shown that it is preferred over a number of existing approaches.

Stochastic sediment property inversion in Shallow Water 06.

PubMed

Michalopoulou, Zoi-Heleni

2017-11-01

Received time-series at a short distance from the source allow the identification of distinct paths; four of these are direct, surface and bottom reflections, and sediment reflection. In this work, a Gibbs sampling method is used for the estimation of the arrival times of these paths and the corresponding probability density functions. The arrival times for the first three paths are then employed along with linearization for the estimation of source range and depth, water column depth, and sound speed in the water. Propagating densities of arrival times through the linearized inverse problem, densities are also obtained for the above parameters, providing maximum a posteriori estimates. These estimates are employed to calculate densities and point estimates of sediment sound speed and thickness using a non-linear, grid-based model. Density computation is an important aspect of this work, because those densities express the uncertainty in the inversion for sediment properties.

Constructing topic models of Internet of Things for information processing.

PubMed

Xin, Jie; Cui, Zhiming; Zhang, Shukui; He, Tianxu; Li, Chunhua; Huang, Haojing

2014-01-01

Internet of Things (IoT) is regarded as a remarkable development of the modern information technology. There is abundant digital products data on the IoT, linking with multiple types of objects/entities. Those associated entities carry rich information and usually in the form of query records. Therefore, constructing high quality topic hierarchies that can capture the term distribution of each product record enables us to better understand users' search intent and benefits tasks such as taxonomy construction, recommendation systems, and other communications solutions for the future IoT. In this paper, we propose a novel record entity topic model (RETM) for IoT environment that is associated with a set of entities and records and a Gibbs sampling-based algorithm is proposed to learn the model. We conduct extensive experiments on real-world datasets and compare our approach with existing methods to demonstrate the advantage of our approach.

First-Year University Chemistry Textbooks' Misrepresentation of Gibbs Energy

ERIC Educational Resources Information Center

Quilez, Juan

2012-01-01

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

Exploring Fourier Series and Gibbs Phenomenon Using Mathematica

ERIC Educational Resources Information Center

Ghosh, Jonaki B.

2011-01-01

This article describes a laboratory module on Fourier series and Gibbs phenomenon which was undertaken by 32 Year 12 students. It shows how the use of CAS played the role of an "amplifier" by making higher level mathematical concepts accessible to students of year 12. Using Mathematica students were able to visualise Fourier series of…

The entropy and Gibbs free energy of formation of the aluminum ion

USGS Publications Warehouse

Hemingway, B.S.; Robie, R.A.

1977-01-01

A reevaluation of the entropy and Gibbs free energy of formation of Al3+(aq) yields -308 ?? 15 J/K??mol and 489.4 ?? 1.4kj/mol for S0298 and ??G0f{hook},298 respectively. The standard electrode potential for aluminum is 1.691 ?? 0.005 volts. ?? 1977.

Surfactant Adsorption: A Revised Physical Chemistry Lab

ERIC Educational Resources Information Center

Bresler, Marc R.; Hagen, John P.

2008-01-01

Many physical chemistry lab courses include an experiment in which students measure surface tension as a function of surfactant concentration. In the traditional experiment, the data are fit to the Gibbs isotherm to determine the molar area for the surfactant, and the critical micelle concentration is used to calculate the Gibbs energy of micelle…

Gibbs energies of transferring triglycine from water into H2O-DMSO solvent

NASA Astrophysics Data System (ADS)

Usacheva, T. R.; Kuz'mina, K. I.; Lan, Pham Thi; Kuz'mina, I. A.; Sharnin, V. A.

2014-08-01

The Gibbs energies of transferring triglycine (3Gly, glycyl-glycyl-glycine) from water into mixtures of water with dimethyl sulfoxide (χDMSO = 0.05, 0.10, and 0.15 mole fractions) at 298.15 K are determined from the interphase distribution. An increased dimethyl sulfoxide (DMSO) concentration in the solvent slightly raises the positive values of Δtr G ○(3Gly), possibly indicating the formation of more stable 3Gly-H2O solvated complexes than ones of 3Gly-DMSO. It is shown that the change in the Gibbs energy of transfer of 3Gly is determined by the enthalpy component. The relationship of 3Gly and 18-crown-6 ether (18C6) solvation's contributions to the change in the Gibbs energy of [3Gly18C6] molecular complex formation in H2O-DMSO solvents is analyzed, and the key role of 3Gly solvation's contribution to the change in the stability of [3Gly18C6] upon moving from H2O to mixtures with DMSO is revealed.

On thermodynamical inconsistency of isotherm equations: Gibbs's thermodynamics.

PubMed

Tóth, József

2003-06-01

It has been proven that all isotherm equations which include the expression 1-Theta contradict the exact Gibbs thermodynamics. These contradictions have been discussed in detail in the case of the Langmuir (L) equation applied to gas/solid (G/S), solid/liquid (S/L), and gas/liquid (G/L) interfaces. In G/S adsorption the L equation can theoretically be applied only at low equilibrium pressures on condition that vg > vs . vg is the molar volume of the adsorbed amount in the gas phase and vs is the same in the Gibbs phase. In S/L and G/L adsorption the L equation is practically applicable only in the domain of very low concentrations. The cause of these contradictions (inconsistencies) is that Gibbs thermodynamics takes excess adsorbed amounts into account; however, the L and other isotherm equations calculate with the absolute adsorbed amount. The two amounts may be practically equal to each other when the limiting conditions mentioned above are fulfilled. It is also discussed how these inconsistent isotherm equations can be transformed into consistent ones.

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

PubMed

Ebenhöh, Oliver; Spelberg, Stephanie

2018-02-19

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

The chemical (not mechanical) paradigm of thermodynamics of colloid and interface science.

PubMed

Kaptay, George

2018-06-01

In the most influential monograph on colloid and interfacial science by Adamson three fundamental equations of "physical chemistry of surfaces" are identified: the Laplace equation, the Kelvin equation and the Gibbs adsorption equation, with a mechanical definition of surface tension by Young as a starting point. Three of them (Young, Laplace and Kelvin) are called here the "mechanical paradigm". In contrary it is shown here that there is only one fundamental equation of the thermodynamics of colloid and interface science and all the above (and other) equations of this field follow as its derivatives. This equation is due to chemical thermodynamics of Gibbs, called here the "chemical paradigm", leading to the definition of surface tension and to 5 rows of equations (see Graphical abstract). The first row is the general equation for interfacial forces, leading to the Young equation, to the Bakker equation and to the Laplace equation, etc. Although the principally wrong extension of the Laplace equation formally leads to the Kelvin equation, using the chemical paradigm it becomes clear that the Kelvin equation is generally incorrect, although it provides right results in special cases. The second row of equations provides equilibrium shapes and positions of phases, including sessile drops of Young, crystals of Wulff, liquids in capillaries, etc. The third row of equations leads to the size-dependent equations of molar Gibbs energies of nano-phases and chemical potentials of their components; from here the corrected versions of the Kelvin equation and its derivatives (the Gibbs-Thomson equation and the Freundlich-Ostwald equation) are derived, including equations for more complex problems. The fourth row of equations is the nucleation theory of Gibbs, also contradicting the Kelvin equation. The fifth row of equations is the adsorption equation of Gibbs, and also the definition of the partial surface tension, leading to the Butler equation and to its derivatives, including the Langmuir equation and the Szyszkowski equation. Positioning the single fundamental equation of Gibbs into the thermodynamic origin of colloid and interface science leads to a coherent set of correct equations of this field. The same provides the chemical (not mechanical) foundation of the chemical (not mechanical) discipline of colloid and interface science. Copyright © 2018 Elsevier B.V. All rights reserved.

A probabilistic model for detecting rigid domains in protein structures.

PubMed

Nguyen, Thach; Habeck, Michael

2016-09-01

Large-scale conformational changes in proteins are implicated in many important biological functions. These structural transitions can often be rationalized in terms of relative movements of rigid domains. There is a need for objective and automated methods that identify rigid domains in sets of protein structures showing alternative conformational states. We present a probabilistic model for detecting rigid-body movements in protein structures. Our model aims to approximate alternative conformational states by a few structural parts that are rigidly transformed under the action of a rotation and a translation. By using Bayesian inference and Markov chain Monte Carlo sampling, we estimate all parameters of the model, including a segmentation of the protein into rigid domains, the structures of the domains themselves, and the rigid transformations that generate the observed structures. We find that our Gibbs sampling algorithm can also estimate the optimal number of rigid domains with high efficiency and accuracy. We assess the power of our method on several thousand entries of the DynDom database and discuss applications to various complex biomolecular systems. The Python source code for protein ensemble analysis is available at: https://github.com/thachnguyen/motion_detection : mhabeck@gwdg.de. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Bayesian Design of Superiority Clinical Trials for Recurrent Events Data with Applications to Bleeding and Transfusion Events in Myelodyplastic Syndrome

PubMed Central

Chen, Ming-Hui; Zeng, Donglin; Hu, Kuolung; Jia, Catherine

2014-01-01

Summary In many biomedical studies, patients may experience the same type of recurrent event repeatedly over time, such as bleeding, multiple infections and disease. In this article, we propose a Bayesian design to a pivotal clinical trial in which lower risk myelodysplastic syndromes (MDS) patients are treated with MDS disease modifying therapies. One of the key study objectives is to demonstrate the investigational product (treatment) effect on reduction of platelet transfusion and bleeding events while receiving MDS therapies. In this context, we propose a new Bayesian approach for the design of superiority clinical trials using recurrent events frailty regression models. Historical recurrent events data from an already completed phase 2 trial are incorporated into the Bayesian design via the partial borrowing power prior of Ibrahim et al. (2012, Biometrics 68, 578–586). An efficient Gibbs sampling algorithm, a predictive data generation algorithm, and a simulation-based algorithm are developed for sampling from the fitting posterior distribution, generating the predictive recurrent events data, and computing various design quantities such as the type I error rate and power, respectively. An extensive simulation study is conducted to compare the proposed method to the existing frequentist methods and to investigate various operating characteristics of the proposed design. PMID:25041037

Efficient algorithms for polyploid haplotype phasing.

PubMed

He, Dan; Saha, Subrata; Finkers, Richard; Parida, Laxmi

2018-05-09

Inference of haplotypes, or the sequence of alleles along the same chromosomes, is a fundamental problem in genetics and is a key component for many analyses including admixture mapping, identifying regions of identity by descent and imputation. Haplotype phasing based on sequencing reads has attracted lots of attentions. Diploid haplotype phasing where the two haplotypes are complimentary have been studied extensively. In this work, we focused on Polyploid haplotype phasing where we aim to phase more than two haplotypes at the same time from sequencing data. The problem is much more complicated as the search space becomes much larger and the haplotypes do not need to be complimentary any more. We proposed two algorithms, (1) Poly-Harsh, a Gibbs Sampling based algorithm which alternatively samples haplotypes and the read assignments to minimize the mismatches between the reads and the phased haplotypes, (2) An efficient algorithm to concatenate haplotype blocks into contiguous haplotypes. Our experiments showed that our method is able to improve the quality of the phased haplotypes over the state-of-the-art methods. To our knowledge, our algorithm for haplotype blocks concatenation is the first algorithm that leverages the shared information across multiple individuals to construct contiguous haplotypes. Our experiments showed that it is both efficient and effective.

Combining the AFLOW GIBBS and elastic libraries to efficiently and robustly screen thermomechanical properties of solids

NASA Astrophysics Data System (ADS)

Toher, Cormac; Oses, Corey; Plata, Jose J.; Hicks, David; Rose, Frisco; Levy, Ohad; de Jong, Maarten; Asta, Mark; Fornari, Marco; Buongiorno Nardelli, Marco; Curtarolo, Stefano

2017-06-01

Thorough characterization of the thermomechanical properties of materials requires difficult and time-consuming experiments. This severely limits the availability of data and is one of the main obstacles for the development of effective accelerated materials design strategies. The rapid screening of new potential materials requires highly integrated, sophisticated, and robust computational approaches. We tackled the challenge by developing an automated, integrated workflow with robust error-correction within the AFLOW framework which combines the newly developed "Automatic Elasticity Library" with the previously implemented GIBBS method. The first extracts the mechanical properties from automatic self-consistent stress-strain calculations, while the latter employs those mechanical properties to evaluate the thermodynamics within the Debye model. This new thermoelastic workflow is benchmarked against a set of 74 experimentally characterized systems to pinpoint a robust computational methodology for the evaluation of bulk and shear moduli, Poisson ratios, Debye temperatures, Grüneisen parameters, and thermal conductivities of a wide variety of materials. The effect of different choices of equations of state and exchange-correlation functionals is examined and the optimum combination of properties for the Leibfried-Schlömann prediction of thermal conductivity is identified, leading to improved agreement with experimental results than the GIBBS-only approach. The framework has been applied to the AFLOW.org data repositories to compute the thermoelastic properties of over 3500 unique materials. The results are now available online by using an expanded version of the REST-API described in the Appendix.

Penalized Weighted Least-Squares Approach to Sinogram Noise Reduction and Image Reconstruction for Low-Dose X-Ray Computed Tomography

PubMed Central

Wang, Jing; Li, Tianfang; Lu, Hongbing; Liang, Zhengrong

2006-01-01

Reconstructing low-dose X-ray CT (computed tomography) images is a noise problem. This work investigated a penalized weighted least-squares (PWLS) approach to address this problem in two dimensions, where the WLS considers first- and second-order noise moments and the penalty models signal spatial correlations. Three different implementations were studied for the PWLS minimization. One utilizes a MRF (Markov random field) Gibbs functional to consider spatial correlations among nearby detector bins and projection views in sinogram space and minimizes the PWLS cost function by iterative Gauss-Seidel algorithm. Another employs Karhunen-Loève (KL) transform to de-correlate data signals among nearby views and minimizes the PWLS adaptively to each KL component by analytical calculation, where the spatial correlation among nearby bins is modeled by the same Gibbs functional. The third one models the spatial correlations among image pixels in image domain also by a MRF Gibbs functional and minimizes the PWLS by iterative successive over-relaxation algorithm. In these three implementations, a quadratic functional regularization was chosen for the MRF model. Phantom experiments showed a comparable performance of these three PWLS-based methods in terms of suppressing noise-induced streak artifacts and preserving resolution in the reconstructed images. Computer simulations concurred with the phantom experiments in terms of noise-resolution tradeoff and detectability in low contrast environment. The KL-PWLS implementation may have the advantage in terms of computation for high-resolution dynamic low-dose CT imaging. PMID:17024831

Third Bose fugacity coefficient in one dimension, as a function of asymptotic quantities

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

Amaya-Tapia, A., E-mail: jano@fis.unam.mx; Larsen, S.Y.; Lassaut, M.

2011-02-15

In one of the very few exact quantum mechanical calculations of fugacity coefficients, [L.R. Dodd, A.M. Gibbs. J. Math. Phys. 15 (1974) 41] obtained b{sub 2} and b{sub 3} for a one dimensional Bose gas, subject to repulsive delta-function interactions, by direct integration of the wave functions. For b{sub 2}, we have shown [A. Amaya-Tapia, S.Y. Larsen, M. Lassaut. Mol. Phys. 103 (2005) 1301-1306. < (arXiv:physics/0405150)>] that Dodd and Gibbs' result can be obtained from a phase shift formalism, if one also includes the contribution of oscillating terms, usually contributing only in one dimension. Now, we develop an exact expressionmore » for b{sub 3}-b{sub 3}{sup 0} (where b{sub 3}{sup 0} is the free particle fugacity coefficient) in terms of sums and differences of three-body eigenphase shifts. Further, we show that if we obtain these eigenphase shifts in a Distorted-Born approximation, then, to first order, we reproduce the leading low temperature behaviour, obtained from an expansion of the twofold integral of Dodd and Gibbs. The contributions of the oscillating terms cancel. The formalism that we propose is not limited to one dimension, but seeks to provide a general method to obtain virial coefficients, fugacity coefficients, in terms of asymptotic quantities. The exact one dimensional results allow us to confirm the validity of our approach in this domain.« less

Re-evaluation of P-T paths across the Himalayan Main Central Thrust

NASA Astrophysics Data System (ADS)

Catlos, E. J.; Harrison, M.; Kelly, E. D.; Ashley, K.; Lovera, O. M.; Etzel, T.; Lizzadro-McPherson, D. J.

2016-12-01

The Main Central Thrust (MCT) is the dominant crustal thickening structure in the Himalayas, juxtaposing high-grade Greater Himalayan Crystalline rocks over the lower-grade Lesser Himalaya Formations. The fault is underlain by a 2 to 12-km-thick sequence of deformed rocks characterized by an apparent inverted metamorphic gradient, termed the MCT shear zone. Garnet-bearing rocks sampled from across the MCT along the Marysandi River in central Nepal contain monazite that decrease in age from Early Miocene (ca. 20 Ma) in the hanging wall to Late Miocene-Pliocene (ca. 7 Ma and 3 Ma) towards structurally lower levels in the shear zone. We obtained high-resolution garnet-zoning pressure-temperature (P-T) paths from 11 of the same rocks used for monazite geochronology using a recently-developed semi-automated Gibbs-free-energy-minimization technique. Quartz-in-garnet Raman barometry refined the locations of the paths. Diffusional re-equilibration of garnet zoning in hanging wall samples prevented accurate path determinations from most Greater Himalayan Crystalline samples, but one that shows a bell-shaped Mn zoning profile shows a slight decrease in P (from 8.2 to 7.6kbar) with increase in T (from 590 to 640ºC). Three MCT shear zone samples were modeled: one yields a simple path increasing in both P and T (6 to 7kbar, 540 to 580ºC); the others yield N-shaped paths that occupy similar P-T space (4 to 5.5 kbar, 500 to 560ºC). Five lower lesser Himalaya garnet-bearing rocks were modeled. One yields a path increasing in both P-T (6 to 7 kbar, 525 to 550ºC) but others show either sharp compression/decompression or N-shape paths (within 4.5-6 kbar and 530-580ºC). The lowermost sample decreases in P (5.5 to 5 kbar) over increasing T (540 to 580°C). No progressive change is seen from one type of path to another within the Lesser Himalayan Formations to the MCT zone. The results using the modeling approach yield lower P-T conditions compared to the Gibbs method and lower core/rim P-T conditions compared to traditional thermometers and barometers. Inclusion barometry suggests that baric estimates from the modeling may be underestimated by 2-4 kbar. Despite uncertainty, path shapes are consistent with a model in which the MCT shear zone experienced a progressive accretion of footwall slivers.

A Multidimensional Item Response Model: Constrained Latent Class Analysis Using the Gibbs Sampler and Posterior Predictive Checks.

ERIC Educational Resources Information Center

Hoijtink, Herbert; Molenaar, Ivo W.

1997-01-01

This paper shows that a certain class of constrained latent class models may be interpreted as a special case of nonparametric multidimensional item response models. Parameters of this latent class model are estimated using an application of the Gibbs sampler, and model fit is investigated using posterior predictive checks. (SLD)

A Generalized Deduction of the Ideal-Solution Model

ERIC Educational Resources Information Center

Leo, Teresa J.; Perez-del-Notario, Pedro; Raso, Miguel A.

2006-01-01

A new general procedure for deriving the Gibbs energy of mixing is developed through general thermodynamic considerations, and the ideal-solution model is obtained as a special particular case of the general one. The deduction of the Gibbs energy of mixing for the ideal-solution model is a rational one and viewed suitable for advanced students who…

Experimental Pragmatics and What Is Said: A Response to Gibbs and Moise.

ERIC Educational Resources Information Center

Nicolle, Steve; Clark, Billy

1999-01-01

Attempted replication of Gibbs and Moise (1997) experiments regarding the recognition of a distinction between what is said and what is implicated. Results showed that, under certain conditions, subject selected implicatures when asked to select the paraphrase best reflecting what a speaker has said. Suggests that results can be explained with the…

On the derivation of linear irreversible thermodynamics for classical fluids

PubMed Central

Theodosopulu, M.; Grecos, A.; Prigogine, I.

1978-01-01

We consider the microscopic derivation of the linearized hydrodynamic equations for an arbitrary simple fluid. Our discussion is based on the concept of hydrodynamical modes, and use is made of the ideas and methods of the theory of subdynamics. We also show that this analysis leads to the Gibbs relation for the entropy of the system. PMID:16592516

Lindeberg theorem for Gibbs-Markov dynamics

NASA Astrophysics Data System (ADS)

Denker, Manfred; Senti, Samuel; Zhang, Xuan

2017-12-01

A dynamical array consists of a family of functions \\{ fn, i: 1≤slant i≤slant k_n, n≥slant 1\\} and a family of initial times \\{τn, i: 1≤slant i≤slant k_n, n≥slant 1\\} . For a dynamical system (X, T) we identify distributional limits for sums of the form for suitable (non-random) constants s_n>0 and an, i\\in { R} . We derive a Lindeberg-type central limit theorem for dynamical arrays. Applications include new central limit theorems for functions which are not locally Lipschitz continuous and central limit theorems for statistical functions of time series obtained from Gibbs-Markov systems. Our results, which hold for more general dynamics, are stated in the context of Gibbs-Markov dynamical systems for convenience.

Generalized Gibbs state with modified Redfield solution: Exact agreement up to second order

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

Thingna, Juzar; Wang, Jian-Sheng; Haenggi, Peter

A novel scheme for the steady state solution of the standard Redfield quantum master equation is developed which yields agreement with the exact result for the corresponding reduced density matrix up to second order in the system-bath coupling strength. We achieve this objective by use of an analytic continuation of the off-diagonal matrix elements of the Redfield solution towards its diagonal limit. Notably, our scheme does not require the provision of yet higher order relaxation tensors. Testing this modified method for a heat bath consisting of a collection of harmonic oscillators we assess that the system relaxes towards its correctmore » coupling-dependent, generalized quantum Gibbs state in second order. We numerically compare our formulation for a damped quantum harmonic system with the nonequilibrium Green's function formalism: we find good agreement at low temperatures for coupling strengths that are even larger than expected from the very regime of validity of the second-order Redfield quantum master equation. Yet another advantage of our method is that it markedly reduces the numerical complexity of the problem; thus, allowing to study efficiently large-sized system Hilbert spaces.« less

Application of recursive Gibbs-Appell formulation in deriving the equations of motion of N-viscoelastic robotic manipulators in 3D space using Timoshenko Beam Theory

NASA Astrophysics Data System (ADS)

Korayem, M. H.; Shafei, A. M.

2013-02-01

The goal of this paper is to describe the application of Gibbs-Appell (G-A) formulation and the assumed modes method to the mathematical modeling of N-viscoelastic link manipulators. The paper's focus is on obtaining accurate and complete equations of motion which encompass the most related structural properties of lightweight elastic manipulators. In this study, two important damping mechanisms, namely, the structural viscoelasticity (Kelvin-Voigt) effect (as internal damping) and the viscous air effect (as external damping) have been considered. To include the effects of shear and rotational inertia, the assumption of Timoshenko beam (TB) theory (TBT) has been applied. Gravity, torsion, and longitudinal elongation effects have also been included in the formulations. To systematically derive the equations of motion and improve the computational efficiency, a recursive algorithm has been used in the modeling of the system. In this algorithm, all the mathematical operations are carried out by only 3×3 and 3×1 matrices. Finally, a computational simulation for a manipulator with two elastic links is performed in order to verify the proposed method.

Q-space truncation and sampling in diffusion spectrum imaging.

PubMed

Tian, Qiyuan; Rokem, Ariel; Folkerth, Rebecca D; Nummenmaa, Aapo; Fan, Qiuyun; Edlow, Brian L; McNab, Jennifer A

2016-12-01

To characterize the q-space truncation and sampling on the spin-displacement probability density function (PDF) in diffusion spectrum imaging (DSI). DSI data were acquired using the MGH-USC connectome scanner (G max  = 300 mT/m) with b max  = 30,000 s/mm 2 , 17 × 17 × 17, 15 × 15 × 15 and 11 × 11 × 11 grids in ex vivo human brains and b max  = 10,000 s/mm 2 , 11 × 11 × 11 grid in vivo. An additional in vivo scan using b max =7,000 s/mm 2 , 11 × 11 × 11 grid was performed with a derated gradient strength of 40 mT/m. PDFs and orientation distribution functions (ODFs) were reconstructed with different q-space filtering and PDF integration lengths, and from down-sampled data by factors of two and three. Both ex vivo and in vivo data showed Gibbs ringing in PDFs, which becomes the main source of artifact in the subsequently reconstructed ODFs. For down-sampled data, PDFs interfere with the first replicas or their ringing, leading to obscured orientations in ODFs. The minimum required q-space sampling density corresponds to a field-of-view approximately equal to twice the mean displacement distance (MDD) of the tissue. The 11 × 11 × 11 grid is suitable for both ex vivo and in vivo DSI experiments. To minimize the effects of Gibbs ringing, ODFs should be reconstructed from unfiltered q-space data with the integration length over the PDF constrained to around the MDD. Magn Reson Med 76:1750-1763, 2016. © 2016 International Society for Magnetic Resonance in Medicine. © 2016 International Society for Magnetic Resonance in Medicine.

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

Das, Chandan K.; Singh, Jayant K., E-mail: jayantks@iitk.ac.in

Three-stage pseudo-supercritical transformation path and multiple-histogram reweighting technique are employed for the determination of solid-liquid coexistence of the Lennard-Jones (12-6) fluid, in a structureless cylindrical pore of radius, R, ranging from 4 to 20 molecular diameters. The Gibbs free energy difference is evaluated using thermodynamic integration method by connecting solid and liquid phases under confinement via one or more intermediate states without any first order phase transition among them. The thermodynamic melting temperature, T{sub m}, is found to oscillate for pore size, R < 8, which is in agreement with the behavior observed for the melting temperature in slit pores.more » However, T{sub m} for almost all pore sizes is less than the bulk case, which is contrary to the behavior seen for the slit pore. The oscillation in T{sub m} decays at around pore radius R = 8, and beyond that shift in the melting temperature with respect to the bulk case is in line with the prediction of the Gibbs-Thomson equation.« less

Quantum chemical approach for condensed-phase thermochemistry (V): Development of rigid-body type harmonic solvation model

NASA Astrophysics Data System (ADS)

Tarumi, Moto; Nakai, Hiromi

2018-05-01

This letter proposes an approximate treatment of the harmonic solvation model (HSM) assuming the solute to be a rigid body (RB-HSM). The HSM method can appropriately estimate the Gibbs free energy for condensed phases even where an ideal gas model used by standard quantum chemical programs fails. The RB-HSM method eliminates calculations for intra-molecular vibrations in order to reduce the computational costs. Numerical assessments indicated that the RB-HSM method can evaluate entropies and internal energies with the same accuracy as the HSM method but with lower calculation costs.

Just Another Gibbs Sampler (JAGS): Flexible Software for MCMC Implementation

ERIC Educational Resources Information Center

Depaoli, Sarah; Clifton, James P.; Cobb, Patrice R.

2016-01-01

A review of the software Just Another Gibbs Sampler (JAGS) is provided. We cover aspects related to history and development and the elements a user needs to know to get started with the program, including (a) definition of the data, (b) definition of the model, (c) compilation of the model, and (d) initialization of the model. An example using a…

An empirical Bayes approach to network recovery using external knowledge.

PubMed

Kpogbezan, Gino B; van der Vaart, Aad W; van Wieringen, Wessel N; Leday, Gwenaël G R; van de Wiel, Mark A

2017-09-01

Reconstruction of a high-dimensional network may benefit substantially from the inclusion of prior knowledge on the network topology. In the case of gene interaction networks such knowledge may come for instance from pathway repositories like KEGG, or be inferred from data of a pilot study. The Bayesian framework provides a natural means of including such prior knowledge. Based on a Bayesian Simultaneous Equation Model, we develop an appealing Empirical Bayes (EB) procedure that automatically assesses the agreement of the used prior knowledge with the data at hand. We use variational Bayes method for posterior densities approximation and compare its accuracy with that of Gibbs sampling strategy. Our method is computationally fast, and can outperform known competitors. In a simulation study, we show that accurate prior data can greatly improve the reconstruction of the network, but need not harm the reconstruction if wrong. We demonstrate the benefits of the method in an analysis of gene expression data from GEO. In particular, the edges of the recovered network have superior reproducibility (compared to that of competitors) over resampled versions of the data. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Quantum-Assisted Learning of Hardware-Embedded Probabilistic Graphical Models

NASA Astrophysics Data System (ADS)

Benedetti, Marcello; Realpe-Gómez, John; Biswas, Rupak; Perdomo-Ortiz, Alejandro

2017-10-01

Mainstream machine-learning techniques such as deep learning and probabilistic programming rely heavily on sampling from generally intractable probability distributions. There is increasing interest in the potential advantages of using quantum computing technologies as sampling engines to speed up these tasks or to make them more effective. However, some pressing challenges in state-of-the-art quantum annealers have to be overcome before we can assess their actual performance. The sparse connectivity, resulting from the local interaction between quantum bits in physical hardware implementations, is considered the most severe limitation to the quality of constructing powerful generative unsupervised machine-learning models. Here, we use embedding techniques to add redundancy to data sets, allowing us to increase the modeling capacity of quantum annealers. We illustrate our findings by training hardware-embedded graphical models on a binarized data set of handwritten digits and two synthetic data sets in experiments with up to 940 quantum bits. Our model can be trained in quantum hardware without full knowledge of the effective parameters specifying the corresponding quantum Gibbs-like distribution; therefore, this approach avoids the need to infer the effective temperature at each iteration, speeding up learning; it also mitigates the effect of noise in the control parameters, making it robust to deviations from the reference Gibbs distribution. Our approach demonstrates the feasibility of using quantum annealers for implementing generative models, and it provides a suitable framework for benchmarking these quantum technologies on machine-learning-related tasks.

Quantum algorithms for Gibbs sampling and hitting-time estimation

DOE PAGES

Chowdhury, Anirban Narayan; Somma, Rolando D.

2017-02-01

In this paper, we present quantum algorithms for solving two problems regarding stochastic processes. The first algorithm prepares the thermal Gibbs state of a quantum system and runs in time almost linear in √Nβ/Ζ and polynomial in log(1/ϵ), where N is the Hilbert space dimension, β is the inverse temperature, Ζ is the partition function, and ϵ is the desired precision of the output state. Our quantum algorithm exponentially improves the dependence on 1/ϵ and quadratically improves the dependence on β of known quantum algorithms for this problem. The second algorithm estimates the hitting time of a Markov chain. Formore » a sparse stochastic matrix Ρ, it runs in time almost linear in 1/(ϵΔ 3/2), where ϵ is the absolute precision in the estimation and Δ is a parameter determined by Ρ, and whose inverse is an upper bound of the hitting time. Our quantum algorithm quadratically improves the dependence on 1/ϵ and 1/Δ of the analog classical algorithm for hitting-time estimation. Finally, both algorithms use tools recently developed in the context of Hamiltonian simulation, spectral gap amplification, and solving linear systems of equations.« less

Learning maximum entropy models from finite-size data sets: A fast data-driven algorithm allows sampling from the posterior distribution.

PubMed

Ferrari, Ulisse

2016-08-01

Maximum entropy models provide the least constrained probability distributions that reproduce statistical properties of experimental datasets. In this work we characterize the learning dynamics that maximizes the log-likelihood in the case of large but finite datasets. We first show how the steepest descent dynamics is not optimal as it is slowed down by the inhomogeneous curvature of the model parameters' space. We then provide a way for rectifying this space which relies only on dataset properties and does not require large computational efforts. We conclude by solving the long-time limit of the parameters' dynamics including the randomness generated by the systematic use of Gibbs sampling. In this stochastic framework, rather than converging to a fixed point, the dynamics reaches a stationary distribution, which for the rectified dynamics reproduces the posterior distribution of the parameters. We sum up all these insights in a "rectified" data-driven algorithm that is fast and by sampling from the parameters' posterior avoids both under- and overfitting along all the directions of the parameters' space. Through the learning of pairwise Ising models from the recording of a large population of retina neurons, we show how our algorithm outperforms the steepest descent method.

About the choice of Gibbs' potential for modelling of FCC ↔ HCP transformation in FeMnSi-based shape memory alloys

NASA Astrophysics Data System (ADS)

Evard, Margarita E.; Volkov, Aleksandr E.; Belyaev, Fedor S.; Ignatova, Anna D.

2018-05-01

The choice of Gibbs' potential for microstructural modeling of FCC ↔ HCP martensitic transformation in FeMn-based shape memory alloys is discussed. Threefold symmetry of the HCP phase is taken into account on specifying internal variables characterizing volume fractions of martensite variants. Constraints imposed on model constants by thermodynamic equilibrium conditions are formulated.

Developpement de techniques numeriques pour l'estimation, la modelisation et la prediction de proprietes thermodynamiques et structurales de systems metalliques a fort ordonnancement chimique

NASA Astrophysics Data System (ADS)

Harvey, Jean-Philippe

In this work, the possibility to calculate and evaluate with a high degree of precision the Gibbs energy of complex multiphase equilibria for which chemical ordering is explicitly and simultaneously considered in the thermodynamic description of solid (short range order and long range order) and liquid (short range order) metallic phases is studied. The cluster site approximation (CSA) and the cluster variation method (CVM) are implemented in a new minimization technique of the Gibbs energy of multicomponent and multiphase systems to describe the thermodynamic behaviour of metallic solid solutions showing strong chemical ordering. The modified quasichemical model in the pair approximation (MQMPA) is also implemented in the new minimization algorithm presented in this work to describe the thermodynamic behaviour of metallic liquid solutions. The constrained minimization technique implemented in this work consists of a sequential quadratic programming technique based on an exact Newton’s method (i.e. the use of exact second derivatives in the determination of the Hessian of the objective function) combined to a line search method to identify a direction of sufficient decrease of the merit function. The implementation of a new algorithm to perform the constrained minimization of the Gibbs energy is justified by the difficulty to identify, in specific cases, the correct multiphase assemblage of a system where the thermodynamic behaviour of the equilibrium phases is described by one of the previously quoted models using the FactSage software (ex.: solid_CSA+liquid_MQMPA; solid1_CSA+solid2_CSA). After a rigorous validation of the constrained Gibbs energy minimization algorithm using several assessed binary and ternary systems found in the literature, the CVM and the CSA models used to describe the energetic behaviour of metallic solid solutions present in systems with key industrial applications such as the Cu-Zr and the Al-Zr systems are parameterized using fully consistent thermodynamic an structural data generated from a Monte Carlo (MC) simulator also implemented in the framework of this project. In this MC simulator, the modified embedded atom model in the second nearest neighbour formalism (MEAM-2NN) is used to describe the cohesive energy of each studied structure. A new Al-Zr MEAM-2NN interatomic potential needed to evaluate the cohesive energy of the condensed phases of this system is presented in this work. The thermodynamic integration (TI) method implemented in the MC simulator allows the evaluation of the absolute Gibbs energy of the considered solid or liquid structures. The original implementation of the TI method allowed us to evaluate theoretically for the first time all the thermodynamic mixing contributions (i.e., mixing enthalpy and mixing entropy contributions) of a metallic liquid (Cu-Zr and Al-Zr) and of a solid solution (face-centered cubic (FCC) Al-Zr solid solution) described by the MEAM-2NN. Thermodynamic and structural data obtained from MC and molecular dynamic simulations are then used to parameterize the CVM for the Al-Zr FCC solid solution and the MQMPA for the Al-Zr and the Cu-Zr liquid phase respectively. The extended thermodynamic study of these systems allow the introduction of a new type of configuration-dependent excess parameters in the definition of the thermodynamic function of solid solutions described by the CVM or the CSA. These parameters greatly improve the precision of these thermodynamic models based on experimental evidences found in the literature. A new parameterization approach of the MQMPA model of metallic liquid solutions is presented throughout this work. In this new approach, calculated pair fractions obtained from MC/MD simulations are taken into account as well as configuration-independent volumetric relaxation effects (regular like excess parameters) in order to parameterize precisely the Gibbs energy function of metallic melts. The generation of a complete set of fully consistent thermodynamic, physical and structural data for solid, liquid, and stoichiometric compounds and the subsequent parameterization of their respective thermodynamic model lead to the first description of the complete Al-Zr phase diagram in the range of composition [0 ≤ XZr ≤ 5 / 9] based on theoretical and fully consistent thermodynamic properties. MC and MD simulations are performed for the Al-Zr system to define for the first time the precise thermodynamic behaviour of the amorphous phase for its entire range of composition. Finally, all the thermodynamic models for the liquid phase, the FCC solid solution and the amorphous phase are used to define conditions based on thermodynamic and volumetric considerations that favor the amorphization of Al-Zr alloys.

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

NASA Technical Reports Server (NTRS)

Isham, M. A.

1992-01-01

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

Strong correlations between the exponent α and the particle number for a Renyi monoatomic gas in Gibbs' statistical mechanics.

PubMed

Plastino, A; Rocca, M C

2017-06-01

Appealing to the 1902 Gibbs formalism for classical statistical mechanics (SM)-the first SM axiomatic theory ever that successfully explained equilibrium thermodynamics-we show that already at the classical level there is a strong correlation between Renyi's exponent α and the number of particles for very simple systems. No reference to heat baths is needed for such a purpose.

GibbsCluster: unsupervised clustering and alignment of peptide sequences.

PubMed

Andreatta, Massimo; Alvarez, Bruno; Nielsen, Morten

2017-07-03

Receptor interactions with short linear peptide fragments (ligands) are at the base of many biological signaling processes. Conserved and information-rich amino acid patterns, commonly called sequence motifs, shape and regulate these interactions. Because of the properties of a receptor-ligand system or of the assay used to interrogate it, experimental data often contain multiple sequence motifs. GibbsCluster is a powerful tool for unsupervised motif discovery because it can simultaneously cluster and align peptide data. The GibbsCluster 2.0 presented here is an improved version incorporating insertion and deletions accounting for variations in motif length in the peptide input. In basic terms, the program takes as input a set of peptide sequences and clusters them into meaningful groups. It returns the optimal number of clusters it identified, together with the sequence alignment and sequence motif characterizing each cluster. Several parameters are available to customize cluster analysis, including adjustable penalties for small clusters and overlapping groups and a trash cluster to remove outliers. As an example application, we used the server to deconvolute multiple specificities in large-scale peptidome data generated by mass spectrometry. The server is available at http://www.cbs.dtu.dk/services/GibbsCluster-2.0. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Density-functional theory computer simulations of CZTS0.25Se0.75 alloy phase diagrams

NASA Astrophysics Data System (ADS)

Chagarov, E.; Sardashti, K.; Haight, R.; Mitzi, D. B.; Kummel, A. C.

2016-08-01

Density-functional theory simulations of CZTS, CZTSe, and CZTS0.25Se0.75 photovoltaic compounds have been performed to investigate the stability of the CZTS0.25Se0.75 alloy vs. decomposition into CZTS, CZTSe, and other secondary compounds. The Gibbs energy for vibrational contributions was estimated by calculating phonon spectra and thermodynamic properties at finite temperatures. It was demonstrated that the CZTS0.25Se0.75 alloy is stabilized not by enthalpy of formation but primarily by the mixing contributions to the Gibbs energy. The Gibbs energy gains/losses for several decomposition reactions were calculated as a function of temperature with/without intermixing and vibration contributions to the Gibbs energy. A set of phase diagrams was built in the multidimensional space of chemical potentials at 300 K and 900 K temperatures to demonstrate alloy stability and boundary compounds at various chemical conditions. It demonstrated for CZTS0.25Se0.75 that the chemical potentials for stability differ between typical processing temperature (˜900 K) and operating temperature (300 K). This implies that as cooling progresses, the flux/concentration of S should be increased in MBE growth to maintain the CZTS0.25Se0.75 in a thermodynamically stable state to minimize phase decomposition.

Temperature-Dependent Estimation of Gibbs Energies Using an Updated Group-Contribution Method.

PubMed

Du, Bin; Zhang, Zhen; Grubner, Sharon; Yurkovich, James T; Palsson, Bernhard O; Zielinski, Daniel C

2018-06-05

Reaction-equilibrium constants determine the metabolite concentrations necessary to drive flux through metabolic pathways. Group-contribution methods offer a way to estimate reaction-equilibrium constants at wide coverage across the metabolic network. Here, we present an updated group-contribution method with 1) additional curated thermodynamic data used in fitting and 2) capabilities to calculate equilibrium constants as a function of temperature. We first collected and curated aqueous thermodynamic data, including reaction-equilibrium constants, enthalpies of reaction, Gibbs free energies of formation, enthalpies of formation, entropy changes of formation of compounds, and proton- and metal-ion-binding constants. Next, we formulated the calculation of equilibrium constants as a function of temperature and calculated the standard entropy change of formation (Δ f S ∘ ) using a model based on molecular properties. The median absolute error in estimating Δ f S ∘ was 0.013 kJ/K/mol. We also estimated magnesium binding constants for 618 compounds using a linear regression model validated against measured data. We demonstrate the improved performance of the current method (8.17 kJ/mol in median absolute residual) over the current state-of-the-art method (11.47 kJ/mol) in estimating the 185 new reactions added in this work. The efforts here fill in gaps for thermodynamic calculations under various conditions, specifically different temperatures and metal-ion concentrations. These, to our knowledge, new capabilities empower the study of thermodynamic driving forces underlying the metabolic function of organisms living under diverse conditions. Copyright © 2018 Biophysical Society. Published by Elsevier Inc. All rights reserved.

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

DOE PAGES

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

2016-03-17

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

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

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

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

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

Unsupervised learning of discriminative edge measures for vehicle matching between nonoverlapping cameras.

PubMed

Shan, Ying; Sawhney, Harpreet S; Kumar, Rakesh

2008-04-01

This paper proposes a novel unsupervised algorithm learning discriminative features in the context of matching road vehicles between two non-overlapping cameras. The matching problem is formulated as a same-different classification problem, which aims to compute the probability of vehicle images from two distinct cameras being from the same vehicle or different vehicle(s). We employ a novel measurement vector that consists of three independent edge-based measures and their associated robust measures computed from a pair of aligned vehicle edge maps. The weight of each measure is determined by an unsupervised learning algorithm that optimally separates the same-different classes in the combined measurement space. This is achieved with a weak classification algorithm that automatically collects representative samples from same-different classes, followed by a more discriminative classifier based on Fisher' s Linear Discriminants and Gibbs Sampling. The robustness of the match measures and the use of unsupervised discriminant analysis in the classification ensures that the proposed method performs consistently in the presence of missing/false features, temporally and spatially changing illumination conditions, and systematic misalignment caused by different camera configurations. Extensive experiments based on real data of over 200 vehicles at different times of day demonstrate promising results.

Quantum Metropolis sampling.

PubMed

Temme, K; Osborne, T J; Vollbrecht, K G; Poulin, D; Verstraete, F

2011-03-03

The original motivation to build a quantum computer came from Feynman, who imagined a machine capable of simulating generic quantum mechanical systems--a task that is believed to be intractable for classical computers. Such a machine could have far-reaching applications in the simulation of many-body quantum physics in condensed-matter, chemical and high-energy systems. Part of Feynman's challenge was met by Lloyd, who showed how to approximately decompose the time evolution operator of interacting quantum particles into a short sequence of elementary gates, suitable for operation on a quantum computer. However, this left open the problem of how to simulate the equilibrium and static properties of quantum systems. This requires the preparation of ground and Gibbs states on a quantum computer. For classical systems, this problem is solved by the ubiquitous Metropolis algorithm, a method that has basically acquired a monopoly on the simulation of interacting particles. Here we demonstrate how to implement a quantum version of the Metropolis algorithm. This algorithm permits sampling directly from the eigenstates of the Hamiltonian, and thus evades the sign problem present in classical simulations. A small-scale implementation of this algorithm should be achievable with today's technology.

Dechlorination Mechanism of CuCl Residue from Zinc Hydrometallurgy by Microwave Roasting

NASA Astrophysics Data System (ADS)

Lu, Shuaidan; Ju, Shaohua; Peng, Jinhui; Zhu, Xiaoping; Srinivasakannan, C.; Zhang, Libo; Tu, Ganfeng

2015-04-01

Removal of chlorine (Cl) from the CuCl residue in the process of zinc hydrometallurgy is of great importance to improve the process economics. The current processing methods result in generation of large quantities of polluted discharge necessitating waste treatment systems. The present work attempts to de-chlorinate the CuCl residue through thermal treatment with application of microwave, towards which the effect of the major experimental factors such as roasting temperature, heating duration and particle size of samples on the process has been investigated. And the changes of Gibbs free energy (ΔG) of the dechlorination reactions are calculated which show that: 1) CuCl can react with H2O and air to produce CuO and HCl(g); 2) CuCl can be oxidized by air into CuO and Cl2 would be released. The tail gas chromatography, XRD and SEM-EDS analysis results of samples before and after microwave roasting verified the thermodynamics study results. Thus, the process of dechlorination by microwave roasting technology is feasible, and the tail gas can be mainly HCl(g) and air which can be absorbed with water and produce hydrochloride easily.

Learning topic models by belief propagation.

PubMed

Zeng, Jia; Cheung, William K; Liu, Jiming

2013-05-01

Latent Dirichlet allocation (LDA) is an important hierarchical Bayesian model for probabilistic topic modeling, which attracts worldwide interest and touches on many important applications in text mining, computer vision and computational biology. This paper represents the collapsed LDA as a factor graph, which enables the classic loopy belief propagation (BP) algorithm for approximate inference and parameter estimation. Although two commonly used approximate inference methods, such as variational Bayes (VB) and collapsed Gibbs sampling (GS), have gained great success in learning LDA, the proposed BP is competitive in both speed and accuracy, as validated by encouraging experimental results on four large-scale document datasets. Furthermore, the BP algorithm has the potential to become a generic scheme for learning variants of LDA-based topic models in the collapsed space. To this end, we show how to learn two typical variants of LDA-based topic models, such as author-topic models (ATM) and relational topic models (RTM), using BP based on the factor graph representations.

Numerical estimation of structure constants in the three-dimensional Ising conformal field theory through Markov chain uv sampler

NASA Astrophysics Data System (ADS)

Herdeiro, Victor

2017-09-01

Herdeiro and Doyon [Phys. Rev. E 94, 043322 (2016), 10.1103/PhysRevE.94.043322] introduced a numerical recipe, dubbed uv sampler, offering precise estimations of the conformal field theory (CFT) data of the planar two-dimensional (2D) critical Ising model. It made use of scale invariance emerging at the critical point in order to sample finite sublattice marginals of the infinite plane Gibbs measure of the model by producing holographic boundary distributions. The main ingredient of the Markov chain Monte Carlo sampler is the invariance under dilation. This paper presents a generalization to higher dimensions with the critical 3D Ising model. This leads to numerical estimations of a subset of the CFT data—scaling weights and structure constants—through fitting of measured correlation functions. The results are shown to agree with the recent most precise estimations from numerical bootstrap methods [Kos, Poland, Simmons-Duffin, and Vichi, J. High Energy Phys. 08 (2016) 036, 10.1007/JHEP08(2016)036].

Temperature lapse rates at restricted thermodynamic equilibrium. Part II: Saturated air and further discussions

NASA Astrophysics Data System (ADS)

Björnbom, Pehr

2016-03-01

In the first part of this work equilibrium temperature profiles in fluid columns with ideal gas or ideal liquid were obtained by numerically minimizing the column energy at constant entropy, equivalent to maximizing column entropy at constant energy. A minimum in internal plus potential energy for an isothermal temperature profile was obtained in line with Gibbs' classical equilibrium criterion. However, a minimum in internal energy alone for adiabatic temperature profiles was also obtained. This led to a hypothesis that the adiabatic lapse rate corresponds to a restricted equilibrium state, a type of state in fact discussed already by Gibbs. In this paper similar numerical results for a fluid column with saturated air suggest that also the saturated adiabatic lapse rate corresponds to a restricted equilibrium state. The proposed hypothesis is further discussed and amended based on the previous and the present numerical results and a theoretical analysis based on Gibbs' equilibrium theory.

A Gibbs point field model for the spatial pattern of coronary capillaries

NASA Astrophysics Data System (ADS)

Karch, R.; Neumann, M.; Neumann, F.; Ullrich, R.; Neumüller, J.; Schreiner, W.

2006-09-01

We propose a Gibbs point field model for the pattern of coronary capillaries in transverse histologic sections from human hearts, based on the physiology of oxygen supply from capillaries to tissue. To specify the potential energy function of the Gibbs point field, we draw on an analogy between the equation of steady-state oxygen diffusion from an array of parallel capillaries to the surrounding tissue and Poisson's equation for the electrostatic potential of a two-dimensional distribution of identical point charges. The influence of factors other than diffusion is treated as a thermal disturbance. On this basis, we arrive at the well-known two-dimensional one-component plasma, a system of identical point charges exhibiting a weak (logarithmic) repulsive interaction that is completely characterized by a single dimensionless parameter. By variation of this parameter, the model is able to reproduce many characteristics of real capillary patterns.

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

NASA Technical Reports Server (NTRS)

Marek, C. John

1996-01-01

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

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

Das, Chandan K.; Singh, Jayant K., E-mail: jayantks@iitk.ac.in

The solid-liquid coexistence of a Lennard-Jones fluid confined in slit pores of variable pore size, H, is studied using molecular dynamics simulations. Three-stage pseudo-supercritical transformation path of Grochola [J. Chem. Phys. 120(5), 2122 (2004)] and multiple histogram reweighting are employed for the confined system, for various pore sizes ranging from 20 to 5 molecular diameters, to compute the solid-liquid coexistence. The Gibbs free energy difference is evaluated using thermodynamic integration method by connecting solid-liquid phases under confinement via one or more intermediate states without any first order phase transition among them. Thermodynamic melting temperature is found to oscillate with wallmore » separation, which is in agreement with the behavior seen for kinetic melting temperature evaluated in an earlier study. However, thermodynamic melting temperature for almost all wall separations is higher than the bulk case, which is contrary to the behavior seen for the kinetic melting temperature. The oscillation founds to decay at around H = 12, and beyond that pore size dependency of the shift in melting point is well represented by the Gibbs-Thompson equation.« less

Computation of thermodynamic equilibrium in systems under stress

NASA Astrophysics Data System (ADS)

Vrijmoed, Johannes C.; Podladchikov, Yuri Y.

2016-04-01

Metamorphic reactions may be partly controlled by the local stress distribution as suggested by observations of phase assemblages around garnet inclusions related to an amphibolite shear zone in granulite of the Bergen Arcs in Norway. A particular example presented in fig. 14 of Mukai et al. [1] is discussed here. A garnet crystal embedded in a plagioclase matrix is replaced on the left side by a high pressure intergrowth of kyanite and quartz and on the right side by chlorite-amphibole. This texture apparently represents disequilibrium. In this case, the minerals adapt to the low pressure ambient conditions only where fluids were present. Alternatively, here we compute that this particular low pressure and high pressure assemblage around a stressed rigid inclusion such as garnet can coexist in equilibrium. To do the computations we developed the Thermolab software package. The core of the software package consists of Matlab functions that generate Gibbs energy of minerals and melts from the Holland and Powell database [2] and aqueous species from the SUPCRT92 database [3]. Most up to date solid solutions are included in a general formulation. The user provides a Matlab script to do the desired calculations using the core functions. Gibbs energy of all minerals, solutions and species are benchmarked versus THERMOCALC, PerpleX [4] and SUPCRT92 and are reproduced within round off computer error. Multi-component phase diagrams have been calculated using Gibbs minimization to benchmark with THERMOCALC and Perple_X. The Matlab script to compute equilibrium in a stressed system needs only two modifications of the standard phase diagram script. Firstly, Gibbs energy of phases considered in the calculation is generated for multiple values of thermodynamic pressure. Secondly, for the Gibbs minimization the proportion of the system at each particular thermodynamic pressure needs to be constrained. The user decides which part of the stress tensor is input as thermodynamic pressure. To compute a case of high and low pressure around a stressed inclusion we first did a Finite Element Method calculation of a rigid inclusion in a viscous matrix under simple shear. From the computed stress distribution we took the local pressure (mean stress) in each grid point of the FEM calculation. This was used as input thermodynamic pressure in the Gibbs minimization and the result showed it is possible to have an equilibrium situation in which chlorite-amphibole is stable in the low pressure domain and kyanite in the high pressure domain of the stress field around the inclusion. Interestingly, the calculation predicts the redistribution of fluid from an average content of fluid in the system. The fluid in equilibrium tends to accumulate in the low pressure areas whereas it leaves the high pressure areas dry. Transport of fluid components occurs not necessarily by fluid flow, but may happen for example by diffusion. We conclude that an apparent disequilibrium texture may be explained by equilibrium under pressure variations, and apparent fluid addition by redistribution of fluid controlled by the local stress distribution. [1] Mukai et al. (2014), Journal of Petrology, 55 (8), p. 1457-1477. [2] Holland and Powell (1998), Journal of Metamorphic Geology, 16, p. 309-343 [3] Johnson et al. (1992), Computers & Geosciences, 18 (7), p. 899-947 [4] Connolly (2005), Earth and Planetary Science Letters, 236, p. 524-541

Heritability of hypothyroidism in the Finnish Hovawart population.

PubMed

Åhlgren, Johanna; Uimari, Pekka

2016-06-07

The Hovawart is a working and companion dog breed of German origin. A few hundred Hovawart dogs are registered annually in Finland. The most common disease with a proposed genetic background in Hovawarts is hypothyroidism. The disease is usually caused by lymphocytic thyroiditis, an autoimmune disorder which destroys the thyroid gland. Hypothyroidism can be treated medically with hormone replacement. Its overall incidence could also be reduced through selection, provided that the trait shows an adequate genetic basis. The aim of this study was to estimate the heritability of hypothyroidism in the Finnish Hovawart population. The pedigree data for the study were provided by the Finnish Kennel Club and the hypothyroidism data by the Finnish Hovawart Club. The data included 4953 dogs born between 1990 and 2010, of which 107 had hypothyroidism and 4846 were unaffected. Prior to the estimation of heritability, we studied the effects of gender, birth year, birth month, and inbreeding on susceptibility to hypothyroidism. Heritability was estimated with the probit model both via restricted maximum likelihood (REML) and Gibbs sampling, using litter and sire of the dog as random effects. None of the studied systematic effects or level of inbreeding had a significant effect on susceptibility to hypothyroidism. The estimated heritability of hypothyroidism varied from 0.47 (SE = 0.18) using REML to 0.62 (SD = 0.21) using Gibbs sampling. Based on our analysis, the heritability of hypothyroidism is moderate to high, suggesting that its prevalence could be decreased through selection. Thus, breeders should notify the breed association of any affected dogs, and their use for breeding should be avoided.

A priori motion models for four-dimensional reconstruction in gated cardiac SPECT

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

Lalush, D.S.; Tsui, B.M.W.; Cui, Lin

1996-12-31

We investigate the benefit of incorporating a priori assumptions about cardiac motion in a fully four-dimensional (4D) reconstruction algorithm for gated cardiac SPECT. Previous work has shown that non-motion-specific 4D Gibbs priors enforcing smoothing in time and space can control noise while preserving resolution. In this paper, we evaluate methods for incorporating known heart motion in the Gibbs prior model. The new model is derived by assigning motion vectors to each 4D voxel, defining the movement of that volume of activity into the neighboring time frames. Weights for the Gibbs cliques are computed based on these {open_quotes}most likely{close_quotes} motion vectors.more » To evaluate, we employ the mathematical cardiac-torso (MCAT) phantom with a new dynamic heart model that simulates the beating and twisting motion of the heart. Sixteen realistically-simulated gated datasets were generated, with noise simulated to emulate a real Tl-201 gated SPECT study. Reconstructions were performed using several different reconstruction algorithms, all modeling nonuniform attenuation and three-dimensional detector response. These include ML-EM with 4D filtering, 4D MAP-EM without prior motion assumption, and 4D MAP-EM with prior motion assumptions. The prior motion assumptions included both the correct motion model and incorrect models. Results show that reconstructions using the 4D prior model can smooth noise and preserve time-domain resolution more effectively than 4D linear filters. We conclude that modeling of motion in 4D reconstruction algorithms can be a powerful tool for smoothing noise and preserving temporal resolution in gated cardiac studies.« less

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

PubMed

Yip, Ngai Yin; Elimelech, Menachem

2012-05-01

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

On the determination of the glass forming ability of AlxZr1-x alloys using molecular dynamics, Monte Carlo simulations, and classical thermodynamics

NASA Astrophysics Data System (ADS)

Harvey, Jean-Philippe; Gheribi, Aïmen E.; Chartrand, Patrice

2012-10-01

In this work, the glass forming ability of Al-Zr alloys is quantified using Monte Carlo (MC) and molecular dynamic (MD) simulations as well as classical thermodynamic calculations. The total energy of each studied structure of the Al-Zr system is described using the modified embedded atom model in the second-nearest-neighbour formalism. The parameterized Al-Zr cross potential which has been extensively validated using available experimental and ab initio data for several solid structures and for the liquid phase is used to evaluate thermodynamic, structural, and physical properties of the glass state and of the fully disordered (FD) face-centered cubic (FCC) solid solution with no short range order (SRO). The local environment of the Al-Zr amorphous phase is identified to be similar to that of a FCC solid structure with short range chemical order. A new approach to model the Gibbs energy of the amorphous phase based on the cluster variation method in the tetrahedron approximation is presented. The Gibbs energy of the fully disordered FCC solid solution with no short range order is determined and compared to the Gibbs energy of the amorphous phase. According to our volumetric and energetic criteria defined in our work to evaluate the possible formation of a glass structure at room temperature and zero pressure, a glass forming range of (0.25≤XZr≤0.75) and of (0.21≤XZr≤0.75) are identified, respectively. All the available quantitative experimental data regarding the amorphization of Al-Zr alloys are compared to the prediction of our MD/MC simulations throughout this study.

Thermodynamic and structural aspects of novel 1,2,4-thiadiazoles in solid and biological mediums.

PubMed

Perlovich, German L; Proshin, Alexey N; Volkova, Tatyana V; Bui, Cong Trinh; Bachurin, Sergey O

2011-10-03

Novel 1,2,4-thiadiazoles were synthesized. Crystal structures of these compounds were solved by X-ray diffraction experiments, and comparative analysis of packing architecture and hydrogen bond networks was carried out. Thermodynamic aspects of sublimation processes of the compounds under study were analyzed using temperature dependencies of vapor pressure. Thermophysical characteristics of the molecular crystals were obtained and compared with the sublimation and structural parameters. The melting points correlate with sublimation Gibbs energies. Moreover, an increase of donor-acceptor interactions in crystal structures leads to growth of Gibbs energy values. Relationships between the melting points and the fragmental contributions to the packing energies were established: R(1)-R(4) fragmental interactions are responsible for the fusion processes of this class of compounds. Solubility and solvation processes of 1,2,4-thiadiazoles in buffer, n-hexane and n-octanol were studied within a wide range of temperature intervals, and their thermodynamic functions were calculated. Specific and nonspecific interactions of molecules resolved in crystals and solvents were estimated and compared. It was found that the melting points correlate with sublimation Gibbs energies. Distribution processes of compounds in buffer/n-octanol and buffer/n-hexane systems (describing different types of membranes) were investigated. Transfer processes of the studied molecules from the buffer to n-octanol/n-hexane phases were analyzed by the diagram method with evaluation of the enthalpic and entropic terms. This approach allowed us to design drug molecules with optimal passive transport properties. Calcium-blocking properties of the substances were evaluated. The trend between the ability to inhibit Glu-Ca uptake and the distribution coefficients in buffer/hexane system was observed.

Revisiting the finite temperature string method for the calculation of reaction tubes and free energies

NASA Astrophysics Data System (ADS)

Vanden-Eijnden, Eric; Venturoli, Maddalena

2009-05-01

An improved and simplified version of the finite temperature string (FTS) method [W. E, W. Ren, and E. Vanden-Eijnden, J. Phys. Chem. B 109, 6688 (2005)] is proposed. Like the original approach, the new method is a scheme to calculate the principal curves associated with the Boltzmann-Gibbs probability distribution of the system, i.e., the curves which are such that their intersection with the hyperplanes perpendicular to themselves coincides with the expected position of the system in these planes (where perpendicular is understood with respect to the appropriate metric). Unlike more standard paths such as the minimum energy path or the minimum free energy path, the location of the principal curve depends on global features of the energy or the free energy landscapes and thereby may remain appropriate in situations where the landscape is rough on the thermal energy scale and/or entropic effects related to the width of the reaction channels matter. Instead of using constrained sampling in hyperplanes as in the original FTS, the new method calculates the principal curve via sampling in the Voronoi tessellation whose generating points are the discretization points along this curve. As shown here, this modification results in greater algorithmic simplicity. As a by-product, it also gives the free energy associated with the Voronoi tessellation. The new method can be applied both in the original Cartesian space of the system or in a set of collective variables. We illustrate FTS on test-case examples and apply it to the study of conformational transitions of the nitrogen regulatory protein C receiver domain using an elastic network model and to the isomerization of solvated alanine dipeptide.

Neural Dynamics as Sampling: A Model for Stochastic Computation in Recurrent Networks of Spiking Neurons

PubMed Central

Buesing, Lars; Bill, Johannes; Nessler, Bernhard; Maass, Wolfgang

2011-01-01

The organization of computations in networks of spiking neurons in the brain is still largely unknown, in particular in view of the inherently stochastic features of their firing activity and the experimentally observed trial-to-trial variability of neural systems in the brain. In principle there exists a powerful computational framework for stochastic computations, probabilistic inference by sampling, which can explain a large number of macroscopic experimental data in neuroscience and cognitive science. But it has turned out to be surprisingly difficult to create a link between these abstract models for stochastic computations and more detailed models of the dynamics of networks of spiking neurons. Here we create such a link and show that under some conditions the stochastic firing activity of networks of spiking neurons can be interpreted as probabilistic inference via Markov chain Monte Carlo (MCMC) sampling. Since common methods for MCMC sampling in distributed systems, such as Gibbs sampling, are inconsistent with the dynamics of spiking neurons, we introduce a different approach based on non-reversible Markov chains that is able to reflect inherent temporal processes of spiking neuronal activity through a suitable choice of random variables. We propose a neural network model and show by a rigorous theoretical analysis that its neural activity implements MCMC sampling of a given distribution, both for the case of discrete and continuous time. This provides a step towards closing the gap between abstract functional models of cortical computation and more detailed models of networks of spiking neurons. PMID:22096452

Limitations in the application of the Gibbs equation to anionic surfactants at the air/water surface: sodium dodecylsulfate and sodium dodecylmonooxyethylenesulfate above and below the CMC.

PubMed

Xu, Hui; Li, Pei Xun; Ma, Kun; Thomas, Robert K; Penfold, Jeffrey; Lu, Jian Ren

2013-07-30

This is a second paper responding to recent papers by Menger et al. and the ensuing discussion about the application of the Gibbs equation to surface tension (ST) data. Using new neutron reflection (NR) measurements on sodium dodecylsulfate (SDS) and sodium dodecylmonooxyethylene sulfate (SLES) above and below their CMCs and with and without added NaCl, in conjunction with the previous ST measurements on SDS by Elworthy and Mysels (EM), we conclude that (i) ST measurements are often seriously compromised by traces of divalent ions, (ii) adsorption does not generally reach saturation at the CMC, making it difficult to obtain the limiting Gibbs slope, and (iii) the significant width of micellization may make it impossible to apply the Gibbs equation in a significant range of concentration below the CMC. Menger et al. proposed ii as a reason for the difficulty of applying the Gibbs equation to ST data. Conclusions i and iii now further emphasize the failings of the ST-Gibbs analysis for determining the limiting coverage at the CMC, especially for SDS. For SDS, adsorption increases above the CMC to a value of 10 × CMC, which is about 25% greater than at the CMC and about the same as at the CMC in the presence of 0.1 M NaCl. In contrast, the adsorption of SLES reaches a limit at the CMC with no further increase up to 10 × CMC, but the addition of 0.1 M NaCl increases the surface excess by 20-25%. The results for SDS are combined with earlier NR results to generate an adsorption isotherm from 2 to 100 mM. The NR results for SDS are compared to the definitive surface tension (ST) measurements of EM, and the surface excesses agree over the range where they can safely be compared, from 2 to 6 mM. This confirms that the anomalous decrease in the slope of EM's σ - ln c curve between 6 mM and the CMC at 8.2 mM results from changes in activity associated with a significant width of micellization. This anomaly shows that it is impossible to apply the Gibbs equation usefully from 6 to 8.2 mM (i.e., the lack of knowledge of the activity in this range is the same as above the CMC (8.2 mM)). It was found that a mislabeling of the original data in EM may have prevented the use of this excellent ST data as a standard by other authors. Although NR and ST results for SDS in the absence of added electrolyte show that the discrepancies can be rationalized, ST is generally shown to be less accurate and more vulnerable to impurities, especially divalent ions, than NR. The radiotracer technique is shown to be less accurate than ST-Gibbs in that the four radiotracer measurements of the surface excess are consistent neither with each other nor with ST and NR. It is also shown that radiotracer results on aerosol-OT are likely to be incorrect. Application of the mass action (MA) model of micellization to the ST curves of SDS and SLES through and above the CMC shows that they can be explained by this model and that they depend on the degree of dissociation of the micelle, which leads to a larger change in the mean activity, and hence the adsorption, for the more highly dissociated SDS micelles than for SLES. Previous measurements of the activity of SDS above the CMC were found to be semiquantitatively consistent with the change in mean activity predicted by the MA model but inconsistent with the combined ST, NR, and Gibbs equation results.

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

NASA Technical Reports Server (NTRS)

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

1979-01-01

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

Generating Natural Language Under Pragmatic Constraints.

DTIC Science & Technology

1987-03-01

central issue, Carter’s loss. concentrating on ,more, pleasant aspects. But what would happen in an extreme case ’.’ what if you, a Carter supporter. are...In [Cohen 78], Cohen studied the effect of the hearer’s knowledge on the selection of appropriate speech act (say, REQUEST vs INFORM OF WANT...utterances is studied in [Clark & Carlson 81], [Clark & Murphy 82]; [Gibbs 79] and [Gibbs 81] discuss the effects of context on the processing of indirect

Air Force Logistics Command DCS/Materiel Management 1988-9 Master Plan

DTIC Science & Technology

1988-10-01

MMMAI, AUTOVON 787-2587 Member: Mr James Gibbs, HQ AFLC/MMMES, AUTOVON 787-3407 PROJECT SPONSOR: Mr Steve Stewart, HQ AFLC/MMME, AUTOVON 787-5280 HQ...AFLC OPR: Mr James Gibbs, HQ AFLC/MMMES, AUTOVON 787-3407 PROBLEM STATEMENT: Item managers do not have a procedure to analyze the economic costs and/or...513) 429-0055 Contractor: The Analytic Sciences Corporation (Contact) Mr Rich Mabe , (513) 426-1040 PROJECT SPONSOR: Lt Col Michael Williams, HQ USAF

Using Theoretical Descriptors in Structural Activity Relationships: 4. Molecular Orbital Basicity and Electrostatic Basicity

DTIC Science & Technology

1988-11-01

rates.6 The Hammet equation , also called the Linear Free Energy Relationship (LFER) because of the relationship of the Gibb’s Free Energy to the... equations for numerous biological and physicochemical properties. Linear Solvation Enery Relationship (LSER), a sub-set of QSAR have been used by...originates from thermodynamics, where Hammet recognized the relationship of structure to the Gibb’s Free Energy, and ultimately to equilibria and reaction

Density-functional theory computer simulations of CZTS{sub 0.25}Se{sub 0.75} alloy phase diagrams

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

Chagarov, E.; Sardashti, K.; Kummel, A. C.

2016-08-14

Density-functional theory simulations of CZTS, CZTSe, and CZTS{sub 0.25}Se{sub 0.75} photovoltaic compounds have been performed to investigate the stability of the CZTS{sub 0.25}Se{sub 0.75} alloy vs. decomposition into CZTS, CZTSe, and other secondary compounds. The Gibbs energy for vibrational contributions was estimated by calculating phonon spectra and thermodynamic properties at finite temperatures. It was demonstrated that the CZTS{sub 0.25}Se{sub 0.75} alloy is stabilized not by enthalpy of formation but primarily by the mixing contributions to the Gibbs energy. The Gibbs energy gains/losses for several decomposition reactions were calculated as a function of temperature with/without intermixing and vibration contributions to themore » Gibbs energy. A set of phase diagrams was built in the multidimensional space of chemical potentials at 300 K and 900 K temperatures to demonstrate alloy stability and boundary compounds at various chemical conditions. It demonstrated for CZTS{sub 0.25}Se{sub 0.75} that the chemical potentials for stability differ between typical processing temperature (∼900 K) and operating temperature (300 K). This implies that as cooling progresses, the flux/concentration of S should be increased in MBE growth to maintain the CZTS{sub 0.25}Se{sub 0.75} in a thermodynamically stable state to minimize phase decomposition.« less

Analysis of Gibbs monolayer adsorbed at the toluene/water interface by UV-visible partial internal reflection spectrometry.

PubMed

Moriya, Yoshio; Hasegawa, Takeshi; Okada, Tetsuo; Ogawa, Nobuaki; Kawai, Erika; Abe, Kosuke; Ogasawara, Masataka; Kato, Sumio; Nakata, Shinichi

2006-11-15

Gibbs monolayers of lipophilic tetraphenylporphyrinatomanganese(III) and hydrophilic diacid of meso-tetrakis(4-sulfonatopheny)porphyrin adsorbed at the liquid-liquid interface have been analyzed by UV-visible external reflection (ER) and partial internal reflection (PIR) spectra measured at different angles of incidence. The angle-dependent ER and PIR spectra over the Brewster angles (thetaERB and thetaIRB) have readily been measured at the toluene/water interface. As preliminarily expected in our previous study, the present study has first proved that the reflection-absorbance of UV-visible PIR spectra quantitatively agrees with the theoretical calculations for the Gibbs monolayer over thetaIRB. In addition, it has also been proved that the absorbance of the PIR spectra is greatly enhanced in comparison to that of the ATR spectra. The enhancement is caused by an optical effect in the monolayer sandwiched between two phases of toluene and water that have different but refractive indices close to each other. This optical enhancement requires an optically perfect contact between the phases, which is difficult to prepare for a solid-solid contact. At the liquid/liquid interface, however, an ideal optical contact is easily realized, which makes the enhancement as much as the theoretical expectation. The PIR spectrometry will be recognized to be a new high-sensitive analytical tool to study Gibbs monolayer at the liquid/liquid interface.

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

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

Lin, Shu-Kun

1996-12-31

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

Passive Sampling for Indoor and Outdoor Exposures to Chlorpyrifos, Azinphos-Methyl, and Oxygen Analogs in a Rural Agricultural Community

PubMed Central

Gibbs, Jenna L.; Yost, Michael G.; Negrete, Maria; Fenske, Richard A.

2016-01-01

Background: Recent studies have highlighted the increased potency of oxygen analogs of organophosphorus pesticides. These pesticides and oxygen analogs have previously been identified in the atmosphere following spray applications in the states of California and Washington. Objectives: We used two passive sampling methods to measure levels of the ollowing organophosphorus pesticides: chlorpyrifos, azinphos-methyl, and their oxygen analogs at 14 farmworker and 9 non-farmworker households in an agricultural region of central Washington State in 2011. Methods: The passive methods included polyurethane foam passive air samplers deployed outdoors and indoors and polypropylene deposition plates deployed indoors. We collected cumulative monthly samples during the pesticide application seasons and during the winter season as a control. Results: Monthly outdoor air concentrations ranged from 9.2 to 199 ng/m3 for chlorpyrifos, 0.03 to 20 ng/m3 for chlorpyrifos-oxon, < LOD (limit of detection) to 7.3 ng/m3 for azinphos-methyl, and < LOD to 0.8 ng/m3 for azinphos-methyl-oxon. Samples from proximal households (≤ 250 m) had significantly higher outdoor air concentrations of chlorpyrifos, chlorpyrifos-oxon, and azinphos-methyl than did samples from nonproximal households (p ≤ 0.02). Overall, indoor air concentrations were lower than outdoors. For example, all outdoor air samples for chlorpyrifos and 97% of samples for azinphos-methyl were > LOD. Indoors, only 78% of air samples for chlorpyrifos and 35% of samples for azinphos-methyl were > LOD. Samples from farmworker households had higher indoor air concentrations of both pesticides than did samples from non-farmworker households. Mean indoor and outdoor air concentration ratios for chlorpyrifos and azinphos-methyl were 0.17 and 0.44, respectively. Conclusions: We identified higher levels in air and on surfaces at both proximal and farmworker households. Our findings further confirm the presence of pesticides and their oxygen analogs in air and highlight their potential for infiltration of indoor living environments. Citation: Gibbs JL, Yost MG, Negrete M, Fenske RA. 2017. Passive sampling for indoor and outdoor exposures to chlorpyrifos, azinphos-methyl, and oxygen analogs in a rural agricultural community. Environ Health Perspect 125:333–341; http://dx.doi.org/10.1289/EHP425 PMID:27517732

Passive Sampling for Indoor and Outdoor Exposures to Chlorpyrifos, Azinphos-Methyl, and Oxygen Analogs in a Rural Agricultural Community.

PubMed

Gibbs, Jenna L; Yost, Michael G; Negrete, Maria; Fenske, Richard A

2017-03-01

Recent studies have highlighted the increased potency of oxygen analogs of organophosphorus pesticides. These pesticides and oxygen analogs have previously been identified in the atmosphere following spray applications in the states of California and Washington. We used two passive sampling methods to measure levels of the ollowing organophosphorus pesticides: chlorpyrifos, azinphos-methyl, and their oxygen analogs at 14 farmworker and 9 non-farmworker households in an agricultural region of central Washington State in 2011. The passive methods included polyurethane foam passive air samplers deployed outdoors and indoors and polypropylene deposition plates deployed indoors. We collected cumulative monthly samples during the pesticide application seasons and during the winter season as a control. Monthly outdoor air concentrations ranged from 9.2 to 199 ng/m 3 for chlorpyrifos, 0.03 to 20 ng/m 3 for chlorpyrifos-oxon, < LOD (limit of detection) to 7.3 ng/m 3 for azinphos-methyl, and < LOD to 0.8 ng/m 3 for azinphos-methyl-oxon. Samples from proximal households (≤ 250 m) had significantly higher outdoor air concentrations of chlorpyrifos, chlorpyrifos-oxon, and azinphos-methyl than did samples from nonproximal households ( p ≤ 0.02). Overall, indoor air concentrations were lower than outdoors. For example, all outdoor air samples for chlorpyrifos and 97% of samples for azinphos-methyl were > LOD. Indoors, only 78% of air samples for chlorpyrifos and 35% of samples for azinphos-methyl were > LOD. Samples from farmworker households had higher indoor air concentrations of both pesticides than did samples from non-farmworker households. Mean indoor and outdoor air concentration ratios for chlorpyrifos and azinphos-methyl were 0.17 and 0.44, respectively. We identified higher levels in air and on surfaces at both proximal and farmworker households. Our findings further confirm the presence of pesticides and their oxygen analogs in air and highlight their potential for infiltration of indoor living environments. Citation: Gibbs JL, Yost MG, Negrete M, Fenske RA. 2017. Passive sampling for indoor and outdoor exposures to chlorpyrifos, azinphos-methyl, and oxygen analogs in a rural agricultural community. Environ Health Perspect 125:333-341; http://dx.doi.org/10.1289/EHP425.

ECG fiducial point extraction using switching Kalman filter.

PubMed

Akhbari, Mahsa; Ghahjaverestan, Nasim Montazeri; Shamsollahi, Mohammad B; Jutten, Christian

2018-04-01

In this paper, we propose a novel method for extracting fiducial points (FPs) of the beats in electrocardiogram (ECG) signals using switching Kalman filter (SKF). In this method, according to McSharry's model, ECG waveforms (P-wave, QRS complex and T-wave) are modeled with Gaussian functions and ECG baselines are modeled with first order auto regressive models. In the proposed method, a discrete state variable called "switch" is considered that affects only the observation equations. We denote a mode as a specific observation equation and switch changes between 7 modes and corresponds to different segments of an ECG beat. At each time instant, the probability of each mode is calculated and compared among two consecutive modes and a path is estimated, which shows the relation of each part of the ECG signal to the mode with the maximum probability. ECG FPs are found from the estimated path. For performance evaluation, the Physionet QT database is used and the proposed method is compared with methods based on wavelet transform, partially collapsed Gibbs sampler (PCGS) and extended Kalman filter. For our proposed method, the mean error and the root mean square error across all FPs are 2 ms (i.e. less than one sample) and 14 ms, respectively. These errors are significantly smaller than those obtained using other methods. The proposed method achieves lesser RMSE and smaller variability with respect to others. Copyright © 2018 Elsevier B.V. All rights reserved.

Methods for thermodynamic evaluation of battery state of health

DOEpatents

Yazami, Rachid; McMenamin, Joseph; Reynier, Yvan; Fultz, Brent T

2013-05-21

Described are systems and methods for accurately characterizing thermodynamic and materials properties of electrodes and battery systems and for characterizing the state of health of electrodes and battery systems. Measurement of physical attributes of electrodes and batteries corresponding to thermodynamically stabilized electrode conditions permit determination of thermodynamic parameters, including state functions such as the Gibbs free energy, enthalpy and entropy of electrode/electrochemical cell reactions, that enable prediction of important performance attributes of electrode materials and battery systems, such as energy, power density, current rate, cycle life and state of health. Also provided are systems and methods for charging a battery according to its state of health.

Methods and systems for thermodynamic evaluation of battery state of health

DOEpatents

Yazami, Rachid; McMenamin, Joseph; Reynier, Yvan; Fultz, Brent T

2014-12-02

Described are systems and methods for accurately characterizing thermodynamic and materials properties of electrodes and battery systems and for characterizing the state of health of electrodes and battery systems. Measurement of physical attributes of electrodes and batteries corresponding to thermodynamically stabilized electrode conditions permit determination of thermodynamic parameters, including state functions such as the Gibbs free energy, enthalpy and entropy of electrode/electrochemical cell reactions, that enable prediction of important performance attributes of electrode materials and battery systems, such as energy, power density, current rate, cycle life and state of health. Also provided are systems and methods for charging a battery according to its state of health.

A stochastic simulation method for the assessment of resistive random access memory retention reliability

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

Berco, Dan, E-mail: danny.barkan@gmail.com; Tseng, Tseung-Yuen, E-mail: tseng@cc.nctu.edu.tw

This study presents an evaluation method for resistive random access memory retention reliability based on the Metropolis Monte Carlo algorithm and Gibbs free energy. The method, which does not rely on a time evolution, provides an extremely efficient way to compare the relative retention properties of metal-insulator-metal structures. It requires a small number of iterations and may be used for statistical analysis. The presented approach is used to compare the relative robustness of a single layer ZrO{sub 2} device with a double layer ZnO/ZrO{sub 2} one, and obtain results which are in good agreement with experimental data.

Accurate age estimation in small-scale societies

PubMed Central

Smith, Daniel; Gerbault, Pascale; Dyble, Mark; Migliano, Andrea Bamberg; Thomas, Mark G.

2017-01-01

Precise estimation of age is essential in evolutionary anthropology, especially to infer population age structures and understand the evolution of human life history diversity. However, in small-scale societies, such as hunter-gatherer populations, time is often not referred to in calendar years, and accurate age estimation remains a challenge. We address this issue by proposing a Bayesian approach that accounts for age uncertainty inherent to fieldwork data. We developed a Gibbs sampling Markov chain Monte Carlo algorithm that produces posterior distributions of ages for each individual, based on a ranking order of individuals from youngest to oldest and age ranges for each individual. We first validate our method on 65 Agta foragers from the Philippines with known ages, and show that our method generates age estimations that are superior to previously published regression-based approaches. We then use data on 587 Agta collected during recent fieldwork to demonstrate how multiple partial age ranks coming from multiple camps of hunter-gatherers can be integrated. Finally, we exemplify how the distributions generated by our method can be used to estimate important demographic parameters in small-scale societies: here, age-specific fertility patterns. Our flexible Bayesian approach will be especially useful to improve cross-cultural life history datasets for small-scale societies for which reliable age records are difficult to acquire. PMID:28696282

Accurate age estimation in small-scale societies.

PubMed

Diekmann, Yoan; Smith, Daniel; Gerbault, Pascale; Dyble, Mark; Page, Abigail E; Chaudhary, Nikhil; Migliano, Andrea Bamberg; Thomas, Mark G

2017-08-01

Precise estimation of age is essential in evolutionary anthropology, especially to infer population age structures and understand the evolution of human life history diversity. However, in small-scale societies, such as hunter-gatherer populations, time is often not referred to in calendar years, and accurate age estimation remains a challenge. We address this issue by proposing a Bayesian approach that accounts for age uncertainty inherent to fieldwork data. We developed a Gibbs sampling Markov chain Monte Carlo algorithm that produces posterior distributions of ages for each individual, based on a ranking order of individuals from youngest to oldest and age ranges for each individual. We first validate our method on 65 Agta foragers from the Philippines with known ages, and show that our method generates age estimations that are superior to previously published regression-based approaches. We then use data on 587 Agta collected during recent fieldwork to demonstrate how multiple partial age ranks coming from multiple camps of hunter-gatherers can be integrated. Finally, we exemplify how the distributions generated by our method can be used to estimate important demographic parameters in small-scale societies: here, age-specific fertility patterns. Our flexible Bayesian approach will be especially useful to improve cross-cultural life history datasets for small-scale societies for which reliable age records are difficult to acquire.

Probabilistic modelling of flood events using the entropy copula

NASA Astrophysics Data System (ADS)

Li, Fan; Zheng, Qian

2016-11-01

The estimation of flood frequency is vital for the flood control strategies and hydraulic structure design. Generating synthetic flood events according to statistical properties of observations is one of plausible methods to analyze the flood frequency. Due to the statistical dependence among the flood event variables (i.e. the flood peak, volume and duration), a multidimensional joint probability estimation is required. Recently, the copula method is widely used for multivariable dependent structure construction, however, the copula family should be chosen before application and the choice process is sometimes rather subjective. The entropy copula, a new copula family, employed in this research proposed a way to avoid the relatively subjective process by combining the theories of copula and entropy. The analysis shows the effectiveness of the entropy copula for probabilistic modelling the flood events of two hydrological gauges, and a comparison of accuracy with the popular copulas was made. The Gibbs sampling technique was applied for trivariate flood events simulation in order to mitigate the calculation difficulties of extending to three dimension directly. The simulation results indicate that the entropy copula is a simple and effective copula family for trivariate flood simulation.

Model-based Clustering of Categorical Time Series with Multinomial Logit Classification

NASA Astrophysics Data System (ADS)

Frühwirth-Schnatter, Sylvia; Pamminger, Christoph; Winter-Ebmer, Rudolf; Weber, Andrea

2010-09-01

A common problem in many areas of applied statistics is to identify groups of similar time series in a panel of time series. However, distance-based clustering methods cannot easily be extended to time series data, where an appropriate distance-measure is rather difficult to define, particularly for discrete-valued time series. Markov chain clustering, proposed by Pamminger and Frühwirth-Schnatter [6], is an approach for clustering discrete-valued time series obtained by observing a categorical variable with several states. This model-based clustering method is based on finite mixtures of first-order time-homogeneous Markov chain models. In order to further explain group membership we present an extension to the approach of Pamminger and Frühwirth-Schnatter [6] by formulating a probabilistic model for the latent group indicators within the Bayesian classification rule by using a multinomial logit model. The parameters are estimated for a fixed number of clusters within a Bayesian framework using an Markov chain Monte Carlo (MCMC) sampling scheme representing a (full) Gibbs-type sampler which involves only draws from standard distributions. Finally, an application to a panel of Austrian wage mobility data is presented which leads to an interesting segmentation of the Austrian labour market.

Hydro-geochemistry and application of water quality index (WQI) for groundwater quality assessment, Anna Nagar, part of Chennai City, Tamil Nadu, India

NASA Astrophysics Data System (ADS)

Krishna kumar, S.; Logeshkumaran, A.; Magesh, N. S.; Godson, Prince S.; Chandrasekar, N.

2015-12-01

In the present study, the geochemical characteristics of groundwater and drinking water quality has been studied. 24 groundwater samples were collected and analyzed for pH, electrical conductivity, total dissolved solids, carbonate, bicarbonate, chloride, sulphate, nitrate, calcium, magnesium, sodium, potassium and total hardness. The results were evaluated and compared with WHO and BIS water quality standards. The studied results reveal that the groundwater is fresh to brackish and moderately high to hard in nature. Na and Cl are dominant ions among cations and anions. Chloride, calcium and magnesium ions are within the allowable limit except few samples. According to Gibbs diagram, the predominant samples fall in the rock-water interaction dominance and evaporation dominance field. The piper trilinear diagram shows that groundwater samples are Na-Cl and mixed CaMgCl type. Based on the WQI results majority of the samples are falling under excellent to good category and suitable for drinking water purposes.

Biochemical thermodynamics: applications of Mathematica.

PubMed

Alberty, Robert A

2006-01-01

The most efficient way to store thermodynamic data on enzyme-catalyzed reactions is to use matrices of species properties. Since equilibrium in enzyme-catalyzed reactions is reached at specified pH values, the thermodynamics of the reactions is discussed in terms of transformed thermodynamic properties. These transformed thermodynamic properties are complicated functions of temperature, pH, and ionic strength that can be calculated from the matrices of species values. The most important of these transformed thermodynamic properties is the standard transformed Gibbs energy of formation of a reactant (sum of species). It is the most important because when this function of temperature, pH, and ionic strength is known, all the other standard transformed properties can be calculated by taking partial derivatives. The species database in this package contains data matrices for 199 reactants. For 94 of these reactants, standard enthalpies of formation of species are known, and so standard transformed Gibbs energies, standard transformed enthalpies, standard transformed entropies, and average numbers of hydrogen atoms can be calculated as functions of temperature, pH, and ionic strength. For reactions between these 94 reactants, the changes in these properties can be calculated over a range of temperatures, pHs, and ionic strengths, and so can apparent equilibrium constants. For the other 105 reactants, only standard transformed Gibbs energies of formation and average numbers of hydrogen atoms at 298.15 K can be calculated. The loading of this package provides functions of pH and ionic strength at 298.15 K for standard transformed Gibbs energies of formation and average numbers of hydrogen atoms for 199 reactants. It also provides functions of temperature, pH, and ionic strength for the standard transformed Gibbs energies of formation, standard transformed enthalpies of formation, standard transformed entropies of formation, and average numbers of hydrogen atoms for 94 reactants. Thus loading this package makes available 774 mathematical functions for these properties. These functions can be added and subtracted to obtain changes in these properties in biochemical reactions and apparent equilibrium constants.

Learning Maximal Entropy Models from finite size datasets: a fast Data-Driven algorithm allows to sample from the posterior distribution

NASA Astrophysics Data System (ADS)

Ferrari, Ulisse

A maximal entropy model provides the least constrained probability distribution that reproduces experimental averages of an observables set. In this work we characterize the learning dynamics that maximizes the log-likelihood in the case of large but finite datasets. We first show how the steepest descent dynamics is not optimal as it is slowed down by the inhomogeneous curvature of the model parameters space. We then provide a way for rectifying this space which relies only on dataset properties and does not require large computational efforts. We conclude by solving the long-time limit of the parameters dynamics including the randomness generated by the systematic use of Gibbs sampling. In this stochastic framework, rather than converging to a fixed point, the dynamics reaches a stationary distribution, which for the rectified dynamics reproduces the posterior distribution of the parameters. We sum up all these insights in a ``rectified'' Data-Driven algorithm that is fast and by sampling from the parameters posterior avoids both under- and over-fitting along all the directions of the parameters space. Through the learning of pairwise Ising models from the recording of a large population of retina neurons, we show how our algorithm outperforms the steepest descent method. This research was supported by a Grant from the Human Brain Project (HBP CLAP).

Combinatorial Study of the Li-Ni-Mn-Co Oxide Pseudoquaternary System for Use in Li-Ion Battery Materials Research.

PubMed

Brown, Colby R; McCalla, Eric; Watson, Cody; Dahn, J R

2015-06-08

Combinatorial synthesis has proven extremely effective in screening for new battery materials for Li-ion battery electrodes. Here, a study in the Li-Ni-Mn-Co-O system is presented, wherein samples with nearly 800 distinct compositions were prepared using a combinatorial and high-throughput method to screen for single-phase materials of high interest as next generation positive electrode materials. X-ray diffraction is used to determine the crystal structure of each sample. The Gibbs' pyramid representing the pseudoquaternary system was studied by making samples within three distinct pseudoternary planes defined at fractional cobalt metal contents of 10%, 20%, and 30% within the Li-Ni-Mn-Co-O system. Two large single-phase regions were observed in the system: the layered region (ordered rocksalt) and cubic spinel region; both of which are of interest for next-generation positive electrodes in lithium-ion batteries. These regions were each found to stretch over a wide range of compositions within the Li-Ni-Mn-Co-O pseudoquaternary system and had complex coexistence regions existing between them. The sample cooling rate was found to have a significant effect on the position of the phase boundaries of the single-phase regions. The results of this work are intended to guide further research by narrowing the composition ranges worthy of study and to illustrate the broad range of applications where solution-based combinatorial synthesis can have significant impact.

Historical and Future Roles of the Tactical Signal Officer

DTIC Science & Technology

1991-03-27

can soil . LTC James. his sigralmen ind ooat crew on tr,e snic m-4Ca scccmolished both feats while under heavy artillery fi-e rrom tne Soanish on...the capture of Fort Malate to Admiral Dewey’s fleet in Manila Bay. Sergeant Gibbs later became Major General Gibbs, and Chief of Signal in 1928.17...kept critical equipment out of operation required in commmand and control, and degraded the unit’s ability to see the enemy at night. These officers

On the Gibbs phenomenon 1: Recovering exponential accuracy from the Fourier partial sum of a non-periodic analytic function

NASA Technical Reports Server (NTRS)

Gottlieb, David; Shu, Chi-Wang; Solomonoff, Alex; Vandeven, Herve

1992-01-01

It is well known that the Fourier series of an analytic or periodic function, truncated after 2N+1 terms, converges exponentially with N, even in the maximum norm, although the function is still analytic. This is known as the Gibbs phenomenon. Here, we show that the first 2N+1 Fourier coefficients contain enough information about the function, so that an exponentially convergent approximation (in the maximum norm) can be constructed.

A kinetic study of jack-bean urease denaturation by a new dithiocarbamate bismuth compound

NASA Astrophysics Data System (ADS)

Menezes, D. C.; Borges, E.; Torres, M. F.; Braga, J. P.

2012-10-01

A kinetic study concerning enzymatic inhibitory effect of a new bismuth dithiocarbamate complex on jack-bean urease is reported. A neural network approach is used to solve the ill-posed inverse problem arising from numerical treatment of the subject. A reaction mechanism for the urease denaturation process is proposed and the rate constants, relaxation time constants, equilibrium constants, activation Gibbs free energies for each reaction step and Gibbs free energies for the transition species are determined.

On the Gibbs phenomenon 5: Recovering exponential accuracy from collocation point values of a piecewise analytic function

NASA Technical Reports Server (NTRS)

Gottlieb, David; Shu, Chi-Wang

1994-01-01

The paper presents a method to recover exponential accuracy at all points (including at the discontinuities themselves), from the knowledge of an approximation to the interpolation polynomial (or trigonometrical polynomial). We show that if we are given the collocation point values (or a highly accurate approximation) at the Gauss or Gauss-Lobatto points, we can reconstruct a uniform exponentially convergent approximation to the function f(x) in any sub-interval of analyticity. The proof covers the cases of Fourier, Chebyshev, Legendre, and more general Gegenbauer collocation methods.

Astrodynamics. Volume 1 - Orbit determination, space navigation, celestial mechanics.

NASA Technical Reports Server (NTRS)

Herrick, S.

1971-01-01

Essential navigational, physical, and mathematical problems of space exploration are covered. The introductory chapters dealing with conic sections, orientation, and the integration of the two-body problem are followed by an introduction to orbit determination and design. Systems of units and constants, as well as ephemerides, representations, reference systems, and data are then dealt with. A detailed attention is given to rendezvous problems and to differential processes in observational orbit correction, and in rendezvous or guidance correction. Finally, the Laplacian methods for determining preliminary orbits, and the orbit methods of Lagrange, Gauss, and Gibbs are reviewed.

Computational Thermodynamics of Materials Zi-Kui Liu and Yi Wang

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

Devanathan, Ram

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

A semi-Lagrangian advection scheme for radioactive tracers in a regional spectral model

NASA Astrophysics Data System (ADS)

Chang, E.-C.; Yoshimura, K.

2015-06-01

In this study, the non-iteration dimensional-split semi-Lagrangian (NDSL) advection scheme is applied to the National Centers for Environmental Prediction (NCEP) regional spectral model (RSM) to alleviate the Gibbs phenomenon. The Gibbs phenomenon is a problem wherein negative values of positive-definite quantities (e.g., moisture and tracers) are generated by the spectral space transformation in a spectral model system. To solve this problem, the spectral prognostic specific humidity and radioactive tracer advection scheme is replaced by the NDSL advection scheme, which considers advection of tracers in a grid system without spectral space transformations. A regional version of the NDSL is developed in this study and is applied to the RSM. Idealized experiments show that the regional version of the NDSL is successful. The model runs for an actual case study suggest that the NDSL can successfully advect radioactive tracers (iodine-131 and cesium-137) without noise from the Gibbs phenomenon. The NDSL can also remove negative specific humidity values produced in spectral calculations without losing detailed features.

Fractional Stochastic Differential Equations Satisfying Fluctuation-Dissipation Theorem

NASA Astrophysics Data System (ADS)

Li, Lei; Liu, Jian-Guo; Lu, Jianfeng

2017-10-01

We propose in this work a fractional stochastic differential equation (FSDE) model consistent with the over-damped limit of the generalized Langevin equation model. As a result of the `fluctuation-dissipation theorem', the differential equations driven by fractional Brownian noise to model memory effects should be paired with Caputo derivatives, and this FSDE model should be understood in an integral form. We establish the existence of strong solutions for such equations and discuss the ergodicity and convergence to Gibbs measure. In the linear forcing regime, we show rigorously the algebraic convergence to Gibbs measure when the `fluctuation-dissipation theorem' is satisfied, and this verifies that satisfying `fluctuation-dissipation theorem' indeed leads to the correct physical behavior. We further discuss possible approaches to analyze the ergodicity and convergence to Gibbs measure in the nonlinear forcing regime, while leave the rigorous analysis for future works. The FSDE model proposed is suitable for systems in contact with heat bath with power-law kernel and subdiffusion behaviors.

Made-to-measure modelling of observed galaxy dynamics

NASA Astrophysics Data System (ADS)

Bovy, Jo; Kawata, Daisuke; Hunt, Jason A. S.

2018-01-01

Amongst dynamical modelling techniques, the made-to-measure (M2M) method for modelling steady-state systems is amongst the most flexible, allowing non-parametric distribution functions in complex gravitational potentials to be modelled efficiently using N-body particles. Here, we propose and test various improvements to the standard M2M method for modelling observed data, illustrated using the simple set-up of a one-dimensional harmonic oscillator. We demonstrate that nuisance parameters describing the modelled system's orientation with respect to the observer - e.g. an external galaxy's inclination or the Sun's position in the Milky Way - as well as the parameters of an external gravitational field can be optimized simultaneously with the particle weights. We develop a method for sampling from the high-dimensional uncertainty distribution of the particle weights. We combine this in a Gibbs sampler with samplers for the nuisance and potential parameters to explore the uncertainty distribution of the full set of parameters. We illustrate our M2M improvements by modelling the vertical density and kinematics of F-type stars in Gaia DR1. The novel M2M method proposed here allows full probabilistic modelling of steady-state dynamical systems, allowing uncertainties on the non-parametric distribution function and on nuisance parameters to be taken into account when constraining the dark and baryonic masses of stellar systems.

A comparison of algorithms for inference and learning in probabilistic graphical models.

PubMed

Frey, Brendan J; Jojic, Nebojsa

2005-09-01

Research into methods for reasoning under uncertainty is currently one of the most exciting areas of artificial intelligence, largely because it has recently become possible to record, store, and process large amounts of data. While impressive achievements have been made in pattern classification problems such as handwritten character recognition, face detection, speaker identification, and prediction of gene function, it is even more exciting that researchers are on the verge of introducing systems that can perform large-scale combinatorial analyses of data, decomposing the data into interacting components. For example, computational methods for automatic scene analysis are now emerging in the computer vision community. These methods decompose an input image into its constituent objects, lighting conditions, motion patterns, etc. Two of the main challenges are finding effective representations and models in specific applications and finding efficient algorithms for inference and learning in these models. In this paper, we advocate the use of graph-based probability models and their associated inference and learning algorithms. We review exact techniques and various approximate, computationally efficient techniques, including iterated conditional modes, the expectation maximization (EM) algorithm, Gibbs sampling, the mean field method, variational techniques, structured variational techniques and the sum-product algorithm ("loopy" belief propagation). We describe how each technique can be applied in a vision model of multiple, occluding objects and contrast the behaviors and performances of the techniques using a unifying cost function, free energy.

Predicting hydration Gibbs energies of alkyl-aromatics using molecular simulation: a comparison of current force fields and the development of a new parameter set for accurate solvation data.

PubMed

Garrido, Nuno M; Jorge, Miguel; Queimada, António J; Gomes, José R B; Economou, Ioannis G; Macedo, Eugénia A

2011-10-14

The Gibbs energy of hydration is an important quantity to understand the molecular behavior in aqueous systems at constant temperature and pressure. In this work we review the performance of some popular force fields, namely TraPPE, OPLS-AA and Gromos, in reproducing the experimental Gibbs energies of hydration of several alkyl-aromatic compounds--benzene, mono-, di- and tri-substituted alkylbenzenes--using molecular simulation techniques. In the second part of the paper, we report a new model that is able to improve such hydration energy predictions, based on Lennard Jones parameters from the recent TraPPE-EH force field and atomic partial charges obtained from natural population analysis of density functional theory calculations. We apply a scaling factor determined by fitting the experimental hydration energy of only two solutes, and then present a simple rule to generate atomic partial charges for different substituted alkyl-aromatics. This rule has the added advantages of eliminating the unnecessary assumption of fixed charge on every substituted carbon atom and providing a simple guideline for extrapolating the charge assignment to any multi-substituted alkyl-aromatic molecule. The point charges derived here yield excellent predictions of experimental Gibbs energies of hydration, with an overall absolute average deviation of less than 0.6 kJ mol(-1). This new parameter set can also give good predictive performance for other thermodynamic properties and liquid structural information.

Stationary wavelet transform for under-sampled MRI reconstruction.

PubMed

Kayvanrad, Mohammad H; McLeod, A Jonathan; Baxter, John S H; McKenzie, Charles A; Peters, Terry M

2014-12-01

In addition to coil sensitivity data (parallel imaging), sparsity constraints are often used as an additional lp-penalty for under-sampled MRI reconstruction (compressed sensing). Penalizing the traditional decimated wavelet transform (DWT) coefficients, however, results in visual pseudo-Gibbs artifacts, some of which are attributed to the lack of translation invariance of the wavelet basis. We show that these artifacts can be greatly reduced by penalizing the translation-invariant stationary wavelet transform (SWT) coefficients. This holds with various additional reconstruction constraints, including coil sensitivity profiles and total variation. Additionally, SWT reconstructions result in lower error values and faster convergence compared to DWT. These concepts are illustrated with extensive experiments on in vivo MRI data with particular emphasis on multiple-channel acquisitions. Copyright © 2014 Elsevier Inc. All rights reserved.

Quantifying uncertainty in geoacoustic inversion. II. Application to broadband, shallow-water data.

PubMed

Dosso, Stan E; Nielsen, Peter L

2002-01-01

This paper applies the new method of fast Gibbs sampling (FGS) to estimate the uncertainties of seabed geoacoustic parameters in a broadband, shallow-water acoustic survey, with the goal of interpreting the survey results and validating the method for experimental data. FGS applies a Bayesian approach to geoacoustic inversion based on sampling the posterior probability density to estimate marginal probability distributions and parameter covariances. This requires knowledge of the statistical distribution of the data errors, including both measurement and theory errors, which is generally not available. Invoking the simplifying assumption of independent, identically distributed Gaussian errors allows a maximum-likelihood estimate of the data variance and leads to a practical inversion algorithm. However, it is necessary to validate these assumptions, i.e., to verify that the parameter uncertainties obtained represent meaningful estimates. To this end, FGS is applied to a geoacoustic experiment carried out at a site off the west coast of Italy where previous acoustic and geophysical studies have been performed. The parameter uncertainties estimated via FGS are validated by comparison with: (i) the variability in the results of inverting multiple independent data sets collected during the experiment; (ii) the results of FGS inversion of synthetic test cases designed to simulate the experiment and data errors; and (iii) the available geophysical ground truth. Comparisons are carried out for a number of different source bandwidths, ranges, and levels of prior information, and indicate that FGS provides reliable and stable uncertainty estimates for the geoacoustic inverse problem.

Rational approximations to rational models: alternative algorithms for category learning.

PubMed

Sanborn, Adam N; Griffiths, Thomas L; Navarro, Daniel J

2010-10-01

Rational models of cognition typically consider the abstract computational problems posed by the environment, assuming that people are capable of optimally solving those problems. This differs from more traditional formal models of cognition, which focus on the psychological processes responsible for behavior. A basic challenge for rational models is thus explaining how optimal solutions can be approximated by psychological processes. We outline a general strategy for answering this question, namely to explore the psychological plausibility of approximation algorithms developed in computer science and statistics. In particular, we argue that Monte Carlo methods provide a source of rational process models that connect optimal solutions to psychological processes. We support this argument through a detailed example, applying this approach to Anderson's (1990, 1991) rational model of categorization (RMC), which involves a particularly challenging computational problem. Drawing on a connection between the RMC and ideas from nonparametric Bayesian statistics, we propose 2 alternative algorithms for approximate inference in this model. The algorithms we consider include Gibbs sampling, a procedure appropriate when all stimuli are presented simultaneously, and particle filters, which sequentially approximate the posterior distribution with a small number of samples that are updated as new data become available. Applying these algorithms to several existing datasets shows that a particle filter with a single particle provides a good description of human inferences.

Detection of mastitis in dairy cattle by use of mixture models for repeated somatic cell scores: a Bayesian approach via Gibbs sampling.

PubMed

Odegård, J; Jensen, J; Madsen, P; Gianola, D; Klemetsdal, G; Heringstad, B

2003-11-01

The distribution of somatic cell scores could be regarded as a mixture of at least two components depending on a cow's udder health status. A heteroscedastic two-component Bayesian normal mixture model with random effects was developed and implemented via Gibbs sampling. The model was evaluated using datasets consisting of simulated somatic cell score records. Somatic cell score was simulated as a mixture representing two alternative udder health statuses ("healthy" or "diseased"). Animals were assigned randomly to the two components according to the probability of group membership (Pm). Random effects (additive genetic and permanent environment), when included, had identical distributions across mixture components. Posterior probabilities of putative mastitis were estimated for all observations, and model adequacy was evaluated using measures of sensitivity, specificity, and posterior probability of misclassification. Fitting different residual variances in the two mixture components caused some bias in estimation of parameters. When the components were difficult to disentangle, so were their residual variances, causing bias in estimation of Pm and of location parameters of the two underlying distributions. When all variance components were identical across mixture components, the mixture model analyses returned parameter estimates essentially without bias and with a high degree of precision. Including random effects in the model increased the probability of correct classification substantially. No sizable differences in probability of correct classification were found between models in which a single cow effect (ignoring relationships) was fitted and models where this effect was split into genetic and permanent environmental components, utilizing relationship information. When genetic and permanent environmental effects were fitted, the between-replicate variance of estimates of posterior means was smaller because the model accounted for random genetic drift.

Comparison of different methods to compute a preliminary orbit of Space Debris using radar observations

NASA Astrophysics Data System (ADS)

Ma, Hélène; Gronchi, Giovanni F.

2014-07-01

We advertise a new method of preliminary orbit determination for space debris using radar observations, which we call Infang †. We can perform a linkage of two sets of four observations collected at close times. The context is characterized by the accuracy of the range ρ, whereas the right ascension α and the declination δ are much more inaccurate due to observational errors. This method can correct α, δ, assuming the exact knowledge of the range ρ. Considering no perturbations from the J 2 effect, but including errors in the observations, we can compare the new method, the classical method of Gibbs, and the more recent Keplerian integrals method. The development of Infang is still on-going and will be further improved and tested.

The thermodynamic properties of benzothiazole and benzoxazole

NASA Astrophysics Data System (ADS)

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

1991-08-01

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

Rotational KMS States and Type I Conformal Nets

NASA Astrophysics Data System (ADS)

Longo, Roberto; Tanimoto, Yoh

2018-01-01

We consider KMS states on a local conformal net on S 1 with respect to rotations. We prove that, if the conformal net is of type I, namely if it admits only type I DHR representations, then the extremal KMS states are the Gibbs states in an irreducible representation. Completely rational nets, the U(1)-current net, the Virasoro nets and their finite tensor products are shown to be of type I. In the completely rational case, we also give a direct proof that all factorial KMS states are Gibbs states.

Diffusive mixing and Tsallis entropy

DOE PAGES

O'Malley, Daniel; Vesselinov, Velimir V.; Cushman, John H.

2015-04-29

Brownian motion, the classical diffusive process, maximizes the Boltzmann-Gibbs entropy. The Tsallis q-entropy, which is non-additive, was developed as an alternative to the classical entropy for systems which are non-ergodic. A generalization of Brownian motion is provided that maximizes the Tsallis entropy rather than the Boltzmann-Gibbs entropy. This process is driven by a Brownian measure with a random diffusion coefficient. In addition, the distribution of this coefficient is derived as a function of q for 1 < q < 3. Applications to transport in porous media are considered.

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

NASA Astrophysics Data System (ADS)

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

2012-12-01

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

Gibbs measures based on 1d (an)harmonic oscillators as mean-field limits

NASA Astrophysics Data System (ADS)

Lewin, Mathieu; Nam, Phan Thành; Rougerie, Nicolas

2018-04-01

We prove that Gibbs measures based on 1D defocusing nonlinear Schrödinger functionals with sub-harmonic trapping can be obtained as the mean-field/large temperature limit of the corresponding grand-canonical ensemble for many bosons. The limit measure is supported on Sobolev spaces of negative regularity, and the corresponding density matrices are not trace-class. The general proof strategy is that of a previous paper of ours, but we have to complement it with Hilbert-Schmidt estimates on reduced density matrices.

Quantitative Boltzmann-Gibbs Principles via Orthogonal Polynomial Duality

NASA Astrophysics Data System (ADS)

Ayala, Mario; Carinci, Gioia; Redig, Frank

2018-06-01

We study fluctuation fields of orthogonal polynomials in the context of particle systems with duality. We thereby obtain a systematic orthogonal decomposition of the fluctuation fields of local functions, where the order of every term can be quantified. This implies a quantitative generalization of the Boltzmann-Gibbs principle. In the context of independent random walkers, we complete this program, including also fluctuation fields in non-stationary context (local equilibrium). For other interacting particle systems with duality such as the symmetric exclusion process, similar results can be obtained, under precise conditions on the n particle dynamics.

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

NASA Astrophysics Data System (ADS)

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

2018-05-01

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

Species Profiles: Life Histories and Environmental Requirements of Coastal Fishes and Invertebrates (North Atlantic), Sandworm and Bloodworm

DTIC Science & Technology

1988-04-01

industry jeopardizing its Bryan, G.W. , and P.E. Gibbs. 1979. future. Natl. Fisherman 59(9):77. Zinc--a major inorganic component of nereid polychaete...Physiol. (A) 52:501-503. search. culture methods and oral administration of a polychlorinated Hamaker , J.1. 1898. The nervous r biphenyl. Veroeff...Environ. Contam. Toxicol. 13:347- Blackburn. 198). The influence of 355. benthic infauna on exchange rates of inorganic nitrogen between sediment Goerke, H

Radial-based tail methods for Monte Carlo simulations of cylindrical interfaces

NASA Astrophysics Data System (ADS)

Goujon, Florent; Bêche, Bruno; Malfreyt, Patrice; Ghoufi, Aziz

2018-03-01

In this work, we implement for the first time the radial-based tail methods for Monte Carlo simulations of cylindrical interfaces. The efficiency of this method is then evaluated through the calculation of surface tension and coexisting properties. We show that the inclusion of tail corrections during the course of the Monte Carlo simulation impacts the coexisting and the interfacial properties. We establish that the long range corrections to the surface tension are the same order of magnitude as those obtained from planar interface. We show that the slab-based tail method does not amend the localization of the Gibbs equimolar dividing surface. Additionally, a non-monotonic behavior of surface tension is exhibited as a function of the radius of the equimolar dividing surface.

Hydrogeochemistry and groundwater quality appraisal of part of south Chennai coastal aquifers, Tamil Nadu, India using WQI and fuzzy logic method

NASA Astrophysics Data System (ADS)

Krishna Kumar, S.; Bharani, R.; Magesh, N. S.; Godson, Prince S.; Chandrasekar, N.

2014-12-01

The present study was carried out to evaluate the groundwater quality and its suitability for drinking purposes in the urban coastal aquifers of part of south Chennai, Tamil Nadu, India. Twenty-three groundwater samples were collected during March 2012. The minimum and maximum values of pH (6.3-8 on scale), electrical conductivity (620-12,150 μS/cm), total dissolved solids (399.28-7,824.6 mg/l), carbonate (0-30 mg/l), bicarbonate (0.9-58.9 mg/l), chloride (70.9-4,067.89 mg/l), sulphate (17.4-105 mg/l), nitrate (0.4-6.0 mg/l), calcium (30-200 mg/l), magnesium (1.2-164 mg/l), sodium (69-1,490 mg/l) and potassium (8-340 mg/l) were recorded in the coastal aquifers of Chennai city. The groundwater samples show that the majority of the sampling points clustered on the NaCl and mixed CaMgCl facies of the piper trilinear diagram. In the Gibbs diagram, the majority of the sampling points fall under rock water and evaporation dominance field. Fuzzy membership classification suggests that the majority of the samples fall under good water type followed by excellent water and poor water categories. Groundwater quality index showing the majority of the samples falls under excellent to poor category of water. A positive correlation was observed with Cl-, SO4 2-, Ca2+, Na+, K+, EC and TDS. The extracted results of the correlation matrix and geochemical analysis suggest that the dominant ions of groundwater (Na+, Ca2+, K+, Cl- and SO4 2-) were derived from seawater intrusion and gypsum dissolution process. Nitrate concentration is most significantly derived from anthropogenic sources.

Dynamics of Contact Line Pinning and Depinning of Droplets Evaporating on Microribs.

PubMed

Mazloomi Moqaddam, Ali; Derome, Dominique; Carmeliet, Jan

2018-05-15

The contact line dynamics of evaporating droplets deposited on a set of parallel microribs is analyzed with the use of a recently developed entropic lattice Boltzmann model for two-phase flow. Upon deposition, part of the droplet penetrates into the space between ribs because of capillary action, whereas the remaining liquid of the droplet remains pinned on top of the microribs. In the first stage, evaporation continues until the droplet undergoes a series of pinning-depinning events, showing alternatively the constant contact radius and constant contact angle modes. While the droplet is pinned, evaporation results in a contact angle reduction, whereas the contact radius remains constant. At a critical contact angle, the contact line depins, the contact radius reduces, and the droplet rearranges to a larger apparent contact angle. This pinning-depinning behavior goes on until the liquid above the microribs is evaporated. By computing the Gibbs free energy taking into account the interfacial energy, pressure terms, and viscous dissipation due to drop internal flow, we found that the mechanism that causes the unpinning of the contact line results from an excess in Gibbs free energy. The spacing distance and the rib height play an important role in controlling the pinning-depinning cycling, the critical contact angle, and the excess Gibbs free energy. However, we found that neither the critical contact angle nor the maximum excess Gibbs free energy depends on the rib width. We show that the different terms, that is, pressure term, viscous dissipation, and interfacial energy, contributing to the excess Gibbs free energy, can be varied differently by varying different geometrical properties of the microribs. It is demonstrated that, by varying the spacing distance between the ribs, the energy barrier is controlled by the interfacial energy while the contribution of the viscous dissipation is dominant if either rib height or width is changed. Main finding of this is study is that, for microrib patterned surfaces, the energy barrier required for the contact line to depin can be enlarged by increasing the spacing or the rib height, which can be important for practical applications.

Effects of Gibbs free energy of interfacial metal oxide on resistive switching characteristics of solution-processed HfOx films

NASA Astrophysics Data System (ADS)

Hsu, Chih-Chieh; Sun, Jhen-Kai; Tsao, Che-Chang; Chuang, Po-Yang

2017-08-01

Effects of bottom electrodes (BEs) of Al, Mo, and Pt on resistive switching characteristics of sol-gel HfOx films were investigated in this work. To avoid influences of plasma or thermal energy on HfOx RS characteristic, the top electrodes were formed by pressing indium balls onto the HfOx surface rather than by using a sputter or an evaporator. When using Mo as the BE, the as-deposited HfOx film can give a forming-free resistive switching behavior with low set/reset voltages of 0.28 V / - 0.54 V. In contrast, non-switching characteristics of the HfOx films were observed when using Al and Pt as the BEs. The HfOx conduction current was found to be highly dependent on the BE. However, when an annealing process at 350 °C in an oxygen ambient was performed to the HfOx films on different BEs, the resistive switching behavior of the HfOx/Mo was absent while it can be found in the HfOx/Al sample. Differences in I-V characteristics of the HfOx films on different BEs were explained by considering Gibbs free energies of interfacial oxide layers. X-ray photoelectron spectroscopy (XPS) depth profile was used to examine the interfacial oxide layer. The resistive switching mechanism was also studied.

Molecular Gibbs Surface Excess and CO2-Hydrate Density Determine the Strong Temperature- and Pressure-Dependent Supercritical CO2-Brine Interfacial Tension.

PubMed

Ji, Jiayuan; Zhao, Lingling; Tao, Lu; Lin, Shangchao

2017-06-29

In CO 2 geological storage, the interfacial tension (IFT) between supercritical CO 2 and brine is critical for the storage capacitance design to prevent CO 2 leakage. IFT relies not only on the interfacial molecule properties but also on the environmental conditions at different storage sites. In this paper, supercritical CO 2 -NaCl solution systems are modeled at 343-373 K and 6-35 MPa under the salinity of 1.89 mol/L using molecular dynamics simulations. After computing and comparing the molecular density profile across the interface, the atomic radial distribution function, the molecular orientation distribution, the molecular Gibbs surface excess (derived from the molecular density profile), and the CO 2 -hydrate number density under the above environmental conditions, we confirm that only the molecular Gibbs surface excess of CO 2 molecules and the CO 2 -hydrate number density correlate strongly with the temperature- and pressure-dependent IFTs. We also compute the populations of two distinct CO 2 -hydrate structures (T-type and H-type) and attribute the observed dependence of IFTs to the dominance of the more stable, surfactant-like T-type CO 2 -hydrates at the interface. On the basis of these new molecular mechanisms behind IFT variations, this study could guide the rational design of suitable injecting environmental pressure and temperature conditions. We believe that the above two molecular-level metrics (Gibbs surface excess and hydrate number density) are of great fundamental importance for understanding the supercritical CO 2 -water interface and engineering applications in geological CO 2 storage.

Knudsen effusion mass spectrometric studies over (USn3+U3Sn7) two-phase region of U-Sn system

NASA Astrophysics Data System (ADS)

Manikandan, P.; Trinadh, V. V.; Bera, Suranjan; Narasimhan, T. S. Lakshmi; Ananthasivan, K.; Joseph, M.; Mudali, U. Kamachi

2017-08-01

Vaporisation studies over (USn3+U3Sn7) ;two-phase; field have been carried out by employing Knudsen effusion mass spectrometry (KEMS) in the temperature range of 1050-1226 K. Sn(g) was the species observed in the mass spectrum of the equilibrium vapour phase over the samples (71.5 at% Sn and 73.0 at% Sn). The partial pressure of Sn(g) was measured as a function of temperature over (USn3+U3Sn7) ;two-phase; field and the p-T relation was derived as log (pSn/Pa) = ((-14580 ± 91)/(T/K)) + (8.82 ± 0.08) (1050-1226 K). The vaporisation reaction 3USn3(s) = U3Sn7(s) + 2Sn(g) was evaluated by second law method. The Gibbs energy of formation of USn3(s) was derived as ΔfGm°(U Sn3 , s , T) (±1.8) = -173.4 + 0.055 T (K) (kJ mol-1) (1050-1226 K). The mass spectrometric studies on this system have been carried out for the first time.

Correlated Topic Vector for Scene Classification.

PubMed

Wei, Pengxu; Qin, Fei; Wan, Fang; Zhu, Yi; Jiao, Jianbin; Ye, Qixiang

2017-07-01

Scene images usually involve semantic correlations, particularly when considering large-scale image data sets. This paper proposes a novel generative image representation, correlated topic vector, to model such semantic correlations. Oriented from the correlated topic model, correlated topic vector intends to naturally utilize the correlations among topics, which are seldom considered in the conventional feature encoding, e.g., Fisher vector, but do exist in scene images. It is expected that the involvement of correlations can increase the discriminative capability of the learned generative model and consequently improve the recognition accuracy. Incorporated with the Fisher kernel method, correlated topic vector inherits the advantages of Fisher vector. The contributions to the topics of visual words have been further employed by incorporating the Fisher kernel framework to indicate the differences among scenes. Combined with the deep convolutional neural network (CNN) features and Gibbs sampling solution, correlated topic vector shows great potential when processing large-scale and complex scene image data sets. Experiments on two scene image data sets demonstrate that correlated topic vector improves significantly the deep CNN features, and outperforms existing Fisher kernel-based features.

Multilevel covariance regression with correlated random effects in the mean and variance structure.

PubMed

Quintero, Adrian; Lesaffre, Emmanuel

2017-09-01

Multivariate regression methods generally assume a constant covariance matrix for the observations. In case a heteroscedastic model is needed, the parametric and nonparametric covariance regression approaches can be restrictive in the literature. We propose a multilevel regression model for the mean and covariance structure, including random intercepts in both components and allowing for correlation between them. The implied conditional covariance function can be different across clusters as a result of the random effect in the variance structure. In addition, allowing for correlation between the random intercepts in the mean and covariance makes the model convenient for skewedly distributed responses. Furthermore, it permits us to analyse directly the relation between the mean response level and the variability in each cluster. Parameter estimation is carried out via Gibbs sampling. We compare the performance of our model to other covariance modelling approaches in a simulation study. Finally, the proposed model is applied to the RN4CAST dataset to identify the variables that impact burnout of nurses in Belgium. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Software for Data Analysis with Graphical Models

NASA Technical Reports Server (NTRS)

Buntine, Wray L.; Roy, H. Scott

1994-01-01

Probabilistic graphical models are being used widely in artificial intelligence and statistics, for instance, in diagnosis and expert systems, as a framework for representing and reasoning with probabilities and independencies. They come with corresponding algorithms for performing statistical inference. This offers a unifying framework for prototyping and/or generating data analysis algorithms from graphical specifications. This paper illustrates the framework with an example and then presents some basic techniques for the task: problem decomposition and the calculation of exact Bayes factors. Other tools already developed, such as automatic differentiation, Gibbs sampling, and use of the EM algorithm, make this a broad basis for the generation of data analysis software.

Numerical time evolution of ETH spin chains by means of matrix product density operators

NASA Astrophysics Data System (ADS)

White, Christopher; Zaletel, Michael; Mong, Roger; Refael, Gil

We introduce a method for approximating density operators of 1D systems that, when combined with a standard framework for time evolution (TEBD), makes possible simulation of the dynamics of strongly thermalizing systems to arbitrary times. We demonstrate that the method works on both near-equilibrium initial states (Gibbs states with spatially varying temperatures) and far-from-equilibrium initial states, including quenches across phase transitions and pure states. This work was supported by the National Science Foundation Graduate Research Fellowship under Grant No. DGE \\x901144469 and by the Caltech IQIM, an NSF Physics Frontiers Center with support of the Gordon and Betty Moore.

Strontium cobaltite oxygen sponge catalyst and methods of use

DOEpatents

Lee, Ho Nyung; Jeen, Hyoungjeen; Choi, Woo Seok; Biegalski, Michael; Folkman, Chad M.; Tung, I-Cheng; Fong, Dillon D.; Freeland, John W.; Shin, Dongwon; Ohta, Hiromichi; Chisholm, Matthew F.

2017-01-24

Rapid, reversible redox activity may be accomplished at significantly reduced temperatures, as low as about 200.degree. C., from epitaxially stabilized, oxygen vacancy ordered SrCoO.sub.2.5 and thermodynamically unfavorable perovskite SrCoO.sub.3-.delta.. The fast, low temperature redox activity in SrCoO.sub.3-.delta. may be attributed to a small Gibbs free energy difference between the two topotactic phases. Epitaxially stabilized thin films of strontium cobaltite provide a catalyst adapted to rapidly transition between oxidation states at substantially low temperatures. Methods of transitioning a strontium cobaltite catalyst from a first oxidation state to a second oxidation state are described.

A semi-Lagrangian advection scheme for radioactive tracers in the NCEP Regional Spectral Model (RSM)

NASA Astrophysics Data System (ADS)

Chang, E.-C.; Yoshimura, K.

2015-10-01

In this study, the non-iteration dimensional-split semi-Lagrangian (NDSL) advection scheme is applied to the National Centers for Environmental Prediction (NCEP) Regional Spectral Model (RSM) to alleviate the Gibbs phenomenon. The Gibbs phenomenon is a problem wherein negative values of positive-definite quantities (e.g., moisture and tracers) are generated by the spectral space transformation in a spectral model system. To solve this problem, the spectral prognostic specific humidity and radioactive tracer advection scheme is replaced by the NDSL advection scheme, which considers advection of tracers in a grid system without spectral space transformations. A regional version of the NDSL is developed in this study and is applied to the RSM. Idealized experiments show that the regional version of the NDSL is successful. The model runs for an actual case study suggest that the NDSL can successfully advect radioactive tracers (iodine-131 and cesium-137) without noise from the Gibbs phenomenon. The NDSL can also remove negative specific humidity values produced in spectral calculations without losing detailed features.

Shielding property for thermal equilibrium states in the quantum Ising model

NASA Astrophysics Data System (ADS)

Móller, N. S.; de Paula, A. L.; Drumond, R. C.

2018-03-01

We show that Gibbs states of nonhomogeneous transverse Ising chains satisfy a shielding property. Namely, whatever the fields on each spin and exchange couplings between neighboring spins are, if the field in one particular site is null, then the reduced states of the subchains to the right and to the left of this site are exactly the Gibbs states of each subchain alone. Therefore, even if there is a strong exchange coupling between the extremal sites of each subchain, the Gibbs states of the each subchain behave as if there is no interaction between them. In general, if a lattice can be divided into two disconnected regions separated by an interface of sites with zero applied field, then we can guarantee a similar result only if the surface contains a single site. Already for an interface with two sites we show an example where the property does not hold. When it holds, however, we show that if a perturbation of the Hamiltonian parameters is done in one side of the lattice, then the other side is completely unchanged, with regard to both its equilibrium state and dynamics.

Thermodynamic properties for bunsenite, NiO, magnetite, Fe3O4, and hematite, Fe2O3, with comments on selected oxygen buffer reactions

USGS Publications Warehouse

Hemingway, B.S.

1990-01-01

Smoothed values of the heat capacities and derived thermodynamic functions are given for bunsenite, magnetite, and hematite for the temperature interval 298.15 to 1800 K. The Gibbs free energy for the reaction Ni + 0.5O2 = NiO is given by the equation ??rG0T = -238.39 + 0.1146T - 3.72 ?? 10-3T ln T and is valid from 298.15 K to 1700 K. The Gibbs free energy (in kJ) of the reaction 2 magnetite + 3 quartz = 3 fayalite + O2 may be calculated from the equation ??rG0T = 474.155 - 0.16120 T in kJ and between 800 and 1400 K. The Gibbs free energy (in kJ) of the reaction 6 hematite = 4 magnetite + O2 may be calculated from the following equations: ??rG0T = 496.215 - 0.27114T, ??rG0T = 514.690 - 0.29753T, ??rG0T = 501.348 - 0.2854T. -from Author

Standard Gibbs energy of formation of Mo 3Te 4 by emf measurements

NASA Astrophysics Data System (ADS)

Mallika, C.; Sreedharan, O. M.

1990-03-01

The emf of the galvanic cells Pt, Mo, MoO 2¦8 YSZ¦'FeO', Fe, Pt (I) and Pt, Fe,'FeO' ¦8 YSZ¦MoO 2, Mo 3Te 4, MoTe 2(α), C, Pt (II) were measured over the temperature ranges 837 to 1151 K and 775 to 1196 K, respectively, using 8 mass% yttria-stabilized zirconia (8 YSZ) as the solid electrolyte. From the emf values, the partial molar Gibbs energy of solution of molybdenum in Mo 3Te 4/MoTe 2(α), Δ ḠMo was found to be Δ ḠMo ± 1.19 ( kJ/mol) = -025.08 + 0.00420T(K) . Using the literature data for the Gibbs energy of formation of MoTe 2(α). the expression ΔG° f( Mo3Te4, s) ± 5.97 (kj/mol) = -253.58 + 0.09214 T( K) was derived for the range 775 to 1196 K. A third-law analysis yielded a value of -209 ± 10 kJ/mol for ΔH° f.298o of Mo 3Te 4(s).

Interfacial interactions between plastic particles in plastics flotation.

PubMed

Wang, Chong-qing; Wang, Hui; Gu, Guo-hua; Fu, Jian-gang; Lin, Qing-quan; Liu, You-nian

2015-12-01

Plastics flotation used for recycling of plastic wastes receives increasing attention for its industrial application. In order to study the mechanism of plastics flotation, the interfacial interactions between plastic particles in flotation system were investigated through calculation of Lifshitz-van der Waals (LW) function, Lewis acid-base (AB) Gibbs function, and the extended Derjaguin-Landau-Verwey-Overbeek potential energy profiles. The results showed that van der Waals force between plastic particles is attraction force in flotation system. The large hydrophobic attraction, caused by the AB Gibbs function, is the dominant interparticle force. Wetting agents present significant effects on the interfacial interactions between plastic particles. It is found that adsorption of wetting agents promotes dispersion of plastic particles and decreases the floatability. Pneumatic flotation may improve the recovery and purity of separated plastics through selective adsorption of wetting agents on plastic surface. The relationships between hydrophobic attraction and surface properties were also examined. It is revealed that there exists a three-order polynomial relationship between the AB Gibbs function and Lewis base component. Our finding provides some insights into mechanism of plastics flotation. Copyright © 2015 Elsevier Ltd. All rights reserved.

Inference with minimal Gibbs free energy in information field theory.

PubMed

Ensslin, Torsten A; Weig, Cornelius

2010-11-01

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

Assessment of groundwater quality: a fusion of geochemical and geophysical information via Bayesian neural networks.

PubMed

Maiti, Saumen; Erram, V C; Gupta, Gautam; Tiwari, Ram Krishna; Kulkarni, U D; Sangpal, R R

2013-04-01

Deplorable quality of groundwater arising from saltwater intrusion, natural leaching and anthropogenic activities is one of the major concerns for the society. Assessment of groundwater quality is, therefore, a primary objective of scientific research. Here, we propose an artificial neural network-based method set in a Bayesian neural network (BNN) framework and employ it to assess groundwater quality. The approach is based on analyzing 36 water samples and inverting up to 85 Schlumberger vertical electrical sounding data. We constructed a priori model by suitably parameterizing geochemical and geophysical data collected from the western part of India. The posterior model (post-inversion) was estimated using the BNN learning procedure and global hybrid Monte Carlo/Markov Chain Monte Carlo optimization scheme. By suitable parameterization of geochemical and geophysical parameters, we simulated 1,500 training samples, out of which 50 % samples were used for training and remaining 50 % were used for validation and testing. We show that the trained model is able to classify validation and test samples with 85 % and 80 % accuracy respectively. Based on cross-correlation analysis and Gibb's diagram of geochemical attributes, the groundwater qualities of the study area were classified into following three categories: "Very good", "Good", and "Unsuitable". The BNN model-based results suggest that groundwater quality falls mostly in the range of "Good" to "Very good" except for some places near the Arabian Sea. The new modeling results powered by uncertainty and statistical analyses would provide useful constrain, which could be utilized in monitoring and assessment of the groundwater quality.

Observation uncertainty in reversible Markov chains.

PubMed

Metzner, Philipp; Weber, Marcus; Schütte, Christof

2010-09-01

In many applications one is interested in finding a simplified model which captures the essential dynamical behavior of a real life process. If the essential dynamics can be assumed to be (approximately) memoryless then a reasonable choice for a model is a Markov model whose parameters are estimated by means of Bayesian inference from an observed time series. We propose an efficient Monte Carlo Markov chain framework to assess the uncertainty of the Markov model and related observables. The derived Gibbs sampler allows for sampling distributions of transition matrices subject to reversibility and/or sparsity constraints. The performance of the suggested sampling scheme is demonstrated and discussed for a variety of model examples. The uncertainty analysis of functions of the Markov model under investigation is discussed in application to the identification of conformations of the trialanine molecule via Robust Perron Cluster Analysis (PCCA+) .

The thermochemistry of london dispersion-driven transition metal reactions: getting the 'right answer for the right reason'.

PubMed

Hansen, Andreas; Bannwarth, Christoph; Grimme, Stefan; Petrović, Predrag; Werlé, Christophe; Djukic, Jean-Pierre

2014-10-01

Reliable thermochemical measurements and theoretical predictions for reactions involving large transition metal complexes in which long-range intramolecular London dispersion interactions contribute significantly to their stabilization are still a challenge, particularly for reactions in solution. As an illustrative and chemically important example, two reactions are investigated where a large dipalladium complex is quenched by bulky phosphane ligands (triphenylphosphane and tricyclohexylphosphane). Reaction enthalpies and Gibbs free energies were measured by isotherm titration calorimetry (ITC) and theoretically 'back-corrected' to yield 0 K gas-phase reaction energies (ΔE). It is shown that the Gibbs free solvation energy calculated with continuum models represents the largest source of error in theoretical thermochemistry protocols. The ('back-corrected') experimental reaction energies were used to benchmark (dispersion-corrected) density functional and wave function theory methods. Particularly, we investigated whether the atom-pairwise D3 dispersion correction is also accurate for transition metal chemistry, and how accurately recently developed local coupled-cluster methods describe the important long-range electron correlation contributions. Both, modern dispersion-corrected density functions (e.g., PW6B95-D3(BJ) or B3LYP-NL), as well as the now possible DLPNO-CCSD(T) calculations, are within the 'experimental' gas phase reference value. The remaining uncertainties of 2-3 kcal mol(-1) can be essentially attributed to the solvation models. Hence, the future for accurate theoretical thermochemistry of large transition metal reactions in solution is very promising.

Ergodic theory and experimental visualization of chaos in 3D flows

NASA Astrophysics Data System (ADS)

Sotiropoulos, Fotis; Mezic, Igor

2000-11-01

In his motivation for the ergodic hypothesis Gibbs invoked an analogy with fluid mixing: “…Yet no fact is more familiar to us than that stirring tends to bring a liquid to a state of uniform mixture, or uniform densities of its components…”. Although proof of the ergodic hypothesis is possible only for the simplest of systems using methods from ergodic theory, the use of the hypothesis has led to many accurate predictions in statistical mechanics. The problem of fluid mixing, however, turned out to be considerably more complicated than Gibbs envisioned. Chaotic advection can indeed lead to efficient mixing even in non-turbulent flows, but many non-mixed islands are known to persist within well-mixed regions. In numerical studies, Poincaré maps can be used to reveal the structure of such islands but their visualization in the laboratory requires laborious experimental procedures and is possible only for certain types of flows. Here we propose the first non-intrusive, simple to implement, and generally applicable technique for constructing experimental Poincaré maps and apply it to a steady, 3D, vortex breakdown bubble. We employ standard laser-induced fluorescence (LIF) and construct Poincaré maps by time averaging a sufficiently long sequence of instantaneous LIF images. We also show that ergodic theory methods provide a rigorous theoretical justification for this approach whose main objective is to reveal the non-ergodic regions of the flow.

Reactions of cisplatin with cysteine and methionine at constant pH; a computational study.

PubMed

Zimmermann, Tomás; Burda, Jaroslav V

2010-02-07

Interactions of hydrated cisplatin complexes cis-[Pt(NH(3))(2)Cl(H(2)O)](+) and cis-[Pt(NH(3))(2)(OH)(H(2)O)](+) with cysteine and methionine in an aqueous solution at constant pH were explored using computational methods. Thermodynamic parameters of considered reactions were studied in a broad pH range, taking up to 4 protonation states of each molecule into account. Reaction free energies at constant pH were obtained from standard Gibbs free energies using the Legendre transformation. Solvation free energies and pK(a) values were calculated using the PCM model with UAHF cavities, recently adapted by us for transition metal complexes. The root mean square error of pK(a) values on a set of model platinum complexes and amino acids was equal to 0.74. At pH 7, the transformed Gibbs free energies differ by up to 15 kcal mol(-1) from the Gibbs free energies of model reactions with a constant number of protons. As for cysteine, calculations confirmed a strong preference for kappaS monodenate bonding in a broad pH range. The most stable product of the second reaction step, which proceeds from monodentate to chelate complex, is the kappa(2)S,N coordinated chelate. The reaction with methionine is more complex. In the first step all three considered methionine donor atoms (N, S and O) are thermodynamically preferred products depending on the platinum complex and the pH. This is in accordance with the experimental observation of a pH dependent migration between N and S donor atoms in a chemically related system. The most stable chelates of platinum with methionine are kappa(2)S,N and kappa(2)N,O bonded complexes. The comparison of reaction free energies of both amino acids suggests, that the bidentate methionine ligand can be displaced even by the monodentate cysteine ligand under certain conditions.

On Detecting Biospheres from Chemical Thermodynamic Disequilibrium in Planetary Atmospheres.

PubMed

Krissansen-Totton, Joshua; Bergsman, David S; Catling, David C

2016-01-01

Atmospheric chemical disequilibrium has been proposed as a method for detecting extraterrestrial biospheres from exoplanet observations. Chemical disequilibrium is potentially a generalized biosignature since it makes no assumptions about particular biogenic gases or metabolisms. Here, we present the first rigorous calculations of the thermodynamic chemical disequilibrium in Solar System atmospheres, in which we quantify the available Gibbs energy: the Gibbs free energy of an observed atmosphere minus that of atmospheric gases reacted to equilibrium. The purely gas phase disequilibrium in Earth's atmosphere is mostly attributable to O2 and CH4. The available Gibbs energy is not unusual compared to other Solar System atmospheres and smaller than that of Mars. However, Earth's fluid envelope contains an ocean, allowing gases to react with water and requiring a multiphase calculation with aqueous species. The disequilibrium in Earth's atmosphere-ocean system (in joules per mole of atmosphere) ranges from ∼20 to 2 × 10(6) times larger than the disequilibria of other atmospheres in the Solar System, where Mars is second to Earth. Only on Earth is the chemical disequilibrium energy comparable to the thermal energy per mole of atmosphere (excluding comparison to Titan with lakes, where quantification is precluded because the mean lake composition is unknown). Earth's disequilibrium is biogenic, mainly caused by the coexistence of N2, O2, and liquid water instead of more stable nitrate. In comparison, the O2-CH4 disequilibrium is minor, although kinetics requires a large CH4 flux into the atmosphere. We identify abiotic processes that cause disequilibrium in the other atmospheres. Our metric requires minimal assumptions and could potentially be calculated from observations of exoplanet atmospheres. However, further work is needed to establish whether thermodynamic disequilibrium is a practical exoplanet biosignature, requiring an assessment of false positives, noisy observations, and other detection challenges. Our Matlab code and databases for these calculations are available, open source.

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

NASA Technical Reports Server (NTRS)

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

1993-01-01

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

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

NASA Astrophysics Data System (ADS)

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

2017-12-01

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

Thermodynamics of BTZ black holes in gravity’s rainbow

NASA Astrophysics Data System (ADS)

Alsaleh, Salwa

2017-05-01

In this paper, we deform the thermodynamics of a BTZ black hole from rainbow functions in gravity’s rainbow. The rainbow functions will be motivated from the results in loop quantum gravity and noncommutative geometry. It will be observed that the thermodynamics gets deformed due to these rainbow functions, indicating the existence of a remnant. However, the Gibbs free energy does not get deformed due to these rainbow functions, and so the critical behavior from Gibbs does not change by this deformation. This is because the deformation in the entropy cancels out the temperature deformation.

Application of the thermorheologically complex nonlinear Adam-Gibbs model for the glass transition to molecular motion in hydrated proteins.

PubMed

Hodge, Ian M

2006-08-01

The nonlinear thermorheologically complex Adam Gibbs (extended "Scherer-Hodge") model for the glass transition is applied to enthalpy relaxation data reported by Sartor, Mayer, and Johari for hydrated methemoglobin. A sensible range in values for the average localized activation energy is obtained (100-200 kJ mol(-1)). The standard deviation in the inferred Gaussian distribution of activation energies, computed from the reported KWW beta-parameter, is approximately 30% of the average, consistent with the suggestion that some relaxation processes in hydrated proteins have exceptionally low activation energies.

On the dispute between Boltzmann and Gibbs entropy

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

Buonsante, Pierfrancesco; Franzosi, Roberto, E-mail: roberto.franzosi@ino.it; Smerzi, Augusto

2016-12-15

The validity of the concept of negative temperature has been recently challenged by arguing that the Boltzmann entropy (that allows negative temperatures) is inconsistent from a mathematical and statistical point of view, whereas the Gibbs entropy (that does not admit negative temperatures) provides the correct definition for the microcanonical entropy. Here we prove that the Boltzmann entropy is thermodynamically and mathematically consistent. Analytical results on two systems supporting negative temperatures illustrate the scenario we propose. In addition we numerically study a lattice system to show that negative temperature equilibrium states are accessible and obey standard statistical mechanics prediction.

A mixture-energy-consistent six-equation two-phase numerical model for fluids with interfaces, cavitation and evaporation waves

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

Pelanti, Marica, E-mail: marica.pelanti@ensta-paristech.fr; Shyue, Keh-Ming, E-mail: shyue@ntu.edu.tw

2014-02-15

We model liquid–gas flows with cavitation by a variant of the six-equation single-velocity two-phase model with stiff mechanical relaxation of Saurel–Petitpas–Berry (Saurel et al., 2009) [9]. In our approach we employ phasic total energy equations instead of the phasic internal energy equations of the classical six-equation system. This alternative formulation allows us to easily design a simple numerical method that ensures consistency with mixture total energy conservation at the discrete level and agreement of the relaxed pressure at equilibrium with the correct mixture equation of state. Temperature and Gibbs free energy exchange terms are included in the equations as relaxationmore » terms to model heat and mass transfer and hence liquid–vapor transition. The algorithm uses a high-resolution wave propagation method for the numerical approximation of the homogeneous hyperbolic portion of the model. In two dimensions a fully-discretized scheme based on a hybrid HLLC/Roe Riemann solver is employed. Thermo-chemical terms are handled numerically via a stiff relaxation solver that forces thermodynamic equilibrium at liquid–vapor interfaces under metastable conditions. We present numerical results of sample tests in one and two space dimensions that show the ability of the proposed model to describe cavitation mechanisms and evaporation wave dynamics.« less

Investigation of thermodynamic parameters in the thermal decomposition of plastic waste-waste lube oil compounds.

PubMed

Kim, Yong Sang; Kim, Young Seok; Kim, Sung Hyun

2010-07-01

Thermal decomposition properties of plastic waste-waste lube oil compounds were investigated under nonisothermal conditions. Polyethylene (PE), polypropylene (PP), polystyrene (PS), and polyethylene terephthalate (PET) were selected as representative household plastic wastes. A plastic waste mixture (PWM) and waste lube oil (WLO) were mixed with mixing ratios of 33, 50, and 67 (w/w) % on a PWM weight basis, and thermogravimetric (TG) experiments were performed from 25 to 600 degrees C. The Flynn-Wall method and the Ozawa-Flynn-Wall method were used for analyses of thermodynamic parameters. In this study, activation energies of PWM/WLO compounds ranged from 73.4 to 229.6 kJ/mol between 0.2 and 0.8 of normalized mass conversions, and the 50% PWM/WLO compound had lower activation energies and enthalpies among the PWM/WLO samples at each mass conversion. At the point of maximum differential mass conversion, the analyzed activation energies, enthalpies, entropies, and Gibbs free energies indicated that mixing PWM and WLO has advantages in reducing energy to decrease the degree of disorder. However, no difference in overall energy that would require overcoming both thermal decomposition reactions and degree of disorder was observed among PWM/WLO compounds under these experimental conditions.

An optimization-based approach for high-order accurate discretization of conservation laws with discontinuous solutions

NASA Astrophysics Data System (ADS)

Zahr, M. J.; Persson, P.-O.

2018-07-01

This work introduces a novel discontinuity-tracking framework for resolving discontinuous solutions of conservation laws with high-order numerical discretizations that support inter-element solution discontinuities, such as discontinuous Galerkin or finite volume methods. The proposed method aims to align inter-element boundaries with discontinuities in the solution by deforming the computational mesh. A discontinuity-aligned mesh ensures the discontinuity is represented through inter-element jumps while smooth basis functions interior to elements are only used to approximate smooth regions of the solution, thereby avoiding Gibbs' phenomena that create well-known stability issues. Therefore, very coarse high-order discretizations accurately resolve the piecewise smooth solution throughout the domain, provided the discontinuity is tracked. Central to the proposed discontinuity-tracking framework is a discrete PDE-constrained optimization formulation that simultaneously aligns the computational mesh with discontinuities in the solution and solves the discretized conservation law on this mesh. The optimization objective is taken as a combination of the deviation of the finite-dimensional solution from its element-wise average and a mesh distortion metric to simultaneously penalize Gibbs' phenomena and distorted meshes. It will be shown that our objective function satisfies two critical properties that are required for this discontinuity-tracking framework to be practical: (1) possesses a local minima at a discontinuity-aligned mesh and (2) decreases monotonically to this minimum in a neighborhood of radius approximately h / 2, whereas other popular discontinuity indicators fail to satisfy the latter. Another important contribution of this work is the observation that traditional reduced space PDE-constrained optimization solvers that repeatedly solve the conservation law at various mesh configurations are not viable in this context since severe overshoot and undershoot in the solution, i.e., Gibbs' phenomena, may make it impossible to solve the discrete conservation law on non-aligned meshes. Therefore, we advocate a gradient-based, full space solver where the mesh and conservation law solution converge to their optimal values simultaneously and therefore never require the solution of the discrete conservation law on a non-aligned mesh. The merit of the proposed method is demonstrated on a number of one- and two-dimensional model problems including the L2 projection of discontinuous functions, Burgers' equation with a discontinuous source term, transonic flow through a nozzle, and supersonic flow around a bluff body. We demonstrate optimal O (h p + 1) convergence rates in the L1 norm for up to polynomial order p = 6 and show that accurate solutions can be obtained on extremely coarse meshes.

In-situ measurements of seismic velocities in the San Francisco Bay Region; part III

USGS Publications Warehouse

Gibbs, James F.; Fumal, Thomas E.; Borcherdt, Roger D.; Roth, Edward F.

1977-01-01

Seismic wave velocities (compressional and shear) are important parameters for estimating the seismic response characteristics of various geologic units when subjected to strong earthquake ground shaking. Seismic velocities of various units often show a strong correlation with the amounts of damage following large earthquakes and have been used as a basis for certain types of seismic zonation studies. In the current program seismic velocities have been measured at 59 locations 1n the San Francisco Bay Region. This report is the third in a series of Open-File Reports and describes the in-situ velocity measurements at locations 35-59. At each location seismic travel times are measured in drill holes, normally at 2.5-m intervals to a depth of 30 m. Geologic logs are determined from drill cuttings, undisturbed (cored) samples, and penetrometer samples. The data provide a detailed comparison of geologic and seismic characteristics and provide parameters for estimating strong earthquake ground motions quantitatively at each of the sites. A major emphasis of this program is to obtain a detailed comparison of geologic and seismic data on a regional scale for use in seismic zonation. There is a variety of geologic and seismic data available in the San Francisco Bay Region for use 1n developing the general zoning techniques which can then be applied to other areas. Shear wave velocities 1n near-surface geologic materials are of especial interest for engineering seismology and seismic zonation studies, yet in general, they are difficult to measure because of contamination by compressional waves. A comparison of various in-situ techniques by Warrick (1974) establishes the reliability of the method utilizing a "horizontal traction" source for sites underlain by bay mud and alluvium. Gibbs, and others (1975a) present data from 12 holes and establishes the reliability of the method for sites underlain by a variety of different rock units and suggest extending the measurements to a large number of sites. Data collected from the first 12 holes also provide an opportunity for developing a routine and efficient procedure for collection and reduction of the data. Gibbs and others (1975b) report preliminary comparisons of the data with the amplification data recorded from nuclear explosions, and the intensity data for the 1906 earthquake. These comparisons show that correlations exist between the three data sets. Average shear wave velocity in each geologic unit form the basis for the preliminary correlations, however, some of the geologic units (that is, granite and Franciscan Formation) exhibit a wide range of shear wave velocity. It is apparent that other factors must be considered in these units, perhaps near surface weathering or fracture spacing. Work is continuing in this area.

Multi-phase-field method for surface tension induced elasticity

NASA Astrophysics Data System (ADS)

Schiedung, Raphael; Steinbach, Ingo; Varnik, Fathollah

2018-01-01

A method, based on the multi-phase-field framework, is proposed that adequately accounts for the effects of a coupling between surface free energy and elastic deformation in solids. The method is validated via a number of analytically solvable problems. In addition to stress states at mechanical equilibrium in complex geometries, the underlying multi-phase-field framework naturally allows us to account for the influence of surface energy induced stresses on phase transformation kinetics. This issue, which is of fundamental importance on the nanoscale, is demonstrated in the limit of fast diffusion for a solid sphere, which melts due to the well-known Gibbs-Thompson effect. This melting process is slowed down when coupled to surface energy induced elastic deformation.

Electrochemical thermodynamic measurement system

DOEpatents

Reynier, Yvan [Meylan, FR; Yazami, Rachid [Los Angeles, CA; Fultz, Brent T [Pasadena, CA

2009-09-29

The present invention provides systems and methods for accurately characterizing thermodynamic and materials properties of electrodes and electrochemical energy storage and conversion systems. Systems and methods of the present invention are configured for simultaneously collecting a suite of measurements characterizing a plurality of interconnected electrochemical and thermodynamic parameters relating to the electrode reaction state of advancement, voltage and temperature. Enhanced sensitivity provided by the present methods and systems combined with measurement conditions that reflect thermodynamically stabilized electrode conditions allow very accurate measurement of thermodynamic parameters, including state functions such as the Gibbs free energy, enthalpy and entropy of electrode/electrochemical cell reactions, that enable prediction of important performance attributes of electrode materials and electrochemical systems, such as the energy, power density, current rate and the cycle life of an electrochemical cell.

An automated and efficient conformation search of L-cysteine and L,L-cystine using the scaled hypersphere search method

NASA Astrophysics Data System (ADS)

Kishimoto, Naoki; Waizumi, Hiroki

2017-10-01

Stable conformers of L-cysteine and L,L-cystine were explored using an automated and efficient conformational searching method. The Gibbs energies of the stable conformers of L-cysteine and L,L-cystine were calculated with G4 and MP2 methods, respectively, at 450, 298.15, and 150 K. By assuming thermodynamic equilibrium and the barrier energies for the conformational isomerization pathways, the estimated ratios of the stable conformers of L-cysteine were compared with those determined by microwave spectroscopy in a previous study. Equilibrium structures of 1:1 and 2:1 cystine-Fe complexes were also calculated, and the energy of insertion of Fe into the disulfide bond was obtained.

Edge-augmented Fourier partial sums with applications to Magnetic Resonance Imaging (MRI)

NASA Astrophysics Data System (ADS)

Larriva-Latt, Jade; Morrison, Angela; Radgowski, Alison; Tobin, Joseph; Iwen, Mark; Viswanathan, Aditya

2017-08-01

Certain applications such as Magnetic Resonance Imaging (MRI) require the reconstruction of functions from Fourier spectral data. When the underlying functions are piecewise-smooth, standard Fourier approximation methods suffer from the Gibbs phenomenon - with associated oscillatory artifacts in the vicinity of edges and an overall reduced order of convergence in the approximation. This paper proposes an edge-augmented Fourier reconstruction procedure which uses only the first few Fourier coefficients of an underlying piecewise-smooth function to accurately estimate jump information and then incorporate it into a Fourier partial sum approximation. We provide both theoretical and empirical results showing the improved accuracy of the proposed method, as well as comparisons demonstrating superior performance over existing state-of-the-art sparse optimization-based methods.

DNA motif alignment by evolving a population of Markov chains.

PubMed

Bi, Chengpeng

2009-01-30

Deciphering cis-regulatory elements or de novo motif-finding in genomes still remains elusive although much algorithmic effort has been expended. The Markov chain Monte Carlo (MCMC) method such as Gibbs motif samplers has been widely employed to solve the de novo motif-finding problem through sequence local alignment. Nonetheless, the MCMC-based motif samplers still suffer from local maxima like EM. Therefore, as a prerequisite for finding good local alignments, these motif algorithms are often independently run a multitude of times, but without information exchange between different chains. Hence it would be worth a new algorithm design enabling such information exchange. This paper presents a novel motif-finding algorithm by evolving a population of Markov chains with information exchange (PMC), each of which is initialized as a random alignment and run by the Metropolis-Hastings sampler (MHS). It is progressively updated through a series of local alignments stochastically sampled. Explicitly, the PMC motif algorithm performs stochastic sampling as specified by a population-based proposal distribution rather than individual ones, and adaptively evolves the population as a whole towards a global maximum. The alignment information exchange is accomplished by taking advantage of the pooled motif site distributions. A distinct method for running multiple independent Markov chains (IMC) without information exchange, or dubbed as the IMC motif algorithm, is also devised to compare with its PMC counterpart. Experimental studies demonstrate that the performance could be improved if pooled information were used to run a population of motif samplers. The new PMC algorithm was able to improve the convergence and outperformed other popular algorithms tested using simulated and biological motif sequences.

Application of the Zero-Order Reaction Rate Model and Transition State Theory to predict porous Ti6Al4V bending strength.

PubMed

Reig, L; Amigó, V; Busquets, D; Calero, J A; Ortiz, J L

2012-08-01

Porous Ti6Al4V samples were produced by microsphere sintering. The Zero-Order Reaction Rate Model and Transition State Theory were used to model the sintering process and to estimate the bending strength of the porous samples developed. The evolution of the surface area during the sintering process was used to obtain sintering parameters (sintering constant, activation energy, frequency factor, constant of activation and Gibbs energy of activation). These were then correlated with the bending strength in order to obtain a simple model with which to estimate the evolution of the bending strength of the samples when the sintering temperature and time are modified: σY=P+B·[lnT·t-ΔGa/R·T]. Although the sintering parameters were obtained only for the microsphere sizes analysed here, the strength of intermediate sizes could easily be estimated following this model. Copyright © 2012 Elsevier B.V. All rights reserved.

A hierarchical Bayesian method for vibration-based time domain force reconstruction problems

NASA Astrophysics Data System (ADS)

Li, Qiaofeng; Lu, Qiuhai

2018-05-01

Traditional force reconstruction techniques require prior knowledge on the force nature to determine the regularization term. When such information is unavailable, the inappropriate term is easily chosen and the reconstruction result becomes unsatisfactory. In this paper, we propose a novel method to automatically determine the appropriate q as in ℓq regularization and reconstruct the force history. The method incorporates all to-be-determined variables such as the force history, precision parameters and q into a hierarchical Bayesian formulation. The posterior distributions of variables are evaluated by a Metropolis-within-Gibbs sampler. The point estimates of variables and their uncertainties are given. Simulations of a cantilever beam and a space truss under various loading conditions validate the proposed method in providing adaptive determination of q and better reconstruction performance than existing Bayesian methods.

Rational computational design for the development of andrographolide molecularly imprinted polymer

NASA Astrophysics Data System (ADS)

Krishnan, Hemavathi; Islam, K. M. Shafiqul; Hamzah, Zainab; Ahmad, Mohd Noor

2017-10-01

Andrographolide is a popular medicinal compound derived from Andrographis Paniculata (AP). Molecularly Imprint Polymer (MIP) is a "Lock and Key" approach, where MIP is the lock and Andrographolide is the key which fits to the MIP lock by both physically and chemically. MIP will be used as selective extraction tool to enrich Andrographolide bioactive compound. Pre-polymerization step is crucial to design MIP. This work investigates molecular interactions and the Gibbs free binding energies on the development of MIP. The structure of Andrographolide (template) and functional monomers were drawn in HyperChem 8.0.10. A hybrid quantum chemical model was used with a few functional monomers. Possible conformations of template and functional monomer as 1:n (n < 4) were designed and simulated to geometrically optimize the complex to the lowest energy in gas phase. The Gibbs free binding energies of each conformation were calculated using semi-empirical PM3 simulation method. Results proved that functional monomers that contain carboxylic group shows higher binding energy compared to those with amine functional group. Itaconic acid (IA) chosen as the best functional monomer at optimum ratio (1:3) of template: monomer to prepare andrographolide MIP. This study demonstrates the importance of studying intermolecular interaction among template, functional monomer and template-monomer ratio in developing MIP.

Disordered crystals from first principles I: Quantifying the configuration space

NASA Astrophysics Data System (ADS)

Kühne, Thomas D.; Prodan, Emil

2018-04-01

This work represents the first chapter of a project on the foundations of first-principle calculations of the electron transport in crystals at finite temperatures. We are interested in the range of temperatures, where most electronic components operate, that is, room temperature and above. The aim is a predictive first-principle formalism that combines ab-initio molecular dynamics and a finite-temperature Kubo-formula for homogeneous thermodynamic phases. The input for this formula is the ergodic dynamical system (Ω , G , dP) defining the thermodynamic crystalline phase, where Ω is the configuration space for the atomic degrees of freedom, G is the space group acting on Ω and dP is the ergodic Gibbs measure relative to the G-action. The present work develops an algorithmic method for quantifying (Ω , G , dP) from first principles. Using the silicon crystal as a working example, we find the Gibbs measure to be extremely well characterized by a multivariate normal distribution, which can be quantified using a small number of parameters. The latter are computed at various temperatures and communicated in the form of a table. Using this table, one can generate large and accurate thermally-disordered atomic configurations to serve, for example, as input for subsequent simulations of the electronic degrees of freedom.

Discontinuous Galerkin method with Gaussian artificial viscosity on graphical processing units for nonlinear acoustics

NASA Astrophysics Data System (ADS)

Tripathi, Bharat B.; Marchiano, Régis; Baskar, Sambandam; Coulouvrat, François

2015-10-01

Propagation of acoustical shock waves in complex geometry is a topic of interest in the field of nonlinear acoustics. For instance, simulation of Buzz Saw Noice requires the treatment of shock waves generated by the turbofan through the engines of aeroplanes with complex geometries and wall liners. Nevertheless, from a numerical point of view it remains a challenge. The two main hurdles are to take into account the complex geometry of the domain and to deal with the spurious oscillations (Gibbs phenomenon) near the discontinuities. In this work, first we derive the conservative hyperbolic system of nonlinear acoustics (up to quadratic nonlinear terms) using the fundamental equations of fluid dynamics. Then, we propose to adapt the classical nodal discontinuous Galerkin method to develop a high fidelity solver for nonlinear acoustics. The discontinuous Galerkin method is a hybrid of finite element and finite volume method and is very versatile to handle complex geometry. In order to obtain better performance, the method is parallelized on Graphical Processing Units. Like other numerical methods, discontinuous Galerkin method suffers with the problem of Gibbs phenomenon near the shock, which is a numerical artifact. Among the various ways to manage these spurious oscillations, we choose the method of parabolic regularization. Although, the introduction of artificial viscosity into the system is a popular way of managing shocks, we propose a new approach of introducing smooth artificial viscosity locally in each element, wherever needed. Firstly, a shock sensor using the linear coefficients of the spectral solution is used to locate the position of the discontinuities. Then, a viscosity coefficient depending on the shock sensor is introduced into the hyperbolic system of equations, only in the elements near the shock. The viscosity is applied as a two-dimensional Gaussian patch with its shape parameters depending on the element dimensions, referred here as Element Centered Smooth Artificial Viscosity. Using this numerical solver, various numerical experiments are presented for one and two-dimensional test cases in homogeneous and quiescent medium. This work is funded by CEFIPRA (Indo-French Centre for the Promotion of Advance Research) and partially aided by EGIDE (Campus France).

Spectroscopic and thermogravimetric study of nickel sulfaquinoxaline complex

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

Tailor, Sanjay M., E-mail: sanjay-tailor10@yahoo.com; Patel, Urmila H.

2016-05-06

The ability of sulfaquinoxaline (4-Amino-N-2-quinoxalinylbenzenesulfonamide) to form metal complexes are investigated. The nickel complex of sulfaquinoxaline is prepared by reflux method and characterized by CHN analysis and IR spectra. The results of IR spectral data suggest that the binding of nickel atom to the sulfonamidic nitrogen are in good agreement. The thermogravimetric analysis (TGA), differential thermal analysis (DTA) and differential thermogravimetric (DTG) analysis of nickel sulfaquinoxaline are carried out from ambient temperature to 750°C in inert nitrogen atmosphere. The activation energy, enthalpy, entropy and Gibbs free energy of nickel sulfaquinoxaline complex is determined from the thermal curves using Broido method.more » The results are reported in this paper.« less

On determining absolute entropy without quantum theory or the third law of thermodynamics

NASA Astrophysics Data System (ADS)

Steane, Andrew M.

2016-04-01

We employ classical thermodynamics to gain information about absolute entropy, without recourse to statistical methods, quantum mechanics or the third law of thermodynamics. The Gibbs-Duhem equation yields various simple methods to determine the absolute entropy of a fluid. We also study the entropy of an ideal gas and the ionization of a plasma in thermal equilibrium. A single measurement of the degree of ionization can be used to determine an unknown constant in the entropy equation, and thus determine the absolute entropy of a gas. It follows from all these examples that the value of entropy at absolute zero temperature does not need to be assigned by postulate, but can be deduced empirically.

Stress versus temperature dependence of activation energies for creep

NASA Technical Reports Server (NTRS)

Freed, A. D.; Raj, S. V.; Walker, K. P.

1992-01-01

The activation energy for creep at low stresses and elevated temperatures is associated with lattice diffusion, where the rate controlling mechanism for deformation is dislocation climb. At higher stresses and intermediate temperatures, the rate controlling mechanism changes from dislocation climb to obstacle-controlled dislocation glide. Along with this change in deformation mechanism occurs a change in the activation energy. When the rate controlling mechanism for deformation is obstacle-controlled dislocation glide, it is shown that a temperature-dependent Gibbs free energy does better than a stress-dependent Gibbs free energy in correlating steady-state creep data for both copper and LiF-22mol percent CaF2 hypereutectic salt.

Impact of uncertainty in expected return estimation on stock price volatility

NASA Astrophysics Data System (ADS)

Kostanjcar, Zvonko; Jeren, Branko; Juretic, Zeljan

2012-11-01

We investigate the origin of volatility in financial markets by defining an analytical model for time evolution of stock share prices. The defined model is similar to the GARCH class of models, but can additionally exhibit bimodal behaviour in the supply-demand structure of the market. Moreover, it differs from existing Ising-type models. It turns out that the constructed model is a solution of a thermodynamic limit of a Gibbs probability measure when the number of traders and the number of stock shares approaches infinity. The energy functional of the Gibbs probability measure is derived from the Nash equilibrium of the underlying game.

On the Gibbs phenomenon 3: Recovering exponential accuracy in a sub-interval from a spectral partial sum of a piecewise analytic function

NASA Technical Reports Server (NTRS)

Gottlieb, David; Shu, Chi-Wang

1993-01-01

The investigation of overcoming Gibbs phenomenon was continued, i.e., obtaining exponential accuracy at all points including at the discontinuities themselves, from the knowledge of a spectral partial sum of a discontinuous but piecewise analytic function. It was shown that if we are given the first N expansion coefficients of an L(sub 2) function f(x) in terms of either the trigonometrical polynomials or the Chebyshev or Legendre polynomials, an exponentially convergent approximation to the point values of f(x) in any sub-interval in which it is analytic can be constructed.

Holographic interferometry of ultrasmall-pressure-induced curvature changes of bilayer lipid membranes

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

Picard, G.; Schneider-Henriquez, J.E.; Fendler, J.H.

Two-exposure interferometric holograms have been shown to sensitively report ultrasmall-pressure (10 natm)-induced curvature changes in glyceryl monooleate (GMO) bilayer lipid membranes (BLMs). The number of concentric fringes observed, and hence the lateral distance between the plane of the Teflon and the BLM, increased linearly with increasing transmembrane pressure and led to a value of 1.1 {plus minus} 0.05 dyn/cm for the surface tension of the BLM. BLMs with appreciable Plateau-Gibbs borders have been shown to undergo nonuniform deformation; the bilayer portion is distorted less than the surrounding Plateau-Gibbs border upon the application of a transmembrane pressure gradient.

Comment on 'Surface thermodynamics, surface stress, equations at surfaces and triple lines for deformable bodies'.

PubMed

Gutman, E M

2010-10-27

In a recent publication by Olives (2010 J. Phys.: Condens. Matter 22 085005) he studied 'the thermodynamics and mechanics of the surface of a deformable body, following and refining the general approach of Gibbs' and believed that 'a new definition of the surface stress is given'. However, using the usual way of deriving the equations of Gibbs-Duhem type the author, nevertheless, has fallen into a mathematical discrepancy because he has tried to unite in one equation different thermodynamic systems and 'a new definition of the surface stress' has appeared known in the usual theory of elasticity.

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

NASA Astrophysics Data System (ADS)

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

2012-07-01

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

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

PubMed

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

2012-07-06

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

On the temperature dependence of the Adam-Gibbs equation around the crossover region in the glass transition

NASA Astrophysics Data System (ADS)

Duque, Michel; Andraca, Adriana; Goldstein, Patricia; del Castillo, Luis Felipe

2018-04-01

The Adam-Gibbs equation has been used for more than five decades, and still a question remains unanswered on the temperature dependence of the chemical potential it includes. Nowadays, it is a well-known fact that in fragile glass formers, actually the behavior of the system depends on the temperature region it is being studied. Transport coefficients change due to the appearance of heterogeneity in the liquid as it is supercooled. Using the different forms for the logarithmic shift factor and the form of the configurational entropy, we evaluate this temperature dependence and present a discussion on our results.

Boiling point determination using adiabatic Gibbs ensemble Monte Carlo simulations: Application to metals described by embedded-atom potentials

NASA Astrophysics Data System (ADS)

Gelb, Lev D.; Chakraborty, Somendra Nath

2011-12-01

The normal boiling points are obtained for a series of metals as described by the "quantum-corrected Sutton Chen" (qSC) potentials [S.-N. Luo, T. J. Ahrens, T. Çağın, A. Strachan, W. A. Goddard III, and D. C. Swift, Phys. Rev. B 68, 134206 (2003)]. Instead of conventional Monte Carlo simulations in an isothermal or expanded ensemble, simulations were done in the constant-NPH adabatic variant of the Gibbs ensemble technique as proposed by Kristóf and Liszi [Chem. Phys. Lett. 261, 620 (1996)]. This simulation technique is shown to be a precise tool for direct calculation of boiling temperatures in high-boiling fluids, with results that are almost completely insensitive to system size or other arbitrary parameters as long as the potential truncation is handled correctly. Results obtained were validated using conventional NVT-Gibbs ensemble Monte Carlo simulations. The qSC predictions for boiling temperatures are found to be reasonably accurate, but substantially underestimate the enthalpies of vaporization in all cases. This appears to be largely due to the systematic overestimation of dimer binding energies by this family of potentials, which leads to an unsatisfactory description of the vapor phase.

Gibbs-Thomson Effect in Planar Nanowires: Orientation and Doping Modulated Growth.

PubMed

Shen, Youde; Chen, Renjie; Yu, Xuechao; Wang, Qijie; Jungjohann, Katherine L; Dayeh, Shadi A; Wu, Tom

2016-07-13

Epitaxy-enabled bottom-up synthesis of self-assembled planar nanowires via the vapor-liquid-solid mechanism is an emerging and promising approach toward large-scale direct integration of nanowire-based devices without postgrowth alignment. Here, by examining large assemblies of indium tin oxide nanowires on yttria-stabilized zirconia substrate, we demonstrate for the first time that the growth dynamics of planar nanowires follows a modified version of the Gibbs-Thomson mechanism, which has been known for the past decades to govern the correlations between thermodynamic supersaturation, growth speed, and nanowire morphology. Furthermore, the substrate orientation strongly influences the growth characteristics of epitaxial planar nanowires as opposed to impact at only the initial nucleation stage in the growth of vertical nanowires. The rich nanowire morphology can be described by a surface-energy-dependent growth model within the Gibbs-Thomson framework, which is further modulated by the tin doping concentration. Our experiments also reveal that the cutoff nanowire diameter depends on the substrate orientation and decreases with increasing tin doping concentration. These results enable a deeper understanding and control over the growth of planar nanowires, and the insights will help advance the fabrication of self-assembled nanowire devices.

Statistical mechanics of money and income

NASA Astrophysics Data System (ADS)

Dragulescu, Adrian; Yakovenko, Victor

2001-03-01

Money: In a closed economic system, money is conserved. Thus, by analogy with energy, the equilibrium probability distribution of money will assume the exponential Boltzmann-Gibbs form characterized by an effective temperature. We demonstrate how the Boltzmann-Gibbs distribution emerges in computer simulations of economic models. We discuss thermal machines, the role of debt, and models with broken time-reversal symmetry for which the Boltzmann-Gibbs law does not hold. Reference: A. Dragulescu and V. M. Yakovenko, "Statistical mechanics of money", Eur. Phys. J. B 17, 723-729 (2000), [cond-mat/0001432]. Income: Using tax and census data, we demonstrate that the distribution of individual income in the United States is exponential. Our calculated Lorenz curve without fitting parameters and Gini coefficient 1/2 agree well with the data. We derive the distribution function of income for families with two earners and show that it also agrees well with the data. The family data for the period 1947-1994 fit the Lorenz curve and Gini coefficient 3/8=0.375 calculated for two-earners families. Reference: A. Dragulescu and V. M. Yakovenko, "Evidence for the exponential distribution of income in the USA", cond-mat/0008305.

Helmholtz and Gibbs ensembles, thermodynamic limit and bistability in polymer lattice models

NASA Astrophysics Data System (ADS)

Giordano, Stefano

2017-12-01

Representing polymers by random walks on a lattice is a fruitful approach largely exploited to study configurational statistics of polymer chains and to develop efficient Monte Carlo algorithms. Nevertheless, the stretching and the folding/unfolding of polymer chains within the Gibbs (isotensional) and the Helmholtz (isometric) ensembles of the statistical mechanics have not been yet thoroughly analysed by means of the lattice methodology. This topic, motivated by the recent introduction of several single-molecule force spectroscopy techniques, is investigated in the present paper. In particular, we analyse the force-extension curves under the Gibbs and Helmholtz conditions and we give a proof of the ensembles equivalence in the thermodynamic limit for polymers represented by a standard random walk on a lattice. Then, we generalize these concepts for lattice polymers that can undergo conformational transitions or, equivalently, for chains composed of bistable or two-state elements (that can be either folded or unfolded). In this case, the isotensional condition leads to a plateau-like force-extension response, whereas the isometric condition causes a sawtooth-like force-extension curve, as predicted by numerous experiments. The equivalence of the ensembles is finally proved also for lattice polymer systems exhibiting conformational transitions.

On-line Gibbs learning. II. Application to perceptron and multilayer networks

NASA Astrophysics Data System (ADS)

Kim, J. W.; Sompolinsky, H.

1998-08-01

In the preceding paper (``On-line Gibbs Learning. I. General Theory'') we have presented the on-line Gibbs algorithm (OLGA) and studied analytically its asymptotic convergence. In this paper we apply OLGA to on-line supervised learning in several network architectures: a single-layer perceptron, two-layer committee machine, and a winner-takes-all (WTA) classifier. The behavior of OLGA for a single-layer perceptron is studied both analytically and numerically for a variety of rules: a realizable perceptron rule, a perceptron rule corrupted by output and input noise, and a rule generated by a committee machine. The two-layer committee machine is studied numerically for the cases of learning a realizable rule as well as a rule that is corrupted by output noise. The WTA network is studied numerically for the case of a realizable rule. The asymptotic results reported in this paper agree with the predictions of the general theory of OLGA presented in paper I. In all the studied cases, OLGA converges to a set of weights that minimizes the generalization error. When the learning rate is chosen as a power law with an optimal power, OLGA converges with a power law that is the same as that of batch learning.

Bayesian Analysis of the Power Spectrum of the Cosmic Microwave Background

NASA Technical Reports Server (NTRS)

Jewell, Jeffrey B.; Eriksen, H. K.; O'Dwyer, I. J.; Wandelt, B. D.

2005-01-01

There is a wealth of cosmological information encoded in the spatial power spectrum of temperature anisotropies of the cosmic microwave background. The sky, when viewed in the microwave, is very uniform, with a nearly perfect blackbody spectrum at 2.7 degrees. Very small amplitude brightness fluctuations (to one part in a million!!) trace small density perturbations in the early universe (roughly 300,000 years after the Big Bang), which later grow through gravitational instability to the large-scale structure seen in redshift surveys... In this talk, I will discuss a Bayesian formulation of this problem; discuss a Gibbs sampling approach to numerically sampling from the Bayesian posterior, and the application of this approach to the first-year data from the Wilkinson Microwave Anisotropy Probe. I will also comment on recent algorithmic developments for this approach to be tractable for the even more massive data set to be returned from the Planck satellite.

Solid state amorphization of nanocrystalline nickel by cryogenic laser shock peening

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

Ye, Chang, E-mail: cye@uakron.edu; Ren, Zhencheng; Zhao, Jingyi

2015-10-07

In this study, complete solid state amorphization in nanocrystalline nickel has been achieved through cryogenic laser shock peening (CLSP). High resolution transmission electron microscopy has revealed the complete amorphous structure of the sample after CLSP processing. A molecular dynamic model has been used to investigate material behavior during the shock loading and the effects of nanoscale grain boundaries on the amorphization process. It has been found that the initial nanoscale grain boundaries increase the initial Gibbs free energy before plastic deformation and also serve as dislocation emission sources during plastic deformation to contribute to defect density increase, leading to themore » amorphization of pure nanocrystalline nickel.« less

Hydrogeochemical quality and suitability studies of groundwater in northern Bangladesh.

PubMed

Islam, M J; Hakim, M A; Hanafi, M M; Juraimi, Abdul Shukor; Aktar, Sharmin; Siddiqa, Aysha; Rahman, A K M Shajedur; Islam, M Atikul; Halim, M A

2014-07-01

Agriculture, rapid urbanization and geochemical processes have direct or indirect effects on the chemical composition of groundwater and aquifer geochemistry. Hydro-chemical investigations, which are significant for assessment of water quality, were carried out to study the sources of dissolved ions in groundwater of Dinajpur district, northern Bangladesh. The groundwater samplish were analyzed for physico-chemical properties like pH, electrical conductance, hardness, alkalinity, total dissolved solids and Ca2+, Mg2+, Na+, K+, CO3(2-), HCO3(-), SO4(2-) and Cl- ions, respectively. Based on the analyses, certain parameters like sodium adsorption ratio, soluble sodium percentage, potential salinity, residual sodium carbonate, Kelly's ratio, permeability index and Gibbs ratio were also calculated. The results showed that the groundwater of study area was fresh, slightly acidic (pH 5.3-6.4) and low in TDS (35-275 mg I(-1)). Ground water of the study area was found suitable for irrigation, drinking and domestic purposes, since most of the parameters analyzed were within the WHO recommended values for drinking water. High concentration of NO3- and Cl- was reported in areas with extensive agriculture and rapid urbanization. Ion-exchange, weathering, oxidation and dissolution of minerals were major geochemical processes governing the groundwater evolution in study area. Gibb's diagram showed that all the samples fell in the rock dominance field. Based on evaluation, it is clear that groundwater quality of the study area was suitable for both domestic and irrigation purposes.

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

NASA Astrophysics Data System (ADS)

Kruskopf, Ari; Visuri, Ville-Valtteri

2017-12-01

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

Methods for studying reaction kinetics in gas chromatography, exemplified by using the 1-chloro-2,2-dimethylaziridine interconversion reaction.

PubMed

Krupcík, J; Mydlová, J; Májek, P; Simon, P; Armstrong, D W

2008-04-04

In this paper, methods are described that are used for studying first-order reaction kinetics by gas chromatography. Basic theory is summarized and illustrated using the interconversion of 1-chloro-2,2-dimethylaziridine enantiomers as a representative example. For the determination of the kinetic and thermodynamic activation data of interconversion the following methods are reviewed: (i) classical kinetic methods where samples of batch-wise kinetic studies are analyzed by enantioselective gas chromatography, (ii) stopped-flow methods performed on one chiral column, (iii) stopped-flow methods performed on an achiral column or empty capillary coupled in series with two chiral columns, (iv) on-flow method performed on an achiral column coupled in series with two chiral columns, and (v) reaction gas chromatography, known as a dynamic gas chromatography, where the interconversion is performed on chiral column during the separation process. The determination of kinetic and thermodynamic activation data by methods (i) through (iv) is straightforward as the experimental data needed for the evaluation (particularly the concentration of reaction constituents) are accessible from the chromatograms. The evaluation of experiments from reaction chromatography method (v) is complex as the concentration bands of reaction constituents are overlapped. The following procedures have been developed to determination peak areas of reaction constituents in such complex chromatograms: (i) methods based on computer-assisted simulations of chromatograms where the kinetic activation parameters for the interconversion of enantiomers are obtained by iterative comparison of experimental and simulated chromatograms, (ii) stochastic methods based on the simulation of Gaussian distribution functions and using a time-dependent probability density function, (iii) approximation function and unified equation, (iv) computer-assisted peak deconvolution methods. Evaluation of the experimental data permits the calculation of apparent rate constants for both the interconversion of the first eluted (k (A-->B)(app)) as well as the second eluted (k(B-->A)(app)) enantiomer. The mean value for all the rate constants (from all the reviewed methods) was found for 1-chloro-2,2-dimethylaziridine A-->B enantiomer interconversion at 100 degrees C: k (A-->B)(app)=21.2 x 10(-4)s(-1) with a standard deviation sigma=10.7 x 10(-4). Evaluating data for reaction chromatography at 100 degrees C {k (app)=k(A-->B)(app)=k(B-->A)(app)=13.9 x 10(-4)s(-1), sigma=3.0 x 10(-4)s(-1)} shows that differences between k(A-->B)(app) and k(B-->A)(app) are the same within experimental error. It was shown both theoretically and experimentally that the Arrhenius activation energy (E(a)) calculated from Arrhenius plots (lnk(app) versus 1/T) is proportional to the enthalpy of activation {E(a)=DeltaH+RT}. Statistical treatment of Gibbs activation energy values gave: DeltaG (app)=110.5kJmol(-1), sigma=2.4kJmol(-1), DeltaG (A-->B)(app)=110.5kJmol(-1), sigma=2.2kJmol(-1), DeltaG (B-->A)(app)=110.3kJmol(-1), sigma=2.8kJmol(-1). This shows that the apparent Gibbs energy barriers for the interconversion of 1-chloro-2,2-dimethylaziridine enantiomers are equal DeltaG (app)=DeltaG(A-->B)(app)=DeltaG(B-->A)(app) and within the given precision of measurement independent of the experimental method used.

Cosmological parameters, shear maps and power spectra from CFHTLenS using Bayesian hierarchical inference

NASA Astrophysics Data System (ADS)

Alsing, Justin; Heavens, Alan; Jaffe, Andrew H.

2017-04-01

We apply two Bayesian hierarchical inference schemes to infer shear power spectra, shear maps and cosmological parameters from the Canada-France-Hawaii Telescope (CFHTLenS) weak lensing survey - the first application of this method to data. In the first approach, we sample the joint posterior distribution of the shear maps and power spectra by Gibbs sampling, with minimal model assumptions. In the second approach, we sample the joint posterior of the shear maps and cosmological parameters, providing a new, accurate and principled approach to cosmological parameter inference from cosmic shear data. As a first demonstration on data, we perform a two-bin tomographic analysis to constrain cosmological parameters and investigate the possibility of photometric redshift bias in the CFHTLenS data. Under the baseline ΛCDM (Λ cold dark matter) model, we constrain S_8 = σ _8(Ω _m/0.3)^{0.5} = 0.67+0.03-0.03 (68 per cent), consistent with previous CFHTLenS analyses but in tension with Planck. Adding neutrino mass as a free parameter, we are able to constrain ∑mν < 4.6 eV (95 per cent) using CFHTLenS data alone. Including a linear redshift-dependent photo-z bias Δz = p2(z - p1), we find p_1=-0.25+0.53-0.60 and p_2 = -0.15+0.17-0.15, and tension with Planck is only alleviated under very conservative prior assumptions. Neither the non-minimal neutrino mass nor photo-z bias models are significantly preferred by the CFHTLenS (two-bin tomography) data.

Estimating Brownian motion dispersal rate, longevity and population density from spatially explicit mark-recapture data on tropical butterflies.

PubMed

Tufto, Jarle; Lande, Russell; Ringsby, Thor-Harald; Engen, Steinar; Saether, Bernt-Erik; Walla, Thomas R; DeVries, Philip J

2012-07-01

1. We develop a Bayesian method for analysing mark-recapture data in continuous habitat using a model in which individuals movement paths are Brownian motions, life spans are exponentially distributed and capture events occur at given instants in time if individuals are within a certain attractive distance of the traps. 2. The joint posterior distribution of the dispersal rate, longevity, trap attraction distances and a number of latent variables representing the unobserved movement paths and time of death of all individuals is computed using Gibbs sampling. 3. An estimate of absolute local population density is obtained simply by dividing the Poisson counts of individuals captured at given points in time by the estimated total attraction area of all traps. Our approach for estimating population density in continuous habitat avoids the need to define an arbitrary effective trapping area that characterized previous mark-recapture methods in continuous habitat. 4. We applied our method to estimate spatial demography parameters in nine species of neotropical butterflies. Path analysis of interspecific variation in demographic parameters and mean wing length revealed a simple network of strong causation. Larger wing length increases dispersal rate, which in turn increases trap attraction distance. However, higher dispersal rate also decreases longevity, thus explaining the surprising observation of a negative correlation between wing length and longevity. © 2012 The Authors. Journal of Animal Ecology © 2012 British Ecological Society.

Generalized Gibbs ensembles for quantum field theories

NASA Astrophysics Data System (ADS)

Essler, F. H. L.; Mussardo, G.; Panfil, M.

2015-05-01

We consider the nonequilibrium dynamics in quantum field theories (QFTs). After being prepared in a density matrix that is not an eigenstate of the Hamiltonian, such systems are expected to relax locally to a stationary state. In the presence of local conservation laws, these stationary states are believed to be described by appropriate generalized Gibbs ensembles. Here we demonstrate that in order to obtain a correct description of the stationary state, it is necessary to take into account conservation laws that are not (ultra)local in the usual sense of QFTs, but fulfill a significantly weaker form of locality. We discuss the implications of our results for integrable QFTs in one spatial dimension.

Change in the Gibbs energy of 18-crown-6 ether transfer from methanol to methanol-acetonitrile mixtures at 298 K

NASA Astrophysics Data System (ADS)

Kuz'mina, I. A.; Usacheva, T. R.; Kuz'mina, K. I.; Volkova, M. A.; Sharnin, V. A.

2015-01-01

The Gibbs energies of the transfer of 18-crown-6 ether from methanol to its mixtures with acetonitrile (χAN = 0.0-1.0 mole fraction) are determined by means of interphase distribution at 298 K. The effect the solvent composition has on the thermodynamic characteristics of the solvation of 18-crown-6 ether is analyzed. An increase in the content of acetonitrile in the mixed solvent enhances the solvation of crown ether due to changes in the energy of the solution. Resolvation of the macrocycle is assumed to be complete at acetonitrile concentrations higher than 0.6 mole fraction.

Employment of Gibbs-Donnan-based concepts for interpretation of the properties of linear polyelectrolyte solutions

USGS Publications Warehouse

Marinsky, J.A.; Reddy, M.M.

1991-01-01

Earlier research has shown that the acid dissociation and metal ion complexation equilibria of linear, weak-acid polyelectrolytes and their cross-linked gel analogues are similarly sensitive to the counterion concentration levels of their solutions. Gibbs-Donnan-based concepts, applicable to the gel, are equally applicable to the linear polyelectrolyte for the accommodation of this sensitivity to ionic strength. This result is presumed to indicate that the linear polyelectrolyte in solution develops counterion-concentrating regions that closely resemble the gel phase of their analogues. Advantage has been taken of this description of linear polyelectrolytes to estimate the solvent uptake by these regions. ?? 1991 American Chemical Society.

Maxwell’s equal area law for Lovelock thermodynamics

NASA Astrophysics Data System (ADS)

Xu, Hao; Xu, Zhen-Ming

We present the construction of Maxwell’s equal area law for the Guass-Bonnet AdS black holes in d = 5, 6 and third-order Lovelock AdS black holes in d = 7, 8. The equal area law can be used to find the number and location of the points of intersection in the plots of Gibbs free energy, so that we can get the thermodynamically preferred solution which corresponds to the first-order phase transition. We obtain the radius of the small and large black holes in the phase transition which share the same Gibbs free energy. The case with two critical points is explored in much more details. The latent heat is also studied.

Phase equilibrium of methane and nitrogen at low temperatures - Application to Titan

NASA Technical Reports Server (NTRS)

Kouvaris, Louis C.; Flasar, F. M.

1991-01-01

Since the vapor phase composition of Titan's methane-nitrogen lower atmosphere is uniquely determined as a function of the Gibbs phase rule, these data are presently computed via integration of the Gibbs-Duhem equation. The thermodynamic consistency of published measurements and calculations of the vapor phase composition is then examined, and the saturated mole fraction of gaseous methane is computed as a function of altitude up to the 700-mbar level. The mole fraction is found to lie approximately halfway between that computed from Raoult's law, for a gas in equilibrium with an ideal solution of liquid nitrogen and methane, and that for a gas in equilibrium with pure liquid methane.

Stress versus temperature dependent activation energies in creep

NASA Technical Reports Server (NTRS)

Freed, A. D.; Raj, S. V.; Walker, K. P.

1990-01-01

The activation energy for creep at low stresses and elevated temperatures is lattice diffusion, where the rate controlling mechanism for deformation is dislocation climb. At higher stresses and intermediate temperatures, the rate controlling mechanism changes from that of dislocation climb to one of obstacle-controlled dislocation glide. Along with this change, there occurs a change in the activation energy. It is shown that a temperature-dependent Gibbs free energy does a good job of correlating steady-state creep data, while a stress-dependent Gibbs free energy does a less desirable job of correlating the same data. Applications are made to copper and a LiF-22 mol. percent CaF2 hypereutectic salt.

A Bayesian state-space approach for damage detection and classification

NASA Astrophysics Data System (ADS)

Dzunic, Zoran; Chen, Justin G.; Mobahi, Hossein; Büyüköztürk, Oral; Fisher, John W.

2017-11-01

The problem of automatic damage detection in civil structures is complex and requires a system that can interpret collected sensor data into meaningful information. We apply our recently developed switching Bayesian model for dependency analysis to the problems of damage detection and classification. The model relies on a state-space approach that accounts for noisy measurement processes and missing data, which also infers the statistical temporal dependency between measurement locations signifying the potential flow of information within the structure. A Gibbs sampling algorithm is used to simultaneously infer the latent states, parameters of the state dynamics, the dependence graph, and any changes in behavior. By employing a fully Bayesian approach, we are able to characterize uncertainty in these variables via their posterior distribution and provide probabilistic estimates of the occurrence of damage or a specific damage scenario. We also implement a single class classification method which is more realistic for most real world situations where training data for a damaged structure is not available. We demonstrate the methodology with experimental test data from a laboratory model structure and accelerometer data from a real world structure during different environmental and excitation conditions.

Joint time/frequency-domain inversion of reflection data for seabed geoacoustic profiles and uncertainties.

PubMed

Dettmer, Jan; Dosso, Stan E; Holland, Charles W

2008-03-01

This paper develops a joint time/frequency-domain inversion for high-resolution single-bounce reflection data, with the potential to resolve fine-scale profiles of sediment velocity, density, and attenuation over small seafloor footprints (approximately 100 m). The approach utilizes sequential Bayesian inversion of time- and frequency-domain reflection data, employing ray-tracing inversion for reflection travel times and a layer-packet stripping method for spherical-wave reflection-coefficient inversion. Posterior credibility intervals from the travel-time inversion are passed on as prior information to the reflection-coefficient inversion. Within the reflection-coefficient inversion, parameter information is passed from one layer packet inversion to the next in terms of marginal probability distributions rotated into principal components, providing an efficient approach to (partially) account for multi-dimensional parameter correlations with one-dimensional, numerical distributions. Quantitative geoacoustic parameter uncertainties are provided by a nonlinear Gibbs sampling approach employing full data error covariance estimation (including nonstationary effects) and accounting for possible biases in travel-time picks. Posterior examination of data residuals shows the importance of including data covariance estimates in the inversion. The joint inversion is applied to data collected on the Malta Plateau during the SCARAB98 experiment.

Thermodynamic calculations for the liquid systems NaK, KCs and LiPb

NASA Astrophysics Data System (ADS)

Alblas, B. P.; Van Der Lugt, W.; Visser, E. G.; De Hosson, J. Th. M.

1982-06-01

The semi-empirical model for the calculation of the Gibbs free energy of mixing via the entropy of mixing, proposed by Visser et al. [1], is used to determine the activity coefficients and the long-wavelength limit of the structure factor, SCC(0). For the liquid alloys systems NaK and KCs the method leads to fairly accurate results, indicating almost ideal behaviour. For the compound-forming liquid alloys systems LiPb the agreement with experiment is less favourable, but the calculations clearly demonstrate the important influence of the volume contraction on the entropy.

Activities in Cu2S-FeS-PbS melts at 1200 °C

NASA Astrophysics Data System (ADS)

Eriç, H.; Timuçin, M.

1981-09-01

The dew-point method was used to determine the vapor pressures of PbS over liquid sulfides of the system Cu2S-FeS-PbS at 1200 °C. From the PbS activity data, activities of Cu2S and FeS were evaluated both in binary and ternary melts by Gibbs-Duhem calculations. The systems Cu2S-PbS and Cu2S-FeS exhibit negative departures from ideal behavior, while the FeS-PbS melts are ideal solutions at 1200 °C.

Boiling point determination using adiabatic Gibbs ensemble Monte Carlo simulations: application to metals described by embedded-atom potentials.

PubMed

Gelb, Lev D; Chakraborty, Somendra Nath

2011-12-14

The normal boiling points are obtained for a series of metals as described by the "quantum-corrected Sutton Chen" (qSC) potentials [S.-N. Luo, T. J. Ahrens, T. Çağın, A. Strachan, W. A. Goddard III, and D. C. Swift, Phys. Rev. B 68, 134206 (2003)]. Instead of conventional Monte Carlo simulations in an isothermal or expanded ensemble, simulations were done in the constant-NPH adabatic variant of the Gibbs ensemble technique as proposed by Kristóf and Liszi [Chem. Phys. Lett. 261, 620 (1996)]. This simulation technique is shown to be a precise tool for direct calculation of boiling temperatures in high-boiling fluids, with results that are almost completely insensitive to system size or other arbitrary parameters as long as the potential truncation is handled correctly. Results obtained were validated using conventional NVT-Gibbs ensemble Monte Carlo simulations. The qSC predictions for boiling temperatures are found to be reasonably accurate, but substantially underestimate the enthalpies of vaporization in all cases. This appears to be largely due to the systematic overestimation of dimer binding energies by this family of potentials, which leads to an unsatisfactory description of the vapor phase. © 2011 American Institute of Physics

Langmuir-Gibbs Surface Phases and Transitions

NASA Astrophysics Data System (ADS)

Ocko, Benjamin; Sloutskin, Eli; Sapir, Zvi; Tamam, Lilach; Deutsch, Moshe; Bain, Colin

2007-03-01

Recent synchrotron x-ray measurements reveal surface ordering transitions in films of medium-length linear hydrocarbons (alkanes), spread on the water surface. Alkanes longer than hexane do not spread on the free surface of water. However, sub-mM concentrations of some anionic surfactants (e.g. CTAB) induce formation of thermodynamically stable alkane monolayers, through a ``pseudo-partial wetting'' phenomenon[1]. The monolayers, incorporating both water-insoluble alkanes (Langmuir) and water-soluble CTAB molecules (Gibbs) are called Langmuir-Gibbs (LG) films. The films formed by alkanes with n <=17 exhibit ordering transition upon cooling [2], below which the molecules are normal to the water surface and hexagonally packed, with CTAB molecules randomly mixed inside the quasi-2D crystal. Alkanes with n>17 can not form ordered LG monolayers, due to the repulsion from the n=16 tails of CTAB. This repulsion arises from the two chains' length mismatch. A demixing transition occurs upon ordering, with a pure alkane quasi-2D crystal forming on top of disordered alkyl tails of CTAB molecules. [1] K.M. Wilkinson et al., Chem. Phys. Phys. Chem. 6, 547 (2005). [2] E. Sloutskin, Z. Sapir, L. Tamam, B.M. Ocko, C.D. Bain, and M. Deutsch, Thin Solid Films, in press; K.M. Wilkinson, L. Qunfang, and C.D. Bain, Soft Matter 2, 66 (2006).

Long-ranged Fermi-Pasta-Ulam systems in thermal contact: Crossover from q-statistics to Boltzmann-Gibbs statistics

NASA Astrophysics Data System (ADS)

Bagchi, Debarshee; Tsallis, Constantino

2017-04-01

The relaxation to equilibrium of two long-range-interacting Fermi-Pasta-Ulam-like models (β type) in thermal contact is numerically studied. These systems, with different sizes and energy densities, are coupled to each other by a few thermal contacts which are short-range harmonic springs. By using the kinetic definition of temperature, we compute the time evolution of temperature and energy density of the two systems. Eventually, for some time t >teq, the temperature and energy density of the coupled system equilibrate to values consistent with standard Boltzmann-Gibbs thermostatistics. The equilibration time teq depends on the system size N as teq ∼Nγ where γ ≃ 1.8. We compute the velocity distribution P (v) of the oscillators of the two systems during the relaxation process. We find that P (v) is non-Gaussian and is remarkably close to a q-Gaussian distribution for all times before thermal equilibrium is reached. During the relaxation process we observe q > 1 while close to t =teq the value of q converges to unity and P (v) approaches a Gaussian. Thus the relaxation phenomenon in long-ranged systems connected by a thermal contact can be generically described as a crossover from q-statistics to Boltzmann-Gibbs statistics.

Occupation times and ergodicity breaking in biased continuous time random walks

NASA Astrophysics Data System (ADS)

Bel, Golan; Barkai, Eli

2005-12-01

Continuous time random walk (CTRW) models are widely used to model diffusion in condensed matter. There are two classes of such models, distinguished by the convergence or divergence of the mean waiting time. Systems with finite average sojourn time are ergodic and thus Boltzmann-Gibbs statistics can be applied. We investigate the statistical properties of CTRW models with infinite average sojourn time; in particular, the occupation time probability density function is obtained. It is shown that in the non-ergodic phase the distribution of the occupation time of the particle on a given lattice point exhibits bimodal U or trimodal W shape, related to the arcsine law. The key points are as follows. (a) In a CTRW with finite or infinite mean waiting time, the distribution of the number of visits on a lattice point is determined by the probability that a member of an ensemble of particles in equilibrium occupies the lattice point. (b) The asymmetry parameter of the probability distribution function of occupation times is related to the Boltzmann probability and to the partition function. (c) The ensemble average is given by Boltzmann-Gibbs statistics for either finite or infinite mean sojourn time, when detailed balance conditions hold. (d) A non-ergodic generalization of the Boltzmann-Gibbs statistical mechanics for systems with infinite mean sojourn time is found.

Complete Scene Recovery and Terrain Classification in Textured Terrain Meshes

PubMed Central

Song, Wei; Cho, Kyungeun; Um, Kyhyun; Won, Chee Sun; Sim, Sungdae

2012-01-01

Terrain classification allows a mobile robot to create an annotated map of its local environment from the three-dimensional (3D) and two-dimensional (2D) datasets collected by its array of sensors, including a GPS receiver, gyroscope, video camera, and range sensor. However, parts of objects that are outside the measurement range of the range sensor will not be detected. To overcome this problem, this paper describes an edge estimation method for complete scene recovery and complete terrain reconstruction. Here, the Gibbs-Markov random field is used to segment the ground from 2D videos and 3D point clouds. Further, a masking method is proposed to classify buildings and trees in a terrain mesh. PMID:23112653

A Step Towards CO2-Neutral Aviation

NASA Technical Reports Server (NTRS)

Brankovic, Andreja; Ryder, Robert C.; Hendricks, Robert C.; Huber, Marcia L.

2008-01-01

An approximation method for evaluation of the caloric equations used in combustion chemistry simulations is described. The method is applied to generate the equations of specific heat, static enthalpy, and Gibb's free energy for fuel mixtures of interest to gas turbine engine manufacturers. Liquid-phase fuel properties are also derived. The fuels investigated include JP-8, synthetic fuel, and two blends of JP-8 and synthetic fuel. The complete set of fuel property equations for both phases are implemented into a computational fluid dynamics (CFD) flow solver database, and multiphase, reacting flow simulations of a well-tested liquid-fueled combustor are performed. The simulations are a first step in understanding combustion system performance and operational issues when using alternate fuels, at practical engine operating conditions.

Thermal behavior and compatibility study of dihydroxylammonium 3,4-dinitraminofurazan

NASA Astrophysics Data System (ADS)

Huang, Haifeng; Shi, Yameng; Yu, Yao; Yang, Jun

2018-04-01

A large number of nitramino-featured energetic salts have been reported and some of them show promising properties. Among them, the dihydroxylammonium 3,4-dinitraminofurazan (HADNAF) is easy to synthesize and shows high calculated detonation performances and acceptable thermal stability. The non-isothermal kinetics parameters of HADNAF including the apparent activation energy (E) and pre-exponential factor (A) of the exothermic decomposition reaction, and activation entropy (ΔS≠), activation enthalpy (ΔH≠), activation Gibbs free energy (ΔG≠) at TP0 of the reaction and the critical temperature of thermal explosion (Tb) were obtained by Kissinger's and Ozawa's method, respectively. Additionally, the compatibility of HADNAF with other materials (e.g. TNT, RDX, HMX, B, Mg) was tested by DSC method.

Applications of physics to economics and finance: Money, income, wealth, and the stock market

NASA Astrophysics Data System (ADS)

Dragulescu, Adrian Antoniu

Several problems arising in Economics and Finance are analyzed using concepts and quantitative methods from Physics. The dissertation is organized as follows: In the first chapter it is argued that in a closed economic system, money is conserved. Thus, by analogy with energy, the equilibrium probability distribution of money must follow the exponential Boltzmann-Gibbs law characterized by an effective temperature equal to the average amount of money per economic agent. The emergence of Boltzmann-Gibbs distribution is demonstrated through computer simulations of economic models. A thermal machine which extracts a monetary profit can be constructed between two economic systems with different temperatures. The role of debt and models with broken time-reversal symmetry for which the Boltzmann-Gibbs law does not hold, are discussed. In the second chapter, using data from several sources, it is found that the distribution of income is described for the great majority of population by an exponential distribution, whereas the high-end tail follows a power law. From the individual income distribution, the probability distribution of income for families with two earners is derived and it is shown that it also agrees well with the data. Data on wealth is presented and it is found that the distribution of wealth has a structure similar to the distribution of income. The Lorenz curve and Gini coefficient were calculated and are shown to be in good agreement with both income and wealth data sets. In the third chapter, the stock-market fluctuations at different time scales are investigated. A model where stock-price dynamics is governed by a geometrical (multiplicative) Brownian motion with stochastic variance is proposed. The corresponding Fokker-Planck equation can be solved exactly. Integrating out the variance, an analytic formula for the time-dependent probability distribution of stock price changes (returns) is found. The formula is in excellent agreement with the Dow-Jones index for the time lags from 1 to 250 trading days. For time lags longer than the relaxation time of variance, the probability distribution can be expressed in a scaling form using a Bessel function. The Dow-Jones data follow the scaling function for seven orders of magnitude.

Classical and quantum Reissner-Nordström black hole thermodynamics and first order phase transition

NASA Astrophysics Data System (ADS)

Ghaffarnejad, Hossein

2016-01-01

First we consider classical Reissner-Nordström black hole (CRNBH) metric which is obtained by solving Einstein-Maxwell metric equation for a point electric charge e inside of a spherical static body with mass M. It has 2 interior and exterior horizons. Using Bekenstein-Hawking entropy theorem we calculate interior and exterior entropy, temperature, Gibbs free energy and heat capacity at constant electric charge. We calculate first derivative of the Gibbs free energy with respect to temperature which become a singular function having a singularity at critical point Mc=2|e|/√{3} with corresponding temperature Tc=1/24π√{3|e|}. Hence we claim first order phase transition is happened there. Temperature same as Gibbs free energy takes absolutely positive (negative) values on the exterior (interior) horizon. The Gibbs free energy takes two different positive values synchronously for 0< T< Tc but not for negative values which means the system is made from two subsystem. For negative temperatures entropy reaches to zero value at Tto-∞ and so takes Bose-Einstein condensation single state. Entropy increases monotonically in case 0< T< Tc. Regarding results of the work presented at Wang and Huang (Phys. Rev. D 63:124014, 2001) we calculate again the mentioned thermodynamical variables for remnant stable final state of evaporating quantum Reissner-Nordström black hole (QRNBH) and obtained results same as one in case of the CRNBH. Finally, we solve mass loss equation of QRNBH against advance Eddington-Finkelstein time coordinate and derive luminosity function. We obtain switching off of QRNBH evaporation before than the mass completely vanishes. It reaches to a could Lukewarm type of RN black hole which its final remnant mass is m_{final}=|e| in geometrical units. Its temperature and luminosity vanish but not in Schwarzschild case of evaporation. Our calculations can be take some acceptable statements about information loss paradox (ILP).

Asymptotic approximations to posterior distributions via conditional moment equations

USGS Publications Warehouse

Yee, J.L.; Johnson, W.O.; Samaniego, F.J.

2002-01-01

We consider asymptotic approximations to joint posterior distributions in situations where the full conditional distributions referred to in Gibbs sampling are asymptotically normal. Our development focuses on problems where data augmentation facilitates simpler calculations, but results hold more generally. Asymptotic mean vectors are obtained as simultaneous solutions to fixed point equations that arise naturally in the development. Asymptotic covariance matrices flow naturally from the work of Arnold & Press (1989) and involve the conditional asymptotic covariance matrices and first derivative matrices for conditional mean functions. When the fixed point equations admit an analytical solution, explicit formulae are subsequently obtained for the covariance structure of the joint limiting distribution, which may shed light on the use of the given statistical model. Two illustrations are given. ?? 2002 Biometrika Trust.

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

PubMed

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

2017-09-14

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

Thermodynamic stability of copper gallates determined from the E.M.F. method

NASA Astrophysics Data System (ADS)

Jendrzejczyk-Handzlik, Dominika; Fitzner, Krzysztof

2015-12-01

Employing following electrochemical cells with the solid YSZ electrolyte: CuO, Cu2O /O2-/ air (pO2 = 0.21​ atm) CuGa2O4, CuGaO2, Ga2O3 /O2-/ air (pO2 = 0.21⁣ a t m) CuGa2O4, CuGaO2, Cu2O /O2-/ air (pO2 = 0.21​ atm) Ni, NiO /O2-/ Ga2O3, CuGaO2, Cu The Gibbs free energy of formation of solid CuGa2O4 and CuGaO2 phases was determined in the temperature range from 1048 to 1223 K. Obtained results were used to derive Gibbs free energy change of the reaction of formation of solid phases from respective oxides: CuO+Ga2O3=CuGa2O4 ∆ GCuGa2O4 0(J/mol) = 21642 - 26.01 × T(± 630) ½Cu2O +½Ga2O3=CuGaO2 ∆ G CuGa O2 0 (J / mol) = - 12879 + 6.29 × T (± 640) Finally, present results were applied to the calculation of oxygen potential diagrams at different temperatures, and consequently, to the prediction of the stability ranges of these both solid phases.

Constitution and thermodynamics of the Mo-Ru, Mo-Pd, Ru-Pd and Mo-Ru-Pd systems

NASA Astrophysics Data System (ADS)

Kleykamp, H.

1989-09-01

The constitution of the Mo-Ru, Mo-Pd and Ru-Pd systems was reinvestigated between 800 and 2000°C. The Mo-Ru system is of the eutectic type, a σ-phase Mo 5Ru 3 exists between 1915 and 1143°C. The Mo-Pd system is characterized by an hcp phase Mo 9Pd 11 and by two peritectic reactions, β- Mo( Pd) + L = Mo9Pd11andMo9Pd11 + L = α- Pd( Mo). Mo 9Pd 11 decomposes eutectoidally at 1370°C. The Ru-Pd system is simple peritectic. The continuous series of the hcp solid solutions between Mo 9Pd 11 and ɛ-Ru(Mo, Pd) in the ternary Mo-Ru-Pd system observed at 1700°C are suppressed below 1370°C near the Mo-Pd boundary system by the formation of a narrow α + β + ɛ three-phase field. Relative partial molar Gibbs energies of Mo, Mo and Ru in the respective binary systems and of Mo in the ternary system were measured by the EMF method with a Zr(Ca)O 2 electrolyte. xsΔ ḠMo∞ quantities were evaluated at 1200 K which give -43 kJ/mol Mo in Ru and -94 kJ/mol Mo in Pd at infinite dilution. Gibbs energies of formation of the Mo-Ru and Mo-Pd systems were calculated.

An Interpolation Method for Obtaining Thermodynamic Properties Near Saturated Liquid and Saturated Vapor Lines

NASA Technical Reports Server (NTRS)

Nguyen, Huy H.; Martin, Michael A.

2004-01-01

The two most common approaches used to formulate thermodynamic properties of pure substances are fundamental (or characteristic) equations of state (Helmholtz and Gibbs functions) and a piecemeal approach that is described in Adebiyi and Russell (1992). This paper neither presents a different method to formulate thermodynamic properties of pure substances nor validates the aforementioned approaches. Rather its purpose is to present a method to generate property tables from existing property packages and a method to facilitate the accurate interpretation of fluid thermodynamic property data from those tables. There are two parts to this paper. The first part of the paper shows how efficient and usable property tables were generated, with the minimum number of data points, using an aerospace industry standard property package. The second part describes an innovative interpolation technique that has been developed to properly obtain thermodynamic properties near the saturated liquid and saturated vapor lines.

Critical evaluation and thermodynamic optimization of the Iron-Rare-Earth systems

NASA Astrophysics Data System (ADS)

Konar, Bikram

Rare-Earth elements by virtue of its typical magnetic, electronic and chemical properties are gaining importance in power, electronics, telecommunications and sustainable green technology related industries. The Magnets from RE-alloys are more powerful than conventional magnets which have more longevity and high temperature workability. The dis-equilibrium in the Rare-Earth element supply and demand has increased the importance of recycling and extraction of REE's from used permanent Magnets. However, lack of the thermodynamic data on RE alloys has made it difficult to design an effective extraction and recycling process. In this regard, Computational Thermodynamic calculations can serve as a cost effective and less time consuming tool to design a waste magnet recycling process. The most common RE permanent magnet is Nd magnet (Nd 2Fe14B). Various elements such as Dy, Tb, Pr, Cu, Co, Ni, etc. are also added to increase its magnetic and mechanical properties. In order to perform reliable thermodynamic calculations for the RE recycling process, accurate thermodynamic database for RE and related alloys are required. The thermodynamic database can be developed using the so-called CALPHAD method. The database development based on the CALPHAD method is essentially the critical evaluation and optimization of all available thermodynamic and phase diagram data. As a results, one set of self-consistent thermodynamic functions for all phases in the given system can be obtained, which can reproduce all reliable thermodynamic and phase diagram data. The database containing the optimized Gibbs energy functions can be used to calculate complex chemical reactions for any high temperature processes. Typically a Gibbs energy minimization routine, such as in FactSage software, can be used to obtain the accurate thermodynamic equilibrium in multicomponent systems. As part of a large thermodynamic database development for permanent magnet recycling and Mg alloy design, all thermodynamic and phase diagram data in the literature for the fourteen Fe-RE binary systems: Fe-La, Fe-Ce, Fe-Pr, Fe-Nd, Fe-Sm, Fe-Gd, Fe-Tb, Fe-Dy, Fe-Ho, Fe-Er, Fe-Tm, Fe-Lu, Fe-Sc and Fe-Y are critically evaluated and optimized to obtain thermodynamic model parameters. The model parameters can be used to calculate phase diagrams and Gibbs energies of all phases as functions of temperature and composition. This database can be incorporated with the present thermodynamic database in FactSage software to perform complex chemical reactions and phase diagram calculations for RE magnet recycling process.

Iterative and function-continuation Fourier deconvolution methods for enhancing mass spectrometer resolution

NASA Technical Reports Server (NTRS)

Ioup, J. W.; Ioup, G. E.; Rayborn, G. H., Jr.; Wood, G. M., Jr.; Upchurch, B. T.

1984-01-01

Mass spectrometer data in the form of ion current versus mass-to-charge ratio often include overlapping mass peaks, especially in low- and medium-resolution instruments. Numerical deconvolution of such data effectively enhances the resolution by decreasing the overlap of mass peaks. In this paper two approaches to deconvolution are presented: a function-domain iterative technique and a Fourier transform method which uses transform-domain function-continuation. Both techniques include data smoothing to reduce the sensitivity of the deconvolution to noise. The efficacy of these methods is demonstrated through application to representative mass spectrometer data and the deconvolved results are discussed and compared to data obtained from a spectrometer with sufficient resolution to achieve separation of the mass peaks studied. A case for which the deconvolution is seriously affected by Gibbs oscillations is analyzed.

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

NASA Technical Reports Server (NTRS)

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

1992-01-01

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

Effect of Surface Excess Energy Transport on the Rupture of an Evaporating Film

NASA Astrophysics Data System (ADS)

Luo, Yan; Zhou, Jianqiu; Yang, Xia; Liu, Rong

2018-05-01

In most of existing works on the instabilities of an evaporating film, the energy boundary condition only takes into account contributions of the evaporation latent heat and the heat conduction in the liquid. We use a new generalized energy boundary condition at the evaporating liquid-vapor interface, in which the contribution of the transport of the Gibbs excess energy is included. We have derived the long-wave equations in which the thickness of film and the interfacial temperature are coupled to describe the dynamics of an evaporating thin film. The results of our computation show that the transport of the Gibbs excess internal energy delay the rupture of thin films due to van de Waals force, evaporating effect and vapor recoil.

Circular dichroism and UV resonance Raman study of the impact of alcohols on the Gibbs free energy landscape of an α-helical peptide†

PubMed Central

Xiong, Kan; Asher, Sanford A

2010-01-01

We used CD and UV resonance Raman spectroscopy to study the impact of alcohols on the conformational equilibria and relative Gibbs free energy landscapes along the Ramanchandran Ψ-coordinate of a mainly poly-ala peptide, AP of sequence AAAAA(AAARA)3A. 2,2,2-trifluroethanol (TFE) most stabilizes the α-helical-like conformations, followed by ethanol, methanol and pure water. The π-bulge conformation is stabilized more than the α-helix, while the 310-helix is destabilized due to the alcohol increased hydrophobicity. Turns are also stabilized by alcohols. We also found that while TFE induces more α-helices, it favors multiple, shorter helix segments. PMID:20225890

Correlations after quantum quenches in the XXZ spin chain: failure of the generalized Gibbs ensemble.

PubMed

Pozsgay, B; Mestyán, M; Werner, M A; Kormos, M; Zaránd, G; Takács, G

2014-09-12

We study the nonequilibrium time evolution of the spin-1/2 anisotropic Heisenberg (XXZ) spin chain, with a choice of dimer product and Néel states as initial states. We investigate numerically various short-ranged spin correlators in the long-time limit and find that they deviate significantly from predictions based on the generalized Gibbs ensemble (GGE) hypotheses. By computing the asymptotic spin correlators within the recently proposed quench-action formalism [Phys. Rev. Lett. 110, 257203 (2013)], however, we find excellent agreement with the numerical data. We, therefore, conclude that the GGE cannot give a complete description even of local observables, while the quench-action formalism correctly captures the steady state in this case.

Relations between dissipated work and Rényi divergences in the generalized Gibbs ensemble

NASA Astrophysics Data System (ADS)

Wei, Bo-Bo

2018-04-01

In this work, we show that the dissipation in a many-body system under an arbitrary nonequilibrium process is related to the Rényi divergences between two states along the forward and reversed dynamics under a very general family of initial conditions. This relation generalizes the links between dissipated work and Rényi divergences to quantum systems with conserved quantities whose equilibrium state is described by the generalized Gibbs ensemble. The relation is applicable for quantum systems with conserved quantities and can be applied to protocols driving the system between integrable and chaotic regimes. We demonstrate our ideas by considering the one-dimensional transverse quantum Ising model and the Jaynes-Cummings model which are driven out of equilibrium.

Vapor-liquid phase equilibria of water modelled by a Kim-Gordon potential

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

Maerzke, K A; McGrath, M J; Kuo, I W

2009-03-16

Gibbs ensemble Monte Carlo simulations were carried out to investigate the properties of a frozen-electron-density (or Kim-Gordon, KG) model of water along the vapor-liquid coexistence curve. Because of its theoretical basis, such a KG model provides for seamless coupling to Kohn-Sham density functional theory for use in mixed quantum mechanics/molecular mechanics (QM/MM) implementations. The Gibbs ensemble simulations indicate rather limited transferability of such a simple KG model to other state points. Specifically, a KG model that was parameterized by Barker and Sprik to the properties of liquid water at 300 K, yields saturated vapor pressures and a critical temperature thatmore » are significantly under- and over-estimated, respectively.« less

Gibbs-Donnan ratio and channel conductance of Tetrahymena cilia in mixed solution of K+ and Ca2+.

PubMed Central

Oosawa, Y; Kasai, M

1988-01-01

A single cation-channel from Tetrahymena cilia was incorporated into planar lipid bilayers. This channel was voltage-independent and is permeable to K+ and Ca2+. In the experiments with mixed solutions where the concentrations of K+ and Ca2+ were varied, the single-channel conductance was found to be influenced by the Gibbs-Donnan ratio. The data are explained by assuming that the binding sites of this channel were always occupied by two potassium ions or one calcium ion under the present experimental conditions (5 mM-90 mM K+ and 0.5 mM-35 mM Ca2+) and these bound cations determined the channel conductivity. PMID:2462927

Generalized Gibbs distribution and energy localization in the semiclassical FPU problem

NASA Astrophysics Data System (ADS)

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

2011-03-01

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

DFT Studies of SN2 Dechlorination of Polychlorinated Biphenyls.

PubMed

Krzemińska, Agnieszka; Paneth, Piotr

2016-06-21

Nucleophilic dechlorination of all 209 PCBs congeners by ethylene glycol anion has been studied theoretically at the DFT level. The obtained Gibbs free energies of activation are in the range 7-22 kcal/mol. The reaction Gibbs free energies indicate that all reactions are virtually irreversible. Due to geometric constrains these reactions undergo rather untypical attack with attacking oxygen atom being nearly perpendicular to the attacked C-Cl bond. The most prone to substitution are chlorine atoms that occupy ortho- (2, 2', 6, 6') positions. These results provide extensive information on the PEG/KOH dependent PCBs degradation. They can also be used in further developments of reaction class transition state theory (RC-TST) for description of complex reactive systems encountered for example in combustion processes.

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

Khodam-Mohammadi, A.; Monshizadeh, M.

We give a review of the existence of Taub-NUT/bolt solutions in Einstein Gauss-Bonnet gravity with the parameter {alpha} in six dimensions. Although the spacetime with base space S{sup 2}xS{sup 2} has a curvature singularity at r=N, which does not admit NUT solutions, we may proceed with the same computations as in the CP{sup 2} case. The investigation of thermodynamics of NUT/bolt solutions in six dimensions is carried out. We compute the finite action, mass, entropy, and temperature of the black hole. Then the validity of the first law of thermodynamics is demonstrated. It is shown that in NUT solutions allmore » thermodynamic quantities for both base spaces are related to each other by substituting {alpha}{sup CP{sup k}}=[(k+1)/k]{alpha}{sup S{sup 2}}{sup xS{sup 2}}{sup x...S{sub k}{sup 2}}. So, no further information is given by investigating NUT solutions in the S{sup 2}xS{sup 2} case. This relation is not true for bolt solutions. A generalization of the thermodynamics of black holes to arbitrary even dimensions is made using a new method based on the Gibbs-Duhem relation and Gibbs free energy for NUT solutions. According to this method, the finite action in Einstein Gauss-Bonnet is obtained by considering the generalized finite action in Einstein gravity with an additional term as a function of {alpha}. Stability analysis is done by investigating the heat capacity and entropy in the allowed range of {alpha}, {lambda}, and N. For NUT solutions in d dimensions, there exists a stable phase at a narrow range of {alpha}. In six-dimensional bolt solutions, the metric is completely stable for B=S{sup 2}xS{sup 2} and is completely unstable for the B=CP{sup 2} case.« less

Analysis of pesticides in surface water, stemflow, and throughfall in an agricultural area in South Georgia, USA.

PubMed

Glinski, Donna A; Purucker, S Thomas; Van Meter, Robin J; Black, Marsha C; Henderson, W Matthew

2018-06-18

To study spray drift contributions to non-targeted habitats, pesticide concentrations in stemflow (water flowing down the trunk of a tree during a rain event), throughfall (water from tree canopy only), and surface water in an agriculturally impacted wetland area near Tifton, Georgia, USA were measured (2015-2016). Agricultural fields and sampling locations were on the University of Georgia's Gibbs Research Farm, Tifton, GA. Samples were screened for more than 160 pesticides, and cumulatively, 32 different pesticides were detected across matrices. Data indicate that herbicides and fungicides were present in all types of environmental samples analyzed while insecticides were only detected in surface water samples. The highest pesticide concentration observed was 10.50 μg/L of metolachlor in an August 2015 surface water sample. Metolachlor, tebuconazole, and fipronil were the most frequently detected herbicide, fungicide, and insecticide, respectively, regardless of sample origin. The most frequently detected pesticide in surface water and stemflow samples was metolachlor (0.09-10.5 μg/L), however, the most commonly detected pesticide in throughfall samples was biphenyl (0.02-0.07 μg/L). These data help determine the importance of indirect chemical exposures to non-targeted habitats by assessing inputs from stemflow and throughfall into surface waters. Copyright © 2018 Elsevier Ltd. All rights reserved.

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

PubMed Central

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

2007-01-01

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

[Continuum based fast Fourier transform processing of infrared spectrum].

PubMed

Liu, Qing-Jie; Lin, Qi-Zhong; Wang, Qin-Jun; Li, Hui; Li, Shuai

2009-12-01

To recognize ground objects with infrared spectrum, high frequency noise removing is one of the most important phases in spectrum feature analysis and extraction. A new method for infrared spectrum preprocessing was given combining spectrum continuum processing and Fast Fourier Transform (CFFT). Continuum was firstly removed from the noise polluted infrared spectrum to standardize hyper-spectra. Then the spectrum was transformed into frequency domain (FD) with fast Fourier transform (FFT), separating noise information from target information After noise eliminating from useful information with a low-pass filter, the filtered FD spectrum was transformed into time domain (TD) with fast Fourier inverse transform. Finally the continuum was recovered to the spectrum, and the filtered infrared spectrum was achieved. Experiment was performed for chlorite spectrum in USGS polluted with two kinds of simulated white noise to validate the filtering ability of CFFT by contrast with cubic function of five point (CFFP) in time domain and traditional FFT in frequency domain. A circle of CFFP has limited filtering effect, so it should work much with more circles and consume more time to achieve better filtering result. As for conventional FFT, Gibbs phenomenon has great effect on preprocessing result at edge bands because of special character of rock or mineral spectra, while works well at middle bands. Mean squared error of CFFT is 0. 000 012 336 with cut-off frequency of 150, while that of FFT and CFFP is 0. 000 061 074 with cut-off frequency of 150 and 0.000 022 963 with 150 working circles respectively. Besides the filtering result of CFFT can be improved by adjusting the filter cut-off frequency, and has little effect on working time. The CFFT method overcomes the Gibbs problem of FFT in spectrum filtering, and can be more convenient, dependable, and effective than traditional TD filter methods.

Predictive thermodynamics for ionic solids and liquids.

PubMed

Glasser, Leslie; Jenkins, H Donald Brooke

2016-08-21

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

Small Changes in the Primary Structure of Transportan 10 Alter the Thermodynamics and Kinetics of its Interaction with Phospholipid Vesicles

PubMed Central

2008-01-01

The kinetics and thermodynamics of binding of transportan 10 (tp10) and four of its variants to phospholipid vesicles, and the kinetics of peptide-induced dye efflux, were compared. Tp10 is a 21-residue, amphipathic, cationic, cell-penetrating peptide similar to helical antimicrobial peptides. The tp10 variants examined include amidated and free peptides, and replacements of tyrosine by tryptophan. Carboxy-terminal amidation or substitution of tryptophan for tyrosine enhance binding and activity. The Gibbs energies of peptide binding to membranes determined experimentally and calculated from the interfacial hydrophobicity scale are in good agreement. The Gibbs energy for insertion into the bilayer core was calculated using hydrophobicity scales of residue transfer from water to octanol and to the membrane/water interface. Peptide-induced efflux becomes faster as the Gibbs energies for binding and insertion of the tp10 variants decrease. If anionic lipids are included, binding and efflux rate increase, as expected because all tp10 variants are cationic and an electrostatic component is added. Whether the most important effect of peptide amidation is the change in charge or an enhancement of helical structure, however, still needs to be established. Nevertheless, it is clear that the changes in efflux rate reflect the differences in the thermodynamics of binding and insertion of the free and amidated peptide groups. PMID:18260641

The Gibbs free energy of nukundamite (Cu3.38Fe0.62S4): A correction and implications for phase equilibria

USGS Publications Warehouse

Seal, R.R.; Inan, E.E.; Hemingway, B.S.

2001-01-01

The Gibbs free energy of formation of nukundamite (Cu3.38Fe0.62S4) was calculated from published experimental studies of the reaction 3.25 Cu3.38Fe0.62S4 + S2 = 11 CuS + 2 FeS2 in order to correct an erroneous expression in the published record. The correct expression describing the Gibbs free energy of formation (kJ???mol-1) of nukundamite relative to the elements and ideal S2 gas is ??fG?? nukundamite T(K) = -549.75 + 0.23242 T + 3.1284 T0.5, with an uncertainty of 0.6%. An evaluation of the phase equilibria of nukundamite with associated phases in the system Cu-Fe-S as a function of temperature and sulfur fugacity indicates that nukundamite is stable from 224 to 501??C at high sulfidation states. At its greatest extent, at 434??C, the stability field of nukundamite is only 0.4 log f(S2) units wide, which explains its rarity. Equilibria between nukundamite and bornite, which limit the stability of both phases, involve bornite compositions that deviate significantly from stoichiometric Cu5FeS4. Under equilibrium conditions in the system Cu-Fe-S, nukundamite + chalcopyrite is not a stable assemblage at any temperature.

Geochemical appraisal of fluoride-laden groundwater in Suri I and II blocks, Birbhum district, West Bengal

NASA Astrophysics Data System (ADS)

Das, Shreya; Nag, S. K.

2017-09-01

The present study has been carried out covering two blocks—Suri I and II in Birbhum district, West Bengal, India. The evaluation focuses on occurrence, distribution and geochemistry in 26 water samples collected from borewells spread across the entire study area homogeneously. Quantitative chemical analysis of groundwater samples collected from the present study area has shown that samples from two locations—Gangta and Dhalla contain fluoride greater than the permissible limit prescribed by WHO during both post-monsoon and pre-monsoon sampling sessions. Significant factor controlling geochemistry of groundwater has been identified to be rock-water interaction processes during both sampling sessions based on the results of Gibb's diagrams. Geochemical modeling studies have revealed that fluorite (CaF2) is, indeed, present as a significant fluoride-bearing mineral in the groundwaters of this study area. Calcite or CaCO3 is one of the most common minerals with which fluorite remains associated, and saturation index calculations have revealed that the calcite-fluorite geochemistry is the dominant factor controlling fluoride concentration in this area during both post- and pre-monsoon. High fluoride waters have also been found to be of `bicarbonate' type showing increase of sodium in water with decrease of calcium.

Ionic depletion at the crystalline Gibbs layer of PEG-capped gold nanoparticle brushes at aqueous surfaces

NASA Astrophysics Data System (ADS)

Wang, Wenjie; Zhang, Honghu; Mallapragada, Surya; Travesset, Alex; Vaknin, David

2017-12-01

In situ surface-sensitive x-ray diffraction and grazing incidence x-ray fluorescence spectroscopy (GIXFS) methods are combined to determine the ionic distributions across the liquid/vapor interfaces of thiolated-polyethylene-glycol-capped gold nanoparticle (PEG-AuNP) solutions. Induced by the addition of salts (i.e., Cs2SO4 ) to PEG-AuNPs solutions, two-dimensional hexagonal lattices of PEG-AuNPs form spontaneously at the aqueous surfaces, as is demonstrated by x-ray reflectivity and grazing incidence small-angle x-ray scattering. By taking advantage of element specificity with the GIXFS method, we find that the cation Cs+ concentration at the crystalline film is significantly reduced in parts of the PEG-AuNP film compared with that in the bulk.

A Step Towards CO2-Neutral Aviation

NASA Technical Reports Server (NTRS)

Brankovic, Andreja; Ryder, Robert C.; Hendricks, Robert C.; Huber, Marcia L.

2007-01-01

An approximation method for evaluation of the caloric equations used in combustion chemistry simulations is described. The method is applied to generate the equations of specific heat, static enthalpy, and Gibb's free energy for fuel mixtures of interest to gas turbine engine manufacturers. Liquid-phase fuel properties are also derived. The fuels include JP-8, synthetic fuel, and two fuel blends consisting of a mixture of JP-8 and synthetic fuel. The complete set of fuel property equations for both phases are implemented into a computational fluid dynamics (CFD) flow solver database, and multi-phase, reacting flow simulations of a well-tested liquid-fueled combustor are performed. The simulations are a first step in understanding combustion system performance and operational issues when using alternate fuels, at practical engine operating conditions.

Reaction path of energetic materials using THOR code

NASA Astrophysics Data System (ADS)

Durães, L.; Campos, J.; Portugal, A.

1998-07-01

The method of predicting reaction path, using THOR code, allows for isobar and isochor adiabatic combustion and CJ detonation regimes, the calculation of the composition and thermodynamic properties of reaction products of energetic materials. THOR code assumes the thermodynamic equilibria of all possible products, for the minimum Gibbs free energy, using HL EoS. The code allows the possibility of estimating various sets of reaction products, obtained successively by the decomposition of the original reacting compound, as a function of the released energy. Two case studies of thermal decomposition procedure were selected, calculated and discussed—pure Ammonium Nitrate and its based explosive ANFO, and Nitromethane—because their equivalence ratio is respectively lower, near and greater than the stoicheiometry. Predictions of reaction path are in good correlation with experimental values, proving the validity of proposed method.

Structure and stability of complexes of agmatine with some functional receptor residues of proteins

NASA Astrophysics Data System (ADS)

Remko, Milan; Broer, Ria; Remková, Anna; Van Duijnen, Piet Th.

2017-04-01

The paper reports the results of a theoretical study of the conformational behavior and basicity of biogenic amine agmatine. The complexes modelling of agmatine - protein interaction are also under scrutiny of our investigation using the Becke3LYP and B97D levels of the density functional theory. The relative stabilities (Gibbs energies) of individual complexes are by both DFT methods described equally. Hydration has a dramatic effect on the hydrogen bonded complexes studied. The pairing acidic carboxylate group with different agmatine species resulted in charged hydrogen bond complexes containing negatively charged acetate species acting as proton acceptors.

Dielectric constant of ionic solutions: a field-theory approach.

PubMed

Levy, Amir; Andelman, David; Orland, Henri

2012-06-01

We study the variation of the dielectric response of a dielectric liquid (e.g. water) when a salt is added to the solution. Employing field-theoretical methods, we expand the Gibbs free energy to first order in a loop expansion and calculate self-consistently the dielectric constant. We predict analytically the dielectric decrement which depends on the ionic strength in a complex way. Furthermore, a qualitative description of the hydration shell is found and is characterized by a single length scale. Our prediction fits rather well a large range of concentrations for different salts using only one fit parameter related to the size of ions and dipoles.

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

NASA Astrophysics Data System (ADS)

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

2018-04-01

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

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

NASA Astrophysics Data System (ADS)

Pistofidis, N.; Vourlias, G.

2010-01-01

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

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

NASA Astrophysics Data System (ADS)

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

2014-03-01

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

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

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

Sobolev, S. L., E-mail: sobolev@icp.ac.ru

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

Tsallis thermostatistics for finite systems: a Hamiltonian approach

NASA Astrophysics Data System (ADS)

Adib, Artur B.; Moreira, Andrã© A.; Andrade, José S., Jr.; Almeida, Murilo P.

2003-05-01

The derivation of the Tsallis generalized canonical distribution from the traditional approach of the Gibbs microcanonical ensemble is revisited (Phys. Lett. A 193 (1994) 140). We show that finite systems whose Hamiltonians obey a generalized homogeneity relation rigorously follow the nonextensive thermostatistics of Tsallis. In the thermodynamical limit, however, our results indicate that the Boltzmann-Gibbs statistics is always recovered, regardless of the type of potential among interacting particles. This approach provides, moreover, a one-to-one correspondence between the generalized entropy and the Hamiltonian structure of a wide class of systems, revealing a possible origin for the intrinsic nonlinear features present in the Tsallis formalism that lead naturally to power-law behavior. Finally, we confirm these exact results through extensive numerical simulations of the Fermi-Pasta-Ulam chain of anharmonic oscillators.

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

NASA Astrophysics Data System (ADS)

Barber, Duncan Henry

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

Ringing Artefact Reduction By An Efficient Likelihood Improvement Method

NASA Astrophysics Data System (ADS)

Fuderer, Miha

1989-10-01

In MR imaging, the extent of the acquired spatial frequencies of the object is necessarily finite. The resulting image shows artefacts caused by "truncation" of its Fourier components. These are known as Gibbs artefacts or ringing artefacts. These artefacts are particularly. visible when the time-saving reduced acquisition method is used, say, when scanning only the lowest 70% of the 256 data lines. Filtering the data results in loss of resolution. A method is described that estimates the high frequency data from the low-frequency data lines, with the likelihood of the image as criterion. It is a computationally very efficient method, since it requires practically only two extra Fourier transforms, in addition to the normal. reconstruction. The results of this method on MR images of human subjects are promising. Evaluations on a 70% acquisition image show about 20% decrease of the error energy after processing. "Error energy" is defined as the total power of the difference to a 256-data-lines reference image. The elimination of ringing artefacts then appears almost complete..

Henry's Constants of Persistent Organic Pollutants by a Group-Contribution Method Based on Scaled-Particle Theory.

PubMed

Razdan, Neil K; Koshy, David M; Prausnitz, John M

2017-11-07

A group-contribution method based on scaled-particle theory was developed to predict Henry's constants for six families of persistent organic pollutants: polychlorinated benzenes, polychlorinated biphenyls, polychlorinated dibenzodioxins, polychlorinated dibenzofurans, polychlorinated naphthalenes, and polybrominated diphenyl ethers. The group-contribution model uses limited experimental data to obtain group-interaction parameters for an easy-to-use method to predict Henry's constants for systems where reliable experimental data are scarce. By using group-interaction parameters obtained from data reduction, scaled-particle theory gives the partial molar Gibbs energy of dissolution, Δg̅ 2 , allowing calculation of Henry's constant, H 2 , for more than 700 organic pollutants. The average deviation between predicted values of log H 2 and experiment is 4%. Application of an approximate van't Hoff equation gives the temperature dependence of Henry's constants for polychlorinated biphenyls, polychlorinated naphthalenes, and polybrominated diphenyl ethers in the environmentally relevant range 0-40 °C.

Reconstructing signals from noisy data with unknown signal and noise covariance.

PubMed

Oppermann, Niels; Robbers, Georg; Ensslin, Torsten A

2011-10-01

We derive a method to reconstruct Gaussian signals from linear measurements with Gaussian noise. This new algorithm is intended for applications in astrophysics and other sciences. The starting point of our considerations is the principle of minimum Gibbs free energy, which was previously used to derive a signal reconstruction algorithm handling uncertainties in the signal covariance. We extend this algorithm to simultaneously uncertain noise and signal covariances using the same principles in the derivation. The resulting equations are general enough to be applied in many different contexts. We demonstrate the performance of the algorithm by applying it to specific example situations and compare it to algorithms not allowing for uncertainties in the noise covariance. The results show that the method we suggest performs very well under a variety of circumstances and is indeed qualitatively superior to the other methods in cases where uncertainty in the noise covariance is present.

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

NASA Astrophysics Data System (ADS)

Vora, Aditya M.

2010-11-01

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

Deep-pelagic (0-3000 m) fish assemblage structure over the Mid-Atlantic Ridge in the area of the Charlie-Gibbs Fracture Zone

NASA Astrophysics Data System (ADS)

Cook, April B.; Sutton, Tracey T.; Galbraith, John K.; Vecchione, Michael

2013-12-01

Only a miniscule fraction of the world’s largest volume of living space, the ocean’s midwater biome, has ever been sampled. As part of the International Census of Marine Life field project on Mid-Atlantic Ridge ecosystems (MAR-ECO), a discrete-depth trawling survey was conducted in 2009 aboard the NOAA FSV Henry B. Bigelow to examine the pelagic faunal assemblage structure and distribution over the Charlie-Gibbs Fracture Zone (CGFZ) of the northern Mid-Atlantic Ridge. Day/night sampling at closely spaced stations allowed the first characterization of diel vertical migration of pelagic nekton over the MAR-ECO study area. Discrete-depth sampling from 0-3000 m was conducted using a Norwegian “Krill” trawl with five codends that were opened and closed via a pre-programmed timer. Seventy-five species of fish were collected, with a maximum diversity and biomass observed between depths of 700-1900 m. A gradient in sea-surface temperature and underlying watermasses, from northwest to southeast, was mirrored by a similar gradient in ichthyofaunal diversity. Using multivariate analyses, eight deep-pelagic fish assemblages were identified, with depth as the primary discriminatory variable. Strong diel vertical migration (DVM) of the mesopelagic fauna was a prevalent feature of the study area, though the numerically dominant fish, Cyclothone microdon (Gonostomatidae), exhibited a broad (0-3000 m) vertical distribution and did not appear to migrate on a diel basis. Three patterns of vertical distribution were observed in the study area: (a) DVM of mesopelagic, and possibly bathypelagic, taxa; (b) broad vertical distribution spanning meso- and bathypelagic depths; and (c) discrete vertical distribution within a limited depth range. Overall species composition and rank order of abundance of fish species agreed with two previous expeditions to the CGFZ (1982-1983 and 2004), suggesting some long-term consistency in the ichthyofaunal composition of the study area, at least in the summer. Frequent captures of putative bathypelagic fishes, shrimps, and cephalopods in the epipelagic zone (0-200 m) were confirmed. The results of this expedition reveal distributional patterns unlike those previously reported for open-ocean ecosystems, with the implication of increased transfer efficiency of surface production to great depths in the mid-North Atlantic.

Note on in situ (scanning) transmission electron microscopy study of liquid samples.

PubMed

Jiang, Nan

2017-08-01

Liquid cell (scanning) transmission electron microscopy has been developed rapidly, using amorphous SiN x membranes as electron transparent windows. The current interpretations of electron beam effects are mainly based on radiolytic processes. In this note, additional effects of the electric field due to electron-beam irradiation are discussed. The electric field can be produced by the charge accumulation due to the emission of secondary and Auger electrons. Besides various beam-induced phenomena, such as nanoparticle precipitation and gas bubble formation and motion, two other effects need to be considered; one is the change of Gibbs free energy of nucleation and the other is the violation of Brownian motion due to ion drifting driven by the electric field. Copyright © 2017 Elsevier B.V. All rights reserved.

Refined two-index entropy and multiscale analysis for complex system

NASA Astrophysics Data System (ADS)

Bian, Songhan; Shang, Pengjian

2016-10-01

As a fundamental concept in describing complex system, entropy measure has been proposed to various forms, like Boltzmann-Gibbs (BG) entropy, one-index entropy, two-index entropy, sample entropy, permutation entropy etc. This paper proposes a new two-index entropy Sq,δ and we find the new two-index entropy is applicable to measure the complexity of wide range of systems in the terms of randomness and fluctuation range. For more complex system, the value of two-index entropy is smaller and the correlation between parameter δ and entropy Sq,δ is weaker. By combining the refined two-index entropy Sq,δ with scaling exponent h(δ), this paper analyzes the complexities of simulation series and classifies several financial markets in various regions of the world effectively.

Semi-blind sparse image reconstruction with application to MRFM.

PubMed

Park, Se Un; Dobigeon, Nicolas; Hero, Alfred O

2012-09-01

We propose a solution to the image deconvolution problem where the convolution kernel or point spread function (PSF) is assumed to be only partially known. Small perturbations generated from the model are exploited to produce a few principal components explaining the PSF uncertainty in a high-dimensional space. Unlike recent developments on blind deconvolution of natural images, we assume the image is sparse in the pixel basis, a natural sparsity arising in magnetic resonance force microscopy (MRFM). Our approach adopts a Bayesian Metropolis-within-Gibbs sampling framework. The performance of our Bayesian semi-blind algorithm for sparse images is superior to previously proposed semi-blind algorithms such as the alternating minimization algorithm and blind algorithms developed for natural images. We illustrate our myopic algorithm on real MRFM tobacco virus data.

Computational investigation of hydrogen storage on B5V3

NASA Astrophysics Data System (ADS)

Guo, Chen; Wang, Chong

2018-05-01

Based on density functional theory method with 6-311+G(d,p) basis set, the structures, stability and hydrogen storage capacity of B5V3 have been theoretically investigated. It is found that a maximum of seven hydrogen molecules can be adsorbed on B5V3 with gravimetric uptake capacity of 6.39 wt%. The uptake capacity exceeds the target set by the US Department of Energy for vehicular application. Moreover, the average adsorption energy of B5V3 01 (7H2) is 0.60 eV/H2 in the desirable range of reversible hydrogen storage. The kinetic stability of H2 adsorbed on B5V3 01 is confirmed by using gap between highest occupied molecular orbital (HOMO)and the lowest unoccupied molecular orbital (LUMO). The gap value of B5V3 01 (7H2) is 2.81 eV, which indicates the compound with high stability. In addition, the thermochemistry calculation (Gibbs free energy corrected adsorption energy) is used to analyse if the adsorption is favourable or not at different temperatures. It can be found that the Gibbs corrected adsorption energy of B5V3 01 (7H2) is still positive at 400 K at 1 atm. It means that the adsorption of seven hydrogen molecules on B5V3 01 is energetically favourable in a fairly wide temperature range. All the results show that B5V3 01 can be considered as a promising material for hydrogen storage.

Life Origination Hydrate Hypothesis (LOH-Hypothesis)

PubMed Central

Ostrovskii, Victor; Kadyshevich, Elena

2012-01-01

The paper develops the Life Origination Hydrate Hypothesis (LOH-hypothesis), according to which living-matter simplest elements (LMSEs, which are N-bases, riboses, nucleosides, nucleotides), DNA- and RNA-like molecules, amino-acids, and proto-cells repeatedly originated on the basis of thermodynamically controlled, natural, and inevitable processes governed by universal physical and chemical laws from CH4, niters, and phosphates under the Earth's surface or seabed within the crystal cavities of the honeycomb methane-hydrate structure at low temperatures; the chemical processes passed slowly through all successive chemical steps in the direction that is determined by a gradual decrease in the Gibbs free energy of reacting systems. The hypothesis formulation method is based on the thermodynamic directedness of natural movement and consists ofan attempt to mentally backtrack on the progression of nature and thus reveal principal milestones alongits route. The changes in Gibbs free energy are estimated for different steps of the living-matter origination process; special attention is paid to the processes of proto-cell formation. Just the occurrence of the gas-hydrate periodic honeycomb matrix filled with LMSEs almost completely in its final state accounts for size limitation in the DNA functional groups and the nonrandom location of N-bases in the DNA chains. The slowness of the low-temperature chemical transformations and their “thermodynamic front” guide the gross process of living matter origination and its successive steps. It is shown that the hypothesis is thermodynamically justified and testable and that many observed natural phenomena count in its favor. PMID:25382120

Mineral-solution equilibria—III. The system Na 2OAl 2O 3SiO 2H 2OHCl

NASA Astrophysics Data System (ADS)

Popp, Robert K.; Frantz, John D.

1980-07-01

Chemical equilibrium between sodium-aluminum silicate minerals and chloride bearing fluid has been experimentally determined in the range 500-700°C at 1 kbar, using rapid-quench hydrothermal methods and two modifications of the Ag + AgCl acid buffer technique. The temperature dependence of the thermodynamic equilibrium constant ( K) for the reaction NaAlSi 3O 8 + HCl o = NaCl o + 1/2Al 2SiO 5, + 5/2SiO 2 + 1/2H 2O Albite Andalusite Qtz. K = (a NaCl o) /(a H 2O ) 1/2/(a HCl o) can be described by the following equation: log k = -4.437 + 5205.6/ T( K) The data from this study are consistent with experimental results reported by MONTOYA and HEMLEY (1975) for lower temperature equilibria defined by the assemblages albite + paragonite + quartz + fluid and paragonite + andalusite + quartz + fluid. Values of the equilibrium constants for the above reactions were used to estimate the difference in Gibbs free energy of formation between NaCl o and HCl o in the range 400-700°C and 1-2 kbar. Similar calculations using data from phase equilibrium studies reported in the literature were made to determine the difference in Gibbs free energy of formation between KCl o and HCl o. These data permit modelling of the chemical interaction between muscovite + kspar + paragonite + albite + quartz assemblages and chloride-bearing hydrothermal fluids.

Polymer-induced phase separation and crystallization in immunoglobulin G solutions.

PubMed

Li, Jianguo; Rajagopalan, Raj; Jiang, Jianwen

2008-05-28

We study the effects of the size of polymer additives and ionic strength on the phase behavior of a nonglobular protein-immunoglobulin G (IgG)-by using a simple four-site model to mimic the shape of IgG. The interaction potential between the protein molecules consists of a Derjaguin-Landau-Verwey-Overbeek-type colloidal potential and an Asakura-Oosawa depletion potential arising from the addition of polymer. Liquid-liquid equilibria and fluid-solid equilibria are calculated by using the Gibbs ensemble Monte Carlo technique and the Gibbs-Duhem integration (GDI) method, respectively. Absolute Helmholtz energy is also calculated to get an initial coexisting point as required by GDI. The results reveal a nonmonotonic dependence of the critical polymer concentration rho(PEG) (*) (i.e., the minimum polymer concentration needed to induce liquid-liquid phase separation) on the polymer-to-protein size ratio q (equivalently, the range of the polymer-induced depletion interaction potential). We have developed a simple equation for estimating the minimum amount of polymer needed to induce the liquid-liquid phase separation and show that rho(PEG) (*) approximately [q(1+q)(3)]. The results also show that the liquid-liquid phase separation is metastable for low-molecular weight polymers (q=0.2) but stable at large molecular weights (q=1.0), thereby indicating that small sizes of polymer are required for protein crystallization. The simulation results provide practical guidelines for the selection of polymer size and ionic strength for protein phase separation and crystallization.

Adsorption characteristics of hexavalent chromium on HCB/TiO2

NASA Astrophysics Data System (ADS)

Zhang, Li; Zhang, Yonggang

2014-10-01

Sol-gel method was adopted to prepare HCB/TiO2 and its adsorption ability of hexavalent chromium, Cr(VI), and removal from aqueous solution were investigated. The samples were characterized by Power X-ray diffraction (XRD) and a transmission electron microscope (TEM) which showed that the TiO2 was deposited on the surface of HCB. FTIR was used to identify the changes of the surface functional groups before and after adsorption. Potentiometric titration method was used to characterize the zero charge (pHpzc) characteristics of the surface of HCB/TiO2 which showed more acidic functional groups containing. Batch experiments showed that initial pH, absorbent dosage, contact time and initial concentration of Cr(VI) were important parameters for the Cr(VI) adsorption studies. The Freundlich isotherm model better reflected the experimental data better. Cr(VI) adsorption process followed the pseudo-second order kinetic model, which illustrated chemical adsorption. The thermodynamic parameters, such as Gibbs free energy (ΔG), changes in enthalpy change (ΔH) and changes in entropy change (ΔS) were also evaluated. Negative value of free energy occurred at temperature range of 25-45 °C, so Cr(VI) adsorption by HCB/TiO2 is spontaneous. Desorption results showed that the adsorption capacity could maintain 80% after five cycles. The maximum adsorption capacity for Cr(VI) was at 27.33 mg g-1 in an acidic medium, of which the value is worth comparable with other low-cost adsorbents.

An efficient Bayesian meta-analysis approach for studying cross-phenotype genetic associations

PubMed Central

Majumdar, Arunabha; Haldar, Tanushree; Bhattacharya, Sourabh; Witte, John S.

2018-01-01

Simultaneous analysis of genetic associations with multiple phenotypes may reveal shared genetic susceptibility across traits (pleiotropy). For a locus exhibiting overall pleiotropy, it is important to identify which specific traits underlie this association. We propose a Bayesian meta-analysis approach (termed CPBayes) that uses summary-level data across multiple phenotypes to simultaneously measure the evidence of aggregate-level pleiotropic association and estimate an optimal subset of traits associated with the risk locus. This method uses a unified Bayesian statistical framework based on a spike and slab prior. CPBayes performs a fully Bayesian analysis by employing the Markov Chain Monte Carlo (MCMC) technique Gibbs sampling. It takes into account heterogeneity in the size and direction of the genetic effects across traits. It can be applied to both cohort data and separate studies of multiple traits having overlapping or non-overlapping subjects. Simulations show that CPBayes can produce higher accuracy in the selection of associated traits underlying a pleiotropic signal than the subset-based meta-analysis ASSET. We used CPBayes to undertake a genome-wide pleiotropic association study of 22 traits in the large Kaiser GERA cohort and detected six independent pleiotropic loci associated with at least two phenotypes. This includes a locus at chromosomal region 1q24.2 which exhibits an association simultaneously with the risk of five different diseases: Dermatophytosis, Hemorrhoids, Iron Deficiency, Osteoporosis and Peripheral Vascular Disease. We provide an R-package ‘CPBayes’ implementing the proposed method. PMID:29432419

Non-Spatial Analysis of Relative Risk of Dengue Disease in Bandung Using Poisson-gamma and Log-normal Models: A Case Study of Dengue Data from Santo Borromeus Hospital in 2013

NASA Astrophysics Data System (ADS)

Irawan, R.; Yong, B.; Kristiani, F.

2017-02-01

Bandung, one of the cities in Indonesia, is vulnerable to dengue disease for both early-stage (Dengue Fever) and severe-stage (Dengue Haemorrhagic Fever and Dengue Shock Syndrome). In 2013, there were 5,749 patients in Bandung and 2,032 of the patients were hospitalized in Santo Borromeus Hospital. In this paper, there are two models, Poisson-gamma and Log-normal models, that use Bayesian inference to estimate the value of the relative risk. The calculation is done by Markov Chain Monte Carlo method which is the simulation using Gibbs Sampling algorithm in WinBUGS 1.4.3 software. The analysis results for dengue disease of 30 sub-districts in Bandung in 2013 based on Santo Borromeus Hospital’s data are Coblong and Bandung Wetan sub-districts had the highest relative risk using both models for the early-stage, severe-stage, and all stages. Meanwhile, Cinambo sub-district had the lowest relative risk using both models for the severe-stage and all stages and BojongloaKaler sub-district had the lowest relative risk using both models for the early-stage. For the model comparison using DIC (Deviance Information Criterion) method, the Log-normal model is a better model for the early-stage and severe-stage, but for the all stages, the Poisson-gamma model is a better model which fits the data.

Co-regulation analysis of co-expressed modules under cold and pathogen stress conditions in tomato.

PubMed

Abedini, Davar; Rashidi Monfared, Sajad

2018-06-01

A primary mechanism for controlling the development of multicellular organisms is transcriptional regulation, which carried out by transcription factors (TFs) that recognize and bind to their binding sites on promoter region. The distance from translation start site, order, orientation, and spacing between cis elements are key factors in the concentration of active nuclear TFs and transcriptional regulation of target genes. In this study, overrepresented motifs in cold and pathogenesis responsive genes were scanned via Gibbs sampling method, this method is based on detection of overrepresented motifs by means of a stochastic optimization strategy that searches for all possible sets of short DNA segments. Then, identified motifs were checked by TRANSFAC, PLACE and Soft Berry databases in order to identify putative TFs which, interact to the motifs. Several cis/trans regulatory elements were found using these databases. Moreover, cross-talk between cold and pathogenesis responsive genes were confirmed. Statistical analysis was used to determine distribution of identified motifs on promoter region. In addition, co-regulation analysis results, illustrated genes in pathogenesis responsive module are divided into two main groups. Also, promoter region was crunched to six subareas in order to draw the pattern of distribution of motifs in promoter subareas. The result showed the majority of motifs are concentrated on 700 nucleotides upstream of the translational start site (ATG). In contrast, this result isn't true in another group. In other words, there was no difference between total and compartmentalized regions in cold responsive genes.

Discrete Fractional Component Monte Carlo Simulation Study of Dilute Nonionic Surfactants at the Air-Water Interface.

PubMed

Yoo, Brian; Marin-Rimoldi, Eliseo; Mullen, Ryan Gotchy; Jusufi, Arben; Maginn, Edward J

2017-09-26

We present a newly developed Monte Carlo scheme to predict bulk surfactant concentrations and surface tensions at the air-water interface for various surfactant interfacial coverages. Since the concentration regimes of these systems of interest are typically very dilute (≪10 -5 mol. frac.), Monte Carlo simulations with the use of insertion/deletion moves can provide the ability to overcome finite system size limitations that often prohibit the use of modern molecular simulation techniques. In performing these simulations, we use the discrete fractional component Monte Carlo (DFCMC) method in the Gibbs ensemble framework, which allows us to separate the bulk and air-water interface into two separate boxes and efficiently swap tetraethylene glycol surfactants C 10 E 4 between boxes. Combining this move with preferential translations, volume biased insertions, and Wang-Landau biasing vastly enhances sampling and helps overcome the classical "insertion problem", often encountered in non-lattice Monte Carlo simulations. We demonstrate that this methodology is both consistent with the original molecular thermodynamic theory (MTT) of Blankschtein and co-workers, as well as their recently modified theory (MD/MTT), which incorporates the results of surfactant infinite dilution transfer free energies and surface tension calculations obtained from molecular dynamics simulations.

Bessel Fourier Orientation Reconstruction (BFOR): An Analytical Diffusion Propagator Reconstruction for Hybrid Diffusion Imaging and Computation of q-Space Indices

PubMed Central

Hosseinbor, A. Pasha; Chung, Moo K.; Wu, Yu-Chien; Alexander, Andrew L.

2012-01-01

The ensemble average propagator (EAP) describes the 3D average diffusion process of water molecules, capturing both its radial and angular contents. The EAP can thus provide richer information about complex tissue microstructure properties than the orientation distribution function (ODF), an angular feature of the EAP. Recently, several analytical EAP reconstruction schemes for multiple q-shell acquisitions have been proposed, such as diffusion propagator imaging (DPI) and spherical polar Fourier imaging (SPFI). In this study, a new analytical EAP reconstruction method is proposed, called Bessel Fourier orientation reconstruction (BFOR), whose solution is based on heat equation estimation of the diffusion signal for each shell acquisition, and is validated on both synthetic and real datasets. A significant portion of the paper is dedicated to comparing BFOR, SPFI, and DPI using hybrid, non-Cartesian sampling for multiple b-value acquisitions. Ways to mitigate the effects of Gibbs ringing on EAP reconstruction are also explored. In addition to analytical EAP reconstruction, the aforementioned modeling bases can be used to obtain rotationally invariant q-space indices of potential clinical value, an avenue which has not yet been thoroughly explored. Three such measures are computed: zero-displacement probability (Po), mean squared displacement (MSD), and generalized fractional anisotropy (GFA). PMID:22963853

Solving Constraint Satisfaction Problems with Networks of Spiking Neurons

PubMed Central

Jonke, Zeno; Habenschuss, Stefan; Maass, Wolfgang

2016-01-01

Network of neurons in the brain apply—unlike processors in our current generation of computer hardware—an event-based processing strategy, where short pulses (spikes) are emitted sparsely by neurons to signal the occurrence of an event at a particular point in time. Such spike-based computations promise to be substantially more power-efficient than traditional clocked processing schemes. However, it turns out to be surprisingly difficult to design networks of spiking neurons that can solve difficult computational problems on the level of single spikes, rather than rates of spikes. We present here a new method for designing networks of spiking neurons via an energy function. Furthermore, we show how the energy function of a network of stochastically firing neurons can be shaped in a transparent manner by composing the networks of simple stereotypical network motifs. We show that this design approach enables networks of spiking neurons to produce approximate solutions to difficult (NP-hard) constraint satisfaction problems from the domains of planning/optimization and verification/logical inference. The resulting networks employ noise as a computational resource. Nevertheless, the timing of spikes plays an essential role in their computations. Furthermore, networks of spiking neurons carry out for the Traveling Salesman Problem a more efficient stochastic search for good solutions compared with stochastic artificial neural networks (Boltzmann machines) and Gibbs sampling. PMID:27065785

Bayesian Hierarchical Random Intercept Model Based on Three Parameter Gamma Distribution

NASA Astrophysics Data System (ADS)

Wirawati, Ika; Iriawan, Nur; Irhamah

2017-06-01

Hierarchical data structures are common throughout many areas of research. Beforehand, the existence of this type of data was less noticed in the analysis. The appropriate statistical analysis to handle this type of data is the hierarchical linear model (HLM). This article will focus only on random intercept model (RIM), as a subclass of HLM. This model assumes that the intercept of models in the lowest level are varied among those models, and their slopes are fixed. The differences of intercepts were suspected affected by some variables in the upper level. These intercepts, therefore, are regressed against those upper level variables as predictors. The purpose of this paper would demonstrate a proven work of the proposed two level RIM of the modeling on per capita household expenditure in Maluku Utara, which has five characteristics in the first level and three characteristics of districts/cities in the second level. The per capita household expenditure data in the first level were captured by the three parameters Gamma distribution. The model, therefore, would be more complex due to interaction of many parameters for representing the hierarchical structure and distribution pattern of the data. To simplify the estimation processes of parameters, the computational Bayesian method couple with Markov Chain Monte Carlo (MCMC) algorithm and its Gibbs Sampling are employed.

Phase relations in the system Cu-Gd-O and Gibbs energy of formation of CuGd[sub 2]O[sub 4

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

Jacob, K.T.; Mathews, T.; Hajra, J.P.

1993-07-01

The phase relations in the system Cu-Gd-O have been determined at 1,273 K by X-ray diffraction, optical microscopy, and electron microprobe analysis of samples equilibrated in quartz ampules and in pure oxygen. Only one ternary compound, CuGd[sub 2]O[sub 4], was found to be stable. The Gibbs free energy of formation of this compound has been measured using the solid-state cell Pt, Cu[sub 2]O + CuGd[sub 2]O[sub 4] + Gd[sub 2]O[sub 3]//(Y[sub 2]O[sub 3])ZrO[sub 2]//CuO + Cu[sub 2]O, Pt in the temperature range of 900 to 1,350 K. For the formation of CuGd[sub 2]O[sub 4] from its binary component oxides, CuOmore » (s) + Gd[sub 2]O[sub 3] (s) [r arrow] CuGd[sub 2]O[sub 4] (s) [Delta]G[degree] = 8230 - 11.2T([plus minus]50)J/mol. Since the formation is endothermic, CuGd[sub 2]O[sub 4] becomes thermodynamically unstable with respect to CuO and Gd[sub 2]O[sub 3] below 735 K. When the oxygen partial pressure over CuGd[sub 2]O[sub 4] is lowered, it decomposes according to the reaction 4CuGd[sub 2]O[sub 4] (s) [r arrow] 4Gd[sub 2]O[sub 3] (s) + 2Cu[sub 2]O (s) + O[sub 2] (g) for which the equilibrium oxygen potential is given by [Delta][mu][sub o][sub 2] = [minus]227,970 + 143.2T([plus minus]500)J/mol. An oxygen potential diagram for the system Cu-Gd-O at 1,273 is presented.« less

Chemolithotrophy in the continental deep subsurface: Sanford Underground Research Facility (SURF), USA

PubMed Central

Osburn, Magdalena R.; LaRowe, Douglas E.; Momper, Lily M.; Amend, Jan P.

2014-01-01

The deep subsurface is an enormous repository of microbial life. However, the metabolic capabilities of these microorganisms and the degree to which they are dependent on surface processes are largely unknown. Due to the logistical difficulty of sampling and inherent heterogeneity, the microbial populations of the terrestrial subsurface are poorly characterized. In an effort to better understand the biogeochemistry of deep terrestrial habitats, we evaluate the energetic yield of chemolithotrophic metabolisms and microbial diversity in the Sanford Underground Research Facility (SURF) in the former Homestake Gold Mine, SD, USA. Geochemical data, energetic modeling, and DNA sequencing were combined with principle component analysis to describe this deep (down to 8100 ft below surface), terrestrial environment. SURF provides access into an iron-rich Paleoproterozoic metasedimentary deposit that contains deeply circulating groundwater. Geochemical analyses of subsurface fluids reveal enormous geochemical diversity ranging widely in salinity, oxidation state (ORP 330 to −328 mV), and concentrations of redox sensitive species (e.g., Fe2+ from near 0 to 6.2 mg/L and Σ S2- from 7 to 2778μg/L). As a direct result of this compositional buffet, Gibbs energy calculations reveal an abundance of energy for microorganisms from the oxidation of sulfur, iron, nitrogen, methane, and manganese. Pyrotag DNA sequencing reveals diverse communities of chemolithoautotrophs, thermophiles, aerobic and anaerobic heterotrophs, and numerous uncultivated clades. Extrapolated across the mine footprint, these data suggest a complex spatial mosaic of subsurface primary productivity that is in good agreement with predicted energy yields. Notably, we report Gibbs energy normalized both per mole of reaction and per kg fluid (energy density) and find the later to be more consistent with observed physiologies and environmental conditions. Further application of this approach will significantly expand our understanding of the deep terrestrial biosphere. PMID:25429287

Entropy Analyses of Four Familiar Processes.

ERIC Educational Resources Information Center

Craig, Norman C.

1988-01-01

Presents entropy analysis of four processes: a chemical reaction, a heat engine, the dissolution of a solid, and osmosis. Discusses entropy, the second law of thermodynamics, and the Gibbs free energy function. (MVL)

Characterization of van der Waals type bimodal,- lambda,- meta- and spinodal phase transitions in liquid mixtures, solid suspensions and thin films.

PubMed

Rosenholm, Jarl B

2018-03-01

The perfect gas law is used as a reference when selecting state variables (P, V, T, n) needed to characterize ideal gases (vapors), liquids and solids. Van der Waals equation of state is used as a reference for models characterizing interactions in liquids, solids and their mixtures. Van der Waals loop introduces meta- and unstable states between the observed gas (vapor)-liquid P-V transitions at low T. These intermediate states are shown to appear also between liquid-liquid, liquid-solid and solid-solid phase transitions. First-order phase transitions are characterized by a sharp discontinuity of first-order partial derivatives (P, S, V) of Helmholtz and Gibbs free energies. Second-order partial derivatives (K T , B, C V , C P , E) consist of a static contribution relating to second-order phase transitions and a relaxation contribution representing the degree of first-order phase transitions. Bimodal (first-order) and spinodal (second-order) phase boundaries are used to separate stable phases from metastable and unstable phases. The boundaries are identified and quantified by partial derivatives of molar Gibbs free energy or chemical potentials with respect to P, S, V and composition (mole fractions). Molecules confined to spread Langmuir monolayers or adsorbed Gibbs monolayers are characterized by equation of state and adsorption isotherms relating to a two-dimensional van der Waals equation of state. The basic work of two-dimensional wetting (cohesion, adsorption, spreading, immersion), have to be adjusted by a horizontal surface pressure in the presence of adsorbed vapor layers. If the adsorption is extended to liquid films a vertical surface pressure (Π) may be added to account for the lateral interaction, thus restoring PV = ΠAh dependence of thin films. Van der Waals attraction, Coulomb repulsion and structural hydration forces contribute to the vertical surface pressure. A van der Waals type coexistence of ordered (dispersed) and disordered (aggregated) phases is shown to exist when liquid vapor is confined in capillaries (condensation-liquefaction-evaporation and flux). This pheno-menon can be experimentally illustrated with suspended nano-sized particles (flocculation-coagulation-peptisation of colloidal sols) being confined in sample holders of varying size. The self-assembled aggregates represent critical self-similar equilibrium structures corres-ponding to rate determining complexes in kinetics. Overall, a self-consistent thermodynamic framework is established for the characterization of two- and three-dimensional phase separations in one-, two- and three-component systems. Copyright © 2018 Elsevier B.V. All rights reserved.

Microemulsification: an approach for analytical determinations.

PubMed

Lima, Renato S; Shiroma, Leandro Y; Teixeira, Alvaro V N C; de Toledo, José R; do Couto, Bruno C; de Carvalho, Rogério M; Carrilho, Emanuel; Kubota, Lauro T; Gobbi, Angelo L

2014-09-16

We address a novel method for analytical determinations that combines simplicity, rapidity, low consumption of chemicals, and portability with high analytical performance taking into account parameters such as precision, linearity, robustness, and accuracy. This approach relies on the effect of the analyte content over the Gibbs free energy of dispersions, affecting the thermodynamic stabilization of emulsions or Winsor systems to form microemulsions (MEs). Such phenomenon was expressed by the minimum volume fraction of amphiphile required to form microemulsion (Φ(ME)), which was the analytical signal of the method. Thus, the measurements can be taken by visually monitoring the transition of the dispersions from cloudy to transparent during the microemulsification, like a titration. It bypasses the employment of electric energy. The performed studies were: phase behavior, droplet dimension by dynamic light scattering, analytical curve, and robustness tests. The reliability of the method was evaluated by determining water in ethanol fuels and monoethylene glycol in complex samples of liquefied natural gas. The dispersions were composed of water-chlorobenzene (water analysis) and water-oleic acid (monoethylene glycol analysis) with ethanol as the hydrotrope phase. The mean hydrodynamic diameter values for the nanostructures in the droplet-based water-chlorobenzene MEs were in the range of 1 to 11 nm. The procedures of microemulsification were conducted by adding ethanol to water-oleic acid (W-O) mixtures with the aid of micropipette and shaking. The Φ(ME) measurements were performed in a thermostatic water bath at 23 °C by direct observation that is based on the visual analyses of the media. The experiments to determine water demonstrated that the analytical performance depends on the composition of ME. It shows flexibility in the developed method. The linear range was fairly broad with limits of linearity up to 70.00% water in ethanol. For monoethylene glycol in water, in turn, the linear range was observed throughout the volume fraction of analyte. The best limits of detection were 0.32% v/v water to ethanol and 0.30% v/v monoethylene glycol to water. Furthermore, the accuracy was highly satisfactory. The natural gas samples provided by the Petrobras exhibited color, particulate material, high ionic strength, and diverse compounds as metals, carboxylic acids, and anions. These samples had a conductivity of up to 2630 μS cm(-1); the conductivity of pure monoethylene glycol was only 0.30 μS cm(-1). Despite such downsides, the method allowed accurate measures bypassing steps such as extraction, preconcentration, and dilution of the sample. In addition, the levels of robustness were promising. This parameter was evaluated by investigating the effect of (i) deviations in volumetric preparation of the dispersions and (ii) changes in temperature over the analyte contents recorded by the method.

Improving Communication Within a Managerial Workgroup

ERIC Educational Resources Information Center

Harvey, Jerry B.; Boettger, C. Russell

1971-01-01

This paper describes an experiment involving the use of laboratory education (Bradford, Gibb, & Benne, 1964; Bennis & Schein, 1965) and was designed on the assumption that improvement of communication in managerial workgroups enhances task effectiveness. (Author)

Cathedral house & crocker fence, Taylor Street east and north ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

Cathedral house & crocker fence, Taylor Street east and north elevations, perspective view from the northeast - Grace Cathedral, George William Gibbs Memorial Hall, 1051 Taylor Street, San Francisco, San Francisco County, CA

Remediation System Evaluation, MacGillis and Gibbs Superfund Site

EPA Pesticide Factsheets

The site was a wood preserving facility that is no longer active. Key contaminants at the site includepentachlorophenol (PCP), chromium, and to a much lesser extent dioxin, arsenic, and polynucleararomatic hydrocarbons (PAHs).

Study of thermodynamic and transport properties of binary liquid mixture of diesel with biodiesel at 298.15K

NASA Astrophysics Data System (ADS)

Suthar, Shyam Sunder; Purohit, Suresh

2018-05-01

Properties of diesel and biodiesel (produced from corn oil) are used. Densities and viscosities of binary mixture of diesel with biodiesel (produced from corn oil) have been computed by using liquid binary mixture law over the entire range of compositions at T=298.15K and atmospheric pressure. From the computed values of density and viscosities, viscosity deviation (Δη), the excess molar volume (VE) and excess Gibbs energy of activation of viscous flow (ΔG#E) have been calculated. The results of excess volume, excess Gibbs energy of activation of viscous flow and viscosity deviation have been fitted to Redlich -Kister models to estimate the binary coefficients. The results are communicated in terms of the molecular interactions and the best suited composition has been found.

Modeling Ignition of HMX with the Gibbs Formulation

NASA Astrophysics Data System (ADS)

Lee, Kibaek; Stewart, D. Scott

2017-06-01

We present a HMX model with the Gibbs formulation in which stress tensor and temperature are assumed to be in local equilibrium, but phase/chemical changes are not assumed to be in equilibrium. We assume multi-components for HMX including beta- and delta-phase, liquid, and gas phase of HMX and its gas products. Isotropic small strain solid model, modified Fried Howard liquid EOS, and ideal gas EOS are used for its relevant component. Phase/chemical changes are characterized as reactions and are in individual reaction rate. Maxwell-Stefan model is used for diffusion. Excited gas products in the local domain lead unreacted HMX solid to the ignition event. Density of the mixture, stress, strain, displacement, mass fractions, and temperature are considered in 1D domain with time histories. Office of Naval Research and Air Force Office of Scientific Research.

High temperature mass spectrometric studies on Usbnd Ga system: Thermodynamic properties over (U3Ga5 + UGa2) and (UGa2 + UGa3) phase regions

NASA Astrophysics Data System (ADS)

Manikandan, P.; Trinadh, V. V.; Bera, Suranjan; Narasimhan, T. S. Lakshmi; Joseph, M.

2016-07-01

Vaporisation studies over gallium rich biphasic regions (U3Ga5 + UGa2) and (UGa2 + UGa3) in the Usbnd Ga system were carried out by Knusen effusion mass spectrometry in the temperature ranges of 1208-1366 K and 1133-1338 K, respectively. Ga(g) was the species observed in the mass spectra of the equilibrium vapour over both phase regions. From temperature dependence measurements, pressure-temperature relations were deduced as: log (pGa/Pa) = (-18216 ± 239)/(T/K) + (12.88 ± 0.18) over (U3Ga5 + UGa2) and log (pGa/Pa) = (-16225 ± 124)/(T/K) + (11.78 ± 0.10) over (UGa2 + UGa3). From these data, Gibbs free energy changes for the reactions 3UGa2(s) = U3Ga5(s) + Ga(g) and UGa3(s) = UGa2(s) + Ga(g) were computed and subsequently Gibbs free energies of formation of U3Ga5(s) and UGa3(s) were deduced as ΔfGTo U3Ga5(s) (±5.5) = -352.4 + 0.133 T(K) (kJ mol-1) (1208-1366 K) and ΔfGTo UGa3(s) (±3.8) = -191.9 + 0.082 T(K) (kJ mol-1) (1133-1338 K). The Gibbs free energy of formation of U3Ga5(s) is being reported for the first time.

Thermodynamic properties of calcium-bismuth alloys determined by emf measurements

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

Kim, H; Boysen, DA; Bradwell, DJ

2012-01-15

The thermodynamic properties of Ca-Bi alloys were determined by electromotive force (emf) measurements to assess the suitability of Ca-Bi electrodes for electrochemical energy storage applications. Emf was measured at ambient pressure as a function of temperature between 723 K and 1173 K using a Ca(s)vertical bar CaF2(s)vertical bar Ca(in Bi) cell for twenty different Ca-Bi alloys spanning the entire range of composition from chi(Ca) = 0 to 1. Reported are the temperature-independent partial molar entropy and enthalpy of calcium for each Ca-Bi alloy. Also given are the measured activities of calcium, the excess partial molar Gibbs energy of bismuth estimatedmore » from the Gibbs-Duhem equation, and the integral change in Gibbs energy for each Ca-Bi alloy at 873 K, 973 K, and 1073 K. Calcium activities at 973 K were found to be nearly constant at a value a(Ca) = 1 x 10(-8) over the composition range chi(Ca) = 0.32-0.56, yielding an emf of similar to 0.77 V. Above chi(Ca) = 0.62 and coincident with Ca5Bi3 formation, the calcium activity approached unity. The Ca-Bi system was also characterized by differential scanning calorimetry over the entire range of composition. Based upon these data along with the emf measurements, a revised Ca-Bi binary phase diagram is proposed. (C) 2011 Elsevier Ltd. All rights reserved.« less

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

PubMed

Latella, Ivan; Pérez-Madrid, Agustín

2013-10-01

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

New active asteroid 313P/Gibbs

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

Jewitt, David; Hui, Man-To; Li, Jing

We present initial observations of the newly discovered active asteroid 313P/Gibbs (formerly P/2014 S4), taken to characterize its nucleus and comet-like activity. The central object has a radius ∼0.5 km (geometric albedo 0.05 assumed). We find no evidence for secondary nuclei and set (with qualifications) an upper limit to the radii of such objects near 20 m, assuming the same albedo. Both aperture photometry and a morphological analysis of the ejected dust show that mass-loss is continuous at rates ∼0.2–0.4 kg s{sup −1}, inconsistent with an impact origin. Large dust particles, with radii ∼50–100 μm, dominate the optical appearance. Atmore » 2.4 AU from the Sun, the surface equilibrium temperatures are too low for thermal or desiccation stresses to be responsible for the ejection of dust. No gas is spectroscopically detected (limiting the gas mass-loss rate to <1.8 kg s{sup −1}). However, the protracted emission of dust seen in our data and the detection of another episode of dust release near perihelion, in archival observations from 2003, are highly suggestive of an origin by the sublimation of ice. Coincidentally, the orbit of 313P/Gibbs is similar to those of several active asteroids independently suspected to be ice sublimators, including P/2012 T1, 238P/Read, and 133P/Elst–Pizarro, suggesting that ice is abundant in the outer asteroid belt.« less

A brief introduction to computer-intensive methods, with a view towards applications in spatial statistics and stereology.

PubMed

Mattfeldt, Torsten

2011-04-01

Computer-intensive methods may be defined as data analytical procedures involving a huge number of highly repetitive computations. We mention resampling methods with replacement (bootstrap methods), resampling methods without replacement (randomization tests) and simulation methods. The resampling methods are based on simple and robust principles and are largely free from distributional assumptions. Bootstrap methods may be used to compute confidence intervals for a scalar model parameter and for summary statistics from replicated planar point patterns, and for significance tests. For some simple models of planar point processes, point patterns can be simulated by elementary Monte Carlo methods. The simulation of models with more complex interaction properties usually requires more advanced computing methods. In this context, we mention simulation of Gibbs processes with Markov chain Monte Carlo methods using the Metropolis-Hastings algorithm. An alternative to simulations on the basis of a parametric model consists of stochastic reconstruction methods. The basic ideas behind the methods are briefly reviewed and illustrated by simple worked examples in order to encourage novices in the field to use computer-intensive methods. © 2010 The Authors Journal of Microscopy © 2010 Royal Microscopical Society.

Evaluation of water quality and hydrogeochemistry of surface and groundwater, Tiruvallur District, Tamil Nadu, India

NASA Astrophysics Data System (ADS)

Krishna Kumar, S.; Hari Babu, S.; Eswar Rao, P.; Selvakumar, S.; Thivya, C.; Muralidharan, S.; Jeyabal, G.

2017-09-01

Water quality of Tiruvallur Taluk of Tiruvallur district, Tamil Nadu, India has been analysed to assess its suitability in relation to domestic and agricultural uses. Thirty water samples, including 8 surface water (S), 22 groundwater samples [15 shallow ground waters (SW) and 7 deep ground waters (DW)], were collected to assess the various physico-chemical parameters such as Temperature, pH, Electrical conductivity (EC), Total dissolved solids (TDS), cations (Ca, Mg, Na, K), anions (CO3, HCO3, Cl, SO4, NO3, PO4) and trace elements (Fe, Mn, Zn). Various irrigation water quality diagrams and parameters such as United states salinity laboratory (USSL), Wilcox, sodium absorption ratio (SAR), sodium percentage (Na %), Residual sodium carbonate (RSC), Residual Sodium Bicarbonate (RSBC) and Kelley's ratio revealed that most of the water samples are suitable for irrigation. Langelier Saturation Index (LSI) values suggest that the water is slightly corrosive and non-scale forming in nature. Gibbs plot suggests that the study area is dominated by evaporation and rock-water dominance process. Piper plot indicates the chemical composition of water, chiefly controlled by dissolution and mixing of irrigation return flow.

Radiation effects on interface reactions of U/Fe, U/(Fe+Cr), and U/(Fe+Cr+Ni)

DOE PAGES

Shao, Lin; Chen, Di; Wei, Chaochen; ...

2014-10-01

We study the effects of radiation damage on interdiffusion and intermetallic phase formation at the interfaces of U/Fe, U/(Fe + Cr), and U/(Fe + Cr + Ni) diffusion couples. Magnetron sputtering is used to deposit thin films of Fe, Fe + Cr, or Fe + Cr + Ni on U substrates to form the diffusion couples. One set of samples are thermally annealed under high vacuum at 450 C or 550 C for one hour. A second set of samples are annealed identically but with concurrent 3.5 MeV Fe++ ion irradiation. The Fe++ ion penetration depth is sufficient to reachmore » the original interfaces. Rutherford backscattering spectrometry analysis with high fidelity spectral simulations is used to obtain interdiffusion profiles, which are used to examine differences in U diffusion and intermetallic phase formation at the buried interfaces. For all three diffusion systems, Fe++ ion irradiations enhance U diffusion. Furthermore, the irradiations accelerate the formation of intermetallic phases. In U/Fe couples, for example, the unirradiated samples show typical interdiffusion governed by Fick’s laws, while the irradiated ones show step-like profiles influenced by Gibbs phase rules.« less

Agricultural Spray Drift Concentrations in Rainwater, Stemflow ...

EPA Pesticide Factsheets

In order to study spray drift contribution to non-targeted habitats, pesticide concentrations were measured in stemflow (water flowing down the trunk of a tree during a rain event), rainfall, and amphibians in an agriculturally impacted wetland area near Tifton, Georgia, USA. Agricultural fields and sampling locations were located on the University of Georgia's Gibbs research farm. Samples were analyzed for >150 pesticides and over 20 different pesticides were detected in these matrices. Data indicated that herbicides (metolachlor and atrazine) and fungicides (tebuconazole) were present with the highest concentrations in stemflow, followed by those in rainfall and amphibian tissue samples. Metolachlor had the highest frequency of detection and highest concentration in rainfall and stemflow samples. Higher concentrations of pesticides were observed in stemflow for a longer period than rainfall. Furthermore, rainfall and stemflow concentrations were compared against aquatic life benchmarks and environmental water screening values to determine if adverse effects would potentially occur for non-targeted organisms. Of the pesticides detected, several had concentrations that exceeded the aquatic life benchmark value. The majority of the time mixtures were present in the different matrices, making it difficult to determine the potential adverse effects that these compounds will have on non-target species, due to unknown potentiating effects. These data help assess the

Oxidation and mobilization of selenium by nitrate in irrigation drainage

USGS Publications Warehouse

Wright, W.G.

1999-01-01

Selenium (Se) can be oxidized by nitrate (NO3-) from irrigation on Cretaceous marine shale in western Colorado. Dissolved Se concentrations are positively correlated with dissolved NO3- concentrations in surface water and ground water samples from irrigated areas. Redox conditions dominate in the mobilization of Se in marine shale hydrogeologic settings; dissolved Se concentrations increase with increasing platinum-electrode potentials. Theoretical calculations for the oxidation of Se by NO3- and oxygen show favorable Gibbs free energies for the oxidation of Se by NO3-, indicating NO3- can act as an electron acceptor for the oxidation of Se. Laboratory batch experiments were performed by adding Mancos Shale samples to zero- dissolved-oxygen water containing 0, 5, 50, and 100 mg/L NO3- as N (mg N/L). Samples were incubated in airtight bottles at 25??C for 188 d; samples collected from the batch experiment bottles show increased Se concentrations over time with increased NO3- concentrations. Pseudo first-order rate constants for NO3- oxidation of Se ranged from 0.0007 to 0.0048/d for 0 to 100 mg N/L NO3- concentrations, respectively. Management of N fertilizer applications in Cretaceous shale settings might help to control the oxidation and mobilization of Se and other trace constituents into the environment.

Ionic depletion at the crystalline Gibbs layer of PEG-capped gold nanoparticle brushes at aqueous surfaces

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

Wang, Wenjie; Zhang, Honghu; Mallapragada, Surya

In situ surface-sensitive x-ray diffraction and grazing incidence x-ray fluorescence spectroscopy (GIXFS) methods are combined to determine the ionic distributions across the liquid/vapor interfaces of thiolated-polyethylene-glycol–capped gold nanoparticle (PEG-AuNP) solutions. Induced by the addition of salts (i.e., Cs 2SO 4) to PEG-AuNPs solutions, two-dimensional hexagonal lattices of PEG-AuNPs form spontaneously at the aqueous surfaces, as is demonstrated by x-ray reflectivity and grazing incidence small-angle x-ray scattering. In conclusion, by taking advantage of element specificity with the GIXFS method, we find that the cation Cs + concentration at the crystalline film is significantly reduced in parts of the PEG-AuNP film comparedmore » with that in the bulk.« less

Nonequilibrium Statistical Operator Method and Generalized Kinetic Equations

NASA Astrophysics Data System (ADS)

Kuzemsky, A. L.

2018-01-01

We consider some principal problems of nonequilibrium statistical thermodynamics in the framework of the Zubarev nonequilibrium statistical operator approach. We present a brief comparative analysis of some approaches to describing irreversible processes based on the concept of nonequilibrium Gibbs ensembles and their applicability to describing nonequilibrium processes. We discuss the derivation of generalized kinetic equations for a system in a heat bath. We obtain and analyze a damped Schrödinger-type equation for a dynamical system in a heat bath. We study the dynamical behavior of a particle in a medium taking the dissipation effects into account. We consider the scattering problem for neutrons in a nonequilibrium medium and derive a generalized Van Hove formula. We show that the nonequilibrium statistical operator method is an effective, convenient tool for describing irreversible processes in condensed matter.

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

PubMed

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

2015-03-01

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

Ionic depletion at the crystalline Gibbs layer of PEG-capped gold nanoparticle brushes at aqueous surfaces

DOE PAGES

Wang, Wenjie; Zhang, Honghu; Mallapragada, Surya; ...

2017-12-14

In situ surface-sensitive x-ray diffraction and grazing incidence x-ray fluorescence spectroscopy (GIXFS) methods are combined to determine the ionic distributions across the liquid/vapor interfaces of thiolated-polyethylene-glycol–capped gold nanoparticle (PEG-AuNP) solutions. Induced by the addition of salts (i.e., Cs 2SO 4) to PEG-AuNPs solutions, two-dimensional hexagonal lattices of PEG-AuNPs form spontaneously at the aqueous surfaces, as is demonstrated by x-ray reflectivity and grazing incidence small-angle x-ray scattering. In conclusion, by taking advantage of element specificity with the GIXFS method, we find that the cation Cs + concentration at the crystalline film is significantly reduced in parts of the PEG-AuNP film comparedmore » with that in the bulk.« less

A two phase Mach number description of the equilibrium flow of nitrogen in ducts

NASA Technical Reports Server (NTRS)

Bursik, J. W.; Hall, R. M.; Adcock, J. B.

1979-01-01

Some additional thermodynamic properties of the usual two-phase form which is linear in the moisture fraction are derived which are useful in the analysis of many kinds of duct flow. The method used is based on knowledge of the vapor pressure and Gibbs function as functions of temperature. With these, additional two-phase functions linear in moisture fraction are generated, which ultimately reveal that the squared ratio of mixture specific volume to mixture sound speed depends on liquid mass fraction and temperature in the same manner as do many weighted mean two-phase properties. This leads to a simple method of calculating two-phase Mach numbers for various duct flows. The matching of one- and two-phase flows at a saturated vapor point with discontinuous Mach number is also discussed.

Bayesian isotonic density regression

PubMed Central

Wang, Lianming; Dunson, David B.

2011-01-01

Density regression models allow the conditional distribution of the response given predictors to change flexibly over the predictor space. Such models are much more flexible than nonparametric mean regression models with nonparametric residual distributions, and are well supported in many applications. A rich variety of Bayesian methods have been proposed for density regression, but it is not clear whether such priors have full support so that any true data-generating model can be accurately approximated. This article develops a new class of density regression models that incorporate stochastic-ordering constraints which are natural when a response tends to increase or decrease monotonely with a predictor. Theory is developed showing large support. Methods are developed for hypothesis testing, with posterior computation relying on a simple Gibbs sampler. Frequentist properties are illustrated in a simulation study, and an epidemiology application is considered. PMID:22822259

Nonparametric, Coupled ,Bayesian ,Dictionary ,and Classifier Learning for Hyperspectral Classification.

PubMed

Akhtar, Naveed; Mian, Ajmal

2017-10-03

We present a principled approach to learn a discriminative dictionary along a linear classifier for hyperspectral classification. Our approach places Gaussian Process priors over the dictionary to account for the relative smoothness of the natural spectra, whereas the classifier parameters are sampled from multivariate Gaussians. We employ two Beta-Bernoulli processes to jointly infer the dictionary and the classifier. These processes are coupled under the same sets of Bernoulli distributions. In our approach, these distributions signify the frequency of the dictionary atom usage in representing class-specific training spectra, which also makes the dictionary discriminative. Due to the coupling between the dictionary and the classifier, the popularity of the atoms for representing different classes gets encoded into the classifier. This helps in predicting the class labels of test spectra that are first represented over the dictionary by solving a simultaneous sparse optimization problem. The labels of the spectra are predicted by feeding the resulting representations to the classifier. Our approach exploits the nonparametric Bayesian framework to automatically infer the dictionary size--the key parameter in discriminative dictionary learning. Moreover, it also has the desirable property of adaptively learning the association between the dictionary atoms and the class labels by itself. We use Gibbs sampling to infer the posterior probability distributions over the dictionary and the classifier under the proposed model, for which, we derive analytical expressions. To establish the effectiveness of our approach, we test it on benchmark hyperspectral images. The classification performance is compared with the state-of-the-art dictionary learning-based classification methods.

Thermal degradation of ternary blend films containing PVA/chitosan/vanillin

NASA Astrophysics Data System (ADS)

Kasai, Deepak; Chougale, Ravindra; Masti, Saraswati; Narasgoudar, Shivayogi

2018-05-01

The ternary chitosan/poly (vinyl alcohol)/vanillin blend films were prepared by solution casting method. The influence of equal weight percent of poly (vinyl alcohol) and vanillin on thermal stability of the chitosan blend films were investigated by using thermogravimetric analysis (TGA). The kinetic parameters such as enthalpy (ΔH*), entropy (ΔS*), and Gibbs free energy (ΔG*) in the first and second decomposition steps based on the thermogravimetric data were calculated. The thermal stabilities of the blend films were confirmed by thermodynamic parameters obtained in the activation energies, which indicated that increase in the equal weight percent of PVA/vanillin decreased the thermal stability of the chitosan film.

Cooperative strings and glassy interfaces

PubMed Central

Salez, Thomas; Salez, Justin; Dalnoki-Veress, Kari; Raphaël, Elie; Forrest, James A.

2015-01-01

We introduce a minimal theory of glass formation based on the ideas of molecular crowding and resultant string-like cooperative rearrangement, and address the effects of free interfaces. In the bulk case, we obtain a scaling expression for the number of particles taking part in cooperative strings, and we recover the Adam–Gibbs description of glassy dynamics. Then, by including thermal dilatation, the Vogel–Fulcher–Tammann relation is derived. Moreover, the random and string-like characters of the cooperative rearrangement allow us to predict a temperature-dependent expression for the cooperative length ξ of bulk relaxation. Finally, we explore the influence of sample boundaries when the system size becomes comparable to ξ. The theory is in agreement with measurements of the glass-transition temperature of thin polymer films, and allows quantification of the temperature-dependent thickness hm of the interfacial mobile layer. PMID:26100908

Hierarchical Dirichlet process model for gene expression clustering

PubMed Central

2013-01-01

Clustering is an important data processing tool for interpreting microarray data and genomic network inference. In this article, we propose a clustering algorithm based on the hierarchical Dirichlet processes (HDP). The HDP clustering introduces a hierarchical structure in the statistical model which captures the hierarchical features prevalent in biological data such as the gene express data. We develop a Gibbs sampling algorithm based on the Chinese restaurant metaphor for the HDP clustering. We apply the proposed HDP algorithm to both regulatory network segmentation and gene expression clustering. The HDP algorithm is shown to outperform several popular clustering algorithms by revealing the underlying hierarchical structure of the data. For the yeast cell cycle data, we compare the HDP result to the standard result and show that the HDP algorithm provides more information and reduces the unnecessary clustering fragments. PMID:23587447

An Improved Mnemonic Diagram for Thermodynamic Relationships.

ERIC Educational Resources Information Center

Rodriguez, Joaquin; Brainard, Alan J.

1989-01-01

Considers pressure, volume, entropy, temperature, Helmholtz free energy, Gibbs free energy, enthalpy, and internal energy. Suggests the mnemonic diagram is for use with simple systems that are defined as macroscopically homogeneous, isotropic, uncharged, and chemically inert. (MVL)

A Mechanical Analogue for Chemical Potential, Extent of Reaction, and the Gibbs Energy.

ERIC Educational Resources Information Center

Glass, Samuel V.; DeKock, Roger L.

1998-01-01

Presents an analogy that relates the one-dimensional mechanical equilibrium of a rigid block between two Hooke's law springs and the chemical equilibrium of two perfect gases using ordinary materials. (PVD)

The African Women's Protocol: bringing attention to reproductive rights and the MDGs.

PubMed

Gerntholtz, Liesl; Gibbs, Andrew; Willan, Samantha

2011-04-01

Andrew Gibbs and colleagues discuss the African Women's Protocol, a framework for ensuring reproductive rights are supported throughout the continent and for supporting interventions to improve women's reproductive health, including the MDGs.

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

Mihaescu, Tatiana, E-mail: mihaescu92tatiana@gmail.com; Isar, Aurelian

We describe the evolution of the quantum entanglement of an open system consisting of two bosonic modes interacting with a common thermal environment, described by two different models. The initial state of the system is taken of Gaussian form. In the case of a thermal bath, characterized by temperature and dissipation constant which correspond to an asymptotic Gibbs state of the system, we show that for a zero temperature of the thermal bath an initial entangled Gaussian state remains entangled for all finite times. For an entangled initial squeezed thermal state, the phenomenon of entanglement sudden death takes place andmore » we calculate the survival time of entanglement. For the second model of the environment, corresponding to a non-Gibbs asymptotic state, we study the possibility of generating entanglement. We show that the generation of the entanglement between two uncoupled bosonic modes is possible only for definite values of the temperature and dissipation constant, which characterize the thermal environment.« less

eQuilibrator--the biochemical thermodynamics calculator.

PubMed

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

2012-01-01

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

AC-67/FLTSATCOM Launch with Isolated Cam Views/ Freeze of Lightning/ Press Conference

NASA Technical Reports Server (NTRS)

1987-01-01

The FLTSATCOM system provides worldwide, high-priority UHF communications between naval aircraft, ships, submarines, and ground stations and between the Strategic Air Command and the national command authority network. This videotape shows the attempted launch of the 6th member of the satellite system on an Atlas Centaur rocket. Within a minute of launch a problem developed. The initial sign of the problem was the loss of telemetry data. The videotape shows three isolated views of the launch, and then a freeze shot of a lightning strike shortly after the launch. The tape then shows a press conference, with Mr. Wolmaster, Mr. Gibbs, and Air Force Colonel Alsbrooke. Mr. Gibbs summarizes the steps that would be taken to review the launch failure. The questions from the press mostly concern the weather conditions, and the possibility that the weather might have caused the mission failure.

eQuilibrator—the biochemical thermodynamics calculator

PubMed Central

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

2012-01-01

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

A possible four-phase coexistence in a single-component system

NASA Astrophysics Data System (ADS)

Akahane, Kenji; Russo, John; Tanaka, Hajime

2016-08-01

For different phases to coexist in equilibrium at constant temperature T and pressure P, the condition of equal chemical potential μ must be satisfied. This condition dictates that, for a single-component system, the maximum number of phases that can coexist is three. Historically this is known as the Gibbs phase rule, and is one of the oldest and venerable rules of thermodynamics. Here we make use of the fact that, by varying model parameters, the Gibbs phase rule can be generalized so that four phases can coexist even in single-component systems. To systematically search for the quadruple point, we use a monoatomic system interacting with a Stillinger-Weber potential with variable tetrahedrality. Our study indicates that the quadruple point provides flexibility in controlling multiple equilibrium phases and may be realized in systems with tunable interactions, which are nowadays feasible in several soft matter systems such as patchy colloids.

On the Gibbs phenomenon 4: Recovering exponential accuracy in a sub-interval from a Gegenbauer partial sum of a piecewise analytic function

NASA Technical Reports Server (NTRS)

Gottlieb, David; Shu, Chi-Wang

1994-01-01

We continue our investigation of overcoming Gibbs phenomenon, i.e., to obtain exponential accuracy at all points (including at the discontinuities themselves), from the knowledge of a spectral partial sum of a discontinuous but piecewise analytic function. We show that if we are given the first N Gegenbauer expansion coefficients, based on the Gegenbauer polynomials C(sub k)(sup mu)(x) with the weight function (1 - x(exp 2))(exp mu - 1/2) for any constant mu is greater than or equal to 0, of an L(sub 1) function f(x), we can construct an exponentially convergent approximation to the point values of f(x) in any subinterval in which the function is analytic. The proof covers the cases of Chebyshev or Legendre partial sums, which are most common in applications.

The Gibbs paradox and the physical criteria for indistinguishability of identical particles

NASA Astrophysics Data System (ADS)

Unnikrishnan, C. S.

2016-08-01

Gibbs paradox in the context of statistical mechanics addresses the issue of additivity of entropy of mixing gases. The usual discussion attributes the paradoxical situation to classical distinguishability of identical particles and credits quantum theory for enabling indistinguishability of identical particles to solve the problem. We argue that indistinguishability of identical particles is already a feature in classical mechanics and this is clearly brought out when the problem is treated in the language of information and associated entropy. We pinpoint the physical criteria for indistinguishability that is crucial for the treatment of the Gibbs’ problem and the consistency of its solution with conventional thermodynamics. Quantum mechanics provides a quantitative criterion, not possible in the classical picture, for the degree of indistinguishability in terms of visibility of quantum interference, or overlap of the states as pointed out by von Neumann, thereby endowing the entropy expression with mathematical continuity and physical reasonableness.

Low-temperature heat capacity and entropy of chalcopyrite (CuFeS2): estimates of the standard molar enthalpy and Gibbs free energy of formation of chalcopyrite and bornite (Cu5FeS4)

USGS Publications Warehouse

Robie, R.A.; Wiggins, L.B.; Barton, P.B.; Hemingway, B.S.

1985-01-01

The heat capacity of CuFeS2 (chalcopyrite) was measured between 6.3 and 303.5 K. At 298.15 K, Cp,mo and Smo(T) are (95.67??0.14) J??K-1??mol-1 and (124.9??0.2) J??K-1??mol-1, respectively. From a consideration of the results of two sets of equilibrium measurements we conclude that ??fHmo(CuFeS2, cr, 298.15 K) = -(193.6??1.6) kJ??mol-1 and that the recent bomb-calorimetric determination by Johnson and Steele (J. Chem. Thermodynamics 1981, 13, 991) is in error. The standard molar Gibbs free energy of formation of bornite (Cu5FeS4) is -(444.9??2.1) kJ??mol-1 at 748 K. ?? 1985.

Compositional Pathways and Capillary Effects during Early-stage Isothermal Precipitation in a Nondilute Ni-Al-Cr Alloy

NASA Technical Reports Server (NTRS)

Sudbrack, Chantal K.; Noebe, Ronald D.; Seidman, David N.

2006-01-01

For a Ni-5.2 Al-14.2 Cr at.% alloy with moderate solute supersaturations, the compositional pathways, as measured with atom-probe tomography, during early to later stage y'(LI2)-precipitation (R = 0.45-10 nm), aged at 873 K, are discussed in light of a multi-component coarsening model. Employing nondilute thermodynamics, detailed model analyses during quasistationary coarsening of the experimental data establish that the y/y' interfacial free-energy is 22- 23+/-7 mJ/sq m. Additionally, solute diffusivities are significantly slower than model estimates. Strong quantitative evidence indicates that an observed y'-supersaturation of Al results from the Gibbs-Thomson effect, providing the first experimental verification of this phenomenon. The Gibbs-Thomson relationship, for a ternary system, as well as differences in measured phase equilibria with CALPHAD assessments, are considered in great detail.

Quenching the XXZ spin chain: quench action approach versus generalized Gibbs ensemble

NASA Astrophysics Data System (ADS)

Mestyán, M.; Pozsgay, B.; Takács, G.; Werner, M. A.

2015-04-01

Following our previous work (Pozsgay et al 2014 Phys. Rev. Lett. 113 117203) we present here a detailed comparison of the quench action approach and the predictions of the generalized Gibbs ensemble, with the result that while the quench action formalism correctly captures the steady state, the GGE does not give a correct description of local short-distance correlation functions. We extend our studies to include another initial state, the so-called q-dimer state. We present important details of our construction, including new results concerning exact overlaps for the dimer and q-dimer states, and we also give an exact solution of the quench-action-based overlap-TBA for the q-dimer. Furthermore, we extend our computations to include the xx spin correlations besides the zz correlations treated previously, and give a detailed discussion of the underlying reasons for the failure of the GGE, especially in the light of new developments.

Thermodynamic data for modeling acid mine drainage problems: compilation and estimation of data for selected soluble iron-sulfate minerals

USGS Publications Warehouse

Hemingway, Bruch S.; Seal, Robert R.; Chou, I-Ming

2002-01-01

Enthalpy of formation, Gibbs energy of formation, and entropy values have been compiled from the literature for the hydrated ferrous sulfate minerals melanterite, rozenite, and szomolnokite, and a variety of other hydrated sulfate compounds. On the basis of this compilation, it appears that there is no evidence for an excess enthalpy of mixing for sulfate-H2O systems, except for the first H2O molecule of crystallization. The enthalpy and Gibbs energy of formation of each H2O molecule of crystallization, except the first, in the iron(II) sulfate - H2O system is -295.15 and -238.0 kJ?mol-1, respectively. The absence of an excess enthalpy of mixing is used as the basis for estimating thermodynamic values for a variety of ferrous, ferric, and mixed-valence sulfate salts of relevance to acid-mine drainage systems.

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

PubMed

Naumov, Sergej; von Sonntag, Clemens

2011-11-01

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

A possible four-phase coexistence in a single-component system

PubMed Central

Akahane, Kenji; Russo, John; Tanaka, Hajime

2016-01-01

For different phases to coexist in equilibrium at constant temperature T and pressure P, the condition of equal chemical potential μ must be satisfied. This condition dictates that, for a single-component system, the maximum number of phases that can coexist is three. Historically this is known as the Gibbs phase rule, and is one of the oldest and venerable rules of thermodynamics. Here we make use of the fact that, by varying model parameters, the Gibbs phase rule can be generalized so that four phases can coexist even in single-component systems. To systematically search for the quadruple point, we use a monoatomic system interacting with a Stillinger–Weber potential with variable tetrahedrality. Our study indicates that the quadruple point provides flexibility in controlling multiple equilibrium phases and may be realized in systems with tunable interactions, which are nowadays feasible in several soft matter systems such as patchy colloids. PMID:27558452

Investigation of Liquid Surface Rheology of Surfactant Solutions by Droplet Shape Oscillations: Experiments

PubMed

Tian; Holt; Apfel

1997-03-01

The experimental results of droplet shape oscillations are reported and applied to the analysis of surface rheological properties of surfactant solutions. An acoustic levitation technique is used to suspend the test drop in air and excite it into quadrupole shape oscillations. The equilibrium surface tension, Gibbs elasticity, and surface dilatational viscosity are determined from the measurements of droplet static shape under different levitation sound pressure, oscillation frequency, and free damping constant. Aqueous solutions of sodium dodecyl sulfate, dodecyltrimethylammonium bromide, and n-octyl beta-d-glucopyranoside are tested with this system. The concentrations of the solutions are below the critical micelle concentration. For these solutions it is found that the surface Gibbs elasticity approaches a maximum at a moderate concentration, and its value is less than that directly calculated from the state equation of a static liquid surface. The surface dilatational viscosity is found to be in a range around 0.1 cps.

A time series model: First-order integer-valued autoregressive (INAR(1))

NASA Astrophysics Data System (ADS)

Simarmata, D. M.; Novkaniza, F.; Widyaningsih, Y.

2017-07-01

Nonnegative integer-valued time series arises in many applications. A time series model: first-order Integer-valued AutoRegressive (INAR(1)) is constructed by binomial thinning operator to model nonnegative integer-valued time series. INAR (1) depends on one period from the process before. The parameter of the model can be estimated by Conditional Least Squares (CLS). Specification of INAR(1) is following the specification of (AR(1)). Forecasting in INAR(1) uses median or Bayesian forecasting methodology. Median forecasting methodology obtains integer s, which is cumulative density function (CDF) until s, is more than or equal to 0.5. Bayesian forecasting methodology forecasts h-step-ahead of generating the parameter of the model and parameter of innovation term using Adaptive Rejection Metropolis Sampling within Gibbs sampling (ARMS), then finding the least integer s, where CDF until s is more than or equal to u . u is a value taken from the Uniform(0,1) distribution. INAR(1) is applied on pneumonia case in Penjaringan, Jakarta Utara, January 2008 until April 2016 monthly.

Studies on silane to 70 GPa

NASA Astrophysics Data System (ADS)

Narayana, C.; Greene, R. G.; Ruoff, A. L.

2008-07-01

Raman and x-ray diffraction studies were made on silane in the diamond anvil cell using three different gaskets, stainless steel, tungsten and rhenium. The structure existing between 10 and 27 GPa is well characterized by the monoclinic space group P21c (#14). While the Gibbs free energy of formation of silane is positive at one atmosphere, it is calculated from the equation of state of silane and its reactants that this becomes negative near 4 GPa and remains negative until 13 GPa and then becomes positive again. At about 27 GPa, where quasi-quantum mechanical calculations suggest there should be a transformation from 4-fold to 6-fold (or even higher), the sample turns black. The Raman modes seize to exist beyond 30 GPa after showing softening above 25 GPa. At higher pressures it turns silvery. The gaskets play a different role as will be discussed. The sample brought back from 70 GPa contains amorphous Si (with attached hydrogen) as well as crystalline silicon. The lowest free energy system at high pressure is the decomposed reactants as observed.

Adsorption of Zinc(II) on diatomite and manganese-oxide-modified diatomite: a kinetic and equilibrium study.

PubMed

Caliskan, Necla; Kul, Ali Riza; Alkan, Salih; Sogut, Eda Gokirmak; Alacabey, Ihsan

2011-10-15

The removal of Zn(II) ions from aqueous solution was studied using natural and MnO(2) modified diatomite samples at different temperatures. The linear Langmuir, Freundlich and Dubinin-Radushkevich (D-R) adsorption equations were applied to describe the equilibrium isotherms. From the D-R model, the mean adsorption energy was calculated as >8 kJ mol(-1), indicating that the adsorption of Zn(II) onto diatomite and Mn-diatomite was physically carried out. In addition, the pseudo-first-order, pseudo-second-order and intraparticle diffusion models were used to determine the kinetic data. The experimental data were well fitted by the pseudo-second-order kinetic model. Thermodynamic parameters such as the enthalpy (ΔH(0)), Gibbs' free energy (ΔG(0)) and entropy (ΔS(0)) were calculated for natural and MnO(2) modified diatomite. These values showed that the adsorption of Zn(II) ions onto diatomite samples was controlled by a physical mechanism and occurred spontaneously. Copyright © 2011 Elsevier B.V. All rights reserved.

A bayesian hierarchical model for classification with selection of functional predictors.

PubMed

Zhu, Hongxiao; Vannucci, Marina; Cox, Dennis D

2010-06-01

In functional data classification, functional observations are often contaminated by various systematic effects, such as random batch effects caused by device artifacts, or fixed effects caused by sample-related factors. These effects may lead to classification bias and thus should not be neglected. Another issue of concern is the selection of functions when predictors consist of multiple functions, some of which may be redundant. The above issues arise in a real data application where we use fluorescence spectroscopy to detect cervical precancer. In this article, we propose a Bayesian hierarchical model that takes into account random batch effects and selects effective functions among multiple functional predictors. Fixed effects or predictors in nonfunctional form are also included in the model. The dimension of the functional data is reduced through orthonormal basis expansion or functional principal components. For posterior sampling, we use a hybrid Metropolis-Hastings/Gibbs sampler, which suffers slow mixing. An evolutionary Monte Carlo algorithm is applied to improve the mixing. Simulation and real data application show that the proposed model provides accurate selection of functional predictors as well as good classification.

Ab Initio Predictions of K, He and Ar Partitioning Between Silicate Melt and Liquid Iron Under High Pressure

NASA Astrophysics Data System (ADS)

Xiong, Z.; Tsuchiya, T.

2017-12-01

Element partitioning is an important property in recording geochemical processes during the core-mantle differentiation. However, experimental measurements of element partitioning coefficients under extreme temperature and pressure condition are still challenging. Theoretical modeling is also not easy, because it requires estimation of high temperature Gibbs free energy, which is not directly accessible by the standard molecular dynamics method. We recently developed an original technique to simulate Gibbs free energy based on the thermodynamics integration method[1]. We apply it to element partitioning of geochemical intriguing trace elements between molten silicate and liquid iron such as potassium, helium and argon as starting examples. Radiogenic potassium in the core can provide energy for Earth's magnetic field, convection in the mantle and outer core[2]. However, its partitioning behavior between silicate and iron remains unclear under high pressure[3,4]. Our calculations suggest that a clear positive temperature dependence of the partitioning coefficient but an insignificant pressure effect. Unlike sulfur and silicon, oxygen dissolved in the metals considerably enhances potassium solubility. Calculated electronic structures reveal alkali-metallic feature of potassium in liquid iron, favoring oxygen with strong electron affinity. Our results suggest that 40K could serve as a potential radiogenic heat source in the outer core if oxygen is the major light element therein.­­ We now further extend our technique to partitioning behaviors of other elements, helium and argon, to get insides into the `helium paradox' and `missing argon' problems. References [1] T. Taniuchi, and T. Tsuchiya, Phys.Rev.B. In press [2] B.A. Buffett, H.E. Huppert, J.R. Lister, and A.W. Woods, Geophys.Res.Lett. 29 (1996) 7989-8006. [3] V.R. Murthy, W. Westrenen, and Y. Fei, Nature. 426 (2003) 163-165. [4] A. Corgne, S.Keshav, Y. Fei, and W.F. McDonough, Earth.Planet.Sci.Lett. 256 (2007) 567-576

Fuzzy-C-Means Clustering Based Segmentation and CNN-Classification for Accurate Segmentation of Lung Nodules

PubMed

K, Jalal Deen; R, Ganesan; A, Merline

2017-07-27

Objective: Accurate segmentation of abnormal and healthy lungs is very crucial for a steadfast computer-aided disease diagnostics. Methods: For this purpose a stack of chest CT scans are processed. In this paper, novel methods are proposed for segmentation of the multimodal grayscale lung CT scan. In the conventional methods using Markov–Gibbs Random Field (MGRF) model the required regions of interest (ROI) are identified. Result: The results of proposed FCM and CNN based process are compared with the results obtained from the conventional method using MGRF model. The results illustrate that the proposed method can able to segment the various kinds of complex multimodal medical images precisely. Conclusion: However, in this paper, to obtain an exact boundary of the regions, every empirical dispersion of the image is computed by Fuzzy C-Means Clustering segmentation. A classification process based on the Convolutional Neural Network (CNN) classifier is accomplished to distinguish the normal tissue and the abnormal tissue. The experimental evaluation is done using the Interstitial Lung Disease (ILD) database. Creative Commons Attribution License

Fuzzy-C-Means Clustering Based Segmentation and CNN-Classification for Accurate Segmentation of Lung Nodules

PubMed Central

K, Jalal Deen; R, Ganesan; A, Merline

2017-01-01

Objective: Accurate segmentation of abnormal and healthy lungs is very crucial for a steadfast computer-aided disease diagnostics. Methods: For this purpose a stack of chest CT scans are processed. In this paper, novel methods are proposed for segmentation of the multimodal grayscale lung CT scan. In the conventional methods using Markov–Gibbs Random Field (MGRF) model the required regions of interest (ROI) are identified. Result: The results of proposed FCM and CNN based process are compared with the results obtained from the conventional method using MGRF model. The results illustrate that the proposed method can able to segment the various kinds of complex multimodal medical images precisely. Conclusion: However, in this paper, to obtain an exact boundary of the regions, every empirical dispersion of the image is computed by Fuzzy C-Means Clustering segmentation. A classification process based on the Convolutional Neural Network (CNN) classifier is accomplished to distinguish the normal tissue and the abnormal tissue. The experimental evaluation is done using the Interstitial Lung Disease (ILD) database. PMID:28749127

Flory Model of Polymer Crystallization, Kauzmann Paradox and Gibbs-DiMarzio Theory of Glass Transition

NASA Astrophysics Data System (ADS)

Corsi, A.; Gujrati, P. D.

2000-03-01

The Flory model of crystallization of polymers is well known and forms the cornerstone of the Gibbs-DiMarzio theory of glass transition. The model has no known exact solution and the original calculation [1] was shown to be incorrect [2]. Still it is interesting to know the order of the phase transition, if it has one. We have studied the thermodynamics of the model in the limit of infinite molecular weight. We have solved it exactly on a recursive lattice with coordination number q=4, relevant for a tetrahedral lattice. Our results show that there is a continuous, i.e. a second-order, transition at which the entropy of the system is continuous. It is finite at all temperatures and approaches 0 as T goes to 0 so that the system is never completely ordered except at T=0. As the temperature is raised above T=0 the system begins to disorder with a degree of disorder that depends on T, which is in accordance with the analysis of Gujrati and Goldstein [2]. Since there is no first order transition there is no Kauzmann paradox. Similarly there is no possible metastable extension in the model which is central to the Gibbs-DiMarzio conjecture for an ideal glass transition. Thus, our solution does not justify their conjecture. [1] P.J. Flory, Proc. R. Soc. London Ser., A234, 60 (1956) [2] P.D. Gujrati, J. Phys. A: Math. Gen., 13, L437 (1980), P.D. Gujrati, M. Goldstein, J. Chem. Phys., 74(4), 2596 (1981)

Recommendations for terminology and databases for biochemical thermodynamics.

PubMed

Alberty, Robert A; Cornish-Bowden, Athel; Goldberg, Robert N; Hammes, Gordon G; Tipton, Keith; Westerhoff, Hans V

2011-05-01

Chemical equations are normally written in terms of specific ionic and elemental species and balance atoms of elements and electric charge. However, in a biochemical context it is usually better to write them with ionic reactants expressed as totals of species in equilibrium with each other. This implies that atoms of elements assumed to be at fixed concentrations, such as hydrogen at a specified pH, should not be balanced in a biochemical equation used for thermodynamic analysis. However, both kinds of equations are needed in biochemistry. The apparent equilibrium constant K' for a biochemical reaction is written in terms of such sums of species and can be used to calculate standard transformed Gibbs energies of reaction Δ(r)G'°. This property for a biochemical reaction can be calculated from the standard transformed Gibbs energies of formation Δ(f)G(i)'° of reactants, which can be calculated from the standard Gibbs energies of formation of species Δ(f)G(j)° and measured apparent equilibrium constants of enzyme-catalyzed reactions. Tables of Δ(r)G'° of reactions and Δ(f)G(i)'° of reactants as functions of pH and temperature are available on the web, as are functions for calculating these properties. Biochemical thermodynamics is also important in enzyme kinetics because apparent equilibrium constant K' can be calculated from experimentally determined kinetic parameters when initial velocities have been determined for both forward and reverse reactions. Specific recommendations are made for reporting experimental results in the literature. Copyright © 2011 Elsevier B.V. All rights reserved.

Theoretical and experimental study on the effects of particle size and temperature on the reaction kinetics of cubic nano-Cu2O

NASA Astrophysics Data System (ADS)

Tang, Huanfeng; Huang, Zaiyin; Xiao, Ming; Liang, Min; Chen, Liying; Tan, XueCai

2017-09-01

The activities, selectivities, and stabilities of nanoparticles in heterogeneous reactions are size-dependent. In order to investigate the influencing laws of particle size and temperature on kinetic parameters in heterogeneous reactions, cubic nano-Cu2O particles of four different sizes in the range of 40-120 nm have been controllably synthesized. In situ microcalorimetry has been used to attain thermodynamic data on the reaction of Cu2O with aqueous HNO3 and, combined with thermodynamic principles and kinetic transition-state theory, the relevant reaction kinetic parameters have been evaluated. The size dependences of the kinetic parameters are discussed in terms of the established kinetic model and the experimental results. It was found that the reaction rate constants increased with decreasing particle size. Accordingly, the apparent activation energy, pre-exponential factor, activation enthalpy, activation entropy, and activation Gibbs energy decreased with decreasing particle size. The reaction rate constants and activation Gibbs energies increased with increasing temperature. Moreover, the logarithms of the apparent activation energies, pre-exponential factors, and rate constants were found to be linearly related to the reciprocal of particle size, consistent with the kinetic models. The influence of particle size on these reaction kinetic parameters may be explained as follows: the apparent activation energy is affected by the partial molar enthalpy, the pre-exponential factor is affected by the partial molar entropy, and the reaction rate constant is affected by the partial molar Gibbs energy. [Figure not available: see fulltext.

Geochemistry and quality parameters of dug and tube well water of Khipro, District Sanghar, Sindh, Pakistan

NASA Astrophysics Data System (ADS)

Bashir, Erum; Huda, Syed Nawaz-ul; Naseem, Shahid; Hamza, Salma; Kaleem, Maria

2017-07-01

Thirty-nine (23 dug and 16 tube well) samples were geochemically evaluated and investigated to ascertain the quality of water in Khipro, Sindh. The analytical results exhibited abundance of major cations and anions in Na+ > Ca2+ > Mg2+ > K+ and Cl- > HCO3 - > SO4 2- sequence. Stiff diagram showed dug well sample have high Na-Cl and moderate Mg-SO4 content as compared to tube well samples. Majority of dug well samples appeared as Na-Cl type on Piper diagram while tube well samples are mixed type. Gibbs diagram reflected evaporation as a dominant phenomenon in dug well; however, tube well samples are declined toward rock dominance. Process of ion exchange was witnessed from Na+ versus Cl- and Ca2+ + Mg2+ versus HCO3 - + SO4 2- plots. Principal component analysis also discriminates dug well and tube well water by means of positive and negative loading based on physical and chemical composition of the groundwater. Studied and computed parameters like pH, EC, TDS, TH, Na+, K+, Ca2+, Mg2+, Cl-, SO4 2-, HCO3 -, sodium adsorption ratio, magnesium adsorption ratio, potential salinity, residual sodium carbonate, Na%, Kelly's ratio, and permeability index were compared with WHO to evaluate studied water for drinking and agricultural purposes. Except Na+ and K+, all chemical constrains are within the allowed limits, set by WHO for drinking water. Similarly, most of the groundwater is moderately suitable for irrigation uses, with few exceptions.

Hedgehogs and foxes (and a bear)

NASA Astrophysics Data System (ADS)

Gibb, Bruce

2017-02-01

The chemical universe is big. Really big. You just won't believe how vastly, hugely, mind-bogglingly big it is. Bruce Gibb reminds us that it's somewhat messy too, and so we succeed by recognizing the limits of our knowledge.

Hard-luck Scheele

NASA Astrophysics Data System (ADS)

Gibb, Bruce C.

2015-11-01

Carl Wilhelm Scheele had a hand in the discovery of at least six elements and contributed to the early development of chemistry in numerous other ways. Bruce Gibb looks into Scheele's story and considers why he doesn't get the credit that he deserves.

A strong shock tube problem calculated by different numerical schemes

NASA Astrophysics Data System (ADS)

Lee, Wen Ho; Clancy, Sean P.

1996-05-01

Calculated results are presented for the solution of a very strong shock tube problem on a coarse mesh using (1) MESA code, (2) UNICORN code, (3) Schulz hydro, and (4) modified TVD scheme. The first two codes are written in Eulerian coordinates, whereas methods (3) and (4) are in Lagrangian coordinates. MESA and UNICORN codes are both of second order and use different monotonic advection method to avoid the Gibbs phenomena. Code (3) uses typical artificial viscosity for inviscid flow, whereas code (4) uses a modified TVD scheme. The test problem is a strong shock tube problem with a pressure ratio of 109 and density ratio of 103 in an ideal gas. For no mass-matching case, Schulz hydro is better than TVD scheme. In the case of mass-matching, there is no difference between them. MESA and UNICORN results are nearly the same. However, the computed positions such as the contact discontinuity (i.e. the material interface) are not as accurate as the Lagrangian methods.

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

Lee, W.H.; Clancy, S.P.

Calculated results are presented for the solution of a very strong shock tube problem on a coarse mesh using (1) MESA code, (2) UNICORN code, (3) Schulz hydro, and (4) modified TVD scheme. The first two codes are written in Eulerian coordinates, whereas methods (3) and (4) are in Lagrangian coordinates. MESA and UNICORN codes are both of second order and use different monotonic advection method to avoid the Gibbs phenomena. Code (3) uses typical artificial viscosity for inviscid flow, whereas code (4) uses a modified TVD scheme. The test problem is a strong shock tube problem with a pressuremore » ratio of 10{sup 9} and density ratio of 10{sup 3} in an ideal gas. For no mass-matching case, Schulz hydro is better than TVD scheme. In the case of mass-matching, there is no difference between them. MESA and UNICORN results are nearly the same. However, the computed positions such as the contact discontinuity (i.e. the material interface) are not as accurate as the Lagrangian methods. {copyright} {ital 1996 American Institute of Physics.}« less

Scientific method discourses in the construction of 'EMF' science: interests, resources and rhetoric in submissions to a public inquiry.

PubMed

Mercer, David

2002-04-01

Since the late 1970s, there has been considerable debate surrounding the question of whether or not exposures to non-ionizing radiation and electric and magnetic fields (EMF), produced by powerlines and electrical and telecommunications technologies, are harmful to health. Whilst there has been some recent evidence of regulatory fatigue, and attempts to enforce closure, the EMF debate nevertheless still continues. This paper will explore the rôle played by competing images of scientific method in the argumentative strategies used by two of the main protagonists in an Australian public inquiry (held in 1990-91) which investigated the EMF issue: 'Inquiry into Community Needs and High Voltage (132kv and above) Transmission Line Development', the so-called Gibbs Inquiry. Apart from documenting some of the epistemologically intricate features of the EMF controversy, the following discussion will also consider the way scientific method discourses can contribute to enhancing the durability of knowledge claims in legal and regulatory settings.

Thermal fluids for CSP systems: Alkaline nitrates/nitrites thermodynamics modelling method

NASA Astrophysics Data System (ADS)

Tizzoni, A. C.; Sau, S.; Corsaro, N.; Giaconia, A.; D'Ottavi, C.; Licoccia, S.

2016-05-01

Molten salt (MS) mixtures are used for the transport (HTF-heat transfer fluid) and storage of heat (HSM-heat storage material) in Concentration Solar Plants (CSP). In general, alkaline and earth-alkaline nitrate/nitrite mixtures are employed. Along with its upper stability temperature, the melting point (liquidus point) of a MS mixture is one of the main parameters which defines its usefulness as a HTF and HSM medium. As a result, we would like to develop a predictive model which will allow us to forecast freezing points for different MS mixture compositions; thus circumventing the need to determine experimentally the phase diagram for each MS mixture. To model ternary/quaternary phase diagram, parameters for the binary subsystems are to be determined, which is the purpose of the concerned work. In a binary system with components A and B, in phase equilibrium conditions (e.g. liquid and solid) the chemical potentials (partial molar Gibbs energy) for each component in each phase are equal. For an ideal solution it is possible to calculate the mixing (A+B) Gibbs energy:ΔG = ΔH - TΔS = RT(xAlnxA + xBlnxB) In case of non-ideal solid/liquid mixtures, such as the nitrates/nitrites compositions investigated in this work, the actual value will differ from the ideal one by an amount defined as the "mixing" (mix) Gibbs free energy. If the resulting mixtures is assumed, as indicated in the previous literature, to follow a "regular solution" model, where all the non-ideality is considered included in the enthalpy of mixing value and considering, for instance, the A component:Δ G ≡0 =(Δ HA-T Δ SA)+(ΔH¯ m i x AL-T ΔS¯ m i x AL)-(ΔH¯ m i x AS-T ΔS¯ m i x AS)where the molar partial amounts can be calculated from the total value by the Gibbs Duhem equation: (ΔH¯m i x AL=ΔHm i x-XB Ld/Δ Hm i x d XB L ) L;(ΔH¯m i x AS=ΔHm i x-XB Sd/Δ Hm i x d XB S ) S and, in general, it is possible to express the mixing enthalpy for solids and liquids as a function of the mol fraction: Δ HL m i x=XA LXB L(a1+b1XA L+c1XA LXB L),Δ HS m i x=XA SXB S(a2+b2XA S+c2XA SXB S) From the latter expressions it can be possible to modelize the phase diagram of a binary mixtures by using the a,b and c couples of parameters. To calculate those coefficients a method commonly employed in literature is to measure the mixing enthalpies, or to use one reported of the enthalpy of mixing (for instance for the liquid state) and calculate the other one using the phase diagram points. A direct ΔHmix (in solid or liquid phase) measurement can be difficult to carry out using common DSC equipment generally present in research laboratories. In fact, such determinations can be, in principle, performed, but the obtained data will be affected by large experimental errors. On the other hand, it is possible to obtain values with great precision regarding the algebraic sum of mixing enthalpies and the phase diagram trend. For this reason, only the phase diagrams are proposed to be used to calculate a, b, c parameters, and, subsequently, the total (liquid-solid algebraic sum) enthalpy of mixing will be employed to verify their validity. At this aim, a C++ code was assessed and used. Three binary mixtures were considered by combining NaNO3, KNO3 and NaNO2.

Bayesian parameter estimation for the Wnt pathway: an infinite mixture models approach.

PubMed

Koutroumpas, Konstantinos; Ballarini, Paolo; Votsi, Irene; Cournède, Paul-Henry

2016-09-01

Likelihood-free methods, like Approximate Bayesian Computation (ABC), have been extensively used in model-based statistical inference with intractable likelihood functions. When combined with Sequential Monte Carlo (SMC) algorithms they constitute a powerful approach for parameter estimation and model selection of mathematical models of complex biological systems. A crucial step in the ABC-SMC algorithms, significantly affecting their performance, is the propagation of a set of parameter vectors through a sequence of intermediate distributions using Markov kernels. In this article, we employ Dirichlet process mixtures (DPMs) to design optimal transition kernels and we present an ABC-SMC algorithm with DPM kernels. We illustrate the use of the proposed methodology using real data for the canonical Wnt signaling pathway. A multi-compartment model of the pathway is developed and it is compared to an existing model. The results indicate that DPMs are more efficient in the exploration of the parameter space and can significantly improve ABC-SMC performance. In comparison to alternative sampling schemes that are commonly used, the proposed approach can bring potential benefits in the estimation of complex multimodal distributions. The method is used to estimate the parameters and the initial state of two models of the Wnt pathway and it is shown that the multi-compartment model fits better the experimental data. Python scripts for the Dirichlet Process Gaussian Mixture model and the Gibbs sampler are available at https://sites.google.com/site/kkoutroumpas/software konstantinos.koutroumpas@ecp.fr. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

On the design of experiments for determining ternary mixture free energies from static light scattering data using a nonlinear partial differential equation

PubMed Central

Wahle, Chris W.; Ross, David S.; Thurston, George M.

2012-01-01

We mathematically design sets of static light scattering experiments to provide for model-independent measurements of ternary liquid mixing free energies to a desired level of accuracy. A parabolic partial differential equation (PDE), linearized from the full nonlinear PDE [D. Ross, G. Thurston, and C. Lutzer, J. Chem. Phys. 129, 064106 (2008)10.1063/1.2937902], describes how data noise affects the free energies to be inferred. The linearized PDE creates a net of spacelike characteristic curves and orthogonal, timelike curves in the composition triangle, and this net governs diffusion of information coming from light scattering measurements to the free energy. Free energy perturbations induced by a light scattering perturbation diffuse along the characteristic curves and towards their concave sides, with a diffusivity that is proportional to the local characteristic curvature radius. Consequently, static light scattering can determine mixing free energies in regions with convex characteristic curve boundaries, given suitable boundary data. The dielectric coefficient is a Lyapunov function for the dynamical system whose trajectories are PDE characteristics. Information diffusion is heterogeneous and system-dependent in the composition triangle, since the characteristics depend on molecular interactions and are tangent to liquid-liquid phase separation coexistence loci at critical points. We find scaling relations that link free energy accuracy, total measurement time, the number of samples, and the interpolation method, and identify the key quantitative tradeoffs between devoting time to measuring more samples, or fewer samples more accurately. For each total measurement time there are optimal sample numbers beyond which more will not improve free energy accuracy. We estimate the degree to which many-point interpolation and optimized measurement concentrations can improve accuracy and save time. For a modest light scattering setup, a sample calculation shows that less than two minutes of measurement time is, in principle, sufficient to determine the dimensionless mixing free energy of a non-associating ternary mixture to within an integrated error norm of 0.003. These findings establish a quantitative framework for designing light scattering experiments to determine the Gibbs free energy of ternary liquid mixtures. PMID:22830693

Thermodynamics of Dilute Solutions.

ERIC Educational Resources Information Center

Jancso, Gabor; Fenby, David V.

1983-01-01

Discusses principles and definitions related to the thermodynamics of dilute solutions. Topics considered include dilute solution, Gibbs-Duhem equation, reference systems (pure gases and gaseous mixtures, liquid mixtures, dilute solutions), real dilute solutions (focusing on solute and solvent), terminology, standard states, and reference systems.…

Learning that Prepares for More Learning: Symbolic Mathematics in Physical Chemistry

ERIC Educational Resources Information Center

Zielinski, Theresa Julia

2004-01-01

The well-crafted templates are useful to learn the new concepts of chemistry. The templates focus on pressure-volume work, the Boltzmann distribution, the Gibbs free energy function, intermolecular potentials, the second virial coefficient and quantum mechanical tunneling.

Thermodynamic properties of liquid Au–Cu–Sn alloys determined from electromotive force measurements

PubMed Central

Guo, Zhongnan; Hindler, Michael; Yuan, Wenxia; Mikula, Adolf

2011-01-01

The thermodynamic properties of the ternary Au–Cu–Sn system were determined with the electromotive force (EMF) method using a liquid electrolyte. Three different cross-sections with constant Au:Cu ratios of 3:1, 1:1, and 1:3 were applied to measure the thermodynamic properties of the ternary system in the temperature range between the liquidus temperature of the alloys and 1023 K. The partial free energies of Sn in liquid Au–Cu–Sn alloys were obtained from EMF data. The integral Gibbs free energy and the integral enthalpy at 900 K were calculated by Gibbs–Duhem integration. The ternary interaction parameters were evaluated using the Redlich–Kister–Muggianu polynomial. PMID:22039311

Pressure induced structural phase transition in metal nitrides: An effective interionic potential calculations

NASA Astrophysics Data System (ADS)

Soni, Shubhangi; Choudhary, K. K.; Kaurav, Netram

2018-05-01

Structural and elastic properties of transition metal nitrides, XN (X = Co, Fe and Cu), are investigated through an effective inter-ionic potential method. The B3(ZnS) type ambient crystal structure of these compounds undergoes to B1(NaCl) type structure with pressure. Structural phase transition pressure in CoN, FeN and CuN was 35, 55 and 35 GPa, respectively, predicated by computing Gibbs' free energy (G) as a function of pressure and has good agreement with available theoretical results. The elastic properties were also estimated as a function of pressure. It is found that the elastic constants increased linearly with increasing pressure due to stronger hybridization, bonding and covalent properties of constituent elements of a compound.

Separating Judicial from Legislative Reasoning in Moral Dilemma Interviews.

PubMed

Langford, Peter E

1997-12-01

Unlike previous studies of the development of reasoning about moral dilemmas, the 2 studies reported separated judicial reasoning (the application of rules) from legislative reasoning (the justification of rules), as well as attending to other aspects of context, using a modification of the weakly interpretive scoring method of Langford and D'Cruz. This assigns justifications to relatively simple conceptually defined categories. Findings were in accord with substantially modified versions of the views of Piaget and Kohlberg, according to which legislative reasoning can be divided into 3 main types of stages in the period 7-21 years: heteronomy (Piaget) or egocentrism (Kohlberg); local groups (attention to group interests, harmony, and reciprocity in local groups), wider groups (attention to these thing in wider groups). Findings contradicted Gibbs's theory.